1 /* sequin5.c
2 * ===========================================================================
3 *
4 * PUBLIC DOMAIN NOTICE
5 * National Center for Biotechnology Information (NCBI)
6 *
7 * This software/database is a "United States Government Work" under the
8 * terms of the United States Copyright Act. It was written as part of
9 * the author's official duties as a United States Government employee and
10 * thus cannot be copyrighted. This software/database is freely available
11 * to the public for use. The National Library of Medicine and the U.S.
12 * Government do not place any restriction on its use or reproduction.
13 * We would, however, appreciate having the NCBI and the author cited in
14 * any work or product based on this material
15 *
16 * Although all reasonable efforts have been taken to ensure the accuracy
17 * and reliability of the software and data, the NLM and the U.S.
18 * Government do not and cannot warrant the performance or results that
19 * may be obtained by using this software or data. The NLM and the U.S.
20 * Government disclaim all warranties, express or implied, including
21 * warranties of performance, merchantability or fitness for any particular
22 * purpose.
23 *
24 * ===========================================================================
25 *
26 * File Name: sequin5.c
27 *
28 * Author: Jonathan Kans
29 *
30 * Version Creation Date: 8/26/97
31 *
32 * $Revision: 6.798 $
33 *
34 * File Description:
35 *
36 * Modifications:
37 * --------------------------------------------------------------------------
38 * Date Name Description of modification
39 * ------- ---------- -----------------------------------------------------
40 *
41 *
42 * ==========================================================================
43 */
44
45 #define USE_BLAST3
46
47 #include "sequin.h"
48 #include <document.h>
49 #include <biosrc.h>
50 #include <jzcoll.h>
51 #include <objsub.h>
52 #ifdef USE_BLAST3
53 #include <netblap3.h>
54 #else
55 #include <netblap2.h>
56 #include <blast2.h>
57 #endif
58 #include <dust.h>
59 #include <pobutil.h>
60 #include <saledit.h>
61 #include <salstruc.h>
62 #include <salfiles.h>
63 #include <salign.h>
64 #include <salsap.h>
65 #include <gbfeat.h>
66 #include <gbftdef.h>
67 #include <satutil.h>
68 #include <rpsutil.h>
69 #include <subutil.h>
70 #include <explore.h>
71 #include <import.h>
72 #include <salutil.h>
73
74 #include <asn2gnbp.h> /* added for parse to flatfile */
75 #include <sqnutils.h> /* added to include SeqEdTranslateOneCDS */
76 #include <seqpanel.h>
77 #include <salpanel.h>
78 #include <tax3api.h> /* added for specific-host corrections */
79 #include <findrepl.h>
80 #include <valid.h> /* added for latloncountry conflict checking */
81 #include <vsmutil.h>
82
83 #define NLM_GENERATED_CODE_PROTO
84 #include <objmacro.h>
85 #include <macroapi.h>
86
87
CommonLaunchBioseqViewer(SeqEntryPtr sep,CharPtr path,Boolean directToEditor)88 static void CommonLaunchBioseqViewer (SeqEntryPtr sep, CharPtr path, Boolean directToEditor)
89
90 {
91 BioseqPtr bsp;
92 BioseqSetPtr bssp;
93 Pointer dataptr;
94 Uint2 datatype;
95 Uint2 entityID;
96 Int2 handled;
97
98 if (sep != NULL) {
99 if (IS_Bioseq (sep)) {
100 datatype = OBJ_BIOSEQ;
101 } else if (IS_Bioseq_set (sep)) {
102 datatype = OBJ_BIOSEQSET;
103 } else {
104 sep = SeqEntryFree (sep);
105 return;
106 }
107 dataptr = (Pointer) sep->data.ptrvalue;
108 entityID = ObjMgrRegister (datatype, dataptr);
109 if (dataptr != NULL && entityID > 0) {
110 if (datatype == OBJ_SEQSUB || datatype == OBJ_SEQENTRY ||
111 datatype == OBJ_BIOSEQ || datatype == OBJ_BIOSEQSET) {
112 WatchCursor ();
113 sep = GetTopSeqEntryForEntityID (entityID);
114 if (sep == NULL) {
115 sep = SeqEntryNew ();
116 if (sep != NULL) {
117 if (datatype == OBJ_BIOSEQ) {
118 bsp = (BioseqPtr) dataptr;
119 sep->choice = 1;
120 sep->data.ptrvalue = bsp;
121 SeqMgrSeqEntry (SM_BIOSEQ, (Pointer) bsp, sep);
122 } else if (datatype == OBJ_BIOSEQSET) {
123 bssp = (BioseqSetPtr) dataptr;
124 sep->choice = 2;
125 sep->data.ptrvalue = bssp;
126 SeqMgrSeqEntry (SM_BIOSEQSET, (Pointer) bssp, sep);
127 } else {
128 sep = SeqEntryFree (sep);
129 }
130 }
131 sep = GetTopSeqEntryForEntityID (entityID);
132 }
133 if (sep != NULL) {
134 SeqEntryPack (sep);
135 }
136 if (directToEditor) {
137 handled = GatherProcLaunch (OMPROC_EDIT, FALSE, entityID, 1,
138 OBJ_BIOSEQ, 0, 0, OBJ_BIOSEQ, 0);
139 } else {
140 if (sep != NULL) {
141 if (! leaveAsOldAsn) {
142 MySeqEntryToAsn3 (sep, TRUE, FALSE, FALSE);
143 }
144 }
145 seqviewprocs.filepath = path;
146 seqviewprocs.forceSeparateViewer = TRUE;
147 handled = GatherProcLaunch (OMPROC_VIEW, FALSE, entityID, 1,
148 OBJ_BIOSEQ, 0, 0, OBJ_BIOSEQ, 0);
149 seqviewprocs.filepath = NULL;
150 }
151 ArrowCursor ();
152 if (handled != OM_MSG_RET_DONE || handled == OM_MSG_RET_NOPROC) {
153 Message (MSG_FATAL, "Unable to launch viewer.");
154 SeqEntryFree (sep);
155 return;
156 } else {
157 SendHelpScrollMessage (helpForm, "Editing the Record", NULL);
158 }
159 ObjMgrSetOptions (OM_OPT_FREE_IF_NO_VIEW, entityID);
160 ObjMgrSetDirtyFlag (entityID, TRUE);
161 } else {
162 Message (MSG_ERROR, "Unable to process object type %d.", (int) datatype);
163 ObjMgrDelete (datatype, dataptr);
164 }
165 }
166 }
167 }
168
169 #define BUFSIZE 128
170
GetSequenceString(BioseqPtr bsp)171 static CharPtr GetSequenceString (BioseqPtr bsp)
172
173 {
174 Char buf [BUFSIZE + 5];
175 Int2 j;
176 ByteStorePtr raw;
177 CharPtr sequence = NULL;
178 SeqPortPtr spp;
179 Uint1 u1Residue;
180
181 if (bsp == NULL) return NULL;
182 if (! ISA_na (bsp->mol)) return NULL;
183 spp = SeqPortNew (bsp, 0, -1, 0, Seq_code_iupacna);
184 if (spp == NULL) return NULL;
185 raw = BSNew (bsp->length + 5);
186 if (raw == NULL) {
187 SeqPortFree (spp);
188 return NULL;
189 }
190
191 j = 0;
192 buf [0] = '\0';
193 while ((u1Residue = SeqPortGetResidue (spp)) != SEQPORT_EOF) {
194 if (IS_residue (u1Residue)) {
195 u1Residue = TO_UPPER(u1Residue);
196 if (u1Residue == 'U') {
197 u1Residue = 'T';
198 }
199 buf [j] = (Char) u1Residue;
200 j++;
201 if (j >= BUFSIZE) {
202 BSWrite (raw, buf, j * sizeof (Char));
203 j = 0;
204 }
205 }
206 }
207 buf [j] = '\0';
208 if (j >= 0) {
209 BSWrite (raw, buf, j * sizeof (Char));
210 }
211 sequence = BSMerge (raw, NULL);
212 BSFree (raw);
213 SeqPortFree (spp);
214 return sequence;
215 }
216
LookForSearchString(CharPtr title,CharPtr str,CharPtr tmp,size_t maxsize)217 static Boolean LookForSearchString (CharPtr title, CharPtr str, CharPtr tmp, size_t maxsize)
218
219 {
220 CharPtr ptr;
221
222 ptr = StringISearch (title, str);
223 if (ptr != NULL) {
224 StringNCpy_0 (tmp, ptr + StringLen (str), maxsize);
225 ptr = StringChr (tmp, ']');
226 if (ptr != NULL) {
227 *ptr = '\0';
228 }
229 return TRUE;
230 }
231 return FALSE;
232 }
233
234 typedef struct geneextendlist {
235 GeneRefPtr grp;
236 SeqLocPtr slp;
237 ObjMgrPtr omp;
238 Boolean rsult;
239 Char label [41];
240 } GeneExtendList, PNTR GeneExtendPtr;
241
GeneExtendFunc(GatherContextPtr gcp)242 static Boolean GeneExtendFunc (GatherContextPtr gcp)
243
244 {
245 BioseqPtr bsp;
246 GeneExtendPtr gep;
247 GeneRefPtr grp;
248 Boolean hasNulls;
249 ObjMgrTypePtr omtp;
250 SeqFeatPtr sfp;
251 SeqLocPtr slp;
252 Char thislabel [41];
253
254 if (gcp == NULL) return TRUE;
255
256 gep = (GeneExtendPtr) gcp->userdata;
257 if (gep == NULL ) return TRUE;
258
259 thislabel [0] = '\0';
260
261 if (gcp->thistype == OBJ_SEQFEAT) {
262 sfp = (SeqFeatPtr) gcp->thisitem;
263 if (sfp != NULL && sfp->data.choice == SEQFEAT_GENE && sfp->data.value.ptrvalue != NULL) {
264 grp = (GeneRefPtr) sfp->data.value.ptrvalue;
265 omtp = ObjMgrTypeFind (gep->omp, gcp->thistype, NULL, NULL);
266 if (omtp == NULL) {
267 return TRUE;
268 }
269 if (omtp->labelfunc != NULL) {
270 (*(omtp->labelfunc)) (gcp->thisitem, thislabel, 40, OM_LABEL_CONTENT);
271 }
272 if (thislabel [0] != '\0') {
273 if (StringICmp (thislabel, gep->label) == 0) {
274 if (/* SeqLocCompare (gep->slp, sfp->location) != SLC_NO_MATCH */
275 SeqLocAinB (gep->slp, sfp->location) <= 0) {
276 bsp = GetBioseqGivenSeqLoc (sfp->location, gcp->entityID);
277 if (bsp != NULL) {
278 slp = SeqLocMerge (bsp, sfp->location, gep->slp, TRUE, FALSE, FALSE);
279 if (slp != NULL) {
280 sfp->location = SeqLocFree (sfp->location);
281 sfp->location = slp;
282 if (bsp->repr == Seq_repr_seg) {
283 slp = SegLocToPartsEx (bsp, sfp->location, TRUE);
284 sfp->location = SeqLocFree (sfp->location);
285 sfp->location = slp;
286 hasNulls = LocationHasNullsBetween (sfp->location);
287 sfp->partial = (sfp->partial || hasNulls);
288 }
289 FreeAllFuzz (slp);
290 gep->rsult = TRUE;
291 }
292 }
293 }
294 return FALSE;
295 }
296 }
297 }
298 }
299 return TRUE;
300 }
301
OligoExtendGene(GeneRefPtr grp,SeqEntryPtr nsep,SeqLocPtr slp)302 static Boolean OligoExtendGene (GeneRefPtr grp, SeqEntryPtr nsep, SeqLocPtr slp)
303
304 {
305 GeneExtendList gel;
306 GatherScope gs;
307 ObjMgrTypePtr omtp;
308 SeqFeatPtr sfp;
309
310 if (grp == NULL || nsep == NULL || slp == NULL) return FALSE;
311 gel.grp = grp;
312 gel.slp = slp;
313 gel.omp = ObjMgrGet ();
314 gel.label [0] = '\0';
315 gel.rsult = FALSE;
316 omtp = ObjMgrTypeFind (gel.omp, OBJ_SEQFEAT, NULL, NULL);
317 if (omtp != NULL && omtp->labelfunc != NULL) {
318 sfp = SeqFeatNew ();
319 if (sfp != NULL) {
320 sfp->data.choice = SEQFEAT_GENE;
321 sfp->data.value.ptrvalue = (Pointer) grp;
322 (*(omtp->labelfunc)) ((Pointer) sfp, gel.label, 40, OM_LABEL_CONTENT);
323 sfp->data.value.ptrvalue = NULL;
324 SeqFeatFree (sfp);
325 }
326 }
327 MemSet ((Pointer)(&gs), 0, sizeof (GatherScope));
328 gs.seglevels = 1;
329 gs.get_feats_location = TRUE;
330 MemSet((Pointer)(gs.ignore), (int)(TRUE), (size_t)(OBJ_MAX * sizeof(Boolean)));
331 gs.ignore[OBJ_BIOSEQ] = FALSE;
332 gs.ignore[OBJ_BIOSEQ_SEG] = FALSE;
333 gs.ignore[OBJ_SEQFEAT] = FALSE;
334 gs.ignore[OBJ_SEQANNOT] = FALSE;
335 GatherSeqEntry (nsep, (Pointer) &gel, GeneExtendFunc, &gs);
336 return gel.rsult;
337 }
338
AddGBQual(SeqFeatPtr sfp,CharPtr qual,CharPtr val)339 static void AddGBQual (SeqFeatPtr sfp, CharPtr qual, CharPtr val)
340
341 {
342 GBQualPtr gbq;
343 GBQualPtr last;
344
345 if (sfp == NULL || StringHasNoText (qual) || StringHasNoText (val)) return;
346 gbq = GBQualNew ();
347 if (gbq == NULL) return;
348 gbq->qual = StringSave (qual);
349 gbq->val = StringSave (val);
350 if (sfp->qual == NULL) {
351 sfp->qual = gbq;
352 } else {
353 last = sfp->qual;
354 while (last->next != NULL) {
355 last = last->next;
356 }
357 last->next = gbq;
358 }
359 }
360
ProcessOligoDefline(SeqFeatPtr sfp,CharPtr title,SeqEntryPtr nsep)361 static void ProcessOligoDefline (SeqFeatPtr sfp, CharPtr title, SeqEntryPtr nsep)
362
363 {
364 BioseqPtr bsp;
365 GeneRefPtr grp;
366 SeqFeatPtr gsfp;
367 SeqLocPtr gslp;
368 Boolean hasNulls;
369 SeqIdPtr sip;
370 Char tmp [256];
371
372 if (sfp == NULL || StringHasNoText (title) || nsep == NULL) return;
373 if (LookForSearchString (title, "[comment=", tmp, sizeof (tmp) - 1)) {
374 sfp->comment = StringSave (tmp);
375 }
376 if (LookForSearchString (title, "[stdname=", tmp, sizeof (tmp) - 1)) {
377 AddGBQual (sfp, "standard_name", tmp);
378 }
379 if (LookForSearchString (title, "[conditions=", tmp, sizeof (tmp) - 1)) {
380 AddGBQual (sfp, "PCR_conditions", tmp);
381 }
382 if (LookForSearchString (title, "[gene=", tmp, sizeof (tmp) - 1)) {
383 grp = CreateNewGeneRef (tmp, NULL, NULL, FALSE);
384 if (grp != NULL) {
385 /*
386 slp = AsnIoMemCopy ((Pointer) sfp->location,
387 (AsnReadFunc) SeqLocAsnRead,
388 (AsnWriteFunc) SeqLocAsnWrite);
389 if (slp != NULL || slp->choice == SEQLOC_INT) {
390 sintp = (SeqIntPtr) slp->data.ptrvalue;
391 if (sintp != NULL) {
392 if (sintp->strand == Seq_strand_minus) {
393 sintp->strand = Seq_strand_plus;
394 } else if (sintp->strand == Seq_strand_plus) {
395 sintp->strand = Seq_strand_minus;
396 }
397 }
398 }
399 */
400 if (OligoExtendGene (grp, nsep, sfp->location) /* || OligoExtendGene (grp, nsep, slp) */) {
401 grp = GeneRefFree (grp);
402 } else {
403 gsfp = CreateNewFeature (nsep, NULL, SEQFEAT_GENE, NULL);
404 if (gsfp != NULL) {
405 gsfp->data.value.ptrvalue = (Pointer) grp;
406 gsfp->location = SeqLocFree (gsfp->location);
407 gsfp->location = AsnIoMemCopy ((Pointer) sfp->location,
408 (AsnReadFunc) SeqLocAsnRead,
409 (AsnWriteFunc) SeqLocAsnWrite);
410 sip = SeqLocId (gsfp->location);
411 if (sip != NULL) {
412 bsp = BioseqFind (sip);
413 } else {
414 bsp = (BioseqPtr) nsep->data.ptrvalue;
415 }
416 if (bsp != NULL) {
417 gslp = SeqLocMerge (bsp, gsfp->location, NULL, TRUE, FALSE, FALSE);
418 if (gslp != NULL) {
419 gsfp->location = SeqLocFree (gsfp->location);
420 gsfp->location = gslp;
421 if (bsp->repr == Seq_repr_seg) {
422 gslp = SegLocToPartsEx (bsp, gsfp->location, TRUE);
423 gsfp->location = SeqLocFree (gsfp->location);
424 gsfp->location = gslp;
425 hasNulls = LocationHasNullsBetween (gsfp->location);
426 gsfp->partial = (gsfp->partial || hasNulls);
427 }
428 FreeAllFuzz (gslp);
429 }
430 }
431 }
432 }
433 /* SeqLocFree (slp); */
434 }
435 }
436 }
437
ProcessOligo(SeqEntryPtr sep,CharPtr sequence,CharPtr title)438 static void ProcessOligo (SeqEntryPtr sep, CharPtr sequence, CharPtr title)
439
440 {
441 BioseqSetPtr bssp;
442 ImpFeatPtr ifp;
443 BioseqPtr nbsp;
444 SeqEntryPtr nsep;
445 SeqFeatPtr sfp;
446 SeqLocPtr slp;
447
448 if (sep == NULL || sequence == NULL) return;
449 if (IS_Bioseq_set (sep)) {
450 bssp = (BioseqSetPtr) sep->data.ptrvalue;
451 if (bssp != NULL && (bssp->_class == 7 ||
452 (IsPopPhyEtcSet (bssp->_class)))) {
453 for (sep = bssp->seq_set; sep != NULL; sep = sep->next) {
454 ProcessOligo (sep, sequence, title);
455 }
456 return;
457 }
458 }
459 nsep = FindNucSeqEntry (sep);
460 if (nsep == NULL) return;
461 if (! IS_Bioseq (nsep)) return;
462 nbsp = (BioseqPtr) nsep->data.ptrvalue;
463 if (nbsp == NULL) return;
464 slp = StringSearchInBioseq (nbsp->id, sequence);
465 if (slp == NULL) return;
466 ifp = ImpFeatNew ();
467 if (ifp != NULL) {
468 ifp->key = StringSave ("primer_bind");
469 sfp = CreateNewFeature (nsep, NULL, SEQFEAT_IMP, NULL);
470 if (sfp != NULL) {
471 sfp->data.value.ptrvalue = (Pointer) ifp;
472 sfp->location = SeqLocFree (sfp->location);
473 sfp->location = slp;
474 ProcessOligoDefline (sfp, title, nsep);
475 }
476 }
477 }
478
479
480 typedef struct edlocdata {
481 FORM_MESSAGE_BLOCK
482 SeqIdPtr sip;
483 BioseqPtr bsp;
484 TexT locusname;
485 PrompT accnnumber;
486 Boolean refgene;
487 } EdLocData, PNTR EdLocPtr;
488
AllToUpper(CharPtr str)489 static CharPtr AllToUpper (CharPtr str)
490
491 {
492 Char ch;
493 CharPtr ptr;
494
495 if (str != NULL) {
496 ptr = str;
497 ch = *ptr;
498 while (ch != '\0') {
499 *ptr = TO_UPPER (ch);
500 ptr++;
501 ch = *ptr;
502 }
503 }
504 return str;
505 }
506
EditLocusActnProc(ForM f)507 static void EditLocusActnProc (ForM f)
508
509 {
510 BioseqPtr bsp;
511 Uint1 choice = SEQID_GENBANK;
512 Int2 count;
513 SeqIdPtr id;
514 EdLocPtr elp;
515 Int2 len;
516 Char num [16];
517 BioseqPtr part;
518 CharPtr ptr;
519 Char str [64];
520 SeqIdPtr sip;
521 SeqLocPtr slp;
522 Char tmp [76];
523 TextSeqIdPtr tsip;
524 ValNode vn;
525
526 elp = (EdLocPtr) GetObjectExtra (f);
527 if (elp != NULL) {
528 sip = elp->sip;
529 bsp = elp->bsp;
530 if (elp->refgene) {
531 choice = SEQID_OTHER;
532 }
533 if (indexerVersion && sip == NULL && bsp != NULL && bsp->id != NULL) {
534 id = bsp->id;
535 while (id->next != NULL) {
536 id = id->next;
537 }
538 tsip = TextSeqIdNew ();
539 if (tsip != NULL) {
540 sip = ValNodeNew (NULL);
541 if (sip != NULL) {
542 sip->choice = choice;
543 sip->data.ptrvalue = (Pointer) tsip;
544 } else {
545 TextSeqIdFree (tsip);
546 }
547 id->next = sip;
548 SeqMgrReplaceInBioseqIndex (bsp);
549 }
550 }
551 if (sip == NULL) return;
552 tsip = (TextSeqIdPtr) sip->data.ptrvalue;
553 if (tsip == NULL) return;
554 tsip->accession = MemFree (tsip->accession);
555 GetTitle (elp->accnnumber, str, sizeof (str) - 1);
556 TrimSpacesAroundString (str);
557 if (! StringHasNoText (str)) {
558 tsip->accession = StringSave (AllToUpper (str));
559 }
560 tsip->name = MemFree (tsip->name);
561 GetTitle (elp->locusname, str, sizeof (str) - 1);
562 if (str [0] != '\0') {
563 if (elp->refgene) {
564 tsip->name = StringSave (str);
565 } else {
566 tsip->name = StringSave (AllToUpper (str));
567 }
568 }
569 if (bsp != NULL && bsp->repr == Seq_repr_seg && bsp->seq_ext != NULL) {
570 if (StringNCmp (str, "SEG_", 4) != 0) {
571 sprintf (tmp, "SEG_%s", str);
572 tsip->name = MemFree (tsip->name);
573 tsip->name = StringSave (tmp);
574 SeqMgrReplaceInBioseqIndex (bsp);
575 }
576 vn.choice = SEQLOC_MIX;
577 vn.next = NULL;
578 vn.data.ptrvalue = bsp->seq_ext;
579 count = 0;
580 slp = SeqLocFindNext (&vn, NULL);
581 while (slp != NULL) {
582 if (slp->choice != SEQLOC_NULL) {
583 count++;
584 }
585 slp = SeqLocFindNext (&vn, slp);
586 }
587 if (count < 10) {
588 len = 1;
589 } else if (count < 100) {
590 len = 2;
591 } else {
592 len = 3;
593 }
594 count = 0;
595 slp = SeqLocFindNext (&vn, NULL);
596 while (slp != NULL) {
597 if (slp->choice != SEQLOC_NULL) {
598 count++;
599 sprintf (num, "%*d", (int) len, (int) count);
600 for (ptr = num; *ptr != '\0'; ptr++) {
601 if (*ptr == ' ') {
602 *ptr = '0';
603 }
604 }
605 sprintf (tmp, "%s%s", str, num);
606 sip = SeqLocId (slp);
607 if (sip != NULL) {
608 part = BioseqFind (sip);
609 if (part != NULL && part->id != NULL) {
610 id = part->id;
611 while (id->choice != choice && id->next != NULL) {
612 id = id->next;
613 }
614 if (id->choice != choice) {
615 tsip = TextSeqIdNew ();
616 if (tsip != NULL) {
617 sip = ValNodeNew (NULL);
618 if (sip != NULL) {
619 sip->choice = choice;
620 sip->data.ptrvalue = (Pointer) tsip;
621 } else {
622 TextSeqIdFree (tsip);
623 }
624 id->next = sip;
625 id = sip;
626 }
627 }
628 if (id != NULL && id->choice == choice) {
629 tsip = (TextSeqIdPtr) id->data.ptrvalue;
630 if (tsip != NULL) {
631 tsip->name = MemFree (tsip->name);
632 if (tmp [0] != '\0') {
633 if (elp->refgene) {
634 tsip->name = StringSave (tmp);
635 } else {
636 tsip->name = StringSave (AllToUpper (tmp));
637 }
638 }
639 }
640 }
641 SeqMgrReplaceInBioseqIndex (part);
642 }
643 }
644 }
645 slp = SeqLocFindNext (&vn, slp);
646 }
647 }
648 ObjMgrSetDirtyFlag (elp->input_entityID, TRUE);
649 ObjMgrSendMsg (OM_MSG_UPDATE, elp->input_entityID, 0, 0);
650 }
651 }
652
EditLocusMessage(ForM f,Int2 mssg)653 static void EditLocusMessage (ForM f, Int2 mssg)
654
655 {
656 EdLocPtr elp;
657
658 elp = (EdLocPtr) GetObjectExtra (f);
659 if (elp != NULL) {
660 switch (mssg) {
661 case VIB_MSG_CLOSE :
662 Remove (f);
663 break;
664 case VIB_MSG_CUT :
665 StdCutTextProc (NULL);
666 break;
667 case VIB_MSG_COPY :
668 StdCopyTextProc (NULL);
669 break;
670 case VIB_MSG_PASTE :
671 StdPasteTextProc (NULL);
672 break;
673 case VIB_MSG_DELETE :
674 StdDeleteTextProc (NULL);
675 break;
676 default :
677 if (elp->appmessage != NULL) {
678 elp->appmessage (f, mssg);
679 }
680 break;
681 }
682 }
683 }
684
685 #define NUM_ORDER 16
686
SeqIdFindGenBankOrOther(SeqIdPtr sip)687 static SeqIdPtr SeqIdFindGenBankOrOther (SeqIdPtr sip)
688
689 {
690 Uint1 order [NUM_ORDER];
691
692 SeqIdBestRank (order, NUM_ORDER);
693 order [SEQID_LOCAL] = 255;
694 order [SEQID_GENBANK] = 1;
695 order [SEQID_EMBL] = 2;
696 order [SEQID_PIR] = 255;
697 order [SEQID_SWISSPROT] = 255;
698 order [SEQID_DDBJ] = 3;
699 order [SEQID_PRF] = 255;
700 order [SEQID_PDB] = 255;
701 order [SEQID_PATENT] = 255;
702 order [SEQID_OTHER] = 2;
703 order [SEQID_GENERAL] = 255;
704 order [SEQID_GIBBSQ] = 255;
705 order [SEQID_GIBBMT] = 255;
706 order [SEQID_GIIM] = 255;
707 order [SEQID_GI] = 255;
708 return SeqIdSelect (sip, order, NUM_ORDER);
709 }
710
EditLocusProc(IteM i)711 void EditLocusProc (IteM i)
712
713 {
714 ButtoN b;
715 BaseFormPtr bfp;
716 BioseqPtr bsp;
717 GrouP c;
718 EdLocPtr elp;
719 GrouP g;
720 StdEditorProcsPtr sepp;
721 SeqIdPtr sip;
722 TextSeqIdPtr tsip;
723 WindoW w;
724
725 #ifdef WIN_MAC
726 bfp = currentFormDataPtr;
727 #else
728 bfp = GetObjectExtra (i);
729 #endif
730 if (bfp == NULL) return;
731 if (bfp->input_itemtype != OBJ_BIOSEQ) return;
732 bsp = GetBioseqGivenIDs (bfp->input_entityID, bfp->input_itemID, bfp->input_itemtype);
733 if (bsp == NULL) return;
734 sip = SeqIdFindGenBankOrOther (bsp->id);
735 /*if (sip == NULL) return;*/
736 elp = (EdLocPtr) MemNew (sizeof (EdLocData));
737 if (elp == NULL) return;
738 w = MovableModalWindow (-50, -33, -10, -10,
739 "Locus and Accession Number",
740 StdCloseWindowProc);
741 SetObjectExtra (w, elp, StdCleanupFormProc);
742 elp->form = (ForM) w;
743 elp->actproc = EditLocusActnProc;
744 elp->formmessage = EditLocusMessage;
745
746 elp->input_entityID = bfp->input_entityID;
747 elp->input_itemID = bfp->input_itemID;
748 elp->input_itemtype = bfp->input_itemtype;
749
750 #ifndef WIN_MAC
751 CreateStdEditorFormMenus (w);
752 #endif
753
754 sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm");
755 if (sepp != NULL) {
756 SetActivate (w, sepp->activateForm);
757 elp->appmessage = sepp->handleMessages;
758 }
759
760 g = HiddenGroup (w, 2, 0, NULL);
761 elp->sip = sip;
762 elp->bsp = bsp;
763 StaticPrompt (g, "Locus: ", 0, dialogTextHeight, systemFont, 'l');
764 elp->locusname = DialogText (g, "", 20, NULL);
765 StaticPrompt (g, "Accession: ", 0, stdLineHeight, systemFont, 'l');
766 elp->accnnumber = StaticPrompt (g, "", 20 * stdCharWidth, stdLineHeight, systemFont, 'l');
767 c = HiddenGroup (w, 2, 0, NULL);
768 b = DefaultButton (c, "Accept", StdAcceptFormButtonProc);
769 SetObjectExtra (b, elp, NULL);
770 PushButton (c, "Cancel", StdCancelButtonProc);
771 AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) c, NULL);
772 if (sip != NULL) {
773 tsip = (TextSeqIdPtr) sip->data.ptrvalue;
774 if (tsip != NULL) {
775 SetTitle (elp->locusname, tsip->name);
776 SetTitle (elp->accnnumber, tsip->accession);
777 }
778 if (sip->choice == SEQID_OTHER) {
779 elp->refgene = TRUE;
780 }
781 }
782 RealizeWindow (w);
783 Select (elp->locusname);
784 Show (w);
785 Select (w);
786 Update ();
787 }
788
789 typedef struct accntolocal
790 {
791 Boolean make_secondary;
792 Boolean convert_prots;
793 Boolean convert_nucs;
794 } AccnToLocalData, PNTR AccnToLocalPtr;
795
LocalSeqIdFromAccession(SeqIdPtr sip,CharPtr str,Int4 str_size)796 static SeqIdPtr LocalSeqIdFromAccession (SeqIdPtr sip, CharPtr str, Int4 str_size)
797 {
798 TextSeqIdPtr tsip;
799 CharPtr text;
800 SeqIdPtr new_sip;
801 ObjectIdPtr oip;
802
803 if (sip == NULL || str == NULL || str_size < 1)
804 {
805 return NULL;
806 }
807 if (sip->choice != SEQID_GENBANK
808 && sip->choice != SEQID_EMBL
809 && sip->choice != SEQID_DDBJ)
810 {
811 return NULL;
812 }
813 if (sip->data.ptrvalue == NULL)
814 {
815 return NULL;
816 }
817 new_sip = ValNodeNew (NULL);
818 if (new_sip == NULL)
819 {
820 return NULL;
821 }
822 tsip = (TextSeqIdPtr) sip->data.ptrvalue;
823 text = NULL;
824 str [0] = '\0';
825 if (tsip->accession != NULL) {
826 text = tsip->accession;
827 } else if (tsip->name != NULL) {
828 text = tsip->name;
829 }
830 if (text != NULL) {
831 StringNCpy_0 (str, text, str_size);
832 oip = ObjectIdNew ();
833 if (oip != NULL) {
834 oip->str = StringSave (text);
835 new_sip->choice = SEQID_LOCAL;
836 new_sip->data.ptrvalue = (Pointer) oip;
837 }
838 }
839 return new_sip;
840 }
841
SeqIdSwap(SeqIdPtr sip1,SeqIdPtr sip2)842 static void SeqIdSwap (SeqIdPtr sip1, SeqIdPtr sip2)
843 {
844 ValNode tmp_sip;
845
846 if (sip1 == NULL || sip2 == NULL)
847 {
848 return;
849 }
850
851 tmp_sip.choice = sip1->choice;
852 tmp_sip.data.ptrvalue = sip1->data.ptrvalue;
853 sip1->choice = sip2->choice;
854 sip1->data.ptrvalue = sip2->data.ptrvalue;
855 sip2->choice = tmp_sip.choice;
856 sip2->data.ptrvalue = tmp_sip.data.ptrvalue;
857 }
858
ConvertSeqIdListToLocalID(SeqIdPtr sip,SeqEntryPtr sep,AccnToLocalPtr atlp)859 static void ConvertSeqIdListToLocalID (SeqIdPtr sip, SeqEntryPtr sep, AccnToLocalPtr atlp)
860
861 {
862 GBBlockPtr gbp;
863 Char str [32];
864 ValNodePtr vnp;
865 BioseqPtr bsp;
866 SeqIdPtr new_sip = NULL;
867
868 if (atlp == NULL) return;
869
870 while (sip != NULL)
871 {
872 bsp = BioseqFind (sip);
873 if (bsp == NULL)
874 {
875 new_sip = LocalSeqIdFromAccession (sip, str, sizeof (str));
876 if (new_sip != NULL)
877 {
878 bsp = BioseqFind (new_sip);
879 }
880 }
881 if (bsp == NULL)
882 {
883 /* have to skip */
884 }
885 else if (ISA_na (bsp->mol) && !atlp->convert_nucs)
886 {
887 /* don't convert the nucleotide ID */
888 }
889 else if (ISA_aa (bsp->mol) && ! atlp->convert_prots)
890 {
891 /* don't convert the protein ID */
892 }
893 else if ((sip->choice == SEQID_GENBANK
894 || sip->choice == SEQID_EMBL
895 || sip->choice == SEQID_DDBJ)
896 && sip->data.ptrvalue != NULL)
897 {
898 new_sip = LocalSeqIdFromAccession (sip, str, sizeof (str));
899 if (new_sip != NULL)
900 {
901 /* replace old sip values with new - new_sip will now be ready for freeing */
902 SeqIdSwap (sip, new_sip);
903
904 /* make secondary if needed */
905 if (atlp->make_secondary && sep != NULL)
906 {
907 vnp = SeqEntryGetSeqDescr (sep, Seq_descr_genbank, NULL);
908 if (vnp == NULL) {
909 vnp = CreateNewDescriptor (sep, Seq_descr_genbank);
910 if (vnp != NULL) {
911 gbp = GBBlockNew ();
912 vnp->data.ptrvalue = (Pointer) gbp;
913 }
914 }
915 if (vnp != NULL) {
916 gbp = (GBBlockPtr) vnp->data.ptrvalue;
917 if (gbp != NULL) {
918 for (vnp = gbp->extra_accessions;
919 vnp != NULL && StringICmp (vnp->data.ptrvalue, str) != 0;
920 vnp = vnp->next) continue;
921 if (vnp == NULL) {
922 vnp = ValNodeCopyStr (&(gbp->extra_accessions), 0, str);
923 }
924 }
925 }
926 }
927 }
928 }
929 new_sip = SeqIdFree (new_sip);
930 sip = sip->next;
931 }
932 }
933
ConvertSeqLocListToLocalID(SeqLocPtr slp,AccnToLocalPtr atlp)934 static void ConvertSeqLocListToLocalID (SeqLocPtr slp, AccnToLocalPtr atlp)
935
936 {
937 SeqLocPtr loc;
938 PackSeqPntPtr psp;
939 SeqBondPtr sbp;
940 SeqIntPtr sinp;
941 SeqIdPtr sip;
942 SeqPntPtr spp;
943
944 while (slp != NULL) {
945 switch (slp->choice) {
946 case SEQLOC_NULL :
947 break;
948 case SEQLOC_EMPTY :
949 case SEQLOC_WHOLE :
950 sip = (SeqIdPtr) slp->data.ptrvalue;
951 ConvertSeqIdListToLocalID (sip, NULL, atlp);
952 break;
953 case SEQLOC_INT :
954 sinp = (SeqIntPtr) slp->data.ptrvalue;
955 if (sinp != NULL) {
956 sip = sinp->id;
957 ConvertSeqIdListToLocalID (sip, NULL, atlp);
958 }
959 break;
960 case SEQLOC_PNT :
961 spp = (SeqPntPtr) slp->data.ptrvalue;
962 if (spp != NULL) {
963 sip = spp->id;
964 ConvertSeqIdListToLocalID (sip, NULL, atlp);
965 }
966 break;
967 case SEQLOC_PACKED_PNT :
968 psp = (PackSeqPntPtr) slp->data.ptrvalue;
969 if (psp != NULL) {
970 sip = psp->id;
971 ConvertSeqIdListToLocalID (sip, NULL, atlp);
972 }
973 break;
974 case SEQLOC_PACKED_INT :
975 case SEQLOC_MIX :
976 case SEQLOC_EQUIV :
977 loc = (SeqLocPtr) slp->data.ptrvalue;
978 while (loc != NULL) {
979 ConvertSeqLocListToLocalID (loc, atlp);
980 loc = loc->next;
981 }
982 break;
983 case SEQLOC_BOND :
984 sbp = (SeqBondPtr) slp->data.ptrvalue;
985 if (sbp != NULL) {
986 spp = (SeqPntPtr) sbp->a;
987 if (spp != NULL) {
988 sip = spp->id;
989 ConvertSeqIdListToLocalID (sip, NULL, atlp);
990 }
991 spp = (SeqPntPtr) sbp->b;
992 if (spp != NULL) {
993 sip = spp->id;
994 ConvertSeqIdListToLocalID (sip, NULL, atlp);
995 }
996 }
997 break;
998 case SEQLOC_FEAT :
999 break;
1000 default :
1001 break;
1002 }
1003 slp = slp->next;
1004 }
1005 }
1006
ChangeAccessionToLocalID(GatherContextPtr gcp)1007 static Boolean ChangeAccessionToLocalID (GatherContextPtr gcp)
1008
1009 {
1010 BioseqPtr bsp;
1011 AccnToLocalPtr atlp;
1012 SeqEntryPtr sep;
1013 SeqFeatPtr sfp;
1014 SeqIdPtr sip;
1015 SeqLocPtr slp;
1016
1017 if (gcp == NULL || gcp->userdata == NULL) return TRUE;
1018 atlp = (AccnToLocalPtr) gcp->userdata;
1019 if (gcp->thisitem == NULL) return TRUE;
1020 switch (gcp->thistype) {
1021 case OBJ_BIOSEQ :
1022 sep = NULL;
1023 bsp = (BioseqPtr) gcp->thisitem;
1024 if (atlp->make_secondary)
1025 {
1026 sep = SeqMgrGetSeqEntryForData (bsp);
1027 }
1028 sip = bsp->id;
1029 ConvertSeqIdListToLocalID (sip, sep, atlp);
1030 SeqMgrReplaceInBioseqIndex (bsp);
1031 break;
1032 case OBJ_SEQFEAT :
1033 sfp = (SeqFeatPtr) gcp->thisitem;
1034 slp = sfp->location;
1035 ConvertSeqLocListToLocalID (slp, atlp);
1036 slp = sfp->product;
1037 ConvertSeqLocListToLocalID (slp, atlp);
1038 break;
1039 default :
1040 break;
1041 }
1042 return TRUE;
1043 }
1044
ConvertToLocalProc(IteM i,Boolean convert_nucs,Boolean convert_prots)1045 static void ConvertToLocalProc (IteM i, Boolean convert_nucs, Boolean convert_prots)
1046
1047 {
1048 MsgAnswer ans;
1049 BaseFormPtr bfp;
1050 GatherScope gs;
1051 AccnToLocalData atld;
1052
1053 #ifdef WIN_MAC
1054 bfp = currentFormDataPtr;
1055 #else
1056 bfp = GetObjectExtra (i);
1057 #endif
1058 if (bfp == NULL) return;
1059 if (bfp->input_itemtype != OBJ_BIOSEQ) return;
1060 ans = Message (MSG_OKC, "Are you sure you want to convert accessions to local IDs?");
1061 if (ans == ANS_CANCEL) return;
1062 ans = Message (MSG_OKC, "Are you REALLY sure you want to convert accessions to local IDs?");
1063 if (ans == ANS_CANCEL) return;
1064 ans = Message (MSG_YN, "Do you want to make the original accessions secondary?");
1065 atld.make_secondary = (Boolean) (ans == ANS_YES);
1066 atld.convert_nucs = convert_nucs;
1067 atld.convert_prots = convert_prots;
1068 MemSet ((Pointer) (&gs), 0, sizeof (GatherScope));
1069 gs.seglevels = 1;
1070 MemSet((Pointer) (gs.ignore), (int) (TRUE), (size_t) (OBJ_MAX * sizeof (Boolean)));
1071 gs.ignore[OBJ_BIOSEQ] = FALSE;
1072 gs.ignore[OBJ_BIOSEQ_SEG] = FALSE;
1073 gs.ignore[OBJ_SEQFEAT] = FALSE;
1074 gs.ignore[OBJ_SEQANNOT] = FALSE;
1075 GatherEntity (bfp->input_entityID, (Pointer) &atld, ChangeAccessionToLocalID, &gs);
1076 ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
1077 ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
1078 }
1079
ConvertToLocalProcOnlyNucs(IteM i)1080 extern void ConvertToLocalProcOnlyNucs (IteM i)
1081 {
1082 ConvertToLocalProc (i, TRUE, FALSE);
1083 }
1084
ConvertToLocalProcOnlyProts(IteM i)1085 extern void ConvertToLocalProcOnlyProts (IteM i)
1086 {
1087 ConvertToLocalProc (i, FALSE, TRUE);
1088 }
1089
ConvertToLocalProcAll(IteM i)1090 extern void ConvertToLocalProcAll (IteM i)
1091 {
1092 ConvertToLocalProc (i, TRUE, TRUE);
1093 }
1094
SeqIdFindBestForPromotion(SeqIdPtr sip)1095 static SeqIdPtr SeqIdFindBestForPromotion (SeqIdPtr sip)
1096
1097 {
1098 return SeqIdFindBest (sip, 0);
1099 }
1100
SeqIdFindWorstForPromotion(SeqIdPtr sip)1101 static SeqIdPtr SeqIdFindWorstForPromotion (SeqIdPtr sip)
1102
1103 {
1104 return SeqIdFindWorst (sip);
1105 }
1106
PromoteSeqId(SeqIdPtr sip,Boolean alsoCheckLocalAccn,Boolean findWorst)1107 static void PromoteSeqId (SeqIdPtr sip, Boolean alsoCheckLocalAccn, Boolean findWorst)
1108
1109 {
1110 SeqIdPtr bestid, newid, oldid;
1111 BioseqPtr bsp;
1112 ObjectIdPtr oip;
1113 TextSeqId tsi;
1114 SeqId vn;
1115
1116 bsp = BioseqFind (sip);
1117 if (bsp == NULL && alsoCheckLocalAccn && sip->choice == SEQID_LOCAL) {
1118 oip = (ObjectIdPtr) sip->data.ptrvalue;
1119 if (oip != NULL && (! StringHasNoText (oip->str))) {
1120 MemSet ((Pointer) &vn, 0, sizeof (SeqId));
1121 MemSet ((Pointer) &tsi, 0, sizeof (TextSeqId));
1122 tsi.accession = oip->str;
1123 vn.choice = SEQID_GENBANK;
1124 vn.data.ptrvalue = (Pointer) &tsi;
1125 bsp = BioseqFind (&vn);
1126 }
1127 }
1128 if (bsp == NULL) return;
1129
1130 if (findWorst) {
1131 bestid = SeqIdFindWorstForPromotion (bsp->id);
1132 } else {
1133 bestid = SeqIdFindBestForPromotion (bsp->id);
1134 }
1135 if (bestid == NULL) return;
1136 newid = SeqIdDup (bestid);
1137 if (newid == NULL) return;
1138
1139 oldid = ValNodeNew (NULL);
1140 if (oldid == NULL) return;
1141
1142 MemCopy (oldid, sip, sizeof (ValNode));
1143 oldid->next = NULL;
1144
1145 sip->choice = newid->choice;
1146 sip->data.ptrvalue = newid->data.ptrvalue;
1147
1148 SeqIdFree (oldid);
1149 ValNodeFree (newid);
1150
1151 SeqIdStripLocus (sip);
1152 }
1153
PromoteSeqIdList(SeqIdPtr sip,Boolean alsoCheckLocalAccn,Boolean findWorst)1154 static void PromoteSeqIdList (SeqIdPtr sip, Boolean alsoCheckLocalAccn, Boolean findWorst)
1155
1156 {
1157 while (sip != NULL) {
1158 PromoteSeqId (sip, alsoCheckLocalAccn, findWorst);
1159 sip = sip->next;
1160 }
1161 }
1162
PromoteSeqLocList(SeqLocPtr slp,Boolean alsoCheckLocalAccn,Boolean findWorst)1163 static void PromoteSeqLocList (SeqLocPtr slp, Boolean alsoCheckLocalAccn, Boolean findWorst)
1164
1165 {
1166 SeqLocPtr loc;
1167 PackSeqPntPtr psp;
1168 SeqBondPtr sbp;
1169 SeqIntPtr sinp;
1170 SeqIdPtr sip;
1171 SeqPntPtr spp;
1172
1173 while (slp != NULL) {
1174 switch (slp->choice) {
1175 case SEQLOC_NULL :
1176 break;
1177 case SEQLOC_EMPTY :
1178 case SEQLOC_WHOLE :
1179 sip = (SeqIdPtr) slp->data.ptrvalue;
1180 PromoteSeqIdList (sip, alsoCheckLocalAccn, findWorst);
1181 break;
1182 case SEQLOC_INT :
1183 sinp = (SeqIntPtr) slp->data.ptrvalue;
1184 if (sinp != NULL) {
1185 sip = sinp->id;
1186 PromoteSeqIdList (sip, alsoCheckLocalAccn, findWorst);
1187 }
1188 break;
1189 case SEQLOC_PNT :
1190 spp = (SeqPntPtr) slp->data.ptrvalue;
1191 if (spp != NULL) {
1192 sip = spp->id;
1193 PromoteSeqIdList (sip, alsoCheckLocalAccn, findWorst);
1194 }
1195 break;
1196 case SEQLOC_PACKED_PNT :
1197 psp = (PackSeqPntPtr) slp->data.ptrvalue;
1198 if (psp != NULL) {
1199 sip = psp->id;
1200 PromoteSeqIdList (sip, alsoCheckLocalAccn, findWorst);
1201 }
1202 break;
1203 case SEQLOC_PACKED_INT :
1204 case SEQLOC_MIX :
1205 case SEQLOC_EQUIV :
1206 loc = (SeqLocPtr) slp->data.ptrvalue;
1207 while (loc != NULL) {
1208 PromoteSeqLocList (loc, alsoCheckLocalAccn, findWorst);
1209 loc = loc->next;
1210 }
1211 break;
1212 case SEQLOC_BOND :
1213 sbp = (SeqBondPtr) slp->data.ptrvalue;
1214 if (sbp != NULL) {
1215 spp = (SeqPntPtr) sbp->a;
1216 if (spp != NULL) {
1217 sip = spp->id;
1218 PromoteSeqIdList (sip, alsoCheckLocalAccn, findWorst);
1219 }
1220 spp = (SeqPntPtr) sbp->b;
1221 if (spp != NULL) {
1222 sip = spp->id;
1223 PromoteSeqIdList (sip, alsoCheckLocalAccn, findWorst);
1224 }
1225 }
1226 break;
1227 case SEQLOC_FEAT :
1228 break;
1229 default :
1230 break;
1231 }
1232 slp = slp->next;
1233 }
1234 }
1235
1236
ChangeGBNameIDs(SeqIdPtr sip,Pointer userdata)1237 static void ChangeGBNameIDs (SeqIdPtr sip, Pointer userdata)
1238
1239 {
1240 Char buf [80];
1241 ObjectIdPtr oip;
1242 TextSeqIdPtr tsip;
1243
1244 if (sip == NULL || sip->choice != SEQID_GENBANK) return;
1245 tsip = (TextSeqIdPtr) sip->data.ptrvalue;
1246 if (tsip == NULL) return;
1247 if (tsip->accession != NULL || StringHasNoText (tsip->name)) return;
1248 StringNCpy (buf, tsip->name, sizeof (buf));
1249 TrimSpacesAroundString (buf);
1250 oip = ObjectIdNew ();
1251 if (oip == NULL) return;
1252 oip->str = StringSave (buf);
1253 sip->choice = SEQID_LOCAL;
1254 sip->data.ptrvalue = (Pointer) oip;
1255 TextSeqIdFree (tsip);
1256 }
1257
ChangeGBNameBioseq(BioseqPtr bsp,Pointer userdata)1258 static void ChangeGBNameBioseq (BioseqPtr bsp, Pointer userdata)
1259
1260 {
1261 VisitSeqIdsInBioseq (bsp, userdata, ChangeGBNameIDs);
1262 SeqMgrReplaceInBioseqIndex (bsp);
1263 }
1264
ChangeGBNameFeature(SeqFeatPtr sfp,Pointer userdata)1265 static void ChangeGBNameFeature (SeqFeatPtr sfp, Pointer userdata)
1266
1267 {
1268 VisitSeqIdsInSeqFeat (sfp, userdata, ChangeGBNameIDs);
1269 }
1270
ChangeGenBankNameToLocal(IteM i)1271 void ChangeGenBankNameToLocal (IteM i)
1272
1273 {
1274 BaseFormPtr bfp;
1275 SeqEntryPtr oldscope, sep;
1276
1277 #ifdef WIN_MAC
1278 bfp = currentFormDataPtr;
1279 #else
1280 bfp = GetObjectExtra (i);
1281 #endif
1282 if (bfp == NULL) return;
1283 sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
1284 if (sep == NULL) return;
1285
1286 oldscope = SeqEntrySetScope (sep);
1287
1288 VisitBioseqsInSep (sep, NULL, ChangeGBNameBioseq);
1289 VisitFeaturesInSep (sep, NULL, ChangeGBNameFeature);
1290
1291 SeqEntrySetScope (oldscope);
1292
1293 ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
1294 ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
1295 }
1296
1297
GetParentForSeqAnnot(SeqAnnotPtr sap)1298 static SeqEntryPtr GetParentForSeqAnnot (SeqAnnotPtr sap)
1299 {
1300 if (sap == NULL || sap->idx.parentptr == NULL) {
1301 return NULL;
1302 }
1303 if (sap->idx.parenttype == OBJ_BIOSEQSET) {
1304 return SeqMgrGetSeqEntryForData (sap->idx.parentptr);
1305 } else if (sap->idx.parenttype == OBJ_BIOSEQ) {
1306 return SeqMgrGetSeqEntryForData (sap->idx.parentptr);
1307 } else {
1308 return NULL;
1309 }
1310 }
1311
1312
PromoteAlignIDsProc(SeqAnnotPtr sp,Pointer data)1313 extern void PromoteAlignIDsProc (SeqAnnotPtr sp, Pointer data)
1314
1315 {
1316 DenseDiagPtr ddp;
1317 DenseSegPtr dsp;
1318 PackSegPtr psp;
1319 SeqAlignPtr sap;
1320 SeqLocPtr slp;
1321 StdSegPtr ssp;
1322 SeqEntryPtr orig_scope, new_scope = NULL;
1323
1324 if (sp == NULL || sp->type != 2) {
1325 return;
1326 }
1327 sap = (SeqAlignPtr) sp->data;
1328 if (sap == NULL) return;
1329
1330 new_scope = GetParentForSeqAnnot(sp);
1331
1332 orig_scope = SeqEntrySetScope (new_scope);
1333
1334 switch (sap->segtype) {
1335 case SAS_DENDIAG :
1336 for (ddp = sap->segs; ddp != NULL; ddp = ddp->next) {
1337 PromoteSeqIdList (ddp->id, TRUE, FALSE);
1338 }
1339 break;
1340 case SAS_DENSEG :
1341 dsp = sap->segs;
1342 if (dsp != NULL) {
1343 PromoteSeqIdList (dsp->ids, TRUE, FALSE);
1344 }
1345 break;
1346 case SAS_STD :
1347 for (ssp = sap->segs; ssp != NULL; ssp = ssp->next) {
1348 PromoteSeqIdList (ssp->ids, TRUE, FALSE);
1349 for (slp = ssp->loc; slp != NULL; slp = slp->next) {
1350 PromoteSeqLocList (slp, TRUE, FALSE);
1351 }
1352 }
1353 break;
1354 case SAS_PACKED :
1355 psp = (PackSegPtr) sap->segs;
1356 if (psp != NULL) {
1357 PromoteSeqIdList (psp->ids, TRUE, FALSE);
1358 }
1359 break;
1360 default :
1361 break;
1362 }
1363
1364 SeqEntrySetScope (orig_scope);
1365 }
1366
1367
RemoveGBIDsProc(GatherObjectPtr gop)1368 static Boolean RemoveGBIDsProc (GatherObjectPtr gop)
1369
1370 {
1371 BioseqPtr bsp;
1372 SeqIdPtr nextid, sip;
1373 SeqIdPtr PNTR previd;
1374
1375 if (gop->itemtype != OBJ_BIOSEQ) return TRUE;
1376 bsp = (BioseqPtr) gop->dataptr;
1377 if (bsp == NULL) return TRUE;
1378
1379 previd = (SeqIdPtr PNTR) &(bsp->id);
1380 sip = bsp->id;
1381 while (sip != NULL) {
1382 nextid = sip->next;
1383 if (sip->choice == SEQID_GENBANK) {
1384 *previd = sip->next;
1385 sip->next = NULL;
1386 SeqIdFree (sip);
1387 } else {
1388 previd = (SeqIdPtr PNTR) &(sip->next);
1389 }
1390 sip = sip->next;
1391 }
1392
1393 return TRUE;
1394 }
1395
RemoveGBIDsFromBioseqs(IteM i)1396 void RemoveGBIDsFromBioseqs (IteM i)
1397
1398 {
1399 MsgAnswer ans;
1400 BaseFormPtr bfp;
1401
1402 #ifdef WIN_MAC
1403 bfp = currentFormDataPtr;
1404 #else
1405 bfp = GetObjectExtra (i);
1406 #endif
1407 if (bfp == NULL) return;
1408
1409 ans = Message (MSG_OKC, "Currently deletes all GenBank SeqIDs");
1410 if (ans == ANS_CANCEL) return;
1411
1412 GatherObjectsInEntity (bfp->input_entityID, 0, NULL, RemoveGBIDsProc, NULL, NULL);
1413
1414 ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
1415 ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
1416 }
1417
RemoveGBProtIDsProc(GatherObjectPtr gop)1418 static Boolean RemoveGBProtIDsProc (GatherObjectPtr gop)
1419
1420 {
1421 BioseqPtr bsp;
1422 SeqIdPtr nextid, sip;
1423 SeqIdPtr PNTR previd;
1424
1425 if (gop->itemtype != OBJ_BIOSEQ) return TRUE;
1426 bsp = (BioseqPtr) gop->dataptr;
1427 if (bsp == NULL) return TRUE;
1428 if (! ISA_aa (bsp->mol)) return TRUE;
1429
1430 previd = (SeqIdPtr PNTR) &(bsp->id);
1431 sip = bsp->id;
1432 while (sip != NULL) {
1433 nextid = sip->next;
1434 if (sip->choice == SEQID_GENBANK) {
1435 *previd = sip->next;
1436 sip->next = NULL;
1437 SeqIdFree (sip);
1438 } else {
1439 previd = (SeqIdPtr PNTR) &(sip->next);
1440 }
1441 sip = sip->next;
1442 }
1443
1444 return TRUE;
1445 }
1446
RemoveGBIDsFromProteins(IteM i)1447 void RemoveGBIDsFromProteins (IteM i)
1448
1449 {
1450 MsgAnswer ans;
1451 BaseFormPtr bfp;
1452
1453 #ifdef WIN_MAC
1454 bfp = currentFormDataPtr;
1455 #else
1456 bfp = GetObjectExtra (i);
1457 #endif
1458 if (bfp == NULL) return;
1459
1460 ans = Message (MSG_OKC, "Currently deletes all GenBank SeqIDs");
1461 if (ans == ANS_CANCEL) return;
1462
1463 GatherObjectsInEntity (bfp->input_entityID, 0, NULL, RemoveGBProtIDsProc, NULL, NULL);
1464
1465 ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
1466 ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
1467 }
1468
RemoveGIProc(GatherObjectPtr gop)1469 static Boolean RemoveGIProc (GatherObjectPtr gop)
1470
1471 {
1472 BioseqPtr bsp;
1473 SeqIdPtr nextid, sip;
1474 SeqIdPtr PNTR previd;
1475
1476 if (gop->itemtype != OBJ_BIOSEQ) return TRUE;
1477 bsp = (BioseqPtr) gop->dataptr;
1478 if (bsp == NULL) return TRUE;
1479
1480 previd = (SeqIdPtr PNTR) &(bsp->id);
1481 sip = bsp->id;
1482 while (sip != NULL) {
1483 nextid = sip->next;
1484 if (sip->choice == SEQID_GI) {
1485 *previd = sip->next;
1486 sip->next = NULL;
1487 SeqIdFree (sip);
1488 } else {
1489 previd = (SeqIdPtr PNTR) &(sip->next);
1490 }
1491 sip = sip->next;
1492 }
1493
1494 return TRUE;
1495 }
1496
RemoveGIsFromBioseqs(IteM i)1497 void RemoveGIsFromBioseqs (IteM i)
1498
1499 {
1500 MsgAnswer ans;
1501 BaseFormPtr bfp;
1502
1503 #ifdef WIN_MAC
1504 bfp = currentFormDataPtr;
1505 #else
1506 bfp = GetObjectExtra (i);
1507 #endif
1508 if (bfp == NULL) return;
1509
1510 ans = Message (MSG_OKC, "Currently deletes all GI SeqIDs");
1511 if (ans == ANS_CANCEL) return;
1512
1513 GatherObjectsInEntity (bfp->input_entityID, 0, NULL, RemoveGIProc, NULL, NULL);
1514
1515 ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
1516 ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
1517 }
1518
1519
DoBuildContig(void)1520 extern Boolean DoBuildContig (void)
1521
1522 {
1523 MsgAnswer ans;
1524 BioseqPtr bsp;
1525 Pointer dataptr;
1526 Uint2 datatype;
1527 Uint2 entityID;
1528 FILE *fp;
1529 Int2 handled;
1530 Char path [PATH_MAX];
1531 SeqEntryPtr sep;
1532
1533 if (! GetInputFileName (path, sizeof (path), NULL, "TEXT")) return FALSE;
1534 fp = FileOpen (path, "r");
1535 if (fp == NULL) return FALSE;
1536 ans = Message (MSG_YN, "Are coordinates on the master (as opposed to the individual accession)?");
1537 sep = ReadContigList (fp, (Boolean) (ans == ANS_YES));
1538 FileClose (fp);
1539 if (sep == NULL || sep->choice != 1) return FALSE;
1540
1541 bsp = (BioseqPtr) sep->data.ptrvalue;
1542 if (bsp == NULL) return FALSE;
1543 datatype = OBJ_BIOSEQ;
1544 dataptr = (Pointer) bsp;
1545 entityID = ObjMgrRegister (datatype, dataptr);
1546 if (dataptr == NULL || entityID == 0) return FALSE;
1547
1548 WatchCursor ();
1549 Update ();
1550 handled = GatherProcLaunch (OMPROC_VIEW, FALSE, entityID, 1,
1551 OBJ_BIOSEQ, 0, 0, OBJ_BIOSEQ, 0);
1552 ArrowCursor ();
1553 Update ();
1554
1555 if (handled != OM_MSG_RET_DONE || handled == OM_MSG_RET_NOPROC) {
1556 Message (MSG_FATAL, "Unable to launch viewer.");
1557 SeqEntryFree (sep);
1558 return FALSE;
1559 }
1560
1561 ObjMgrSetOptions (OM_OPT_FREE_IF_NO_VIEW, entityID);
1562 ObjMgrSetDirtyFlag (entityID, TRUE);
1563 return TRUE;
1564 }
1565
DoParseTrinomial(BioSourcePtr biop,Pointer userdata)1566 static void DoParseTrinomial (BioSourcePtr biop, Pointer userdata)
1567
1568 {
1569 BinomialOrgNamePtr bonp;
1570 OrgModPtr omp;
1571 OrgNamePtr onp;
1572 OrgRefPtr orp;
1573 CharPtr str;
1574
1575 if (biop == NULL) return;
1576 orp = biop->org;
1577 if (orp == NULL) return;
1578 onp = orp->orgname;
1579 if (onp == NULL) return;
1580 if (onp->choice != 1) return;
1581 bonp = (BinomialOrgNamePtr) onp->data;
1582 if (bonp == NULL) return;
1583 if (StringHasNoText (bonp->subspecies)) return;
1584 for (omp = onp->mod; omp != NULL; omp = omp->next) {
1585 if (omp->subtype == ORGMOD_sub_species) return;
1586 }
1587 str = bonp->subspecies;
1588 if (StringNICmp (str, "subsp. ", 7) == 0) {
1589 str += 7;
1590 if (StringHasNoText (str)) return;
1591 }
1592 omp = OrgModNew ();
1593 if (omp == NULL) return;
1594 omp->subtype = ORGMOD_sub_species;
1595 omp->subname = StringSave (str);
1596 omp->next = onp->mod;
1597 onp->mod = omp;
1598 }
1599
1600 extern void ParseTrinomial (IteM i);
ParseTrinomial(IteM i)1601 extern void ParseTrinomial (IteM i)
1602
1603 {
1604 BaseFormPtr bfp;
1605 SeqEntryPtr sep;
1606
1607 #ifdef WIN_MAC
1608 bfp = currentFormDataPtr;
1609 #else
1610 bfp = GetObjectExtra (i);
1611 #endif
1612 if (bfp == NULL) return;
1613 sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
1614 if (sep == NULL) return;
1615
1616 VisitBioSourcesInSep (sep, NULL, DoParseTrinomial);
1617
1618 ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
1619 ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
1620 Update ();
1621 }
1622
1623
1624
1625 #define NUM_SITES 27
1626 static CharPtr siteString [NUM_SITES] = {
1627 "", "active site", "binding site", "cleavage site", "inhibition site", "modified site",
1628 "glycosylation site", "myristoylation site", "mutagenized site", "metal binding site",
1629 "phosphorylation site", "acetylation site", "amidation site", "methylation site",
1630 "hydroxylation site", "sulfatation site", "oxidative deamination site",
1631 "pyrrolidone carboxylic acid site", "gamma carboxyglutamic acid site",
1632 "blocked site", "lipid binding site", "np binding site", "DNA binding site",
1633 "signal peptide", "transit peptide", "transmembrane region", "nitrosylation"
1634 };
1635
1636 /*=========================================================================*/
1637 /* */
1638 /* SeqLocAdjustByOffset () */
1639 /* */
1640 /*=========================================================================*/
1641
SeqLocAdjustByOffset(SeqLocPtr slp,Int4 offset)1642 extern void SeqLocAdjustByOffset (SeqLocPtr slp,
1643 Int4 offset)
1644 {
1645 SeqIntPtr sinp;
1646
1647 switch (slp->choice) {
1648 case SEQLOC_INT :
1649 sinp = (SeqIntPtr) slp->data.ptrvalue;
1650 if (NULL == sinp)
1651 break;
1652 sinp->from += offset;
1653 sinp->to += offset;
1654 break;
1655 case SEQLOC_EMPTY :
1656 case SEQLOC_NULL :
1657 case SEQLOC_WHOLE :
1658 case SEQLOC_PNT :
1659 case SEQLOC_PACKED_PNT :
1660 case SEQLOC_PACKED_INT :
1661 case SEQLOC_MIX :
1662 case SEQLOC_EQUIV :
1663 case SEQLOC_BOND :
1664 case SEQLOC_FEAT :
1665 default :
1666 break;
1667 }
1668 }
1669
1670
ConvertImpToSpecialRNA(SeqFeatPtr sfp,Uint2 featdef_to,Pointer extradata)1671 static Boolean ConvertImpToSpecialRNA
1672 (SeqFeatPtr sfp,
1673 Uint2 featdef_to,
1674 Pointer extradata)
1675 {
1676 RnaRefPtr rrp;
1677
1678 if (sfp == NULL || sfp->data.choice != SEQFEAT_IMP)
1679 {
1680 return FALSE;
1681 }
1682 rrp = RnaRefNew ();
1683 if (rrp != NULL) {
1684 sfp->data.value.ptrvalue = ImpFeatFree ((ImpFeatPtr) sfp->data.value.ptrvalue);
1685 sfp->data.choice = SEQFEAT_RNA;
1686 sfp->data.value.ptrvalue = (Pointer) rrp;
1687 if (featdef_to == FEATDEF_precursor_RNA) {
1688 rrp->type = 1;
1689 } else {
1690 rrp->type = 255;
1691 }
1692 }
1693 return TRUE;
1694 }
1695
ConvertRegionToRNA(SeqFeatPtr sfp,Uint2 featdef_to,Pointer extradata)1696 static Boolean ConvertRegionToRNA
1697 (SeqFeatPtr sfp,
1698 Uint2 featdef_to,
1699 Pointer extradata)
1700 {
1701 RnaRefPtr rrp;
1702 CharPtr str;
1703
1704 if (sfp == NULL || sfp->data.choice != SEQFEAT_REGION)
1705 {
1706 return FALSE;
1707 }
1708
1709 rrp = RnaRefNew ();
1710 if (NULL == rrp)
1711 {
1712 return FALSE;
1713 }
1714
1715 str = (CharPtr) sfp->data.value.ptrvalue;
1716 sfp->data.choice = SEQFEAT_RNA;
1717 sfp->data.value.ptrvalue = (Pointer) rrp;
1718
1719 if (featdef_to == FEATDEF_precursor_RNA) {
1720 rrp->type = 1;
1721 } else {
1722 rrp->type = 255;
1723 }
1724
1725 if (! StringHasNoText (str)) {
1726 rrp->ext.choice = 1;
1727 rrp->ext.value.ptrvalue = str;
1728 }
1729 return TRUE;
1730 }
1731
1732
CommentShouldBeProduct(CharPtr comment)1733 static Boolean CommentShouldBeProduct (CharPtr comment)
1734 {
1735 CharPtr search1 = "internal transcribed spacer ";
1736 CharPtr search2 = "ITS";
1737 CharPtr found;
1738 Int4 len;
1739
1740 if (StringHasNoText (comment)) {
1741 return FALSE;
1742 }
1743 if ((found = StringISearch (comment, search1)) != NULL
1744 && (len = StringLen (search1)) < StringLen (found)
1745 && (*(found + len) == '1' || *(found + len) == '2' || *(found + len) == '3')) {
1746 return TRUE;
1747 }
1748
1749 if ((found = StringISearch (comment, search2)) != NULL
1750 && (len = StringLen (search2)) < StringLen (found)
1751 && (*(found + len) == '1' || *(found + len) == '2' || *(found + len) == '3')) {
1752 return TRUE;
1753 }
1754 return FALSE;
1755 }
1756
1757
ConvertImpToRNA(SeqFeatPtr sfp,Uint2 featdef_to,Pointer extradata)1758 static Boolean ConvertImpToRNA
1759 (SeqFeatPtr sfp,
1760 Uint2 featdef_to,
1761 Pointer extradata)
1762 {
1763 RnaRefPtr rrp;
1764 RNAGenPtr rgp;
1765 Boolean was_misc_feat = FALSE;
1766
1767 if (sfp == NULL || sfp->data.choice != SEQFEAT_IMP)
1768 {
1769 return FALSE;
1770 }
1771 if (sfp->idx.subtype == FEATDEF_misc_feature) {
1772 was_misc_feat = TRUE;
1773 }
1774
1775 rrp = RnaRefNew ();
1776 if (NULL == rrp)
1777 return FALSE;
1778
1779 sfp->data.value.ptrvalue =
1780 ImpFeatFree ((ImpFeatPtr) sfp->data.value.ptrvalue);
1781 sfp->data.choice = SEQFEAT_RNA;
1782 sfp->data.value.ptrvalue = (Pointer) rrp;
1783
1784 switch (featdef_to) {
1785 case FEATDEF_preRNA :
1786 rrp->type = 1;
1787 break;
1788 case FEATDEF_mRNA :
1789 rrp->type = 2;
1790 break;
1791 case FEATDEF_tRNA :
1792 rrp->type = 3;
1793 break;
1794 case FEATDEF_rRNA :
1795 rrp->type = 4;
1796 break;
1797 case FEATDEF_snRNA :
1798 rrp->type = 5;
1799 break;
1800 case FEATDEF_scRNA :
1801 rrp->type = 6;
1802 break;
1803 case FEATDEF_snoRNA :
1804 rrp->type = 7;
1805 break;
1806 case FEATDEF_ncRNA :
1807 rrp->type = 8;
1808 rrp->ext.choice = 3;
1809 rrp->ext.value.ptrvalue = RNAGenNew ();
1810 break;
1811 case FEATDEF_tmRNA :
1812 rrp->type = 9;
1813 rrp->ext.choice = 3;
1814 rrp->ext.value.ptrvalue = RNAGenNew ();
1815 break;
1816 case FEATDEF_misc_RNA:
1817 rrp->type = 10;
1818 rrp->ext.choice = 3;
1819 rgp = RNAGenNew ();
1820 rrp->ext.value.ptrvalue = rgp;
1821 if (was_misc_feat && CommentShouldBeProduct(sfp->comment)) {
1822 rgp->product = sfp->comment;
1823 sfp->comment = NULL;
1824 }
1825 break;
1826 case FEATDEF_otherRNA :
1827 if (was_misc_feat && CommentShouldBeProduct(sfp->comment)) {
1828 rrp->type = 10;
1829 rrp->ext.choice = 3;
1830 rgp = RNAGenNew ();
1831 rrp->ext.value.ptrvalue = rgp;
1832 rgp->product = sfp->comment;
1833 sfp->comment = NULL;
1834 } else {
1835 rrp->type = 255;
1836 rrp->ext.choice = 1;
1837 rrp->ext.value.ptrvalue = StringSave ("misc_RNA");
1838 }
1839 break;
1840 default :
1841 break;
1842 }
1843 return TRUE;
1844 }
1845
ConvertCommentToMiscFeat(SeqFeatPtr sfp,Uint2 featdef_to,Pointer extradata)1846 static Boolean ConvertCommentToMiscFeat (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata)
1847 {
1848 ImpFeatPtr ifp;
1849
1850 if (sfp == NULL || sfp->data.choice != SEQFEAT_COMMENT || sfp->data.value.ptrvalue != NULL)
1851 {
1852 return FALSE;
1853 }
1854
1855 ifp = ImpFeatNew ();
1856 if (ifp != NULL) {
1857 ifp->key = StringSave ("misc_feature");
1858 sfp->data.choice = SEQFEAT_IMP;
1859 sfp->data.value.ptrvalue = (Pointer) ifp;
1860 return TRUE;
1861 }
1862 return FALSE;
1863 }
1864
ConvertGeneToImpFeat(SeqFeatPtr sfp,Uint2 featdef_to,Pointer extradata)1865 static Boolean ConvertGeneToImpFeat
1866 (SeqFeatPtr sfp,
1867 Uint2 featdef_to,
1868 Pointer extradata)
1869 {
1870 return ConvertGeneToImpFeatFunc (sfp, featdef_to);
1871 }
1872
ConvertRNAToMiscFeat(SeqFeatPtr sfp,Uint2 featdef_to,Pointer extradata)1873 static Boolean ConvertRNAToMiscFeat
1874 (SeqFeatPtr sfp,
1875 Uint2 featdef_to,
1876 Pointer extradata)
1877 {
1878 return ConvertRNAToImpFeat (sfp, featdef_to);
1879 }
1880
ConvertSiteToMiscFeat(SeqFeatPtr sfp,Uint2 featdef_to,Pointer extradata)1881 static Boolean ConvertSiteToMiscFeat
1882 (SeqFeatPtr sfp,
1883 Uint2 featdef_to,
1884 Pointer extradata)
1885 {
1886 GBQualPtr gbqual;
1887 ImpFeatPtr ifp;
1888 Int2 sitetype;
1889
1890 if (sfp == NULL || sfp->data.choice != SEQFEAT_SITE)
1891 {
1892 return FALSE;
1893 }
1894
1895 ifp = ImpFeatNew ();
1896 if (NULL == ifp)
1897 {
1898 return FALSE;
1899 }
1900
1901 sitetype = (Int2) sfp->data.value.intvalue;
1902 sfp->data.choice = SEQFEAT_IMP;
1903 sfp->data.value.ptrvalue = (Pointer) ifp;
1904 ifp->key = StringSave ("misc_feature");
1905 if (sitetype > 0 && sitetype < NUM_SITES) {
1906 gbqual = GBQualNew ();
1907 if (gbqual != NULL) {
1908 gbqual->qual = StringSave ("note");
1909 gbqual->val = StringSave (siteString [sitetype]);
1910 gbqual->next = sfp->qual;
1911 sfp->qual = gbqual;
1912 }
1913 }
1914 return TRUE;
1915 }
1916
ConvertProtToRegion(SeqFeatPtr sfp,Uint2 featdef_to,Pointer extradata)1917 static Boolean ConvertProtToRegion
1918 (SeqFeatPtr sfp,
1919 Uint2 featdef_to,
1920 Pointer extradata)
1921 {
1922 ProtRefPtr prp;
1923 ValNodePtr vnp;
1924 CharPtr str;
1925
1926 if (sfp == NULL || sfp->data.choice != SEQFEAT_PROT)
1927 {
1928 return FALSE;
1929 }
1930 prp = (ProtRefPtr) sfp->data.value.ptrvalue;
1931 if (NULL == prp)
1932 {
1933 return FALSE;
1934 }
1935
1936 vnp = prp->name;
1937 if (vnp != NULL && vnp->next == NULL) {
1938 str = (CharPtr) vnp->data.ptrvalue;
1939 if (! StringHasNoText (str)) {
1940 vnp->data.ptrvalue = NULL;
1941 sfp->data.value.ptrvalue = ProtRefFree (prp);
1942 sfp->data.choice = SEQFEAT_REGION;
1943 sfp->data.value.ptrvalue = (Pointer) str;
1944 }
1945 }
1946 return TRUE;
1947 }
1948
1949
ConvertRegionToProt(SeqFeatPtr sfp,Uint2 featdef_to,Pointer extradata)1950 static Boolean ConvertRegionToProt
1951 (SeqFeatPtr sfp,
1952 Uint2 featdef_to,
1953 Pointer extradata)
1954 {
1955 return ConvertRegionToProtFunc (sfp, featdef_to);
1956 }
1957
1958
ConvertRNAToNcRNA(SeqFeatPtr sfp)1959 static Boolean ConvertRNAToNcRNA
1960 (SeqFeatPtr sfp)
1961 {
1962 RnaRefPtr rrp;
1963 tRNAPtr trp;
1964 RNAGenPtr rgp = NULL;
1965
1966 if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA) return FALSE;
1967
1968 rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
1969 if (NULL == rrp) {
1970 rrp = RnaRefNew ();
1971 sfp->data.value.ptrvalue = rrp;
1972 }
1973
1974 if (rrp->ext.choice == 2) {
1975 trp = (tRNAPtr) rrp->ext.value.ptrvalue;
1976 if (trp != NULL) {
1977 trp->anticodon = SeqLocFree (trp->anticodon);
1978 trp = MemFree (trp);
1979 rrp->ext.value.ptrvalue = trp;
1980 }
1981 rrp->ext.choice = 0;
1982 }
1983
1984 /* might be converting from other ncRNA, tmRNA, or misc_RNA */
1985 if (rrp->ext.choice == 1) {
1986 rgp = RNAGenNew ();
1987 rgp->product = rrp->ext.value.ptrvalue;
1988 rrp->ext.choice = 3;
1989 rrp->ext.value.ptrvalue = rgp;
1990 } else if (rrp->ext.choice == 0) {
1991 rgp = RNAGenNew ();
1992 rrp->ext.choice = 3;
1993 rrp->ext.value.ptrvalue = rgp;
1994 } else if (rrp->ext.choice == 3) {
1995 rgp = rrp->ext.value.ptrvalue;
1996 if (rgp == NULL) {
1997 rgp = RNAGenNew ();
1998 rrp->ext.value.ptrvalue = rgp;
1999 }
2000 }
2001
2002 if (rgp != NULL) {
2003 if (rrp->type == 5) {
2004 rgp->_class = StringSave ("snRNA");
2005 } else if (rrp->type == 6) {
2006 rgp->_class = StringSave ("scRNA");
2007 } else if (rrp->type == 7) {
2008 rgp->_class = StringSave ("snoRNA");
2009 }
2010 }
2011
2012 rrp->type = 8;
2013 return TRUE;
2014 }
2015
2016
ConvertFromncRNAtoMiscRNA(SeqFeatPtr sfp)2017 static void ConvertFromncRNAtoMiscRNA (SeqFeatPtr sfp)
2018 {
2019 RnaRefPtr rrp;
2020 RNAGenPtr rgp;
2021 CharPtr tmp;
2022
2023 if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA) return;
2024 rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
2025 if (rrp == NULL || rrp->ext.choice != 3) {
2026 return;
2027 }
2028
2029 rgp = (RNAGenPtr) rrp->ext.value.ptrvalue;
2030 if (rgp == NULL) {
2031 return;
2032 }
2033
2034 /* if no product but has comment, promote comment to product */
2035 if (rgp->product == NULL && !StringHasNoText (sfp->comment)) {
2036 rgp->product = sfp->comment;
2037 sfp->comment = NULL;
2038 }
2039
2040 /* move ncRNA_class elsewhere */
2041 if (!StringHasNoText (rgp->_class)) {
2042 if (StringCmp (rgp->_class, "other") == 0) {
2043 rgp->_class = MemFree (rgp->_class);
2044 } else if (rgp->product == NULL) {
2045 rgp->product = rgp->_class;
2046 rgp->_class = NULL;
2047 } else {
2048 if (StringHasNoText (sfp->comment)) {
2049 sfp->comment = MemFree (sfp->comment);
2050 sfp->comment = StringSave (rgp->_class);
2051 } else {
2052 tmp = (CharPtr) MemNew (sizeof (Char) * (StringLen (sfp->comment) + StringLen (rgp->_class) + 3));
2053 sprintf (tmp, "%s; %s", sfp->comment, rgp->_class);
2054 sfp->comment = MemFree (sfp->comment);
2055 sfp->comment = tmp;
2056 }
2057 rgp->_class = MemFree (rgp->_class);
2058 }
2059 }
2060 }
2061
2062
ConvertRNAToRNA(SeqFeatPtr sfp,Uint2 featdef_to,Pointer extradata)2063 static Boolean ConvertRNAToRNA
2064 (SeqFeatPtr sfp,
2065 Uint2 featdef_to,
2066 Pointer extradata)
2067 {
2068 RnaRefPtr rrp;
2069 Boolean from_misc = FALSE, to_misc = FALSE;
2070 GBQualPtr gbq, gbq_p = NULL;
2071
2072 rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
2073 if (NULL == rrp)
2074 return FALSE;
2075
2076 if (rrp->type == 255) {
2077 from_misc = TRUE;
2078 }
2079
2080 switch (featdef_to) {
2081 case FEATDEF_preRNA :
2082 rrp->type = 1;
2083 break;
2084 case FEATDEF_mRNA :
2085 rrp->type = 2;
2086 break;
2087 case FEATDEF_tRNA :
2088 rrp->type = 3;
2089 break;
2090 case FEATDEF_rRNA :
2091 rrp->type = 4;
2092 break;
2093 case FEATDEF_snRNA :
2094 rrp->type = 5;
2095 to_misc = TRUE;
2096 break;
2097 case FEATDEF_scRNA :
2098 rrp->type = 6;
2099 to_misc = TRUE;
2100 break;
2101 case FEATDEF_snoRNA :
2102 rrp->type = 7;
2103 to_misc = TRUE;
2104 break;
2105 case FEATDEF_ncRNA :
2106 return ConvertRNAToNcRNA (sfp);
2107 break;
2108 case FEATDEF_otherRNA :
2109 rrp->type = 255;
2110 ConvertFromncRNAtoMiscRNA (sfp);
2111 break;
2112 default:
2113 break;
2114 }
2115 if (from_misc && !to_misc && rrp->ext.choice == 1 && StringCmp (rrp->ext.value.ptrvalue, "misc_RNA") == 0) {
2116 /* move product qual to string */
2117 gbq = sfp->qual;
2118 while (gbq != NULL && StringCmp (gbq->qual, "product") != 0) {
2119 gbq_p = gbq;
2120 gbq = gbq->next;
2121 }
2122 if (gbq == NULL) {
2123 rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
2124 rrp->ext.choice = 0;
2125 } else {
2126 rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
2127 rrp->ext.value.ptrvalue = gbq->val;
2128 gbq->val = NULL;
2129 if (gbq_p == NULL) {
2130 sfp->qual = gbq->next;
2131 } else {
2132 gbq_p->next = gbq->next;
2133 }
2134 gbq->next = NULL;
2135 gbq = GBQualFree (gbq);
2136 }
2137 }
2138 return TRUE;
2139 }
2140
ConvertncRNAToMiscBinding(SeqFeatPtr sfp,Uint2 featdef_to,Pointer extradata)2141 static Boolean ConvertncRNAToMiscBinding
2142 (SeqFeatPtr sfp,
2143 Uint2 featdef_to,
2144 Pointer extradata)
2145 {
2146 RnaRefPtr rrp;
2147 RNAGenPtr rgp;
2148 Boolean asked = TRUE, replace = FALSE, use_semicolon = TRUE;
2149 ImpFeatPtr ifp;
2150
2151 rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
2152 if (NULL == rrp)
2153 return FALSE;
2154
2155 if (rrp->ext.choice == 1) {
2156 /* move product to note */
2157 AppendOrReplaceString (&(sfp->comment), rrp->ext.value.ptrvalue, &asked, &replace, &use_semicolon);
2158 } else if (rrp->ext.choice == 3 && (rgp = (RNAGenPtr) rrp->ext.value.ptrvalue) != NULL
2159 && !StringHasNoText (rgp->product)) {
2160 AppendOrReplaceString (&(sfp->comment), rgp->product, &asked, &replace, &use_semicolon);
2161 }
2162 rrp = RnaRefFree (rrp);
2163 sfp->data.choice = SEQFEAT_IMP;
2164 ifp = ImpFeatNew ();
2165 ifp->key = StringSave ("misc_binding");
2166 sfp->data.value.ptrvalue = ifp;
2167 sfp->idx.subtype = 0;
2168
2169 return TRUE;
2170 }
2171
ConvertProtToProt(SeqFeatPtr sfp,Uint2 featdef_to,Pointer extradata)2172 static Boolean ConvertProtToProt
2173 (SeqFeatPtr sfp,
2174 Uint2 featdef_to,
2175 Pointer extradata)
2176 {
2177 return ConvertProtToProtFunc (sfp, featdef_to);
2178 }
2179
2180
ConvertImpToProt(SeqFeatPtr sfp,Uint2 featdef_to,Pointer extradata)2181 static Boolean ConvertImpToProt (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata)
2182 {
2183 return ConvertImpToProtFunc (sfp, featdef_to);
2184 }
2185
2186
ConvertProtToImp(SeqFeatPtr sfp,Uint2 featdef_to,Pointer extradata)2187 static Boolean ConvertProtToImp (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata)
2188 {
2189 return ConvertProtToImpFunc (sfp, featdef_to);
2190 }
2191
2192
ConvertBioSrcToRepeatRegionEx(SeqFeatPtr sfp,Uint2 featdef_to,Pointer extradata)2193 static Boolean ConvertBioSrcToRepeatRegionEx (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata)
2194 {
2195 return ConvertBioSrcToRepeatRegion (sfp, featdef_to);
2196 }
2197
2198
ConvertCDSToMatPeptide(SeqFeatPtr sfp,Uint2 featdef_to,Pointer extradata)2199 static Boolean ConvertCDSToMatPeptide (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata)
2200 {
2201 return AutoConvertCDSToMiscFeat (sfp, extradata == NULL ? TRUE : !(*((BoolPtr) extradata)));
2202 }
2203
2204
ConvertMiscFeatureToCDSFunction(SeqFeatPtr sfp,Uint2 featdef_to,Pointer extradata)2205 static Boolean ConvertMiscFeatureToCDSFunction (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata)
2206 {
2207 return ConvertMiscFeatToCodingRegion (sfp);
2208 }
2209
2210
ConvertmRNAToCodingRegionFunction(SeqFeatPtr sfp,Uint2 featdef_to,Pointer extradata)2211 static Boolean ConvertmRNAToCodingRegionFunction (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata)
2212 {
2213 return ConvertmRNAToCodingRegion (sfp);
2214 }
2215
2216
ConverttRNAToGeneFunction(SeqFeatPtr sfp,Uint2 featdef_to,Pointer extradata)2217 static Boolean ConverttRNAToGeneFunction (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata)
2218 {
2219 return ConverttRNAToGene (sfp);
2220 }
2221
2222
ConvertMiscFeatureToGeneFunction(SeqFeatPtr sfp,Uint2 featdef_to,Pointer extradata)2223 static Boolean ConvertMiscFeatureToGeneFunction (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata)
2224 {
2225 return ConvertMiscFeatToGene (sfp);
2226 }
2227
2228
2229 extern EnumFieldAssoc enum_bond_alist [];
2230 extern EnumFieldAssoc enum_site_alist [];
2231
2232
2233 static GbFeatName EditQualifierList[] = {
2234 {"allele", Class_text},
2235 {"anticodon", Class_pos_aa},
2236 {"bound_moiety", Class_text},
2237 {"chromosome", Class_text},
2238 {"citation", Class_bracket_int},
2239 {"codon", Class_seq_aa},
2240 {"codon_start", Class_int_or},
2241 {"compare", Class_text },
2242 {"cons_splice", Class_site},
2243 {"db_xref", Class_text},
2244 {"direction", Class_L_R_B},
2245 {"EC_number", Class_ecnum},
2246 {"evidence", Class_exper},
2247 {"exception", Class_text},
2248 {"experiment", Class_text},
2249 {"frequency", Class_text},
2250 {"function", Class_text},
2251 {"gene", Class_text},
2252 {"gdb_xref", Class_text},
2253 {"label", Class_token},
2254 {"map", Class_text},
2255 {"mobile_element", Class_text},
2256 {"mod_base", Class_token}, {"note", Class_note},
2257 {"number", Class_number},
2258 #ifdef INTERNAL_NCBI_SEQUIN
2259 {"old_locus_tag", Class_text},
2260 #endif
2261 {"operon", Class_text},
2262 {"organism", Class_text},
2263 {"partial", Class_none}, {"PCR_conditions", Class_text},
2264 {"phenotype", Class_text},
2265 {"plasmid", Class_text}, {"product", Class_text},
2266 {"pseudo", Class_none},
2267 {"rearranged", Class_none}, { "replace", Class_text},
2268 {"rpt_family", Class_text}, {"rpt_type", Class_rpt},
2269 {"rpt_unit", Class_token}, {"rpt_unit_seq", Class_token}, {"rpt_unit_range", Class_token},
2270 {"satellite", Class_text},
2271 {"sequenced_mol", Class_text},
2272 {"standard_name", Class_text},
2273 {"translation", Class_text}, {"transl_except", Class_pos_aa},
2274 {"transl_table", Class_int},
2275 {"usedin", Class_token},
2276 {"focus", Class_none},
2277 {"protein_id", Class_text},
2278 {"organelle", Class_text}, {"transcript_id", Class_text},
2279 {"transgenic", Class_none}, {"environmental_sample", Class_none},
2280 {"locus_tag", Class_text}, {"mol_type", Class_text},
2281 {"segment", Class_text}
2282 };
2283
2284 const Int4 NumEditQualifiers = sizeof (EditQualifierList) / sizeof (GbFeatName);
2285 #define QUAL_EVIDENCE 13
2286 #define QUAL_EXPERIMENT 15
2287
2288
ENUM_ALIST(biosource_genome_alistX)2289 static ENUM_ALIST(biosource_genome_alistX)
2290 {" ", 0},
2291 {"Apicoplast", 16},
2292 {"Chloroplast", 2},
2293 {"Chromatophore", 22},
2294 {"Chromoplast", 3},
2295 {"Chromosome", 21},
2296 {"Cyanelle", 12},
2297 {"Endogenous-virus", 19},
2298 {"Extrachromosomal", 8},
2299 {"Genomic", 1},
2300 {"Hydrogenosome", 20},
2301 {"Insertion Sequence", 11},
2302 {"Kinetoplast", 4},
2303 {"Leucoplast", 17},
2304 {"Macronuclear", 7},
2305 {"Mitochondrion", 5},
2306 {"Nucleomorph", 15},
2307 {"Plasmid", 9},
2308 {"Plastid", 6},
2309 {"Proplastid", 18},
2310 {"Proviral", 13},
2311 {"Transposon", 10},
2312 END_ENUM_ALIST
2313
2314 static ENUM_ALIST(orgref_textfield_alist)
2315 {" ", 0},
2316 {"Scientific Name", 1},
2317 {"Common Name", 2},
2318 {"Lineage", 3},
2319 {"Division", 4},
2320 END_ENUM_ALIST
2321
2322 typedef struct sourceformdata {
2323 FEATURE_FORM_BLOCK
2324
2325 Int2 type;
2326 ButtoN applyToParts;
2327 TexT onlyThisPart;
2328 GrouP sourceGroup;
2329 GrouP modGrp;
2330 GrouP genGrp;
2331 GrouP refGrp;
2332 GrouP txtGrp;
2333 GrouP originGrp;
2334 PopuP frommod;
2335 PopuP tomod;
2336 PopuP fromgen;
2337 PopuP togen;
2338 PopuP fromref;
2339 PopuP toref;
2340 PopuP toorigin;
2341 PopuP fromorigin;
2342 TexT findthis;
2343 TexT replacewith;
2344 GrouP applyChoiceGrp; /* This is the group for the radio buttons for the
2345 * constraint on which biosources to operate on.
2346 */
2347 PopuP qual_to_have; /* This is the control that indicates which qualifier
2348 * should be present to operate on a biosource.
2349 */
2350 TexT text_to_have; /* This is the control that indicates the text that
2351 * should be present in the biosource to be operated on.
2352 */
2353 Int4 applyChoiceVal; /* This is the value of the applyChoiceGrp choice. */
2354 CharPtr text_to_have_str;/* This is the contents of the text_to_have box. */
2355 Int4 qual_to_have_val;/* This is the subtype for the qual to have. */
2356
2357 Int2 choice;
2358 Int2 fromval;
2359 Int2 toval;
2360 Int2 onlythis;
2361 CharPtr findStr;
2362 CharPtr replaceStr;
2363
2364 Boolean replaceOldAsked;
2365 Boolean doReplaceAll;
2366 Boolean use_semicolon;
2367 ButtoN leaveDlgUp;
2368 } SourceFormData, PNTR SourceFormPtr;
2369
2370 Uint2 mod_widths [] = {
2371 0, 25
2372 };
2373
2374 Uint2 mod_types [] = {
2375 TAGLIST_POPUP, TAGLIST_TEXT
2376 };
2377
2378
FindTypeForModNameText(CharPtr cp)2379 extern Uint1 FindTypeForModNameText (CharPtr cp)
2380 {
2381 Uint1 subtype;
2382
2383 subtype = EquivalentSubSourceEx (cp, TRUE);
2384 if (subtype == 0) {
2385 subtype = EquivalentOrgMod (cp);
2386 if (subtype > 200) {
2387 /* function that calls this expects less than 100 vals for orgmod */
2388 /* need to adjust for old-lineage and old-name */
2389 subtype -= 200;
2390 }
2391 } else {
2392 /* function that calls this uses >100 to decide if subsource */
2393 subtype += 100;
2394 }
2395 if (subtype == 0) {
2396 subtype = SUBSRC_other;
2397 }
2398 return subtype;
2399 }
2400
2401
AppendOrReplaceString(CharPtr PNTR string_loc,CharPtr new_value,Boolean PNTR asked_question,Boolean PNTR do_replace,Boolean PNTR use_semicolon)2402 extern void AppendOrReplaceString (
2403 CharPtr PNTR string_loc,
2404 CharPtr new_value,
2405 Boolean PNTR asked_question,
2406 Boolean PNTR do_replace,
2407 Boolean PNTR use_semicolon
2408 )
2409 {
2410 MsgAnswer ans;
2411 CharPtr tmp_value, tmp_new_value;
2412
2413 if (string_loc == NULL
2414 || new_value == NULL
2415 || asked_question == NULL
2416 || do_replace == NULL
2417 || use_semicolon == NULL)
2418 {
2419 return;
2420 }
2421
2422 if (! *asked_question && !StringHasNoText (*string_loc))
2423 {
2424 *asked_question = TRUE;
2425 ArrowCursor ();
2426 ans = Message (MSG_YN, "Do you wish to overwrite existing content?");
2427 *do_replace = (Boolean) (ans == ANS_YES);
2428 if (! *use_semicolon)
2429 {
2430 if (! *do_replace)
2431 {
2432 ans = Message (MSG_YN, "Separate items with semicolon?");
2433 *use_semicolon = (Boolean) (ans == ANS_YES);
2434 }
2435 }
2436 WatchCursor ();
2437 Update ();
2438 }
2439 if (*do_replace || StringHasNoText (*string_loc))
2440 {
2441 MemFree (*string_loc);
2442 *string_loc = StringSave (new_value);
2443 }
2444 else
2445 {
2446 tmp_value = MemNew (StringLen (*string_loc) + StringLen ( new_value) + 3);
2447 if (tmp_value == NULL) return;
2448 StringCpy (tmp_value, *string_loc);
2449 TrimSpacesAroundString (tmp_value);
2450 if (*use_semicolon)
2451 {
2452 StringCat (tmp_value, "; ");
2453 }
2454 else
2455 {
2456 StringCat (tmp_value, " ");
2457 }
2458 tmp_new_value = StringSave (new_value);
2459 TrimSpacesAroundString (tmp_new_value);
2460 StringCat (tmp_value, tmp_new_value);
2461 MemFree (tmp_new_value);
2462 MemFree (*string_loc);
2463 *string_loc = tmp_value;
2464 }
2465 }
2466
ENUM_ALIST(origin_alist)2467 static ENUM_ALIST(origin_alist)
2468 {" ", ORG_DEFAULT },
2469 {"Natural", ORG_NATURAL },
2470 {"Natural Mutant", ORG_NATMUT },
2471 {"Mutant", ORG_MUT },
2472 {"Artificial", ORG_ARTIFICIAL },
2473 {"Synthetic", ORG_SYNTHETIC },
2474 {"Other", ORG_OTHER },
2475 END_ENUM_ALIST
2476
2477
2478 typedef struct setsample
2479 {
2480 GetFeatureFieldString fieldstring_func;
2481 GetDescriptorFieldString descrstring_func;
2482 Uint2 entityID;
2483 ValNodePtr field_list;
2484 FreeValNodeProc free_vn_proc;
2485 CopyValNodeDataProc copy_vn_proc;
2486 MatchValNodeProc match_vn_proc;
2487 NameFromValNodeProc label_vn_proc;
2488
2489 FilterSetPtr fsp;
2490 } SetSampleData, PNTR SetSamplePtr;
2491
IntValNodeCopy(ValNodePtr vnp)2492 static ValNodePtr IntValNodeCopy (ValNodePtr vnp)
2493 {
2494 ValNodePtr vnp_new;
2495
2496 if (vnp == NULL)
2497 {
2498 return NULL;
2499 }
2500 vnp_new = ValNodeNew (NULL);
2501 if (vnp_new != NULL)
2502 {
2503 vnp_new->choice = vnp->choice;
2504 vnp_new->data.intvalue = vnp->data.intvalue;
2505 }
2506 return vnp_new;
2507 }
2508
IntValNodeMatch(ValNodePtr vnp1,ValNodePtr vnp2)2509 static Boolean IntValNodeMatch (ValNodePtr vnp1, ValNodePtr vnp2)
2510 {
2511 if (vnp1 == NULL && vnp2 == NULL)
2512 {
2513 return TRUE;
2514 }
2515 else if (vnp1 == NULL || vnp2 == NULL)
2516 {
2517 return FALSE;
2518 }
2519 else if (vnp1->data.intvalue == vnp2->data.intvalue)
2520 {
2521 return TRUE;
2522 }
2523 else
2524 {
2525 return FALSE;
2526 }
2527 }
2528
LocationConstraintXClearText(LocationConstraintXPtr lcp)2529 static void LocationConstraintXClearText (LocationConstraintXPtr lcp)
2530 {
2531 if (lcp != NULL)
2532 {
2533 lcp->left = -1;
2534 lcp->right = -1;
2535 }
2536 }
2537
LocationConstraintXFree(LocationConstraintXPtr lcp)2538 static LocationConstraintXPtr LocationConstraintXFree (LocationConstraintXPtr lcp)
2539 {
2540 lcp = MemFree (lcp);
2541 return lcp;
2542 }
2543
LocationConstraintXCopy(LocationConstraintXPtr lcp)2544 static LocationConstraintXPtr LocationConstraintXCopy (LocationConstraintXPtr lcp)
2545 {
2546 LocationConstraintXPtr lcp_new;
2547 if (lcp == NULL)
2548 {
2549 return NULL;
2550 }
2551 lcp_new = (LocationConstraintXPtr) MemNew (sizeof (LocationConstraintXData));
2552 if (lcp_new != NULL)
2553 {
2554 lcp_new->left = lcp->left;
2555 lcp_new->right = lcp->right;
2556 lcp_new->interval_end_choice = lcp->interval_end_choice;
2557 lcp_new->match_choice = lcp->match_choice;
2558 lcp_new->strand = lcp->strand;
2559 lcp_new->sequence_type = lcp->sequence_type;
2560 }
2561 return lcp_new;
2562 }
2563
StringConstraintXFree(StringConstraintXPtr scp)2564 extern StringConstraintXPtr StringConstraintXFree (StringConstraintXPtr scp)
2565 {
2566 if (scp == NULL) return NULL;
2567 scp->match_text = MemFree (scp->match_text);
2568 scp = MemFree (scp);
2569 return scp;
2570 }
2571
StringConstraintClearText(StringConstraintXPtr scp)2572 static void StringConstraintClearText (StringConstraintXPtr scp)
2573 {
2574 if (scp != NULL)
2575 {
2576 scp->match_text = MemFree (scp->match_text);
2577 }
2578 }
2579
StringConstraintCopy(StringConstraintXPtr scp)2580 static StringConstraintXPtr StringConstraintCopy (StringConstraintXPtr scp)
2581 {
2582 StringConstraintXPtr scp_new;
2583 if (scp == NULL)
2584 {
2585 return NULL;
2586 }
2587
2588 scp_new = (StringConstraintXPtr) MemNew (sizeof (StringConstraintData));
2589 if (scp_new != NULL)
2590 {
2591 scp_new->match_text = StringSave (scp->match_text);
2592 scp_new->match_location = scp->match_location;
2593 scp_new->insensitive = scp->insensitive;
2594 scp_new->whole_word = scp->whole_word;
2595 scp_new->not_present = scp->not_present;
2596 }
2597 return scp_new;
2598 }
2599
ValNodeFuncFree(ValNodePtr vnp,FreeValNodeProc free_vn_proc)2600 extern ValNodePtr ValNodeFuncFree (ValNodePtr vnp, FreeValNodeProc free_vn_proc)
2601 {
2602 if (vnp == NULL)
2603 {
2604 return NULL;
2605 }
2606 vnp->next = ValNodeFuncFree (vnp->next, free_vn_proc);
2607 if (free_vn_proc != NULL)
2608 {
2609 free_vn_proc (vnp);
2610 }
2611 ValNodeFree (vnp);
2612 return NULL;
2613 }
2614
ChoiceConstraintFree(ChoiceConstraintPtr scp)2615 extern ChoiceConstraintPtr ChoiceConstraintFree (ChoiceConstraintPtr scp)
2616 {
2617 if (scp == NULL) return NULL;
2618 scp->qual_choice = ValNodeFuncFree (scp->qual_choice, scp->free_vn_proc);
2619 scp->qual_choice_match = ValNodeFuncFree (scp->qual_choice, scp->free_vn_proc);
2620 scp->string_constraint = StringConstraintXFree (scp->string_constraint);
2621 scp->pseudo_constraint = MemFree (scp->pseudo_constraint);
2622 scp = MemFree (scp);
2623 return scp;
2624 }
2625
QualChoiceCopy(ValNodePtr vnp,CopyValNodeDataProc copy_vn_proc)2626 static ValNodePtr QualChoiceCopy (ValNodePtr vnp, CopyValNodeDataProc copy_vn_proc)
2627 {
2628 ValNodePtr new_list = NULL;
2629
2630 if (vnp == NULL || copy_vn_proc == NULL)
2631 {
2632 return NULL;
2633 }
2634
2635 new_list = copy_vn_proc (vnp);
2636 new_list->next = QualChoiceCopy (vnp->next, copy_vn_proc);
2637 return new_list;
2638 }
2639
ChoiceConstraintCopy(ChoiceConstraintPtr ccp)2640 static ChoiceConstraintPtr ChoiceConstraintCopy (ChoiceConstraintPtr ccp)
2641 {
2642 ChoiceConstraintPtr ccp_new;
2643 if (ccp == NULL || ccp->copy_vn_proc == NULL)
2644 {
2645 return NULL;
2646 }
2647 ccp_new = (ChoiceConstraintPtr) MemNew (sizeof (ChoiceConstraintData));
2648 if (ccp_new != NULL)
2649 {
2650 ccp_new->constraint_type = ccp->constraint_type;
2651 ccp_new->qual_choice = QualChoiceCopy (ccp->qual_choice, ccp->copy_vn_proc);
2652 ccp_new->qual_choice_match = QualChoiceCopy (ccp->qual_choice_match, ccp->copy_vn_proc);
2653 ccp_new->string_constraint = StringConstraintCopy (ccp->string_constraint);
2654 ccp_new->copy_vn_proc = ccp->copy_vn_proc;
2655 ccp_new->free_vn_proc = ccp->free_vn_proc;
2656 }
2657 return ccp_new;
2658 }
2659
ChoiceConstraintClearText(ChoiceConstraintPtr scp)2660 static void ChoiceConstraintClearText (ChoiceConstraintPtr scp)
2661 {
2662 if (scp != NULL)
2663 {
2664 StringConstraintClearText (scp->string_constraint);
2665 }
2666 }
2667
2668
FilterSetClearText(FilterSetPtr fsp)2669 extern void FilterSetClearText (FilterSetPtr fsp)
2670 {
2671 if (fsp != NULL)
2672 {
2673 StringConstraintClearText (fsp->scp);
2674 ChoiceConstraintClearText (fsp->ccp);
2675 LocationConstraintXClearText (fsp->lcp);
2676 StringConstraintClearText (fsp->id_list);
2677 }
2678 }
2679
FilterSetNew(void)2680 extern FilterSetPtr FilterSetNew (void)
2681 {
2682 FilterSetPtr fsp_new;
2683 fsp_new = (FilterSetPtr) MemNew (sizeof (FilterSetData));
2684 if (fsp_new != NULL)
2685 {
2686 fsp_new->scp = NULL;
2687 fsp_new->ccp = NULL;
2688 fsp_new->lcp = NULL;
2689 fsp_new->cgp = NULL;
2690 fsp_new->id_list = NULL;
2691 }
2692 return fsp_new;
2693 }
2694
FilterSetFree(FilterSetPtr fsp)2695 extern FilterSetPtr FilterSetFree (FilterSetPtr fsp)
2696 {
2697 if (fsp != NULL)
2698 {
2699 fsp->scp = StringConstraintXFree (fsp->scp);
2700 fsp->ccp = ChoiceConstraintFree (fsp->ccp);
2701 fsp->lcp = LocationConstraintXFree (fsp->lcp);
2702 fsp->cgp = ChoiceConstraintFree (fsp->cgp);
2703 fsp->id_list = StringConstraintXFree (fsp->id_list);
2704 fsp = MemFree (fsp);
2705 }
2706 return fsp;
2707 }
2708
FilterSetCopy(FilterSetPtr fsp)2709 static FilterSetPtr FilterSetCopy (FilterSetPtr fsp)
2710 {
2711 FilterSetPtr fsp_new;
2712
2713 if (fsp == NULL)
2714 {
2715 return NULL;
2716 }
2717 fsp_new = (FilterSetPtr) MemNew (sizeof (FilterSetData));
2718 if (fsp_new != NULL)
2719 {
2720 fsp_new->scp = StringConstraintCopy (fsp->scp);
2721 fsp_new->ccp = ChoiceConstraintCopy (fsp->ccp);
2722 fsp_new->lcp = LocationConstraintXCopy (fsp->lcp);
2723 fsp_new->cgp = ChoiceConstraintCopy (fsp->cgp);
2724 fsp_new->id_list = StringConstraintCopy (fsp->id_list);
2725 }
2726 return fsp_new;
2727 }
2728
2729
SetSampleFree(SetSamplePtr ssp)2730 static SetSamplePtr SetSampleFree (SetSamplePtr ssp)
2731 {
2732 ValNodePtr vnp;
2733
2734 if (ssp == NULL)
2735 {
2736 return NULL;
2737 }
2738 if (ssp->free_vn_proc != NULL)
2739 {
2740 for (vnp = ssp->field_list; vnp != NULL; vnp = vnp->next)
2741 {
2742 (ssp->free_vn_proc)(vnp);
2743 }
2744 }
2745 ssp->field_list = ValNodeFree (ssp->field_list);
2746
2747 ssp = MemFree (ssp);
2748 return ssp;
2749 }
2750
SetSampleCopy(SetSamplePtr ssp)2751 static SetSamplePtr SetSampleCopy (SetSamplePtr ssp)
2752 {
2753 SetSamplePtr ssp_new;
2754 ValNodePtr vnp_old, vnp_new, vnp_last = NULL;
2755
2756 if (ssp == NULL)
2757 {
2758 return NULL;
2759 }
2760 ssp_new = (SetSamplePtr) MemNew (sizeof (SetSampleData));
2761 if (ssp_new != NULL)
2762 {
2763 ssp_new->fieldstring_func = ssp->fieldstring_func;
2764 ssp_new->descrstring_func = ssp->descrstring_func;
2765 ssp_new->free_vn_proc = ssp->free_vn_proc;
2766 ssp_new->copy_vn_proc = ssp->copy_vn_proc;
2767 ssp_new->match_vn_proc = ssp->match_vn_proc;
2768 ssp_new->label_vn_proc = ssp->label_vn_proc;
2769
2770 ssp_new->entityID = ssp->entityID;
2771 ssp_new->field_list = NULL;
2772 for (vnp_old = ssp->field_list; vnp_old != NULL; vnp_old = vnp_old->next)
2773 {
2774 vnp_new = (ssp_new->copy_vn_proc)(vnp_old);
2775 if (vnp_last == NULL)
2776 {
2777 ssp_new->field_list = vnp_new;
2778 }
2779 else
2780 {
2781 vnp_last->next = vnp_new;
2782 }
2783 vnp_last = vnp_new;
2784 }
2785 ssp_new->fsp = FilterSetCopy (ssp->fsp);
2786 }
2787 return ssp_new;
2788 }
2789
2790 #define PARSE_FIELD_DEFLINE 1
2791 #define PARSE_FIELD_BIOSRC_STRING 2
2792 #define PARSE_FIELD_SOURCE_QUAL 3
2793 #define PARSE_FIELD_GENE_FIELD 4
2794 #define PARSE_FIELD_RNA_FIELD 5
2795 #define PARSE_FIELD_CDS_COMMENT 6
2796 #define PARSE_FIELD_PROTEIN_FIELD 7
2797 #define PARSE_FIELD_IMPORT_QUAL 8
2798 #define PARSE_FIELD_FEATURE_NOTE 9
2799 #define PARSE_FIELD_COMMENT_DESC 10
2800 #define PARSE_FIELD_DBXREF 11
2801
2802 #define MAX_PARSE_FIELD_TYPE 11
2803 #define SEARCH_FIELD_PUBLICATION 12
2804
2805 #define PARSE_FIELD_FIRST_FEATURE 4
2806 #define PARSE_FIELD_LAST_FEATURE 9
2807
2808 extern Boolean DoesLocationMatchConstraint (SeqLocPtr slp, LocationConstraintXPtr lcp);
2809
2810 typedef struct acceptpolicy
2811 {
2812 Boolean leave_dlg_up;
2813 } AcceptPolicyData, PNTR AcceptPolicyPtr;
2814
2815 typedef struct acceptcanceldialog
2816 {
2817 DIALOG_MESSAGE_BLOCK
2818 Nlm_AcceptActnProc accept_actn;
2819 Nlm_CancelActnProc cancel_actn;
2820 Nlm_ClearActnProc clear_actn;
2821 Nlm_ClearTextActnProc clear_text_actn;
2822 WindoW w;
2823
2824 ButtoN accept_btn;
2825
2826 ButtoN leave_dlg_up_btn;
2827 } AcceptCancelDialogData, PNTR AcceptCancelDialogPtr;
2828
AcceptCancelDialogAccept(ButtoN b)2829 static void AcceptCancelDialogAccept (ButtoN b)
2830 {
2831 AcceptCancelDialogPtr acdp;
2832
2833 acdp = (AcceptCancelDialogPtr) GetObjectExtra (b);
2834 if (acdp == NULL) return;
2835
2836 if (acdp->accept_actn != NULL)
2837 {
2838 if (!((acdp->accept_actn) (acdp->userdata)))
2839 {
2840 return;
2841 }
2842 }
2843 if (! GetStatus (acdp->leave_dlg_up_btn))
2844 {
2845 Remove (acdp->w);
2846 }
2847 }
2848
AcceptCancelDialogCancel(ButtoN b)2849 static void AcceptCancelDialogCancel (ButtoN b)
2850 {
2851 AcceptCancelDialogPtr acdp;
2852
2853 acdp = (AcceptCancelDialogPtr) GetObjectExtra (b);
2854 if (acdp == NULL) return;
2855
2856 if (acdp->cancel_actn != NULL)
2857 {
2858 (acdp->cancel_actn) (acdp->userdata);
2859 }
2860 Remove (acdp->w);
2861 }
2862
AcceptCancelDialogClear(ButtoN b)2863 static void AcceptCancelDialogClear (ButtoN b)
2864 {
2865 AcceptCancelDialogPtr acdp;
2866
2867 acdp = (AcceptCancelDialogPtr) GetObjectExtra (b);
2868 if (acdp == NULL || acdp->clear_actn == NULL) return;
2869
2870 (acdp->clear_actn) (acdp->userdata);
2871 }
2872
AcceptCancelDialogClearText(ButtoN b)2873 static void AcceptCancelDialogClearText (ButtoN b)
2874 {
2875 AcceptCancelDialogPtr acdp;
2876
2877 acdp = (AcceptCancelDialogPtr) GetObjectExtra (b);
2878 if (acdp == NULL || acdp->clear_text_actn == NULL) return;
2879
2880 (acdp->clear_text_actn) (acdp->userdata);
2881 }
2882
AcceptPolicyToAcceptCancelDialog(DialoG d,Pointer data)2883 static void AcceptPolicyToAcceptCancelDialog (DialoG d, Pointer data)
2884
2885 {
2886 AcceptCancelDialogPtr acdp;
2887 AcceptPolicyPtr app;
2888
2889 acdp = (AcceptCancelDialogPtr) GetObjectExtra (d);
2890 app = (AcceptPolicyPtr) data;
2891 if (acdp == NULL || app == NULL)
2892 {
2893 return;
2894 }
2895
2896 SetStatus (acdp->leave_dlg_up_btn, app->leave_dlg_up);
2897 }
2898
AcceptCancelDialogToAcceptPolicy(DialoG d)2899 static Pointer AcceptCancelDialogToAcceptPolicy (DialoG d)
2900 {
2901 AcceptCancelDialogPtr acdp;
2902 AcceptPolicyPtr app;
2903
2904 acdp = (AcceptCancelDialogPtr) GetObjectExtra (d);
2905 if (acdp == NULL)
2906 {
2907 return NULL;
2908 }
2909
2910 app = (AcceptPolicyPtr) MemNew (sizeof (AcceptPolicyData));
2911 if (app != NULL)
2912 {
2913 app->leave_dlg_up = GetStatus (acdp->leave_dlg_up_btn);
2914 }
2915 return app;
2916 }
2917
AcceptCancelMessage(DialoG d,Int2 mssg)2918 static void AcceptCancelMessage (DialoG d, Int2 mssg)
2919
2920 {
2921 AcceptCancelDialogPtr acdp;
2922
2923 acdp = (AcceptCancelDialogPtr) GetObjectExtra (d);
2924 if (acdp != NULL) {
2925 switch (mssg) {
2926 case VIB_MSG_INIT :
2927 /* reset accept policy */
2928 SetStatus (acdp->leave_dlg_up_btn, FALSE);
2929 break;
2930 case VIB_MSG_ENTER :
2931 Select (acdp->accept_btn);
2932 break;
2933 default :
2934 break;
2935 }
2936 }
2937 }
2938
TestAcceptCancelDialog(DialoG d)2939 static ValNodePtr TestAcceptCancelDialog (DialoG d)
2940
2941 {
2942 return NULL;
2943 }
2944
AcceptCancelDialog(GrouP parent,Nlm_AcceptActnProc accept_actn,Nlm_CancelActnProc cancel_actn,Nlm_ClearActnProc clear_actn,Nlm_ClearTextActnProc clear_text_actn,Pointer userdata,WindoW w)2945 extern DialoG AcceptCancelDialog
2946 (GrouP parent,
2947 Nlm_AcceptActnProc accept_actn,
2948 Nlm_CancelActnProc cancel_actn,
2949 Nlm_ClearActnProc clear_actn,
2950 Nlm_ClearTextActnProc clear_text_actn,
2951 Pointer userdata,
2952 WindoW w)
2953 {
2954 AcceptCancelDialogPtr acdp;
2955 GrouP grp, policy_grp = NULL, other_grp;
2956 ButtoN b;
2957
2958 acdp = (AcceptCancelDialogPtr) MemNew (sizeof (AcceptCancelDialogData));
2959 grp = HiddenGroup (parent, -1, 0, NULL);
2960 SetObjectExtra (grp, acdp, StdCleanupExtraProc);
2961 SetGroupSpacing (grp, 10, 10);
2962
2963 acdp->dialog = (DialoG) grp;
2964 acdp->todialog = AcceptPolicyToAcceptCancelDialog;
2965 acdp->fromdialog = AcceptCancelDialogToAcceptPolicy;
2966 acdp->dialogmessage = AcceptCancelMessage;
2967 acdp->testdialog = TestAcceptCancelDialog;
2968
2969 acdp->accept_actn = accept_actn;
2970 acdp->cancel_actn = cancel_actn;
2971 acdp->clear_actn = clear_actn;
2972 acdp->clear_text_actn = clear_text_actn;
2973 acdp->userdata = userdata;
2974 acdp->w = w;
2975
2976 policy_grp = HiddenGroup (grp, 3, 0, NULL);
2977 SetGroupSpacing (policy_grp, 10, 10);
2978
2979 b = PushButton (policy_grp, "Clear", AcceptCancelDialogClear);
2980 SetObjectExtra (b, acdp, NULL);
2981
2982 b = PushButton (policy_grp, "Clear Text", AcceptCancelDialogClearText);
2983 SetObjectExtra (b, acdp, NULL);
2984
2985 acdp->leave_dlg_up_btn = CheckBox (policy_grp, "Leave Dialog Up", NULL);
2986
2987 other_grp = HiddenGroup (grp, 5, 0, NULL);
2988 SetGroupSpacing (other_grp, 10, 10);
2989 acdp->accept_btn = PushButton (other_grp, "Accept", AcceptCancelDialogAccept);
2990 SetObjectExtra (acdp->accept_btn, acdp, NULL);
2991
2992 b = PushButton (other_grp, "Cancel", AcceptCancelDialogCancel);
2993 SetObjectExtra (b, acdp, NULL);
2994
2995 AlignObjects (ALIGN_CENTER, (HANDLE) policy_grp, (HANDLE) other_grp, NULL);
2996
2997 return (DialoG) grp;
2998 }
2999
3000
EnableAcceptCancelDialogAccept(DialoG d)3001 extern void EnableAcceptCancelDialogAccept (DialoG d)
3002 {
3003 AcceptCancelDialogPtr acdp;
3004
3005 acdp = (AcceptCancelDialogPtr) GetObjectExtra (d);
3006
3007 if (acdp == NULL) return;
3008
3009 InvalObject (acdp->accept_btn);
3010 SafeEnable (acdp->accept_btn);
3011 Update ();
3012 }
3013
DisableAcceptCancelDialogAccept(DialoG d)3014 extern void DisableAcceptCancelDialogAccept (DialoG d)
3015 {
3016 AcceptCancelDialogPtr acdp;
3017
3018 acdp = (AcceptCancelDialogPtr) GetObjectExtra (d);
3019
3020 if (acdp == NULL) return;
3021
3022 InvalObject (acdp->accept_btn);
3023 SafeDisable (acdp->accept_btn);
3024 Update ();
3025 }
3026
3027
3028
3029
3030
ValNodeAppend(ValNodePtr list,ValNodePtr second_list)3031 static ValNodePtr ValNodeAppend (ValNodePtr list, ValNodePtr second_list)
3032 {
3033 ValNodePtr last_vnp;
3034
3035 if (list == NULL)
3036 {
3037 list = second_list;
3038 }
3039 else if (second_list != NULL)
3040 {
3041 last_vnp = list;
3042 while (last_vnp != NULL && last_vnp->next != NULL)
3043 {
3044 last_vnp = last_vnp->next;
3045 }
3046 last_vnp->next = second_list;
3047 }
3048 return list;
3049 }
3050
FindFeatureTypeCallback(SeqFeatPtr sfp,Pointer userdata)3051 static void FindFeatureTypeCallback (SeqFeatPtr sfp, Pointer userdata)
3052 {
3053 BoolPtr type_list;
3054
3055 if (sfp == NULL || userdata == NULL) return;
3056
3057 type_list = (BoolPtr) userdata;
3058 type_list[sfp->idx.subtype] = TRUE;
3059 }
3060
3061
AddFeatureToList(ValNodePtr PNTR list,FeatDefPtr curr)3062 static void AddFeatureToList (ValNodePtr PNTR list, FeatDefPtr curr)
3063 {
3064 Char str [256];
3065
3066 if (list == NULL || curr == NULL) return;
3067
3068 if (curr->featdef_key == FEATDEF_PUB)
3069 {
3070 StringNCpy_0 (str, curr->typelabel, sizeof (str) - 15);
3071 StringCat (str, " (Publication)");
3072 ValNodeAddPointer (list, curr->featdef_key, StringSave (str));
3073 }
3074 else if (curr->featdef_key == FEATDEF_BIOSRC)
3075 {
3076 ValNodeAddPointer (list, FEATDEF_BIOSRC, StringSave ("BioSource"));
3077 }
3078 else if (curr->featdef_key == FEATDEF_otherRNA)
3079 {
3080 ValNodeAddPointer (list, FEATDEF_otherRNA, StringSave ("misc_RNA"));
3081 }
3082 else if (curr->featdef_key == FEATDEF_misc_RNA ||
3083 curr->featdef_key == FEATDEF_precursor_RNA ||
3084 curr->featdef_key == FEATDEF_mat_peptide ||
3085 curr->featdef_key == FEATDEF_sig_peptide ||
3086 curr->featdef_key == FEATDEF_transit_peptide ||
3087 curr->featdef_key == FEATDEF_Imp_CDS)
3088 {
3089 StringNCpy_0 (str, curr->typelabel, sizeof (str) - 10);
3090 StringCat (str, "_imp");
3091 ValNodeAddPointer (list, curr->featdef_key, StringSave (str));
3092 }
3093 else
3094 {
3095 ValNodeAddPointer (list, curr->featdef_key, StringSave (curr->typelabel));
3096 }
3097 }
3098
BuildFeatureDialogList(Boolean list_most_used_first,SeqEntryPtr sep)3099 extern ValNodePtr BuildFeatureDialogList (Boolean list_most_used_first, SeqEntryPtr sep)
3100 {
3101 ValNodePtr feature_choice_list = NULL;
3102 ValNodePtr import_feature_list = NULL;
3103 ValNodePtr least_liked_feature_list = NULL;
3104 ValNodePtr most_used_feature_list = NULL;
3105 ValNodePtr unused_list = NULL;
3106 FeatDefPtr curr;
3107 Uint1 key;
3108 CharPtr label = NULL;
3109 Boolean feature_type_list[256];
3110 Boolean only_most_used = TRUE;
3111 Int4 i;
3112
3113 if (sep == NULL) {
3114 for (i = 0; i < 255; i++) {
3115 feature_type_list[i] = TRUE;
3116 }
3117 } else {
3118 for (i = 0; i < 255; i++) {
3119 feature_type_list[i] = FALSE;
3120 }
3121 VisitFeaturesInSep (sep, feature_type_list, FindFeatureTypeCallback);
3122 }
3123
3124 curr = FeatDefFindNext (NULL, &key, &label, FEATDEF_ANY, TRUE);
3125 while (curr != NULL) {
3126 if (key == FEATDEF_BAD
3127 || key == FEATDEF_Imp_CDS
3128 || key == FEATDEF_source
3129 || key == FEATDEF_ORG
3130 || IsUnwantedFeatureType (key)
3131 || IsRegulatorySubtype (key))
3132 {
3133 curr = FeatDefFindNext (curr, &key, &label, FEATDEF_ANY, TRUE);
3134 continue;
3135 }
3136 else if (!feature_type_list[key])
3137 {
3138 AddFeatureToList (&unused_list, curr);
3139 curr = FeatDefFindNext (curr, &key, &label, FEATDEF_ANY, TRUE);
3140 continue;
3141 }
3142
3143 if (curr->featdef_key == FEATDEF_otherRNA) {
3144 AddFeatureToList (&feature_choice_list, curr);
3145 if (list_most_used_first) {
3146 AddFeatureToList (&most_used_feature_list, curr);
3147 }
3148 }
3149 else if (curr->featdef_key == FEATDEF_misc_RNA ||
3150 curr->featdef_key == FEATDEF_precursor_RNA ||
3151 curr->featdef_key == FEATDEF_mat_peptide ||
3152 curr->featdef_key == FEATDEF_sig_peptide ||
3153 curr->featdef_key == FEATDEF_transit_peptide ||
3154 curr->featdef_key == FEATDEF_Imp_CDS)
3155 {
3156 AddFeatureToList (&import_feature_list, curr);
3157 }
3158 else if (curr->featdef_key == FEATDEF_TXINIT)
3159 {
3160 AddFeatureToList (&least_liked_feature_list, curr);
3161 }
3162 else
3163 {
3164 ValNodeAddPointer (&feature_choice_list, curr->featdef_key, StringSave (curr->typelabel));
3165 }
3166
3167 if (list_most_used_first)
3168 {
3169 /* also build most used list */
3170 if (curr->featdef_key == FEATDEF_CDS
3171 || curr->featdef_key == FEATDEF_exon
3172 || curr->featdef_key == FEATDEF_GENE
3173 || curr->featdef_key == FEATDEF_intron
3174 || curr->featdef_key == FEATDEF_mRNA
3175 || curr->featdef_key == FEATDEF_rRNA
3176 || curr->featdef_key == FEATDEF_PROT)
3177 {
3178 ValNodeAddPointer (&most_used_feature_list, curr->featdef_key,
3179 StringSave (curr->typelabel));
3180 }
3181 else
3182 {
3183 only_most_used = FALSE;
3184 }
3185 }
3186
3187 curr = FeatDefFindNext (curr, &key, &label, FEATDEF_ANY, TRUE);
3188 }
3189
3190 most_used_feature_list = SortValNode (most_used_feature_list,
3191 CompareFeatureValNodeStrings);
3192 feature_choice_list = SortValNode (feature_choice_list,
3193 CompareFeatureValNodeStrings);
3194 import_feature_list = SortValNode (import_feature_list,
3195 CompareFeatureValNodeStrings);
3196 least_liked_feature_list = SortValNode (least_liked_feature_list,
3197 CompareFeatureValNodeStrings);
3198 unused_list = SortValNode (unused_list, CompareFeatureValNodeStrings);
3199
3200 if (most_used_feature_list != NULL && only_most_used) {
3201 feature_choice_list = ValNodeFreeData (feature_choice_list);
3202 feature_choice_list = most_used_feature_list;
3203 least_liked_feature_list = ValNodeFreeData(least_liked_feature_list);
3204 import_feature_list = ValNodeFreeData(least_liked_feature_list);
3205 } else {
3206 feature_choice_list = ValNodeAppend (most_used_feature_list, feature_choice_list);
3207 feature_choice_list = ValNodeAppend (feature_choice_list, least_liked_feature_list);
3208 feature_choice_list = ValNodeAppend (feature_choice_list, import_feature_list);
3209 }
3210 feature_choice_list = ValNodeAppend (feature_choice_list, unused_list);
3211
3212 return feature_choice_list;
3213 }
3214
BuildImportList(void)3215 static ValNodePtr BuildImportList (void)
3216 {
3217 ValNodePtr import_feature_list = NULL;
3218 FeatDefPtr curr;
3219 Uint1 key;
3220 CharPtr label = NULL;
3221 Char str [256];
3222
3223 curr = FeatDefFindNext (NULL, &key, &label, FEATDEF_ANY, TRUE);
3224 while (curr != NULL) {
3225 if (FindFeatFromFeatDefType (key) == SEQFEAT_IMP && !IsUnwantedFeatureType(key))
3226 {
3227 ValNodeAddPointer (&import_feature_list, curr->featdef_key, StringSave (str));
3228 }
3229
3230 curr = FeatDefFindNext (curr, &key, &label, FEATDEF_ANY, TRUE);
3231 }
3232 return import_feature_list;
3233 }
3234
RemoveFeatureSelectionDuplicates(ValNodePtr orig_list)3235 static void RemoveFeatureSelectionDuplicates (ValNodePtr orig_list)
3236 {
3237 ValNodePtr vnp1, vnp2, prev_vnp, next_vnp;
3238
3239 if (orig_list == NULL || orig_list->next == NULL)
3240 {
3241 return;
3242 }
3243
3244 vnp1 = orig_list;
3245 while (vnp1 != NULL && vnp1->next != NULL)
3246 {
3247 vnp2 = vnp1->next;
3248 prev_vnp = vnp1;
3249 while (vnp2 != NULL)
3250 {
3251 next_vnp = vnp2->next;
3252 if (vnp2->choice == vnp1->choice)
3253 {
3254 prev_vnp->next = next_vnp;
3255 vnp2->next = NULL;
3256 vnp2 = ValNodeFreeData (vnp2);
3257 }
3258 else
3259 {
3260 prev_vnp = vnp2;
3261 }
3262 vnp2 = next_vnp;
3263 }
3264 vnp1 = vnp1->next;
3265 }
3266 }
3267
FeatureSelectionRemap(ValNodePtr orig_list)3268 static ValNodePtr FeatureSelectionRemap (ValNodePtr orig_list)
3269 {
3270 ValNodePtr vnp, vnp_next, prev_vnp, repl_vnp = NULL;
3271
3272 if (orig_list == NULL)
3273 {
3274 return NULL;
3275 }
3276
3277 vnp = orig_list;
3278 prev_vnp = NULL;
3279 while (vnp != NULL && repl_vnp == NULL)
3280 {
3281 vnp_next = vnp->next;
3282 /* replace FEATDEF_IMP with list of import features */
3283 if (vnp->choice == FEATDEF_IMP)
3284 {
3285 /* build replacement list */
3286 repl_vnp = BuildImportList ();
3287
3288 ValNodeLink (&repl_vnp, vnp->next);
3289
3290 if (prev_vnp == NULL)
3291 {
3292 orig_list = repl_vnp;
3293 }
3294 else
3295 {
3296 prev_vnp->next = repl_vnp;
3297 }
3298
3299 vnp->next = NULL;
3300 ValNodeFreeData (vnp);
3301 }
3302 else
3303 {
3304 prev_vnp = vnp;
3305 }
3306 vnp = vnp_next;
3307 }
3308
3309 RemoveFeatureSelectionDuplicates (orig_list);
3310
3311 return orig_list;
3312 }
3313
3314 extern DialoG
FeatureSelectionDialogEx(GrouP h,Boolean allow_multi,SeqEntryPtr sep,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)3315 FeatureSelectionDialogEx
3316 (GrouP h,
3317 Boolean allow_multi,
3318 SeqEntryPtr sep,
3319 Nlm_ChangeNotifyProc change_notify,
3320 Pointer change_userdata)
3321 {
3322 DialoG dlg;
3323 ValNodePtr feature_choice_list, vnp, vnp_next, vnp_prev;
3324 Boolean found_import = FALSE;
3325
3326 feature_choice_list = BuildFeatureDialogList (TRUE, sep);
3327
3328 if (!allow_multi)
3329 {
3330 /* remove Import option */
3331 vnp_prev = NULL;
3332 for (vnp = feature_choice_list; vnp != NULL && !found_import; vnp = vnp_next)
3333 {
3334 vnp_next = vnp->next;
3335 if (vnp->choice == FEATDEF_IMP)
3336 {
3337 if (vnp_prev == NULL)
3338 {
3339 feature_choice_list = vnp_next;
3340 }
3341 else
3342 {
3343 vnp_prev->next = vnp_next;
3344 }
3345 vnp->next = NULL;
3346 vnp = ValNodeFreeData (vnp);
3347 found_import = TRUE;
3348 }
3349 else
3350 {
3351 vnp_prev = vnp;
3352 }
3353 }
3354 }
3355
3356 /* note - the ValNodeSelectionDialog will free the feature_choice_list when done */
3357
3358 dlg = ValNodeSelectionDialogEx (h, feature_choice_list, TALL_SELECTION_LIST,
3359 ValNodeStringName,
3360 ValNodeSimpleDataFree, ValNodeStringCopy,
3361 ValNodeChoiceMatch, "feature list",
3362 change_notify, change_userdata, allow_multi, FALSE,
3363 allow_multi ? FeatureSelectionRemap : NULL);
3364 return dlg;
3365 }
3366
3367 extern DialoG
FeatureSelectionDialog(GrouP h,Boolean allow_multi,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)3368 FeatureSelectionDialog
3369 (GrouP h,
3370 Boolean allow_multi,
3371 Nlm_ChangeNotifyProc change_notify,
3372 Pointer change_userdata)
3373 {
3374 return FeatureSelectionDialogEx(h, allow_multi, NULL, change_notify, change_userdata);
3375 }
3376
3377 extern DialoG
DescriptorSelectionDialog(GrouP h,Boolean allow_multi,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)3378 DescriptorSelectionDialog
3379 (GrouP h,
3380 Boolean allow_multi,
3381 Nlm_ChangeNotifyProc change_notify,
3382 Pointer change_userdata)
3383 {
3384 ValNodePtr descriptor_list = BuildDescriptorValNodeList ();
3385 return ValNodeSelectionDialogEx (h, descriptor_list, TALL_SELECTION_LIST,
3386 ValNodeStringName,
3387 ValNodeSimpleDataFree, ValNodeStringCopy,
3388 ValNodeChoiceMatch, "descriptor list",
3389 change_notify, change_userdata, allow_multi, FALSE,
3390 NULL);
3391 }
3392
3393
SourceQualValNodeName(ValNodePtr vnp)3394 extern CharPtr SourceQualValNodeName (ValNodePtr vnp)
3395 {
3396 SourceQualDescPtr sqdp;
3397
3398 if (vnp == NULL || vnp->data.ptrvalue == NULL)
3399 {
3400 return NULL;
3401 }
3402 else if (vnp->choice == 0)
3403 {
3404 sqdp = (SourceQualDescPtr) vnp->data.ptrvalue;
3405 return StringSave (sqdp->name);
3406 }
3407 else
3408 {
3409 return StringSave (vnp->data.ptrvalue);
3410 }
3411 }
3412
SourceQualValNodeDataCopy(ValNodePtr vnp)3413 extern ValNodePtr SourceQualValNodeDataCopy (ValNodePtr vnp)
3414 {
3415 SourceQualDescPtr sqdp, new_sqdp = NULL;
3416 ValNodePtr vnp_copy = NULL;
3417
3418 if (vnp != NULL && vnp->data.ptrvalue != NULL)
3419 {
3420 if (vnp->choice == 0)
3421 {
3422 sqdp = (SourceQualDescPtr) vnp->data.ptrvalue;
3423 new_sqdp = (SourceQualDescPtr) MemNew (sizeof (SourceQualDescData));
3424 if (new_sqdp != NULL)
3425 {
3426 MemCpy (new_sqdp, sqdp, sizeof (SourceQualDescData));
3427 }
3428 ValNodeAddPointer (&vnp_copy, vnp->choice, new_sqdp);
3429 }
3430 else
3431 {
3432 ValNodeAddPointer (&vnp_copy, vnp->choice, StringSave (vnp->data.ptrvalue));
3433 }
3434 }
3435 return vnp_copy;
3436 }
3437
3438
SourceQualValNodeCopy(ValNodePtr vnp)3439 NLM_EXTERN ValNodePtr LIBCALL SourceQualValNodeCopy (ValNodePtr vnp)
3440 {
3441 return SourceQualValNodeDataCopy(vnp);
3442 }
3443
3444
SourceQualValNodeMatch(ValNodePtr vnp1,ValNodePtr vnp2)3445 extern Boolean SourceQualValNodeMatch (ValNodePtr vnp1, ValNodePtr vnp2)
3446 {
3447 SourceQualDescPtr sqdp1, sqdp2;
3448 Boolean rval = FALSE;
3449
3450 if (vnp1 == NULL || vnp2 == NULL
3451 || vnp1->data.ptrvalue == NULL || vnp2->data.ptrvalue == NULL)
3452 {
3453 rval = FALSE;
3454 }
3455 else if (vnp1->choice != vnp2->choice)
3456 {
3457 rval = FALSE;
3458 }
3459 else if (vnp1->choice == 0)
3460 {
3461 sqdp1 = (SourceQualDescPtr) vnp1->data.ptrvalue;
3462 sqdp2 = (SourceQualDescPtr) vnp2->data.ptrvalue;
3463
3464 if (sqdp1->subtype == sqdp2->subtype
3465 && ((sqdp1->isOrgMod && sqdp2->isOrgMod)
3466 || (!sqdp1->isOrgMod && ! sqdp2->isOrgMod)))
3467 {
3468 rval = TRUE;
3469 }
3470 else
3471 {
3472 rval = FALSE;
3473 }
3474 }
3475 else
3476 {
3477 if (StringCmp (vnp1->data.ptrvalue, vnp2->data.ptrvalue) == 0)
3478 {
3479 rval = TRUE;
3480 }
3481 else
3482 {
3483 rval = FALSE;
3484 }
3485 }
3486 return rval;
3487 }
3488
SourceQualTypeSelectionDialogEx(GrouP h,Boolean allow_multi,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata,Int2 list_height,Boolean show_discouraged,Boolean show_discontinued)3489 static DialoG SourceQualTypeSelectionDialogEx
3490 (GrouP h,
3491 Boolean allow_multi,
3492 Nlm_ChangeNotifyProc change_notify,
3493 Pointer change_userdata,
3494 Int2 list_height,
3495 Boolean show_discouraged,
3496 Boolean show_discontinued)
3497
3498 {
3499 DialoG dlg;
3500 ValNodePtr qual_choice_list;
3501
3502 if (allow_multi)
3503 {
3504 qual_choice_list = ValNodeNew (NULL);
3505 qual_choice_list->choice = 1;
3506 qual_choice_list->data.ptrvalue = StringSave ("All Notes");
3507 qual_choice_list->next = GetSourceQualDescList (TRUE, TRUE, show_discouraged, show_discontinued);
3508 }
3509 else
3510 {
3511 qual_choice_list = GetSourceQualDescList (TRUE, TRUE, show_discouraged, show_discontinued);
3512 }
3513 /* note - the ValNodeSelectionDialog will free the qual_choice_list when done */
3514 dlg = ValNodeSelectionDialog (h, qual_choice_list, list_height, SourceQualValNodeName,
3515 ValNodeSimpleDataFree, SourceQualValNodeDataCopy,
3516 SourceQualValNodeMatch, "feature list",
3517 change_notify, change_userdata, allow_multi);
3518
3519 return dlg;
3520 }
3521
SourceQualTypeSelectionDialog(GrouP h,Boolean allow_multi,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)3522 extern DialoG SourceQualTypeSelectionDialog
3523 (GrouP h,
3524 Boolean allow_multi,
3525 Nlm_ChangeNotifyProc change_notify,
3526 Pointer change_userdata)
3527
3528 {
3529 return SourceQualTypeSelectionDialogEx (h, allow_multi, change_notify,
3530 change_userdata, 6, FALSE, FALSE);
3531 }
3532
SourceQualTypeDiscSelectionDialog(GrouP h,Boolean allow_multi,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)3533 static DialoG SourceQualTypeDiscSelectionDialog
3534 (GrouP h,
3535 Boolean allow_multi,
3536 Nlm_ChangeNotifyProc change_notify,
3537 Pointer change_userdata)
3538
3539 {
3540 return SourceQualTypeSelectionDialogEx (h, allow_multi, change_notify,
3541 change_userdata, 6, TRUE, TRUE);
3542 }
3543
SourceQualTypeConstraintSelectionDialog(GrouP h,Boolean allow_multi,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)3544 static DialoG SourceQualTypeConstraintSelectionDialog
3545 (GrouP h,
3546 Boolean allow_multi,
3547 Nlm_ChangeNotifyProc change_notify,
3548 Pointer change_userdata)
3549
3550 {
3551 return SourceQualTypeSelectionDialogEx (h, allow_multi, change_notify,
3552 change_userdata, 4, TRUE, FALSE);
3553 }
3554
SourceStringConstraintSelectionDialog(GrouP h,Boolean allow_multi,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)3555 static DialoG SourceStringConstraintSelectionDialog
3556 (GrouP h,
3557 Boolean allow_multi,
3558 Nlm_ChangeNotifyProc change_notify,
3559 Pointer change_userdata)
3560
3561 {
3562 DialoG dlg;
3563 ValNodePtr qual_choice_list = NULL;
3564
3565 /* ignore allow_multi */
3566
3567 ValNodeAddPointer (&qual_choice_list, 1, StringSave ("Organism or Any Qual"));
3568 ValNodeAddPointer (&qual_choice_list, 1, StringSave ("Organism"));
3569 qual_choice_list->next->next = GetSourceQualDescList (TRUE, TRUE, TRUE, FALSE);
3570 ValNodeAddPointer (&qual_choice_list, 1, StringSave ("Lineage"));
3571 ValNodeAddPointer (&qual_choice_list, 1, StringSave ("Location"));
3572
3573 /* note - the ValNodeSelectionDialog will free the qual_choice_list when done */
3574 dlg = ValNodeSelectionDialog (h, qual_choice_list, 4, SourceQualValNodeName,
3575 ValNodeSimpleDataFree, SourceQualValNodeDataCopy,
3576 SourceQualValNodeMatch, "feature list",
3577 change_notify, change_userdata, FALSE);
3578
3579 return dlg;
3580 }
3581
OrgModSpecialMatch(OrgModPtr mod,FilterSetPtr fsp)3582 static Boolean OrgModSpecialMatch (OrgModPtr mod, FilterSetPtr fsp)
3583 {
3584 SourceQualDescPtr sqdp;
3585
3586 if (mod == NULL)
3587 {
3588 return FALSE;
3589 }
3590 if (fsp == NULL
3591 || fsp->ccp == NULL
3592 || fsp->ccp->constraint_type != CHOICE_CONSTRAINT_STRING
3593 || fsp->ccp->string_constraint == NULL
3594 || fsp->ccp->qual_choice == NULL
3595 || fsp->ccp->qual_choice->data.ptrvalue == NULL)
3596 {
3597 return TRUE;
3598 }
3599
3600 sqdp = (SourceQualDescPtr) fsp->ccp->qual_choice->data.ptrvalue;
3601 if (sqdp->subtype != mod->subtype)
3602 {
3603 return TRUE;
3604 }
3605
3606 if (DoesStringMatchConstraintX (mod->subname, fsp->ccp->string_constraint))
3607 {
3608 if (fsp->ccp->string_constraint->not_present)
3609 {
3610 return FALSE;
3611 }
3612 else
3613 {
3614 return TRUE;
3615 }
3616 }
3617 else
3618 {
3619 if (fsp->ccp->string_constraint->not_present)
3620 {
3621 return TRUE;
3622 }
3623 else
3624 {
3625 return FALSE;
3626 }
3627 }
3628 }
3629
SubSrcSpecialMatch(SubSourcePtr ssp,FilterSetPtr fsp)3630 static Boolean SubSrcSpecialMatch (SubSourcePtr ssp, FilterSetPtr fsp)
3631 {
3632 SourceQualDescPtr sqdp;
3633
3634 if (ssp == NULL)
3635 {
3636 return FALSE;
3637 }
3638 if (fsp == NULL
3639 || fsp->ccp == NULL
3640 || fsp->ccp->constraint_type != CHOICE_CONSTRAINT_STRING
3641 || fsp->ccp->string_constraint == NULL
3642 || fsp->ccp->qual_choice == NULL
3643 || fsp->ccp->qual_choice->data.ptrvalue == NULL)
3644 {
3645 return TRUE;
3646 }
3647
3648 sqdp = (SourceQualDescPtr) fsp->ccp->qual_choice->data.ptrvalue;
3649 if (sqdp->subtype != ssp->subtype)
3650 {
3651 return TRUE;
3652 }
3653 if (DoesStringMatchConstraintX (ssp->name, fsp->ccp->string_constraint))
3654 {
3655 if (fsp->ccp->string_constraint->not_present)
3656 {
3657 return FALSE;
3658 }
3659 else
3660 {
3661 return TRUE;
3662 }
3663 }
3664 else
3665 {
3666 if (fsp->ccp->string_constraint->not_present)
3667 {
3668 return TRUE;
3669 }
3670 else
3671 {
3672 return FALSE;
3673 }
3674 }
3675 }
3676
3677
GetSubfield(CharPtr str,Uint1 subfield)3678 static CharPtr GetSubfield (CharPtr str, Uint1 subfield)
3679 {
3680 CharPtr cp, cp2;
3681 Int4 num_colons = 0;
3682 CharPtr new_val = NULL;
3683
3684 if (StringHasNoText (str)) {
3685 return NULL;
3686 }
3687
3688 cp = StringChr (str, ':');
3689 while (cp != NULL) {
3690 num_colons ++;
3691 cp = StringChr (cp + 1, ':');
3692 }
3693
3694 if (subfield == 0) {
3695 new_val = StringSave (str);
3696 } else if (subfield == 1) {
3697 if (num_colons == 0) {
3698 return NULL;
3699 } else {
3700 cp = StringChr (str, ':');
3701 new_val = (CharPtr) MemNew (sizeof (Char) * (cp - str + 1));
3702 StringNCpy (new_val, str, cp - str);
3703 new_val[cp - str] = 0;
3704 }
3705 } else if (subfield == 2) {
3706 if (num_colons == 0 || num_colons == 1) {
3707 return NULL;
3708 } else {
3709 cp = StringChr (str, ':');
3710 cp2 = StringChr (cp + 1, ':');
3711 new_val = (CharPtr) MemNew (sizeof (Char) * (cp2 - cp));
3712 StringNCpy (new_val, cp + 1, cp2 - cp - 1);
3713 new_val[cp2 - cp - 1] = 0;
3714 }
3715 } else {
3716 if (num_colons == 0) {
3717 new_val = StringSave (str);
3718 } else {
3719 cp = StringRChr (str, ':');
3720 new_val = StringSave (cp + 1);
3721 }
3722 }
3723 return new_val;
3724 }
3725
3726
3727 static CharPtr
GetSourceQualQualValueFromBiop(BioSourcePtr biop,SourceQualDescPtr sqdp,FilterSetPtr fsp)3728 GetSourceQualQualValueFromBiop
3729 (BioSourcePtr biop,
3730 SourceQualDescPtr sqdp,
3731 FilterSetPtr fsp)
3732 {
3733 CharPtr str = NULL, field, tmp_str;
3734 OrgModPtr mod;
3735 SubSourcePtr ssp;
3736
3737 if (biop == NULL || sqdp == NULL)
3738 {
3739 return NULL;
3740 }
3741
3742 if (sqdp->isOrgMod)
3743 {
3744 if (biop->org != NULL && biop->org->orgname != NULL)
3745 {
3746 mod = biop->org->orgname->mod;
3747 while (mod != NULL)
3748 {
3749 if (mod->subtype == sqdp->subtype
3750 && !StringHasNoText (mod->subname)
3751 && OrgModSpecialMatch (mod, fsp))
3752 {
3753 field = GetSubfield (mod->subname, sqdp->subfield);
3754 if (!StringHasNoText (field)) {
3755 if (str == NULL) {
3756 str = field;
3757 } else {
3758 tmp_str = (CharPtr) MemNew ((StringLen (str) + StringLen (field) + 3) * sizeof (Char));
3759 StringCpy (tmp_str, str);
3760 StringCat (tmp_str, "; ");
3761 StringCat (tmp_str, field);
3762 field = MemFree (field);
3763 str = MemFree (str);
3764 str = tmp_str;
3765 }
3766 } else {
3767 field = MemFree (field);
3768 }
3769 }
3770 mod = mod->next;
3771 }
3772 }
3773 }
3774 else
3775 {
3776 ssp = biop->subtype;
3777 while (ssp != NULL)
3778 {
3779 if (ssp->subtype == sqdp->subtype
3780 && !StringHasNoText (ssp->name)
3781 && SubSrcSpecialMatch (ssp, fsp))
3782 {
3783 field = GetSubfield (ssp->name, sqdp->subfield);
3784 if (!StringHasNoText (field)) {
3785 if (str == NULL) {
3786 str = field;
3787 } else {
3788 tmp_str = (CharPtr) MemNew ((StringLen (str) + StringLen (field) + 3) * sizeof (Char));
3789 StringCpy (tmp_str, str);
3790 StringCat (tmp_str, "; ");
3791 StringCat (tmp_str, field);
3792 field = MemFree (field);
3793 str = MemFree (str);
3794 str = tmp_str;
3795 }
3796 } else {
3797 field = MemFree (field);
3798 }
3799 }
3800 ssp = ssp->next;
3801 }
3802 }
3803 return str;
3804 }
3805
GetLocationFromSource(BioSourcePtr biop,ValNodePtr vnp)3806 static CharPtr GetLocationFromSource (BioSourcePtr biop, ValNodePtr vnp)
3807 {
3808 Nlm_EnumFieldAssocPtr eap;
3809
3810 if (biop == NULL)
3811 {
3812 return NULL;
3813 }
3814
3815 for (eap = biosource_genome_alistX;
3816 eap->name != NULL && eap->value != biop->genome;
3817 eap++)
3818 {
3819 }
3820
3821 if (eap != NULL && eap->name != NULL && !StringHasNoText (eap->name))
3822 {
3823 return StringSave (eap->name);
3824 }
3825 else
3826 {
3827 return NULL;
3828 }
3829 }
3830
GetLocationFromSourceFeature(SeqFeatPtr sfp,ValNodePtr vnp,FilterSetPtr fsp)3831 static CharPtr GetLocationFromSourceFeature (SeqFeatPtr sfp, ValNodePtr vnp, FilterSetPtr fsp)
3832 {
3833 if (sfp != NULL && sfp->data.choice == SEQFEAT_BIOSRC)
3834 {
3835 return GetLocationFromSource (sfp->data.value.ptrvalue, vnp);
3836 }
3837 else
3838 {
3839 return NULL;
3840 }
3841 }
3842
3843 static CharPtr
GetLocationFromSourceDescriptor(SeqDescrPtr sdp,ValNodePtr vnp,FilterSetPtr fsp)3844 GetLocationFromSourceDescriptor
3845 (SeqDescrPtr sdp,
3846 ValNodePtr vnp,
3847 FilterSetPtr fsp)
3848 {
3849 if (sdp != NULL && sdp->choice == Seq_descr_source)
3850 {
3851 return GetLocationFromSource (sdp->data.ptrvalue, vnp);
3852 }
3853 else
3854 {
3855 return NULL;
3856 }
3857 }
3858
GetOriginFromSource(BioSourcePtr biop,ValNodePtr vnp)3859 static CharPtr GetOriginFromSource (BioSourcePtr biop, ValNodePtr vnp)
3860 {
3861 Nlm_EnumFieldAssocPtr eap;
3862
3863 if (biop == NULL)
3864 {
3865 return NULL;
3866 }
3867
3868 for (eap = origin_alist;
3869 eap->name != NULL && eap->value != biop->origin;
3870 eap++)
3871 {
3872 }
3873
3874 if (eap != NULL && eap->name != NULL && !StringHasNoText (eap->name))
3875 {
3876 return StringSave (eap->name);
3877 }
3878 else
3879 {
3880 return NULL;
3881 }
3882 }
3883
3884 static CharPtr
GetOriginFromSourceFeature(SeqFeatPtr sfp,ValNodePtr vnp,FilterSetPtr fsp)3885 GetOriginFromSourceFeature
3886 (SeqFeatPtr sfp,
3887 ValNodePtr vnp,
3888 FilterSetPtr fsp)
3889 {
3890 if (sfp != NULL && sfp->data.choice == SEQFEAT_BIOSRC)
3891 {
3892 return GetOriginFromSource (sfp->data.value.ptrvalue, vnp);
3893 }
3894 else
3895 {
3896 return NULL;
3897 }
3898 }
3899
3900 static CharPtr
GetOriginFromSourceDescriptor(SeqDescrPtr sdp,ValNodePtr vnp,FilterSetPtr fsp)3901 GetOriginFromSourceDescriptor
3902 (SeqDescrPtr sdp,
3903 ValNodePtr vnp,
3904 FilterSetPtr fsp)
3905 {
3906 if (sdp != NULL && sdp->choice == Seq_descr_source)
3907 {
3908 return GetOriginFromSource (sdp->data.ptrvalue, vnp);
3909 }
3910 else
3911 {
3912 return NULL;
3913 }
3914 }
3915
GetStringFromSource(BioSourcePtr biop,ValNodePtr vnp)3916 static CharPtr GetStringFromSource (BioSourcePtr biop, ValNodePtr vnp)
3917 {
3918 Nlm_EnumFieldAssocPtr eap;
3919
3920 if (biop == NULL)
3921 {
3922 return NULL;
3923 }
3924
3925 for (eap = orgref_textfield_alist;
3926 eap->name != NULL && StringCmp (vnp->data.ptrvalue, eap->name) != 0;
3927 eap++)
3928 {
3929 }
3930
3931 if (eap != NULL && eap->name != NULL)
3932 {
3933 switch (eap->value)
3934 {
3935 case 1:
3936 if (biop->org != NULL && !StringHasNoText (biop->org->taxname))
3937 {
3938 return StringSave (biop->org->taxname);
3939 }
3940 break;
3941 case 2:
3942 if (biop->org != NULL && !StringHasNoText (biop->org->common))
3943 {
3944 return StringSave (biop->org->common);
3945 }
3946 break;
3947 case 3:
3948 if (biop->org != NULL && biop->org->orgname != NULL
3949 && !StringHasNoText (biop->org->orgname->lineage))
3950 {
3951 return StringSave (biop->org->orgname->lineage);
3952 }
3953 break;
3954 case 4:
3955 if (biop->org != NULL && biop->org->orgname != NULL
3956 && !StringHasNoText (biop->org->orgname->div))
3957 {
3958 return StringSave (biop->org->orgname->div);
3959 }
3960 break;
3961 }
3962 }
3963 return NULL;
3964 }
3965
GetStringFromSourceFeature(SeqFeatPtr sfp,ValNodePtr vnp,FilterSetPtr fsp)3966 static CharPtr GetStringFromSourceFeature (SeqFeatPtr sfp, ValNodePtr vnp, FilterSetPtr fsp)
3967 {
3968 if (sfp != NULL && sfp->data.choice == SEQFEAT_BIOSRC)
3969 {
3970 return GetStringFromSource (sfp->data.value.ptrvalue, vnp);
3971 }
3972 else
3973 {
3974 return NULL;
3975 }
3976 }
3977
StringAppend(CharPtr str1,CharPtr str2)3978 static CharPtr StringAppend (CharPtr str1, CharPtr str2)
3979 {
3980 CharPtr new_str;
3981
3982 if (str1 == NULL && str2 == NULL)
3983 {
3984 return NULL;
3985 }
3986 else if (str1 == NULL)
3987 {
3988 return StringSave (str2);
3989 }
3990 else if (str2 == NULL)
3991 {
3992 return StringSave (str1);
3993 }
3994 else
3995 {
3996 new_str = (CharPtr) MemNew ((StringLen (str1) + StringLen (str2) + 3) * sizeof (Char));
3997 if (new_str != NULL)
3998 {
3999 sprintf (new_str, "%s; %s", str1, str2);
4000 }
4001 return new_str;
4002 }
4003 }
4004
GetStringFromSourceDescriptor(SeqDescrPtr sdp,ValNodePtr vnp,FilterSetPtr fsp)4005 static CharPtr GetStringFromSourceDescriptor (SeqDescrPtr sdp, ValNodePtr vnp, FilterSetPtr fsp)
4006 {
4007 if (sdp != NULL && sdp->choice == Seq_descr_source)
4008 {
4009 return GetStringFromSource (sdp->data.ptrvalue, vnp);
4010 }
4011 else
4012 {
4013 return NULL;
4014 }
4015 }
4016
4017 static CharPtr
GetSourceQualStringFromBioSource(BioSourcePtr biop,ValNodePtr vnp,FilterSetPtr fsp)4018 GetSourceQualStringFromBioSource
4019 (BioSourcePtr biop,
4020 ValNodePtr vnp,
4021 FilterSetPtr fsp)
4022 {
4023 CharPtr str = NULL, str1 = NULL, str2 = NULL;
4024 SourceQualDescData sqdd;
4025
4026 if (biop == NULL || vnp == NULL)
4027 {
4028 return NULL;
4029 }
4030
4031 while (vnp != NULL && str == NULL)
4032 {
4033 if (vnp->choice == 0)
4034 {
4035 str = GetSourceQualQualValueFromBiop (biop, vnp->data.ptrvalue, fsp);
4036 }
4037 else if (vnp->choice == 1)
4038 {
4039 if (StringCmp (vnp->data.ptrvalue, "Location") == 0)
4040 {
4041 str = GetLocationFromSource (biop, vnp);
4042 }
4043 else if (StringCmp (vnp->data.ptrvalue, "Origin") == 0)
4044 {
4045 str = GetOriginFromSource (biop, vnp);
4046 }
4047 else if (StringCmp (vnp->data.ptrvalue, "All Notes") == 0)
4048 {
4049 sqdd.name = "note";
4050 sqdd.isOrgMod = TRUE;
4051 sqdd.subtype = 255;
4052 str1 = GetSourceQualQualValueFromBiop (biop, &sqdd, fsp);
4053 sqdd.isOrgMod = FALSE;
4054 str2 = GetSourceQualQualValueFromBiop (biop, &sqdd, fsp);
4055 str = StringAppend (str1, str2);
4056 str1 = MemFree (str1);
4057 str2 = MemFree (str2);
4058 }
4059 else
4060 {
4061 str = GetStringFromSource (biop, vnp);
4062 }
4063 }
4064 vnp = vnp->next;
4065 }
4066 return str;
4067 }
4068
4069 static CharPtr
GetSourceQualDescrString(SeqDescrPtr sdp,ValNodePtr vnp,FilterSetPtr fsp)4070 GetSourceQualDescrString
4071 (SeqDescrPtr sdp,
4072 ValNodePtr vnp,
4073 FilterSetPtr fsp)
4074 {
4075 if (sdp == NULL || sdp->choice != Seq_descr_source || vnp == NULL)
4076 {
4077 return NULL;
4078 }
4079 return GetSourceQualStringFromBioSource (sdp->data.ptrvalue, vnp, fsp);
4080 }
4081
4082 static CharPtr
GetSourceQualFeatureString(SeqFeatPtr sfp,ValNodePtr vnp,FilterSetPtr fsp)4083 GetSourceQualFeatureString
4084 (SeqFeatPtr sfp,
4085 ValNodePtr vnp,
4086 FilterSetPtr fsp)
4087 {
4088 if (sfp == NULL || sfp->data.choice != SEQFEAT_BIOSRC || vnp == NULL)
4089 {
4090 return NULL;
4091 }
4092
4093 return GetSourceQualStringFromBioSource (sfp->data.value.ptrvalue, vnp, fsp);
4094 }
4095
ApplyLocationToBiop(BioSourcePtr biop,ApplyValuePtr avp)4096 static void ApplyLocationToBiop (BioSourcePtr biop, ApplyValuePtr avp)
4097 {
4098 if (biop == NULL || avp == NULL || avp->field_list == NULL)
4099 {
4100 return;
4101 }
4102
4103 if (avp->etp == NULL
4104 || avp->etp->existing_text_choice == eExistingTextChoiceReplaceOld
4105 || biop->genome == 0)
4106 {
4107 biop->genome = avp->field_list->choice;
4108 }
4109 }
4110
ApplyLocationToSourceFeature(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)4111 static void ApplyLocationToSourceFeature (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
4112 {
4113 if (sfp != NULL && sfp->data.choice == SEQFEAT_BIOSRC)
4114 {
4115 ApplyLocationToBiop (sfp->data.value.ptrvalue, userdata);
4116 }
4117 }
4118
ApplyLocationToSourceDescriptor(SeqDescrPtr sdp,Pointer userdata,FilterSetPtr fsp)4119 static void ApplyLocationToSourceDescriptor (SeqDescrPtr sdp, Pointer userdata, FilterSetPtr fsp)
4120 {
4121 if (sdp != NULL && sdp->choice == Seq_descr_source)
4122 {
4123 ApplyLocationToBiop (sdp->data.ptrvalue, userdata);
4124 }
4125 }
4126
RemoveLocationFromBiop(BioSourcePtr biop,ApplyValuePtr avp)4127 static void RemoveLocationFromBiop (BioSourcePtr biop, ApplyValuePtr avp)
4128 {
4129 if (biop == NULL || avp == NULL || avp->field_list == NULL)
4130 {
4131 return;
4132 }
4133
4134 if (biop->genome == avp->field_list->choice)
4135 {
4136 biop->genome = 0;
4137 }
4138 }
4139
RemoveLocationFromSourceFeature(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)4140 static void RemoveLocationFromSourceFeature (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
4141 {
4142 if (sfp != NULL && sfp->data.choice == SEQFEAT_BIOSRC)
4143 {
4144 RemoveLocationFromBiop (sfp->data.value.ptrvalue, userdata);
4145 }
4146 }
4147
RemoveLocationFromSourceDescriptor(SeqDescrPtr sdp,Pointer userdata,FilterSetPtr fsp)4148 static void RemoveLocationFromSourceDescriptor (SeqDescrPtr sdp, Pointer userdata, FilterSetPtr fsp)
4149 {
4150 if (sdp != NULL && sdp->choice == Seq_descr_source)
4151 {
4152 RemoveLocationFromBiop (sdp->data.ptrvalue, userdata);
4153 }
4154 }
4155
ApplyOriginToBiop(BioSourcePtr biop,ApplyValuePtr avp)4156 static void ApplyOriginToBiop (BioSourcePtr biop, ApplyValuePtr avp)
4157 {
4158 if (biop == NULL || avp == NULL || avp->field_list == NULL)
4159 {
4160 return;
4161 }
4162
4163 if (avp->etp == NULL
4164 || avp->etp->existing_text_choice == eExistingTextChoiceReplaceOld
4165 || biop->origin == 0)
4166 {
4167 biop->origin = avp->field_list->choice;
4168 }
4169 }
4170
ApplyOriginToSourceFeature(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)4171 static void ApplyOriginToSourceFeature (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
4172 {
4173 if (sfp != NULL && sfp->data.choice == SEQFEAT_BIOSRC)
4174 {
4175 ApplyOriginToBiop (sfp->data.value.ptrvalue, userdata);
4176 }
4177 }
4178
ApplyOriginToSourceDescriptor(SeqDescrPtr sdp,Pointer userdata,FilterSetPtr fsp)4179 static void ApplyOriginToSourceDescriptor (SeqDescrPtr sdp, Pointer userdata, FilterSetPtr fsp)
4180 {
4181 if (sdp != NULL && sdp->choice == Seq_descr_source)
4182 {
4183 ApplyOriginToBiop (sdp->data.ptrvalue, userdata);
4184 }
4185 }
4186
RemoveOriginFromBiop(BioSourcePtr biop,ApplyValuePtr avp)4187 static void RemoveOriginFromBiop (BioSourcePtr biop, ApplyValuePtr avp)
4188 {
4189 if (biop == NULL || avp == NULL || avp->field_list == NULL)
4190 {
4191 return;
4192 }
4193
4194 if (biop->origin == avp->field_list->choice)
4195 {
4196 biop->origin = 0;
4197 }
4198 }
4199
RemoveOriginFromSourceFeature(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)4200 static void RemoveOriginFromSourceFeature (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
4201 {
4202 if (sfp != NULL && sfp->data.choice == SEQFEAT_BIOSRC)
4203 {
4204 RemoveOriginFromBiop (sfp->data.value.ptrvalue, userdata);
4205 }
4206 }
4207
RemoveOriginFromSourceDescriptor(SeqDescrPtr sdp,Pointer userdata,FilterSetPtr fsp)4208 static void RemoveOriginFromSourceDescriptor (SeqDescrPtr sdp, Pointer userdata, FilterSetPtr fsp)
4209 {
4210 if (sdp != NULL && sdp->choice == Seq_descr_source)
4211 {
4212 RemoveOriginFromBiop (sdp->data.ptrvalue, userdata);
4213 }
4214 }
4215
ApplyStringToSource(BioSourcePtr biop,Pointer userdata)4216 static void ApplyStringToSource (BioSourcePtr biop, Pointer userdata)
4217 {
4218 ApplyValuePtr avp;
4219
4220 if (biop == NULL || userdata == NULL)
4221 {
4222 return;
4223 }
4224
4225 avp = (ApplyValuePtr) userdata;
4226 if (avp == NULL || avp->field_list == NULL)
4227 {
4228 return;
4229 }
4230
4231 if (StringHasNoText (avp->text_to_replace))
4232 {
4233 if (biop->org == NULL)
4234 {
4235 biop->org = OrgRefNew();
4236 }
4237 if (biop->org->orgname == NULL
4238 && (avp->field_list->choice == 3
4239 || avp->field_list->choice == 4))
4240 {
4241 biop->org->orgname = OrgNameNew ();
4242 }
4243 }
4244
4245 switch (avp->field_list->choice)
4246 {
4247 case 1:
4248 biop->org->taxname = HandleApplyValue (biop->org->taxname, avp);
4249 break;
4250 case 2:
4251 biop->org->common = HandleApplyValue (biop->org->common, avp);
4252 break;
4253 case 3:
4254 biop->org->orgname->lineage = HandleApplyValue (biop->org->orgname->lineage, avp);
4255 break;
4256 case 4:
4257 biop->org->orgname->div = HandleApplyValue (biop->org->orgname->div, avp);
4258 break;
4259 }
4260 }
4261
ApplyStringToSourceFeature(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)4262 static void ApplyStringToSourceFeature (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
4263 {
4264 if (sfp != NULL && sfp->data.choice == SEQFEAT_BIOSRC)
4265 {
4266 ApplyStringToSource (sfp->data.value.ptrvalue, userdata);
4267 }
4268 }
4269
ApplyStringToSourceDescriptor(SeqDescrPtr sdp,Pointer userdata,FilterSetPtr fsp)4270 static void ApplyStringToSourceDescriptor (SeqDescrPtr sdp, Pointer userdata, FilterSetPtr fsp)
4271 {
4272 if (sdp != NULL && sdp->choice == Seq_descr_source)
4273 {
4274 ApplyStringToSource (sdp->data.ptrvalue, userdata);
4275 }
4276 }
4277
RemoveStringFromSource(BioSourcePtr biop,Pointer userdata)4278 static void RemoveStringFromSource (BioSourcePtr biop, Pointer userdata)
4279 {
4280 ApplyValuePtr avp;
4281
4282 if (biop == NULL || biop->org == NULL || userdata == NULL)
4283 {
4284 return;
4285 }
4286
4287 avp = (ApplyValuePtr) userdata;
4288 if (avp == NULL || avp->field_list == NULL)
4289 {
4290 return;
4291 }
4292
4293 switch (avp->field_list->choice)
4294 {
4295 case 1:
4296 biop->org->taxname = MemFree (biop->org->taxname);
4297 break;
4298 case 2:
4299 biop->org->common = MemFree (biop->org->common);
4300 break;
4301 case 3:
4302 if (biop->org->orgname != NULL)
4303 {
4304 biop->org->orgname->lineage = MemFree (biop->org->orgname->lineage);
4305 }
4306 break;
4307 case 4:
4308 if (biop->org->orgname != NULL)
4309 {
4310 biop->org->orgname->div = MemFree (biop->org->orgname->div);
4311 }
4312 break;
4313 }
4314 }
4315
RemoveStringFromSourceFeature(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)4316 static void RemoveStringFromSourceFeature (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
4317 {
4318 if (sfp != NULL && sfp->data.choice == SEQFEAT_BIOSRC)
4319 {
4320 RemoveStringFromSource (sfp->data.value.ptrvalue, userdata);
4321 }
4322 }
4323
RemoveStringFromSourceDescriptor(SeqDescrPtr sdp,Pointer userdata,FilterSetPtr fsp)4324 static void RemoveStringFromSourceDescriptor (SeqDescrPtr sdp, Pointer userdata, FilterSetPtr fsp)
4325 {
4326 if (sdp != NULL && sdp->choice == Seq_descr_source)
4327 {
4328 RemoveStringFromSource (sdp->data.ptrvalue, userdata);
4329 }
4330 }
4331
4332 static void SqnRemoveSourceQualFromBioSource (BioSourcePtr biop, Pointer userdata, FilterSetPtr fsp);
4333
RemoveSubfield(CharPtr orig,Uint1 subfield)4334 static CharPtr RemoveSubfield (CharPtr orig, Uint1 subfield)
4335 {
4336 CharPtr cp, cp2;
4337 Int4 num_colons = 0;
4338 CharPtr new_val;
4339
4340 cp = StringChr (orig, ':');
4341 while (cp != NULL) {
4342 num_colons ++;
4343 cp = StringChr (cp + 1, ':');
4344 }
4345 new_val = orig;
4346
4347 if (subfield == 0) {
4348 new_val = MemFree (new_val);
4349 } else if (subfield == 1) {
4350 if (num_colons == 0) {
4351 /* no INST, just specID, nothing to remove */
4352 } else if (num_colons == 1) {
4353 cp = StringChr (orig, ':');
4354 new_val = StringSave (cp + 1);
4355 orig = MemFree (orig);
4356 } else {
4357 cp = StringChr (orig, ':');
4358 new_val = StringSave (cp);
4359 orig = MemFree (orig);
4360 }
4361 } else if (subfield == 2) {
4362 if (num_colons == 0 || num_colons == 1) {
4363 /* no COLL, nothing to remove */
4364 } else {
4365 cp = StringChr (orig, ':');
4366 cp2 = StringChr (cp + 1, ':');
4367 new_val = (CharPtr) MemNew (sizeof (Char) * (cp - orig + StringLen (cp2) + 1));
4368 StringNCpy (new_val, orig, cp - orig);
4369 StringCat (new_val, cp2);
4370 orig = MemFree (orig);
4371 if (StringCmp (new_val, ":") == 0) {
4372 new_val = MemFree (new_val);
4373 }
4374 }
4375 } else {
4376 /* specid */
4377 if (num_colons == 0) {
4378 new_val = MemFree (new_val);
4379 } else {
4380 cp = StringRChr (new_val, ':');
4381 *(cp + 1) = 0;
4382 }
4383 }
4384 return new_val;
4385 }
4386
4387
ApplyToSubfield(CharPtr orig,ApplyValuePtr avp,Uint1 subfield)4388 static CharPtr ApplyToSubfield (CharPtr orig, ApplyValuePtr avp, Uint1 subfield)
4389 {
4390 CharPtr cp, cp2;
4391 Int4 num_colons = 0, len;
4392 CharPtr new_field, new_val;
4393
4394 cp = StringChr (orig, ':');
4395 while (cp != NULL) {
4396 num_colons ++;
4397 cp = StringChr (cp + 1, ':');
4398 }
4399
4400 new_val = orig;
4401 if (subfield == 0) {
4402 /* whole field */
4403 new_val = HandleApplyValue (orig, avp);
4404 } else if (subfield == 1) {
4405 /* INST */
4406 if (num_colons == 0) {
4407 /* all we have is the specID, we are adding INST */
4408 new_field = HandleApplyValue (NULL, avp);
4409 if (!StringHasNoText (new_field)) {
4410 new_val = (CharPtr) MemNew (sizeof (Char) * (StringLen (new_field) + StringLen (orig) + 2));
4411 sprintf (new_val, "%s:%s", new_field, orig == NULL ? "" : orig);
4412 orig = MemFree (orig);
4413 } else {
4414 new_val = orig;
4415 }
4416 new_field = MemFree (new_field);
4417 } else {
4418 cp = StringChr (orig, ':');
4419 len = cp - orig + 1;
4420 new_field = (CharPtr) MemNew (sizeof (Char) * len);
4421 StringNCpy (new_field, orig, len - 1);
4422 new_field[len - 1] = 0;
4423 new_field = HandleApplyValue (new_field, avp);
4424 new_val = (CharPtr) MemNew (sizeof (Char) * (StringLen (new_field) + StringLen (cp) + 1));
4425 sprintf (new_val, "%s%s", new_field == NULL ? "" : new_field, cp);
4426 orig = MemFree (orig);
4427 new_field = MemFree (new_field);
4428 }
4429 } else if (subfield == 2) {
4430 /* COLL */
4431 if (num_colons == 0) {
4432 /* add blank INST, then COLL, then existing specID */
4433 new_field = HandleApplyValue (NULL, avp);
4434 if (!StringHasNoText (new_field)) {
4435 new_val = (CharPtr) MemNew (sizeof (Char) * (3 + StringLen (new_field) + StringLen (orig)));
4436 sprintf (new_val, ":%s:%s", new_field, orig == NULL ? "" : orig);
4437 orig = MemFree (orig);
4438 } else {
4439 new_val = orig;
4440 }
4441 new_field = MemFree (new_field);
4442 } else if (num_colons == 1) {
4443 /* have INST and specID */
4444 new_field = HandleApplyValue (NULL, avp);
4445 if (!StringHasNoText (new_field)) {
4446 new_val = (CharPtr) MemNew (sizeof (Char) * (3 + StringLen (new_field) + StringLen (orig)));
4447 cp = StringChr (orig, ':');
4448 len = cp - orig;
4449 StringNCpy (new_val, orig, len);
4450 StringCat (new_val, ":");
4451 StringCat (new_val, new_field);
4452 StringCat (new_val, cp);
4453 orig = MemFree (orig);
4454 } else {
4455 new_val = orig;
4456 }
4457 new_field = MemFree (new_field);
4458 } else {
4459 cp = StringChr (orig, ':');
4460 cp2 = StringChr (cp + 1, ':');
4461 len = cp2 - cp;
4462 new_field = (CharPtr) MemNew (sizeof (Char) * len);
4463 StringNCpy (new_field, cp + 1, len - 1);
4464 new_field[len - 1] = 0;
4465 new_field = HandleApplyValue (new_field, avp);
4466 new_val = (CharPtr) MemNew (sizeof (Char) * (cp - orig + 1 + StringLen (new_field) + StringLen (cp2) + 1));
4467 StringNCpy (new_val, orig, cp - orig + 1);
4468 StringCat (new_val, new_field);
4469 StringCat (new_val, cp2);
4470 orig = MemFree (orig);
4471 new_field = MemFree (new_field);
4472 }
4473 } else {
4474 /* specid */
4475 if (num_colons == 0) {
4476 new_val = HandleApplyValue (orig, avp);
4477 } else {
4478 cp = StringRChr (orig, ':');
4479 new_field = StringSave (cp + 1);
4480 new_field = HandleApplyValue (new_field, avp);
4481 new_val = (CharPtr) MemNew (sizeof (Char) + (cp - orig + 1 + StringLen (new_field) + 1));
4482 StringNCpy (new_val, orig, cp - orig + 1);
4483 StringCat (new_val, new_field);
4484 orig = MemFree (orig);
4485 new_field = MemFree (new_field);
4486 }
4487 }
4488 return new_val;
4489 }
4490
4491
ApplySourceQualBioSourceCallback(BioSourcePtr biop,Pointer userdata,FilterSetPtr fsp)4492 static void ApplySourceQualBioSourceCallback (BioSourcePtr biop, Pointer userdata, FilterSetPtr fsp)
4493 {
4494 ApplyValuePtr avp;
4495 SourceQualDescPtr sqdp;
4496 OrgModPtr mod = NULL, last_mod = NULL;
4497 SubSourcePtr ssp = NULL, last_ssp = NULL;
4498 Boolean found = FALSE;
4499 Boolean is_nontext;
4500
4501 if (biop == NULL || userdata == NULL)
4502 {
4503 return;
4504 }
4505
4506 avp = (ApplyValuePtr) userdata;
4507 if (avp->field_list == NULL || avp->field_list->data.ptrvalue == NULL)
4508 {
4509 return;
4510 }
4511
4512 /* don't apply to All Notes */
4513 if (avp->field_list->choice != 0)
4514 {
4515 return;
4516 }
4517
4518 sqdp = (SourceQualDescPtr) avp->field_list->data.ptrvalue;
4519
4520 is_nontext = IsNonTextModifier (sqdp->name);
4521 if (is_nontext && StringHasNoText (avp->new_text))
4522 {
4523 SqnRemoveSourceQualFromBioSource (biop, avp, fsp);
4524 return;
4525 }
4526
4527 if (!StringHasNoText (avp->text_to_replace))
4528 {
4529 found = TRUE;
4530 }
4531
4532 if (sqdp->isOrgMod)
4533 {
4534 if (biop->org == NULL)
4535 {
4536 biop->org = OrgRefNew ();
4537 }
4538 if (biop->org != NULL && biop->org->orgname == NULL)
4539 {
4540 biop->org->orgname = OrgNameNew ();
4541 }
4542 if (biop->org != NULL && biop->org->orgname != NULL)
4543 {
4544 mod = biop->org->orgname->mod;
4545 while (mod != NULL)
4546 {
4547 if (mod->subtype == sqdp->subtype)
4548 {
4549 if (!is_nontext)
4550 {
4551 mod->subname = ApplyToSubfield (mod->subname, avp, sqdp->subfield);
4552 }
4553 found = TRUE;
4554 }
4555 last_mod = mod;
4556 mod = mod->next;
4557 }
4558 if (!found)
4559 {
4560 mod = OrgModNew ();
4561 mod->subtype = sqdp->subtype;
4562 if (is_nontext)
4563 {
4564 mod->subname = StringSave ("");
4565 }
4566 else
4567 {
4568 mod->subname = ApplyToSubfield (mod->subname, avp, sqdp->subfield);
4569 }
4570 if (last_mod == NULL)
4571 {
4572 biop->org->orgname->mod = mod;
4573 }
4574 else
4575 {
4576 last_mod->next = mod;
4577 }
4578 }
4579 }
4580 }
4581 else
4582 {
4583 ssp = biop->subtype;
4584 while (ssp != NULL)
4585 {
4586 if (ssp->subtype == sqdp->subtype)
4587 {
4588 if (! is_nontext)
4589 {
4590 ssp->name = ApplyToSubfield (ssp->name, avp, sqdp->subfield);
4591 }
4592 found = TRUE;
4593 }
4594 last_ssp = ssp;
4595 ssp = ssp->next;
4596 }
4597 if (!found)
4598 {
4599 ssp = SubSourceNew ();
4600 ssp->subtype = sqdp->subtype;
4601 if (is_nontext)
4602 {
4603 ssp->name = StringSave ("");
4604 }
4605 else
4606 {
4607 ssp->name = ApplyToSubfield (ssp->name, avp, sqdp->subfield);
4608 }
4609 if (last_ssp == NULL)
4610 {
4611 biop->subtype = ssp;
4612 }
4613 else
4614 {
4615 last_ssp->next = ssp;
4616 }
4617 }
4618 }
4619 }
4620
ApplySourceQualFeatureCallback(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)4621 static void ApplySourceQualFeatureCallback (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
4622 {
4623 if (sfp == NULL || sfp->data.choice != SEQFEAT_BIOSRC || userdata == NULL)
4624 {
4625 return;
4626 }
4627 ApplySourceQualBioSourceCallback (sfp->data.value.ptrvalue, userdata, fsp);
4628 }
4629
ApplySourceQualDescriptorCallback(SeqDescrPtr sdp,Pointer userdata,FilterSetPtr fsp)4630 static void ApplySourceQualDescriptorCallback (SeqDescrPtr sdp, Pointer userdata, FilterSetPtr fsp)
4631 {
4632 if (sdp == NULL || sdp->choice != Seq_descr_source || userdata == NULL)
4633 {
4634 return;
4635 }
4636 ApplySourceQualBioSourceCallback (sdp->data.ptrvalue, userdata, fsp);
4637 }
4638
RemoveOrgModFromBioSource(BioSourcePtr biop,Uint1 subtype,Uint1 subfield,FilterSetPtr fsp)4639 static void RemoveOrgModFromBioSource (BioSourcePtr biop, Uint1 subtype, Uint1 subfield, FilterSetPtr fsp)
4640 {
4641 OrgModPtr mod = NULL, prev_mod = NULL, next_mod;
4642
4643 if (biop != NULL && biop->org != NULL && biop->org->orgname != NULL)
4644 {
4645 mod = biop->org->orgname->mod;
4646 while (mod != NULL)
4647 {
4648 next_mod = mod->next;
4649 if (mod->subtype == subtype
4650 && OrgModSpecialMatch (mod, fsp))
4651 {
4652 mod->subname = RemoveSubfield (mod->subname, subfield);
4653 if (StringHasNoText (mod->subname)) {
4654 if (prev_mod == NULL)
4655 {
4656 biop->org->orgname->mod = mod->next;
4657 }
4658 else
4659 {
4660 prev_mod->next = mod->next;
4661 }
4662 mod->next = NULL;
4663 OrgModFree (mod);
4664 } else {
4665 prev_mod = mod;
4666 }
4667 }
4668 else
4669 {
4670 prev_mod = mod;
4671 }
4672 mod = next_mod;
4673 }
4674 }
4675 }
4676
RemoveSubSourceFromBioSource(BioSourcePtr biop,Uint2 subtype,Uint1 subfield,FilterSetPtr fsp)4677 static void RemoveSubSourceFromBioSource (BioSourcePtr biop, Uint2 subtype, Uint1 subfield, FilterSetPtr fsp)
4678 {
4679 SubSourcePtr ssp = NULL, prev_ssp = NULL, next_ssp;
4680
4681 if (biop != NULL)
4682 {
4683 ssp = biop->subtype;
4684 while (ssp != NULL)
4685 {
4686 next_ssp = ssp->next;
4687 if (ssp->subtype == subtype
4688 && SubSrcSpecialMatch (ssp, fsp))
4689 {
4690 ssp->name = RemoveSubfield (ssp->name, subfield);
4691 if (StringHasNoText (ssp->name)) {
4692 if (prev_ssp == NULL)
4693 {
4694 biop->subtype = ssp->next;
4695 }
4696 else
4697 {
4698 prev_ssp->next = ssp->next;
4699 }
4700 ssp->next = NULL;
4701 SubSourceFree (ssp);
4702 } else {
4703 prev_ssp = ssp;
4704 }
4705 }
4706 else
4707 {
4708 prev_ssp = ssp;
4709 }
4710 ssp = next_ssp;
4711 }
4712 }
4713 }
4714
SqnRemoveSourceQualFromBioSource(BioSourcePtr biop,Pointer userdata,FilterSetPtr fsp)4715 static void SqnRemoveSourceQualFromBioSource (BioSourcePtr biop, Pointer userdata, FilterSetPtr fsp)
4716 {
4717 ApplyValuePtr avp;
4718 SourceQualDescPtr sqdp;
4719
4720 if (biop == NULL || userdata == NULL)
4721 {
4722 return;
4723 }
4724
4725 avp = (ApplyValuePtr) userdata;
4726 if (avp->field_list == NULL || avp->field_list->data.ptrvalue == NULL)
4727 {
4728 return;
4729 }
4730 if (avp->field_list->choice == 0)
4731 {
4732 sqdp = (SourceQualDescPtr) avp->field_list->data.ptrvalue;
4733 if (sqdp->isOrgMod)
4734 {
4735 RemoveOrgModFromBioSource (biop, sqdp->subtype, sqdp->subfield, fsp);
4736 }
4737 else
4738 {
4739 RemoveSubSourceFromBioSource (biop, sqdp->subtype, sqdp->subfield, fsp);
4740 }
4741 }
4742 else if (avp->field_list->choice == 1
4743 && StringCmp (avp->field_list->data.ptrvalue, "All Notes") == 0)
4744 {
4745 RemoveOrgModFromBioSource (biop, 255, 0, fsp);
4746 RemoveSubSourceFromBioSource (biop, 255, 0, fsp);
4747 }
4748 }
4749
RemoveSourceQualFromSourceFeature(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)4750 static void RemoveSourceQualFromSourceFeature (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
4751 {
4752 if (sfp == NULL || sfp->data.choice != SEQFEAT_BIOSRC || userdata == NULL)
4753 {
4754 return;
4755 }
4756 SqnRemoveSourceQualFromBioSource (sfp->data.value.ptrvalue, userdata, fsp);
4757 }
4758
RemoveSourceQualFromSourceDescriptor(SeqDescrPtr sdp,Pointer userdata,FilterSetPtr fsp)4759 static void RemoveSourceQualFromSourceDescriptor (SeqDescrPtr sdp, Pointer userdata, FilterSetPtr fsp)
4760 {
4761 if (sdp == NULL || sdp->choice != Seq_descr_source || userdata == NULL)
4762 {
4763 return;
4764 }
4765 SqnRemoveSourceQualFromBioSource (sdp->data.ptrvalue, userdata, fsp);
4766 }
4767
SourceLocationSelectionDialogEx(GrouP h,Boolean allow_multi,Boolean allow_discontinued,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)4768 static DialoG SourceLocationSelectionDialogEx
4769 (GrouP h,
4770 Boolean allow_multi,
4771 Boolean allow_discontinued,
4772 Nlm_ChangeNotifyProc change_notify,
4773 Pointer change_userdata)
4774
4775 {
4776 DialoG dlg;
4777 ValNodePtr choice_list = NULL;
4778 Nlm_EnumFieldAssocPtr eap = biosource_genome_alistX;
4779
4780 if (eap == NULL)
4781 {
4782 return NULL;
4783 }
4784
4785 while (eap->name != NULL)
4786 {
4787 if (!StringHasNoText (eap->name)
4788 && (allow_discontinued ||
4789 (StringCmp (eap->name, "Insertion Sequence") != 0
4790 && StringCmp (eap->name, "Transposon") != 0)))
4791 {
4792 ValNodeAddPointer (&choice_list, eap->value, StringSave (eap->name));
4793 }
4794 eap++;
4795 }
4796
4797 /* note - the ValNodeSelectionDialog will free the qual_choice_list
4798 * when done */
4799 dlg = ValNodeSelectionDialog (h, choice_list, TALL_SELECTION_LIST,
4800 ValNodeStringName,
4801 ValNodeSimpleDataFree, ValNodeStringCopy,
4802 ValNodeChoiceMatch, "Location",
4803 change_notify, change_userdata, allow_multi);
4804
4805 return dlg;
4806 }
4807
4808
SourceLocationSelectionDialog(GrouP h,Boolean allow_multi,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)4809 static DialoG SourceLocationSelectionDialog
4810 (GrouP h,
4811 Boolean allow_multi,
4812 Nlm_ChangeNotifyProc change_notify,
4813 Pointer change_userdata)
4814 {
4815 return SourceLocationSelectionDialogEx (h, allow_multi, FALSE,
4816 change_notify, change_userdata);
4817 }
4818
4819
SourceLocationDiscSelectionDialog(GrouP h,Boolean allow_multi,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)4820 static DialoG SourceLocationDiscSelectionDialog
4821 (GrouP h,
4822 Boolean allow_multi,
4823 Nlm_ChangeNotifyProc change_notify,
4824 Pointer change_userdata)
4825 {
4826 return SourceLocationSelectionDialogEx (h, allow_multi, TRUE,
4827 change_notify, change_userdata);
4828 }
4829
4830
SourceOriginSelectionDialog(GrouP h,Boolean allow_multi,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)4831 static DialoG SourceOriginSelectionDialog
4832 (GrouP h,
4833 Boolean allow_multi,
4834 Nlm_ChangeNotifyProc change_notify,
4835 Pointer change_userdata)
4836
4837 {
4838 return EnumAssocSelectionDialog (h, origin_alist, "Origin",
4839 allow_multi, change_notify, change_userdata);
4840 }
4841
SourceStringSelectionDialog(GrouP h,Boolean allow_multi,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)4842 static DialoG SourceStringSelectionDialog
4843 (GrouP h,
4844 Boolean allow_multi,
4845 Nlm_ChangeNotifyProc change_notify,
4846 Pointer change_userdata)
4847
4848 {
4849 return EnumAssocSelectionDialog (h, orgref_textfield_alist, "string",
4850 allow_multi, change_notify, change_userdata);
4851 }
4852
4853
4854 static CharPtr
GetStringFromStringDescriptor(SeqDescrPtr sdp,ValNodePtr vnp,FilterSetPtr fsp)4855 GetStringFromStringDescriptor
4856 (SeqDescrPtr sdp,
4857 ValNodePtr vnp,
4858 FilterSetPtr fsp)
4859 {
4860 if (sdp == NULL || vnp == NULL || sdp->choice != vnp->data.intvalue)
4861 {
4862 return NULL;
4863 }
4864 return StringSave (sdp->data.ptrvalue);
4865 }
4866
GBQualSelectionDialog(GrouP h,Boolean allow_multi,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)4867 static DialoG GBQualSelectionDialog
4868 (GrouP h,
4869 Boolean allow_multi,
4870 Nlm_ChangeNotifyProc change_notify,
4871 Pointer change_userdata)
4872
4873 {
4874 DialoG dlg;
4875 ValNodePtr choice_name_list = NULL;
4876 Int4 i;
4877
4878 for (i = 0; i < NumEditQualifiers; i++)
4879 {
4880 ValNodeAddPointer (&choice_name_list, 0, EditQualifierList[i].name);
4881 }
4882
4883 dlg = SelectionDialog (h, change_notify, change_userdata,
4884 allow_multi, "genbank qualifier",
4885 choice_name_list, TALL_SELECTION_LIST);
4886 ValNodeFree (choice_name_list);
4887 return dlg;
4888 }
4889
GetDbtagStringLen(DbtagPtr db_tag)4890 static Int4 GetDbtagStringLen (DbtagPtr db_tag)
4891 {
4892 Int4 len;
4893
4894 if (db_tag == NULL)
4895 {
4896 return 0;
4897 }
4898
4899 len = StringLen (db_tag->db) + 2;
4900 if (db_tag->tag != NULL)
4901 {
4902 if (db_tag->tag->str != NULL)
4903 {
4904 len += StringLen (db_tag->tag->str);
4905 }
4906 else
4907 {
4908 len += 10;
4909 }
4910 }
4911 return len;
4912 }
4913
GetDbxrefString(SeqFeatPtr sfp)4914 static CharPtr GetDbxrefString (SeqFeatPtr sfp)
4915 {
4916 ValNodePtr vnp;
4917 Int4 len = 0;
4918 CharPtr str = NULL, cp;
4919
4920 if (sfp == NULL || sfp->dbxref == NULL)
4921 {
4922 return NULL;
4923 }
4924
4925 for (vnp = sfp->dbxref; vnp != NULL; vnp = vnp->next)
4926 {
4927 len += GetDbtagStringLen (vnp->data.ptrvalue) + 1;
4928 }
4929
4930 if (len == 0)
4931 {
4932 return NULL;
4933 }
4934
4935 str = (CharPtr) MemNew ((len + 1) * sizeof (Char));
4936 if (str != NULL)
4937 {
4938 for (vnp = sfp->dbxref; vnp != NULL; vnp = vnp->next)
4939 {
4940 cp = GetDbtagString (vnp->data.ptrvalue);
4941 if (cp != NULL)
4942 {
4943 StringCat (str, cp);
4944 StringCat (str, ";");
4945 }
4946 }
4947 }
4948 if (StringLen (str) >1)
4949 {
4950 /* remove final semicolon */
4951 str [StringLen (str) - 2] = 0;
4952 }
4953 return str;
4954 }
4955
GetGBQualString(SeqFeatPtr sfp,ValNodePtr vnp,FilterSetPtr fsp)4956 static CharPtr GetGBQualString (SeqFeatPtr sfp, ValNodePtr vnp, FilterSetPtr fsp)
4957 {
4958 GBQualPtr gbqual;
4959 CharPtr str = NULL;
4960 Int4 field_choice;
4961 RnaRefPtr rrp;
4962 GeneRefPtr grp;
4963
4964 if (sfp == NULL)
4965 {
4966 return NULL;
4967 }
4968 while (vnp != NULL && str == NULL)
4969 {
4970 field_choice = vnp->data.intvalue;
4971 if (StringICmp (EditQualifierList[field_choice - 1].name, "note") == 0)
4972 {
4973 if (!StringHasNoText (sfp->comment))
4974 {
4975 str = StringSave (sfp->comment);
4976 }
4977 }
4978 else if (StringICmp (EditQualifierList[field_choice - 1].name, "exception") == 0)
4979 {
4980 if (!StringHasNoText (sfp->except_text))
4981 {
4982 str = StringSave (sfp->except_text);
4983 }
4984 }
4985 else if (StringICmp (EditQualifierList[field_choice - 1].name, "product") == 0
4986 && sfp->data.choice == SEQFEAT_RNA)
4987 {
4988 rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
4989 if (rrp != NULL && rrp->ext.choice == 1
4990 && !StringHasNoText (rrp->ext.value.ptrvalue))
4991 {
4992 str = StringSave (rrp->ext.value.ptrvalue);
4993 }
4994 }
4995 else if (StringICmp (EditQualifierList [field_choice - 1].name, "map") == 0
4996 && sfp->data.choice == SEQFEAT_GENE)
4997 {
4998 grp = (GeneRefPtr) sfp->data.value.ptrvalue;
4999 if (grp != NULL && !StringHasNoText (grp->maploc))
5000 {
5001 str = StringSave (grp->maploc);
5002 }
5003 }
5004 else if (StringICmp (EditQualifierList [field_choice - 1].name, "db_xref") == 0)
5005 {
5006 str = GetDbxrefString (sfp);
5007 }
5008 else if (StringICmp (EditQualifierList [field_choice - 1].name, "evidence") == 0)
5009 {
5010 if (sfp->exp_ev == 1)
5011 {
5012 str = StringSave ("experimental");
5013 }
5014 else if (sfp->exp_ev == 2)
5015 {
5016 str = StringSave ("non-experimental");
5017 }
5018 }
5019 else
5020 {
5021 gbqual = sfp->qual;
5022 while (gbqual != NULL && str == NULL)
5023 {
5024 if (field_choice > 0 && field_choice < NumEditQualifiers + 1
5025 && StringCmp (gbqual->qual, EditQualifierList[field_choice - 1].name) == 0
5026 && !StringHasNoText (gbqual->val))
5027 {
5028 str = StringSave (gbqual->val);
5029 }
5030 gbqual = gbqual->next;
5031 }
5032 }
5033 vnp = vnp->next;
5034 }
5035 return str;
5036 }
5037
DbtagFromString(CharPtr str)5038 static DbtagPtr DbtagFromString (CharPtr str)
5039 {
5040 DbtagPtr db_tag;
5041 CharPtr cp, idp;
5042 Boolean use_id = TRUE;
5043
5044 if (StringHasNoText (str))
5045 {
5046 return NULL;
5047 }
5048
5049 cp = StringChr (str, ':');
5050 if (cp == NULL)
5051 {
5052 return NULL;
5053 }
5054
5055 db_tag = DbtagNew ();
5056 if (db_tag != NULL)
5057 {
5058 db_tag->db = (CharPtr) MemNew ((cp - str + 1) * sizeof (Char));
5059 StringNCpy (db_tag->db, str, cp - str);
5060 db_tag->db [cp - str] = 0;
5061
5062 idp = cp + 1;
5063 while (*idp != 0 && use_id)
5064 {
5065 if (!isdigit (*idp))
5066 {
5067 use_id = FALSE;
5068 }
5069 idp++;
5070 }
5071 db_tag->tag = ObjectIdNew ();
5072 if (use_id)
5073 {
5074 db_tag->tag->id = atoi (cp + 1);
5075 db_tag->tag->str = NULL;
5076 }
5077 else
5078 {
5079 db_tag->tag->id = 0;
5080 db_tag->tag->str = StringSave (cp + 1);
5081 }
5082 }
5083 return db_tag;
5084 }
5085
HandleApplyValueForObjectID(ObjectIdPtr oip,ApplyValuePtr avp)5086 static void HandleApplyValueForObjectID (ObjectIdPtr oip, ApplyValuePtr avp)
5087 {
5088 CharPtr tmp_str = NULL;
5089 CharPtr cp;
5090 Boolean is_num = TRUE;
5091
5092 if (oip == NULL || avp == NULL)
5093 {
5094 return;
5095 }
5096
5097 if (oip->str == NULL)
5098 {
5099 tmp_str = (CharPtr) MemNew (10 * sizeof (Char));
5100 sprintf (tmp_str, "%d", oip->id);
5101
5102 }
5103 else
5104 {
5105 tmp_str = oip->str;
5106 oip->str = NULL;
5107 }
5108 tmp_str = HandleApplyValue (tmp_str, avp);
5109
5110 for (cp = tmp_str; cp != NULL && *cp != 0 && is_num; cp++)
5111 {
5112 if (!isdigit (*cp))
5113 {
5114 is_num = FALSE;
5115 }
5116 }
5117 if (is_num)
5118 {
5119 oip->id = atoi (tmp_str);
5120 tmp_str = MemFree (tmp_str);
5121 }
5122 else
5123 {
5124 oip->str = tmp_str;
5125 }
5126 }
5127
EditDbxref(SeqFeatPtr sfp,ApplyValuePtr avp,FilterSetPtr fsp)5128 static void EditDbxref (SeqFeatPtr sfp, ApplyValuePtr avp, FilterSetPtr fsp)
5129 {
5130 ValNodePtr vnp;
5131 DbtagPtr db_tag_new, db_tag_to_replace, db_tag;
5132 CharPtr cp;
5133
5134 if (sfp == NULL || avp == NULL)
5135 {
5136 return;
5137 }
5138
5139 db_tag_new = DbtagFromString (avp->new_text);
5140 db_tag_to_replace = DbtagFromString (avp->text_to_replace);
5141
5142 if (db_tag_new == NULL && db_tag_to_replace == NULL)
5143 {
5144 for (vnp = sfp->dbxref; vnp != NULL; vnp = vnp->next)
5145 {
5146 db_tag = (DbtagPtr) vnp->data.ptrvalue;
5147 if (db_tag != NULL)
5148 {
5149 db_tag->db = HandleApplyValue (db_tag->db, avp);
5150 HandleApplyValueForObjectID (db_tag->tag, avp);
5151 }
5152 }
5153 }
5154 else if (db_tag_new != NULL && db_tag_to_replace != NULL)
5155 {
5156 for (vnp = sfp->dbxref; vnp != NULL; vnp = vnp->next)
5157 {
5158 db_tag = (DbtagPtr) vnp->data.ptrvalue;
5159 if (db_tag != NULL)
5160 {
5161 cp = GetDbtagString (db_tag);
5162 cp = HandleApplyValue (cp, avp);
5163 db_tag = DbtagFree (db_tag);
5164 db_tag = DbtagFromString (cp);
5165 vnp->data.ptrvalue = db_tag;
5166 cp = MemFree (cp);
5167 }
5168 }
5169 }
5170 }
5171
RemoveDbxrefList(ValNodePtr vnp)5172 static ValNodePtr RemoveDbxrefList (ValNodePtr vnp)
5173
5174 {
5175 ValNodePtr next;
5176
5177 while (vnp != NULL) {
5178 next = vnp->next;
5179 DbtagFree ((DbtagPtr) vnp->data.ptrvalue);
5180 MemFree (vnp);
5181 vnp = next;
5182 }
5183 return NULL;
5184 }
5185
SetDbxrefFromString(SeqFeatPtr sfp,ApplyValuePtr avp,FilterSetPtr fsp)5186 static void SetDbxrefFromString (SeqFeatPtr sfp, ApplyValuePtr avp, FilterSetPtr fsp)
5187 {
5188 DbtagPtr new_tag;
5189
5190 if (sfp == NULL || avp == NULL)
5191 {
5192 return;
5193 }
5194
5195 if (StringHasNoText (avp->text_to_replace))
5196 {
5197 /* this is an apply */
5198 if (avp->etp != NULL)
5199 {
5200 if (avp->etp->existing_text_choice == eExistingTextChoiceLeaveOld
5201 && sfp->dbxref != NULL)
5202 {
5203 return;
5204 }
5205 else if (avp->etp->existing_text_choice == eExistingTextChoiceReplaceOld)
5206 {
5207 sfp->dbxref = RemoveDbxrefList (sfp->dbxref);
5208 }
5209 }
5210
5211 new_tag = DbtagFromString (avp->new_text);
5212 if (new_tag != NULL)
5213 {
5214 ValNodeAddPointer (&(sfp->dbxref), 0, new_tag);
5215 }
5216 }
5217 else
5218 {
5219 EditDbxref (sfp, avp, fsp);
5220 }
5221
5222 }
5223
5224 static void SetRNAProduct (SeqFeatPtr sfp, ApplyValuePtr avp);
5225
SetGBQualString(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)5226 static void SetGBQualString (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
5227 {
5228 GBQualPtr gbqual, gbqual_last = NULL;
5229 ApplyValuePtr avp;
5230 Boolean found = FALSE;
5231 GeneRefPtr grp;
5232
5233 if (sfp == NULL || userdata == NULL)
5234 {
5235 return;
5236 }
5237 avp = (ApplyValuePtr) userdata;
5238 if (avp->field_list == NULL
5239 || avp->field_list->data.intvalue < 1
5240 || avp->field_list->data.intvalue >= NumEditQualifiers + 1)
5241 {
5242 return;
5243 }
5244
5245 if (StringICmp (EditQualifierList[avp->field_list->data.intvalue - 1].name, "note") == 0)
5246 {
5247 sfp->comment = HandleApplyValue (sfp->comment, avp);
5248 return;
5249 }
5250 else if (StringICmp (EditQualifierList[avp->field_list->data.intvalue - 1].name, "exception") == 0)
5251 {
5252 sfp->except_text = HandleApplyValue (sfp->except_text, avp);
5253 return;
5254 }
5255 else if (StringICmp (EditQualifierList[avp->field_list->data.intvalue - 1].name, "product") == 0
5256 && sfp->data.choice == SEQFEAT_RNA)
5257 {
5258 SetRNAProduct (sfp, avp);
5259 return;
5260 }
5261 else if (StringICmp (EditQualifierList [avp->field_list->data.intvalue - 1].name, "map") == 0
5262 && sfp->data.choice == SEQFEAT_GENE)
5263 {
5264 grp = (GeneRefPtr) sfp->data.value.ptrvalue;
5265 if (grp != NULL)
5266 {
5267 grp->maploc = HandleApplyValue (grp->maploc, avp);
5268 return;
5269 }
5270 }
5271 else if (StringICmp (EditQualifierList [avp->field_list->data.intvalue - 1].name, "db_xref") == 0)
5272 {
5273 SetDbxrefFromString (sfp, avp, fsp);
5274 return;
5275 }
5276
5277
5278 if (!StringHasNoText (avp->text_to_replace))
5279 {
5280 found = TRUE;
5281 }
5282
5283 gbqual = sfp->qual;
5284 while (gbqual != NULL)
5285 {
5286 gbqual_last = gbqual;
5287 if (StringCmp (gbqual->qual, EditQualifierList[avp->field_list->data.intvalue - 1].name) == 0)
5288 {
5289 gbqual->val = HandleApplyValue (gbqual->val, avp);
5290 found = TRUE;
5291 }
5292 gbqual = gbqual->next;
5293 }
5294 if (!found)
5295 {
5296 gbqual = GBQualNew ();
5297 if (gbqual != NULL)
5298 {
5299 gbqual->qual = StringSave (EditQualifierList[avp->field_list->data.intvalue - 1].name);
5300 gbqual->val = StringSave (avp->new_text);
5301 if (gbqual_last == NULL)
5302 {
5303 sfp->qual = gbqual;
5304 }
5305 else
5306 {
5307 gbqual_last->next = gbqual;
5308 }
5309 }
5310 }
5311 }
5312
RemoveGBQualField(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)5313 static void RemoveGBQualField (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
5314 {
5315 GBQualPtr gbqual, gbqual_last = NULL, gbqual_next;
5316 ApplyValuePtr avp;
5317 RnaRefPtr rrp;
5318 GeneRefPtr grp;
5319
5320 if (sfp == NULL || userdata == NULL)
5321 {
5322 return;
5323 }
5324 avp = (ApplyValuePtr) userdata;
5325 if (avp->field_list == NULL
5326 || avp->field_list->data.intvalue < 1
5327 || avp->field_list->data.intvalue >= NumEditQualifiers + 1)
5328 {
5329 return;
5330 }
5331
5332 if (StringICmp (EditQualifierList[avp->field_list->data.intvalue - 1].name, "note") == 0)
5333 {
5334 sfp->comment = MemFree (sfp->comment);
5335 return;
5336 }
5337 else if (StringICmp (EditQualifierList[avp->field_list->data.intvalue - 1].name, "exception") == 0)
5338 {
5339 sfp->except_text = MemFree (sfp->except_text);
5340 return;
5341 }
5342 else if (StringICmp (EditQualifierList[avp->field_list->data.intvalue - 1].name, "product") == 0
5343 && sfp->data.choice == SEQFEAT_RNA)
5344 {
5345 rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
5346 if (rrp != NULL && rrp->ext.choice == 1)
5347 {
5348 rrp->ext.choice = 0;
5349 rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
5350 }
5351 return;
5352 }
5353 else if (StringICmp (EditQualifierList [avp->field_list->data.intvalue - 1].name, "map") == 0
5354 && sfp->data.choice == SEQFEAT_GENE)
5355 {
5356 grp = (GeneRefPtr) sfp->data.value.ptrvalue;
5357 if (grp != NULL)
5358 {
5359 grp->maploc = MemFree (grp->maploc);
5360 }
5361 }
5362 else if (StringICmp (EditQualifierList [avp->field_list->data.intvalue - 1].name, "db_xref") == 0)
5363 {
5364 sfp->dbxref = RemoveDbxrefList (sfp->dbxref);
5365 }
5366
5367
5368 gbqual = sfp->qual;
5369 while (gbqual != NULL)
5370 {
5371 gbqual_next = gbqual->next;
5372 if (StringCmp (gbqual->qual, EditQualifierList[avp->field_list->data.intvalue - 1].name) == 0)
5373 {
5374 if (gbqual_last == NULL)
5375 {
5376 sfp->qual = gbqual->next;
5377 }
5378 else
5379 {
5380 gbqual_last->next = gbqual->next;
5381 }
5382 gbqual->next = NULL;
5383 GBQualFree (gbqual);
5384 }
5385 else
5386 {
5387 gbqual_last = gbqual;
5388 }
5389 gbqual = gbqual_next;
5390 }
5391 }
5392
5393
RemoveGoTerm(SeqFeatPtr sfp,CharPtr term_name)5394 static void RemoveGoTerm (SeqFeatPtr sfp, CharPtr term_name)
5395 {
5396 UserObjectPtr uop;
5397 ObjectIdPtr oip;
5398 UserFieldPtr curr, curr_next, prev = NULL;
5399
5400 if (sfp == NULL || sfp->ext == NULL || StringHasNoText (term_name))
5401 {
5402 return;
5403 }
5404
5405 uop = (UserObjectPtr) sfp->ext;
5406 oip = uop->type;
5407 if (oip == NULL || StringICmp (oip->str, "GeneOntology") != 0) return;
5408
5409 for (curr = uop->data; curr != NULL; curr = curr_next)
5410 {
5411 curr_next = curr->next;
5412 oip = curr->label;
5413 if (oip != NULL && StringICmp (oip->str, term_name) == 0)
5414 {
5415 if (prev == NULL)
5416 {
5417 uop->data = curr->next;
5418 }
5419 else
5420 {
5421 prev->next = curr->next;
5422 }
5423 curr->next = NULL;
5424 UserFieldFree (curr);
5425 }
5426 else
5427 {
5428 prev = curr;
5429 }
5430 }
5431
5432 if (uop->data == NULL)
5433 {
5434 sfp->ext = UserObjectFree (sfp->ext);
5435 }
5436
5437 }
5438
5439
RemoveGBQualByNameConstraint(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)5440 static void RemoveGBQualByNameConstraint (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
5441 {
5442 GBQualPtr gbqual, gbqual_last = NULL, gbqual_next;
5443 RnaRefPtr rrp;
5444 GeneRefPtr grp;
5445 StringConstraintXPtr scp;
5446
5447 if (sfp == NULL || userdata == NULL)
5448 {
5449 return;
5450 }
5451 scp = (StringConstraintXPtr) userdata;
5452 if (scp == NULL)
5453 {
5454 return;
5455 }
5456
5457 if (DoesStringMatchConstraintX ("note", scp))
5458 {
5459 sfp->comment = MemFree (sfp->comment);
5460 }
5461
5462 if (DoesStringMatchConstraintX ("exception", scp))
5463 {
5464 sfp->except_text = MemFree (sfp->except_text);
5465 }
5466
5467 if (DoesStringMatchConstraintX ("product", scp) && sfp->data.choice == SEQFEAT_RNA)
5468 {
5469 rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
5470 if (rrp != NULL && rrp->ext.choice == 1)
5471 {
5472 rrp->ext.choice = 0;
5473 rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
5474 }
5475 }
5476
5477 if (DoesStringMatchConstraintX ("map", scp) && sfp->data.choice == SEQFEAT_GENE)
5478 {
5479 grp = (GeneRefPtr) sfp->data.value.ptrvalue;
5480 if (grp != NULL)
5481 {
5482 grp->maploc = MemFree (grp->maploc);
5483 }
5484 }
5485
5486 if (DoesStringMatchConstraintX ("db_xref", scp))
5487 {
5488 sfp->dbxref = RemoveDbxrefList (sfp->dbxref);
5489 }
5490
5491 if (DoesStringMatchConstraintX ("go_process", scp))
5492 {
5493 RemoveGoTerm (sfp, "process");
5494 }
5495
5496 if (DoesStringMatchConstraintX ("go_function", scp))
5497 {
5498 RemoveGoTerm (sfp, "function");
5499 }
5500
5501 if (DoesStringMatchConstraintX ("go_component", scp))
5502 {
5503 RemoveGoTerm (sfp, "component");
5504 }
5505
5506 gbqual = sfp->qual;
5507 while (gbqual != NULL)
5508 {
5509 gbqual_next = gbqual->next;
5510 if (DoesStringMatchConstraintX (gbqual->qual, scp))
5511 {
5512 if (gbqual_last == NULL)
5513 {
5514 sfp->qual = gbqual->next;
5515 }
5516 else
5517 {
5518 gbqual_last->next = gbqual->next;
5519 }
5520 gbqual->next = NULL;
5521 GBQualFree (gbqual);
5522 }
5523 else
5524 {
5525 gbqual_last = gbqual;
5526 }
5527 gbqual = gbqual_next;
5528 }
5529 }
5530
5531
GetFeatureNote(SeqFeatPtr sfp,ValNodePtr vnp,FilterSetPtr fsp)5532 static CharPtr GetFeatureNote (SeqFeatPtr sfp, ValNodePtr vnp, FilterSetPtr fsp)
5533 {
5534 if (sfp == NULL || StringHasNoText (sfp->comment))
5535 {
5536 return NULL;
5537 }
5538 else
5539 {
5540 return StringSave (sfp->comment);
5541 }
5542 }
5543
5544
StripFieldNameFromText(CharPtr text,NameFromValNodeProc field_name_func,ValNodePtr field_vnp)5545 static void StripFieldNameFromText(CharPtr text,
5546 NameFromValNodeProc field_name_func,
5547 ValNodePtr field_vnp)
5548 {
5549 CharPtr src, dst;
5550 CharPtr field_name = NULL;
5551 Uint4 field_name_len;
5552
5553 if (StringHasNoText (text) || field_name_func == NULL)
5554 {
5555 return;
5556 }
5557
5558 field_name = field_name_func(field_vnp);
5559 field_name_len = StringLen (field_name);
5560
5561 if (!StringHasNoText (field_name) && StringNICmp(text, field_name, field_name_len) == 0
5562 && StringLen (text) > field_name_len
5563 && text[field_name_len] == ' ')
5564 {
5565 src = text + field_name_len + 1;
5566 while (*src == ' ')
5567 {
5568 src++;
5569 }
5570 dst = text;
5571 while (*src != 0)
5572 {
5573 *dst = *src;
5574 dst++;
5575 src++;
5576 }
5577 *dst = 0;
5578 }
5579 field_name = MemFree (field_name);
5580 }
5581
5582
ReplaceStringForParse(CharPtr src_text,TextPortionXPtr text_portion)5583 static CharPtr ReplaceStringForParse(CharPtr src_text, TextPortionXPtr text_portion)
5584 {
5585 CharPtr found_loc;
5586 Int4 found_len;
5587 CharPtr dst_txt = NULL, cp;
5588
5589 if (src_text == NULL || text_portion == NULL) {
5590 return NULL;
5591 }
5592 /* for parse, replace the source text with the portion we want */
5593 found_loc = NULL;
5594 found_len = 0;
5595 FindTextPortionXInString (src_text, text_portion, &found_loc, &found_len);
5596 if (found_loc != NULL)
5597 {
5598 dst_txt = (CharPtr)MemNew (found_len + 1);
5599 StringNCpy (dst_txt, found_loc, found_len);
5600 dst_txt[found_len] = 0;
5601 cp = found_loc + found_len;
5602 while (*cp != 0) {
5603 *found_loc = *cp;
5604 found_loc++;
5605 cp++;
5606 }
5607 *found_loc = 0;
5608 }
5609 return dst_txt;
5610 }
5611
5612
ConvertFeatureFieldCallback(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)5613 static void ConvertFeatureFieldCallback (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
5614 {
5615 ConvertFieldPtr cfp;
5616 CharPtr src_text;
5617 CharPtr dst_text = NULL;
5618 ApplyValueData avd;
5619
5620 if (sfp == NULL || userdata == NULL)
5621 {
5622 return;
5623 }
5624
5625 cfp = (ConvertFieldPtr) userdata;
5626
5627 if (cfp->src_field_list == NULL || cfp->dst_field_list == NULL
5628 || cfp->get_str_func == NULL || cfp->set_str_func == NULL
5629 || cfp->remove_str_func == NULL)
5630 {
5631 return;
5632 }
5633
5634 avd.text_to_replace = NULL;
5635 avd.where_to_replace = EditApplyFindLocation_anywhere;
5636 src_text = (cfp->get_str_func)(sfp, cfp->src_field_list, cfp->fsp);
5637
5638 if (cfp->strip_name_from_text)
5639 {
5640 StripFieldNameFromText(src_text, cfp->name_field_func, cfp->dst_field_list);
5641 }
5642
5643 if (StringHasNoText (src_text))
5644 {
5645 src_text = MemFree (src_text);
5646 return;
5647 }
5648
5649 if (cfp->convert_type == CONVERT_TYPE_SWAP)
5650 {
5651 /* for swap, we already know what we're doing with existing text -
5652 * we're putting it where the new text used to be. */
5653 avd.etp = NULL;
5654 /* and we need to get the destination text before it's replaced */
5655 dst_text = (cfp->get_str_func)(sfp, cfp->dst_field_list, cfp->fsp);
5656 if (cfp->strip_name_from_text)
5657 {
5658 StripFieldNameFromText(dst_text, cfp->name_field_func, cfp->src_field_list);
5659 }
5660 }
5661 else if (cfp->convert_type == CONVERT_TYPE_PARSE)
5662 {
5663 /* for parse, replace the source text with the portion we want */
5664 dst_text = src_text;
5665 src_text = ReplaceStringForParse(src_text, cfp->text_portion);
5666 if (src_text == NULL)
5667 {
5668 dst_text = MemFree (dst_text);
5669 return;
5670 }
5671 if (!cfp->remove_parsed) {
5672 dst_text = MemFree (dst_text);
5673 }
5674 avd.etp = cfp->etp;
5675 }
5676 else
5677 {
5678 avd.etp = cfp->etp;
5679 }
5680
5681
5682 /* put src_text in the dst_field */
5683 avd.field_list = cfp->dst_field_list;
5684 avd.new_text = src_text;
5685 (cfp->set_str_func) (sfp, &avd, cfp->fsp);
5686
5687 if (cfp->convert_type == CONVERT_TYPE_SWAP
5688 || (cfp->convert_type == CONVERT_TYPE_PARSE && cfp->remove_parsed))
5689 {
5690 /* put dst_text in the src_field */
5691 avd.field_list = cfp->src_field_list;
5692 avd.new_text = dst_text;
5693 (cfp->set_str_func) (sfp, &avd, cfp->fsp);
5694 }
5695 else if (cfp->convert_type == CONVERT_TYPE_MOVE)
5696 {
5697 /* remove old src_field */
5698 avd.etp = NULL;
5699 avd.field_list = cfp->src_field_list;
5700 avd.new_text = NULL;
5701 (cfp->remove_str_func) (sfp, &avd, cfp->fsp);
5702 }
5703 }
5704
ConvertDescriptorFieldCallback(SeqDescrPtr sdp,Pointer userdata,FilterSetPtr fsp)5705 static void ConvertDescriptorFieldCallback (SeqDescrPtr sdp, Pointer userdata, FilterSetPtr fsp)
5706 {
5707 ConvertFieldPtr cfp;
5708 CharPtr src_text;
5709 CharPtr dst_text;
5710 ApplyValueData avd;
5711
5712 if (sdp == NULL || userdata == NULL)
5713 {
5714 return;
5715 }
5716
5717 cfp = (ConvertFieldPtr) userdata;
5718
5719 if (cfp->src_field_list == NULL || cfp->dst_field_list == NULL
5720 || cfp->get_d_str_func == NULL || cfp->set_d_str_func == NULL
5721 || cfp->remove_d_str_func == NULL)
5722 {
5723 return;
5724 }
5725
5726 avd.text_to_replace = NULL;
5727 avd.where_to_replace = EditApplyFindLocation_anywhere;
5728 src_text = (cfp->get_d_str_func)(sdp, cfp->src_field_list, cfp->fsp);
5729 if (cfp->strip_name_from_text)
5730 {
5731 StripFieldNameFromText(src_text, cfp->name_field_func, cfp->dst_field_list);
5732 }
5733
5734 if (StringHasNoText (src_text))
5735 {
5736 src_text = MemFree (src_text);
5737 return;
5738 }
5739
5740 if (cfp->convert_type == CONVERT_TYPE_SWAP)
5741 {
5742 /* for swap, we already know what we're doing with existing text -
5743 * we're putting it where the new text used to be. */
5744 avd.etp = NULL;
5745 /* and we need to get the destination text before it's replaced */
5746 dst_text = (cfp->get_d_str_func)(sdp, cfp->dst_field_list, cfp->fsp);
5747 if (cfp->strip_name_from_text)
5748 {
5749 StripFieldNameFromText(dst_text, cfp->name_field_func, cfp->src_field_list);
5750 }
5751
5752 }
5753 else if (cfp->convert_type == CONVERT_TYPE_PARSE)
5754 {
5755 /* for parse, replace the source text with the portion we want */
5756 dst_text = src_text;
5757 src_text = ReplaceStringForParse(src_text, cfp->text_portion);
5758 if (src_text == NULL)
5759 {
5760 dst_text = MemFree (dst_text);
5761 return;
5762 }
5763 if (!cfp->remove_parsed) {
5764 dst_text = MemFree (dst_text);
5765 }
5766 avd.etp = cfp->etp;
5767 }
5768 else
5769 {
5770 avd.etp = cfp->etp;
5771 }
5772
5773 /* put src_text in the dst_field */
5774 avd.field_list = cfp->dst_field_list;
5775 avd.new_text = src_text;
5776 (cfp->set_d_str_func) (sdp, &avd, cfp->fsp);
5777
5778 if (cfp->convert_type == CONVERT_TYPE_SWAP
5779 || (cfp->convert_type == CONVERT_TYPE_PARSE && cfp->remove_parsed))
5780 {
5781 /* put dst_text in the src_field */
5782 avd.etp = NULL;
5783 avd.field_list = cfp->src_field_list;
5784 avd.new_text = dst_text;
5785 (cfp->set_d_str_func) (sdp, &avd, cfp->fsp);
5786 }
5787 else if (cfp->convert_type == CONVERT_TYPE_MOVE)
5788 {
5789 /* remove old src_field */
5790 avd.etp = NULL;
5791 avd.field_list = cfp->src_field_list;
5792 avd.new_text = NULL;
5793 (cfp->remove_d_str_func) (sdp, &avd, cfp->fsp);
5794 }
5795 }
5796
ConvertNonTextFeatureFieldCallback(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)5797 static void ConvertNonTextFeatureFieldCallback (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
5798 {
5799 ConvertFieldPtr cfp;
5800 CharPtr curr_val = NULL;
5801 CharPtr src_val;
5802 ApplyValueData avd;
5803
5804 if (sfp == NULL || userdata == NULL)
5805 {
5806 return;
5807 }
5808
5809 cfp = (ConvertFieldPtr) userdata;
5810
5811 if (cfp->src_field_list == NULL || cfp->dst_field_list == NULL
5812 || cfp->get_str_func == NULL || cfp->set_str_func == NULL
5813 || cfp->name_field_func == NULL)
5814 {
5815 return;
5816 }
5817
5818 curr_val = (cfp->get_str_func)(sfp, NULL, NULL);
5819 src_val = (cfp->name_field_func)(cfp->src_field_list);
5820 if (StringCmp (curr_val, src_val) == 0)
5821 {
5822 avd.where_to_replace = EditApplyFindLocation_anywhere;
5823 avd.field_list = cfp->dst_field_list;
5824 avd.etp = NULL;
5825 (cfp->set_str_func) (sfp, &avd, cfp->fsp);
5826 }
5827 curr_val = MemFree (curr_val);
5828 src_val = MemFree (src_val);
5829 }
5830
ConvertNonTextDescriptorFieldCallback(SeqDescrPtr sdp,Pointer userdata,FilterSetPtr fsp)5831 static void ConvertNonTextDescriptorFieldCallback (SeqDescrPtr sdp, Pointer userdata, FilterSetPtr fsp)
5832 {
5833 ConvertFieldPtr cfp;
5834 CharPtr curr_val = NULL;
5835 CharPtr src_val;
5836 ApplyValueData avd;
5837
5838 if (sdp == NULL || userdata == NULL)
5839 {
5840 return;
5841 }
5842
5843 cfp = (ConvertFieldPtr) userdata;
5844
5845 if (cfp->src_field_list == NULL || cfp->dst_field_list == NULL
5846 || cfp->get_d_str_func == NULL || cfp->set_d_str_func == NULL
5847 || cfp->name_field_func == NULL)
5848 {
5849 return;
5850 }
5851
5852 curr_val = (cfp->get_d_str_func)(sdp, NULL, NULL);
5853 src_val = (cfp->name_field_func)(cfp->src_field_list);
5854 if (StringCmp (curr_val, src_val) == 0)
5855 {
5856 avd.where_to_replace = EditApplyFindLocation_anywhere;
5857 avd.field_list = cfp->dst_field_list;
5858 avd.etp = NULL;
5859 (cfp->set_d_str_func) (sdp, &avd, cfp->fsp);
5860 }
5861 curr_val = MemFree (curr_val);
5862 src_val = MemFree (src_val);
5863 }
5864
5865 #define FEATUREFIELD_NONE 0
5866
5867 typedef struct featurefieldselection
5868 {
5869 DIALOG_MESSAGE_BLOCK
5870 PopuP feature_field;
5871
5872 Boolean allow_none;
5873 Int4 num_fields;
5874 Nlm_ChangeNotifyProc change_notify;
5875 Pointer change_userdata;
5876 } FeatureFieldSelectionData, PNTR FeatureFieldSelectionPtr;
5877
5878
FeatureFieldSelectionChange(PopuP p)5879 static void FeatureFieldSelectionChange (PopuP p)
5880 {
5881 FeatureFieldSelectionPtr dlg;
5882
5883 dlg = (FeatureFieldSelectionPtr) GetObjectExtra (p);
5884 if (dlg == NULL)
5885 {
5886 return;
5887 }
5888 if (dlg->change_notify != NULL)
5889 {
5890 (dlg->change_notify) (dlg->change_userdata);
5891 }
5892 }
5893
ResetFeatureFieldSelection(FeatureFieldSelectionPtr dlg)5894 static void ResetFeatureFieldSelection (FeatureFieldSelectionPtr dlg)
5895 {
5896 if (dlg == NULL)
5897 {
5898 return;
5899 }
5900 SetValue (dlg->feature_field, 1);
5901 FeatureFieldSelectionChange (dlg->feature_field);
5902 }
5903
FeatureFieldToDialog(DialoG d,Pointer data)5904 static void FeatureFieldToDialog (DialoG d, Pointer data)
5905 {
5906 FeatureFieldSelectionPtr dlg;
5907 ValNodePtr vnp;
5908 Int4 feature_field;
5909
5910 dlg = (FeatureFieldSelectionPtr) GetObjectExtra (d);
5911 if (dlg == NULL)
5912 {
5913 return;
5914 }
5915
5916 vnp = (ValNodePtr) data;
5917 if (vnp == NULL)
5918 {
5919 ResetFeatureFieldSelection (dlg);
5920 }
5921 else
5922 {
5923 feature_field = vnp->data.intvalue;
5924 if (feature_field < FEATUREFIELD_NONE || feature_field > dlg->num_fields + 1)
5925 {
5926 feature_field = FEATUREFIELD_NONE;
5927 }
5928 if (dlg->allow_none)
5929 {
5930 feature_field ++;
5931 }
5932 SetValue (dlg->feature_field, feature_field);
5933 }
5934 }
5935
DialogToFeatureField(DialoG d)5936 static Pointer DialogToFeatureField (DialoG d)
5937 {
5938 FeatureFieldSelectionPtr dlg;
5939 ValNodePtr vnp = NULL;
5940 Int4 feature_field;
5941
5942 dlg = (FeatureFieldSelectionPtr) GetObjectExtra (d);
5943 if (dlg == NULL)
5944 {
5945 return NULL;
5946 }
5947
5948 feature_field = GetValue (dlg->feature_field);
5949 if (dlg->allow_none)
5950 {
5951 feature_field --;
5952 }
5953 if (feature_field > FEATUREFIELD_NONE)
5954 {
5955 vnp = ValNodeNew (NULL);
5956 if (vnp != NULL)
5957 {
5958 vnp->data.intvalue = feature_field;
5959 }
5960 }
5961 return vnp;
5962 }
5963
FeatureFieldMessage(DialoG d,Int2 mssg)5964 static void FeatureFieldMessage (DialoG d, Int2 mssg)
5965
5966 {
5967 FeatureFieldSelectionPtr dlg;
5968
5969 dlg = (FeatureFieldSelectionPtr) GetObjectExtra (d);
5970 if (dlg != NULL) {
5971 switch (mssg) {
5972 case VIB_MSG_INIT :
5973 /* reset list */
5974 ResetFeatureFieldSelection (dlg);
5975 break;
5976 case VIB_MSG_ENTER :
5977 Select (dlg->feature_field);
5978 break;
5979 default :
5980 break;
5981 }
5982 }
5983 }
5984
TestFeatureFieldDialog(DialoG d)5985 static ValNodePtr TestFeatureFieldDialog (DialoG d)
5986
5987 {
5988 return NULL;
5989 }
5990
FeatureFieldSelectionDialogEx(GrouP h,Boolean allow_none,CharPtr none_txt,Int4 num_fields,CharPtr PNTR field_names,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)5991 static DialoG FeatureFieldSelectionDialogEx
5992 (GrouP h,
5993 Boolean allow_none,
5994 CharPtr none_txt,
5995 Int4 num_fields,
5996 CharPtr PNTR field_names,
5997 Nlm_ChangeNotifyProc change_notify,
5998 Pointer change_userdata)
5999 {
6000 FeatureFieldSelectionPtr dlg;
6001 GrouP p;
6002 Int4 k;
6003
6004 dlg = (FeatureFieldSelectionPtr) MemNew (sizeof (FeatureFieldSelectionData));
6005 if (dlg == NULL)
6006 {
6007 return NULL;
6008 }
6009
6010 p = HiddenGroup (h, 1, 0, NULL);
6011 SetObjectExtra (p, dlg, StdCleanupExtraProc);
6012
6013 dlg->dialog = (DialoG) p;
6014 dlg->todialog = FeatureFieldToDialog;
6015 dlg->fromdialog = DialogToFeatureField;
6016 dlg->dialogmessage = FeatureFieldMessage;
6017 dlg->testdialog = TestFeatureFieldDialog;
6018 dlg->allow_none = allow_none;
6019 dlg->num_fields = num_fields;
6020 dlg->change_notify = change_notify;
6021 dlg->change_userdata = change_userdata;
6022
6023 dlg->feature_field = PopupList (p, TRUE, FeatureFieldSelectionChange);
6024 if (dlg->allow_none)
6025 {
6026 PopupItem (dlg->feature_field, none_txt);
6027 }
6028 for (k = 0; k < dlg->num_fields; k++)
6029 {
6030 PopupItem (dlg->feature_field, field_names[k]);
6031 }
6032 SetValue (dlg->feature_field, 1);
6033 SetObjectExtra (dlg->feature_field, dlg, NULL);
6034 return (DialoG) p;
6035 }
6036
6037 extern DialoG
FeatureFieldSelectionDialog(GrouP h,Boolean allow_none,Int4 num_fields,CharPtr PNTR field_names,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)6038 FeatureFieldSelectionDialog
6039 (GrouP h,
6040 Boolean allow_none,
6041 Int4 num_fields,
6042 CharPtr PNTR field_names,
6043 Nlm_ChangeNotifyProc change_notify,
6044 Pointer change_userdata)
6045 {
6046 return FeatureFieldSelectionDialogEx (h, allow_none, "None",
6047 num_fields, field_names,
6048 change_notify, change_userdata);
6049 }
6050
FeatureFieldSelectionDialogAny(GrouP h,Boolean allow_none,Int4 num_fields,CharPtr PNTR field_names,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)6051 static DialoG FeatureFieldSelectionDialogAny
6052 (GrouP h,
6053 Boolean allow_none,
6054 Int4 num_fields,
6055 CharPtr PNTR field_names,
6056 Nlm_ChangeNotifyProc change_notify,
6057 Pointer change_userdata)
6058 {
6059 return FeatureFieldSelectionDialogEx (h, allow_none, "Any Field",
6060 num_fields, field_names,
6061 change_notify, change_userdata);
6062 }
6063
6064
6065 static CharPtr gene_field_list [] =
6066 {
6067 "locus", "description", "comment", "allele", "maploc", "locus_tag", "synonym", "old_locus_tag"
6068 };
6069
6070 #define GENEFIELD_LOCUS 1
6071 #define GENEFIELD_DESCRIPTION 2
6072 #define GENEFIELD_COMMENT 3
6073 #define GENEFIELD_ALLELE 4
6074 #define GENEFIELD_MAPLOC 5
6075 #define GENEFIELD_LOCUS_TAG 6
6076 #define GENEFIELD_SYNONYM 7
6077 #define GENEFIELD_OLD_LOCUS_TAG 8
6078
6079 static int num_gene_fields = sizeof (gene_field_list) / sizeof (CharPtr);
6080
6081 extern DialoG
GeneFieldSelectionDialog(GrouP h,Boolean allow_none,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)6082 GeneFieldSelectionDialog
6083 (GrouP h,
6084 Boolean allow_none,
6085 Nlm_ChangeNotifyProc change_notify,
6086 Pointer change_userdata)
6087 {
6088 return FeatureFieldSelectionDialog (h, allow_none,
6089 num_gene_fields, gene_field_list,
6090 change_notify, change_userdata);
6091 }
6092
6093 extern CharPtr
GetGeneFieldString(SeqFeatPtr sfp,ValNodePtr gene_field,FilterSetPtr fsp)6094 GetGeneFieldString
6095 (SeqFeatPtr sfp,
6096 ValNodePtr gene_field,
6097 FilterSetPtr fsp)
6098 {
6099 ValNodePtr vnp;
6100 CharPtr str = NULL;
6101 GeneRefPtr grp;
6102 GBQualPtr qual;
6103
6104 if (sfp == NULL || gene_field == NULL)
6105 {
6106 return NULL;
6107 }
6108
6109 if (sfp->data.choice == SEQFEAT_GENE)
6110 {
6111 grp = (GeneRefPtr) sfp->data.value.ptrvalue;
6112 }
6113 else
6114 {
6115 grp = SeqMgrGetGeneXref (sfp);
6116 }
6117
6118 if (sfp->data.choice != SEQFEAT_GENE && grp != NULL)
6119 {
6120 vnp = NULL;
6121 }
6122
6123 vnp = gene_field;
6124 while (vnp != NULL && vnp->data.intvalue != FEATUREFIELD_NONE && StringHasNoText (str))
6125 {
6126 str = NULL;
6127 switch (vnp->data.intvalue)
6128 {
6129 case GENEFIELD_LOCUS:
6130 if (grp != NULL)
6131 {
6132 str = grp->locus;
6133 }
6134 break;
6135 case GENEFIELD_DESCRIPTION:
6136 if (grp != NULL)
6137 {
6138 str = grp->desc;
6139 }
6140 break;
6141 case GENEFIELD_COMMENT:
6142 if (sfp->data.choice == SEQFEAT_GENE)
6143 {
6144 str = sfp->comment;
6145 }
6146 break;
6147 case GENEFIELD_ALLELE:
6148 if (grp != NULL)
6149 {
6150 str = grp->allele;
6151 }
6152 break;
6153 case GENEFIELD_MAPLOC:
6154 if (grp != NULL)
6155 {
6156 str = grp->maploc;
6157 }
6158 break;
6159 case GENEFIELD_SYNONYM:
6160 if (grp != NULL && grp->syn != NULL)
6161 {
6162 str = grp->syn->data.ptrvalue;
6163 }
6164 break;
6165 case GENEFIELD_LOCUS_TAG:
6166 if (grp != NULL)
6167 {
6168 str = grp->locus_tag;
6169 }
6170 break;
6171 case GENEFIELD_OLD_LOCUS_TAG:
6172 qual = sfp->qual;
6173 while (qual != NULL && StringICmp (qual->qual, "old_locus_tag") != 0)
6174 {
6175 qual = qual->next;
6176 }
6177 if (qual != NULL)
6178 {
6179 str = qual->val;
6180 }
6181 break;
6182 }
6183 vnp = vnp->next;
6184 }
6185 if (StringHasNoText (str))
6186 {
6187 str = NULL;
6188 }
6189 else
6190 {
6191 str = StringSave (str);
6192 }
6193 return str;
6194 }
6195
RemoveGeneFieldString(SeqFeatPtr sfp,ValNodePtr gene_field)6196 extern void RemoveGeneFieldString (SeqFeatPtr sfp, ValNodePtr gene_field)
6197 {
6198 ValNodePtr vnp;
6199 Boolean found_nonempty = FALSE;
6200 GeneRefPtr grp;
6201 ValNodePtr syn_remove;
6202 GBQualPtr qual, prevqual;
6203
6204 if (sfp == NULL || gene_field == NULL)
6205 {
6206 return;
6207 }
6208
6209 if (sfp->data.choice == SEQFEAT_GENE)
6210 {
6211 grp = (GeneRefPtr) sfp->data.value.ptrvalue;
6212 }
6213 else
6214 {
6215 grp = SeqMgrGetGeneXref (sfp);
6216 }
6217
6218 if (grp == NULL)
6219 {
6220 return;
6221 }
6222
6223 vnp = gene_field;
6224 while (vnp != NULL && vnp->data.intvalue != FEATUREFIELD_NONE && !found_nonempty)
6225 {
6226 switch (vnp->data.intvalue)
6227 {
6228 case GENEFIELD_LOCUS:
6229 if (grp != NULL && !StringHasNoText (grp->locus))
6230 {
6231 found_nonempty = TRUE;
6232 if (vnp->choice != 0)
6233 {
6234 grp->locus = MemFree (grp->locus);
6235 }
6236 }
6237 break;
6238 case GENEFIELD_DESCRIPTION:
6239 if (grp != NULL && !StringHasNoText (grp->desc))
6240 {
6241 found_nonempty = TRUE;
6242 if (vnp->choice != 0)
6243 {
6244 grp->desc = MemFree (grp->desc);
6245 }
6246 }
6247 break;
6248 case GENEFIELD_COMMENT:
6249 if (!StringHasNoText (sfp->comment))
6250 {
6251 found_nonempty = TRUE;
6252 if (vnp->choice != 0)
6253 {
6254 sfp->comment = MemFree (sfp->comment);
6255 }
6256 }
6257 break;
6258 case GENEFIELD_ALLELE:
6259 if (grp != NULL && !StringHasNoText (grp->allele))
6260 {
6261 found_nonempty = TRUE;
6262 if (vnp->choice != 0)
6263 {
6264 grp->allele = MemFree (grp->allele);
6265 }
6266 }
6267 break;
6268 case GENEFIELD_MAPLOC:
6269 if (grp != NULL && !StringHasNoText (grp->maploc))
6270 {
6271 found_nonempty = TRUE;
6272 if (vnp->choice != 0)
6273 {
6274 grp->maploc = MemFree (grp->maploc);
6275 }
6276 }
6277 break;
6278 case GENEFIELD_SYNONYM:
6279 if (grp != NULL && grp->syn != NULL && !StringHasNoText (grp->syn->data.ptrvalue))
6280 {
6281 found_nonempty = TRUE;
6282 if (vnp->choice != 0)
6283 {
6284 syn_remove = grp->syn;
6285 grp->syn = grp->syn->next;
6286 syn_remove->next = NULL;
6287 ValNodeFreeData (syn_remove);
6288 }
6289 }
6290 break;
6291 case GENEFIELD_LOCUS_TAG:
6292 if (grp != NULL && !StringHasNoText (grp->locus_tag))
6293 {
6294 found_nonempty = TRUE;
6295 if (vnp->choice != 0)
6296 {
6297 grp->locus_tag = MemFree (grp->locus_tag);
6298 }
6299 }
6300 break;
6301 case GENEFIELD_OLD_LOCUS_TAG:
6302 prevqual = NULL;
6303 qual = sfp->qual;
6304 while (qual != NULL)
6305 {
6306 if (StringICmp (qual->qual, "old_locus_tag") == 0)
6307 {
6308 if (prevqual == NULL)
6309 {
6310 sfp->qual = qual->next;
6311 qual->next = NULL;
6312 qual = GBQualFree (qual);
6313 qual = sfp->qual;
6314 }
6315 else
6316 {
6317 prevqual->next = qual->next;
6318 qual->next = NULL;
6319 qual = GBQualFree (qual);
6320 qual = prevqual->next;
6321 }
6322 }
6323 else
6324 {
6325 prevqual = qual;
6326 qual = qual->next;
6327 }
6328 }
6329 break;
6330 }
6331 vnp = vnp->next;
6332 }
6333 }
6334
SetGeneFieldString(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)6335 static void SetGeneFieldString (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
6336 {
6337 GeneRefPtr grp;
6338 ApplyValuePtr avp;
6339 Boolean found;
6340 GBQualPtr qual, qual_last;
6341
6342 if (sfp == NULL || userdata == NULL)
6343 {
6344 return;
6345 }
6346 avp = (ApplyValuePtr) userdata;
6347 if (avp->field_list == NULL)
6348 {
6349 return;
6350 }
6351
6352 if (sfp->data.choice == SEQFEAT_GENE)
6353 {
6354 grp = (GeneRefPtr) sfp->data.value.ptrvalue;
6355 }
6356 else
6357 {
6358 grp = SeqMgrGetGeneXref (sfp);
6359 }
6360
6361 if (grp == NULL && sfp->data.choice == SEQFEAT_GENE)
6362 {
6363 grp = GeneRefNew ();
6364 sfp->data.value.ptrvalue = grp;
6365 }
6366
6367 if (grp == NULL)
6368 {
6369 return;
6370 }
6371
6372 switch (avp->field_list->data.intvalue)
6373 {
6374 case GENEFIELD_LOCUS:
6375 grp->locus = HandleApplyValue (grp->locus, avp);
6376 break;
6377 case GENEFIELD_DESCRIPTION:
6378 grp->desc = HandleApplyValue (grp->desc, avp);
6379 break;
6380 case GENEFIELD_COMMENT:
6381 sfp->comment = HandleApplyValue (sfp->comment, avp);
6382 break;
6383 case GENEFIELD_ALLELE:
6384 grp->allele = HandleApplyValue (grp->allele, avp);
6385 break;
6386 case GENEFIELD_MAPLOC:
6387 grp->maploc = HandleApplyValue (grp->maploc, avp);
6388 break;
6389 case GENEFIELD_SYNONYM:
6390 if (grp->syn == NULL || !StringHasNoText (avp->text_to_replace)) {
6391 grp->syn = ApplyValueToValNodeStringList (grp->syn, 0, avp);
6392 } else {
6393 grp->syn->data.ptrvalue = HandleApplyValue (grp->syn->data.ptrvalue, avp);
6394 }
6395 break;
6396 case GENEFIELD_LOCUS_TAG:
6397 grp->locus_tag = HandleApplyValue (grp->locus_tag, avp);
6398 break;
6399 case GENEFIELD_OLD_LOCUS_TAG:
6400 qual = sfp->qual;
6401 qual_last = NULL;
6402 found = FALSE;
6403 while (qual != NULL && !found)
6404 {
6405 qual_last = qual;
6406 if (StringCmp (qual->qual, "old_locus_tag") == 0)
6407 {
6408 qual->val = HandleApplyValue (qual->val, avp);
6409 found = TRUE;
6410 }
6411 qual = qual->next;
6412 }
6413 if (!found)
6414 {
6415 qual = GBQualNew ();
6416 if (qual != NULL)
6417 {
6418 qual->qual = StringSave ("old_locus_tag");
6419 qual->val = StringSave (avp->new_text);
6420 if (qual_last == NULL)
6421 {
6422 sfp->qual = qual;
6423 }
6424 else
6425 {
6426 qual_last->next = qual;
6427 }
6428 }
6429 }
6430 break;
6431 }
6432 }
6433
6434 static CharPtr mrna_field_list [] =
6435 {
6436 "product", "comment"
6437 };
6438
6439 #define MRNAFIELD_PRODUCT 1
6440 #define MRNAFIELD_COMMENT 2
6441
6442 static int num_mrna_fields = sizeof (mrna_field_list) / sizeof (CharPtr);
6443
6444 extern DialoG
MRNAFieldSelectionDialog(GrouP h,Boolean allow_none,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)6445 MRNAFieldSelectionDialog
6446 (GrouP h,
6447 Boolean allow_none,
6448 Nlm_ChangeNotifyProc change_notify,
6449 Pointer change_userdata)
6450 {
6451 return FeatureFieldSelectionDialog (h, allow_none,
6452 num_mrna_fields, mrna_field_list,
6453 change_notify, change_userdata);
6454 }
6455
6456 extern CharPtr
GetmRNAFieldString(SeqFeatPtr sfp,ValNodePtr mrna_field,FilterSetPtr fsp)6457 GetmRNAFieldString
6458 (SeqFeatPtr sfp,
6459 ValNodePtr mrna_field,
6460 FilterSetPtr fsp)
6461 {
6462 ValNodePtr vnp;
6463 CharPtr str = NULL;
6464 RnaRefPtr rrp;
6465
6466 if (sfp == NULL || mrna_field == NULL || sfp->idx.subtype != FEATDEF_mRNA)
6467 {
6468 return NULL;
6469 }
6470
6471 vnp = mrna_field;
6472 rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
6473
6474 while (vnp != NULL && vnp->data.intvalue != FEATUREFIELD_NONE && StringHasNoText (str))
6475 {
6476 str = NULL;
6477 switch (vnp->data.intvalue)
6478 {
6479 case MRNAFIELD_PRODUCT:
6480 if (rrp != NULL)
6481 {
6482 str = rrp->ext.value.ptrvalue;
6483 }
6484 break;
6485 case MRNAFIELD_COMMENT:
6486 str = sfp->comment;
6487 break;
6488 }
6489 vnp = vnp->next;
6490 }
6491 if (StringHasNoText (str))
6492 {
6493 str = NULL;
6494 }
6495 else
6496 {
6497 str = StringSave (str);
6498 }
6499 return str;
6500 }
6501
RemovemRNAFieldString(SeqFeatPtr sfp,ValNodePtr mrna_field)6502 extern void RemovemRNAFieldString (SeqFeatPtr sfp, ValNodePtr mrna_field)
6503 {
6504 ValNodePtr vnp;
6505 Boolean found_nonempty = FALSE;
6506 RnaRefPtr rrp;
6507
6508 if (sfp == NULL || mrna_field == NULL || sfp->idx.subtype != FEATDEF_mRNA)
6509 {
6510 return;
6511 }
6512
6513 vnp = mrna_field;
6514 rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
6515 while (vnp != NULL && vnp->data.intvalue != FEATUREFIELD_NONE && !found_nonempty)
6516 {
6517 switch (vnp->data.intvalue)
6518 {
6519 case MRNAFIELD_PRODUCT:
6520 if (rrp != NULL && !StringHasNoText (rrp->ext.value.ptrvalue))
6521 {
6522 found_nonempty = TRUE;
6523 if (vnp->choice != 0)
6524 {
6525 rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
6526 }
6527 }
6528 break;
6529 case MRNAFIELD_COMMENT:
6530 if (!StringHasNoText (sfp->comment))
6531 {
6532 found_nonempty = TRUE;
6533 if (vnp->choice != 0)
6534 {
6535 sfp->comment = MemFree (sfp->comment);
6536 }
6537 }
6538 break;
6539 }
6540 vnp = vnp->next;
6541 }
6542 }
6543
SetmRNAFieldString(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)6544 static void SetmRNAFieldString (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
6545 {
6546 RnaRefPtr rrp;
6547 ApplyValuePtr avp;
6548 Int4 field_choice;
6549
6550 if (sfp == NULL || userdata == NULL || sfp->idx.subtype != FEATDEF_mRNA)
6551 {
6552 return;
6553 }
6554
6555 avp = (ApplyValuePtr) userdata;
6556 if (avp->field_list == NULL)
6557 {
6558 return;
6559 }
6560
6561 rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
6562 if (rrp == NULL)
6563 {
6564 rrp = RnaRefNew ();
6565 if (rrp == NULL)
6566 {
6567 return;
6568 }
6569 sfp->data.value.ptrvalue = rrp;
6570 }
6571 field_choice = avp->field_list->data.intvalue;
6572 switch (avp->field_list->data.intvalue)
6573 {
6574 case MRNAFIELD_PRODUCT:
6575 if (rrp->ext.choice == 0)
6576 {
6577 rrp->ext.choice = 1;
6578 rrp->ext.value.ptrvalue = NULL;
6579 }
6580 rrp->ext.value.ptrvalue = HandleApplyValue (rrp->ext.value.ptrvalue, avp);
6581 break;
6582 case MRNAFIELD_COMMENT:
6583 sfp->comment = HandleApplyValue (sfp->comment,avp);
6584 break;
6585 }
6586 }
6587
GetCDSComment(SeqFeatPtr sfp,ValNodePtr vnp,FilterSetPtr fsp)6588 static CharPtr GetCDSComment (SeqFeatPtr sfp, ValNodePtr vnp, FilterSetPtr fsp)
6589 {
6590 if (sfp == NULL || sfp->data.choice != SEQFEAT_CDREGION || StringHasNoText (sfp->comment))
6591 {
6592 return NULL;
6593 }
6594 else
6595 {
6596 return StringSave (sfp->comment);
6597 }
6598 }
6599
SetCDSComment(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)6600 static void SetCDSComment (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
6601 {
6602 ApplyValuePtr avp;
6603
6604 if (sfp == NULL || userdata == NULL || sfp->data.choice != SEQFEAT_CDREGION)
6605 {
6606 return;
6607 }
6608
6609 avp = (ApplyValuePtr) userdata;
6610
6611 sfp->comment = HandleApplyValue (sfp->comment, avp);
6612 }
6613
RemoveCDSComment(SeqFeatPtr sfp,ValNodePtr vnp)6614 static void RemoveCDSComment (SeqFeatPtr sfp, ValNodePtr vnp)
6615 {
6616 if (sfp == NULL || sfp->data.choice != SEQFEAT_CDREGION)
6617 {
6618 return;
6619 }
6620 sfp->comment = MemFree (sfp->comment);
6621 }
6622
6623 extern CharPtr
GetCDSFieldString(SeqFeatPtr sfp,ValNodePtr cds_field,FilterSetPtr fsp)6624 GetCDSFieldString
6625 (SeqFeatPtr sfp,
6626 ValNodePtr cds_field,
6627 FilterSetPtr fsp)
6628 {
6629 ValNodePtr vnp;
6630 CharPtr str = NULL;
6631 BioseqPtr prot_bsp;
6632 SeqFeatPtr prot_sfp;
6633 SeqMgrFeatContext prot_context;
6634 ProtRefPtr prp;
6635
6636 if (sfp == NULL || cds_field == NULL || sfp->idx.subtype != FEATDEF_CDS)
6637 {
6638 return NULL;
6639 }
6640
6641 vnp = cds_field;
6642
6643 while (vnp != NULL && vnp->data.intvalue != FEATUREFIELD_NONE && StringHasNoText (str))
6644 {
6645 str = NULL;
6646 switch (vnp->data.intvalue)
6647 {
6648 case MRNAFIELD_PRODUCT:
6649 prot_bsp = BioseqFind (SeqLocId (sfp->product));
6650 prot_sfp = SeqMgrGetNextFeature (prot_bsp, NULL, SEQFEAT_PROT, 0, &prot_context);
6651 if (prot_sfp != NULL && prot_sfp->data.value.ptrvalue != NULL) {
6652 prp = (ProtRefPtr) prot_sfp->data.value.ptrvalue;
6653 if (prp->name != NULL && !StringHasNoText (prp->name->data.ptrvalue)) {
6654 str = prp->name->data.ptrvalue;
6655 }
6656 }
6657 break;
6658 case MRNAFIELD_COMMENT:
6659 str = sfp->comment;
6660 break;
6661 }
6662 vnp = vnp->next;
6663 }
6664 if (StringHasNoText (str))
6665 {
6666 str = NULL;
6667 }
6668 else
6669 {
6670 str = StringSave (str);
6671 }
6672 return str;
6673 }
6674
RemoveCDSFieldString(SeqFeatPtr sfp,ValNodePtr cds_field)6675 extern void RemoveCDSFieldString (SeqFeatPtr sfp, ValNodePtr cds_field)
6676 {
6677 ValNodePtr vnp;
6678 Boolean found_nonempty = FALSE;
6679 BioseqPtr prot_bsp;
6680 SeqFeatPtr prot_sfp;
6681 SeqMgrFeatContext prot_context;
6682 ProtRefPtr prp;
6683
6684 if (sfp == NULL || cds_field == NULL || sfp->idx.subtype != FEATDEF_CDS)
6685 {
6686 return;
6687 }
6688
6689 vnp = cds_field;
6690 while (vnp != NULL && vnp->data.intvalue != FEATUREFIELD_NONE && !found_nonempty)
6691 {
6692 switch (vnp->data.intvalue)
6693 {
6694 case MRNAFIELD_PRODUCT:
6695 prot_bsp = BioseqFind (SeqLocId (sfp->product));
6696 prot_sfp = SeqMgrGetNextFeature (prot_bsp, NULL, SEQFEAT_PROT, 0, &prot_context);
6697 if (prot_sfp != NULL && prot_sfp->data.value.ptrvalue != NULL) {
6698 prp = (ProtRefPtr) prot_sfp->data.value.ptrvalue;
6699 if (prp->name != NULL && !StringHasNoText (prp->name->data.ptrvalue)) {
6700 found_nonempty = TRUE;
6701 if (vnp->choice != 0) {
6702 prp->name = ValNodeFreeData (prp->name);
6703 }
6704 }
6705 }
6706 break;
6707 case MRNAFIELD_COMMENT:
6708 if (!StringHasNoText (sfp->comment))
6709 {
6710 found_nonempty = TRUE;
6711 if (vnp->choice != 0)
6712 {
6713 sfp->comment = MemFree (sfp->comment);
6714 }
6715 }
6716 break;
6717 }
6718 vnp = vnp->next;
6719 }
6720 }
6721
6722 #define PROTEINFIELD_NAME 1
6723 #define PROTEINFIELD_DESC 2
6724 #define PROTEINFIELD_EC_NUM 3
6725 #define PROTEINFIELD_ACTIVITY 4
6726 #define PROTEINFIELD_COMMENT 5
6727 #define PROTEINFIELD_MATPEPTIDE_NAME 6
6728 #define PROTEINFIELD_MATPEPTIDE_DESC 7
6729 #define PROTEINFIELD_MATPEPTIDE_COMMENT 8
6730
6731 static CharPtr protein_field_list [] =
6732 {
6733 "name", "description", "E.C. number", "activity", "comment", "mat_peptide name", "mat_peptide description", "mat_peptide comment"
6734 };
6735
6736 static int num_protein_fields = sizeof (protein_field_list) / sizeof (CharPtr);
6737
6738 extern DialoG
ProteinFieldSelectionDialog(GrouP h,Boolean allow_none,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)6739 ProteinFieldSelectionDialog
6740 (GrouP h,
6741 Boolean allow_none,
6742 Nlm_ChangeNotifyProc change_notify,
6743 Pointer change_userdata)
6744 {
6745 return FeatureFieldSelectionDialog (h, allow_none,
6746 num_protein_fields, protein_field_list,
6747 change_notify, change_userdata);
6748 }
6749
GetProteinFieldString(SeqFeatPtr sfp,ValNodePtr protein_field,FilterSetPtr fsp)6750 extern CharPtr GetProteinFieldString (SeqFeatPtr sfp, ValNodePtr protein_field, FilterSetPtr fsp)
6751 {
6752 ValNodePtr vnp, val_vnp;
6753 CharPtr str = NULL;
6754 ProtRefPtr prp = NULL;
6755 Int4 field_choice;
6756 SeqFeatXrefPtr xref;
6757
6758 if (sfp == NULL || protein_field == NULL || (sfp->data.choice != SEQFEAT_PROT && sfp->data.choice != SEQFEAT_CDREGION))
6759 {
6760 return NULL;
6761 }
6762
6763 vnp = protein_field;
6764 if (sfp->data.choice == SEQFEAT_PROT) {
6765 prp = (ProtRefPtr) sfp->data.value.ptrvalue;
6766 } else if (sfp->data.choice == SEQFEAT_CDREGION) {
6767 xref = sfp->xref;
6768 while (xref != NULL && xref->data.choice != SEQFEAT_PROT) {
6769 xref = xref->next;
6770 }
6771 if (xref != NULL) {
6772 prp = xref->data.value.ptrvalue;
6773 }
6774 }
6775
6776
6777 while (vnp != NULL && vnp->data.intvalue != FEATUREFIELD_NONE && StringHasNoText (str))
6778 {
6779 str = NULL;
6780 field_choice = vnp->data.intvalue;
6781 switch (field_choice)
6782 {
6783 case PROTEINFIELD_NAME:
6784 if (prp != NULL && prp->name != NULL && (sfp->idx.subtype == FEATDEF_PROT || sfp->idx.subtype == FEATDEF_CDS))
6785 {
6786 val_vnp = prp->name;
6787 str = val_vnp->data.ptrvalue;
6788 }
6789 break;
6790 case PROTEINFIELD_DESC:
6791 if (prp != NULL && sfp->idx.subtype == FEATDEF_PROT)
6792 {
6793 str = prp->desc;
6794 }
6795 break;
6796 case PROTEINFIELD_EC_NUM:
6797 if (prp != NULL && prp->ec != NULL && sfp->idx.subtype == FEATDEF_PROT)
6798 {
6799 val_vnp = prp->ec;
6800 str = val_vnp->data.ptrvalue;
6801 }
6802 break;
6803 case PROTEINFIELD_ACTIVITY:
6804 if (prp != NULL && prp->activity != NULL && sfp->idx.subtype == FEATDEF_PROT)
6805 {
6806 val_vnp = prp->activity;
6807 str = val_vnp->data.ptrvalue;
6808 }
6809 break;
6810 case PROTEINFIELD_COMMENT:
6811 if (sfp->idx.subtype == FEATDEF_PROT)
6812 {
6813 str = sfp->comment;
6814 }
6815 break;
6816 case PROTEINFIELD_MATPEPTIDE_NAME:
6817 if (prp != NULL && prp->name != NULL && sfp->idx.subtype == FEATDEF_mat_peptide_aa)
6818 {
6819 val_vnp = prp->name;
6820 str = val_vnp->data.ptrvalue;
6821 }
6822 break;
6823 case PROTEINFIELD_MATPEPTIDE_DESC:
6824 if (sfp->idx.subtype == FEATDEF_mat_peptide_aa && prp != NULL)
6825 {
6826 str = prp->desc;
6827 }
6828 break;
6829 case PROTEINFIELD_MATPEPTIDE_COMMENT:
6830 if (sfp->idx.subtype == FEATDEF_mat_peptide_aa)
6831 {
6832 str = sfp->comment;
6833 }
6834 break;
6835 }
6836 vnp = vnp->next;
6837 }
6838 if (StringHasNoText (str))
6839 {
6840 str = NULL;
6841 }
6842 else
6843 {
6844 str = StringSave (str);
6845 }
6846 return str;
6847 }
6848
RemoveProteinFieldString(SeqFeatPtr sfp,ValNodePtr protein_field)6849 static void RemoveProteinFieldString (SeqFeatPtr sfp, ValNodePtr protein_field)
6850 {
6851 ValNodePtr vnp;
6852 ProtRefPtr prp = NULL;
6853 Int4 field_choice;
6854 SeqFeatXrefPtr xref = NULL, prev;
6855
6856 if (sfp == NULL || protein_field == NULL)
6857 {
6858 return;
6859 }
6860
6861 vnp = protein_field;
6862 if (sfp->idx.subtype == FEATDEF_PROT
6863 || sfp->idx.subtype == FEATDEF_mat_peptide_aa) {
6864 prp = (ProtRefPtr) sfp->data.value.ptrvalue;
6865 } else if (sfp->idx.subtype == FEATDEF_CDS) {
6866 xref = sfp->xref;
6867 while (xref != NULL && xref->data.choice != SEQFEAT_PROT) {
6868 xref = xref->next;
6869 }
6870 if (xref != NULL) {
6871 prp = xref->data.value.ptrvalue;
6872 }
6873 }
6874
6875 while (vnp != NULL && vnp->data.intvalue != FEATUREFIELD_NONE)
6876 {
6877 field_choice = vnp->data.intvalue;
6878 switch (field_choice)
6879 {
6880 case PROTEINFIELD_NAME:
6881 if (prp != NULL && prp->name != NULL && sfp->idx.subtype == FEATDEF_PROT)
6882 {
6883 prp->name = ValNodeFreeData (prp->name);
6884 }
6885 break;
6886 case PROTEINFIELD_DESC:
6887 if (prp != NULL && sfp->idx.subtype == FEATDEF_PROT)
6888 {
6889 prp->desc = MemFree (prp->desc);
6890 }
6891 break;
6892 case PROTEINFIELD_EC_NUM:
6893 if (prp != NULL && prp->ec != NULL && sfp->idx.subtype == FEATDEF_PROT)
6894 {
6895 prp->ec = ValNodeFreeData (prp->ec);
6896 }
6897 break;
6898 case PROTEINFIELD_ACTIVITY:
6899 if (prp != NULL && prp->activity != NULL && sfp->idx.subtype == FEATDEF_PROT)
6900 {
6901 prp->activity = ValNodeFreeData (prp->activity);
6902 }
6903 break;
6904 case PROTEINFIELD_COMMENT:
6905 if (sfp->idx.subtype == FEATDEF_PROT)
6906 {
6907 sfp->comment = MemFree (sfp->comment);
6908 }
6909 break;
6910 case PROTEINFIELD_MATPEPTIDE_NAME:
6911 if (prp != NULL && prp->name != NULL && sfp->idx.subtype == FEATDEF_mat_peptide_aa)
6912 {
6913 prp->name = ValNodeFreeData (prp->name);
6914 }
6915 break;
6916 case PROTEINFIELD_MATPEPTIDE_DESC:
6917 if (prp != NULL && sfp->idx.subtype == FEATDEF_mat_peptide_aa)
6918 {
6919 prp->desc = MemFree (prp->desc);
6920 }
6921 break;
6922 case PROTEINFIELD_MATPEPTIDE_COMMENT:
6923 if (sfp->idx.subtype == FEATDEF_mat_peptide_aa)
6924 {
6925 sfp->comment = MemFree (sfp->comment);
6926 }
6927 break;
6928 }
6929 vnp = vnp->next;
6930 }
6931
6932 /* remove protein xref if empty */
6933 if (prp != NULL && xref != NULL
6934 && prp->name == NULL
6935 && StringHasNoText (prp->desc)
6936 && prp->ec == NULL
6937 && prp->activity == NULL
6938 && prp->db == NULL) {
6939 prp = ProtRefFree(prp);
6940 xref->data.value.ptrvalue = NULL;
6941 if (sfp->xref == xref) {
6942 sfp->xref = xref->next;
6943 } else {
6944 prev = sfp->xref;
6945 while (prev != NULL && prev->next != xref) {
6946 prev = prev->next;
6947 }
6948 if (prev != NULL) {
6949 prev->next = xref->next;
6950 }
6951 }
6952 xref = SeqFeatXrefFree(xref);
6953 }
6954 }
6955
6956 extern ValNodePtr ApplyValueToValNodeStringListAsText (ValNodePtr list, Int2 choice, ApplyValuePtr avp);
6957
SetProteinFieldString(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)6958 static void SetProteinFieldString (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
6959 {
6960 ProtRefPtr prp;
6961 ApplyValuePtr avp;
6962
6963 if (sfp == NULL || userdata == NULL)
6964 {
6965 return;
6966 }
6967 if (sfp->idx.subtype != FEATDEF_PROT && sfp->idx.subtype != FEATDEF_mat_peptide_aa)
6968 {
6969 return;
6970 }
6971
6972 avp = (ApplyValuePtr) userdata;
6973 if (avp->field_list == NULL)
6974 {
6975 return;
6976 }
6977
6978 if (sfp->idx.subtype == FEATDEF_PROT)
6979 {
6980 if (avp->field_list->data.intvalue == PROTEINFIELD_MATPEPTIDE_NAME
6981 || avp->field_list->data.intvalue == PROTEINFIELD_MATPEPTIDE_DESC
6982 || avp->field_list->data.intvalue == PROTEINFIELD_MATPEPTIDE_COMMENT)
6983 {
6984 return;
6985 }
6986 }
6987 else if (sfp->idx.subtype == FEATDEF_mat_peptide_aa)
6988 {
6989 if (avp->field_list->data.intvalue != PROTEINFIELD_MATPEPTIDE_NAME
6990 && avp->field_list->data.intvalue != PROTEINFIELD_MATPEPTIDE_DESC
6991 && avp->field_list->data.intvalue != PROTEINFIELD_MATPEPTIDE_COMMENT)
6992 {
6993 return;
6994 }
6995 }
6996 else
6997 {
6998 return;
6999 }
7000
7001 prp = (ProtRefPtr) sfp->data.value.ptrvalue;
7002 if (prp == NULL)
7003 {
7004 prp = ProtRefNew ();
7005 if (prp == NULL)
7006 {
7007 return;
7008 }
7009 sfp->data.value.ptrvalue = prp;
7010 }
7011
7012 switch (avp->field_list->data.intvalue)
7013 {
7014 case PROTEINFIELD_NAME:
7015 case PROTEINFIELD_MATPEPTIDE_NAME:
7016 if (prp->name == NULL || !StringHasNoText(avp->text_to_replace))
7017 {
7018 prp->name = ApplyValueToValNodeStringList (prp->name, 0, avp);
7019 }
7020 else
7021 {
7022 prp->name->data.ptrvalue = HandleApplyValue (prp->name->data.ptrvalue, avp);
7023 }
7024 break;
7025 case PROTEINFIELD_DESC:
7026 case PROTEINFIELD_MATPEPTIDE_DESC:
7027 prp->desc = HandleApplyValue (prp->desc, avp);
7028 break;
7029 case PROTEINFIELD_EC_NUM:
7030 prp->ec = ApplyValueToValNodeStringListAsText (prp->ec, 0, avp);
7031 break;
7032 case PROTEINFIELD_ACTIVITY:
7033 if (prp->activity == NULL || !StringHasNoText(avp->text_to_replace))
7034 {
7035 prp->activity = ApplyValueToValNodeStringList (prp->activity, 0, avp);
7036 }
7037 else
7038 {
7039 prp->activity->data.ptrvalue = HandleApplyValue (prp->activity->data.ptrvalue, avp);
7040 }
7041 break;
7042 case PROTEINFIELD_COMMENT:
7043 case PROTEINFIELD_MATPEPTIDE_COMMENT:
7044 sfp->comment = HandleApplyValue (sfp->comment, avp);
7045 break;
7046 }
7047 }
7048
BuildCDSGeneFieldList(Int4Ptr num_fields)7049 static CharPtr PNTR BuildCDSGeneFieldList (Int4Ptr num_fields)
7050 {
7051 CharPtr PNTR field_name_list;
7052 Int4 i, k;
7053 Char tmp[100];
7054
7055 if (num_fields == NULL)
7056 {
7057 return NULL;
7058 }
7059 *num_fields = 1 + num_gene_fields + num_mrna_fields + num_protein_fields;
7060 field_name_list = (CharPtr PNTR) MemNew (*num_fields * sizeof (CharPtr));
7061 if (field_name_list == NULL)
7062 {
7063 return NULL;
7064 }
7065
7066 field_name_list [0] = StringSave ("CDS comment");
7067 k = 1;
7068 for (i = 0; i < num_gene_fields; i++)
7069 {
7070 sprintf (tmp, "Gene %s", gene_field_list [i]);
7071 field_name_list [k++] = StringSave (tmp);
7072 }
7073 for (i = 0; i < num_mrna_fields; i++)
7074 {
7075 sprintf (tmp, "mRNA %s", mrna_field_list [i]);
7076 field_name_list [k++] = StringSave (tmp);
7077 }
7078 for (i = 0; i < num_protein_fields; i++)
7079 {
7080 if (StringNCmp (protein_field_list [i], "mat_peptide", 11) == 0)
7081 {
7082 sprintf (tmp, "%s", protein_field_list [i]);
7083 tmp [0] = toupper (tmp [0]);
7084 }
7085 else
7086 {
7087 sprintf (tmp, "Protein %s", protein_field_list [i]);
7088 }
7089 field_name_list [k++] = StringSave (tmp);
7090 }
7091 return field_name_list;
7092 }
7093
FreeCDSGeneFieldList(CharPtr PNTR field_name_list,Int4 num_fields)7094 static void FreeCDSGeneFieldList (CharPtr PNTR field_name_list, Int4 num_fields)
7095 {
7096 Int4 i;
7097
7098 if (field_name_list == NULL || num_fields == 0)
7099 {
7100 return;
7101 }
7102
7103 for (i = 0; i < num_fields; i++)
7104 {
7105 field_name_list [i] = MemFree (field_name_list [i]);
7106 }
7107 field_name_list = MemFree (field_name_list);
7108 }
7109
7110 extern DialoG
CDSGeneProtFieldSelectionDialog(GrouP h,Boolean allow_none,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)7111 CDSGeneProtFieldSelectionDialog
7112 (GrouP h,
7113 Boolean allow_none,
7114 Nlm_ChangeNotifyProc change_notify,
7115 Pointer change_userdata)
7116 {
7117 CharPtr PNTR field_name_list;
7118 Int4 num_fields = 0;
7119 DialoG d;
7120
7121 field_name_list = BuildCDSGeneFieldList (&num_fields);
7122
7123 d = FeatureFieldSelectionDialog (h, allow_none,
7124 num_fields, field_name_list,
7125 change_notify, change_userdata);
7126 FreeCDSGeneFieldList (field_name_list, num_fields);
7127 return d;
7128 }
7129
7130 static DialoG
CDSGeneProtFieldConstraintSelectionDialog(GrouP h,Boolean allow_none,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)7131 CDSGeneProtFieldConstraintSelectionDialog
7132 (GrouP h,
7133 Boolean allow_none,
7134 Nlm_ChangeNotifyProc change_notify,
7135 Pointer change_userdata)
7136 {
7137 CharPtr PNTR field_name_list;
7138 Int4 num_fields = 0;
7139 DialoG d;
7140
7141 field_name_list = BuildCDSGeneFieldList (&num_fields);
7142
7143 d = FeatureFieldSelectionDialogAny (h, allow_none,
7144 num_fields, field_name_list,
7145 change_notify, change_userdata);
7146 FreeCDSGeneFieldList (field_name_list, num_fields);
7147 return d;
7148 }
7149
7150
IsCDSetProteinProductChoice(ValNodePtr vnp)7151 extern Boolean IsCDSetProteinProductChoice (ValNodePtr vnp)
7152 {
7153 if (vnp != NULL && vnp->data.intvalue == 2 + num_gene_fields + num_mrna_fields) {
7154 return TRUE;
7155 } else {
7156 return FALSE;
7157 }
7158 }
7159
7160
IsCDSetProteinQualChoice(ValNodePtr vnp)7161 static Boolean IsCDSetProteinQualChoice (ValNodePtr vnp)
7162 {
7163 if (vnp != NULL
7164 && vnp->data.intvalue > 1 + num_gene_fields + num_mrna_fields
7165 && vnp->data.intvalue <= 1 + num_gene_fields + num_mrna_fields + num_protein_fields)
7166 {
7167 return TRUE;
7168 }
7169 else
7170 {
7171 return FALSE;
7172 }
7173 }
7174
IsCDSetMatPeptideQualChoice(ValNodePtr vnp)7175 static Boolean IsCDSetMatPeptideQualChoice (ValNodePtr vnp)
7176 {
7177 if (IsCDSetProteinQualChoice (vnp)
7178 && StringNICmp (protein_field_list[vnp->data.intvalue - num_gene_fields - num_mrna_fields - 2],
7179 "mat_peptide", 11) == 0)
7180 {
7181 return TRUE;
7182 }
7183 else
7184 {
7185 return FALSE;
7186 }
7187 }
7188
IsCDSetMRNAQualChoice(ValNodePtr vnp)7189 static Boolean IsCDSetMRNAQualChoice (ValNodePtr vnp)
7190 {
7191 if (vnp != NULL
7192 && vnp->data.intvalue > 1 + num_gene_fields
7193 && vnp->data.intvalue <= 1 + num_gene_fields + num_mrna_fields)
7194 {
7195 return TRUE;
7196 }
7197 else
7198 {
7199 return FALSE;
7200 }
7201 }
7202
IsCDSetGeneQualChoice(ValNodePtr vnp)7203 static Boolean IsCDSetGeneQualChoice (ValNodePtr vnp)
7204 {
7205 if (vnp != NULL
7206 && vnp->data.intvalue > 1
7207 && vnp->data.intvalue <= 1 + num_gene_fields)
7208 {
7209 return TRUE;
7210 }
7211 else
7212 {
7213 return FALSE;
7214 }
7215 }
7216
IsCDSetCDSQualChoice(ValNodePtr vnp)7217 static Boolean IsCDSetCDSQualChoice (ValNodePtr vnp)
7218 {
7219 if (vnp != NULL && vnp->data.intvalue == 1)
7220 {
7221 return TRUE;
7222 }
7223 else
7224 {
7225 return FALSE;
7226 }
7227 }
7228
GetCDSGeneProtField(SeqFeatPtr sfp,ValNodePtr vnp,FilterSetPtr fsp)7229 extern CharPtr GetCDSGeneProtField (SeqFeatPtr sfp, ValNodePtr vnp, FilterSetPtr fsp)
7230 {
7231 CharPtr str = NULL;
7232 ValNode vn;
7233 Int4 field_choice;
7234
7235 if (sfp == NULL || vnp == NULL)
7236 {
7237 return NULL;
7238 }
7239
7240 while (vnp != NULL && str == NULL)
7241 {
7242 vn.choice = vnp->choice;
7243 vn.next = NULL;
7244
7245 field_choice = vnp->data.intvalue;
7246
7247 if (IsCDSetCDSQualChoice(vnp))
7248 {
7249 /* CDS Comment */
7250 str = GetCDSComment (sfp, NULL, NULL);
7251 }
7252 else if (IsCDSetGeneQualChoice (vnp))
7253 {
7254 vn.data.intvalue = vnp->data.intvalue - 1;
7255 str = GetGeneFieldString (sfp, &vn, NULL);
7256 }
7257 else if (IsCDSetMRNAQualChoice (vnp))
7258 {
7259 vn.data.intvalue = vnp->data.intvalue - num_gene_fields - 1;
7260 str = GetmRNAFieldString (sfp, &vn, NULL);
7261 }
7262 else if (IsCDSetProteinQualChoice (vnp))
7263 {
7264 vn.data.intvalue = vnp->data.intvalue - num_gene_fields - num_mrna_fields - 1;
7265 str = GetProteinFieldString (sfp, &vn, NULL);
7266 }
7267 vnp = vnp->next;
7268 }
7269 return str;
7270 }
7271
7272 /* we could have multiple mat_peptides in a CDSset, some that match the constraint and some that do not */
DoesConstraintDisqualifyFeature(SeqFeatPtr sfp,ChoiceConstraintPtr ccp)7273 static Boolean DoesConstraintDisqualifyFeature (SeqFeatPtr sfp, ChoiceConstraintPtr ccp)
7274 {
7275 Boolean is_disqualified = FALSE;
7276 Boolean does_match = FALSE;
7277 CharPtr str;
7278
7279 if (sfp == NULL || ccp == NULL
7280 || ccp->constraint_type == CHOICE_CONSTRAINT_ANY
7281 || sfp->idx.subtype != FEATDEF_mat_peptide_aa
7282 || !IsCDSetMatPeptideQualChoice(ccp->qual_choice))
7283 {
7284 is_disqualified = FALSE;
7285 }
7286 else if (ccp->constraint_type == CHOICE_CONSTRAINT_QUAL_PRESENT && ccp->qual_choice != NULL)
7287 {
7288 str = GetCDSGeneProtField (sfp, ccp->qual_choice, NULL);
7289 if (str == NULL)
7290 {
7291 is_disqualified = TRUE;
7292 }
7293 MemFree (str);
7294 }
7295 else if (ccp->constraint_type == CHOICE_CONSTRAINT_STRING)
7296 {
7297 str = GetCDSGeneProtField (sfp, ccp->qual_choice, NULL);
7298 does_match = DoesStringMatchConstraintX (str, ccp->string_constraint);
7299 MemFree (str);
7300 if (ccp->string_constraint != NULL && ccp->string_constraint->not_present)
7301 {
7302 does_match = ! does_match;
7303 }
7304 if (!does_match)
7305 {
7306 is_disqualified = TRUE;
7307 }
7308 }
7309 return is_disqualified;
7310
7311 }
7312
RemoveCDSGeneProtField(SeqFeatPtr sfp,ValNodePtr vnp,FilterSetPtr fsp)7313 extern void RemoveCDSGeneProtField (SeqFeatPtr sfp, ValNodePtr vnp, FilterSetPtr fsp)
7314 {
7315 ValNode vn;
7316
7317 if (sfp == NULL || vnp == NULL)
7318 {
7319 return;
7320 }
7321
7322 if (fsp != NULL && fsp->cgp != NULL && DoesConstraintDisqualifyFeature (sfp, fsp->cgp))
7323 {
7324 return;
7325 }
7326
7327 while (vnp != NULL)
7328 {
7329 vn.choice = vnp->choice;
7330 vn.next = NULL;
7331
7332 if (vnp->data.intvalue == 1)
7333 {
7334 /* CDS Comment */
7335 RemoveCDSComment (sfp, NULL);
7336 }
7337 else if (vnp->data.intvalue <= 1 + num_gene_fields)
7338 {
7339 vn.data.intvalue = vnp->data.intvalue - 1;
7340 RemoveGeneFieldString (sfp, &vn);
7341 }
7342 else if (vnp->data.intvalue <= 1 + num_gene_fields + num_mrna_fields)
7343 {
7344 vn.data.intvalue = vnp->data.intvalue - num_gene_fields - 1;
7345 RemovemRNAFieldString (sfp, &vn);
7346 }
7347 else if (vnp->data.intvalue <= 1 + num_gene_fields + num_mrna_fields + num_protein_fields)
7348 {
7349 vn.data.intvalue = vnp->data.intvalue - num_gene_fields - num_mrna_fields - 1;
7350 RemoveProteinFieldString (sfp, &vn);
7351 }
7352 vnp = vnp->next;
7353 }
7354 }
7355
7356
FeatDefTypeFromFieldList(ValNodePtr vnp)7357 extern Uint2 FeatDefTypeFromFieldList (ValNodePtr vnp)
7358 {
7359 if (vnp == NULL)
7360 {
7361 return 0;
7362 }
7363 else if (IsCDSetCDSQualChoice(vnp))
7364 {
7365 return FEATDEF_CDS;
7366 }
7367 else if (IsCDSetGeneQualChoice (vnp))
7368 {
7369 return FEATDEF_GENE;
7370 }
7371 else if (IsCDSetMRNAQualChoice(vnp))
7372 {
7373 return FEATDEF_mRNA;
7374 }
7375 else if (IsCDSetProteinQualChoice (vnp))
7376 {
7377 if (IsCDSetMatPeptideQualChoice (vnp))
7378 {
7379 return FEATDEF_mat_peptide_aa;
7380 }
7381 else
7382 {
7383 return FEATDEF_PROT;
7384 }
7385 }
7386 else
7387 {
7388 return 0;
7389 }
7390 }
7391
7392
7393 /* return TRUE if actually set field, FALSE otherwise */
7394 extern Boolean
SetCDSGeneProtField(SeqFeatPtr sfp,ValNodePtr vnp,ApplyValuePtr avp,FilterSetPtr fsp)7395 SetCDSGeneProtField
7396 (SeqFeatPtr sfp,
7397 ValNodePtr vnp,
7398 ApplyValuePtr avp,
7399 FilterSetPtr fsp)
7400 {
7401 ValNode vn;
7402 ApplyValueData local_avd;
7403 Uint2 choice;
7404
7405 if (sfp == NULL || vnp == NULL || avp == NULL)
7406 {
7407 return FALSE;
7408 }
7409
7410 choice = FeatDefTypeFromFieldList (vnp);
7411 if (FindFeatFromFeatDefType(choice) != sfp->data.choice)
7412 {
7413 return FALSE;
7414 }
7415
7416 if (fsp != NULL && fsp->cgp != NULL && DoesConstraintDisqualifyFeature (sfp, fsp->cgp))
7417 {
7418 return FALSE;
7419 }
7420
7421 vn.choice = vnp->choice;
7422 vn.next = NULL;
7423 local_avd.field_list = &vn;
7424 local_avd.new_text = avp->new_text;
7425 local_avd.etp = avp->etp;
7426 local_avd.text_to_replace = avp->text_to_replace;
7427 local_avd.where_to_replace = avp->where_to_replace;
7428
7429 if (vnp->data.intvalue == 1)
7430 {
7431 /* CDS Comment */
7432 SetCDSComment (sfp, &local_avd, NULL);
7433 }
7434 else if (vnp->data.intvalue <= 1 + num_gene_fields)
7435 {
7436 vn.data.intvalue = vnp->data.intvalue - 1;
7437 SetGeneFieldString (sfp, &local_avd, NULL);
7438 }
7439 else if (vnp->data.intvalue <= 1 + num_gene_fields + num_mrna_fields)
7440 {
7441 vn.data.intvalue = vnp->data.intvalue - num_gene_fields - 1;
7442 SetmRNAFieldString (sfp, &local_avd, NULL);
7443 }
7444 else if (vnp->data.intvalue <= 1 + num_gene_fields + num_mrna_fields + num_protein_fields)
7445 {
7446 vn.data.intvalue = vnp->data.intvalue - num_gene_fields - num_mrna_fields - 1;
7447 SetProteinFieldString (sfp, &local_avd, NULL);
7448 }
7449
7450 /* no need to free any part of local_avd */
7451
7452 return TRUE;
7453 }
7454
7455 #define RNAFIELD_PRODUCT 1
7456 #define RNAFIELD_COMMENT 2
7457 #define RNAFIELD_CODONS_RECOGNIZED 3
7458 #define RNAFIELD_NCRNA_CLASS 4
7459 #define RNAFIELD_ANTICODON 5
7460 #define RNAFIELD_TRANSCRIPT_ID 6
7461
7462 static CharPtr rna_field_list [] =
7463 {
7464 "Product", "Comment", "Codons Recognized", "ncRNA class", "Anticodon", "Transcript ID"
7465 };
7466
7467 static Int4 num_rna_fields = sizeof (rna_field_list) / sizeof (CharPtr);
7468
GetRNAFieldName(ValNodePtr vnp)7469 static CharPtr GetRNAFieldName (ValNodePtr vnp)
7470 {
7471 CharPtr label = NULL;
7472
7473 if (vnp != NULL && vnp->data.intvalue >= 1)
7474 {
7475 if (vnp->data.intvalue <= num_rna_fields)
7476 {
7477 label = StringSave (rna_field_list [vnp->data.intvalue - 1]);
7478 }
7479 else if (vnp->data.intvalue <= num_rna_fields + num_gene_fields)
7480 {
7481 label = (CharPtr) MemNew ((StringLen (gene_field_list [vnp->data.intvalue - 1 - num_rna_fields]) + 6) * sizeof (Char));
7482 if (label != NULL)
7483 {
7484 sprintf (label, "Gene %s", gene_field_list [vnp->data.intvalue - 1 - num_rna_fields]);
7485 }
7486 }
7487 }
7488 return label;
7489 }
7490
7491 extern DialoG
RNAAddFieldSelectionDialog(GrouP h,Boolean allow_multi,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)7492 RNAAddFieldSelectionDialog
7493 (GrouP h,
7494 Boolean allow_multi,
7495 Nlm_ChangeNotifyProc change_notify,
7496 Pointer change_userdata)
7497 {
7498 ValNodePtr choice_list = NULL;
7499 DialoG dlg;
7500 Int4 i;
7501
7502 for (i = 0; i < 4; i++)
7503 {
7504 ValNodeAddInt (&choice_list, 0, i + 1);
7505 }
7506 for (i = 0; i < num_gene_fields; i++)
7507 {
7508 ValNodeAddInt (&choice_list, 0, i + num_rna_fields + 1);
7509 }
7510
7511 dlg = ValNodeSelectionDialog (h, choice_list, TALL_SELECTION_LIST,
7512 GetRNAFieldName, NULL,
7513 IntValNodeCopy, IntValNodeMatch,
7514 "RNA field", change_notify, change_userdata,
7515 FALSE);
7516
7517 return dlg;
7518 }
7519
7520 extern DialoG
RNARemoveFieldSelectionDialog(GrouP h,Boolean allow_multi,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)7521 RNARemoveFieldSelectionDialog
7522 (GrouP h,
7523 Boolean allow_multi,
7524 Nlm_ChangeNotifyProc change_notify,
7525 Pointer change_userdata)
7526 {
7527 ValNodePtr choice_list = NULL;
7528 DialoG dlg;
7529 Int4 i;
7530
7531 for (i = 0; i < num_rna_fields; i++)
7532 {
7533 ValNodeAddInt (&choice_list, 0, i + 1);
7534 }
7535 for (i = 0; i < num_gene_fields; i++)
7536 {
7537 ValNodeAddInt (&choice_list, 0, i + num_rna_fields + 1);
7538 }
7539
7540 dlg = ValNodeSelectionDialog (h, choice_list, TALL_SELECTION_LIST,
7541 GetRNAFieldName, NULL,
7542 IntValNodeCopy, IntValNodeMatch,
7543 "RNA field", change_notify, change_userdata,
7544 FALSE);
7545
7546 return dlg;
7547 }
7548
7549 extern DialoG
RNAFieldSelectionDialog(GrouP h,Boolean allow_multi,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)7550 RNAFieldSelectionDialog
7551 (GrouP h,
7552 Boolean allow_multi,
7553 Nlm_ChangeNotifyProc change_notify,
7554 Pointer change_userdata)
7555 {
7556 ValNodePtr choice_list = NULL;
7557 DialoG dlg;
7558 Int4 i;
7559
7560 for (i = 0; i < 4; i++)
7561 {
7562 ValNodeAddInt (&choice_list, 0, i + 1);
7563 }
7564 for (i = 0; i < num_gene_fields; i++)
7565 {
7566 ValNodeAddInt (&choice_list, 0, i + num_rna_fields + 1);
7567 }
7568
7569 dlg = ValNodeSelectionDialog (h, choice_list, TALL_SELECTION_LIST,
7570 GetRNAFieldName, NULL,
7571 IntValNodeCopy, IntValNodeMatch,
7572 "RNA field", change_notify, change_userdata,
7573 FALSE);
7574
7575 return dlg;
7576 }
7577
7578 static CharPtr rna_subtype_list [] = { "misc_RNA", "preRna", "mRNA", "tRNA",
7579 "rRNA", "ncRNA", "tmRNA"};
7580 static Int2 num_rna_subtypes = sizeof (rna_subtype_list) / sizeof (CharPtr);
7581
GetRNASubtypeName(ValNodePtr vnp)7582 static CharPtr GetRNASubtypeName (ValNodePtr vnp)
7583 {
7584 CharPtr label = NULL;
7585
7586 if (vnp != NULL && vnp->choice < num_rna_subtypes)
7587 {
7588 label = StringSave (rna_subtype_list[vnp->choice]);
7589 }
7590 return label;
7591 }
7592
RNASubtypeSelectionDialog(GrouP h,Boolean allow_multi,SeqEntryPtr sep,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)7593 static DialoG RNASubtypeSelectionDialog
7594 (GrouP h,
7595 Boolean allow_multi,
7596 SeqEntryPtr sep,
7597 Nlm_ChangeNotifyProc change_notify,
7598 Pointer change_userdata)
7599 {
7600 ValNodePtr choice_list = NULL;
7601 DialoG dlg;
7602
7603 ValNodeAddInt (&choice_list, 0, FEATDEF_otherRNA);
7604 ValNodeAddInt (&choice_list, 1, FEATDEF_preRNA);
7605 ValNodeAddInt (&choice_list, 2, FEATDEF_mRNA);
7606 ValNodeAddInt (&choice_list, 3, FEATDEF_tRNA);
7607 ValNodeAddInt (&choice_list, 4, FEATDEF_rRNA);
7608 ValNodeAddInt (&choice_list, 5, FEATDEF_ncRNA);
7609 ValNodeAddInt (&choice_list, 6, FEATDEF_tmRNA);
7610
7611 dlg = ValNodeSelectionDialog (h, choice_list, TALL_SELECTION_LIST,
7612 GetRNASubtypeName, NULL,
7613 IntValNodeCopy, IntValNodeMatch,
7614 "RNA subtype", change_notify, change_userdata,
7615 allow_multi);
7616 return dlg;
7617 }
7618
7619
GetRNAFieldString(SeqFeatPtr sfp,ValNodePtr vnp,FilterSetPtr fsp)7620 extern CharPtr GetRNAFieldString (SeqFeatPtr sfp, ValNodePtr vnp, FilterSetPtr fsp)
7621 {
7622 RnaRefPtr rrp;
7623 CharPtr str = NULL;
7624 ValNode vn;
7625 GeneRefPtr grp;
7626 SeqFeatPtr gene;
7627 SeqMgrFeatContext context;
7628 Int4 field_choice;
7629 GBQualPtr qual;
7630
7631 if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA || vnp == NULL)
7632 {
7633 return NULL;
7634 }
7635
7636 rrp = sfp->data.value.ptrvalue;
7637
7638 while (vnp != NULL && str == NULL)
7639 {
7640 field_choice = vnp->data.intvalue;
7641 switch (vnp->data.intvalue)
7642 {
7643 case RNAFIELD_PRODUCT :
7644 str = GetRNAProductString (sfp, NULL);
7645 break;
7646 case RNAFIELD_COMMENT :
7647 if (!StringHasNoText (sfp->comment))
7648 {
7649 str = StringSave (sfp->comment);
7650 }
7651 break;
7652 case RNAFIELD_NCRNA_CLASS :
7653 for (qual = sfp->qual; qual != NULL && str == NULL; qual = qual->next)
7654 {
7655 if (StringCmp (qual->qual, "ncRNA_class") == 0
7656 && !StringHasNoText (qual->val))
7657 {
7658 str = StringSave (qual->val);
7659 }
7660 }
7661 break;
7662 default:
7663 if (vnp->data.intvalue >= num_rna_fields + 1)
7664 {
7665 vn.choice = 0;
7666 vn.next = NULL;
7667 vn.data.intvalue = vnp->data.intvalue - num_rna_fields;
7668 grp = SeqMgrGetGeneXref (sfp);
7669 if (grp == NULL)
7670 {
7671 gene = SeqMgrGetOverlappingGene (sfp->location, &context);
7672 str = GetGeneFieldString (gene, &vn, NULL);
7673 }
7674 else
7675 {
7676 str = GetGeneFieldString (sfp, &vn, NULL);
7677 }
7678 }
7679 break;
7680
7681 }
7682 vnp = vnp->next;
7683 }
7684 return str;
7685 }
7686
7687
IsParseabletRNAName(CharPtr name_string)7688 static Boolean IsParseabletRNAName (CharPtr name_string)
7689 {
7690 if (StringHasNoText(name_string))
7691 {
7692 return TRUE;
7693 }
7694 else if (StringNICmp (name_string, "trna-", 5) != 0)
7695 {
7696 return FALSE;
7697 }
7698 else if (StringLen (name_string) != 8)
7699 {
7700 return FALSE;
7701 }
7702 else if (ParseTRnaString (name_string, NULL, NULL, TRUE) == 0)
7703 {
7704 return FALSE;
7705 }
7706 else
7707 {
7708 return TRUE;
7709 }
7710 }
7711
7712
SettRNAName(SeqFeatPtr sfp,ApplyValuePtr avp)7713 static void SettRNAName (SeqFeatPtr sfp, ApplyValuePtr avp)
7714 {
7715 RnaRefPtr rrp;
7716 tRNAPtr trp;
7717 Uint1 new_aa;
7718 CharPtr name_string;
7719 Boolean justTrnaText = FALSE;
7720 Uint1 codon [6];
7721 GBQualPtr gbqual, gbqual_last = NULL;
7722
7723 if (sfp == NULL || sfp->data.value.ptrvalue == NULL
7724 || sfp->idx.subtype != FEATDEF_tRNA
7725 || avp == NULL)
7726 {
7727 return;
7728 }
7729
7730 rrp = sfp->data.value.ptrvalue;
7731 if (rrp->ext.choice == 0)
7732 {
7733 trp = MemNew (sizeof (tRNA));
7734 trp->aatype = 0;
7735 MemSet (trp->codon, 255, sizeof (trp->codon));
7736 trp->anticodon = NULL;
7737 rrp->ext.value.ptrvalue = trp;
7738 rrp->ext.choice = 2;
7739 }
7740 if (rrp->ext.choice != 2)
7741 {
7742 return;
7743 }
7744 trp = (tRNAPtr) rrp->ext.value.ptrvalue;
7745
7746 name_string = GetRNAProductString (sfp, NULL);
7747 name_string = HandleApplyValue (name_string, avp);
7748 if (!IsParseabletRNAName(name_string))
7749 {
7750 if (trp->anticodon == NULL
7751 && trp->codon[0] == 255
7752 && trp->codon[1] == 255
7753 && trp->codon[2] == 255
7754 && trp->codon[3] == 255
7755 && trp->codon[4] == 255
7756 && trp->codon[5] == 255)
7757 {
7758 trp = MemFree (trp);
7759 rrp->ext.choice = 1;
7760 rrp->ext.value.ptrvalue = name_string;
7761 }
7762 else
7763 {
7764 trp->aa = 0;
7765 gbqual = sfp->qual;
7766 while (gbqual != NULL)
7767 {
7768 gbqual_last = gbqual;
7769 gbqual = gbqual->next;
7770 }
7771 gbqual = GBQualNew ();
7772 gbqual->qual = StringSave ("product");
7773 gbqual->val = name_string;
7774 if (gbqual_last == NULL)
7775 {
7776 sfp->qual = gbqual;
7777 }
7778 else
7779 {
7780 gbqual->next = gbqual_last->next;
7781 gbqual_last->next = gbqual;
7782 }
7783 }
7784 }
7785 else
7786 {
7787 new_aa = ParseTRnaString (name_string, &justTrnaText, codon, TRUE);
7788 trp->aa = new_aa;
7789 trp->aatype = 2;
7790 name_string = MemFree (name_string);
7791 }
7792 }
7793
7794
SetRNAProduct(SeqFeatPtr sfp,ApplyValuePtr avp)7795 static void SetRNAProduct (SeqFeatPtr sfp, ApplyValuePtr avp)
7796 {
7797 RnaRefPtr rrp;
7798 GBQualPtr gbq, prev_gbq = NULL;
7799
7800 if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA || sfp->data.value.ptrvalue == NULL || avp == NULL)
7801 {
7802 return;
7803 }
7804
7805 rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
7806
7807 gbq = sfp->qual;
7808 while (gbq != NULL && StringCmp (gbq->qual, "product") != 0)
7809 {
7810 prev_gbq = gbq;
7811 gbq = gbq->next;
7812 }
7813 if (gbq != NULL)
7814 {
7815 gbq->val = HandleApplyValue (gbq->val, avp);
7816 if (StringHasNoText (gbq->val))
7817 {
7818 if (prev_gbq == NULL)
7819 {
7820 sfp->qual = gbq->next;
7821 }
7822 else
7823 {
7824 prev_gbq->next = gbq->next;
7825 }
7826 gbq->next = NULL;
7827 gbq = GBQualFree (gbq);
7828 }
7829 }
7830 else if (sfp->idx.subtype == FEATDEF_tRNA || rrp->ext.choice == 2)
7831 {
7832 SettRNAName (sfp, avp);
7833 }
7834 else if (rrp->ext.choice == 1
7835 && (StringCmp (rrp->ext.value.ptrvalue, "ncRNA") == 0
7836 || StringCmp (rrp->ext.value.ptrvalue, "tmRNA") == 0
7837 || StringCmp (rrp->ext.value.ptrvalue, "misc_RNA") == 0))
7838 {
7839 gbq = GBQualNew();
7840 gbq->qual = StringSave ("product");
7841 gbq->val = HandleApplyValue (gbq->val, avp);
7842 gbq->next = sfp->qual;
7843 sfp->qual = gbq;
7844 }
7845 else if (rrp->ext.choice == 1 || rrp->ext.choice == 0)
7846 {
7847 rrp->ext.value.ptrvalue = HandleApplyValue (rrp->ext.value.ptrvalue, avp);
7848 if (StringHasNoText (rrp->ext.value.ptrvalue))
7849 {
7850 rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
7851 rrp->ext.choice = 0;
7852 }
7853 else
7854 {
7855 rrp->ext.choice = 1;
7856 }
7857 }
7858 }
7859
7860
SetRNAFieldString(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)7861 static void SetRNAFieldString (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
7862 {
7863 RnaRefPtr rrp;
7864 ApplyValuePtr avp;
7865 SeqFeatPtr gene;
7866 GeneRefPtr grp;
7867 SeqMgrFeatContext context;
7868 GBQualPtr qual;
7869 Boolean found = FALSE;
7870
7871 if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA || userdata == NULL)
7872 {
7873 return;
7874 }
7875
7876 avp = (ApplyValuePtr) userdata;
7877 if (avp->field_list == NULL)
7878 {
7879 return;
7880 }
7881
7882 rrp = sfp->data.value.ptrvalue;
7883
7884 switch (avp->field_list->data.intvalue)
7885 {
7886 case RNAFIELD_PRODUCT :
7887 SetRNAProduct (sfp, avp);
7888 break;
7889 case RNAFIELD_COMMENT :
7890 sfp->comment = HandleApplyValue (sfp->comment, avp);
7891 break;
7892 case RNAFIELD_NCRNA_CLASS :
7893 for (qual = sfp->qual; qual != NULL; qual = qual->next)
7894 {
7895 if (StringCmp (qual->qual, "ncRNA_class") == 0)
7896 {
7897 qual->val = HandleApplyValue (qual->val, avp);
7898 found = TRUE;
7899 }
7900 }
7901 if (!found)
7902 {
7903 qual = GBQualNew ();
7904 qual->qual = StringSave ("ncRNA_class");
7905 qual->val = StringSave (avp->new_text);
7906 qual->next = sfp->qual;
7907 sfp->qual = qual;
7908 }
7909 break;
7910 default:
7911 if (avp->field_list->data.intvalue >= num_rna_fields + 1)
7912 {
7913 avp->field_list->data.intvalue -= num_rna_fields;
7914 grp = SeqMgrGetGeneXref (sfp);
7915 if (grp == NULL)
7916 {
7917 gene = SeqMgrGetOverlappingGene (sfp->location, &context);
7918 SetGeneFieldString (gene, avp, fsp);
7919 }
7920 else
7921 {
7922 SetGeneFieldString (sfp, avp, fsp);
7923 }
7924 avp->field_list->data.intvalue += num_rna_fields;
7925 }
7926 break;
7927 }
7928 }
7929
7930
RemoveRNAProduct(SeqFeatPtr sfp)7931 static void RemoveRNAProduct (SeqFeatPtr sfp)
7932 {
7933 RnaRefPtr rrp;
7934 GBQualPtr gbq, prev_gbq = NULL;
7935 tRNAPtr trp;
7936
7937 if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA || sfp->data.value.ptrvalue == NULL)
7938 {
7939 return;
7940 }
7941
7942 rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
7943
7944 gbq = sfp->qual;
7945 while (gbq != NULL && StringCmp (gbq->qual, "product") != 0)
7946 {
7947 prev_gbq = gbq;
7948 gbq = gbq->next;
7949 }
7950 if (gbq != NULL)
7951 {
7952 if (prev_gbq == NULL)
7953 {
7954 sfp->qual = gbq->next;
7955 }
7956 else
7957 {
7958 prev_gbq->next = gbq->next;
7959 }
7960 gbq->next = NULL;
7961 gbq = GBQualFree (gbq);
7962 }
7963 else if (rrp->ext.choice == 1
7964 && (StringCmp (rrp->ext.value.ptrvalue, "ncRNA") == 0
7965 || StringCmp (rrp->ext.value.ptrvalue, "tmRNA") == 0
7966 || StringCmp (rrp->ext.value.ptrvalue, "misc_RNA") == 0))
7967 {
7968 /* do nothing - already have no product */
7969 }
7970 else if (rrp->ext.choice == 0)
7971 {
7972 /* do nothing - already have no product */
7973 }
7974 else if (rrp->ext.choice == 1)
7975 {
7976 rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
7977 rrp->ext.choice = 0;
7978 }
7979 else if (rrp->ext.choice == 2)
7980 {
7981 trp = (tRNAPtr) rrp->ext.value.ptrvalue;
7982 if (trp != NULL)
7983 {
7984 trp->aatype = 0;
7985 }
7986 }
7987 }
7988
7989
RemoveRNAField(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)7990 static void RemoveRNAField (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
7991 {
7992 RnaRefPtr rrp;
7993 tRNAPtr trp;
7994 ApplyValuePtr avp;
7995 SeqFeatPtr gene;
7996 GeneRefPtr grp;
7997 ValNode vn;
7998 SeqMgrFeatContext context;
7999 GBQualPtr qual, qual_prev = NULL, qual_next;
8000
8001 if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA || userdata == NULL)
8002 {
8003 return;
8004 }
8005
8006 avp = (ApplyValuePtr) userdata;
8007 if (avp->field_list == NULL)
8008 {
8009 return;
8010 }
8011
8012 rrp = sfp->data.value.ptrvalue;
8013
8014 switch (avp->field_list->data.intvalue)
8015 {
8016 case RNAFIELD_PRODUCT :
8017 RemoveRNAProduct (sfp);
8018 break;
8019 case RNAFIELD_COMMENT :
8020 sfp->comment = MemFree (sfp->comment);
8021 break;
8022 case RNAFIELD_NCRNA_CLASS :
8023 qual = sfp->qual;
8024 while (qual != NULL)
8025 {
8026 qual_next = qual->next;
8027 if (StringCmp (qual->qual, "ncRNA_class") == 0)
8028 {
8029 if (qual_prev == NULL)
8030 {
8031 sfp->qual = qual_next;
8032 }
8033 else
8034 {
8035 qual_prev->next = qual_next;
8036 }
8037 qual->next = NULL;
8038 qual = GBQualFree (qual);
8039 }
8040 else
8041 {
8042 qual_prev = qual;
8043 }
8044 qual = qual_next;
8045 }
8046 break;
8047 case RNAFIELD_ANTICODON :
8048 if (rrp->ext.choice == 2) {
8049 trp = (tRNAPtr) rrp->ext.value.ptrvalue;
8050 if (trp != NULL && trp->anticodon != NULL) {
8051 trp->anticodon = SeqLocFree (trp->anticodon);
8052 }
8053 }
8054 break;
8055 case RNAFIELD_CODONS_RECOGNIZED :
8056 if (rrp->ext.choice == 2) {
8057 trp = (tRNAPtr) rrp->ext.value.ptrvalue;
8058 if (trp != NULL) {
8059 trp->codon [0] = 255;
8060 trp->codon [1] = 255;
8061 trp->codon [2] = 255;
8062 trp->codon [3] = 255;
8063 trp->codon [4] = 255;
8064 trp->codon [5] = 255;
8065 }
8066 }
8067 break;
8068 case RNAFIELD_TRANSCRIPT_ID :
8069 sfp->product = SeqLocFree (sfp->product);
8070 break;
8071 default:
8072 if (avp->field_list->data.intvalue >= num_rna_fields + 1)
8073 {
8074 vn.choice = 1;
8075 vn.next = NULL;
8076 vn.data.intvalue = avp->field_list->data.intvalue - num_rna_fields;
8077 grp = SeqMgrGetGeneXref (sfp);
8078 if (grp == NULL)
8079 {
8080 gene = SeqMgrGetOverlappingGene (sfp->location, &context);
8081 RemoveGeneFieldString (gene, &vn);
8082 }
8083 else
8084 {
8085 RemoveGeneFieldString (sfp, &vn);
8086 }
8087 }
8088 break;
8089 }
8090 }
8091
8092 typedef struct exonfieldselection
8093 {
8094 DIALOG_MESSAGE_BLOCK
8095 PopuP exon_field;
8096
8097 Boolean allow_none;
8098 Nlm_ChangeNotifyProc change_notify;
8099 Pointer change_userdata;
8100 } ExonFieldSelectionData, PNTR ExonFieldSelectionPtr;
8101
8102 #define EXONFIELD_ALLELE 1
8103 #define EXONFIELD_COMMENT 2
8104 #define EXONFIELD_EC_NUMBER 3
8105 #define EXONFIELD_FUNCTION 4
8106 #define EXONFIELD_OLD_LOCUS_TAG 5
8107 #define EXONFIELD_NUMBER 6
8108 #define EXONFIELD_PRODUCT 7
8109
8110 static CharPtr exon_field_list [] =
8111 {
8112 "allele", "comment", "EC_number", "function", "old_locus_tag", "number", "product"
8113 };
8114 #define NUM_EXON_FIELDS 7
8115
8116 extern DialoG
ExonFieldSelectionDialog(GrouP h,Boolean allow_none,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)8117 ExonFieldSelectionDialog
8118 (GrouP h,
8119 Boolean allow_none,
8120 Nlm_ChangeNotifyProc change_notify,
8121 Pointer change_userdata)
8122 {
8123 return FeatureFieldSelectionDialog (h, allow_none,
8124 NUM_EXON_FIELDS, exon_field_list,
8125 change_notify, change_userdata);
8126
8127 }
8128
GetExonFieldString(SeqFeatPtr sfp,ValNodePtr exon_field)8129 extern CharPtr GetExonFieldString (SeqFeatPtr sfp, ValNodePtr exon_field)
8130 {
8131 ValNodePtr vnp;
8132 CharPtr str = NULL;
8133 GBQualPtr gbqual;
8134
8135 if (sfp == NULL || exon_field == NULL || sfp->idx.subtype != FEATDEF_exon)
8136 {
8137 return NULL;
8138 }
8139
8140 vnp = exon_field;
8141 while (vnp != NULL && StringHasNoText (str))
8142 {
8143 str = NULL;
8144 if (vnp->data.intvalue == EXONFIELD_COMMENT)
8145 {
8146 str = sfp->comment;
8147 }
8148 else
8149 {
8150 gbqual = sfp->qual;
8151 while (gbqual != NULL && StringHasNoText (str))
8152 {
8153 if (vnp->data.intvalue < NUM_EXON_FIELDS + 1
8154 && vnp->data.intvalue >= 1
8155 && StringCmp (gbqual->qual, exon_field_list[vnp->data.intvalue - 1]) == 0)
8156 {
8157 str = gbqual->val;
8158 }
8159 gbqual = gbqual->next;
8160 }
8161 }
8162 vnp = vnp->next;
8163 }
8164 if (StringHasNoText (str))
8165 {
8166 str = NULL;
8167 }
8168 else
8169 {
8170 str = StringSave (str);
8171 }
8172 return str;
8173 }
8174
RemoveExonFieldString(SeqFeatPtr sfp,ValNodePtr exon_field)8175 extern void RemoveExonFieldString (SeqFeatPtr sfp, ValNodePtr exon_field)
8176 {
8177 ValNodePtr vnp;
8178 Boolean found_nonempty = FALSE;
8179 GBQualPtr gbqual, prev_qual;
8180
8181 if (sfp == NULL || exon_field == NULL || sfp->idx.subtype != FEATDEF_exon)
8182 {
8183 return;
8184 }
8185
8186 vnp = exon_field;
8187 while (vnp != NULL && !found_nonempty)
8188 {
8189 if (vnp->data.intvalue == EXONFIELD_COMMENT)
8190 {
8191 if (!StringHasNoText (sfp->comment))
8192 {
8193 found_nonempty = TRUE;
8194 if (vnp->choice != 0)
8195 {
8196 sfp->comment = MemFree (sfp->comment);
8197 }
8198 }
8199 }
8200 else
8201 {
8202 gbqual = sfp->qual;
8203 prev_qual = NULL;
8204 while (gbqual != NULL)
8205 {
8206 if (vnp->data.intvalue <= NUM_EXON_FIELDS + 1
8207 && vnp->data.intvalue >= 1
8208 && StringCmp (gbqual->qual, exon_field_list[vnp->data.intvalue - 1]) == 0)
8209 {
8210 if (!StringHasNoText (gbqual->val))
8211 {
8212 found_nonempty = TRUE;
8213 if (vnp->choice != 0)
8214 {
8215 if (prev_qual == NULL)
8216 {
8217 sfp->qual = gbqual->next;
8218 } else {
8219 prev_qual->next = gbqual->next;
8220 }
8221 gbqual->next = NULL;
8222 GBQualFree (gbqual);
8223 return;
8224 }
8225 }
8226 }
8227 prev_qual = gbqual;
8228 gbqual = gbqual->next;
8229 }
8230 }
8231 vnp = vnp->next;
8232 }
8233 }
8234
8235
8236 #define PARSE_FIELD_BIOSRC_TAXNAME 1
8237 #define PARSE_FIELD_BIOSRC_LINEAGE 2
8238 #define PARSE_FIELD_BIOSRC_DIVISION 3
8239
8240 static CharPtr biosrc_string_list [] =
8241 {
8242 "Organism Name", "Lineage", "Division"
8243 };
8244
8245 static int num_biosrc_strings = sizeof (biosrc_string_list) / sizeof (CharPtr);
8246
BioSourceStringDialog(GrouP h,Boolean allow_multi,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)8247 extern DialoG BioSourceStringDialog
8248 (GrouP h,
8249 Boolean allow_multi,
8250 Nlm_ChangeNotifyProc change_notify,
8251 Pointer change_userdata)
8252 {
8253 return FeatureFieldSelectionDialog (h, allow_multi,
8254 num_biosrc_strings, biosrc_string_list,
8255 change_notify, change_userdata);
8256 }
8257
GetSourceStringFromBioSource(BioSourcePtr biop,ValNodePtr vnp)8258 static CharPtr GetSourceStringFromBioSource (BioSourcePtr biop, ValNodePtr vnp)
8259 {
8260 if (biop == NULL || vnp == NULL || biop->org == NULL)
8261 {
8262 return NULL;
8263 }
8264
8265 if (vnp->data.intvalue == PARSE_FIELD_BIOSRC_TAXNAME
8266 && !StringHasNoText (biop->org->taxname))
8267 {
8268 return StringSave (biop->org->taxname);
8269 }
8270 else if (vnp->data.intvalue == PARSE_FIELD_BIOSRC_LINEAGE
8271 && biop->org->orgname != NULL
8272 && !StringHasNoText (biop->org->orgname->lineage))
8273 {
8274 return StringSave (biop->org->orgname->lineage);
8275 }
8276 else if (vnp->data.intvalue == PARSE_FIELD_BIOSRC_DIVISION
8277 && biop->org->orgname != NULL
8278 && !StringHasNoText (biop->org->orgname->div))
8279 {
8280 return StringSave (biop->org->orgname->div);
8281 }
8282 else
8283 {
8284 return NULL;
8285 }
8286 }
8287
8288 static CharPtr
GetSourceFeatureString(SeqFeatPtr sfp,ValNodePtr vnp,FilterSetPtr fsp)8289 GetSourceFeatureString
8290 (SeqFeatPtr sfp,
8291 ValNodePtr vnp,
8292 FilterSetPtr fsp)
8293 {
8294 if (sfp == NULL || sfp->data.choice != SEQFEAT_BIOSRC || vnp == NULL)
8295 {
8296 return NULL;
8297 }
8298
8299 return GetSourceStringFromBioSource (sfp->data.value.ptrvalue, vnp);
8300 }
8301
8302 static CharPtr
GetSourceDescriptorString(SeqDescrPtr sdp,ValNodePtr vnp,FilterSetPtr fsp)8303 GetSourceDescriptorString
8304 (SeqDescrPtr sdp,
8305 ValNodePtr vnp,
8306 FilterSetPtr fsp)
8307 {
8308 if (sdp == NULL || sdp->choice != Seq_descr_source || vnp == NULL)
8309 {
8310 return NULL;
8311 }
8312 return GetSourceStringFromBioSource (sdp->data.ptrvalue, vnp);
8313 }
8314
8315
GetDbxrefFromBioSource(BioSourcePtr biop,ValNodePtr vnp)8316 static CharPtr GetDbxrefFromBioSource (BioSourcePtr biop, ValNodePtr vnp)
8317 {
8318 ValNodePtr dbx;
8319 DbtagPtr dbtag;
8320 Char buf[20];
8321
8322 if (biop == NULL || vnp == NULL || vnp->data.ptrvalue == NULL || biop->org == NULL)
8323 {
8324 return NULL;
8325 }
8326
8327 dbx = biop->org->db;
8328 while (dbx != NULL)
8329 {
8330 dbtag = (DbtagPtr) dbx->data.ptrvalue;
8331 if (dbtag != NULL && dbtag->tag != NULL
8332 && StringCmp (dbtag->db, vnp->data.ptrvalue) == 0)
8333 {
8334 if (dbtag->tag->str == NULL)
8335 {
8336 sprintf (buf, "%d", dbtag->tag->id);
8337 return StringSave (buf);
8338 }
8339 else
8340 {
8341 return StringSave (dbtag->tag->str);
8342 }
8343 }
8344 dbx = dbx->next;
8345 }
8346 return NULL;
8347 }
8348
8349 static CharPtr
GetBioSourceFeatureDbxrefString(SeqFeatPtr sfp,ValNodePtr vnp,FilterSetPtr fsp)8350 GetBioSourceFeatureDbxrefString
8351 (SeqFeatPtr sfp,
8352 ValNodePtr vnp,
8353 FilterSetPtr fsp)
8354 {
8355 if (sfp == NULL || sfp->data.choice != SEQFEAT_BIOSRC || vnp == NULL)
8356 {
8357 return NULL;
8358 }
8359
8360 return GetDbxrefFromBioSource (sfp->data.value.ptrvalue, vnp);
8361 }
8362
8363 static CharPtr
GetBioSourceDescriptorDbxrefString(SeqDescrPtr sdp,ValNodePtr vnp,FilterSetPtr fsp)8364 GetBioSourceDescriptorDbxrefString
8365 (SeqDescrPtr sdp,
8366 ValNodePtr vnp,
8367 FilterSetPtr fsp)
8368 {
8369 if (sdp == NULL || sdp->choice != Seq_descr_source || vnp == NULL)
8370 {
8371 return NULL;
8372 }
8373 return GetDbxrefFromBioSource (sdp->data.ptrvalue, vnp);
8374 }
8375
8376
8377 #define TEXT_PORTION_START_AFTER 1
8378 #define TEXT_PORTION_START_WITH 2
8379 #define TEXT_PORTION_END_AFTER 1
8380 #define TEXT_PORTION_END_WITH 2
8381
8382 typedef struct textportiondialog
8383 {
8384 DIALOG_MESSAGE_BLOCK
8385
8386 GrouP start_choice;
8387 TexT start_text;
8388 GrouP end_choice;
8389 TexT end_text;
8390 ButtoN rem_before;
8391 ButtoN also_rem_before;
8392 ButtoN rem_after;
8393 ButtoN also_rem_after;
8394 ButtoN insensitive;
8395 ButtoN whole_word;
8396
8397 Boolean inside;
8398
8399 Nlm_ChangeNotifyProc change_notify;
8400 Pointer change_userdata;
8401 } TextPortionXDialogData, PNTR TextPortionXDialogPtr;
8402
8403
OutsideEnableDisable(TextPortionXDialogPtr tp)8404 static void OutsideEnableDisable (TextPortionXDialogPtr tp)
8405 {
8406 if (tp == NULL || tp->inside)
8407 {
8408 return;
8409 }
8410 if (GetStatus (tp->rem_before))
8411 {
8412 Enable (tp->start_text);
8413 Enable (tp->also_rem_before);
8414 }
8415 else
8416 {
8417 Disable (tp->start_text);
8418 Disable (tp->also_rem_before);
8419 }
8420 if (GetStatus (tp->rem_after))
8421 {
8422 Enable (tp->end_text);
8423 Enable (tp->also_rem_after);
8424 }
8425 else
8426 {
8427 Disable (tp->end_text);
8428 Disable (tp->also_rem_after);
8429 }
8430 }
8431
ResetTextPortionXDialog(TextPortionXDialogPtr tp)8432 static void ResetTextPortionXDialog (TextPortionXDialogPtr tp)
8433 {
8434 if (tp == NULL)
8435 {
8436 return;
8437 }
8438 if (tp->inside)
8439 {
8440 SetValue (tp->start_choice, TEXT_PORTION_START_AFTER);
8441 SetValue (tp->end_choice, TEXT_PORTION_END_AFTER);
8442 }
8443 else
8444 {
8445 SetStatus (tp->rem_before, FALSE);
8446 SetStatus (tp->also_rem_before, FALSE);
8447 SetStatus (tp->rem_after, FALSE);
8448 SetStatus (tp->also_rem_after, FALSE);
8449 }
8450 SetTitle (tp->start_text, "");
8451 SetTitle (tp->end_text, "");
8452 SetStatus (tp->insensitive, FALSE);
8453 SetStatus (tp->whole_word, FALSE);
8454 OutsideEnableDisable (tp);
8455 }
8456
TextPortionXToDialog(DialoG d,Pointer data)8457 static void TextPortionXToDialog (DialoG d, Pointer data)
8458 {
8459 TextPortionXDialogPtr tdlg;
8460 TextPortionXPtr tdata;
8461 Int4 start_choice, end_choice;
8462
8463 tdlg = (TextPortionXDialogPtr) GetObjectExtra (d);
8464 if (tdlg == NULL)
8465 {
8466 return;
8467 }
8468 tdata = (TextPortionXPtr) data;
8469 ResetTextPortionXDialog (tdlg);
8470 if (tdata != NULL)
8471 {
8472 start_choice = tdata->end_choice;
8473 end_choice = tdata->end_choice;
8474 if (start_choice < TEXT_PORTION_START_AFTER || start_choice > TEXT_PORTION_START_WITH)
8475 {
8476 start_choice = TEXT_PORTION_START_AFTER;
8477 }
8478 if (end_choice < TEXT_PORTION_END_AFTER || end_choice > TEXT_PORTION_END_WITH)
8479 {
8480 end_choice = TEXT_PORTION_END_AFTER;
8481 }
8482 if (tdlg->inside)
8483 {
8484 SetValue (tdlg->start_choice, start_choice);
8485 SetValue (tdlg->end_choice, end_choice);
8486 }
8487 else
8488 {
8489 SetStatus (tdlg->rem_before, StringHasNoText (tdata->start_text));
8490 SetStatus (tdlg->rem_after, StringHasNoText (tdata->end_text));
8491 if (start_choice == TEXT_PORTION_START_AFTER)
8492 {
8493 SetStatus (tdlg->also_rem_before, TRUE);
8494 }
8495 else
8496 {
8497 SetStatus (tdlg->also_rem_before, FALSE);
8498 }
8499 if (end_choice == TEXT_PORTION_END_AFTER)
8500 {
8501 SetStatus (tdlg->also_rem_after, TRUE);
8502 }
8503 else
8504 {
8505 SetStatus (tdlg->also_rem_after, FALSE);
8506 }
8507 }
8508 if (tdata->start_text != NULL)
8509 {
8510 SetTitle (tdlg->start_text, tdata->start_text);
8511 }
8512 if (tdata->end_text != NULL)
8513 {
8514 SetTitle (tdlg->end_text, tdata->end_text);
8515 }
8516 SetStatus (tdlg->insensitive, tdata->insensitive);
8517 SetStatus (tdlg->whole_word, tdata->whole_word);
8518 }
8519 OutsideEnableDisable (tdlg);
8520 }
8521
DialogToTextPortionX(DialoG d)8522 static Pointer DialogToTextPortionX (DialoG d)
8523 {
8524 TextPortionXDialogPtr tdlg;
8525 TextPortionXPtr tdata;
8526
8527 tdlg = (TextPortionXDialogPtr) GetObjectExtra (d);
8528 if (tdlg == NULL)
8529 {
8530 return NULL;
8531 }
8532
8533 tdata = (TextPortionXPtr) MemNew (sizeof (TextPortionXData));
8534 if (tdata != NULL)
8535 {
8536 if (tdlg->inside)
8537 {
8538 tdata->start_choice = GetValue (tdlg->start_choice);
8539 tdata->end_choice = GetValue (tdlg->end_choice);
8540 tdata->start_text = JustSaveStringFromText (tdlg->start_text);
8541 tdata->end_text = JustSaveStringFromText (tdlg->end_text);
8542 }
8543 else
8544 {
8545 if (GetStatus (tdlg->rem_before))
8546 {
8547 tdata->start_text = JustSaveStringFromText (tdlg->start_text);
8548 }
8549 else
8550 {
8551 tdata->start_text = NULL;
8552 }
8553 if (GetStatus (tdlg->rem_after))
8554 {
8555 tdata->end_text = JustSaveStringFromText (tdlg->end_text);
8556 }
8557 else
8558 {
8559 tdata->end_text = NULL;
8560 }
8561
8562 if (GetStatus (tdlg->also_rem_before))
8563 {
8564 tdata->start_choice = TEXT_PORTION_START_AFTER;
8565 }
8566 else
8567 {
8568 tdata->start_choice = TEXT_PORTION_START_WITH;
8569 }
8570 if (GetStatus (tdlg->also_rem_after))
8571 {
8572 tdata->end_choice = TEXT_PORTION_END_AFTER;
8573 }
8574 else
8575 {
8576 tdata->end_choice = TEXT_PORTION_END_WITH;
8577 }
8578
8579 }
8580
8581 tdata->insensitive = GetStatus (tdlg->insensitive);
8582 tdata->whole_word = GetStatus (tdlg->whole_word);
8583 }
8584 return tdata;
8585 }
8586
TextPortionXMessage(DialoG d,Int2 mssg)8587 static void TextPortionXMessage (DialoG d, Int2 mssg)
8588
8589 {
8590 TextPortionXDialogPtr tp;
8591
8592 tp = (TextPortionXDialogPtr) GetObjectExtra (d);
8593 if (tp != NULL) {
8594 switch (mssg) {
8595 case VIB_MSG_INIT :
8596 ResetTextPortionXDialog (tp);
8597 break;
8598 case VIB_MSG_ENTER :
8599 Select (tp->start_text);
8600 break;
8601 case NUM_VIB_MSG + 1 :
8602 SetTitle (tp->start_text, "");
8603 SetTitle (tp->end_text, "");
8604 break;
8605 default :
8606 break;
8607 }
8608 }
8609 }
8610
TestTextPortionXDialog(DialoG d)8611 static ValNodePtr TestTextPortionXDialog (DialoG d)
8612
8613 {
8614 return NULL;
8615 }
8616
ChangeTextPortionXGroup(GrouP g)8617 static void ChangeTextPortionXGroup (GrouP g)
8618 {
8619 TextPortionXDialogPtr tp;
8620
8621 tp = (TextPortionXDialogPtr) GetObjectExtra (g);
8622 if (tp == NULL) return;
8623
8624 if (tp->change_notify != NULL)
8625 {
8626 (tp->change_notify) (tp->change_userdata);
8627 }
8628 }
8629
ChangeTextPortionXText(TexT t)8630 static void ChangeTextPortionXText (TexT t)
8631 {
8632 TextPortionXDialogPtr tp;
8633
8634 tp = (TextPortionXDialogPtr) GetObjectExtra (t);
8635 if (tp == NULL) return;
8636
8637 if (tp->change_notify != NULL)
8638 {
8639 (tp->change_notify) (tp->change_userdata);
8640 }
8641 }
8642
8643
ChangeTextPortionXBtn(ButtoN b)8644 static void ChangeTextPortionXBtn (ButtoN b)
8645 {
8646 TextPortionXDialogPtr tp;
8647
8648 tp = (TextPortionXDialogPtr) GetObjectExtra (b);
8649 if (tp == NULL) return;
8650 OutsideEnableDisable (tp);
8651
8652 if (tp->change_notify != NULL)
8653 {
8654 (tp->change_notify) (tp->change_userdata);
8655 }
8656 }
8657
8658
8659
TextPortionXDialogEx(GrouP h,Boolean inside,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)8660 extern DialoG TextPortionXDialogEx (GrouP h, Boolean inside, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
8661 {
8662 TextPortionXDialogPtr tp;
8663 GrouP p, g1, g2;
8664
8665 tp = (TextPortionXDialogPtr) MemNew (sizeof (TextPortionXDialogData));
8666 if (tp == NULL)
8667 {
8668 return NULL;
8669 }
8670
8671 p = HiddenGroup (h, -1, 0, NULL);
8672 SetObjectExtra (p, tp, StdCleanupExtraProc);
8673
8674 tp->dialog = (DialoG) p;
8675 tp->todialog = TextPortionXToDialog;
8676 tp->fromdialog = DialogToTextPortionX;
8677 tp->dialogmessage = TextPortionXMessage;
8678 tp->testdialog = TestTextPortionXDialog;
8679
8680 tp->change_notify = change_notify;
8681 tp->change_userdata = change_userdata;
8682 tp->inside = inside;
8683
8684 g1 = HiddenGroup (p, 3, 0, NULL);
8685 SetGroupSpacing (g1, 10, 10);
8686
8687 if (inside)
8688 {
8689 StaticPrompt (g1, "Between", 0, popupMenuHeight, programFont, 'r');
8690 tp->start_choice = HiddenGroup (g1, 2, 0, ChangeTextPortionXGroup);
8691 RadioButton (tp->start_choice, "just after");
8692 RadioButton (tp->start_choice, "starting at");
8693 SetValue (tp->start_choice, TEXT_PORTION_START_AFTER);
8694 SetObjectExtra (tp->start_choice, tp, NULL);
8695
8696 tp->start_text = DialogText (g1, "", 10, ChangeTextPortionXText);
8697 SetObjectExtra (tp->start_text, tp, NULL);
8698
8699 StaticPrompt (g1, "And", 0, popupMenuHeight, programFont, 'r');
8700 tp->end_choice = HiddenGroup (g1, 2, 0, ChangeTextPortionXGroup);
8701 RadioButton (tp->end_choice, "up to");
8702 RadioButton (tp->end_choice, "including");
8703 SetValue (tp->end_choice, TEXT_PORTION_END_AFTER);
8704 SetObjectExtra (tp->end_choice, tp, NULL);
8705
8706 tp->end_text = DialogText (g1, "", 10, ChangeTextPortionXText);
8707 SetObjectExtra (tp->end_text, tp, NULL);
8708 }
8709 else
8710 {
8711 tp->rem_before = CheckBox (g1, "Before", ChangeTextPortionXBtn);
8712 SetObjectExtra (tp->rem_before, tp, NULL);
8713 tp->start_text = DialogText (g1, "", 10, ChangeTextPortionXText);
8714 SetObjectExtra (tp->start_text, tp, NULL);
8715 tp->also_rem_before = CheckBox (g1, "Also Remove Entered Text", ChangeTextPortionXBtn);
8716
8717 tp->rem_after = CheckBox (g1, "After", ChangeTextPortionXBtn);
8718 SetObjectExtra (tp->rem_after, tp, NULL);
8719 tp->end_text = DialogText (g1, "", 10, ChangeTextPortionXText);
8720 SetObjectExtra (tp->end_text, tp, NULL);
8721 tp->also_rem_after = CheckBox (g1, "Also Remove Entered Text", ChangeTextPortionXBtn);
8722 }
8723
8724 g2 = HiddenGroup (p, 2, 0, NULL);
8725 tp->insensitive = CheckBox (g2, "Case insensitive", ChangeTextPortionXBtn);
8726 SetObjectExtra (tp->insensitive, tp, NULL);
8727 tp->whole_word = CheckBox (g2, "Whole word", ChangeTextPortionXBtn);
8728 SetObjectExtra (tp->whole_word, tp, NULL);
8729
8730 AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) g2, NULL);
8731
8732 ResetTextPortionXDialog (tp);
8733 return (DialoG) p;
8734 }
8735
TextPortionXDialog(GrouP h)8736 extern DialoG TextPortionXDialog (GrouP h)
8737 {
8738 return TextPortionXDialogEx (h, TRUE, NULL, NULL);
8739 }
8740
TextPortionXFree(TextPortionXPtr tp)8741 extern TextPortionXPtr TextPortionXFree (TextPortionXPtr tp)
8742 {
8743 if (tp == NULL) return NULL;
8744 tp->start_text = MemFree (tp->start_text);
8745 tp->end_text = MemFree (tp->end_text);
8746 tp = MemFree (tp->end_text);
8747 return tp;
8748 }
8749
8750
TextPortionXNew(void)8751 static TextPortionXPtr TextPortionXNew (void)
8752 {
8753 TextPortionXPtr tp;
8754
8755 tp = (TextPortionXPtr) MemNew (sizeof (TextPortionXData));
8756 return tp;
8757 }
8758
8759
IsWholeWordMatch(CharPtr start,CharPtr found,Int4 match_len)8760 static Boolean IsWholeWordMatch (CharPtr start, CharPtr found, Int4 match_len)
8761 {
8762 Boolean rval = TRUE;
8763 Char char_after;
8764 Char char_before;
8765
8766 if (match_len == 0)
8767 {
8768 rval = TRUE;
8769 }
8770 else if (start == NULL || found == NULL)
8771 {
8772 rval = FALSE;
8773 }
8774 else
8775 {
8776 char_after = *(found + match_len);
8777 if (found != start)
8778 {
8779 char_before = *(found - 1);
8780 if (isalpha ((Int4) char_before) || isdigit ((Int4) char_before))
8781 {
8782 rval = FALSE;
8783 }
8784 }
8785 if (char_after != 0 && (isalpha ((Int4) char_after) || isdigit ((Int4)char_after)))
8786 {
8787 rval = FALSE;
8788 }
8789 }
8790 return rval;
8791 }
8792
8793 extern void
FindTextPortionXInString(CharPtr str,TextPortionXPtr tp,CharPtr PNTR ploc,Int4Ptr plen)8794 FindTextPortionXInString
8795 (CharPtr str,
8796 TextPortionXPtr tp,
8797 CharPtr PNTR ploc,
8798 Int4Ptr plen)
8799 {
8800 CharPtr found_start, found_end;
8801 Int4 found_len;
8802
8803 if (ploc == NULL || plen == NULL || tp == NULL)
8804 {
8805 return;
8806 }
8807 *ploc = NULL;
8808 *plen = 0;
8809
8810 if (str == NULL)
8811 {
8812 return;
8813 }
8814
8815 if (tp->start_text == NULL || tp->start_text [0] == 0)
8816 {
8817 found_start = str;
8818 }
8819 else
8820 {
8821 if (tp->insensitive)
8822 {
8823 found_start = StringISearch (str, tp->start_text);
8824 }
8825 else
8826 {
8827 found_start = StringSearch (str, tp->start_text);
8828 }
8829
8830 if (tp->whole_word && ! IsWholeWordMatch (str, found_start, StringLen (tp->start_text)))
8831 {
8832 found_start = NULL;
8833 }
8834 }
8835
8836 if (found_start == NULL)
8837 {
8838 return;
8839 }
8840
8841
8842
8843 if (tp->start_choice == TEXT_PORTION_START_AFTER)
8844 {
8845 found_start += StringLen (tp->start_text);
8846 }
8847
8848 if (tp->end_text == NULL || tp->end_text [0] == 0)
8849 {
8850 found_len = StringLen (found_start);
8851 }
8852 else
8853 {
8854 if (tp->insensitive)
8855 {
8856 found_end = StringISearch (found_start, tp->end_text);
8857 }
8858 else
8859 {
8860 found_end = StringSearch (found_start, tp->end_text);
8861 }
8862 if (tp->whole_word && ! IsWholeWordMatch (str, found_end, StringLen (tp->end_text)))
8863 {
8864 found_end = NULL;
8865 }
8866
8867 if (found_end == NULL)
8868 {
8869 found_len = 0;
8870 }
8871 else if (tp->end_choice == TEXT_PORTION_END_WITH)
8872 {
8873 found_len = (Int4)(found_end - found_start) + StringLen (tp->end_text);
8874 }
8875 else
8876 {
8877 found_len = found_end - found_start;
8878 }
8879 }
8880
8881 if (found_len > 0)
8882 {
8883 *ploc = found_start;
8884 *plen = found_len;
8885 }
8886 }
8887
ClearDialogBtn(ButtoN b)8888 static void ClearDialogBtn (ButtoN b)
8889 {
8890 DialoG d;
8891
8892 d = (DialoG) GetObjectExtra (b);
8893
8894 PointerToDialog (d, NULL);
8895 }
8896
8897 typedef struct changecasedlg {
8898 DIALOG_MESSAGE_BLOCK
8899 GrouP change_case;
8900 GrouP options;
8901 ButtoN keep_cap_before_punct;
8902 ButtoN keep_cap_before_cap;
8903 ButtoN keep_cap_before_digit;
8904 ButtoN remove_comma;
8905 } ChangeCaseDlgData, PNTR ChangeCaseDlgPtr;
8906
8907 typedef enum {
8908 eChangeCaseNone = 1,
8909 eChangeCaseAllLower,
8910 eChangeCaseCapFirst,
8911 eChangeCaseLowerFirstRestNoChange,
8912 eChangeCaseOptions
8913 } EChangeCaseRule;
8914
8915 typedef struct changecase {
8916 EChangeCaseRule change;
8917 FixProductCapData fc;
8918 } ChangeCaseData, PNTR ChangeCasePtr;
8919
8920
ChangeCapitalizationChoice(GrouP g)8921 static void ChangeCapitalizationChoice (GrouP g)
8922 {
8923 ChangeCaseDlgPtr dlg;
8924
8925 dlg = (ChangeCaseDlgPtr) GetObjectExtra (g);
8926 if (dlg == NULL) {
8927 return;
8928 }
8929
8930 if (GetValue (dlg->change_case) == eChangeCaseOptions) {
8931 Enable (dlg->options);
8932 } else {
8933 Disable (dlg->options);
8934 }
8935 }
8936
8937
DataToChangeCaseDialog(DialoG d,Pointer data)8938 static void DataToChangeCaseDialog (DialoG d, Pointer data)
8939 {
8940 ChangeCasePtr ccp = (ChangeCasePtr) data;
8941 ChangeCaseDlgPtr dlg = (ChangeCaseDlgPtr) GetObjectExtra (d);
8942 if (dlg == NULL) return;
8943
8944 if (ccp == NULL || ccp->change == eChangeCaseNone) {
8945 SetValue (dlg->change_case, eChangeCaseNone);
8946 } else {
8947 SetValue (dlg->change_case, ccp->change);
8948 if (ccp->change == eChangeCaseOptions) {
8949 SetStatus (dlg->keep_cap_before_cap, ccp->fc.keep_cap_before_cap);
8950 SetStatus (dlg->keep_cap_before_punct, ccp->fc.keep_cap_before_punct);
8951 SetStatus (dlg->keep_cap_before_digit, ccp->fc.keep_cap_before_digit);
8952 if (StringChr (ccp->fc.remove_list, ',') == NULL) {
8953 SetStatus (dlg->remove_comma, FALSE);
8954 } else {
8955 SetStatus (dlg->remove_comma, TRUE);
8956 }
8957 }
8958 }
8959 ChangeCapitalizationChoice (dlg->options);
8960 }
8961
ChangeCaseDialogToData(DialoG d)8962 static Pointer ChangeCaseDialogToData (DialoG d)
8963 {
8964 ChangeCaseDlgPtr dlg = (ChangeCaseDlgPtr) GetObjectExtra (d);
8965 ChangeCasePtr ccp = (ChangeCasePtr) MemNew (sizeof (ChangeCaseData));
8966
8967 if (dlg == NULL) {
8968 ccp->change = eChangeCaseNone;
8969 MemSet (&(ccp->fc), 0, sizeof (FixProductCapData));
8970 } else {
8971 ccp->change = GetValue (dlg->change_case);
8972 if (ccp->change == eChangeCaseOptions) {
8973 ccp->fc.keep_cap_before_cap = GetStatus (dlg->keep_cap_before_cap);
8974 ccp->fc.keep_cap_before_punct = GetStatus (dlg->keep_cap_before_punct);
8975 ccp->fc.keep_cap_before_digit = GetStatus (dlg->keep_cap_before_digit);
8976 if (GetStatus (dlg->remove_comma)) {
8977 ccp->fc.remove_list = ",";
8978 } else {
8979 ccp->fc.remove_list = NULL;
8980 }
8981 } else {
8982 MemSet (&(ccp->fc), 0, sizeof (FixProductCapData));
8983 }
8984 }
8985 return ccp;
8986 }
8987
8988
ChangeCaseDialog(GrouP h)8989 static DialoG ChangeCaseDialog (GrouP h)
8990 {
8991 ChangeCaseDlgPtr dlg;
8992 GrouP p;
8993
8994 dlg = (ChangeCaseDlgPtr) MemNew (sizeof (ChangeCaseDlgData));
8995 if (dlg == NULL)
8996 {
8997 return NULL;
8998 }
8999
9000 p = HiddenGroup (h, -1, 0, NULL);
9001 SetObjectExtra (p, dlg, StdCleanupExtraProc);
9002 SetGroupSpacing (p, 10, 10);
9003
9004 dlg->dialog = (DialoG) p;
9005 dlg->todialog = DataToChangeCaseDialog;
9006 dlg->fromdialog = ChangeCaseDialogToData;
9007 dlg->dialogmessage = NULL;
9008 dlg->testdialog = NULL;
9009
9010 dlg->change_case = NormalGroup (p, 3, 0, "Capitalization", programFont, ChangeCapitalizationChoice);
9011 SetObjectExtra (dlg->change_case, dlg, NULL);
9012 SetGroupSpacing (dlg->change_case, 10, 10);
9013
9014 RadioButton (dlg->change_case, "No change");
9015 RadioButton (dlg->change_case, "To lower");
9016 RadioButton (dlg->change_case, "First cap, rest lower");
9017 RadioButton (dlg->change_case, "First lower, rest no change");
9018 RadioButton (dlg->change_case, "Special options");
9019
9020 dlg->options = HiddenGroup (p, 0, 4, NULL);
9021 dlg->keep_cap_before_punct = CheckBox (dlg->options, "Keep caps before punctuation", NULL);
9022 dlg->keep_cap_before_cap = CheckBox (dlg->options, "Keep caps before caps", NULL);
9023 dlg->keep_cap_before_digit = CheckBox (dlg->options, "Keep caps before numbers", NULL);
9024 dlg->remove_comma = CheckBox (dlg->options, "Remove comma", NULL);
9025
9026 SetValue (dlg->change_case, eChangeCaseNone);
9027 Disable (dlg->options);
9028
9029 return (DialoG) p;
9030 }
9031
9032
ChangeCase(CharPtr PNTR pText,ChangeCasePtr ccp,ValNodePtr orgnames)9033 static void ChangeCase (CharPtr PNTR pText, ChangeCasePtr ccp, ValNodePtr orgnames)
9034 {
9035 if (ccp != NULL) {
9036 switch (ccp->change) {
9037 case eChangeCaseNone:
9038 break;
9039 case eChangeCaseAllLower:
9040 FixCapitalizationInTitle (pText, FALSE, orgnames);
9041 break;
9042 case eChangeCaseCapFirst:
9043 FixCapitalizationInTitle (pText, TRUE, orgnames);
9044 break;
9045 case eChangeCaseLowerFirstRestNoChange:
9046 if (pText != NULL && *pText != NULL && isalpha (**pText)) {
9047 **pText = tolower (**pText);
9048 }
9049 break;
9050 case eChangeCaseOptions:
9051 FixProductCapitalizationInString (pText, &(ccp->fc));
9052 break;
9053 }
9054 }
9055 }
9056
9057 typedef struct stringconstraintdialog
9058 {
9059 DIALOG_MESSAGE_BLOCK
9060 PopuP match_choice;
9061 TexT match_text;
9062 ButtoN insensitive;
9063 ButtoN whole_word;
9064 } StringConstraintDialogXData, PNTR StringConstraintDialogXPtr;
9065
ResetStringConstraintDialogX(StringConstraintDialogXPtr scdp)9066 static void ResetStringConstraintDialogX (StringConstraintDialogXPtr scdp)
9067 {
9068 if (scdp == NULL) return;
9069
9070 SetValue (scdp->match_choice, 1);
9071 SetTitle (scdp->match_text, "");
9072 SetStatus (scdp->insensitive, FALSE);
9073 SetStatus (scdp->whole_word, FALSE);
9074 }
9075
9076
GetPopupPosForStringConstraint(StringConstraintXPtr scp)9077 static Int4 GetPopupPosForStringConstraint (StringConstraintXPtr scp)
9078 {
9079 Int4 rval = 1;
9080
9081 if (scp == NULL) return 1;
9082
9083 switch (scp->match_location)
9084 {
9085 case eStringConstraintContains:
9086 if (scp->not_present)
9087 {
9088 rval = 2;
9089 } else {
9090 rval = 1;
9091 }
9092 break;
9093 case eStringConstraintEquals:
9094 if (scp->not_present) {
9095 rval = 4;
9096 } else {
9097 rval = 3;
9098 }
9099 break;
9100 case eStringConstraintStarts:
9101 if (scp->not_present) {
9102 rval = 9;
9103 } else {
9104 rval = 5;
9105 }
9106 break;
9107 case eStringConstraintEnds:
9108 if (scp->not_present) {
9109 rval = 10;
9110 } else {
9111 rval = 6;
9112 }
9113 break;
9114 case eStringConstraintInList:
9115 if (scp->not_present) {
9116 rval = 8;
9117 } else {
9118 rval = 7;
9119 }
9120 break;
9121 }
9122 return rval;
9123 }
9124
9125
StringConstraintToDialog(DialoG d,Pointer data)9126 static void StringConstraintToDialog (DialoG d, Pointer data)
9127
9128 {
9129 StringConstraintDialogXPtr scdp;
9130 StringConstraintXPtr scp;
9131
9132 scdp = (StringConstraintDialogXPtr) GetObjectExtra (d);
9133 scp = (StringConstraintXPtr) data;
9134 if (scdp == NULL)
9135 {
9136 return;
9137 }
9138
9139 if (scp == NULL)
9140 {
9141 ResetStringConstraintDialogX (scdp);
9142 }
9143 else
9144 {
9145 SetValue (scdp->match_choice, GetPopupPosForStringConstraint (scp));
9146
9147 if (StringHasNoText (scp->match_text))
9148 {
9149 SetTitle (scdp->match_text, " ");
9150 }
9151 else
9152 {
9153 SetTitle (scdp->match_text, scp->match_text);
9154 }
9155
9156 SetStatus (scdp->insensitive, scp->insensitive);
9157 SetStatus (scdp->whole_word, scp->whole_word);
9158 }
9159 }
9160
DialogToStringConstraint(DialoG d)9161 static Pointer DialogToStringConstraint (DialoG d)
9162
9163 {
9164 StringConstraintDialogXPtr scdp;
9165 StringConstraintXPtr scp;
9166 Int4 match_choice;
9167
9168 scdp = (StringConstraintDialogXPtr) GetObjectExtra (d);
9169 if (scdp == NULL)
9170 {
9171 return NULL;
9172 }
9173 scp = (StringConstraintXPtr) MemNew (sizeof (StringConstraintData));
9174 if (scp != NULL)
9175 {
9176 scp->match_text = SaveStringFromText (scdp->match_text);
9177 scp->insensitive = GetStatus (scdp->insensitive);
9178 scp->whole_word = GetStatus (scdp->whole_word);
9179 match_choice = GetValue (scdp->match_choice);
9180 switch (match_choice)
9181 {
9182 case 1:
9183 scp->match_location = eStringConstraintContains;
9184 scp->not_present = FALSE;
9185 break;
9186 case 2:
9187 scp->match_location = eStringConstraintContains;
9188 scp->not_present = TRUE;
9189 break;
9190 case 3:
9191 scp->match_location = eStringConstraintEquals;
9192 scp->not_present = FALSE;
9193 break;
9194 case 4:
9195 scp->match_location = eStringConstraintEquals;
9196 scp->not_present = TRUE;
9197 break;
9198 case 5:
9199 scp->match_location = eStringConstraintStarts;
9200 scp->not_present = FALSE;
9201 break;
9202 case 6:
9203 scp->match_location = eStringConstraintEnds;
9204 scp->not_present = FALSE;
9205 break;
9206 case 7:
9207 scp->match_location = eStringConstraintInList;
9208 scp->not_present = FALSE;
9209 break;
9210 case 8:
9211 scp->match_location = eStringConstraintInList;
9212 scp->not_present = TRUE;
9213 break;
9214 case 9:
9215 scp->match_location = eStringConstraintStarts;
9216 scp->not_present = TRUE;
9217 break;
9218 case 10:
9219 scp->match_location = eStringConstraintEnds;
9220 scp->not_present = TRUE;
9221 break;
9222 default:
9223 scp->match_location = eStringConstraintContains;
9224 scp->not_present = FALSE;
9225 break;
9226 }
9227 }
9228 return scp;
9229 }
9230
StringConstraintMessage(DialoG d,Int2 mssg)9231 static void StringConstraintMessage (DialoG d, Int2 mssg)
9232
9233 {
9234 StringConstraintDialogXPtr scdp;
9235
9236 scdp = (StringConstraintDialogXPtr) GetObjectExtra (d);
9237 if (scdp != NULL) {
9238 switch (mssg) {
9239 case VIB_MSG_INIT :
9240 ResetStringConstraintDialogX (scdp);
9241 break;
9242 case VIB_MSG_ENTER :
9243 Select (scdp->match_text);
9244 break;
9245 default :
9246 break;
9247 }
9248 }
9249 }
9250
TestStringConstraintDialogX(DialoG d)9251 static ValNodePtr TestStringConstraintDialogX (DialoG d)
9252
9253 {
9254 return NULL;
9255 }
9256
StringConstraintDialogX(GrouP h,CharPtr label,Boolean clear_btn)9257 extern DialoG StringConstraintDialogX (GrouP h, CharPtr label, Boolean clear_btn)
9258
9259 {
9260 StringConstraintDialogXPtr scdp;
9261 GrouP p, g, k;
9262 ButtoN b = NULL;
9263
9264 scdp = (StringConstraintDialogXPtr) MemNew (sizeof (StringConstraintDialogXData));
9265 if (scdp == NULL)
9266 {
9267 return NULL;
9268 }
9269
9270 p = HiddenGroup (h, -1, 0, NULL);
9271 SetObjectExtra (p, scdp, StdCleanupExtraProc);
9272
9273 scdp->dialog = (DialoG) p;
9274 scdp->todialog = StringConstraintToDialog;
9275 scdp->fromdialog = DialogToStringConstraint;
9276 scdp->dialogmessage = StringConstraintMessage;
9277 scdp->testdialog = TestStringConstraintDialogX;
9278
9279 g = HiddenGroup (p, 3, 0, NULL);
9280 SetGroupSpacing (g, 10, 10);
9281
9282 if (!StringHasNoText (label))
9283 {
9284 StaticPrompt (g, label, 0, dialogTextHeight, systemFont, 'l');
9285 }
9286
9287 scdp->match_choice = PopupList (g, TRUE, NULL);
9288 PopupItem (scdp->match_choice, "Contains");
9289 PopupItem (scdp->match_choice, "Does not contain");
9290 PopupItem (scdp->match_choice, "Equals");
9291 PopupItem (scdp->match_choice, "Does not equal");
9292 PopupItem (scdp->match_choice, "Starts with");
9293 PopupItem (scdp->match_choice, "Ends with");
9294 PopupItem (scdp->match_choice, "Is one of");
9295 PopupItem (scdp->match_choice, "Is not one of");
9296 PopupItem (scdp->match_choice, "Does not start with");
9297 PopupItem (scdp->match_choice, "Does not end with");
9298 SetValue (scdp->match_choice, 1);
9299 scdp->match_text = DialogText (g, "", 15, NULL);
9300
9301 k = HiddenGroup (p, 3, 0, NULL);
9302 SetGroupSpacing (k, 10, 10);
9303 scdp->insensitive = CheckBox (k, "Case Insensitive", NULL);
9304 scdp->whole_word = CheckBox (k, "Whole Word", NULL);
9305
9306 if (clear_btn)
9307 {
9308 b = PushButton (p, "Clear Constraint", ClearDialogBtn);
9309 SetObjectExtra (b, p, NULL);
9310 }
9311
9312 AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) k, (HANDLE) b, NULL);
9313
9314 return (DialoG) p;
9315 }
9316
9317
9318 typedef struct pseudoconstraintdialog
9319 {
9320 DIALOG_MESSAGE_BLOCK
9321 GrouP pseudo_choice;
9322 DialoG feature_choice;
9323 } PseudoConstraintDialogData, PNTR PseudoConstraintDialogPtr;
9324
ENUM_ALIST(pseudoconstraint_alist)9325 static ENUM_ALIST(pseudoconstraint_alist)
9326 {"Any Feature", FEATDEF_ANY },
9327 {"CDS", FEATDEF_CDS },
9328 {"Gene", FEATDEF_GENE },
9329 {"mRNA", FEATDEF_mRNA },
9330 END_ENUM_ALIST
9331
9332 static void ResetPseudoConstraintDialog (PseudoConstraintDialogPtr pcdp)
9333 {
9334 if (pcdp != NULL)
9335 {
9336 SetValue (pcdp->pseudo_choice, 1);
9337 SendMessageToDialog (pcdp->feature_choice, VIB_MSG_INIT);
9338 }
9339 }
9340
PseudoConstraintToDialog(DialoG d,Pointer data)9341 static void PseudoConstraintToDialog (DialoG d, Pointer data)
9342 {
9343 PseudoConstraintDialogPtr pcdp;
9344 PseudoConstraintPtr pcp;
9345 ValNode vn;
9346
9347 pcdp = (PseudoConstraintDialogPtr) GetObjectExtra (d);
9348
9349 if (pcdp != NULL)
9350 {
9351 ResetPseudoConstraintDialog (pcdp);
9352 pcp = (PseudoConstraintPtr) data;
9353 if (pcp != NULL)
9354 {
9355 if (pcp->is_pseudo)
9356 {
9357 SetValue (pcdp->pseudo_choice, 1);
9358 }
9359 else
9360 {
9361 SetValue (pcdp->pseudo_choice, 2);
9362 }
9363 vn.choice = pcp->featdef_type;
9364 vn.data.ptrvalue = NULL;
9365 vn.next = NULL;
9366 PointerToDialog (pcdp->feature_choice, &vn);
9367 }
9368 }
9369 }
9370
DialogToPseudoConstraint(DialoG d)9371 static Pointer DialogToPseudoConstraint (DialoG d)
9372 {
9373 PseudoConstraintDialogPtr pcdp;
9374 PseudoConstraintPtr pcp;
9375 ValNodePtr vnp;
9376
9377 pcdp = (PseudoConstraintDialogPtr) GetObjectExtra (d);
9378 if (pcdp == NULL) return NULL;
9379 pcp = (PseudoConstraintPtr) MemNew (sizeof (PseudoConstraintData));
9380 if (pcp != NULL)
9381 {
9382 if (GetValue (pcdp->pseudo_choice) == 1)
9383 {
9384 pcp->is_pseudo = TRUE;
9385 }
9386 else
9387 {
9388 pcp->is_pseudo = FALSE;
9389 }
9390 vnp = DialogToPointer (pcdp->feature_choice);
9391 if (vnp == NULL)
9392 {
9393 pcp->featdef_type = FEATDEF_ANY;
9394 }
9395 else
9396 {
9397 pcp->featdef_type = vnp->choice;
9398 }
9399 ValNodeFreeData (vnp);
9400 }
9401 return pcp;
9402 }
9403
PseudoConstraintMessage(DialoG d,Int2 mssg)9404 static void PseudoConstraintMessage (DialoG d, Int2 mssg)
9405
9406 {
9407 PseudoConstraintDialogPtr pcdp;
9408
9409 pcdp = (PseudoConstraintDialogPtr) GetObjectExtra (d);
9410 if (pcdp != NULL) {
9411 switch (mssg) {
9412 case VIB_MSG_INIT :
9413 ResetPseudoConstraintDialog (pcdp);
9414 break;
9415 case VIB_MSG_ENTER :
9416 Select (pcdp->feature_choice);
9417 break;
9418 default :
9419 break;
9420 }
9421 }
9422 }
9423
TestPseudoConstraintDialog(DialoG d)9424 static ValNodePtr TestPseudoConstraintDialog (DialoG d)
9425
9426 {
9427 return NULL;
9428 }
9429
PseudoConstraintDialog(GrouP h)9430 static DialoG PseudoConstraintDialog (GrouP h)
9431 {
9432 PseudoConstraintDialogPtr pcdp;
9433 GrouP p;
9434
9435 pcdp = (PseudoConstraintDialogPtr) MemNew (sizeof (PseudoConstraintDialogData));
9436 if (pcdp == NULL)
9437 {
9438 return NULL;
9439 }
9440
9441 p = HiddenGroup (h, 2, 0, NULL);
9442 SetObjectExtra (p, pcdp, StdCleanupExtraProc);
9443 SetGroupSpacing (p, 10, 10);
9444
9445 pcdp->dialog = (DialoG) p;
9446 pcdp->todialog = PseudoConstraintToDialog;
9447 pcdp->fromdialog = DialogToPseudoConstraint;
9448 pcdp->dialogmessage = PseudoConstraintMessage;
9449 pcdp->testdialog = TestPseudoConstraintDialog;
9450
9451 pcdp->feature_choice = EnumAssocSelectionDialog (p, pseudoconstraint_alist,
9452 "feature", FALSE, NULL, NULL);
9453
9454 pcdp->pseudo_choice = HiddenGroup (p, 2, 0, NULL);
9455 RadioButton (pcdp->pseudo_choice, "Is Pseudo");
9456 RadioButton (pcdp->pseudo_choice, "Is Not Pseudo");
9457 SetValue (pcdp->pseudo_choice, 1);
9458
9459 return (DialoG) p;
9460 }
9461
9462 typedef struct choiceconstraintdialog
9463 {
9464 DIALOG_MESSAGE_BLOCK
9465 GrouP constraint_type;
9466 DialoG present_qual_choice;
9467 DialoG string_qual_choice;
9468 DialoG string_constraint;
9469 DialoG pseudo_constraint;
9470 DialoG match_1;
9471 DialoG match_2;
9472 FreeValNodeProc free_vn_proc;
9473 CopyValNodeDataProc copy_vn_proc;
9474 } ChoiceConstraintDialogData, PNTR ChoiceConstraintDialogPtr;
9475
ChangeChoiceConstraintType(GrouP p)9476 static void ChangeChoiceConstraintType (GrouP p)
9477 {
9478 ChoiceConstraintDialogPtr scdp;
9479 Int4 constraint_type;
9480
9481 scdp = (ChoiceConstraintDialogPtr) GetObjectExtra (p);
9482 if (scdp == NULL)
9483 {
9484 return;
9485 }
9486
9487 constraint_type = GetValue (scdp->constraint_type);
9488 if (constraint_type == CHOICE_CONSTRAINT_QUAL_PRESENT)
9489 {
9490 Enable (scdp->present_qual_choice);
9491 Disable (scdp->string_qual_choice);
9492 Disable (scdp->string_constraint);
9493 Disable (scdp->match_1);
9494 Disable (scdp->match_2);
9495 SafeDisable (scdp->pseudo_constraint);
9496 }
9497 else if (constraint_type == CHOICE_CONSTRAINT_STRING)
9498 {
9499 Enable (scdp->string_qual_choice);
9500 Enable (scdp->string_constraint);
9501 Disable (scdp->present_qual_choice);
9502 Disable (scdp->match_1);
9503 Disable (scdp->match_2);
9504 SafeDisable (scdp->pseudo_constraint);
9505 }
9506 else if (constraint_type == CHOICE_CONSTRAINT_MATCH)
9507 {
9508 Enable (scdp->match_1);
9509 Enable (scdp->match_2);
9510 Disable (scdp->string_qual_choice);
9511 Disable (scdp->string_constraint);
9512 Disable (scdp->present_qual_choice);
9513 SafeDisable (scdp->pseudo_constraint);
9514 }
9515 else if (constraint_type == CHOICE_CONSTRAINT_PSEUDO)
9516 {
9517 Disable (scdp->present_qual_choice);
9518 Disable (scdp->string_qual_choice);
9519 Disable (scdp->string_constraint);
9520 Disable (scdp->match_1);
9521 Disable (scdp->match_2);
9522 Enable (scdp->pseudo_constraint);
9523 }
9524 else
9525 {
9526 Disable (scdp->present_qual_choice);
9527 Disable (scdp->string_qual_choice);
9528 Disable (scdp->string_constraint);
9529 Disable (scdp->match_1);
9530 Disable (scdp->match_2);
9531 SafeDisable (scdp->pseudo_constraint);
9532 }
9533 }
9534
ResetChoiceConstraintDialog(ChoiceConstraintDialogPtr scdp)9535 static void ResetChoiceConstraintDialog (ChoiceConstraintDialogPtr scdp)
9536 {
9537 if (scdp != NULL)
9538 {
9539 SetValue (scdp->constraint_type, CHOICE_CONSTRAINT_ANY);
9540 PointerToDialog (scdp->present_qual_choice, NULL);
9541 PointerToDialog (scdp->string_qual_choice, NULL);
9542 PointerToDialog (scdp->string_constraint, NULL);
9543 PointerToDialog (scdp->pseudo_constraint, NULL);
9544 ChangeChoiceConstraintType (scdp->constraint_type);
9545 }
9546 }
9547
ChoiceConstraintToDialog(DialoG d,Pointer data)9548 static void ChoiceConstraintToDialog (DialoG d, Pointer data)
9549 {
9550 ChoiceConstraintDialogPtr src_dlg;
9551 ChoiceConstraintPtr src_data;
9552 Int4 constraint_type;
9553
9554 src_dlg = (ChoiceConstraintDialogPtr) GetObjectExtra (d);
9555 if (src_dlg == NULL)
9556 {
9557 return;
9558 }
9559 src_data = (ChoiceConstraintPtr) data;
9560 if (src_data == NULL)
9561 {
9562 ResetChoiceConstraintDialog (src_dlg);
9563 }
9564 else
9565 {
9566 constraint_type = src_data->constraint_type;
9567 if (constraint_type < CHOICE_CONSTRAINT_ANY || constraint_type > CHOICE_CONSTRAINT_PSEUDO)
9568 {
9569 constraint_type = CHOICE_CONSTRAINT_ANY;
9570 }
9571 SetValue (src_dlg->constraint_type, constraint_type);
9572 if (constraint_type == CHOICE_CONSTRAINT_QUAL_PRESENT)
9573 {
9574 PointerToDialog (src_dlg->present_qual_choice, src_data->qual_choice);
9575 }
9576 else if (constraint_type == CHOICE_CONSTRAINT_STRING)
9577 {
9578 PointerToDialog (src_dlg->string_qual_choice, src_data->qual_choice);
9579 PointerToDialog (src_dlg->string_constraint, src_data->string_constraint);
9580 }
9581 else if (constraint_type == CHOICE_CONSTRAINT_MATCH)
9582 {
9583 PointerToDialog (src_dlg->match_1, src_data->qual_choice);
9584 PointerToDialog (src_dlg->match_2, src_data->qual_choice_match);
9585 }
9586 else if (constraint_type == CHOICE_CONSTRAINT_PSEUDO)
9587 {
9588 PointerToDialog (src_dlg->pseudo_constraint, src_data->pseudo_constraint);
9589 }
9590 ChangeChoiceConstraintType (src_dlg->constraint_type);
9591 }
9592 }
9593
DialogToChoiceConstraint(DialoG d)9594 static Pointer DialogToChoiceConstraint (DialoG d)
9595 {
9596 ChoiceConstraintDialogPtr src_dlg;
9597 ChoiceConstraintPtr src_data;
9598
9599 src_dlg = (ChoiceConstraintDialogPtr) GetObjectExtra (d);
9600 if (src_dlg == NULL)
9601 {
9602 return NULL;
9603 }
9604
9605 src_data = (ChoiceConstraintPtr) MemNew (sizeof (ChoiceConstraintData));
9606 if (src_data != NULL)
9607 {
9608 src_data->constraint_type = GetValue (src_dlg->constraint_type);
9609 if (src_data->constraint_type == CHOICE_CONSTRAINT_QUAL_PRESENT)
9610 {
9611 src_data->qual_choice = DialogToPointer (src_dlg->present_qual_choice);
9612 }
9613 else if (src_data->constraint_type == CHOICE_CONSTRAINT_STRING)
9614 {
9615 src_data->qual_choice = DialogToPointer (src_dlg->string_qual_choice);
9616 src_data->string_constraint = DialogToPointer (src_dlg->string_constraint);
9617 }
9618 else if (src_data->constraint_type == CHOICE_CONSTRAINT_MATCH)
9619 {
9620 src_data->qual_choice = DialogToPointer (src_dlg->match_1);
9621 src_data->qual_choice_match = DialogToPointer (src_dlg->match_2);
9622 }
9623 else if (src_data->constraint_type == CHOICE_CONSTRAINT_PSEUDO)
9624 {
9625 src_data->pseudo_constraint = DialogToPointer (src_dlg->pseudo_constraint);
9626 }
9627 src_data->free_vn_proc = src_dlg->free_vn_proc;
9628 src_data->copy_vn_proc = src_dlg->copy_vn_proc;
9629 }
9630 return src_data;
9631 }
9632
ChoiceConstraintMessage(DialoG d,Int2 mssg)9633 static void ChoiceConstraintMessage (DialoG d, Int2 mssg)
9634
9635 {
9636 ChoiceConstraintDialogPtr scdp;
9637
9638 scdp = (ChoiceConstraintDialogPtr) GetObjectExtra (d);
9639 if (scdp != NULL) {
9640 switch (mssg) {
9641 case VIB_MSG_INIT :
9642 ResetChoiceConstraintDialog (scdp);
9643 break;
9644 case VIB_MSG_ENTER :
9645 Select (scdp->constraint_type);
9646 break;
9647 default :
9648 break;
9649 }
9650 }
9651 }
9652
TestChoiceConstraintDialog(DialoG d)9653 static ValNodePtr TestChoiceConstraintDialog (DialoG d)
9654
9655 {
9656 return NULL;
9657 }
9658
9659 extern DialoG
ConstraintChoiceDialog(GrouP h,FeatureFieldSelectionProc func_present,FeatureFieldSelectionProc func_string,FreeValNodeProc free_vn_proc,CopyValNodeDataProc copy_vn_proc,CharPtr any_name,CharPtr present_name,Boolean clear_btn,Boolean use_pseudo)9660 ConstraintChoiceDialog
9661 (GrouP h,
9662 FeatureFieldSelectionProc func_present,
9663 FeatureFieldSelectionProc func_string,
9664 FreeValNodeProc free_vn_proc,
9665 CopyValNodeDataProc copy_vn_proc,
9666 CharPtr any_name,
9667 CharPtr present_name,
9668 Boolean clear_btn,
9669 Boolean use_pseudo)
9670 {
9671 ChoiceConstraintDialogPtr scdp;
9672 GrouP p, q;
9673 ButtoN b = NULL;
9674
9675 scdp = (ChoiceConstraintDialogPtr) MemNew (sizeof (ChoiceConstraintDialogData));
9676 if (scdp == NULL)
9677 {
9678 return NULL;
9679 }
9680
9681 p = HiddenGroup (h, -1, 0, NULL);
9682 SetObjectExtra (p, scdp, StdCleanupExtraProc);
9683 SetGroupSpacing (p, 10, 10);
9684
9685 scdp->dialog = (DialoG) p;
9686 scdp->todialog = ChoiceConstraintToDialog;
9687 scdp->fromdialog = DialogToChoiceConstraint;
9688 scdp->dialogmessage = ChoiceConstraintMessage;
9689 scdp->testdialog = TestChoiceConstraintDialog;
9690
9691 scdp->constraint_type = HiddenGroup (p, 2, 0, ChangeChoiceConstraintType);
9692 RadioButton (scdp->constraint_type, any_name);
9693 StaticPrompt (scdp->constraint_type, "", 0, dialogTextHeight, systemFont, 'l');
9694
9695 RadioButton (scdp->constraint_type, present_name);
9696 scdp->present_qual_choice = func_present (scdp->constraint_type, FALSE, NULL, NULL);
9697
9698 RadioButton (scdp->constraint_type, "When");
9699 q = HiddenGroup (scdp->constraint_type, 2, 0, NULL);
9700 scdp->string_qual_choice = func_string (q, TRUE, NULL, NULL);
9701 scdp->string_constraint = StringConstraintDialogX (q, NULL, FALSE);
9702
9703 RadioButton (scdp->constraint_type, "When");
9704 q = HiddenGroup (scdp->constraint_type, 3, 0, NULL);
9705 scdp->match_1 = func_string (q, TRUE, NULL, NULL);
9706 StaticPrompt (q, "Equals", 0, dialogTextHeight, systemFont, 'l');
9707 scdp->match_2 = func_string (q, TRUE, NULL, NULL);
9708
9709 if (use_pseudo)
9710 {
9711 RadioButton (scdp->constraint_type, "When");
9712 scdp->pseudo_constraint = PseudoConstraintDialog (scdp->constraint_type);
9713 }
9714 else
9715 {
9716 scdp->pseudo_constraint = NULL;
9717 }
9718
9719 SetValue (scdp->constraint_type, CHOICE_CONSTRAINT_ANY);
9720 SetObjectExtra (scdp->constraint_type, scdp, NULL);
9721
9722 Disable (scdp->present_qual_choice);
9723 Disable (scdp->string_qual_choice);
9724 Disable (scdp->string_constraint);
9725 Disable (scdp->match_1);
9726 Disable (scdp->match_2);
9727
9728 scdp->free_vn_proc = free_vn_proc;
9729 scdp->copy_vn_proc = copy_vn_proc;
9730
9731 if (clear_btn)
9732 {
9733 b = PushButton (p, "Clear Constraint", ClearDialogBtn);
9734 SetObjectExtra (b, p, NULL);
9735 }
9736
9737 AlignObjects (ALIGN_CENTER, (HANDLE) scdp->constraint_type, (HANDLE) b, NULL);
9738
9739 return (DialoG) p;
9740 }
9741
SourceConstraintDialogX(GrouP h,Boolean clear_btn)9742 extern DialoG SourceConstraintDialogX (GrouP h, Boolean clear_btn)
9743 {
9744 return ConstraintChoiceDialog (h, SourceQualTypeConstraintSelectionDialog,
9745 SourceStringConstraintSelectionDialog,
9746 ValNodeSimpleDataFree,
9747 SourceQualValNodeDataCopy,
9748 "For any source", "When qualifier present:",
9749 clear_btn,
9750 FALSE);
9751 }
9752
9753
CDSGeneProtConstraintDialog(GrouP h,Boolean clear_btn)9754 extern DialoG CDSGeneProtConstraintDialog (GrouP h, Boolean clear_btn)
9755 {
9756 return ConstraintChoiceDialog (h, CDSGeneProtFieldSelectionDialog,
9757 CDSGeneProtFieldConstraintSelectionDialog,
9758 NULL, IntValNodeCopy,
9759 "For any CDS-Gene-Prot-mRNA set",
9760 "When field present:",
9761 clear_btn, TRUE);
9762 }
9763
9764 typedef struct LocationConstraintXdialog
9765 {
9766 DIALOG_MESSAGE_BLOCK
9767 PopuP interval_end_choice;
9768 PopuP interval_match_choice;
9769 PopuP endpoint_match_choice;
9770 TexT only_val;
9771 TexT first_val;
9772 TexT second_val;
9773 PrompT second_val_prompt;
9774 PopuP strand;
9775 PopuP sequence_type;
9776 Boolean show_interval_controls;
9777 } LocationConstraintXDialogData, PNTR LocationConstraintXDialogPtr;
9778
ShowLocationChoiceControls(PopuP p)9779 static void ShowLocationChoiceControls (PopuP p)
9780
9781 {
9782 LocationConstraintXDialogPtr lcdp;
9783 Int4 match_choice;
9784
9785 lcdp = (LocationConstraintXDialogPtr) GetObjectExtra (p);
9786 if (lcdp == NULL || lcdp->interval_end_choice == NULL) return;
9787
9788 if (GetValue (lcdp->interval_end_choice) == LOCATION_CONSTRAINT_WHOLE_INTERVAL)
9789 {
9790 Show (lcdp->interval_match_choice);
9791 Hide (lcdp->endpoint_match_choice);
9792 if (p == lcdp->interval_end_choice)
9793 {
9794 SetValue (lcdp->interval_match_choice, GetValue (lcdp->endpoint_match_choice));
9795 }
9796 match_choice = GetValue (lcdp->interval_match_choice);
9797 }
9798 else
9799 {
9800 Hide (lcdp->interval_match_choice);
9801 Show (lcdp->endpoint_match_choice);
9802 if (p == lcdp->interval_end_choice)
9803 {
9804 SetValue (lcdp->endpoint_match_choice, GetValue (lcdp->interval_match_choice));
9805 }
9806 match_choice = GetValue (lcdp->endpoint_match_choice);
9807 }
9808
9809 switch (match_choice)
9810 {
9811 case LOCATION_CONSTRAINT_ANY :
9812 Hide (lcdp->only_val);
9813 Hide (lcdp->first_val);
9814 Hide (lcdp->second_val_prompt);
9815 Hide (lcdp->second_val);
9816 break;
9817 case LOCATION_CONSTRAINT_UPSTREAM :
9818 case LOCATION_CONSTRAINT_DOWNSTREAM :
9819 Show (lcdp->only_val);
9820 Hide (lcdp->first_val);
9821 Hide (lcdp->second_val_prompt);
9822 Hide (lcdp->second_val);
9823 break;
9824 case LOCATION_CONSTRAINT_CONTAINED :
9825 case LOCATION_CONSTRAINT_NOT_IN :
9826 case LOCATION_CONSTRAINT_OVERLAP :
9827 case LOCATION_CONSTRAINT_EQUAL :
9828 Hide (lcdp->only_val);
9829 Show (lcdp->first_val);
9830 Show (lcdp->second_val_prompt);
9831 Show (lcdp->second_val);
9832 break;
9833 }
9834 }
9835
ResetLocationConstraintXDialog(LocationConstraintXDialogPtr lcdp)9836 static void ResetLocationConstraintXDialog (LocationConstraintXDialogPtr lcdp)
9837 {
9838 if (lcdp == NULL) return;
9839
9840 SafeSetValue (lcdp->interval_end_choice, LOCATION_CONSTRAINT_WHOLE_INTERVAL);
9841 SafeSetValue (lcdp->interval_match_choice, LOCATION_CONSTRAINT_ANY);
9842 SafeSetTitle (lcdp->only_val, "");
9843 SafeSetTitle (lcdp->first_val, "");
9844 SafeSetTitle (lcdp->second_val, "");
9845 SetValue (lcdp->strand, LOCATION_CONSTRAINT_ANY_STRAND);
9846 SetValue (lcdp->sequence_type, LOCATION_CONSTRAINT_ANY_SEQ);
9847 ShowLocationChoiceControls (lcdp->interval_end_choice);
9848 }
9849
LocationConstraintXToDialog(DialoG d,Pointer data)9850 static void LocationConstraintXToDialog (DialoG d, Pointer data)
9851
9852 {
9853 LocationConstraintXDialogPtr lcdp;
9854 LocationConstraintXPtr lcp;
9855 Int4 interval_end_choice;
9856 Int4 match_choice;
9857 Char tmp [15];
9858 Int4 strand;
9859 Int4 sequence_type;
9860
9861 lcdp = (LocationConstraintXDialogPtr) GetObjectExtra (d);
9862 if (lcdp == NULL)
9863 {
9864 return;
9865 }
9866 lcp = (LocationConstraintXPtr) data;
9867
9868 ResetLocationConstraintXDialog (lcdp);
9869 if (lcp != NULL)
9870 {
9871 interval_end_choice = lcp->interval_end_choice;
9872 if (interval_end_choice < LOCATION_CONSTRAINT_WHOLE_INTERVAL
9873 || interval_end_choice > LOCATION_CONSTRAINT_STOP_ENDPOINT)
9874 {
9875 interval_end_choice = LOCATION_CONSTRAINT_WHOLE_INTERVAL;
9876 }
9877 match_choice = lcp->match_choice;
9878 if (match_choice < LOCATION_CONSTRAINT_ANY)
9879 {
9880 match_choice = LOCATION_CONSTRAINT_ANY;
9881 }
9882 else if (match_choice > LOCATION_CONSTRAINT_EQUAL)
9883 {
9884 match_choice = LOCATION_CONSTRAINT_EQUAL;
9885 }
9886 if (match_choice > LOCATION_CONSTRAINT_NOT_IN && interval_end_choice != LOCATION_CONSTRAINT_WHOLE_INTERVAL)
9887 {
9888 interval_end_choice = LOCATION_CONSTRAINT_WHOLE_INTERVAL;
9889 }
9890
9891 SetValue (lcdp->interval_end_choice, interval_end_choice);
9892 if (interval_end_choice == LOCATION_CONSTRAINT_WHOLE_INTERVAL)
9893 {
9894 SetValue (lcdp->interval_match_choice, match_choice);
9895 }
9896 else
9897 {
9898 SetValue (lcdp->endpoint_match_choice, match_choice);
9899 }
9900 switch (match_choice)
9901 {
9902 case LOCATION_CONSTRAINT_ANY :
9903 break;
9904 case LOCATION_CONSTRAINT_UPSTREAM :
9905 case LOCATION_CONSTRAINT_DOWNSTREAM :
9906 if (lcp->left >= 0)
9907 {
9908 sprintf (tmp, "%d", lcp->left + 1);
9909 SetTitle (lcdp->only_val, tmp);
9910 }
9911 break;
9912 case LOCATION_CONSTRAINT_CONTAINED :
9913 case LOCATION_CONSTRAINT_NOT_IN :
9914 case LOCATION_CONSTRAINT_OVERLAP :
9915 case LOCATION_CONSTRAINT_EQUAL :
9916 if (lcp->left >= 0)
9917 {
9918 sprintf (tmp, "%d", lcp->left + 1);
9919 SetTitle (lcdp->first_val, tmp);
9920 }
9921 if (lcp->right >= 0)
9922 {
9923 sprintf (tmp, "%d", lcp->right + 1);
9924 SetTitle (lcdp->second_val, tmp);
9925 }
9926 break;
9927 }
9928 strand = lcp->strand;
9929 if (strand < LOCATION_CONSTRAINT_ANY_STRAND || strand > LOCATION_CONSTRAINT_MINUS_STRAND)
9930 {
9931 strand = LOCATION_CONSTRAINT_ANY_STRAND;
9932 }
9933 SetValue (lcdp->strand, strand);
9934 sequence_type = lcp->sequence_type;
9935 if (sequence_type < LOCATION_CONSTRAINT_ANY_SEQ || sequence_type > LOCATION_CONSTRAINT_PROT_SEQ)
9936 {
9937 sequence_type = LOCATION_CONSTRAINT_ANY_SEQ;
9938 }
9939 SetValue (lcdp->sequence_type, LOCATION_CONSTRAINT_ANY_SEQ);
9940 }
9941 ShowLocationChoiceControls (lcdp->interval_match_choice);
9942 }
9943
DialogToLocationConstraintX(DialoG d)9944 static Pointer DialogToLocationConstraintX (DialoG d)
9945
9946 {
9947 LocationConstraintXDialogPtr lcdp;
9948 LocationConstraintXPtr lcp;
9949 CharPtr tmp;
9950
9951 lcdp = (LocationConstraintXDialogPtr) GetObjectExtra (d);
9952 if (lcdp == NULL)
9953 {
9954 return NULL;
9955 }
9956 lcp = (LocationConstraintXPtr) MemNew (sizeof (LocationConstraintXData));
9957 if (lcp != NULL)
9958 {
9959 if (lcdp->show_interval_controls)
9960 {
9961 lcp->interval_end_choice = GetValue (lcdp->interval_end_choice);
9962 if (lcp->interval_end_choice == LOCATION_CONSTRAINT_WHOLE_INTERVAL)
9963 {
9964 lcp->match_choice = GetValue (lcdp->interval_match_choice);
9965 }
9966 else
9967 {
9968 lcp->match_choice = GetValue (lcdp->endpoint_match_choice);
9969 }
9970 switch (lcp->match_choice)
9971 {
9972 case LOCATION_CONSTRAINT_ANY :
9973 break;
9974 case LOCATION_CONSTRAINT_UPSTREAM :
9975 case LOCATION_CONSTRAINT_DOWNSTREAM :
9976 tmp = SaveStringFromText (lcdp->only_val);
9977 if (StringHasNoText (tmp))
9978 {
9979 lcp->left = 0;
9980 }
9981 else
9982 {
9983 lcp->left = atoi (tmp) - 1;
9984 }
9985 tmp = MemFree (tmp);
9986 break;
9987 case LOCATION_CONSTRAINT_CONTAINED :
9988 case LOCATION_CONSTRAINT_NOT_IN :
9989 case LOCATION_CONSTRAINT_OVERLAP :
9990 case LOCATION_CONSTRAINT_EQUAL :
9991 tmp = SaveStringFromText (lcdp->first_val);
9992 if (StringHasNoText (tmp))
9993 {
9994 lcp->left = 0;
9995 }
9996 else
9997 {
9998 lcp->left = atoi (tmp) - 1;
9999 }
10000 tmp = MemFree (tmp);
10001 tmp = SaveStringFromText (lcdp->second_val);
10002 if (StringHasNoText (tmp))
10003 {
10004 lcp->right = 0;
10005 }
10006 else
10007 {
10008 lcp->right = atoi (tmp) - 1;
10009 }
10010 tmp = MemFree (tmp);
10011 break;
10012 }
10013 }
10014 else
10015 {
10016 lcp->match_choice = LOCATION_CONSTRAINT_ANY;
10017 lcp->left = 0;
10018 lcp->right = 0;
10019 }
10020 lcp->strand = GetValue (lcdp->strand);
10021 lcp->sequence_type = GetValue (lcdp->sequence_type);
10022 }
10023 return lcp;
10024 }
10025
LocationConstraintXMessage(DialoG d,Int2 mssg)10026 static void LocationConstraintXMessage (DialoG d, Int2 mssg)
10027
10028 {
10029 LocationConstraintXDialogPtr lcdp;
10030
10031 lcdp = (LocationConstraintXDialogPtr) GetObjectExtra (d);
10032 if (lcdp != NULL) {
10033 switch (mssg) {
10034 case VIB_MSG_INIT :
10035 ResetLocationConstraintXDialog (lcdp);
10036 break;
10037 case VIB_MSG_ENTER :
10038 if (lcdp->show_interval_controls)
10039 {
10040 Select (lcdp->interval_end_choice);
10041 }
10042 else
10043 {
10044 Select (lcdp->strand);
10045 }
10046 break;
10047 default :
10048 break;
10049 }
10050 }
10051 }
10052
TestLocationConstraintXDialog(DialoG d)10053 static ValNodePtr TestLocationConstraintXDialog (DialoG d)
10054
10055 {
10056 return NULL;
10057 }
10058
10059
10060 extern DialoG
LocationConstraintXDialog(GrouP h,Boolean show_interval_controls,Boolean clear_btn)10061 LocationConstraintXDialog
10062 (GrouP h,
10063 Boolean show_interval_controls,
10064 Boolean clear_btn)
10065
10066 {
10067 LocationConstraintXDialogPtr lcdp;
10068 GrouP p, g, k, val_grp, strand_grp, g2, g3, g4;
10069 ButtoN b = NULL;
10070
10071 lcdp = (LocationConstraintXDialogPtr) MemNew (sizeof (LocationConstraintXDialogData));
10072 if (lcdp == NULL)
10073 {
10074 return NULL;
10075 }
10076
10077 p = HiddenGroup (h, -1, 0, NULL);
10078 SetObjectExtra (p, lcdp, StdCleanupExtraProc);
10079
10080 lcdp->dialog = (DialoG) p;
10081 lcdp->todialog = LocationConstraintXToDialog;
10082 lcdp->fromdialog = DialogToLocationConstraintX;
10083 lcdp->dialogmessage = LocationConstraintXMessage;
10084 lcdp->testdialog = TestLocationConstraintXDialog;
10085
10086 lcdp->show_interval_controls = show_interval_controls;
10087
10088 if (lcdp->show_interval_controls)
10089 {
10090 g = HiddenGroup (p, 6, 0, NULL);
10091 SetGroupSpacing (g, 10, 10);
10092 lcdp->interval_end_choice = PopupList (g, TRUE, ShowLocationChoiceControls);
10093 PopupItem (lcdp->interval_end_choice, "Entire location");
10094 PopupItem (lcdp->interval_end_choice, "Start");
10095 PopupItem (lcdp->interval_end_choice, "Stop");
10096 SetValue (lcdp->interval_end_choice, 1);
10097 SetObjectExtra (lcdp->interval_end_choice, lcdp, NULL);
10098
10099 StaticPrompt (g, "is", 0, dialogTextHeight, systemFont, 'l');
10100
10101 k = HiddenGroup (g, 0, 0, NULL);
10102 lcdp->interval_match_choice = PopupList (k, TRUE, ShowLocationChoiceControls);
10103 PopupItem (lcdp->interval_match_choice, "Any location");
10104 PopupItem (lcdp->interval_match_choice, "Upstream from");
10105 PopupItem (lcdp->interval_match_choice, "Downstream from");
10106 PopupItem (lcdp->interval_match_choice, "Contained in");
10107 PopupItem (lcdp->interval_match_choice, "Not in");
10108 PopupItem (lcdp->interval_match_choice, "Overlaps");
10109 PopupItem (lcdp->interval_match_choice, "Equal to");
10110 SetValue (lcdp->interval_match_choice, 1);
10111 SetObjectExtra (lcdp->interval_match_choice, lcdp, NULL);
10112
10113 lcdp->endpoint_match_choice = PopupList (k, TRUE, ShowLocationChoiceControls);
10114 PopupItem (lcdp->endpoint_match_choice, "Any location");
10115 PopupItem (lcdp->endpoint_match_choice, "Upstream from");
10116 PopupItem (lcdp->endpoint_match_choice, "Downstream from");
10117 PopupItem (lcdp->endpoint_match_choice, "Contained in");
10118 PopupItem (lcdp->endpoint_match_choice, "Not in");
10119 SetValue (lcdp->endpoint_match_choice, 1);
10120 SetObjectExtra (lcdp->endpoint_match_choice, lcdp, NULL);
10121
10122 g2 = HiddenGroup (g, 2, 0, NULL);
10123 SetGroupSpacing (g2, 10, 10);
10124 val_grp = HiddenGroup (g2, 0, 0, NULL);
10125 lcdp->only_val = DialogText (val_grp, "", 5, NULL);
10126 g3 = HiddenGroup (val_grp, 3, 0, NULL);
10127 lcdp->first_val = DialogText (g3, "", 5, NULL);
10128 lcdp->second_val_prompt = StaticPrompt (g3, "to", 0, dialogTextHeight, systemFont, 'l');
10129 lcdp->second_val = DialogText (g3, "", 5, NULL);
10130 AlignObjects (ALIGN_CENTER, (HANDLE) lcdp->only_val, (HANDLE) g3, NULL);
10131 }
10132 else
10133 {
10134 g = HiddenGroup (p, 2, 0, NULL);
10135 }
10136
10137 strand_grp = HiddenGroup (g, 2, 0, NULL);
10138 StaticPrompt (strand_grp, "on", 0, dialogTextHeight, systemFont, 'l');
10139 lcdp->strand = PopupList (strand_grp, TRUE, NULL);
10140 PopupItem (lcdp->strand, "Any strand");
10141 PopupItem (lcdp->strand, "Plus strand");
10142 PopupItem (lcdp->strand, "Minus strand");
10143 SetValue (lcdp->strand, LOCATION_CONSTRAINT_ANY_STRAND);
10144
10145 g4 = HiddenGroup (g, 3, 0, NULL);
10146 SetGroupSpacing (g4, 10, 10);
10147 StaticPrompt (g4, "on", 0, dialogTextHeight, systemFont, 'l');
10148 lcdp->sequence_type = PopupList (g4, TRUE, NULL);
10149 PopupItem (lcdp->sequence_type, "nucleotide and protein sequences");
10150 PopupItem (lcdp->sequence_type, "nucleotide sequences only");
10151 PopupItem (lcdp->sequence_type, "protein sequences only");
10152 SetValue (lcdp->sequence_type, LOCATION_CONSTRAINT_ANY_SEQ);
10153
10154 if (clear_btn)
10155 {
10156 b = PushButton (p, "Clear Constraint", ClearDialogBtn);
10157 SetObjectExtra (b, p, NULL);
10158 }
10159
10160 AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) b, NULL);
10161
10162 ShowLocationChoiceControls (lcdp->interval_match_choice);
10163 return (DialoG) p;
10164 }
10165
DoesStrandMatchConstraint(SeqLocPtr slp,LocationConstraintXPtr lcp)10166 static Boolean DoesStrandMatchConstraint (SeqLocPtr slp, LocationConstraintXPtr lcp)
10167 {
10168 Uint2 strand;
10169 Boolean rval = FALSE;
10170
10171 if (slp == NULL)
10172 {
10173 rval = FALSE;
10174 }
10175 else if (lcp == NULL || lcp->strand == LOCATION_CONSTRAINT_ANY_STRAND)
10176 {
10177 rval = TRUE;
10178 }
10179 else
10180 {
10181 strand = SeqLocStrand (slp);
10182 if (strand == Seq_strand_minus)
10183 {
10184 if (lcp->strand == LOCATION_CONSTRAINT_MINUS_STRAND)
10185 {
10186 rval = TRUE;
10187 }
10188 else
10189 {
10190 rval = FALSE;
10191 }
10192 }
10193 else
10194 {
10195 if (lcp->strand == LOCATION_CONSTRAINT_PLUS_STRAND)
10196 {
10197 rval = TRUE;
10198 }
10199 else
10200 {
10201 rval = FALSE;
10202 }
10203 }
10204 }
10205 return rval;
10206 }
10207
DoesSequenceTypeMatchContraint(SeqLocPtr slp,LocationConstraintXPtr lcp)10208 static Boolean DoesSequenceTypeMatchContraint (SeqLocPtr slp, LocationConstraintXPtr lcp)
10209 {
10210 Boolean rval = FALSE;
10211 BioseqPtr bsp;
10212
10213 if (slp == NULL)
10214 {
10215 rval = FALSE;
10216 }
10217 else if (lcp == NULL || lcp->sequence_type == LOCATION_CONSTRAINT_ANY_SEQ)
10218 {
10219 rval = TRUE;
10220 }
10221 else
10222 {
10223 bsp = BioseqFindFromSeqLoc (slp);
10224 if (bsp != NULL)
10225 {
10226 if (ISA_na (bsp->mol) && lcp->sequence_type == LOCATION_CONSTRAINT_NUC_SEQ)
10227 {
10228 rval = TRUE;
10229 }
10230 else if (ISA_aa (bsp->mol) && lcp->sequence_type == LOCATION_CONSTRAINT_PROT_SEQ)
10231 {
10232 rval = TRUE;
10233 }
10234 }
10235 }
10236 return rval;
10237 }
10238
DoesLocationMatchConstraint(SeqLocPtr slp,LocationConstraintXPtr lcp)10239 extern Boolean DoesLocationMatchConstraint (SeqLocPtr slp, LocationConstraintXPtr lcp)
10240
10241 {
10242 Boolean rval = FALSE;
10243 Int4 loc_start, loc_stop, endpoint = 0;
10244
10245 if (slp == NULL)
10246 {
10247 return FALSE;
10248 }
10249
10250 if (lcp == NULL)
10251 {
10252 rval = TRUE;
10253 }
10254 else if (! DoesStrandMatchConstraint (slp, lcp))
10255 {
10256 rval = FALSE;
10257 }
10258 else if (! DoesSequenceTypeMatchContraint (slp, lcp))
10259 {
10260 rval = FALSE;
10261 }
10262 else
10263 {
10264 switch (lcp->match_choice)
10265 {
10266 case LOCATION_CONSTRAINT_ANY :
10267 rval = TRUE;
10268 break;
10269 case LOCATION_CONSTRAINT_UPSTREAM :
10270 if (lcp->interval_end_choice == LOCATION_CONSTRAINT_WHOLE_INTERVAL
10271 || lcp->interval_end_choice == LOCATION_CONSTRAINT_STOP_ENDPOINT)
10272 {
10273 endpoint = SeqLocStop (slp);
10274 }
10275 else
10276 {
10277 endpoint = SeqLocStart (slp);
10278 }
10279 if (endpoint < lcp->left)
10280 {
10281 rval = TRUE;
10282 }
10283 break;
10284 case LOCATION_CONSTRAINT_DOWNSTREAM :
10285 if (lcp->interval_end_choice == LOCATION_CONSTRAINT_WHOLE_INTERVAL
10286 || lcp->interval_end_choice == LOCATION_CONSTRAINT_START_ENDPOINT)
10287 {
10288 endpoint = SeqLocStart (slp);
10289 }
10290 else
10291 {
10292 endpoint = SeqLocStop (slp);
10293 }
10294 if (endpoint > lcp->left)
10295 {
10296 rval = TRUE;
10297 }
10298 break;
10299 case LOCATION_CONSTRAINT_CONTAINED :
10300 if (lcp->interval_end_choice == LOCATION_CONSTRAINT_WHOLE_INTERVAL)
10301 {
10302 loc_start = SeqLocStart (slp);
10303 loc_stop = SeqLocStop (slp);
10304 }
10305 else
10306 {
10307 if (lcp->interval_end_choice == LOCATION_CONSTRAINT_START_ENDPOINT)
10308 {
10309 endpoint = SeqLocStart (slp);
10310 }
10311 else
10312 {
10313 endpoint = SeqLocStop (slp);
10314 }
10315 loc_start = endpoint;
10316 loc_stop = endpoint;
10317 }
10318 if (loc_start >= lcp->left && loc_stop <= lcp->right)
10319 {
10320 rval = TRUE;
10321 }
10322 break;
10323 case LOCATION_CONSTRAINT_NOT_IN :
10324 if (lcp->interval_end_choice == LOCATION_CONSTRAINT_WHOLE_INTERVAL)
10325 {
10326 loc_start = SeqLocStart (slp);
10327 loc_stop = SeqLocStop (slp);
10328 }
10329 else
10330 {
10331 if (lcp->interval_end_choice == LOCATION_CONSTRAINT_START_ENDPOINT)
10332 {
10333 endpoint = SeqLocStart (slp);
10334 }
10335 else
10336 {
10337 endpoint = SeqLocStop (slp);
10338 }
10339 loc_start = endpoint;
10340 loc_stop = endpoint;
10341 }
10342 if (loc_stop <= lcp->left || loc_start >= lcp->right)
10343 {
10344 rval = TRUE;
10345 }
10346 break;
10347 case LOCATION_CONSTRAINT_OVERLAP :
10348 loc_start = SeqLocStart (slp);
10349 loc_stop = SeqLocStop (slp);
10350 if (loc_start <= lcp->left && loc_stop >= lcp->left)
10351 {
10352 rval = TRUE;
10353 }
10354 else if (loc_start <= lcp->right && loc_stop >= lcp->right)
10355 {
10356 rval = TRUE;
10357 }
10358 else if (loc_start >= lcp->left && loc_stop <= lcp->right)
10359 {
10360 rval = TRUE;
10361 }
10362 break;
10363 case LOCATION_CONSTRAINT_EQUAL :
10364 loc_start = SeqLocStart (slp);
10365 loc_stop = SeqLocStop (slp);
10366 if (loc_start == lcp->left && loc_stop == lcp->right)
10367 {
10368 rval = TRUE;
10369 }
10370 break;
10371 }
10372 }
10373 return rval;
10374 }
10375
10376 typedef struct filterform
10377 {
10378 DIALOG_MESSAGE_BLOCK
10379
10380 DialoG string_constraint;
10381 DialoG source_constraint;
10382 DialoG location_constraint;
10383 DialoG cds_gene_prot_constraint;
10384 DialoG id_list_constraint;
10385
10386 DialoG tbs;
10387 DialoG pages[6];
10388 Int4 current_page;
10389
10390 } FilterFormData, PNTR FilterFormPtr;
10391
FilterToDialog(DialoG d,Pointer userdata)10392 static void FilterToDialog (DialoG d, Pointer userdata)
10393 {
10394 FilterFormPtr dlg;
10395 FilterSetPtr dlg_data;
10396
10397 dlg = (FilterFormPtr) GetObjectExtra (d);
10398
10399 if (dlg == NULL)
10400 {
10401 return;
10402 }
10403 dlg_data = (FilterSetPtr) userdata;
10404 PointerToDialog (dlg->string_constraint, NULL);
10405 PointerToDialog (dlg->source_constraint, NULL);
10406 PointerToDialog (dlg->location_constraint, NULL);
10407 PointerToDialog (dlg->cds_gene_prot_constraint, NULL);
10408 PointerToDialog (dlg->id_list_constraint, NULL);
10409
10410 if (dlg_data != NULL)
10411 {
10412 PointerToDialog (dlg->string_constraint, dlg_data->scp);
10413 PointerToDialog (dlg->source_constraint, dlg_data->ccp);
10414 PointerToDialog (dlg->location_constraint, dlg_data->lcp);
10415 PointerToDialog (dlg->cds_gene_prot_constraint, dlg_data->cgp);
10416 PointerToDialog (dlg->id_list_constraint, dlg_data->id_list);
10417 }
10418 }
10419
ApplyNthPage(FilterFormPtr dlg,FilterSetPtr dlg_data,Int4 page)10420 static void ApplyNthPage (FilterFormPtr dlg, FilterSetPtr dlg_data, Int4 page)
10421 {
10422 if (page < 0) return;
10423
10424 /* adjust page value to reflect missing pages */
10425 if (dlg->source_constraint == NULL)
10426 {
10427 page++;
10428 }
10429 if (dlg->string_constraint == NULL && page >= 1)
10430 {
10431 page++;
10432 }
10433 if (dlg->location_constraint == NULL && page >= 2)
10434 {
10435 page++;
10436 }
10437 if (dlg->cds_gene_prot_constraint == NULL && page >= 3)
10438 {
10439 page++;
10440 }
10441 if (dlg->id_list_constraint == NULL && page >= 4)
10442 {
10443 page++;
10444 }
10445
10446 switch (page)
10447 {
10448 case 0:
10449 dlg_data->ccp = DialogToPointer (dlg->source_constraint);
10450 break;
10451 case 1:
10452 dlg_data->scp = DialogToPointer (dlg->string_constraint);
10453 break;
10454 case 2:
10455 dlg_data->lcp = DialogToPointer (dlg->location_constraint);
10456 break;
10457 case 3:
10458 dlg_data->cgp = DialogToPointer (dlg->cds_gene_prot_constraint);
10459 break;
10460 case 4:
10461 dlg_data->id_list = DialogToPointer (dlg->id_list_constraint);
10462 break;
10463 }
10464
10465 }
10466
10467
DialogToFilter(DialoG d)10468 static Pointer DialogToFilter (DialoG d)
10469 {
10470 FilterFormPtr dlg;
10471 FilterSetPtr dlg_data;
10472
10473 dlg = (FilterFormPtr) GetObjectExtra (d);
10474
10475 if (dlg == NULL)
10476 {
10477 return NULL;
10478 }
10479 dlg_data = (FilterSetPtr) MemNew (sizeof (FilterSetData));
10480
10481 if (dlg_data != NULL)
10482 {
10483 if (dlg->tbs == NULL)
10484 {
10485 dlg_data->scp = DialogToPointer (dlg->string_constraint);
10486 dlg_data->ccp = DialogToPointer (dlg->source_constraint);
10487 dlg_data->lcp = DialogToPointer (dlg->location_constraint);
10488 dlg_data->cgp = DialogToPointer (dlg->cds_gene_prot_constraint);
10489 dlg_data->id_list = DialogToPointer (dlg->id_list_constraint);
10490 }
10491 else
10492 {
10493 /* only take one value */
10494 ApplyNthPage (dlg, dlg_data, dlg->current_page);
10495 }
10496 }
10497 return dlg_data;
10498 }
10499
FilterFormMessage(DialoG d,Int2 mssg)10500 static void FilterFormMessage (DialoG d, Int2 mssg)
10501
10502 {
10503 }
10504
TestFilterFormDialog(DialoG d)10505 static ValNodePtr TestFilterFormDialog (DialoG d)
10506
10507 {
10508 return NULL;
10509 }
10510
ChangeFilterPage(VoidPtr data,Int2 newval,Int2 oldval)10511 static void ChangeFilterPage (VoidPtr data, Int2 newval, Int2 oldval)
10512
10513 {
10514 FilterFormPtr ffp;
10515
10516 ffp = (FilterFormPtr) data;
10517 if (ffp != NULL) {
10518 ffp->current_page = newval;
10519 SafeHide (ffp->pages [oldval]);
10520 Update ();
10521 SafeShow (ffp->pages [newval]);
10522 Update ();
10523 }
10524 }
10525
ClearAllConstraints(ButtoN b)10526 static void ClearAllConstraints (ButtoN b)
10527 {
10528 FilterFormPtr ffp;
10529
10530 ffp = (FilterFormPtr) GetObjectExtra (b);
10531 if (ffp != NULL)
10532 {
10533 PointerToDialog (ffp->dialog, NULL);
10534 }
10535 }
10536
10537 extern DialoG
FilterGroup(GrouP h,Boolean has_string_constraint,Boolean has_source_constraint,Boolean has_location_constraint,Boolean has_cds_gene_prot_constraint,Boolean has_id_list_constraint,CharPtr string_constraint_label)10538 FilterGroup
10539 (GrouP h,
10540 Boolean has_string_constraint,
10541 Boolean has_source_constraint,
10542 Boolean has_location_constraint,
10543 Boolean has_cds_gene_prot_constraint,
10544 Boolean has_id_list_constraint,
10545 CharPtr string_constraint_label)
10546 {
10547 GrouP g, k;
10548 FilterFormPtr ffp;
10549 Int4 num_pages = 0;
10550 CharPtr filterTabs[5];
10551 Int4 i;
10552 ButtoN clear_constraints = NULL;
10553
10554 if (! has_string_constraint
10555 && ! has_source_constraint
10556 && ! has_location_constraint
10557 && ! has_cds_gene_prot_constraint
10558 && ! has_id_list_constraint)
10559 {
10560 return NULL;
10561 }
10562
10563 ffp = (FilterFormPtr) MemNew (sizeof (FilterFormData));
10564 if (ffp == NULL)
10565 {
10566 return NULL;
10567 }
10568
10569 g = NormalGroup (h, -1, 0, NULL, programFont, NULL);
10570 SetObjectExtra (g, ffp, StdCleanupExtraProc);
10571
10572 ffp->dialog = (DialoG) g;
10573 ffp->todialog = FilterToDialog;
10574 ffp->fromdialog = DialogToFilter;
10575 ffp->dialogmessage = FilterFormMessage;
10576 ffp->testdialog = TestFilterFormDialog;
10577
10578 ffp->current_page = 0;
10579
10580 if (has_source_constraint)
10581 {
10582 filterTabs [num_pages++] = "Source Constraint";
10583 }
10584 if (has_string_constraint)
10585 {
10586 filterTabs [num_pages++] = "String Constraint";
10587 }
10588 if (has_location_constraint)
10589 {
10590 filterTabs [num_pages++] = "Location Constraint";
10591 }
10592 if (has_cds_gene_prot_constraint)
10593 {
10594 filterTabs [num_pages++] = "CDS-Gene-Prot-mRNA Set Constraint";
10595 }
10596 if (has_id_list_constraint)
10597 {
10598 filterTabs [num_pages++] = "Sequence ID Constraint";
10599 }
10600 filterTabs [num_pages] = NULL;
10601
10602 if (num_pages > 1)
10603 {
10604
10605 ffp->tbs = CreateFolderTabs (g, filterTabs, 0,
10606 0, 0, PROGRAM_FOLDER_TAB,
10607 ChangeFilterPage, (Pointer) ffp);
10608 k = HiddenGroup (g, 0, 0, NULL);
10609 num_pages = 0;
10610 if (has_source_constraint)
10611 {
10612 ffp->source_constraint = SourceConstraintDialogX (k, FALSE);
10613 ffp->pages [num_pages++] = ffp->source_constraint;
10614 }
10615 if (has_string_constraint)
10616 {
10617 ffp->string_constraint = StringConstraintDialogX (k, string_constraint_label, FALSE);
10618 ffp->pages [num_pages++] = ffp->string_constraint;
10619 }
10620 if (has_location_constraint)
10621 {
10622 ffp->location_constraint = LocationConstraintXDialog (k, FALSE, FALSE);
10623 ffp->pages [num_pages++] = ffp->location_constraint;
10624 }
10625 if (has_cds_gene_prot_constraint)
10626 {
10627 ffp->cds_gene_prot_constraint = CDSGeneProtConstraintDialog (k, FALSE);
10628 ffp->pages [num_pages++] = ffp->cds_gene_prot_constraint;
10629 }
10630 if (has_id_list_constraint)
10631 {
10632 ffp->id_list_constraint = StringConstraintDialogX (k, "Where sequence ID", FALSE);
10633 ffp->pages[num_pages++] = ffp->id_list_constraint;
10634 }
10635 for (i = 1; i < num_pages; i++)
10636 {
10637 Hide (ffp->pages [i]);
10638 }
10639 AlignObjects (ALIGN_CENTER, (HANDLE) ffp->pages [0],
10640 (HANDLE) ffp->pages [1],
10641 (HANDLE) ffp->pages [2],
10642 (HANDLE) ffp->pages [3],
10643 NULL);
10644 clear_constraints = PushButton (g, "Clear Constraints", ClearAllConstraints);
10645 SetObjectExtra (clear_constraints, ffp, NULL);
10646 AlignObjects (ALIGN_CENTER, (HANDLE) ffp->tbs, (HANDLE) k, (HANDLE) clear_constraints, NULL);
10647 }
10648 else
10649 {
10650 if (has_source_constraint)
10651 {
10652 ffp->source_constraint = SourceConstraintDialogX (g, TRUE);
10653 }
10654 else if (has_string_constraint)
10655 {
10656 ffp->string_constraint = StringConstraintDialogX (g, string_constraint_label, TRUE);
10657 }
10658 else if (has_location_constraint)
10659 {
10660 ffp->location_constraint = LocationConstraintXDialog (g, FALSE, TRUE);
10661 }
10662 else if (has_cds_gene_prot_constraint)
10663 {
10664 ffp->cds_gene_prot_constraint = CDSGeneProtConstraintDialog (g, TRUE);
10665 }
10666 else if (has_id_list_constraint)
10667 {
10668 ffp->id_list_constraint = StringConstraintDialogX (g, "Where sequence ID", TRUE);
10669 }
10670 }
10671 return (DialoG) g;
10672 }
10673
10674 /* Operations on constrained features and descriptors */
10675 typedef struct objecthasstring
10676 {
10677 StringConstraintXPtr scp;
10678 Boolean found;
10679 } ObjectHasStringData, PNTR ObjectHasStringPtr;
10680
10681 typedef struct constraintop
10682 {
10683 FilterSetPtr fsp;
10684 ObjMgrPtr omp;
10685 ObjMgrTypePtr omtp;
10686 AsnIoPtr aip;
10687 Uint2 entityID;
10688 ObjectHasStringData ohsd;
10689 Pointer userdata;
10690 FeatureActionProc feature_action;
10691 Uint1 seqFeatChoice;
10692 Uint1 featDefChoice;
10693 DescriptorActionProc descriptor_action;
10694 Uint1 descriptorChoice;
10695 } ConstraintOpData, PNTR ConstraintOpPtr;
10696
DoesStringMatchConstraintX(CharPtr pchSource,StringConstraintXPtr scp)10697 extern Boolean DoesStringMatchConstraintX (CharPtr pchSource, StringConstraintXPtr scp)
10698 {
10699 CharPtr pFound;
10700 Boolean rval = FALSE;
10701 Char char_after = 0;
10702
10703 if (pchSource == NULL) return FALSE;
10704
10705 if (scp == NULL || StringHasNoText (scp->match_text)) return TRUE;
10706
10707 switch (scp->match_location)
10708 {
10709 case eStringConstraintContains:
10710 if (scp->insensitive)
10711 {
10712 pFound = StringISearch (pchSource, scp->match_text);
10713 }
10714 else
10715 {
10716 pFound = StringSearch (pchSource, scp->match_text);
10717 }
10718 if (pFound == NULL)
10719 {
10720 rval = FALSE;
10721 }
10722 else if (scp->whole_word)
10723 {
10724 rval = IsWholeWordMatch (pchSource, pFound, StringLen (scp->match_text));
10725 while (!rval && pFound != NULL)
10726 {
10727 if (scp->insensitive)
10728 {
10729 pFound = StringISearch (pFound + 1, scp->match_text);
10730 }
10731 else
10732 {
10733 pFound = StringSearch (pFound + 1, scp->match_text);
10734 }
10735 if (pFound != NULL)
10736 {
10737 rval = IsWholeWordMatch (pchSource, pFound, StringLen (scp->match_text));
10738 }
10739 }
10740 }
10741 else
10742 {
10743 rval = TRUE;
10744 }
10745 break;
10746 case eStringConstraintStarts:
10747 if (scp->insensitive)
10748 {
10749 pFound = StringISearch (pchSource, scp->match_text);
10750 }
10751 else
10752 {
10753 pFound = StringSearch (pchSource, scp->match_text);
10754 }
10755 if (pFound == pchSource)
10756 {
10757 if (scp->whole_word)
10758 {
10759 rval = IsWholeWordMatch (pchSource, pFound, StringLen (scp->match_text));
10760 }
10761 else
10762 {
10763 rval = TRUE;
10764 }
10765 }
10766 break;
10767 case eStringConstraintEnds:
10768 if (scp->insensitive)
10769 {
10770 pFound = StringISearch (pchSource, scp->match_text);
10771 }
10772 else
10773 {
10774 pFound = StringSearch (pchSource, scp->match_text);
10775 }
10776 while (pFound != NULL && !rval) {
10777 char_after = *(pFound + StringLen (scp->match_text));
10778 if (char_after == 0)
10779 {
10780 if (scp->whole_word)
10781 {
10782 rval = IsWholeWordMatch (pchSource, pFound, StringLen (scp->match_text));
10783 }
10784 else
10785 {
10786 rval = TRUE;
10787 }
10788 /* stop the search, we're at the end of the string */
10789 pFound = NULL;
10790 }
10791 else
10792 {
10793 if (scp->insensitive)
10794 {
10795 pFound = StringISearch (pFound + 1, scp->match_text);
10796 }
10797 else
10798 {
10799 pFound = StringSearch (pFound + 1, scp->match_text);
10800 }
10801 }
10802 }
10803 break;
10804 case eStringConstraintEquals:
10805 if (scp->insensitive)
10806 {
10807 if (StringICmp (pchSource, scp->match_text) == 0)
10808 {
10809 rval = TRUE;
10810 }
10811 }
10812 else
10813 {
10814 if (StringCmp (pchSource, scp->match_text) == 0)
10815 {
10816 rval = TRUE;
10817 }
10818 }
10819 break;
10820 case eStringConstraintInList:
10821 if (scp->insensitive)
10822 {
10823 pFound = StringISearch (scp->match_text, pchSource);
10824 }
10825 else
10826 {
10827 pFound = StringSearch (scp->match_text, pchSource);
10828 }
10829 if (pFound == NULL)
10830 {
10831 rval = FALSE;
10832 }
10833 else
10834 {
10835 rval = IsWholeWordMatch (scp->match_text, pFound, StringLen (pchSource));
10836 while (!rval && pFound != NULL)
10837 {
10838 if (scp->insensitive)
10839 {
10840 pFound = StringISearch (pFound + 1, pchSource);
10841 }
10842 else
10843 {
10844 pFound = StringSearch (pFound + 1, pchSource);
10845 }
10846 if (pFound != NULL)
10847 {
10848 rval = IsWholeWordMatch (scp->match_text, pFound, StringLen (pchSource));
10849 }
10850 }
10851 }
10852 if (!rval) {
10853 /* look for spans */
10854 rval = IsStringInSpanInList (pchSource, scp->match_text);
10855 }
10856 break;
10857 }
10858 return rval;
10859 }
10860
AsnWriteConstraintCallBack(AsnExpOptStructPtr pAEOS)10861 static void LIBCALLBACK AsnWriteConstraintCallBack (AsnExpOptStructPtr pAEOS)
10862
10863 {
10864 CharPtr pchSource;
10865 ObjectHasStringPtr ohsp;
10866
10867 ohsp = (ObjectHasStringPtr) pAEOS->data;
10868 if (ISA_STRINGTYPE (AsnFindBaseIsa (pAEOS->atp)))
10869 {
10870 pchSource = (CharPtr) pAEOS->dvp->ptrvalue;
10871 ohsp->found |= DoesStringMatchConstraintX (pchSource, ohsp->scp);
10872 }
10873 }
10874
10875 static Boolean
DoesObjectMatchStringConstraint(ObjMgrTypePtr omtp,AsnIoPtr aip,Pointer ptr,ObjectHasStringPtr ohsp)10876 DoesObjectMatchStringConstraint
10877 (ObjMgrTypePtr omtp,
10878 AsnIoPtr aip,
10879 Pointer ptr,
10880 ObjectHasStringPtr ohsp)
10881
10882 {
10883 SeqFeatPtr sfp;
10884 SeqMgrFeatContext fcontext;
10885 CharPtr search_txt = NULL;
10886
10887 if (omtp == NULL || ohsp == NULL)
10888 {
10889 return FALSE;
10890 }
10891 ohsp->found = FALSE;
10892 (omtp->asnwrite) (ptr, aip, NULL);
10893
10894 if (!ohsp->found && omtp->datatype == OBJ_SEQFEAT)
10895 {
10896 sfp = (SeqFeatPtr) ptr;
10897 if (SeqMgrFeaturesAreIndexed(sfp->idx.entityID) == 0) {
10898 SeqMgrIndexFeatures (sfp->idx.entityID, NULL);
10899 }
10900
10901 sfp = SeqMgrGetDesiredFeature (sfp->idx.entityID, NULL, sfp->idx.itemID, 0, sfp, &fcontext);
10902 ohsp->found = DoesStringMatchConstraintX (fcontext.label, ohsp->scp);
10903 if (!ohsp->found && sfp != NULL && sfp->idx.subtype == FEATDEF_tRNA)
10904 {
10905 search_txt = (CharPtr) MemNew ((StringLen (fcontext.label) + 6) * sizeof (Char));
10906 if (search_txt != NULL)
10907 {
10908 sprintf (search_txt, "tRNA-%s", fcontext.label);
10909 ohsp->found = DoesStringMatchConstraintX (search_txt, ohsp->scp);
10910 search_txt = MemFree (search_txt);
10911 }
10912 }
10913 }
10914 return ohsp->found;
10915 }
10916
10917
DoesSourceHaveOneQualPresent(BioSourcePtr biop,SourceQualDescPtr sqdp)10918 static Boolean DoesSourceHaveOneQualPresent (BioSourcePtr biop, SourceQualDescPtr sqdp)
10919 {
10920 OrgModPtr mod;
10921 SubSourcePtr ssp;
10922 Boolean is_present = FALSE;
10923
10924 if (biop == NULL || sqdp == NULL)
10925 {
10926 return FALSE;
10927 }
10928
10929 if (sqdp->isOrgMod)
10930 {
10931 if (biop->org != NULL && biop->org->orgname != NULL)
10932 {
10933 mod = biop->org->orgname->mod;
10934 while (mod != NULL && mod->subtype != sqdp->subtype)
10935 {
10936 mod = mod->next;
10937 }
10938 if (mod != NULL && mod->subtype == sqdp->subtype)
10939 {
10940 is_present = TRUE;
10941 }
10942 }
10943 }
10944 else
10945 {
10946 ssp = biop->subtype;
10947 while (ssp != NULL && ssp->subtype != sqdp->subtype)
10948 {
10949 ssp = ssp->next;
10950 }
10951 if (ssp != NULL && ssp->subtype == sqdp->subtype)
10952 {
10953 is_present = TRUE;
10954 }
10955 }
10956 return is_present;
10957 }
10958
DoesSourceHaveQualPresent(BioSourcePtr biop,ValNodePtr qual_list)10959 static Boolean DoesSourceHaveQualPresent (BioSourcePtr biop, ValNodePtr qual_list)
10960 {
10961 ValNodePtr vnp;
10962 Boolean qual_found = FALSE;
10963
10964 if (biop == NULL)
10965 {
10966 return FALSE;
10967 }
10968 if (qual_list == NULL)
10969 {
10970 return TRUE;
10971 }
10972
10973 for (vnp = qual_list; vnp != NULL && !qual_found; vnp = vnp->next)
10974 {
10975 qual_found = DoesSourceHaveOneQualPresent (biop, (SourceQualDescPtr) vnp->data.ptrvalue);
10976 }
10977
10978 return qual_found;
10979 }
10980
IsMatchAny(ValNodePtr vnp)10981 static Boolean IsMatchAny (ValNodePtr vnp)
10982 {
10983 if (vnp == NULL
10984 || vnp->data.ptrvalue == NULL
10985 || (vnp->choice > 0 && StringICmp (vnp->data.ptrvalue, "Organism or Any Qual") == 0))
10986 {
10987 return TRUE;
10988 } else {
10989 return FALSE;
10990 }
10991 }
10992
DoFieldsMatch(BioSourcePtr biop,ChoiceConstraintPtr ccp)10993 static Boolean DoFieldsMatch (BioSourcePtr biop, ChoiceConstraintPtr ccp)
10994 {
10995 ValNodePtr swap, swap2;
10996 ValNodePtr qual_choice_list = NULL, vnp1, vnp2;
10997 Boolean rval = FALSE;
10998 ChoiceConstraintData tmp_const;
10999 StringConstraintData scd;
11000 SourceQualDescPtr sqdp;
11001 CharPtr location;
11002 OrgModPtr mod = NULL;
11003 SubSourcePtr ssp;
11004
11005 if (biop == NULL) return FALSE;
11006 if (ccp == NULL) return TRUE;
11007
11008 /* Init temporary choice constraint */
11009 MemSet (&tmp_const, 0, sizeof (ChoiceConstraintData));
11010 MemSet (&scd, 0, sizeof (StringConstraintData));
11011 scd.match_location = eStringConstraintEquals;
11012 tmp_const.string_constraint = &scd;
11013 tmp_const.constraint_type = CHOICE_CONSTRAINT_STRING;
11014
11015 if (IsMatchAny (ccp->qual_choice) && IsMatchAny (ccp->qual_choice_match)) {
11016 /* both are wildcards */
11017 ValNodeAddPointer (&qual_choice_list, 1, StringSave ("Organism"));
11018 qual_choice_list->next = GetSourceQualDescList (TRUE, TRUE, TRUE, FALSE);
11019 ValNodeAddPointer (&qual_choice_list, 1, StringSave ("Lineage"));
11020 ValNodeAddPointer (&qual_choice_list, 1, StringSave ("Location"));
11021
11022 /* save original wildcards */
11023 swap = ccp->qual_choice;
11024 swap2 = ccp->qual_choice_match;
11025 for (vnp1 = qual_choice_list; vnp1 != NULL && vnp1->next != NULL && !rval; vnp1 = vnp1->next) {
11026 ccp->qual_choice = vnp1;
11027 for (vnp2 = vnp1->next; vnp2 != NULL && !rval; vnp2 = vnp2->next) {
11028 ccp->qual_choice_match = vnp2;
11029 if (DoFieldsMatch (biop, ccp)) {
11030 rval = TRUE;
11031 }
11032 }
11033 }
11034 /* put original wildcards back */
11035 ccp->qual_choice = swap;
11036 ccp->qual_choice_match = swap2;
11037 qual_choice_list = ValNodeFreeData (qual_choice_list);
11038 } else if (IsMatchAny (ccp->qual_choice) || IsMatchAny (ccp->qual_choice_match)) {
11039 /* one is a wild card */
11040 ValNodeAddPointer (&qual_choice_list, 1, StringSave ("Organism"));
11041 qual_choice_list->next = GetSourceQualDescList (TRUE, TRUE, TRUE, FALSE);
11042 ValNodeAddPointer (&qual_choice_list, 1, StringSave ("Lineage"));
11043 ValNodeAddPointer (&qual_choice_list, 1, StringSave ("Location"));
11044
11045 /* if one wild card, make it the first one */
11046 if (IsMatchAny (ccp->qual_choice_match)) {
11047 swap = ccp->qual_choice;
11048 ccp->qual_choice = ccp->qual_choice_match;
11049 ccp->qual_choice_match = swap;
11050 }
11051 /* save original wildcard */
11052 swap = ccp->qual_choice;
11053 for (vnp1 = qual_choice_list; vnp1 != NULL && !rval; vnp1 = vnp1->next) {
11054 if (SourceQualValNodeMatch (vnp1, ccp->qual_choice_match)) {
11055 /* don't compare something to itself */
11056 continue;
11057 } else {
11058 ccp->qual_choice = vnp1;
11059 rval = DoFieldsMatch (biop, ccp);
11060 }
11061 }
11062 /* put original wildcard back */
11063 ccp->qual_choice = swap;
11064 qual_choice_list = ValNodeFreeData (qual_choice_list);
11065 }
11066 else if (ccp->qual_choice->choice > 0)
11067 {
11068 tmp_const.qual_choice = ccp->qual_choice_match;
11069 if (StringICmp (ccp->qual_choice->data.ptrvalue, "Organism") == 0)
11070 {
11071 if (biop->org != NULL && !StringHasNoText (biop->org->taxname))
11072 {
11073 tmp_const.string_constraint->match_text = biop->org->taxname;
11074 rval = DoesOneSourceMatchConstraint (biop, &tmp_const);
11075 }
11076 }
11077 else if (StringICmp (ccp->qual_choice->data.ptrvalue, "Lineage") == 0)
11078 {
11079 if (biop->org != NULL && biop->org->orgname != NULL && !StringHasNoText (biop->org->orgname->lineage))
11080 {
11081 tmp_const.string_constraint->match_text = biop->org->orgname->lineage;
11082 rval = DoesOneSourceMatchConstraint (biop, &tmp_const);
11083 }
11084 }
11085 else if (StringICmp (ccp->qual_choice->data.ptrvalue, "Location") == 0)
11086 {
11087 location = GetLocationFromSource (biop, NULL);
11088 tmp_const.string_constraint->match_text = location;
11089 if (!StringHasNoText (location)) {
11090 rval = DoesOneSourceMatchConstraint (biop, &tmp_const);
11091 }
11092 location = MemFree (location);
11093 }
11094 }
11095 else
11096 {
11097 tmp_const.qual_choice = ccp->qual_choice_match;
11098 sqdp = (SourceQualDescPtr) ccp->qual_choice->data.ptrvalue;
11099 if (sqdp->isOrgMod)
11100 {
11101 if (biop->org != NULL && biop->org->orgname != NULL)
11102 {
11103 mod = biop->org->orgname->mod;
11104 }
11105 while (! rval && mod != NULL)
11106 {
11107 if (mod->subtype == sqdp->subtype && !StringHasNoText (mod->subname))
11108 {
11109 tmp_const.string_constraint->match_text = mod->subname;
11110 rval = DoesOneSourceMatchConstraint (biop, &tmp_const);
11111 }
11112 mod = mod->next;
11113 }
11114 }
11115 else
11116 {
11117 ssp = biop->subtype;
11118 while (!rval && ssp != NULL)
11119 {
11120 if (ssp->subtype == sqdp->subtype && !StringHasNoText (ssp->name))
11121 {
11122 tmp_const.string_constraint->match_text = ssp->name;
11123 rval = DoesOneSourceMatchConstraint (biop, &tmp_const);
11124 }
11125 ssp = ssp->next;
11126 }
11127 }
11128 }
11129 return rval;
11130 }
11131
11132 extern Boolean
DoesOneSourceMatchConstraint(BioSourcePtr biop,ChoiceConstraintPtr scp)11133 DoesOneSourceMatchConstraint
11134 (BioSourcePtr biop, ChoiceConstraintPtr scp)
11135 {
11136 Boolean does_match = FALSE;
11137 OrgModPtr mod = NULL;
11138 SubSourcePtr ssp;
11139 SourceQualDescPtr sqdp;
11140 CharPtr location;
11141
11142 if (scp == NULL || scp->constraint_type == CHOICE_CONSTRAINT_ANY)
11143 {
11144 return TRUE;
11145 }
11146 if (biop == NULL)
11147 {
11148 return FALSE;
11149 }
11150
11151 if (scp->constraint_type == CHOICE_CONSTRAINT_STRING)
11152 {
11153 if (IsMatchAny (scp->qual_choice))
11154 {
11155 if (biop->org != NULL)
11156 {
11157 does_match = DoesStringMatchConstraintX (biop->org->taxname, scp->string_constraint);
11158 if (biop->org->orgname != NULL)
11159 {
11160 mod = biop->org->orgname->mod;
11161 }
11162 while (! does_match && mod != NULL)
11163 {
11164 does_match = DoesStringMatchConstraintX (mod->subname, scp->string_constraint);
11165 mod = mod->next;
11166 }
11167 }
11168 ssp = biop->subtype;
11169 while (!does_match && ssp != NULL)
11170 {
11171 does_match = DoesStringMatchConstraintX (ssp->name, scp->string_constraint);
11172 ssp = ssp->next;
11173 }
11174 }
11175 else if (scp->qual_choice->choice > 0 && StringICmp (scp->qual_choice->data.ptrvalue, "Organism") == 0)
11176 {
11177 if (biop->org != NULL)
11178 {
11179 does_match = DoesStringMatchConstraintX (biop->org->taxname, scp->string_constraint);
11180 }
11181 }
11182 else if (scp->qual_choice->choice > 0 && StringICmp (scp->qual_choice->data.ptrvalue, "Lineage") == 0)
11183 {
11184 if (biop->org != NULL && biop->org->orgname != NULL)
11185 {
11186 does_match = DoesStringMatchConstraintX (biop->org->orgname->lineage,
11187 scp->string_constraint);
11188 }
11189 }
11190 else if (scp->qual_choice->choice > 0 && StringICmp (scp->qual_choice->data.ptrvalue, "Location") == 0)
11191 {
11192 location = GetLocationFromSource (biop, NULL);
11193 does_match = DoesStringMatchConstraintX (location, scp->string_constraint);
11194 location = MemFree (location);
11195 }
11196 else
11197 {
11198 sqdp = (SourceQualDescPtr) scp->qual_choice->data.ptrvalue;
11199 if (sqdp->isOrgMod)
11200 {
11201 if (biop->org != NULL && biop->org->orgname != NULL)
11202 {
11203 mod = biop->org->orgname->mod;
11204 }
11205 while (! does_match && mod != NULL)
11206 {
11207 if (mod->subtype == sqdp->subtype)
11208 {
11209 does_match = DoesStringMatchConstraintX (mod->subname, scp->string_constraint);
11210 }
11211 mod = mod->next;
11212 }
11213 }
11214 else
11215 {
11216 ssp = biop->subtype;
11217 while (!does_match && ssp != NULL)
11218 {
11219 if (ssp->subtype == sqdp->subtype)
11220 {
11221 does_match = DoesStringMatchConstraintX (ssp->name, scp->string_constraint);
11222 }
11223 ssp = ssp->next;
11224 }
11225 }
11226 }
11227 if (scp->string_constraint->not_present)
11228 {
11229 does_match = ! does_match;
11230 }
11231 }
11232 else if (scp->constraint_type == CHOICE_CONSTRAINT_MATCH)
11233 {
11234 does_match = DoFieldsMatch (biop, scp);
11235 }
11236 else
11237 {
11238 does_match = DoesSourceHaveQualPresent (biop, scp->qual_choice);
11239 }
11240 return does_match;
11241 }
11242
SeqEntryConstrainedFeaturesCallback(SeqFeatPtr sfp,Pointer userdata)11243 static void SeqEntryConstrainedFeaturesCallback (SeqFeatPtr sfp, Pointer userdata)
11244 {
11245 SeqMgrFeatContext fcontext;
11246 ConstraintOpPtr cop;
11247 Boolean feature_matches = TRUE;
11248
11249 if (sfp == NULL || userdata == NULL) return;
11250 cop = (ConstraintOpPtr) userdata;
11251 sfp = SeqMgrGetDesiredFeature (sfp->idx.entityID, NULL, sfp->idx.itemID, 0, sfp, &fcontext);
11252 if (sfp == NULL) return;
11253
11254 if (cop->seqFeatChoice != 0 && cop->seqFeatChoice != sfp->data.choice) return;
11255 if (cop->featDefChoice != 0 && cop->featDefChoice != sfp->idx.subtype) return;
11256
11257 if (cop->fsp != NULL && cop->fsp->scp != NULL)
11258 {
11259 if (cop->fsp->scp->not_present)
11260 {
11261 if (DoesObjectMatchStringConstraint (cop->omtp, cop->aip, (Pointer) sfp, &(cop->ohsd))
11262 || DoesStringMatchConstraintX (fcontext.label, cop->fsp->scp))
11263 {
11264 feature_matches = FALSE;
11265 }
11266 }
11267 else
11268 {
11269 if (! DoesObjectMatchStringConstraint (cop->omtp, cop->aip, (Pointer) sfp, &(cop->ohsd))
11270 && ! DoesStringMatchConstraintX (fcontext.label, cop->fsp->scp))
11271 {
11272 feature_matches = FALSE;
11273 }
11274 }
11275 }
11276 if (cop->fsp != NULL && cop->fsp->lcp != NULL)
11277 {
11278 if (! DoesLocationMatchConstraint (sfp->location, cop->fsp->lcp))
11279 {
11280 feature_matches = FALSE;
11281 }
11282 }
11283
11284 if (feature_matches)
11285 {
11286 (cop->feature_action) (sfp, cop->userdata, cop->fsp);
11287 }
11288 }
11289
11290
BioseqConstrainedFeaturesCallback(BioseqPtr bsp,Pointer userdata)11291 static void BioseqConstrainedFeaturesCallback (BioseqPtr bsp, Pointer userdata)
11292 {
11293 ConstraintOpPtr cop;
11294 SeqFeatPtr sfp;
11295 ObjMgrDataPtr omdp;
11296 BioseqExtraPtr bspextra;
11297 Int4 index;
11298
11299 if (bsp == NULL || userdata == NULL) return;
11300 cop = (ConstraintOpPtr) userdata;
11301
11302 omdp = SeqMgrGetOmdpForBioseq (bsp);
11303 if (omdp == NULL || omdp->datatype != OBJ_BIOSEQ) return;
11304
11305 bspextra = (BioseqExtraPtr) omdp->extradata;
11306 if (bspextra == NULL) {
11307 SeqMgrIndexFeatures (bsp->idx.entityID, NULL);
11308 omdp = SeqMgrGetOmdpForBioseq (bsp);
11309 if (omdp == NULL || omdp->datatype != OBJ_BIOSEQ) return;
11310
11311 bspextra = (BioseqExtraPtr) omdp->extradata;
11312 }
11313 if (bspextra == NULL) return;
11314
11315 for (index = 0; index < bspextra->numfeats; index++)
11316 {
11317 sfp = bspextra->featsByPos[index]->sfp;
11318 SeqEntryConstrainedFeaturesCallback (sfp, userdata);
11319 }
11320 }
11321
11322
SeqEntryConstrainedDescriptorsCallback(SeqDescrPtr sdp,Pointer userdata)11323 static void SeqEntryConstrainedDescriptorsCallback (SeqDescrPtr sdp, Pointer userdata)
11324 {
11325 ConstraintOpPtr cop;
11326 Boolean descriptor_matches = TRUE;
11327
11328 if (sdp == NULL || userdata == NULL) return;
11329 cop = (ConstraintOpPtr) userdata;
11330
11331 if (cop != NULL && cop->descriptorChoice != 0 && cop->descriptorChoice != sdp->choice)
11332 {
11333 return;
11334 }
11335
11336 if (cop != NULL && cop->fsp != NULL && cop->fsp->scp != NULL)
11337 {
11338 if (cop->fsp->scp->not_present)
11339 {
11340 if (DoesObjectMatchStringConstraint (cop->omtp, cop->aip, (Pointer) sdp, &(cop->ohsd)))
11341 {
11342 descriptor_matches = FALSE;
11343 }
11344 }
11345 else
11346 {
11347 if (! DoesObjectMatchStringConstraint (cop->omtp, cop->aip, (Pointer) sdp, &(cop->ohsd)))
11348 {
11349 descriptor_matches = FALSE;
11350 }
11351 }
11352 }
11353 if (descriptor_matches)
11354 {
11355 (cop->descriptor_action) (sdp, cop->userdata, cop->fsp);
11356 }
11357 }
11358
11359
ConstrainedSourceCallback(SeqEntryPtr sep,ConstraintOpPtr cop)11360 static void ConstrainedSourceCallback (SeqEntryPtr sep, ConstraintOpPtr cop)
11361 {
11362 BioseqPtr bsp;
11363 BioseqSetPtr bssp = NULL;
11364 SeqAnnotPtr sap = NULL;
11365 SeqDescrPtr sdp = NULL;
11366 SeqFeatPtr sfp;
11367 Boolean found = FALSE;
11368
11369 if (sep == NULL || sep->data.ptrvalue == NULL || cop == NULL || cop->fsp == NULL)
11370 {
11371 return;
11372 }
11373
11374 if (IS_Bioseq (sep))
11375 {
11376 bsp = (BioseqPtr) sep->data.ptrvalue;
11377 sap = bsp->annot;
11378 sdp = bsp->descr;
11379 }
11380 else if (IS_Bioseq_set (sep))
11381 {
11382 bssp = (BioseqSetPtr) sep->data.ptrvalue;
11383 sap = bssp->annot;
11384 sdp = bssp->descr;
11385 }
11386 while (sap != NULL && !found)
11387 {
11388 if (sap->type == 1)
11389 {
11390 sfp = (SeqFeatPtr) sap->data;
11391 while (sfp != NULL && ! found)
11392 {
11393 if (sfp->data.choice == SEQFEAT_BIOSRC
11394 && DoesOneSourceMatchConstraint (sfp->data.value.ptrvalue, cop->fsp->ccp))
11395 {
11396 found = TRUE;
11397 }
11398 sfp = sfp->next;
11399 }
11400 }
11401 sap = sap->next;
11402 }
11403
11404 while (sdp != NULL && !found)
11405 {
11406 if (sdp->choice == Seq_descr_source
11407 && DoesOneSourceMatchConstraint (sdp->data.ptrvalue, cop->fsp->ccp))
11408 {
11409 found = TRUE;
11410 }
11411 sdp = sdp->next;
11412 }
11413 if (found)
11414 {
11415 if (cop->feature_action != NULL)
11416 {
11417 cop->omtp = ObjMgrTypeFind (cop->omp, OBJ_SEQFEAT, NULL, NULL);
11418 if (cop->omtp != NULL)
11419 {
11420 VisitBioseqsInSep (sep, cop, BioseqConstrainedFeaturesCallback);
11421 }
11422 }
11423
11424 if (cop->descriptor_action != NULL)
11425 {
11426 cop->omtp = ObjMgrTypeFind (cop->omp, OBJ_SEQDESC, NULL, NULL);
11427 if (cop->omtp != NULL)
11428 {
11429 VisitDescriptorsInSep (sep, cop, SeqEntryConstrainedDescriptorsCallback);
11430 }
11431 }
11432 }
11433 else if (bssp != NULL)
11434 {
11435 ConstrainedSourceCallback (bssp->seq_set, cop);
11436 }
11437 ConstrainedSourceCallback (sep->next, cop);
11438 }
11439
11440
ConstrainedBioseqCallback(SeqEntryPtr sep,ConstraintOpPtr cop)11441 static void ConstrainedBioseqCallback (SeqEntryPtr sep, ConstraintOpPtr cop)
11442 {
11443 BioseqPtr bsp = NULL;
11444 BioseqSetPtr bssp = NULL;
11445 SeqFeatPtr sfp;
11446 SeqDescPtr sdp;
11447 SeqMgrFeatContext fcontext;
11448 SeqMgrDescContext dcontext;
11449
11450 if (sep == NULL || sep->data.ptrvalue == NULL || cop == NULL || cop->fsp == NULL)
11451 {
11452 return;
11453 }
11454
11455 if (IS_Bioseq (sep))
11456 {
11457 bsp = (BioseqPtr) sep->data.ptrvalue;
11458 }
11459 else if (IS_Bioseq_set (sep))
11460 {
11461 bssp = (BioseqSetPtr) sep->data.ptrvalue;
11462 }
11463
11464 if (bsp != NULL && DoesIDListMeetStringConstraint (bsp->id, cop->fsp->id_list))
11465 {
11466 if (cop->feature_action != NULL)
11467 {
11468 cop->omtp = ObjMgrTypeFind (cop->omp, OBJ_SEQFEAT, NULL, NULL);
11469 if (cop->omtp != NULL)
11470 {
11471 for (sfp = SeqMgrGetNextFeature (bsp, NULL, 0, 0, &fcontext);
11472 sfp != NULL;
11473 sfp = SeqMgrGetNextFeature (bsp, sfp, 0, 0, &fcontext))
11474 {
11475 SeqEntryConstrainedFeaturesCallback (sfp, cop);
11476 }
11477 }
11478 }
11479
11480 if (cop->descriptor_action != NULL)
11481 {
11482 cop->omtp = ObjMgrTypeFind (cop->omp, OBJ_SEQDESC, NULL, NULL);
11483 if (cop->omtp != NULL)
11484 {
11485 for (sdp = SeqMgrGetNextDescriptor (bsp, NULL, 0, &dcontext);
11486 sdp != NULL;
11487 sdp = SeqMgrGetNextDescriptor (bsp, sdp, 0, &dcontext))
11488 {
11489 SeqEntryConstrainedDescriptorsCallback (sdp, cop);
11490 }
11491 }
11492 }
11493 }
11494 else if (bssp != NULL)
11495 {
11496 ConstrainedBioseqCallback (bssp->seq_set, cop);
11497 }
11498 ConstrainedBioseqCallback (sep->next, cop);
11499 }
11500
11501
11502 extern void
OperateOnSeqEntryConstrainedObjects(SeqEntryPtr sep,FilterSetPtr fsp,FeatureActionProc feature_action,DescriptorActionProc descriptor_action,Uint1 seqFeatChoice,Uint1 featDefChoice,Uint1 descriptorChoice,Pointer userdata)11503 OperateOnSeqEntryConstrainedObjects
11504 (SeqEntryPtr sep,
11505 FilterSetPtr fsp,
11506 FeatureActionProc feature_action,
11507 DescriptorActionProc descriptor_action,
11508 Uint1 seqFeatChoice,
11509 Uint1 featDefChoice,
11510 Uint1 descriptorChoice,
11511 Pointer userdata)
11512 {
11513 ConstraintOpData cod;
11514 AsnExpOptPtr aeop;
11515 SeqEntryPtr old_scope;
11516 BioseqPtr bsp = NULL;
11517 SeqFeatPtr sfp;
11518 SeqDescrPtr sdp;
11519 SeqMgrFeatContext fcontext;
11520 SeqMgrDescContext dcontext;
11521
11522 if (sep == NULL) return;
11523 if (feature_action == NULL && descriptor_action == NULL) return;
11524
11525 cod.omp = ObjMgrGet ();
11526 if (cod.omp == NULL) return;
11527
11528 cod.fsp = fsp;
11529 cod.feature_action = feature_action;
11530 cod.descriptor_action = descriptor_action;
11531 cod.userdata = userdata;
11532 cod.entityID = SeqMgrGetEntityIDForSeqEntry (sep);
11533 cod.seqFeatChoice = seqFeatChoice;
11534 cod.featDefChoice = featDefChoice;
11535 cod.descriptorChoice = descriptorChoice;
11536
11537 old_scope = SeqEntrySetScope (sep);
11538
11539 cod.aip = AsnIoNullOpen ();
11540 if (fsp == NULL)
11541 {
11542 cod.ohsd.scp = NULL;
11543 }
11544 else
11545 {
11546 cod.ohsd.scp = fsp->scp;
11547 }
11548
11549 aeop = AsnExpOptNew (cod.aip, NULL, NULL, AsnWriteConstraintCallBack);
11550 if (aeop != NULL) {
11551 aeop->user_data = (Pointer) &(cod.ohsd);
11552 }
11553
11554 if (IS_Bioseq (sep))
11555 {
11556 bsp = (BioseqPtr) sep->data.ptrvalue;
11557 }
11558
11559 if (fsp == NULL || (fsp->ccp == NULL && fsp->id_list == NULL)
11560 || (fsp->ccp != NULL && fsp->ccp->constraint_type == CHOICE_CONSTRAINT_ANY)
11561 || (fsp->id_list != NULL && bsp != NULL && DoesIDListMeetStringConstraint (bsp->id, fsp->id_list)))
11562 {
11563 if (feature_action != NULL)
11564 {
11565 cod.omtp = ObjMgrTypeFind (cod.omp, OBJ_SEQFEAT, NULL, NULL);
11566 if (cod.omtp != NULL)
11567 {
11568 if (bsp == NULL)
11569 {
11570 VisitBioseqsInSep (sep, &cod, BioseqConstrainedFeaturesCallback);
11571 }
11572 else
11573 {
11574 sfp = SeqMgrGetNextFeature (bsp, NULL, 0, 0, &fcontext);
11575 while (sfp != NULL)
11576 {
11577 SeqEntryConstrainedFeaturesCallback (sfp, &cod);
11578 sfp = SeqMgrGetNextFeature (bsp, sfp, 0, 0, &fcontext);
11579 }
11580 }
11581 }
11582 }
11583
11584 if (descriptor_action != NULL)
11585 {
11586 cod.omtp = ObjMgrTypeFind (cod.omp, OBJ_SEQDESC, NULL, NULL);
11587 if (cod.omtp != NULL)
11588 {
11589 if (bsp == NULL)
11590 {
11591 VisitDescriptorsInSep (sep, &cod, SeqEntryConstrainedDescriptorsCallback);
11592 }
11593 else
11594 {
11595 sdp = SeqMgrGetNextDescriptor (bsp, NULL, 0, &dcontext);
11596 while (sdp != NULL)
11597 {
11598 SeqEntryConstrainedDescriptorsCallback (sdp, &cod);
11599 sdp = SeqMgrGetNextDescriptor (bsp, sdp, 0, &dcontext);
11600 }
11601 }
11602 }
11603 }
11604 }
11605 else if (fsp->id_list != NULL)
11606 {
11607 ConstrainedBioseqCallback (sep, &cod);
11608 }
11609 else
11610 {
11611 ConstrainedSourceCallback (sep, &cod);
11612 }
11613
11614 AsnIoClose (cod.aip);
11615 SeqEntrySetScope (old_scope);
11616 }
11617
GetSampleNew(void)11618 extern GetSamplePtr GetSampleNew (void)
11619 {
11620 GetSamplePtr gsp;
11621
11622 gsp = (GetSamplePtr) MemNew (sizeof (GetSampleData));
11623 if (gsp != NULL)
11624 {
11625 gsp->all_same = TRUE;
11626 gsp->sample_text = NULL;
11627 gsp->num_found = 0;
11628 gsp->feat_dest_list = NULL;
11629 gsp->descr_dest_list = NULL;
11630
11631 gsp->fieldstring_func = NULL;
11632 gsp->descrstring_func = NULL;
11633 gsp->requested_field = NULL;
11634 gsp->free_vn_proc = NULL;
11635 gsp->copy_vn_proc = NULL;
11636 }
11637 return gsp;
11638 }
11639
GetSampleFree(GetSamplePtr gsp)11640 extern GetSamplePtr GetSampleFree (GetSamplePtr gsp)
11641 {
11642 if (gsp != NULL)
11643 {
11644 gsp->sample_text = MemFree (gsp->sample_text);
11645 if (gsp->free_vn_proc != NULL)
11646 {
11647 (gsp->free_vn_proc)(gsp->requested_field);
11648 }
11649 gsp->requested_field = ValNodeFree (gsp->requested_field);
11650 gsp->feat_dest_list = ValNodeFree (gsp->feat_dest_list);
11651 gsp->descr_dest_list = ValNodeFree (gsp->descr_dest_list);
11652 gsp = MemFree (gsp);
11653 }
11654 return gsp;
11655 }
11656
GetSampleCopy(GetSamplePtr gsp)11657 static GetSamplePtr GetSampleCopy (GetSamplePtr gsp)
11658 {
11659 GetSamplePtr copy_gsp;
11660 ValNodePtr copy_vnp;
11661
11662 if (gsp == NULL)
11663 {
11664 return NULL;
11665 }
11666
11667 copy_gsp = (GetSamplePtr) MemNew (sizeof (GetSampleData));
11668 if (copy_gsp != NULL)
11669 {
11670 copy_gsp->fieldstring_func = gsp->fieldstring_func;
11671 copy_gsp->descrstring_func = gsp->descrstring_func;
11672 copy_gsp->free_vn_proc = gsp->free_vn_proc;
11673 copy_gsp->copy_vn_proc = gsp->copy_vn_proc;
11674 if (copy_gsp->copy_vn_proc != NULL)
11675 {
11676 copy_gsp->requested_field = (gsp->copy_vn_proc) (gsp->requested_field);
11677 }
11678 copy_gsp->sample_text = StringSave (gsp->sample_text);
11679 copy_gsp->num_found = gsp->num_found;
11680 copy_gsp->all_same = gsp->all_same;
11681
11682 copy_vnp = gsp->feat_dest_list;
11683 copy_gsp->feat_dest_list = NULL;
11684 while (copy_vnp != NULL)
11685 {
11686 ValNodeAddPointer (&(copy_gsp->feat_dest_list), copy_vnp->choice, copy_vnp->data.ptrvalue);
11687 copy_vnp = copy_vnp->next;
11688 }
11689
11690 copy_vnp = gsp->descr_dest_list;
11691 copy_gsp->descr_dest_list = NULL;
11692 while (copy_vnp != NULL)
11693 {
11694 ValNodeAddPointer (&(copy_gsp->descr_dest_list), copy_vnp->choice, copy_vnp->data.ptrvalue);
11695 copy_vnp = copy_vnp->next;
11696 }
11697
11698 }
11699 return copy_gsp;
11700 }
11701
AddValNodeLists(ValNodePtr vnp1,ValNodePtr vnp2)11702 static ValNodePtr AddValNodeLists (ValNodePtr vnp1, ValNodePtr vnp2)
11703 {
11704 ValNodePtr new_list = NULL, copy_vnp, check_vnp;
11705
11706 /* copy first list */
11707 copy_vnp = vnp1;
11708 while (copy_vnp != NULL)
11709 {
11710 ValNodeAddPointer (&(new_list), copy_vnp->choice, copy_vnp->data.ptrvalue);
11711 copy_vnp = copy_vnp->next;
11712 }
11713
11714 copy_vnp = vnp2;
11715 while (copy_vnp != NULL)
11716 {
11717 /* check to see if destination is already in the list */
11718 check_vnp = new_list;
11719 while (check_vnp != NULL && check_vnp->data.ptrvalue != copy_vnp->data.ptrvalue)
11720 {
11721 check_vnp = check_vnp->next;
11722 }
11723
11724 if (check_vnp == NULL)
11725 {
11726 /* add to list if not present */
11727 ValNodeAddPointer (&new_list, copy_vnp->choice, copy_vnp->data.ptrvalue);
11728 }
11729 else if (check_vnp->choice < 250)
11730 {
11731 /* do not increase choice beyond 250 */
11732 check_vnp->choice ++;
11733 }
11734
11735 copy_vnp = copy_vnp->next;
11736 }
11737 return new_list;
11738 }
11739
GetSampleAdd(GetSamplePtr gsp1,GetSamplePtr gsp2)11740 static GetSamplePtr GetSampleAdd (GetSamplePtr gsp1, GetSamplePtr gsp2)
11741 {
11742 GetSamplePtr sum_gsp;
11743
11744 if (gsp1 == NULL && gsp2 == NULL)
11745 {
11746 sum_gsp = NULL;
11747 }
11748 else if (gsp1 == NULL)
11749 {
11750 sum_gsp = GetSampleCopy (gsp2);
11751 }
11752 else if (gsp2 == NULL)
11753 {
11754 sum_gsp = GetSampleCopy (gsp1);
11755 }
11756 else
11757 {
11758 sum_gsp = (GetSamplePtr) MemNew (sizeof (GetSampleData));
11759 if (sum_gsp != NULL)
11760 {
11761 sum_gsp->fieldstring_func = gsp1->fieldstring_func;
11762 sum_gsp->descrstring_func = gsp1->descrstring_func;
11763 sum_gsp->requested_field = gsp1->requested_field;
11764 gsp1->requested_field = NULL;
11765 sum_gsp->sample_text = StringSave (gsp1->sample_text);
11766 sum_gsp->num_found = gsp1->num_found + gsp2->num_found;
11767 if (gsp1->num_found == 0)
11768 {
11769 sum_gsp->all_same = gsp2->all_same;
11770 }
11771 else if (gsp2->num_found == 0)
11772 {
11773 sum_gsp->all_same = gsp1->all_same;
11774 }
11775 else if (!gsp1->all_same || ! gsp2->all_same)
11776 {
11777 sum_gsp->all_same = FALSE;
11778 }
11779 else if (StringCmp (gsp1->sample_text, gsp2->sample_text) == 0)
11780 {
11781 sum_gsp->all_same = TRUE;
11782 }
11783 else
11784 {
11785 sum_gsp->all_same = FALSE;
11786 }
11787
11788 /* combine destination lists */
11789 sum_gsp->feat_dest_list = AddValNodeLists (gsp1->feat_dest_list, gsp2->feat_dest_list);
11790
11791 }
11792 }
11793 return sum_gsp;
11794 }
11795
11796
GetSampleFeatureCallback(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)11797 static void GetSampleFeatureCallback (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
11798 {
11799 GetSamplePtr cp;
11800 CharPtr str;
11801 ValNodePtr check_vnp;
11802
11803 if (sfp == NULL || userdata == NULL)
11804 {
11805 return;
11806 }
11807
11808 cp = (GetSamplePtr) userdata;
11809 if (cp->fieldstring_func == NULL)
11810 {
11811 return;
11812 }
11813
11814 check_vnp = cp->feat_dest_list;
11815 while (check_vnp != NULL && check_vnp->data.ptrvalue != sfp)
11816 {
11817 check_vnp = check_vnp->next;
11818 }
11819 if (check_vnp == NULL)
11820 {
11821 ValNodeAddPointer (&(cp->feat_dest_list), 1, sfp);
11822 }
11823 else
11824 {
11825 if (check_vnp->choice < 250)
11826 {
11827 check_vnp->choice ++;
11828 }
11829 return;
11830 }
11831
11832 str = cp->fieldstring_func (sfp, cp->requested_field, NULL);
11833 if (!StringHasNoText (str) || (fsp != NULL && fsp->scp != NULL && fsp->scp->not_present))
11834 {
11835 cp->num_found ++;
11836 if (cp->sample_text == NULL)
11837 {
11838 cp->sample_text = str;
11839 }
11840 else
11841 {
11842 if (StringCmp (str, cp->sample_text) != 0)
11843 {
11844 cp->all_same = FALSE;
11845 }
11846 str = MemFree (str);
11847 }
11848 }
11849 }
11850
GetSampleDescriptorCallback(SeqDescrPtr sdp,Pointer userdata,FilterSetPtr fsp)11851 static void GetSampleDescriptorCallback (SeqDescrPtr sdp, Pointer userdata, FilterSetPtr fsp)
11852 {
11853 GetSamplePtr cp;
11854 CharPtr str;
11855 ValNodePtr check_vnp;
11856
11857 if (sdp == NULL || userdata == NULL)
11858 {
11859 return;
11860 }
11861
11862 cp = (GetSamplePtr) userdata;
11863 if (cp->descrstring_func == NULL)
11864 {
11865 return;
11866 }
11867
11868 check_vnp = cp->descr_dest_list;
11869 while (check_vnp != NULL && check_vnp->data.ptrvalue != sdp)
11870 {
11871 check_vnp = check_vnp->next;
11872 }
11873 if (check_vnp == NULL)
11874 {
11875 ValNodeAddPointer (&(cp->descr_dest_list), 1, sdp);
11876 }
11877 else
11878 {
11879 if (check_vnp->choice < 250)
11880 {
11881 check_vnp->choice ++;
11882 }
11883 return;
11884 }
11885
11886 str = cp->descrstring_func (sdp, cp->requested_field, NULL);
11887 if (!StringHasNoText (str))
11888 {
11889 cp->num_found ++;
11890 if (cp->sample_text == NULL)
11891 {
11892 cp->sample_text = str;
11893 }
11894 else
11895 {
11896 if (StringCmp (str, cp->sample_text) != 0)
11897 {
11898 cp->all_same = FALSE;
11899 }
11900 str = MemFree (str);
11901 }
11902 }
11903 }
11904
CheckForExistingTextInSeqEntry(SeqEntryPtr sep,ValNodePtr requested_field,GetFeatureFieldString fieldstring_func,GetDescriptorFieldString descrstring_func,FreeValNodeProc free_vn_proc,CopyValNodeDataProc copy_vn_proc,FilterSetPtr fsp,Uint1 seqfeat_choice,Uint1 featdef_choice,Uint1 descr_choice)11905 static GetSamplePtr CheckForExistingTextInSeqEntry
11906 (SeqEntryPtr sep,
11907 ValNodePtr requested_field,
11908 GetFeatureFieldString fieldstring_func,
11909 GetDescriptorFieldString descrstring_func,
11910 FreeValNodeProc free_vn_proc,
11911 CopyValNodeDataProc copy_vn_proc,
11912 FilterSetPtr fsp,
11913 Uint1 seqfeat_choice,
11914 Uint1 featdef_choice,
11915 Uint1 descr_choice)
11916 {
11917 GetSamplePtr gsp;
11918
11919 gsp = (GetSamplePtr) MemNew (sizeof (GetSampleData));
11920 if (gsp != NULL)
11921 {
11922 gsp->sample_text = NULL;
11923 gsp->fieldstring_func = fieldstring_func;
11924 gsp->descrstring_func = descrstring_func;
11925 gsp->free_vn_proc = free_vn_proc;
11926 gsp->copy_vn_proc = copy_vn_proc;
11927 gsp->requested_field = (gsp->copy_vn_proc) (requested_field);
11928 gsp->num_found = 0;
11929 gsp->all_same = TRUE;
11930 OperateOnSeqEntryConstrainedObjects (sep, fsp, GetSampleFeatureCallback,
11931 GetSampleDescriptorCallback,
11932 seqfeat_choice, featdef_choice,
11933 descr_choice, gsp);
11934 }
11935 return gsp;
11936 }
11937
CheckForExistingText(Uint2 entityID,ValNodePtr requested_field,GetFeatureFieldString fieldstring_func,GetDescriptorFieldString descrstring_func,FreeValNodeProc free_vn_proc,CopyValNodeDataProc copy_vn_proc,FilterSetPtr fsp,Uint1 seqfeat_choice,Uint1 featdef_choice,Uint1 descr_choice)11938 static GetSamplePtr CheckForExistingText
11939 (Uint2 entityID,
11940 ValNodePtr requested_field,
11941 GetFeatureFieldString fieldstring_func,
11942 GetDescriptorFieldString descrstring_func,
11943 FreeValNodeProc free_vn_proc,
11944 CopyValNodeDataProc copy_vn_proc,
11945 FilterSetPtr fsp,
11946 Uint1 seqfeat_choice,
11947 Uint1 featdef_choice,
11948 Uint1 descr_choice)
11949 {
11950 SeqEntryPtr sep;
11951
11952 sep = GetTopSeqEntryForEntityID (entityID);
11953 return CheckForExistingTextInSeqEntry (sep, requested_field,
11954 fieldstring_func, descrstring_func,
11955 free_vn_proc, copy_vn_proc, fsp,
11956 seqfeat_choice, featdef_choice, descr_choice);
11957 }
11958
HandleApplyValue(CharPtr orig_text,ApplyValuePtr avp)11959 extern CharPtr HandleApplyValue (CharPtr orig_text, ApplyValuePtr avp)
11960 {
11961 CharPtr new_str, cp_found;
11962 Int4 found_len, replace_len, new_len;
11963
11964 if (avp == NULL)
11965 {
11966 return orig_text;
11967 }
11968 else if (StringHasNoText (orig_text))
11969 {
11970 if (StringHasNoText (avp->text_to_replace))
11971 {
11972 MemFree (orig_text);
11973 return StringSave (avp->new_text);
11974 }
11975 else
11976 {
11977 return orig_text;
11978 }
11979 }
11980 else if (StringHasNoText (avp->text_to_replace))
11981 {
11982 return HandleExistingText (orig_text, StringSave (avp->new_text), avp->etp);
11983 }
11984 else
11985 {
11986 found_len = StringLen (avp->text_to_replace);
11987 replace_len = StringLen (avp->new_text);
11988 cp_found = StringISearch (orig_text, avp->text_to_replace);
11989 if (avp->where_to_replace == EditApplyFindLocation_beginning
11990 && cp_found != orig_text) {
11991 cp_found = NULL;
11992 }
11993 while (cp_found != NULL)
11994 {
11995 if (avp->where_to_replace == EditApplyFindLocation_end
11996 && cp_found != orig_text + StringLen (orig_text) - found_len) {
11997 cp_found = StringISearch (cp_found + found_len, avp->text_to_replace);
11998 } else {
11999 new_len = StringLen (orig_text) + 1 - found_len + replace_len;
12000 new_str = (CharPtr) MemNew (new_len * sizeof (Char));
12001 if (new_str != NULL)
12002 {
12003 if (cp_found != orig_text)
12004 {
12005 StringNCpy (new_str, orig_text, cp_found - orig_text);
12006 }
12007 StringCat (new_str, avp->new_text);
12008 StringCat (new_str, cp_found + found_len);
12009 cp_found = new_str + (cp_found - orig_text) + replace_len;
12010 orig_text = MemFree (orig_text);
12011 orig_text = new_str;
12012 }
12013 cp_found = StringISearch (cp_found, avp->text_to_replace);
12014 }
12015 }
12016 return orig_text;
12017 }
12018 }
12019
ApplyValueToValNodeStringList(ValNodePtr list,Int2 choice,ApplyValuePtr avp)12020 extern ValNodePtr ApplyValueToValNodeStringList (ValNodePtr list, Int2 choice, ApplyValuePtr avp)
12021 {
12022 ValNodePtr vnp;
12023
12024 if (avp == NULL)
12025 {
12026 return NULL;
12027 }
12028
12029 if (!StringHasNoText (avp->text_to_replace))
12030 {
12031 for (vnp = list; vnp != NULL; vnp = vnp->next)
12032 {
12033 vnp->data.ptrvalue = HandleApplyValue (vnp->data.ptrvalue, avp);
12034 }
12035 }
12036 else
12037 {
12038 ValNodeAddPointer (&list, choice, StringSave (avp->new_text));
12039 }
12040 return list;
12041 }
12042
12043
12044
MakeSemicolonStringsIntoSeparateItems(ValNodePtr PNTR list)12045 static void MakeSemicolonStringsIntoSeparateItems (ValNodePtr PNTR list)
12046 {
12047 ValNodePtr prev = NULL, vnp_next, vnp, vnp_new;
12048 CharPtr cp;
12049
12050 if (list == NULL || *list == NULL) return;
12051
12052 vnp = *list;
12053 while (vnp != NULL)
12054 {
12055 vnp_next = vnp->next;
12056 if (StringHasNoText (vnp->data.ptrvalue))
12057 {
12058 if (prev == NULL)
12059 {
12060 *list = vnp_next;
12061 }
12062 else
12063 {
12064 prev->next = vnp_next;
12065 }
12066 vnp->next = NULL;
12067 vnp = ValNodeFreeData (vnp);
12068 }
12069 else if ((cp = StringChr (vnp->data.ptrvalue, ';')) != NULL)
12070 {
12071 vnp_new = ValNodeNew (NULL);
12072 vnp_new->choice = vnp->choice;
12073 vnp_new->data.ptrvalue = StringSave (cp + 1);
12074 vnp_new->next = vnp_next;
12075 *cp = 0;
12076 vnp->next = vnp_new;
12077 vnp_next = vnp_new;
12078 prev = vnp;
12079 }
12080 else
12081 {
12082 prev = vnp;
12083 }
12084 vnp = vnp_next;
12085 }
12086 }
12087
12088
ApplyValueToValNodeStringListAsText(ValNodePtr list,Int2 choice,ApplyValuePtr avp)12089 extern ValNodePtr ApplyValueToValNodeStringListAsText (ValNodePtr list, Int2 choice, ApplyValuePtr avp)
12090 {
12091 ValNodePtr vnp;
12092
12093 if (avp == NULL)
12094 {
12095 return NULL;
12096 }
12097
12098 if (!StringHasNoText (avp->text_to_replace))
12099 {
12100 for (vnp = list; vnp != NULL; vnp = vnp->next)
12101 {
12102 vnp->data.ptrvalue = HandleApplyValue (vnp->data.ptrvalue, avp);
12103 }
12104 }
12105 else
12106 {
12107 if (avp->etp == NULL
12108 || avp->etp->existing_text_choice == eExistingTextChoiceReplaceOld)
12109 {
12110 list = ValNodeFree (list);
12111 ValNodeAddPointer (&list, choice, StringSave (avp->new_text));
12112 }
12113 else if (avp->etp->existing_text_choice == eExistingTextChoiceAppendSemi)
12114 {
12115 ValNodeAddPointer (&list, choice, StringSave (avp->new_text));
12116 }
12117 else if (avp->etp->existing_text_choice == eExistingTextChoicePrefixSemi)
12118 {
12119 vnp = ValNodeNew(NULL);
12120 vnp->choice = (Uint1) choice;
12121 vnp->data.ptrvalue = StringSave (avp->new_text);
12122 vnp->next = list;
12123 list = vnp;
12124 }
12125 else if (avp->etp->existing_text_choice == eExistingTextChoiceLeaveOld)
12126 {
12127 if (list == NULL)
12128 {
12129 ValNodeAddPointer (&list, choice, StringSave (avp->new_text));
12130 }
12131 } else {
12132 for (vnp = list; vnp != NULL; vnp = vnp->next)
12133 {
12134 vnp->data.ptrvalue = HandleApplyValue (vnp->data.ptrvalue, avp);
12135 }
12136 }
12137 }
12138
12139 if (avp->etp == NULL || avp->etp->existing_text_choice != eExistingTextChoiceLeaveOld)
12140 {
12141 MakeSemicolonStringsIntoSeparateItems (&list);
12142 }
12143 return list;
12144 }
12145
12146
12147 typedef struct parsefielddialog
12148 {
12149 DIALOG_MESSAGE_BLOCK
12150 DialoG parse_field_type;
12151 DialoG biosrc_string_choice;
12152 DialoG source_qual_choice;
12153 DialoG gene_field;
12154 DialoG rna_subtype;
12155 DialoG rna_field;
12156 DialoG protein_field;
12157 DialoG import_feature;
12158 DialoG import_qual;
12159 DialoG feature;
12160 GrouP dbxref_grp;
12161 TexT dbxref_db;
12162 GrouP feat_or_desc;
12163 Nlm_ChangeNotifyProc change_notify;
12164 Pointer change_userdata;
12165 Boolean is_search_field;
12166 } ParseFieldDialogData, PNTR ParseFieldDialogPtr;
12167
ChangeParseFieldType(Pointer data)12168 static void ChangeParseFieldType (Pointer data)
12169 {
12170 ParseFieldDialogPtr dlg;
12171 ValNodePtr vnp;
12172
12173 dlg = (ParseFieldDialogPtr) data;
12174 if (dlg == NULL)
12175 {
12176 return;
12177 }
12178 vnp = DialogToPointer (dlg->parse_field_type);
12179 Hide (dlg->biosrc_string_choice);
12180 Hide (dlg->feat_or_desc);
12181 Hide (dlg->source_qual_choice);
12182 Hide (dlg->gene_field);
12183 Hide (dlg->rna_subtype);
12184 Hide (dlg->rna_field);
12185 Hide (dlg->protein_field);
12186 Hide (dlg->import_feature);
12187 Hide (dlg->import_qual);
12188 Hide (dlg->feature);
12189 Hide (dlg->dbxref_grp);
12190 if (vnp != NULL)
12191 {
12192 switch (vnp->choice)
12193 {
12194 case PARSE_FIELD_BIOSRC_STRING:
12195 Show (dlg->biosrc_string_choice);
12196 Show (dlg->feat_or_desc);
12197 break;
12198 case PARSE_FIELD_SOURCE_QUAL:
12199 Show (dlg->source_qual_choice);
12200 Show (dlg->feat_or_desc);
12201 break;
12202 case PARSE_FIELD_GENE_FIELD:
12203 Show (dlg->gene_field);
12204 break;
12205 case PARSE_FIELD_RNA_FIELD:
12206 Show (dlg->rna_subtype);
12207 Show (dlg->rna_field);
12208 break;
12209 case PARSE_FIELD_PROTEIN_FIELD:
12210 Show (dlg->protein_field);
12211 break;
12212 case PARSE_FIELD_IMPORT_QUAL:
12213 Show (dlg->import_feature);
12214 Show (dlg->import_qual);
12215 break;
12216 case PARSE_FIELD_FEATURE_NOTE:
12217 Show (dlg->feature);
12218 break;
12219 case PARSE_FIELD_DBXREF:
12220 Show (dlg->dbxref_grp);
12221 break;
12222 }
12223 }
12224 if (dlg->change_notify != NULL)
12225 {
12226 (dlg->change_notify)(dlg->change_userdata);
12227 }
12228 }
12229
ResetParseFieldDialog(ParseFieldDialogPtr dlg)12230 static void ResetParseFieldDialog (ParseFieldDialogPtr dlg)
12231 {
12232 ValNode vn;
12233
12234 if (dlg == NULL)
12235 {
12236 return;
12237 }
12238 vn.choice = PARSE_FIELD_DEFLINE;
12239 vn.data.ptrvalue = NULL;
12240 vn.next = NULL;
12241 PointerToDialog (dlg->parse_field_type, &vn);
12242 ChangeParseFieldType (dlg);
12243 }
12244
ParseFieldToDialog(DialoG d,Pointer data)12245 static void ParseFieldToDialog (DialoG d, Pointer data)
12246 {
12247 ParseFieldDialogPtr dlg;
12248 ParseFieldPtr parse_field;
12249 Int4 parse_field_type;
12250 ValNode vn;
12251
12252 dlg = (ParseFieldDialogPtr) GetObjectExtra (d);
12253 if (dlg == NULL)
12254 {
12255 return;
12256 }
12257 ResetParseFieldDialog (dlg);
12258 parse_field = (ParseFieldPtr) data;
12259 if (parse_field != NULL)
12260 {
12261 parse_field_type = parse_field->parse_field_type;
12262 if (parse_field_type < PARSE_FIELD_DEFLINE
12263 || (dlg->is_search_field && parse_field_type > SEARCH_FIELD_PUBLICATION)
12264 || (!dlg->is_search_field && parse_field_type > MAX_PARSE_FIELD_TYPE))
12265 {
12266 parse_field_type = PARSE_FIELD_DEFLINE;
12267 }
12268 vn.choice = parse_field_type;
12269 vn.data.ptrvalue = NULL;
12270 vn.next = NULL;
12271 PointerToDialog (dlg->parse_field_type, &vn);
12272 switch (parse_field_type)
12273 {
12274 case PARSE_FIELD_BIOSRC_STRING:
12275 PointerToDialog (dlg->biosrc_string_choice, parse_field->feature_field);
12276 if (parse_field->do_desc && parse_field->do_feat)
12277 {
12278 SetValue (dlg->feat_or_desc, 1);
12279 }
12280 else if (parse_field->do_desc)
12281 {
12282 SetValue (dlg->feat_or_desc, 2);
12283 }
12284 else if (parse_field->do_feat)
12285 {
12286 SetValue (dlg->feat_or_desc, 3);
12287 }
12288 else
12289 {
12290 SetValue (dlg->feat_or_desc, 1);
12291 }
12292 break;
12293 case PARSE_FIELD_SOURCE_QUAL:
12294 PointerToDialog (dlg->source_qual_choice, parse_field->feature_field);
12295 if (parse_field->do_desc && parse_field->do_feat)
12296 {
12297 SetValue (dlg->feat_or_desc, 1);
12298 }
12299 else if (parse_field->do_desc)
12300 {
12301 SetValue (dlg->feat_or_desc, 2);
12302 }
12303 else if (parse_field->do_feat)
12304 {
12305 SetValue (dlg->feat_or_desc, 3);
12306 }
12307 else
12308 {
12309 SetValue (dlg->feat_or_desc, 1);
12310 }
12311 break;
12312 case PARSE_FIELD_DBXREF:
12313 if (parse_field->feature_field == NULL || parse_field->feature_field->data.ptrvalue == NULL)
12314 {
12315 SetTitle (dlg->dbxref_db, "");
12316 }
12317 else
12318 {
12319 SetTitle (dlg->dbxref_db, parse_field->feature_field->data.ptrvalue);
12320 }
12321 if (parse_field->do_desc && parse_field->do_feat)
12322 {
12323 SetValue (dlg->feat_or_desc, 1);
12324 }
12325 else if (parse_field->do_desc)
12326 {
12327 SetValue (dlg->feat_or_desc, 2);
12328 }
12329 else if (parse_field->do_feat)
12330 {
12331 SetValue (dlg->feat_or_desc, 3);
12332 }
12333 else
12334 {
12335 SetValue (dlg->feat_or_desc, 1);
12336 }
12337 break;
12338 case PARSE_FIELD_GENE_FIELD:
12339 PointerToDialog (dlg->gene_field, parse_field->feature_field);
12340 break;
12341 case PARSE_FIELD_RNA_FIELD:
12342 PointerToDialog (dlg->rna_subtype, parse_field->feature_subtype);
12343 PointerToDialog (dlg->rna_field, parse_field->feature_field);
12344 break;
12345 case PARSE_FIELD_PROTEIN_FIELD:
12346 PointerToDialog (dlg->protein_field, parse_field->feature_field);
12347 break;
12348 case PARSE_FIELD_IMPORT_QUAL:
12349 PointerToDialog (dlg->import_feature, parse_field->feature_subtype);
12350 PointerToDialog (dlg->import_qual, parse_field->feature_field);
12351 break;
12352 case PARSE_FIELD_FEATURE_NOTE:
12353 PointerToDialog (dlg->feature, parse_field->feature_field);
12354 break;
12355 case SEARCH_FIELD_PUBLICATION:
12356 /* nothing to do here */
12357 break;
12358 }
12359 }
12360 ChangeParseFieldType (dlg);
12361 }
12362
DialogToParseField(DialoG d)12363 static Pointer DialogToParseField (DialoG d)
12364 {
12365 ParseFieldDialogPtr dlg;
12366 ParseFieldPtr parse_field;
12367 Int4 val;
12368 ValNodePtr vnp;
12369
12370 dlg = (ParseFieldDialogPtr) GetObjectExtra (d);
12371 if (dlg == NULL)
12372 {
12373 return NULL;
12374 }
12375 vnp = DialogToPointer (dlg->parse_field_type);
12376 if (vnp == NULL)
12377 {
12378 return NULL;
12379 }
12380
12381 parse_field = (ParseFieldPtr) MemNew (sizeof (ParseFieldData));
12382 if (parse_field != NULL)
12383 {
12384 parse_field->parse_field_type = vnp->choice;
12385 parse_field->feature_field = NULL;
12386 switch (parse_field->parse_field_type)
12387 {
12388 case PARSE_FIELD_BIOSRC_STRING:
12389 parse_field->feature_field = DialogToPointer (dlg->biosrc_string_choice);
12390 val = GetValue (dlg->feat_or_desc);
12391 switch (val)
12392 {
12393 case 2:
12394 parse_field->do_desc = TRUE;
12395 parse_field->do_feat = FALSE;
12396 break;
12397 case 3:
12398 parse_field->do_desc = FALSE;
12399 parse_field->do_feat = TRUE;
12400 break;
12401 case 1:
12402 default:
12403 parse_field->do_desc = TRUE;
12404 parse_field->do_feat = TRUE;
12405 break;
12406 }
12407 break;
12408 case PARSE_FIELD_SOURCE_QUAL:
12409 parse_field->feature_field = DialogToPointer (dlg->source_qual_choice);
12410 val = GetValue (dlg->feat_or_desc);
12411 switch (val)
12412 {
12413 case 2:
12414 parse_field->do_desc = TRUE;
12415 parse_field->do_feat = FALSE;
12416 break;
12417 case 3:
12418 parse_field->do_desc = FALSE;
12419 parse_field->do_feat = TRUE;
12420 break;
12421 case 1:
12422 default:
12423 parse_field->do_desc = TRUE;
12424 parse_field->do_feat = TRUE;
12425 break;
12426 }
12427 break;
12428 case PARSE_FIELD_DBXREF:
12429 if (!TextHasNoText (dlg->dbxref_db))
12430 {
12431 ValNodeAddPointer (&(parse_field->feature_field), 0, SaveStringFromText (dlg->dbxref_db));
12432 }
12433 val = GetValue (dlg->feat_or_desc);
12434 switch (val)
12435 {
12436 case 2:
12437 parse_field->do_desc = TRUE;
12438 parse_field->do_feat = FALSE;
12439 break;
12440 case 3:
12441 parse_field->do_desc = FALSE;
12442 parse_field->do_feat = TRUE;
12443 break;
12444 case 1:
12445 default:
12446 parse_field->do_desc = TRUE;
12447 parse_field->do_feat = TRUE;
12448 break;
12449 }
12450 break;
12451 case PARSE_FIELD_GENE_FIELD:
12452 parse_field->feature_field = DialogToPointer (dlg->gene_field);
12453 break;
12454 case PARSE_FIELD_RNA_FIELD:
12455 parse_field->feature_subtype = DialogToPointer (dlg->rna_subtype);
12456 parse_field->feature_field = DialogToPointer (dlg->rna_field);
12457 break;
12458 case PARSE_FIELD_PROTEIN_FIELD:
12459 parse_field->feature_field = DialogToPointer (dlg->protein_field);
12460 break;
12461 case PARSE_FIELD_IMPORT_QUAL:
12462 parse_field->feature_subtype = DialogToPointer (dlg->import_feature);
12463 parse_field->feature_field = DialogToPointer (dlg->import_qual);
12464 break;
12465 case PARSE_FIELD_FEATURE_NOTE:
12466 parse_field->feature_field = DialogToPointer (dlg->feature);
12467 break;
12468 case SEARCH_FIELD_PUBLICATION:
12469 /* nothing to do here */
12470 break;
12471 }
12472 }
12473 vnp = ValNodeFreeData (vnp);
12474 return parse_field;
12475 }
12476
ParseFieldMessage(DialoG d,Int2 mssg)12477 static void ParseFieldMessage (DialoG d, Int2 mssg)
12478
12479 {
12480 ParseFieldDialogPtr dlg;
12481
12482 dlg = (ParseFieldDialogPtr) GetObjectExtra (d);
12483 if (dlg != NULL) {
12484 switch (mssg) {
12485 case VIB_MSG_INIT :
12486 ResetParseFieldDialog (dlg);
12487 break;
12488 case VIB_MSG_ENTER :
12489 Select (dlg->parse_field_type);
12490 break;
12491 default :
12492 break;
12493 }
12494 }
12495 }
12496
TestParseFieldDialog(DialoG d)12497 static ValNodePtr TestParseFieldDialog (DialoG d)
12498
12499 {
12500 ValNodePtr head = NULL;
12501 ParseFieldDialogPtr dlg;
12502 Int4 parse_field_type;
12503 ValNodePtr vnp;
12504
12505 dlg = (ParseFieldDialogPtr) GetObjectExtra (d);
12506
12507 if (dlg != NULL)
12508 {
12509 vnp = DialogToPointer (dlg->parse_field_type);
12510 if (vnp == NULL)
12511 {
12512 head = AddStringToValNodeChain (head, "destination type", 1);
12513 }
12514 else
12515 {
12516 parse_field_type = vnp->choice;
12517 vnp = ValNodeFreeData (vnp);
12518 switch (parse_field_type)
12519 {
12520 case PARSE_FIELD_DEFLINE:
12521 case PARSE_FIELD_CDS_COMMENT:
12522 case PARSE_FIELD_COMMENT_DESC:
12523 /* don't need any extra information */
12524 break;
12525 case PARSE_FIELD_BIOSRC_STRING:
12526 vnp = DialogToPointer (dlg->biosrc_string_choice);
12527 if (vnp == NULL)
12528 {
12529 head = AddStringToValNodeChain (head, "biosrc string type", 1);
12530 }
12531 ValNodeFree (vnp);
12532 break;
12533 case PARSE_FIELD_SOURCE_QUAL:
12534 vnp = DialogToPointer (dlg->source_qual_choice);
12535 if (vnp == NULL)
12536 {
12537 head = AddStringToValNodeChain (head, "source qual type", 1);
12538 }
12539 ValNodeFree (vnp);
12540 break;
12541 case PARSE_FIELD_GENE_FIELD:
12542 vnp = DialogToPointer (dlg->gene_field);
12543 if (vnp == NULL || vnp->data.intvalue == FEATUREFIELD_NONE)
12544 {
12545 head = AddStringToValNodeChain (head, "gene field", 1);
12546 }
12547 ValNodeFree (vnp);
12548 break;
12549 case PARSE_FIELD_RNA_FIELD:
12550 vnp = DialogToPointer (dlg->rna_subtype);
12551 if (vnp == NULL)
12552 {
12553 head = AddStringToValNodeChain (head, "RNA subtype", 1);
12554 }
12555 ValNodeFree (vnp);
12556 vnp = DialogToPointer (dlg->rna_field);
12557 if (vnp == NULL || vnp->data.intvalue == FEATUREFIELD_NONE)
12558 {
12559 head = AddStringToValNodeChain (head, "RNA field", 1);
12560 }
12561 ValNodeFree (vnp);
12562 break;
12563 case PARSE_FIELD_PROTEIN_FIELD:
12564 vnp = DialogToPointer (dlg->protein_field);
12565 if (vnp == NULL || vnp->data.intvalue == FEATUREFIELD_NONE)
12566 {
12567 head = AddStringToValNodeChain (head, "protein field", 1);
12568 }
12569 ValNodeFree (vnp);
12570 break;
12571 case PARSE_FIELD_IMPORT_QUAL:
12572 vnp = DialogToPointer (dlg->import_qual);
12573 if (vnp == NULL)
12574 {
12575 ValNodeAddPointer (&head, 1, "import qualifier");
12576 }
12577 ValNodeFree (vnp);
12578 vnp = DialogToPointer (dlg->import_feature);
12579 if (vnp == NULL)
12580 {
12581 ValNodeAddPointer (&head, 1, "import feature");
12582 }
12583 ValNodeFree (vnp);
12584 break;
12585 case PARSE_FIELD_FEATURE_NOTE:
12586 vnp = DialogToPointer (dlg->feature);
12587 if (vnp == NULL)
12588 {
12589 ValNodeAddPointer (&head, 1, "feature");
12590 ValNodeFree (vnp);
12591 }
12592 break;
12593 case PARSE_FIELD_DBXREF:
12594 if (TextHasNoText (dlg->dbxref_db))
12595 {
12596 ValNodeAddPointer (&head, 1, "specify database");
12597 }
12598 break;
12599 case SEARCH_FIELD_PUBLICATION:
12600 if (!dlg->is_search_field)
12601 {
12602 head = AddStringToValNodeChain (head, "field type", 1);
12603 }
12604 break;
12605 default:
12606 head = AddStringToValNodeChain (head, "field type", 1);
12607 break;
12608 }
12609 }
12610 }
12611
12612 return head;
12613 }
12614
12615
GetParseFieldDestList(Boolean include_pub,Boolean include_dbxref)12616 static ValNodePtr GetParseFieldDestList (Boolean include_pub, Boolean include_dbxref)
12617 {
12618 ValNodePtr list = NULL;
12619
12620 ValNodeAddPointer (&list, PARSE_FIELD_DEFLINE, StringSave ("Definition Line"));
12621 ValNodeAddPointer (&list, PARSE_FIELD_BIOSRC_STRING, StringSave ("Biosource"));
12622 ValNodeAddPointer (&list, PARSE_FIELD_SOURCE_QUAL, StringSave ("Source Qualifier"));
12623 ValNodeAddPointer (&list, PARSE_FIELD_GENE_FIELD, StringSave ("Gene Field"));
12624 ValNodeAddPointer (&list, PARSE_FIELD_RNA_FIELD, StringSave ("RNA Field"));
12625 ValNodeAddPointer (&list, PARSE_FIELD_CDS_COMMENT, StringSave ("CDS Comment"));
12626 ValNodeAddPointer (&list, PARSE_FIELD_PROTEIN_FIELD, StringSave ("Protein Field"));
12627 ValNodeAddPointer (&list, PARSE_FIELD_IMPORT_QUAL, StringSave ("Import Feature"));
12628 ValNodeAddPointer (&list, PARSE_FIELD_FEATURE_NOTE, StringSave ("Feature Note"));
12629 ValNodeAddPointer (&list, PARSE_FIELD_COMMENT_DESC, StringSave ("Comment Descriptor"));
12630 if (include_dbxref)
12631 {
12632 ValNodeAddPointer (&list, PARSE_FIELD_DBXREF, StringSave ("Dbxref"));
12633 }
12634 if (include_pub)
12635 {
12636 ValNodeAddPointer (&list, SEARCH_FIELD_PUBLICATION, StringSave ("Publication"));
12637 }
12638 return list;
12639 }
12640
12641
ChangeParseFieldDestText(TexT t)12642 static void ChangeParseFieldDestText (TexT t)
12643 {
12644 ParseFieldDialogPtr dlg;
12645
12646 dlg = (ParseFieldDialogPtr) GetObjectExtra (t);
12647 if (dlg != NULL && dlg->change_notify != NULL)
12648 {
12649 (dlg->change_notify) (dlg->change_userdata);
12650 }
12651 }
12652
12653
ParseFieldDestDialogEx(GrouP h,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata,Boolean is_search_field,Boolean include_dbxref)12654 extern DialoG ParseFieldDestDialogEx
12655 (GrouP h,
12656 Nlm_ChangeNotifyProc change_notify,
12657 Pointer change_userdata,
12658 Boolean is_search_field,
12659 Boolean include_dbxref)
12660 {
12661 ParseFieldDialogPtr dlg;
12662 GrouP p, m, g;
12663 GrouP subgrp;
12664 ValNodePtr choice_list;
12665 ValNode vn;
12666
12667 dlg = (ParseFieldDialogPtr) MemNew (sizeof (ParseFieldDialogData));
12668 if (dlg == NULL)
12669 {
12670 return NULL;
12671 }
12672
12673 p = HiddenGroup (h, -1, 0, NULL);
12674 SetObjectExtra (p, dlg, StdCleanupExtraProc);
12675
12676 dlg->dialog = (DialoG) p;
12677 dlg->todialog = ParseFieldToDialog;
12678 dlg->fromdialog = DialogToParseField;
12679 dlg->dialogmessage = ParseFieldMessage;
12680 dlg->testdialog = TestParseFieldDialog;
12681 dlg->change_notify = change_notify;
12682 dlg->change_userdata = change_userdata;
12683 dlg->is_search_field = is_search_field;
12684
12685 m = HiddenGroup (p, 2, 0, NULL);
12686
12687 choice_list = GetParseFieldDestList (is_search_field, include_dbxref);
12688 dlg->parse_field_type = ValNodeSelectionDialog (m, choice_list, TALL_SELECTION_LIST, ValNodeStringName,
12689 ValNodeSimpleDataFree, ValNodeStringCopy,
12690 ValNodeChoiceMatch, "parse destination",
12691 ChangeParseFieldType, dlg, FALSE);
12692
12693 subgrp = HiddenGroup (m, 0, 0, NULL);
12694 dlg->biosrc_string_choice = BioSourceStringDialog (subgrp, FALSE, change_notify, change_userdata);
12695 Hide (dlg->biosrc_string_choice);
12696 dlg->source_qual_choice = SourceQualTypeSelectionDialog (subgrp, FALSE, change_notify, change_userdata);
12697 Hide (dlg->source_qual_choice);
12698 dlg->gene_field = GeneFieldSelectionDialog (subgrp, FALSE, change_notify, change_userdata);
12699 Hide (dlg->gene_field);
12700 g = HiddenGroup (subgrp, 2, 0, NULL);
12701 dlg->rna_subtype = RNASubtypeSelectionDialog (g, FALSE, NULL, change_notify, change_userdata);
12702 Hide (dlg->rna_subtype);
12703 dlg->rna_field = RNAFieldSelectionDialog (g, FALSE,
12704 change_notify,
12705 change_userdata);
12706 Hide (dlg->rna_field);
12707 dlg->protein_field = ProteinFieldSelectionDialog (subgrp, FALSE, change_notify, change_userdata);
12708 Hide (dlg->protein_field);
12709 g = HiddenGroup (subgrp, 2, 0, NULL);
12710 dlg->import_feature = FeatureSelectionDialog (g, TRUE, change_notify, change_userdata);
12711 Hide (dlg->import_feature);
12712 dlg->import_qual = GBQualSelectionDialog (g, FALSE, change_notify, change_userdata);
12713 Hide (dlg->import_qual);
12714 dlg->feature = FeatureSelectionDialog (subgrp, TRUE, change_notify, change_userdata);
12715 Hide (dlg->feature);
12716 if (include_dbxref)
12717 {
12718 dlg->dbxref_grp = HiddenGroup (subgrp, 2, 0, NULL);
12719 StaticPrompt (dlg->dbxref_grp, "Database:", 0, 0, programFont, 'r');
12720 dlg->dbxref_db = DialogText (dlg->dbxref_grp, "", 5, ChangeParseFieldDestText);
12721 SetObjectExtra (dlg->dbxref_db, dlg, NULL);
12722 Hide (dlg->dbxref_grp);
12723 }
12724 else
12725 {
12726 dlg->dbxref_db = NULL;
12727 }
12728
12729 vn.choice = PARSE_FIELD_DEFLINE;
12730 vn.data.ptrvalue = NULL;
12731 vn.next = NULL;
12732 PointerToDialog (dlg->parse_field_type, &vn);
12733
12734 dlg->feat_or_desc = HiddenGroup (p, 3, 0, NULL);
12735 RadioButton (dlg->feat_or_desc, "Descriptors and Features");
12736 RadioButton (dlg->feat_or_desc, "Descriptors Only");
12737 RadioButton (dlg->feat_or_desc, "Features Only");
12738 SetValue (dlg->feat_or_desc, 1);
12739 Hide (dlg->feat_or_desc);
12740
12741 AlignObjects (ALIGN_CENTER, (HANDLE) m, (HANDLE) dlg->feat_or_desc, NULL);
12742
12743 return (DialoG) p;
12744 }
12745
ParseFieldDestDialog(GrouP h,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)12746 extern DialoG ParseFieldDestDialog
12747 (GrouP h,
12748 Nlm_ChangeNotifyProc change_notify,
12749 Pointer change_userdata)
12750 {
12751 return ParseFieldDestDialogEx (h, change_notify, change_userdata, FALSE, FALSE);
12752 }
12753 /* Search Field dialog is identical to ParseFieldDestDialog except that it allows
12754 * an additional option, Publication.
12755 */
SearchFieldDialog(GrouP h,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)12756 extern DialoG SearchFieldDialog
12757 (GrouP h,
12758 Nlm_ChangeNotifyProc change_notify,
12759 Pointer change_userdata)
12760 {
12761 return ParseFieldDestDialogEx (h, change_notify, change_userdata, TRUE, FALSE);
12762 }
12763
12764
12765 typedef enum
12766 {
12767 eParseFieldSrcDefLine = 1,
12768 eParseFieldSrcGenBankFlatFile,
12769 eParseFieldSrcLocalID,
12770 eParseFieldSrcTaxName,
12771 eParseFieldSrcSourceQual,
12772 eParseFieldSrcComment,
12773 eParseFieldSrcBankitComment,
12774 eParseFieldSrcStructuredComment,
12775 eParseFieldSrcTaxNameAfterNomial,
12776 eParseFieldSrcFileID
12777 } EParseFieldSrc;
12778
12779 const Int4 MAX_PARSE_FIELD = eParseFieldSrcFileID;
12780
12781 static CharPtr parse_src_field_list [] =
12782 {
12783 "Definition Line", "GenBank Flatfile", "Local ID", "Organism Name", "Source Qualifier", "Comment", "Bankit Comment",
12784 "Structured Comment", "Taxname after Binomial/Trinomial", "File ID"
12785 };
12786
12787 static int num_parse_src_fields = sizeof (parse_src_field_list) / sizeof (CharPtr);
12788
12789 typedef struct parsefieldsrc
12790 {
12791 Int4 parse_field;
12792 SourceQualDescPtr sqdp;
12793 CharPtr comment_field;
12794 } ParseFieldSrcData, PNTR ParseFieldSrcPtr;
12795
ParseFieldSrcFree(ParseFieldSrcPtr pfsp)12796 static ParseFieldSrcPtr ParseFieldSrcFree (ParseFieldSrcPtr pfsp)
12797 {
12798 if (pfsp != NULL) {
12799 pfsp->comment_field = MemFree (pfsp->comment_field);
12800 pfsp->sqdp = MemFree (pfsp->sqdp);
12801 pfsp = MemFree (pfsp);
12802 }
12803 return pfsp;
12804 }
12805
12806 typedef struct parsefieldsrcdlg
12807 {
12808 DIALOG_MESSAGE_BLOCK
12809 DialoG parse_field;
12810 PopuP comment_field;
12811 ValNodePtr comment_field_list;
12812 DialoG src_qual;
12813 Nlm_ChangeNotifyProc change_notify;
12814 Pointer change_userdata;
12815 } ParseFieldSrcDlgData, PNTR ParseFieldSrcDlgPtr;
12816
CleanupParseFieldSrcDialog(GraphiC g,VoidPtr data)12817 static void CleanupParseFieldSrcDialog (GraphiC g, VoidPtr data)
12818 {
12819 ParseFieldSrcDlgPtr dlg;
12820
12821 dlg = (ParseFieldSrcDlgPtr) data;
12822 if (dlg != NULL) {
12823 dlg->comment_field_list = ValNodeFreeData(dlg->comment_field_list);
12824 }
12825 StdCleanupExtraProc (g, data);
12826 }
12827
ResetParseFieldSourceDialog(ParseFieldSrcDlgPtr dlg)12828 static void ResetParseFieldSourceDialog (ParseFieldSrcDlgPtr dlg)
12829 {
12830 if (dlg == NULL) {
12831 return;
12832 }
12833 SendMessageToDialog (dlg->parse_field, VIB_MSG_INIT);
12834 SetValue (dlg->comment_field, 0);
12835 Hide (dlg->comment_field);
12836 }
12837
ParseFieldSourceDialogMessage(DialoG d,Int2 mssg)12838 static void ParseFieldSourceDialogMessage (DialoG d, Int2 mssg)
12839
12840 {
12841 ParseFieldSrcDlgPtr dlg;
12842
12843 dlg = (ParseFieldSrcDlgPtr) GetObjectExtra (d);
12844 if (dlg != NULL) {
12845 switch (mssg) {
12846 case VIB_MSG_INIT :
12847 /* reset list */
12848 ResetParseFieldSourceDialog (dlg);
12849 break;
12850 default :
12851 break;
12852 }
12853 }
12854 }
12855
ParseFieldChange(Pointer userdata)12856 static void ParseFieldChange (Pointer userdata)
12857 {
12858 ParseFieldSrcDlgPtr dlg;
12859 ValNodePtr vnp;
12860
12861 dlg = (ParseFieldSrcDlgPtr) userdata;
12862 if (dlg == NULL) return;
12863
12864 vnp = DialogToPointer (dlg->parse_field);
12865 if (vnp == NULL || vnp->data.intvalue != eParseFieldSrcStructuredComment) {
12866 Hide (dlg->comment_field);
12867 } else {
12868 Show (dlg->comment_field);
12869 }
12870 if (vnp == NULL || vnp->data.intvalue != eParseFieldSrcSourceQual) {
12871 Hide (dlg->src_qual);
12872 } else {
12873 Show (dlg->src_qual);
12874 }
12875
12876 if (dlg->change_notify != NULL) {
12877 (dlg->change_notify)(dlg->change_userdata);
12878 }
12879 }
12880
FindCommentFieldPosition(CharPtr comment_field,ValNodePtr comment_list)12881 static Int4 FindCommentFieldPosition (CharPtr comment_field, ValNodePtr comment_list)
12882 {
12883 Int4 pos = 1;
12884 ValNodePtr vnp;
12885
12886 if (StringHasNoText (comment_field) || comment_list == NULL) {
12887 return 0;
12888 }
12889
12890 vnp = comment_list;
12891 while (vnp != NULL && StringCmp (comment_field, vnp->data.ptrvalue) != 0) {
12892 vnp = vnp->next;
12893 pos++;
12894 }
12895 if (vnp == NULL) {
12896 pos = 0;
12897 }
12898 return pos;
12899 }
12900
DataToParseFieldSrcDialog(DialoG d,Pointer data)12901 static void DataToParseFieldSrcDialog(DialoG d, Pointer data)
12902 {
12903 ParseFieldSrcDlgPtr dlg;
12904 ParseFieldSrcPtr pfsp;
12905 ValNode vn;
12906
12907 dlg = (ParseFieldSrcDlgPtr) GetObjectExtra (d);
12908 if (dlg != NULL) {
12909 pfsp = (ParseFieldSrcPtr) data;
12910 if (pfsp == NULL) {
12911 ResetParseFieldSourceDialog (dlg);
12912 } else {
12913 vn.data.intvalue = pfsp->parse_field;
12914 vn.next = NULL;
12915 vn.choice = 0;
12916 PointerToDialog (dlg->parse_field, &vn);
12917 SetValue (dlg->comment_field, FindCommentFieldPosition (pfsp->comment_field, dlg->comment_field_list));
12918 vn.data.ptrvalue = pfsp->sqdp;
12919 PointerToDialog (dlg->src_qual, &vn);
12920 }
12921 }
12922 ParseFieldChange (dlg);
12923 }
12924
ParseFieldSrcDialogToData(DialoG d)12925 static Pointer ParseFieldSrcDialogToData(DialoG d)
12926 {
12927 ParseFieldSrcDlgPtr dlg;
12928 ParseFieldSrcPtr pfsp;
12929 ValNodePtr vnp;
12930 Int4 field_pos;
12931
12932 dlg = (ParseFieldSrcDlgPtr) GetObjectExtra (d);
12933 if (dlg == NULL) {
12934 return NULL;
12935 }
12936
12937 pfsp = (ParseFieldSrcPtr) MemNew (sizeof (ParseFieldSrcData));
12938 vnp = DialogToPointer (dlg->parse_field);
12939 if (vnp != NULL) {
12940 pfsp->parse_field = vnp->data.intvalue;
12941 vnp = ValNodeFree (vnp);
12942 }
12943 pfsp->comment_field = NULL;
12944 pfsp->sqdp = NULL;
12945 if (pfsp->parse_field == eParseFieldSrcStructuredComment) {
12946 field_pos = GetValue (dlg->comment_field);
12947 if (field_pos > 0) {
12948 vnp = dlg->comment_field_list;
12949 field_pos --;
12950 while (field_pos > 0 && vnp != NULL) {
12951 vnp = vnp->next;
12952 field_pos --;
12953 }
12954 if (vnp != NULL) {
12955 pfsp->comment_field = StringSave (vnp->data.ptrvalue);
12956 }
12957 }
12958 } else if (pfsp->parse_field == eParseFieldSrcSourceQual) {
12959 vnp = DialogToPointer (dlg->src_qual);
12960 if (vnp != NULL) {
12961 pfsp->sqdp = vnp->data.ptrvalue;
12962 vnp->data.ptrvalue = NULL;
12963 vnp = ValNodeFreeData (vnp);
12964 }
12965 }
12966
12967 return pfsp;
12968 }
12969
AddCommentFieldName(SeqDescrPtr sdp,Pointer userdata)12970 static void AddCommentFieldName (SeqDescrPtr sdp, Pointer userdata)
12971 {
12972 UserObjectPtr uop;
12973 ObjectIdPtr oip;
12974 UserFieldPtr ufp;
12975 ValNodePtr vnp;
12976 Boolean found;
12977 ValNodePtr PNTR comment_field_list = (ValNodePtr PNTR) userdata;
12978
12979 if (comment_field_list == NULL
12980 || sdp->choice != Seq_descr_user
12981 || sdp->extended == 0
12982 || sdp->data.ptrvalue == NULL) {
12983 return;
12984 }
12985
12986 uop = (UserObjectPtr) sdp->data.ptrvalue;
12987 oip = uop->type;
12988 if (oip != NULL && StringCmp (oip->str, "StructuredComment") == 0)
12989 {
12990 for (ufp = uop->data; ufp != NULL; ufp = ufp->next)
12991 {
12992 oip = ufp->label;
12993 if (oip != NULL && !StringHasNoText (oip->str))
12994 {
12995 found = FALSE;
12996 vnp = *comment_field_list;
12997 while (vnp != NULL && !found) {
12998 if (StringCmp (vnp->data.ptrvalue, oip->str) == 0) {
12999 found = TRUE;
13000 }
13001 vnp = vnp->next;
13002 }
13003 if (!found) {
13004 ValNodeAddPointer (comment_field_list, 0, StringSave (oip->str));
13005 }
13006 }
13007 }
13008 }
13009 }
13010
13011
TestParseFieldSource(DialoG d)13012 static ValNodePtr TestParseFieldSource (DialoG d)
13013
13014 {
13015 ParseFieldSrcDlgPtr dlg;
13016 ValNodePtr head = NULL, vnp, vnp2;
13017
13018 dlg = (ParseFieldSrcDlgPtr) GetObjectExtra (d);
13019
13020 vnp = DialogToPointer (dlg->parse_field);
13021 if (vnp == NULL)
13022 {
13023 head = AddStringToValNodeChain (head, "field choice", 1);
13024 }
13025 else if (vnp->data.intvalue == eParseFieldSrcSourceQual)
13026 {
13027 vnp2 = DialogToPointer (dlg->src_qual);
13028 if (vnp2 == NULL)
13029 {
13030 head = AddStringToValNodeChain (head, "source qual", 1);
13031 }
13032 vnp2 = ValNodeFree (vnp2);
13033 }
13034
13035 vnp = ValNodeFree (vnp);
13036
13037 return head;
13038 }
13039
13040
ParseFieldSourceDialog(GrouP h,SeqEntryPtr sep,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)13041 extern DialoG ParseFieldSourceDialog
13042 (GrouP h,
13043 SeqEntryPtr sep,
13044 Nlm_ChangeNotifyProc change_notify,
13045 Pointer change_userdata)
13046 {
13047 ParseFieldSrcDlgPtr dlg;
13048 GrouP p, k;
13049 ValNodePtr vnp;
13050
13051 dlg = (ParseFieldSrcDlgPtr) MemNew (sizeof (ParseFieldSrcDlgData));
13052 if (dlg == NULL)
13053 {
13054 return NULL;
13055 }
13056
13057 p = HiddenGroup (h, 2, 0, NULL);
13058
13059 SetObjectExtra (p, dlg, CleanupParseFieldSrcDialog);
13060
13061 dlg->dialog = (DialoG) p;
13062 dlg->todialog = DataToParseFieldSrcDialog;
13063 dlg->fromdialog = ParseFieldSrcDialogToData;
13064 dlg->dialogmessage = ParseFieldSourceDialogMessage;
13065 dlg->testdialog = TestParseFieldSource;
13066 dlg->change_notify = change_notify;
13067 dlg->change_userdata = change_userdata;
13068
13069 dlg->parse_field = FeatureFieldSelectionDialog (p, FALSE,
13070 num_parse_src_fields, parse_src_field_list,
13071 ParseFieldChange, dlg);
13072
13073 k = HiddenGroup (p, 0, 0, NULL);
13074 dlg->comment_field = PopupList (k, TRUE, NULL);
13075 dlg->src_qual = SourceQualTypeSelectionDialogEx (k, FALSE, change_notify,
13076 change_userdata, 6, FALSE, FALSE);
13077 AlignObjects (ALIGN_CENTER, (HANDLE) dlg->comment_field, (HANDLE) dlg->src_qual, NULL);
13078
13079 /* Add to comment_field list all user fields found in SeqEntry sep */
13080 VisitDescriptorsInSep (sep, &(dlg->comment_field_list), AddCommentFieldName);
13081 for (vnp = dlg->comment_field_list; vnp != NULL; vnp = vnp->next) {
13082 PopupItem (dlg->comment_field, vnp->data.ptrvalue);
13083 }
13084
13085 return (DialoG) p;
13086 }
13087
13088 typedef struct sampledialog
13089 {
13090 DIALOG_MESSAGE_BLOCK
13091 DoC doc;
13092 Int2 start_item;
13093 Int2 start_row;
13094 Int2 start_col;
13095 Int2 end_item;
13096 Int2 end_row;
13097 Int2 end_col;
13098 SetSamplePtr ssp;
13099 } SampleDialogData, PNTR SampleDialogPtr;
13100
TruncateStringAfterTwoLines(CharPtr str,Uint4 char_per_line)13101 static void TruncateStringAfterTwoLines (CharPtr str, Uint4 char_per_line)
13102 {
13103 CharPtr cp;
13104 Uint4 string_len;
13105
13106 if (StringHasNoText (str))
13107 {
13108 return;
13109 }
13110
13111 string_len = StringLen (str);
13112 if (string_len < char_per_line)
13113 {
13114 return;
13115 }
13116
13117 cp = str + char_per_line;
13118 while (! isspace ((Int4)(*cp)) && cp > str)
13119 {
13120 cp--;
13121 }
13122 if (cp == str)
13123 {
13124 if (string_len > 2 * char_per_line)
13125 {
13126 str [2 * char_per_line] = 0;
13127 }
13128 }
13129 else
13130 {
13131 if (StringLen (cp) > char_per_line)
13132 {
13133 cp[char_per_line] = 0;
13134 }
13135 }
13136
13137 }
13138
13139 typedef struct exportsample
13140 {
13141 ValNodePtr row_list;
13142 SetSamplePtr ssp;
13143 } ExportSampleData, PNTR ExportSamplePtr;
13144
ExportSampleDialogCallback(BioseqPtr bsp,Pointer userdata)13145 static void ExportSampleDialogCallback (BioseqPtr bsp, Pointer userdata)
13146 {
13147 ExportSamplePtr esp;
13148 SeqFeatPtr sfp;
13149 SeqMgrFeatContext fcontext;
13150 SeqDescrPtr sdp;
13151 SeqMgrDescContext dcontext;
13152 Char tmp[128];
13153 CharPtr val_str = NULL, new_val_str, tmp_val_str;
13154 ValNodePtr sample_field, sample_field_next;
13155 ValNodePtr new_row = NULL;
13156 SeqIdPtr sip;
13157
13158 if (bsp == NULL || userdata == NULL || ! ISA_na (bsp->mol))
13159 {
13160 return;
13161 }
13162
13163 esp = (ExportSamplePtr) userdata;
13164
13165 sip = SeqIdFindBest (bsp->id, 0);
13166 SeqIdWrite (sip, tmp, PRINTID_REPORT, sizeof (tmp));
13167
13168 ValNodeAddPointer (&new_row, 0, StringSave (tmp));
13169
13170 for (sample_field = esp->ssp->field_list;
13171 sample_field != NULL;
13172 sample_field = sample_field->next)
13173 {
13174 sample_field_next = sample_field->next;
13175 sample_field->next = NULL;
13176 val_str = NULL;
13177
13178 if (esp->ssp->descrstring_func != NULL)
13179 {
13180 sdp = SeqMgrGetNextDescriptor (bsp, NULL, 0, &dcontext);
13181 while (sdp != NULL)
13182 {
13183 new_val_str = (esp->ssp->descrstring_func) (sdp, sample_field, NULL);
13184 tmp_val_str = StringAppend (val_str, new_val_str);
13185 val_str = MemFree (val_str);
13186 new_val_str = MemFree (new_val_str);
13187 val_str = tmp_val_str;
13188 tmp_val_str = NULL;
13189 sdp = SeqMgrGetNextDescriptor (bsp, sdp, 0, &dcontext);
13190 }
13191 }
13192 if (esp->ssp->fieldstring_func != NULL)
13193 {
13194 sfp = SeqMgrGetNextFeature (bsp, NULL, 0, 0, &fcontext);
13195 while (sfp != NULL)
13196 {
13197 new_val_str = (esp->ssp->fieldstring_func)(sfp, sample_field, NULL);
13198 tmp_val_str = StringAppend (val_str, new_val_str);
13199 val_str = MemFree (val_str);
13200 new_val_str = MemFree (new_val_str);
13201 val_str = tmp_val_str;
13202 tmp_val_str = NULL;
13203 sfp = SeqMgrGetNextFeature (bsp, sfp, 0, 0, &fcontext);
13204 }
13205 }
13206 ValNodeAddPointer (&new_row, 0, val_str);
13207 sample_field->next = sample_field_next;
13208 }
13209 ValNodeAddPointer (&(esp->row_list), 0, new_row);
13210 }
13211
GetTableDataColumnWidths(ValNodePtr row_list)13212 static void GetTableDataColumnWidths (ValNodePtr row_list)
13213 {
13214 ValNodePtr row_vnp, col_vnp, header_vnp;
13215
13216 if (row_list == NULL || row_list->next == NULL)
13217 {
13218 return;
13219 }
13220
13221 /* only collect widths for data columns, not header, so we can detect empty rows */
13222 for (row_vnp = row_list->next; row_vnp != NULL; row_vnp = row_vnp->next)
13223 {
13224 for (col_vnp = row_vnp->data.ptrvalue, header_vnp = row_list->data.ptrvalue;
13225 col_vnp != NULL && header_vnp != NULL;
13226 col_vnp = col_vnp->next, header_vnp = header_vnp->next)
13227 {
13228 if (!StringHasNoText (col_vnp->data.ptrvalue))
13229 {
13230 header_vnp->choice = MAX (header_vnp->choice, StringLen (col_vnp->data.ptrvalue));
13231 }
13232 }
13233 }
13234 }
13235
RemoveTableEmptyColumns(ValNodePtr row_list)13236 static void RemoveTableEmptyColumns (ValNodePtr row_list)
13237 {
13238 ValNodePtr row_vnp, col_vnp, header_vnp, col_vnp_next, col_vnp_prev;
13239 ValNodePtr column_list;
13240
13241 if (row_list == NULL)
13242 {
13243 return;
13244 }
13245
13246 /* remove data columns */
13247 for (row_vnp = row_list->next; row_vnp != NULL; row_vnp = row_vnp->next)
13248 {
13249 column_list = row_vnp->data.ptrvalue;
13250 col_vnp_prev = NULL;
13251 for (col_vnp = column_list, header_vnp = row_list->data.ptrvalue;
13252 col_vnp != NULL && header_vnp != NULL;
13253 col_vnp = col_vnp_next, header_vnp = header_vnp->next)
13254 {
13255 col_vnp_next = col_vnp->next;
13256 if (header_vnp->choice == 0)
13257 {
13258 if (col_vnp_prev == NULL)
13259 {
13260 row_vnp->data.ptrvalue = col_vnp_next;
13261 column_list = row_vnp->data.ptrvalue;
13262 }
13263 else
13264 {
13265 col_vnp_prev->next = col_vnp_next;
13266 }
13267 col_vnp->next = NULL;
13268 ValNodeFreeData (col_vnp);
13269 }
13270 else
13271 {
13272 col_vnp_prev = col_vnp;
13273 }
13274 }
13275 }
13276
13277 /* remove headers for empty columns */
13278 col_vnp_prev = NULL;
13279 for (col_vnp = row_list->data.ptrvalue;
13280 col_vnp != NULL;
13281 col_vnp = col_vnp_next)
13282 {
13283 col_vnp_next = col_vnp->next;
13284 if (col_vnp->choice == 0)
13285 {
13286 if (col_vnp_prev == NULL)
13287 {
13288 row_list->data.ptrvalue = col_vnp_next;
13289 }
13290 else
13291 {
13292 col_vnp_prev->next = col_vnp_next;
13293 }
13294 col_vnp->next = NULL;
13295 ValNodeFreeData (col_vnp);
13296 }
13297 else
13298 {
13299 col_vnp_prev = col_vnp;
13300 }
13301 }
13302 }
13303
ExportSampleDialogData(SampleDialogPtr dlg)13304 static void ExportSampleDialogData (SampleDialogPtr dlg)
13305 {
13306 Char path [PATH_MAX];
13307 ExportSampleData esd;
13308 SeqEntryPtr sep;
13309 CharPtr sample_label;
13310 ValNodePtr sample_field;
13311 FILE *fp;
13312 ValNodePtr new_row = NULL;
13313
13314 if (dlg == NULL || dlg->ssp == NULL || dlg->ssp->label_vn_proc == NULL)
13315 {
13316 return;
13317 }
13318
13319 sep = GetTopSeqEntryForEntityID (dlg->ssp->entityID);
13320 if (sep == NULL)
13321 {
13322 return;
13323 }
13324 if (! GetOutputFileName (path, sizeof (path), NULL)) return;
13325 fp = FileOpen (path, "w");
13326 if (fp == NULL)
13327 {
13328 Message (MSG_ERROR, "Unable to open %s", path);
13329 return;
13330 }
13331 WatchCursor ();
13332 Update ();
13333 esd.ssp = dlg->ssp;
13334 ValNodeAddPointer (&new_row, 0, StringSave ("Sequence"));
13335
13336 for (sample_field = dlg->ssp->field_list;
13337 sample_field != NULL;
13338 sample_field = sample_field->next)
13339 {
13340 sample_label = (dlg->ssp->label_vn_proc) (sample_field);
13341 ValNodeAddPointer (&new_row, 0, StringSave (sample_label));
13342 }
13343 esd.row_list = NULL;
13344 ValNodeAddPointer (&(esd.row_list), 0, new_row);
13345
13346 VisitBioseqsInSep (sep, &esd, ExportSampleDialogCallback);
13347
13348 GetTableDataColumnWidths (esd.row_list);
13349 RemoveTableEmptyColumns (esd.row_list);
13350
13351 PrintTableDisplayRowListToFile (esd.row_list, fp);
13352 esd.row_list = FreeTableDisplayRowList (esd.row_list);
13353
13354 FileClose (fp);
13355 ArrowCursor();
13356 Update();
13357 }
13358
RefreshSampleDialog(SampleDialogPtr dlg)13359 static void RefreshSampleDialog (SampleDialogPtr dlg)
13360 {
13361 SeqEntryPtr sep;
13362 RecT r;
13363 ParData ParFmt = {FALSE, FALSE, FALSE, FALSE, FALSE, 0, 0};
13364 ColData ColFmt[] =
13365 {
13366 {0, 0, 80, 0, NULL, 'l', TRUE, FALSE, FALSE, FALSE, FALSE},
13367 {0, 0, 80, 0, NULL, 'l', TRUE, FALSE, FALSE, FALSE, FALSE},
13368 {0, 0, 80, 0, NULL, 'l', TRUE, FALSE, FALSE, FALSE, TRUE}
13369 };
13370 GetSampleData gsd;
13371 CharPtr new_line;
13372 ValNodePtr sample_field, sample_field_next;
13373 CharPtr sample_label = NULL;
13374 Int4 max_char_per_line;
13375
13376 if (dlg == NULL)
13377 {
13378 return;
13379 }
13380 Reset (dlg->doc);
13381 if (dlg->ssp == NULL || dlg->ssp->field_list == NULL
13382 || (dlg->ssp->fieldstring_func == NULL && dlg->ssp->descrstring_func == NULL))
13383 {
13384 return;
13385 }
13386
13387 sep = GetTopSeqEntryForEntityID (dlg->ssp->entityID);
13388 if (sep == NULL)
13389 {
13390 return;
13391 }
13392 gsd.sample_text = NULL;
13393 gsd.fieldstring_func = dlg->ssp->fieldstring_func;
13394 gsd.descrstring_func = dlg->ssp->descrstring_func;
13395
13396 ObjectRect (dlg->doc, &r);
13397 InsetRect (&r, 4, 4);
13398 ColFmt[0].pixWidth = (r.right - r.left) / 3;
13399 ColFmt[1].pixWidth = (r.right - r.left) / 4;
13400 ColFmt[2].pixWidth = (r.right - r.left) - ColFmt[0].pixWidth - ColFmt[1].pixWidth;
13401
13402 SelectFont (programFont);
13403 max_char_per_line = ColFmt[2].pixWidth / CharWidth ('0');
13404
13405
13406 for (sample_field = dlg->ssp->field_list; sample_field != NULL; sample_field = sample_field->next)
13407 {
13408 sample_field_next = sample_field->next;
13409 sample_field->next = NULL;
13410 gsd.requested_field = sample_field;
13411 gsd.num_found = 0;
13412 gsd.all_same = TRUE;
13413 gsd.feat_dest_list = NULL;
13414 gsd.descr_dest_list = NULL;
13415
13416 OperateOnSeqEntryConstrainedObjects (sep, dlg->ssp->fsp, GetSampleFeatureCallback,
13417 GetSampleDescriptorCallback,
13418 0, 0, 0, &gsd);
13419 if (gsd.num_found > 0)
13420 {
13421 sample_label = (dlg->ssp->label_vn_proc) (sample_field);
13422 new_line = (CharPtr) MemNew (
13423 (StringLen (sample_label)
13424 + StringLen (gsd.sample_text) + 20)
13425 * sizeof (Char));
13426 if (new_line != NULL)
13427 {
13428 if (gsd.all_same)
13429 {
13430 sprintf (new_line, "%s\t(%d same)\t", sample_label, gsd.num_found);
13431 }
13432 else
13433 {
13434 sprintf (new_line, "%s\t(%d mixed)\t", sample_label, gsd.num_found);
13435 }
13436 if (!StringHasNoText (gsd.sample_text))
13437 {
13438 TruncateStringAfterTwoLines (gsd.sample_text, max_char_per_line);
13439 StringCat (new_line, gsd.sample_text);
13440 }
13441 StringCat (new_line, "\n");
13442 AppendText (dlg->doc, new_line, &ParFmt, ColFmt, programFont);
13443 MemFree (new_line);
13444 }
13445 sample_label = MemFree (sample_label);
13446 }
13447 gsd.sample_text = MemFree (gsd.sample_text);
13448 sample_field->next = sample_field_next;
13449 }
13450 InvalDocument (dlg->doc);
13451 }
13452
PopulateSampleDialog(DialoG d,Pointer userdata)13453 static void PopulateSampleDialog (DialoG d, Pointer userdata)
13454 {
13455 SampleDialogPtr dlg;
13456 SetSamplePtr ssp;
13457
13458 dlg = (SampleDialogPtr) GetObjectExtra (d);
13459 if (dlg == NULL || userdata == NULL)
13460 {
13461 return;
13462 }
13463 ssp = (SetSamplePtr) userdata;
13464 dlg->ssp = SetSampleFree (dlg->ssp);
13465 dlg->ssp = SetSampleCopy (ssp);
13466 }
13467
13468 static void
GetSampleDialogStartAndEnd(SampleDialogPtr dlg,Int2Ptr start_item,Int2Ptr start_row,Int2Ptr start_col,Int2Ptr end_item,Int2Ptr end_row,Int2Ptr end_col)13469 GetSampleDialogStartAndEnd
13470 (SampleDialogPtr dlg,
13471 Int2Ptr start_item,
13472 Int2Ptr start_row,
13473 Int2Ptr start_col,
13474 Int2Ptr end_item,
13475 Int2Ptr end_row,
13476 Int2Ptr end_col)
13477 {
13478 if (dlg == NULL || start_item == NULL || start_row == NULL
13479 || start_col == NULL || end_item == NULL
13480 || end_row == NULL || end_col == NULL)
13481 {
13482 return;
13483 }
13484
13485 if (dlg->start_item < 0)
13486 {
13487 *start_item = -1;
13488 *start_row = -1;
13489 *start_col = -1;
13490 *end_item = -1;
13491 *end_row = -1;
13492 *end_col = -1;
13493 }
13494 else if (dlg->end_item < 0)
13495 {
13496 *start_item = dlg->start_item;
13497 *start_row = dlg->start_row;
13498 *start_col = dlg->start_col;
13499 *end_item = *start_item;
13500 *end_row = *start_row;
13501 *end_col = *start_col;
13502 }
13503 else if (dlg->start_item <= dlg->end_item)
13504 {
13505 *start_item = dlg->start_item;
13506 *end_item = dlg->end_item;
13507 if (dlg->start_row <= dlg->end_row)
13508 {
13509 *start_row = dlg->start_row;
13510 *end_row = dlg->end_row;
13511 if (dlg->start_col <= dlg->end_col)
13512 {
13513 *start_col = dlg->start_col;
13514 *end_col = dlg->end_col;
13515 }
13516 else
13517 {
13518 *start_col = dlg->end_col;
13519 *end_col = dlg->start_col;
13520 }
13521 }
13522 else
13523 {
13524 *start_row = dlg->end_row;
13525 *start_col = dlg->end_col;
13526 *end_row = dlg->start_row;
13527 *end_col = dlg->start_col;
13528 }
13529 }
13530 else
13531 {
13532 *start_item = dlg->end_item;
13533 *start_row = dlg->end_row;
13534 *start_col = dlg->end_col;
13535 *end_item = dlg->start_item;
13536 *end_row = dlg->start_row;
13537 *end_col = dlg->start_col;
13538 }
13539
13540 }
13541
SampleDialogCopy(SampleDialogPtr dlg)13542 static void SampleDialogCopy (SampleDialogPtr dlg)
13543 {
13544 Int2 start_row = 0, end_row = 0, tmp_row, first_row, last_row;
13545 Int2 start_col = 0, end_col = 0, first_col, last_col;
13546 Int2 start_item = 0, end_item = 0, tmp_item;
13547 CharPtr str;
13548 ValNodePtr strings = NULL;
13549 Int2 num_rows, num_cols;
13550
13551 if (dlg->start_row < 0)
13552 {
13553 return;
13554 }
13555
13556 GetSampleDialogStartAndEnd (dlg, &start_item, &start_row, &start_col,
13557 &end_item, &end_row, &end_col);
13558
13559 first_row = start_row;
13560 first_col = start_col;
13561 for (tmp_item = start_item; tmp_item <= end_item; tmp_item++)
13562 {
13563 GetItemParams (dlg->doc, tmp_item, NULL, &num_rows, &num_cols, NULL, NULL);
13564 if (tmp_item == end_item)
13565 {
13566 last_row = end_row;
13567 }
13568 else
13569 {
13570 last_row = num_rows;
13571 }
13572 for (tmp_row = first_row; tmp_row <= last_row; tmp_row++)
13573 {
13574 if (tmp_row == last_row && tmp_item == end_item)
13575 {
13576 last_col = end_col;
13577 }
13578 else
13579 {
13580 last_col = num_cols;
13581 }
13582 str = GetDocText (dlg->doc, tmp_item, tmp_row, 3);
13583 ValNodeAddPointer (&strings, 0, str);
13584 }
13585 first_row = 1;
13586 }
13587 str = MergeValNodeStrings (strings, FALSE);
13588
13589 StringToClipboard (str);
13590 MemFree (str);
13591 strings = ValNodeFreeData (strings);
13592 }
13593
InvalidateSampleDialogRows(DoC d,Int2 start_item,Int2 end_item)13594 static void InvalidateSampleDialogRows (DoC d, Int2 start_item, Int2 end_item)
13595 {
13596 Int2 num_rows;
13597 if (d == NULL)
13598 {
13599 return;
13600 }
13601 if (start_item < 1)
13602 {
13603 start_item = 1;
13604 }
13605 if (end_item < 1)
13606 {
13607 end_item = start_item;
13608 }
13609 while (start_item <= end_item)
13610 {
13611 GetItemParams (d, start_item, NULL, &num_rows, NULL, NULL, NULL);
13612 InvalDocRows (d, start_item, 1, num_rows);
13613 start_item++;
13614 }
13615 }
13616
SampleDialogOnClick(DoC d,PoinT pt)13617 static void SampleDialogOnClick (DoC d, PoinT pt)
13618 {
13619 SampleDialogPtr dlg;
13620 Int2 pos_item, pos_row, pos_col;
13621 Int2 start_item = 0, start_row, start_col;
13622 Int2 end_item = -1, end_row, end_col;
13623
13624 dlg = (SampleDialogPtr) GetObjectExtra (d);
13625 if (dlg == NULL) return;
13626
13627 MapDocPoint (d, pt, &(pos_item), &(pos_row), &(pos_col), NULL);
13628 if (dlg->start_item == pos_item
13629 && dlg->start_row == pos_row
13630 && dlg->start_col == pos_col)
13631 {
13632 dlg->start_row = -1;
13633 dlg->start_col = -1;
13634
13635 }
13636 else
13637 {
13638 if (dlg->start_item > -1)
13639 {
13640 GetSampleDialogStartAndEnd (dlg, &start_item, &start_row, &start_col,
13641 &end_item, &end_row, &end_col);
13642 }
13643 dlg->start_item = pos_item;
13644 dlg->start_row = pos_row;
13645 dlg->start_col = pos_col;
13646 }
13647 dlg->end_item = -1;
13648 dlg->end_row = -1;
13649 dlg->end_col = -1;
13650 InvalidateSampleDialogRows (d, start_item, end_item);
13651 InvalidateSampleDialogRows (d, pos_item, pos_item);
13652 }
13653
SampleDialogOnDrag(DoC d,PoinT pt)13654 static void SampleDialogOnDrag (DoC d, PoinT pt)
13655 {
13656 SampleDialogPtr dlg;
13657
13658 dlg = (SampleDialogPtr) GetObjectExtra (d);
13659 if (dlg == NULL) return;
13660
13661 MapDocPoint (d, pt, &(dlg->end_item), &(dlg->end_row), &(dlg->end_col), NULL);
13662 InvalDocument (d);
13663 }
13664
SampleDialogOnRelease(DoC d,PoinT pt)13665 static void SampleDialogOnRelease (DoC d, PoinT pt)
13666 {
13667 SampleDialogPtr dlg;
13668
13669 dlg = (SampleDialogPtr) GetObjectExtra (d);
13670 if (dlg == NULL) return;
13671
13672 MapDocPoint (d, pt, &(dlg->end_item), &(dlg->end_row), &(dlg->end_col), NULL);
13673 InvalDocument (d);
13674 }
13675
SampleDialogInvert(DoC d,Int2 item,Int2 row,Int2 col)13676 static Boolean SampleDialogInvert (DoC d, Int2 item, Int2 row, Int2 col)
13677 {
13678 SampleDialogPtr dlg;
13679 Int2 start_item = 0, start_row = 0, start_col = 0;
13680 Int2 end_item = 0, end_row = 0, end_col = 0;
13681 Boolean rval = FALSE;
13682
13683 dlg = (SampleDialogPtr) GetObjectExtra (d);
13684 if (dlg == NULL) return FALSE;
13685
13686 if (dlg->start_row < 0)
13687 {
13688 return FALSE;
13689 }
13690
13691 if (dlg->end_item == -1)
13692 {
13693 if(dlg->start_item == item
13694 && dlg->start_row == row
13695 && dlg->start_col == col)
13696 {
13697 return TRUE;
13698 }
13699 else
13700 {
13701 return FALSE;
13702 }
13703 }
13704 GetSampleDialogStartAndEnd (dlg, &start_item, &start_row, &start_col,
13705 &end_item, &end_row, &end_col);
13706 if (start_item <= item && end_item >= item)
13707 {
13708 rval = TRUE;
13709 if (start_item == item)
13710 {
13711 if (start_row == row)
13712 {
13713 if (start_col > col)
13714 {
13715 rval = FALSE;
13716 }
13717 }
13718 else if (start_row > row)
13719 {
13720 rval = FALSE;
13721 }
13722 }
13723
13724 if (end_item == item)
13725 {
13726 if (end_row == row)
13727 {
13728 if (end_col < col)
13729 {
13730 rval = FALSE;
13731 }
13732 }
13733 else if (end_row < row)
13734 {
13735 rval = FALSE;
13736 }
13737 }
13738 }
13739 if (col == 3)
13740 {
13741 return rval;
13742 }
13743 else
13744 {
13745 return FALSE;
13746 }
13747 }
13748
SampleDialogOnKey(SlatE s,Char ch)13749 static void SampleDialogOnKey (SlatE s, Char ch)
13750 {
13751 DoC d;
13752 SampleDialogPtr dlg;
13753
13754 d = (DoC) s;
13755 Select (d);
13756 dlg = (SampleDialogPtr) GetObjectExtra (d);
13757 if (dlg == NULL) return;
13758 CaptureSlateFocus ((SlatE) s);
13759
13760 #ifdef WIN_MSWIN
13761 if (ch == 3)
13762 {
13763 SampleDialogCopy (dlg);
13764 }
13765 #else
13766 if (ctrlKey)
13767 {
13768 if (ch == 'c')
13769 {
13770 SampleDialogCopy (dlg);
13771 }
13772 }
13773 #endif
13774 }
13775
SampleDialogMessage(DialoG d,Int2 mssg)13776 static void SampleDialogMessage (DialoG d, Int2 mssg)
13777
13778 {
13779 SampleDialogPtr dlg;
13780
13781 dlg = (SampleDialogPtr) GetObjectExtra (d);
13782 if (dlg != NULL) {
13783 switch (mssg) {
13784 case VIB_MSG_INIT :
13785 /* reset list */
13786 RefreshSampleDialog (dlg);
13787 break;
13788 default :
13789 break;
13790 }
13791 }
13792 }
13793
CleanupSampleDialog(GraphiC g,VoidPtr data)13794 static void CleanupSampleDialog (GraphiC g, VoidPtr data)
13795 {
13796 SampleDialogPtr dlg;
13797
13798 dlg = (SampleDialogPtr) data;
13799 if (dlg != NULL) {
13800 dlg->ssp = SetSampleFree (dlg->ssp);
13801 }
13802 StdCleanupExtraProc (g, data);
13803 }
13804
RefreshSampleBtn(ButtoN b)13805 static void RefreshSampleBtn (ButtoN b)
13806 {
13807 SampleDialogPtr dlg;
13808
13809 dlg = (SampleDialogPtr) GetObjectExtra (b);
13810 RefreshSampleDialog (dlg);
13811 }
13812
ExportSampleBtn(ButtoN b)13813 static void ExportSampleBtn (ButtoN b)
13814 {
13815 SampleDialogPtr dlg;
13816
13817 dlg = (SampleDialogPtr) GetObjectExtra (b);
13818 ExportSampleDialogData (dlg);
13819 }
13820
SampleDialog(GrouP h)13821 extern DialoG SampleDialog (GrouP h)
13822 {
13823 SampleDialogPtr dlg;
13824 GrouP p, g;
13825 ButtoN b;
13826
13827 dlg = (SampleDialogPtr) MemNew (sizeof (SampleDialogData));
13828 if (dlg == NULL)
13829 {
13830 return NULL;
13831 }
13832
13833 p = HiddenGroup (h, -1, 0, NULL);
13834
13835 SetObjectExtra (p, dlg, CleanupSampleDialog);
13836
13837 dlg->dialog = (DialoG) p;
13838 dlg->todialog = PopulateSampleDialog;
13839 dlg->fromdialog = NULL;
13840 dlg->dialogmessage = SampleDialogMessage;
13841 dlg->testdialog = NULL;
13842
13843 dlg->doc = DocumentPanel (p, stdCharWidth * 27, stdLineHeight * 8);
13844 SetObjectExtra (dlg->doc, dlg, NULL);
13845 SetDocProcs (dlg->doc, SampleDialogOnClick, SampleDialogOnDrag, SampleDialogOnRelease, NULL);
13846 SetDocShade (dlg->doc, NULL, NULL, SampleDialogInvert, NULL);
13847 SetDocAutoAdjust (dlg->doc, TRUE);
13848 SetSlateChar ((SlatE) dlg->doc, SampleDialogOnKey);
13849
13850 g = HiddenGroup (p, 2, 0, NULL);
13851 b = PushButton (g, "Refresh Qualifiers", RefreshSampleBtn);
13852 SetObjectExtra (b, dlg, NULL);
13853 b = PushButton (g, "Export Qualifiers", ExportSampleBtn);
13854 SetObjectExtra (b, dlg, NULL);
13855
13856 AlignObjects (ALIGN_CENTER, (HANDLE) dlg->doc, (HANDLE) g, NULL);
13857
13858 return (DialoG) p;
13859 }
13860
13861 typedef struct featurefieldchoicedialog
13862 {
13863 DIALOG_MESSAGE_BLOCK
13864 DialoG first_choice;
13865 DialoG second_choice;
13866 DialoG third_choice;
13867 ButtoN remove_first;
13868 ButtoN remove_second;
13869 ButtoN remove_third;
13870
13871 Nlm_ChangeNotifyProc change_notify;
13872 Pointer change_userdata;
13873 } FeatureFieldChoiceDialogData, PNTR FeatureFieldChoiceDialogPtr;
13874
FeatureFieldChoiceChange(Pointer data)13875 static void FeatureFieldChoiceChange (Pointer data)
13876 {
13877 FeatureFieldChoiceDialogPtr dlg;
13878 ValNodePtr vnp;
13879
13880 dlg = (FeatureFieldChoiceDialogPtr) data;
13881 if (dlg == NULL)
13882 {
13883 return;
13884 }
13885
13886 Disable (dlg->remove_first);
13887 Disable (dlg->remove_second);
13888 Disable (dlg->remove_third);
13889
13890 Disable (dlg->second_choice);
13891 Disable (dlg->third_choice);
13892
13893 vnp = DialogToPointer (dlg->first_choice);
13894 if (vnp != NULL)
13895 {
13896 ValNodeFree (vnp);
13897 Enable (dlg->second_choice);
13898 Enable (dlg->remove_first);
13899 vnp = DialogToPointer (dlg->second_choice);
13900 if (vnp != NULL)
13901 {
13902 ValNodeFree (vnp);
13903 Enable (dlg->third_choice);
13904 Enable (dlg->remove_second);
13905 vnp = DialogToPointer (dlg->third_choice);
13906 if (vnp != NULL)
13907 {
13908 ValNodeFree (vnp);
13909 Enable (dlg->remove_third);
13910 }
13911 }
13912 }
13913 if (dlg->change_notify != NULL)
13914 {
13915 (dlg->change_notify)(dlg->change_userdata);
13916 }
13917 }
13918
ResetFeatureFieldChoiceDialog(FeatureFieldChoiceDialogPtr dlg)13919 static void ResetFeatureFieldChoiceDialog (FeatureFieldChoiceDialogPtr dlg)
13920 {
13921 if (dlg == NULL)
13922 {
13923 return;
13924 }
13925 PointerToDialog (dlg->first_choice, NULL);
13926 PointerToDialog (dlg->second_choice, NULL);
13927 PointerToDialog (dlg->third_choice, NULL);
13928 if (dlg->remove_first != NULL)
13929 {
13930 SetStatus (dlg->remove_first, FALSE);
13931 }
13932 if (dlg->remove_second != NULL)
13933 {
13934 SetStatus (dlg->remove_second, FALSE);
13935 }
13936 if (dlg->remove_third != NULL)
13937 {
13938 SetStatus (dlg->remove_third, FALSE);
13939 }
13940 FeatureFieldChoiceChange (dlg);
13941 }
13942
FeatureFieldChoiceToDialog(DialoG d,Pointer data)13943 static void FeatureFieldChoiceToDialog (DialoG d, Pointer data)
13944 {
13945 FeatureFieldChoiceDialogPtr dlg;
13946 ValNodePtr feature_field;
13947
13948 dlg = (FeatureFieldChoiceDialogPtr) GetObjectExtra (d);
13949 if (dlg == NULL)
13950 {
13951 return;
13952 }
13953
13954 ResetFeatureFieldChoiceDialog (dlg);
13955 feature_field = (ValNodePtr) data;
13956 if (feature_field != NULL)
13957 {
13958 PointerToDialog (dlg->first_choice, feature_field);
13959 if (feature_field->choice != 0 && dlg->remove_first != NULL)
13960 {
13961 SetStatus (dlg->remove_first, TRUE);
13962 }
13963 feature_field = feature_field->next;
13964 if (feature_field != NULL)
13965 {
13966 PointerToDialog (dlg->second_choice, feature_field);
13967 if (feature_field->choice != 0 && dlg->remove_second != NULL)
13968 {
13969 SetStatus (dlg->remove_second, TRUE);
13970 }
13971 feature_field = feature_field->next;
13972 if (feature_field != NULL)
13973 {
13974 if (feature_field->choice != 0 && dlg->remove_third != NULL)
13975 {
13976 SetStatus (dlg->remove_third, TRUE);
13977 }
13978 PointerToDialog (dlg->third_choice, feature_field);
13979 }
13980 }
13981 }
13982 FeatureFieldChoiceChange (dlg);
13983 }
13984
DialogToFeatureFieldChoice(DialoG d)13985 static Pointer DialogToFeatureFieldChoice (DialoG d)
13986 {
13987 FeatureFieldChoiceDialogPtr dlg;
13988 ValNodePtr choice_list = NULL;
13989 ValNodePtr feature_field, vnp_prev;
13990
13991 dlg = (FeatureFieldChoiceDialogPtr) GetObjectExtra (d);
13992 if (dlg == NULL)
13993 {
13994 return NULL;
13995 }
13996
13997 feature_field = DialogToPointer (dlg->first_choice);
13998 if (feature_field != NULL)
13999 {
14000 if (dlg->remove_first != NULL && GetStatus (dlg->remove_first))
14001 {
14002 feature_field->choice = 1;
14003 }
14004 choice_list = feature_field;
14005
14006 feature_field = DialogToPointer (dlg->second_choice);
14007 if (feature_field != NULL)
14008 {
14009 if (dlg->remove_second != NULL && GetStatus (dlg->remove_second))
14010 {
14011 feature_field->choice = 1;
14012 }
14013 choice_list->next = feature_field;
14014 vnp_prev = feature_field;
14015
14016 feature_field = DialogToPointer (dlg->third_choice);
14017 if (feature_field != NULL)
14018 {
14019 if (dlg->remove_third != NULL && GetStatus (dlg->remove_third))
14020 {
14021 feature_field->choice = 1;
14022 }
14023 vnp_prev->next = feature_field;
14024 }
14025 else
14026 {
14027 ValNodeFree (feature_field);
14028 }
14029 }
14030 else
14031 {
14032 ValNodeFree (feature_field);
14033 }
14034 }
14035 else
14036 {
14037 ValNodeFree (feature_field);
14038 }
14039 return choice_list;
14040 }
14041
FeatureFieldChoiceMessage(DialoG d,Int2 mssg)14042 static void FeatureFieldChoiceMessage (DialoG d, Int2 mssg)
14043
14044 {
14045 FeatureFieldChoiceDialogPtr dlg;
14046
14047 dlg = (FeatureFieldChoiceDialogPtr) GetObjectExtra (d);
14048 if (dlg != NULL) {
14049 switch (mssg) {
14050 case VIB_MSG_INIT :
14051 /* reset list */
14052 ResetFeatureFieldChoiceDialog (dlg);
14053 break;
14054 case VIB_MSG_ENTER :
14055 Select (dlg->first_choice);
14056 break;
14057 default :
14058 break;
14059 }
14060 }
14061 }
14062
TestFeatureFieldChoice(DialoG d)14063 static ValNodePtr TestFeatureFieldChoice (DialoG d)
14064
14065 {
14066 FeatureFieldChoiceDialogPtr dlg;
14067 ValNodePtr head = NULL;
14068 ValNodePtr vnp;
14069
14070 dlg = (FeatureFieldChoiceDialogPtr) GetObjectExtra (d);
14071 vnp = DialogToPointer (d);
14072 if (vnp == NULL)
14073 {
14074 head = AddStringToValNodeChain (head, "feature field choice", 1);
14075 }
14076 else
14077 {
14078 ValNodeFree (vnp);
14079 }
14080 return head;
14081 }
14082
FeatureFieldChoiceDialog(GrouP h,FeatureFieldSelectionProc make_fieldlist_dlg,Boolean offer_to_remove,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)14083 extern DialoG FeatureFieldChoiceDialog
14084 (GrouP h,
14085 FeatureFieldSelectionProc make_fieldlist_dlg,
14086 Boolean offer_to_remove,
14087 Nlm_ChangeNotifyProc change_notify,
14088 Pointer change_userdata)
14089 {
14090 FeatureFieldChoiceDialogPtr dlg;
14091 GrouP p, g;
14092
14093 if (make_fieldlist_dlg == NULL)
14094 {
14095 return NULL;
14096 }
14097
14098 dlg = (FeatureFieldChoiceDialogPtr) MemNew (sizeof (FeatureFieldChoiceDialogData));
14099 if (dlg == NULL)
14100 {
14101 return NULL;
14102 }
14103
14104 p = HiddenGroup (h, 0, 6, NULL);
14105 SetObjectExtra (p, dlg, StdCleanupExtraProc);
14106
14107 dlg->dialog = (DialoG) p;
14108 dlg->todialog = FeatureFieldChoiceToDialog;
14109 dlg->fromdialog = DialogToFeatureFieldChoice;
14110 dlg->dialogmessage = FeatureFieldChoiceMessage;
14111 dlg->testdialog = TestFeatureFieldChoice;
14112 dlg->change_notify = change_notify;
14113 dlg->change_userdata = change_userdata;
14114
14115 g = HiddenGroup (p, 3, 0, NULL);
14116 StaticPrompt (g, "1st Choice", 0, 0, programFont, 'c');
14117 dlg->first_choice = (make_fieldlist_dlg) (g, TRUE, FeatureFieldChoiceChange, dlg);
14118 if (offer_to_remove)
14119 {
14120 dlg->remove_first = CheckBox (g, "Remove if used", NULL);
14121 Disable (dlg->remove_first);
14122 }
14123 else
14124 {
14125 dlg->remove_first = NULL;
14126 }
14127
14128 g = HiddenGroup (p, 3, 0, NULL);
14129 StaticPrompt (g, "2nd Choice", 0, 0, programFont, 'c');
14130 dlg->second_choice = (make_fieldlist_dlg) (g, TRUE, FeatureFieldChoiceChange, dlg);
14131 if (offer_to_remove)
14132 {
14133 dlg->remove_second = CheckBox (g, "Remove if used", NULL);
14134 Disable (dlg->remove_second);
14135 }
14136 else
14137 {
14138 dlg->remove_second = NULL;
14139 }
14140 Disable (dlg->second_choice);
14141
14142 g = HiddenGroup (p, 3, 0, NULL);
14143 StaticPrompt (g, "3rd Choice", 0, 0, programFont, 'c');
14144 dlg->third_choice = (make_fieldlist_dlg) (g, TRUE, FeatureFieldChoiceChange, dlg);
14145 if (offer_to_remove)
14146 {
14147 dlg->remove_third = CheckBox (g, "Remove if used", NULL);
14148 Disable (dlg->remove_third);
14149 }
14150 else
14151 {
14152 dlg->remove_third = NULL;
14153 }
14154 Disable (dlg->third_choice);
14155
14156 return (DialoG) p;
14157 }
14158
14159
14160 typedef ValNodePtr (*AdjustConvertFeatureListFunc) PROTO ((ValNodePtr, Pointer, BaseFormPtr, BoolPtr cancel));
14161 typedef Pointer (*CollectConvertFeatureOptionsFunc) PROTO ((ValNodePtr, BaseFormPtr, BoolPtr cancel));
14162 typedef Pointer (*FreeConvertFeatureOptionsFunc) PROTO ((Pointer));
14163 typedef Boolean (*ConvertFeatureTypeFunc) PROTO ((SeqFeatPtr, Uint2, Pointer));
14164 typedef void (*ConversionCleanupFunc) PROTO ((Uint2, Pointer));
14165
14166 typedef struct convertfeatureprocs {
14167 Uint2 seqfeat_from;
14168 Uint2 featdef_from;
14169 Uint2 seqfeat_to;
14170 Uint2 featdef_to;
14171 AdjustConvertFeatureListFunc adjust_features;
14172 CollectConvertFeatureOptionsFunc collect_options;
14173 FreeConvertFeatureOptionsFunc free_options;
14174 ConvertFeatureTypeFunc convert_func;
14175 ConversionCleanupFunc cleanup_func;
14176 CharPtr help_text;
14177 } ConvertFeatureProcsData, PNTR ConvertFeatureProcsPtr;
14178
14179 static Pointer SimpleOptsFree (Pointer);
14180 static Boolean ConvertCDSToRNAEx (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
14181 static Boolean ConvertGeneToRNAEx (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
14182 static ValNodePtr AdjustConvertFeaturesForBioSrcToRepeatRegion (ValNodePtr feat_list, Pointer extradata, BaseFormPtr bfp, BoolPtr cancel);
14183 static Boolean ConvertBioSrcToRepeatRegionEx (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
14184 static ValNodePtr AdjustCDSToMiscFeatList (ValNodePtr feat_list, Pointer extradata, BaseFormPtr bfp, BoolPtr cancel);
14185 static Pointer GetCDSConversionOpts (ValNodePtr feat_list, BaseFormPtr bfp, BoolPtr cancel);
14186 static Boolean CDSToMiscFeatConvertFunc (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
14187 static void CDSToMiscFeatConversionCleanup (Uint2 entityID, Pointer extradata);
14188 static Boolean ConvertImpToProt (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
14189 static Boolean ConvertProtToImp (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
14190 static Boolean ConvertImpToSpecialRNA (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
14191 static Boolean ConvertRegionToImp (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
14192 static Boolean ConvertRegionToRNA (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
14193 static Boolean ConvertImpToRNA (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
14194 static Boolean ConvertCommentToMiscFeat (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
14195 static Boolean ConvertGeneToImpFeat (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
14196 static Boolean ConvertRNAToMiscFeat (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
14197 static Boolean ConvertSiteToMiscFeat (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
14198 static Boolean ConvertProtToRegion (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
14199 static Boolean ConvertRegionToProt (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
14200 static Pointer GetBondOpts (ValNodePtr feat_list, BaseFormPtr bfp, BoolPtr cancel);
14201 static Pointer GetSiteOpts (ValNodePtr feat_list, BaseFormPtr bfp, BoolPtr cancel);
14202 static Boolean ConvertToSiteOrBond (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
14203 static Pointer GetRegionOpts (ValNodePtr feat_list, BaseFormPtr bfp, BoolPtr cancel);
14204 static ValNodePtr AdjustRegionConversionFeatures (ValNodePtr feat_list, Pointer extradata, BaseFormPtr bfp, BoolPtr cancel);
14205 static Boolean ConvertAnyToRegion (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
14206 static Boolean ConvertImpToImp (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
14207 static Boolean ConvertRNAToRNA (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
14208 static Boolean ConvertProtToProt (SeqFeatPtr, Uint2 featdef_to, Pointer extradata);
14209 static Boolean ConvertCDSToMatPeptide (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata);
14210 static Boolean ConvertMiscFeatureToCDSFunction (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata);
14211 static Boolean ConvertMiscFeatureToGeneFunction (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata);
14212 static Boolean ConvertmRNAToCodingRegionFunction (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata);
14213 static Boolean ConverttRNAToGeneFunction (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata);
14214
14215 static ConvertFeatureProcsData ConvertFeaturesTable[] = {
14216 { SEQFEAT_CDREGION, FEATDEF_CDS, SEQFEAT_RNA, FEATDEF_ANY,
14217 NULL, GetCDSConversionOpts, SimpleOptsFree, ConvertCDSToRNAEx, NULL,
14218 "Delete protein product sequence.\nClear product field if transcript ID removal was requested.\nIf converting to tRNA and anticodon value can be parsed from label, set aa value, and add any text that could not be parsed into an anticodon value to the feature note.\nIf converting to other RNA, put label in RNA product." },
14219 { SEQFEAT_GENE, FEATDEF_GENE, SEQFEAT_RNA, FEATDEF_ANY,
14220 NULL, NULL, NULL, ConvertGeneToRNAEx, NULL,
14221 "If converting to tRNA and anticodon value can be parsed from label, set aa value, and add any text that could not be parsed into an anticodon value to the feature note. If converting to other RNA, put label in RNA product. Also append gene locus, allele, description, map location, and locus tag to comment (as long as these values are not already in the label and therefore in the RNA product)." },
14222 { SEQFEAT_BIOSRC, FEATDEF_BIOSRC, SEQFEAT_IMP, FEATDEF_repeat_region,
14223 AdjustConvertFeaturesForBioSrcToRepeatRegion, NULL, NULL, ConvertBioSrcToRepeatRegionEx, NULL,
14224 "Creates a repeat_region with mobile_element qualifiers for the transposon and/or insertion sequence qualifiers on the BioSource. All other BioSource information is discarded." },
14225 { SEQFEAT_CDREGION, FEATDEF_CDS, SEQFEAT_IMP, FEATDEF_misc_feature,
14226 AdjustCDSToMiscFeatList, GetCDSConversionOpts, SimpleOptsFree, CDSToMiscFeatConvertFunc, CDSToMiscFeatConversionCleanup,
14227 "Copy comment from coding region to new misc_feature and remove product field. If not pseudo coding region, add product name from protein feature to new misc_feature comment and delete product sequence." },
14228 { SEQFEAT_IMP, FEATDEF_ANY, SEQFEAT_PROT, FEATDEF_ANY,
14229 NULL, NULL, NULL, ConvertImpToProt, NULL,
14230 "Original feature must be on nucleotide sequence and be contained in coding region location. Coding region must have product protein sequence. New feature is created on product protein sequence so that the translated location will be as close as possible to the original nucleotide location (may not be exact because of codon boundaries)." },
14231 { SEQFEAT_PROT, FEATDEF_mat_peptide_aa, SEQFEAT_IMP, FEATDEF_ANY,
14232 NULL, NULL, NULL, ConvertProtToImp, NULL,
14233 "Original feature must be on a protein sequence that is a product of a coding region.\nNew feature will be created on same sequence as coding region.\n"
14234 "If protein feature has name, this will be saved as /product qualifier on new feature.\nIf protein feature does not have name but does have description, this will be saved as /product qualifier on new feature.\n"
14235 "EC_number values from the protein feature will be saved as /EC_number qualifiers on the new feature.\nActivity values will be saved as /function qualifiers on the new feature.\n"
14236 "Db_xref values from the protein feature will be saved as /db_xref qualifers on the new feature." },
14237 { SEQFEAT_PROT, FEATDEF_sig_peptide_aa, SEQFEAT_IMP, FEATDEF_ANY,
14238 NULL, NULL, NULL, ConvertProtToImp, NULL,
14239 "Original feature must be on a protein sequence that is a product of a coding region.\nNew feature will be created on same sequence as coding region.\n"
14240 "If protein feature has name, this will be saved as /product qualifier on new feature.\nIf protein feature does not have name but does have description, this will be saved as /product qualifier on new feature.\n"
14241 "EC_number values from the protein feature will be saved as /EC_number qualifiers on the new feature.\nActivity values will be saved as /function qualifiers on the new feature.\n"
14242 "Db_xref values from the protein feature will be saved as /db_xref qualifers on the new feature." },
14243 { SEQFEAT_PROT, FEATDEF_transit_peptide_aa, SEQFEAT_IMP, FEATDEF_ANY,
14244 NULL, NULL, NULL, ConvertProtToImp, NULL,
14245 "Original feature must be on a protein sequence that is a product of a coding region.\nNew feature will be created on same sequence as coding region.\n"
14246 "If protein feature has name, this will be saved as /product qualifier on new feature.\nIf protein feature does not have name but does have description, this will be saved as /product qualifier on new feature.\n"
14247 "EC_number values from the protein feature will be saved as /EC_number qualifiers on the new feature.\nActivity values will be saved as /function qualifiers on the new feature.\n"
14248 "Db_xref values from the protein feature will be saved as /db_xref qualifers on the new feature." },
14249 { SEQFEAT_IMP, FEATDEF_misc_feature, SEQFEAT_CDREGION, FEATDEF_CDS,
14250 NULL, NULL, NULL, ConvertMiscFeatureToCDSFunction, NULL,
14251 "Use misc_feature comment for coding region product name." },
14252 { SEQFEAT_RNA, FEATDEF_mRNA, SEQFEAT_CDREGION, FEATDEF_CDS,
14253 NULL, NULL, NULL, ConvertmRNAToCodingRegionFunction, NULL,
14254 "Convert mRNA to coding region, use mRNA product for protein feature" },
14255 { SEQFEAT_RNA, FEATDEF_tRNA, SEQFEAT_GENE, FEATDEF_GENE,
14256 NULL, NULL, NULL, ConverttRNAToGeneFunction, NULL,
14257 "Convert tRNA to gene, use tRNA product for gene description" },
14258 { SEQFEAT_IMP, FEATDEF_misc_feature, SEQFEAT_GENE, FEATDEF_GENE,
14259 NULL, NULL, NULL, ConvertMiscFeatureToGeneFunction, NULL,
14260 "Use misc_feature comment for gene locus." },
14261 { SEQFEAT_IMP, FEATDEF_ANY, SEQFEAT_RNA, FEATDEF_misc_RNA,
14262 NULL, NULL, NULL, ConvertImpToSpecialRNA, NULL,
14263 "Creates a misc_RNA. Import feature key is discarded." },
14264 { SEQFEAT_IMP, FEATDEF_ANY, SEQFEAT_RNA, FEATDEF_precursor_RNA,
14265 NULL, NULL, NULL, ConvertImpToSpecialRNA, NULL,
14266 "Creates a precursor RNA. Import feature key is discarded." },
14267 { SEQFEAT_REGION, FEATDEF_REGION, SEQFEAT_IMP, FEATDEF_ANY,
14268 NULL, NULL, NULL, ConvertRegionToImp, NULL,
14269 "Creates a misc_feature with the region name saved as a /note qualifier." },
14270 { SEQFEAT_REGION, FEATDEF_REGION, SEQFEAT_RNA, FEATDEF_misc_RNA,
14271 NULL, NULL, NULL, ConvertRegionToRNA, NULL,
14272 "Creates a misc_RNA feature with the region name as the product name." },
14273 { SEQFEAT_REGION, FEATDEF_REGION, SEQFEAT_RNA, FEATDEF_precursor_RNA,
14274 NULL, NULL, NULL, ConvertRegionToRNA, NULL,
14275 "Creates a precursor RNA feature with the region name as the product name." },
14276 { SEQFEAT_IMP, FEATDEF_ANY, SEQFEAT_RNA, FEATDEF_ANY,
14277 NULL, NULL, NULL, ConvertImpToRNA, NULL,
14278 "Creates an RNA feature of the specified type." },
14279 { SEQFEAT_COMMENT, FEATDEF_ANY, SEQFEAT_IMP, FEATDEF_misc_feature,
14280 NULL, NULL, NULL, ConvertCommentToMiscFeat, NULL,
14281 "Creates a misc_feature with the same note as the original. Note the flatfile display for the feature is the same." },
14282 { SEQFEAT_GENE, FEATDEF_GENE, SEQFEAT_IMP, FEATDEF_ANY,
14283 NULL, NULL, NULL, ConvertGeneToImpFeat, NULL,
14284 "Creates an import feature with the gene description and locus prepended to the original comment, separated by semicolons." },
14285 { SEQFEAT_RNA, FEATDEF_ANY, SEQFEAT_IMP, FEATDEF_misc_feature,
14286 NULL, NULL, NULL, ConvertRNAToMiscFeat, NULL,
14287 "Creates a misc_feature and adds the RNA product name to the comment." } ,
14288 { SEQFEAT_SITE, FEATDEF_ANY, SEQFEAT_IMP, FEATDEF_misc_feature,
14289 NULL, NULL, NULL, ConvertSiteToMiscFeat, NULL,
14290 "Creates a misc_feature with the site type name as a /note qualifier." } ,
14291 { SEQFEAT_PROT, FEATDEF_mat_peptide_aa, SEQFEAT_REGION, FEATDEF_REGION,
14292 NULL, NULL, NULL, ConvertProtToRegion, NULL,
14293 "Creates a Region feature with the protein name as the region name." },
14294 { SEQFEAT_PROT, FEATDEF_sig_peptide_aa, SEQFEAT_REGION, FEATDEF_REGION,
14295 NULL, NULL, NULL, ConvertProtToRegion, NULL,
14296 "Creates a Region feature with the protein name as the region name." },
14297 { SEQFEAT_PROT, FEATDEF_transit_peptide_aa, SEQFEAT_REGION, FEATDEF_REGION,
14298 NULL, NULL, NULL, ConvertProtToRegion, NULL,
14299 "Creates a Region feature with the protein name as the region name." },
14300 { SEQFEAT_REGION, FEATDEF_REGION, SEQFEAT_PROT, FEATDEF_mat_peptide_aa,
14301 NULL, NULL, NULL, ConvertRegionToProt, NULL,
14302 "If feature is on nucleotide sequence, will create feature on protein product sequence for overlapping coding region. Protein name will be region name." },
14303 { SEQFEAT_REGION, FEATDEF_REGION, SEQFEAT_PROT, FEATDEF_sig_peptide_aa,
14304 NULL, NULL, NULL, ConvertRegionToProt, NULL,
14305 "If feature is on nucleotide sequence, will create feature on protein product sequence for overlapping coding region. Protein name will be region name." },
14306 { SEQFEAT_REGION, FEATDEF_REGION, SEQFEAT_PROT, FEATDEF_transit_peptide_aa,
14307 NULL, NULL, NULL, ConvertRegionToProt, NULL,
14308 "If feature is on nucleotide sequence, will create feature on protein product sequence for overlapping coding region. Protein name will be region name." },
14309 { SEQFEAT_REGION, FEATDEF_REGION, SEQFEAT_PROT, FEATDEF_preprotein,
14310 NULL, NULL, NULL, ConvertRegionToProt, NULL,
14311 "If feature is on nucleotide sequence, will create feature on protein product sequence for overlapping coding region. Protein name will be region name." },
14312 { 0, FEATDEF_ANY, SEQFEAT_BOND, FEATDEF_BOND,
14313 NULL, GetBondOpts, SimpleOptsFree, ConvertToSiteOrBond, NULL,
14314 "Create Bond feature with specified bond type. Location is a SeqLocBond with a point at the start of the original location and a point at the end of the original location. All feature ID, partialness, except, comment, product, location, genbank qualifiers, title, citation, experimental evidence, gene xrefs, db xrefs, and pseudo-ness information is discarded." },
14315 { 0, FEATDEF_ANY, SEQFEAT_SITE, FEATDEF_SITE,
14316 NULL, GetSiteOpts, SimpleOptsFree, ConvertToSiteOrBond, NULL,
14317 "Create Site feature with specified site type. All feature ID, partialness, except, comment, product, location, genbank qualifiers, title, citation, experimental evidence, gene xrefs, db xrefs, and pseudo-ness information is discarded." },
14318 { 0, FEATDEF_ANY, SEQFEAT_REGION, FEATDEF_REGION,
14319 AdjustRegionConversionFeatures, GetRegionOpts, SimpleOptsFree, ConvertAnyToRegion, NULL,
14320 "Create Region feature on nucleotide sequence or protein product sequence of overlapping coding region as specified. Use comment on feature for region name.\n"
14321 "All feature ID, partialness, except, comment, product, location, genbank qualifiers, title, citation, experimental evidence, gene xrefs, db xrefs, and pseudo-ness information is discarded." },
14322 { SEQFEAT_IMP, FEATDEF_ANY, SEQFEAT_IMP, FEATDEF_ANY,
14323 NULL, NULL, NULL, ConvertImpToImp, NULL,
14324 "Changes type of import feature." },
14325 { SEQFEAT_RNA, FEATDEF_ANY, SEQFEAT_RNA, FEATDEF_ANY,
14326 NULL, NULL, NULL, ConvertRNAToRNA, NULL,
14327 "Changes type of RNA feature." },
14328 { SEQFEAT_RNA, FEATDEF_ncRNA, SEQFEAT_IMP, FEATDEF_misc_binding,
14329 NULL, NULL, NULL, ConvertncRNAToMiscBinding, NULL,
14330 "Changes ncRNA to misc_binding." },
14331 { SEQFEAT_PROT, FEATDEF_ANY, SEQFEAT_PROT, FEATDEF_ANY,
14332 NULL, NULL, NULL, ConvertProtToProt, NULL,
14333 "Changes type of protein feature." },
14334 { SEQFEAT_CDREGION, FEATDEF_CDS, SEQFEAT_PROT, FEATDEF_mat_peptide_aa,
14335 NULL, NULL, NULL, ConvertCDSToMatPeptide, NULL,
14336 "If coding region is overlapped by another coding region, will convert the coding region to a mat-peptide on the overlapping coding region's protein sequence, otherwise if you have checked \"Leave Original Feature\" it will create a mat-peptide with the same protein names and description on the protein sequence for the coding region." }
14337 };
14338
14339 static Int4 num_convert_feature_table_lines = sizeof (ConvertFeaturesTable) / sizeof (ConvertFeatureProcsData);
14340
GetConvertFeatureTableLine(Uint2 seqfeat_from,Uint2 featdef_from,Uint2 seqfeat_to,Uint2 featdef_to)14341 static Int4 GetConvertFeatureTableLine (Uint2 seqfeat_from, Uint2 featdef_from, Uint2 seqfeat_to, Uint2 featdef_to)
14342 {
14343 Int4 i, table_line_num = -1;
14344
14345 for (i = 0; i < num_convert_feature_table_lines && table_line_num == -1; i++)
14346 {
14347 if ((ConvertFeaturesTable[i].seqfeat_from == 0 || ConvertFeaturesTable[i].seqfeat_from == seqfeat_from)
14348 && (ConvertFeaturesTable[i].featdef_from == FEATDEF_ANY || ConvertFeaturesTable[i].featdef_from == featdef_from)
14349 && (ConvertFeaturesTable[i].seqfeat_to == 0 || ConvertFeaturesTable[i].seqfeat_to == seqfeat_to)
14350 && (ConvertFeaturesTable[i].featdef_to == FEATDEF_ANY || ConvertFeaturesTable[i].featdef_to == featdef_to))
14351 {
14352 table_line_num = i;
14353 }
14354 }
14355 return table_line_num;
14356 }
14357
14358
14359 typedef struct featureselremconform
14360 {
14361 FORM_MESSAGE_BLOCK
14362 DialoG feature_select;
14363 DialoG constraints;
14364 DialoG accept_cancel;
14365 PopuP action_choice;
14366 DialoG feature_select_to;
14367 PrompT from_prompt;
14368 PrompT to_prompt;
14369 DialoG feature_select_from;
14370 GrouP remove_grp;
14371 GrouP convert_grp;
14372 ButtoN clear_constraints_on_action_change;
14373 ButtoN leave_original_feature_btn; /* checkbox for conversion only */
14374
14375 DoC help_text; /* for conversion only - describes conversion */
14376
14377 /* used for convert callback */
14378 Uint1 featdef_to;
14379 Boolean renormalize_nucprot;
14380 Boolean leave_original_feature;
14381 ValNodePtr feat_list;
14382 BaseFormPtr bfp;
14383 } FeatureSelRemConvFormData, PNTR FeatureSelRemConvFormPtr;
14384
CleanupFeatureSelRemConvForm(GraphiC g,VoidPtr data)14385 static void CleanupFeatureSelRemConvForm (GraphiC g, VoidPtr data)
14386
14387 {
14388 FeatureSelRemConvFormPtr mrfp;
14389
14390 mrfp = (FeatureSelRemConvFormPtr) data;
14391 if (mrfp != NULL) {
14392 }
14393 StdCleanupFormProc (g, data);
14394 }
14395
FeatureRemoveClearText(Pointer data)14396 static void FeatureRemoveClearText (Pointer data)
14397 {
14398 FeatureSelRemConvFormPtr mrfp;
14399 FilterSetPtr fsp;
14400
14401 mrfp = (FeatureSelRemConvFormPtr) data;
14402 if (mrfp == NULL) return;
14403
14404 fsp = DialogToPointer (mrfp->constraints);
14405 FilterSetClearText (fsp);
14406 PointerToDialog (mrfp->constraints, fsp);
14407 FilterSetFree (fsp);
14408 }
14409
FeatureRemoveClear(Pointer data)14410 static void FeatureRemoveClear (Pointer data)
14411 {
14412 FeatureSelRemConvFormPtr mrfp;
14413
14414 mrfp = (FeatureSelRemConvFormPtr) data;
14415 if (mrfp == NULL) return;
14416
14417 PointerToDialog (mrfp->feature_select, NULL);
14418 PointerToDialog (mrfp->constraints, NULL);
14419 PointerToDialog (mrfp->feature_select_to, NULL);
14420 PointerToDialog (mrfp->feature_select_from, NULL);
14421 SetStatus (mrfp->leave_original_feature_btn, FALSE);
14422 }
14423
FeatureRemoveChangeNotify(Pointer userdata)14424 static void FeatureRemoveChangeNotify (Pointer userdata)
14425 {
14426 FeatureSelRemConvFormPtr mrfp;
14427 ValNodePtr err_list = NULL, vnp_from, vnp_to;
14428 Int4 table_line;
14429 RecT r;
14430 Boolean need_original = FALSE;
14431
14432 mrfp = (FeatureSelRemConvFormPtr) userdata;
14433 if (mrfp == NULL) return;
14434
14435 if (mrfp->action_choice == NULL)
14436 {
14437 /* just the remove dialog */
14438 err_list = TestDialog (mrfp->feature_select);
14439 }
14440 else if (GetValue (mrfp->action_choice) == FEATURE_CONVERT)
14441 {
14442 /* convert dialog in choice */
14443 if (mrfp->feature_select_from != NULL)
14444 {
14445 err_list = TestDialog (mrfp->feature_select_from);
14446 }
14447 else
14448 {
14449 err_list = TestDialog (mrfp->feature_select);
14450 }
14451 if (err_list == NULL && mrfp->feature_select_to != NULL)
14452 {
14453 err_list = TestDialog (mrfp->feature_select_to);
14454 }
14455 /* set help text */
14456 Reset (mrfp->help_text);
14457 vnp_from = (ValNodePtr) DialogToPointer (mrfp->feature_select_from);
14458 vnp_to = (ValNodePtr) DialogToPointer (mrfp->feature_select_to);
14459 if (vnp_from == NULL || vnp_to == NULL)
14460 {
14461 AppendText (mrfp->help_text, "No conversion selected", NULL, NULL, systemFont);
14462 }
14463 else if (vnp_from->choice == vnp_to->choice)
14464 {
14465 AppendText (mrfp->help_text, "Can't convert from and to the same type", NULL, NULL, systemFont);
14466 ValNodeAddPointer (&err_list, 0, "Can't convert from and to the same type");
14467 }
14468 else
14469 {
14470 /* set help text */
14471 table_line = GetConvertFeatureTableLine (FindFeatFromFeatDefType (vnp_from->choice),
14472 vnp_from->choice,
14473 FindFeatFromFeatDefType (vnp_to->choice),
14474 vnp_to->choice);
14475 if (table_line < 0)
14476 {
14477 AppendText (mrfp->help_text, "Conversion not supported", NULL, NULL, systemFont);
14478 }
14479 else if (ConvertFeaturesTable[table_line].help_text == NULL)
14480 {
14481 AppendText (mrfp->help_text, "No description available", NULL, NULL, systemFont);
14482 }
14483 else
14484 {
14485 AppendText (mrfp->help_text, ConvertFeaturesTable[table_line].help_text, NULL, NULL, systemFont);
14486 }
14487
14488 /* if converting from CDS to site, bond, or region, "leave original" must be checked */
14489 if ((vnp_from->choice == FEATDEF_CDS
14490 || vnp_from->choice == FEATDEF_ANY)
14491 && (vnp_to->choice == FEATDEF_SITE
14492 || vnp_to->choice == FEATDEF_BOND
14493 || vnp_to->choice == FEATDEF_REGION))
14494 {
14495 need_original = TRUE;
14496 AppendText (mrfp->help_text, "If converting from CDS to site or bond, or region, you must check Leave Original Feature.", NULL, NULL, systemFont);
14497 }
14498 }
14499 vnp_from = ValNodeFreeData (vnp_from);
14500 vnp_to = ValNodeFreeData (vnp_to);
14501 ObjectRect (mrfp->help_text, &r);
14502 InvalRect (&r);
14503
14504 }
14505 else
14506 {
14507 /* single feature dialog in choice */
14508 if (mrfp->feature_select != NULL)
14509 {
14510 err_list = TestDialog (mrfp->feature_select);
14511 }
14512 }
14513
14514 if (err_list == NULL && (!need_original || GetStatus (mrfp->leave_original_feature_btn)))
14515 {
14516 EnableAcceptCancelDialogAccept (mrfp->accept_cancel);
14517 }
14518 else
14519 {
14520 DisableAcceptCancelDialogAccept (mrfp->accept_cancel);
14521 }
14522 ValNodeFree (err_list);
14523 }
14524
14525
FeatureRemoveChangeButton(ButtoN b)14526 static void FeatureRemoveChangeButton (ButtoN b)
14527 {
14528 FeatureSelRemConvFormPtr mrfp;
14529
14530 mrfp = (FeatureSelRemConvFormPtr) GetObjectExtra (b);
14531 if (mrfp == NULL) return;
14532 FeatureRemoveChangeNotify (mrfp);
14533 }
14534
14535
FeatureRemoveOrConvertCenterAction(PopuP p)14536 static void FeatureRemoveOrConvertCenterAction (PopuP p)
14537 {
14538 FeatureSelRemConvFormPtr mrfp;
14539
14540 mrfp = (FeatureSelRemConvFormPtr) GetObjectExtra (p);
14541 if (mrfp == NULL) return;
14542
14543 if (GetValue (p) == 2)
14544 {
14545 Hide (mrfp->remove_grp);
14546 Show (mrfp->convert_grp);
14547 }
14548 else
14549 {
14550 Show (mrfp->remove_grp);
14551 Hide (mrfp->convert_grp);
14552 }
14553
14554 if (GetStatus (mrfp->clear_constraints_on_action_change))
14555 {
14556 PointerToDialog (mrfp->feature_select, NULL);
14557 PointerToDialog (mrfp->feature_select_from, NULL);
14558 PointerToDialog (mrfp->feature_select_to, NULL);
14559 PointerToDialog (mrfp->constraints, NULL);
14560 }
14561 FeatureRemoveChangeNotify ((Pointer) mrfp);
14562 }
14563
14564
14565
SelectFeatureCallback(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)14566 static void SelectFeatureCallback (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
14567
14568 {
14569 if (sfp == NULL) return;
14570 ObjMgrAlsoSelect (sfp->idx.entityID, sfp->idx.itemID, OBJ_SEQFEAT, 0, NULL);
14571 }
14572
DeselectFeatureCallback(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)14573 static void DeselectFeatureCallback (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
14574
14575 {
14576 if (sfp == NULL) return;
14577 ObjMgrDeSelect (sfp->idx.entityID, sfp->idx.itemID, OBJ_SEQFEAT, 0, NULL);
14578 }
14579
14580 typedef struct removefeature
14581 {
14582 ValNodePtr bsplist;
14583 ValNodePtr bssplist;
14584 } RemoveFeatureData, PNTR RemoveFeaturePtr;
14585
RemoveFeatureCallback(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)14586 static void RemoveFeatureCallback (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
14587 {
14588 RemoveFeaturePtr rfp;
14589 SeqIdPtr sip;
14590 BioseqPtr productbsp, productcdna;
14591 BioseqSetPtr productnps;
14592
14593 if (sfp == NULL || userdata == NULL) return;
14594 rfp = (RemoveFeaturePtr) userdata;
14595
14596 sfp->idx.deleteme = TRUE;
14597 if (sfp->data.choice == SEQFEAT_CDREGION)
14598 {
14599 if (sfp->product != NULL)
14600 {
14601 sip = SeqLocId (sfp->product);
14602 if (sip != NULL)
14603 {
14604 productbsp = BioseqFind (sip);
14605 if (productbsp != NULL)
14606 {
14607 ValNodeAddPointer (&(rfp->bsplist), 0, (Pointer) productbsp);
14608 }
14609 }
14610 }
14611 }
14612 else if (sfp->data.choice == SEQFEAT_RNA)
14613 {
14614 if (sfp->product != NULL)
14615 {
14616 sip = SeqLocId (sfp->product);
14617 if (sip != NULL)
14618 {
14619 productcdna = BioseqFind (sip);
14620 if (productcdna != NULL && productcdna->idx.parenttype == OBJ_BIOSEQSET)
14621 {
14622 productnps = (BioseqSetPtr) productcdna->idx.parentptr;
14623 if (productnps != NULL && productnps->_class == BioseqseqSet_class_nuc_prot)
14624 {
14625 ValNodeAddPointer (&(rfp->bssplist), 0, (Pointer) productnps);
14626 }
14627 }
14628 }
14629 }
14630 }
14631 }
14632
14633
ConvertRegionToImp(SeqFeatPtr sfp,Uint2 featdef_to,Pointer extradata)14634 static Boolean ConvertRegionToImp (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata)
14635 {
14636 return ConvertRegionToImpFunc (sfp, featdef_to);
14637 }
14638
14639
14640 static Boolean
ConvertToBondSiteOrRegion(SeqFeatPtr sfp,Int4 site_or_bond_type,Uint2 featdef_to,Boolean create_prot_feats)14641 ConvertToBondSiteOrRegion
14642 (SeqFeatPtr sfp,
14643 Int4 site_or_bond_type,
14644 Uint2 featdef_to,
14645 Boolean create_prot_feats)
14646 {
14647 BioseqPtr bsp;
14648 SeqLocPtr slp;
14649 SeqEntryPtr sep;
14650 SeqMgrFeatContext context;
14651 SeqFeatPtr newsfp;
14652 SeqIdPtr sip;
14653 CharPtr comment;
14654 SeqBondPtr sbp;
14655 SeqPntPtr spp;
14656 Boolean no_cds = FALSE;
14657
14658 if (sfp == NULL)
14659 {
14660 return FALSE;
14661 }
14662
14663 if (site_or_bond_type == -1 && featdef_to != FEATDEF_REGION)
14664 {
14665 return FALSE;
14666 }
14667
14668 bsp = BioseqFindFromSeqLoc (sfp->location);
14669 sfp = SeqMgrGetDesiredFeature (0, bsp, 0, 0, sfp, &context);
14670 if (sfp == NULL || bsp == NULL) return FALSE;
14671
14672 if (ISA_aa (bsp->mol))
14673 {
14674 if (create_prot_feats)
14675 {
14676 slp = (SeqLocPtr) AsnIoMemCopy (sfp->location, (AsnReadFunc) SeqLocAsnRead, (AsnWriteFunc) SeqLocAsnWrite);
14677 }
14678 else
14679 {
14680 slp = FindNucleotideLocationForProteinFeatureConversion (sfp->location);
14681 }
14682 }
14683 else if (create_prot_feats)
14684 {
14685 slp = GetProteinLocationForNucleotideFeatureConversion (sfp->location, &no_cds);
14686 if (no_cds) {
14687 Message (MSG_ERROR, "Unable to find CDS covering %s", context.label);
14688 return FALSE;
14689 }
14690 } else {
14691 slp = (SeqLocPtr) AsnIoMemCopy (sfp->location, (AsnReadFunc) SeqLocAsnRead, (AsnWriteFunc) SeqLocAsnWrite);
14692 }
14693
14694 bsp = GetBioseqGivenSeqLoc (slp, context.entityID);
14695 if (bsp == NULL) {
14696 Message (MSG_ERROR, "Unable to find target %s bioseq for %s", create_prot_feats ? "protein" : "nucleotide", context.label);
14697 slp = SeqLocFree (slp);
14698 return FALSE;
14699 }
14700
14701 sep = SeqMgrGetSeqEntryForData (bsp);
14702 if (sep == NULL) {
14703 Message (MSG_ERROR, "Unable to find target %s seq-entry for %s", create_prot_feats ? "protein" : "nucleotide", context.label);
14704 return FALSE;
14705 }
14706
14707 comment = sfp->comment;
14708
14709 newsfp = NULL;
14710 if (featdef_to == FEATDEF_BOND || featdef_to == FEATDEF_SITE) {
14711 newsfp = SeqFeatNew ();
14712 if (newsfp != NULL)
14713 {
14714 newsfp->data.choice = FindFeatFromFeatDefType(featdef_to);
14715 newsfp->data.value.intvalue = site_or_bond_type;
14716 sfp->comment = NULL;
14717 }
14718 } else if (featdef_to == FEATDEF_REGION) {
14719 newsfp = SeqFeatNew ();
14720 if (newsfp != NULL)
14721 {
14722 newsfp->data.choice = FindFeatFromFeatDefType(featdef_to);
14723 newsfp->data.value.ptrvalue = sfp->comment;
14724 sfp->comment = NULL;
14725 comment = NULL;
14726 }
14727 }
14728 if (newsfp != NULL) {
14729 sfp->idx.deleteme = TRUE;
14730 CreateNewFeature (sep, NULL, FindFeatFromFeatDefType(featdef_to), newsfp);
14731 newsfp->location = slp;
14732 newsfp->comment = comment;
14733 if (featdef_to == FEATDEF_BOND) {
14734 if (slp->choice != SEQLOC_BOND) {
14735 sip = SeqLocId (slp);
14736 if (sip != NULL) {
14737 sbp = SeqBondNew ();
14738 if (sbp != NULL) {
14739 slp = ValNodeNew (NULL);
14740 if (slp != NULL) {
14741 slp->choice = SEQLOC_BOND;
14742 slp->data.ptrvalue = (Pointer) sbp;
14743 spp = SeqPntNew ();
14744 if (spp != NULL) {
14745 spp->strand = SeqLocStrand (newsfp->location);
14746 spp->id = SeqIdStripLocus (SeqIdDup (SeqIdFindBest (sip, 0)));
14747 spp->point = SeqLocStart (newsfp->location);
14748 sbp->a = spp;
14749 }
14750 spp = SeqPntNew ();
14751 if (spp != NULL) {
14752 spp->strand = SeqLocStrand (newsfp->location);
14753 spp->id = SeqIdStripLocus (SeqIdDup (SeqIdFindBest (sip, 0)));
14754 spp->point = SeqLocStop (newsfp->location);
14755 sbp->b = spp;
14756 }
14757 newsfp->location = SeqLocFree (newsfp->location);
14758 newsfp->location = slp;
14759 }
14760 }
14761 }
14762 }
14763 }
14764 }
14765 if (newsfp == NULL)
14766 {
14767 return FALSE;
14768 }
14769 else
14770 {
14771 return TRUE;
14772 }
14773 }
14774
14775
14776 typedef struct origfeat
14777 {
14778 SeqEntryPtr sep;
14779 SeqFeatPtr sfp;
14780 } OrigFeatData, PNTR OrigFeatPtr;
14781
14782
AddDuplicateFeature(SeqFeatPtr sfp_orig,ValNodePtr PNTR feat_list)14783 static ValNodePtr AddDuplicateFeature (SeqFeatPtr sfp_orig, ValNodePtr PNTR feat_list)
14784 {
14785 SeqEntryPtr sep;
14786 BioseqPtr bsp;
14787 OrigFeatPtr ofp;
14788
14789 if (sfp_orig == NULL || feat_list == NULL) return NULL;
14790 bsp = BioseqFindFromSeqLoc (sfp_orig->location);
14791 if (bsp == NULL) return NULL;
14792 sep = SeqMgrGetSeqEntryForData (bsp);
14793 if (sep == NULL) return NULL;
14794
14795 ofp = (OrigFeatPtr) MemNew (sizeof (OrigFeatData));
14796 if (ofp == NULL) return NULL;
14797
14798 ofp->sep = sep;
14799 ofp->sfp = (SeqFeatPtr) AsnIoMemCopy (sfp_orig, (AsnReadFunc) SeqFeatAsnRead,
14800 (AsnWriteFunc) SeqFeatAsnWrite);
14801
14802 return ValNodeAddPointer (feat_list, 0, ofp);
14803 }
14804
SimpleOptsFree(Pointer data)14805 static Pointer SimpleOptsFree (Pointer data)
14806 {
14807 return MemFree (data);
14808 }
14809
14810 static Boolean
ConvertCDSToRNAEx(SeqFeatPtr sfp,Uint2 toFeatSubType,Pointer extradata)14811 ConvertCDSToRNAEx
14812 (SeqFeatPtr sfp,
14813 Uint2 toFeatSubType,
14814 Pointer extradata)
14815 {
14816 CDSConversionOptsPtr opts;
14817 Boolean remove_mRNA = FALSE;
14818 Boolean remove_gene = FALSE;
14819 Boolean remove_transcript_id = FALSE;
14820 Boolean remove_only_pseudo = FALSE;
14821
14822
14823 if (sfp == NULL || sfp->data.choice != SEQFEAT_CDREGION) return FALSE;
14824
14825 opts = (CDSConversionOptsPtr) extradata;
14826 if (opts != NULL) {
14827 remove_mRNA = opts->remove_mrna;
14828 remove_gene = opts->remove_gene;
14829 remove_transcript_id = opts->remove_transcript_id;
14830 remove_only_pseudo = opts->only_pseudo;
14831 }
14832 if (remove_only_pseudo && !sfp->pseudo) {
14833 return FALSE;
14834 }
14835 ApplyCDSOptionsToFeature (sfp, remove_mRNA, remove_gene, remove_transcript_id, FALSE);
14836 return ConvertCDSToRNA (sfp, toFeatSubType);
14837 }
14838
14839
ConvertGeneToRNAEx(SeqFeatPtr sfp,Uint2 featdef_to,Pointer extradata)14840 static Boolean ConvertGeneToRNAEx (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata)
14841 {
14842 return ConvertGeneToRNA (sfp, featdef_to);
14843 }
14844
14845
CreateClickableListForSourceFeats(ValNodePtr feat_list)14846 static ValNodePtr CreateClickableListForSourceFeats (ValNodePtr feat_list)
14847 {
14848 ValNodePtr transposon_only_list = NULL;
14849 ValNodePtr insertion_seq_only_list = NULL;
14850 ValNodePtr transposon_and_insertion_seq_list = NULL;
14851 ValNodePtr note_only_list = NULL;
14852 ValNodePtr no_data_list = NULL;
14853 ValNodePtr vnp;
14854 CharPtr transposon_txt, insertion_seq_txt, note_txt;
14855 SeqFeatPtr sfp;
14856 BioSourcePtr biop;
14857 Boolean is_transposon;
14858 Boolean is_insertion_seq;
14859 ClickableItemPtr cip;
14860 ValNodePtr clickable_list = NULL;
14861
14862 for (vnp = feat_list; vnp != NULL; vnp = vnp->next) {
14863 sfp = (SeqFeatPtr) vnp->data.ptrvalue;
14864 biop = (BioSourcePtr) sfp->data.value.ptrvalue;
14865 is_transposon = FALSE;
14866 is_insertion_seq = FALSE;
14867 transposon_txt = SubSourceText (biop, SUBSRC_transposon_name, &is_transposon);
14868 insertion_seq_txt = SubSourceText (biop, SUBSRC_insertion_seq_name, &is_insertion_seq);
14869 note_txt = NoteText (biop, sfp->comment);
14870
14871 if (is_transposon && is_insertion_seq) {
14872 ValNodeAddPointer (&transposon_and_insertion_seq_list, OBJ_SEQFEAT, vnp->data.ptrvalue);
14873 } else if (is_transposon) {
14874 ValNodeAddPointer (&transposon_only_list, OBJ_SEQFEAT, vnp->data.ptrvalue);
14875 } else if (is_insertion_seq) {
14876 ValNodeAddPointer (&insertion_seq_only_list, OBJ_SEQFEAT, vnp->data.ptrvalue);
14877 } else if (!StringHasNoText (note_txt)) {
14878 ValNodeAddPointer (¬e_only_list, OBJ_SEQFEAT, vnp->data.ptrvalue);
14879 } else {
14880 ValNodeAddPointer (&no_data_list, OBJ_SEQFEAT, vnp->data.ptrvalue);
14881 }
14882 }
14883
14884 if (transposon_and_insertion_seq_list != NULL) {
14885 cip = NewClickableItem (0, "%d source features have both transposon-name and insertion-seq-name.", transposon_and_insertion_seq_list);
14886 ValNodeAddPointer (&clickable_list, 0, cip);
14887 }
14888 if (transposon_only_list != NULL) {
14889 cip = NewClickableItem (0, "%d source features have transposon-name.", transposon_only_list);
14890 cip->chosen = TRUE;
14891 ValNodeAddPointer (&clickable_list, 0, cip);
14892 }
14893 if (insertion_seq_only_list != NULL) {
14894 cip = NewClickableItem (0, "%d source features have insertion-seq-name.", insertion_seq_only_list);
14895 cip->chosen = TRUE;
14896 ValNodeAddPointer (&clickable_list, 0, cip);
14897 }
14898 if (note_only_list != NULL) {
14899 cip = NewClickableItem (0, "%d source features have notes, but neither transposon-name nor insertion-seq-name.", note_only_list);
14900 ValNodeAddPointer (&clickable_list, 0, cip);
14901 }
14902 if (no_data_list != NULL) {
14903 cip = NewClickableItem (0, "%d source features have no notes, no transposon-name, and no insertion-seq-name.", no_data_list);
14904 ValNodeAddPointer (&clickable_list, 0, cip);
14905 }
14906
14907 return clickable_list;
14908 }
14909
14910
AdjustConvertFeaturesForBioSrcToRepeatRegion(ValNodePtr feat_list,Pointer extradata,BaseFormPtr bfp,BoolPtr cancel)14911 static ValNodePtr AdjustConvertFeaturesForBioSrcToRepeatRegion (ValNodePtr feat_list, Pointer extradata, BaseFormPtr bfp, BoolPtr cancel)
14912 {
14913 ValNodePtr clickable_list;
14914
14915 *cancel = FALSE;
14916 clickable_list = CreateClickableListForSourceFeats (feat_list);
14917 feat_list = ValNodeFree (feat_list);
14918 feat_list = ChooseFeaturesForConversion (clickable_list, bfp, "Available Data", "Features");
14919 /* NOTE - the clickable_list will be freed by the dialog - do not free it again here */
14920 if (feat_list == NULL)
14921 {
14922 *cancel = TRUE;
14923 }
14924 return feat_list;
14925 }
14926
14927
RemoveNonPseudoFeatures(ValNodePtr PNTR feat_list)14928 static void RemoveNonPseudoFeatures (ValNodePtr PNTR feat_list)
14929 {
14930 ValNodePtr prev = NULL, next_vnp, vnp;
14931 SeqFeatPtr sfp;
14932
14933 vnp = *feat_list;
14934 while (vnp != NULL) {
14935 next_vnp = vnp->next;
14936 sfp = (SeqFeatPtr) vnp->data.ptrvalue;
14937 if (sfp != NULL && !sfp->pseudo) {
14938 if (prev == NULL) {
14939 *feat_list = vnp->next;
14940 } else {
14941 prev->next = vnp->next;
14942 }
14943 vnp->next = NULL;
14944 vnp = ValNodeFree (vnp);
14945 } else {
14946 prev = vnp;
14947 }
14948 vnp = next_vnp;
14949 }
14950 }
14951
14952
GetCDSConversionOpts(ValNodePtr feat_list,BaseFormPtr bfp,BoolPtr cancel)14953 static Pointer GetCDSConversionOpts (ValNodePtr feat_list, BaseFormPtr bfp, BoolPtr cancel)
14954 {
14955 Boolean all_are_pseudo = TRUE, any_are_pseudo = FALSE, any_gps = FALSE;
14956 CDSConversionOptsPtr opts;
14957 ValNodePtr vnp;
14958 SeqFeatPtr sfp;
14959
14960 for (vnp = feat_list; vnp != NULL; vnp = vnp->next)
14961 {
14962 sfp = (SeqFeatPtr) vnp->data.ptrvalue;
14963 if (sfp != NULL)
14964 {
14965 if (sfp->pseudo)
14966 {
14967 any_are_pseudo = TRUE;
14968 }
14969 else
14970 {
14971 all_are_pseudo = FALSE;
14972 }
14973 if (!any_gps)
14974 {
14975 any_gps = IsFeatInGPS (sfp);
14976 }
14977 }
14978 }
14979
14980 opts = GetCDSConversionOptions (all_are_pseudo, any_are_pseudo, any_gps, cancel);
14981
14982 return opts;
14983 }
14984
14985
AdjustCDSToMiscFeatList(ValNodePtr feat_list,Pointer extradata,BaseFormPtr bfp,BoolPtr cancel)14986 static ValNodePtr AdjustCDSToMiscFeatList (ValNodePtr feat_list, Pointer extradata, BaseFormPtr bfp, BoolPtr cancel)
14987 {
14988 CDSConversionOptsPtr opts;
14989
14990 if (feat_list == NULL || extradata == NULL || cancel == NULL) return feat_list;
14991 opts = (CDSConversionOptsPtr) extradata;
14992 *cancel = FALSE;
14993 if (opts->only_pseudo) {
14994 /* remove features that are not pseudo */
14995 RemoveNonPseudoFeatures (&feat_list);
14996 }
14997 return feat_list;
14998 }
14999
15000
CDSToMiscFeatConversionCleanup(Uint2 entityID,Pointer extradata)15001 static void CDSToMiscFeatConversionCleanup (Uint2 entityID, Pointer extradata)
15002 {
15003 SeqEntryPtr sep;
15004
15005 DeleteMarkedObjects (entityID, 0, NULL);
15006 sep = GetTopSeqEntryForEntityID (entityID);
15007 RenormalizeNucProtSets (sep, TRUE);
15008 }
15009
15010
CDSToMiscFeatConvertFunc(SeqFeatPtr sfp,Uint2 featdef_to,Pointer extradata)15011 static Boolean CDSToMiscFeatConvertFunc (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata)
15012 {
15013 CDSConversionOptsPtr opts;
15014 Boolean rval = FALSE;
15015
15016 opts = (CDSConversionOptsPtr) extradata;
15017 if (opts == NULL || sfp == NULL || sfp->data.choice != SEQFEAT_CDREGION)
15018 {
15019 return FALSE;
15020 }
15021 else if (sfp->pseudo)
15022 {
15023 rval = ConvertOnePseudoCDSToMiscFeat (sfp);
15024 }
15025 else
15026 {
15027 /* do other here */
15028
15029 rval = ConvertOneCDSToMiscFeat (sfp, FALSE, FALSE, opts);
15030 }
15031 return TRUE;
15032 }
15033
15034
15035 typedef struct siteorbond {
15036 Int4 site_or_bond_type;
15037 } SiteOrBondData, PNTR SiteOrBondPtr;
15038
GetSiteOrBondOpts(ValNodePtr feat_list,BaseFormPtr bfp,BoolPtr cancel,Uint2 toFeat)15039 static Pointer GetSiteOrBondOpts (ValNodePtr feat_list, BaseFormPtr bfp, BoolPtr cancel, Uint2 toFeat)
15040 {
15041 EnumFieldAssocPtr al;
15042 CharPtr mssg;
15043 UIEnum val;
15044 SiteOrBondPtr opts = NULL;
15045
15046 *cancel = FALSE;
15047 al = NULL;
15048 mssg = NULL;
15049 if (toFeat == FEATDEF_BOND) {
15050 al = enum_bond_alist;
15051 mssg = "Select type of bond";
15052 } else if (toFeat == FEATDEF_SITE) {
15053 al = enum_site_alist;
15054 mssg = "Select type of site";
15055 } else {
15056 *cancel = TRUE;
15057 return NULL;
15058 }
15059
15060 if (al == NULL || ! AlistMessage (al, &val, 1, mssg))
15061 {
15062 *cancel = TRUE;
15063 }
15064 else
15065 {
15066 opts = (SiteOrBondPtr) MemNew (sizeof (SiteOrBondData));
15067 opts->site_or_bond_type = (Int4) val;
15068 }
15069 return opts;
15070 }
15071
15072
GetSiteOpts(ValNodePtr feat_list,BaseFormPtr bfp,BoolPtr cancel)15073 static Pointer GetSiteOpts (ValNodePtr feat_list, BaseFormPtr bfp, BoolPtr cancel)
15074 {
15075 return GetSiteOrBondOpts (feat_list, bfp, cancel, FEATDEF_SITE);
15076 }
15077
15078
GetBondOpts(ValNodePtr feat_list,BaseFormPtr bfp,BoolPtr cancel)15079 static Pointer GetBondOpts (ValNodePtr feat_list, BaseFormPtr bfp, BoolPtr cancel)
15080 {
15081 return GetSiteOrBondOpts (feat_list, bfp, cancel, FEATDEF_BOND);
15082 }
15083
15084
ConvertToSiteOrBond(SeqFeatPtr sfp,Uint2 featdef_to,Pointer extradata)15085 static Boolean ConvertToSiteOrBond (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata)
15086 {
15087 SiteOrBondPtr opts = NULL;
15088
15089 opts = (SiteOrBondPtr) extradata;
15090 if (sfp == NULL || opts == NULL) return FALSE;
15091
15092 return ConvertToBondSiteOrRegion (sfp, opts->site_or_bond_type, featdef_to, TRUE);
15093 }
15094
15095 typedef struct regionopts {
15096 Boolean create_prot_feats;
15097 } RegionOptsData, PNTR RegionOptsPtr;
15098
15099
GetBadProteinConversionFeatures(ValNodePtr feat_list)15100 static ValNodePtr GetBadProteinConversionFeatures (ValNodePtr feat_list)
15101 {
15102 ValNodePtr no_cds_list = NULL, bad_coordinates_list = NULL, err_list = NULL, vnp;
15103 Boolean no_cds;
15104 SeqLocPtr slp;
15105 SeqFeatPtr sfp;
15106 BioseqPtr bsp;
15107
15108 for (vnp = feat_list; vnp != NULL; vnp = vnp->next) {
15109 sfp = (SeqFeatPtr) vnp->data.ptrvalue;
15110 bsp = BioseqFindFromSeqLoc (sfp->location);
15111 if (bsp != NULL && ISA_aa (bsp->mol))
15112 {
15113 slp = FindNucleotideLocationForProteinFeatureConversion (sfp->location);
15114 if (slp == NULL)
15115 {
15116 no_cds = TRUE;
15117 }
15118 }
15119 else
15120 {
15121 slp = GetProteinLocationForNucleotideFeatureConversion (sfp->location, &no_cds);
15122 }
15123 if (slp == NULL) {
15124 if (no_cds) {
15125 ValNodeAddPointer (&no_cds_list, OBJ_SEQFEAT, sfp);
15126 } else {
15127 ValNodeAddPointer (&bad_coordinates_list, OBJ_SEQFEAT, sfp);
15128 }
15129 } else {
15130 slp = SeqLocFree (slp);
15131 }
15132 }
15133
15134 if (no_cds_list != NULL) {
15135 ValNodeAddPointer (&err_list, 0, NewClickableItem (0, "%d features have no overlapping coding region", no_cds_list));
15136 }
15137 if (bad_coordinates_list != NULL) {
15138 ValNodeAddPointer (&err_list, 0, NewClickableItem (0, "%d features do not stop or start on codon boundaries", bad_coordinates_list));
15139 }
15140 return err_list;
15141 }
15142
15143
GetRegionOpts(ValNodePtr feat_list,BaseFormPtr bfp,BoolPtr cancel)15144 static Pointer GetRegionOpts (ValNodePtr feat_list, BaseFormPtr bfp, BoolPtr cancel)
15145 {
15146 ValNodePtr err_list;
15147 WindoW w;
15148 GrouP h, nuc_prot_choice, c;
15149 DialoG bad_prot_feats = NULL;
15150 ButtoN b;
15151 ModalAcceptCancelData acd;
15152 Boolean rval = FALSE;
15153 RegionOptsPtr opts = NULL;
15154
15155 *cancel = FALSE;
15156
15157 if (feat_list == NULL) return NULL;
15158
15159 err_list = GetBadProteinConversionFeatures (feat_list);
15160
15161 w = MovableModalWindow(-20, -13, -10, -10, "Create Nucleotide or Protein Features", NULL);
15162 h = HiddenGroup (w, -1, 0, NULL);
15163 SetGroupSpacing (h, 10, 10);
15164
15165 if (err_list != NULL) {
15166 bad_prot_feats = CreateClickableListDialog (h, "Reasons", "Original Features",
15167 ScrollToDiscrepancyItem, EditDiscrepancyItem, NULL,
15168 GetDiscrepancyItemText);
15169 PointerToDialog (bad_prot_feats, err_list);
15170 }
15171
15172 nuc_prot_choice = HiddenGroup (h, 0, 2, NULL);
15173 RadioButton (nuc_prot_choice, "Create Nucleotide Features");
15174 RadioButton (nuc_prot_choice, err_list == NULL ? "Create Protein Features" : "Create Protein Features (features listed above will be skipped)");
15175 SetValue (nuc_prot_choice, err_list == NULL ? 2 : 1);
15176
15177 c = HiddenGroup (h, 2, 0, NULL);
15178 SetGroupSpacing (c, 10, 10);
15179 b = PushButton (c, "Accept", ModalAcceptButton);
15180 SetObjectExtra (b, &acd, NULL);
15181 b = PushButton (c, "Cancel", ModalCancelButton);
15182 SetObjectExtra (b, &acd, NULL);
15183 AlignObjects (ALIGN_CENTER, (HANDLE) nuc_prot_choice,
15184 (HANDLE) c,
15185 (HANDLE) bad_prot_feats,
15186 NULL);
15187 Show (w);
15188 Select (w);
15189 acd.accepted = FALSE;
15190 acd.cancelled = FALSE;
15191 while (!acd.accepted && ! acd.cancelled)
15192 {
15193 ProcessExternalEvent ();
15194 Update ();
15195 }
15196 ProcessAnEvent ();
15197 if (acd.cancelled)
15198 {
15199 *cancel = TRUE;
15200 }
15201 else
15202 {
15203 opts = (RegionOptsPtr) MemNew (sizeof (RegionOptsData));
15204 if (GetValue (nuc_prot_choice) == 2)
15205 {
15206 opts->create_prot_feats = TRUE;
15207 }
15208 else
15209 {
15210 opts->create_prot_feats = FALSE;
15211 }
15212 }
15213 Remove (w);
15214
15215 return opts;
15216 }
15217
15218
RemoveClickableItemFeaturesFromFeatureList(ClickableItemPtr cip,ValNodePtr PNTR feat_list)15219 static void RemoveClickableItemFeaturesFromFeatureList (ClickableItemPtr cip, ValNodePtr PNTR feat_list)
15220 {
15221 ValNodePtr vnp_i, vnp_p, vnp_r;
15222
15223 if (cip == NULL || feat_list == NULL || *feat_list == NULL) return;
15224 for (vnp_i = cip->item_list; vnp_i != NULL; vnp_i = vnp_i->next) {
15225 if (vnp_i->choice != OBJ_SEQFEAT || vnp_i->data.ptrvalue == NULL) continue;
15226 vnp_p = NULL;
15227 vnp_r = *feat_list;
15228 while (vnp_r != NULL && vnp_r->data.ptrvalue != vnp_i->data.ptrvalue) {
15229 vnp_p = vnp_r;
15230 vnp_r = vnp_r->next;
15231 }
15232 if (vnp_r != NULL) {
15233 if (vnp_p == NULL) {
15234 *feat_list = vnp_r->next;
15235 } else {
15236 vnp_p->next = vnp_r->next;
15237 }
15238 vnp_r->next = NULL;
15239 vnp_r = ValNodeFree (vnp_r);
15240 }
15241 }
15242 for (vnp_i = cip->subcategories; vnp_i != NULL; vnp_i = vnp_i->next) {
15243 RemoveClickableItemFeaturesFromFeatureList (vnp_i->data.ptrvalue, feat_list);
15244 }
15245 }
15246
15247
AdjustRegionConversionFeatures(ValNodePtr feat_list,Pointer extradata,BaseFormPtr bfp,BoolPtr cancel)15248 static ValNodePtr AdjustRegionConversionFeatures (ValNodePtr feat_list, Pointer extradata, BaseFormPtr bfp, BoolPtr cancel)
15249 {
15250 RegionOptsPtr opts = (RegionOptsPtr) extradata;
15251 ValNodePtr err_list, vnp_c;
15252
15253 *cancel = FALSE;
15254 if (opts == NULL || !opts->create_prot_feats) return feat_list;
15255
15256 err_list = GetBadProteinConversionFeatures (feat_list);
15257
15258 for (vnp_c = err_list; vnp_c != NULL; vnp_c = vnp_c->next) {
15259 RemoveClickableItemFeaturesFromFeatureList (vnp_c->data.ptrvalue, &feat_list);
15260 }
15261 return feat_list;
15262 }
15263
15264
ConvertAnyToRegion(SeqFeatPtr sfp,Uint2 featdef_to,Pointer extradata)15265 static Boolean ConvertAnyToRegion (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata)
15266 {
15267 RegionOptsPtr opts = (RegionOptsPtr) extradata;
15268
15269 if (opts == NULL || sfp == NULL) return FALSE;
15270 return ConvertToBondSiteOrRegion (sfp, 0, FEATDEF_REGION, opts->create_prot_feats);
15271 }
15272
15273
ConvertImpToImp(SeqFeatPtr sfp,Uint2 featdef_to,Pointer extradata)15274 static Boolean ConvertImpToImp (SeqFeatPtr sfp, Uint2 featdef_to, Pointer extradata)
15275 {
15276 return ConvertImpToImpFunc (sfp, featdef_to);
15277 }
15278
15279
CollectFeaturesToBeConverted(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)15280 static void CollectFeaturesToBeConverted (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
15281 {
15282 ValNodePtr PNTR feat_list = (ValNodePtr PNTR) userdata;
15283
15284 ValNodeAddPointer (feat_list, OBJ_SEQFEAT, sfp);
15285 }
15286
15287
MoveInferenceToOverlappingGene(SeqFeatPtr sfp)15288 static void MoveInferenceToOverlappingGene (SeqFeatPtr sfp)
15289 {
15290 GBQualPtr qual, qual_prev= NULL, qual_next;
15291 SeqFeatPtr gene;
15292
15293 if (sfp == NULL) return;
15294
15295 gene = GetGeneForFeature (sfp);
15296 if (gene == NULL || gene->idx.deleteme || gene == sfp) return;
15297
15298 qual = sfp->qual;
15299 while (qual != NULL) {
15300 qual_next = qual->next;
15301 if (StringCmp (qual->qual, "inference") == 0) {
15302 if (qual_prev == NULL) {
15303 sfp->qual = qual->next;
15304 } else {
15305 qual_prev->next = qual->next;
15306 }
15307 qual->next = NULL;
15308 qual->next = gene->qual;
15309 gene->qual = qual;
15310 } else {
15311 qual_prev = qual;
15312 }
15313 qual = qual_next;
15314 }
15315 }
15316
15317
NewConvertFeaturesByList(SeqEntryPtr sep,FilterSetPtr fsp,Uint1 featdef_from,FeatureSelRemConvFormPtr mrfp)15318 static Boolean NewConvertFeaturesByList (SeqEntryPtr sep, FilterSetPtr fsp, Uint1 featdef_from, FeatureSelRemConvFormPtr mrfp)
15319 {
15320 ValNodePtr feat_list = NULL, sel_feat_list = NULL, vnp;
15321 Boolean not_match = FALSE;
15322 Boolean only_pseudo = FALSE;
15323 SelStructPtr sel;
15324 SeqFeatPtr sfp;
15325 SeqMgrFeatContext fcontext;
15326 Int4 table_line_num = -1;
15327 Uint2 seqfeat_from, seqfeat_to;
15328 Pointer extradata = NULL;
15329 Boolean cancel = FALSE;
15330 ValNodePtr dup_feat_vnp = NULL;
15331 OrigFeatPtr ofp;
15332 Boolean removed_cds = FALSE;
15333 BioseqPtr protBsp;
15334
15335 OperateOnSeqEntryConstrainedObjects (sep, fsp,
15336 CollectFeaturesToBeConverted,
15337 NULL, 0, featdef_from, 0, &feat_list);
15338 sel = ObjMgrGetSelected ();
15339 while (sel != NULL) {
15340 if (sel->entityID == mrfp->input_entityID && sel->itemtype == OBJ_SEQFEAT) {
15341 sfp = SeqMgrGetDesiredFeature (sel->entityID, NULL, sel->itemID, 0, NULL, &fcontext);
15342 if (sfp != NULL) {
15343 vnp = feat_list;
15344 while (vnp != NULL && vnp->data.ptrvalue != sfp) {
15345 vnp = vnp->next;
15346 }
15347 if (vnp == NULL) {
15348 not_match = TRUE;
15349 }
15350 ValNodeAddPointer (&sel_feat_list, OBJ_SEQFEAT, sfp);
15351 }
15352 }
15353 sel = sel->next;
15354 }
15355 if (sel_feat_list != NULL) {
15356 feat_list = ValNodeFree (feat_list);
15357 if (not_match
15358 && Message (MSG_YN,
15359 "Selected feature%s do%s not match options - apply to selected feature anyway?",
15360 sel_feat_list->next == NULL ? "" : "s",
15361 sel_feat_list->next == NULL ? "es" : "") == ANS_NO) {
15362 sel_feat_list = ValNodeFree (sel_feat_list);
15363 return FALSE;
15364 }
15365 feat_list = sel_feat_list;
15366 }
15367
15368 if (feat_list == NULL) {
15369 Message (MSG_ERROR, "No features of the specified type exist to be converted!");
15370 return FALSE;
15371 }
15372
15373 /* find line in table that applies */
15374 seqfeat_from = FindFeatFromFeatDefType (featdef_from);
15375 seqfeat_to = FindFeatFromFeatDefType (mrfp->featdef_to);
15376
15377 table_line_num = GetConvertFeatureTableLine (seqfeat_from, featdef_from, seqfeat_to, mrfp->featdef_to);
15378 if (table_line_num < 0 || ConvertFeaturesTable[table_line_num].convert_func == NULL)
15379 {
15380 Message (MSG_ERROR, "This conversion not supported - contact"
15381 " sequindev for instructions.");
15382 return FALSE;
15383 }
15384
15385 /* collect extra data if necessary */
15386 if (ConvertFeaturesTable[table_line_num].collect_options != NULL)
15387 {
15388 extradata = (ConvertFeaturesTable[table_line_num].collect_options) (feat_list, mrfp->bfp, &cancel);
15389 if (cancel)
15390 {
15391 feat_list = ValNodeFree (feat_list);
15392 /* free extradata */
15393 if (ConvertFeaturesTable[table_line_num].free_options != NULL)
15394 {
15395 (ConvertFeaturesTable[table_line_num].free_options) (extradata);
15396 }
15397 return FALSE;
15398 }
15399 }
15400 else if (featdef_from == FEATDEF_CDS && mrfp->featdef_to == FEATDEF_mat_peptide_aa)
15401 {
15402 extradata = &(mrfp->leave_original_feature);
15403 }
15404
15405 /* adjust feature list if necessary */
15406 if (ConvertFeaturesTable[table_line_num].adjust_features != NULL)
15407 {
15408 feat_list = (ConvertFeaturesTable[table_line_num].adjust_features) (feat_list, extradata, mrfp->bfp, &cancel);
15409 if (cancel || feat_list == NULL)
15410 {
15411 feat_list = ValNodeFree (feat_list);
15412 /* free extradata */
15413 if (ConvertFeaturesTable[table_line_num].free_options != NULL)
15414 {
15415 (ConvertFeaturesTable[table_line_num].free_options) (extradata);
15416 }
15417 return FALSE;
15418 }
15419 }
15420
15421 /* process list */
15422 for (vnp = feat_list; vnp != NULL; vnp = vnp->next)
15423 {
15424 sfp = (SeqFeatPtr) vnp->data.ptrvalue;
15425 if (sfp == NULL) continue;
15426 protBsp = NULL;
15427 if (sfp->data.choice == SEQFEAT_CDREGION && !mrfp->leave_original_feature)
15428 {
15429 protBsp = BioseqFindFromSeqLoc (sfp->product);
15430 if (protBsp != NULL)
15431 {
15432 protBsp->idx.deleteme = TRUE;
15433 }
15434 removed_cds = TRUE;
15435 }
15436
15437 dup_feat_vnp = NULL;
15438 if (mrfp->leave_original_feature)
15439 {
15440 /* need a list of duplicate features that we can add to the appropriate SeqEntrys
15441 * when we are done with the conversions.
15442 */
15443 dup_feat_vnp = AddDuplicateFeature (sfp, &(mrfp->feat_list));
15444 }
15445
15446 if (ConvertFeaturesTable[table_line_num].convert_func (sfp, mrfp->featdef_to, extradata))
15447 {
15448 /* set the subtype to zero so that it will be reindexed */
15449 sfp->idx.subtype = 0;
15450 if (mrfp->featdef_to == FEATDEF_misc_feature)
15451 {
15452 MoveInferenceToOverlappingGene (sfp);
15453 }
15454 }
15455 else if (dup_feat_vnp != NULL && dup_feat_vnp->data.ptrvalue != NULL)
15456 {
15457 /* feature wasn't removed, for whatever reason */
15458 /* remove the duplicate feature from the list to be added later */
15459 ofp = (OrigFeatPtr) dup_feat_vnp->data.ptrvalue;
15460 ofp->sfp = SeqFeatFree (ofp->sfp);
15461 ofp->sep = NULL;
15462
15463 /* don't remove protein product if feature wasn't removed */
15464 if (protBsp != NULL)
15465 {
15466 protBsp->idx.deleteme = FALSE;
15467 }
15468 }
15469 else if (sfp->data.choice == SEQFEAT_CDREGION)
15470 {
15471 /* failed to convert feature, don't remove product */
15472 if (protBsp != NULL)
15473 {
15474 protBsp->idx.deleteme = FALSE;
15475 }
15476 }
15477 }
15478
15479 feat_list = ValNodeFree (feat_list);
15480
15481 /* do cleanup tasks */
15482 if (ConvertFeaturesTable[table_line_num].cleanup_func != NULL)
15483 {
15484 (ConvertFeaturesTable[table_line_num].cleanup_func) (mrfp->input_entityID, extradata);
15485 }
15486
15487 /* free extradata */
15488 if (ConvertFeaturesTable[table_line_num].free_options != NULL)
15489 {
15490 (ConvertFeaturesTable[table_line_num].free_options) (extradata);
15491 }
15492
15493 if (removed_cds)
15494 {
15495 DeleteMarkedObjects (mrfp->input_entityID, 0, NULL);
15496 RenormalizeNucProtSets (sep, TRUE);
15497 }
15498
15499 return TRUE;
15500 }
15501
15502
RemoveProteinProducts(ValNodePtr bsplist,Uint2 entityID,SeqEntryPtr sep)15503 static void RemoveProteinProducts (ValNodePtr bsplist, Uint2 entityID, SeqEntryPtr sep)
15504 {
15505 MsgAnswer ans;
15506 ValNodePtr tmp;
15507 BioseqPtr bsp;
15508 Uint4 itemID;
15509 OMProcControl ompc;
15510
15511 if (bsplist == NULL)
15512 {
15513 return;
15514 }
15515 ans = Message (MSG_YN, "Remove protein products?");
15516 if (ans == ANS_YES) {
15517 for (tmp = bsplist; tmp != NULL; tmp = tmp->next) {
15518 bsp = (BioseqPtr) tmp->data.ptrvalue;
15519 itemID = GetItemIDGivenPointer (entityID, OBJ_BIOSEQ, (Pointer) bsp);
15520 if (itemID > 0) {
15521 MemSet ((Pointer) (&ompc), 0, sizeof (OMProcControl));
15522 ompc.do_not_reload_from_cache = TRUE;
15523 ompc.input_entityID = entityID;
15524 ompc.input_itemID = itemID;
15525 ompc.input_itemtype = OBJ_BIOSEQ;
15526 if (! DetachDataForProc (&ompc, FALSE)) {
15527 Message (MSG_POSTERR, "DetachDataForProc failed");
15528 }
15529 SeqMgrDeleteFromBioseqIndex (bsp);
15530 }
15531 }
15532 ans = Message (MSG_YN, "Renormalize Nuc-Prot sets?");
15533 if (ans == ANS_YES)
15534 {
15535 RemoveOrphanProteins (entityID, sep);
15536 RenormalizeNucProtSets (sep, TRUE);
15537 }
15538 }
15539 }
15540
RemoveCDNANucProtProducts(ValNodePtr bssplist,Uint2 entityID)15541 static void RemoveCDNANucProtProducts (ValNodePtr bssplist, Uint2 entityID)
15542 {
15543 MsgAnswer ans;
15544 ValNodePtr tmp;
15545 BioseqSetPtr bssp;
15546 Uint4 itemID;
15547 OMProcControl ompc;
15548
15549 if (bssplist == NULL)
15550 {
15551 return;
15552 }
15553
15554 ans = Message (MSG_YN, "Remove cDNA nuc-prot products?");
15555 if (ans != ANS_YES)
15556 {
15557 return;
15558 }
15559
15560 for (tmp = bssplist; tmp != NULL; tmp = tmp->next)
15561 {
15562 bssp = (BioseqSetPtr) tmp->data.ptrvalue;
15563 itemID = GetItemIDGivenPointer (entityID, OBJ_BIOSEQSET, (Pointer) bssp);
15564 if (itemID > 0) {
15565 MemSet ((Pointer) (&ompc), 0, sizeof (OMProcControl));
15566 ompc.do_not_reload_from_cache = TRUE;
15567 ompc.input_entityID = entityID;
15568 ompc.input_itemID = itemID;
15569 ompc.input_itemtype = OBJ_BIOSEQSET;
15570 if (! DetachDataForProc (&ompc, FALSE)) {
15571 Message (MSG_POSTERR, "DetachDataForProc failed");
15572 }
15573 }
15574 }
15575 }
15576
15577
FeatureRemoveOrConvertAction(Pointer userdata)15578 static Boolean FeatureRemoveOrConvertAction (Pointer userdata)
15579 {
15580 FeatureSelRemConvFormPtr mrfp;
15581 FilterSetPtr fsp;
15582 SeqEntryPtr sep;
15583 ValNodePtr feature_type_list, vnp;
15584 Int4 window_action;
15585 Uint1 feat_def_choice;
15586 RemoveFeatureData rfd;
15587 OrigFeatPtr ofp;
15588 SeqFeatPtr sfp;
15589 Boolean rval = TRUE;
15590 SeqEntryPtr create_sep;
15591
15592 if (userdata == NULL) return FALSE;
15593
15594 mrfp = (FeatureSelRemConvFormPtr) userdata;
15595 window_action = GetValue (mrfp->action_choice);
15596
15597 fsp = (FilterSetPtr) DialogToPointer (mrfp->constraints);
15598
15599 sep = GetTopSeqEntryForEntityID (mrfp->input_entityID);
15600 if (sep == NULL) return FALSE;
15601
15602 if (window_action == FEATURE_CONVERT)
15603 {
15604 vnp = (ValNodePtr) DialogToPointer (mrfp->feature_select_to);
15605 if (vnp == NULL)
15606 {
15607 FilterSetFree (fsp);
15608 return FALSE;
15609 }
15610 mrfp->featdef_to = vnp->choice;
15611 /* NOTE - I do not need to use ValNodeFreeData because I'm using
15612 * the data.ptrvalue in mrfp->featname_to and will free it when I free
15613 * mrfp.
15614 */
15615 vnp = ValNodeFree (vnp);
15616 feature_type_list = (ValNodePtr) DialogToPointer (mrfp->feature_select_from);
15617 mrfp->leave_original_feature = GetStatus (mrfp->leave_original_feature_btn);
15618 }
15619 else
15620 {
15621 feature_type_list = (ValNodePtr) DialogToPointer (mrfp->feature_select);
15622 }
15623 if (feature_type_list == NULL)
15624 {
15625 FilterSetFree (fsp);
15626 return FALSE;
15627 }
15628
15629 for (vnp = feature_type_list; vnp != NULL; vnp = vnp->next)
15630 {
15631 feat_def_choice = vnp->choice;
15632 if (feat_def_choice == 255)
15633 {
15634 feat_def_choice = 0;
15635 }
15636 switch (window_action)
15637 {
15638 case FEATURE_CONVERT:
15639 rval = NewConvertFeaturesByList (sep, fsp, feat_def_choice, mrfp);
15640 break;
15641 case FEATURE_REMOVE:
15642 rfd.bsplist = NULL;
15643 rfd.bssplist = NULL;
15644 OperateOnSeqEntryConstrainedObjects (sep, fsp,
15645 RemoveFeatureCallback,
15646 NULL, 0, feat_def_choice, 0, &rfd);
15647 RemoveProteinProducts (rfd.bsplist, mrfp->input_entityID, sep);
15648 RemoveCDNANucProtProducts (rfd.bssplist, mrfp->input_entityID);
15649 rfd.bsplist = ValNodeFree (rfd.bsplist);
15650 rfd.bssplist = ValNodeFree (rfd.bssplist);
15651 break;
15652 case FEATURE_SELECT:
15653 OperateOnSeqEntryConstrainedObjects (sep, fsp,
15654 SelectFeatureCallback,
15655 NULL, 0, feat_def_choice, 0, NULL);
15656 break;
15657 case FEATURE_DESELECT:
15658 OperateOnSeqEntryConstrainedObjects (sep, fsp,
15659 DeselectFeatureCallback,
15660 NULL, 0, feat_def_choice, 0, NULL);
15661 break;
15662 }
15663 }
15664
15665 ValNodeFree (feature_type_list);
15666 FilterSetFree (fsp);
15667
15668 if (window_action == FEATURE_REMOVE || window_action == FEATURE_CONVERT)
15669 {
15670 DeleteMarkedObjects (mrfp->input_entityID, 0, NULL);
15671 }
15672
15673 if (window_action == FEATURE_CONVERT && mrfp->leave_original_feature)
15674 {
15675 for (vnp = mrfp->feat_list; vnp != NULL; vnp = vnp->next)
15676 {
15677 ofp = (OrigFeatPtr) vnp->data.ptrvalue;
15678 if (ofp == NULL || ofp->sep == NULL || ofp->sfp == NULL)
15679 {
15680 continue;
15681 }
15682 if (IS_Bioseq_set (ofp->sep)) {
15683 create_sep = FindNucSeqEntry (ofp->sep);
15684 } else {
15685 create_sep = ofp->sep;
15686 }
15687 sfp = CreateNewFeature (create_sep, NULL, ofp->sfp->data.choice, ofp->sfp);
15688 }
15689 }
15690 mrfp->feat_list = ValNodeFreeData (mrfp->feat_list);
15691
15692 if (mrfp->renormalize_nucprot) {
15693 RenormalizeNucProtSets (sep, TRUE);
15694 }
15695
15696 ObjMgrSetDirtyFlag (mrfp->input_entityID, TRUE);
15697 ObjMgrSendMsg (OM_MSG_UPDATE, mrfp->input_entityID, 0, 0);
15698 Update ();
15699 return rval;
15700 }
15701
FeatureRemoveOrConvertBaseForm(BaseFormPtr bfp,Int4 first_action)15702 NLM_EXTERN void FeatureRemoveOrConvertBaseForm (BaseFormPtr bfp, Int4 first_action)
15703 {
15704 FeatureSelRemConvFormPtr mrfp;
15705 WindoW w;
15706 GrouP h, k, g, n;
15707 SeqEntryPtr sep;
15708
15709 if (bfp == NULL) return;
15710
15711 mrfp = (FeatureSelRemConvFormPtr) MemNew (sizeof (FeatureSelRemConvFormData));
15712 if (mrfp == NULL) return;
15713
15714 mrfp->bfp = bfp;
15715
15716 w = FixedWindow (-50, -33, -10, -10, "Remove or Convert Features", StdCloseWindowProc);
15717 SetObjectExtra (w, mrfp, CleanupFeatureSelRemConvForm);
15718 mrfp->form = (ForM) w;
15719 mrfp->input_entityID = bfp->input_entityID;
15720
15721 sep = GetTopSeqEntryForEntityID(bfp->input_entityID);
15722
15723 h = HiddenGroup (w, -1, 0, NULL);
15724 SetGroupSpacing (h, 10, 10);
15725
15726 if (first_action < FEATURE_REMOVE || first_action > FEATURE_DESELECT)
15727 {
15728 first_action = FEATURE_REMOVE;
15729 }
15730 mrfp->action_choice = PopupList (h, TRUE, FeatureRemoveOrConvertCenterAction);
15731 PopupItem (mrfp->action_choice, "Remove Features");
15732 PopupItem (mrfp->action_choice, "Convert Features");
15733 SetValue (mrfp->action_choice, first_action);
15734 SetObjectExtra (mrfp->action_choice, mrfp, NULL);
15735
15736 mrfp->clear_constraints_on_action_change = CheckBox (h, "Clear when changing actions", NULL);
15737 SetStatus (mrfp->clear_constraints_on_action_change, TRUE);
15738
15739 n = HiddenGroup (h, 0, 0, NULL);
15740 mrfp->remove_grp = HiddenGroup (n, 0, 1, NULL);
15741 mrfp->feature_select = FeatureSelectionDialogEx (mrfp->remove_grp, TRUE, sep,
15742 FeatureRemoveChangeNotify,
15743 mrfp);
15744
15745 mrfp->convert_grp = HiddenGroup (n, 3, 0, NULL);
15746 k = HiddenGroup (mrfp->convert_grp, 0, 2, NULL);
15747 mrfp->from_prompt = StaticPrompt (k, "From", 0, dialogTextHeight, systemFont, 'l');
15748 mrfp->feature_select_from = FeatureSelectionDialogEx (k, FALSE, sep,
15749 FeatureRemoveChangeNotify,
15750 mrfp);
15751 AlignObjects (ALIGN_CENTER, (HANDLE) mrfp->from_prompt, (HANDLE) mrfp->feature_select_from, NULL);
15752 k = HiddenGroup (mrfp->convert_grp, 0, 2, NULL);
15753 mrfp->to_prompt = StaticPrompt (k, "To", 0, dialogTextHeight, systemFont, 'l');
15754 mrfp->feature_select_to = FeatureSelectionDialog (k, FALSE,
15755 FeatureRemoveChangeNotify,
15756 mrfp);
15757 AlignObjects (ALIGN_CENTER, (HANDLE) mrfp->to_prompt, (HANDLE) mrfp->feature_select_to, NULL);
15758 AlignObjects (ALIGN_CENTER, (HANDLE) mrfp->remove_grp, (HANDLE) mrfp->convert_grp, NULL);
15759
15760 g = HiddenGroup (mrfp->convert_grp, 0, 2, NULL);
15761 StaticPrompt (g, "Conversion Function", 0, dialogTextHeight, systemFont, 'c');
15762 SelectFont (systemFont);
15763 mrfp->help_text = DocumentPanel (g, stdCharWidth * 12, LineHeight () * (TALL_SELECTION_LIST + 1));
15764
15765 mrfp->leave_original_feature_btn = CheckBox (mrfp->convert_grp, "Leave Original Feature", FeatureRemoveChangeButton);
15766 SetObjectExtra (mrfp->leave_original_feature_btn, mrfp, NULL);
15767 SetStatus (mrfp->leave_original_feature_btn, FALSE);
15768 AlignObjects (ALIGN_CENTER, (HANDLE) k, (HANDLE) mrfp->leave_original_feature_btn, NULL);
15769
15770 mrfp->feat_list = NULL;
15771 mrfp->constraints = FilterGroup (h, TRUE, FALSE, TRUE, FALSE, TRUE, "Where feature text");
15772 mrfp->accept_cancel = AcceptCancelDialog (h, FeatureRemoveOrConvertAction, NULL, FeatureRemoveClear, FeatureRemoveClearText, (Pointer)mrfp, w);
15773 AlignObjects (ALIGN_CENTER, (HANDLE) mrfp->action_choice,
15774 (HANDLE) mrfp->clear_constraints_on_action_change,
15775 (HANDLE) n,
15776 (HANDLE) mrfp->constraints,
15777 (HANDLE) mrfp->accept_cancel, NULL);
15778
15779 FeatureRemoveOrConvertCenterAction (mrfp->action_choice);
15780
15781 Show (w);
15782 }
15783
15784
FeatureRemoveOrConvert(IteM i,Int4 first_action)15785 static void FeatureRemoveOrConvert (IteM i, Int4 first_action)
15786 {
15787 BaseFormPtr bfp;
15788
15789 #ifdef WIN_MAC
15790 bfp = currentFormDataPtr;
15791 #else
15792 bfp = GetObjectExtra (i);
15793 #endif
15794 FeatureRemoveOrConvertBaseForm (bfp, first_action);
15795 }
15796
15797
FeatureRemove(IteM i)15798 extern void FeatureRemove (IteM i)
15799 {
15800 FeatureRemoveOrConvert (i, FEATURE_REMOVE);
15801 }
15802
ConvertFeatures(IteM i)15803 extern void ConvertFeatures (IteM i)
15804 {
15805 FeatureRemoveOrConvert (i, FEATURE_CONVERT);
15806 }
15807
SelectFeatureAction(Pointer userdata)15808 static Boolean SelectFeatureAction (Pointer userdata)
15809 {
15810 FeatureSelRemConvFormPtr mrfp;
15811 FilterSetPtr fsp;
15812 SeqEntryPtr sep;
15813 ValNodePtr feature_type_list, vnp;
15814 Uint1 feat_def_choice;
15815
15816 if (userdata == NULL) return FALSE;
15817
15818 mrfp = (FeatureSelRemConvFormPtr) userdata;
15819 fsp = (FilterSetPtr) DialogToPointer (mrfp->constraints);
15820
15821 sep = GetTopSeqEntryForEntityID (mrfp->input_entityID);
15822 if (sep == NULL) return FALSE;
15823
15824 feature_type_list = (ValNodePtr) DialogToPointer (mrfp->feature_select);
15825 if (feature_type_list == NULL)
15826 {
15827 FilterSetFree (fsp);
15828 return FALSE;
15829 }
15830
15831 for (vnp = feature_type_list; vnp != NULL; vnp = vnp->next)
15832 {
15833 feat_def_choice = vnp->choice;
15834 if (feat_def_choice == 255)
15835 {
15836 feat_def_choice = 0;
15837 }
15838 OperateOnSeqEntryConstrainedObjects (sep, fsp,
15839 SelectFeatureCallback,
15840 NULL, 0, feat_def_choice, 0, NULL);
15841 }
15842
15843 ValNodeFree (feature_type_list);
15844 FilterSetFree (fsp);
15845
15846 ObjMgrSetDirtyFlag (mrfp->input_entityID, TRUE);
15847 ObjMgrSendMsg (OM_MSG_UPDATE, mrfp->input_entityID, 0, 0);
15848 Update ();
15849 return TRUE;
15850 }
15851
SelectFeatures(IteM i)15852 extern void SelectFeatures (IteM i)
15853 {
15854 BaseFormPtr bfp;
15855 FeatureSelRemConvFormPtr mrfp;
15856 WindoW w;
15857 GrouP h;
15858 SeqEntryPtr sep;
15859
15860 #ifdef WIN_MAC
15861 bfp = currentFormDataPtr;
15862 #else
15863 bfp = GetObjectExtra (i);
15864 #endif
15865 if (bfp == NULL) return;
15866
15867 mrfp = (FeatureSelRemConvFormPtr) MemNew (sizeof (FeatureSelRemConvFormData));
15868 if (mrfp == NULL) return;
15869
15870 w = FixedWindow (-50, -33, -10, -10, "Select Features", StdCloseWindowProc);
15871 SetObjectExtra (w, mrfp, CleanupFeatureSelRemConvForm);
15872 mrfp->form = (ForM) w;
15873 mrfp->input_entityID = bfp->input_entityID;
15874 sep = GetTopSeqEntryForEntityID(bfp->input_entityID);
15875
15876 h = HiddenGroup (w, -1, 0, NULL);
15877 SetGroupSpacing (h, 10, 10);
15878
15879 mrfp->feature_select = FeatureSelectionDialogEx (h, TRUE, sep,
15880 FeatureRemoveChangeNotify,
15881 mrfp);
15882
15883 mrfp->constraints = FilterGroup (h, TRUE, FALSE, TRUE, FALSE, FALSE, "Where feature text");
15884 mrfp->accept_cancel = AcceptCancelDialog (h, SelectFeatureAction, NULL, FeatureRemoveClear, FeatureRemoveClearText, (Pointer)mrfp, w);
15885 AlignObjects (ALIGN_CENTER, (HANDLE) mrfp->feature_select,
15886 (HANDLE) mrfp->constraints,
15887 (HANDLE) mrfp->accept_cancel, NULL);
15888
15889 Show (w);
15890 }
15891
15892
15893 typedef struct reverseintervalsform
15894 {
15895 FORM_MESSAGE_BLOCK
15896 DialoG feature_select;
15897 DialoG constraints;
15898 DialoG accept_cancel;
15899
15900 ValNodePtr feat_list;
15901 BaseFormPtr bfp;
15902 } ReverseIntervalsFormData, PNTR ReverseIntervalsFormPtr;
15903
ReverseIntervalsChangeNotify(Pointer userdata)15904 static void ReverseIntervalsChangeNotify (Pointer userdata)
15905 {
15906 ReverseIntervalsFormPtr fp;
15907 ValNodePtr err_list;
15908
15909 fp = (ReverseIntervalsFormPtr) userdata;
15910 if (fp == NULL) return;
15911
15912 err_list = TestDialog (fp->feature_select);
15913
15914 if (err_list == NULL)
15915 {
15916 EnableAcceptCancelDialogAccept (fp->accept_cancel);
15917 }
15918 else
15919 {
15920 DisableAcceptCancelDialogAccept (fp->accept_cancel);
15921 }
15922 ValNodeFree (err_list);
15923 }
15924
ReverseIntervalsClearText(Pointer data)15925 static void ReverseIntervalsClearText (Pointer data)
15926 {
15927 ReverseIntervalsFormPtr mrfp;
15928 FilterSetPtr fsp;
15929
15930 mrfp = (ReverseIntervalsFormPtr) data;
15931 if (mrfp == NULL) return;
15932
15933 fsp = DialogToPointer (mrfp->constraints);
15934 FilterSetClearText (fsp);
15935 PointerToDialog (mrfp->constraints, fsp);
15936 FilterSetFree (fsp);
15937 }
15938
ReverseIntervalsClear(Pointer data)15939 static void ReverseIntervalsClear (Pointer data)
15940 {
15941 ReverseIntervalsFormPtr mrfp;
15942
15943 mrfp = (ReverseIntervalsFormPtr) data;
15944 if (mrfp == NULL) return;
15945
15946 PointerToDialog (mrfp->feature_select, NULL);
15947 PointerToDialog (mrfp->constraints, NULL);
15948 }
15949
ReverseLocationIntervalOrder(SeqLocPtr slp)15950 static void ReverseLocationIntervalOrder (SeqLocPtr slp)
15951 {
15952 SeqLocPtr subslp_list = NULL, subslp, subslp_next;
15953 PackSeqPntPtr pspp;
15954 Int4 pnt_num, swap;
15955
15956 if (slp == NULL
15957 || slp->choice == SEQLOC_NULL
15958 || slp->choice == SEQLOC_EMPTY
15959 || slp->choice == SEQLOC_WHOLE
15960 || slp->choice == SEQLOC_INT
15961 || slp->choice == SEQLOC_PNT
15962 || slp->choice == SEQLOC_BOND
15963 || slp->choice == SEQLOC_FEAT) {
15964 return;
15965 }
15966 if (slp->choice == SEQLOC_MIX
15967 || slp->choice == SEQLOC_PACKED_INT
15968 || slp->choice == SEQLOC_EQUIV) {
15969 for (subslp = slp->data.ptrvalue;
15970 subslp != NULL;
15971 subslp = subslp_next) {
15972 subslp_next = subslp->next;
15973 subslp->next = subslp_list;
15974 subslp_list = subslp;
15975 ReverseLocationIntervalOrder (subslp);
15976 }
15977 slp->data.ptrvalue = subslp_list;
15978 } else if (slp->choice == SEQLOC_PACKED_PNT) {
15979 pspp = (PackSeqPntPtr) slp->data.ptrvalue;
15980 if (pspp != NULL) {
15981 for (pnt_num = 0; pnt_num < pspp->used / 2; pnt_num++) {
15982 swap = pspp->pnts[pnt_num];
15983 pspp->pnts[pnt_num] = pspp->pnts[pspp->used - 1 - pnt_num];
15984 pspp->pnts[pspp->used - 1 - pnt_num] = swap;
15985 }
15986 }
15987 }
15988 }
15989
ReverseIntervalsCallback(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)15990 static void ReverseIntervalsCallback (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
15991
15992 {
15993 if (sfp == NULL || sfp->location == NULL) return;
15994
15995 ReverseLocationIntervalOrder (sfp->location);
15996 }
15997
15998
ReverseIntervalsAction(Pointer userdata)15999 static Boolean ReverseIntervalsAction (Pointer userdata)
16000 {
16001 ReverseIntervalsFormPtr mrfp;
16002 FilterSetPtr fsp;
16003 SeqEntryPtr sep;
16004 ValNodePtr feature_type_list, vnp;
16005 Uint1 feat_def_choice;
16006
16007 if (userdata == NULL) return FALSE;
16008
16009 mrfp = (ReverseIntervalsFormPtr) userdata;
16010 fsp = (FilterSetPtr) DialogToPointer (mrfp->constraints);
16011
16012 sep = GetTopSeqEntryForEntityID (mrfp->input_entityID);
16013 if (sep == NULL) return FALSE;
16014
16015 feature_type_list = (ValNodePtr) DialogToPointer (mrfp->feature_select);
16016 if (feature_type_list == NULL)
16017 {
16018 FilterSetFree (fsp);
16019 return FALSE;
16020 }
16021
16022 for (vnp = feature_type_list; vnp != NULL; vnp = vnp->next)
16023 {
16024 feat_def_choice = vnp->choice;
16025 if (feat_def_choice == 255)
16026 {
16027 feat_def_choice = 0;
16028 }
16029 OperateOnSeqEntryConstrainedObjects (sep, fsp,
16030 ReverseIntervalsCallback,
16031 NULL, 0, feat_def_choice, 0, NULL);
16032 }
16033
16034 ValNodeFree (feature_type_list);
16035 FilterSetFree (fsp);
16036
16037 ObjMgrSetDirtyFlag (mrfp->input_entityID, TRUE);
16038 ObjMgrSendMsg (OM_MSG_UPDATE, mrfp->input_entityID, 0, 0);
16039 Update ();
16040 return TRUE;
16041 }
16042
ReverseFeatureIntervals(IteM i)16043 extern void ReverseFeatureIntervals (IteM i)
16044 {
16045 BaseFormPtr bfp;
16046 ReverseIntervalsFormPtr fp;
16047 WindoW w;
16048 GrouP h;
16049 SeqEntryPtr sep;
16050
16051 #ifdef WIN_MAC
16052 bfp = currentFormDataPtr;
16053 #else
16054 bfp = GetObjectExtra (i);
16055 #endif
16056 if (bfp == NULL) return;
16057
16058 fp = (ReverseIntervalsFormPtr) MemNew (sizeof (ReverseIntervalsFormData));
16059 if (fp == NULL) return;
16060
16061 w = FixedWindow (-50, -33, -10, -10, "Reverse Feature Intervals", StdCloseWindowProc);
16062 SetObjectExtra (w, fp, StdCleanupFormProc);
16063 fp->form = (ForM) w;
16064 fp->input_entityID = bfp->input_entityID;
16065 sep = GetTopSeqEntryForEntityID(bfp->input_entityID);
16066
16067 h = HiddenGroup (w, -1, 0, NULL);
16068 SetGroupSpacing (h, 10, 10);
16069
16070 fp->feature_select = FeatureSelectionDialogEx (h, TRUE, sep,
16071 ReverseIntervalsChangeNotify,
16072 fp);
16073
16074 fp->constraints = FilterGroup (h, TRUE, FALSE, TRUE, FALSE, FALSE, "Where feature text");
16075 fp->accept_cancel = AcceptCancelDialog (h, ReverseIntervalsAction, NULL, ReverseIntervalsClear, ReverseIntervalsClearText, (Pointer)fp, w);
16076 AlignObjects (ALIGN_CENTER, (HANDLE) fp->feature_select,
16077 (HANDLE) fp->constraints,
16078 (HANDLE) fp->accept_cancel, NULL);
16079
16080 Show (w);
16081 }
16082
16083
16084
ParseFieldFree(ParseFieldPtr pfp)16085 extern ParseFieldPtr ParseFieldFree (ParseFieldPtr pfp)
16086 {
16087 if (pfp != NULL)
16088 {
16089 switch (pfp->parse_field_type) {
16090 case PARSE_FIELD_SOURCE_QUAL :
16091 case PARSE_FIELD_FEATURE_NOTE:
16092 case PARSE_FIELD_DBXREF:
16093 pfp->feature_field = ValNodeFreeData (pfp->feature_field);
16094 break;
16095 case PARSE_FIELD_DEFLINE:
16096 case PARSE_FIELD_BIOSRC_STRING:
16097 case PARSE_FIELD_GENE_FIELD:
16098 case PARSE_FIELD_RNA_FIELD:
16099 case PARSE_FIELD_CDS_COMMENT:
16100 case PARSE_FIELD_COMMENT_DESC:
16101 case PARSE_FIELD_IMPORT_QUAL:
16102 case PARSE_FIELD_PROTEIN_FIELD:
16103 pfp->feature_field = ValNodeFree (pfp->feature_field);
16104 break;
16105 default:
16106 pfp->feature_field = ValNodeFree (pfp->feature_field);
16107 }
16108
16109 if (pfp->parse_field_type == PARSE_FIELD_RNA_FIELD)
16110 {
16111 pfp->feature_subtype = ValNodeFree (pfp->feature_subtype);
16112 }
16113 else
16114 {
16115 pfp->feature_subtype = ValNodeFreeData (pfp->feature_subtype);
16116 }
16117 pfp = MemFree (pfp);
16118 }
16119 return pfp;
16120 }
16121
16122
16123 #define AECR_APPLY 1
16124 #define AECR_EDIT 2
16125 #define AECR_CONVERT 3
16126 #define AECR_SWAP 4
16127 #define AECR_PARSE 5
16128 #define AECR_REMOVE 6
16129 #define NUM_AECR 6
16130
16131
FeatureEditor(IteM i,Int4 first_action)16132 static void FeatureEditor (IteM i, Int4 first_action)
16133 {
16134 BaseFormPtr bfp;
16135
16136 #ifdef WIN_MAC
16137 bfp = currentFormDataPtr;
16138 #else
16139 bfp = GetObjectExtra (i);
16140 #endif
16141 if (bfp == NULL) return;
16142 FeatureEditorBaseForm (bfp, first_action);
16143 }
16144
16145
FeatureEvidenceEditor(IteM i)16146 extern void FeatureEvidenceEditor (IteM i)
16147 {
16148 FeatureEditor(i, FEAT_ED_EVIDENCE);
16149 }
16150
FeatureExceptionEditor(IteM i)16151 extern void FeatureExceptionEditor (IteM i)
16152 {
16153 FeatureEditor(i, FEAT_ED_EXCEPTION);
16154 }
16155
FeaturePartialEditor(IteM i)16156 extern void FeaturePartialEditor (IteM i)
16157 {
16158 FeatureEditor(i, FEAT_ED_PARTIAL);
16159 }
16160
FeatureStrandEditor(IteM i)16161 extern void FeatureStrandEditor (IteM i)
16162 {
16163 FeatureEditor(i, FEAT_ED_STRAND);
16164 }
16165
FeatureCitationEditor(IteM i)16166 extern void FeatureCitationEditor (IteM i)
16167 {
16168 FeatureEditor(i, FEAT_ED_CITATION);
16169 }
16170
FeatureExperimentEditor(IteM i)16171 extern void FeatureExperimentEditor (IteM i)
16172 {
16173 FeatureEditor(i, FEAT_ED_EXPERIMENT);
16174 }
16175
FeatureInferenceEditor(IteM i)16176 extern void FeatureInferenceEditor (IteM i)
16177 {
16178 FeatureEditor(i, FEAT_ED_INFERENCE);
16179 }
16180
FeaturePseudoEditor(IteM i)16181 extern void FeaturePseudoEditor (IteM i)
16182 {
16183 FeatureEditor (i, FEAT_ED_PSEUDO);
16184 }
16185
16186 typedef struct cdset
16187 {
16188 ValNodePtr cds_list;
16189 ValNodePtr gene_list;
16190 ValNodePtr prot_list;
16191 ValNodePtr mrna_list;
16192 } CDSetData, PNTR CDSetPtr;
16193
FreeCDSetList(ValNodePtr vnp)16194 static ValNodePtr FreeCDSetList (ValNodePtr vnp)
16195 {
16196 CDSetPtr cdsp;
16197
16198 if (vnp != NULL)
16199 {
16200 FreeCDSetList (vnp->next);
16201 vnp->next = NULL;
16202 cdsp = (CDSetPtr) vnp->data.ptrvalue;
16203 if (cdsp != NULL)
16204 {
16205 cdsp->cds_list = ValNodeFree (cdsp->cds_list);
16206 cdsp->gene_list = ValNodeFree (cdsp->gene_list);
16207 cdsp->prot_list = ValNodeFree (cdsp->prot_list);
16208 cdsp->mrna_list = ValNodeFree (cdsp->mrna_list);
16209 }
16210 ValNodeFreeData (vnp);
16211 }
16212 return NULL;
16213 }
16214
GetCDSGeneProtFieldName(ValNodePtr vnp)16215 extern CharPtr GetCDSGeneProtFieldName (ValNodePtr vnp)
16216 {
16217 CharPtr PNTR field_name_list = NULL;
16218 Int4 num_fields = 0;
16219 CharPtr label = NULL;
16220
16221 field_name_list = BuildCDSGeneFieldList (&num_fields);
16222 if (field_name_list != NULL
16223 && vnp->data.intvalue > 0 && vnp->data.intvalue <= num_fields)
16224 {
16225 label = StringSave (field_name_list [vnp->data.intvalue - 1]);
16226 }
16227 FreeCDSGeneFieldList (field_name_list, num_fields);
16228 return label;
16229 }
16230
GetCDSGeneProtSample(GrouP h,Uint2 entityID)16231 static DialoG GetCDSGeneProtSample (GrouP h, Uint2 entityID)
16232 {
16233 CharPtr PNTR field_name_list = NULL;
16234 Int4 num_fields = 0, i;
16235 DialoG d = NULL;
16236 SetSampleData ssd;
16237
16238 field_name_list = BuildCDSGeneFieldList (&num_fields);
16239 if (field_name_list != NULL)
16240 {
16241 ssd.entityID = entityID;
16242 ssd.field_list = NULL;
16243 for (i = 0; i < num_fields; i++)
16244 {
16245 ValNodeAddInt (&ssd.field_list, 0, i + 1);
16246 }
16247 ssd.fieldstring_func = GetCDSGeneProtField;
16248 ssd.descrstring_func = NULL;
16249 ssd.fsp = NULL;
16250 ssd.free_vn_proc = NULL;
16251 ssd.copy_vn_proc = IntValNodeCopy;
16252 ssd.match_vn_proc = IntValNodeMatch;
16253 ssd.label_vn_proc = GetCDSGeneProtFieldName;
16254
16255
16256 d = SampleDialog (h);
16257 PointerToDialog (d, &ssd);
16258 FreeCDSGeneFieldList (field_name_list, num_fields);
16259 }
16260 return d;
16261 }
16262
16263
16264 typedef struct buildcdset2
16265 {
16266 ValNodePtr cds_list;
16267 ValNodePtr mrna_list;
16268 ValNodePtr gene_list;
16269 } BuildCDSet2Data, PNTR BuildCDSet2Ptr;
16270
BuildCDSet2Callback(SeqFeatPtr sfp,Pointer userdata)16271 static void BuildCDSet2Callback (SeqFeatPtr sfp, Pointer userdata)
16272 {
16273 BuildCDSet2Ptr b;
16274
16275 if (sfp == NULL || sfp->idx.deleteme || userdata == NULL) return;
16276 b = (BuildCDSet2Ptr) userdata;
16277 if (sfp->data.choice == SEQFEAT_CDREGION)
16278 {
16279 ValNodeAddPointer (&(b->cds_list), OBJ_SEQFEAT, sfp);
16280 }
16281 else if (sfp->data.choice == SEQFEAT_GENE)
16282 {
16283 ValNodeAddPointer (&(b->gene_list), OBJ_SEQFEAT, sfp);
16284 }
16285 else if (sfp->idx.subtype == FEATDEF_mRNA)
16286 {
16287 ValNodeAddPointer (&(b->mrna_list), OBJ_SEQFEAT, sfp);
16288 }
16289 else if (SeqMgrGetGeneXref (sfp) != NULL)
16290 {
16291 ValNodeAddPointer (&(b->gene_list), OBJ_SEQFEAT, sfp);
16292 }
16293 }
16294
16295
UnmarkFeatureList(ValNodePtr list)16296 static void UnmarkFeatureList (ValNodePtr list)
16297 {
16298 SeqFeatPtr sfp;
16299
16300 while (list != NULL)
16301 {
16302 sfp = list->data.ptrvalue;
16303 if (sfp != NULL)
16304 {
16305 sfp->idx.deleteme = FALSE;
16306 }
16307 list = list->next;
16308 }
16309 }
16310
16311
GetGeneForCDSetFeature(SeqFeatPtr sfp)16312 static SeqFeatPtr GetGeneForCDSetFeature (SeqFeatPtr sfp)
16313 {
16314 GeneRefPtr grp;
16315 SeqFeatPtr gene = NULL;
16316 SeqMgrFeatContext fcontext;
16317
16318 grp = SeqMgrGetGeneXref (sfp);
16319 if (grp == NULL)
16320 {
16321 gene = SeqMgrGetOverlappingGene (sfp->location, &fcontext);
16322 }
16323 else if (!SeqMgrGeneIsSuppressed (grp))
16324 {
16325 if (!StringHasNoText (grp->locus_tag))
16326 {
16327 gene = SeqMgrGetGeneByLocusTag (BioseqFindFromSeqLoc (sfp->location), grp->locus_tag, &fcontext);
16328 }
16329 }
16330 return gene;
16331 }
16332
16333
BuildCDSetFromCodingRegion(SeqFeatPtr cds,BoolPtr indexing_needed)16334 static CDSetPtr BuildCDSetFromCodingRegion (SeqFeatPtr cds, BoolPtr indexing_needed)
16335 {
16336 SeqMgrFeatContext fcontext;
16337 SeqFeatPtr gene = NULL, mrna, prot;
16338 BioseqPtr protbsp;
16339 CDSetPtr cdsp;
16340 ProtRefPtr prp;
16341
16342 if (cds == NULL || cds->data.choice != SEQFEAT_CDREGION) return NULL;
16343
16344 cdsp = (CDSetPtr) MemNew (sizeof (CDSetData));
16345 ValNodeAddPointer (&(cdsp->cds_list), 0, cds);
16346
16347 gene = GetGeneForCDSetFeature (cds);
16348 if (gene != NULL)
16349 {
16350 ValNodeAddPointer (&(cdsp->gene_list), 0, gene);
16351 /* mark gene, so that we'll know it isn't lonely */
16352 gene->idx.deleteme = TRUE;
16353 }
16354
16355 mrna = SeqMgrGetOverlappingmRNA (cds->location, &fcontext);
16356 if (mrna != NULL)
16357 {
16358 ValNodeAddPointer (&(cdsp->mrna_list), 0, mrna);
16359 /* mark mrna, so that we'll know it's already in a set */
16360 mrna->idx.deleteme = TRUE;
16361 }
16362
16363 if (cds->product != NULL)
16364 {
16365 protbsp = BioseqFindFromSeqLoc (cds->product);
16366 if (protbsp != NULL)
16367 {
16368 prot = SeqMgrGetNextFeature (protbsp, NULL, SEQFEAT_PROT, FEATDEF_PROT, &fcontext);
16369 /* if there is no full-length protein feature, make one */
16370 if (prot == NULL)
16371 {
16372 prp = ProtRefNew ();
16373 prot = CreateNewFeatureOnBioseq (protbsp, SEQFEAT_PROT, NULL);
16374 if (prot != NULL)
16375 {
16376 prot->data.value.ptrvalue = prp;
16377 if (indexing_needed != NULL)
16378 {
16379 *indexing_needed = TRUE;
16380 }
16381 }
16382 }
16383 if (prot != NULL)
16384 {
16385 ValNodeAddPointer (&(cdsp->prot_list), 0, prot);
16386 }
16387
16388 /* also add in mat_peptides from protein feature */
16389 prot = SeqMgrGetNextFeature (protbsp, NULL, SEQFEAT_PROT, FEATDEF_mat_peptide_aa, &fcontext);
16390 while (prot != NULL)
16391 {
16392 ValNodeAddPointer (&(cdsp->prot_list), 0, prot);
16393 prot = SeqMgrGetNextFeature (protbsp, prot, SEQFEAT_PROT, FEATDEF_mat_peptide_aa, &fcontext);
16394 }
16395 }
16396 }
16397 return cdsp;
16398 }
16399
16400
BuildCDSetFrommRNA(SeqFeatPtr mrna)16401 static CDSetPtr BuildCDSetFrommRNA (SeqFeatPtr mrna)
16402 {
16403 SeqFeatPtr gene;
16404 CDSetPtr cdsp;
16405
16406 if (mrna == NULL || mrna->idx.deleteme || mrna->idx.subtype != FEATDEF_mRNA) return NULL;
16407
16408 cdsp = (CDSetPtr) MemNew (sizeof (CDSetData));
16409 ValNodeAddPointer (&(cdsp->mrna_list), 0, mrna);
16410
16411 gene = GetGeneForCDSetFeature (mrna);
16412 if (gene != NULL)
16413 {
16414 ValNodeAddPointer (&(cdsp->gene_list), 0, gene);
16415 /* mark gene, so that we'll know it isn't lonely */
16416 gene->idx.deleteme = TRUE;
16417 }
16418
16419 return cdsp;
16420 }
16421
16422
16423 static Boolean DoesCDSetMatchConstraint (CDSetPtr cdsp, ChoiceConstraintPtr ccp);
16424
BuildCDSet2List(Uint2 entityID,ChoiceConstraintPtr ccp)16425 static ValNodePtr BuildCDSet2List (Uint2 entityID, ChoiceConstraintPtr ccp)
16426 {
16427 SeqEntryPtr sep;
16428 BuildCDSet2Data b;
16429 CDSetPtr cdsp;
16430 ValNodePtr vnp, vnp_next, vnp_prev;
16431 ValNodePtr cdset_list = NULL;
16432 SeqFeatPtr cds, gene, mrna;
16433 Boolean need_indexing = FALSE;
16434
16435 sep = GetTopSeqEntryForEntityID (entityID);
16436
16437 b.cds_list = NULL;
16438 b.gene_list = NULL;
16439 b.mrna_list = NULL;
16440
16441 VisitFeaturesInSep (sep, &b, BuildCDSet2Callback);
16442
16443 /* build cdsets that have coding regions */
16444 for (vnp = b.cds_list; vnp != NULL; vnp = vnp->next)
16445 {
16446 cds = (SeqFeatPtr) vnp->data.ptrvalue;
16447 if (cds == NULL) continue;
16448 cdsp = BuildCDSetFromCodingRegion (cds, &need_indexing);
16449 if (cdsp != NULL)
16450 {
16451 ValNodeAddPointer (&cdset_list, 0, cdsp);
16452 }
16453 }
16454 if (need_indexing)
16455 {
16456 /* indexing because we have created full-length protein features */
16457 SeqMgrIndexFeatures (entityID, NULL);
16458 }
16459
16460 /* build cdsets for mrna features that don't have coding regions */
16461 for (vnp = b.mrna_list; vnp != NULL; vnp = vnp->next)
16462 {
16463 mrna = (SeqFeatPtr) vnp->data.ptrvalue;
16464 if (mrna == NULL || mrna->idx.deleteme) continue;
16465 cdsp = BuildCDSetFrommRNA (mrna);
16466 if (cdsp != NULL)
16467 {
16468 ValNodeAddPointer (&cdset_list, 0, cdsp);
16469 }
16470 }
16471
16472 /* build cdsets for lonely genes / features with gene xrefs that are not coding regions or mrnas */
16473 for (vnp = b.gene_list; vnp != NULL; vnp = vnp->next)
16474 {
16475 gene = (SeqFeatPtr) vnp->data.ptrvalue;
16476 if (gene == NULL || gene->idx.deleteme) continue;
16477 cdsp = (CDSetPtr) MemNew (sizeof (CDSetData));
16478 ValNodeAddPointer (&(cdsp->gene_list), 0, gene);
16479 ValNodeAddPointer (&cdset_list, 0, cdsp);
16480 }
16481
16482 /* now unmark features */
16483 UnmarkFeatureList (b.cds_list);
16484 UnmarkFeatureList (b.mrna_list);
16485 UnmarkFeatureList (b.gene_list);
16486
16487 b.cds_list = ValNodeFree (b.cds_list);
16488 b.mrna_list = ValNodeFree (b.mrna_list);
16489 b.gene_list = ValNodeFree (b.gene_list);
16490
16491 /* now remove sets that don't match our choice constraint */
16492 vnp_prev = NULL;
16493 for (vnp = cdset_list; vnp != NULL; vnp = vnp_next)
16494 {
16495 vnp_next = vnp->next;
16496 if (!DoesCDSetMatchConstraint (vnp->data.ptrvalue, ccp))
16497 {
16498 if (vnp_prev == NULL)
16499 {
16500 cdset_list = vnp->next;
16501 }
16502 else
16503 {
16504 vnp_prev->next = vnp->next;
16505 }
16506 vnp->next = NULL;
16507 FreeCDSetList (vnp);
16508 }
16509 else
16510 {
16511 vnp_prev = vnp;
16512 }
16513 }
16514
16515 return cdset_list;
16516 }
16517
16518 typedef struct buildcdset
16519 {
16520 ValNodePtr cdset_list;
16521 ValNodePtr lonely_gene_list;
16522 } BuildCDSetData, PNTR BuildCDSetPtr;
16523
16524
GetCDSetField(CDSetPtr cdsp,ValNodePtr vnp)16525 static CharPtr GetCDSetField (CDSetPtr cdsp, ValNodePtr vnp)
16526 {
16527 ValNodePtr sfp_vnp;
16528 CharPtr str = NULL;
16529
16530 if (cdsp == NULL || vnp == NULL)
16531 {
16532 return NULL;
16533 }
16534
16535 for (sfp_vnp = cdsp->cds_list; sfp_vnp != NULL && str == NULL; sfp_vnp = sfp_vnp->next)
16536 {
16537 str = GetCDSGeneProtField (sfp_vnp->data.ptrvalue, vnp, NULL);
16538 }
16539 for (sfp_vnp = cdsp->gene_list; sfp_vnp != NULL && str == NULL; sfp_vnp = sfp_vnp->next)
16540 {
16541 str = GetCDSGeneProtField (sfp_vnp->data.ptrvalue, vnp, NULL);
16542 }
16543 for (sfp_vnp = cdsp->prot_list; sfp_vnp != NULL && str == NULL; sfp_vnp = sfp_vnp->next)
16544 {
16545 str = GetCDSGeneProtField (sfp_vnp->data.ptrvalue, vnp, NULL);
16546 }
16547 for (sfp_vnp = cdsp->mrna_list; sfp_vnp != NULL && str == NULL; sfp_vnp = sfp_vnp->next)
16548 {
16549 str = GetCDSGeneProtField (sfp_vnp->data.ptrvalue, vnp, NULL);
16550 }
16551 return str;
16552 }
16553
SetCDSetField(CDSetPtr cdsp,ValNodePtr vnp,ApplyValuePtr avp,FilterSetPtr fsp)16554 static Boolean SetCDSetField (CDSetPtr cdsp, ValNodePtr vnp, ApplyValuePtr avp, FilterSetPtr fsp)
16555 {
16556 ValNodePtr sfp_vnp;
16557 Boolean rval = FALSE;
16558
16559 if (cdsp == NULL || vnp == NULL || avp == NULL)
16560 {
16561 return FALSE;
16562 }
16563
16564 for (sfp_vnp = cdsp->cds_list; sfp_vnp != NULL ; sfp_vnp = sfp_vnp->next)
16565 {
16566 rval |= SetCDSGeneProtField (sfp_vnp->data.ptrvalue, vnp, avp, fsp);
16567 }
16568 for (sfp_vnp = cdsp->gene_list; sfp_vnp != NULL; sfp_vnp = sfp_vnp->next)
16569 {
16570 if (sfp_vnp->choice == 0) /* don't set again if already set */
16571 {
16572 rval |= SetCDSGeneProtField (sfp_vnp->data.ptrvalue, vnp, avp, fsp);
16573 }
16574 }
16575 for (sfp_vnp = cdsp->prot_list; sfp_vnp != NULL; sfp_vnp = sfp_vnp->next)
16576 {
16577 rval |= SetCDSGeneProtField (sfp_vnp->data.ptrvalue, vnp, avp, fsp);
16578 }
16579 for (sfp_vnp = cdsp->mrna_list; sfp_vnp != NULL; sfp_vnp = sfp_vnp->next)
16580 {
16581 rval |= SetCDSGeneProtField (sfp_vnp->data.ptrvalue, vnp, avp, fsp);
16582 }
16583 return rval;
16584 }
16585
RemoveCDSetField(CDSetPtr cdsp,ValNodePtr vnp,FilterSetPtr fsp)16586 static void RemoveCDSetField (CDSetPtr cdsp, ValNodePtr vnp, FilterSetPtr fsp)
16587 {
16588 ValNodePtr sfp_vnp;
16589 CharPtr str = NULL;
16590
16591 if (cdsp == NULL || vnp == NULL)
16592 {
16593 return;
16594 }
16595
16596 for (sfp_vnp = cdsp->cds_list; sfp_vnp != NULL && str == NULL; sfp_vnp = sfp_vnp->next)
16597 {
16598 RemoveCDSGeneProtField (sfp_vnp->data.ptrvalue, vnp, fsp);
16599 }
16600 for (sfp_vnp = cdsp->gene_list; sfp_vnp != NULL && str == NULL; sfp_vnp = sfp_vnp->next)
16601 {
16602 RemoveCDSGeneProtField (sfp_vnp->data.ptrvalue, vnp, fsp);
16603 }
16604 for (sfp_vnp = cdsp->prot_list; sfp_vnp != NULL && str == NULL; sfp_vnp = sfp_vnp->next)
16605 {
16606 RemoveCDSGeneProtField (sfp_vnp->data.ptrvalue, vnp, fsp);
16607 }
16608 for (sfp_vnp = cdsp->mrna_list; sfp_vnp != NULL && str == NULL; sfp_vnp = sfp_vnp->next)
16609 {
16610 RemoveCDSGeneProtField (sfp_vnp->data.ptrvalue, vnp, fsp);
16611 }
16612 }
16613
GetCDSetPseudoMatch(CDSetPtr cdsp,Int4 featdef_type,Boolean is_pseudo)16614 static Boolean GetCDSetPseudoMatch (CDSetPtr cdsp, Int4 featdef_type, Boolean is_pseudo)
16615 {
16616 ValNodePtr sfp_vnp;
16617 CharPtr str = NULL;
16618 SeqFeatPtr sfp;
16619 GeneRefPtr grp;
16620 Boolean gene_is_pseudo;
16621
16622 if (cdsp == NULL)
16623 {
16624 return FALSE;
16625 }
16626
16627 if (featdef_type == FEATDEF_CDS || featdef_type == FEATDEF_ANY)
16628 {
16629 for (sfp_vnp = cdsp->cds_list; sfp_vnp != NULL && str == NULL; sfp_vnp = sfp_vnp->next)
16630 {
16631 sfp = sfp_vnp->data.ptrvalue;
16632 if (sfp != NULL && ((is_pseudo && sfp->pseudo) || (!is_pseudo && ! sfp->pseudo)))
16633 {
16634 return TRUE;
16635 }
16636 }
16637 }
16638 if (featdef_type == FEATDEF_GENE || featdef_type == FEATDEF_ANY)
16639 {
16640 for (sfp_vnp = cdsp->gene_list; sfp_vnp != NULL && str == NULL; sfp_vnp = sfp_vnp->next)
16641 {
16642 sfp = sfp_vnp->data.ptrvalue;
16643 if (sfp != NULL)
16644 {
16645 gene_is_pseudo = FALSE;
16646 if (sfp->pseudo)
16647 {
16648 gene_is_pseudo = TRUE;
16649 }
16650 if (sfp->data.choice == SEQFEAT_GENE)
16651 {
16652 grp = (GeneRefPtr) sfp->data.value.ptrvalue;
16653 if (grp != NULL && grp->pseudo)
16654 {
16655 gene_is_pseudo = TRUE;
16656 }
16657 }
16658 if ((is_pseudo && gene_is_pseudo) || (!is_pseudo && ! gene_is_pseudo))
16659 {
16660 return TRUE;
16661 }
16662 }
16663 }
16664 }
16665 if (featdef_type == FEATDEF_mRNA || featdef_type == FEATDEF_ANY)
16666 {
16667 for (sfp_vnp = cdsp->mrna_list; sfp_vnp != NULL && str == NULL; sfp_vnp = sfp_vnp->next)
16668 {
16669 sfp = sfp_vnp->data.ptrvalue;
16670 if (sfp != NULL && ((is_pseudo && sfp->pseudo) || (!is_pseudo && ! sfp->pseudo)))
16671 {
16672 return TRUE;
16673 }
16674 }
16675 }
16676 return FALSE;
16677 }
16678
DoCDSFieldsMatch(CDSetPtr cdsp,ValNodePtr qual_choice,ValNodePtr qual_choice_match)16679 static Boolean DoCDSFieldsMatch (CDSetPtr cdsp, ValNodePtr qual_choice, ValNodePtr qual_choice_match)
16680 {
16681 CharPtr str1, str2;
16682 Int4 field_choice, field_choice2;
16683 ValNode field_vn, field_vn2;
16684 Boolean does_match = FALSE;
16685
16686 if (qual_choice == NULL && qual_choice_match == NULL)
16687 {
16688 /* both are wildcards */
16689 field_vn.next = NULL;
16690 field_vn.choice = 0;
16691 field_vn2.next = NULL;
16692 field_vn2.choice = 0;
16693
16694 for (field_choice = 1;
16695 ! does_match && field_choice < num_gene_fields + num_mrna_fields + num_protein_fields;
16696 field_choice++)
16697 {
16698 field_vn.data.intvalue = field_choice;
16699 str1 = GetCDSetField (cdsp, &field_vn);
16700 if (!StringHasNoText (str1)) {
16701 for (field_choice2 = field_choice + 1;
16702 ! does_match && field_choice2 < 1 + num_gene_fields + num_mrna_fields + num_protein_fields;
16703 field_choice2++)
16704 {
16705 field_vn2.data.intvalue = field_choice2;
16706 str2 = GetCDSetField (cdsp, &field_vn2);
16707 if (StringCmp (str1, str2) == 0)
16708 {
16709 does_match = TRUE;
16710 }
16711 str2 = MemFree (str2);
16712 }
16713 }
16714 str1 = MemFree (str1);
16715 }
16716 }
16717 else if (qual_choice == NULL || qual_choice_match == NULL)
16718 {
16719 /* one is a wildcard */
16720 /* make sure it is the first one */
16721 if (qual_choice_match == NULL)
16722 {
16723 qual_choice_match = qual_choice;
16724 qual_choice = NULL;
16725 }
16726 field_vn.next = NULL;
16727 field_vn.choice = 0;
16728 str2 = GetCDSetField (cdsp, qual_choice_match);
16729 if (!StringHasNoText (str2)) {
16730 for (field_choice = 1;
16731 ! does_match && field_choice < num_gene_fields + num_mrna_fields + num_protein_fields;
16732 field_choice++)
16733 {
16734 if (field_choice != qual_choice_match->data.intvalue) {
16735 /* don't compare something to itself */
16736 field_vn.data.intvalue = field_choice;
16737 str1 = GetCDSetField (cdsp, &field_vn);
16738 if (StringCmp (str1, str2) == 0)
16739 {
16740 does_match = TRUE;
16741 }
16742 str1 = MemFree (str1);
16743 }
16744 }
16745 }
16746 str2 = MemFree (str2);
16747 } else {
16748 str1 = GetCDSetField (cdsp, qual_choice);
16749 str2 = GetCDSetField (cdsp, qual_choice_match);
16750 if (!StringHasNoText (str1) && StringCmp (str1, str2) == 0)
16751 {
16752 does_match = TRUE;
16753 }
16754 str1 = MemFree (str1);
16755 str2 = MemFree (str2);
16756 }
16757 return does_match;
16758 }
16759
16760
DoesCDSetMatchConstraint(CDSetPtr cdsp,ChoiceConstraintPtr ccp)16761 static Boolean DoesCDSetMatchConstraint (CDSetPtr cdsp, ChoiceConstraintPtr ccp)
16762 {
16763 Boolean does_match = FALSE;
16764 CharPtr str;
16765 Int4 field_choice;
16766 ValNode field_vn;
16767 ValNodePtr sfp_vnp;
16768
16769 if (cdsp == NULL)
16770 {
16771 return FALSE;
16772 }
16773 if (ccp == NULL || ccp->constraint_type == CHOICE_CONSTRAINT_ANY)
16774 {
16775 does_match = TRUE;
16776 }
16777 else if (ccp->constraint_type == CHOICE_CONSTRAINT_QUAL_PRESENT)
16778 {
16779 if (ccp->qual_choice == NULL)
16780 {
16781 does_match = TRUE;
16782 }
16783 else
16784 {
16785 str = GetCDSetField (cdsp, ccp->qual_choice);
16786 if (str != NULL)
16787 {
16788 MemFree (str);
16789 does_match = TRUE;
16790 }
16791 }
16792 }
16793 else if (ccp->constraint_type == CHOICE_CONSTRAINT_STRING)
16794 {
16795 if (ccp->qual_choice == NULL)
16796 {
16797 field_vn.next = NULL;
16798 field_vn.choice = 0;
16799 for (field_choice = 1;
16800 ! does_match && field_choice < 1 + num_gene_fields + num_mrna_fields + num_protein_fields;
16801 field_choice++)
16802 {
16803 field_vn.data.intvalue = field_choice;
16804 str = GetCDSetField (cdsp, &field_vn);
16805 does_match = DoesStringMatchConstraintX (str, ccp->string_constraint);
16806 MemFree (str);
16807 }
16808 if (ccp->string_constraint != NULL && ccp->string_constraint->not_present)
16809 {
16810 does_match = ! does_match;
16811 }
16812 }
16813 else if (IsCDSetMatPeptideQualChoice(ccp->qual_choice))
16814 {
16815 /* if we're matching protein fields, we need to look at all of them */
16816 for (sfp_vnp = cdsp->prot_list; sfp_vnp != NULL && !does_match; sfp_vnp = sfp_vnp->next)
16817 {
16818 str = GetCDSGeneProtField (sfp_vnp->data.ptrvalue, ccp->qual_choice, NULL);
16819 does_match = DoesStringMatchConstraintX (str, ccp->string_constraint);
16820 if (ccp->string_constraint != NULL && ccp->string_constraint->not_present)
16821 {
16822 does_match = ! does_match;
16823 }
16824 MemFree (str);
16825 }
16826 }
16827 else
16828 {
16829 str = GetCDSetField (cdsp, ccp->qual_choice);
16830 does_match = DoesStringMatchConstraintX (str, ccp->string_constraint);
16831 MemFree (str);
16832 if (ccp->string_constraint != NULL && ccp->string_constraint->not_present)
16833 {
16834 does_match = ! does_match;
16835 }
16836 }
16837 }
16838 else if (ccp->constraint_type == CHOICE_CONSTRAINT_MATCH)
16839 {
16840 does_match = DoCDSFieldsMatch (cdsp, ccp->qual_choice, ccp->qual_choice_match);
16841 }
16842 else if (ccp->constraint_type == CHOICE_CONSTRAINT_PSEUDO)
16843 {
16844 if (ccp->pseudo_constraint == NULL)
16845 {
16846 does_match = TRUE;
16847 }
16848 else
16849 {
16850 does_match = GetCDSetPseudoMatch (cdsp,
16851 ccp->pseudo_constraint->featdef_type,
16852 ccp->pseudo_constraint->is_pseudo);
16853 }
16854 }
16855 return does_match;
16856 }
16857
GetNewFeatureLocation(ValNodePtr feat_list,Uint2 choice,Uint2 choice_from)16858 static SeqLocPtr GetNewFeatureLocation(ValNodePtr feat_list, Uint2 choice, Uint2 choice_from)
16859 {
16860 ValNodePtr vnp;
16861 SeqFeatPtr sfp;
16862 BioseqPtr bsp = NULL;
16863 SeqLocPtr slp = NULL;
16864
16865 for (vnp = feat_list; vnp != NULL && slp == NULL; vnp = vnp->next)
16866 {
16867 sfp = vnp->data.ptrvalue;
16868 if (sfp != NULL)
16869 {
16870 if (choice == FEATDEF_PROT || choice == FEATDEF_mat_peptide_aa)
16871 {
16872 bsp = BioseqFindFromSeqLoc (sfp->product);
16873 slp = SeqLocWholeNew (bsp);
16874 }
16875 else
16876 {
16877 if (choice_from == sfp->idx.subtype || (sfp->idx.subtype == FEATDEF_CDS && (choice_from == FEATDEF_PROT || choice_from == FEATDEF_mat_peptide_aa)))
16878 {
16879 slp = (SeqLocPtr) AsnIoMemCopy (sfp->location, (AsnReadFunc) SeqLocAsnRead, (AsnWriteFunc) SeqLocAsnWrite);
16880 }
16881 else
16882 {
16883 bsp = BioseqFindFromSeqLoc (sfp->location);
16884 slp = SeqLocWholeNew (bsp);
16885 }
16886 }
16887 }
16888 }
16889 return slp;
16890 }
16891
16892
BuildOneNewCDSGeneProtFeature(CDSetPtr cdsp,Uint2 choice,Uint2 choice_from)16893 static SeqFeatPtr BuildOneNewCDSGeneProtFeature (CDSetPtr cdsp, Uint2 choice, Uint2 choice_from)
16894 {
16895 BioseqPtr bsp = NULL;
16896 SeqLocPtr slp = NULL, slp_tmp, slp_sum;
16897 SeqFeatPtr sfp = NULL;
16898 RnaRefPtr rrp;
16899 ProtRefPtr prp;
16900
16901 if (cdsp == NULL)
16902 {
16903 return NULL;
16904 }
16905
16906 if (choice == FEATDEF_PROT || choice == FEATDEF_mat_peptide_aa)
16907 {
16908 slp = GetNewFeatureLocation(cdsp->cds_list, choice, choice_from);
16909 }
16910 else
16911 {
16912 /* get location from CDS features */
16913 if (choice_from == 0 || choice_from == FEATDEF_CDS || choice_from == FEATDEF_PROT || choice_from == FEATDEF_mat_peptide_aa)
16914 {
16915 slp = GetNewFeatureLocation(cdsp->cds_list, choice, choice_from);
16916 }
16917
16918 /* get location from mRNA features */
16919 if ((choice_from == 0 && slp == NULL) || choice_from == FEATDEF_mRNA)
16920 {
16921 slp_tmp = GetNewFeatureLocation(cdsp->mrna_list, choice, choice_from);
16922 if (slp == NULL)
16923 {
16924 slp = slp_tmp;
16925 }
16926 else
16927 {
16928 bsp = BioseqFindFromSeqLoc (sfp->location);
16929 if (bsp != NULL)
16930 {
16931 slp_sum = SeqLocMerge (bsp, slp_tmp, slp, TRUE, FALSE, FALSE);
16932 slp = SeqLocFree (slp);
16933 slp_tmp = SeqLocFree (slp_tmp);
16934 slp = slp_sum;
16935 slp_sum = NULL;
16936 }
16937 }
16938 }
16939
16940 /* get location from gene features */
16941 if ((choice_from == 0 && slp == NULL) || choice_from == FEATDEF_GENE)
16942 {
16943 slp_tmp = GetNewFeatureLocation(cdsp->gene_list, choice, choice_from);
16944 if (slp == NULL)
16945 {
16946 slp = slp_tmp;
16947 }
16948 else
16949 {
16950 bsp = BioseqFindFromSeqLoc (sfp->location);
16951 if (bsp != NULL)
16952 {
16953 slp_sum = SeqLocMerge (bsp, slp_tmp, slp, TRUE, FALSE, FALSE);
16954 slp = SeqLocFree (slp);
16955 slp_tmp = SeqLocFree (slp_tmp);
16956 slp = slp_sum;
16957 slp_sum = NULL;
16958 }
16959 }
16960 }
16961 }
16962
16963 bsp = BioseqFindFromSeqLoc (slp);
16964 if (bsp != NULL && slp != NULL)
16965 {
16966 sfp = CreateNewFeatureOnBioseq (bsp, FindFeatFromFeatDefType(choice), slp);
16967 switch (choice)
16968 {
16969 case FEATDEF_mRNA:
16970 rrp = RnaRefNew ();
16971 rrp->type = 2;
16972 sfp->data.value.ptrvalue = rrp;
16973 break;
16974 case FEATDEF_GENE:
16975 sfp->data.value.ptrvalue = GeneRefNew();
16976 break;
16977 case FEATDEF_CDS:
16978 sfp->data.value.ptrvalue = CdRegionNew();
16979 break;
16980 case FEATDEF_PROT:
16981 case FEATDEF_mat_peptide_aa:
16982 prp = ProtRefNew();
16983 if (choice == FEATDEF_mat_peptide_aa)
16984 {
16985 prp->processed = 2;
16986 }
16987 sfp->data.value.ptrvalue = prp;
16988 break;
16989 }
16990 }
16991 return sfp;
16992 }
16993
BuildNewCDSGeneProtFeature(CDSetPtr cdsp,ValNodePtr vnp,ValNodePtr field_from)16994 static SeqFeatPtr BuildNewCDSGeneProtFeature (CDSetPtr cdsp, ValNodePtr vnp, ValNodePtr field_from)
16995 {
16996 SeqFeatPtr new_sfp = NULL, sfp;
16997 Uint2 choice_to, choice_from;
16998 ValNodePtr v;
16999 Boolean found;
17000
17001 if (cdsp == NULL || vnp == NULL)
17002 {
17003 return NULL;
17004 }
17005
17006 choice_to = FeatDefTypeFromFieldList (vnp);
17007 choice_from = FeatDefTypeFromFieldList (field_from);
17008
17009 switch (choice_to)
17010 {
17011 case FEATDEF_CDS:
17012 if (choice_from != 0 && cdsp->cds_list == NULL)
17013 {
17014 /* add new CDS */
17015 new_sfp = BuildOneNewCDSGeneProtFeature (cdsp, choice_to, choice_from);
17016 if (new_sfp != NULL)
17017 {
17018 ValNodeAddPointer (&(cdsp->cds_list), 0, new_sfp);
17019 }
17020 }
17021 break;
17022 case FEATDEF_GENE:
17023 if ((choice_from != 0 || vnp->data.intvalue - 1 == GENEFIELD_LOCUS) && cdsp->gene_list == NULL)
17024 {
17025 /* add new gene */
17026 new_sfp = BuildOneNewCDSGeneProtFeature (cdsp, choice_to, choice_from);
17027 if (new_sfp != NULL)
17028 {
17029 ValNodeAddPointer (&(cdsp->gene_list), 0, new_sfp);
17030 }
17031 }
17032 break;
17033 case FEATDEF_mRNA:
17034 if (choice_from != 0 && cdsp->mrna_list == NULL)
17035 {
17036 /* add new mrna */
17037 new_sfp = BuildOneNewCDSGeneProtFeature (cdsp, choice_to, choice_from);
17038 if (new_sfp != NULL)
17039 {
17040 ValNodeAddPointer (&(cdsp->mrna_list), 0, new_sfp);
17041 }
17042 }
17043 break;
17044 case FEATDEF_PROT:
17045 case FEATDEF_mat_peptide_aa:
17046 if (choice_from != 0 && cdsp->cds_list != NULL)
17047 {
17048 found = FALSE;
17049 for (v = cdsp->prot_list; v != NULL && !found; v = v->next)
17050 {
17051 sfp = (SeqFeatPtr) v->data.ptrvalue;
17052 if (sfp != NULL && sfp->idx.subtype == choice_to)
17053 {
17054 found = FALSE;
17055 }
17056 }
17057 if (!found)
17058 {
17059 new_sfp = BuildOneNewCDSGeneProtFeature (cdsp, choice_to, choice_from);
17060 if (new_sfp != NULL)
17061 {
17062 /* set subtype so other functions will work */
17063 new_sfp->idx.subtype = choice_to;
17064 ValNodeAddPointer (&(cdsp->mrna_list), 0, new_sfp);
17065 }
17066 }
17067 }
17068 break;
17069 }
17070 return new_sfp;
17071 }
17072
CDSetOnBioseq(CDSetPtr cdsp,BioseqPtr bsp)17073 static Boolean CDSetOnBioseq (CDSetPtr cdsp, BioseqPtr bsp)
17074 {
17075 SeqFeatPtr sfp;
17076 Boolean is_on_bioseq = FALSE;
17077 ValNodePtr sfp_vnp;
17078
17079 if (cdsp == NULL || bsp == NULL) return FALSE;
17080
17081 for (sfp_vnp = cdsp->cds_list; sfp_vnp != NULL && !is_on_bioseq; sfp_vnp = sfp_vnp->next)
17082 {
17083 sfp = sfp_vnp->data.ptrvalue;
17084 if (sfp != NULL && BioseqFindFromSeqLoc (sfp->location) == bsp) {
17085 is_on_bioseq = TRUE;
17086 }
17087 }
17088 for (sfp_vnp = cdsp->gene_list; sfp_vnp != NULL && !is_on_bioseq; sfp_vnp = sfp_vnp->next)
17089 {
17090 sfp = sfp_vnp->data.ptrvalue;
17091 if (sfp != NULL && BioseqFindFromSeqLoc (sfp->location) == bsp) {
17092 is_on_bioseq = TRUE;
17093 }
17094 }
17095 for (sfp_vnp = cdsp->mrna_list; sfp_vnp != NULL && !is_on_bioseq; sfp_vnp = sfp_vnp->next)
17096 {
17097 sfp = sfp_vnp->data.ptrvalue;
17098 if (sfp != NULL && BioseqFindFromSeqLoc (sfp->location) == bsp) {
17099 is_on_bioseq = TRUE;
17100 }
17101 }
17102 return is_on_bioseq;
17103 }
17104
ValNodeDataAlreadyInValNodeList(ValNodePtr list,ValNodePtr findme)17105 static Boolean ValNodeDataAlreadyInValNodeList (ValNodePtr list, ValNodePtr findme)
17106 {
17107 if (findme == NULL) return FALSE;
17108 while (list != NULL)
17109 {
17110 if (list->data.ptrvalue == findme->data.ptrvalue)
17111 {
17112 return TRUE;
17113 }
17114 list = list->next;
17115 }
17116 return FALSE;
17117 }
17118
BuildGeneForSegSet(BioseqSetPtr segset,ValNodePtr PNTR cdset_list,Boolean lonely_ok)17119 static void BuildGeneForSegSet (BioseqSetPtr segset, ValNodePtr PNTR cdset_list, Boolean lonely_ok)
17120 {
17121 SeqEntryPtr this_sep, master_sep = NULL;
17122 BioseqSetPtr part_set = NULL;
17123 SeqLocPtr slp = NULL, slp_new, slp_last = NULL;
17124 SeqFeatPtr sfp;
17125 SeqMgrFeatContext context;
17126 ValNodePtr vnp, add_gene_to = NULL;
17127 Boolean on_part;
17128 CDSetPtr cdsp;
17129
17130 if (segset == NULL || segset->seq_set == NULL)
17131 {
17132 return;
17133 }
17134
17135 this_sep = segset->seq_set;
17136 while (this_sep != NULL && (part_set == NULL || master_sep == NULL))
17137 {
17138 if (IS_Bioseq_set (this_sep))
17139 {
17140 part_set = (BioseqSetPtr) this_sep->data.ptrvalue;
17141 if (part_set != NULL && part_set->_class != BioseqseqSet_class_parts)
17142 {
17143 part_set = NULL;
17144 }
17145 }
17146 else if (IS_Bioseq (this_sep))
17147 {
17148 master_sep = this_sep;
17149 }
17150 this_sep = this_sep->next;
17151 }
17152 if (part_set != NULL && master_sep != NULL)
17153 {
17154 this_sep = part_set->seq_set;
17155 sfp = SeqMgrGetNextFeature (master_sep->data.ptrvalue, NULL,
17156 SEQFEAT_GENE, FEATDEF_GENE, &context);
17157
17158 while (this_sep != NULL && sfp == NULL)
17159 {
17160 if (IS_Bioseq (this_sep))
17161 {
17162 sfp = SeqMgrGetNextFeature (this_sep->data.ptrvalue, NULL,
17163 SEQFEAT_GENE, FEATDEF_GENE, &context);
17164 }
17165 this_sep = this_sep->next;
17166 }
17167 if (sfp != NULL)
17168 {
17169 return;
17170 }
17171
17172 /* no other genes anywhere in segmented set. Any cdsets? */
17173 for (vnp = *cdset_list; vnp != NULL; vnp = vnp->next)
17174 {
17175 cdsp = (CDSetPtr) vnp->data.ptrvalue;
17176 if (CDSetOnBioseq(cdsp, master_sep->data.ptrvalue)
17177 && !ValNodeDataAlreadyInValNodeList(add_gene_to, vnp))
17178 {
17179 ValNodeAddPointer (&add_gene_to, 0, cdsp);
17180 }
17181 else
17182 {
17183 on_part = FALSE;
17184 for (this_sep = part_set->seq_set; this_sep != NULL && !on_part; this_sep = this_sep->next)
17185 {
17186 if (CDSetOnBioseq(cdsp, this_sep->data.ptrvalue)
17187 && !ValNodeDataAlreadyInValNodeList(add_gene_to, vnp))
17188 {
17189 ValNodeAddPointer (&add_gene_to, 0, cdsp);
17190 on_part = TRUE;
17191 }
17192 }
17193 }
17194 }
17195
17196 if (add_gene_to != NULL || lonely_ok) {
17197 /* create gene */
17198 this_sep = part_set->seq_set;
17199 while (this_sep != NULL)
17200 {
17201 if (IS_Bioseq (this_sep))
17202 {
17203 slp_new = SeqLocWholeNew (this_sep->data.ptrvalue);
17204 if (slp_new != NULL)
17205 {
17206 if (slp_last == NULL)
17207 {
17208 slp = slp_new;
17209 }
17210 else
17211 {
17212 slp_last = ValNodeNew (slp);
17213 slp_last->choice = SEQLOC_NULL;
17214 slp_last->next = slp_new;
17215 }
17216 slp_last = slp_new;
17217 }
17218 }
17219 this_sep = this_sep->next;
17220 }
17221 slp_new = ValNodeNew (NULL);
17222 slp_new->choice = SEQLOC_MIX;
17223 slp_new->data.ptrvalue = slp;
17224 sfp = CreateNewFeature (master_sep, NULL, SEQFEAT_GENE, NULL);
17225 sfp->location = SeqLocFree (sfp->location);
17226 sfp->location = slp_new;
17227 sfp->data.value.ptrvalue = GeneRefNew ();
17228
17229 /* add to sets */
17230 if (add_gene_to == NULL)
17231 {
17232 cdsp = (CDSetPtr) MemNew (sizeof (CDSetData));
17233 MemSet (cdsp, 0, sizeof (CDSetData));
17234 ValNodeAddPointer (&(cdsp->gene_list), 0, sfp);
17235 ValNodeAddPointer (cdset_list, 0, cdsp);
17236 }
17237 else
17238 {
17239 for (vnp = add_gene_to; vnp != NULL; vnp = vnp->next)
17240 {
17241 cdsp = (CDSetPtr) vnp->data.ptrvalue;
17242 ValNodeAddPointer (&(cdsp->gene_list), 0, sfp);
17243 }
17244 }
17245 }
17246 add_gene_to = ValNodeFree (add_gene_to);
17247 }
17248 }
17249
LoneGeneOkWithFilter(FilterSetPtr fsp)17250 static Boolean LoneGeneOkWithFilter (FilterSetPtr fsp)
17251 {
17252 if (fsp == NULL || fsp->cgp == NULL
17253 || fsp->cgp->constraint_type == CHOICE_CONSTRAINT_ANY
17254 || (fsp->cgp->constraint_type == CHOICE_CONSTRAINT_QUAL_PRESENT
17255 && fsp->cgp->qual_choice == NULL))
17256 {
17257 return TRUE;
17258 }
17259 else
17260 {
17261 return FALSE;
17262 }
17263 }
17264
BuildNewGenes(SeqEntryPtr sep,ValNodePtr PNTR cdset_list,Boolean lonely_ok)17265 static void BuildNewGenes (SeqEntryPtr sep, ValNodePtr PNTR cdset_list, Boolean lonely_ok)
17266 {
17267 BioseqSetPtr bssp = NULL;
17268 BioseqPtr bsp = NULL;
17269 SeqFeatPtr sfp;
17270 SeqMgrFeatContext context;
17271 SeqLocPtr slp = NULL;
17272 ValNodePtr vnp;
17273 CDSetPtr cdsp;
17274 ValNodePtr add_gene_to;
17275
17276 if (sep == NULL)
17277 {
17278 return;
17279 }
17280
17281 if (IS_Bioseq (sep))
17282 {
17283 bsp = (BioseqPtr) sep->data.ptrvalue;
17284 if (ISA_na (bsp->mol))
17285 {
17286 sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_GENE, FEATDEF_GENE, &context);
17287 if (sfp == NULL)
17288 {
17289 /* are there any sets already on this Bioseq? */
17290 add_gene_to = NULL;
17291 for (vnp = *cdset_list; vnp != NULL; vnp = vnp->next)
17292 {
17293 cdsp = (CDSetPtr) vnp->data.ptrvalue;
17294 if (CDSetOnBioseq(cdsp, bsp))
17295 {
17296 if (cdsp->gene_list == NULL)
17297 {
17298 ValNodeAddPointer (&add_gene_to, 0, cdsp);
17299 }
17300 }
17301 }
17302 if (add_gene_to != NULL || lonely_ok)
17303 {
17304 slp = SeqLocWholeNew (bsp);
17305 sfp = CreateNewFeatureOnBioseq (bsp, SEQFEAT_GENE, slp);
17306 sfp->data.value.ptrvalue = GeneRefNew();
17307 if (add_gene_to == NULL)
17308 {
17309 cdsp = (CDSetPtr) MemNew (sizeof (CDSetData));
17310 MemSet (cdsp, 0, sizeof (CDSetData));
17311 ValNodeAddPointer (&(cdsp->gene_list), 0, sfp);
17312 ValNodeAddPointer (cdset_list, 0, cdsp);
17313 }
17314 else
17315 {
17316 for (vnp = add_gene_to; vnp != NULL; vnp = vnp->next)
17317 {
17318 cdsp = (CDSetPtr) vnp->data.ptrvalue;
17319 ValNodeAddPointer (&(cdsp->gene_list), 0, sfp);
17320 }
17321 }
17322 }
17323 add_gene_to = ValNodeFree (add_gene_to);
17324 }
17325 }
17326 }
17327 else if (IS_Bioseq_set (sep))
17328 {
17329 bssp = (BioseqSetPtr) sep->data.ptrvalue;
17330 if (bssp->_class == BioseqseqSet_class_segset)
17331 {
17332 BuildGeneForSegSet (bssp, cdset_list, lonely_ok);
17333 }
17334 else
17335 {
17336 BuildNewGenes (bssp->seq_set, cdset_list, lonely_ok);
17337 }
17338 }
17339 BuildNewGenes (sep->next, cdset_list, lonely_ok);
17340 }
17341
17342 typedef Boolean (*Nlm_TestAECRChoiceProc) PROTO((Pointer));
17343 typedef DialoG (*Nlm_AECRMakeDlgProc) PROTO ((GrouP, Int4, Nlm_ChangeNotifyProc, Pointer, Uint2));
17344 typedef DialoG (*Nlm_SampleDialogProc) PROTO ((GrouP, Uint2));
17345 typedef DialoG (*Nlm_FieldListDlgProc) PROTO ((GrouP, Boolean, Nlm_ChangeNotifyProc, Pointer));
17346 typedef DialoG (*Nlm_SubtypeListDlgProc) PROTO ((GrouP, Boolean, SeqEntryPtr, Nlm_ChangeNotifyProc, Pointer));
17347
17348 #define AECR_VIB_MSG_SET_DEFAULT (NUM_VIB_MSG + 1)
17349 #define AECR_VIB_MSG_CLEAR_TEXT (NUM_VIB_MSG + 2)
17350 #define AECR_VIB_MSG_AUTOPOPULATE (NUM_VIB_MSG + 3)
17351
17352 typedef void (*Nlm_ChangeAECRActionProc) PROTO ((DialoG, DialoG));
17353
17354 typedef struct applyeditconvertremove
17355 {
17356 FORM_MESSAGE_BLOCK
17357 DialoG aecr_pages [NUM_AECR];
17358 DialoG accept_cancel;
17359 PopuP action_popup;
17360 DialoG constraints;
17361 ButtoN clear_constraints_on_action_change;
17362 Nlm_ChangeAECRActionProc change_action;
17363 Int4 prev_page;
17364 Boolean crippled;
17365 Int4 crippled_action;
17366 } ApplyEditConvertRemoveData, PNTR ApplyEditConvertRemovePtr;
17367
ApplyEditConvertRemoveChangeNotify(Pointer userdata)17368 static void ApplyEditConvertRemoveChangeNotify (Pointer userdata)
17369 {
17370 ApplyEditConvertRemovePtr mp;
17371 Int4 action_choice;
17372 ValNodePtr err_list;
17373
17374 mp = (ApplyEditConvertRemovePtr) userdata;
17375 if (mp == NULL)
17376 {
17377 return;
17378 }
17379
17380 if (mp->crippled)
17381 {
17382 action_choice = mp->crippled_action;
17383 }
17384 else
17385 {
17386 action_choice = GetValue (mp->action_popup);
17387 }
17388
17389 if (action_choice > 0 && action_choice <= NUM_AECR)
17390 {
17391 err_list = TestDialog (mp->aecr_pages [action_choice - 1]);
17392 if (err_list != NULL)
17393 {
17394 err_list = ValNodeFree (err_list);
17395 DisableAcceptCancelDialogAccept (mp->accept_cancel);
17396 }
17397 else
17398 {
17399 EnableAcceptCancelDialogAccept (mp->accept_cancel);
17400 }
17401 }
17402 else
17403 {
17404 DisableAcceptCancelDialogAccept (mp->accept_cancel);
17405 return;
17406 }
17407 }
17408
17409
ApplyEditConvertRemoveClearText(Pointer userdata)17410 static void ApplyEditConvertRemoveClearText (Pointer userdata)
17411 {
17412 ApplyEditConvertRemovePtr mp;
17413 FilterSetPtr fsp;
17414 Int4 i;
17415
17416 mp = (ApplyEditConvertRemovePtr) userdata;
17417 if (mp != NULL)
17418 {
17419 for (i = 0; i < NUM_AECR; i++)
17420 {
17421 SendMessageToDialog (mp->aecr_pages[i], AECR_VIB_MSG_CLEAR_TEXT);
17422 }
17423 fsp = DialogToPointer (mp->constraints);
17424 FilterSetClearText (fsp);
17425 PointerToDialog (mp->constraints, fsp);
17426 FilterSetFree (fsp);
17427 ApplyEditConvertRemoveChangeNotify (mp);
17428 }
17429 }
17430
ApplyEditConvertRemoveClear(Pointer userdata)17431 static void ApplyEditConvertRemoveClear (Pointer userdata)
17432 {
17433 ApplyEditConvertRemovePtr mp;
17434 Int4 i;
17435
17436 mp = (ApplyEditConvertRemovePtr) userdata;
17437 if (mp != NULL)
17438 {
17439 for (i = 0; i < NUM_AECR; i++)
17440 {
17441 PointerToDialog (mp->aecr_pages[i], NULL);
17442 }
17443 PointerToDialog (mp->constraints, NULL);
17444 ApplyEditConvertRemoveChangeNotify (mp);
17445 }
17446 }
17447
17448 static void
ChangeApplyEditConvertRemoveAction(ApplyEditConvertRemovePtr mp,Int4 action_choice)17449 ChangeApplyEditConvertRemoveAction
17450 (ApplyEditConvertRemovePtr mp,
17451 Int4 action_choice)
17452 {
17453 Int4 i;
17454
17455 if (mp == NULL || action_choice < AECR_APPLY || action_choice > NUM_AECR)
17456 {
17457 return;
17458 }
17459
17460 for (i = 0; i < NUM_AECR; i++)
17461 {
17462 if (i + 1 == action_choice)
17463 {
17464 Show (mp->aecr_pages[i]);
17465 }
17466 else
17467 {
17468 Hide (mp->aecr_pages[i]);
17469 }
17470 }
17471
17472 if (GetStatus (mp->clear_constraints_on_action_change))
17473 {
17474 PointerToDialog (mp->constraints, NULL);
17475 PointerToDialog (mp->aecr_pages [action_choice - 1], NULL);
17476 }
17477
17478 if (mp->change_action != NULL)
17479 {
17480 if (mp->prev_page < AECR_APPLY || mp->prev_page > NUM_AECR)
17481 {
17482 (mp->change_action) (NULL, mp->aecr_pages [action_choice - 1]);
17483 }
17484 else
17485 {
17486 (mp->change_action) (mp->aecr_pages [mp->prev_page - 1],
17487 mp->aecr_pages [action_choice - 1]);
17488 }
17489 }
17490
17491 mp->prev_page = action_choice;
17492
17493 if (action_choice == AECR_APPLY)
17494 {
17495 SendMessageToDialog (mp->aecr_pages[AECR_APPLY - 1], AECR_VIB_MSG_AUTOPOPULATE);
17496 }
17497 else if (action_choice == AECR_EDIT)
17498 {
17499 SendMessageToDialog (mp->aecr_pages[AECR_EDIT - 1], AECR_VIB_MSG_AUTOPOPULATE);
17500 }
17501
17502 ApplyEditConvertRemoveChangeNotify (mp);
17503 }
17504
ChangeApplyEditConvertRemoveActionPopup(PopuP p)17505 static void ChangeApplyEditConvertRemoveActionPopup (PopuP p)
17506 {
17507 ApplyEditConvertRemovePtr mp;
17508 Int4 action_choice;
17509
17510 mp = (ApplyEditConvertRemovePtr) GetObjectExtra (p);
17511 if (mp == NULL)
17512 {
17513 return;
17514 }
17515
17516 action_choice = GetValue (mp->action_popup);
17517 ChangeApplyEditConvertRemoveAction (mp, action_choice);
17518 }
17519 typedef struct samplebtn
17520 {
17521 Uint2 entityID;
17522 Nlm_SampleDialogProc make_sample_dlg;
17523 CharPtr title;
17524 } SampleBtnData, PNTR SampleBtnPtr;
17525
AECRSampleButton(ButtoN b)17526 static void AECRSampleButton (ButtoN b)
17527 {
17528 SampleBtnPtr sbp;
17529 WindoW w;
17530
17531 sbp = GetObjectExtra (b);
17532 if (sbp != NULL && sbp->make_sample_dlg != NULL)
17533 {
17534 w = FixedWindow (-50, -33, -10, -10, sbp->title, StdCloseWindowProc);
17535 (sbp->make_sample_dlg) (w, sbp->entityID);
17536 Show (w);
17537 }
17538 }
17539
17540 static void
ApplyEditConvertRemoveCombo(IteM i,Int4 first_action_choice,Boolean crippled,CharPtr title,Nlm_AECRMakeDlgProc make_dlg,Boolean show_sample,Nlm_SampleDialogProc make_sample_dlg,Boolean string_constraint,Boolean source_constraint,Boolean location_constraint,Boolean cds_gene_prot_constraint,Boolean id_list_constraint,CharPtr string_constraint_label,Nlm_AcceptActnProc accept_actn,Nlm_CancelActnProc cancel_actn,Nlm_ChangeAECRActionProc change_action,OkToPreSample presample_check_proc)17541 ApplyEditConvertRemoveCombo
17542 (IteM i,
17543 Int4 first_action_choice,
17544 Boolean crippled,
17545 CharPtr title,
17546 Nlm_AECRMakeDlgProc make_dlg,
17547 Boolean show_sample,
17548 Nlm_SampleDialogProc make_sample_dlg,
17549 Boolean string_constraint,
17550 Boolean source_constraint,
17551 Boolean location_constraint,
17552 Boolean cds_gene_prot_constraint,
17553 Boolean id_list_constraint,
17554 CharPtr string_constraint_label,
17555 Nlm_AcceptActnProc accept_actn,
17556 Nlm_CancelActnProc cancel_actn,
17557 Nlm_ChangeAECRActionProc change_action,
17558 OkToPreSample presample_check_proc)
17559 {
17560 BaseFormPtr bfp;
17561 ApplyEditConvertRemovePtr mp;
17562 WindoW w;
17563 GrouP h, g1, k, n, m;
17564 Int4 page_num;
17565 SampleBtnPtr sbp;
17566 ButtoN b;
17567 DialoG sample_dlg = NULL;
17568
17569 #ifdef WIN_MAC
17570 bfp = currentFormDataPtr;
17571 #else
17572 bfp = GetObjectExtra (i);
17573 #endif
17574 if (bfp == NULL) return;
17575
17576 mp = (ApplyEditConvertRemovePtr) MemNew (sizeof (ApplyEditConvertRemoveData));
17577 if (mp == NULL) return;
17578
17579 if (first_action_choice < AECR_APPLY || first_action_choice > AECR_REMOVE)
17580 {
17581 first_action_choice = AECR_APPLY;
17582 }
17583 mp->crippled = crippled;
17584 mp->crippled_action = first_action_choice;
17585
17586 w = FixedWindow (-50, -33, -10, -10, title, StdCloseWindowProc);
17587 SetObjectExtra (w, mp, StdCleanupExtraProc);
17588 SetObjectExtra (w, mp, NULL);
17589 mp->form = (ForM) w;
17590 mp->input_entityID = bfp->input_entityID;
17591
17592 #ifndef WIN_MAC
17593 CreateStandardEditMenu (w);
17594 #endif
17595
17596 n = HiddenGroup (w, -1, 0, NULL);
17597 SetGroupSpacing (n, 10, 10);
17598
17599 k = HiddenGroup (n, 2, 0, NULL);
17600 SetGroupSpacing (k, 10, 10);
17601 if (show_sample && make_sample_dlg != NULL && ! mp->crippled)
17602 {
17603 sample_dlg = make_sample_dlg (k, mp->input_entityID);
17604 }
17605
17606 h = HiddenGroup (k, -1, 0, NULL);
17607 SetGroupSpacing (h, 10, 10);
17608
17609 if (!mp->crippled)
17610 {
17611 m = HiddenGroup (h, 2, 0, NULL);
17612 SetGroupSpacing (m, 10, 10);
17613
17614 if (!show_sample && make_sample_dlg != NULL)
17615 {
17616 sbp = (SampleBtnPtr) MemNew (sizeof (SampleBtnData));
17617 sbp->entityID = mp->input_entityID;
17618 sbp->title = title;
17619 sbp->make_sample_dlg = make_sample_dlg;
17620 b = PushButton (m, "Show Qualifiers", AECRSampleButton);
17621 SetObjectExtra (b, sbp, StdCleanupExtraProc);
17622 }
17623
17624 mp->action_popup = PopupList (m, TRUE, ChangeApplyEditConvertRemoveActionPopup);
17625 SetObjectExtra (mp->action_popup, mp, NULL);
17626 PopupItem (mp->action_popup, "Apply");
17627 PopupItem (mp->action_popup, "Edit");
17628 PopupItem (mp->action_popup, "Convert");
17629 PopupItem (mp->action_popup, "Swap");
17630 PopupItem (mp->action_popup, "Parse");
17631 PopupItem (mp->action_popup, "Remove");
17632 SetValue (mp->action_popup, first_action_choice);
17633
17634 mp->change_action = change_action;
17635
17636 mp->clear_constraints_on_action_change = CheckBox (h, "Clear when changing actions", NULL);
17637 SetStatus (mp->clear_constraints_on_action_change, TRUE);
17638 }
17639
17640 g1 = HiddenGroup (h, 0, 0, NULL);
17641 for (page_num = 0; page_num < NUM_AECR; page_num++)
17642 {
17643 mp->aecr_pages [page_num] = make_dlg (g1, page_num + 1,
17644 ApplyEditConvertRemoveChangeNotify,
17645 mp, mp->input_entityID);
17646 }
17647 AlignObjects (ALIGN_CENTER, (HANDLE) mp->aecr_pages[0],
17648 (HANDLE) mp->aecr_pages[1],
17649 (HANDLE) mp->aecr_pages[2],
17650 (HANDLE) mp->aecr_pages[3],
17651 (HANDLE) mp->aecr_pages[4],
17652 (HANDLE) mp->aecr_pages[5],
17653 NULL);
17654
17655 if (! mp->crippled)
17656 {
17657 AlignObjects (ALIGN_CENTER, (HANDLE) m,
17658 (HANDLE) mp->clear_constraints_on_action_change,
17659 (HANDLE) g1,
17660 (HANDLE) NULL);
17661 mp->constraints = FilterGroup (n, string_constraint, source_constraint,
17662 location_constraint, cds_gene_prot_constraint,
17663 id_list_constraint,
17664 string_constraint_label);
17665
17666 }
17667
17668 mp->accept_cancel = AcceptCancelDialog (n, accept_actn, cancel_actn,
17669 ApplyEditConvertRemoveClear,
17670 ApplyEditConvertRemoveClearText,
17671 (Pointer)mp, w);
17672
17673 if (mp->crippled)
17674 {
17675 AlignObjects (ALIGN_CENTER, (HANDLE) k, (HANDLE) mp->accept_cancel, NULL);
17676 }
17677 else
17678 {
17679 AlignObjects (ALIGN_CENTER, (HANDLE) k,
17680 (HANDLE) mp->constraints,
17681 (HANDLE) mp->accept_cancel,
17682 NULL);
17683 }
17684
17685 mp->prev_page = -1;
17686 ChangeApplyEditConvertRemoveAction (mp, first_action_choice);
17687 /* initialize sample values if conditions are met */
17688 if (sample_dlg != NULL && (presample_check_proc == NULL || presample_check_proc(mp->input_entityID))) {
17689 SendMessageToDialog (sample_dlg, VIB_MSG_INIT);
17690 }
17691 Show (w);
17692 }
17693
17694
CountFeaturesCallback(SeqFeatPtr sfp,Pointer userdata)17695 static void CountFeaturesCallback(SeqFeatPtr sfp, Pointer userdata)
17696 {
17697 Int4Ptr pTotal;
17698
17699 if (userdata == NULL || sfp == NULL) {
17700 return;
17701 }
17702
17703 pTotal = (Int4Ptr) userdata;
17704
17705 (*pTotal) ++;
17706 }
17707
17708
CheckFeaturesForPresample(Uint2 entityID)17709 static Boolean CheckFeaturesForPresample (Uint2 entityID)
17710 {
17711 SeqEntryPtr sep;
17712 Int4 total = 0;
17713
17714 sep = GetTopSeqEntryForEntityID(entityID);
17715 if (sep == NULL) {
17716 return FALSE;
17717 }
17718
17719 VisitFeaturesInSep(sep, &total, CountFeaturesCallback);
17720
17721 if (total > 1500) {
17722 return FALSE;
17723 } else {
17724 return TRUE;
17725 }
17726 }
17727
17728
17729 typedef struct conversionconflict
17730 {
17731 ConvertFieldPtr cfp;
17732 GetSamplePtr gsp;
17733 } ConversionConflictData, PNTR ConversionConflictPtr;
17734
GetConversionConflictsFeatureCallback(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)17735 static void GetConversionConflictsFeatureCallback (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
17736 {
17737 ConversionConflictPtr ccp;
17738 CharPtr src_str, dst_str;
17739
17740 if (sfp == NULL || userdata == NULL)
17741 {
17742 return;
17743 }
17744
17745 ccp = (ConversionConflictPtr) userdata;
17746
17747 if (ccp->cfp == NULL
17748 || ccp->cfp->src_field_list == NULL
17749 || ccp->cfp->dst_field_list == NULL
17750 || ccp->cfp->get_str_func == NULL
17751 || ccp->gsp == NULL)
17752 {
17753 return;
17754 }
17755
17756 src_str = (ccp->cfp->get_str_func) (sfp, ccp->cfp->src_field_list, ccp->cfp->fsp);
17757
17758 if (ccp->cfp->convert_type == CONVERT_TYPE_PARSE)
17759 {
17760 dst_str = src_str;
17761 src_str = ReplaceStringForParse(src_str, ccp->cfp->text_portion);
17762 dst_str = MemFree (dst_str);
17763 if (src_str == NULL)
17764 {
17765 return;
17766 }
17767 }
17768
17769 if (!StringHasNoText (src_str))
17770 {
17771 dst_str = (ccp->cfp->get_str_func) (sfp, ccp->cfp->dst_field_list, ccp->cfp->fsp);
17772 if (!StringHasNoText (dst_str))
17773 {
17774 ccp->gsp->num_found ++;
17775 if (ccp->gsp->sample_text == NULL)
17776 {
17777 ccp->gsp->sample_text = dst_str;
17778 }
17779 else
17780 {
17781 if (StringCmp (dst_str, ccp->gsp->sample_text) != 0)
17782 {
17783 ccp->gsp->all_same = FALSE;
17784 }
17785 dst_str = MemFree (dst_str);
17786 }
17787 }
17788 src_str = MemFree (src_str);
17789 }
17790 }
17791
GetConversionConflictsDescriptorCallback(SeqDescPtr sdp,Pointer userdata,FilterSetPtr fsp)17792 static void GetConversionConflictsDescriptorCallback (SeqDescPtr sdp, Pointer userdata, FilterSetPtr fsp)
17793 {
17794 ConversionConflictPtr ccp;
17795 CharPtr src_str, dst_str;
17796
17797 if (sdp == NULL || userdata == NULL)
17798 {
17799 return;
17800 }
17801
17802 ccp = (ConversionConflictPtr) userdata;
17803
17804 if (ccp->cfp == NULL
17805 || ccp->cfp->src_field_list == NULL
17806 || ccp->cfp->dst_field_list == NULL
17807 || ccp->cfp->get_d_str_func == NULL
17808 || ccp->gsp == NULL)
17809 {
17810 return;
17811 }
17812
17813 src_str = (ccp->cfp->get_d_str_func) (sdp, ccp->cfp->src_field_list, ccp->cfp->fsp);
17814
17815 if (ccp->cfp->convert_type == CONVERT_TYPE_PARSE)
17816 {
17817 dst_str = src_str;
17818 src_str = ReplaceStringForParse(src_str, ccp->cfp->text_portion);
17819 dst_str = MemFree (dst_str);
17820 if (src_str == NULL)
17821 {
17822 return;
17823 }
17824 }
17825
17826 if (!StringHasNoText (src_str))
17827 {
17828 dst_str = (ccp->cfp->get_d_str_func) (sdp, ccp->cfp->dst_field_list, ccp->cfp->fsp);
17829 if (!StringHasNoText (dst_str))
17830 {
17831 ccp->gsp->num_found ++;
17832 if (ccp->gsp->sample_text == NULL)
17833 {
17834 ccp->gsp->sample_text = dst_str;
17835 }
17836 else
17837 {
17838 if (StringCmp (dst_str, ccp->gsp->sample_text) != 0)
17839 {
17840 ccp->gsp->all_same = FALSE;
17841 }
17842 dst_str = MemFree (dst_str);
17843 }
17844 }
17845 src_str = MemFree (src_str);
17846 }
17847 }
17848
CheckForConversionExistingTextInSeqEntry(SeqEntryPtr sep,ConvertFieldPtr cfp,FilterSetPtr fsp,Uint1 seqfeat_choice,Uint1 featdef_choice,Uint1 descr_choice)17849 static GetSamplePtr CheckForConversionExistingTextInSeqEntry
17850 (SeqEntryPtr sep,
17851 ConvertFieldPtr cfp,
17852 FilterSetPtr fsp,
17853 Uint1 seqfeat_choice,
17854 Uint1 featdef_choice,
17855 Uint1 descr_choice)
17856 {
17857 ConversionConflictData ccd;
17858
17859 ccd.cfp = cfp;
17860 ccd.gsp = (GetSamplePtr) MemNew (sizeof (GetSampleData));
17861 if (ccd.gsp != NULL)
17862 {
17863 ccd.gsp->sample_text = NULL;
17864 ccd.gsp->fieldstring_func = NULL;
17865 ccd.gsp->descrstring_func = NULL;
17866 ccd.gsp->free_vn_proc = NULL;
17867 ccd.gsp->copy_vn_proc = NULL;
17868 ccd.gsp->requested_field = NULL;
17869 ccd.gsp->num_found = 0;
17870 ccd.gsp->all_same = TRUE;
17871 OperateOnSeqEntryConstrainedObjects (sep, fsp, GetConversionConflictsFeatureCallback,
17872 GetConversionConflictsDescriptorCallback,
17873 seqfeat_choice, featdef_choice, descr_choice, &ccd);
17874 }
17875 return ccd.gsp;
17876 }
17877
17878 NLM_EXTERN void
AddEditApplyDataToApplyValue(Int4 action_choice,EditApplyPtr edit_apply,ApplyValuePtr avp)17879 AddEditApplyDataToApplyValue
17880 (Int4 action_choice,
17881 EditApplyPtr edit_apply,
17882 ApplyValuePtr avp)
17883 {
17884 if (avp == NULL)
17885 {
17886 return;
17887 }
17888
17889 if (edit_apply == NULL)
17890 {
17891 avp->text_to_replace = NULL;
17892 avp->new_text = NULL;
17893 avp->where_to_replace = EditApplyFindLocation_anywhere;
17894
17895 return;
17896 }
17897
17898 if (action_choice == AECR_EDIT)
17899 {
17900 avp->text_to_replace = StringSave (edit_apply->find_txt);
17901 avp->new_text = StringSave (edit_apply->repl_txt);
17902 avp->where_to_replace = edit_apply->find_location;
17903 }
17904 else if (action_choice == AECR_APPLY)
17905 {
17906 avp->new_text = StringSave (edit_apply->apply_txt);
17907 avp->text_to_replace = NULL;
17908 avp->where_to_replace = EditApplyFindLocation_anywhere;
17909 }
17910 else
17911 {
17912 avp->text_to_replace = NULL;
17913 avp->new_text = NULL;
17914 avp->where_to_replace = EditApplyFindLocation_anywhere;
17915 }
17916 }
17917
17918 #define AECR_DATA_BLOCK \
17919 ValNodePtr field_list; \
17920 ValNodePtr field_list_to; \
17921 ValNodePtr subtype_list; \
17922 Boolean leave_on_original; \
17923 Boolean strip_name_from_text; \
17924 EditApplyPtr edit_apply; \
17925 TextPortionXPtr text_portion; \
17926 Boolean remove_parsed; \
17927 FreeValNodeProc free_field_vn_proc; \
17928 FreeValNodeProc free_subtype_vn_proc;
17929
17930 typedef struct simpleaecr
17931 {
17932 AECR_DATA_BLOCK
17933 } SimpleAECRData, PNTR SimpleAECRPtr;
17934
AECRDataBlockFreeContents(SimpleAECRPtr sp)17935 static void AECRDataBlockFreeContents (SimpleAECRPtr sp)
17936 {
17937 if (sp != NULL)
17938 {
17939 sp->field_list = ValNodeFuncFree (sp->field_list, sp->free_field_vn_proc);
17940 sp->field_list_to = ValNodeFuncFree (sp->field_list_to, sp->free_field_vn_proc);
17941 sp->subtype_list = ValNodeFuncFree (sp->subtype_list, sp->free_subtype_vn_proc);
17942 sp->edit_apply = EditApplyFree (sp->edit_apply);
17943 sp->text_portion = TextPortionXFree(sp->text_portion);
17944 }
17945 }
17946
SimpleAECRFree(SimpleAECRPtr sp)17947 static SimpleAECRPtr SimpleAECRFree (SimpleAECRPtr sp)
17948 {
17949 if (sp != NULL)
17950 {
17951 AECRDataBlockFreeContents (sp);
17952 sp = MemFree (sp);
17953 }
17954 return sp;
17955 }
17956
17957 /* This function is used to autopopulate the new_text and find fields */
17958 typedef CharPtr (*GetAutoPopulateTextFunc) PROTO ((ValNodePtr, ValNodePtr, Uint2));
17959
17960 #define AECR_BLOCK \
17961 DIALOG_MESSAGE_BLOCK \
17962 DialoG field_list; \
17963 DialoG field_list_to; \
17964 DialoG subtype_list; \
17965 ButtoN leave_on_original; \
17966 ButtoN strip_name_from_text; \
17967 DialoG edit_apply; \
17968 DialoG text_portion; \
17969 ButtoN remove_parsed; \
17970 Int4 action_choice; \
17971 /* These are necessary to produce the SimpleAECR structure for output */ \
17972 FreeValNodeProc free_field_vn_proc; \
17973 FreeValNodeProc free_subtype_vn_proc; \
17974 /* These are used for autopopulating text fields */ \
17975 GetAutoPopulateTextFunc get_autopopulate_text; \
17976 Nlm_ChangeNotifyProc change_notify; \
17977 Pointer change_userdata; \
17978 Uint2 entityID;
17979
17980 typedef struct simpleaecrdlg
17981 {
17982 AECR_BLOCK
17983 } SimpleAECRDlgData, PNTR SimpleAECRDlgPtr;
17984
ClearTextSimpleAECRDlg(SimpleAECRDlgPtr dlg)17985 static void ClearTextSimpleAECRDlg (SimpleAECRDlgPtr dlg)
17986 {
17987 if (dlg != NULL)
17988 {
17989 PointerToDialog (dlg->edit_apply, NULL);
17990 PointerToDialog (dlg->text_portion, NULL);
17991 }
17992 }
17993
ResetSimpleAECRDlg(SimpleAECRDlgPtr dlg)17994 static void ResetSimpleAECRDlg (SimpleAECRDlgPtr dlg)
17995 {
17996 if (dlg != NULL)
17997 {
17998 PointerToDialog (dlg->field_list, NULL);
17999 PointerToDialog (dlg->field_list_to, NULL);
18000 PointerToDialog (dlg->subtype_list, NULL);
18001 PointerToDialog (dlg->text_portion, NULL);
18002 SafeSetStatus (dlg->leave_on_original, FALSE);
18003 SafeSetStatus (dlg->strip_name_from_text, FALSE);
18004 SafeSetStatus (dlg->remove_parsed, FALSE);
18005 ClearTextSimpleAECRDlg (dlg);
18006 }
18007 }
18008
SimpleAECRToDialog(DialoG d,Pointer userdata)18009 static void SimpleAECRToDialog (DialoG d, Pointer userdata)
18010 {
18011 SimpleAECRDlgPtr dlg;
18012 SimpleAECRPtr data;
18013
18014 dlg = (SimpleAECRDlgPtr) GetObjectExtra (d);
18015 if (dlg == NULL)
18016 {
18017 return;
18018 }
18019
18020 ResetSimpleAECRDlg (dlg);
18021 data = (SimpleAECRPtr) userdata;
18022 if (data != NULL)
18023 {
18024 PointerToDialog (dlg->field_list, data->field_list);
18025 PointerToDialog (dlg->field_list_to, data->field_list_to);
18026 SendMessageToDialog (dlg->field_list_to, NUM_VIB_MSG + 1);
18027 PointerToDialog (dlg->subtype_list, data->subtype_list);
18028 PointerToDialog (dlg->edit_apply, data->edit_apply);
18029 PointerToDialog (dlg->text_portion, data->text_portion);
18030 SafeSetValue (dlg->leave_on_original, data->leave_on_original);
18031 SafeSetValue (dlg->strip_name_from_text, data->strip_name_from_text);
18032 SafeSetStatus (dlg->remove_parsed, data->remove_parsed);
18033 dlg->free_field_vn_proc = data->free_field_vn_proc;
18034 dlg->free_subtype_vn_proc = data->free_subtype_vn_proc;
18035 }
18036 else
18037 {
18038 SendMessageToDialog (dlg->field_list, NUM_VIB_MSG + 1);
18039 SendMessageToDialog (dlg->field_list_to, NUM_VIB_MSG + 1);
18040 }
18041 }
18042
DialogToSimpleAECR(DialoG d)18043 static Pointer DialogToSimpleAECR (DialoG d)
18044 {
18045 SimpleAECRDlgPtr dlg;
18046 SimpleAECRPtr data;
18047
18048 dlg = (SimpleAECRDlgPtr) GetObjectExtra (d);
18049 if (dlg == NULL)
18050 {
18051 return NULL;
18052 }
18053
18054 data = (SimpleAECRPtr) MemNew (sizeof (SimpleAECRData));
18055 if (data != NULL)
18056 {
18057 data->field_list = DialogToPointer (dlg->field_list);
18058 data->field_list_to = DialogToPointer (dlg->field_list_to);
18059 data->subtype_list = DialogToPointer (dlg->subtype_list);
18060 data->edit_apply = DialogToPointer (dlg->edit_apply);
18061 data->text_portion = DialogToPointer (dlg->text_portion);
18062 if (dlg->remove_parsed == NULL) {
18063 data->remove_parsed = FALSE;
18064 }
18065 else
18066 {
18067 data->remove_parsed = GetStatus (dlg->remove_parsed);
18068 }
18069 if (dlg->leave_on_original != NULL)
18070 {
18071 data->leave_on_original = GetStatus (dlg->leave_on_original);
18072 }
18073 else
18074 {
18075 data->leave_on_original = FALSE;
18076 }
18077 if (dlg->strip_name_from_text != NULL)
18078 {
18079 data->strip_name_from_text = GetStatus (dlg->strip_name_from_text);
18080 }
18081 else
18082 {
18083 data->strip_name_from_text = FALSE;
18084 }
18085 data->free_field_vn_proc = dlg->free_field_vn_proc;
18086 data->free_subtype_vn_proc = dlg->free_subtype_vn_proc;
18087 }
18088 return data;
18089 }
18090
SimpleAECRDialogChangeNotify(Pointer userdata)18091 static void SimpleAECRDialogChangeNotify (Pointer userdata)
18092 {
18093 SimpleAECRDlgPtr dlg;
18094 CharPtr autopopulate_text;
18095 EditApplyPtr eap;
18096 ValNodePtr subtype_list, field_list;
18097
18098 dlg = (SimpleAECRDlgPtr) userdata;
18099 if (dlg == NULL)
18100 {
18101 return;
18102 }
18103
18104 if (dlg->get_autopopulate_text != NULL
18105 && (dlg->action_choice == AECR_APPLY || dlg->action_choice == AECR_EDIT))
18106 {
18107 eap = DialogToPointer (dlg->edit_apply);
18108 subtype_list = DialogToPointer (dlg->subtype_list);
18109 field_list = DialogToPointer (dlg->field_list);
18110 autopopulate_text = (dlg->get_autopopulate_text) (subtype_list, field_list, dlg->entityID);
18111 subtype_list = ValNodeFuncFree (subtype_list, dlg->free_subtype_vn_proc);
18112 field_list = ValNodeFuncFree (field_list, dlg->free_field_vn_proc);
18113 if (dlg->action_choice == AECR_APPLY)
18114 {
18115 eap->apply_txt = MemFree (eap->find_txt);
18116 eap->apply_txt = autopopulate_text;
18117 }
18118 else
18119 {
18120 eap->find_txt = MemFree (eap->find_txt);
18121 eap->find_txt = autopopulate_text;
18122 }
18123 PointerToDialog (dlg->edit_apply, eap);
18124 EditApplyFree (eap);
18125 }
18126
18127 if (dlg->change_notify != NULL)
18128 {
18129 (dlg->change_notify) (dlg->change_userdata);
18130 }
18131 }
18132
18133
SimpleAECRMessage(DialoG d,Int2 mssg)18134 static void SimpleAECRMessage (DialoG d, Int2 mssg)
18135
18136 {
18137 SimpleAECRDlgPtr dlg;
18138
18139 dlg = (SimpleAECRDlgPtr) GetObjectExtra (d);
18140 if (dlg != NULL) {
18141 switch (mssg)
18142 {
18143 case VIB_MSG_INIT :
18144 /* reset list */
18145 ResetSimpleAECRDlg (dlg);
18146 break;
18147 case VIB_MSG_ENTER :
18148 if (dlg->subtype_list != NULL)
18149 {
18150 Select (dlg->subtype_list);
18151 }
18152 else
18153 {
18154 Select (dlg->field_list);
18155 }
18156 break;
18157 case AECR_VIB_MSG_SET_DEFAULT :
18158 SendMessageToDialog (dlg->field_list, AECR_VIB_MSG_SET_DEFAULT);
18159 SendMessageToDialog (dlg->field_list_to, AECR_VIB_MSG_SET_DEFAULT);
18160 SendMessageToDialog (dlg->subtype_list, AECR_VIB_MSG_SET_DEFAULT);
18161 ClearTextSimpleAECRDlg (dlg);
18162 break;
18163 case AECR_VIB_MSG_AUTOPOPULATE:
18164 SimpleAECRDialogChangeNotify (dlg);
18165 break;
18166 case AECR_VIB_MSG_CLEAR_TEXT :
18167 ClearTextSimpleAECRDlg (dlg);
18168 break;
18169 default :
18170 break;
18171 }
18172 }
18173 }
18174
TestSimpleAECR(DialoG d)18175 static ValNodePtr TestSimpleAECR (DialoG d)
18176 {
18177 SimpleAECRDlgPtr dlg;
18178 ValNodePtr err_list = NULL;
18179 ValNodePtr total_err_list = NULL;
18180
18181 dlg = (SimpleAECRDlgPtr) GetObjectExtra (d);
18182 if (dlg == NULL)
18183 {
18184 return FALSE;
18185 }
18186
18187 total_err_list = TestDialog (dlg->field_list);
18188
18189 if (dlg->subtype_list != NULL)
18190 {
18191 err_list = TestDialog (dlg->subtype_list);
18192 total_err_list = ValNodeAppend (total_err_list, err_list);
18193 }
18194
18195 err_list = NULL;
18196 switch (dlg->action_choice)
18197 {
18198 case AECR_CONVERT:
18199 case AECR_SWAP:
18200 err_list = TestDialog (dlg->field_list_to);
18201 break;
18202 case AECR_APPLY:
18203 case AECR_EDIT:
18204 err_list = TestDialog (dlg->edit_apply);
18205 break;
18206 }
18207
18208 total_err_list = ValNodeAppend (total_err_list, err_list);
18209
18210 return total_err_list;
18211 }
18212
SimpleAECRButtonChange(ButtoN b)18213 static void SimpleAECRButtonChange (ButtoN b)
18214 {
18215 SimpleAECRDlgPtr dlg;
18216
18217 dlg = (SimpleAECRDlgPtr) GetObjectExtra (b);
18218 if (dlg == NULL) return;
18219
18220 if (dlg->change_notify != NULL)
18221 {
18222 (dlg->change_notify) (dlg->change_userdata);
18223 }
18224 }
18225
SimpleAECRDialogEx(GrouP h,Int4 action_choice,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata,FreeValNodeProc free_field_vn_proc,FreeValNodeProc free_subtype_vn_proc,Nlm_FieldListDlgProc fieldlist_dlg_proc,Nlm_SubtypeListDlgProc subtypelist_dlg_proc,GetAutoPopulateTextFunc get_autopopulate_text,CharPtr field_label,CharPtr subtype_label,Boolean is_text,Boolean strip_name,Uint2 entityID)18226 static DialoG SimpleAECRDialogEx
18227 (GrouP h,
18228 Int4 action_choice,
18229 Nlm_ChangeNotifyProc change_notify,
18230 Pointer change_userdata,
18231 FreeValNodeProc free_field_vn_proc,
18232 FreeValNodeProc free_subtype_vn_proc,
18233 Nlm_FieldListDlgProc fieldlist_dlg_proc,
18234 Nlm_SubtypeListDlgProc subtypelist_dlg_proc,
18235 GetAutoPopulateTextFunc get_autopopulate_text,
18236 CharPtr field_label,
18237 CharPtr subtype_label,
18238 Boolean is_text,
18239 Boolean strip_name,
18240 Uint2 entityID)
18241 {
18242 SimpleAECRDlgPtr dlg;
18243 GrouP p, g1;
18244 SeqEntryPtr sep;
18245
18246 dlg = (SimpleAECRDlgPtr) MemNew (sizeof (SimpleAECRDlgData));
18247 if (dlg == NULL)
18248 {
18249 return NULL;
18250 }
18251
18252 p = HiddenGroup (h, -1, 0, NULL);
18253 SetObjectExtra (p, dlg, StdCleanupExtraProc);
18254 SetGroupSpacing (p, 10, 10);
18255
18256 dlg->dialog = (DialoG) p;
18257 dlg->todialog = SimpleAECRToDialog;
18258 dlg->fromdialog = DialogToSimpleAECR;
18259 dlg->dialogmessage = SimpleAECRMessage;
18260 dlg->testdialog = TestSimpleAECR;
18261 dlg->action_choice = action_choice;
18262 dlg->free_field_vn_proc = free_field_vn_proc;
18263 dlg->free_subtype_vn_proc = free_subtype_vn_proc;
18264 dlg->change_notify = change_notify;
18265 dlg->change_userdata = change_userdata;
18266 dlg->get_autopopulate_text = get_autopopulate_text;
18267 dlg->entityID = entityID;
18268 dlg->strip_name_from_text = NULL;
18269
18270 dlg->subtype_list = NULL;
18271
18272 sep = GetTopSeqEntryForEntityID(entityID);
18273
18274 if (action_choice == AECR_CONVERT || action_choice == AECR_SWAP || action_choice == AECR_PARSE)
18275 {
18276 if (subtypelist_dlg_proc == NULL)
18277 {
18278 g1 = HiddenGroup (p, 2, 0, NULL);
18279 }
18280 else
18281 {
18282 g1 = HiddenGroup (p, 3, 0, NULL);
18283 StaticPrompt (g1, subtype_label, 0, dialogTextHeight, systemFont, 'l');
18284 }
18285 StaticPrompt (g1, "From", 0, dialogTextHeight, systemFont, 'l');
18286 StaticPrompt (g1, "To", 0, dialogTextHeight, systemFont, 'l');
18287
18288 if (subtypelist_dlg_proc != NULL)
18289 {
18290 dlg->subtype_list = (subtypelist_dlg_proc) (g1, TRUE, sep, change_notify, change_userdata);
18291 }
18292 dlg->field_list = fieldlist_dlg_proc (g1, FALSE,
18293 change_notify,
18294 change_userdata);
18295 dlg->field_list_to = fieldlist_dlg_proc (g1, FALSE,
18296 change_notify,
18297 change_userdata);
18298 if (action_choice == AECR_CONVERT && is_text)
18299 {
18300 dlg->leave_on_original = CheckBox (p, "Leave on original", SimpleAECRButtonChange);
18301 SetObjectExtra (dlg->leave_on_original, dlg, NULL);
18302 }
18303 if (strip_name)
18304 {
18305 dlg->strip_name_from_text = CheckBox (p, "Strip name from text", SimpleAECRButtonChange);
18306 SetObjectExtra (dlg->strip_name_from_text, dlg, NULL);
18307 }
18308 }
18309 else
18310 {
18311 if (subtypelist_dlg_proc == NULL)
18312 {
18313 g1 = HiddenGroup (p, 1, 0, NULL);
18314
18315 }
18316 else
18317 {
18318 g1 = HiddenGroup (p, 2, 0, NULL);
18319 StaticPrompt (g1, subtype_label, 0, dialogTextHeight, systemFont, 'l');
18320 }
18321 StaticPrompt (g1, field_label, 0, dialogTextHeight, systemFont, 'l');
18322 if (action_choice == AECR_REMOVE)
18323 {
18324 if (subtypelist_dlg_proc != NULL)
18325 {
18326 dlg->subtype_list = (subtypelist_dlg_proc) (g1, TRUE, sep, change_notify, change_userdata);
18327 }
18328 dlg->field_list = fieldlist_dlg_proc (g1, TRUE,
18329 change_notify,
18330 change_userdata);
18331 }
18332 else
18333 {
18334 if (subtypelist_dlg_proc != NULL)
18335 {
18336 dlg->subtype_list = (subtypelist_dlg_proc) (g1, TRUE, sep,
18337 SimpleAECRDialogChangeNotify,
18338 dlg);
18339 }
18340 dlg->field_list = fieldlist_dlg_proc (g1, FALSE,
18341 SimpleAECRDialogChangeNotify,
18342 dlg);
18343 }
18344 }
18345
18346 if (is_text && (action_choice == AECR_APPLY || action_choice == AECR_EDIT))
18347 {
18348 dlg->edit_apply = EditApplyDialog (p,
18349 action_choice == AECR_APPLY ? eEditApplyChoice_Apply : eEditApplyChoice_Edit,
18350 "New Text", NULL,
18351 change_notify, change_userdata);
18352 dlg->text_portion = NULL;
18353 dlg->remove_parsed = NULL;
18354 }
18355 else if (action_choice == AECR_PARSE)
18356 {
18357 dlg->edit_apply = NULL;
18358 if (is_text) {
18359 dlg->text_portion = TextPortionXDialog(p);
18360 }
18361 dlg->remove_parsed = CheckBox (p, "Remove from parsed field", SimpleAECRButtonChange);
18362 SetObjectExtra (dlg->remove_parsed, dlg, NULL);
18363 }
18364 else
18365 {
18366 dlg->edit_apply = NULL;
18367 dlg->text_portion = NULL;
18368 dlg->remove_parsed = NULL;
18369 }
18370
18371 if (action_choice == AECR_CONVERT)
18372 {
18373 if (is_text)
18374 {
18375 AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) dlg->leave_on_original, (HANDLE) dlg->strip_name_from_text, NULL);
18376 }
18377 else
18378 {
18379 AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) dlg->strip_name_from_text, NULL);
18380 }
18381 }
18382 else if (action_choice == AECR_SWAP)
18383 {
18384 AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) dlg->strip_name_from_text, NULL);
18385 }
18386 else if (action_choice == AECR_PARSE)
18387 {
18388 AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) dlg->text_portion, (HANDLE) dlg->remove_parsed, NULL);
18389 }
18390 else
18391 {
18392 AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) dlg->edit_apply, NULL);
18393 }
18394 return (DialoG) p;
18395 }
18396
SimpleAECRDialog(GrouP h,Int4 action_choice,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata,FreeValNodeProc free_field_vn_proc,FreeValNodeProc free_subtype_vn_proc,Nlm_FieldListDlgProc fieldlist_dlg_proc,Nlm_SubtypeListDlgProc subtypelist_dlg_proc,GetAutoPopulateTextFunc get_autopopulate_text,CharPtr field_label,CharPtr subtype_label,Boolean is_text,Uint2 entityID)18397 static DialoG SimpleAECRDialog
18398 (GrouP h,
18399 Int4 action_choice,
18400 Nlm_ChangeNotifyProc change_notify,
18401 Pointer change_userdata,
18402 FreeValNodeProc free_field_vn_proc,
18403 FreeValNodeProc free_subtype_vn_proc,
18404 Nlm_FieldListDlgProc fieldlist_dlg_proc,
18405 Nlm_SubtypeListDlgProc subtypelist_dlg_proc,
18406 GetAutoPopulateTextFunc get_autopopulate_text,
18407 CharPtr field_label,
18408 CharPtr subtype_label,
18409 Boolean is_text,
18410 Uint2 entityID)
18411 {
18412 return SimpleAECRDialogEx(h, action_choice, change_notify, change_userdata,
18413 free_field_vn_proc, free_subtype_vn_proc,
18414 fieldlist_dlg_proc, subtypelist_dlg_proc,
18415 get_autopopulate_text,
18416 field_label, subtype_label,
18417 is_text, FALSE, entityID);
18418 }
18419
18420 static CharPtr
CDSGeneProtAutopopulate(ValNodePtr subtype_list,ValNodePtr field_list,Uint2 entityID)18421 CDSGeneProtAutopopulate
18422 (ValNodePtr subtype_list,
18423 ValNodePtr field_list,
18424 Uint2 entityID)
18425 {
18426 GetSamplePtr gsp;
18427 CharPtr rval;
18428
18429 gsp = CheckForExistingText (entityID, field_list,
18430 GetCDSGeneProtField,
18431 NULL,
18432 NULL,
18433 IntValNodeCopy,
18434 NULL,
18435 0, 0, 0);
18436 rval = gsp->sample_text;
18437 gsp->sample_text = NULL;
18438 GetSampleFree (gsp);
18439 return rval;
18440 }
18441
18442 typedef struct cdsgeneprotaecrdlg
18443 {
18444 AECR_BLOCK
18445 ButtoN also_mrna;
18446 } CDSGeneProtAECRDlgData, PNTR CDSGeneProtAECRDlgPtr;
18447
18448 typedef struct cdsgeneprotaecr
18449 {
18450 AECR_DATA_BLOCK
18451 Boolean also_mrna;
18452 } CDSGeneProtAECRData, PNTR CDSGeneProtAECRPtr;
18453
18454
CDSGeneProtAECRFree(CDSGeneProtAECRPtr sp)18455 static CDSGeneProtAECRPtr CDSGeneProtAECRFree (CDSGeneProtAECRPtr sp)
18456 {
18457 if (sp != NULL)
18458 {
18459 AECRDataBlockFreeContents ((SimpleAECRPtr) sp);
18460 sp = MemFree (sp);
18461 }
18462 return sp;
18463 }
18464
18465
PointerToCDSGeneProtAECRDialog(DialoG d,Pointer userdata)18466 static void PointerToCDSGeneProtAECRDialog (DialoG d, Pointer userdata)
18467 {
18468 CDSGeneProtAECRDlgPtr dlg;
18469 CDSGeneProtAECRPtr data;
18470
18471 dlg = (CDSGeneProtAECRDlgPtr) GetObjectExtra (d);
18472 if (dlg == NULL) return;
18473 data = (CDSGeneProtAECRPtr) userdata;
18474 SimpleAECRToDialog (d, userdata);
18475 if (data != NULL)
18476 {
18477 SetStatus (dlg->also_mrna, data->also_mrna);
18478 }
18479
18480 }
18481
18482
ShowingProteinName(CDSGeneProtAECRDlgPtr dlg)18483 static Boolean ShowingProteinName (CDSGeneProtAECRDlgPtr dlg)
18484 {
18485 ValNodePtr vnp_from, vnp_to;
18486 Int4 protein_name_field_num = 2 + num_gene_fields + num_mrna_fields;
18487 Boolean rval = FALSE;
18488
18489 if (dlg == NULL) return FALSE;
18490
18491 vnp_from = DialogToPointer (dlg->field_list);
18492 vnp_to = DialogToPointer (dlg->field_list_to);
18493
18494 if ((vnp_from != NULL && vnp_from->data.intvalue == protein_name_field_num)
18495 || (vnp_to != NULL && vnp_to->data.intvalue == protein_name_field_num))
18496 {
18497 rval = TRUE;
18498 }
18499 vnp_from = ValNodeFree (vnp_from);
18500 vnp_to = ValNodeFree (vnp_to);
18501
18502 return rval;
18503 }
18504
18505
CDSGeneProtAECRDialogToPointer(DialoG d)18506 static Pointer CDSGeneProtAECRDialogToPointer (DialoG d)
18507 {
18508 CDSGeneProtAECRDlgPtr dlg;
18509 SimpleAECRPtr subset;
18510 CDSGeneProtAECRPtr data = NULL;
18511
18512 dlg = (CDSGeneProtAECRDlgPtr) GetObjectExtra (d);
18513 if (dlg == NULL) return NULL;
18514
18515 subset = DialogToSimpleAECR (d);
18516 if (subset != NULL)
18517 {
18518 data = (CDSGeneProtAECRPtr) MemNew (sizeof (CDSGeneProtAECRData));
18519 MemCpy (data, subset, sizeof (SimpleAECRData));
18520 MemSet (subset, 0, sizeof (SimpleAECRData));
18521 subset = MemFree (subset);
18522 if (ShowingProteinName (dlg))
18523 {
18524 data->also_mrna = GetStatus (dlg->also_mrna);
18525 }
18526 else
18527 {
18528 data->also_mrna = FALSE;
18529 }
18530 }
18531 return data;
18532 }
18533
18534
CDSGeneProtAECRDialogChange(Pointer data)18535 static void CDSGeneProtAECRDialogChange (Pointer data)
18536 {
18537 CDSGeneProtAECRDlgPtr dlg;
18538
18539 dlg = (CDSGeneProtAECRDlgPtr) data;
18540 if (dlg == NULL) return;
18541
18542 if (ShowingProteinName (dlg))
18543 {
18544 Show (dlg->also_mrna);
18545 }
18546 else
18547 {
18548 Hide (dlg->also_mrna);
18549 }
18550
18551 SimpleAECRDialogChangeNotify (dlg);
18552 }
18553
18554
CDSGeneProtAECRDialog(GrouP h,Int4 action_choice,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata,Uint2 entityID)18555 static DialoG CDSGeneProtAECRDialog
18556 (GrouP h,
18557 Int4 action_choice,
18558 Nlm_ChangeNotifyProc change_notify,
18559 Pointer change_userdata,
18560 Uint2 entityID)
18561 {
18562 CDSGeneProtAECRDlgPtr dlg;
18563 GrouP p, g1;
18564 SeqEntryPtr sep;
18565
18566 dlg = (CDSGeneProtAECRDlgPtr) MemNew (sizeof (CDSGeneProtAECRDlgData));
18567 if (dlg == NULL)
18568 {
18569 return NULL;
18570 }
18571
18572 p = HiddenGroup (h, -1, 0, NULL);
18573 SetObjectExtra (p, dlg, StdCleanupExtraProc);
18574 SetGroupSpacing (p, 10, 10);
18575
18576 dlg->dialog = (DialoG) p;
18577 dlg->todialog = PointerToCDSGeneProtAECRDialog;
18578 dlg->fromdialog = CDSGeneProtAECRDialogToPointer;
18579 dlg->dialogmessage = SimpleAECRMessage;
18580 dlg->testdialog = TestSimpleAECR;
18581 dlg->action_choice = action_choice;
18582 dlg->free_field_vn_proc = NULL;
18583 dlg->free_subtype_vn_proc = NULL;
18584 dlg->change_notify = change_notify;
18585 dlg->change_userdata = change_userdata;
18586 dlg->get_autopopulate_text = CDSGeneProtAutopopulate;
18587 dlg->entityID = entityID;
18588 dlg->strip_name_from_text = NULL;
18589
18590 dlg->subtype_list = NULL;
18591
18592 sep = GetTopSeqEntryForEntityID(entityID);
18593
18594 if (action_choice == AECR_CONVERT || action_choice == AECR_SWAP || action_choice == AECR_PARSE)
18595 {
18596 g1 = HiddenGroup (p, 2, 0, NULL);
18597 StaticPrompt (g1, "From", 0, dialogTextHeight, systemFont, 'l');
18598 StaticPrompt (g1, "To", 0, dialogTextHeight, systemFont, 'l');
18599
18600 dlg->field_list = CDSGeneProtFieldSelectionDialog (g1, FALSE,
18601 CDSGeneProtAECRDialogChange,
18602 dlg);
18603 dlg->field_list_to = CDSGeneProtFieldSelectionDialog (g1, FALSE,
18604 CDSGeneProtAECRDialogChange,
18605 dlg);
18606 if (action_choice == AECR_CONVERT)
18607 {
18608 dlg->leave_on_original = CheckBox (p, "Leave on original", NULL);
18609 }
18610 }
18611 else
18612 {
18613 g1 = HiddenGroup (p, 1, 0, NULL);
18614 StaticPrompt (g1, "Field", 0, dialogTextHeight, systemFont, 'l');
18615 if (action_choice == AECR_REMOVE)
18616 {
18617 dlg->field_list = CDSGeneProtFieldSelectionDialog (g1, TRUE,
18618 CDSGeneProtAECRDialogChange,
18619 dlg);
18620 }
18621 else
18622 {
18623 dlg->field_list = CDSGeneProtFieldSelectionDialog (g1, FALSE,
18624 CDSGeneProtAECRDialogChange,
18625 dlg);
18626 }
18627 }
18628
18629 if (action_choice == AECR_APPLY || action_choice == AECR_EDIT)
18630 {
18631 dlg->edit_apply = EditApplyDialog (p,
18632 action_choice == AECR_APPLY ? eEditApplyChoice_Apply : eEditApplyChoice_Edit,
18633 "New Text", NULL,
18634 change_notify, change_userdata);
18635 dlg->text_portion = NULL;
18636 dlg->remove_parsed = NULL;
18637 }
18638 else if (action_choice == AECR_PARSE)
18639 {
18640 dlg->edit_apply = NULL;
18641 dlg->text_portion = TextPortionXDialog(p);
18642 dlg->remove_parsed = CheckBox (p, "Remove from parsed field", NULL);
18643 }
18644 else
18645 {
18646 dlg->edit_apply = NULL;
18647 dlg->text_portion = NULL;
18648 dlg->remove_parsed = NULL;
18649 }
18650
18651 dlg->also_mrna = CheckBox (p, "Make mRNA product match CDS protein name", NULL);
18652
18653 if (action_choice == AECR_CONVERT)
18654 {
18655 AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) dlg->leave_on_original, (HANDLE) dlg->also_mrna, NULL);
18656 }
18657 else if (action_choice == AECR_SWAP)
18658 {
18659 AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) dlg->strip_name_from_text, (HANDLE) dlg->also_mrna, NULL);
18660 }
18661 else if (action_choice == AECR_PARSE)
18662 {
18663 AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) dlg->text_portion, (HANDLE) dlg->remove_parsed, (HANDLE) dlg->also_mrna, NULL);
18664 }
18665 else
18666 {
18667 AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) dlg->edit_apply, (HANDLE) dlg->also_mrna, NULL);
18668 }
18669 return (DialoG) p;
18670 }
18671
18672
AddStringToSample(CharPtr str,GetSamplePtr gsp)18673 static void AddStringToSample (CharPtr str, GetSamplePtr gsp)
18674 {
18675 if (gsp == NULL) return;
18676
18677 if (str != NULL)
18678 {
18679 gsp->num_found ++;
18680 }
18681 if (gsp->sample_text == NULL)
18682 {
18683 gsp->sample_text = StringSave (str);
18684 }
18685 else
18686 {
18687 if (StringCmp (str, gsp->sample_text) != 0)
18688 {
18689 gsp->all_same = FALSE;
18690 }
18691 }
18692 }
18693
18694 static GetSamplePtr
GetCDSGeneProtAECRSample(ValNodePtr cdset_list,ValNodePtr field_list,ValNodePtr field_list_to,FilterSetPtr fsp)18695 GetCDSGeneProtAECRSample
18696 (ValNodePtr cdset_list,
18697 ValNodePtr field_list,
18698 ValNodePtr field_list_to,
18699 FilterSetPtr fsp)
18700 {
18701 GetSamplePtr gsp;
18702 ValNodePtr cdset_vnp, sfp_vnp;
18703 CharPtr str;
18704 CDSetPtr cdsp;
18705
18706 gsp = (GetSamplePtr) MemNew (sizeof (GetSampleData));
18707 if (gsp == NULL)
18708 {
18709 return NULL;
18710 }
18711 gsp->free_vn_proc = NULL;
18712 gsp->copy_vn_proc = IntValNodeCopy;
18713 for (cdset_vnp = cdset_list; cdset_vnp != NULL; cdset_vnp = cdset_vnp->next)
18714 {
18715 cdsp = (CDSetPtr) cdset_vnp->data.ptrvalue;
18716 if (IsCDSetMatPeptideQualChoice(field_list) || IsCDSetMatPeptideQualChoice(field_list_to))
18717 {
18718 /* need to look at all mat_peptide features */
18719 for (sfp_vnp = cdsp->prot_list; sfp_vnp != NULL; sfp_vnp = sfp_vnp->next)
18720 {
18721 if (fsp != NULL && fsp->cgp != NULL && DoesConstraintDisqualifyFeature (sfp_vnp->data.ptrvalue, fsp->cgp))
18722 {
18723 /* this feature will be skipped in the action, so it should not be included in the sample */
18724 }
18725 else
18726 {
18727 str = GetCDSGeneProtField (sfp_vnp->data.ptrvalue, field_list, fsp);
18728 if (str != NULL && field_list_to != NULL)
18729 {
18730 str = GetCDSGeneProtField (sfp_vnp->data.ptrvalue, field_list_to, fsp);
18731 }
18732 AddStringToSample (str, gsp);
18733 str = MemFree (str);
18734 }
18735 }
18736 } else {
18737 str = GetCDSetField (cdsp, field_list);
18738 if (str != NULL && field_list_to != NULL)
18739 {
18740 str = MemFree (str);
18741 str = GetCDSetField (cdset_vnp->data.ptrvalue, field_list_to);
18742 }
18743 AddStringToSample (str, gsp);
18744 str = MemFree (str);
18745 }
18746 }
18747 return gsp;
18748 }
18749
FeatureTypeMissingFromCDSet(CDSetPtr cdsp,Uint2 choice)18750 static Boolean FeatureTypeMissingFromCDSet (CDSetPtr cdsp, Uint2 choice)
18751 {
18752 ValNodePtr vnp;
18753 SeqFeatPtr sfp;
18754 Boolean is_missing = TRUE;
18755
18756 if (cdsp == NULL) return TRUE;
18757 switch (choice)
18758 {
18759 case FEATDEF_CDS:
18760 if (cdsp->cds_list != NULL)
18761 {
18762 is_missing = FALSE;
18763 }
18764 break;
18765 case FEATDEF_GENE:
18766 if (cdsp->gene_list != NULL)
18767 {
18768 is_missing = FALSE;
18769 }
18770 break;
18771 case FEATDEF_mRNA:
18772 if (cdsp->mrna_list != NULL)
18773 {
18774 is_missing = FALSE;
18775 }
18776 break;
18777 case FEATDEF_PROT:
18778 case FEATDEF_mat_peptide_aa:
18779 for (vnp = cdsp->prot_list; vnp != NULL; vnp = vnp->next)
18780 {
18781 sfp = (SeqFeatPtr) vnp->data.ptrvalue;
18782 if (sfp != NULL && sfp->idx.subtype == choice)
18783 {
18784 is_missing = FALSE;
18785 }
18786 }
18787 break;
18788 }
18789 return is_missing;
18790 }
18791
18792 static Int4
CountMissingFeatures(ValNodePtr cdset_list,ValNodePtr field_list,ValNodePtr field_list_to,FilterSetPtr fsp)18793 CountMissingFeatures
18794 (ValNodePtr cdset_list,
18795 ValNodePtr field_list,
18796 ValNodePtr field_list_to,
18797 FilterSetPtr fsp)
18798 {
18799 ValNodePtr cdset_vnp, sfp_vnp;
18800 CharPtr str;
18801 CDSetPtr cdsp;
18802 Uint2 choice_from, choice_to;
18803 Int4 num_missing = 0;
18804
18805 choice_from = FeatDefTypeFromFieldList (field_list);
18806 choice_to = FeatDefTypeFromFieldList (field_list_to);
18807
18808 if (choice_from == 0 || choice_to == 0 || choice_from == choice_to)
18809 {
18810 return 0;
18811 }
18812
18813 for (cdset_vnp = cdset_list; cdset_vnp != NULL; cdset_vnp = cdset_vnp->next)
18814 {
18815 cdsp = (CDSetPtr) cdset_vnp->data.ptrvalue;
18816
18817 if (choice_from == FEATDEF_mat_peptide_aa)
18818 {
18819 /* need to look at all mat_peptide features */
18820 for (sfp_vnp = cdsp->prot_list; sfp_vnp != NULL; sfp_vnp = sfp_vnp->next)
18821 {
18822 if (fsp != NULL && fsp->cgp != NULL && DoesConstraintDisqualifyFeature (sfp_vnp->data.ptrvalue, fsp->cgp))
18823 {
18824 /* this feature will be skipped in the action, so it doesn't count towards missing sets */
18825 }
18826 else
18827 {
18828 str = GetCDSGeneProtField (sfp_vnp->data.ptrvalue, field_list, fsp);
18829 if (str != NULL)
18830 {
18831 if (FeatureTypeMissingFromCDSet (cdsp, choice_to))
18832 {
18833 num_missing++;
18834 }
18835 }
18836 str = MemFree (str);
18837 }
18838 }
18839 } else {
18840 str = GetCDSetField (cdsp, field_list);
18841 if (str != NULL)
18842 {
18843 if (FeatureTypeMissingFromCDSet (cdsp, choice_to))
18844 {
18845 num_missing++;
18846 }
18847 }
18848 str = MemFree (str);
18849 }
18850 }
18851 return num_missing;
18852 }
18853
18854
18855 /* things get tricksy when we're dealing with mat_peptides, because there
18856 * can be more than one of them in the CDS-mRNA-Gene-Prot group.
18857 */
18858
CDSGeneProtApplyToAllThatMatchFilter(CharPtr str_src,CDSetPtr cdsp,ValNodePtr field_list_to,FilterSetPtr fsp,ExistingTextPtr etp)18859 static Boolean CDSGeneProtApplyToAllThatMatchFilter
18860 (CharPtr str_src,
18861 CDSetPtr cdsp,
18862 ValNodePtr field_list_to,
18863 FilterSetPtr fsp,
18864 ExistingTextPtr etp)
18865 {
18866 ApplyValueData avd;
18867
18868 avd.where_to_replace = EditApplyFindLocation_anywhere;
18869
18870 /* build gene if we're applying to gene but gene doesn't already exist */
18871 BuildNewCDSGeneProtFeature (cdsp, field_list_to, NULL);
18872 avd.field_list = NULL;
18873 avd.new_text = str_src;
18874 avd.text_to_replace = NULL;
18875 avd.etp = etp;
18876
18877 return SetCDSetField (cdsp, field_list_to, &avd, fsp);
18878 }
18879
CDSGeneProtApplyToOneFeature(CharPtr str_src,SeqFeatPtr sfp,ValNodePtr field_list_to,FilterSetPtr fsp,ExistingTextPtr etp)18880 static Boolean CDSGeneProtApplyToOneFeature
18881 (CharPtr str_src,
18882 SeqFeatPtr sfp,
18883 ValNodePtr field_list_to,
18884 FilterSetPtr fsp,
18885 ExistingTextPtr etp)
18886 {
18887 ApplyValueData avd;
18888
18889 avd.where_to_replace = EditApplyFindLocation_anywhere;
18890
18891 avd.field_list = NULL;
18892 avd.new_text = str_src;
18893 avd.text_to_replace = NULL;
18894 avd.etp = etp;
18895
18896 return SetCDSGeneProtField (sfp, field_list_to, &avd, fsp);
18897 }
18898
18899
CopyProteinNameTomRNAName(CDSetPtr cdsp)18900 static void CopyProteinNameTomRNAName (CDSetPtr cdsp)
18901 {
18902 Int4 protein_name_field_num = 2 + num_gene_fields + num_mrna_fields;
18903 Int4 mrna_product_field_num = 2 + num_gene_fields;
18904 ValNode vn_src, vn_dst;
18905 ApplyValueData avd;
18906
18907 vn_src.data.intvalue = protein_name_field_num;
18908 vn_src.next = NULL;
18909 vn_src.choice = 0;
18910
18911 vn_dst.data.intvalue = mrna_product_field_num;
18912 vn_dst.next = NULL;
18913 vn_dst.choice = 0;
18914
18915 avd.new_text = GetCDSetField (cdsp, &vn_src);
18916 avd.etp = NULL;
18917 avd.field_list = NULL;
18918 avd.text_to_replace = NULL;
18919 avd.where_to_replace = EditApplyFindLocation_anywhere;
18920 SetCDSetField (cdsp, &vn_dst, &avd, NULL);
18921 }
18922
CDSGeneProtConvert(CDSetPtr cdsp,CDSGeneProtAECRPtr sp,FilterSetPtr fsp,ExistingTextPtr etp,Boolean build_missing)18923 static void CDSGeneProtConvert
18924 (CDSetPtr cdsp,
18925 CDSGeneProtAECRPtr sp,
18926 FilterSetPtr fsp,
18927 ExistingTextPtr etp,
18928 Boolean build_missing)
18929 {
18930 CharPtr str_src = NULL;
18931 CharPtr str_dst = NULL;
18932 ValNodePtr sfp_vnp;
18933 SeqFeatPtr sfp;
18934 Boolean able_to_apply = FALSE;
18935 Boolean change_made = FALSE;
18936
18937 if (IsCDSetMatPeptideQualChoice(sp->field_list))
18938 {
18939 for (sfp_vnp = cdsp->prot_list; sfp_vnp != NULL; sfp_vnp = sfp_vnp->next)
18940 {
18941 sfp = sfp_vnp->data.ptrvalue;
18942 able_to_apply = FALSE;
18943 if (fsp == NULL || !DoesConstraintDisqualifyFeature(sfp, fsp->cgp)) {
18944 str_src = GetCDSGeneProtField (sfp_vnp->data.ptrvalue, sp->field_list, NULL);
18945 if (str_src != NULL)
18946 {
18947 if (IsCDSetMatPeptideQualChoice (sp->field_list_to))
18948 {
18949 CDSGeneProtApplyToOneFeature (str_src, sfp, sp->field_list_to, fsp, etp);
18950 change_made = TRUE;
18951 }
18952 else
18953 {
18954 if (build_missing)
18955 {
18956 BuildNewCDSGeneProtFeature (cdsp, sp->field_list_to, sp->field_list);
18957 }
18958 able_to_apply = CDSGeneProtApplyToAllThatMatchFilter (str_src, cdsp, sp->field_list_to, fsp, etp);
18959 if (able_to_apply)
18960 {
18961 change_made = TRUE;
18962 }
18963 }
18964 if (!sp->leave_on_original && able_to_apply)
18965 {
18966 sp->field_list->choice = 1;
18967 RemoveCDSGeneProtField (sfp, sp->field_list, fsp);
18968 change_made = TRUE;
18969 }
18970 }
18971 }
18972 }
18973 }
18974 else
18975 {
18976 str_src = GetCDSetField (cdsp, sp->field_list);
18977 if (str_src != NULL)
18978 {
18979 if (build_missing)
18980 {
18981 BuildNewCDSGeneProtFeature (cdsp, sp->field_list_to, sp->field_list);
18982 }
18983 able_to_apply = CDSGeneProtApplyToAllThatMatchFilter (str_src, cdsp, sp->field_list_to, fsp, etp);
18984 if (!sp->leave_on_original && able_to_apply)
18985 {
18986 sp->field_list->choice = 1;
18987 RemoveCDSetField (cdsp, sp->field_list, fsp);
18988 }
18989 if (able_to_apply)
18990 {
18991 change_made = TRUE;
18992 }
18993 }
18994 }
18995 if (sp->also_mrna && change_made)
18996 {
18997 CopyProteinNameTomRNAName (cdsp);
18998 }
18999
19000 }
19001
CDSGeneProtSwap(CDSetPtr cdsp,CDSGeneProtAECRPtr sp,FilterSetPtr fsp,ExistingTextPtr etp,Boolean build_missing)19002 static void CDSGeneProtSwap
19003 (CDSetPtr cdsp,
19004 CDSGeneProtAECRPtr sp,
19005 FilterSetPtr fsp,
19006 ExistingTextPtr etp,
19007 Boolean build_missing)
19008 {
19009 CharPtr str_src = NULL;
19010 CharPtr str_dst = NULL;
19011 ValNodePtr sfp_vnp_src, sfp_vnp_dst, vnp_swap;
19012 SeqFeatPtr sfp_src, sfp_dst;
19013 ApplyValueData avd;
19014 Uint2 choice_to, choice_from;
19015 Boolean change_made = FALSE;
19016
19017 avd.where_to_replace = EditApplyFindLocation_anywhere;
19018
19019 choice_from = FeatDefTypeFromFieldList (sp->field_list);
19020 choice_to = FeatDefTypeFromFieldList (sp->field_list_to);
19021
19022 if (choice_from == FEATDEF_mat_peptide_aa || choice_to == FEATDEF_mat_peptide_aa)
19023 {
19024 /* make sure mat_peptide qual if in field_list */
19025 if (!IsCDSetMatPeptideQualChoice(sp->field_list))
19026 {
19027 vnp_swap = sp->field_list;
19028 sp->field_list = sp->field_list_to;
19029 sp->field_list_to = vnp_swap;
19030 }
19031 for (sfp_vnp_src = cdsp->prot_list; sfp_vnp_src != NULL; sfp_vnp_src = sfp_vnp_src->next)
19032 {
19033 sfp_src = sfp_vnp_src->data.ptrvalue;
19034 if (fsp == NULL || !DoesConstraintDisqualifyFeature(sfp_src, fsp->cgp))
19035 {
19036 str_src = GetCDSGeneProtField (sfp_src, sp->field_list, NULL);
19037 if (IsCDSetMatPeptideQualChoice(sp->field_list_to))
19038 {
19039 for (sfp_vnp_dst = cdsp->prot_list; sfp_vnp_dst != NULL; sfp_vnp_dst = sfp_vnp_dst->next)
19040 {
19041 sfp_dst = sfp_vnp_dst->data.ptrvalue;
19042 if (fsp == NULL || !DoesConstraintDisqualifyFeature(sfp_dst, fsp->cgp))
19043 {
19044 str_dst = GetCDSGeneProtField (sfp_dst, sp->field_list_to, NULL);
19045 if (!StringHasNoText (str_src) || !StringHasNoText (str_dst))
19046 {
19047 if (build_missing)
19048 {
19049 BuildNewCDSGeneProtFeature (cdsp, sp->field_list, sp->field_list_to);
19050 BuildNewCDSGeneProtFeature (cdsp, sp->field_list_to, sp->field_list);
19051 }
19052 if (!FeatureTypeMissingFromCDSet(cdsp, choice_from)
19053 && !FeatureTypeMissingFromCDSet(cdsp, choice_to))
19054 {
19055 avd.etp = NULL;
19056 avd.text_to_replace = NULL;
19057 avd.new_text = StringSave (str_src);
19058 avd.field_list = NULL;
19059 SetCDSGeneProtField (sfp_dst, sp->field_list_to, &avd, fsp);
19060 avd.new_text = StringSave (str_dst);
19061 SetCDSGeneProtField (sfp_src, sp->field_list, &avd, fsp);
19062 change_made = TRUE;
19063 }
19064 }
19065 str_dst = MemFree (str_dst);
19066 }
19067 }
19068 }
19069 else
19070 {
19071 str_dst = GetCDSetField (cdsp, sp->field_list_to);
19072 if (!StringHasNoText (str_src) || !StringHasNoText (str_dst))
19073 {
19074 if (build_missing)
19075 {
19076 BuildNewCDSGeneProtFeature (cdsp, sp->field_list, sp->field_list_to);
19077 BuildNewCDSGeneProtFeature (cdsp, sp->field_list_to, sp->field_list);
19078 }
19079 if (!FeatureTypeMissingFromCDSet(cdsp, choice_from)
19080 && !FeatureTypeMissingFromCDSet(cdsp, choice_to))
19081 {
19082 avd.etp = NULL;
19083 avd.text_to_replace = NULL;
19084 avd.new_text = StringSave (str_src);
19085 avd.field_list = NULL;
19086 SetCDSetField (cdsp, sp->field_list_to, &avd, fsp);
19087 avd.new_text = StringSave (str_dst);
19088 SetCDSGeneProtField (sfp_src, sp->field_list, &avd, fsp);
19089 change_made = TRUE;
19090 }
19091 }
19092 str_dst = MemFree (str_dst);
19093 }
19094 str_src = MemFree (str_src);
19095 }
19096 }
19097 }
19098 else
19099 {
19100 str_src = GetCDSetField (cdsp, sp->field_list);
19101 str_dst = GetCDSetField (cdsp, sp->field_list_to);
19102 if (!StringHasNoText (str_src) || !StringHasNoText (str_dst))
19103 {
19104 if (build_missing)
19105 {
19106 BuildNewCDSGeneProtFeature (cdsp, sp->field_list, sp->field_list_to);
19107 BuildNewCDSGeneProtFeature (cdsp, sp->field_list_to, sp->field_list);
19108 }
19109 if (!FeatureTypeMissingFromCDSet(cdsp, choice_from)
19110 && !FeatureTypeMissingFromCDSet(cdsp, choice_to))
19111 {
19112 avd.etp = NULL;
19113 avd.text_to_replace = NULL;
19114 avd.new_text = str_src;
19115 avd.field_list = NULL;
19116 SetCDSetField (cdsp, sp->field_list_to, &avd, fsp);
19117 avd.new_text = str_dst;
19118 SetCDSetField (cdsp, sp->field_list, &avd, fsp);
19119 change_made = TRUE;
19120 }
19121 }
19122 }
19123 if (change_made && sp->also_mrna)
19124 {
19125 CopyProteinNameTomRNAName (cdsp);
19126 }
19127 }
19128
19129
CDSGeneProtParse(CDSetPtr cdsp,CDSGeneProtAECRPtr sp,FilterSetPtr fsp,ExistingTextPtr etp,Boolean build_missing)19130 static void CDSGeneProtParse
19131 (CDSetPtr cdsp,
19132 CDSGeneProtAECRPtr sp,
19133 FilterSetPtr fsp,
19134 ExistingTextPtr etp,
19135 Boolean build_missing)
19136 {
19137 CharPtr str_src = NULL;
19138 CharPtr str_dst = NULL;
19139 ValNodePtr sfp_vnp;
19140 SeqFeatPtr sfp;
19141 ApplyValueData avd;
19142 Boolean able_to_apply;
19143 Boolean change_made = FALSE;
19144
19145 avd.where_to_replace = EditApplyFindLocation_anywhere;
19146
19147 if (IsCDSetMatPeptideQualChoice(sp->field_list))
19148 {
19149 for (sfp_vnp = cdsp->prot_list; sfp_vnp != NULL; sfp_vnp = sfp_vnp->next)
19150 {
19151 sfp = sfp_vnp->data.ptrvalue;
19152 if (fsp == NULL || !DoesConstraintDisqualifyFeature(sfp, fsp->cgp))
19153 {
19154 str_src = GetCDSGeneProtField (sfp, sp->field_list, NULL);
19155 str_dst = str_src;
19156 str_src = ReplaceStringForParse(str_src, sp->text_portion);
19157 if (!sp->remove_parsed) {
19158 str_dst = MemFree (str_dst);
19159 }
19160
19161 if (str_src != NULL) {
19162 if (build_missing)
19163 {
19164 BuildNewCDSGeneProtFeature (cdsp, sp->field_list_to, sp->field_list);
19165 }
19166 able_to_apply = FALSE;
19167 if (IsCDSetMatPeptideQualChoice (sp->field_list_to))
19168 {
19169 able_to_apply = CDSGeneProtApplyToOneFeature (str_src, sfp, sp->field_list_to, fsp, etp);
19170 }
19171 else
19172 {
19173 able_to_apply = CDSGeneProtApplyToAllThatMatchFilter (str_src, cdsp, sp->field_list_to, fsp, etp);
19174 }
19175 if (sp->remove_parsed && able_to_apply) {
19176 CDSGeneProtApplyToOneFeature (str_dst, sfp, sp->field_list, fsp, NULL);
19177 }
19178 if (able_to_apply)
19179 {
19180 change_made = TRUE;
19181 }
19182 str_src = MemFree (str_src);
19183 }
19184 str_dst = MemFree (str_dst);
19185 }
19186 }
19187 }
19188 else
19189 {
19190 str_src = GetCDSetField (cdsp, sp->field_list);
19191 str_dst = str_src;
19192 str_src = ReplaceStringForParse(str_src, sp->text_portion);
19193 if (!sp->remove_parsed) {
19194 str_dst = MemFree (str_dst);
19195 }
19196 if (str_src != NULL) {
19197 if (build_missing)
19198 {
19199 BuildNewCDSGeneProtFeature (cdsp, sp->field_list_to, sp->field_list);
19200 }
19201 able_to_apply = CDSGeneProtApplyToAllThatMatchFilter (str_src, cdsp, sp->field_list_to, fsp, etp);
19202 if (sp->remove_parsed && able_to_apply) {
19203 CDSGeneProtApplyToAllThatMatchFilter (str_dst, cdsp, sp->field_list, fsp, NULL);
19204 }
19205 if (able_to_apply)
19206 {
19207 change_made = TRUE;
19208 }
19209 str_src = MemFree (str_src);
19210 }
19211 str_dst = MemFree (str_dst);
19212 }
19213
19214 if (sp->also_mrna && change_made)
19215 {
19216 CopyProteinNameTomRNAName (cdsp);
19217 }
19218 }
19219
CDSGeneProtEdit(CDSetPtr cdsp,CDSGeneProtAECRPtr sp,FilterSetPtr fsp,ExistingTextPtr etp)19220 static void CDSGeneProtEdit
19221 (CDSetPtr cdsp,
19222 CDSGeneProtAECRPtr sp,
19223 FilterSetPtr fsp,
19224 ExistingTextPtr etp)
19225 {
19226 ApplyValueData avd;
19227
19228 avd.where_to_replace = EditApplyFindLocation_anywhere;
19229
19230 avd.field_list = sp->field_list;
19231 avd.etp = NULL;
19232 AddEditApplyDataToApplyValue (AECR_EDIT, sp->edit_apply, &avd);
19233 SetCDSetField (cdsp, sp->field_list, &avd, fsp);
19234 avd.text_to_replace = MemFree (avd.text_to_replace);
19235 avd.new_text = MemFree (avd.new_text);
19236 if (sp->also_mrna)
19237 {
19238 CopyProteinNameTomRNAName (cdsp);
19239 }
19240 }
19241
CollectCDSetList(Uint2 entityID,FilterSetPtr fsp)19242 static ValNodePtr CollectCDSetList (Uint2 entityID, FilterSetPtr fsp)
19243 {
19244 ValNodePtr cdset_list;
19245
19246 /* need to create a list of sets */
19247 cdset_list = BuildCDSet2List (entityID, fsp == NULL || fsp->cgp == NULL ? NULL : fsp->cgp);
19248
19249 return cdset_list;
19250 }
19251
19252
MarkAlreadyEditedGenes(CDSetPtr cdsp,ValNodePtr cdset_list)19253 static void MarkAlreadyEditedGenes (CDSetPtr cdsp, ValNodePtr cdset_list)
19254 {
19255 ValNodePtr gene_vnp, list_vnp, genecheck_vnp;
19256 CDSetPtr check_cdsp;
19257
19258 if (cdsp == NULL || cdset_list == NULL || cdsp->gene_list == NULL) return;
19259
19260 for (gene_vnp = cdsp->gene_list; gene_vnp != NULL; gene_vnp = gene_vnp->next)
19261 {
19262 if (gene_vnp->choice > 0) continue;
19263 for (list_vnp = cdset_list; list_vnp != NULL; list_vnp = list_vnp->next)
19264 {
19265 check_cdsp = (CDSetPtr) list_vnp->data.ptrvalue;
19266 if (check_cdsp != NULL)
19267 {
19268 for (genecheck_vnp = check_cdsp->gene_list; genecheck_vnp != NULL; genecheck_vnp = genecheck_vnp->next)
19269 {
19270 if (genecheck_vnp->data.ptrvalue == gene_vnp->data.ptrvalue)
19271 {
19272 genecheck_vnp->choice = 1;
19273 }
19274 }
19275 }
19276 }
19277 }
19278 }
19279
19280
CDSGeneProtAECRAction(Pointer userdata)19281 static Boolean CDSGeneProtAECRAction (Pointer userdata)
19282 {
19283 ApplyEditConvertRemovePtr ap;
19284 CDSGeneProtAECRPtr sp;
19285 Int4 action_choice;
19286 SeqEntryPtr sep;
19287 FilterSetPtr fsp;
19288 GetSamplePtr gsp = NULL;
19289 Boolean rval = TRUE;
19290 ValNodePtr cdset_list, cdset_vnp;
19291 ExistingTextPtr etp = NULL;
19292 Int4 num_missing;
19293 Boolean build_missing = FALSE;
19294 MsgAnswer ans;
19295
19296 ap = (ApplyEditConvertRemovePtr) userdata;
19297 if (ap == NULL)
19298 {
19299 return FALSE;
19300 }
19301
19302 WatchCursor ();
19303 Update ();
19304
19305 if (ap->crippled)
19306 {
19307 action_choice = ap->crippled_action;
19308 }
19309 else
19310 {
19311 action_choice = GetValue (ap->action_popup);
19312 }
19313 if (action_choice < 1 || action_choice > NUM_AECR)
19314 {
19315 return FALSE;
19316 }
19317 sp = (CDSGeneProtAECRPtr) DialogToPointer (ap->aecr_pages[action_choice - 1]);
19318
19319 sep = GetTopSeqEntryForEntityID (ap->input_entityID);
19320 if (sp->field_list == NULL
19321 || ((action_choice == AECR_CONVERT || action_choice == AECR_SWAP)
19322 && sp->field_list == NULL))
19323 {
19324 sp = CDSGeneProtAECRFree (sp);
19325 ArrowCursor ();
19326 Update ();
19327 return FALSE;
19328 }
19329
19330 fsp = (FilterSetPtr) DialogToPointer (ap->constraints);
19331
19332 /* need to create a list of sets */
19333 cdset_list = CollectCDSetList (ap->input_entityID, fsp);
19334
19335 /* find existing text and how to handle it */
19336 if (action_choice == AECR_CONVERT || action_choice == AECR_APPLY || action_choice == AECR_PARSE)
19337 {
19338 gsp = GetCDSGeneProtAECRSample (cdset_list, sp->field_list, sp->field_list_to, fsp);
19339 etp = GetExistingTextHandlerInfo (gsp == NULL ? 0 : gsp->num_found, FALSE);
19340 gsp = GetSampleFree (gsp);
19341 if (etp != NULL && etp->existing_text_choice == eExistingTextChoiceCancel)
19342 {
19343 rval = FALSE;
19344 }
19345 }
19346
19347 num_missing = CountMissingFeatures (cdset_list, sp->field_list, sp->field_list_to, fsp);
19348 if (action_choice == AECR_SWAP)
19349 {
19350 num_missing += CountMissingFeatures (cdset_list, sp->field_list_to, sp->field_list, fsp);
19351 }
19352 if (num_missing > 0)
19353 {
19354 ans = Message (MSG_YNC, "There are %d fields where the feature to which the field should be applied does not exist. Do you want to create these features?", num_missing);
19355 if (ans == ANS_CANCEL)
19356 {
19357 rval = FALSE;
19358 } else if (ans == ANS_YES) {
19359 build_missing = TRUE;
19360 }
19361 }
19362
19363 if (rval)
19364 {
19365 /* if we are applying gene locus, we need to make sure every sequence has a gene
19366 * and we need to recollect the cdset_list
19367 */
19368 if ((action_choice == AECR_APPLY || action_choice == AECR_PARSE)
19369 && sp->field_list != NULL
19370 && sp->field_list->data.intvalue == 1 + GENEFIELD_LOCUS)
19371 {
19372 BuildNewGenes (sep, &cdset_list, LoneGeneOkWithFilter(fsp));
19373 }
19374
19375 for (cdset_vnp = cdset_list; cdset_vnp != NULL; cdset_vnp = cdset_vnp->next)
19376 {
19377 if (action_choice == AECR_CONVERT)
19378 {
19379 CDSGeneProtConvert (cdset_vnp->data.ptrvalue, sp, fsp, etp, build_missing);
19380 }
19381 else if (action_choice == AECR_SWAP)
19382 {
19383 CDSGeneProtSwap (cdset_vnp->data.ptrvalue, sp, fsp, etp, build_missing);
19384 }
19385 else if (action_choice == AECR_PARSE)
19386 {
19387 CDSGeneProtParse (cdset_vnp->data.ptrvalue, sp, fsp, etp, build_missing);
19388 }
19389 else if (action_choice == AECR_APPLY)
19390 {
19391 CDSGeneProtApplyToAllThatMatchFilter (sp->edit_apply->apply_txt, cdset_vnp->data.ptrvalue, sp->field_list, fsp, etp);
19392 }
19393 else if (action_choice == AECR_REMOVE)
19394 {
19395 sp->field_list->choice = 1;
19396 RemoveCDSetField (cdset_vnp->data.ptrvalue, sp->field_list, fsp);
19397 if (sp->also_mrna)
19398 {
19399 CopyProteinNameTomRNAName (cdset_vnp->data.ptrvalue);
19400 }
19401 }
19402 else if (action_choice == AECR_EDIT)
19403 {
19404 CDSGeneProtEdit (cdset_vnp->data.ptrvalue, sp, fsp, etp);
19405 }
19406 if (((action_choice == AECR_APPLY || action_choice == AECR_EDIT) && IsCDSetGeneQualChoice (sp->field_list))
19407 || ((action_choice == AECR_PARSE || action_choice == AECR_CONVERT) && IsCDSetGeneQualChoice (sp->field_list_to))
19408 || (action_choice == AECR_SWAP && (IsCDSetGeneQualChoice (sp->field_list) || IsCDSetGeneQualChoice (sp->field_list_to))))
19409 {
19410 MarkAlreadyEditedGenes (cdset_vnp->data.ptrvalue, cdset_vnp->next);
19411 }
19412 }
19413 }
19414 FilterSetFree (fsp);
19415 sp = CDSGeneProtAECRFree (sp);
19416 FreeCDSetList (cdset_list);
19417
19418 if (rval)
19419 {
19420 ObjMgrSetDirtyFlag (ap->input_entityID, TRUE);
19421 ObjMgrSendMsg (OM_MSG_UPDATE, ap->input_entityID, 0, 0);
19422 }
19423 ArrowCursor ();
19424 Update ();
19425
19426 return rval;
19427
19428 }
19429
19430 static void
CDSGeneProtApplyEditConvertRemove(IteM i,Int4 first_action_choice,Boolean crippled)19431 CDSGeneProtApplyEditConvertRemove
19432 (IteM i,
19433 Int4 first_action_choice,
19434 Boolean crippled)
19435 {
19436 ApplyEditConvertRemoveCombo (i, first_action_choice, crippled,
19437 "CDS-Gene-Prot-mRNA",
19438 CDSGeneProtAECRDialog,
19439 TRUE, GetCDSGeneProtSample,
19440 FALSE, FALSE, FALSE, TRUE, FALSE, NULL,
19441 CDSGeneProtAECRAction, NULL, NULL,
19442 CheckFeaturesForPresample);
19443 }
19444
ApplyCDSGeneProt(IteM i)19445 extern void ApplyCDSGeneProt (IteM i)
19446 {
19447 CDSGeneProtApplyEditConvertRemove (i, AECR_APPLY, FALSE);
19448 }
19449
PublicApplyCDSGeneProt(IteM i)19450 extern void PublicApplyCDSGeneProt (IteM i)
19451 {
19452 CDSGeneProtApplyEditConvertRemove (i, AECR_APPLY, TRUE);
19453 }
19454
EditCDSGeneProt(IteM i)19455 extern void EditCDSGeneProt (IteM i)
19456 {
19457 CDSGeneProtApplyEditConvertRemove (i, AECR_EDIT, FALSE);
19458 }
19459
PublicEditCDSGeneProt(IteM i)19460 extern void PublicEditCDSGeneProt (IteM i)
19461 {
19462 CDSGeneProtApplyEditConvertRemove (i, AECR_EDIT, TRUE);
19463 }
19464
ConvertCDSGeneProt(IteM i)19465 extern void ConvertCDSGeneProt (IteM i)
19466 {
19467 CDSGeneProtApplyEditConvertRemove (i, AECR_CONVERT, FALSE);
19468 }
19469
SwapCDSGeneProt(IteM i)19470 extern void SwapCDSGeneProt (IteM i)
19471 {
19472 CDSGeneProtApplyEditConvertRemove (i, AECR_SWAP, FALSE);
19473 }
19474
RemoveCDSGeneProt(IteM i)19475 extern void RemoveCDSGeneProt (IteM i)
19476 {
19477 CDSGeneProtApplyEditConvertRemove (i, AECR_REMOVE, FALSE);
19478 }
19479
19480 #define QUALKIND_SOURCE_QUAL 1
19481 #define QUALKIND_STRINGS 2
19482 #define QUALKIND_LOCATION 3
19483 #define QUALKIND_ORIGIN 4
19484
19485 typedef struct sourcequalaecrdata
19486 {
19487 Int4 qual_kind;
19488 SimpleAECRPtr source_qual;
19489 SimpleAECRPtr location;
19490 SimpleAECRPtr origin;
19491 SimpleAECRPtr strings;
19492
19493 TaxnameOptionsPtr taxname_options;
19494 } SourceQualAECRData, PNTR SourceQualAECRPtr;
19495
SourceQualAECRFree(SourceQualAECRPtr sp)19496 static SourceQualAECRPtr SourceQualAECRFree (SourceQualAECRPtr sp)
19497 {
19498 if (sp != NULL)
19499 {
19500 sp->source_qual = SimpleAECRFree (sp->source_qual);
19501 sp->taxname_options = MemFree (sp->taxname_options);
19502 sp = MemFree (sp);
19503 }
19504 return sp;
19505 }
19506
19507 typedef struct sourcequalaecrdlg
19508 {
19509 DIALOG_MESSAGE_BLOCK
19510 GrouP qual_kind;
19511
19512 DialoG source_qual;
19513 DialoG location;
19514 DialoG origin;
19515 DialoG strings;
19516
19517 DialoG taxname_options;
19518
19519 Int4 action_choice;
19520 Nlm_ChangeNotifyProc change_notify;
19521 Pointer change_userdata;
19522
19523 } SourceQualAECRDlgData, PNTR SourceQualAECRDlgPtr;
19524
19525
AreTaxNameOptionsRelevant(Int4 action_choice,SimpleAECRPtr sp)19526 static Boolean AreTaxNameOptionsRelevant (Int4 action_choice, SimpleAECRPtr sp)
19527 {
19528 Boolean relevant = FALSE;
19529 if (sp == NULL) return FALSE;
19530
19531 switch (action_choice)
19532 {
19533 case AECR_APPLY:
19534 case AECR_EDIT:
19535 case AECR_REMOVE:
19536 if (sp->field_list != NULL && sp->field_list->choice == 1)
19537 {
19538 relevant = TRUE;
19539 }
19540 break;
19541 case AECR_SWAP:
19542 if ((sp->field_list != NULL && sp->field_list->choice == 1)
19543 || (sp->field_list_to != NULL && sp->field_list_to->choice == 1))
19544 {
19545 relevant = TRUE;
19546 }
19547 break;
19548 case AECR_CONVERT:
19549 if ((sp->field_list != NULL && sp->field_list->choice == 1 && !sp->leave_on_original)
19550 || (sp->field_list_to != NULL && sp->field_list_to->choice == 1))
19551 {
19552 relevant = TRUE;
19553 }
19554 break;
19555 case AECR_PARSE:
19556 if ((sp->field_list != NULL && sp->field_list->choice == 1 && sp->remove_parsed)
19557 || (sp->field_list_to != NULL && sp->field_list_to->choice == 1))
19558 {
19559 relevant = TRUE;
19560 }
19561 break;
19562 default:
19563 relevant = FALSE;
19564 break;
19565 }
19566 return relevant;
19567 }
19568
ChangeQualKind(GrouP g)19569 static void ChangeQualKind (GrouP g)
19570 {
19571 SourceQualAECRDlgPtr dlg;
19572 Int4 qual_kind;
19573 SimpleAECRPtr sp;
19574
19575 dlg = (SourceQualAECRDlgPtr) GetObjectExtra (g);
19576 if (dlg == NULL)
19577 {
19578 return;
19579 }
19580
19581 Hide (dlg->source_qual);
19582 Hide (dlg->location);
19583 Hide (dlg->origin);
19584 Hide (dlg->strings);
19585 Hide (dlg->taxname_options);
19586 qual_kind = GetValue (dlg->qual_kind);
19587 switch (qual_kind)
19588 {
19589 case QUALKIND_SOURCE_QUAL :
19590 Show (dlg->source_qual);
19591 break;
19592 case QUALKIND_LOCATION :
19593 Show (dlg->location);
19594 break;
19595 case QUALKIND_ORIGIN :
19596 Show (dlg->origin);
19597 break;
19598 case QUALKIND_STRINGS :
19599 Show (dlg->strings);
19600 Show (dlg->taxname_options);
19601 sp = DialogToPointer (dlg->strings);
19602 if (AreTaxNameOptionsRelevant (dlg->action_choice, sp))
19603 {
19604 Enable (dlg->taxname_options);
19605 }
19606 else
19607 {
19608 Disable (dlg->taxname_options);
19609 }
19610 sp = SimpleAECRFree (sp);
19611 break;
19612 }
19613 if (dlg->change_notify != NULL)
19614 {
19615 (dlg->change_notify)(dlg->change_userdata);
19616 }
19617 }
19618
ResetSourceQualAECRDlg(SourceQualAECRDlgPtr dlg)19619 static void ResetSourceQualAECRDlg (SourceQualAECRDlgPtr dlg)
19620 {
19621 if (dlg == NULL)
19622 {
19623 return;
19624 }
19625
19626 PointerToDialog (dlg->source_qual, NULL);
19627 PointerToDialog (dlg->location, NULL);
19628 PointerToDialog (dlg->origin, NULL);
19629 PointerToDialog (dlg->strings, NULL);
19630 ChangeQualKind (dlg->qual_kind);
19631 PointerToDialog (dlg->taxname_options, NULL);
19632 }
19633
ClearTextSourceQualAECRDlg(SourceQualAECRDlgPtr dlg)19634 static void ClearTextSourceQualAECRDlg (SourceQualAECRDlgPtr dlg)
19635 {
19636 if (dlg == NULL)
19637 {
19638 return;
19639 }
19640 SendMessageToDialog (dlg->source_qual, AECR_VIB_MSG_CLEAR_TEXT);
19641 SendMessageToDialog (dlg->location, AECR_VIB_MSG_CLEAR_TEXT);
19642 SendMessageToDialog (dlg->origin, AECR_VIB_MSG_CLEAR_TEXT);
19643 SendMessageToDialog (dlg->strings, AECR_VIB_MSG_CLEAR_TEXT);
19644 }
19645
SourceQualAECRToDialog(DialoG d,Pointer userdata)19646 static void SourceQualAECRToDialog (DialoG d, Pointer userdata)
19647 {
19648 SourceQualAECRDlgPtr dlg;
19649 SourceQualAECRPtr data;
19650
19651 dlg = (SourceQualAECRDlgPtr) GetObjectExtra (d);
19652 if (dlg == NULL)
19653 {
19654 return;
19655 }
19656
19657 ResetSourceQualAECRDlg (dlg);
19658
19659 data = (SourceQualAECRPtr) userdata;
19660 if (data == NULL)
19661 {
19662 return;
19663 }
19664 PointerToDialog (dlg->source_qual, data->source_qual);
19665 PointerToDialog (dlg->location, data->location);
19666 PointerToDialog (dlg->origin, data->origin);
19667 PointerToDialog (dlg->strings, data->strings);
19668
19669 if (data->qual_kind < QUALKIND_SOURCE_QUAL)
19670 {
19671 SetValue (dlg->qual_kind, QUALKIND_SOURCE_QUAL);
19672 }
19673 else if (data->qual_kind > QUALKIND_STRINGS
19674 && (dlg->action_choice == AECR_EDIT || dlg->action_choice == AECR_SWAP))
19675 {
19676 SetValue (dlg->qual_kind, QUALKIND_STRINGS);
19677 PointerToDialog (dlg->taxname_options, data->taxname_options);
19678 }
19679 else if (data->qual_kind > QUALKIND_ORIGIN)
19680 {
19681 SetValue (dlg->qual_kind, QUALKIND_ORIGIN);
19682 }
19683 else
19684 {
19685 SetValue (dlg->qual_kind, data->qual_kind);
19686 }
19687 ChangeQualKind (dlg->qual_kind);
19688 }
19689
DialogToSourceQualAECR(DialoG d)19690 static Pointer DialogToSourceQualAECR (DialoG d)
19691 {
19692 SourceQualAECRDlgPtr dlg;
19693 SourceQualAECRPtr data;
19694
19695 dlg = (SourceQualAECRDlgPtr) GetObjectExtra (d);
19696 if (dlg == NULL)
19697 {
19698 return NULL;
19699 }
19700
19701 data = (SourceQualAECRPtr) MemNew (sizeof (SourceQualAECRData));
19702 if (data != NULL)
19703 {
19704 data->taxname_options = NULL;
19705 data->qual_kind = GetValue (dlg->qual_kind);
19706 switch (data->qual_kind)
19707 {
19708 case QUALKIND_SOURCE_QUAL :
19709 data->source_qual = DialogToPointer (dlg->source_qual);
19710 break;
19711 case QUALKIND_LOCATION :
19712 data->location = DialogToPointer (dlg->location);
19713 break;
19714 case QUALKIND_ORIGIN :
19715 data->origin = DialogToPointer (dlg->origin);
19716 break;
19717 case QUALKIND_STRINGS :
19718 data->strings = DialogToPointer (dlg->strings);
19719 if (AreTaxNameOptionsRelevant (dlg->action_choice, data->strings))
19720 {
19721 data->taxname_options = DialogToPointer (dlg->taxname_options);
19722 }
19723 break;
19724 }
19725
19726 }
19727 return data;
19728 }
19729
SourceQualAECRMessage(DialoG d,Int2 mssg)19730 static void SourceQualAECRMessage (DialoG d, Int2 mssg)
19731
19732 {
19733 SourceQualAECRDlgPtr dlg;
19734
19735 dlg = (SourceQualAECRDlgPtr) GetObjectExtra (d);
19736 if (dlg != NULL) {
19737 switch (mssg)
19738 {
19739 case VIB_MSG_INIT :
19740 /* reset list */
19741 ResetSourceQualAECRDlg (dlg);
19742 break;
19743 case VIB_MSG_ENTER :
19744 Select (dlg->qual_kind);
19745 break;
19746 case AECR_VIB_MSG_SET_DEFAULT :
19747 SetValue (dlg->qual_kind, QUALKIND_SOURCE_QUAL);
19748 SendMessageToDialog (dlg->source_qual, AECR_VIB_MSG_SET_DEFAULT);
19749 SendMessageToDialog (dlg->location, AECR_VIB_MSG_SET_DEFAULT);
19750 SendMessageToDialog (dlg->origin, AECR_VIB_MSG_SET_DEFAULT);
19751 SendMessageToDialog (dlg->strings, AECR_VIB_MSG_SET_DEFAULT);
19752 PointerToDialog (dlg->taxname_options, NULL);
19753 ChangeQualKind (dlg->qual_kind);
19754 break;
19755 case AECR_VIB_MSG_CLEAR_TEXT :
19756 ClearTextSourceQualAECRDlg (dlg);
19757 break;
19758 default :
19759 break;
19760 }
19761 }
19762 }
19763
TestSourceQualAECR(DialoG d)19764 static ValNodePtr TestSourceQualAECR (DialoG d)
19765 {
19766 SourceQualAECRDlgPtr dlg;
19767 ValNodePtr total_err_list = NULL;
19768 Int4 qual_kind;
19769
19770 dlg = (SourceQualAECRDlgPtr) GetObjectExtra (d);
19771 if (dlg == NULL)
19772 {
19773 return FALSE;
19774 }
19775
19776 qual_kind = GetValue (dlg->qual_kind);
19777 switch (qual_kind)
19778 {
19779 case QUALKIND_SOURCE_QUAL :
19780 total_err_list = TestDialog (dlg->source_qual);
19781 break;
19782 case QUALKIND_LOCATION :
19783 total_err_list = TestDialog (dlg->location);
19784 break;
19785 case QUALKIND_ORIGIN :
19786 total_err_list = TestDialog (dlg->origin);
19787 break;
19788 case QUALKIND_STRINGS :
19789 total_err_list = TestDialog (dlg->strings);
19790 break;
19791 default:
19792 ValNodeAddPointer (&total_err_list, 0, "qual kind");
19793 break;
19794 }
19795 return total_err_list;
19796 }
19797
19798 typedef struct applysourcequaldlg
19799 {
19800 DIALOG_MESSAGE_BLOCK
19801 DialoG field_list;
19802 DialoG edit_apply;
19803 PopuP true_false;
19804 Nlm_ChangeNotifyProc change_notify;
19805 Pointer change_userdata;
19806 Uint2 entityID;
19807
19808 } ApplySourceQualDlgData, PNTR ApplySourceQualDlgPtr;
19809
SourceQualChangeNotify(Pointer userdata)19810 static void SourceQualChangeNotify (Pointer userdata)
19811 {
19812 ApplySourceQualDlgPtr dlg;
19813 ValNodePtr vnp;
19814 SourceQualDescPtr sqdp;
19815
19816 dlg = (ApplySourceQualDlgPtr) userdata;
19817 if (dlg == NULL)
19818 {
19819 return;
19820 }
19821
19822 vnp = (ValNodePtr) DialogToPointer (dlg->field_list);
19823 if (vnp == NULL || vnp->data.ptrvalue == NULL)
19824 {
19825 Hide (dlg->edit_apply);
19826 Hide (dlg->true_false);
19827 }
19828 else
19829 {
19830 sqdp = (SourceQualDescPtr) vnp->data.ptrvalue;
19831 if (IsNonTextModifier (sqdp->name))
19832 {
19833 Hide (dlg->true_false);
19834 Hide (dlg->edit_apply);
19835 }
19836 else
19837 {
19838 Show (dlg->edit_apply);
19839 Hide (dlg->true_false);
19840 }
19841 }
19842 vnp = ValNodeFreeData (vnp);
19843
19844 if (dlg->change_notify != NULL)
19845 {
19846 (dlg->change_notify) (dlg->change_userdata);
19847 }
19848 }
19849
ClearTextApplySourceQualDialog(ApplySourceQualDlgPtr dlg)19850 static void ClearTextApplySourceQualDialog (ApplySourceQualDlgPtr dlg)
19851 {
19852 if (dlg != NULL)
19853 {
19854 PointerToDialog (dlg->edit_apply, NULL);
19855 }
19856 }
19857
ResetApplySourceQualDialog(ApplySourceQualDlgPtr dlg)19858 static void ResetApplySourceQualDialog (ApplySourceQualDlgPtr dlg)
19859 {
19860 if (dlg == NULL)
19861 {
19862 return;
19863 }
19864 PointerToDialog (dlg->field_list, NULL);
19865 PointerToDialog (dlg->edit_apply, NULL);
19866 SetValue (dlg->true_false, 1);
19867 SourceQualChangeNotify (dlg);
19868 }
19869
ApplySourceQualToDialog(DialoG d,Pointer data)19870 static void ApplySourceQualToDialog (DialoG d, Pointer data)
19871 {
19872 ApplySourceQualDlgPtr dlg;
19873 SimpleAECRPtr sap;
19874 SourceQualDescPtr sqdp;
19875
19876 dlg = (ApplySourceQualDlgPtr) GetObjectExtra (d);
19877 if (dlg == NULL)
19878 {
19879 return;
19880 }
19881 ResetApplySourceQualDialog (dlg);
19882
19883 sap = (SimpleAECRPtr) data;
19884 if (sap != NULL)
19885 {
19886 PointerToDialog (dlg->field_list, sap->field_list);
19887
19888 if (sap->field_list != NULL && sap->field_list->data.ptrvalue != NULL)
19889 {
19890 sqdp = (SourceQualDescPtr) sap->field_list->data.ptrvalue;
19891 if (IsNonTextModifier (sqdp->name))
19892 {
19893 if (sap->edit_apply == NULL
19894 || StringHasNoText (sap->edit_apply->apply_txt))
19895 {
19896 SetValue (dlg->true_false, 2);
19897 }
19898 else
19899 {
19900 SetValue (dlg->true_false, 1);
19901 }
19902 }
19903 else
19904 {
19905 PointerToDialog (dlg->edit_apply, sap->edit_apply);
19906 }
19907 }
19908 }
19909 SourceQualChangeNotify (dlg);
19910 }
19911
DialogToApplySourceQual(DialoG d)19912 static Pointer DialogToApplySourceQual (DialoG d)
19913 {
19914 ApplySourceQualDlgPtr dlg;
19915 SimpleAECRPtr sap;
19916 SourceQualDescPtr sqdp;
19917
19918 dlg = (ApplySourceQualDlgPtr) GetObjectExtra (d);
19919 if (dlg == NULL)
19920 {
19921 return NULL;
19922 }
19923
19924 sap = (SimpleAECRPtr) MemNew (sizeof (SimpleAECRData));
19925 if (sap == NULL)
19926 {
19927 return NULL;
19928 }
19929 sap->field_list = DialogToPointer (dlg->field_list);
19930 sap->edit_apply = DialogToPointer (dlg->edit_apply);
19931 if (sap->field_list != NULL && sap->field_list->data.ptrvalue != NULL)
19932 {
19933 sqdp = (SourceQualDescPtr) sap->field_list->data.ptrvalue;
19934 if (IsNonTextModifier (sqdp->name))
19935 {
19936 sap->edit_apply->apply_txt = MemFree (sap->edit_apply->apply_txt);
19937 if (GetValue (dlg->true_false) == 1)
19938 {
19939 sap->edit_apply->apply_txt = StringSave ("TRUE");
19940 }
19941 }
19942 }
19943
19944 sap->free_field_vn_proc = ValNodeSimpleDataFree;
19945 sap->free_subtype_vn_proc = NULL;
19946 return sap;
19947 }
19948
ApplySourceQualMessage(DialoG d,Int2 mssg)19949 static void ApplySourceQualMessage (DialoG d, Int2 mssg)
19950
19951 {
19952 ApplySourceQualDlgPtr dlg;
19953
19954 dlg = (ApplySourceQualDlgPtr) GetObjectExtra (d);
19955 if (dlg != NULL) {
19956 switch (mssg)
19957 {
19958 case VIB_MSG_INIT :
19959 /* reset list */
19960 ResetApplySourceQualDialog (dlg);
19961 break;
19962 case VIB_MSG_ENTER :
19963 Select (dlg->field_list);
19964 break;
19965 case AECR_VIB_MSG_SET_DEFAULT :
19966 SendMessageToDialog (dlg->field_list, AECR_VIB_MSG_SET_DEFAULT);
19967 ClearTextApplySourceQualDialog (dlg);
19968 break;
19969 case AECR_VIB_MSG_CLEAR_TEXT :
19970 ClearTextApplySourceQualDialog (dlg);
19971 break;
19972 case AECR_VIB_MSG_AUTOPOPULATE:
19973 SourceQualChangeNotify (dlg);
19974 break;
19975 default :
19976 break;
19977 }
19978 }
19979 }
19980
TestApplySourceQual(DialoG d)19981 static ValNodePtr TestApplySourceQual (DialoG d)
19982 {
19983 ApplySourceQualDlgPtr dlg;
19984 ValNodePtr err_list = NULL;
19985 ValNodePtr total_err_list = NULL;
19986 ValNodePtr field_list;
19987 SourceQualDescPtr sqdp;
19988
19989 dlg = (ApplySourceQualDlgPtr) GetObjectExtra (d);
19990 if (dlg == NULL)
19991 {
19992 return NULL;
19993 }
19994
19995 err_list = TestDialog (dlg->field_list);
19996 total_err_list = ValNodeAppend (total_err_list, err_list);
19997
19998 field_list = DialogToPointer (dlg->field_list);
19999 if (field_list != NULL && field_list->data.ptrvalue != NULL)
20000 {
20001 sqdp = (SourceQualDescPtr) field_list->data.ptrvalue;
20002 if (IsNonTextModifier (sqdp->name))
20003 {
20004 /* any true or false value is valid */
20005 }
20006 else
20007 {
20008 err_list = TestDialog (dlg->edit_apply);
20009 total_err_list = ValNodeAppend (total_err_list, err_list);
20010 }
20011 }
20012 field_list = ValNodeFreeData (field_list);
20013
20014 return total_err_list;
20015 }
20016
ApplySourceQualDialog(GrouP h,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata,Uint2 entityID)20017 static DialoG ApplySourceQualDialog
20018 (GrouP h,
20019 Nlm_ChangeNotifyProc change_notify,
20020 Pointer change_userdata,
20021 Uint2 entityID)
20022 {
20023 ApplySourceQualDlgPtr dlg;
20024 GrouP p, g1, g2;
20025
20026 dlg = (ApplySourceQualDlgPtr) MemNew (sizeof (ApplySourceQualDlgData));
20027 if (dlg == NULL)
20028 {
20029 return NULL;
20030 }
20031
20032 p = HiddenGroup (h, -1, 0, NULL);
20033 SetObjectExtra (p, dlg, StdCleanupExtraProc);
20034 SetGroupSpacing (p, 10, 10);
20035
20036 dlg->dialog = (DialoG) p;
20037 dlg->todialog = ApplySourceQualToDialog;
20038 dlg->fromdialog = DialogToApplySourceQual;
20039 dlg->dialogmessage = ApplySourceQualMessage;
20040 dlg->testdialog = TestApplySourceQual;
20041 dlg->change_notify = change_notify;
20042 dlg->change_userdata = change_userdata;
20043 dlg->entityID = entityID;
20044
20045 g1 = HiddenGroup (p, 1, 0, NULL);
20046 StaticPrompt (g1, "Qualifier", 0, dialogTextHeight, systemFont, 'l');
20047
20048 dlg->field_list = SourceQualTypeSelectionDialog (g1, FALSE,
20049 SourceQualChangeNotify,
20050 dlg);
20051
20052 g2 = HiddenGroup (p, 0, 0, NULL);
20053 dlg->edit_apply = EditApplyDialog (g2, eEditApplyChoice_Apply, "New Text", NULL,
20054 change_notify, change_userdata);
20055
20056 dlg->true_false = PopupList (g2, TRUE, NULL);
20057 PopupItem (dlg->true_false, "TRUE");
20058 PopupItem (dlg->true_false, "FALSE");
20059 SetValue (dlg->true_false, 1);
20060
20061 Hide (dlg->edit_apply);
20062 Hide (dlg->true_false);
20063
20064 AlignObjects (ALIGN_CENTER, (HANDLE) dlg->edit_apply, (HANDLE) dlg->true_false, NULL);
20065
20066 AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) g2, NULL);
20067
20068 SourceQualChangeNotify (dlg);
20069
20070 return (DialoG) p;
20071 }
20072
ConvertSourceQualDialog(GrouP h,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata,Uint2 entityID)20073 static DialoG ConvertSourceQualDialog
20074 (GrouP h,
20075 Nlm_ChangeNotifyProc change_notify,
20076 Pointer change_userdata,
20077 Uint2 entityID)
20078 {
20079 SimpleAECRDlgPtr dlg;
20080 GrouP p, g1;
20081
20082 dlg = (SimpleAECRDlgPtr) MemNew (sizeof (SimpleAECRDlgData));
20083 if (dlg == NULL)
20084 {
20085 return NULL;
20086 }
20087
20088 p = HiddenGroup (h, -1, 0, NULL);
20089 SetObjectExtra (p, dlg, StdCleanupExtraProc);
20090 SetGroupSpacing (p, 10, 10);
20091
20092 dlg->dialog = (DialoG) p;
20093 dlg->todialog = SimpleAECRToDialog;
20094 dlg->fromdialog = DialogToSimpleAECR;
20095 dlg->dialogmessage = SimpleAECRMessage;
20096 dlg->testdialog = TestSimpleAECR;
20097 dlg->action_choice = AECR_CONVERT;
20098 dlg->free_field_vn_proc = ValNodeSimpleDataFree;
20099 dlg->free_subtype_vn_proc = NULL;
20100 dlg->change_notify = change_notify;
20101 dlg->change_userdata = change_userdata;
20102 dlg->get_autopopulate_text = NULL;
20103 dlg->entityID = entityID;
20104
20105 dlg->subtype_list = NULL;
20106
20107 g1 = HiddenGroup (p, 2, 0, NULL);
20108 StaticPrompt (g1, "From", 0, dialogTextHeight, systemFont, 'l');
20109 StaticPrompt (g1, "To", 0, dialogTextHeight, systemFont, 'l');
20110
20111 dlg->field_list = SourceQualTypeDiscSelectionDialog (g1, FALSE,
20112 change_notify,
20113 change_userdata);
20114 dlg->field_list_to = SourceQualTypeSelectionDialog (g1, FALSE,
20115 change_notify,
20116 change_userdata);
20117 dlg->leave_on_original = CheckBox (p, "Leave on original", NULL);
20118 dlg->strip_name_from_text = CheckBox (p, "Strip name from text", NULL);
20119
20120 dlg->edit_apply = NULL;
20121
20122 AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) dlg->leave_on_original, (HANDLE) dlg->strip_name_from_text, NULL);
20123 return (DialoG) p;
20124 }
20125
20126
ConvertSourceLocationDialog(GrouP h,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata,Uint2 entityID)20127 static DialoG ConvertSourceLocationDialog
20128 (GrouP h,
20129 Nlm_ChangeNotifyProc change_notify,
20130 Pointer change_userdata,
20131 Uint2 entityID)
20132 {
20133 SimpleAECRDlgPtr dlg;
20134 GrouP p, g1;
20135
20136 dlg = (SimpleAECRDlgPtr) MemNew (sizeof (SimpleAECRDlgData));
20137 if (dlg == NULL)
20138 {
20139 return NULL;
20140 }
20141
20142 p = HiddenGroup (h, -1, 0, NULL);
20143 SetObjectExtra (p, dlg, StdCleanupExtraProc);
20144 SetGroupSpacing (p, 10, 10);
20145
20146 dlg->dialog = (DialoG) p;
20147 dlg->todialog = SimpleAECRToDialog;
20148 dlg->fromdialog = DialogToSimpleAECR;
20149 dlg->dialogmessage = SimpleAECRMessage;
20150 dlg->testdialog = TestSimpleAECR;
20151 dlg->action_choice = AECR_CONVERT;
20152 dlg->free_field_vn_proc = ValNodeSimpleDataFree;
20153 dlg->free_subtype_vn_proc = NULL;
20154 dlg->change_notify = change_notify;
20155 dlg->change_userdata = change_userdata;
20156 dlg->get_autopopulate_text = NULL;
20157 dlg->entityID = entityID;
20158
20159 dlg->subtype_list = NULL;
20160
20161 g1 = HiddenGroup (p, 2, 0, NULL);
20162 StaticPrompt (g1, "From", 0, dialogTextHeight, systemFont, 'l');
20163 StaticPrompt (g1, "To", 0, dialogTextHeight, systemFont, 'l');
20164
20165 dlg->field_list = SourceLocationDiscSelectionDialog (g1, FALSE,
20166 change_notify,
20167 change_userdata);
20168 dlg->field_list_to = SourceLocationSelectionDialog (g1, FALSE,
20169 change_notify,
20170 change_userdata);
20171 dlg->leave_on_original = CheckBox (p, "Leave on original", NULL);
20172
20173 dlg->edit_apply = NULL;
20174
20175 AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) dlg->leave_on_original, NULL);
20176 return (DialoG) p;
20177 }
20178
20179
ChangeTaxonomyStrings(Pointer data)20180 static void ChangeTaxonomyStrings (Pointer data)
20181 {
20182 SourceQualAECRDlgPtr dlg;
20183 SimpleAECRPtr sp;
20184
20185 dlg = (SourceQualAECRDlgPtr) data;
20186 if (dlg == NULL) return;
20187
20188 if (GetValue (dlg->qual_kind) == QUALKIND_STRINGS)
20189 {
20190 sp = DialogToPointer (dlg->strings);
20191 if (AreTaxNameOptionsRelevant (dlg->action_choice, sp))
20192 {
20193 Enable (dlg->taxname_options);
20194 }
20195 else
20196 {
20197 Disable (dlg->taxname_options);
20198 }
20199 sp = SimpleAECRFree (sp);
20200 }
20201 if (dlg->change_notify != NULL)
20202 {
20203 (dlg->change_notify)(dlg->change_userdata);
20204 }
20205
20206 }
20207
SourceQualAECRDialog(GrouP h,Int4 action_choice,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata,Uint2 entityID)20208 static DialoG SourceQualAECRDialog
20209 (GrouP h,
20210 Int4 action_choice,
20211 Nlm_ChangeNotifyProc change_notify,
20212 Pointer change_userdata,
20213 Uint2 entityID)
20214 {
20215
20216 SourceQualAECRDlgPtr dlg;
20217 GrouP p, g1;
20218
20219 dlg = (SourceQualAECRDlgPtr) MemNew (sizeof (SourceQualAECRDlgData));
20220 if (dlg == NULL)
20221 {
20222 return NULL;
20223 }
20224
20225 p = HiddenGroup (h, -1, 0, NULL);
20226 SetObjectExtra (p, dlg, StdCleanupExtraProc);
20227 SetGroupSpacing (p, 10, 10);
20228
20229 dlg->dialog = (DialoG) p;
20230 dlg->todialog = SourceQualAECRToDialog;
20231 dlg->fromdialog = DialogToSourceQualAECR;
20232 dlg->dialogmessage = SourceQualAECRMessage;
20233 dlg->testdialog = TestSourceQualAECR;
20234 dlg->action_choice = action_choice;
20235 dlg->change_notify = change_notify;
20236 dlg->change_userdata = change_userdata;
20237
20238 dlg->qual_kind = HiddenGroup (p, 4, 0, ChangeQualKind);
20239 SetObjectExtra (dlg->qual_kind, dlg, NULL);
20240 RadioButton (dlg->qual_kind, "Qualifiers");
20241 RadioButton (dlg->qual_kind, "Taxonomy");
20242 if (action_choice != AECR_EDIT && action_choice != AECR_SWAP)
20243 {
20244 RadioButton (dlg->qual_kind, "Location");
20245 RadioButton (dlg->qual_kind, "Origin");
20246 }
20247 SetValue (dlg->qual_kind, QUALKIND_SOURCE_QUAL);
20248
20249 g1 = HiddenGroup (p, 0, 0, NULL);
20250 /* Source Qualifiers dialog */
20251 if (action_choice == AECR_APPLY)
20252 {
20253 dlg->source_qual = ApplySourceQualDialog (g1,
20254 change_notify,
20255 change_userdata,
20256 entityID);
20257 }
20258 else if (action_choice == AECR_REMOVE)
20259 {
20260 dlg->source_qual = SimpleAECRDialog (g1, action_choice,
20261 change_notify, change_userdata,
20262 ValNodeSimpleDataFree, NULL,
20263 SourceQualTypeDiscSelectionDialog, NULL, NULL,
20264 "Qualifier", NULL, TRUE, entityID);
20265 }
20266 else if (action_choice == AECR_CONVERT)
20267 {
20268 dlg->source_qual = ConvertSourceQualDialog (g1,
20269 change_notify,
20270 change_userdata,
20271 entityID);
20272 }
20273 else if (action_choice == AECR_SWAP)
20274 {
20275 dlg->source_qual = SimpleAECRDialogEx (g1, action_choice,
20276 change_notify, change_userdata,
20277 ValNodeSimpleDataFree, NULL,
20278 SourceQualTypeSelectionDialog, NULL, NULL,
20279 "Qualifier", NULL, TRUE, TRUE, entityID);
20280 }
20281 else
20282 {
20283 dlg->source_qual = SimpleAECRDialog (g1, action_choice,
20284 change_notify, change_userdata,
20285 ValNodeSimpleDataFree, NULL,
20286 SourceQualTypeSelectionDialog, NULL, NULL,
20287 "Qualifier", NULL, TRUE, entityID);
20288 }
20289
20290 /* Taxonomy Strings dialog */
20291 dlg->strings = SimpleAECRDialog (g1, action_choice, ChangeTaxonomyStrings, dlg,
20292 ValNodeSimpleDataFree, NULL,
20293 SourceStringSelectionDialog, NULL, NULL,
20294 "Taxonomy", NULL, TRUE, entityID);
20295
20296 if (action_choice != AECR_EDIT && action_choice != AECR_SWAP)
20297 {
20298 /* Location Dialog */
20299 if (action_choice == AECR_APPLY)
20300 {
20301 dlg->location = SimpleAECRDialog (g1, action_choice,
20302 change_notify, change_userdata,
20303 ValNodeSimpleDataFree, NULL,
20304 SourceLocationSelectionDialog, NULL,
20305 NULL, "Location", NULL, FALSE, entityID);
20306 }
20307 else if (action_choice == AECR_CONVERT)
20308 {
20309 dlg->location = ConvertSourceLocationDialog (g1,
20310 change_notify,
20311 change_userdata,
20312 entityID);
20313 }
20314 else
20315 {
20316 dlg->location = SimpleAECRDialog (g1, action_choice,
20317 change_notify, change_userdata,
20318 ValNodeSimpleDataFree, NULL,
20319 SourceLocationDiscSelectionDialog,
20320 NULL, NULL, "Location", NULL, FALSE,
20321 entityID);
20322 }
20323
20324 /* Origin Dialog */
20325 dlg->origin = SimpleAECRDialog (g1, action_choice, change_notify, change_userdata,
20326 ValNodeSimpleDataFree, NULL,
20327 SourceOriginSelectionDialog, NULL, NULL,
20328 "Origin", NULL, FALSE, entityID);
20329 }
20330
20331 dlg->taxname_options = TaxnameOptionsDialog (p, change_notify, change_userdata);
20332
20333 Disable (dlg->taxname_options);
20334
20335 AlignObjects (ALIGN_CENTER, (HANDLE) dlg->source_qual,
20336 (HANDLE) dlg->location,
20337 (HANDLE) dlg->origin,
20338 (HANDLE) dlg->strings,
20339 NULL);
20340
20341 AlignObjects (ALIGN_CENTER, (HANDLE) dlg->qual_kind,
20342 (HANDLE) g1,
20343 (HANDLE) dlg->taxname_options,
20344 NULL);
20345
20346 ChangeQualKind (dlg->qual_kind);
20347 return (DialoG) p;
20348 }
20349
20350
BioSourceHasMultipleQuals(BioSourcePtr biop,SourceQualDescPtr sqdp,FilterSetPtr fsp)20351 static Boolean BioSourceHasMultipleQuals (BioSourcePtr biop, SourceQualDescPtr sqdp, FilterSetPtr fsp)
20352 {
20353 OrgModPtr mod;
20354 SubSourcePtr ssp;
20355 Boolean found_one = FALSE;
20356
20357 if (biop == NULL || sqdp == NULL) return FALSE;
20358
20359 if (sqdp->isOrgMod)
20360 {
20361 if (biop->org != NULL && biop->org->orgname != NULL)
20362 {
20363 mod = biop->org->orgname->mod;
20364 while (mod != NULL)
20365 {
20366 if (mod->subtype == sqdp->subtype
20367 && !StringHasNoText (mod->subname)
20368 && OrgModSpecialMatch (mod, fsp))
20369 {
20370 if (found_one) {
20371 return TRUE;
20372 } else {
20373 found_one = TRUE;
20374 }
20375 }
20376 mod = mod->next;
20377 }
20378 }
20379 }
20380 else
20381 {
20382 ssp = biop->subtype;
20383 while (ssp != NULL)
20384 {
20385 if (ssp->subtype == sqdp->subtype
20386 && !StringHasNoText (ssp->name)
20387 && SubSrcSpecialMatch (ssp, fsp))
20388 {
20389 if (found_one) {
20390 return TRUE;
20391 } else {
20392 found_one = TRUE;
20393 }
20394 }
20395 ssp = ssp->next;
20396 }
20397 }
20398 return FALSE;
20399 }
20400
CheckBioSrcListForMultipleQuals(ValNodePtr biosrc_list,SourceQualDescPtr sqdp,FilterSetPtr fsp)20401 static Boolean CheckBioSrcListForMultipleQuals (ValNodePtr biosrc_list, SourceQualDescPtr sqdp, FilterSetPtr fsp)
20402 {
20403 ValNodePtr vnp;
20404 SeqFeatPtr sfp;
20405 SeqDescrPtr sdp;
20406 Boolean has_multiple = FALSE;
20407
20408 if (sqdp == NULL) return FALSE;
20409
20410 for (vnp = biosrc_list; vnp != NULL && !has_multiple; vnp = vnp->next)
20411 {
20412 if (vnp->data.ptrvalue == NULL) continue;
20413 if (vnp->choice == OBJ_SEQFEAT)
20414 {
20415 sfp = (SeqFeatPtr) vnp->data.ptrvalue;
20416 if (sfp->data.choice == SEQFEAT_BIOSRC)
20417 {
20418 has_multiple = BioSourceHasMultipleQuals ((BioSourcePtr)sfp->data.value.ptrvalue, sqdp, fsp);
20419 }
20420 }
20421 else if (vnp->choice == OBJ_SEQDESC)
20422 {
20423 sdp = (SeqDescrPtr) vnp->data.ptrvalue;
20424 if (sdp->choice == Seq_descr_source)
20425 {
20426 has_multiple = BioSourceHasMultipleQuals ((BioSourcePtr)sdp->data.ptrvalue, sqdp, fsp);
20427 }
20428 }
20429 }
20430 return has_multiple;
20431 }
20432
20433
20434 typedef struct taxnameoptionsdlg
20435 {
20436 DIALOG_MESSAGE_BLOCK
20437 ButtoN remove_taxref;
20438 ButtoN remove_common;
20439 ButtoN remove_old_name;
20440 Nlm_ChangeNotifyProc change_notify;
20441 Pointer change_userdata;
20442 } TaxnameOptionsDlgData, PNTR TaxnameOptionsDlgPtr;
20443
TaxnameOptionsToDialog(DialoG d,Pointer data)20444 static void TaxnameOptionsToDialog (DialoG d, Pointer data)
20445 {
20446 TaxnameOptionsDlgPtr dlg;
20447 TaxnameOptionsPtr top;
20448
20449 dlg = (TaxnameOptionsDlgPtr) GetObjectExtra (d);
20450 if (dlg == NULL) return;
20451
20452 top = (TaxnameOptionsPtr) data;
20453 if (top == NULL)
20454 {
20455 SetStatus (dlg->remove_taxref, TRUE);
20456 SetStatus (dlg->remove_common, TRUE);
20457 SetStatus (dlg->remove_old_name, TRUE);
20458 }
20459 else
20460 {
20461 SetStatus (dlg->remove_taxref, top->remove_taxref);
20462 SetStatus (dlg->remove_common, top->remove_common);
20463 SetStatus (dlg->remove_old_name, top->remove_old_name);
20464 }
20465 if (dlg->change_notify != NULL)
20466 {
20467 (dlg->change_notify) (dlg->change_userdata);
20468 }
20469 }
20470
TaxnameOptionsFromDialog(DialoG d)20471 static Pointer TaxnameOptionsFromDialog (DialoG d)
20472 {
20473 TaxnameOptionsDlgPtr dlg;
20474 TaxnameOptionsPtr top;
20475
20476 dlg = (TaxnameOptionsDlgPtr) GetObjectExtra (d);
20477 if (dlg == NULL) return NULL;
20478
20479 top = (TaxnameOptionsPtr) MemNew (sizeof (TaxnameOptionsData));
20480 top->remove_taxref = GetStatus (dlg->remove_taxref);
20481 top->remove_common = GetStatus (dlg->remove_common);
20482 top->remove_old_name = GetStatus (dlg->remove_old_name);
20483 return top;
20484 }
20485
20486
ChangeTaxnameOptions(ButtoN b)20487 static void ChangeTaxnameOptions (ButtoN b)
20488 {
20489 TaxnameOptionsDlgPtr dlg;
20490
20491 dlg = (TaxnameOptionsDlgPtr) GetObjectExtra (b);
20492 if (dlg != NULL && dlg->change_notify != NULL)
20493 {
20494 (dlg->change_notify) (dlg->change_userdata);
20495 }
20496 }
20497
20498
TaxnameOptionsDialog(GrouP h,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)20499 extern DialoG TaxnameOptionsDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
20500 {
20501 TaxnameOptionsDlgPtr dlg;
20502 GrouP p;
20503
20504 dlg = (TaxnameOptionsDlgPtr) MemNew (sizeof (TaxnameOptionsDlgData));
20505 if (dlg == NULL)
20506 {
20507 return NULL;
20508 }
20509
20510 p = HiddenGroup (h, 3, 0, NULL);
20511 SetObjectExtra (p, dlg, StdCleanupExtraProc);
20512 SetGroupSpacing (p, 10, 10);
20513
20514 dlg->dialog = (DialoG) p;
20515 dlg->todialog = TaxnameOptionsToDialog;
20516 dlg->fromdialog = TaxnameOptionsFromDialog;
20517 dlg->change_notify = change_notify;
20518 dlg->change_userdata = change_userdata;
20519
20520 dlg->remove_taxref = CheckBox (p, "Remove taxonomy xref", ChangeTaxnameOptions);
20521 SetObjectExtra (dlg->remove_taxref, dlg, NULL);
20522 SetStatus (dlg->remove_taxref, TRUE);
20523 dlg->remove_common = CheckBox (p, "Remove GenBank common name", ChangeTaxnameOptions);
20524 SetObjectExtra (dlg->remove_common, dlg, NULL);
20525 SetStatus (dlg->remove_common, TRUE);
20526 dlg->remove_old_name = CheckBox (p, "Remove old_name qualifier", ChangeTaxnameOptions);
20527 SetObjectExtra (dlg->remove_old_name, dlg, NULL);
20528 SetStatus (dlg->remove_old_name, TRUE);
20529 return (DialoG) p;
20530 }
20531
ApplyTaxnameOptionsToBioSource(BioSourcePtr biop,TaxnameOptionsPtr top)20532 extern void ApplyTaxnameOptionsToBioSource (BioSourcePtr biop, TaxnameOptionsPtr top)
20533 {
20534 if (biop == NULL || top == NULL) return;
20535
20536 if (top->remove_taxref)
20537 {
20538 RemoveTaxRef (biop->org);
20539 }
20540 if (top->remove_old_name)
20541 {
20542 RemoveOldName (biop->org);
20543 }
20544 if (top->remove_common)
20545 {
20546 if (biop->org != NULL)
20547 {
20548 biop->org->common = MemFree (biop->org->common);
20549 }
20550 }
20551 }
20552
HandleTaxnameOptionsFeature(SeqFeatPtr sfp,TaxnameOptionsPtr top)20553 static void HandleTaxnameOptionsFeature (SeqFeatPtr sfp, TaxnameOptionsPtr top)
20554 {
20555 if (sfp == NULL || sfp->data.choice != SEQFEAT_BIOSRC || top == NULL)
20556 {
20557 return;
20558 }
20559 ApplyTaxnameOptionsToBioSource (sfp->data.value.ptrvalue, top);
20560 }
20561
HandleTaxnameOptionsDescriptorCallback(SeqDescrPtr sdp,TaxnameOptionsPtr top)20562 static void HandleTaxnameOptionsDescriptorCallback (SeqDescrPtr sdp, TaxnameOptionsPtr top)
20563 {
20564 if (sdp == NULL || sdp->choice != Seq_descr_source || top == NULL)
20565 {
20566 return;
20567 }
20568 ApplyTaxnameOptionsToBioSource (sdp->data.ptrvalue, top);
20569 }
20570
20571
HandleTaxnameOptionsForBioSourceList(ValNodePtr biosrc_list,TaxnameOptionsPtr top)20572 static void HandleTaxnameOptionsForBioSourceList (ValNodePtr biosrc_list, TaxnameOptionsPtr top)
20573 {
20574 ValNodePtr vnp;
20575
20576 if (top == NULL) return;
20577 for (vnp = biosrc_list; vnp != NULL; vnp = vnp->next)
20578 {
20579 if (vnp->choice == OBJ_SEQFEAT)
20580 {
20581 HandleTaxnameOptionsFeature (vnp->data.ptrvalue, top);
20582 }
20583 else if (vnp->choice == OBJ_SEQDESC)
20584 {
20585 HandleTaxnameOptionsDescriptorCallback (vnp->data.ptrvalue, top);
20586 }
20587 }
20588 }
20589
CollectBioSourceFeatureFieldCallback(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)20590 static void CollectBioSourceFeatureFieldCallback (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
20591 {
20592 if (sfp == NULL || userdata == NULL)
20593 {
20594 return;
20595 }
20596 ValNodeAddPointer ((ValNodePtr PNTR) userdata, OBJ_SEQFEAT, sfp);
20597 }
20598
CollectBioSourceDescriptorFieldCallback(SeqDescrPtr sdp,Pointer userdata,FilterSetPtr fsp)20599 static void CollectBioSourceDescriptorFieldCallback (SeqDescrPtr sdp, Pointer userdata, FilterSetPtr fsp)
20600 {
20601 if (sdp == NULL || userdata == NULL)
20602 {
20603 return;
20604 }
20605
20606 ValNodeAddPointer ((ValNodePtr PNTR) userdata, OBJ_SEQDESC, sdp);
20607 }
20608
20609
RemoveSourceQualEditNonMatches(ValNodePtr PNTR biosrc_list,ApplyValuePtr avp)20610 static void RemoveSourceQualEditNonMatches (ValNodePtr PNTR biosrc_list, ApplyValuePtr avp)
20611 {
20612 ValNodePtr vnp_prev = NULL, vnp_next, vnp_this;
20613 CharPtr val1, val2;
20614 Boolean do_remove;
20615
20616 if (biosrc_list == NULL || avp == NULL || StringHasNoText (avp->text_to_replace))
20617 {
20618 return;
20619 }
20620
20621 vnp_this = *biosrc_list;
20622 while (vnp_this != NULL)
20623 {
20624 vnp_next = vnp_this->next;
20625 do_remove = FALSE;
20626 if (vnp_this->choice == OBJ_SEQFEAT)
20627 {
20628 val1 = GetSourceQualFeatureString (vnp_this->data.ptrvalue, avp->field_list, NULL);
20629 }
20630 else if (vnp_this->choice == OBJ_SEQDESC)
20631 {
20632 val1 = GetSourceQualDescrString (vnp_this->data.ptrvalue, avp->field_list, NULL);
20633 }
20634 else
20635 {
20636 val1 = NULL;
20637 }
20638 if (val1 == NULL)
20639 {
20640 do_remove = TRUE;
20641 }
20642 else
20643 {
20644 val2 = HandleApplyValue (StringSave (val1), avp);
20645 if (StringCmp (val1, val2) == 0)
20646 {
20647 do_remove = TRUE;
20648 }
20649 val1 = MemFree (val1);
20650 val2 = MemFree (val2);
20651 }
20652 if (do_remove)
20653 {
20654 if (vnp_prev == NULL)
20655 {
20656 *biosrc_list = vnp_this->next;
20657 }
20658 else
20659 {
20660 vnp_prev->next = vnp_this->next;
20661 }
20662 vnp_this->next = NULL;
20663 vnp_this = ValNodeFree (vnp_this);
20664 }
20665 else
20666 {
20667 vnp_prev = vnp_this;
20668 }
20669 vnp_this = vnp_next;
20670 }
20671 }
20672
20673
20674 static Boolean
SourceQualQualApplyEditConvertRemoveAction(ApplyEditConvertRemovePtr ap,SimpleAECRPtr sp,Int4 action_choice,SetFeatureFieldString feature_apply_action,SetDescriptorFieldString descriptor_apply_action,RemoveFeatureFieldString feature_remove_action,RemoveDescriptorFieldString descriptor_remove_action,CopyValNodeDataProc copy_vn_proc,GetFeatureFieldString fieldstring_func,GetDescriptorFieldString descrstring_func,Boolean non_text,NameFromValNodeProc name_field_func,TaxnameOptionsPtr top)20675 SourceQualQualApplyEditConvertRemoveAction
20676 (ApplyEditConvertRemovePtr ap,
20677 SimpleAECRPtr sp,
20678 Int4 action_choice,
20679 SetFeatureFieldString feature_apply_action,
20680 SetDescriptorFieldString descriptor_apply_action,
20681 RemoveFeatureFieldString feature_remove_action,
20682 RemoveDescriptorFieldString descriptor_remove_action,
20683 CopyValNodeDataProc copy_vn_proc,
20684 GetFeatureFieldString fieldstring_func,
20685 GetDescriptorFieldString descrstring_func,
20686 Boolean non_text,
20687 NameFromValNodeProc name_field_func,
20688 TaxnameOptionsPtr top)
20689
20690 {
20691 SeqEntryPtr sep;
20692 ApplyValueData avd;
20693 ConvertFieldData cfd;
20694 FilterSetPtr fsp;
20695 GetSamplePtr gsp;
20696 Boolean rval = TRUE;
20697 ValNodePtr vnp;
20698 CharPtr field_name = NULL;
20699 MsgAnswer ans;
20700 ValNodePtr biosrc_list = NULL;
20701 SourceQualDescPtr multi_sqdp = NULL;
20702
20703 sep = GetTopSeqEntryForEntityID (ap->input_entityID);
20704 if (sp == NULL
20705 || sp->field_list == NULL
20706 || feature_apply_action == NULL
20707 || descriptor_apply_action == NULL
20708 || feature_remove_action == NULL
20709 || descriptor_remove_action == NULL
20710 || ((action_choice == AECR_CONVERT || action_choice == AECR_SWAP || action_choice == AECR_PARSE)
20711 && sp->field_list == NULL))
20712 {
20713 return FALSE;
20714 }
20715
20716 WatchCursor ();
20717 Update ();
20718
20719 avd.where_to_replace = EditApplyFindLocation_anywhere;
20720
20721 fsp = (FilterSetPtr) DialogToPointer (ap->constraints);
20722
20723 /* collect list of BioSources that will be acted upon */
20724 OperateOnSeqEntryConstrainedObjects (sep, fsp,
20725 CollectBioSourceFeatureFieldCallback,
20726 CollectBioSourceDescriptorFieldCallback,
20727 SEQFEAT_BIOSRC, 0, Seq_descr_source,
20728 &biosrc_list);
20729
20730 if (action_choice == AECR_CONVERT || action_choice == AECR_SWAP || action_choice == AECR_PARSE)
20731 {
20732 /* check for multiple sources */
20733 if ((sp->field_list->choice == 0
20734 && (multi_sqdp = sp->field_list->data.ptrvalue) != NULL
20735 && CheckBioSrcListForMultipleQuals(biosrc_list, multi_sqdp, fsp))
20736 || (action_choice == AECR_SWAP && sp->field_list_to->choice == 0
20737 && (multi_sqdp = sp->field_list_to->data.ptrvalue) != NULL
20738 && CheckBioSrcListForMultipleQuals(biosrc_list, multi_sqdp, fsp))) {
20739 if (name_field_func != NULL) {
20740 if (action_choice == AECR_SWAP && multi_sqdp == sp->field_list_to->data.ptrvalue) {
20741 field_name = name_field_func(sp->field_list_to);
20742 } else {
20743 field_name = name_field_func(sp->field_list);
20744 }
20745 }
20746 if (field_name != NULL) {
20747 ans = Message (MSG_OKC, "One or more BioSources has multiple source quals. These will be combined. Do you want to continue?");
20748 } else {
20749 ans = Message (MSG_OKC, "One or more BioSources has multiple %s source quals. These will be combined. Do you want to continue?", field_name);
20750 }
20751 field_name = MemFree (field_name);
20752 if (ans == ANS_CANCEL) {
20753 FilterSetFree (fsp);
20754 ArrowCursor();
20755 Update();
20756 return FALSE;
20757 }
20758 }
20759 cfd.src_field_list = sp->field_list;
20760 cfd.dst_field_list = sp->field_list_to;
20761 cfd.etp = NULL;
20762 cfd.get_str_func = fieldstring_func;
20763 cfd.set_str_func = feature_apply_action;
20764 cfd.remove_str_func = feature_remove_action;
20765 cfd.get_d_str_func = descrstring_func;
20766 cfd.set_d_str_func = descriptor_apply_action;
20767 cfd.remove_d_str_func = descriptor_remove_action;
20768 cfd.fsp = fsp;
20769 cfd.strip_name_from_text = sp->strip_name_from_text;
20770 cfd.remove_parsed = sp->remove_parsed;
20771 cfd.name_field_func = name_field_func;
20772 cfd.text_portion = sp->text_portion;
20773 if (action_choice == AECR_CONVERT)
20774 {
20775 if (sp->leave_on_original)
20776 {
20777 cfd.convert_type = CONVERT_TYPE_COPY;
20778 }
20779 else
20780 {
20781 cfd.convert_type = CONVERT_TYPE_MOVE;
20782 }
20783 }
20784 else if (action_choice == AECR_SWAP)
20785 {
20786 cfd.convert_type = CONVERT_TYPE_SWAP;
20787 }
20788 else if (action_choice == AECR_PARSE)
20789 {
20790 cfd.convert_type = CONVERT_TYPE_PARSE;
20791 }
20792 if ((cfd.convert_type == CONVERT_TYPE_MOVE || cfd.convert_type == CONVERT_TYPE_COPY || cfd.convert_type == CONVERT_TYPE_PARSE)
20793 && ! non_text)
20794 {
20795 gsp = CheckForConversionExistingTextInSeqEntry (sep, &cfd, fsp,
20796 SEQFEAT_BIOSRC, 0,
20797 Seq_descr_source);
20798 cfd.etp = GetExistingTextHandlerInfo (gsp == NULL ? 0 : gsp->num_found, non_text);
20799 gsp = GetSampleFree (gsp);
20800 if (cfd.etp != NULL && cfd.etp->existing_text_choice == eExistingTextChoiceCancel)
20801 {
20802 rval = FALSE;
20803 }
20804 }
20805 else
20806 {
20807 cfd.etp = NULL;
20808 }
20809
20810 if (rval)
20811 {
20812 if (non_text)
20813 {
20814 OperateOnSeqEntryConstrainedObjects (sep, fsp,
20815 ConvertNonTextFeatureFieldCallback,
20816 ConvertNonTextDescriptorFieldCallback,
20817 SEQFEAT_BIOSRC, 0, Seq_descr_source,
20818 &cfd);
20819 }
20820 else
20821 {
20822 OperateOnSeqEntryConstrainedObjects (sep, fsp,
20823 ConvertFeatureFieldCallback,
20824 ConvertDescriptorFieldCallback,
20825 SEQFEAT_BIOSRC, 0, Seq_descr_source,
20826 &cfd);
20827 }
20828
20829 }
20830 cfd.etp = MemFree (cfd.etp);
20831 }
20832 else
20833 {
20834 avd.field_list = sp->field_list;
20835
20836 /* get handling for existing text */
20837 if (action_choice == AECR_APPLY)
20838 {
20839 gsp = CheckForExistingText (ap->input_entityID,
20840 avd.field_list,
20841 fieldstring_func,
20842 descrstring_func,
20843 ValNodeSimpleDataFree,
20844 copy_vn_proc,
20845 fsp, SEQFEAT_BIOSRC, 0, Seq_descr_source);
20846 avd.etp = GetExistingTextHandlerInfo (gsp == NULL ? 0 : gsp->num_found, non_text);
20847 gsp = GetSampleFree (gsp);
20848
20849 if (avd.etp != NULL
20850 && avd.etp->existing_text_choice == eExistingTextChoiceCancel)
20851 {
20852 rval = FALSE;
20853 }
20854 }
20855 else
20856 {
20857 avd.etp = NULL;
20858 }
20859
20860 if (rval)
20861 {
20862 AddEditApplyDataToApplyValue (action_choice, sp->edit_apply, &avd);
20863
20864 if (action_choice == AECR_EDIT)
20865 {
20866 /* remove items that don't contain text that will be replaced */
20867 RemoveSourceQualEditNonMatches (&biosrc_list, &avd);
20868 }
20869
20870
20871 if (action_choice == AECR_EDIT || action_choice == AECR_APPLY)
20872 {
20873 OperateOnSeqEntryConstrainedObjects (sep, fsp,
20874 feature_apply_action,
20875 descriptor_apply_action,
20876 SEQFEAT_BIOSRC, 0, Seq_descr_source, &avd);
20877 }
20878 else if (action_choice == AECR_REMOVE)
20879 {
20880 for (vnp = sp->field_list; vnp != NULL; vnp = vnp->next)
20881 {
20882 avd.field_list = vnp;
20883 OperateOnSeqEntryConstrainedObjects (sep, fsp,
20884 feature_remove_action,
20885 descriptor_remove_action,
20886 SEQFEAT_BIOSRC, 0, Seq_descr_source, &avd);
20887 }
20888 }
20889
20890 avd.text_to_replace = MemFree (avd.text_to_replace);
20891 avd.new_text = MemFree (avd.new_text);
20892 }
20893 avd.etp = MemFree (avd.etp);
20894 }
20895
20896 FilterSetFree (fsp);
20897
20898 if (rval)
20899 {
20900 /* Handle taxname options */
20901 HandleTaxnameOptionsForBioSourceList (biosrc_list, top);
20902
20903 ObjMgrSetDirtyFlag (ap->input_entityID, TRUE);
20904 ObjMgrSendMsg (OM_MSG_UPDATE, ap->input_entityID, 0, 0);
20905 }
20906 biosrc_list = ValNodeFree (biosrc_list);
20907 ArrowCursor ();
20908 Update ();
20909
20910 return rval;
20911 }
20912
SourceQualApplyEditConvertRemoveAction(Pointer userdata)20913 static Boolean SourceQualApplyEditConvertRemoveAction (Pointer userdata)
20914 {
20915 ApplyEditConvertRemovePtr ap;
20916 SourceQualAECRPtr sp;
20917 Int4 action_choice;
20918 Boolean rval = FALSE;
20919
20920 ap = (ApplyEditConvertRemovePtr) userdata;
20921 if (ap == NULL)
20922 {
20923 return FALSE;
20924 }
20925
20926 if (ap->crippled)
20927 {
20928 action_choice = ap->crippled_action;
20929 }
20930 else
20931 {
20932 action_choice = GetValue (ap->action_popup);
20933 }
20934 if (action_choice < 1 || action_choice > NUM_AECR)
20935 {
20936 return FALSE;
20937 }
20938 sp = (SourceQualAECRPtr) DialogToPointer (ap->aecr_pages[action_choice - 1]);
20939
20940 switch (sp->qual_kind)
20941 {
20942 case QUALKIND_SOURCE_QUAL :
20943 rval = SourceQualQualApplyEditConvertRemoveAction (ap, sp->source_qual,
20944 action_choice,
20945 ApplySourceQualFeatureCallback,
20946 ApplySourceQualDescriptorCallback,
20947 RemoveSourceQualFromSourceFeature,
20948 RemoveSourceQualFromSourceDescriptor,
20949 SourceQualValNodeDataCopy,
20950 GetSourceQualFeatureString,
20951 GetSourceQualDescrString,
20952 FALSE,
20953 SourceQualValNodeName,
20954 NULL);
20955 break;
20956 case QUALKIND_STRINGS :
20957 rval = SourceQualQualApplyEditConvertRemoveAction (ap, sp->strings,
20958 action_choice,
20959 ApplyStringToSourceFeature,
20960 ApplyStringToSourceDescriptor,
20961 RemoveStringFromSourceFeature,
20962 RemoveStringFromSourceDescriptor,
20963 ValNodeStringCopy,
20964 GetStringFromSourceFeature,
20965 GetStringFromSourceDescriptor,
20966 FALSE,
20967 NULL,
20968 sp->taxname_options);
20969 break;
20970 case QUALKIND_LOCATION :
20971 rval = SourceQualQualApplyEditConvertRemoveAction (ap, sp->location,
20972 action_choice,
20973 ApplyLocationToSourceFeature,
20974 ApplyLocationToSourceDescriptor,
20975 RemoveLocationFromSourceFeature,
20976 RemoveLocationFromSourceDescriptor,
20977 ValNodeStringCopy,
20978 GetLocationFromSourceFeature,
20979 GetLocationFromSourceDescriptor,
20980 TRUE,
20981 ValNodeStringName,
20982 NULL);
20983 break;
20984 case QUALKIND_ORIGIN :
20985 rval = SourceQualQualApplyEditConvertRemoveAction (ap, sp->origin,
20986 action_choice,
20987 ApplyOriginToSourceFeature,
20988 ApplyOriginToSourceDescriptor,
20989 RemoveOriginFromSourceFeature,
20990 RemoveOriginFromSourceDescriptor,
20991 ValNodeStringCopy,
20992 GetOriginFromSourceFeature,
20993 GetOriginFromSourceDescriptor,
20994 TRUE,
20995 ValNodeStringName,
20996 NULL);
20997 break;
20998 }
20999 sp = SourceQualAECRFree (sp);
21000 return rval;
21001 }
21002
ChangeSourceQualAction(DialoG prev_page,DialoG new_page)21003 static void ChangeSourceQualAction (DialoG prev_page, DialoG new_page)
21004 {
21005 SourceQualAECRPtr prev_sp, new_sp;
21006
21007 if (prev_page == NULL || new_page == NULL)
21008 {
21009 return;
21010 }
21011
21012 prev_sp = (SourceQualAECRPtr) DialogToPointer (prev_page);
21013 new_sp = (SourceQualAECRPtr) DialogToPointer (new_page);
21014 if (prev_sp != NULL && new_sp != NULL)
21015 {
21016 new_sp->qual_kind = prev_sp->qual_kind;
21017 PointerToDialog (new_page, new_sp);
21018 }
21019 new_sp = SourceQualAECRFree (new_sp);
21020 prev_sp = SourceQualAECRFree (prev_sp);
21021 }
21022
GetSourceQualSample(GrouP h,Uint2 entityID)21023 static DialoG GetSourceQualSample (GrouP h, Uint2 entityID)
21024 {
21025 DialoG d;
21026 SetSampleData ssd;
21027
21028 d = SampleDialog (h);
21029 ssd.fieldstring_func = GetSourceQualFeatureString;
21030 ssd.descrstring_func = GetSourceQualDescrString;
21031 ssd.entityID = entityID;
21032 ssd.field_list = GetSourceQualDescList (TRUE, TRUE, TRUE, FALSE);
21033 ValNodeAddPointer (&(ssd.field_list), 1, StringSave ("Scientific Name"));
21034 ValNodeAddPointer (&(ssd.field_list), 1, StringSave ("Location"));
21035
21036 ssd.fsp = NULL;
21037 ssd.free_vn_proc = ValNodeSimpleDataFree;
21038 ssd.copy_vn_proc = SourceQualValNodeDataCopy;
21039 ssd.match_vn_proc = SourceQualValNodeMatch;
21040 ssd.label_vn_proc = SourceQualValNodeName;
21041 PointerToDialog (d, &ssd);
21042 return d;
21043 }
21044
21045 static void
SourceQualApplyEditConvertRemove(IteM i,Int4 first_action_choice,Boolean crippled)21046 SourceQualApplyEditConvertRemove
21047 (IteM i,
21048 Int4 first_action_choice,
21049 Boolean crippled)
21050 {
21051 ApplyEditConvertRemoveCombo (i, first_action_choice, crippled,
21052 "Source Qual",
21053 SourceQualAECRDialog,
21054 FALSE, GetSourceQualSample,
21055 FALSE, TRUE, FALSE, FALSE, FALSE, NULL,
21056 SourceQualApplyEditConvertRemoveAction, NULL,
21057 ChangeSourceQualAction, NULL);
21058 }
21059
ApplySourceQual(IteM i)21060 extern void ApplySourceQual (IteM i)
21061 {
21062 SourceQualApplyEditConvertRemove (i, AECR_APPLY, FALSE);
21063 }
21064
PublicApplySourceQual(IteM i)21065 extern void PublicApplySourceQual (IteM i)
21066 {
21067 SourceQualApplyEditConvertRemove (i, AECR_APPLY, TRUE);
21068 }
21069
EditSourceQual(IteM i)21070 extern void EditSourceQual (IteM i)
21071 {
21072 SourceQualApplyEditConvertRemove (i, AECR_EDIT, FALSE);
21073 }
21074
PublicEditSourceQual(IteM i)21075 extern void PublicEditSourceQual (IteM i)
21076 {
21077 SourceQualApplyEditConvertRemove (i, AECR_EDIT, TRUE);
21078 }
21079
ConvertSourceQual(IteM i)21080 extern void ConvertSourceQual (IteM i)
21081 {
21082 SourceQualApplyEditConvertRemove (i, AECR_CONVERT, FALSE);
21083 }
21084
SwapSourceQual(IteM i)21085 extern void SwapSourceQual (IteM i)
21086 {
21087 SourceQualApplyEditConvertRemove (i, AECR_SWAP, FALSE);
21088 }
21089
RemoveSourceQual(IteM i)21090 extern void RemoveSourceQual (IteM i)
21091 {
21092 SourceQualApplyEditConvertRemove (i, AECR_REMOVE, FALSE);
21093 }
21094
21095 static CharPtr rna_sample_field_list [] = { "Product",
21096 "Comment" };
21097 static Int2 num_rna_sample_fields = sizeof (rna_sample_field_list) / sizeof (CharPtr);
21098
21099
GetRNASampleFieldString(SeqFeatPtr sfp,ValNodePtr vnp,FilterSetPtr fsp)21100 static CharPtr GetRNASampleFieldString (SeqFeatPtr sfp, ValNodePtr vnp, FilterSetPtr fsp)
21101 {
21102 RnaRefPtr rrp;
21103 CharPtr str = NULL;
21104 Int2 rna_subtype, rna_field_type;
21105 GeneRefPtr grp;
21106 SeqFeatPtr gene;
21107 ValNode vn;
21108 SeqMgrFeatContext fcontext;
21109
21110 if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA || vnp == NULL)
21111 {
21112 return NULL;
21113 }
21114
21115 rrp = sfp->data.value.ptrvalue;
21116
21117 while (vnp != NULL && str == NULL)
21118 {
21119 rna_subtype = (vnp->data.intvalue - 1) / (num_rna_sample_fields + num_gene_fields);
21120 rna_field_type = (vnp->data.intvalue - 1) % (num_rna_sample_fields + num_gene_fields);
21121 switch (rna_subtype)
21122 {
21123 case 0:
21124 if (rrp->type != 255
21125 || (rrp->ext.choice == 1
21126 && (StringCmp (rrp->ext.value.ptrvalue, "ncRNA") == 0
21127 || StringCmp (rrp->ext.value.ptrvalue, "tmRNA") == 0)))
21128 {
21129 vnp = vnp->next;
21130 continue;
21131 }
21132 break;
21133 case 1:
21134 case 2:
21135 case 3:
21136 case 4:
21137 if (rna_subtype != rrp->type)
21138 {
21139 vnp = vnp->next;
21140 continue;
21141 }
21142 break;
21143 case 5:
21144 if (rrp->type != 255
21145 || rrp->ext.choice != 1
21146 || StringCmp (rrp->ext.value.ptrvalue, "ncRNA") != 0)
21147 {
21148 vnp = vnp->next;
21149 continue;
21150 }
21151 break;
21152 case 6:
21153 if (rrp->type != 255
21154 || rrp->ext.choice != 1
21155 || StringCmp (rrp->ext.value.ptrvalue, "tmRNA") != 0)
21156 {
21157 vnp = vnp->next;
21158 continue;
21159 }
21160 break;
21161 }
21162
21163 switch (rna_field_type)
21164 {
21165 case 0 :
21166 str = GetRNAProductString (sfp, NULL);
21167 break;
21168 case 1 :
21169 if (!StringHasNoText (sfp->comment))
21170 {
21171 str = StringSave (sfp->comment);
21172 }
21173 break;
21174 default :
21175 vn.next = NULL;
21176 vn.choice = 0;
21177 vn.data.intvalue = rna_field_type - num_rna_sample_fields + 1;
21178 grp = SeqMgrGetGeneXref (sfp);
21179 if (grp == NULL)
21180 {
21181 gene = SeqMgrGetOverlappingGene (sfp->location, &fcontext);
21182 str = GetGeneFieldString (gene, &vn, NULL);
21183 }
21184 else
21185 {
21186 str = GetGeneFieldString (sfp, &vn, NULL);
21187 }
21188 break;
21189 }
21190 vnp = vnp->next;
21191 }
21192 return str;
21193 }
21194
GetRNAQualSampleName(ValNodePtr vnp)21195 static CharPtr GetRNAQualSampleName (ValNodePtr vnp)
21196 {
21197 CharPtr label = NULL;
21198 Int2 rna_subtype, rna_field_type;
21199
21200 if (vnp == NULL)
21201 {
21202 return NULL;
21203 }
21204 rna_subtype = (vnp->data.intvalue - 1) / (num_rna_sample_fields + num_gene_fields);
21205 rna_field_type = (vnp->data.intvalue - 1) % (num_rna_sample_fields + num_gene_fields);
21206
21207 if (rna_field_type < num_rna_sample_fields)
21208 {
21209 label = (CharPtr) MemNew ((StringLen (rna_subtype_list [rna_subtype])
21210 + StringLen (rna_sample_field_list[rna_field_type])
21211 + 2) * sizeof (Char));
21212 if (label != NULL)
21213 {
21214 sprintf (label, "%s %s", rna_subtype_list [rna_subtype],
21215 rna_sample_field_list[rna_field_type]);
21216 }
21217 }
21218 else if (rna_field_type < num_rna_sample_fields + num_gene_fields)
21219 {
21220 label = (CharPtr) MemNew ((StringLen (rna_subtype_list [rna_subtype])
21221 + StringLen (gene_field_list[rna_field_type - num_rna_sample_fields])
21222 + 7) * sizeof (Char));
21223 if (label != NULL)
21224 {
21225 sprintf (label, "%s Gene %s", rna_subtype_list [rna_subtype],
21226 gene_field_list[rna_field_type - num_rna_sample_fields]);
21227 }
21228 }
21229 return label;
21230 }
21231
GetRNAQualSample(GrouP h,Uint2 entityID)21232 static DialoG GetRNAQualSample (GrouP h, Uint2 entityID)
21233 {
21234 DialoG d;
21235 SetSampleData ssd;
21236 Int2 rna_subtype, field_type;
21237 Int4 list_index;
21238
21239 d = SampleDialog (h);
21240 ssd.fieldstring_func = GetRNASampleFieldString;
21241 ssd.descrstring_func = NULL;
21242 ssd.entityID = entityID;
21243
21244 /* construct RNA field list for separate types of RNAs */
21245 ssd.free_vn_proc = NULL;
21246 ssd.copy_vn_proc = IntValNodeCopy;
21247 ssd.match_vn_proc = IntValNodeMatch;
21248 ssd.label_vn_proc = GetRNAQualSampleName;
21249
21250 ssd.field_list = NULL;
21251 for (rna_subtype = 0; rna_subtype < num_rna_subtypes; rna_subtype++)
21252 {
21253 for (field_type = 0; field_type < num_rna_sample_fields; field_type++)
21254 {
21255 list_index = (rna_subtype * (num_rna_sample_fields + num_gene_fields)) + field_type;
21256 ValNodeAddInt (&ssd.field_list, 0, list_index + 1);
21257 }
21258 for (field_type = 0; field_type < num_gene_fields; field_type ++)
21259 {
21260 list_index = (rna_subtype * (num_rna_sample_fields + num_gene_fields))
21261 + field_type + num_rna_sample_fields;
21262 ValNodeAddInt (&ssd.field_list, 0, list_index + 1);
21263 }
21264 }
21265 ssd.fsp = NULL;
21266 PointerToDialog (d, &ssd);
21267
21268 /* now free up field list (SampleDialog maintains its own copy */
21269 ssd.field_list = ValNodeFree (ssd.field_list);
21270
21271 return d;
21272 }
21273
21274 typedef struct aecrrnaqual
21275 {
21276 ValNodePtr field_list;
21277 ValNodePtr field_list_to;
21278 RnaTypePtr rna_type;
21279 EditApplyPtr edit_apply;
21280 ValNodePtr codons;
21281 SeqLocPtr anticodon;
21282 TextPortionXPtr text_portion;
21283 Boolean leave_on_original;
21284 Boolean remove_parsed;
21285 } AECRRNAQualData, PNTR AECRRNAQualPtr;
21286
AECRRNAQualFree(AECRRNAQualPtr ap)21287 static AECRRNAQualPtr AECRRNAQualFree (AECRRNAQualPtr ap)
21288 {
21289 if (ap != NULL)
21290 {
21291 ap->field_list = ValNodeFree (ap->field_list);
21292 ap->field_list_to = ValNodeFree (ap->field_list_to);
21293 ap->rna_type = RnaTypeFree (ap->rna_type);
21294 ap->edit_apply = EditApplyFree (ap->edit_apply);
21295 ap->codons = ValNodeFreeData (ap->codons);
21296 ap = MemFree (ap);
21297 }
21298 return ap;
21299 }
21300
21301 typedef struct aecrrnaqualdlg
21302 {
21303 DIALOG_MESSAGE_BLOCK
21304 DialoG field_list;
21305 DialoG field_list_to;
21306 DialoG rna_type;
21307 DialoG edit_apply;
21308 DialoG codons;
21309 DialoG ncrna_class;
21310 DialoG text_portion;
21311 ButtoN leave_on_original;
21312 ButtoN remove_parsed;
21313
21314 Nlm_ChangeNotifyProc change_notify;
21315 Pointer change_userdata;
21316 Uint2 entityID;
21317
21318 /* The following is used to create the anticodon location dialog */
21319 FeatureForm ff;
21320 DialoG anticodon;
21321 } AECRRNAQualDlgData, PNTR AECRRNAQualDlgPtr;
21322
ClearTextAECRRNAQualDlg(AECRRNAQualDlgPtr dlg)21323 static void ClearTextAECRRNAQualDlg (AECRRNAQualDlgPtr dlg)
21324 {
21325 if (dlg != NULL)
21326 {
21327 PointerToDialog (dlg->edit_apply, NULL);
21328 PointerToDialog (dlg->codons, NULL);
21329 PointerToDialog (dlg->ncrna_class, NULL);
21330 }
21331 }
21332
ResetAECRRNAQualDlg(AECRRNAQualDlgPtr dlg)21333 static void ResetAECRRNAQualDlg (AECRRNAQualDlgPtr dlg)
21334 {
21335 if (dlg != NULL)
21336 {
21337 PointerToDialog (dlg->field_list, NULL);
21338 PointerToDialog (dlg->field_list_to, NULL);
21339 SendMessageToDialog (dlg->field_list, NUM_VIB_MSG + 1);
21340 PointerToDialog (dlg->rna_type, NULL);
21341 PointerToDialog (dlg->text_portion, NULL);
21342 SafeSetStatus (dlg->leave_on_original, FALSE);
21343 SafeSetStatus (dlg->remove_parsed, FALSE);
21344 ClearTextAECRRNAQualDlg (dlg);
21345 }
21346 }
21347
AECRRNAQualToDialog(DialoG d,Pointer userdata)21348 static void AECRRNAQualToDialog (DialoG d, Pointer userdata)
21349 {
21350 AECRRNAQualDlgPtr dlg;
21351 AECRRNAQualPtr data;
21352
21353 dlg = (AECRRNAQualDlgPtr) GetObjectExtra (d);
21354 if (dlg == NULL)
21355 {
21356 return;
21357 }
21358
21359 ResetAECRRNAQualDlg (dlg);
21360 data = (AECRRNAQualPtr) userdata;
21361 if (data != NULL)
21362 {
21363 PointerToDialog (dlg->field_list, data->field_list);
21364 PointerToDialog (dlg->field_list_to, data->field_list_to);
21365 PointerToDialog (dlg->rna_type, data->rna_type);
21366 PointerToDialog (dlg->edit_apply, data->edit_apply);
21367 PointerToDialog (dlg->codons, data->codons);
21368 if (data->field_list != NULL && data->field_list->data.intvalue == RNAFIELD_NCRNA_CLASS) {
21369 if (data->edit_apply == NULL) {
21370 PointerToDialog (dlg->ncrna_class, NULL);
21371 } else {
21372 PointerToDialog (dlg->ncrna_class, data->edit_apply->apply_txt);
21373 }
21374 }
21375 PointerToDialog (dlg->anticodon, data->anticodon);
21376 PointerToDialog (dlg->text_portion, data->text_portion);
21377 SafeSetStatus (dlg->leave_on_original, data->leave_on_original);
21378 SafeSetStatus (dlg->remove_parsed, data->remove_parsed);
21379 }
21380 }
21381
DialogToAECRRNAQual(DialoG d)21382 static Pointer DialogToAECRRNAQual (DialoG d)
21383 {
21384 AECRRNAQualDlgPtr dlg;
21385 AECRRNAQualPtr data;
21386
21387 dlg = (AECRRNAQualDlgPtr) GetObjectExtra (d);
21388 if (dlg == NULL)
21389 {
21390 return NULL;
21391 }
21392
21393 data = (AECRRNAQualPtr) MemNew (sizeof (AECRRNAQualData));
21394 if (data != NULL)
21395 {
21396 data->field_list = DialogToPointer (dlg->field_list);
21397 data->field_list_to = DialogToPointer (dlg->field_list_to);
21398 data->rna_type = DialogToPointer (dlg->rna_type);
21399 if (data->field_list != NULL && data->field_list->data.intvalue == RNAFIELD_NCRNA_CLASS
21400 && dlg->ncrna_class != NULL) {
21401 data->edit_apply = EditApplyNew ();
21402 data->edit_apply->apply_txt = DialogToPointer (dlg->ncrna_class);
21403 } else {
21404 data->edit_apply = DialogToPointer (dlg->edit_apply);
21405 }
21406 data->codons = DialogToPointer (dlg->codons);
21407 data->anticodon = DialogToPointer (dlg->anticodon);
21408 data->text_portion = DialogToPointer (dlg->text_portion);
21409 data->leave_on_original = (dlg->leave_on_original == NULL) ? FALSE : GetStatus (dlg->leave_on_original);
21410 data->remove_parsed = (dlg->remove_parsed == NULL) ? FALSE : GetStatus (dlg->remove_parsed);
21411 }
21412 return data;
21413 }
21414
21415 static ValNodePtr GetRNAFeatureList (SeqEntryPtr sep, FilterSetPtr fsp, RnaTypePtr rtp);
21416 static GetSamplePtr GetRnaExistingTextForList (ValNodePtr rna_list, ValNodePtr requested_field);
21417
21418 static CharPtr
RNAQualAutopopulate(RnaTypePtr rna_type,ValNodePtr field_list,Uint2 entityID)21419 RNAQualAutopopulate
21420 (RnaTypePtr rna_type,
21421 ValNodePtr field_list,
21422 Uint2 entityID)
21423 {
21424 SeqEntryPtr sep;
21425 GetSamplePtr gsp;
21426 ValNodePtr rna_list;
21427 CharPtr rval = NULL;
21428
21429 sep = GetTopSeqEntryForEntityID (entityID);
21430 rna_list = GetRNAFeatureList (sep, NULL, rna_type);
21431 gsp = GetRnaExistingTextForList (rna_list, field_list);
21432 if (gsp != NULL && !StringHasNoText (gsp->sample_text))
21433 {
21434 rval = gsp->sample_text;
21435 gsp->sample_text = NULL;
21436 }
21437 GetSampleFree (gsp);
21438 rna_list = ValNodeFree (rna_list);
21439 return rval;
21440 }
21441
RNAQualChangeNotify(Pointer userdata)21442 static void RNAQualChangeNotify (Pointer userdata)
21443 {
21444 AECRRNAQualDlgPtr dlg;
21445 ValNodePtr field_list = NULL;
21446 RnaTypePtr rna_type;
21447 EditApplyPtr eap;
21448 CharPtr ncrna_class;
21449
21450 dlg = (AECRRNAQualDlgPtr) userdata;
21451 if (dlg == NULL)
21452 {
21453 return;
21454 }
21455
21456 field_list = DialogToPointer (dlg->field_list);
21457 if (field_list == NULL)
21458 {
21459 Hide (dlg->edit_apply);
21460 Hide (dlg->anticodon);
21461 Hide (dlg->codons);
21462 Hide (dlg->ncrna_class);
21463 }
21464 else if (field_list->data.intvalue == RNAFIELD_CODONS_RECOGNIZED)
21465 {
21466 Show (dlg->codons);
21467 Hide (dlg->edit_apply);
21468 Hide (dlg->anticodon);
21469 Hide (dlg->ncrna_class);
21470 }
21471 else if (field_list->data.intvalue == RNAFIELD_ANTICODON)
21472 {
21473 Show (dlg->anticodon);
21474 Hide (dlg->edit_apply);
21475 Hide (dlg->codons);
21476 Hide (dlg->ncrna_class);
21477 }
21478 else if (field_list->data.intvalue == RNAFIELD_NCRNA_CLASS && dlg->ncrna_class != NULL)
21479 {
21480 Show (dlg->ncrna_class);
21481 Hide (dlg->codons);
21482 Hide (dlg->edit_apply);
21483 Hide (dlg->anticodon);
21484 /* autopopulate */
21485 rna_type = DialogToPointer (dlg->rna_type);
21486 ncrna_class = RNAQualAutopopulate (rna_type, field_list, dlg->entityID);
21487 PointerToDialog (dlg->ncrna_class, ncrna_class);
21488 ncrna_class = MemFree (ncrna_class);
21489 }
21490 else
21491 {
21492 Show (dlg->edit_apply);
21493 Hide (dlg->codons);
21494 Hide (dlg->anticodon);
21495 Hide (dlg->ncrna_class);
21496
21497 /* autopopulate text fields */
21498 if (dlg->edit_apply != NULL)
21499 {
21500 rna_type = DialogToPointer (dlg->rna_type);
21501 eap = DialogToPointer (dlg->edit_apply);
21502 eap->apply_txt = MemFree (eap->apply_txt);
21503 eap->apply_txt = RNAQualAutopopulate (rna_type, field_list, dlg->entityID);
21504 PointerToDialog (dlg->edit_apply, eap);
21505 EditApplyFree (eap);
21506 rna_type = RnaTypeFree (rna_type);
21507 }
21508 }
21509
21510 field_list = ValNodeFree (field_list);
21511
21512 if (dlg->change_notify != NULL)
21513 {
21514 (dlg->change_notify)(dlg->change_userdata);
21515 }
21516 }
21517
AECRRNAQualMessage(DialoG d,Int2 mssg)21518 static void AECRRNAQualMessage (DialoG d, Int2 mssg)
21519
21520 {
21521 AECRRNAQualDlgPtr dlg;
21522
21523 dlg = (AECRRNAQualDlgPtr) GetObjectExtra (d);
21524 if (dlg != NULL) {
21525 switch (mssg)
21526 {
21527 case VIB_MSG_INIT :
21528 /* reset list */
21529 ResetAECRRNAQualDlg (dlg);
21530 break;
21531 case VIB_MSG_ENTER :
21532 Select (dlg->rna_type);
21533 break;
21534 case AECR_VIB_MSG_SET_DEFAULT :
21535 SendMessageToDialog (dlg->field_list, AECR_VIB_MSG_SET_DEFAULT);
21536 SendMessageToDialog (dlg->rna_type, AECR_VIB_MSG_SET_DEFAULT);
21537 ClearTextAECRRNAQualDlg (dlg);
21538 break;
21539 case AECR_VIB_MSG_CLEAR_TEXT :
21540 ClearTextAECRRNAQualDlg (dlg);
21541 break;
21542 case AECR_VIB_MSG_AUTOPOPULATE:
21543 RNAQualChangeNotify (dlg);
21544 break;
21545 default :
21546 break;
21547 }
21548 }
21549 }
21550
TestAECRRNAQual(DialoG d)21551 static ValNodePtr TestAECRRNAQual (DialoG d)
21552 {
21553 AECRRNAQualDlgPtr dlg;
21554 ValNodePtr total_err_list = NULL;
21555 ValNodePtr field_list;
21556
21557 dlg = (AECRRNAQualDlgPtr) GetObjectExtra (d);
21558 if (dlg == NULL)
21559 {
21560 return NULL;
21561 }
21562
21563 total_err_list = TestDialog (dlg->rna_type);
21564
21565 ValNodeLink (&total_err_list, TestDialog (dlg->field_list));
21566
21567 field_list = DialogToPointer (dlg->field_list);
21568 if (field_list != NULL) {
21569 if (field_list->data.intvalue == RNAFIELD_NCRNA_CLASS && dlg->ncrna_class != NULL) {
21570 ValNodeLink (&total_err_list, TestDialog (dlg->ncrna_class));
21571 } else if (field_list->data.intvalue != RNAFIELD_CODONS_RECOGNIZED) {
21572 ValNodeLink (&total_err_list, TestDialog (dlg->edit_apply));
21573 }
21574 }
21575
21576 return total_err_list;
21577 }
21578
21579
AECRRNAQualButtonChange(ButtoN b)21580 static void AECRRNAQualButtonChange (ButtoN b)
21581 {
21582 AECRRNAQualDlgPtr dlg;
21583
21584 dlg = (AECRRNAQualDlgPtr) GetObjectExtra (b);
21585 if (dlg == NULL) return;
21586
21587 if (dlg->change_notify != NULL)
21588 {
21589 (dlg->change_notify) (dlg->change_userdata);
21590 }
21591 }
21592
21593
RNAQualListDialog(GrouP h,Int4 action_choice,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata,Uint2 entityID)21594 static DialoG RNAQualListDialog
21595 (GrouP h,
21596 Int4 action_choice,
21597 Nlm_ChangeNotifyProc change_notify,
21598 Pointer change_userdata,
21599 Uint2 entityID)
21600 {
21601 AECRRNAQualDlgPtr dlg;
21602 GrouP p, g1, g2 = NULL;
21603 SeqEntryPtr sep;
21604
21605 dlg = (AECRRNAQualDlgPtr) MemNew (sizeof (AECRRNAQualDlgData));
21606 if (dlg == NULL)
21607 {
21608 return NULL;
21609 }
21610
21611 p = HiddenGroup (h, -1, 0, NULL);
21612 SetObjectExtra (p, dlg, StdCleanupExtraProc);
21613 SetGroupSpacing (p, 10, 10);
21614
21615 dlg->dialog = (DialoG) p;
21616 dlg->todialog = AECRRNAQualToDialog;
21617 dlg->fromdialog = DialogToAECRRNAQual;
21618 dlg->dialogmessage = AECRRNAQualMessage;
21619 dlg->testdialog = TestAECRRNAQual;
21620 dlg->change_notify = change_notify;
21621 dlg->change_userdata = change_userdata;
21622 dlg->entityID = entityID;
21623
21624
21625 if (action_choice == AECR_CONVERT || action_choice == AECR_SWAP || action_choice == AECR_PARSE)
21626 {
21627 g1 = HiddenGroup (p, 3, 0, NULL);
21628 StaticPrompt (g1, "", 0, dialogTextHeight, systemFont, 'l');
21629 StaticPrompt (g1, "From", 0, dialogTextHeight, systemFont, 'l');
21630 StaticPrompt (g1, "To", 0, dialogTextHeight, systemFont, 'l');
21631 dlg->rna_type = RnaTypeDialog (g1, TRUE, RNAQualChangeNotify, dlg);
21632
21633 dlg->field_list = RNAFieldSelectionDialog (g1, FALSE,
21634 change_notify,
21635 change_userdata);
21636 dlg->field_list_to = RNAFieldSelectionDialog (g1, FALSE,
21637 change_notify,
21638 change_userdata);
21639 if (action_choice == AECR_CONVERT)
21640 {
21641 dlg->leave_on_original = CheckBox (p, "Leave on original", AECRRNAQualButtonChange);
21642 SetObjectExtra (dlg->leave_on_original, dlg, NULL);
21643 }
21644 }
21645 else
21646 {
21647 g1 = HiddenGroup (p, 2, 0, NULL);
21648 StaticPrompt (g1, "", 0, dialogTextHeight, systemFont, 'l');
21649 StaticPrompt (g1, "RNA Field", 0, dialogTextHeight, systemFont, 'l');
21650 dlg->rna_type = RnaTypeDialog (g1, TRUE, RNAQualChangeNotify, dlg);
21651 if (action_choice == AECR_REMOVE)
21652 {
21653 dlg->field_list = RNARemoveFieldSelectionDialog (g1, TRUE,
21654 RNAQualChangeNotify, dlg);
21655 }
21656 else
21657 {
21658 dlg->field_list = RNAFieldSelectionDialog (g1, FALSE,
21659 RNAQualChangeNotify,
21660 dlg);
21661 }
21662 }
21663
21664 if (action_choice == AECR_APPLY)
21665 {
21666 g2 = HiddenGroup (p, 0, 0, NULL);
21667 dlg->edit_apply = EditApplyDialog (g2, eEditApplyChoice_Apply, "New Text", NULL,
21668 change_notify, change_userdata);
21669
21670 dlg->codons = CreateVisibleStringDialog (g2, 3, -1, 4);
21671
21672 dlg->ncrna_class = CreatencRNAClassDialog (g2, FALSE, change_notify, change_userdata);
21673
21674 sep = GetTopSeqEntryForEntityID (entityID);
21675
21676 dlg->anticodon = NULL;
21677 /*
21678 dlg->anticodon = CreateIntervalEditorDialogEx (g2, NULL, 2, 2, sep, TRUE, FALSE,
21679 TRUE, TRUE, FALSE,
21680 &(dlg->ff),
21681 NULL); */
21682
21683 AlignObjects (ALIGN_CENTER, (HANDLE) dlg->edit_apply,
21684 (HANDLE) dlg->codons,
21685 (HANDLE) dlg->ncrna_class,
21686 (HANDLE) dlg->anticodon,
21687 NULL);
21688 }
21689 else if (action_choice == AECR_EDIT)
21690 {
21691 g2 = HiddenGroup (p, 1, 0, NULL);
21692 dlg->edit_apply = EditApplyDialog (g2, eEditApplyChoice_Edit,
21693 "New Text", NULL,
21694 change_notify, change_userdata);
21695 dlg->text_portion = NULL;
21696 dlg->remove_parsed = NULL;
21697 }
21698 else if (action_choice == AECR_PARSE)
21699 {
21700 g2 = HiddenGroup (p, -1, 0, NULL);
21701 dlg->edit_apply = NULL;
21702 dlg->text_portion = TextPortionXDialog(p);
21703 dlg->remove_parsed = CheckBox (p, "Remove from parsed field", SimpleAECRButtonChange);
21704 SetObjectExtra (dlg->remove_parsed, dlg, NULL);
21705 AlignObjects (ALIGN_CENTER, (HANDLE) dlg->edit_apply, (HANDLE) dlg->remove_parsed, NULL);
21706 }
21707 else
21708 {
21709 dlg->edit_apply = NULL;
21710 dlg->text_portion = NULL;
21711 dlg->remove_parsed = NULL;
21712 }
21713
21714
21715 AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) g2, NULL);
21716
21717 RNAQualChangeNotify (dlg);
21718
21719 return (DialoG) p;
21720 }
21721
21722
ApplyRNACodonsCallback(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)21723 static void ApplyRNACodonsCallback (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
21724 {
21725 ValNodePtr codons;
21726 RnaRefPtr rrp;
21727
21728 if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA)
21729 {
21730 return;
21731 }
21732
21733 rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
21734 codons = (ValNodePtr) userdata;
21735 if (rrp != NULL && rrp->type == 3 && rrp->ext.choice == 2)
21736 {
21737 AddCodonListTotRNA (rrp->ext.value.ptrvalue, codons);
21738 }
21739 }
21740
ApplyRNAAnticodonCallback(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)21741 static void ApplyRNAAnticodonCallback (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
21742 {
21743 RnaRefPtr rrp;
21744 tRNAPtr trp;
21745 SeqLocPtr anticodon_loc, slp;
21746
21747 if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA
21748 || sfp->data.value.ptrvalue == NULL)
21749 {
21750 return;
21751 }
21752
21753 anticodon_loc = (SeqLocPtr) userdata;
21754
21755 rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
21756
21757 if (rrp->ext.choice == 2)
21758 {
21759 trp = (tRNAPtr) rrp->ext.value.ptrvalue;
21760 if (trp != NULL)
21761 {
21762 trp->anticodon = SeqLocFree (trp->anticodon);
21763 if (anticodon_loc != NULL)
21764 {
21765 slp = (SeqLocPtr) AsnIoMemCopy (anticodon_loc,
21766 (AsnReadFunc) SeqLocAsnRead,
21767 (AsnWriteFunc) SeqLocAsnWrite);
21768
21769 slp = SeqLocReplaceID (slp, SeqLocId (sfp->location));
21770 trp->anticodon = slp;
21771 }
21772 }
21773 }
21774 }
21775
21776
CollectRNAFeaturesCallback(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)21777 static void CollectRNAFeaturesCallback (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
21778 {
21779 if (sfp != NULL && sfp->data.choice == SEQFEAT_RNA && userdata != NULL)
21780 {
21781 ValNodeAddPointer ((ValNodePtr PNTR) userdata, OBJ_SEQFEAT, sfp);
21782 }
21783
21784 }
21785
21786
GetRNAFeatureList(SeqEntryPtr sep,FilterSetPtr fsp,RnaTypePtr rtp)21787 static ValNodePtr GetRNAFeatureList (SeqEntryPtr sep, FilterSetPtr fsp, RnaTypePtr rtp)
21788 {
21789 ValNodePtr rna_list = NULL, vnp_rna;
21790 ValNodePtr not_match;
21791 SeqFeatPtr sfp;
21792 Boolean matches;
21793
21794 if (sep == NULL) return NULL;
21795
21796 OperateOnSeqEntryConstrainedObjects (sep, fsp, CollectRNAFeaturesCallback,
21797 NULL, SEQFEAT_RNA, 0, 0, &rna_list);
21798
21799 if (rtp != NULL)
21800 {
21801 for (vnp_rna = rna_list; vnp_rna != NULL; vnp_rna = vnp_rna->next)
21802 {
21803 matches = FALSE;
21804 sfp = vnp_rna->data.ptrvalue;
21805 if (!MatchesRnaType (sfp, rtp))
21806 {
21807 vnp_rna->choice = 0;
21808 }
21809 }
21810
21811 not_match = ValNodeExtractList (&rna_list, 0);
21812 not_match = ValNodeFree (not_match);
21813 }
21814 return rna_list;
21815 }
21816
21817
GetRnaExistingTextForList(ValNodePtr rna_list,ValNodePtr requested_field)21818 static GetSamplePtr GetRnaExistingTextForList (ValNodePtr rna_list, ValNodePtr requested_field)
21819 {
21820 GetSamplePtr gsp;
21821 ValNodePtr vnp;
21822 SeqFeatPtr sfp;
21823
21824 if (rna_list == NULL || requested_field == NULL) return NULL;
21825
21826 gsp = GetSampleNew ();
21827 gsp->sample_text = NULL;
21828 gsp->fieldstring_func = GetRNAFieldString;
21829 gsp->descrstring_func = NULL;
21830 gsp->free_vn_proc = NULL;
21831 gsp->copy_vn_proc = IntValNodeCopy;
21832 gsp->requested_field = (gsp->copy_vn_proc) (requested_field);
21833 gsp->num_found = 0;
21834 gsp->all_same = TRUE;
21835
21836 for (vnp = rna_list; vnp != NULL; vnp = vnp->next)
21837 {
21838 sfp = vnp->data.ptrvalue;
21839 GetSampleFeatureCallback (sfp, gsp, NULL);
21840 }
21841 return gsp;
21842 }
21843
21844
ApplyToRNAList(ValNodePtr rna_list,AECRRNAQualPtr rp,FilterSetPtr fsp)21845 static Boolean ApplyToRNAList (ValNodePtr rna_list, AECRRNAQualPtr rp, FilterSetPtr fsp)
21846 {
21847 ValNodePtr vnp_rna;
21848 SeqFeatPtr sfp;
21849 ApplyValueData avd;
21850 Boolean rval = TRUE;
21851 GetSamplePtr gsp;
21852
21853 if (rna_list == NULL || rp == NULL || rp->field_list == NULL)
21854 {
21855 return FALSE;
21856 }
21857
21858 if (rp->field_list->data.intvalue == RNAFIELD_CODONS_RECOGNIZED)
21859 {
21860 for (vnp_rna = rna_list; vnp_rna != NULL; vnp_rna = vnp_rna->next)
21861 {
21862 sfp = vnp_rna->data.ptrvalue;
21863 if (sfp->idx.subtype == FEATDEF_tRNA)
21864 {
21865 ApplyRNACodonsCallback (sfp, rp->codons, fsp);
21866 }
21867 }
21868 }
21869 else if (rp->field_list->data.intvalue == RNAFIELD_ANTICODON)
21870 {
21871 for (vnp_rna = rna_list; vnp_rna != NULL; vnp_rna = vnp_rna->next)
21872 {
21873 sfp = vnp_rna->data.ptrvalue;
21874 if (sfp->idx.subtype == FEATDEF_tRNA)
21875 {
21876 ApplyRNAAnticodonCallback (sfp, rp->anticodon, fsp);
21877 }
21878 }
21879 }
21880 else
21881 {
21882 avd.field_list = rp->field_list;
21883 avd.where_to_replace = EditApplyFindLocation_anywhere;
21884
21885 /* get handling for existing text */
21886 gsp = GetRnaExistingTextForList (rna_list, rp->field_list);
21887 avd.etp = GetExistingTextHandlerInfo (gsp == NULL ? 0 : gsp->num_found, FALSE);
21888 gsp = GetSampleFree (gsp);
21889
21890 if (avd.etp != NULL
21891 && avd.etp->existing_text_choice == eExistingTextChoiceCancel)
21892 {
21893 rval = FALSE;
21894 }
21895
21896 if (rval)
21897 {
21898 AddEditApplyDataToApplyValue (AECR_APPLY, rp->edit_apply, &avd);
21899
21900 for (vnp_rna = rna_list; vnp_rna != NULL; vnp_rna = vnp_rna->next)
21901 {
21902 sfp = vnp_rna->data.ptrvalue;
21903 SetRNAFieldString (sfp, &avd, fsp);
21904 }
21905 avd.text_to_replace = MemFree (avd.text_to_replace);
21906 avd.new_text = MemFree (avd.new_text);
21907 }
21908 avd.etp = MemFree (avd.etp);
21909 }
21910 return rval;
21911 }
21912
21913
21914 static Boolean
RNAQualConvertSwapParseList(ValNodePtr rna_list,AECRRNAQualPtr rp,Int4 action_choice,FilterSetPtr fsp)21915 RNAQualConvertSwapParseList
21916 (ValNodePtr rna_list,
21917 AECRRNAQualPtr rp,
21918 Int4 action_choice,
21919 FilterSetPtr fsp)
21920 {
21921 ConvertFieldData cfd;
21922 ConversionConflictData ccd;
21923 ValNodePtr vnp_rna;
21924 ApplyValueData avd;
21925 Boolean rval = TRUE;
21926 SeqFeatPtr sfp;
21927
21928 if (rna_list == NULL
21929 || rp == NULL
21930 || action_choice < AECR_EDIT
21931 || action_choice > NUM_AECR
21932 || rp->field_list == NULL
21933 || rp->field_list_to == NULL)
21934 {
21935 return FALSE;
21936 }
21937
21938 avd.where_to_replace = EditApplyFindLocation_anywhere;
21939
21940 cfd.src_field_list = rp->field_list;
21941 cfd.dst_field_list = rp->field_list_to;
21942 cfd.etp = NULL;
21943 cfd.convert_type = CONVERT_TYPE_MOVE;
21944 cfd.get_str_func = GetRNAFieldString;
21945 cfd.set_str_func = SetRNAFieldString;
21946 cfd.remove_str_func = RemoveRNAField;
21947 cfd.get_d_str_func = NULL;
21948 cfd.set_d_str_func = NULL;
21949 cfd.remove_d_str_func = NULL;
21950 cfd.fsp = fsp;
21951 cfd.strip_name_from_text = FALSE;
21952 cfd.name_field_func = NULL;
21953 cfd.text_portion = rp->text_portion;
21954 cfd.remove_parsed = rp->remove_parsed;
21955
21956 if (action_choice == AECR_CONVERT)
21957 {
21958 if (rp->leave_on_original)
21959 {
21960 cfd.convert_type = CONVERT_TYPE_COPY;
21961 }
21962 else
21963 {
21964 cfd.convert_type = CONVERT_TYPE_MOVE;
21965 }
21966 }
21967 else if (action_choice == AECR_SWAP)
21968 {
21969 cfd.convert_type = CONVERT_TYPE_SWAP;
21970 }
21971 else if (action_choice == AECR_PARSE)
21972 {
21973 cfd.convert_type = CONVERT_TYPE_PARSE;
21974 }
21975
21976 if (cfd.convert_type == CONVERT_TYPE_MOVE || cfd.convert_type == CONVERT_TYPE_COPY || cfd.convert_type == CONVERT_TYPE_PARSE)
21977 {
21978 /* get existing text sample */
21979 ccd.cfp = &cfd;
21980 ccd.gsp = GetSampleNew();
21981
21982 for (vnp_rna = rna_list; vnp_rna != NULL; vnp_rna = vnp_rna->next)
21983 {
21984 sfp = vnp_rna->data.ptrvalue;
21985 GetConversionConflictsFeatureCallback (sfp, &ccd, fsp);
21986 }
21987 cfd.etp = GetExistingTextHandlerInfo (ccd.gsp == NULL ? 0 : ccd.gsp->num_found, FALSE);
21988 ccd.gsp = GetSampleFree (ccd.gsp);
21989 if (cfd.etp != NULL && cfd.etp->existing_text_choice == eExistingTextChoiceCancel)
21990 {
21991 rval = FALSE;
21992 }
21993 }
21994 else
21995 {
21996 cfd.etp = NULL;
21997 }
21998
21999 if (rval)
22000 {
22001 for (vnp_rna = rna_list; vnp_rna != NULL; vnp_rna = vnp_rna->next)
22002 {
22003 sfp = vnp_rna->data.ptrvalue;
22004 ConvertFeatureFieldCallback (sfp, &cfd, fsp);
22005 }
22006 }
22007
22008 return rval;
22009 }
22010
22011
RNAQualEditRemoveList(ValNodePtr rna_list,AECRRNAQualPtr rp,Int4 action_choice,FilterSetPtr fsp)22012 static Boolean RNAQualEditRemoveList
22013 (ValNodePtr rna_list,
22014 AECRRNAQualPtr rp,
22015 Int4 action_choice,
22016 FilterSetPtr fsp)
22017 {
22018 SeqFeatPtr sfp;
22019 ValNodePtr vnp_rna;
22020 ApplyValueData avd;
22021 Boolean rval = TRUE;
22022
22023 if (rna_list == NULL
22024 || rp == NULL
22025 || (action_choice != AECR_EDIT && action_choice != AECR_REMOVE)
22026 || rp->field_list == NULL)
22027 {
22028 return FALSE;
22029 }
22030
22031 avd.where_to_replace = EditApplyFindLocation_anywhere;
22032 avd.field_list = rp->field_list;
22033 avd.etp = NULL;
22034 AddEditApplyDataToApplyValue (action_choice, rp->edit_apply, &avd);
22035
22036 for (vnp_rna = rna_list; vnp_rna != NULL; vnp_rna = vnp_rna->next)
22037 {
22038 sfp = vnp_rna->data.ptrvalue;
22039 if (action_choice == AECR_EDIT)
22040 {
22041 SetRNAFieldString (sfp, &avd, fsp);
22042 }
22043 else if (action_choice == AECR_REMOVE)
22044 {
22045 RemoveRNAField (sfp, &avd, fsp);
22046 }
22047 }
22048
22049 avd.text_to_replace = MemFree (avd.text_to_replace);
22050 avd.new_text = MemFree (avd.new_text);
22051 return TRUE;
22052 }
22053
22054
22055
22056
AcceptRNAQualApplyEditRemoveConvert(Pointer userdata)22057 static Boolean AcceptRNAQualApplyEditRemoveConvert (Pointer userdata)
22058 {
22059 ApplyEditConvertRemovePtr ap;
22060 AECRRNAQualPtr rp;
22061 Int4 action_choice;
22062 Boolean rval = TRUE;
22063 FilterSetPtr fsp;
22064 ValNodePtr rna_list;
22065 SeqEntryPtr sep;
22066
22067 ap = (ApplyEditConvertRemovePtr) userdata;
22068 if (ap == NULL)
22069 {
22070 return FALSE;
22071 }
22072
22073 WatchCursor ();
22074 Update ();
22075
22076 if (ap->crippled)
22077 {
22078 action_choice = ap->crippled_action;
22079 }
22080 else
22081 {
22082 action_choice = GetValue (ap->action_popup);
22083 }
22084
22085 rp = (AECRRNAQualPtr) DialogToPointer (ap->aecr_pages[action_choice - 1]);
22086 if (rp == NULL) return FALSE;
22087
22088 fsp = (FilterSetPtr) DialogToPointer (ap->constraints);
22089 sep = GetTopSeqEntryForEntityID (ap->input_entityID);
22090 rna_list = GetRNAFeatureList (sep, fsp, rp->rna_type);
22091
22092 if (action_choice == AECR_APPLY)
22093 {
22094 rval = ApplyToRNAList (rna_list, rp, fsp);
22095 }
22096 else if (action_choice == AECR_CONVERT || action_choice == AECR_SWAP
22097 || action_choice == AECR_PARSE)
22098 {
22099 rval = RNAQualConvertSwapParseList (rna_list, rp, action_choice, fsp);
22100 }
22101 else if (action_choice > AECR_APPLY && action_choice <= NUM_AECR)
22102 {
22103 rval = RNAQualEditRemoveList (rna_list, rp, action_choice, fsp);
22104 }
22105
22106 if (rval)
22107 {
22108 ObjMgrSetDirtyFlag (ap->input_entityID, TRUE);
22109 ObjMgrSendMsg (OM_MSG_UPDATE, ap->input_entityID, 0, 0);
22110 }
22111 ArrowCursor ();
22112 Update ();
22113
22114 return rval;
22115 }
22116
22117 static void
RNAQualApplyEditRemoveConvert(IteM i,Int4 first_action_choice,Boolean crippled)22118 RNAQualApplyEditRemoveConvert
22119 (IteM i,
22120 Int4 first_action_choice,
22121 Boolean crippled)
22122 {
22123 ApplyEditConvertRemoveCombo (i, first_action_choice, crippled,
22124 "RNA Qualifiers",
22125 RNAQualListDialog, TRUE, GetRNAQualSample,
22126 TRUE, FALSE, TRUE, FALSE, FALSE, "Where feature text",
22127 AcceptRNAQualApplyEditRemoveConvert, NULL, NULL,
22128 CheckFeaturesForPresample);
22129 }
22130
PublicApplyRNAQual(IteM i)22131 extern void PublicApplyRNAQual (IteM i)
22132 {
22133 RNAQualApplyEditRemoveConvert (i, AECR_APPLY, TRUE);
22134 }
22135
EditRNAQual(IteM i)22136 extern void EditRNAQual (IteM i)
22137 {
22138 RNAQualApplyEditRemoveConvert (i, AECR_EDIT, FALSE);
22139 }
22140
PublicEditRNAQual(IteM i)22141 extern void PublicEditRNAQual (IteM i)
22142 {
22143 RNAQualApplyEditRemoveConvert (i, AECR_EDIT, TRUE);
22144 }
22145
ConvertRNAQual(IteM i)22146 extern void ConvertRNAQual (IteM i)
22147 {
22148 RNAQualApplyEditRemoveConvert (i, AECR_CONVERT, FALSE);
22149 }
22150
SwapRNAQual(IteM i)22151 extern void SwapRNAQual (IteM i)
22152 {
22153 RNAQualApplyEditRemoveConvert (i, AECR_SWAP, FALSE);
22154 }
22155
RemoveRNAQual(IteM i)22156 extern void RemoveRNAQual (IteM i)
22157 {
22158 RNAQualApplyEditRemoveConvert (i, AECR_REMOVE, FALSE);
22159 }
22160
22161
22162 typedef struct removegbqualdlg
22163 {
22164 DIALOG_MESSAGE_BLOCK
22165 DialoG field_list;
22166 DialoG subtype_list;
22167 GrouP list_or_txt_grp;
22168 DialoG qual_name_constraint;
22169
22170 /* These are necessary to produce the SimpleAECR structure for output */
22171 FreeValNodeProc free_field_vn_proc;
22172 FreeValNodeProc free_subtype_vn_proc;
22173
22174 Nlm_ChangeNotifyProc change_notify;
22175 Pointer change_userdata;
22176 Uint2 entityID;
22177
22178 } RemoveGBQualDlgData, PNTR RemoveGBQualDlgPtr;
22179
22180
22181 typedef struct removegbqual
22182 {
22183 ValNodePtr field_list;
22184 ValNodePtr subtype_list;
22185 StringConstraintXPtr scp;
22186 Boolean use_field_list;
22187 } RemoveGBQualData, PNTR RemoveGBQualPtr;
22188
RemoveGBQualFree(RemoveGBQualPtr ap)22189 static RemoveGBQualPtr RemoveGBQualFree (RemoveGBQualPtr ap)
22190 {
22191 if (ap != NULL)
22192 {
22193 ap->field_list = ValNodeFree (ap->field_list);
22194 ap->subtype_list = ValNodeFree (ap->subtype_list);
22195 ap->scp = StringConstraintXFree (ap->scp);
22196 ap = MemFree (ap);
22197 }
22198 return ap;
22199 }
22200
22201
ClearTextRemoveGBQualDlg(RemoveGBQualDlgPtr dlg)22202 static void ClearTextRemoveGBQualDlg (RemoveGBQualDlgPtr dlg)
22203 {
22204 if (dlg != NULL)
22205 {
22206 PointerToDialog (dlg->qual_name_constraint, NULL);
22207 }
22208 }
22209
ResetRemoveGBQualDlg(RemoveGBQualDlgPtr dlg)22210 static void ResetRemoveGBQualDlg (RemoveGBQualDlgPtr dlg)
22211 {
22212 if (dlg != NULL)
22213 {
22214 PointerToDialog (dlg->field_list, NULL);
22215 SendMessageToDialog (dlg->field_list, NUM_VIB_MSG + 1);
22216 PointerToDialog (dlg->subtype_list, NULL);
22217 ClearTextRemoveGBQualDlg (dlg);
22218 SetValue (dlg->list_or_txt_grp, 1);
22219 Enable (dlg->subtype_list);
22220 Disable (dlg->qual_name_constraint);
22221 }
22222 }
22223
22224
RemoveGBQualToDialog(DialoG d,Pointer userdata)22225 static void RemoveGBQualToDialog (DialoG d, Pointer userdata)
22226 {
22227 RemoveGBQualDlgPtr dlg;
22228 RemoveGBQualPtr data;
22229
22230 dlg = (RemoveGBQualDlgPtr) GetObjectExtra (d);
22231 if (dlg == NULL)
22232 {
22233 return;
22234 }
22235
22236 data = (RemoveGBQualPtr) userdata;
22237 if (data == NULL)
22238 {
22239 PointerToDialog (dlg->field_list, NULL);
22240 PointerToDialog (dlg->subtype_list, NULL);
22241 ClearTextRemoveGBQualDlg (dlg);
22242 SetValue (dlg->list_or_txt_grp, 1);
22243 Enable (dlg->subtype_list);
22244 Disable (dlg->qual_name_constraint);
22245 }
22246 else
22247 {
22248 PointerToDialog (dlg->field_list, data->field_list);
22249 PointerToDialog (dlg->subtype_list, data->subtype_list);
22250 PointerToDialog (dlg->qual_name_constraint, data->scp);
22251 if (data->use_field_list)
22252 {
22253 SetValue (dlg->list_or_txt_grp, 1);
22254 Enable (dlg->subtype_list);
22255 Disable (dlg->qual_name_constraint);
22256 }
22257 else
22258 {
22259 SetValue (dlg->list_or_txt_grp, 2);
22260 Disable (dlg->subtype_list);
22261 Enable (dlg->qual_name_constraint);
22262 }
22263 }
22264 }
22265
22266
DialogToRemoveGBQual(DialoG d)22267 static Pointer DialogToRemoveGBQual (DialoG d)
22268 {
22269 RemoveGBQualDlgPtr dlg;
22270 RemoveGBQualPtr data;
22271
22272 dlg = (RemoveGBQualDlgPtr) GetObjectExtra (d);
22273 if (dlg == NULL)
22274 {
22275 return NULL;
22276 }
22277
22278 data = (RemoveGBQualPtr) MemNew (sizeof (RemoveGBQualData));
22279 if (data != NULL)
22280 {
22281 data->field_list = DialogToPointer (dlg->field_list);
22282 data->subtype_list = DialogToPointer (dlg->subtype_list);
22283 data->scp = DialogToPointer (dlg->qual_name_constraint);
22284 if (GetValue (dlg->list_or_txt_grp) == 1)
22285 {
22286 data->use_field_list = TRUE;
22287 }
22288 else
22289 {
22290 data->use_field_list = FALSE;
22291 }
22292 }
22293 return data;
22294 }
22295
22296
RemoveGBQualMessage(DialoG d,Int2 mssg)22297 static void RemoveGBQualMessage (DialoG d, Int2 mssg)
22298
22299 {
22300 RemoveGBQualDlgPtr dlg;
22301
22302 dlg = (RemoveGBQualDlgPtr) GetObjectExtra (d);
22303 if (dlg != NULL) {
22304 switch (mssg)
22305 {
22306 case VIB_MSG_INIT :
22307 /* reset list */
22308 ResetRemoveGBQualDlg (dlg);
22309 break;
22310 case VIB_MSG_ENTER :
22311 if (dlg->subtype_list != NULL)
22312 {
22313 Select (dlg->subtype_list);
22314 }
22315 else
22316 {
22317 Select (dlg->field_list);
22318 }
22319 break;
22320 case AECR_VIB_MSG_SET_DEFAULT :
22321 SendMessageToDialog (dlg->field_list, AECR_VIB_MSG_SET_DEFAULT);
22322 SendMessageToDialog (dlg->subtype_list, AECR_VIB_MSG_SET_DEFAULT);
22323 ClearTextRemoveGBQualDlg (dlg);
22324 break;
22325 case AECR_VIB_MSG_CLEAR_TEXT :
22326 ClearTextRemoveGBQualDlg (dlg);
22327 break;
22328 case AECR_VIB_MSG_AUTOPOPULATE:
22329 break;
22330 default :
22331 break;
22332 }
22333 }
22334 }
22335
TestRemoveGBQual(DialoG d)22336 static ValNodePtr TestRemoveGBQual (DialoG d)
22337 {
22338 RemoveGBQualDlgPtr dlg;
22339 ValNodePtr err_list = NULL;
22340 ValNodePtr total_err_list = NULL;
22341
22342 dlg = (RemoveGBQualDlgPtr) GetObjectExtra (d);
22343 if (dlg == NULL)
22344 {
22345 return NULL;
22346 }
22347
22348 total_err_list = TestDialog (dlg->subtype_list);
22349
22350 if (GetValue (dlg->list_or_txt_grp) == 1)
22351 {
22352 err_list = TestDialog (dlg->field_list);
22353 total_err_list = ValNodeAppend (total_err_list, err_list);
22354 }
22355
22356 return total_err_list;
22357 }
22358
22359
GBQualChangeNotify(GrouP b)22360 static void GBQualChangeNotify (GrouP b)
22361 {
22362 RemoveGBQualDlgPtr dlg;
22363
22364 dlg = (RemoveGBQualDlgPtr) GetObjectExtra (b);
22365 if (dlg == NULL)
22366 {
22367 return;
22368 }
22369
22370 if (GetValue (dlg->list_or_txt_grp) == 1)
22371 {
22372 Enable (dlg->field_list);
22373 Disable (dlg->qual_name_constraint);
22374 }
22375 else
22376 {
22377 Disable (dlg->field_list);
22378 Enable (dlg->qual_name_constraint);
22379 }
22380
22381 if (dlg->change_notify != NULL)
22382 {
22383 (dlg->change_notify)(dlg->change_userdata);
22384 }
22385 }
22386
22387
GBQualRemoveDialog(GrouP h,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata,Uint2 entityID)22388 static DialoG GBQualRemoveDialog
22389 (GrouP h,
22390 Nlm_ChangeNotifyProc change_notify,
22391 Pointer change_userdata,
22392 Uint2 entityID)
22393 {
22394 RemoveGBQualDlgPtr dlg;
22395 GrouP p, g1;
22396 SeqEntryPtr sep;
22397
22398 dlg = (RemoveGBQualDlgPtr) MemNew (sizeof (RemoveGBQualDlgData));
22399 if (dlg == NULL)
22400 {
22401 return NULL;
22402 }
22403
22404 p = HiddenGroup (h, -1, 0, NULL);
22405 SetObjectExtra (p, dlg, StdCleanupExtraProc);
22406 SetGroupSpacing (p, 10, 10);
22407
22408 dlg->dialog = (DialoG) p;
22409 dlg->todialog = RemoveGBQualToDialog;
22410 dlg->fromdialog = DialogToRemoveGBQual;
22411 dlg->dialogmessage = RemoveGBQualMessage;
22412 dlg->testdialog = TestRemoveGBQual;
22413 dlg->change_notify = change_notify;
22414 dlg->change_userdata = change_userdata;
22415 dlg->entityID = entityID;
22416 sep = GetTopSeqEntryForEntityID(entityID);
22417
22418 g1 = HiddenGroup (p, 2, 0, NULL);
22419 StaticPrompt (g1, "Feature", 0, dialogTextHeight, systemFont, 'l');
22420 StaticPrompt (g1, "Qualifier", 0, dialogTextHeight, systemFont, 'l');
22421 dlg->subtype_list = FeatureSelectionDialogEx (g1, TRUE, sep,
22422 change_notify,
22423 change_userdata);
22424 dlg->list_or_txt_grp = HiddenGroup (g1, 2, 0, GBQualChangeNotify);
22425 SetObjectExtra (dlg->list_or_txt_grp, dlg, NULL);
22426 RadioButton (dlg->list_or_txt_grp, "Choose from Standard List");
22427 RadioButton (dlg->list_or_txt_grp, "Select Qual Name Constraint");
22428 dlg->field_list = GBQualSelectionDialog (dlg->list_or_txt_grp, FALSE,
22429 change_notify,
22430 change_userdata);
22431 dlg->qual_name_constraint = StringConstraintDialogX (dlg->list_or_txt_grp, "Where qualifier name contains", FALSE);
22432 SetValue (dlg->list_or_txt_grp, 1);
22433 Disable (dlg->qual_name_constraint);
22434
22435 return (DialoG) p;
22436 }
22437
22438
22439 static DialoG
GBQualListDialog(GrouP h,Int4 action_choice,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata,Uint2 entityID)22440 GBQualListDialog
22441 (GrouP h,
22442 Int4 action_choice,
22443 Nlm_ChangeNotifyProc change_notify,
22444 Pointer change_userdata,
22445 Uint2 entityID)
22446 {
22447 if (action_choice == AECR_REMOVE)
22448 {
22449 return GBQualRemoveDialog (h, change_notify, change_userdata, entityID);
22450 }
22451 else
22452 {
22453 return SimpleAECRDialog (h, action_choice, change_notify, change_userdata,
22454 NULL, ValNodeSimpleDataFree,
22455 GBQualSelectionDialog, FeatureSelectionDialogEx, NULL,
22456 "Qualifier", "Feature", TRUE, entityID);
22457 }
22458 }
22459
22460 static GetSamplePtr
GetGBQualExistingText(SeqEntryPtr sep,ValNodePtr feature_type_list,ValNodePtr requested_field,FilterSetPtr fsp)22461 GetGBQualExistingText
22462 (SeqEntryPtr sep,
22463 ValNodePtr feature_type_list,
22464 ValNodePtr requested_field,
22465 FilterSetPtr fsp)
22466 {
22467 ValNodePtr vnp;
22468 GetSamplePtr gsp;
22469
22470 if (sep == NULL || feature_type_list == NULL)
22471 {
22472 return NULL;
22473 }
22474
22475 gsp = (GetSamplePtr) MemNew (sizeof (GetSampleData));
22476 if (gsp == NULL)
22477 {
22478 return NULL;
22479 }
22480 gsp->sample_text = NULL;
22481 gsp->fieldstring_func = GetGBQualString;
22482 gsp->descrstring_func = NULL;
22483 gsp->free_vn_proc = NULL;
22484 gsp->copy_vn_proc = IntValNodeCopy;
22485
22486 gsp->requested_field = (gsp->copy_vn_proc) (requested_field);
22487 gsp->num_found = 0;
22488 gsp->all_same = TRUE;
22489 for (vnp = feature_type_list; vnp != NULL; vnp = vnp->next)
22490 {
22491 OperateOnSeqEntryConstrainedObjects (sep, fsp, GetSampleFeatureCallback,
22492 NULL,
22493 0, vnp->choice, 0, gsp);
22494 }
22495 return gsp;
22496 }
22497
22498
AcceptGBQualApplyEditRemoveConvert(Pointer userdata)22499 static Boolean AcceptGBQualApplyEditRemoveConvert (Pointer userdata)
22500 {
22501 ApplyEditConvertRemovePtr ap;
22502 SimpleAECRPtr gp = NULL;
22503 RemoveGBQualPtr rgp = NULL;
22504 Int4 action_choice;
22505 SeqEntryPtr sep;
22506 ApplyValueData avd;
22507 ConvertFieldData cfd;
22508 FilterSetPtr fsp;
22509 GetSamplePtr gsp = NULL, gsp_new, gsp_sum;
22510 ValNodePtr vnp, qual_vnp;
22511 Boolean rval = TRUE;
22512
22513 ValNodePtr field_list = NULL;
22514 ValNodePtr subtype_list = NULL;
22515 EditApplyPtr eap = NULL;
22516
22517
22518 ap = (ApplyEditConvertRemovePtr) userdata;
22519 if (ap == NULL)
22520 {
22521 return FALSE;
22522 }
22523
22524 if (ap->crippled)
22525 {
22526 action_choice = ap->crippled_action;
22527 }
22528 else
22529 {
22530 action_choice = GetValue (ap->action_popup);
22531 }
22532 if (action_choice < 1 || action_choice > NUM_AECR)
22533 {
22534 return FALSE;
22535 }
22536
22537 avd.where_to_replace = EditApplyFindLocation_anywhere;
22538
22539 if (action_choice == AECR_REMOVE)
22540 {
22541 rgp = (RemoveGBQualPtr) DialogToPointer (ap->aecr_pages[action_choice - 1]);
22542 if (rgp == NULL)
22543 {
22544 return FALSE;
22545 }
22546 field_list = rgp->field_list;
22547 subtype_list = rgp->subtype_list;
22548 }
22549 else
22550 {
22551 gp = (SimpleAECRPtr) DialogToPointer (ap->aecr_pages[action_choice - 1]);
22552 if (gp == NULL)
22553 {
22554 return FALSE;
22555 }
22556 field_list = gp->field_list;
22557 subtype_list = gp->subtype_list;
22558 eap = gp->edit_apply;
22559 }
22560
22561 WatchCursor ();
22562 Update ();
22563
22564 sep = GetTopSeqEntryForEntityID (ap->input_entityID);
22565 if (subtype_list == NULL || (action_choice != AECR_REMOVE && field_list == NULL)
22566 || (action_choice == AECR_REMOVE && rgp->use_field_list && field_list == NULL)
22567 || ((action_choice == AECR_CONVERT || action_choice == AECR_SWAP || action_choice == AECR_PARSE)
22568 && gp->field_list_to == NULL))
22569 {
22570 gp = SimpleAECRFree (gp);
22571 rgp = RemoveGBQualFree (rgp);
22572 ArrowCursor ();
22573 Update ();
22574 return FALSE;
22575 }
22576
22577 fsp = (FilterSetPtr) DialogToPointer (ap->constraints);
22578
22579 if (action_choice == AECR_CONVERT || action_choice == AECR_SWAP || action_choice == AECR_PARSE)
22580 {
22581 cfd.src_field_list = gp->field_list;
22582 cfd.dst_field_list = gp->field_list_to;
22583 cfd.etp = NULL;
22584 cfd.get_str_func = GetGBQualString;
22585 cfd.set_str_func = SetGBQualString;
22586 cfd.remove_str_func = RemoveGBQualField;
22587 cfd.get_d_str_func = NULL;
22588 cfd.set_d_str_func = NULL;
22589 cfd.remove_d_str_func = NULL;
22590 cfd.fsp = fsp;
22591 cfd.strip_name_from_text = gp->strip_name_from_text;
22592 cfd.remove_parsed = gp->remove_parsed;
22593 cfd.name_field_func = NULL;
22594 cfd.text_portion = gp->text_portion;
22595
22596 if (action_choice == AECR_CONVERT)
22597 {
22598 if (gp->leave_on_original)
22599 {
22600 cfd.convert_type = CONVERT_TYPE_COPY;
22601 }
22602 else
22603 {
22604 cfd.convert_type = CONVERT_TYPE_MOVE;
22605 }
22606 }
22607 else if (action_choice == AECR_SWAP)
22608 {
22609 cfd.convert_type = CONVERT_TYPE_SWAP;
22610 }
22611 else if (action_choice == AECR_PARSE)
22612 {
22613 cfd.convert_type = CONVERT_TYPE_PARSE;
22614 }
22615
22616 if (cfd.convert_type == CONVERT_TYPE_MOVE || cfd.convert_type == CONVERT_TYPE_COPY || cfd.convert_type == CONVERT_TYPE_PARSE)
22617 {
22618 /* get existing text data */
22619 gsp_sum = NULL;
22620 for (vnp = gp->subtype_list; vnp != NULL; vnp = vnp->next)
22621 {
22622 gsp = CheckForConversionExistingTextInSeqEntry (sep, &cfd, fsp,
22623 0,
22624 vnp->choice,
22625 0);
22626 gsp_new = GetSampleAdd (gsp_sum, gsp);
22627 gsp = GetSampleFree (gsp);
22628 gsp_sum = GetSampleFree (gsp_sum);
22629 gsp_sum = gsp_new;
22630 }
22631 cfd.etp = GetExistingTextHandlerInfo (gsp_sum == NULL ? 0 : gsp_sum->num_found, FALSE);
22632 gsp_sum = GetSampleFree (gsp_sum);
22633 if (cfd.etp != NULL && cfd.etp->existing_text_choice == eExistingTextChoiceCancel)
22634 {
22635 rval = FALSE;
22636 }
22637 }
22638 else
22639 {
22640 cfd.etp = NULL;
22641 }
22642
22643 if (rval)
22644 {
22645 for (vnp = gp->subtype_list; vnp != NULL; vnp = vnp->next)
22646 {
22647 OperateOnSeqEntryConstrainedObjects (sep, fsp, ConvertFeatureFieldCallback,
22648 NULL, 0, vnp->choice, 0, &cfd);
22649 }
22650 }
22651 cfd.etp = MemFree (cfd.etp);
22652 }
22653 else if (action_choice == AECR_REMOVE && rgp != NULL && ! rgp->use_field_list)
22654 {
22655 for (vnp = subtype_list; vnp != NULL; vnp = vnp->next)
22656 {
22657 OperateOnSeqEntryConstrainedObjects (sep, fsp, RemoveGBQualByNameConstraint,
22658 NULL, 0, vnp->choice, 0, rgp->scp);
22659 }
22660 }
22661 else
22662 {
22663 avd.field_list = field_list;
22664
22665 /* get handling for existing text */
22666 if (action_choice == AECR_APPLY)
22667 {
22668 gsp = GetGBQualExistingText (sep, subtype_list,
22669 avd.field_list,
22670 fsp);
22671 avd.etp = GetExistingTextHandlerInfo (gsp == NULL ? 0 : gsp->num_found, FALSE);
22672 gsp = GetSampleFree (gsp);
22673
22674 if (avd.etp != NULL
22675 && avd.etp->existing_text_choice == eExistingTextChoiceCancel)
22676 {
22677 rval = FALSE;
22678 }
22679 }
22680 else
22681 {
22682 avd.etp = NULL;
22683 }
22684
22685 AddEditApplyDataToApplyValue (action_choice, eap, &avd);
22686
22687 for (vnp = subtype_list; vnp != NULL; vnp = vnp->next)
22688 {
22689 if (action_choice == AECR_EDIT || action_choice == AECR_APPLY)
22690 {
22691 OperateOnSeqEntryConstrainedObjects (sep, fsp, SetGBQualString,
22692 NULL, 0, vnp->choice, 0, &avd);
22693 }
22694 else if (action_choice == AECR_REMOVE)
22695 {
22696 for (qual_vnp = field_list; qual_vnp != NULL; qual_vnp = qual_vnp->next)
22697 {
22698 avd.field_list = qual_vnp;
22699 OperateOnSeqEntryConstrainedObjects (sep, fsp, RemoveGBQualField,
22700 NULL, 0, vnp->choice, 0, &avd);
22701 }
22702 }
22703 }
22704
22705 avd.text_to_replace = MemFree (avd.text_to_replace);
22706 avd.new_text = MemFree (avd.new_text);
22707 }
22708 FilterSetFree (fsp);
22709 gp = SimpleAECRFree (gp);
22710 rgp = RemoveGBQualFree (rgp);
22711
22712 if (rval)
22713 {
22714 ObjMgrSetDirtyFlag (ap->input_entityID, TRUE);
22715 ObjMgrSendMsg (OM_MSG_UPDATE, ap->input_entityID, 0, 0);
22716 }
22717 ArrowCursor ();
22718 Update ();
22719
22720 return rval;
22721 }
22722
22723
GetGBQualSampleName(ValNodePtr vnp)22724 static CharPtr GetGBQualSampleName (ValNodePtr vnp)
22725 {
22726 CharPtr label = NULL;
22727 Int2 feature_subtype, gb_field_choice;
22728 ValNodePtr feature_list, f_vnp;
22729 Int4 num_feature_choices;
22730 CharPtr feature_label = "";
22731
22732 if (vnp == NULL)
22733 {
22734 return NULL;
22735 }
22736
22737 feature_list = BuildFeatureDialogList (FALSE, NULL);
22738 num_feature_choices = ValNodeLen (feature_list);
22739
22740 feature_subtype = (vnp->data.intvalue - 1) / NumEditQualifiers;
22741 gb_field_choice = (vnp->data.intvalue - 1) % NumEditQualifiers;
22742
22743 for (f_vnp = feature_list; f_vnp != NULL; f_vnp = f_vnp->next)
22744 {
22745 if (f_vnp->choice == feature_subtype)
22746 {
22747 feature_label = f_vnp->data.ptrvalue;
22748 }
22749 }
22750
22751
22752 label = (CharPtr) MemNew ((StringLen (feature_label)
22753 + StringLen (EditQualifierList[gb_field_choice].name)
22754 + 2) * sizeof (Char));
22755 if (label != NULL)
22756 {
22757 sprintf (label, "%s %s", feature_label,
22758 EditQualifierList[gb_field_choice].name);
22759 }
22760 ValNodeFreeData (feature_list);
22761 return label;
22762 }
22763
GetGBQualSampleFieldString(SeqFeatPtr sfp,ValNodePtr vnp,FilterSetPtr fsp)22764 static CharPtr GetGBQualSampleFieldString (SeqFeatPtr sfp, ValNodePtr vnp, FilterSetPtr fsp)
22765 {
22766 CharPtr str = NULL;
22767 Int2 feature_subtype, gb_field_choice;
22768 ValNode vn;
22769
22770 if (sfp == NULL || vnp == NULL)
22771 {
22772 return NULL;
22773 }
22774
22775 feature_subtype = (vnp->data.intvalue - 1) / NumEditQualifiers;
22776 gb_field_choice = (vnp->data.intvalue - 1) % NumEditQualifiers;
22777
22778 if (feature_subtype != sfp->idx.subtype)
22779 {
22780 return NULL;
22781 }
22782
22783 vn.next = NULL;
22784 vn.choice = 0;
22785 vn.data.intvalue = gb_field_choice + 1;
22786 str = GetGBQualString (sfp, &vn, NULL);
22787
22788 return str;
22789 }
22790
GetGBQualSample(GrouP h,Uint2 entityID)22791 static DialoG GetGBQualSample (GrouP h, Uint2 entityID)
22792 {
22793 DialoG d;
22794 SetSampleData ssd;
22795 Int4 qual_choice, list_index;
22796 ValNodePtr feature_list, f_vnp;
22797
22798 d = SampleDialog (h);
22799 ssd.fieldstring_func = GetGBQualSampleFieldString;
22800 ssd.descrstring_func = NULL;
22801 ssd.entityID = entityID;
22802 ssd.free_vn_proc = NULL;
22803 ssd.copy_vn_proc = IntValNodeCopy;
22804 ssd.match_vn_proc = IntValNodeMatch;
22805 ssd.label_vn_proc = GetGBQualSampleName;
22806 ssd.fsp = NULL;
22807
22808 /* construct list of Features and GBQualifiers */
22809 ssd.field_list = NULL;
22810
22811 feature_list = BuildFeatureDialogList (FALSE, NULL);
22812
22813 for (f_vnp = feature_list; f_vnp != NULL; f_vnp = f_vnp->next)
22814 {
22815 for (qual_choice = 0; qual_choice < NumEditQualifiers; qual_choice++)
22816 {
22817 list_index = f_vnp->choice * NumEditQualifiers
22818 + qual_choice;
22819 ValNodeAddInt (&ssd.field_list, 0, list_index + 1);
22820 }
22821 }
22822
22823 PointerToDialog (d, &ssd);
22824
22825 /* now free up field list (SampleDialog maintains its own copy */
22826 ssd.field_list = ValNodeFree (ssd.field_list);
22827 feature_list = ValNodeFreeData (feature_list);
22828 return d;
22829 }
22830
22831 static void
GBQualApplyEditRemoveConvert(IteM i,Int4 first_action_choice,Boolean crippled)22832 GBQualApplyEditRemoveConvert
22833 (IteM i,
22834 Int4 first_action_choice,
22835 Boolean crippled)
22836 {
22837 ApplyEditConvertRemoveCombo (i, first_action_choice, crippled,
22838 "Import Qualifiers",
22839 GBQualListDialog, FALSE, GetGBQualSample,
22840 TRUE, FALSE, TRUE, FALSE, FALSE, "Where feature text",
22841 AcceptGBQualApplyEditRemoveConvert, NULL, NULL,
22842 CheckFeaturesForPresample);
22843 }
22844
ApplyGBQual(IteM i)22845 extern void ApplyGBQual (IteM i)
22846 {
22847 GBQualApplyEditRemoveConvert (i, AECR_APPLY, FALSE);
22848 }
22849
PublicApplyGBQual(IteM i)22850 extern void PublicApplyGBQual (IteM i)
22851 {
22852 GBQualApplyEditRemoveConvert (i, AECR_APPLY, TRUE);
22853 }
22854
EditGBQual(IteM i)22855 extern void EditGBQual (IteM i)
22856 {
22857 GBQualApplyEditRemoveConvert (i, AECR_EDIT, FALSE);
22858 }
22859
PublicEditGBQual(IteM i)22860 extern void PublicEditGBQual (IteM i)
22861 {
22862 GBQualApplyEditRemoveConvert (i, AECR_EDIT, TRUE);
22863 }
22864
ConvertGBQual(IteM i)22865 extern void ConvertGBQual (IteM i)
22866 {
22867 GBQualApplyEditRemoveConvert (i, AECR_CONVERT, FALSE);
22868 }
22869
SwapGBQual(IteM i)22870 extern void SwapGBQual (IteM i)
22871 {
22872 GBQualApplyEditRemoveConvert (i, AECR_SWAP, FALSE);
22873 }
22874
RemoveGBQual(IteM i)22875 extern void RemoveGBQual (IteM i)
22876 {
22877 GBQualApplyEditRemoveConvert (i, AECR_REMOVE, FALSE);
22878 }
22879
22880
22881 typedef enum
22882 {
22883 eAllTargetsAllActions_BioSource = 0,
22884 eAllTargetsAllActions_GBQual,
22885 eAllTargetsAllActions_RNAQual,
22886 eAllTargetsAllActions_CDSGeneProtmRNA,
22887 eNumAllTargetsAllActions
22888 } EAllTargetsAllActions;
22889
22890 typedef struct allactionsalltargetsdlg
22891 {
22892 DIALOG_MESSAGE_BLOCK
22893 DialoG tbs; /* folder tab for switching between target types */
22894 Int2 currentPage;
22895 GrouP target_pages [eNumAllTargetsAllActions];
22896 DialoG aecr_pages [NUM_AECR * eNumAllTargetsAllActions];
22897 PopuP action_popup;
22898
22899 DialoG accept_cancel;
22900 DialoG constraints;
22901 ButtoN clear_constraints_on_action_change;
22902 Nlm_ChangeAECRActionProc change_action;
22903 Int4 prev_page;
22904 Boolean crippled;
22905 Int4 crippled_action;
22906 Uint2 entityID;
22907 Nlm_ChangeNotifyProc change_notify;
22908 Pointer change_userdata;
22909 } AllActionsAllTargetsDlgData, PNTR AllActionsAllTargetsDlgPtr;
22910
22911
AllActionsAllTargets(IteM i)22912 extern void AllActionsAllTargets (IteM i)
22913 {
22914
22915 }
22916
22917 typedef struct locustagtooldlocustag
22918 {
22919 FORM_MESSAGE_BLOCK
22920 DialoG constraints;
22921 DialoG accept_cancel;
22922
22923 SeqEntryPtr sep;
22924 } LocusTagToOldLocusTagData, PNTR LocusTagToOldLocusTagPtr;
22925
LocusTagToOldLocusTagActionClear(Pointer userdata)22926 static void LocusTagToOldLocusTagActionClear (Pointer userdata)
22927 {
22928 LocusTagToOldLocusTagPtr mp;
22929
22930 mp = (LocusTagToOldLocusTagPtr) userdata;
22931 if (mp == NULL)
22932 {
22933 return;
22934 }
22935 PointerToDialog (mp->constraints, NULL);
22936 }
22937
LocusTagToOldLocusTagActionClearText(Pointer userdata)22938 static void LocusTagToOldLocusTagActionClearText (Pointer userdata)
22939 {
22940 LocusTagToOldLocusTagPtr mp;
22941 FilterSetPtr fsp;
22942
22943 mp = (LocusTagToOldLocusTagPtr) userdata;
22944 if (mp == NULL)
22945 {
22946 return;
22947 }
22948 fsp = (FilterSetPtr) DialogToPointer (mp->constraints);
22949 FilterSetClearText (fsp);
22950 PointerToDialog (mp->constraints, fsp);
22951 FilterSetFree (fsp);
22952 }
22953
22954
22955 static void
ConvertGeneLocusTagToOldLocusTagCallback(SeqFeatPtr gene,Pointer userdata,FilterSetPtr fsp)22956 ConvertGeneLocusTagToOldLocusTagCallback
22957 (SeqFeatPtr gene,
22958 Pointer userdata,
22959 FilterSetPtr fsp)
22960 {
22961 GeneRefPtr grp;
22962 CharPtr locus_tag;
22963 GBQualPtr new_qual, prev_qual;
22964 LocusTagToOldLocusTagPtr mp;
22965
22966 if (gene == NULL || gene->data.choice != SEQFEAT_GENE || userdata == NULL) return;
22967
22968 mp = (LocusTagToOldLocusTagPtr)userdata;
22969
22970 grp = (GeneRefPtr) gene->data.value.ptrvalue;
22971 if (grp == NULL || StringHasNoText (grp->locus_tag))
22972 {
22973 return;
22974 }
22975 locus_tag = grp->locus_tag;
22976 grp->locus_tag = NULL;
22977
22978 new_qual = GBQualNew ();
22979 if (new_qual == NULL) return;
22980 new_qual->qual = StringSave ("old_locus_tag");
22981 new_qual->val = locus_tag;
22982 new_qual->next = NULL;
22983
22984 if (gene->qual == NULL)
22985 {
22986 gene->qual = new_qual;
22987 }
22988 else
22989 {
22990 for (prev_qual = gene->qual; prev_qual->next != NULL; prev_qual = prev_qual->next)
22991 {
22992 }
22993 prev_qual->next = new_qual;
22994 }
22995 }
22996
LocusTagToOldLocusTagAction(Pointer userdata)22997 static Boolean LocusTagToOldLocusTagAction (Pointer userdata)
22998 {
22999 LocusTagToOldLocusTagPtr mp;
23000 FilterSetPtr fsp;
23001
23002 mp = (LocusTagToOldLocusTagPtr) userdata;
23003 if (mp == NULL)
23004 {
23005 return FALSE;
23006 }
23007
23008 WatchCursor ();
23009 Update ();
23010
23011 mp->sep = GetTopSeqEntryForEntityID (mp->input_entityID);
23012 fsp = (FilterSetPtr) DialogToPointer (mp->constraints);
23013 OperateOnSeqEntryConstrainedObjects (mp->sep, fsp, ConvertGeneLocusTagToOldLocusTagCallback,
23014 NULL, SEQFEAT_GENE, 0, 0, mp);
23015 ObjMgrSetDirtyFlag (mp->input_entityID, TRUE);
23016 ObjMgrSendMsg (OM_MSG_UPDATE, mp->input_entityID, 0, 0);
23017 ArrowCursor ();
23018 Update ();
23019 return TRUE;
23020 }
23021
ConvertLocusTagToOldLocusTag(IteM i)23022 extern void ConvertLocusTagToOldLocusTag (IteM i)
23023 {
23024 BaseFormPtr bfp;
23025 LocusTagToOldLocusTagPtr mp;
23026 WindoW w;
23027 GrouP h;
23028
23029 #ifdef WIN_MAC
23030 bfp = currentFormDataPtr;
23031 #else
23032 bfp = GetObjectExtra (i);
23033 #endif
23034 if (bfp == NULL) return;
23035
23036 mp = (LocusTagToOldLocusTagPtr) MemNew (sizeof (LocusTagToOldLocusTagData));
23037 if (mp == NULL) return;
23038
23039 w = FixedWindow (-50, -33, -10, -10, "Convert Locus Tag to Old Locus Tag", StdCloseWindowProc);
23040 SetObjectExtra (w, mp, StdCleanupExtraProc);
23041 SetObjectExtra (w, mp, NULL);
23042 mp->form = (ForM) w;
23043 mp->input_entityID = bfp->input_entityID;
23044
23045 h = HiddenGroup (w, -1, 0, NULL);
23046 SetGroupSpacing (h, 10, 10);
23047
23048 mp->constraints = FilterGroup (h, TRUE, FALSE, TRUE, FALSE, FALSE, "Where feature text");
23049 mp->accept_cancel = AcceptCancelDialog (h, LocusTagToOldLocusTagAction, NULL,
23050 LocusTagToOldLocusTagActionClear,
23051 LocusTagToOldLocusTagActionClearText,
23052 (Pointer)mp, w);
23053 AlignObjects (ALIGN_CENTER, (HANDLE) mp->constraints,
23054 (HANDLE) mp->accept_cancel,
23055 NULL);
23056 Show (w);
23057 }
23058
GetLastLineageFromString(CharPtr lineage)23059 static CharPtr GetLastLineageFromString (CharPtr lineage)
23060 {
23061 CharPtr last_semicolon, lineage_start, penultimate_semicolon;
23062
23063
23064 if (StringHasNoText (lineage))
23065 {
23066 return lineage;
23067 }
23068
23069 last_semicolon = StringRChr (lineage, ';');
23070 if (last_semicolon == NULL)
23071 {
23072 return lineage;
23073 }
23074
23075 /* skip past semicolon */
23076 lineage_start = last_semicolon + 1;
23077
23078 /* skip over whitespace */
23079 lineage_start += StringSpn (lineage_start, " \t");
23080
23081 if (StringICmp (lineage_start, "environmental samples") == 0
23082 && last_semicolon != lineage)
23083 {
23084 *last_semicolon = 0;
23085 penultimate_semicolon = StringRChr (lineage, ';');
23086 if (penultimate_semicolon == NULL)
23087 {
23088 lineage_start = lineage;
23089 }
23090 else
23091 {
23092 lineage_start = penultimate_semicolon + 1;
23093 }
23094 lineage_start += StringSpn (lineage_start, " \t");
23095 }
23096 return lineage_start;
23097 }
23098
ExportLastLineageCallback(BioseqPtr bsp,Pointer userdata)23099 static void ExportLastLineageCallback (BioseqPtr bsp, Pointer userdata)
23100 {
23101 LogInfoPtr lip;
23102 SeqFeatPtr sfp;
23103 SeqMgrFeatContext fcontext;
23104 SeqDescrPtr sdp;
23105 SeqMgrDescContext dcontext;
23106 SeqIdPtr sip;
23107 Char tmp[128];
23108 CharPtr val_str = NULL;
23109 ValNode lineage_field;
23110 CharPtr last_lineage;
23111 Boolean found_text = FALSE;
23112
23113 if (bsp == NULL || userdata == NULL || ISA_aa (bsp->mol))
23114 {
23115 return;
23116 }
23117
23118 lip = (LogInfoPtr) userdata;
23119
23120 sip = SeqIdFindBest (bsp->id, 0);
23121 SeqIdWrite (sip, tmp, PRINTID_REPORT, sizeof (tmp));
23122
23123 fprintf (lip->fp, "%s", tmp);
23124
23125 lineage_field.next = NULL;
23126 lineage_field.choice = 1;
23127 lineage_field.data.ptrvalue = "Lineage";
23128
23129 sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext);
23130 while (sdp != NULL)
23131 {
23132 val_str = GetSourceQualDescrString (sdp, &lineage_field, NULL);
23133 last_lineage = GetLastLineageFromString (val_str);
23134 if (last_lineage != NULL)
23135 {
23136 if (found_text)
23137 {
23138 fprintf (lip->fp, ";%s", last_lineage);
23139 }
23140 else
23141 {
23142 fprintf (lip->fp, "\t%s", last_lineage);
23143 }
23144 val_str = MemFree (val_str);
23145 found_text = TRUE;
23146 }
23147 sdp = SeqMgrGetNextDescriptor (bsp, sdp, 0, &dcontext);
23148 }
23149
23150 sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_BIOSRC, 0, &fcontext);
23151 while (sfp != NULL)
23152 {
23153 val_str = GetSourceQualFeatureString (sfp, &lineage_field, NULL);
23154 last_lineage = GetLastLineageFromString (val_str);
23155 if (last_lineage != NULL)
23156 {
23157 if (found_text)
23158 {
23159 fprintf (lip->fp, ";%s", last_lineage);
23160 }
23161 else
23162 {
23163 fprintf (lip->fp, "\t%s", last_lineage);
23164 }
23165 val_str = MemFree (val_str);
23166 found_text = TRUE;
23167 }
23168 sfp = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_BIOSRC, 0, &fcontext);
23169 }
23170 fprintf (lip->fp, "\n");
23171 lip->data_in_log = TRUE;
23172 }
23173
ExportLastLineage(IteM i)23174 extern void ExportLastLineage (IteM i)
23175 {
23176 BaseFormPtr bfp;
23177 SeqEntryPtr sep;
23178 LogInfoPtr lip;
23179
23180 #ifdef WIN_MAC
23181 bfp = currentFormDataPtr;
23182 #else
23183 bfp = GetObjectExtra (i);
23184 #endif
23185 if (bfp == NULL) return;
23186
23187 sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
23188 if (sep == NULL) return;
23189
23190 lip = OpenLog ("Lineage");
23191 WatchCursor ();
23192 Update ();
23193 VisitBioseqsInSep (sep, lip, ExportLastLineageCallback);
23194 CloseLog (lip);
23195 lip = FreeLog (lip);
23196 ArrowCursor ();
23197 Update ();
23198 }
23199
23200 typedef struct combinecds
23201 {
23202 FORM_MESSAGE_BLOCK
23203 GrouP action_choice_grp;
23204 GrouP new_cds_grp;
23205 ButtoN cover_sequence_btn;
23206 DialoG string_constraint_dlg;
23207
23208 Int2 action_choice;
23209 Boolean cover_sequence;
23210 StringConstraintXPtr string_constraint;
23211 LogInfoPtr lip;
23212
23213 /* for string constraint */
23214 ObjectHasStringData ohsd;
23215 ObjMgrTypePtr omtp;
23216 AsnIoPtr aip;
23217
23218 /* for finding location for master CDS */
23219 Int4 left_end;
23220 Int4 right_end;
23221 Boolean partial5;
23222 Boolean partial3;
23223 Uint1 strand;
23224 SeqFeatPtr first_cds;
23225
23226 /* for product name for master CDS */
23227 GrouP prod_name_choice_grp;
23228 TexT prod_name_txt;
23229 } CombineCDSData, PNTR CombineCDSPtr;
23230
23231
GetProteinForCDS(SeqFeatPtr sfp)23232 static SeqFeatPtr GetProteinForCDS (SeqFeatPtr sfp)
23233 {
23234 BioseqPtr protbsp;
23235 SeqMgrFeatContext context;
23236
23237 if (sfp == NULL
23238 || sfp->data.choice != SEQFEAT_CDREGION
23239 || sfp->product == NULL
23240 || (protbsp = BioseqFind(SeqLocId (sfp->product))) == NULL) {
23241 return NULL;
23242 }
23243 return SeqMgrGetNextFeature (protbsp, NULL, SEQFEAT_PROT, FEATDEF_PROT, &context);
23244 }
23245
23246
DoesCDSFieldMatchStringConstraint(SeqFeatPtr sfp,CombineCDSPtr ccp)23247 static Boolean DoesCDSFieldMatchStringConstraint (SeqFeatPtr sfp, CombineCDSPtr ccp)
23248 {
23249 SeqFeatPtr prot;
23250 SeqMgrFeatContext fcontext;
23251
23252 if (sfp == NULL || ccp == NULL) {
23253 return FALSE;
23254 } else if (ccp->ohsd.scp == NULL) {
23255 return TRUE;
23256 } else if (DoesObjectMatchStringConstraint (ccp->omtp, ccp->aip, sfp, &(ccp->ohsd))) {
23257 return TRUE;
23258 } else if ((prot = GetProteinForCDS(sfp)) != NULL && DoesObjectMatchStringConstraint (ccp->omtp, ccp->aip, prot, &(ccp->ohsd))) {
23259 return TRUE;
23260 }
23261 sfp = SeqMgrGetDesiredFeature (ccp->input_entityID, NULL, 0, 0, sfp, &fcontext);
23262 if (sfp != NULL && DoesStringMatchConstraintX (fcontext.label, ccp->ohsd.scp))
23263 {
23264 return TRUE;
23265 }
23266 prot = SeqMgrGetDesiredFeature (ccp->input_entityID, NULL, 0, 0, prot, &fcontext);
23267 if (prot != NULL && DoesStringMatchConstraintX (fcontext.label, ccp->ohsd.scp))
23268 {
23269 return TRUE;
23270 }
23271 return FALSE;
23272 }
23273
23274
GetCombinedCDSLocationCallback(SeqFeatPtr sfp,Pointer userdata)23275 static void GetCombinedCDSLocationCallback (SeqFeatPtr sfp, Pointer userdata)
23276 {
23277 CombineCDSPtr ccp;
23278 Int4 start, stop;
23279 Boolean partial5, partial3;
23280 Uint1 strand;
23281
23282 if (sfp == NULL
23283 || sfp->data.choice != SEQFEAT_CDREGION
23284 || sfp->location == NULL
23285 || userdata == NULL)
23286 {
23287 return;
23288 }
23289
23290 ccp = (CombineCDSPtr) userdata;
23291
23292 if (!DoesCDSFieldMatchStringConstraint(sfp, ccp)) {
23293 return;
23294 }
23295
23296 start = SeqLocStart (sfp->location);
23297 stop = SeqLocStop (sfp->location);
23298 strand = SeqLocStrand (sfp->location);
23299 CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
23300 if (start < ccp->left_end)
23301 {
23302 ccp->first_cds = sfp;
23303 ccp->left_end = start;
23304 if (strand == Seq_strand_minus)
23305 {
23306 ccp->partial3 = partial3;
23307 }
23308 else
23309 {
23310 ccp->partial5 = partial5;
23311 }
23312 ccp->strand = strand;
23313 }
23314
23315 if (stop > ccp->right_end)
23316 {
23317 ccp->right_end = stop;
23318 if (strand == Seq_strand_minus)
23319 {
23320 ccp->partial5 = partial5;
23321 }
23322 else
23323 {
23324 ccp->partial3 = partial3;
23325 }
23326 ccp->strand = strand;
23327 }
23328 }
23329
23330
ApplyProductName(CombineCDSPtr ccp,SeqFeatPtr new_cds)23331 static void ApplyProductName (CombineCDSPtr ccp, SeqFeatPtr new_cds)
23332 {
23333 BioseqPtr first_prot_bsp, new_prot_bsp;
23334 SeqFeatPtr first_prot = NULL;
23335 ProtRefPtr prp;
23336 CharPtr product_name = NULL;
23337
23338 if (ccp == NULL || new_cds == NULL)
23339 {
23340 return;
23341 }
23342
23343 if (GetValue (ccp->prod_name_choice_grp) == 1)
23344 {
23345 first_prot_bsp = BioseqFindFromSeqLoc (ccp->first_cds->product);
23346 if (first_prot_bsp != NULL)
23347 {
23348 first_prot = GetProtFeature (first_prot_bsp);
23349 if (first_prot != NULL)
23350 {
23351 prp = (ProtRefPtr) first_prot->data.value.ptrvalue;
23352 if (prp != NULL && prp->name != NULL
23353 && ! StringHasNoText (prp->name->data.ptrvalue))
23354 {
23355 product_name = StringSave (prp->name->data.ptrvalue);
23356 }
23357 }
23358 }
23359 }
23360 else
23361 {
23362 product_name = SaveStringFromText (ccp->prod_name_txt);
23363 if (StringHasNoText (product_name))
23364 {
23365 product_name = MemFree (product_name);
23366 }
23367 }
23368
23369 if (product_name != NULL)
23370 {
23371 new_prot_bsp = BioseqFindFromSeqLoc (new_cds->product);
23372 if (new_prot_bsp != NULL)
23373 {
23374 first_prot = GetProtFeature (new_prot_bsp);
23375 if (first_prot != NULL)
23376 {
23377 prp = (ProtRefPtr) first_prot->data.value.ptrvalue;
23378 if (prp != NULL)
23379 {
23380 ValNodeAddPointer (&(prp->name), 0, product_name);
23381 product_name = NULL;
23382 }
23383 }
23384 }
23385 }
23386 product_name = MemFree (product_name);
23387 }
23388
GetMasterCDSLocation(BioseqPtr bsp,CombineCDSPtr ccp)23389 static SeqLocPtr GetMasterCDSLocation (BioseqPtr bsp, CombineCDSPtr ccp)
23390 {
23391 SeqFeatPtr sfp;
23392 SeqMgrFeatContext fcontext;
23393 SeqLocPtr cover_loc;
23394
23395 if (bsp == NULL || ! ISA_na (bsp->mol) || ccp == NULL)
23396 {
23397 return NULL;
23398 }
23399
23400 /* create location for master CDS */
23401 ccp->left_end = bsp->length - 1;
23402 ccp->right_end = 0;
23403 ccp->partial5 = FALSE;
23404 ccp->partial3 = FALSE;
23405
23406 sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_CDREGION, 0, &fcontext);
23407 if (sfp == NULL)
23408 {
23409 return NULL;
23410 }
23411 if (ccp->cover_sequence)
23412 {
23413 ccp->left_end = 0;
23414 ccp->right_end = bsp->length - 1;
23415 ccp->partial5 = FALSE;
23416 ccp->partial3 = FALSE;
23417 ccp->first_cds = sfp;
23418 }
23419 else
23420 {
23421 while (sfp != NULL)
23422 {
23423 GetCombinedCDSLocationCallback (sfp, ccp);
23424 sfp = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_CDREGION, 0, &fcontext);
23425 }
23426 if (ccp->left_end > ccp->right_end || ccp->first_cds == NULL)
23427 {
23428 return NULL;
23429 }
23430 }
23431
23432 cover_loc = SeqLocIntNew (ccp->left_end, ccp->right_end, ccp->strand, bsp->id);
23433 SetSeqLocPartial (cover_loc, ccp->partial5, ccp->partial3);
23434
23435 return cover_loc;
23436 }
23437
23438
CreateMasterCodingRegions(BioseqPtr bsp,Pointer userdata)23439 static void CreateMasterCodingRegions (BioseqPtr bsp, Pointer userdata)
23440 {
23441 CombineCDSPtr ccp;
23442 SeqLocPtr cover_loc;
23443 SeqFeatPtr cds;
23444
23445
23446 if (bsp == NULL || userdata == NULL)
23447 {
23448 return;
23449 }
23450
23451 ccp = (CombineCDSPtr) userdata;
23452
23453 cover_loc = GetMasterCDSLocation (bsp, ccp);
23454 if (cover_loc == NULL)
23455 {
23456 return;
23457 }
23458
23459 cds = CreateNewFeatureOnBioseq (bsp, SEQFEAT_CDREGION, cover_loc);
23460 cds->partial = (ccp->partial5 | ccp->partial3);
23461
23462 cds->data.value.ptrvalue = AsnIoMemCopy (ccp->first_cds->data.value.ptrvalue,
23463 (AsnReadFunc) CdRegionAsnRead,
23464 (AsnWriteFunc) CdRegionAsnWrite);
23465 RetranslateOneCDS (cds, ccp->first_cds->idx.entityID, TRUE, FALSE);
23466
23467 ApplyProductName (ccp, cds);
23468 }
23469
23470
ConvertCDSToMatPeptideNoOverlap(SeqFeatPtr sfp,LogInfoPtr lip)23471 static Boolean ConvertCDSToMatPeptideNoOverlap (SeqFeatPtr sfp, LogInfoPtr lip)
23472 {
23473 SeqMgrFeatContext fcontext;
23474
23475 if (sfp == NULL || sfp->data.choice != SEQFEAT_CDREGION) {
23476 return FALSE;
23477 }
23478 if (!CreateMatPeptideFromCDS (sfp)) {
23479 SeqMgrGetDesiredFeature (sfp->idx.entityID, NULL, sfp->idx.itemID, 0, sfp, &fcontext);
23480 if (lip != NULL && lip->fp != NULL) {
23481 fprintf (lip->fp, "Coding region %s has no product sequence\n", fcontext.label);
23482 lip->data_in_log = TRUE;
23483 } else {
23484 Message (MSG_ERROR, "Coding region %s has no product sequence\n", fcontext.label);
23485 }
23486 return FALSE;
23487 } else {
23488 return TRUE;
23489 }
23490 }
23491
23492
ConvertCDSToMatPeptideNoOverlapCallback(BioseqPtr bsp,Pointer userdata)23493 static void ConvertCDSToMatPeptideNoOverlapCallback (BioseqPtr bsp, Pointer userdata)
23494 {
23495 LogInfoPtr lip;
23496 SeqMgrFeatContext fcontext;
23497 SeqFeatPtr sfp;
23498
23499 if (bsp == NULL || ISA_aa (bsp->mol)) {
23500 return;
23501 }
23502
23503 lip = (LogInfoPtr) userdata;
23504 for (sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_CDREGION, 0, &fcontext);
23505 sfp != NULL;
23506 sfp = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_CDREGION, 0, &fcontext)) {
23507 ConvertCDSToMatPeptideNoOverlap (sfp, lip);
23508 }
23509 }
23510
23511
ConvertCDSToMatPeptideOverlap(SeqFeatPtr sfp,SeqFeatPtr top_cds,LogInfoPtr lip)23512 static void ConvertCDSToMatPeptideOverlap (SeqFeatPtr sfp, SeqFeatPtr top_cds, LogInfoPtr lip)
23513 {
23514 SeqMgrFeatContext gene_context;
23515 SeqFeatPtr gene;
23516
23517 if (sfp == NULL || top_cds == NULL || sfp->data.choice != SEQFEAT_CDREGION || top_cds->data.choice != SEQFEAT_CDREGION) {
23518 return;
23519 }
23520
23521 if (!ConvertCDSToMatPeptideForOverlappingCDS (sfp, top_cds, TRUE)) {
23522 if (lip != NULL && lip->fp != NULL)
23523 {
23524 fprintf (lip->fp, "Invalid coordinates for mat_peptide conversion\n");
23525 lip->data_in_log = TRUE;
23526 }
23527 else
23528 {
23529 Message (MSG_ERROR, "Invalid coordinates for mat_peptide conversion");
23530 }
23531 } else {
23532 /* Mark gene with same location for deletion */
23533 gene = SeqMgrGetOverlappingGene (sfp->location, &gene_context);
23534 if (gene != NULL && SeqLocCompare (gene->location, sfp->location) == SLC_A_EQ_B)
23535 {
23536 gene->idx.deleteme = 1;
23537 }
23538 }
23539 }
23540
23541
ConvertInnerCDSsToMatPeptidesCallback(BioseqPtr bsp,Pointer userdata)23542 static void ConvertInnerCDSsToMatPeptidesCallback (BioseqPtr bsp, Pointer userdata)
23543 {
23544 LogInfoPtr lip;
23545 SeqFeatPtr sfp = NULL;
23546 ValNodePtr top_level_cds_list = NULL;
23547 SeqMgrFeatContext context;
23548 ValNodePtr vnp;
23549 SeqFeatPtr top_cds;
23550
23551 if (bsp == NULL || ! ISA_na (bsp->mol)) return;
23552 lip = (LogInfoPtr) userdata;
23553
23554 sfp = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_CDREGION, 0, &context);
23555 while (sfp != NULL)
23556 {
23557 top_cds = NULL;
23558 for (vnp = top_level_cds_list;
23559 vnp != NULL && top_cds == NULL;
23560 vnp = vnp->next)
23561 {
23562 top_cds = (SeqFeatPtr) vnp->data.ptrvalue;
23563 if (top_cds != NULL)
23564 {
23565 if (SeqLocCompare (top_cds->location, sfp->location) != SLC_B_IN_A)
23566 {
23567 top_cds = NULL;
23568 }
23569 }
23570 }
23571
23572 if (top_cds == NULL)
23573 {
23574 /* add to list of top level CDSs */
23575 ValNodeAddPointer (&top_level_cds_list, 0, sfp);
23576 }
23577 else
23578 {
23579 ConvertCDSToMatPeptideOverlap (sfp, top_cds, lip);
23580 }
23581 sfp = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_CDREGION, 0, &context);
23582 }
23583 ValNodeFree (top_level_cds_list);
23584 }
23585
23586
DoCombineCDS(ButtoN b)23587 static void DoCombineCDS (ButtoN b)
23588 {
23589 CombineCDSPtr ccp;
23590 SeqEntryPtr sep, old_scope;
23591 ObjMgrPtr omp;
23592 AsnExpOptPtr aeop;
23593
23594 ccp = (CombineCDSPtr) GetObjectExtra (b);
23595 if (ccp == NULL)
23596 {
23597 return;
23598 }
23599
23600 sep = GetTopSeqEntryForEntityID (ccp->input_entityID);
23601 if (NULL == sep)
23602 return;
23603
23604 old_scope = SeqEntrySetScope (sep);
23605
23606 omp = ObjMgrGet ();
23607 if (omp == NULL) return;
23608
23609 ccp->action_choice = GetValue (ccp->action_choice_grp);
23610 ccp->cover_sequence = GetStatus (ccp->cover_sequence_btn);
23611 ccp->string_constraint = DialogToPointer (ccp->string_constraint_dlg);
23612
23613 WatchCursor ();
23614 Update ();
23615
23616 ccp->lip = OpenLog ("Combine CDS Features");
23617
23618 if (ccp->string_constraint != NULL)
23619 {
23620 ccp->omtp = ObjMgrTypeFind (omp, OBJ_SEQFEAT, NULL, NULL);
23621 ccp->aip = AsnIoNullOpen ();
23622 ccp->ohsd.scp = ccp->string_constraint;
23623 aeop = AsnExpOptNew (ccp->aip, NULL, NULL, AsnWriteConstraintCallBack);
23624 if (aeop != NULL) {
23625 aeop->user_data = (Pointer) &(ccp->ohsd);
23626 }
23627 }
23628 else
23629 {
23630 ccp->omtp = NULL;
23631 ccp->aip = NULL;
23632 ccp->ohsd.scp = NULL;
23633 aeop = NULL;
23634 }
23635
23636 if (ccp->action_choice == 2) {
23637 VisitBioseqsInSep (sep, ccp, CreateMasterCodingRegions);
23638 SeqMgrIndexFeatures (ccp->input_entityID, NULL);
23639 }
23640
23641 if (ccp->action_choice == 1 || ccp->action_choice == 2) {
23642 VisitBioseqsInSep (sep, ccp->lip, ConvertInnerCDSsToMatPeptidesCallback);
23643 } else {
23644 VisitBioseqsInSep (sep, ccp->lip, ConvertCDSToMatPeptideNoOverlapCallback);
23645 }
23646
23647 AsnIoClose (ccp->aip);
23648 SeqEntrySetScope (old_scope);
23649
23650 CloseLog (ccp->lip);
23651 FreeLog (ccp->lip);
23652 ccp->string_constraint = StringConstraintXFree (ccp->string_constraint);
23653 Remove (ccp->form);
23654 DeleteMarkedObjects (ccp->input_entityID, 0, NULL);
23655 ObjMgrSetDirtyFlag (ccp->input_entityID, TRUE);
23656 ObjMgrSendMsg (OM_MSG_UPDATE, ccp->input_entityID, 0, 0);
23657 ArrowCursor ();
23658 Update ();
23659 }
23660
EnableNewCDSControls(GrouP g)23661 static void EnableNewCDSControls (GrouP g)
23662 {
23663 CombineCDSPtr ccp;
23664
23665 ccp = (CombineCDSPtr) GetObjectExtra (g);
23666 if (ccp == NULL) return;
23667
23668 if (GetValue (ccp->action_choice_grp) == 2)
23669 {
23670 Enable (ccp->new_cds_grp);
23671 }
23672 else
23673 {
23674 Disable (ccp->new_cds_grp);
23675 }
23676 }
23677
EnableProdName(GrouP g)23678 static void EnableProdName (GrouP g)
23679 {
23680 CombineCDSPtr ccp;
23681
23682 ccp = (CombineCDSPtr) GetObjectExtra (g);
23683 if (ccp == NULL) return;
23684
23685 if (GetValue (ccp->prod_name_choice_grp) == 1)
23686 {
23687 Disable (ccp->prod_name_txt);
23688 }
23689 else
23690 {
23691 Enable (ccp->prod_name_txt);
23692 }
23693 }
23694
CombineMultipleCDS(IteM i)23695 extern void CombineMultipleCDS (IteM i)
23696 {
23697 BaseFormPtr bfp;
23698 CombineCDSPtr ccp;
23699 WindoW w;
23700 GrouP h, c;
23701 ButtoN b;
23702
23703 #ifdef WIN_MAC
23704 bfp = currentFormDataPtr;
23705 #else
23706 bfp = GetObjectExtra (i);
23707 #endif
23708 if (bfp == NULL) return;
23709
23710 ccp = (CombineCDSPtr) MemNew (sizeof (CombineCDSData));
23711 if (ccp == NULL) return;
23712
23713 w = FixedWindow (-50, -33, -10, -10, "Convert CDS to Mat-peptide", StdCloseWindowProc);
23714 SetObjectExtra (w, ccp, StdCleanupExtraProc);
23715 ccp->form = (ForM) w;
23716 ccp->input_entityID = bfp->input_entityID;
23717
23718 h = HiddenGroup (w, -1, 0, NULL);
23719 SetGroupSpacing (h, 10, 10);
23720
23721 ccp->action_choice_grp = HiddenGroup (h, 0, 3, EnableNewCDSControls);
23722 RadioButton (ccp->action_choice_grp, "Convert inner CDSs to mat_peptides");
23723 RadioButton (ccp->action_choice_grp, "Merge multiple CDSs into one CDS and convert inner CDSs to mat_peptides");
23724 RadioButton (ccp->action_choice_grp, "Create mat-peptide from protein on each CDS");
23725 SetValue (ccp->action_choice_grp, 1);
23726 SetObjectExtra (ccp->action_choice_grp, ccp, NULL);
23727
23728 ccp->new_cds_grp = HiddenGroup (h, -1, 0, NULL);
23729 ccp->cover_sequence_btn = CheckBox (ccp->new_cds_grp, "New CDS should cover entire sequence", NULL);
23730 SetStatus (ccp->cover_sequence_btn, FALSE);
23731
23732 ccp->prod_name_choice_grp = HiddenGroup (ccp->new_cds_grp, 0, 2, EnableProdName);
23733 SetObjectExtra (ccp->prod_name_choice_grp, ccp, NULL);
23734 RadioButton (ccp->prod_name_choice_grp, "Use product name from first CDS");
23735 RadioButton (ccp->prod_name_choice_grp, "Use this product name:");
23736 StaticPrompt (ccp->prod_name_choice_grp, "", 0, 0, programFont, 'l');
23737 ccp->prod_name_txt = DialogText (ccp->prod_name_choice_grp, " ", 10, NULL);
23738 SetValue (ccp->prod_name_choice_grp, 1);
23739 Disable (ccp->prod_name_txt);
23740
23741 ccp->string_constraint_dlg = StringConstraintDialogX (ccp->new_cds_grp, "Where CDS field", TRUE);
23742 Disable (ccp->new_cds_grp);
23743
23744 AlignObjects (ALIGN_CENTER, (HANDLE) ccp->cover_sequence_btn,
23745 (HANDLE) ccp->prod_name_choice_grp,
23746 (HANDLE) ccp->string_constraint_dlg,
23747 NULL);
23748
23749 c = HiddenGroup (h, 2, 0, NULL);
23750 b = PushButton (c, "Accept", DoCombineCDS);
23751 SetObjectExtra (b, ccp, NULL);
23752 b = PushButton (c, "Cancel", StdCancelButtonProc);
23753
23754 AlignObjects (ALIGN_CENTER, (HANDLE) ccp->action_choice_grp,
23755 (HANDLE) ccp->new_cds_grp,
23756 (HANDLE) c,
23757 NULL);
23758 RealizeWindow (w);
23759 Show (w);
23760 Select (w);
23761 Update ();
23762 }
23763
23764
MoveToProteinSequenceCallback(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)23765 static void MoveToProteinSequenceCallback (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
23766 {
23767 SeqLocPtr prot_loc;
23768 SeqFeatPtr overlapping_cds, new_sfp;
23769 SeqMgrFeatContext cds_context, fcontext;
23770 Int4 offset;
23771 CdRegionPtr crp;
23772 BioseqPtr prot_bsp;
23773 LogInfoPtr lip;
23774
23775 if (sfp == NULL) {
23776 return;
23777 }
23778
23779 lip = (LogInfoPtr) userdata;
23780
23781 overlapping_cds = SeqMgrGetOverlappingCDS(sfp->location, &cds_context);
23782 if (overlapping_cds == NULL) {
23783 SeqMgrGetDesiredFeature (sfp->idx.entityID, NULL, sfp->idx.itemID, 0, sfp, &fcontext);
23784 if (lip != NULL && lip->fp != NULL)
23785 {
23786 fprintf (lip->fp, "No overlapping coding region for %s\n", fcontext.label);
23787 lip->data_in_log = TRUE;
23788 }
23789 else
23790 {
23791 Message (MSG_ERROR, "No overlapping coding region for %s\n", fcontext.label);
23792 }
23793 return;
23794 }
23795
23796 prot_bsp = BioseqFindFromSeqLoc(overlapping_cds->product);
23797 if (prot_bsp == NULL) {
23798 if (lip != NULL && lip->fp != NULL)
23799 {
23800 fprintf (lip->fp, "No protein product for %s\n", cds_context.label);
23801 lip->data_in_log = TRUE;
23802 }
23803 else
23804 {
23805 Message (MSG_ERROR, "No protein product for %s\n", cds_context.label);
23806 }
23807 return;
23808 }
23809
23810 offset = cds_context.left;
23811 crp = (CdRegionPtr) overlapping_cds->data.value.ptrvalue;
23812 if (crp != NULL) {
23813 if (crp->frame == 2)
23814 {
23815 offset += 1;
23816 }
23817 else if (crp->frame == 3)
23818 {
23819 offset += 2;
23820 }
23821 }
23822
23823 prot_loc = BuildProtLoc (overlapping_cds, sfp->location, NULL);
23824 if (prot_loc == NULL)
23825 {
23826 SeqMgrGetDesiredFeature (sfp->idx.entityID, NULL, sfp->idx.itemID, 0, sfp, &fcontext);
23827 if (lip != NULL && lip->fp != NULL)
23828 {
23829 fprintf (lip->fp, "Unable to translate coordinates for %s\n", fcontext.label);
23830 lip->data_in_log = TRUE;
23831 }
23832 else
23833 {
23834 Message (MSG_ERROR, "Unable to translate coordinates for %s\n", fcontext.label);
23835 }
23836 }
23837 else
23838 {
23839 new_sfp = CreateNewFeatureOnBioseq (prot_bsp, sfp->data.choice, prot_loc);
23840 if (new_sfp != NULL)
23841 {
23842 new_sfp->data.value.ptrvalue = sfp->data.value.ptrvalue;
23843 sfp->data.value.ptrvalue = NULL;
23844 sfp->idx.deleteme = TRUE;
23845 }
23846 }
23847
23848 }
23849
23850
23851 typedef struct maptoprotein {
23852 FORM_MESSAGE_BLOCK
23853 DialoG feature_selection;
23854 DialoG constraints;
23855 } MapToProteinData, PNTR MapToProteinPtr;
23856
23857
MapToProteinSequence(ButtoN b)23858 static void MapToProteinSequence(ButtoN b)
23859 {
23860 SeqEntryPtr sep;
23861 MapToProteinPtr mtpp;
23862 FilterSetPtr fsp;
23863 LogInfoPtr lip;
23864 ValNodePtr feature_type_list, vnp;
23865 Uint1 feat_def_choice;
23866
23867 mtpp = (MapToProteinPtr) GetObjectExtra (b);
23868 if (mtpp == NULL) {
23869 return;
23870 }
23871
23872 feature_type_list = (ValNodePtr) DialogToPointer (mtpp->feature_selection);
23873 if (feature_type_list != NULL)
23874 {
23875 sep = GetTopSeqEntryForEntityID (mtpp->input_entityID);
23876 fsp = DialogToPointer (mtpp->constraints);
23877 lip = OpenLog ("Map to Protein Sequence");
23878
23879 for (vnp = feature_type_list; vnp != NULL; vnp = vnp->next)
23880 {
23881 feat_def_choice = vnp->choice;
23882 if (feat_def_choice == 255)
23883 {
23884 feat_def_choice = 0;
23885 }
23886 OperateOnSeqEntryConstrainedObjects (sep, fsp, MoveToProteinSequenceCallback,
23887 NULL, 0, feat_def_choice, 0, lip);
23888 }
23889 fsp = FilterSetFree (fsp);
23890 CloseLog (lip);
23891 lip = FreeLog (lip);
23892 DeleteMarkedObjects (mtpp->input_entityID, 0, NULL);
23893 ObjMgrSetDirtyFlag (mtpp->input_entityID, TRUE);
23894 ObjMgrSendMsg (OM_MSG_UPDATE, mtpp->input_entityID, 0, 0);
23895 Update ();
23896 Remove (mtpp->form);
23897 ValNodeFree (feature_type_list);
23898 }
23899 }
23900
23901
MapFeaturesToProteinSequence(IteM i)23902 extern void MapFeaturesToProteinSequence(IteM i)
23903 {
23904 ButtoN b;
23905 BaseFormPtr bfp;
23906 GrouP c;
23907 GrouP g;
23908 WindoW w;
23909 MapToProteinPtr mtpp;
23910 PrompT p;
23911 SeqEntryPtr sep;
23912
23913 #ifdef WIN_MAC
23914 bfp = currentFormDataPtr;
23915 #else
23916 bfp = GetObjectExtra (i);
23917 #endif
23918 if (bfp == NULL) return;
23919
23920 mtpp = (MapToProteinPtr) MemNew (sizeof (MapToProteinData));
23921 if (mtpp == NULL) return;
23922 mtpp->input_entityID = bfp->input_entityID;
23923 sep = GetTopSeqEntryForEntityID(bfp->input_entityID);
23924 w = MovableModalWindow (-50, -33, -10, -10,
23925 "Map to Protein Sequence",
23926 StdCloseWindowProc);
23927 SetObjectExtra (w, mtpp, StdCleanupFormProc);
23928 mtpp->form = (ForM) w;
23929
23930 g = HiddenGroup (w, -1, 0, NULL);
23931 p = StaticPrompt (g, "Move features to protein of type", 0, dialogTextHeight, systemFont, 'l');
23932
23933 mtpp->feature_selection = FeatureSelectionDialogEx (g, TRUE, sep, NULL, NULL);
23934 mtpp->constraints = FilterGroup (g, TRUE, FALSE, FALSE, FALSE, FALSE, "Where feature text");
23935 AlignObjects (ALIGN_CENTER, (HANDLE) p, (HANDLE) mtpp->feature_selection, (HANDLE) mtpp->constraints, NULL);
23936
23937 c = HiddenGroup (w, 2, 0, NULL);
23938 b = DefaultButton (c, "Accept", MapToProteinSequence);
23939 SetObjectExtra (b, mtpp, NULL);
23940 PushButton (c, "Cancel", StdCancelButtonProc);
23941 AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) c, NULL);
23942 RealizeWindow (w);
23943 Show (w);
23944 Select (w);
23945 Update ();
23946 }
23947
23948
23949 typedef struct uniquevaluecollection {
23950 ValNodePtr requested_field;
23951 GetFeatureFieldString fieldstring_func;
23952 GetDescriptorFieldString descrstring_func;
23953 FreeValNodeProc free_vn_proc;
23954 CopyValNodeDataProc copy_vn_proc;
23955 ValNodePtr value_lists;
23956 } UniqueValueCollectionData, PNTR UniqueValueCollectionPtr;
23957
23958
FindExistingCategory(CharPtr description,ValNodePtr category_list)23959 static ClickableItemPtr FindExistingCategory (CharPtr description, ValNodePtr category_list)
23960 {
23961 ClickableItemPtr cip;
23962
23963 while (category_list != NULL) {
23964 cip = (ClickableItemPtr) category_list->data.ptrvalue;
23965 if (cip != NULL &&
23966 (StringCmp (description, cip->description) == 0
23967 || (StringHasNoText (description) && StringHasNoText (cip->description)))) {
23968 return cip;
23969 }
23970 category_list = category_list->next;
23971 }
23972 return NULL;
23973 }
23974
23975
DataInValNodeList(ValNodePtr list,Uint1 choice,Pointer ptrvalue)23976 static ValNodePtr DataInValNodeList (ValNodePtr list, Uint1 choice, Pointer ptrvalue)
23977 {
23978 while (list != NULL) {
23979 if (choice == list->choice && ptrvalue == list->data.ptrvalue) {
23980 return list;
23981 }
23982 list = list->next;
23983 }
23984 return NULL;
23985 }
23986
23987
CombineClickableItemLists(ValNodePtr PNTR list1,ValNodePtr list2)23988 static void CombineClickableItemLists (ValNodePtr PNTR list1, ValNodePtr list2)
23989 {
23990 ValNodePtr add_vnp, prev_vnp = NULL, next_vnp;
23991
23992 if (*list1 == NULL) {
23993 *list1 = list2;
23994 return;
23995 } else if (list2 == NULL) {
23996 return;
23997 }
23998
23999 add_vnp = list2;
24000 while (add_vnp != NULL) {
24001 next_vnp = add_vnp->next;
24002 if (DataInValNodeList (*list1, add_vnp->choice, add_vnp->data.ptrvalue)) {
24003 if (prev_vnp == NULL) {
24004 list2 = next_vnp;
24005 } else {
24006 prev_vnp->next = next_vnp;
24007 }
24008 add_vnp->next = NULL;
24009 ValNodeFree (add_vnp);
24010 } else {
24011 prev_vnp = add_vnp;
24012 }
24013 add_vnp = next_vnp;
24014 }
24015 ValNodeLink (list1, list2);
24016 }
24017
24018
CombineClickableLists(ValNodePtr PNTR list1,ValNodePtr list2)24019 static void CombineClickableLists (ValNodePtr PNTR list1, ValNodePtr list2)
24020 {
24021 ClickableItemPtr cip1, cip2;
24022 ValNodePtr vnp;
24023 for (vnp = list2; vnp != NULL; vnp = vnp->next) {
24024 cip2 = vnp->data.ptrvalue;
24025 if (cip2 != NULL) {
24026 cip1 = FindExistingCategory (cip2->description, *list1);
24027 if (cip1 == NULL) {
24028 ValNodeAddPointer (list1, 0, cip2);
24029 vnp->data.ptrvalue = NULL;
24030 } else {
24031 CombineClickableItemLists (&(cip1->item_list), cip2->item_list);
24032 cip2->item_list = NULL;
24033 }
24034 }
24035 }
24036 list2 = FreeClickableList (list2);
24037 }
24038
24039
GetUniqueValuesFeatureCallback(SeqFeatPtr sfp,Pointer userdata,FilterSetPtr fsp)24040 static void GetUniqueValuesFeatureCallback (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
24041 {
24042 UniqueValueCollectionPtr uvcp;
24043 CharPtr str;
24044 ValNodePtr check_vnp;
24045 ClickableItemPtr cip;
24046
24047 if (sfp == NULL || userdata == NULL)
24048 {
24049 return;
24050 }
24051
24052 uvcp = (UniqueValueCollectionPtr) userdata;
24053 if (uvcp->fieldstring_func == NULL)
24054 {
24055 return;
24056 }
24057
24058 str = uvcp->fieldstring_func (sfp, uvcp->requested_field, NULL);
24059 if (str == NULL) {
24060 return;
24061 }
24062 cip = FindExistingCategory (str, uvcp->value_lists);
24063 if (cip == NULL) {
24064 cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
24065 MemSet (cip, 0, sizeof (ClickableItemData));
24066 cip->description = str;
24067 ValNodeAddPointer (&cip->item_list, OBJ_SEQFEAT, sfp);
24068 ValNodeAddPointer (&(uvcp->value_lists), 0, cip);
24069 } else {
24070 str = MemFree (str);
24071 /* make sure feature isn't already in the list */
24072 for (check_vnp = cip->item_list; check_vnp != NULL; check_vnp = check_vnp->next) {
24073 if (check_vnp->choice == OBJ_SEQFEAT && sfp == check_vnp->data.ptrvalue) break;
24074 }
24075 if (check_vnp == NULL) {
24076 ValNodeAddPointer (&cip->item_list, OBJ_SEQFEAT, sfp);
24077 }
24078 }
24079 }
24080
GetUniqueValuesDescriptorCallback(SeqDescrPtr sdp,Pointer userdata,FilterSetPtr fsp)24081 static void GetUniqueValuesDescriptorCallback (SeqDescrPtr sdp, Pointer userdata, FilterSetPtr fsp)
24082 {
24083 UniqueValueCollectionPtr uvcp;
24084 ClickableItemPtr cip;
24085 CharPtr str;
24086 ValNodePtr check_vnp;
24087
24088 if (sdp == NULL || userdata == NULL)
24089 {
24090 return;
24091 }
24092
24093 uvcp = (UniqueValueCollectionPtr) userdata;
24094 if (uvcp->descrstring_func == NULL)
24095 {
24096 return;
24097 }
24098
24099 str = uvcp->descrstring_func (sdp, uvcp->requested_field, NULL);
24100
24101 cip = FindExistingCategory (str, uvcp->value_lists);
24102
24103 if (cip == NULL) {
24104 cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
24105 MemSet (cip, 0, sizeof (ClickableItemData));
24106 cip->description = str;
24107 ValNodeAddPointer (&cip->item_list, OBJ_SEQDESC, sdp);
24108 ValNodeAddPointer (&(uvcp->value_lists), 0, cip);
24109 } else {
24110 str = MemFree (str);
24111 /* make sure feature isn't already in the list */
24112 for (check_vnp = cip->item_list; check_vnp != NULL; check_vnp = check_vnp->next) {
24113 if (check_vnp->choice == OBJ_SEQDESC && sdp == check_vnp->data.ptrvalue) break;
24114 }
24115 if (check_vnp == NULL) {
24116 ValNodeAddPointer (&cip->item_list, OBJ_SEQDESC, sdp);
24117 }
24118 }
24119 }
24120
24121
CheckForUniqueValuesInSeqEntry(SeqEntryPtr sep,ValNodePtr requested_field,GetFeatureFieldString fieldstring_func,GetDescriptorFieldString descrstring_func,FreeValNodeProc free_vn_proc,CopyValNodeDataProc copy_vn_proc,FilterSetPtr fsp,Uint1 seqfeat_choice,Uint1 featdef_choice,Uint1 descr_choice)24122 static ValNodePtr CheckForUniqueValuesInSeqEntry
24123 (SeqEntryPtr sep,
24124 ValNodePtr requested_field,
24125 GetFeatureFieldString fieldstring_func,
24126 GetDescriptorFieldString descrstring_func,
24127 FreeValNodeProc free_vn_proc,
24128 CopyValNodeDataProc copy_vn_proc,
24129 FilterSetPtr fsp,
24130 Uint1 seqfeat_choice,
24131 Uint1 featdef_choice,
24132 Uint1 descr_choice)
24133 {
24134 UniqueValueCollectionData uvcd;
24135
24136 uvcd.fieldstring_func = fieldstring_func;
24137 uvcd.descrstring_func = descrstring_func;
24138 uvcd.free_vn_proc = free_vn_proc;
24139 uvcd.copy_vn_proc = copy_vn_proc;
24140 uvcd.requested_field = (copy_vn_proc) (requested_field);
24141 uvcd.value_lists = NULL;
24142 OperateOnSeqEntryConstrainedObjects (sep, fsp, GetUniqueValuesFeatureCallback,
24143 GetUniqueValuesDescriptorCallback,
24144 seqfeat_choice, featdef_choice,
24145 descr_choice, &uvcd);
24146 return uvcd.value_lists;
24147 }
24148
24149
24150 static ValNodePtr
GetUniqueValueListForSeqEntry(SeqEntryPtr sep,Uint2 entityID,ParseFieldPtr dst_field_data,FilterSetPtr fsp)24151 GetUniqueValueListForSeqEntry
24152 (SeqEntryPtr sep,
24153 Uint2 entityID,
24154 ParseFieldPtr dst_field_data,
24155 FilterSetPtr fsp)
24156 {
24157 ValNodePtr unique_values = NULL;
24158 ValNodePtr requested_field = NULL, vnp;
24159 SeqEntryPtr orig_sep;
24160
24161 if (sep == NULL || dst_field_data == NULL)
24162 {
24163 return NULL;
24164 }
24165
24166 switch (dst_field_data->parse_field_type)
24167 {
24168 case PARSE_FIELD_SOURCE_QUAL :
24169 unique_values = CheckForUniqueValuesInSeqEntry (sep,
24170 dst_field_data->feature_field,
24171 GetSourceQualFeatureString,
24172 GetSourceQualDescrString,
24173 ValNodeSimpleDataFree,
24174 SourceQualValNodeDataCopy,
24175 fsp,
24176 SEQFEAT_BIOSRC, 0,
24177 Seq_descr_source);
24178 break;
24179 case PARSE_FIELD_DEFLINE:
24180 requested_field = ValNodeNew (NULL);
24181 requested_field->data.intvalue = Seq_descr_title;
24182 unique_values = CheckForUniqueValuesInSeqEntry (sep, requested_field,
24183 NULL,
24184 GetStringFromStringDescriptor,
24185 NULL, IntValNodeCopy,
24186 fsp, 0, 0, Seq_descr_title);
24187 requested_field = ValNodeFree (requested_field);
24188 break;
24189 case PARSE_FIELD_BIOSRC_STRING:
24190 unique_values = CheckForUniqueValuesInSeqEntry (sep,
24191 dst_field_data->feature_field,
24192 GetSourceFeatureString,
24193 GetSourceDescriptorString,
24194 NULL, IntValNodeCopy,
24195 fsp,
24196 SEQFEAT_BIOSRC, 0,
24197 Seq_descr_source);
24198 break;
24199 case PARSE_FIELD_DBXREF:
24200 unique_values = CheckForUniqueValuesInSeqEntry (sep, dst_field_data->feature_field,
24201 GetBioSourceFeatureDbxrefString,
24202 GetBioSourceDescriptorDbxrefString,
24203 ValNodeSimpleDataFree,
24204 ValNodeStringCopy,
24205 fsp,
24206 SEQFEAT_BIOSRC, 0, Seq_descr_source);
24207 break;
24208 case PARSE_FIELD_GENE_FIELD:
24209 unique_values = CheckForUniqueValuesInSeqEntry (sep,
24210 dst_field_data->feature_field,
24211 GetGeneFieldString,
24212 NULL,
24213 NULL, IntValNodeCopy,
24214 fsp,
24215 SEQFEAT_GENE, 0, 0);
24216 break;
24217 case PARSE_FIELD_RNA_FIELD:
24218 unique_values = CheckForUniqueValuesInSeqEntry (sep,
24219 dst_field_data->feature_field,
24220 GetRNAFieldString,
24221 NULL,
24222 NULL, IntValNodeCopy,
24223 fsp,
24224 SEQFEAT_RNA,
24225 dst_field_data->feature_subtype == NULL ? 0 : dst_field_data->feature_subtype->data.intvalue,
24226 0);
24227 break;
24228 case PARSE_FIELD_CDS_COMMENT:
24229 unique_values = CheckForUniqueValuesInSeqEntry (sep,
24230 NULL,
24231 GetCDSComment,
24232 NULL,
24233 NULL, IntValNodeCopy,
24234 fsp,
24235 SEQFEAT_CDREGION, FEATDEF_CDS, 0);
24236 break;
24237 case PARSE_FIELD_COMMENT_DESC:
24238 requested_field = ValNodeNew (NULL);
24239 requested_field->data.intvalue = Seq_descr_comment;
24240
24241 unique_values = CheckForUniqueValuesInSeqEntry (sep, requested_field,
24242 NULL,
24243 GetStringFromStringDescriptor,
24244 NULL, IntValNodeCopy,
24245 fsp, 0, 0, Seq_descr_comment);
24246 requested_field = ValNodeFree (requested_field);
24247 break;
24248 case PARSE_FIELD_PROTEIN_FIELD:
24249 unique_values = CheckForUniqueValuesInSeqEntry (sep,
24250 dst_field_data->feature_field,
24251 GetProteinFieldString,
24252 NULL,
24253 NULL, IntValNodeCopy,
24254 fsp,
24255 SEQFEAT_PROT, 0, 0);
24256 break;
24257 case PARSE_FIELD_IMPORT_QUAL:
24258 orig_sep = sep;
24259 for (vnp = dst_field_data->feature_subtype; vnp != NULL; vnp = vnp->next)
24260 {
24261 CombineClickableLists (&unique_values,
24262 CheckForUniqueValuesInSeqEntry (sep,
24263 dst_field_data->feature_field,
24264 GetGBQualString,
24265 NULL,
24266 NULL, IntValNodeCopy,
24267 fsp, 0, vnp->choice, 0));
24268 /* if we are also looking at features other than mat_peptides, use
24269 * original SeqEntry */
24270 sep = orig_sep;
24271 }
24272 break;
24273 case PARSE_FIELD_FEATURE_NOTE:
24274 orig_sep = sep;
24275 for (vnp = dst_field_data->feature_field; vnp != NULL; vnp = vnp->next)
24276 {
24277 CombineClickableLists (&unique_values,
24278 CheckForUniqueValuesInSeqEntry (sep, vnp,
24279 GetFeatureNote,
24280 NULL,
24281 ValNodeSimpleDataFree,
24282 ValNodeStringCopy,
24283 fsp, 0, vnp->choice, 0));
24284 /* if we are also looking at features other than mat_peptides, use
24285 * original SeqEntry */
24286 sep = orig_sep;
24287 }
24288 break;
24289 }
24290 return unique_values;
24291 }
24292
24293
GetSeqEntryListForItem(ValNodePtr vnp)24294 static ValNodePtr GetSeqEntryListForItem (ValNodePtr vnp)
24295 {
24296 SeqFeatPtr sfp;
24297 SeqDescrPtr sdp;
24298 ObjValNodePtr ovp;
24299 SeqEntryPtr sep = NULL;
24300 BioseqPtr bsp;
24301 BioseqSetPtr bssp;
24302 ValNodePtr sep_list = NULL;
24303
24304 if (vnp == NULL || vnp->data.ptrvalue == NULL) return NULL;
24305
24306 if (vnp->choice == OBJ_SEQFEAT) {
24307 sfp = vnp->data.ptrvalue;
24308 sep = GetBestTopParentForData (sfp->idx.entityID, BioseqFindFromSeqLoc (sfp->location));
24309 ValNodeAddPointer (&sep_list, OBJ_SEQENTRY, sep);
24310 } else if (vnp->choice == OBJ_SEQDESC) {
24311 sdp = vnp->data.ptrvalue;
24312 if (sdp->extended != 0) {
24313 ovp = (ObjValNodePtr) sdp;
24314 if (ovp->idx.parenttype == OBJ_BIOSEQSET) {
24315 bssp = (BioseqSetPtr) ovp->idx.parentptr;
24316 if (bssp != NULL) {
24317 /* nuc_prot sets, segsets, and members of parts should travel together */
24318 if (bssp->_class == BioseqseqSet_class_nuc_prot) {
24319 sep = SeqMgrGetSeqEntryForData (bssp);
24320 if (sep != NULL) {
24321 ValNodeAddPointer (&sep_list, OBJ_SEQENTRY, sep);
24322 }
24323 } else if (bssp->_class == BioseqseqSet_class_segset
24324 || bssp->_class == BioseqseqSet_class_parts) {
24325 sep = bssp->seq_set;
24326 if (sep != NULL && IS_Bioseq (sep)) {
24327 bsp = sep->data.ptrvalue;
24328 sep = GetBestTopParentForData (bsp->idx.entityID, bsp);
24329 if (sep != NULL) {
24330 ValNodeAddPointer (&sep_list, OBJ_SEQENTRY, sep);
24331 }
24332 }
24333 } else {
24334 sep = bssp->seq_set;
24335 while (sep != NULL) {
24336 ValNodeAddPointer (&sep_list, OBJ_SEQENTRY, sep);
24337 sep = sep->next;
24338 }
24339 }
24340 }
24341 } else if (ovp->idx.parenttype == OBJ_BIOSEQ) {
24342 sep = GetBestTopParentForData (ovp->idx.entityID, ovp->idx.parentptr);
24343 if (sep != NULL) {
24344 ValNodeAddPointer (&sep_list, OBJ_SEQENTRY, sep);
24345 }
24346 }
24347 }
24348 } else if (vnp->choice == OBJ_BIOSEQ) {
24349 bsp = (BioseqPtr) vnp->data.ptrvalue;
24350 sep = GetBestTopParentForData (bsp->idx.entityID, bsp);
24351 ValNodeAddPointer (&sep_list, OBJ_SEQENTRY, sep);
24352 } else if (vnp->choice == OBJ_SEQENTRY) {
24353 sep = vnp->data.ptrvalue;
24354 ValNodeAddPointer (&sep_list, OBJ_SEQENTRY, sep);
24355 }
24356 return sep_list;
24357 }
24358
24359
RemoveItemAndCategory(ClickableItemPtr cip,Uint1 choice,Pointer ptrvalue)24360 static Boolean RemoveItemAndCategory (ClickableItemPtr cip, Uint1 choice, Pointer ptrvalue)
24361 {
24362 ValNodePtr vnp, prev = NULL;
24363 Boolean found = FALSE;
24364 CharPtr description = NULL;
24365 ClickableItemPtr subcat;
24366
24367 vnp = cip->item_list;
24368 while (vnp != NULL) {
24369 if (vnp->choice == choice && vnp->data.ptrvalue == ptrvalue) {
24370 found = TRUE;
24371 if (prev == NULL) {
24372 cip->item_list = vnp->next;
24373 } else {
24374 prev->next = vnp->next;
24375 }
24376 vnp->next = NULL;
24377 description = GetDiscrepancyItemText (vnp);
24378 vnp = ValNodeFree (vnp);
24379 } else {
24380 prev = vnp;
24381 vnp = vnp->next;
24382 }
24383 }
24384 if (found) {
24385 /* also remove subcategory */
24386 prev = NULL;
24387 vnp = cip->subcategories;
24388 while (vnp != NULL) {
24389 subcat = (ClickableItemPtr) vnp->data.ptrvalue;
24390 if (subcat != NULL && StringCmp (subcat->description, description) == 0) {
24391 if (prev == NULL) {
24392 cip->subcategories = vnp->next;
24393 } else {
24394 prev->next = vnp->next;
24395 }
24396 vnp->next = NULL;
24397 vnp = FreeClickableList (vnp);
24398 } else {
24399 prev = vnp;
24400 vnp = vnp->next;
24401 }
24402 }
24403 }
24404 return found;
24405 }
24406
RearrangeForSeqEntriesInMultipleCategories(ValNodePtr value_lists)24407 static ValNodePtr RearrangeForSeqEntriesInMultipleCategories (ValNodePtr value_lists)
24408 {
24409 ClickableItemPtr cip1, cip2, existing_cat;
24410 ValNodePtr vnp, check_vnp, last_vnp, vnp_item1, prev, vnp_next;
24411 Boolean found;
24412 CharPtr new_description;
24413
24414 /* now check for SeqEntries that appear in multiple lists */
24415 for (vnp = value_lists; vnp != NULL && vnp->next != NULL; vnp = vnp->next) {
24416 if (vnp->data.ptrvalue == NULL) continue;
24417 last_vnp = vnp->next;
24418 while (last_vnp->next != NULL) {
24419 last_vnp = last_vnp->next;
24420 }
24421 cip1 = (ClickableItemPtr) vnp->data.ptrvalue;
24422 for (vnp_item1 = cip1->item_list;
24423 vnp_item1 != NULL;
24424 vnp_item1 = vnp_next) {
24425 vnp_next = vnp_item1->next;
24426 found = FALSE;
24427 if (vnp_item1->data.ptrvalue != NULL && vnp_item1->choice == OBJ_SEQENTRY) {
24428 check_vnp = vnp->next;
24429 while (check_vnp != NULL && !found) {
24430 if (check_vnp->data.ptrvalue != NULL) {
24431 cip2 = check_vnp->data.ptrvalue;
24432 found = RemoveItemAndCategory (cip2, vnp_item1->choice, vnp_item1->data.ptrvalue);
24433 }
24434 if (!found) {
24435 if (check_vnp == last_vnp) {
24436 check_vnp = NULL;
24437 } else {
24438 check_vnp = check_vnp->next;
24439 }
24440 }
24441 }
24442 }
24443 if (found) {
24444 /* need to take this SeqEntry out of both lists, put in new category */
24445 new_description = (CharPtr) MemNew (sizeof (Char) * (StringLen (cip1->description)
24446 + StringLen (cip2->description) + 6));
24447 if (StringCmp (cip1->description, cip2->description) < 0) {
24448 sprintf (new_description, "%s AND %s", cip1->description, cip2->description);
24449 } else {
24450 sprintf (new_description, "%s AND %s", cip2->description, cip1->description);
24451 }
24452 existing_cat = FindExistingCategory (new_description, check_vnp->next);
24453 if (existing_cat == NULL) {
24454 /* make new category, add to end of list */
24455 existing_cat = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
24456 MemSet (existing_cat, 0, sizeof (ClickableItemData));
24457 existing_cat->description = new_description;
24458 ValNodeAddPointer (&value_lists, 0, existing_cat);
24459 } else {
24460 new_description = MemFree (new_description);
24461 }
24462 /* don't add item twice */
24463 if (!DataInValNodeList (existing_cat->item_list, vnp_item1->choice, vnp_item1->data.ptrvalue)) {
24464 ValNodeAddPointer (&(existing_cat->item_list), vnp_item1->choice, vnp_item1->data.ptrvalue);
24465 }
24466 /* remove from cip1 */
24467 RemoveItemAndCategory (cip1, vnp_item1->choice, vnp_item1->data.ptrvalue);
24468 }
24469 }
24470 }
24471
24472 /* remove empty categories */
24473 for (vnp = value_lists, prev = NULL; vnp != NULL; vnp = vnp_next) {
24474 vnp_next = vnp->next;
24475 cip1 = (ClickableItemPtr) vnp->data.ptrvalue;
24476 if (cip1 == NULL || cip1->item_list == NULL) {
24477 if (prev == NULL) {
24478 value_lists = vnp->next;
24479 } else {
24480 prev->next = vnp->next;
24481 }
24482 vnp->next = NULL;
24483 vnp = FreeClickableList (vnp);
24484 } else {
24485 prev = vnp;
24486 }
24487 }
24488 return value_lists;
24489 }
24490
24491
ChangeUniqueValueListsToSeqEntryLists(ValNodePtr value_lists)24492 static ValNodePtr ChangeUniqueValueListsToSeqEntryLists (ValNodePtr value_lists)
24493 {
24494 ValNodePtr vnp, vnp_item, new_item_list, new_vnp, sep_list, sep_vnp;
24495 ClickableItemPtr cip, subcat;
24496 SeqEntryPtr sep;
24497 CharPtr description;
24498
24499 /* First, add SeqEntry for each feature or descriptor to the item list */
24500 for (vnp = value_lists; vnp != NULL; vnp = vnp->next) {
24501 cip = (ClickableItemPtr) vnp->data.ptrvalue;
24502 new_item_list = NULL;
24503 if (cip != NULL) {
24504 for (vnp_item = cip->item_list; vnp_item != NULL; vnp_item = vnp_item->next) {
24505 if (vnp_item->data.ptrvalue == NULL) continue;
24506 sep_list = GetSeqEntryListForItem (vnp_item);
24507 for (sep_vnp = sep_list; sep_vnp != NULL; sep_vnp = sep_vnp->next) {
24508 sep = sep_vnp->data.ptrvalue;
24509 new_vnp = DataInValNodeList (new_item_list, OBJ_SEQENTRY, sep);
24510 /* add to list for this category */
24511 if (new_vnp == NULL) {
24512 new_vnp = ValNodeAddPointer (&new_item_list, OBJ_SEQENTRY, sep);
24513 }
24514 description = GetDiscrepancyItemText(new_vnp);
24515 subcat = FindExistingCategory (description, cip->subcategories);
24516 if (subcat == NULL) {
24517 subcat = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
24518 MemSet (subcat, 0, sizeof (ClickableItemData));
24519 subcat->description = description;
24520 ValNodeAddPointer (&(cip->subcategories), 0, subcat);
24521 } else {
24522 description = MemFree (description);
24523 }
24524 /* don't add item twice */
24525 if (!DataInValNodeList (subcat->item_list, vnp_item->choice, vnp_item->data.ptrvalue)) {
24526 ValNodeAddPointer (&(subcat->item_list), vnp_item->choice, vnp_item->data.ptrvalue);
24527 }
24528 }
24529 sep_list = ValNodeFree (sep_list);
24530 }
24531
24532 cip->item_list = ValNodeFree (cip->item_list);
24533 cip->item_list = new_item_list;
24534 }
24535 }
24536 value_lists = RearrangeForSeqEntriesInMultipleCategories (value_lists);
24537 return value_lists;
24538 }
24539
24540
GetMolTypes(SeqDescrPtr sdp,Pointer userdata)24541 static void GetMolTypes (SeqDescrPtr sdp, Pointer userdata)
24542 {
24543 ValNodePtr PNTR type_list;
24544 ClickableItemPtr cip;
24545 CharPtr str;
24546 MolInfoPtr mip;
24547
24548 if (sdp == NULL || sdp->choice != Seq_descr_molinfo || sdp->data.ptrvalue == NULL || userdata == NULL)
24549 {
24550 return;
24551 }
24552
24553 type_list = (ValNodePtr PNTR) userdata;
24554
24555 mip = (MolInfoPtr) sdp->data.ptrvalue;
24556 /* don't look for peptides */
24557 if (mip->biomol == 8) return;
24558
24559 str = GetMoleculeTypeName (mip->biomol);
24560
24561 cip = FindExistingCategory (str, *type_list);
24562
24563 if (cip == NULL) {
24564 cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
24565 MemSet (cip, 0, sizeof (ClickableItemData));
24566 cip->description = StringSave (str);
24567 ValNodeAddPointer (&cip->item_list, OBJ_SEQDESC, sdp);
24568 ValNodeAddPointer (type_list, 0, cip);
24569 } else {
24570 /* make sure feature isn't already in the list */
24571 if (DataInValNodeList (cip->item_list, OBJ_SEQDESC, sdp) == NULL) {
24572 ValNodeAddPointer (&cip->item_list, OBJ_SEQDESC, sdp);
24573 }
24574 }
24575 }
24576
GetMolClasses(BioseqPtr bsp,Pointer userdata)24577 static void GetMolClasses (BioseqPtr bsp, Pointer userdata)
24578 {
24579 ValNodePtr PNTR type_list;
24580 ClickableItemPtr cip;
24581 CharPtr str;
24582
24583 if (bsp == NULL || ISA_aa(bsp->mol) || userdata == NULL)
24584 {
24585 return;
24586 }
24587
24588 type_list = (ValNodePtr PNTR) userdata;
24589
24590 str = GetMoleculeClassName (bsp->mol);
24591
24592 cip = FindExistingCategory (str, *type_list);
24593
24594 if (cip == NULL) {
24595 cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
24596 MemSet (cip, 0, sizeof (ClickableItemData));
24597 cip->description = StringSave (str);
24598 ValNodeAddPointer (&cip->item_list, OBJ_BIOSEQ, bsp);
24599 ValNodeAddPointer (type_list, 0, cip);
24600 } else {
24601 /* make sure feature isn't already in the list */
24602 if (DataInValNodeList (cip->item_list, OBJ_BIOSEQ, bsp) == NULL) {
24603 ValNodeAddPointer (&cip->item_list, OBJ_BIOSEQ, bsp);
24604 }
24605 }
24606 }
24607
GetMolTopologies(BioseqPtr bsp,Pointer userdata)24608 static void GetMolTopologies (BioseqPtr bsp, Pointer userdata)
24609 {
24610 ValNodePtr PNTR type_list;
24611 ClickableItemPtr cip;
24612 CharPtr str;
24613
24614 if (bsp == NULL || ISA_aa(bsp->mol) || userdata == NULL)
24615 {
24616 return;
24617 }
24618
24619 type_list = (ValNodePtr PNTR) userdata;
24620
24621 str = GetMoleculeTopologyName (bsp->topology);
24622
24623 cip = FindExistingCategory (str, *type_list);
24624
24625 if (cip == NULL) {
24626 cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
24627 MemSet (cip, 0, sizeof (ClickableItemData));
24628 cip->description = StringSave (str);
24629 ValNodeAddPointer (&cip->item_list, OBJ_BIOSEQ, bsp);
24630 ValNodeAddPointer (type_list, 0, cip);
24631 } else {
24632 /* make sure feature isn't already in the list */
24633 if (DataInValNodeList (cip->item_list, OBJ_BIOSEQ, bsp) == NULL) {
24634 ValNodeAddPointer (&cip->item_list, OBJ_BIOSEQ, bsp);
24635 }
24636 }
24637 }
24638
24639
24640 typedef struct segfeatures {
24641 Uint2 featdef;
24642 ValNodePtr feature_list;
24643 } SegFeaturesData, PNTR SegFeaturesPtr;
24644
FindFeaturesForSeg(SeqFeatPtr sfp,Pointer userdata)24645 static void FindFeaturesForSeg (SeqFeatPtr sfp, Pointer userdata)
24646 {
24647 SegFeaturesPtr fp;
24648
24649 if (sfp == NULL || userdata == NULL) return;
24650
24651 fp = (SegFeaturesPtr) userdata;
24652
24653 if (sfp->idx.subtype == fp->featdef) {
24654 ValNodeAddPointer (&(fp->feature_list), OBJ_SEQFEAT, sfp);
24655 }
24656 }
24657
24658 typedef struct segdescriptors {
24659 Uint2 desc_type;
24660 ValNodePtr descriptor_list;
24661 } SegDescriptorsData, PNTR SegDescriptorsPtr;
24662
FindDescriptorsForSeg(SeqDescrPtr sdp,Pointer userdata)24663 static void FindDescriptorsForSeg (SeqDescrPtr sdp, Pointer userdata)
24664 {
24665 SegDescriptorsPtr fp;
24666
24667 if (sdp == NULL || userdata == NULL) return;
24668
24669 fp = (SegDescriptorsPtr) userdata;
24670
24671 if (sdp->choice == fp->desc_type) {
24672 ValNodeAddPointer (&(fp->descriptor_list), OBJ_SEQDESC, sdp);
24673 }
24674 }
24675
24676
24677 extern ValNodePtr
CreateSeqEntryListsForUniqueValues(SeqEntryPtr sep,Uint2 entityID,ParseFieldPtr dst_field_data,FilterSetPtr fsp)24678 CreateSeqEntryListsForUniqueValues
24679 (SeqEntryPtr sep,
24680 Uint2 entityID,
24681 ParseFieldPtr dst_field_data,
24682 FilterSetPtr fsp)
24683 {
24684 ValNodePtr value_lists;
24685
24686 value_lists = GetUniqueValueListForSeqEntry (sep, entityID, dst_field_data, fsp);
24687
24688 value_lists = ChangeUniqueValueListsToSeqEntryLists (value_lists);
24689 return value_lists;
24690 }
24691
AddPubFeatureWithText(SeqFeatPtr sfp,Pointer userdata)24692 static void AddPubFeatureWithText (SeqFeatPtr sfp, Pointer userdata)
24693 {
24694 ValNodePtr PNTR pub_list;
24695
24696 if (sfp == NULL || userdata == NULL) return;
24697 pub_list = (ValNodePtr PNTR) userdata;
24698
24699 ValNodeAddPointer (pub_list, OBJ_SEQFEAT, sfp);
24700 }
24701
AddPubDescriptorWithText(SeqDescrPtr sdp,Pointer userdata)24702 static void AddPubDescriptorWithText (SeqDescrPtr sdp, Pointer userdata)
24703 {
24704 ValNodePtr PNTR pub_list;
24705
24706 if (sdp == NULL || userdata == NULL || sdp->choice != Seq_descr_pub) return;
24707 pub_list = (ValNodePtr PNTR) userdata;
24708
24709 ValNodeAddPointer (pub_list, OBJ_SEQDESC, sdp);
24710 }
24711
GetTextPubListsForSeqEntry(SeqEntryPtr sep,CharPtr search_text)24712 static ValNodePtr GetTextPubListsForSeqEntry (SeqEntryPtr sep, CharPtr search_text)
24713 {
24714 FeaturesWithTextData ftd;
24715 DescriptorsWithTextData dtd;
24716 ValNodePtr obj_list = NULL;
24717
24718 ftd.seqFeatChoice = SEQFEAT_PUB;
24719 ftd.featDefChoice = FEATDEF_PUB;
24720 ftd.search_text = search_text;
24721 ftd.act_when_string_not_present = FALSE;
24722 ftd.case_insensitive = TRUE;
24723 ftd.whole_word = FALSE;
24724 ftd.no_text = FALSE;
24725 ftd.callback = AddPubFeatureWithText;
24726 ftd.userdata = &obj_list;
24727
24728 dtd.search_text = search_text;
24729 dtd.act_when_string_not_present = FALSE;
24730 dtd.case_insensitive = TRUE;
24731 dtd.whole_word = FALSE;
24732 dtd.no_text = FALSE;
24733 dtd.callback = AddPubDescriptorWithText;
24734 dtd.userdata = &obj_list;
24735
24736 OperateOnSeqEntryFeaturesWithText (sep, &ftd);
24737 OperateOnSeqEntryDescriptorsWithText (sep, &dtd);
24738
24739 return obj_list;
24740 }
24741
GetTextSeqEntryListForSeqEntry(SeqEntryPtr sep,Uint2 entityID,CharPtr search_text,ParseFieldPtr dst_field_data)24742 static ValNodePtr GetTextSeqEntryListForSeqEntry (SeqEntryPtr sep, Uint2 entityID, CharPtr search_text, ParseFieldPtr dst_field_data)
24743 {
24744 ValNodePtr value_lists = NULL;
24745 ValNodePtr obj_list = NULL, tmp_list, vnp;
24746 ClickableItemPtr cip;
24747 CharPtr desc_fmt = "%d sequences contain %s";
24748 StringConstraintData scd;
24749 ChoiceConstraintData ccd;
24750 FilterSetData fsd;
24751
24752 if (dst_field_data == NULL) {
24753 /* do nothing */
24754 } else if (dst_field_data->parse_field_type == SEARCH_FIELD_PUBLICATION) {
24755 obj_list = GetTextPubListsForSeqEntry(sep, search_text);
24756 } else {
24757 scd.match_text = search_text;
24758 scd.match_location = 1;
24759 scd.insensitive = TRUE;
24760 scd.whole_word = FALSE;
24761 scd.not_present = FALSE;
24762
24763 ccd.constraint_type = CHOICE_CONSTRAINT_STRING;
24764 ccd.qual_choice =
24765 ccd.qual_choice_match = NULL;
24766 ccd.string_constraint = &scd;
24767 ccd.pseudo_constraint = NULL;
24768 ccd.free_vn_proc = NULL;
24769 ccd.copy_vn_proc = NULL;
24770
24771 MemSet (&fsd, 0, sizeof (FilterSetData));
24772 fsd.ccp = &ccd;
24773
24774 tmp_list = GetUniqueValueListForSeqEntry (sep, entityID, dst_field_data, NULL);
24775
24776 for (vnp = tmp_list; vnp != NULL; vnp = vnp->next) {
24777 cip = (ClickableItemPtr) vnp->data.ptrvalue;
24778 if (cip != NULL && StringISearch (cip->description, search_text) != NULL) {
24779 ValNodeLink (&obj_list, cip->item_list);
24780 cip->item_list = NULL;
24781 }
24782 }
24783 tmp_list = FreeClickableList (tmp_list);
24784 }
24785 if (obj_list != NULL) {
24786 cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
24787 MemSet (cip, 0, sizeof (ClickableItemData));
24788 cip->description = StringSave (search_text);
24789 cip->item_list = obj_list;
24790 cip->chosen = TRUE;
24791 ValNodeAddPointer (&value_lists, 0, cip);
24792 value_lists = ChangeUniqueValueListsToSeqEntryLists (value_lists);
24793 /* rename description */
24794 if (value_lists != NULL) {
24795 cip = value_lists->data.ptrvalue;
24796 if (cip != NULL) {
24797 cip->description = MemFree (cip->description);
24798 cip->description = (CharPtr) MemNew (sizeof(Char) * (StringLen (desc_fmt) + StringLen (search_text) + 15));
24799 sprintf (cip->description, desc_fmt, ValNodeLen (cip->item_list), search_text);
24800 }
24801 }
24802 }
24803
24804 return value_lists;
24805 }
24806
24807 typedef enum vectorhitlevel {
24808 eVectorHitLevelSuspect = 1,
24809 eVectorHitLevelWeak,
24810 eVectorHitLevelModerate,
24811 eVectorHitLevelStrong } EVectorHitLevel;
24812
24813 typedef struct vectorcontaminationoptions {
24814 Int4 internal_level;
24815 Int4 end5_level;
24816 Int4 end3_level;
24817 ValNodePtr bioseq_list;
24818 } VectorContaminationOptionsData, PNTR VectorContaminationOptionsPtr;
24819
24820 typedef struct vectorcontaminationoptionsdlg {
24821 DIALOG_MESSAGE_BLOCK
24822
24823 ButtoN internal;
24824 ButtoN end5;
24825 ButtoN end3;
24826 GrouP internal_level;
24827 GrouP end5_level;
24828 GrouP end3_level;
24829
24830 Nlm_ChangeNotifyProc change_notify;
24831 Pointer change_userdata;
24832 } VectorContaminationOptionsDlgData, PNTR VectorContaminationOptionsDlgPtr;
24833
DataToVectorContaminationOptionsDlg(DialoG d,Pointer data)24834 static void DataToVectorContaminationOptionsDlg (DialoG d, Pointer data)
24835 {
24836 VectorContaminationOptionsDlgPtr dlg;
24837 VectorContaminationOptionsPtr options;
24838
24839 dlg = (VectorContaminationOptionsDlgPtr) GetObjectExtra (d);
24840 if (dlg == NULL) {
24841 return;
24842 }
24843
24844 options = (VectorContaminationOptionsPtr) data;
24845 if (options == NULL) {
24846 SetStatus (dlg->internal, FALSE);
24847 SetStatus (dlg->end5, FALSE);
24848 SetStatus (dlg->end3, FALSE);
24849 SetValue (dlg->internal_level, eVectorHitLevelStrong);
24850 SetValue (dlg->end5_level, eVectorHitLevelStrong);
24851 SetValue (dlg->end3_level, eVectorHitLevelStrong);
24852 } else {
24853 if (options->internal_level == 0) {
24854 SetStatus (dlg->internal, FALSE);
24855 } else {
24856 SetStatus (dlg->internal, TRUE);
24857 SetValue (dlg->internal_level, options->internal_level);
24858 }
24859
24860 if (options->end5_level == 0) {
24861 SetStatus (dlg->end5, FALSE);
24862 } else {
24863 SetStatus (dlg->end5, TRUE);
24864 SetValue (dlg->end5_level, options->end5_level);
24865 }
24866 if (options->end3_level == 0) {
24867 SetStatus (dlg->end3, FALSE);
24868 } else {
24869 SetStatus (dlg->end3, TRUE);
24870 SetValue (dlg->end3_level, options->end3_level);
24871 }
24872 }
24873 }
24874
24875
VectorContaminationOptionsDlgToData(DialoG d)24876 static Pointer VectorContaminationOptionsDlgToData (DialoG d)
24877 {
24878 VectorContaminationOptionsDlgPtr dlg;
24879 VectorContaminationOptionsPtr options = NULL;
24880
24881 dlg = (VectorContaminationOptionsDlgPtr) GetObjectExtra (d);
24882 if (dlg == NULL) {
24883 return NULL;
24884 }
24885
24886 options = (VectorContaminationOptionsPtr) MemNew (sizeof (VectorContaminationOptionsData));
24887 if (GetStatus (dlg->internal)) {
24888 options->internal_level = GetValue (dlg->internal_level);
24889 } else {
24890 options->internal_level = 0;
24891 }
24892 if (GetStatus (dlg->end5)) {
24893 options->end5_level = GetValue (dlg->end5_level);
24894 } else {
24895 options->end5_level = 0;
24896 }
24897 if (GetStatus (dlg->end3)) {
24898 options->end3_level = GetValue (dlg->end3_level);
24899 } else {
24900 options->end3_level = 0;
24901 }
24902
24903 options->bioseq_list = NULL;
24904 return (Pointer) options;
24905 }
24906
24907
ChangeVectorContaminationButton(ButtoN b)24908 static void ChangeVectorContaminationButton (ButtoN b)
24909 {
24910 VectorContaminationOptionsDlgPtr dlg;
24911
24912 dlg = (VectorContaminationOptionsDlgPtr) GetObjectExtra (b);
24913 if (dlg == NULL) {
24914 return;
24915 }
24916
24917 if (GetStatus (dlg->internal)) {
24918 Enable (dlg->internal_level);
24919 } else {
24920 Disable (dlg->internal_level);
24921 }
24922 if (GetStatus (dlg->end5)) {
24923 Enable (dlg->end5_level);
24924 } else {
24925 Disable (dlg->end5_level);
24926 }
24927 if (GetStatus (dlg->end3)) {
24928 Enable (dlg->end3_level);
24929 } else {
24930 Disable (dlg->end3_level);
24931 }
24932
24933 if (dlg->change_notify != NULL) {
24934 (dlg->change_notify)(dlg->change_userdata);
24935 }
24936 }
24937
24938
ChangeVectorContaminationGroup(GrouP g)24939 static void ChangeVectorContaminationGroup (GrouP g)
24940 {
24941 VectorContaminationOptionsDlgPtr dlg;
24942
24943 dlg = (VectorContaminationOptionsDlgPtr) GetObjectExtra (g);
24944 if (dlg != NULL && dlg->change_notify != NULL) {
24945 (dlg->change_notify)(dlg->change_userdata);
24946 }
24947 }
24948
24949
VectorContaminationOptionsDialog(GrouP h,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)24950 static DialoG VectorContaminationOptionsDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
24951 {
24952 VectorContaminationOptionsDlgPtr dlg;
24953 GrouP p;
24954
24955 dlg = (VectorContaminationOptionsDlgPtr) MemNew (sizeof (VectorContaminationOptionsDlgData));
24956 if (dlg == NULL)
24957 {
24958 return NULL;
24959 }
24960
24961 p = HiddenGroup (h, 2, 0, NULL);
24962 SetObjectExtra (p, dlg, StdCleanupExtraProc);
24963 SetGroupSpacing (p, 10, 10);
24964
24965 dlg->dialog = (DialoG) p;
24966 dlg->todialog = DataToVectorContaminationOptionsDlg;
24967 dlg->fromdialog = VectorContaminationOptionsDlgToData;
24968 dlg->dialogmessage = NULL;
24969 dlg->testdialog = NULL;
24970 dlg->change_notify = change_notify;
24971 dlg->change_userdata = change_userdata;
24972
24973 dlg->internal = CheckBox (p, "Internal", ChangeVectorContaminationButton);
24974 SetObjectExtra (dlg->internal, dlg, NULL);
24975 dlg->internal_level = HiddenGroup (p, 4, 0, ChangeVectorContaminationGroup);
24976 SetObjectExtra (dlg->internal_level, dlg, NULL);
24977 RadioButton (dlg->internal_level, "Suspect");
24978 RadioButton (dlg->internal_level, "Weak");
24979 RadioButton (dlg->internal_level, "Moderate");
24980 RadioButton (dlg->internal_level, "Strong");
24981 SetValue (dlg->internal_level, 1);
24982 Disable (dlg->internal_level);
24983
24984 dlg->end5 = CheckBox (p, "5' End", ChangeVectorContaminationButton);
24985 SetObjectExtra (dlg->end5, dlg, NULL);
24986 dlg->end5_level = HiddenGroup (p, 4, 0, ChangeVectorContaminationGroup);
24987 SetObjectExtra (dlg->end5_level, dlg, NULL);
24988 RadioButton (dlg->end5_level, "Suspect");
24989 RadioButton (dlg->end5_level, "Weak");
24990 RadioButton (dlg->end5_level, "Moderate");
24991 RadioButton (dlg->end5_level, "Strong");
24992 SetValue (dlg->end5_level, 1);
24993 Disable (dlg->end5_level);
24994
24995 dlg->end3 = CheckBox (p, "3' End", ChangeVectorContaminationButton);
24996 SetObjectExtra (dlg->end3, dlg, NULL);
24997 dlg->end3_level = HiddenGroup (p, 4, 0, ChangeVectorContaminationGroup);
24998 SetObjectExtra (dlg->end3_level, dlg, NULL);
24999 RadioButton (dlg->end3_level, "Suspect");
25000 RadioButton (dlg->end3_level, "Weak");
25001 RadioButton (dlg->end3_level, "Moderate");
25002 RadioButton (dlg->end3_level, "Strong");
25003 SetValue (dlg->end3_level, 1);
25004 Disable (dlg->end3_level);
25005
25006 return (DialoG) p;
25007 }
25008
25009
25010 typedef struct chooseseqsbylen {
25011 ValNodePtr bsp_list;
25012 Int4 min;
25013 Int4 max;
25014 } ChooseSeqsByLenData, PNTR ChooseSeqsByLenPtr;
25015
25016
25017 typedef struct chooseseqsbylendlg {
25018 DIALOG_MESSAGE_BLOCK
25019 TexT min;
25020 TexT max;
25021 Nlm_ChangeNotifyProc change_notify;
25022 Pointer change_userdata;
25023 } ChooseSeqsByLenDlgData, PNTR ChooseSeqsByLenDlgPtr;
25024
25025
DataToChooseSeqsByLenDlg(DialoG d,Pointer data)25026 static void DataToChooseSeqsByLenDlg (DialoG d, Pointer data)
25027 {
25028 ChooseSeqsByLenDlgPtr dlg;
25029 ChooseSeqsByLenPtr options;
25030 Char buf[255];
25031
25032 dlg = (ChooseSeqsByLenDlgPtr) GetObjectExtra (d);
25033 if (dlg == NULL) {
25034 return;
25035 }
25036
25037 options = (ChooseSeqsByLenPtr) data;
25038 if (options == NULL) {
25039 SetTitle (dlg->min, "0");
25040 SetTitle (dlg->max, "0");
25041 } else {
25042 sprintf (buf, "%d", options->min);
25043 SetTitle (dlg->min, buf);
25044 sprintf (buf, "%d", options->max);
25045 SetTitle (dlg->max, buf);
25046 }
25047 }
25048
25049
ChooseSeqsByLenDlgToData(DialoG d)25050 static Pointer ChooseSeqsByLenDlgToData (DialoG d)
25051 {
25052 ChooseSeqsByLenDlgPtr dlg;
25053 ChooseSeqsByLenPtr options = NULL;
25054 CharPtr buf;
25055
25056 dlg = (ChooseSeqsByLenDlgPtr) GetObjectExtra (d);
25057 if (dlg == NULL) {
25058 return NULL;
25059 }
25060
25061 options = (ChooseSeqsByLenPtr) MemNew (sizeof (ChooseSeqsByLenData));
25062 if (TextHasNoText (dlg->min)) {
25063 options->min = 0;
25064 } else {
25065 buf = SaveStringFromText (dlg->min);
25066 options->min = atoi (buf);
25067 buf = MemFree (buf);
25068 }
25069 if (TextHasNoText (dlg->max)) {
25070 options->max = 0;
25071 } else {
25072 buf = SaveStringFromText (dlg->max);
25073 options->max = atoi (buf);
25074 buf = MemFree (buf);
25075 }
25076 return (Pointer) options;
25077 }
25078
25079
ChangeChooseSeqsByLenText(TexT t)25080 static void ChangeChooseSeqsByLenText (TexT t)
25081 {
25082 ChooseSeqsByLenDlgPtr dlg;
25083
25084 dlg = (ChooseSeqsByLenDlgPtr) GetObjectExtra (t);
25085 if (dlg == NULL) {
25086 return;
25087 }
25088
25089 if (dlg->change_notify != NULL) {
25090 (dlg->change_notify)(dlg->change_userdata);
25091 }
25092 }
25093
25094
ChooseSeqsByLenDialog(GrouP h,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata)25095 static DialoG ChooseSeqsByLenDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
25096 {
25097 ChooseSeqsByLenDlgPtr dlg;
25098 GrouP p;
25099
25100 dlg = (ChooseSeqsByLenDlgPtr) MemNew (sizeof (ChooseSeqsByLenDlgData));
25101 if (dlg == NULL)
25102 {
25103 return NULL;
25104 }
25105
25106 p = HiddenGroup (h, 2, 0, NULL);
25107 SetObjectExtra (p, dlg, StdCleanupExtraProc);
25108 SetGroupSpacing (p, 10, 10);
25109
25110 dlg->dialog = (DialoG) p;
25111 dlg->todialog = DataToChooseSeqsByLenDlg;
25112 dlg->fromdialog = ChooseSeqsByLenDlgToData;
25113 dlg->dialogmessage = NULL;
25114 dlg->testdialog = NULL;
25115 dlg->change_notify = change_notify;
25116 dlg->change_userdata = change_userdata;
25117
25118 StaticPrompt (p, "Minimum length", 0, dialogTextHeight, programFont, 'c');
25119 dlg->min = DialogText (p, "0", 10, ChangeChooseSeqsByLenText);
25120 SetObjectExtra (dlg->min, dlg, NULL);
25121 StaticPrompt (p, "Maximum length", 0, dialogTextHeight, programFont, 'c');
25122 dlg->max = DialogText (p, "50", 10, ChangeChooseSeqsByLenText);
25123 SetObjectExtra (dlg->max, dlg, NULL);
25124
25125 return (DialoG) p;
25126 }
25127
25128
25129 typedef enum {
25130 eSegPageId = 1,
25131 eSegPageText,
25132 eSegPageField,
25133 eSegPageMolInfo,
25134 eSegPageFeatureType,
25135 eSegPageDescriptorType,
25136 eSegPageLength,
25137 eSegPageVectorContamination,
25138 eSegPageNumFinalSets,
25139 eSegPageFile,
25140 eSegPageConstraint,
25141 eSegPageStructuredCommentField,
25142 eNumSegPages
25143 } ESegPage;
25144
25145 typedef struct segbyfield {
25146 FORM_MESSAGE_BLOCK
25147 GrouP seg_choice_grp;
25148
25149 GrouP pages[eNumSegPages];
25150 /* for segregating by field */
25151 DialoG field_dlg;
25152 DialoG group_list_dlg;
25153
25154 /* for segregating by molinfo */
25155 ButtoN mol_type_btn;
25156 ButtoN mol_class_btn;
25157 ButtoN mol_topology_btn;
25158
25159 /* for segregating by feature */
25160 DialoG feature_select;
25161
25162 /* for segregating by descriptor */
25163 DialoG descriptor_select;
25164
25165 /* for segregating by text */
25166 DialoG search_field;
25167 TexT search_text;
25168
25169 /* for segregating by ID */
25170 DialoG id_constraint_dlg;
25171
25172 /* for segregating by length */
25173 DialoG len_options;
25174
25175 /* for segregating by vector contamination */
25176 DialoG vector_options;
25177
25178 /* for segregating into a specific number of sets */
25179 TexT num_sets;
25180
25181 /* for segregating by any constraint */
25182 DialoG seq_constraint_dlg;
25183
25184 /* for segregating by structured comment field */
25185 DialoG struc_comm_field;
25186
25187 Nlm_BtnActnProc actn;
25188 ButtoN accept;
25189 ButtoN leave_dlg_up;
25190 BioseqSetPtr target_set;
25191 ValNodePtr value_lists;
25192 } SegByFieldData, PNTR SegByFieldPtr;
25193
25194 static void ChangeSegChoice (GrouP g);
25195
25196
PullChosenIntoOneGroup(ValNodePtr PNTR value_list,ClickableItemPtr chosen)25197 static void PullChosenIntoOneGroup (ValNodePtr PNTR value_list, ClickableItemPtr chosen)
25198 {
25199 ValNodePtr vnp_prev = NULL, vnp_next, vnp_this;
25200 ClickableItemPtr cip;
25201
25202 if (value_list == NULL || chosen == NULL) return;
25203
25204 vnp_this = *value_list;
25205 while (vnp_this != NULL)
25206 {
25207 vnp_next = vnp_this->next;
25208 cip = (ClickableItemPtr) vnp_this->data.ptrvalue;
25209 if (cip == NULL)
25210 {
25211 vnp_this->next = NULL;
25212 if (vnp_prev == NULL)
25213 {
25214 *value_list = vnp_next;
25215 }
25216 else
25217 {
25218 vnp_prev->next = vnp_next;
25219 }
25220 vnp_this = ValNodeFree (vnp_this);
25221 }
25222 else if (cip->chosen)
25223 {
25224 vnp_this->next = NULL;
25225 if (vnp_prev == NULL)
25226 {
25227 *value_list = vnp_next;
25228 }
25229 else
25230 {
25231 vnp_prev->next = vnp_next;
25232 }
25233 ValNodeLink (&(chosen->item_list), cip->item_list);
25234 cip->item_list = NULL;
25235 vnp_this = FreeClickableList (vnp_this);
25236 }
25237 else
25238 {
25239 PullChosenIntoOneGroup (&(cip->subcategories), chosen);
25240 vnp_prev = vnp_this;
25241 }
25242 vnp_this = vnp_next;
25243 }
25244 }
25245
25246
NumChosenThatContainSequencesInAlignments(ValNodePtr value_lists,Boolean count_all)25247 static Int4 NumChosenThatContainSequencesInAlignments (ValNodePtr value_lists, Boolean count_all)
25248 {
25249 Int4 rval = 0;
25250 ClickableItemPtr cip;
25251 ValNodePtr vnp, vnp_item;
25252 BioseqPtr bsp;
25253 BioseqSetPtr bssp;
25254 SeqEntryPtr sep;
25255
25256 if (value_lists == NULL)
25257 {
25258 return 0;
25259 }
25260
25261 for (vnp = value_lists; vnp != NULL; vnp = vnp->next)
25262 {
25263 cip = (ClickableItemPtr) vnp->data.ptrvalue;
25264 if (cip == NULL)
25265 {
25266 /* ignore */
25267 }
25268 else if (cip->chosen || count_all)
25269 {
25270 if (cip->item_list == NULL)
25271 {
25272 rval += NumChosenThatContainSequencesInAlignments (cip->subcategories, TRUE);
25273 }
25274 else
25275 {
25276 for (vnp_item = cip->item_list; vnp_item != NULL; vnp_item = vnp_item->next)
25277 {
25278 if (vnp_item->choice == OBJ_BIOSEQ)
25279 {
25280 bsp = (BioseqPtr) vnp_item->data.ptrvalue;
25281 if (bsp != NULL && IsBioseqInAnyAlignment (bsp, bsp->idx.entityID))
25282 {
25283 rval++;
25284 }
25285 }
25286 else if (vnp_item->choice == OBJ_BIOSEQSET)
25287 {
25288 bssp = (BioseqSetPtr) vnp_item->data.ptrvalue;
25289 if (bssp != NULL && AreAnyElementsOfSetInAnyAlignment (bssp, bssp->idx.entityID))
25290 {
25291 rval++;
25292 }
25293 }
25294 else if (vnp_item->choice == OBJ_SEQENTRY)
25295 {
25296 sep = vnp_item->data.ptrvalue;
25297 if (IS_Bioseq (sep))
25298 {
25299 bsp = (BioseqPtr) sep->data.ptrvalue;
25300 if (bsp != NULL && IsBioseqInAnyAlignment (bsp, bsp->idx.entityID))
25301 {
25302 rval++;
25303 }
25304 }
25305 else if (IS_Bioseq_set(sep))
25306 {
25307 bssp = (BioseqSetPtr) sep->data.ptrvalue;
25308 if (bssp != NULL && AreAnyElementsOfSetInAnyAlignment (bssp, bssp->idx.entityID))
25309 {
25310 rval++;
25311 }
25312 }
25313 }
25314 }
25315 }
25316 }
25317 else
25318 {
25319 rval += NumChosenThatContainSequencesInAlignments (cip->subcategories, FALSE);
25320 }
25321 }
25322
25323 return rval;
25324 }
25325
25326
RemoveAlignmentsWithChosenSegregateSequences(ValNodePtr value_lists,Uint2 entityID,Boolean all_chosen)25327 static void RemoveAlignmentsWithChosenSegregateSequences (ValNodePtr value_lists, Uint2 entityID, Boolean all_chosen)
25328 {
25329 ClickableItemPtr cip;
25330 ValNodePtr vnp, vnp_item;
25331 BioseqPtr bsp;
25332 SeqEntryPtr sep;
25333
25334 if (value_lists == NULL)
25335 {
25336 return;
25337 }
25338
25339 for (vnp = value_lists; vnp != NULL; vnp = vnp->next)
25340 {
25341 cip = (ClickableItemPtr) vnp->data.ptrvalue;
25342 if (cip == NULL)
25343 {
25344 /* ignore */
25345 }
25346 else if (cip->chosen || all_chosen)
25347 {
25348 if (cip->item_list == NULL)
25349 {
25350 RemoveAlignmentsWithChosenSegregateSequences (cip->subcategories, entityID, TRUE);
25351 }
25352 else
25353 {
25354 for (vnp_item = cip->item_list; vnp_item != NULL; vnp_item = vnp_item->next)
25355 {
25356 if (vnp_item->choice == OBJ_BIOSEQ)
25357 {
25358 bsp = (BioseqPtr) vnp_item->data.ptrvalue;
25359 RemoveAlignmentsWithSequence (bsp, entityID);
25360 }
25361 else if (vnp_item->choice == OBJ_BIOSEQSET)
25362 {
25363 RemoveAlignmentsWithElementsOfSet (vnp_item->data.ptrvalue, entityID);
25364 }
25365 else if (vnp_item->choice == OBJ_SEQENTRY)
25366 {
25367 sep = vnp_item->data.ptrvalue;
25368 if (IS_Bioseq (sep))
25369 {
25370 bsp = (BioseqPtr) sep->data.ptrvalue;
25371 RemoveAlignmentsWithSequence (bsp, entityID);
25372 }
25373 else if (IS_Bioseq_set(sep))
25374 {
25375 RemoveAlignmentsWithElementsOfSet (sep->data.ptrvalue, entityID);
25376 }
25377 }
25378
25379 }
25380 }
25381 }
25382 else
25383 {
25384 RemoveAlignmentsWithChosenSegregateSequences (cip->subcategories, entityID, FALSE);
25385 }
25386 }
25387 }
25388
PropagateDescriptorBeforeSegregate(SeqEntryPtr sep)25389 static void PropagateDescriptorBeforeSegregate(SeqEntryPtr sep)
25390 {
25391 BioseqSetPtr bssp;
25392
25393 if (sep == NULL || !IS_Bioseq_set(sep)
25394 || (bssp = (BioseqSetPtr) sep->data.ptrvalue) == NULL
25395 || bssp->_class == BioseqseqSet_class_nuc_prot) {
25396 return;
25397 }
25398 SetDescriptorPropagate(bssp);
25399 for (sep = bssp->seq_set; sep != NULL; sep = sep->next) {
25400 PropagateDescriptorBeforeSegregate(sep);
25401 }
25402 }
25403
25404
SegregateByField_Callback(ButtoN b)25405 static void SegregateByField_Callback (ButtoN b)
25406 {
25407 SegByFieldPtr sfp;
25408 Int4 num_chosen = 0, num_in_align;
25409 ClickableItemPtr cip;
25410 Int2 val;
25411 MsgAnswer ans;
25412 SeqEntryPtr sep, orig_sep;
25413
25414 sfp = (SegByFieldPtr) GetObjectExtra (b);
25415 if (sfp == NULL) return;
25416
25417 num_chosen = CountChosenDiscrepancies (sfp->value_lists, FALSE);
25418 if (num_chosen < 1) {
25419 if (ANS_OK == Message (MSG_OKC, "You have not chosen any groups. Create all?")) {
25420 ChooseAllDiscrepancies (sfp->value_lists);
25421 } else {
25422 return;
25423 }
25424 }
25425
25426 sep = GetTopSeqEntryForEntityID (sfp->input_entityID);
25427 if (sep == NULL) {
25428 Message (MSG_ERROR, "No Seq-entry to segregate!");
25429 } else if (!IS_Bioseq_set(sep)) {
25430 Message (MSG_ERROR, "Cannot segregate a single sequence!");
25431 }
25432
25433 orig_sep = SeqEntrySetScope (sep);
25434 num_in_align = NumChosenThatContainSequencesInAlignments(sfp->value_lists, FALSE);
25435 SeqEntrySetScope (orig_sep);
25436 if (num_in_align > 0) {
25437 ans = Message (MSG_YNC, "%d sequences are in alignments. Do you want to remove the alignments?", num_in_align);
25438 if (ans == ANS_CANCEL) {
25439 ChangeSegChoice (sfp->seg_choice_grp);
25440 return;
25441 } else if (ans == ANS_YES) {
25442 RemoveAlignmentsWithChosenSegregateSequences (sfp->value_lists, sfp->input_entityID, FALSE);
25443 }
25444 }
25445
25446 RemovePopsetTitles (sep);
25447 PropagateDescriptorBeforeSegregate (sep);
25448
25449 val = GetValue (sfp->seg_choice_grp);
25450 if (val == eSegPageId || val == eSegPageVectorContamination || val == eSegPageLength || val == eSegPageConstraint) {
25451 /* put all selected sequences into one group */
25452 cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
25453 cip->chosen = TRUE;
25454 PullChosenIntoOneGroup (&(sfp->value_lists), cip);
25455 ValNodeAddPointer (&(sfp->value_lists), 0, cip);
25456 }
25457
25458 sfp->target_set = MakeGroupsForUniqueValues (sfp->target_set, sfp->value_lists);
25459
25460 if (GetStatus (sfp->leave_dlg_up)) {
25461 ChangeSegChoice (sfp->seg_choice_grp);
25462 } else {
25463 Remove (sfp->form);
25464 }
25465 }
25466
ChangeSegField(Pointer userdata)25467 static void ChangeSegField (Pointer userdata)
25468 {
25469 SegByFieldPtr sfp = (SegByFieldPtr) userdata;
25470 SeqEntryPtr sep;
25471 ParseFieldPtr dst_field_data;
25472
25473 if (sfp == NULL || sfp->target_set == NULL) return;
25474
25475 WatchCursor();
25476 Update();
25477 sep = SeqMgrGetSeqEntryForData (sfp->target_set);
25478
25479 PointerToDialog (sfp->group_list_dlg, NULL);
25480 sfp->value_lists = FreeClickableList (sfp->value_lists);
25481
25482 dst_field_data = DialogToPointer (sfp->field_dlg);
25483 if (dst_field_data == NULL) {
25484 Disable (sfp->accept);
25485 return;
25486 }
25487
25488 sfp->value_lists = CreateSeqEntryListsForUniqueValues (sep, sfp->target_set->idx.entityID, dst_field_data, NULL);
25489 dst_field_data = ParseFieldFree (dst_field_data);
25490 PointerToDialog (sfp->group_list_dlg, sfp->value_lists);
25491 Enable (sfp->accept);
25492 ArrowCursor();
25493 Update();
25494 }
25495
25496
ChangeSegStructuredCommentField(Pointer userdata)25497 static void ChangeSegStructuredCommentField (Pointer userdata)
25498 {
25499 SegByFieldPtr sfp = (SegByFieldPtr) userdata;
25500 SeqEntryPtr sep;
25501 ValNodePtr vnp;
25502
25503 if (sfp == NULL || sfp->target_set == NULL) return;
25504
25505 sep = SeqMgrGetSeqEntryForData (sfp->target_set);
25506
25507 PointerToDialog (sfp->group_list_dlg, NULL);
25508 sfp->value_lists = FreeClickableList (sfp->value_lists);
25509
25510 vnp = DialogToPointer (sfp->struc_comm_field);
25511 if (vnp == NULL) {
25512 Disable (sfp->accept);
25513 return;
25514 }
25515
25516 WatchCursor();
25517 Update();
25518
25519 sfp->value_lists = GetUniqueValuesForStructuredCommentField (sep, vnp->data.ptrvalue);
25520 sfp->value_lists = ChangeUniqueValueListsToSeqEntryLists (sfp->value_lists);
25521 vnp = ValNodeFreeData (vnp);
25522
25523 PointerToDialog (sfp->group_list_dlg, sfp->value_lists);
25524 Enable (sfp->accept);
25525 ArrowCursor();
25526 Update();
25527 }
25528
25529
SegTextChangeNotify(Pointer userdata)25530 static void SegTextChangeNotify (Pointer userdata)
25531 {
25532 SegByFieldPtr sfp = (SegByFieldPtr) userdata;
25533 SeqEntryPtr sep;
25534 ParseFieldPtr dst_field_data;
25535 CharPtr search_text;
25536
25537 if (sfp == NULL || sfp->target_set == NULL) return;
25538
25539 WatchCursor();
25540 Update();
25541 sep = SeqMgrGetSeqEntryForData (sfp->target_set);
25542
25543 PointerToDialog (sfp->group_list_dlg, NULL);
25544 sfp->value_lists = FreeClickableList (sfp->value_lists);
25545
25546 if (TextHasNoText (sfp->search_text)) {
25547 Disable (sfp->accept);
25548 ArrowCursor();
25549 Update();
25550 return;
25551 }
25552 dst_field_data = DialogToPointer (sfp->search_field);
25553 if (dst_field_data == NULL) {
25554 Disable (sfp->accept);
25555 ArrowCursor();
25556 Update();
25557 return;
25558 }
25559 search_text = SaveStringFromText (sfp->search_text);
25560
25561 sfp->value_lists = GetTextSeqEntryListForSeqEntry (sep, sfp->target_set->idx.entityID, search_text, dst_field_data);
25562
25563 search_text = MemFree (search_text);
25564
25565 dst_field_data = ParseFieldFree (dst_field_data);
25566 PointerToDialog (sfp->group_list_dlg, sfp->value_lists);
25567 if (sfp->value_lists == NULL) {
25568 Disable(sfp->accept);
25569 } else {
25570 Enable (sfp->accept);
25571 }
25572 ArrowCursor();
25573 Update();
25574 }
25575
SegTextChange(TexT t)25576 static void SegTextChange (TexT t)
25577 {
25578 SegByFieldPtr sfp;
25579
25580 sfp = (SegByFieldPtr) GetObjectExtra (t);
25581
25582 SegTextChangeNotify (sfp);
25583
25584 }
25585
25586
IsBankitId(SeqIdPtr sip)25587 static Boolean IsBankitId (SeqIdPtr sip)
25588 {
25589 DbtagPtr dbtag;
25590
25591 if (sip == NULL || sip->choice != SEQID_GENERAL) {
25592 return FALSE;
25593 }
25594 if ((dbtag = (DbtagPtr) sip->data.ptrvalue) == NULL) {
25595 return FALSE;
25596 }
25597 if (StringCmp (dbtag->db, "BankIt") == 0) {
25598 return TRUE;
25599 } else {
25600 return FALSE;
25601 }
25602 }
25603
25604
ClickableItemForBioseq(BioseqPtr bsp)25605 NLM_EXTERN ClickableItemPtr ClickableItemForBioseq (BioseqPtr bsp)
25606 {
25607 ClickableItemPtr cip = NULL;
25608 SeqIdPtr sip, sip2;
25609 Char id_str[3][100];
25610 Int4 num_id = 1, len = 0;
25611 Int4 i;
25612
25613 if (bsp != NULL && ! ISA_aa (bsp->mol))
25614 {
25615 cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
25616 sip = SeqIdFindBest (bsp->id, SEQID_GENBANK);
25617 SeqIdWrite (sip, id_str[0], PRINTID_REPORT, sizeof (id_str[0]) - 1);
25618 len = StringLen (id_str[0]) + 1;
25619 if (!IsBankitId(sip)) {
25620 sip2 = bsp->id;
25621 while (sip2 != NULL && !IsBankitId(sip2)) {
25622 sip2 = sip2->next;
25623 }
25624 if (sip2 != NULL) {
25625 SeqIdWrite (sip2, id_str[1], PRINTID_REPORT, sizeof (id_str[1]) - 1);
25626 len += StringLen (id_str[1]) + 1;
25627 num_id++;
25628 }
25629 }
25630 if (!IsNCBIFileID(sip)) {
25631 sip2 = bsp->id;
25632 while (sip2 != NULL && !IsNCBIFileID(sip2)) {
25633 sip2 = sip2->next;
25634 }
25635 if (sip2 != NULL) {
25636 SeqIdWrite (sip2, id_str[1], PRINTID_REPORT, sizeof (id_str[1]) - 1);
25637 len += StringLen (id_str[1]) + 1;
25638 num_id++;
25639 }
25640 }
25641
25642 /* space for length */
25643 len += 20;
25644
25645 cip->description = (CharPtr) MemNew (sizeof (Char) * len);
25646 sprintf (cip->description, "%s", id_str[0]);
25647 for (i = 1; i < num_id; i++) {
25648 StringCat (cip->description, "|");
25649 StringCat (cip->description, id_str[i]);
25650 }
25651 sprintf (cip->description + StringLen (cip->description), ":%d", bsp->length);
25652
25653 ValNodeAddPointer (&(cip->item_list), OBJ_BIOSEQ, bsp);
25654 }
25655 return cip;
25656 }
25657
25658
ListAllSequences(BioseqPtr bsp,Pointer userdata)25659 extern void ListAllSequences (BioseqPtr bsp, Pointer userdata)
25660 {
25661 ClickableItemPtr cip;
25662
25663 cip = ClickableItemForBioseq (bsp);
25664 if (cip != NULL)
25665 {
25666 ValNodeAddPointer ((ValNodePtr PNTR) userdata, 0, cip);
25667 }
25668 }
25669
25670
ChooseSegId(Pointer userdata)25671 static void ChooseSegId (Pointer userdata)
25672 {
25673 SegByFieldPtr sfp = (SegByFieldPtr) userdata;
25674 SeqEntryPtr sep;
25675
25676 if (sfp == NULL || sfp->target_set == NULL) return;
25677
25678 WatchCursor();
25679 Update();
25680 sep = SeqMgrGetSeqEntryForData (sfp->target_set);
25681
25682 PointerToDialog (sfp->group_list_dlg, NULL);
25683 sfp->value_lists = FreeClickableList (sfp->value_lists);
25684
25685 VisitBioseqsInSep (sep, &sfp->value_lists, ListAllSequences);
25686
25687 PointerToDialog (sfp->group_list_dlg, sfp->value_lists);
25688 if (sfp->value_lists == NULL) {
25689 Disable(sfp->accept);
25690 } else {
25691 Enable (sfp->accept);
25692 }
25693 ArrowCursor();
25694 Update();
25695 }
25696
25697
DoesLevelStringMatchLevel(CharPtr str,Int4 level)25698 static Boolean DoesLevelStringMatchLevel (CharPtr str, Int4 level)
25699 {
25700 Boolean rval = FALSE;
25701
25702 switch (level) {
25703 case eVectorHitLevelSuspect:
25704 if (StringISearch (str, "suspect") != NULL) {
25705 rval = TRUE;
25706 }
25707 /* note - absence of break is deliberate */
25708 case eVectorHitLevelWeak:
25709 if (StringISearch (str, "weak") != NULL) {
25710 rval = TRUE;
25711 }
25712 /* note - absence of break is deliberate */
25713 case eVectorHitLevelModerate:
25714 if (StringISearch (str, "moderate") != NULL) {
25715 rval = TRUE;
25716 }
25717 /* note - absence of break is deliberate */
25718 case eVectorHitLevelStrong:
25719 if (StringISearch (str, "strong") != NULL) {
25720 rval = TRUE;
25721 }
25722 break;
25723 }
25724 return rval;
25725 }
25726
25727
DoesVectorMatchOptions(ClickableItemPtr cip,VectorContaminationOptionsPtr options)25728 static Boolean DoesVectorMatchOptions (ClickableItemPtr cip, VectorContaminationOptionsPtr options)
25729 {
25730 Boolean rval = FALSE;
25731
25732 if (cip == NULL || options == NULL || StringHasNoText (cip->description)) {
25733 return FALSE;
25734 }
25735
25736 if (options->internal_level > 0
25737 && StringNICmp (cip->description, "Internal", 8) == 0
25738 && DoesLevelStringMatchLevel (cip->description, options->internal_level)) {
25739 rval = TRUE;
25740 } else if (options->end5_level > 0
25741 && StringNICmp (cip->description, "5'", 2) == 0
25742 && DoesLevelStringMatchLevel (cip->description, options->end5_level)) {
25743 rval = TRUE;
25744 } else if (options->end3_level > 0
25745 && StringNICmp (cip->description, "3'", 2) == 0
25746 && DoesLevelStringMatchLevel (cip->description, options->end3_level)) {
25747 rval = TRUE;
25748 }
25749 return rval;
25750 }
25751
25752
GetVectorBioseqList(BioseqPtr bsp,Pointer data)25753 static void GetVectorBioseqList (BioseqPtr bsp, Pointer data)
25754 {
25755 VectorContaminationOptionsPtr options;
25756 SeqFeatPtr sfp;
25757 SeqMgrFeatContext fcontext;
25758 Boolean isvector;
25759 GBQualPtr gbq;
25760 Int4 last_right;
25761 ClickableItemPtr cip = NULL, cip_match;
25762 ValNodePtr vector_list = NULL, vnp;
25763 Int4 desc_len = 0;
25764 Boolean is_match = FALSE;
25765
25766 if (bsp == NULL || data == NULL) {
25767 return;
25768 }
25769
25770 options = (VectorContaminationOptionsPtr) data;
25771
25772 for (sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_IMP, FEATDEF_misc_feature, &fcontext);
25773 sfp != NULL;
25774 sfp = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_IMP, FEATDEF_misc_feature, &fcontext)) {
25775 for (isvector = FALSE, gbq = sfp->qual; gbq != NULL; gbq = gbq->next) {
25776 if (StringCmp (gbq->qual, "standard_name") == 0) {
25777 if (StringCmp (gbq->val, "Vector Contamination") == 0) {
25778 isvector = TRUE;
25779 }
25780 }
25781 }
25782 if (isvector) {
25783 if (cip != NULL && last_right >= fcontext.left - 1) {
25784 ValNodeAddPointer (&(cip->item_list), OBJ_SEQFEAT, sfp);
25785 last_right = fcontext.right;
25786 } else {
25787 /* calculate description for previous list */
25788 CalculateVectorDescription (cip);
25789 cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
25790 if (cip != NULL) {
25791 cip->clickable_item_type = 0;
25792 cip->callback_func = NULL;
25793 cip->datafree_func = NULL;
25794 cip->callback_data = NULL;
25795 cip->item_list = NULL;
25796 cip->subcategories = NULL;
25797 cip->expanded = FALSE;
25798 cip->level = 0;
25799 cip->description = NULL;
25800
25801 ValNodeAddPointer (&(cip->item_list), OBJ_SEQFEAT, sfp);
25802
25803 ValNodeAddPointer (&vector_list, 0, cip);
25804 last_right = fcontext.right;
25805 }
25806 }
25807 }
25808 }
25809 /* calculate description for last item */
25810 CalculateVectorDescription (cip);
25811
25812 /* now determine whether we have a hit that matches our requirements */
25813 for (vnp = vector_list; vnp != NULL; vnp = vnp->next) {
25814 cip = vnp->data.ptrvalue;
25815 if (DoesVectorMatchOptions (cip, options)) {
25816 is_match = TRUE;
25817 }
25818 desc_len += StringLen (cip->description) + 2;
25819 }
25820
25821 if (is_match) {
25822 cip_match = MemNew (sizeof (ClickableItemData));
25823 cip_match->description = (CharPtr) MemNew (sizeof (Char) * desc_len);
25824 cip_match->description[0] = 0;
25825 for (vnp = vector_list; vnp != NULL; vnp = vnp->next) {
25826 cip = vnp->data.ptrvalue;
25827 StringCat (cip_match->description, cip->description);
25828 if (vnp->next != NULL) {
25829 StringCat (cip_match->description, ";");
25830 }
25831 }
25832 ValNodeAddPointer (&(cip_match->item_list), OBJ_BIOSEQ, bsp);
25833 cip_match->chosen = TRUE;
25834 ValNodeAddPointer (&(options->bioseq_list), 0, cip_match);
25835 }
25836 vector_list = FreeClickableList (vector_list);
25837 }
25838
25839
ChooseVectorSeqs(Pointer userdata)25840 static void ChooseVectorSeqs (Pointer userdata)
25841 {
25842 SegByFieldPtr sfp = (SegByFieldPtr) userdata;
25843 SeqEntryPtr sep;
25844 VectorContaminationOptionsPtr options;
25845
25846 if (sfp == NULL || sfp->target_set == NULL) return;
25847
25848 WatchCursor();
25849 Update();
25850 sep = SeqMgrGetSeqEntryForData (sfp->target_set);
25851
25852 PointerToDialog (sfp->group_list_dlg, NULL);
25853 sfp->value_lists = FreeClickableList (sfp->value_lists);
25854
25855 options = DialogToPointer (sfp->vector_options);
25856
25857 VisitBioseqsInSep (sep, options, GetVectorBioseqList);
25858
25859 sfp->value_lists = options->bioseq_list;
25860 options->bioseq_list = NULL;
25861
25862 options = MemFree (options);
25863
25864 PointerToDialog (sfp->group_list_dlg, sfp->value_lists);
25865 if (sfp->value_lists == NULL) {
25866 Disable(sfp->accept);
25867 } else {
25868 Enable (sfp->accept);
25869 }
25870 ArrowCursor();
25871 Update();
25872 }
25873
25874
SeqsByLenCallback(BioseqPtr bsp,Pointer userdata)25875 static void SeqsByLenCallback (BioseqPtr bsp, Pointer userdata)
25876 {
25877 ChooseSeqsByLenPtr p = (ChooseSeqsByLenPtr) userdata;
25878 ClickableItemPtr cip_match;
25879 CharPtr fmt = "%s %d";
25880 Char id_str[45];
25881
25882 if (bsp == NULL || ISA_aa (bsp->mol) || p == NULL) {
25883 return;
25884 }
25885
25886 if (bsp->length >= p->min && bsp->length <= p->max) {
25887 cip_match = MemNew (sizeof (ClickableItemData));
25888
25889 /* create description (use ID and length ) */
25890 SeqIdWrite (SeqIdFindBest (bsp->id, SEQID_GENBANK), id_str, PRINTID_REPORT, sizeof (id_str) - 1);
25891 cip_match->description = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (id_str) + 15));
25892 sprintf (cip_match->description, fmt, id_str, bsp->length);
25893
25894 ValNodeAddPointer (&(cip_match->item_list), OBJ_BIOSEQ, bsp);
25895 cip_match->chosen = TRUE;
25896 ValNodeAddPointer (&(p->bsp_list), 0, cip_match);
25897 }
25898 }
25899
25900
ChooseSeqsByLen(Pointer userdata)25901 static void ChooseSeqsByLen (Pointer userdata)
25902 {
25903 SegByFieldPtr sfp = (SegByFieldPtr) userdata;
25904 SeqEntryPtr sep;
25905 ChooseSeqsByLenPtr options;
25906
25907 if (sfp == NULL || sfp->target_set == NULL) return;
25908
25909 WatchCursor();
25910 Update();
25911 sep = SeqMgrGetSeqEntryForData (sfp->target_set);
25912
25913 PointerToDialog (sfp->group_list_dlg, NULL);
25914 sfp->value_lists = FreeClickableList (sfp->value_lists);
25915
25916 options = DialogToPointer (sfp->len_options);
25917
25918 VisitBioseqsInSep (sep, options, SeqsByLenCallback);
25919
25920 sfp->value_lists = options->bsp_list;
25921 options->bsp_list = NULL;
25922
25923 options = MemFree (options);
25924 PointerToDialog (sfp->group_list_dlg, sfp->value_lists);
25925 if (sfp->value_lists == NULL) {
25926 Disable(sfp->accept);
25927 } else {
25928 Enable (sfp->accept);
25929 }
25930 ArrowCursor();
25931 Update();
25932 }
25933
25934
ChangeMol(ButtoN b)25935 static void ChangeMol (ButtoN b)
25936 {
25937 SegByFieldPtr sfp;
25938 SeqEntryPtr sep;
25939
25940 sfp = (SegByFieldPtr) GetObjectExtra (b);
25941
25942 if (sfp == NULL) return;
25943
25944 WatchCursor ();
25945 Update();
25946 sep = SeqMgrGetSeqEntryForData (sfp->target_set);
25947
25948 PointerToDialog (sfp->group_list_dlg, NULL);
25949 sfp->value_lists = FreeClickableList (sfp->value_lists);
25950
25951 if (GetStatus (sfp->mol_class_btn)) {
25952 VisitBioseqsInSep (sep, &(sfp->value_lists), GetMolClasses);
25953 }
25954 if (GetStatus (sfp->mol_type_btn)) {
25955 VisitDescriptorsInSep (sep, &(sfp->value_lists), GetMolTypes);
25956 }
25957 if (GetStatus (sfp->mol_topology_btn)) {
25958 VisitBioseqsInSep (sep, &(sfp->value_lists), GetMolTopologies);
25959 }
25960
25961 sfp->value_lists = ChangeUniqueValueListsToSeqEntryLists (sfp->value_lists);
25962
25963 PointerToDialog (sfp->group_list_dlg, sfp->value_lists);
25964 if (ValNodeLen (sfp->value_lists) < 2) {
25965 Disable(sfp->accept);
25966 } else {
25967 Enable (sfp->accept);
25968 }
25969 ArrowCursor();
25970 Update();
25971 }
25972
25973
SegFeatureChangeNotify(Pointer userdata)25974 static void SegFeatureChangeNotify (Pointer userdata)
25975 {
25976 SegByFieldPtr sfp = (SegByFieldPtr) userdata;
25977 SeqEntryPtr sep;
25978 SegFeaturesData sfd;
25979 ClickableItemPtr cip;
25980 ValNodePtr vnp;
25981 CharPtr desc_fmt = "%d %ss";
25982
25983 if (sfp == NULL) return;
25984
25985 vnp = DialogToPointer (sfp->feature_select);
25986 if (vnp == NULL) {
25987 PointerToDialog (sfp->group_list_dlg, NULL);
25988 sfp->value_lists = FreeClickableList (sfp->value_lists);
25989 Disable (sfp->accept);
25990 return;
25991 }
25992
25993 WatchCursor ();
25994 Update();
25995 sep = SeqMgrGetSeqEntryForData (sfp->target_set);
25996
25997 PointerToDialog (sfp->group_list_dlg, NULL);
25998 sfp->value_lists = FreeClickableList (sfp->value_lists);
25999
26000 sfd.featdef = vnp->choice;
26001 sfd.feature_list = NULL;
26002 VisitFeaturesInSep (sep, &sfd, FindFeaturesForSeg);
26003
26004 if (sfd.feature_list != NULL) {
26005 cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
26006 MemSet (cip, 0, sizeof (ClickableItemData));
26007 cip->description = (CharPtr) MemNew (sizeof(Char) * (StringLen (desc_fmt) + StringLen (vnp->data.ptrvalue) + 15));
26008 sprintf (cip->description, desc_fmt, ValNodeLen (sfd.feature_list), vnp->data.ptrvalue);
26009 cip->item_list = sfd.feature_list;
26010 cip->chosen = TRUE;
26011 ValNodeAddPointer (&(sfp->value_lists), 0, cip);
26012 sfp->value_lists = ChangeUniqueValueListsToSeqEntryLists (sfp->value_lists);
26013 }
26014 vnp = ValNodeFree (vnp);
26015
26016 PointerToDialog (sfp->group_list_dlg, sfp->value_lists);
26017
26018 if (sfp->value_lists == NULL) {
26019 Disable (sfp->accept);
26020 } else {
26021 Enable (sfp->accept);
26022 }
26023 ArrowCursor();
26024 Update();
26025 }
26026
SegDescriptorChangeNotify(Pointer data)26027 static void SegDescriptorChangeNotify (Pointer data)
26028 {
26029 SegByFieldPtr sfp;
26030 ValNodePtr vnp;
26031 SegDescriptorsData sdd;
26032 ClickableItemPtr cip;
26033 CharPtr desc_fmt = "%d %ss";
26034 SeqEntryPtr sep;
26035
26036 sfp = (SegByFieldPtr) data;
26037 if (sfp == NULL) return;
26038
26039 vnp = DialogToPointer (sfp->descriptor_select);
26040 if (vnp == NULL) {
26041 PointerToDialog (sfp->group_list_dlg, NULL);
26042 sfp->value_lists = FreeClickableList (sfp->value_lists);
26043 Disable (sfp->accept);
26044 return;
26045 }
26046
26047 WatchCursor ();
26048 Update();
26049 sep = SeqMgrGetSeqEntryForData (sfp->target_set);
26050
26051 PointerToDialog (sfp->group_list_dlg, NULL);
26052 sfp->value_lists = FreeClickableList (sfp->value_lists);
26053
26054 sdd.desc_type = vnp->choice;
26055 sdd.descriptor_list = NULL;
26056 VisitDescriptorsInSep (sep, &sdd, FindDescriptorsForSeg);
26057
26058 if (sdd.descriptor_list != NULL) {
26059 cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
26060 MemSet (cip, 0, sizeof (ClickableItemData));
26061 cip->description = (CharPtr) MemNew (sizeof(Char) * (StringLen (desc_fmt) + StringLen (vnp->data.ptrvalue) + 15));
26062 sprintf (cip->description, desc_fmt, ValNodeLen (sdd.descriptor_list), vnp->data.ptrvalue);
26063 cip->item_list = sdd.descriptor_list;
26064 cip->chosen = TRUE;
26065 ValNodeAddPointer (&(sfp->value_lists), 0, cip);
26066 sfp->value_lists = ChangeUniqueValueListsToSeqEntryLists (sfp->value_lists);
26067 }
26068 vnp = ValNodeFree (vnp);
26069
26070 PointerToDialog (sfp->group_list_dlg, sfp->value_lists);
26071
26072 if (sfp->value_lists == NULL) {
26073 Disable (sfp->accept);
26074 } else {
26075 Enable (sfp->accept);
26076 }
26077 ArrowCursor();
26078 Update();
26079
26080 }
26081
ChooseSeqsForNumSets(Pointer data)26082 static void ChooseSeqsForNumSets (Pointer data)
26083 {
26084 SegByFieldPtr sfp;
26085 SeqEntryPtr sep;
26086 Int4 num_sets;
26087 CharPtr str;
26088
26089 sfp = (SegByFieldPtr) data;
26090 if (sfp == NULL) return;
26091
26092 str = SaveStringFromText (sfp->num_sets);
26093 if (str == NULL) {
26094 Disable (sfp->accept);
26095 return;
26096 }
26097
26098 num_sets = atoi (str);
26099 str = MemFree (str);
26100 if (num_sets < 1) {
26101 Disable (sfp->accept);
26102 return;
26103 }
26104
26105 WatchCursor ();
26106 Update();
26107 sep = SeqMgrGetSeqEntryForData (sfp->target_set);
26108
26109 PointerToDialog (sfp->group_list_dlg, NULL);
26110 sfp->value_lists = FreeClickableList (sfp->value_lists);
26111
26112 sfp->value_lists = PrepareSequenceListForSegregateByNumberOfSets (num_sets, sep);
26113
26114 PointerToDialog (sfp->group_list_dlg, sfp->value_lists);
26115
26116 if (sfp->value_lists == NULL) {
26117 Disable (sfp->accept);
26118 } else {
26119 Enable (sfp->accept);
26120 }
26121 ArrowCursor();
26122 Update();
26123 }
26124
SegNumSetsChange(TexT t)26125 static void SegNumSetsChange (TexT t)
26126 {
26127 SegByFieldPtr sfp;
26128
26129 sfp = (SegByFieldPtr) GetObjectExtra (t);
26130
26131 ChooseSeqsForNumSets (sfp);
26132 }
26133
26134
GroupSeqByFileCallback(BioseqPtr bsp,Pointer data)26135 static void GroupSeqByFileCallback (BioseqPtr bsp, Pointer data)
26136 {
26137 ValNodePtr PNTR list;
26138 ValNodePtr vnp;
26139 SeqIdPtr sip;
26140 DbtagPtr dbtag;
26141 Char id_buf[15];
26142 CharPtr id = NULL, last_slash;
26143 ClickableItemPtr cip;
26144 Boolean found = FALSE;
26145
26146 if (bsp == NULL || ISA_aa (bsp->mol) || (list = (ValNodePtr PNTR) data) == NULL) {
26147 return;
26148 }
26149
26150 sip = bsp->id;
26151 while (sip != NULL && !IsNCBIFileID(sip)) {
26152 sip = sip->next;
26153 }
26154
26155 if (sip != NULL && (dbtag = (DbtagPtr) sip->data.ptrvalue) != NULL) {
26156 if (dbtag->tag->id > 0) {
26157 sprintf (id_buf, "%d", dbtag->tag->id);
26158 id = id_buf;
26159 } else {
26160 id = dbtag->tag->str;
26161 }
26162 id = StringSave (id);
26163 if ((last_slash = StringRChr (id, '/')) != NULL) {
26164 *last_slash = 0;
26165 }
26166 for (vnp = *list; vnp != NULL && !found; vnp = vnp->next) {
26167 cip = (ClickableItemPtr) vnp->data.ptrvalue;
26168 if (cip != NULL && StringCmp (id, cip->description) == 0) {
26169 ValNodeAddPointer (&cip->item_list, OBJ_BIOSEQ, bsp);
26170 found = TRUE;
26171 id = MemFree (id);
26172 }
26173 }
26174 if (!found) {
26175 cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
26176 cip->description = id;
26177 ValNodeAddPointer (&cip->item_list, OBJ_BIOSEQ, bsp);
26178 ValNodeAddPointer (list, 0, cip);
26179 }
26180 }
26181 }
26182
26183
ChooseFile(SegByFieldPtr sfp)26184 static void ChooseFile (SegByFieldPtr sfp)
26185 {
26186 SeqEntryPtr sep;
26187
26188 if (sfp == NULL) return;
26189
26190 WatchCursor ();
26191 Update();
26192 sep = SeqMgrGetSeqEntryForData (sfp->target_set);
26193
26194 PointerToDialog (sfp->group_list_dlg, NULL);
26195 sfp->value_lists = FreeClickableList (sfp->value_lists);
26196
26197 VisitBioseqsInSep (sep, &(sfp->value_lists), GroupSeqByFileCallback);
26198
26199 PointerToDialog (sfp->group_list_dlg, sfp->value_lists);
26200
26201 if (sfp->value_lists == NULL) {
26202 Disable (sfp->accept);
26203 } else {
26204 Enable (sfp->accept);
26205 }
26206 ArrowCursor();
26207 Update();
26208 }
26209
26210
ChangeSegChoice(GrouP g)26211 static void ChangeSegChoice (GrouP g)
26212 {
26213 SegByFieldPtr sfp;
26214 Int4 seg_choice, i;
26215
26216 sfp = (SegByFieldPtr) GetObjectExtra (g);
26217 if (sfp == NULL) return;
26218
26219 seg_choice = GetValue (sfp->seg_choice_grp);
26220
26221 for (i = 0; i < eNumSegPages; i++) {
26222 if (i != seg_choice - 1) {
26223 SafeHide (sfp->pages[i]);
26224 }
26225 }
26226 Update ();
26227
26228 for (i = 0; i < eNumSegPages; i++) {
26229 if (i == seg_choice - 1) {
26230 SafeShow (sfp->pages[i]);
26231 }
26232 }
26233 Update ();
26234
26235 switch (seg_choice) {
26236 case eSegPageField:
26237 ChangeSegField (sfp);
26238 break;
26239 case eSegPageMolInfo:
26240 ChangeMol(sfp->mol_class_btn);
26241 break;
26242 case eSegPageFeatureType:
26243 SegFeatureChangeNotify (sfp);
26244 break;
26245 case eSegPageDescriptorType:
26246 SegDescriptorChangeNotify (sfp);
26247 break;
26248 case eSegPageText:
26249 SegTextChangeNotify (sfp);
26250 break;
26251 case eSegPageId:
26252 case eSegPageConstraint:
26253 ChooseSegId (sfp);
26254 break;
26255 case eSegPageVectorContamination:
26256 ChooseVectorSeqs (sfp);
26257 break;
26258 case eSegPageLength:
26259 ChooseSeqsByLen (sfp);
26260 break;
26261 case eSegPageNumFinalSets:
26262 ChooseSeqsForNumSets (sfp);
26263 break;
26264 case eSegPageFile:
26265 ChooseFile(sfp);
26266 break;
26267 case eSegPageStructuredCommentField:
26268 ChangeSegStructuredCommentField (sfp);
26269 break;
26270 }
26271 if (seg_choice == eSegPageId || seg_choice == eSegPageConstraint
26272 || seg_choice == eSegPageVectorContamination || seg_choice == eSegPageLength) {
26273 SetClickableListDialogTitles (sfp->group_list_dlg, "Sequences for New Set", "",
26274 "Use checkbox to mark sequences for new set",
26275 "Single click to navigate to sequence in record");
26276 SetClickableListDisplayChosen (sfp->group_list_dlg, TRUE);
26277 } else {
26278 SetClickableListDialogTitles (sfp->group_list_dlg, "New Sets", "Sequences in Highlighted Set",
26279 "Use checkbox to mark sets to create",
26280 "");
26281 SetClickableListDisplayChosen (sfp->group_list_dlg, FALSE);
26282 }
26283 }
26284
26285
ChooseCategories(ValNodePtr value_list,Boolean do_choose)26286 extern void ChooseCategories (ValNodePtr value_list, Boolean do_choose)
26287 {
26288 ClickableItemPtr cip;
26289
26290 while (value_list != NULL) {
26291 cip = (ClickableItemPtr) value_list->data.ptrvalue;
26292 if (cip != NULL) {
26293 cip->chosen = do_choose;
26294 ChooseCategories (cip->subcategories, FALSE);
26295 }
26296 value_list = value_list->next;
26297 }
26298 }
26299
26300
SelectSegCategories(ButtoN b)26301 static void SelectSegCategories (ButtoN b)
26302 {
26303 SegByFieldPtr sfp;
26304
26305 sfp = (SegByFieldPtr) GetObjectExtra (b);
26306 if (sfp != NULL) {
26307 ChooseCategories (sfp->value_lists, TRUE);
26308 PointerToDialog (sfp->group_list_dlg, sfp->value_lists);
26309 }
26310 }
26311
26312
UnselectSegCategories(ButtoN b)26313 static void UnselectSegCategories (ButtoN b)
26314 {
26315 SegByFieldPtr sfp;
26316
26317 sfp = (SegByFieldPtr) GetObjectExtra (b);
26318 if (sfp != NULL) {
26319 ChooseCategories (sfp->value_lists, FALSE);
26320 PointerToDialog (sfp->group_list_dlg, sfp->value_lists);
26321 }
26322 }
26323
26324
ResortMarkedSegCategories(ButtoN b)26325 static void ResortMarkedSegCategories (ButtoN b)
26326 {
26327 SegByFieldPtr sfp;
26328
26329 sfp = (SegByFieldPtr) GetObjectExtra (b);
26330 if (sfp != NULL) {
26331 sfp->value_lists = ValNodeSort (sfp->value_lists, SortVnpByClickableItemChosen);
26332 PointerToDialog (sfp->group_list_dlg, sfp->value_lists);
26333 }
26334 }
26335
26336
SelectSequenceIDsForSegregate(ButtoN b)26337 static void SelectSequenceIDsForSegregate (ButtoN b)
26338 {
26339 SegByFieldPtr sfp;
26340
26341 sfp = (SegByFieldPtr) GetObjectExtra (b);
26342 if (sfp == NULL) return;
26343
26344 ChooseCategoriesForSegregateIdDialog(sfp->id_constraint_dlg, sfp->value_lists);
26345 PointerToDialog (sfp->group_list_dlg, sfp->value_lists);
26346 }
26347
26348
SelectSequenceIDsByConstraintForSegregate(ButtoN b)26349 static void SelectSequenceIDsByConstraintForSegregate (ButtoN b)
26350 {
26351 SegByFieldPtr sfp;
26352
26353 sfp = (SegByFieldPtr) GetObjectExtra (b);
26354 if (sfp == NULL) return;
26355
26356 ChooseCategoriesForSegregateConstraintDialog(sfp->seq_constraint_dlg, sfp->value_lists);
26357 PointerToDialog (sfp->group_list_dlg, sfp->value_lists);
26358 }
26359
26360
UnselectSequenceIdsByConstraintForSegregate(ButtoN b)26361 static void UnselectSequenceIdsByConstraintForSegregate (ButtoN b)
26362 {
26363 SegByFieldPtr sfp;
26364
26365 sfp = (SegByFieldPtr) GetObjectExtra (b);
26366 if (sfp == NULL) return;
26367
26368 UnchooseCategoriesForSegregateConstraintDialog(sfp->seq_constraint_dlg, sfp->value_lists);
26369 PointerToDialog (sfp->group_list_dlg, sfp->value_lists);
26370 }
26371
26372
CleanupSegregateByFieldForm(GraphiC g,VoidPtr data)26373 static void CleanupSegregateByFieldForm (GraphiC g, VoidPtr data)
26374
26375 {
26376 SegByFieldPtr sfp;
26377
26378 sfp = (SegByFieldPtr) data;
26379 if (sfp != NULL) {
26380 sfp->value_lists = FreeClickableList (sfp->value_lists);
26381 }
26382 StdCleanupFormProc (g, data);
26383 }
26384
26385
CreateSegregateFormMenus(WindoW w)26386 static void CreateSegregateFormMenus (WindoW w)
26387
26388 {
26389 BaseFormPtr bfp;
26390 MenU m;
26391
26392 bfp = (BaseFormPtr) GetObjectExtra (w);
26393 if (bfp != NULL) {
26394 m = PulldownMenu (w, "File");
26395 FormCommandItem (m, "Accept", bfp, VIB_MSG_ACCEPT);
26396 FormCommandItem (m, "Cancel", bfp, VIB_MSG_CLOSE);
26397 }
26398 }
26399
SegregateFormMessage(ForM f,Int2 mssg)26400 static void SegregateFormMessage (ForM f, Int2 mssg)
26401 {
26402 SegByFieldPtr frm;
26403
26404 frm = (SegByFieldPtr) GetObjectExtra (f);
26405 if (frm != NULL) {
26406 switch (mssg) {
26407 case VIB_MSG_ACCEPT :
26408 frm->actn(frm->accept);
26409 break;
26410 case VIB_MSG_CLOSE:
26411 Remove ((WindoW)(frm->form));
26412 break;
26413 default :
26414 break;
26415 }
26416 }
26417 }
26418
26419
NewSegregateBioseqSet(BioseqSetPtr bssp,Nlm_BtnActnProc actn,ESegPage default_type,CharPtr title)26420 static Int2 NewSegregateBioseqSet (BioseqSetPtr bssp, Nlm_BtnActnProc actn, ESegPage default_type, CharPtr title)
26421 {
26422 GrouP c;
26423 SegByFieldPtr cfp;
26424 GrouP h, k, page_grp, g1, g2, g3;
26425 PrompT p, p2;
26426 StdEditorProcsPtr sepp;
26427 WindoW w;
26428 ButtoN b;
26429
26430
26431 /* Create a new window, and a struct */
26432 /* to pass around the data in. */
26433
26434 cfp = (SegByFieldPtr) MemNew (sizeof (SegByFieldData));
26435 if (cfp == NULL)
26436 return OM_MSG_RET_ERROR;
26437 cfp->target_set = bssp;
26438 cfp->actn = actn;
26439
26440 w = FixedWindow (-50, -33, -10, -10, title,
26441 StdCloseWindowProc);
26442 SetObjectExtra (w, cfp, CleanupSegregateByFieldForm);
26443 cfp->form = (ForM) w;
26444
26445 sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm");
26446 if (sepp != NULL) {
26447 SetActivate (w, sepp->activateForm);
26448 cfp->appmessage = sepp->handleMessages;
26449 }
26450
26451 cfp->input_entityID = bssp->idx.entityID;
26452 cfp->input_itemID = bssp->idx.itemID;
26453 cfp->input_itemtype = OBJ_BIOSEQSET;
26454 cfp->formmessage = SegregateFormMessage;
26455
26456 sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm");
26457 if (sepp != NULL) {
26458 SetActivate (w, sepp->activateForm);
26459 cfp->appmessage = sepp->handleMessages;
26460 }
26461
26462 h = HiddenGroup (w, -1, 0, NULL);
26463 SetGroupSpacing (h, 10, 10);
26464
26465 cfp->group_list_dlg = CreateClickableListDialogEx (h, "New Sets", "Sequences for New Set",
26466 "Use checkbox to mark sets to create",
26467 "",
26468 ScrollToDiscrepancyItem, EditDiscrepancyItem, NULL,
26469 GetDiscrepancyItemText,
26470 stdCharWidth * 30,
26471 stdCharWidth * 30 + 5,
26472 TRUE, FALSE);
26473
26474 g3 = NormalGroup (h, 2, 0, "", programFont, NULL);
26475 SetGroupSpacing (g3, 10, 10);
26476 StaticPrompt (g3, "Segregate Based on", 0, dialogTextHeight, programFont, 'c');
26477 cfp->seg_choice_grp = HiddenGroup (g3, eNumSegPages, 0, ChangeSegChoice);
26478 SetObjectExtra (cfp->seg_choice_grp, cfp, NULL);
26479 SetGroupSpacing (cfp->seg_choice_grp, 10, 10);
26480
26481 RadioButton (cfp->seg_choice_grp, "ID");
26482 RadioButton (cfp->seg_choice_grp, "Text");
26483 RadioButton (cfp->seg_choice_grp, "Field");
26484 RadioButton (cfp->seg_choice_grp, "MolInfo");
26485 RadioButton (cfp->seg_choice_grp, "Feature Type");
26486 RadioButton (cfp->seg_choice_grp, "Descriptor Type");
26487 RadioButton (cfp->seg_choice_grp, "Nucleotide Sequence Length");
26488 RadioButton (cfp->seg_choice_grp, "Vector Contamination");
26489 RadioButton (cfp->seg_choice_grp, "Number of Sets");
26490 RadioButton (cfp->seg_choice_grp, "File Name");
26491 RadioButton (cfp->seg_choice_grp, "Constraint");
26492 RadioButton (cfp->seg_choice_grp, "Structured Comment Field");
26493
26494 page_grp = HiddenGroup (h, 0, 0, NULL);
26495 /* identical fields */
26496 cfp->pages[eSegPageField - 1] = HiddenGroup (page_grp, 2, 0, NULL);
26497 SetGroupSpacing (cfp->pages[eSegPageField - 1], 10, 10);
26498 p = StaticPrompt (cfp->pages[eSegPageField - 1], "Segregate sequences with identical", 0, dialogTextHeight,
26499 programFont, 'c');
26500 cfp->field_dlg = ParseFieldDestDialog (cfp->pages[eSegPageField - 1], ChangeSegField, cfp);
26501
26502 /* molinfo */
26503 cfp->pages[eSegPageMolInfo - 1] = HiddenGroup (page_grp, 0, 4, NULL);
26504 SetGroupSpacing (cfp->pages[eSegPageMolInfo - 1], 10, 10);
26505 cfp->mol_class_btn = CheckBox (cfp->pages[eSegPageMolInfo - 1], "Molecule Class", ChangeMol);
26506 SetObjectExtra (cfp->mol_class_btn, cfp, NULL);
26507 SetStatus (cfp->mol_class_btn, TRUE);
26508 cfp->mol_type_btn = CheckBox (cfp->pages[eSegPageMolInfo - 1], "Molecule Type", ChangeMol);
26509 SetObjectExtra (cfp->mol_type_btn, cfp, NULL);
26510 SetStatus (cfp->mol_type_btn, TRUE);
26511 cfp->mol_topology_btn = CheckBox (cfp->pages[eSegPageMolInfo - 1], "Molecule Topology", ChangeMol);
26512 SetObjectExtra (cfp->mol_topology_btn, cfp, NULL);
26513 SetStatus (cfp->mol_topology_btn, TRUE);
26514
26515 /* features */
26516 cfp->pages[eSegPageFeatureType - 1] = HiddenGroup (page_grp, 2, 0, NULL);
26517 SetGroupSpacing (cfp->pages[eSegPageFeatureType - 1], 10, 10);
26518 StaticPrompt (cfp->pages[eSegPageFeatureType - 1], "Segregate by Feature", 0, dialogTextHeight,
26519 programFont, 'c');
26520 cfp->feature_select = FeatureSelectionDialogEx (cfp->pages[eSegPageFeatureType - 1], FALSE, NULL,
26521 SegFeatureChangeNotify,
26522 cfp);
26523
26524 /* descriptors */
26525 cfp->pages[eSegPageDescriptorType - 1] = HiddenGroup (page_grp, 2, 0, NULL);
26526 SetGroupSpacing (cfp->pages[eSegPageDescriptorType - 1], 10, 10);
26527 StaticPrompt (cfp->pages[eSegPageDescriptorType - 1], "Segregate by Descriptor", 0, dialogTextHeight,
26528 programFont, 'c');
26529 cfp->descriptor_select = DescriptorSelectionDialog (cfp->pages[eSegPageDescriptorType - 1], FALSE,
26530 SegDescriptorChangeNotify, cfp);
26531
26532 /* text */
26533 cfp->pages[eSegPageText - 1] = HiddenGroup (page_grp, 4, 0, NULL);
26534 SetGroupSpacing (cfp->pages[eSegPageText - 1], 10, 10);
26535 StaticPrompt (cfp->pages[eSegPageText - 1], "Create set with sequences where", 0, dialogTextHeight, programFont, 'l');
26536 cfp->search_text = DialogText (cfp->pages[eSegPageText - 1], "", 10, SegTextChange);
26537 SetObjectExtra (cfp->search_text, cfp, NULL);
26538 StaticPrompt (cfp->pages[eSegPageText - 1], "appears in", 0, dialogTextHeight, programFont, 'l');
26539 cfp->search_field = SearchFieldDialog (cfp->pages[eSegPageText - 1], SegTextChangeNotify, cfp);
26540
26541 /* id */
26542 cfp->pages[eSegPageId - 1] = HiddenGroup (page_grp, -1, 0, NULL);
26543 SetGroupSpacing (cfp->pages[eSegPageId - 1], 10, 10);
26544 p2 = StaticPrompt (cfp->pages[eSegPageId - 1], "Create set with marked sequences", 0, dialogTextHeight, programFont, 'l');
26545 g1 = HiddenGroup (cfp->pages[eSegPageId - 1], 3, 0, NULL);
26546 g2 = HiddenGroup (cfp->pages[eSegPageId - 1], 2, 0, NULL);
26547 cfp->id_constraint_dlg = SegregateIdDialog (g2);
26548 b = PushButton (g2, "Mark", SelectSequenceIDsForSegregate);
26549 SetObjectExtra (b, cfp, NULL);
26550 AlignObjects (ALIGN_CENTER, (HANDLE) p2, (HANDLE) g1, (HANDLE) g2, NULL);
26551
26552 /* length */
26553 cfp->pages[eSegPageLength - 1] = HiddenGroup (page_grp, -1, 0, NULL);
26554 SetGroupSpacing (cfp->pages[eSegPageLength - 1], 10, 10);
26555 cfp->len_options = ChooseSeqsByLenDialog (cfp->pages[eSegPageLength - 1], ChooseSeqsByLen, cfp);
26556
26557 /* vector contamination */
26558 cfp->pages[eSegPageVectorContamination - 1] = HiddenGroup (page_grp, -1, 0, NULL);
26559 SetGroupSpacing (cfp->pages[eSegPageVectorContamination - 1], 10, 10);
26560 cfp->vector_options = VectorContaminationOptionsDialog (cfp->pages[eSegPageVectorContamination - 1], ChooseVectorSeqs, cfp);
26561
26562 /* number of sets */
26563 cfp->pages[eSegPageNumFinalSets - 1] = HiddenGroup (page_grp, 2, 0, NULL);
26564 SetGroupSpacing (cfp->pages[eSegPageNumFinalSets - 1], 10, 10);
26565 StaticPrompt (cfp->pages[eSegPageNumFinalSets - 1], "Number of sets to create", 0, dialogTextHeight, programFont, 'l');
26566 cfp->num_sets = DialogText (cfp->pages[eSegPageNumFinalSets - 1], "", 10, SegNumSetsChange);
26567 SetObjectExtra (cfp->num_sets, cfp, NULL);
26568
26569 /* don't need controls for File */
26570 cfp->pages[eSegPageFile - 1] = NULL;
26571
26572 /* constraint */
26573 cfp->pages[eSegPageConstraint- 1] = HiddenGroup (page_grp, -1, 0, NULL);
26574 SetGroupSpacing (cfp->pages[eSegPageConstraint - 1], 10, 10);
26575 p2 = StaticPrompt (cfp->pages[eSegPageConstraint - 1], "Create set with marked sequences", 0, dialogTextHeight, programFont, 'l');
26576 g1 = HiddenGroup (cfp->pages[eSegPageConstraint - 1], 2, 0, NULL);
26577 cfp->seq_constraint_dlg = SegregateConstraintDialog (g1);
26578 g2 = HiddenGroup (g1, 0, 2, NULL);
26579 SetGroupSpacing (g2, 10, 10);
26580 b = PushButton (g2, "Mark", SelectSequenceIDsByConstraintForSegregate);
26581 SetObjectExtra (b, cfp, NULL);
26582 b = PushButton (g2, "Unmark", UnselectSequenceIdsByConstraintForSegregate);
26583 SetObjectExtra (b, cfp, NULL);
26584 AlignObjects (ALIGN_CENTER, (HANDLE) p2, (HANDLE) g1, NULL);
26585
26586 cfp->pages[eSegPageStructuredCommentField - 1] = HiddenGroup (page_grp, 2, 0, NULL);
26587 SetGroupSpacing (cfp->pages[eSegPageStructuredCommentField - 1], 10, 10);
26588 StaticPrompt (cfp->pages[eSegPageStructuredCommentField - 1], "Choose Structured Comment Field Name", 0, dialogTextHeight, programFont, 'l');
26589 cfp->struc_comm_field = ValNodeSelectionDialog (cfp->pages[eSegPageStructuredCommentField - 1],
26590 GetStructuredCommentFieldNames(SeqMgrGetSeqEntryForData(bssp)),
26591 8, ValNodeStringName, ValNodeSimpleDataFree,
26592 ValNodeStringCopy, ValNodeStringMatch, "fieldname",
26593 ChangeSegStructuredCommentField, cfp, FALSE);
26594
26595 AlignObjects (ALIGN_CENTER, (HANDLE) cfp->pages[0],
26596 (HANDLE) cfp->pages[1],
26597 (HANDLE) cfp->pages[2],
26598 (HANDLE) cfp->pages[3],
26599 (HANDLE) cfp->pages[4],
26600 (HANDLE) cfp->pages[5],
26601 (HANDLE) cfp->pages[6],
26602 (HANDLE) cfp->pages[7],
26603 (HANDLE) cfp->pages[8],
26604 (HANDLE) cfp->pages[9],
26605 (HANDLE) cfp->pages[10],
26606 (HANDLE) cfp->pages[11],
26607 (HANDLE) cfp->pages[12],
26608 NULL);
26609
26610 SetValue (cfp->seg_choice_grp, default_type);
26611
26612 /* add select all/unselect all buttons */
26613 k = HiddenGroup (h, 3, 0, NULL);
26614 b = PushButton (k, "Mark All", SelectSegCategories);
26615 SetObjectExtra (b, cfp, NULL);
26616 b = PushButton (k, "Unmark All", UnselectSegCategories);
26617 SetObjectExtra (b, cfp, NULL);
26618 b = PushButton (k, "Resort Marked", ResortMarkedSegCategories);
26619 SetObjectExtra (b, cfp, NULL);
26620
26621 /* Add Accept and Cancel buttons */
26622
26623 c = HiddenGroup (h, 3, 0, NULL);
26624 cfp->accept = DefaultButton (c, "Accept", actn);
26625 SetObjectExtra (cfp->accept, cfp, NULL);
26626 Disable (cfp->accept);
26627 PushButton (c, "Cancel", StdCancelButtonProc);
26628 cfp->leave_dlg_up = CheckBox (c, "Leave Dialog Up", NULL);
26629
26630 /* Line things up nicely */
26631
26632 AlignObjects (ALIGN_CENTER, (HANDLE) g3,
26633 (HANDLE) cfp->group_list_dlg,
26634 (HANDLE) page_grp,
26635 (HANDLE) k,
26636 (HANDLE) c, NULL);
26637
26638 /* initialize the display */
26639 ChangeSegChoice (cfp->seg_choice_grp);
26640
26641 /* Display the window now */
26642 CreateSegregateFormMenus(w);
26643 RealizeWindow (w);
26644 Show (w);
26645 Select (w);
26646 Select (cfp->accept);
26647 Update ();
26648 return OM_MSG_RET_OK;
26649 }
26650
SegregateSetsByFieldEx(Pointer data,Nlm_BtnActnProc actn,ESegPage default_type,CharPtr title)26651 static Int2 LIBCALLBACK SegregateSetsByFieldEx (Pointer data, Nlm_BtnActnProc actn, ESegPage default_type, CharPtr title)
26652 {
26653 OMProcControlPtr ompcp;
26654
26655 /* Check parameters and get a pointer to the current data */
26656
26657 ompcp = (OMProcControlPtr) data;
26658 if (ompcp == NULL
26659 || ompcp->input_itemtype != OBJ_BIOSEQSET
26660 || ompcp->input_data == NULL) {
26661 Message (MSG_ERROR, "You must select a set to segregate!");
26662 return OM_MSG_RET_ERROR;
26663 }
26664 return NewSegregateBioseqSet (ompcp->input_data, actn, default_type, title);
26665 }
26666
26667
SegregateSetsByField(Pointer data)26668 extern Int2 LIBCALLBACK SegregateSetsByField (Pointer data)
26669 {
26670 return SegregateSetsByFieldEx (data, SegregateByField_Callback, eSegPageText, "Segregate Sets");
26671 }
26672
26673
SegregateBioseqSetEntityID(Uint2 entityID)26674 NLM_EXTERN void SegregateBioseqSetEntityID (Uint2 entityID)
26675 {
26676 SeqEntryPtr sep;
26677
26678 sep = GetTopSeqEntryForEntityID (entityID);
26679 if (sep == NULL || !IS_Bioseq_set (sep)) {
26680 Message (MSG_ERROR, "This record does not have a top-levelset!");
26681 } else {
26682 NewSegregateBioseqSet (FindTopLevelSetForDesktopFunction((BioseqSetPtr) sep->data.ptrvalue), SegregateByField_Callback, eSegPageText, "Segregate Sets");
26683 }
26684 }
26685
26686
NewSegregateBioseqSetMenuItem(IteM i)26687 extern void NewSegregateBioseqSetMenuItem (IteM i)
26688 {
26689 BaseFormPtr bfp;
26690
26691 #ifdef WIN_MAC
26692 bfp = currentFormDataPtr;
26693 #else
26694 bfp = GetObjectExtra (i);
26695 #endif
26696 if (bfp == NULL) return;
26697
26698 SegregateBioseqSetEntityID (bfp->input_entityID);
26699 }
26700
26701
26702 typedef struct unsequester{
26703 SeqEntryPtr sep;
26704 BioseqSetPtr orig_parent;
26705 Int4 set_pos;
26706 } UnsequesterData, PNTR UnsequesterPtr;
26707
26708
UnsequesterNew(SeqEntryPtr sep,BioseqSetPtr parent,Int4 set_pos)26709 static UnsequesterPtr UnsequesterNew (SeqEntryPtr sep, BioseqSetPtr parent, Int4 set_pos)
26710 {
26711 UnsequesterPtr u;
26712
26713 u = (UnsequesterPtr) MemNew (sizeof (UnsequesterData));
26714 u->sep = sep;
26715 u->orig_parent = parent;
26716 u->set_pos = set_pos;
26717 return u;
26718 }
26719
26720
GetUnsequesterForSep(SeqEntryPtr sep,ValNodePtr list)26721 static UnsequesterPtr GetUnsequesterForSep (SeqEntryPtr sep, ValNodePtr list)
26722 {
26723 UnsequesterPtr u;
26724
26725 while (list != NULL) {
26726 if ((u = list->data.ptrvalue) != NULL && u->sep == sep) {
26727 return u;
26728 } else {
26729 list = list->next;
26730 }
26731 }
26732 return NULL;
26733 }
26734
26735
26736 static ValNodePtr unsequester_list = NULL;
26737
26738 static BioseqSetPtr sequester_set = NULL;
26739 static const CharPtr SEQUESTER_BACKUP_FILE = "sequestr.bkp";
26740 static Boolean doReportAfterUnsequester = 0;
26741
SetDoReportAfterUnsequester(Int4 report_type)26742 NLM_EXTERN void SetDoReportAfterUnsequester (Int4 report_type)
26743 {
26744 doReportAfterUnsequester = report_type;
26745 }
26746
26747
26748 static const CharPtr placeholder_id_string = "ABCDEFGHIJKLMNOPQRSTUVWXYZMagicCookiePlaceHolderABCDEFGHIJKLMNOPQRSTUVWXYZ";
26749
PlaceholderBioseq(void)26750 static BioseqPtr PlaceholderBioseq (void)
26751 {
26752 BioseqPtr bsp;
26753 ObjectIdPtr oip;
26754
26755 oip = ObjectIdNew ();
26756 oip->str = StringSave (placeholder_id_string);
26757 bsp = BioseqNew ();
26758 bsp->id = ValNodeNew (NULL);
26759 bsp->id->choice = SEQID_LOCAL;
26760 bsp->id->data.ptrvalue = oip;
26761 return bsp;
26762 }
26763
26764
IsPlaceholderBioseq(BioseqPtr bsp)26765 static Boolean IsPlaceholderBioseq (BioseqPtr bsp)
26766 {
26767 ObjectIdPtr oip;
26768
26769 if (bsp == NULL || bsp->id == NULL
26770 || bsp->id->choice != SEQID_LOCAL
26771 || (oip = (ObjectIdPtr) bsp->id->data.ptrvalue) == NULL
26772 || StringCmp (oip->str, placeholder_id_string) != 0) {
26773 return FALSE;
26774 } else {
26775 return TRUE;
26776 }
26777 }
26778
26779
26780 /* sequesters is different from segregate - we aren't creating a permanent new set with
26781 * the combined descriptors of the previous set; we're creating a temporary holding set.
26782 */
SequesterCategorySeqEntries(BioseqSetPtr newset,ClickableItemPtr category)26783 static void SequesterCategorySeqEntries (BioseqSetPtr newset, ClickableItemPtr category)
26784 {
26785 ValNodePtr vnp_item;
26786 SeqEntryPtr sep, last_sep, prev_sep, remove_sep, set_sep, tmp_sep;
26787 BioseqSetPtr bssp, orig_parent, prev_new_parent = NULL, prev_orig_parent = NULL;
26788 BioseqPtr bsp;
26789 Int4 set_pos;
26790
26791 if (newset == NULL || category == NULL || (category->item_list == NULL && category->subcategories == NULL)) return;
26792
26793 if (category->chosen) {
26794 last_sep = newset->seq_set;
26795 while (last_sep != NULL && last_sep->next != NULL) {
26796 last_sep = last_sep->next;
26797 }
26798
26799 for (vnp_item = category->item_list; vnp_item != NULL; vnp_item = vnp_item->next) {
26800 sep = GetBestSeqEntryForItem (vnp_item);
26801 if (sep == NULL || sep->data.ptrvalue == NULL) continue;
26802 orig_parent = NULL;
26803 if (IS_Bioseq (sep)) {
26804 bsp = sep->data.ptrvalue;
26805 if (bsp->idx.parenttype == OBJ_BIOSEQSET) {
26806 orig_parent = bsp->idx.parentptr;
26807 bsp->idx.parentptr = NULL;
26808 }
26809 } else if (IS_Bioseq_set (sep)) {
26810 bssp = sep->data.ptrvalue;
26811 if (bssp->idx.parenttype == OBJ_BIOSEQSET) {
26812 orig_parent = bssp->idx.parentptr;
26813 bssp->idx.parentptr = NULL;
26814 }
26815 } else {
26816 continue;
26817 }
26818
26819 if (orig_parent == NULL) {
26820 continue;
26821 }
26822
26823 /* remove this seq-entry from the original parent */
26824 prev_sep = NULL;
26825 set_pos = 0;
26826 for (remove_sep = orig_parent->seq_set;
26827 remove_sep != NULL && remove_sep != sep;
26828 remove_sep = remove_sep->next) {
26829 prev_sep = remove_sep;
26830 set_pos++;
26831 }
26832 if (remove_sep == sep) {
26833 if (prev_sep == NULL) {
26834 orig_parent->seq_set = orig_parent->seq_set->next;
26835 if (orig_parent->seq_set == NULL) {
26836 orig_parent->seq_set = SeqEntryNew ();
26837 orig_parent->seq_set->choice = 1;
26838 orig_parent->seq_set->data.ptrvalue = PlaceholderBioseq();
26839 SeqMgrLinkSeqEntry (orig_parent->seq_set, OBJ_BIOSEQSET, orig_parent);
26840 }
26841 } else {
26842 prev_sep->next = sep->next;
26843 }
26844 sep->next = NULL;
26845 }
26846
26847 /* if this seq-entry is from the same parent as the previous one, just add this to
26848 * our current placeholder.
26849 */
26850 if (prev_orig_parent != orig_parent) {
26851 prev_new_parent = BioseqSetNew ();
26852 prev_new_parent->_class = orig_parent->_class;
26853 /* add descriptors from the orig_parent to the new parent */
26854 AddNewUniqueDescriptors (&(prev_new_parent->descr), orig_parent->descr);
26855
26856 /* add annotations from the orig_parent to the new parent */
26857 AddNewUniqueAnnotations (&(prev_new_parent->annot), orig_parent->annot);
26858
26859 /* add new parent to set */
26860 set_sep = SeqEntryNew ();
26861 set_sep->choice = 2;
26862 set_sep->data.ptrvalue = prev_new_parent;
26863
26864 if (newset->seq_set == NULL) {
26865 newset->seq_set = set_sep;
26866 } else {
26867 for (tmp_sep = newset->seq_set; tmp_sep->next != NULL; tmp_sep = tmp_sep->next) {
26868 }
26869 tmp_sep->next = set_sep;
26870 }
26871 SeqMgrLinkSeqEntry (set_sep, OBJ_BIOSEQSET, newset);
26872 last_sep = NULL;
26873 }
26874 /* add seqentry to new parent */
26875 if (last_sep == NULL) {
26876 prev_new_parent->seq_set = sep;
26877 } else {
26878 last_sep->next = sep;
26879 }
26880 last_sep = sep;
26881
26882 SeqMgrLinkSeqEntry (sep, OBJ_BIOSEQSET, prev_new_parent);
26883
26884 /* create unsequester entry */
26885 ValNodeAddPointer (&unsequester_list, 0, UnsequesterNew (sep, orig_parent, set_pos));
26886
26887 prev_orig_parent = orig_parent;
26888 }
26889 } else {
26890 for (vnp_item = category->subcategories; vnp_item != NULL; vnp_item = vnp_item->next) {
26891 SequesterCategorySeqEntries (newset, vnp_item->data.ptrvalue);
26892 }
26893 }
26894 }
26895
26896
RestoreSequesteredSets(ForM f)26897 static void RestoreSequesteredSets (ForM f)
26898 {
26899 Uint2 new_entityID;
26900 BaseFormPtr bfp;
26901 BioseqViewFormPtr vfp;
26902
26903 bfp = GetBaseFormForEntityID (sequester_set->idx.entityID);
26904 if (bfp == NULL) {
26905 return;
26906 }
26907 SequinSeqViewFormMessage (f, VIB_MSG_CLOSE);
26908
26909 new_entityID = RestoreEntityIDFromFile (SEQUESTER_BACKUP_FILE, bfp->input_entityID);
26910 if (new_entityID != 0) {
26911 bfp->input_entityID = new_entityID;
26912 ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
26913 ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
26914 }
26915 Show (bfp->form);
26916 vfp = (BioseqViewFormPtr) bfp;
26917 Show (vfp->toolForm);
26918
26919 sequester_set = NULL;
26920 }
26921
26922
IsSeqDescInSet(SeqDescrPtr sdp,SeqDescrPtr set)26923 static Boolean IsSeqDescInSet (SeqDescrPtr sdp, SeqDescrPtr set)
26924 {
26925 while (set != NULL) {
26926 if (AsnIoMemComp (sdp, set, (AsnWriteFunc) SeqDescAsnWrite)) {
26927 return TRUE;
26928 } else {
26929 set = set->next;
26930 }
26931 }
26932 return FALSE;
26933 }
26934
PropagateToSeqEntryIfNotDup(SeqEntryPtr sep,SeqDescrPtr sdp)26935 static SeqDescrPtr PropagateToSeqEntryIfNotDup (SeqEntryPtr sep, SeqDescrPtr sdp)
26936 {
26937 BioseqPtr bsp;
26938 BioseqSetPtr bssp;
26939 SeqDescrPtr new_sdp = NULL;
26940
26941 if (sep != NULL && sep->data.ptrvalue != NULL) {
26942 if (IS_Bioseq (sep)) {
26943 bsp = (BioseqPtr) sep->data.ptrvalue;
26944 if (!IsSeqDescInSet (sdp, bsp->descr)) {
26945 new_sdp = AsnIoMemCopy ((Pointer) sdp,
26946 (AsnReadFunc) SeqDescrAsnRead,
26947 (AsnWriteFunc) SeqDescrAsnWrite);
26948 ValNodeLink (&(bsp->descr), new_sdp);
26949 }
26950 } else if (IS_Bioseq_set (sep)) {
26951 bssp = (BioseqSetPtr) sep->data.ptrvalue;
26952 if (!IsSeqDescInSet (sdp, bssp->descr)) {
26953 new_sdp = AsnIoMemCopy ((Pointer) sdp,
26954 (AsnReadFunc) SeqDescrAsnRead,
26955 (AsnWriteFunc) SeqDescrAsnWrite);
26956 ValNodeLink (&(bssp->descr), new_sdp);
26957 }
26958 }
26959 }
26960 return new_sdp;
26961 }
26962
26963
AddSepBackToSet(SeqEntryPtr add_back_sep,BioseqSetPtr bssp,SeqDescrPtr parent_descriptors,Int4 set_pos)26964 static void AddSepBackToSet (SeqEntryPtr add_back_sep, BioseqSetPtr bssp, SeqDescrPtr parent_descriptors, Int4 set_pos)
26965 {
26966 ObjMgrDataPtr omdptop;
26967 ObjMgrData omdata;
26968 Uint2 parenttype;
26969 Pointer parentptr;
26970 SeqEntryPtr sep, prev, tmp;
26971 SeqDescrPtr sdp, new_sdp, sdp_tmp;
26972 ObjValNodePtr ovp, new_ovp;
26973 Boolean found;
26974 Int4 pos;
26975 BioseqPtr bsp;
26976
26977 /* any descriptors currently on bssp that are not in parent_descriptors must be propagated */
26978 /* mark parent descriptor as found, so we don't add it again */
26979 for (sdp = bssp->descr; sdp != NULL; sdp = sdp->next) {
26980 if (sdp->extended == 0) {
26981 continue;
26982 }
26983 /* don't copy set titles */
26984 if (sdp->choice == Seq_descr_title) {
26985 continue;
26986 }
26987 ovp = (ObjValNodePtr) sdp;
26988 found = FALSE;
26989 for (new_sdp = parent_descriptors; new_sdp != NULL && !found; new_sdp = new_sdp->next) {
26990 if (new_sdp->extended == 0) {
26991 continue;
26992 }
26993 new_ovp = (ObjValNodePtr) new_sdp;
26994 if (new_ovp->idx.deleteme) {
26995 continue;
26996 }
26997 if (AsnIoMemComp (sdp, new_sdp, (AsnWriteFunc) SeqDescAsnWrite)) {
26998 found = TRUE;
26999 new_ovp->idx.deleteme = TRUE;
27000 }
27001 }
27002 if (!found) {
27003 /* propagate descriptor to members of bssp */
27004 sdp_tmp = sdp->next;
27005 sdp->next = NULL;
27006 for (sep = bssp->seq_set; sep != NULL; sep = sep->next) {
27007 PropagateToSeqEntryIfNotDup (sep, sdp);
27008 }
27009 sdp->next = sdp_tmp;
27010 ovp->idx.deleteme = TRUE;
27011 }
27012 }
27013 /* now add any parent descriptors that weren't marked to the contents of add_back_sep
27014 * (and unmark those that were marked) */
27015 for (new_sdp = parent_descriptors; new_sdp != NULL; new_sdp = new_sdp->next) {
27016 if (new_sdp->extended == 0) {
27017 continue;
27018 }
27019 new_ovp = (ObjValNodePtr) new_sdp;
27020 if (new_ovp->idx.deleteme) {
27021 new_ovp->idx.deleteme = FALSE;
27022 } else {
27023 /* add to added_back_sep */
27024 PropagateToSeqEntryIfNotDup (add_back_sep, new_sdp);
27025 }
27026 }
27027
27028 /* mark placeholders in destination set for removal */
27029 for (tmp = bssp->seq_set; tmp != NULL; tmp = tmp->next) {
27030 if (IS_Bioseq (tmp) && (bsp = tmp->data.ptrvalue) != NULL && IsPlaceholderBioseq (bsp)) {
27031 bsp->idx.deleteme = TRUE;
27032 }
27033 }
27034
27035 sep = SeqMgrGetSeqEntryForData (bssp);
27036 SaveSeqEntryObjMgrData (sep, &omdptop, &omdata);
27037 GetSeqEntryParent (sep, &parentptr, &parenttype);
27038 prev = NULL;
27039 pos = 0;
27040 for (tmp = bssp->seq_set; tmp != NULL && pos < set_pos; tmp = tmp->next) {
27041 prev = tmp;
27042 pos++;
27043 }
27044 if (prev == NULL) {
27045 add_back_sep->next = bssp->seq_set;
27046 bssp->seq_set = add_back_sep;
27047 } else {
27048 add_back_sep->next = tmp;
27049 prev->next = add_back_sep;
27050 }
27051 SeqMgrLinkSeqEntry (add_back_sep, OBJ_BIOSEQSET, bssp);
27052
27053 SeqMgrLinkSeqEntry (sep, parenttype, parentptr);
27054 RestoreSeqEntryObjMgrData (sep, omdptop, &omdata);
27055 }
27056
27057
ReintegrateSequesteredSets(Uint2 entityID)27058 static void ReintegrateSequesteredSets (Uint2 entityID)
27059 {
27060 BaseFormPtr bfp;
27061 BioseqViewFormPtr vfp;
27062 SeqEntryPtr new_parent_sep, sep, add_back_sep, next_sep;
27063 BioseqSetPtr top_bssp, bssp;
27064 UnsequesterPtr u;
27065
27066 add_back_sep = GetTopSeqEntryForEntityID (entityID);
27067 if (!IS_Bioseq_set (add_back_sep)) {
27068 return;
27069 }
27070 bfp = GetBaseFormForEntityID (entityID);
27071 RemoveSeqEntryViewer (bfp->form);
27072
27073 /* remove any popset titles created */
27074 RemovePopsetTitles (add_back_sep);
27075
27076 /* we created a genbank set to hold the actual parent sets */
27077 top_bssp = (BioseqSetPtr) add_back_sep->data.ptrvalue;
27078
27079 /* propagate any other descriptors that ended up on the top-level set
27080 * (like cit-sub-updates)
27081 */
27082 SetDescriptorPropagate(top_bssp);
27083
27084 /* need to process entries in seq_set in reverse, so that the set_pos will be
27085 * correct relative to when the seq-entry was removed */
27086 ValNodeReverse (&(top_bssp->seq_set));
27087 new_parent_sep = top_bssp->seq_set;
27088
27089 while (new_parent_sep != NULL) {
27090 bssp = new_parent_sep->data.ptrvalue;
27091 ValNodeReverse (&(bssp->seq_set));
27092 sep = bssp->seq_set;
27093
27094 while (sep != NULL) {
27095 next_sep = sep->next;
27096 sep->next = NULL;
27097 u = GetUnsequesterForSep (sep, unsequester_list);
27098 if (u == NULL || u->orig_parent == NULL) {
27099 AddSepBackToSet (sep, sequester_set, bssp->descr, 0);
27100 } else {
27101 AddSepBackToSet (sep, u->orig_parent, bssp->descr, u->set_pos);
27102 }
27103 sep = next_sep;
27104 }
27105 bssp->seq_set = NULL;
27106 new_parent_sep = new_parent_sep->next;
27107 }
27108
27109 ObjMgrDelete (OBJ_SEQENTRY, add_back_sep);
27110 top_bssp->seq_set = NULL;
27111 top_bssp->idx.deleteme = TRUE;
27112 DeleteMarkedObjects (entityID, 0, NULL);
27113
27114 sep = GetTopSeqEntryForEntityID (sequester_set->idx.entityID);
27115 DeleteMarkedObjects (sequester_set->idx.entityID, 0, NULL);
27116 ObjMgrSetDirtyFlag (sequester_set->idx.entityID, TRUE);
27117 ObjMgrSendMsg (OM_MSG_UPDATE, sequester_set->idx.entityID, 0, 0);
27118
27119 bfp = GetBaseFormForEntityID (sequester_set->idx.entityID);
27120 if (bfp != NULL) {
27121 Show (bfp->form);
27122 vfp = (BioseqViewFormPtr) bfp;
27123 Show (vfp->toolForm);
27124 }
27125
27126 }
27127
27128
FinishedSequester(void)27129 static void FinishedSequester (void)
27130 {
27131 sequester_set = NULL;
27132 unsequester_list = ValNodeFreeData (unsequester_list);
27133 FileRemove(SEQUESTER_BACKUP_FILE);
27134 if (doReportAfterUnsequester > 0) {
27135 CreateReportWindow (doReportAfterUnsequester);
27136 doReportAfterUnsequester = 0;
27137 }
27138 }
27139
27140
SequesterShutdown(ForM f)27141 static void SequesterShutdown (ForM f)
27142 {
27143 MsgAnswer ans;
27144 BaseFormPtr bfp;
27145
27146 bfp = (BaseFormPtr) GetObjectExtra (f);
27147 if (bfp != NULL) {
27148 ans = Message (MSG_YNC, "Accept changes and add sequences back to original set? Hit No to continue working, Cancel to restore original set");
27149 if (ans == ANS_YES) {
27150 ReintegrateSequesteredSets (bfp->input_entityID);
27151 FinishedSequester();
27152 } else if (ans == ANS_CANCEL) {
27153 RestoreSequesteredSets (f);
27154 FinishedSequester();
27155 }
27156 }
27157 }
27158
27159
SequesterFormMessage(ForM f,Int2 mssg)27160 static void SequesterFormMessage (ForM f, Int2 mssg)
27161
27162 {
27163 BaseFormPtr bfp;
27164
27165 bfp = (BaseFormPtr) GetObjectExtra (f);
27166 if (bfp != NULL) {
27167 switch (mssg) {
27168 case VIB_MSG_CLOSE :
27169 case VIB_MSG_QUIT :
27170 case VIB_MSG_ACCEPT :
27171 SequesterShutdown (f);
27172 break;
27173 default:
27174 SequinSeqViewFormMessage (f, mssg);
27175 break;
27176 }
27177 }
27178 }
27179
27180
SequesterSets(ButtoN b)27181 static void SequesterSets (ButtoN b)
27182 {
27183 SegByFieldPtr sfp;
27184 Int4 num_chosen = 0;
27185 ValNodePtr vnp;
27186 ClickableItemPtr cip;
27187 Int2 val;
27188 SeqEntryPtr top_sep, pulled_sep;
27189 BioseqSetPtr new_set;
27190 ObjMgrDataPtr omdptop;
27191 ObjMgrData omdata;
27192 Uint2 parenttype;
27193 Pointer parentptr;
27194 Uint2 entityID;
27195 FormMessageFunc old_message_handler;
27196 BaseFormPtr bfp;
27197 BioseqViewFormPtr vfp;
27198
27199 sfp = (SegByFieldPtr) GetObjectExtra (b);
27200 if (sfp == NULL) return;
27201
27202 if (unsequester_list != NULL || sequester_set != NULL) {
27203 Message (MSG_ERROR, "You are already sequestering a set. You cannot sequester until you have restored these sequences to the original set.");
27204 return;
27205 }
27206
27207 WriteTheEntityID (sfp->input_entityID, SEQUESTER_BACKUP_FILE, FALSE);
27208
27209 num_chosen = CountChosenDiscrepancies (sfp->value_lists, FALSE);
27210 if (num_chosen < 1) {
27211 if (ANS_OK == Message (MSG_OKC, "You have not chosen any groups. Create all?")) {
27212 ChooseAllDiscrepancies (sfp->value_lists);
27213 } else {
27214 return;
27215 }
27216 }
27217
27218 val = GetValue (sfp->seg_choice_grp);
27219 if (val == eSegPageId || val == eSegPageVectorContamination || val == eSegPageLength) {
27220 /* put all selected sequences into one group */
27221 cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
27222 cip->chosen = TRUE;
27223 PullChosenIntoOneGroup (&(sfp->value_lists), cip);
27224 ValNodeAddPointer (&(sfp->value_lists), 0, cip);
27225 }
27226
27227 sequester_set = sfp->target_set;
27228
27229 /* create a new set with just the chosen sequences */
27230 top_sep = SeqMgrGetSeqEntryForData (sfp->target_set);
27231 SaveSeqEntryObjMgrData (top_sep, &omdptop, &omdata);
27232 GetSeqEntryParent (top_sep, &parentptr, &parenttype);
27233
27234 new_set = BioseqSetNew ();
27235 new_set->_class = BioseqseqSet_class_genbank;
27236
27237 for (vnp = sfp->value_lists; vnp != NULL; vnp = vnp->next) {
27238 cip = (ClickableItemPtr) vnp->data.ptrvalue;
27239 if (cip == NULL || (!cip->chosen && ! AnyDiscrepanciesChosen (cip->subcategories))) {
27240 continue;
27241 }
27242
27243 /* add SeqEntries for this category here */
27244 SequesterCategorySeqEntries (new_set, cip);
27245
27246 }
27247
27248 RestoreSeqEntryObjMgrData (top_sep, omdptop, &omdata);
27249 DeleteMarkedObjects (sfp->input_entityID, 0, NULL);
27250 ObjMgrSetDirtyFlag (sfp->input_entityID, TRUE);
27251 ObjMgrSendMsg (OM_MSG_UPDATE, sfp->input_entityID, 0, 0);
27252
27253 pulled_sep = SeqEntryNew ();
27254 pulled_sep->choice = 2;
27255 pulled_sep->data.ptrvalue = new_set;
27256 SeqMgrLinkSeqEntry (pulled_sep, 0, NULL);
27257
27258 entityID = ObjMgrRegister (OBJ_SEQENTRY, pulled_sep);
27259 seqviewprocs.filepath = NULL;
27260 seqviewprocs.forceSeparateViewer = TRUE;
27261 old_message_handler = seqviewprocs.handleMessages;
27262 seqviewprocs.handleMessages = SequesterFormMessage;
27263
27264
27265 SeqEntrySetScope (NULL);
27266 GatherProcLaunch (OMPROC_VIEW, FALSE, entityID, 1,
27267 OBJ_BIOSEQ, 0, 0, OBJ_BIOSEQ, 0);
27268
27269 seqviewprocs.handleMessages = old_message_handler;
27270
27271 /* hide viewer with the remaining sequences */
27272 bfp = GetBaseFormForEntityID (sfp->input_entityID);
27273 if (bfp != NULL) {
27274 Hide (bfp->form);
27275 vfp = (BioseqViewFormPtr) bfp;
27276 Hide (vfp->toolForm);
27277 }
27278
27279 if (GetStatus (sfp->leave_dlg_up)) {
27280 ChangeSegChoice (sfp->seg_choice_grp);
27281 } else {
27282 Remove (sfp->form);
27283 }
27284 }
27285
OkToSequester(void)27286 NLM_EXTERN Boolean OkToSequester (void)
27287 {
27288 if (unsequester_list != NULL || sequester_set != NULL) {
27289 return FALSE;
27290 } else {
27291 return TRUE;
27292 }
27293 }
27294
27295
SequesterClickableItem(Uint2 entityID,ClickableItemPtr cip)27296 NLM_EXTERN Uint2 SequesterClickableItem (Uint2 entityID, ClickableItemPtr cip)
27297 {
27298 SeqEntryPtr sep;
27299 BioseqSetPtr bssp, new_set;
27300 ObjMgrDataPtr omdptop;
27301 ObjMgrData omdata;
27302 Uint2 parenttype;
27303 Pointer parentptr;
27304 Uint2 new_entityID;
27305 FormMessageFunc old_message_handler;
27306 BaseFormPtr bfp;
27307 BioseqViewFormPtr vfp;
27308 SeqEntryPtr pulled_sep;
27309
27310 if (unsequester_list != NULL || sequester_set != NULL) {
27311 Message (MSG_ERROR, "You are already sequestering a set. You cannot sequester until you have restored these sequences to the original set.");
27312 return 0;
27313 }
27314
27315 sep = GetTopSeqEntryForEntityID (entityID);
27316 if (sep == NULL || !IS_Bioseq_set (sep)) {
27317 Message (MSG_ERROR, "This record does not have a top-levelset!");
27318 return 0;
27319 }
27320
27321 bssp = FindTopLevelSetForDesktopFunction((BioseqSetPtr) sep->data.ptrvalue);
27322 if (bssp == NULL) {
27323 Message (MSG_ERROR, "Unable to find top level set");
27324 return 0;
27325 }
27326
27327 WriteTheEntityID (entityID, SEQUESTER_BACKUP_FILE, FALSE);
27328 sequester_set = bssp;
27329
27330 /* create a new set with just the chosen sequences */
27331 SaveSeqEntryObjMgrData (sep, &omdptop, &omdata);
27332 GetSeqEntryParent (sep, &parentptr, &parenttype);
27333
27334 new_set = BioseqSetNew ();
27335 new_set->_class = BioseqseqSet_class_genbank;
27336
27337 SequesterCategorySeqEntries (new_set, cip);
27338
27339 RestoreSeqEntryObjMgrData (sep, omdptop, &omdata);
27340 DeleteMarkedObjects (entityID, 0, NULL);
27341 ObjMgrSetDirtyFlag (entityID, TRUE);
27342 ObjMgrSendMsg (OM_MSG_UPDATE, entityID, 0, 0);
27343
27344 pulled_sep = SeqEntryNew ();
27345 pulled_sep->choice = 2;
27346 pulled_sep->data.ptrvalue = new_set;
27347 SeqMgrLinkSeqEntry (pulled_sep, 0, NULL);
27348
27349 new_entityID = ObjMgrRegister (OBJ_SEQENTRY, pulled_sep);
27350 seqviewprocs.filepath = NULL;
27351 seqviewprocs.forceSeparateViewer = TRUE;
27352 old_message_handler = seqviewprocs.handleMessages;
27353 seqviewprocs.handleMessages = SequesterFormMessage;
27354
27355
27356 SeqEntrySetScope (NULL);
27357 GatherProcLaunch (OMPROC_VIEW, FALSE, new_entityID, 1,
27358 OBJ_BIOSEQ, 0, 0, OBJ_BIOSEQ, 0);
27359
27360 seqviewprocs.handleMessages = old_message_handler;
27361
27362 /* hide viewer with the remaining sequences */
27363 bfp = GetBaseFormForEntityID (entityID);
27364 if (bfp != NULL) {
27365 Hide (bfp->form);
27366 vfp = (BioseqViewFormPtr) bfp;
27367 Hide (vfp->toolForm);
27368 }
27369 return new_entityID;
27370 }
27371
27372
SequesterSequenceList(Uint2 entityID,ValNodePtr bsp_list)27373 NLM_EXTERN void LIBCALLBACK SequesterSequenceList (Uint2 entityID, ValNodePtr bsp_list)
27374 {
27375 ClickableItemData cid;
27376 Uint2 new_entityID;
27377 BaseFormPtr bfp;
27378
27379 if (bsp_list == NULL) {
27380 return;
27381 }
27382
27383 MemSet (&cid, 0, sizeof (ClickableItemData));
27384 cid.chosen = TRUE;
27385 cid.item_list = bsp_list;
27386 if ((new_entityID = SequesterClickableItem (entityID, &cid)) > 0) {
27387 /* get rid of existing validator window, replace with validator for new sequences */
27388 FreeValidateWindow ();
27389 bfp = GetBaseFormForEntityID (new_entityID);
27390 ValSeqEntryForm (bfp->form);
27391 }
27392 }
27393
27394
SequesterSequences(Pointer data)27395 extern Int2 LIBCALLBACK SequesterSequences (Pointer data)
27396 {
27397 /* note - in future, will need to make sequester dialog modal. */
27398 return SegregateSetsByFieldEx (data, SequesterSets, eSegPageId, "Sequester Sets");
27399 }
27400
27401
SequesterSequencesEntityID(Uint2 entityID)27402 extern void SequesterSequencesEntityID (Uint2 entityID)
27403 {
27404 SeqEntryPtr sep;
27405
27406 sep = GetTopSeqEntryForEntityID (entityID);
27407 if (sep == NULL || !IS_Bioseq_set (sep)) {
27408 Message (MSG_ERROR, "This record does not have a top-level set!");
27409 } else {
27410 NewSegregateBioseqSet (FindTopLevelSetForDesktopFunction((BioseqSetPtr) sep->data.ptrvalue), SequesterSets, eSegPageId, "Sequester Sets");
27411 }
27412 }
27413
27414
SequesterSequencesMenuItem(IteM i)27415 extern void SequesterSequencesMenuItem (IteM i)
27416 {
27417 BaseFormPtr bfp;
27418
27419 #ifdef WIN_MAC
27420 bfp = currentFormDataPtr;
27421 #else
27422 bfp = GetObjectExtra (i);
27423 #endif
27424 if (bfp == NULL) return;
27425
27426 SequesterSequencesEntityID (bfp->input_entityID);
27427 }
27428
27429
SegregateSequenceList(Uint2 entityID,ValNodePtr bsp_list)27430 NLM_EXTERN void LIBCALLBACK SegregateSequenceList (Uint2 entityID, ValNodePtr bsp_list)
27431 {
27432 SeqEntryPtr sep;
27433 BioseqSetPtr bssp;
27434 ClickableItemData cid;
27435 ValNodePtr list = NULL;
27436
27437 if (bsp_list == NULL) {
27438 return;
27439 }
27440
27441 sep = GetTopSeqEntryForEntityID (entityID);
27442 if (sep == NULL || !IS_Bioseq_set (sep)) {
27443 Message (MSG_ERROR, "This record does not have a top-level set!");
27444 return;
27445 }
27446
27447 bssp = FindTopLevelSetForDesktopFunction((BioseqSetPtr) sep->data.ptrvalue);
27448 if (bssp == NULL) {
27449 Message (MSG_ERROR, "Unable to find top level set");
27450 return;
27451 }
27452
27453 MemSet (&cid, 0, sizeof (ClickableItemData));
27454 cid.item_list = bsp_list;
27455 cid.chosen = TRUE;
27456 ValNodeAddPointer (&list, 0, &cid);
27457
27458 MakeGroupsForUniqueValues (bssp, list);
27459 list = ValNodeFree (list);
27460 }
27461
27462
FormatBoxColumn(ColPtr col)27463 static void FormatBoxColumn (ColPtr col)
27464 {
27465 if (col == NULL) return;
27466 col->pixWidth = stdCharWidth;
27467 col->pixInset = 0;
27468 col->charWidth = 0;
27469 col->charInset = 0;
27470 col->font = NULL;
27471 col->just = 'l';
27472 col->wrap = 1;
27473 col->bar = 0;
27474 col->underline = 0;
27475 col->left = 0;
27476 col->last = FALSE;
27477 }
27478
AllocateDocColumnsForFieldList(BulkEdFieldPtr field_list,Int4Ptr p_len,Int4 last_sorted_col,Int4 display_offset,Int4 columns_shown)27479 static ColPtr AllocateDocColumnsForFieldList (BulkEdFieldPtr field_list, Int4Ptr p_len, Int4 last_sorted_col, Int4 display_offset, Int4 columns_shown)
27480 {
27481 Int4 i, num_columns = 4, len = 0, col;
27482 ColPtr col_list;
27483
27484 if (field_list == NULL) {
27485 return NULL;
27486 }
27487
27488 /* set the font so that the pixwidth will be correct */
27489 SelectFont (programFont);
27490
27491 /* start with 3 columns, one for expand/collapse and one for checkbox for row selection, one for right scroll, and one for final blank */
27492 for (i = 0; field_list[i].name != NULL; i++) {
27493 num_columns ++;
27494 }
27495 col_list = (ColPtr) MemNew (num_columns * sizeof (ColData));
27496 col = 0;
27497 FormatBoxColumn (col_list + col);
27498 len += col_list[col].pixWidth;
27499 col++;
27500
27501 for (i = 0; field_list[i].name != NULL; i++) {
27502 if (i < display_offset) {
27503 continue;
27504 } else if (i >= display_offset + columns_shown) {
27505 break;
27506 }
27507 if (i == last_sorted_col) {
27508 FormatBoxColumn (col_list + col);
27509 len += col_list[col].pixWidth;
27510 col++;
27511 }
27512 len += (field_list[i].format_col_func) (col_list + col, field_list[i].name);
27513 col_list[col].last = FALSE;
27514 col++;
27515 }
27516
27517 /* right scroll */
27518 FormatBoxColumn (col_list + col);
27519 len += col_list[col].pixWidth;
27520 col++;
27521
27522 /* final blank column */
27523 col_list[col].pixWidth = 0;
27524 col_list[col].pixInset = 0;
27525 col_list[col].charWidth = 0;
27526 col_list[col].charInset = 0;
27527 col_list[col].font = NULL;
27528 col_list[col].just = 'l';
27529 col_list[col].wrap = 1;
27530 col_list[col].bar = 0;
27531 col_list[col].underline = 0;
27532 col_list[col].left = 0;
27533 col_list[col].last = TRUE;
27534 if (p_len != NULL) {
27535 *p_len = len;
27536 }
27537 return col_list;
27538 }
27539
27540 typedef struct bulkeditorrow {
27541 ValNodePtr values_list;
27542 ValNodePtr object_list;
27543 struct bulkeditorrow PNTR subrows;
27544 Int4 copied_to_meta;
27545 Int4 copied_to_sub;
27546 Boolean expanded;
27547 Boolean selected;
27548 } BulkEditorRowData, PNTR BulkEditorRowPtr;
27549
FreeBulkEditorValues(ValNodePtr values,BulkEdFieldPtr field_list)27550 static ValNodePtr FreeBulkEditorValues (ValNodePtr values, BulkEdFieldPtr field_list)
27551 {
27552 ValNodePtr vnp;
27553 Int4 col;
27554
27555 for (col = 0, vnp = values;
27556 vnp != NULL;
27557 col++, vnp = vnp->next) {
27558 if (field_list[col].free_func == NULL) {
27559 vnp->data.ptrvalue = MemFree (vnp->data.ptrvalue);
27560 } else {
27561 (field_list[col].free_func) (vnp->data.ptrvalue);
27562 vnp->data.ptrvalue = NULL;
27563 }
27564 }
27565 values = ValNodeFree (values);
27566 return values;
27567 }
27568
FreeBulkEditorValuesList(ValNodePtr PNTR values_list,Int4 num_rows,BulkEdFieldPtr field_list)27569 static void FreeBulkEditorValuesList (ValNodePtr PNTR values_list, Int4 num_rows, BulkEdFieldPtr field_list)
27570 {
27571 Int4 i;
27572
27573 if (values_list == NULL || field_list == NULL) return;
27574 for (i = 0; i < num_rows; i++) {
27575 values_list[i] = FreeBulkEditorValues (values_list[i], field_list);
27576 }
27577 values_list = MemFree (values_list);
27578 }
27579
FreeBulkEditorRows(BulkEditorRowPtr rows,BulkEdFieldPtr field_list)27580 static BulkEditorRowPtr FreeBulkEditorRows (BulkEditorRowPtr rows, BulkEdFieldPtr field_list)
27581 {
27582 Int4 row_num;
27583
27584 if (rows == NULL) return NULL;
27585 for (row_num = 0; rows[row_num].object_list != NULL; row_num++) {
27586 rows[row_num].values_list = FreeBulkEditorValues (rows[row_num].values_list, field_list);
27587 rows[row_num].object_list = ValNodeFree (rows[row_num].object_list);
27588 FreeBulkEditorRows (rows[row_num].subrows, field_list);
27589 rows[row_num].subrows = NULL;
27590 }
27591 rows = MemFree (rows);
27592 return rows;
27593 }
27594
27595
CopyToSingleBulkEditRow(BulkEditorRowPtr dst,BulkEditorRowPtr src,BulkEdFieldPtr field_list)27596 static void CopyToSingleBulkEditRow (BulkEditorRowPtr dst, BulkEditorRowPtr src, BulkEdFieldPtr field_list)
27597 {
27598 ValNodePtr vnp;
27599 Int4 col;
27600
27601 if (dst == NULL || src == NULL) return;
27602
27603 /* copy values */
27604 dst->values_list = NULL;
27605 for (vnp = src->values_list, col = 0; vnp != NULL; vnp = vnp->next, col++) {
27606 ValNodeAddPointer (&(dst->values_list), vnp->choice, field_list[col].copy_func(vnp->data.ptrvalue));
27607 }
27608
27609 /* copy object */
27610 dst->object_list = NULL;
27611 ValNodeAddPointer (&(dst->object_list), src->object_list->choice, src->object_list->data.ptrvalue);
27612
27613 /* copy selection */
27614 dst->selected = src->selected;
27615 }
27616
27617
ExpandAllBulkEditRows(BulkEditorRowPtr row_list)27618 static void ExpandAllBulkEditRows (BulkEditorRowPtr row_list)
27619 {
27620 Int4 row_num;
27621
27622 if (row_list == NULL) return;
27623 for (row_num = 0; row_list[row_num].object_list != NULL; row_num++) {
27624 if (row_list[row_num].subrows != NULL) {
27625 row_list[row_num].expanded = TRUE;
27626 }
27627 }
27628 }
27629
CollapseAllBulkEditRows(BulkEditorRowPtr row_list)27630 static void CollapseAllBulkEditRows (BulkEditorRowPtr row_list)
27631 {
27632 Int4 row_num;
27633
27634 if (row_list == NULL) return;
27635 for (row_num = 0; row_list[row_num].object_list != NULL; row_num++) {
27636 if (row_list[row_num].subrows != NULL) {
27637 row_list[row_num].expanded = FALSE;
27638 }
27639 }
27640 }
27641
27642
27643 /* sort_col is zero-based data column, already corrected for selection and expansion columns */
GetTextForBulkEditorRow(BulkEditorRowPtr berp,BulkEdFieldPtr field_list,Int4 sort_col,Int4 display_offset,Int4 columns_shown)27644 static CharPtr GetTextForBulkEditorRow (BulkEditorRowPtr berp, BulkEdFieldPtr field_list, Int4 sort_col, Int4 display_offset, Int4 columns_shown)
27645 {
27646 ValNodePtr column_values = NULL, vnp;
27647 Int4 text_len = 6, col;
27648 CharPtr str, line_text = NULL, tmp_str;
27649
27650 if (berp == NULL) return NULL;
27651 for (vnp = berp->values_list, col = 0; vnp != NULL; vnp = vnp->next, col++) {
27652 if (col < display_offset) {
27653 continue;
27654 } else if (col >= display_offset + columns_shown) {
27655 break;
27656 }
27657 if (field_list[col].display_func == NULL) {
27658 str = NULL;
27659 } else {
27660 str = (field_list[col].display_func)(vnp->data.ptrvalue);
27661 }
27662 if (str == NULL) {
27663 str = StringSave ("");
27664 }
27665 if (berp->subrows != NULL && col == sort_col) {
27666 tmp_str = (CharPtr) MemNew (sizeof (Char) * (18 + StringLen (str)));
27667 sprintf (tmp_str, "%s%s(%d)", field_list[col].draw_col_func == NULL ? "" : " ",
27668 str, ValNodeLen (berp->object_list));
27669 str = MemFree (str);
27670 str = tmp_str;
27671 }
27672 ValNodeAddPointer (&column_values, 0, str);
27673 text_len += StringLen (str) + 1;
27674 }
27675 line_text = (CharPtr) MemNew (text_len * sizeof (Char));
27676 line_text[0] = 0;
27677 /* add blank column for row selector */
27678 StringCat (line_text, "\t");
27679 for (vnp = column_values, col = display_offset; vnp != NULL; vnp = vnp->next, col++) {
27680 if (col == sort_col) {
27681 /* add blank column for expand/collapse */
27682 StringCat (line_text, "\t");
27683 }
27684 StringCat (line_text, vnp->data.ptrvalue);
27685 StringCat (line_text, "\t");
27686 }
27687 column_values = ValNodeFreeData (column_values);
27688 /* add blank column at end, to allow last real column to be highlighted when blank */
27689 StringCat (line_text, "\t\n");
27690 return line_text;
27691 }
27692
27693
DataPosFromBulkEdDlgRow(Int2 row,BulkEditorRowPtr row_list,Int4Ptr pRowNum,Int4Ptr pSubNum)27694 static Boolean DataPosFromBulkEdDlgRow (Int2 row, BulkEditorRowPtr row_list, Int4Ptr pRowNum, Int4Ptr pSubNum)
27695 {
27696 Int4 row_num = 0, sub_num;
27697 Int2 display_row = 1;
27698
27699 if (row < 1 || row_list == NULL || pRowNum == NULL || pSubNum == NULL) return FALSE;
27700
27701 while (row_list[row_num].object_list != NULL) {
27702 if (display_row == row) {
27703 *pRowNum = row_num;
27704 *pSubNum = -1;
27705 return TRUE;
27706 }
27707 display_row++;
27708 if (row_list[row_num].subrows != NULL && row_list[row_num].expanded) {
27709 sub_num = 0;
27710 while (display_row != row && row_list[row_num].subrows[sub_num].object_list != NULL) {
27711 display_row++;
27712 sub_num++;
27713 }
27714 if (row_list[row_num].subrows[sub_num].object_list == NULL) {
27715 sub_num = -1;
27716 } else {
27717 if (display_row == row) {
27718 *pRowNum = row_num;
27719 *pSubNum = sub_num;
27720 return TRUE;
27721 }
27722 }
27723 }
27724 row_num++;
27725 }
27726 *pRowNum = -1;
27727 *pSubNum = -1;
27728 return FALSE;
27729 }
27730
27731
BulkEdDlgRowFromDataPos(Int4 row_num,Int4 sub_num,BulkEditorRowPtr row_list)27732 static Int4 BulkEdDlgRowFromDataPos (Int4 row_num, Int4 sub_num, BulkEditorRowPtr row_list)
27733 {
27734 Int4 i, j, display_row = 1;
27735
27736 if (row_list == NULL) return 0;
27737 /* count subrows also passed */
27738 for (i = 0; row_list[i].object_list != NULL && i < row_num; i++) {
27739 display_row++;
27740 if (row_list[i].subrows != NULL && row_list[i].expanded) {
27741 for (j = 0; row_list[i].subrows[j].object_list != NULL; j++) {
27742 display_row++;
27743 }
27744 }
27745 }
27746 if (sub_num > -1) {
27747 display_row += sub_num + 1;
27748 }
27749 return display_row;
27750 }
27751
27752
BulkEdDataColumnFromDocColumn(Int4 doc_col,Int4 sort_col,Int4 display_offset)27753 static Int4 BulkEdDataColumnFromDocColumn (Int4 doc_col, Int4 sort_col, Int4 display_offset)
27754 {
27755 /* subtract offset (document maps first column to 1) */
27756 doc_col--;
27757 /* subtract selection column */
27758 doc_col--;
27759
27760 /* skip over columns not shown */
27761 doc_col += display_offset;
27762
27763 /* subtract expand/collapse column */
27764 if (doc_col > sort_col && sort_col >= display_offset) {
27765 doc_col--;
27766 }
27767 return doc_col;
27768 }
27769
27770
GetBulkEditorRowValueByColumn(BulkEditorRowPtr berp,Int4 col)27771 static ValNodePtr GetBulkEditorRowValueByColumn (BulkEditorRowPtr berp, Int4 col)
27772 {
27773 Int4 i;
27774 ValNodePtr vnp;
27775
27776 if (col < 0) return NULL;
27777
27778 for (i = 0, vnp = berp->values_list;
27779 i < col && vnp != NULL;
27780 i++, vnp = vnp->next) {}
27781 return vnp;
27782 }
27783
27784
SelectBulkEditorRows(BulkEditorRowPtr berp,Boolean val)27785 static void SelectBulkEditorRows (BulkEditorRowPtr berp, Boolean val)
27786 {
27787 if (berp == NULL) return;
27788
27789 while (berp->object_list != NULL) {
27790 berp->selected = val;
27791 SelectBulkEditorRows (berp->subrows, val);
27792 berp++;
27793 }
27794 }
27795
27796
CountBulkEditorRowsSelected(BulkEditorRowPtr berp)27797 static Int4 CountBulkEditorRowsSelected (BulkEditorRowPtr berp)
27798 {
27799 Int4 num = 0;
27800 if (berp == NULL) return 0;
27801
27802 while (berp->object_list != NULL) {
27803 if (berp->subrows == NULL) {
27804 if (berp->selected) {
27805 num++;
27806 }
27807 } else {
27808 num+= CountBulkEditorRowsSelected (berp->subrows);
27809 }
27810 berp++;
27811 }
27812 return num;
27813 }
27814
27815
GetBulkEditorSelectedObjects(BulkEditorRowPtr berp,ValNodePtr PNTR object_list)27816 static void GetBulkEditorSelectedObjects (BulkEditorRowPtr berp, ValNodePtr PNTR object_list)
27817 {
27818 ValNodePtr vnp;
27819 if (berp == NULL || object_list == NULL) return;
27820
27821 while (berp->object_list != NULL) {
27822 if (berp->subrows == NULL) {
27823 if (berp->selected) {
27824 for (vnp = berp->object_list; vnp != NULL; vnp = vnp->next) {
27825 ValNodeAddPointer (object_list, vnp->choice, vnp->data.ptrvalue);
27826 }
27827 }
27828 } else {
27829 GetBulkEditorSelectedObjects (berp->subrows, object_list);
27830 }
27831 berp++;
27832 }
27833 }
27834
27835
AllBulkEditorRowsSelected(BulkEditorRowPtr berp)27836 static Boolean AllBulkEditorRowsSelected (BulkEditorRowPtr berp)
27837 {
27838 if (berp == NULL) return FALSE;
27839
27840 while (berp->object_list != NULL) {
27841 /* note - don't need to check subrows, because metarow would
27842 * have been unselected if any subrows were unselected */
27843 if (!berp->selected) {
27844 return FALSE;
27845 }
27846 berp++;
27847 }
27848 return TRUE;
27849 }
27850
27851
SelectBulkEditorRowsByStringConstraint(BulkEditorRowPtr berp,BulkEdFieldPtr field_list,Int4 col,StringConstraintXPtr scp,Boolean val)27852 static void SelectBulkEditorRowsByStringConstraint (BulkEditorRowPtr berp, BulkEdFieldPtr field_list, Int4 col, StringConstraintXPtr scp, Boolean val)
27853 {
27854 ValNodePtr vnp;
27855 CharPtr str = NULL;
27856 Boolean match;
27857
27858 if (berp == NULL || field_list == NULL || col < 0 || field_list[col].display_func == NULL) return;
27859
27860 while (berp->object_list != NULL) {
27861 if (berp->subrows == NULL) {
27862 vnp = GetBulkEditorRowValueByColumn (berp, col);
27863 if (vnp != NULL) {
27864 str = field_list[col].display_func(vnp->data.ptrvalue);
27865 }
27866 match = DoesStringMatchConstraintX (str, scp);
27867 str = MemFree (str);
27868 if (scp != NULL && scp->not_present) {
27869 match = !match;
27870 }
27871 if (match) {
27872 berp->selected = val;
27873 }
27874 } else {
27875 SelectBulkEditorRowsByStringConstraint (berp->subrows, field_list, col, scp, val);
27876 berp->selected = AllBulkEditorRowsSelected (berp->subrows);
27877 }
27878 berp++;
27879 }
27880 }
27881
27882
27883 /* call nulls and null values bigger */
27884 /* return 0 if a and b are equal, -1 if a is smaller, and 1 if b is smaller */
CompareBulkRowValues(Pointer val_a,Pointer val_b,BulkDisplayFieldFunc display_func)27885 static Int4 CompareBulkRowValues (Pointer val_a, Pointer val_b, BulkDisplayFieldFunc display_func)
27886 {
27887 CharPtr str_a, str_b;
27888 Int4 rval = 0;
27889
27890 if (val_a == NULL && val_b == NULL) {
27891 rval = 0;
27892 } else if (val_a == NULL) {
27893 rval = 1;
27894 } else if (val_b == NULL) {
27895 rval = -1;
27896 } else if (display_func == NULL) {
27897 rval = 0;
27898 } else {
27899 str_a = display_func(val_a);
27900 str_b = display_func(val_b);
27901 rval = StringCmp (str_a, str_b);
27902 }
27903 return rval;
27904 }
27905
27906 /* call nulls and null values bigger */
27907 /* return 0 if a and b are equal, -1 if a is smaller, and 1 if b is smaller */
CompareBulkRows(BulkEditorRowPtr row_a,BulkEditorRowPtr row_b,Int4 sort_column,BulkEdFieldPtr field_list)27908 static Int4 CompareBulkRows (BulkEditorRowPtr row_a, BulkEditorRowPtr row_b, Int4 sort_column, BulkEdFieldPtr field_list)
27909 {
27910 Int4 col;
27911 ValNodePtr vnp_a, vnp_b;
27912 Int4 rval = 0;
27913
27914 if (row_a == NULL && row_b == NULL) {
27915 rval = 0;
27916 } else if (row_a == NULL) {
27917 rval = 1;
27918 } else if (row_b == NULL) {
27919 rval = -1;
27920 } else if (row_a->values_list == NULL && row_b->values_list == NULL) {
27921 rval = 0;
27922 } else if (row_a->values_list == NULL) {
27923 rval = 1;
27924 } else if (row_b->values_list == NULL) {
27925 rval = -1;
27926 } else {
27927 col = 0;
27928 vnp_a = GetBulkEditorRowValueByColumn (row_a, sort_column);
27929 vnp_b = GetBulkEditorRowValueByColumn (row_b, sort_column);
27930
27931 if (vnp_a == NULL && vnp_b == NULL) {
27932 rval = 0;
27933 } else if (vnp_a == NULL) {
27934 rval = 1;
27935 } else if (vnp_b == NULL) {
27936 rval = -1;
27937 } else {
27938 rval = CompareBulkRowValues (vnp_a->data.ptrvalue, vnp_b->data.ptrvalue, field_list[sort_column].display_func);
27939 }
27940 }
27941 return rval;
27942 }
27943
CountIndividualRows(BulkEditorRowPtr row_list)27944 static Int4 CountIndividualRows (BulkEditorRowPtr row_list)
27945 {
27946 Int4 num_rows = 0, row_num;
27947
27948 if (row_list == NULL) return 0;
27949
27950 for (row_num = 0; row_list[row_num].object_list != NULL; row_num++) {
27951 if (row_list[row_num].subrows == NULL) {
27952 num_rows++;
27953 } else {
27954 num_rows += CountIndividualRows(row_list[row_num].subrows);
27955 }
27956 }
27957 return num_rows;
27958 }
27959
27960
SetDefaultCopiedToValues(BulkEditorRowPtr row_list)27961 static void SetDefaultCopiedToValues (BulkEditorRowPtr row_list)
27962 {
27963 Int4 row_num;
27964
27965 if (row_list == NULL) return;
27966
27967 for (row_num = 0; row_list[row_num].object_list != NULL; row_num++) {
27968 row_list[row_num].copied_to_meta = -1;
27969 row_list[row_num].copied_to_sub = -1;
27970 if (row_list[row_num].subrows != NULL) {
27971 SetDefaultCopiedToValues(row_list[row_num].subrows);
27972 }
27973 }
27974 }
27975
27976
SummarizeOneSubrowSet(BulkEditorRowPtr row,Int4 last_sorted_col)27977 static void SummarizeOneSubrowSet (BulkEditorRowPtr row, Int4 last_sorted_col)
27978 {
27979 Int4 i, num_columns, row_num;
27980 ValNodePtr vnp;
27981 BoolPtr all_present, any_present, all_same;
27982 CharPtr PNTR values;
27983
27984 if (row == NULL || row->subrows == NULL)
27985 {
27986 return;
27987 }
27988 /* count columns */
27989 for (num_columns = 0, vnp = row->values_list; vnp != NULL; num_columns++, vnp = vnp->next)
27990 {}
27991
27992 all_present = (BoolPtr) MemNew (sizeof (Boolean) * num_columns);
27993 any_present = (BoolPtr) MemNew (sizeof (Boolean) * num_columns);
27994 all_same = (BoolPtr) MemNew (sizeof (Boolean) * num_columns);
27995 values = (CharPtr PNTR) MemNew (sizeof (CharPtr) * num_columns);
27996
27997 for (i = 0; i < num_columns; i++)
27998 {
27999 all_present[i] = TRUE;
28000 any_present[i] = FALSE;
28001 all_same[i] = TRUE;
28002 values[i] = NULL;
28003 }
28004
28005 for (row_num = 0; row->subrows[row_num].object_list != NULL; row_num++)
28006 {
28007 for (i = 0, vnp = row->subrows[row_num].values_list; vnp != NULL && i < num_columns; i++, vnp = vnp->next)
28008 {
28009 if (StringHasNoText (vnp->data.ptrvalue))
28010 {
28011 all_present[i] = FALSE;
28012 }
28013 else
28014 {
28015 any_present[i] = TRUE;
28016 if (values[i] == NULL)
28017 {
28018 values[i] = vnp->data.ptrvalue;
28019 }
28020 else if (StringCmp (values[i], vnp->data.ptrvalue) != 0)
28021 {
28022 all_same[i] = FALSE;
28023 }
28024 }
28025 }
28026 while (i < num_columns)
28027 {
28028 all_present[i] = FALSE;
28029 i++;
28030 }
28031 }
28032
28033 for (i = 0, vnp = row->values_list; vnp != NULL; i++, vnp = vnp->next)
28034 {
28035 if (i == last_sorted_col) {
28036 continue;
28037 }
28038 vnp->data.ptrvalue = MemFree (vnp->data.ptrvalue);
28039 if (any_present[i]) {
28040 if (all_present[i]) {
28041 if (all_same[i]) {
28042 vnp->data.ptrvalue = StringSave (values[i]);
28043 } else {
28044 vnp->data.ptrvalue = StringSave ("All present, mixed");
28045 }
28046 } else if (all_same[i]) {
28047 vnp->data.ptrvalue = StringSave ("Some missing, one unique");
28048 } else {
28049 vnp->data.ptrvalue = StringSave ("Some missing, mixed");
28050 }
28051 }
28052 }
28053 all_present = MemFree (all_present);
28054 any_present = MemFree (any_present);
28055 all_same = MemFree (all_same);
28056 values = MemFree (values);
28057 }
28058
28059
AddSummaryInfoToMetaRows(BulkEditorRowPtr row_list,Int4 last_sorted_col)28060 static void AddSummaryInfoToMetaRows (BulkEditorRowPtr row_list, Int4 last_sorted_col)
28061 {
28062 Int4 row_num;
28063
28064 if (row_list == NULL) return;
28065
28066 for (row_num = 0; row_list[row_num].object_list != NULL; row_num++) {
28067 SummarizeOneSubrowSet(row_list + row_num, last_sorted_col);
28068 AddSummaryInfoToMetaRows(row_list[row_num].subrows, last_sorted_col);
28069 }
28070 }
28071
28072
28073 static BulkEdFieldPtr s_CurrentSortingFieldList;
28074 static Int4 s_CurrentSortColumn;
28075
28076
SortVnpByBulkEditorRow(VoidPtr ptr1,VoidPtr ptr2)28077 NLM_EXTERN int LIBCALLBACK SortVnpByBulkEditorRow (VoidPtr ptr1, VoidPtr ptr2)
28078
28079 {
28080 BulkEditorRowPtr row1;
28081 BulkEditorRowPtr row2;
28082 ValNodePtr vnp1;
28083 ValNodePtr vnp2;
28084
28085 if (ptr1 != NULL && ptr2 != NULL) {
28086 vnp1 = *((ValNodePtr PNTR) ptr1);
28087 vnp2 = *((ValNodePtr PNTR) ptr2);
28088 if (vnp1 != NULL && vnp2 != NULL) {
28089
28090 row1 = (BulkEditorRowPtr) vnp1->data.ptrvalue;
28091 row2 = (BulkEditorRowPtr) vnp2->data.ptrvalue;
28092 if (row1 != NULL && row2 != NULL) {
28093 return CompareBulkRows (row1, row2, s_CurrentSortColumn, s_CurrentSortingFieldList);
28094 }
28095 }
28096 }
28097 return 0;
28098 }
28099
28100
FlatCopyRows(BulkEditorRowPtr new_rows,BulkEditorRowPtr orig_rows,BulkEdFieldPtr field_list)28101 static Int4 FlatCopyRows (BulkEditorRowPtr new_rows, BulkEditorRowPtr orig_rows, BulkEdFieldPtr field_list)
28102 {
28103 Int4 num_n = 0, num_o = 0;
28104
28105 while (orig_rows[num_o].object_list != NULL) {
28106 if (orig_rows[num_o].subrows != NULL) {
28107 num_n += FlatCopyRows (new_rows + num_n, orig_rows[num_o].subrows, field_list);
28108 } else {
28109 CopyToSingleBulkEditRow (new_rows + num_n, orig_rows + num_o, field_list);
28110 num_n++;
28111 }
28112 num_o++;
28113 }
28114 return num_n;
28115 }
28116
28117
AddBulkEditorRowsToBlock(ValNodeBlockPtr vb,BulkEditorRowPtr rows)28118 static void AddBulkEditorRowsToBlock (ValNodeBlockPtr vb, BulkEditorRowPtr rows)
28119 {
28120 Int4 i = 0;
28121
28122 if (rows == NULL) {
28123 return;
28124 }
28125 while (rows[i].object_list != NULL) {
28126 if (rows[i].subrows == NULL) {
28127 ValNodeAddPointerToEnd (vb, 0, rows + i);
28128 } else {
28129 AddBulkEditorRowsToBlock (vb, rows[i].subrows);
28130 }
28131 i++;
28132 }
28133 }
28134
28135
SortBulkEditorRowsByValue(BulkEditorRowPtr orig_rows,BulkEdFieldPtr field_list,Int4 new_sort_column)28136 static BulkEditorRowPtr SortBulkEditorRowsByValue (BulkEditorRowPtr orig_rows, BulkEdFieldPtr field_list, Int4 new_sort_column)
28137 {
28138 Int4 num_individual_rows = 0;
28139 ValNodeBlock vb;
28140 Int4 i;
28141 ValNodePtr vnp;
28142 BulkEditorRowPtr new_rows;
28143
28144 /* count individual rows (will need this many or fewer) */
28145 num_individual_rows = CountIndividualRows(orig_rows);
28146 new_rows = (BulkEditorRowPtr) MemNew (sizeof (BulkEditorRowData) * (num_individual_rows + 1));
28147 MemSet (new_rows, 0, sizeof (BulkEditorRowData) * (num_individual_rows + 1));
28148
28149 InitValNodeBlock (&vb, NULL);
28150 AddBulkEditorRowsToBlock (&vb, orig_rows);
28151 s_CurrentSortingFieldList = field_list;
28152 s_CurrentSortColumn = new_sort_column;
28153
28154 vb.head = ValNodeSort (vb.head, SortVnpByBulkEditorRow);
28155 for (vnp = vb.head, i = 0; vnp != NULL; vnp = vnp->next, i++) {
28156 CopyToSingleBulkEditRow (new_rows + i, vnp->data.ptrvalue, field_list);
28157 }
28158 return new_rows;
28159 }
28160
28161
ZeroOutBulkEditorRow(BulkEditorRowPtr row,BulkEdFieldPtr field_list)28162 static void ZeroOutBulkEditorRow (BulkEditorRowPtr row, BulkEdFieldPtr field_list)
28163 {
28164 row->values_list = FreeBulkEditorValues (row->values_list, field_list);
28165 row->object_list = ValNodeFree (row->object_list);
28166 FreeBulkEditorRows (row->subrows, field_list);
28167 row->subrows = NULL;
28168 }
28169
28170
ResortBulkEditorRows(BulkEditorRowPtr orig_rows,BulkEdFieldPtr field_list,Int4 new_sort_column)28171 static BulkEditorRowPtr ResortBulkEditorRows (BulkEditorRowPtr orig_rows, BulkEdFieldPtr field_list, Int4 new_sort_column)
28172 {
28173 Int4 num_individual_rows = 0;
28174 Int4 row_num, sub_num, last_inserted = 0, comp, col;
28175 Int4 smallest_pos = 0, insert_pos = 0;
28176 BulkEditorRowPtr new_rows = NULL, smallest = NULL;
28177 ValNodePtr matches = NULL, vnp;
28178 Boolean all_selected;
28179 BulkEditorRowData swap;
28180
28181 new_rows = SortBulkEditorRowsByValue (orig_rows, field_list, new_sort_column);
28182 /* count individual rows (will need this many or fewer) */
28183 num_individual_rows = CountIndividualRows(orig_rows);
28184
28185 for (row_num = 0; new_rows[row_num].object_list != NULL; row_num++) {
28186 if (smallest == NULL) {
28187 smallest = new_rows + row_num;
28188 smallest_pos = row_num;
28189 } else {
28190 comp = CompareBulkRows (new_rows + row_num, smallest, new_sort_column, field_list);
28191 if (comp == 0) {
28192 /* equal - will be combined into meta row after first non-match is found */
28193 } else {
28194 if (smallest_pos < row_num - 1) {
28195 /* move first match to temporary location */
28196 CopyToSingleBulkEditRow (&swap, smallest, field_list);
28197 /* create meta row */
28198 ZeroOutBulkEditorRow (new_rows + insert_pos, field_list);
28199 /* add value for only sort column */
28200 for (col = 0, vnp = swap.values_list; vnp != NULL; col++, vnp = vnp->next) {
28201 if (col == new_sort_column) {
28202 ValNodeAddPointer (&(new_rows[insert_pos].values_list), vnp->choice, field_list[col].copy_func(vnp->data.ptrvalue));
28203 } else {
28204 ValNodeAddPointer (&(new_rows[insert_pos].values_list), 0, NULL);
28205 }
28206 }
28207 /* add features and subrows */
28208 new_rows[insert_pos].subrows = (BulkEditorRowPtr) MemNew (sizeof(BulkEditorRowData) * (row_num - smallest_pos + 1));
28209 MemSet (new_rows[insert_pos].subrows, 0, sizeof(BulkEditorRowData) * (row_num - smallest_pos + 1));
28210 /* copy in swap row */
28211 sub_num = 0;
28212 ValNodeAddPointer (&(new_rows[insert_pos].object_list), swap.object_list->choice, swap.object_list->data.ptrvalue);
28213 CopyToSingleBulkEditRow (new_rows[insert_pos].subrows + sub_num, &swap, field_list);
28214 all_selected = swap.selected;
28215 sub_num++;
28216 while (sub_num + smallest_pos < row_num) {
28217 ValNodeAddPointer (&(new_rows[insert_pos].object_list), new_rows[smallest_pos + sub_num].object_list->choice, new_rows[smallest_pos + sub_num].object_list->data.ptrvalue);
28218 CopyToSingleBulkEditRow (new_rows[insert_pos].subrows + sub_num, new_rows + smallest_pos + sub_num, field_list);
28219 all_selected &= new_rows[smallest_pos + sub_num].selected;
28220 sub_num++;
28221 }
28222 new_rows[insert_pos].selected = all_selected;
28223 } else {
28224 if (insert_pos != row_num - 1) {
28225 ZeroOutBulkEditorRow (new_rows + insert_pos, field_list);
28226 CopyToSingleBulkEditRow (new_rows + insert_pos, new_rows + row_num - 1, field_list);
28227 }
28228 }
28229 insert_pos++;
28230 smallest_pos = row_num;
28231 smallest = new_rows + smallest_pos;
28232 }
28233 }
28234 }
28235
28236 /* final row */
28237 if (smallest_pos < row_num - 1) {
28238 /* move first match to temporary location */
28239 CopyToSingleBulkEditRow (&swap, smallest, field_list);
28240 /* create meta row */
28241 ZeroOutBulkEditorRow (new_rows + insert_pos, field_list);
28242 /* add value for only sort column */
28243 for (col = 0, vnp = swap.values_list; vnp != NULL; col++, vnp = vnp->next) {
28244 if (col == new_sort_column) {
28245 ValNodeAddPointer (&(new_rows[insert_pos].values_list), vnp->choice, field_list[col].copy_func(vnp->data.ptrvalue));
28246 } else {
28247 ValNodeAddPointer (&(new_rows[insert_pos].values_list), 0, NULL);
28248 }
28249 }
28250 /* add features and subrows */
28251 new_rows[insert_pos].subrows = (BulkEditorRowPtr) MemNew (sizeof(BulkEditorRowData) * (row_num - smallest_pos + 1));
28252 MemSet (new_rows[insert_pos].subrows, 0, sizeof(BulkEditorRowData) * (row_num - smallest_pos + 1));
28253 /* copy in swap row */
28254 sub_num = 0;
28255 ValNodeAddPointer (&(new_rows[insert_pos].object_list), swap.object_list->choice, swap.object_list->data.ptrvalue);
28256 CopyToSingleBulkEditRow (new_rows[insert_pos].subrows + sub_num, &swap, field_list);
28257 all_selected = swap.selected;
28258 sub_num++;
28259 while (sub_num + smallest_pos < row_num) {
28260 ValNodeAddPointer (&(new_rows[insert_pos].object_list), new_rows[smallest_pos + sub_num].object_list->choice, new_rows[smallest_pos + sub_num].object_list->data.ptrvalue);
28261 CopyToSingleBulkEditRow (new_rows[insert_pos].subrows + sub_num, new_rows + smallest_pos + sub_num, field_list);
28262 all_selected &= new_rows[smallest_pos + sub_num].selected;
28263 sub_num++;
28264 }
28265 new_rows[insert_pos].selected = all_selected;
28266 } else {
28267 if (insert_pos != row_num - 1) {
28268 ZeroOutBulkEditorRow (new_rows + insert_pos, field_list);
28269 CopyToSingleBulkEditRow (new_rows + insert_pos, new_rows + row_num - 1, field_list);
28270 }
28271 }
28272 insert_pos++;
28273
28274 while (insert_pos < num_individual_rows) {
28275 ZeroOutBulkEditorRow (new_rows + insert_pos, field_list);
28276 insert_pos++;
28277 }
28278
28279 AddSummaryInfoToMetaRows (new_rows, new_sort_column);
28280 return new_rows;
28281 }
28282
28283
28284 /* sort_column is zero-based data column, already corrected for selection and expansion columns */
AllSubrowsSameValue(BulkEditorRowPtr berp,BulkEdFieldPtr field_list,Int4 sort_column)28285 static Boolean AllSubrowsSameValue (BulkEditorRowPtr berp, BulkEdFieldPtr field_list, Int4 sort_column)
28286 {
28287 Int4 i;
28288 Boolean all_same = TRUE;
28289
28290 if (berp == NULL || berp->subrows == NULL || berp->subrows[0].object_list == NULL) {
28291 return TRUE;
28292 }
28293
28294 for (i = 1; berp->subrows[i].object_list != NULL && all_same; i++) {
28295 if (CompareBulkRows (berp->subrows + i - 1, berp->subrows + i, sort_column, field_list) != 0) {
28296 all_same = FALSE;
28297 }
28298 }
28299
28300 return all_same;
28301 }
28302
28303
28304 /* sort_column is zero-based data column, already corrected for selection and expansion columns */
28305 /* look to see if data in columns is different from data in editor */
AnyChangeInBulkFields(BulkEditorRowPtr berp,BulkEdFieldPtr field_list,DialoG editor,Int4 sort_column)28306 static Boolean AnyChangeInBulkFields (BulkEditorRowPtr berp, BulkEdFieldPtr field_list, DialoG editor, Int4 sort_column)
28307 {
28308 Pointer m_data;
28309 ValNodePtr vnp;
28310 Int4 comp;
28311
28312 if (berp == NULL || berp->subrows == NULL || berp->subrows[0].object_list == NULL) return FALSE;
28313 if (field_list == NULL || editor == NULL) return FALSE;
28314
28315 if (!AllSubrowsSameValue (berp, field_list, sort_column)) {
28316 return TRUE;
28317 }
28318
28319 /* find value for sort_column from first subrow */
28320 vnp = GetBulkEditorRowValueByColumn (berp, sort_column);
28321
28322 if (vnp == NULL) return TRUE;
28323
28324 /* compare with data from editor */
28325 m_data = DialogToPointer (editor);
28326
28327 comp = CompareBulkRowValues (m_data, vnp->data.ptrvalue, field_list[sort_column].display_func);
28328
28329 /* free data from editor */
28330 if (field_list[sort_column].free_func) {
28331 (field_list[sort_column].free_func)(m_data);
28332 }
28333
28334 if (comp == 0) {
28335 return FALSE;
28336 } else {
28337 return TRUE;
28338 }
28339 }
28340
28341
28342 /* col is zero-based data column, already corrected for selection and expansion columns */
ApplyValueToOneBulkEditorRow(BulkEditorRowPtr berp,Int2 col,BulkEdFieldPtr field_list,DialoG editor)28343 static void ApplyValueToOneBulkEditorRow (BulkEditorRowPtr berp, Int2 col, BulkEdFieldPtr field_list, DialoG editor)
28344 {
28345 ValNodePtr vnp;
28346
28347 if (berp == NULL || field_list == NULL || editor == NULL) return;
28348
28349 vnp = GetBulkEditorRowValueByColumn (berp, col);
28350
28351 if (vnp != NULL) {
28352 if (field_list[col].free_func == NULL) {
28353 vnp->data.ptrvalue = MemFree (vnp->data.ptrvalue);
28354 } else {
28355 (field_list[col].free_func) (vnp->data.ptrvalue);
28356 vnp->data.ptrvalue = NULL;
28357 }
28358 vnp->data.ptrvalue = DialogToPointer (editor);
28359 }
28360 }
28361
28362
PopulateSingleBulkEditRowFromData(BulkEditorRowPtr berp,Uint1 data_choice,Pointer data,BulkEdFieldPtr field_list,Pointer metadata)28363 static void PopulateSingleBulkEditRowFromData (BulkEditorRowPtr berp, Uint1 data_choice, Pointer data, BulkEdFieldPtr field_list, Pointer metadata)
28364 {
28365 Int4 col;
28366
28367 /* add values for all columns */
28368 for (col = 0; field_list[col].name != NULL; col++) {
28369 ValNodeAddPointer (&(berp->values_list), 0, (field_list[col].get_func (data_choice, data, metadata)));
28370 }
28371 /* add feature */
28372 ValNodeAddPointer (&(berp->object_list), data_choice, data);
28373 }
28374
MakeBulkEditorRowsFromObjectList(ValNodePtr object_list,BulkEdFieldPtr field_list,Int4 sort_column,Pointer metadata)28375 static BulkEditorRowPtr MakeBulkEditorRowsFromObjectList (ValNodePtr object_list, BulkEdFieldPtr field_list, Int4 sort_column, Pointer metadata)
28376 {
28377 ValNodePtr vnp;
28378 BulkEditorRowPtr bulk_ed_rows = NULL, sorted_rows = NULL;
28379 Int4 num_rows, row_num;
28380
28381 if (object_list == NULL || field_list == NULL) return NULL;
28382
28383 /* first, create list with one row per object */
28384 num_rows = ValNodeLen (object_list);
28385
28386 bulk_ed_rows = (BulkEditorRowPtr) MemNew (sizeof (BulkEditorRowData) * (num_rows + 1));
28387 MemSet (bulk_ed_rows, 0, sizeof (BulkEditorRowData) * (num_rows + 1));
28388
28389 for (vnp = object_list, row_num = 0; vnp != NULL; vnp = vnp->next, row_num++)
28390 {
28391 PopulateSingleBulkEditRowFromData (bulk_ed_rows + row_num, vnp->choice, vnp->data.ptrvalue, field_list, metadata);
28392 }
28393
28394 if (sort_column >= 0)
28395 {
28396 /* Now resort rows for column */
28397 sorted_rows = ResortBulkEditorRows (bulk_ed_rows, field_list, sort_column);
28398 bulk_ed_rows = FreeBulkEditorRows (bulk_ed_rows, field_list);
28399 bulk_ed_rows = sorted_rows;
28400 }
28401 return bulk_ed_rows;
28402 }
28403
28404
28405 static Boolean IsBulkEditorColumnEmpty (BulkEditorRowPtr row_list, Int4 column);
28406
IsBulkEditorRowColumnEmpty(BulkEditorRowPtr row,Int4 column)28407 static Boolean IsBulkEditorRowColumnEmpty (BulkEditorRowPtr row, Int4 column)
28408 {
28409 ValNodePtr vnp;
28410 Int4 pos;
28411
28412 if (row == NULL) {
28413 return TRUE;
28414 }
28415
28416 for (pos = 0, vnp = row->values_list;
28417 pos < column && vnp != NULL;
28418 pos++, vnp = vnp->next)
28419 {
28420 }
28421 if (pos == column && vnp != NULL && !StringHasNoText (vnp->data.ptrvalue))
28422 {
28423 return FALSE;
28424 }
28425 else
28426 {
28427 return IsBulkEditorColumnEmpty(row->subrows, column);
28428 }
28429 }
28430
28431
IsBulkEditorColumnEmpty(BulkEditorRowPtr row_list,Int4 column)28432 static Boolean IsBulkEditorColumnEmpty (BulkEditorRowPtr row_list, Int4 column)
28433 {
28434 Boolean rval = TRUE;
28435 Int4 i;
28436
28437 if (row_list == NULL)
28438 {
28439 return TRUE;
28440 }
28441 for (i = 0; row_list[i].object_list != NULL && rval; i++)
28442 {
28443 rval = IsBulkEditorRowColumnEmpty (row_list + i, column);
28444 }
28445 return rval;
28446 }
28447
28448
28449 static Int4
AddRowsToListBySelection(BulkEditorRowPtr dest,BulkEditorRowPtr src,BulkEdFieldPtr field_list,Int4 last_inserted,Boolean selected)28450 AddRowsToListBySelection
28451 (BulkEditorRowPtr dest,
28452 BulkEditorRowPtr src,
28453 BulkEdFieldPtr field_list,
28454 Int4 last_inserted,
28455 Boolean selected)
28456 {
28457 Int4 row_num;
28458
28459 if (dest == NULL || src == NULL) return last_inserted;
28460
28461 for (row_num = 0; src[row_num].object_list != NULL; row_num++) {
28462 if (src[row_num].subrows == NULL) {
28463 if ((src[row_num].selected && selected)
28464 || (!src[row_num].selected && !selected)) {
28465 CopyToSingleBulkEditRow (dest + last_inserted, src + row_num, field_list);
28466 src[row_num].copied_to_meta = last_inserted;
28467 src[row_num].copied_to_sub = 0;
28468 last_inserted++;
28469 }
28470 } else {
28471 last_inserted = AddRowsToListBySelection(dest, src[row_num].subrows, field_list, last_inserted, selected);
28472 }
28473 }
28474 return last_inserted;
28475 }
28476
ResortBulkEditorRowsBySelected(BulkEditorRowPtr orig_rows,BulkEdFieldPtr field_list)28477 static BulkEditorRowPtr ResortBulkEditorRowsBySelected (BulkEditorRowPtr orig_rows, BulkEdFieldPtr field_list)
28478 {
28479 Int4 num_individual_rows;
28480 Int4 last_inserted = 0;
28481 BulkEditorRowPtr new_rows = NULL;
28482
28483 /* count individual rows (will need this many or fewer) */
28484 num_individual_rows = CountIndividualRows(orig_rows);
28485
28486 /* set default copied_to values */
28487 SetDefaultCopiedToValues (orig_rows);
28488
28489 new_rows = (BulkEditorRowPtr) MemNew (sizeof (BulkEditorRowData) * (num_individual_rows + 1));
28490 MemSet (new_rows, 0, sizeof (BulkEditorRowData) * (num_individual_rows + 1));
28491
28492 /* add selected rows first */
28493 last_inserted = AddRowsToListBySelection(new_rows, orig_rows, field_list, last_inserted, TRUE);
28494
28495 /* add unselected rows */
28496 last_inserted = AddRowsToListBySelection(new_rows, orig_rows, field_list, last_inserted, FALSE);
28497
28498 return new_rows;
28499 }
28500
28501
28502
28503
28504
28505 typedef enum {
28506 eBulkApplyField = 1,
28507 eBulkEditField,
28508 eBulkConvertField,
28509 eBulkParseField,
28510 eBulkSwapField,
28511 eBulkRemoveField,
28512 eBulkCapitalizeField
28513 } EBulkAction;
28514
GetFieldNumFromPopupValue(Int4 popup_val,BulkEdFieldPtr field_list,Boolean edit_only)28515 static Int4 GetFieldNumFromPopupValue (Int4 popup_val, BulkEdFieldPtr field_list, Boolean edit_only)
28516 {
28517 Int4 i, pval = 1;
28518
28519 for (i = 0; field_list[i].name != NULL; i++) {
28520 if (field_list[i].create_dlg_func != NULL || (!edit_only && field_list[i].display_func != NULL)) {
28521 if (pval == popup_val) {
28522 return i;
28523 } else {
28524 pval++;
28525 }
28526 }
28527 }
28528 return -1;
28529 }
28530
28531
MakeBulkEditorFieldListPopup(GrouP g,BulkEdFieldPtr field_list,Boolean edit_only)28532 static PopuP MakeBulkEditorFieldListPopup (GrouP g, BulkEdFieldPtr field_list, Boolean edit_only)
28533 {
28534 PopuP p;
28535 Int4 i;
28536
28537 if (field_list == NULL) return NULL;
28538
28539 p = PopupList (g, TRUE, NULL);
28540 for (i = 0; field_list[i].name != NULL; i++) {
28541 if (field_list[i].create_dlg_func != NULL || (!edit_only && field_list[i].display_func != NULL)) {
28542 PopupItem (p, field_list[i].name);
28543 }
28544 }
28545 return p;
28546 }
28547
28548
MakeBulkEditorFieldListDialog(GrouP g,BulkEdFieldPtr field_list,Boolean edit_only)28549 static DialoG MakeBulkEditorFieldListDialog (GrouP g, BulkEdFieldPtr field_list, Boolean edit_only)
28550 {
28551 ValNodeBlock block;
28552 Int4 i;
28553
28554 if (field_list == NULL) return NULL;
28555 InitValNodeBlock (&block, NULL);
28556
28557 for (i = 0; field_list[i].name != NULL; i++) {
28558 if (field_list[i].create_dlg_func != NULL || (!edit_only && field_list[i].display_func != NULL)) {
28559 ValNodeAddPointerToEnd (&block, i, StringSave (field_list[i].name));
28560 }
28561 }
28562 return ValNodeSelectionDialog (g, block.head, TALL_SELECTION_LIST, ValNodeStringName, ValNodeSimpleDataFree, ValNodeStringCopy, ValNodeChoiceMatch, "field", NULL, NULL, FALSE);
28563 }
28564
28565
SetBulkEditorFieldListDialogValue(DialoG d,Int4 val)28566 static void SetBulkEditorFieldListDialogValue (DialoG d, Int4 val)
28567 {
28568 ValNode vn;
28569
28570 MemSet (&vn, 0, sizeof (ValNode));
28571 vn.choice = val;
28572 PointerToDialog (d, &vn);
28573 }
28574
28575
ResetBulkEditorFieldListDialogValue(DialoG d,BulkEdFieldPtr field_list)28576 static void ResetBulkEditorFieldListDialogValue (DialoG d, BulkEdFieldPtr field_list)
28577 {
28578 SetBulkEditorFieldListDialogValue(d, GetFieldNumFromPopupValue(1, field_list, TRUE));
28579 }
28580
28581
GetBulkEditorFieldListDialogValue(DialoG d)28582 static Int4 GetBulkEditorFieldListDialogValue (DialoG d)
28583 {
28584 Int4 val = 0;
28585 ValNodePtr vnp;
28586
28587 vnp = DialogToPointer (d);
28588 if (vnp != NULL) {
28589 val = vnp->choice;
28590 vnp = ValNodeFree (vnp);
28591 }
28592 return val;
28593 }
28594
28595
28596
28597 typedef struct onefieldbulkedit
28598 {
28599 Int4 field;
28600 EditApplyPtr edit_apply;
28601 ChangeCasePtr capitalization;
28602 } OneFieldBulkEditData, PNTR OneFieldBulkEditPtr;
28603
28604
OneFieldBulkEditNew(void)28605 static OneFieldBulkEditPtr OneFieldBulkEditNew (void)
28606 {
28607 OneFieldBulkEditPtr ofp;
28608
28609 ofp = (OneFieldBulkEditPtr) MemNew (sizeof (OneFieldBulkEditData));
28610 return ofp;
28611 }
28612
28613
OneFieldBulkEditFree(OneFieldBulkEditPtr ofp)28614 static OneFieldBulkEditPtr OneFieldBulkEditFree (OneFieldBulkEditPtr ofp)
28615 {
28616 if (ofp != NULL) {
28617 ofp->edit_apply = EditApplyFree (ofp->edit_apply);
28618 ofp->capitalization = MemFree (ofp->capitalization);
28619 ofp = MemFree (ofp);
28620 }
28621 return ofp;
28622 }
28623
28624
GetDlgFieldNumFromMasterFieldNum(BulkEdFieldPtr master_field_list,BulkEdFieldPtr field_list,Int4 master_field)28625 static Int4 GetDlgFieldNumFromMasterFieldNum (BulkEdFieldPtr master_field_list, BulkEdFieldPtr field_list, Int4 master_field)
28626 {
28627 Int4 m = 0, f = 0;
28628
28629 while (master_field_list[m].name != NULL && m < master_field) {
28630 if (StringCmp (master_field_list[m].name, field_list[f].name) == 0) {
28631 f++;
28632 }
28633 m++;
28634 }
28635
28636 return f;
28637 }
28638
28639
GetMasterFieldNumFromDlgFieldNum(BulkEdFieldPtr master_field_list,BulkEdFieldPtr field_list,Int4 dlg_field)28640 static Int4 GetMasterFieldNumFromDlgFieldNum (BulkEdFieldPtr master_field_list, BulkEdFieldPtr field_list, Int4 dlg_field)
28641 {
28642 Int4 m = 0;
28643
28644 while (master_field_list[m].name != NULL && StringCmp (master_field_list[m].name, field_list[dlg_field].name) != 0) {
28645 m++;
28646 }
28647
28648 return m;
28649
28650 }
28651
28652
AdjustOneFieldForMaster(OneFieldBulkEditPtr ofp,BulkEdFieldPtr master_field_list,BulkEdFieldPtr field_list)28653 static void AdjustOneFieldForMaster (OneFieldBulkEditPtr ofp, BulkEdFieldPtr master_field_list, BulkEdFieldPtr field_list)
28654 {
28655 if (ofp == NULL || master_field_list == NULL || field_list == NULL) {
28656 return;
28657 }
28658
28659 ofp->field = GetDlgFieldNumFromMasterFieldNum (master_field_list, field_list, ofp->field);
28660 }
28661
28662
28663 typedef CharPtr (*Nlm_GetAutopopulateTextProc) PROTO ((Pointer, Int4));
28664
28665 typedef struct onefieldbulkeditdlg
28666 {
28667 DIALOG_MESSAGE_BLOCK
28668 Nlm_ChangeNotifyProc change_notify;
28669 Pointer change_userdata;
28670 BulkEdFieldPtr field_list;
28671 DialoG edit_apply;
28672 DialoG capitalization;
28673 DialoG field_dlg;
28674
28675 Nlm_GetAutopopulateTextProc autopopulate_func;
28676 Pointer autopopulate_data;
28677 } OneFieldBulkEditDialogData, PNTR OneFieldBulkEditDialogPtr;
28678
28679
OneFieldBulkEditToDialog(DialoG d,Pointer data)28680 static void OneFieldBulkEditToDialog (DialoG d, Pointer data)
28681 {
28682 OneFieldBulkEditDialogPtr dlg;
28683 OneFieldBulkEditPtr dlg_data;
28684
28685 dlg = (OneFieldBulkEditDialogPtr) GetObjectExtra (d);
28686 if (dlg == NULL) return;
28687
28688 dlg_data = (OneFieldBulkEditPtr) data;
28689 if (dlg_data == NULL) {
28690 ResetBulkEditorFieldListDialogValue (dlg->field_dlg, dlg->field_list);
28691 PointerToDialog (dlg->edit_apply, NULL);
28692 PointerToDialog (dlg->capitalization, NULL);
28693 } else {
28694 SetBulkEditorFieldListDialogValue (dlg->field_dlg, dlg_data->field);
28695 PointerToDialog (dlg->edit_apply, dlg_data->edit_apply);
28696 PointerToDialog (dlg->capitalization, dlg_data->capitalization);
28697 }
28698 if (dlg->change_notify != NULL) {
28699 (dlg->change_notify) (dlg->change_userdata);
28700 }
28701 }
28702
28703
OneFieldBulkEditDialogToPointer(DialoG d)28704 static Pointer OneFieldBulkEditDialogToPointer (DialoG d)
28705 {
28706 OneFieldBulkEditDialogPtr dlg;
28707 OneFieldBulkEditPtr dlg_data;
28708
28709 dlg = (OneFieldBulkEditDialogPtr) GetObjectExtra (d);
28710 if (dlg == NULL) return NULL;
28711
28712 dlg_data = (OneFieldBulkEditPtr) MemNew (sizeof (OneFieldBulkEditData));
28713 dlg_data->field = GetBulkEditorFieldListDialogValue (dlg->field_dlg);
28714 dlg_data->edit_apply = DialogToPointer (dlg->edit_apply);
28715 dlg_data->capitalization = DialogToPointer (dlg->capitalization);
28716
28717 return dlg_data;
28718 }
28719
28720
OneFieldBulkEditMsg(DialoG d,Int2 mssg)28721 static void OneFieldBulkEditMsg (DialoG d, Int2 mssg)
28722
28723 {
28724 OneFieldBulkEditDialogPtr dlg;
28725
28726 dlg = (OneFieldBulkEditDialogPtr) GetObjectExtra (d);
28727 if (dlg != NULL) {
28728 if (mssg == AECR_VIB_MSG_CLEAR_TEXT) {
28729 SendMessageToDialog (dlg->edit_apply, NUM_VIB_MSG + 1);
28730 }
28731 }
28732 }
28733
28734
OneFieldAutopopulate(ButtoN b)28735 static void OneFieldAutopopulate(ButtoN b)
28736 {
28737 OneFieldBulkEditDialogPtr dlg;
28738 CharPtr txt;
28739 EditApplyPtr edit_apply;
28740 Int4 field;
28741
28742 dlg = (OneFieldBulkEditDialogPtr) GetObjectExtra (b);
28743 if (dlg != NULL && dlg->autopopulate_func != NULL) {
28744 field = GetBulkEditorFieldListDialogValue (dlg->field_dlg);
28745 txt = (dlg->autopopulate_func) (dlg->autopopulate_data, field);
28746 edit_apply = DialogToPointer (dlg->edit_apply);
28747 if (edit_apply == NULL) {
28748 edit_apply = EditApplyNew();
28749 }
28750 edit_apply->find_txt = MemFree (edit_apply->find_txt);
28751 edit_apply->find_txt = StringSave (txt);
28752 edit_apply->apply_txt = MemFree (edit_apply->apply_txt);
28753 edit_apply->apply_txt = StringSave (txt);
28754 PointerToDialog (dlg->edit_apply, edit_apply);
28755 edit_apply = EditApplyFree (edit_apply);
28756 txt = MemFree (txt);
28757 }
28758 }
28759
28760
OneFieldClearText(ButtoN b)28761 static void OneFieldClearText(ButtoN b)
28762 {
28763 OneFieldBulkEditDialogPtr dlg;
28764 EditApplyPtr edit_apply;
28765
28766 dlg = (OneFieldBulkEditDialogPtr) GetObjectExtra (b);
28767 if (dlg != NULL) {
28768 edit_apply = DialogToPointer (dlg->edit_apply);
28769 if (edit_apply != NULL) {
28770 edit_apply->find_txt = MemFree (edit_apply->find_txt);
28771 edit_apply->repl_txt = MemFree (edit_apply->repl_txt);
28772 edit_apply->apply_txt = MemFree (edit_apply->apply_txt);
28773 PointerToDialog (dlg->edit_apply, edit_apply);
28774 edit_apply = EditApplyFree (edit_apply);
28775 }
28776 }
28777 }
28778
28779
OneFieldBulkEditDialog(GrouP h,EBulkAction action_choice,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata,BulkEdFieldPtr field_list,Nlm_GetAutopopulateTextProc autopopulate_func,Pointer autopopulate_data)28780 static DialoG OneFieldBulkEditDialog
28781 (GrouP h,
28782 EBulkAction action_choice,
28783 Nlm_ChangeNotifyProc change_notify,
28784 Pointer change_userdata,
28785 BulkEdFieldPtr field_list,
28786 Nlm_GetAutopopulateTextProc autopopulate_func,
28787 Pointer autopopulate_data
28788 )
28789
28790 {
28791 OneFieldBulkEditDialogPtr dlg;
28792 GrouP p, g1, g2 = NULL;
28793 ButtoN b;
28794
28795 dlg = (OneFieldBulkEditDialogPtr) MemNew (sizeof (OneFieldBulkEditDialogData));
28796 if (dlg == NULL)
28797 {
28798 return NULL;
28799 }
28800
28801 p = HiddenGroup (h, -1, 0, NULL);
28802 SetObjectExtra (p, dlg, StdCleanupExtraProc);
28803 SetGroupSpacing (p, 10, 10);
28804
28805 dlg->dialog = (DialoG) p;
28806 dlg->todialog = OneFieldBulkEditToDialog;
28807 dlg->fromdialog = OneFieldBulkEditDialogToPointer;
28808 dlg->dialogmessage = OneFieldBulkEditMsg;
28809 dlg->testdialog = NULL;
28810
28811 dlg->field_list = field_list;
28812 dlg->autopopulate_func = autopopulate_func;
28813 dlg->autopopulate_data = autopopulate_data;
28814
28815 g1 = HiddenGroup (p, 2, 0, NULL);
28816 SetGroupSpacing (g1, 10, 10);
28817 dlg->field_dlg = MakeBulkEditorFieldListDialog (g1, field_list, TRUE);
28818 ResetBulkEditorFieldListDialogValue (dlg->field_dlg, dlg->field_list);
28819
28820 if (action_choice == eBulkApplyField)
28821 {
28822 dlg->edit_apply = EditApplyDialog (g1, eEditApplyChoice_Apply, NULL, NULL, NULL, NULL);
28823 }
28824 else if (action_choice == eBulkEditField)
28825 {
28826 dlg->edit_apply = EditApplyDialog (g1, eEditApplyChoice_Edit, NULL, NULL, NULL, NULL);
28827 }
28828 else if (action_choice == eBulkCapitalizeField)
28829 {
28830 dlg->capitalization = ChangeCaseDialog (g1);
28831 }
28832
28833 if (autopopulate_func != NULL) {
28834 g2 = HiddenGroup (p, 2, 0, NULL);
28835 SetGroupSpacing (g2, 10, 10);
28836 b = PushButton (g2, "Autopopulate", OneFieldAutopopulate);
28837 SetObjectExtra (b, dlg, NULL);
28838 b = PushButton (g2, "Clear Text", OneFieldClearText);
28839 SetObjectExtra (b, dlg, NULL);
28840 }
28841 AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) g2, NULL);
28842
28843 return (DialoG) p;
28844 }
28845
28846
28847 typedef struct twofieldbulkedit
28848 {
28849 Int4 field_from;
28850 Int4 field_to;
28851 Boolean strip_name;
28852 Boolean leave_on_original;
28853 Boolean remove_parsed;
28854 TextPortionXPtr text_portion;
28855 } TwoFieldBulkEditData, PNTR TwoFieldBulkEditPtr;
28856
28857
TwoFieldBulkEditNew(void)28858 static TwoFieldBulkEditPtr TwoFieldBulkEditNew (void)
28859 {
28860 TwoFieldBulkEditPtr tfp;
28861
28862 tfp = (TwoFieldBulkEditPtr) MemNew (sizeof (TwoFieldBulkEditData));
28863 return tfp;
28864 }
28865
28866
TwoFieldBulkEditFree(TwoFieldBulkEditPtr tfp)28867 static TwoFieldBulkEditPtr TwoFieldBulkEditFree (TwoFieldBulkEditPtr tfp)
28868 {
28869 if (tfp != NULL) {
28870 tfp->text_portion = TextPortionXFree (tfp->text_portion);
28871 tfp = MemFree (tfp);
28872 }
28873 return tfp;
28874 }
28875
28876
AdjustTwoFieldsForMaster(TwoFieldBulkEditPtr tfp,BulkEdFieldPtr master_field_list,BulkEdFieldPtr field_list)28877 static void AdjustTwoFieldsForMaster (TwoFieldBulkEditPtr tfp, BulkEdFieldPtr master_field_list, BulkEdFieldPtr field_list)
28878 {
28879 if (tfp == NULL || master_field_list == NULL || field_list == NULL) {
28880 return;
28881 }
28882
28883 tfp->field_to = GetDlgFieldNumFromMasterFieldNum (master_field_list, field_list, tfp->field_to);
28884 tfp->field_from = GetDlgFieldNumFromMasterFieldNum (master_field_list, field_list, tfp->field_from);
28885 }
28886
28887
28888 typedef struct twofieldbulkeditdlg
28889 {
28890 DIALOG_MESSAGE_BLOCK
28891 Nlm_ChangeNotifyProc change_notify;
28892 Pointer change_userdata;
28893 BulkEdFieldPtr field_list;
28894 ButtoN strip_name;
28895 ButtoN leave_on_original;
28896 ButtoN remove_parsed;
28897 DialoG text_portion;
28898 DialoG field_from;
28899 DialoG field_to;
28900
28901 Nlm_GetAutopopulateTextProc autopopulate_func;
28902 Pointer autopopulate_data;
28903 } TwoFieldBulkEditDialogData, PNTR TwoFieldBulkEditDialogPtr;
28904
28905
TwoFieldBulkEditToDialog(DialoG d,Pointer data)28906 static void TwoFieldBulkEditToDialog (DialoG d, Pointer data)
28907 {
28908 TwoFieldBulkEditDialogPtr dlg;
28909 TwoFieldBulkEditPtr dlg_data;
28910
28911 dlg = (TwoFieldBulkEditDialogPtr) GetObjectExtra (d);
28912 if (dlg == NULL) return;
28913
28914 dlg_data = (TwoFieldBulkEditPtr) data;
28915 if (dlg_data == NULL) {
28916 ResetBulkEditorFieldListDialogValue (dlg->field_from, dlg->field_list);
28917 ResetBulkEditorFieldListDialogValue (dlg->field_to, dlg->field_list);
28918 if (dlg->leave_on_original != NULL) {
28919 SetStatus (dlg->leave_on_original, FALSE);
28920 }
28921 if (dlg->strip_name != NULL) {
28922 SetStatus (dlg->strip_name, FALSE);
28923 }
28924 if (dlg->remove_parsed != NULL) {
28925 SetStatus (dlg->remove_parsed, FALSE);
28926 }
28927 PointerToDialog (dlg->text_portion, NULL);
28928 } else {
28929 SetBulkEditorFieldListDialogValue (dlg->field_from, dlg_data->field_from);
28930 SetBulkEditorFieldListDialogValue (dlg->field_to, dlg_data->field_from);
28931 if (dlg->leave_on_original != NULL) {
28932 SetStatus (dlg->leave_on_original, dlg_data->leave_on_original);
28933 }
28934 if (dlg->strip_name != NULL) {
28935 SetStatus (dlg->strip_name, dlg_data->strip_name);
28936 }
28937 if (dlg->remove_parsed != NULL) {
28938 SetStatus (dlg->remove_parsed, dlg_data->remove_parsed);
28939 }
28940 PointerToDialog (dlg->text_portion, dlg_data->text_portion);
28941 }
28942 if (dlg->change_notify != NULL) {
28943 (dlg->change_notify) (dlg->change_userdata);
28944 }
28945 }
28946
28947
TwoFieldBulkEditDialogToPointer(DialoG d)28948 static Pointer TwoFieldBulkEditDialogToPointer (DialoG d)
28949 {
28950 TwoFieldBulkEditDialogPtr dlg;
28951 TwoFieldBulkEditPtr dlg_data;
28952
28953 dlg = (TwoFieldBulkEditDialogPtr) GetObjectExtra (d);
28954 if (dlg == NULL) return NULL;
28955
28956 dlg_data = (TwoFieldBulkEditPtr) MemNew (sizeof (TwoFieldBulkEditData));
28957 dlg_data->field_from = GetBulkEditorFieldListDialogValue (dlg->field_from);
28958 dlg_data->field_to = GetBulkEditorFieldListDialogValue (dlg->field_to);
28959 dlg_data->leave_on_original = dlg->leave_on_original == NULL ? FALSE : GetStatus (dlg->leave_on_original);
28960 dlg_data->strip_name = dlg->strip_name == NULL ? FALSE : GetStatus (dlg->strip_name);
28961 dlg_data->remove_parsed = dlg->remove_parsed == NULL ? FALSE : GetStatus (dlg->remove_parsed);
28962 dlg_data->text_portion = DialogToPointer (dlg->text_portion);
28963
28964 return dlg_data;
28965 }
28966
28967
TwoFieldBulkEditMsg(DialoG d,Int2 mssg)28968 static void TwoFieldBulkEditMsg (DialoG d, Int2 mssg)
28969
28970 {
28971 TwoFieldBulkEditDialogPtr dlg;
28972
28973 dlg = (TwoFieldBulkEditDialogPtr) GetObjectExtra (d);
28974 if (dlg != NULL) {
28975 if (mssg == AECR_VIB_MSG_CLEAR_TEXT) {
28976 SendMessageToDialog (dlg->text_portion, NUM_VIB_MSG + 1);
28977 }
28978 }
28979 }
28980
28981
TwoFieldAutopopulate(ButtoN b)28982 static void TwoFieldAutopopulate(ButtoN b)
28983 {
28984 TwoFieldBulkEditDialogPtr dlg;
28985 CharPtr txt;
28986 TextPortionXPtr text_portion;
28987 Int4 field;
28988
28989 dlg = (TwoFieldBulkEditDialogPtr) GetObjectExtra (b);
28990 if (dlg != NULL && dlg->autopopulate_func != NULL) {
28991 field = GetBulkEditorFieldListDialogValue (dlg->field_from);
28992 txt = (dlg->autopopulate_func) (dlg->autopopulate_data, field);
28993 text_portion = DialogToPointer (dlg->text_portion);
28994 if (text_portion == NULL) {
28995 text_portion = TextPortionXNew();
28996 }
28997 text_portion->start_text = MemFree (text_portion->start_text);
28998 text_portion->start_text = StringSave (txt);
28999 text_portion->end_text = MemFree (text_portion->end_text);
29000 text_portion->end_text = StringSave (txt);
29001 PointerToDialog (dlg->text_portion, text_portion);
29002 text_portion = TextPortionXFree (text_portion);
29003 txt = MemFree (txt);
29004 }
29005 }
29006
29007
TwoFieldClearText(ButtoN b)29008 static void TwoFieldClearText(ButtoN b)
29009 {
29010 TwoFieldBulkEditDialogPtr dlg;
29011 TextPortionXPtr text_portion;
29012
29013 dlg = (TwoFieldBulkEditDialogPtr) GetObjectExtra (b);
29014 if (dlg != NULL) {
29015 text_portion = DialogToPointer (dlg->text_portion);
29016 if (text_portion != NULL) {
29017 text_portion->start_text = MemFree (text_portion->start_text);
29018 text_portion->end_text = MemFree (text_portion->end_text);
29019 PointerToDialog (dlg->text_portion, text_portion);
29020 text_portion = TextPortionXFree (text_portion);
29021 }
29022 }
29023 }
29024
29025
TwoFieldBulkEditDialog(GrouP h,EBulkAction action_choice,Nlm_ChangeNotifyProc change_notify,Pointer change_userdata,BulkEdFieldPtr field_list,Boolean strip_name,Nlm_GetAutopopulateTextProc autopopulate_func,Pointer autopopulate_data)29026 static DialoG TwoFieldBulkEditDialog
29027 (GrouP h,
29028 EBulkAction action_choice,
29029 Nlm_ChangeNotifyProc change_notify,
29030 Pointer change_userdata,
29031 BulkEdFieldPtr field_list,
29032 Boolean strip_name,
29033 Nlm_GetAutopopulateTextProc autopopulate_func,
29034 Pointer autopopulate_data
29035 )
29036
29037 {
29038 TwoFieldBulkEditDialogPtr dlg;
29039 GrouP p, g1, g2, g3 = NULL;
29040 ButtoN b;
29041
29042 dlg = (TwoFieldBulkEditDialogPtr) MemNew (sizeof (TwoFieldBulkEditDialogData));
29043 if (dlg == NULL)
29044 {
29045 return NULL;
29046 }
29047
29048 p = HiddenGroup (h, -1, 0, NULL);
29049 SetObjectExtra (p, dlg, StdCleanupExtraProc);
29050 SetGroupSpacing (p, 10, 10);
29051
29052 dlg->dialog = (DialoG) p;
29053 dlg->todialog = TwoFieldBulkEditToDialog;
29054 dlg->fromdialog = TwoFieldBulkEditDialogToPointer;
29055 dlg->dialogmessage = TwoFieldBulkEditMsg;
29056 dlg->testdialog = NULL;
29057
29058 dlg->field_list = field_list;
29059 dlg->autopopulate_func = autopopulate_func;
29060 dlg->autopopulate_data = autopopulate_data;
29061
29062 g1 = HiddenGroup (p, 2, 0, NULL);
29063 StaticPrompt (g1, "From", 0, dialogTextHeight, systemFont, 'l');
29064 StaticPrompt (g1, "To", 0, dialogTextHeight, systemFont, 'l');
29065
29066 dlg->field_from = MakeBulkEditorFieldListDialog (g1, field_list, TRUE);
29067 ResetBulkEditorFieldListDialogValue (dlg->field_from, field_list);
29068 dlg->field_to = MakeBulkEditorFieldListDialog (g1, field_list, TRUE);
29069 ResetBulkEditorFieldListDialogValue (dlg->field_to, field_list);
29070
29071 if (action_choice == eBulkParseField)
29072 {
29073 dlg->text_portion = TextPortionXDialog(p);
29074 }
29075
29076 g2 = HiddenGroup (p, 3, 0, NULL);
29077
29078 if (action_choice == eBulkParseField)
29079 {
29080 dlg->remove_parsed = CheckBox (g2, "Remove from parsed field", NULL);
29081
29082 if (autopopulate_func != NULL) {
29083 g3 = HiddenGroup (p, 2, 0, NULL);
29084 SetGroupSpacing (g3, 10, 10);
29085 b = PushButton (g3, "Autopopulate", TwoFieldAutopopulate);
29086 SetObjectExtra (b, dlg, NULL);
29087 b = PushButton (g3, "Clear Text", TwoFieldClearText);
29088 SetObjectExtra (b, dlg, NULL);
29089 }
29090 }
29091
29092 if (action_choice == eBulkConvertField)
29093 {
29094 dlg->leave_on_original = CheckBox (g2, "Leave on original", NULL);
29095 }
29096 if (strip_name)
29097 {
29098 dlg->strip_name = CheckBox (g2, "Strip name from text", NULL);
29099 }
29100
29101 AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE)g2, (HANDLE) dlg->text_portion, (HANDLE) g3, NULL);
29102 return (DialoG) p;
29103 }
29104
29105
BulkDrawCollapseExpand(Boolean val,RectPtr r)29106 static void BulkDrawCollapseExpand (Boolean val, RectPtr r)
29107 {
29108 RecT rct;
29109
29110 if (r == NULL) return;
29111
29112 rct = *r;
29113 rct.bottom = rct.top + stdLineHeight - 4;
29114 rct.right = rct.left + stdLineHeight - 4;
29115 InsetRect (&rct, 2, 2);
29116 FrameRect (&rct);
29117
29118 Gray();
29119 if (val) {
29120 /* draw minus */
29121 MoveTo (rct.left, (rct.top + rct.bottom) / 2);
29122 LineTo (rct.right - 1, (rct.top + rct.bottom) / 2);
29123 } else {
29124 /* draw plus */
29125 MoveTo (rct.left, (rct.top + rct.bottom) / 2);
29126 LineTo (rct.right - 1, (rct.top + rct.bottom) / 2);
29127 MoveTo ((rct.left + rct.right) / 2, rct.top);
29128 LineTo ((rct.left + rct.right) / 2, rct.bottom);
29129 }
29130 Black();
29131 }
29132
29133
BulkDrawSelect(Boolean val,RectPtr r)29134 static void BulkDrawSelect (Boolean val, RectPtr r)
29135 {
29136 RecT rct;
29137
29138 if (r == NULL) return;
29139
29140 rct = *r;
29141 rct.bottom = rct.top + stdLineHeight - 4;
29142 rct.right = rct.left + stdLineHeight - 4;
29143 InsetRect (&rct, 2, 2);
29144 FrameRect (&rct);
29145
29146 if (val) {
29147 /* draw X */
29148 MoveTo (rct.left, rct.top);
29149 LineTo (rct.right - 1, rct.bottom - 1);
29150 MoveTo (rct.right, rct.top);
29151 LineTo (rct.left, rct.bottom - 1);
29152 }
29153 }
29154
29155
29156 typedef struct bulkeditordlg {
29157 DIALOG_MESSAGE_BLOCK
29158 DoC title_doc;
29159 DoC doc;
29160 BulkEdFieldPtr master_field_list;
29161 BulkEdFieldPtr field_list;
29162 ColPtr col_list;
29163 ParData par_fmt;
29164 BulkEditorRowPtr row_list;
29165 DialoG PNTR editor_list;
29166 GrouP ed_btn_grp;
29167 Int4 num_columns;
29168 Int4 num_master_columns;
29169 Int2 last_viewed_row;
29170 Int2 last_viewed_col; /* this will always refer to the data column */
29171 Int2 last_sorted_col; /* this will always refer to the data column */
29172 /* for columns shown in display when there are extra */
29173 Int4 display_offset;
29174 Int4 columns_shown;
29175
29176 /* These are for the bulk edit actions */
29177 PopuP bulk_action;
29178 GrouP action_pages[8];
29179
29180 DialoG bulk_apply;
29181 DialoG bulk_edit;
29182 DialoG bulk_convert;
29183 DialoG bulk_parse;
29184 DialoG bulk_swap;
29185 DialoG bulk_remove;
29186 DialoG bulk_capitalize;
29187
29188 GrouP sel_unsel_grp;
29189 PopuP check_constraint_field;
29190 DialoG check_constraint;
29191 PrompT check_status;
29192
29193 Boolean any_editing;
29194 Boolean collapse_by_default;
29195 ClickableCallback single_click_func;
29196 ClickableCallback double_click_func;
29197 Pointer metadata;
29198 SeqEntryPtr sep;
29199 } BulkEditorDlgData, PNTR BulkEditorDlgPtr;
29200
29201
InitBulkEdTitleDoc(BulkEditorDlgPtr dlg,DoC doc)29202 static void InitBulkEdTitleDoc (BulkEditorDlgPtr dlg, DoC doc)
29203 {
29204 Int4 i, text_len = 9;
29205 CharPtr line_text;
29206
29207 if (dlg == NULL || doc == NULL) {
29208 return;
29209 }
29210
29211 Reset (doc);
29212 for (i = 0; i < dlg->display_offset + dlg->columns_shown; i++) {
29213 if (i < dlg->display_offset) {
29214 continue;
29215 }
29216 text_len += StringLen (dlg->field_list[i].name) + 1;
29217 }
29218
29219 line_text = (CharPtr) MemNew (text_len * sizeof (Char));
29220 line_text[0] = 0;
29221 /* add blank column for row selection/scrolling */
29222 if (dlg->display_offset > 0) {
29223 StringCat (line_text, "<");
29224 }
29225 StringCat (line_text, "\t");
29226
29227 for (i = 0; i < dlg->display_offset + dlg->columns_shown - 1; i++) {
29228 if (i < dlg->display_offset) {
29229 continue;
29230 }
29231 if (i == dlg->last_sorted_col) {
29232 /* add blank column for expand/collapse */
29233 StringCat (line_text, "\t");
29234 }
29235 StringCat (line_text, dlg->field_list[i].name);
29236 StringCat (line_text, "\t");
29237 }
29238 if (i == dlg->last_sorted_col) {
29239 /* add blank column for expand/collapse */
29240 StringCat (line_text, "\t");
29241 }
29242 StringCat (line_text, dlg->field_list[i].name);
29243 /* add blank column at end */
29244 if (dlg->display_offset + dlg->columns_shown < dlg->num_columns) {
29245 StringCat (line_text, "\t>\n");
29246 } else {
29247 StringCat (line_text, "\t\n");
29248 }
29249
29250 AppendText (doc, line_text, &(dlg->par_fmt), dlg->col_list, programFont);
29251 line_text = MemFree (line_text);
29252 }
29253
29254
29255 /* redraw, set scroll position */
UpdateBulkEdDisplay(BulkEditorDlgPtr dlg)29256 static void UpdateBulkEdDisplay (BulkEditorDlgPtr dlg)
29257 {
29258 Int4 i, text_len = 0, sub_num;
29259 CharPtr line_text;
29260 BaR sb;
29261 Int4 offset = 0;
29262 Int2 first_shown = 0;
29263
29264 if (dlg == NULL) {
29265 return;
29266 }
29267
29268 /* Get original scroll position */
29269 sb = GetSlateVScrollBar ((SlatE)dlg->doc);
29270 offset = 0;
29271 GetScrlParams4 (dlg->doc, &offset, &first_shown, NULL);
29272
29273 Reset (dlg->doc);
29274
29275 if (dlg->row_list == NULL) {
29276 return;
29277 }
29278
29279 for (i = 0; dlg->row_list[i].object_list != NULL; i++) {
29280 line_text = GetTextForBulkEditorRow(dlg->row_list + i, dlg->field_list, dlg->last_sorted_col, dlg->display_offset, dlg->columns_shown);
29281 AppendText (dlg->doc, line_text, &(dlg->par_fmt), dlg->col_list, programFont);
29282 line_text = MemFree (line_text);
29283 if (dlg->row_list[i].subrows != NULL && dlg->row_list[i].expanded) {
29284 for (sub_num = 0; dlg->row_list[i].subrows[sub_num].object_list != NULL; sub_num++) {
29285 line_text = GetTextForBulkEditorRow(dlg->row_list[i].subrows + sub_num, dlg->field_list, dlg->last_sorted_col, dlg->display_offset, dlg->columns_shown);
29286 AppendText (dlg->doc, line_text, &(dlg->par_fmt), dlg->col_list, programFont);
29287 line_text = MemFree (line_text);
29288 }
29289 }
29290 }
29291
29292 /* restore original scroll position */
29293 GetItemParams4 (dlg->doc, first_shown, &offset, NULL, NULL, NULL, NULL);
29294 offset = MIN (offset, GetBarMax (sb));
29295 SetScrlParams4 (dlg->doc, offset);
29296 }
29297
29298
RedrawAfterColumnShift(BulkEditorDlgPtr dlg)29299 static void RedrawAfterColumnShift (BulkEditorDlgPtr dlg)
29300 {
29301 RecT r;
29302 Int4 width = 0;
29303
29304 ResetClip();
29305 /* reset column widths */
29306 dlg->col_list = MemFree (dlg->col_list);
29307 SelectFont (systemFont);
29308 dlg->col_list = AllocateDocColumnsForFieldList (dlg->field_list, &width, dlg->last_sorted_col, dlg->display_offset, dlg->columns_shown);
29309
29310 /* set data */
29311 InitBulkEdTitleDoc (dlg, dlg->title_doc);
29312 UpdateBulkEdDisplay (dlg);
29313 /* redraw highlight etc. */
29314 ObjectRect (dlg->title_doc, &r);
29315 InvalRect (&r);
29316 ObjectRect (dlg->doc, &r);
29317 InvalRect (&r);
29318 Update ();
29319 }
29320
29321
29322 /* col is zero-based data column, already corrected for selection and expansion columns */
BulkEdDlgToField(Int2 row,Int2 col,BulkEditorDlgPtr dlg)29323 static void BulkEdDlgToField (Int2 row, Int2 col, BulkEditorDlgPtr dlg)
29324 {
29325 Int4 i;
29326 Int4 bulk_row, sub_num;
29327 Int2 edit_col, last_edit_col;
29328
29329 if (row < 1 || col < 0 || dlg == NULL) return;
29330
29331 if (!DataPosFromBulkEdDlgRow (row, dlg->row_list, &bulk_row, &sub_num)) return;
29332
29333 /* don't apply values if editing master row and column other than sort */
29334 if (sub_num < 0 && col != dlg->last_sorted_col && dlg->row_list[bulk_row].subrows != NULL) return;
29335
29336 edit_col = GetMasterFieldNumFromDlgFieldNum (dlg->master_field_list, dlg->field_list, col);
29337
29338 if (dlg->editor_list[edit_col] == NULL) return;
29339
29340 if (sub_num < 0) {
29341 /* if applying to all, get confirmation */
29342 if (dlg->row_list[bulk_row].subrows != NULL) {
29343 /* if nothing changed, no need to ask, nothing to do */
29344 last_edit_col = GetMasterFieldNumFromDlgFieldNum (dlg->master_field_list, dlg->field_list, dlg->last_sorted_col);
29345 if (!AnyChangeInBulkFields(dlg->row_list + bulk_row, dlg->field_list, dlg->editor_list[last_edit_col], dlg->last_sorted_col)) {
29346 return;
29347 } else if (ANS_CANCEL == Message (MSG_OKC, "Apply value to all features in collapsible group?")) {
29348 return;
29349 }
29350 }
29351 ApplyValueToOneBulkEditorRow (dlg->row_list + bulk_row, col, dlg->field_list, dlg->editor_list[edit_col]);
29352 if (dlg->row_list[bulk_row].subrows != NULL) {
29353 for (i = 0; dlg->row_list[bulk_row].subrows[i].object_list != NULL; i++) {
29354 ApplyValueToOneBulkEditorRow (dlg->row_list[bulk_row].subrows + i, col, dlg->field_list, dlg->editor_list[edit_col]);
29355 }
29356 }
29357 } else {
29358 ApplyValueToOneBulkEditorRow (dlg->row_list[bulk_row].subrows + sub_num, col, dlg->field_list, dlg->editor_list[edit_col]);
29359 }
29360 UpdateBulkEdDisplay (dlg);
29361 }
29362
29363
29364 /* col is zero-based data column, already corrected for selection and expansion columns */
29365 /* if col is -1, hide everything (sorted by selection) */
ShowBulkFieldEditor(BulkEditorDlgPtr dlg,Int4 bulk_row,Int4 sub_num,Int2 col)29366 static void ShowBulkFieldEditor (BulkEditorDlgPtr dlg, Int4 bulk_row, Int4 sub_num, Int2 col)
29367 {
29368 BulkEditorRowPtr berp;
29369 ValNodePtr vnp;
29370 Int2 i;
29371 Int4 edit_col;
29372
29373 for (i = 0; i < dlg->num_master_columns; i++) {
29374 SafeHide (dlg->editor_list[i]);
29375 }
29376 SafeHide (dlg->ed_btn_grp);
29377
29378 if (col < 0) return;
29379
29380 if (sub_num < 0) {
29381 berp = dlg->row_list + bulk_row;
29382 } else {
29383 berp = dlg->row_list[bulk_row].subrows + sub_num;
29384 }
29385
29386 /* only show editor dialog if sorted column or not master row */
29387 if (col == dlg->last_sorted_col || berp->subrows == NULL) {
29388 vnp = GetBulkEditorRowValueByColumn (berp, col);
29389
29390 edit_col = GetMasterFieldNumFromDlgFieldNum (dlg->master_field_list, dlg->field_list, col);
29391
29392 if (vnp == NULL) {
29393 PointerToDialog (dlg->editor_list[edit_col], NULL);
29394 } else {
29395 PointerToDialog (dlg->editor_list[edit_col], vnp->data.ptrvalue);
29396 }
29397 if (dlg->editor_list[edit_col] != NULL) {
29398 Show (dlg->editor_list[edit_col]);
29399 Show (dlg->ed_btn_grp);
29400 }
29401 }
29402 }
29403
29404
SetBulkEditorSortColumn(DialoG dialog,Int4 col)29405 NLM_EXTERN void SetBulkEditorSortColumn (DialoG dialog, Int4 col)
29406 {
29407 BulkEditorDlgPtr dlg;
29408 Int4 bulk_row_num = -1, bulk_sub_num = -1;
29409 RecT r;
29410 Int4 offset = 0, i;
29411 BulkEditorRowPtr sorted_rows;
29412
29413 dlg = (BulkEditorDlgPtr) GetObjectExtra (dialog);
29414 if (dlg == NULL) return;
29415
29416 if (col < -1 || col >= dlg->num_columns) return;
29417 ResetClip();
29418
29419 /* save value of column listed */
29420 dlg->last_sorted_col = col;
29421
29422 if (col < 0) {
29423 sorted_rows = ResortBulkEditorRowsBySelected (dlg->row_list, dlg->field_list);
29424 } else {
29425 sorted_rows = ResortBulkEditorRows (dlg->row_list, dlg->field_list, dlg->last_sorted_col);
29426 if (dlg->collapse_by_default) {
29427 CollapseAllBulkEditRows (sorted_rows);
29428 } else {
29429 ExpandAllBulkEditRows (sorted_rows);
29430 }
29431 }
29432 /* get new position from old row */
29433 if (DataPosFromBulkEdDlgRow (dlg->last_viewed_row, dlg->row_list, &bulk_row_num, &bulk_sub_num)) {
29434 if (bulk_sub_num > -1) {
29435 dlg->last_viewed_row = BulkEdDlgRowFromDataPos (dlg->row_list[bulk_row_num].subrows[bulk_sub_num].copied_to_meta,
29436 dlg->row_list[bulk_row_num].subrows[bulk_sub_num].copied_to_sub,
29437 sorted_rows);
29438 } else {
29439 dlg->last_viewed_row = BulkEdDlgRowFromDataPos (dlg->row_list[bulk_row_num].copied_to_meta,
29440 dlg->row_list[bulk_row_num].copied_to_sub,
29441 sorted_rows);
29442 }
29443 dlg->last_viewed_col = dlg->last_sorted_col;
29444 }
29445
29446 dlg->row_list = FreeBulkEditorRows (dlg->row_list, dlg->field_list);
29447 dlg->row_list = sorted_rows;
29448
29449
29450 /* reformat the columns */
29451 dlg->col_list = AllocateDocColumnsForFieldList (dlg->field_list, NULL, dlg->last_sorted_col, dlg->display_offset, dlg->columns_shown);
29452 ResetClip();
29453 InitBulkEdTitleDoc (dlg, dlg->title_doc);
29454 ObjectRect (dlg->title_doc, &r);
29455 InvalRect (&r);
29456
29457 UpdateBulkEdDisplay (dlg);
29458
29459 if (dlg->last_viewed_row > 0) {
29460 /* show appropriate editor for highlighted item */
29461 if (DataPosFromBulkEdDlgRow (dlg->last_viewed_row, dlg->row_list, &bulk_row_num, &bulk_sub_num)) {
29462 ShowBulkFieldEditor (dlg, bulk_row_num, bulk_sub_num, dlg->last_sorted_col);
29463 } else {
29464 dlg->last_viewed_row = 0;
29465 dlg->last_viewed_col = 0;
29466 for (i = 0; i < dlg->num_master_columns; i++) {
29467 SafeHide (dlg->editor_list[i]);
29468 }
29469 Hide (dlg->ed_btn_grp);
29470 }
29471
29472 /* scroll to new position of last_viewed */
29473 GetItemParams4 (dlg->doc, dlg->last_viewed_row, &offset, NULL, NULL, NULL, NULL);
29474 SetScrlParams4 (dlg->doc, offset);
29475 }
29476
29477 /* redraw highlight etc. */
29478 ObjectRect (dlg->title_doc, &r);
29479 InvalRect (&r);
29480 ObjectRect (dlg->doc, &r);
29481 InvalRect (&r);
29482 Update ();
29483 }
29484
29485
29486 /* clicking on a column in the title indicates that we should sort by this column. */
ClickBulkTitle(DoC d,PoinT pt)29487 static void ClickBulkTitle (DoC d, PoinT pt)
29488 {
29489 BulkEditorDlgPtr dlg;
29490 Int2 item;
29491 Int2 row;
29492 Int2 col;
29493
29494 MapDocPoint (d, pt, &item, &row, &col, NULL);
29495 if (item < 1) {
29496 return;
29497 }
29498 dlg = (BulkEditorDlgPtr) GetObjectExtra (d);
29499 if (dlg == NULL) return;
29500 if (col == 1) {
29501 if (dlg->display_offset > 0) {
29502 dlg->display_offset --;
29503 RedrawAfterColumnShift (dlg);
29504 return;
29505 }
29506 } else if (dlg->col_list[col].last) {
29507 if (dlg->display_offset < dlg->num_columns - dlg->columns_shown) {
29508 dlg->display_offset ++;
29509 RedrawAfterColumnShift(dlg);
29510 }
29511 return;
29512 }
29513
29514
29515 if (col - 2 == dlg->last_sorted_col) {
29516 /* clicked on checkbox column */
29517 col = -1;
29518 } else {
29519 col = BulkEdDataColumnFromDocColumn(col, dlg->last_sorted_col, dlg->display_offset);
29520 }
29521
29522 SetBulkEditorSortColumn (dlg->dialog, col);
29523 }
29524
29525
UpdateCheckStatus(BulkEditorDlgPtr dlg)29526 static void UpdateCheckStatus (BulkEditorDlgPtr dlg)
29527 {
29528 Int4 num_selected;
29529 CharPtr status_fmt = "%d feature%s currently checked";
29530 Char status_str[50];
29531
29532 if (dlg == NULL) return;
29533
29534 num_selected = CountBulkEditorRowsSelected (dlg->row_list);
29535 sprintf (status_str, status_fmt, num_selected, num_selected == 1 ? "" : "s");
29536 SetTitle (dlg->check_status, status_str);
29537 }
29538
29539
29540 /* when clicking on field, show editor (if available), change selection, collapse/expand,
29541 * set last viewed row, populate data from previously displayed editor
29542 */
ClickBulkEdField(DoC d,PoinT pt)29543 static void ClickBulkEdField (DoC d, PoinT pt)
29544 {
29545 BulkEditorDlgPtr dlg;
29546 BulkEditorRowPtr berp;
29547 Int2 item;
29548 Int2 row;
29549 Int2 col;
29550 RecT r;
29551 ValNodePtr vnp;
29552 Int4 bulk_row = -1, sub_num = -1;
29553 Boolean dblclick = dblClick;
29554
29555 dlg = (BulkEditorDlgPtr) GetObjectExtra (d);
29556 if (dlg == NULL) return;
29557
29558 MapDocPoint (d, pt, &item, &row, &col, NULL);
29559
29560 if (!DataPosFromBulkEdDlgRow (item, dlg->row_list, &bulk_row, &sub_num)) {
29561 return;
29562 }
29563
29564 if (sub_num < 0) {
29565 berp = dlg->row_list + bulk_row;
29566 } else {
29567 berp = dlg->row_list[bulk_row].subrows + sub_num;
29568 }
29569
29570 if (col == 1) {
29571 /* do selection */
29572 berp->selected = !berp->selected;
29573 if (berp->subrows != NULL) {
29574 SelectBulkEditorRows (berp->subrows, berp->selected);
29575 } else if (sub_num > -1) {
29576 /* this is a subrow - metarow can no longer be selected
29577 * if this is not selected.
29578 */
29579 if (dlg->row_list[bulk_row].selected && !berp->selected) {
29580 dlg->row_list[bulk_row].selected = FALSE;
29581 } else if (AllBulkEditorRowsSelected(dlg->row_list[bulk_row].subrows)) {
29582 /* all child rows are now selected, so select metarow */
29583 dlg->row_list[bulk_row].selected = TRUE;
29584 }
29585 }
29586 UpdateCheckStatus (dlg);
29587 ObjectRect (dlg->doc, &r);
29588 InvalRect (&r);
29589 Update ();
29590 return;
29591 } else if (col == dlg->last_sorted_col + 2 - dlg->display_offset) {
29592 /* do expand/collapse */
29593 if (berp->subrows != NULL) {
29594 berp->expanded = !berp->expanded;
29595 UpdateBulkEdDisplay (dlg);
29596 ObjectRect (dlg->doc, &r);
29597 InvalRect (&r);
29598 Update ();
29599 }
29600 return;
29601 } else {
29602 /* adjust to account for checkbox column */
29603 col = BulkEdDataColumnFromDocColumn(col, dlg->last_sorted_col, dlg->display_offset);
29604 }
29605 if (item < 1 || col < 0 || col >= dlg->num_columns) return;
29606 /* took out this line - use Apply button instead, less confusing */
29607 /*BulkEdDlgToField (dlg->last_viewed_row, dlg->last_viewed_col, dlg); */
29608 ResetClip();
29609
29610 ShowBulkFieldEditor (dlg, bulk_row, sub_num, col);
29611
29612 if (dlg->field_list[col].release_cell_func != NULL) {
29613 vnp = GetBulkEditorRowValueByColumn (berp, col);
29614 if (vnp != NULL) {
29615 vnp->data.ptrvalue = (dlg->field_list[col].release_cell_func) (vnp->data.ptrvalue);
29616 }
29617 }
29618 dlg->last_viewed_row = item;
29619 dlg->last_viewed_col = col;
29620
29621 /* redraw highlight etc. */
29622 ObjectRect (dlg->doc, &r);
29623 InvalRect (&r);
29624 Update ();
29625
29626
29627 if (dblclick) {
29628 if (dlg->double_click_func != NULL) {
29629 (dlg->double_click_func) (berp->object_list, NULL);
29630 }
29631 } else {
29632 if (dlg->single_click_func != NULL) {
29633 (dlg->single_click_func) (berp->object_list, NULL);
29634 }
29635 }
29636 }
29637
29638
ApplyBulkEditingChange(ButtoN b)29639 static void ApplyBulkEditingChange (ButtoN b)
29640 {
29641 BulkEditorDlgPtr dlg;
29642 RecT r;
29643
29644 dlg = (BulkEditorDlgPtr) GetObjectExtra (b);
29645 if (dlg == NULL) return;
29646
29647 BulkEdDlgToField (dlg->last_viewed_row, dlg->last_viewed_col, dlg);
29648
29649 /* redraw highlight etc. */
29650 Select (dlg->dialog);
29651 ObjectRect (dlg->doc, &r);
29652 InvalRect (&r);
29653 Update ();
29654
29655 }
29656
29657
HighlightBulkEdField(DoC d,Int2 item,Int2 row,Int2 col)29658 static Boolean HighlightBulkEdField (DoC d, Int2 item, Int2 row, Int2 col)
29659
29660 {
29661 BulkEditorDlgPtr dlg;
29662
29663 dlg = (BulkEditorDlgPtr) GetObjectExtra (d);
29664 if (dlg == NULL) return FALSE;
29665
29666 if (col == 1 || col == dlg->last_sorted_col + 1) {
29667 /* don't highlight selection column or expansion column */
29668 return FALSE;
29669 }
29670
29671 col = BulkEdDataColumnFromDocColumn (col, dlg->last_sorted_col, dlg->display_offset);
29672
29673 if (item == dlg->last_viewed_row && col == dlg->last_viewed_col) {
29674 return TRUE;
29675 } else {
29676 return FALSE;
29677 }
29678 }
29679
DrawBulkEdCell(DoC d,RectPtr r,Int2 item,Int2 firstLine)29680 static void DrawBulkEdCell (DoC d, RectPtr r, Int2 item, Int2 firstLine)
29681
29682 {
29683 Int2 lineHeight;
29684 RecT rct;
29685 Int2 format_col, data_col;
29686 BulkEditorDlgPtr dlg;
29687 BulkEditorRowPtr berp;
29688 ValNodePtr vnp;
29689 Int4 bulk_row_num = -1, bulk_sub_num = -1;
29690
29691 dlg = (BulkEditorDlgPtr) GetObjectExtra (d);
29692 if (dlg == NULL || r == NULL || item <= 0 || firstLine != 0) {
29693 return;
29694 }
29695
29696 GetItemParams (d, item, NULL, NULL, NULL, &lineHeight, NULL);
29697 rct = *r;
29698
29699 if (!DataPosFromBulkEdDlgRow (item, dlg->row_list, &bulk_row_num, &bulk_sub_num)) {
29700 return;
29701 }
29702
29703 /* draw lines at top of each row after the first that does not have subrows */
29704 if (bulk_row_num > 0 && bulk_sub_num < 0) {
29705 MoveTo (rct.left, rct.top);
29706 LineTo (rct.right, rct.top);
29707 }
29708
29709 if (bulk_sub_num < 0) {
29710 berp = dlg->row_list + bulk_row_num;
29711 } else {
29712 berp = dlg->row_list[bulk_row_num].subrows + bulk_sub_num;
29713 }
29714
29715 /* for column 0, draw selection box */
29716 format_col = 0;
29717 rct.right = rct.left + dlg->col_list[format_col].pixWidth - 1;
29718 BulkDrawSelect (berp->selected, &rct);
29719 rct.left = rct.right + 1;
29720 format_col++;
29721
29722 for (data_col = 0, vnp = berp->values_list;
29723 data_col < dlg->num_columns && vnp != NULL;
29724 data_col++, vnp = vnp->next) {
29725
29726 if (data_col < dlg->display_offset) {
29727 continue;
29728 } else if (data_col >= dlg->display_offset + dlg->columns_shown) {
29729 break;
29730 }
29731
29732 rct.right = rct.left + dlg->col_list[format_col].pixWidth - 1;
29733 if (data_col == dlg->last_sorted_col) {
29734 /* draw box if expandable */
29735 if (bulk_sub_num == -1
29736 && dlg->row_list[bulk_row_num].subrows != NULL) {
29737 BulkDrawCollapseExpand (dlg->row_list[bulk_row_num].expanded, &rct);
29738 }
29739 rct.left = rct.right + 1;
29740 format_col++;
29741 rct.right = rct.left + dlg->col_list[format_col].pixWidth - 1;
29742 }
29743 if (dlg->field_list[data_col].draw_col_func != NULL) {
29744 (dlg->field_list[data_col].draw_col_func)(vnp->data.ptrvalue, &rct);
29745 }
29746 rct.left = rct.right + 1;
29747 format_col++;
29748 }
29749 }
29750
29751
GetFirstBulkEditValue(Pointer data,Int4 col)29752 static CharPtr GetFirstBulkEditValue (Pointer data, Int4 col)
29753 {
29754 BulkEditorDlgPtr dlg;
29755 CharPtr txt = NULL;
29756 Int4 i;
29757
29758 if ((dlg = (BulkEditorDlgPtr) data) == NULL
29759 || col < 0 || col >= dlg->num_master_columns
29760 || dlg->master_field_list[col].get_func == NULL)
29761 {
29762 return NULL;
29763 }
29764
29765 for (i = 0; dlg->row_list[i].object_list != NULL && txt == NULL; i++)
29766 {
29767 txt = (dlg->master_field_list[col].get_func)(dlg->row_list[i].object_list->choice, dlg->row_list[i].object_list->data.ptrvalue, dlg->metadata);
29768 if (StringHasNoText (txt)) {
29769 txt = MemFree (txt);
29770 }
29771 }
29772 return txt;
29773 }
29774
29775
CleanupBulkEditorDialog(GraphiC g,VoidPtr data)29776 static void CleanupBulkEditorDialog (GraphiC g, VoidPtr data)
29777 {
29778 BulkEditorDlgPtr dlg;
29779
29780 dlg = (BulkEditorDlgPtr) data;
29781 if (dlg != NULL) {
29782 dlg->row_list = FreeBulkEditorRows(dlg->row_list, dlg->field_list);
29783 /* field list has pointers to non-freeable data, just free container */
29784 dlg->field_list = MemFree (dlg->field_list);
29785 /* col_list is structures */
29786 dlg->col_list = MemFree (dlg->col_list);
29787 }
29788 StdCleanupExtraProc (g, data);
29789 }
29790
ApplyBulkEditorRowToObject(BulkEditorRowPtr berp,ValNodePtr target,BulkEdFieldPtr field_list,Pointer metadata,LogInfoPtr lip)29791 static void ApplyBulkEditorRowToObject (
29792 BulkEditorRowPtr berp,
29793 ValNodePtr target,
29794 BulkEdFieldPtr field_list,
29795 Pointer metadata,
29796 LogInfoPtr lip
29797 )
29798 {
29799 ValNodePtr vnp_val;
29800 Int4 i;
29801 Pointer orig_val;
29802 CharPtr orig_txt, new_txt, txt;
29803
29804 if (berp == NULL || target == NULL || field_list == NULL) return;
29805
29806 for (i = 0, vnp_val = berp->values_list;
29807 vnp_val != NULL;
29808 i++, vnp_val = vnp_val->next) {
29809 if (field_list[i].set_func != NULL) {
29810 if (lip != NULL) {
29811 orig_val = (field_list[i].get_func) (target->choice, target->data.ptrvalue, metadata);
29812 orig_txt = (field_list[i].display_func) (orig_val);
29813 new_txt = (field_list[i].display_func)(vnp_val->data.ptrvalue);
29814 if (StringCmp (orig_txt, new_txt) != 0) {
29815 txt = GetDiscrepancyItemText (target);
29816 fprintf (lip->fp, "Changed '%s' to '%s' for %s on %s\n",
29817 orig_txt, new_txt, field_list[i].name, txt);
29818 txt = MemFree (txt);
29819 lip->data_in_log = TRUE;
29820 }
29821 orig_txt = MemFree (orig_txt);
29822 new_txt = MemFree (new_txt);
29823 field_list[i].free_func(orig_val);
29824 }
29825 (field_list[i].set_func) (target->data.ptrvalue, vnp_val->data.ptrvalue);
29826 }
29827 }
29828 }
29829
ApplyBulkEditorToObjectList(DialoG d,Boolean do_log)29830 NLM_EXTERN void ApplyBulkEditorToObjectList (DialoG d, Boolean do_log)
29831 {
29832 BulkEditorDlgPtr dlg;
29833 Int4 row, i;
29834 LogInfoPtr lip = NULL;
29835
29836 dlg = (BulkEditorDlgPtr) GetObjectExtra (d);
29837 if (dlg == NULL) return;
29838
29839 if (do_log) {
29840 lip = OpenLog ("Bulk Edit Changes");
29841 }
29842
29843 for (row = 0; dlg->row_list[row].object_list != NULL; row++) {
29844 if (dlg->row_list[row].subrows == NULL) {
29845 ApplyBulkEditorRowToObject (dlg->row_list + row,
29846 dlg->row_list[row].object_list,
29847 dlg->field_list,
29848 dlg->metadata,
29849 lip);
29850 } else {
29851 for (i = 0; dlg->row_list[row].subrows[i].object_list != NULL; i++) {
29852 ApplyBulkEditorRowToObject (dlg->row_list[row].subrows + i,
29853 dlg->row_list[row].subrows[i].object_list,
29854 dlg->field_list,
29855 dlg->metadata,
29856 lip);
29857 }
29858 }
29859 }
29860 if (do_log) {
29861 CloseLog (lip);
29862 lip = FreeLog (lip);
29863 }
29864 }
29865
29866
ExportBulkEditorRow(BulkEditorRowPtr berp,ValNodePtr target,BulkEdFieldPtr field_list,Pointer metadata,FILE * fp)29867 static void ExportBulkEditorRow (
29868 BulkEditorRowPtr berp,
29869 ValNodePtr target,
29870 BulkEdFieldPtr field_list,
29871 Pointer metadata,
29872 FILE *fp
29873 )
29874 {
29875 ValNodePtr vnp_val;
29876 Int4 i;
29877 Pointer orig_val;
29878 CharPtr orig_txt, new_txt;
29879
29880 if (berp == NULL || target == NULL || field_list == NULL) return;
29881
29882 /* first, print original values */
29883 for (i = 0, vnp_val = berp->values_list;
29884 vnp_val != NULL;
29885 i++, vnp_val = vnp_val->next) {
29886 orig_val = (field_list[i].get_func) (target->choice, target->data.ptrvalue, metadata);
29887 orig_txt = (field_list[i].display_func) (orig_val);
29888 fprintf (fp, "%s\t", orig_txt == NULL ? "" : orig_txt);
29889 orig_txt = MemFree (orig_txt);
29890 field_list[i].free_func(orig_val);
29891 }
29892
29893 /* now print values that can be set */
29894 for (i = 0, vnp_val = berp->values_list;
29895 vnp_val != NULL;
29896 i++, vnp_val = vnp_val->next) {
29897 if (field_list[i].set_str_func != NULL && field_list[i].set_func != NULL) {
29898 new_txt = (field_list[i].display_func)(vnp_val->data.ptrvalue);
29899 fprintf (fp, "%s\t", new_txt == NULL ? "" : new_txt);
29900 new_txt = MemFree (new_txt);
29901 }
29902 }
29903 fprintf (fp, "\n");
29904 }
29905
29906
ExportBulkEditorTable(DialoG d)29907 NLM_EXTERN void ExportBulkEditorTable (DialoG d)
29908 {
29909 BulkEditorDlgPtr dlg;
29910 Int4 row, i;
29911 Char path [PATH_MAX];
29912 FILE *fp;
29913
29914 dlg = (BulkEditorDlgPtr) GetObjectExtra (d);
29915 if (dlg == NULL) return;
29916
29917 if (! GetOutputFileName (path, sizeof (path), NULL)) return;
29918 fp = FileOpen (path, "w");
29919 if (fp == NULL)
29920 {
29921 Message (MSG_ERROR, "Unable to open %s", path);
29922 return;
29923 }
29924
29925 /* print header */
29926 /* first, print original values */
29927 for (i = 0; dlg->field_list[i].name != NULL; i++) {
29928 fprintf (fp, "Original %s\t", dlg->field_list[i].name);
29929 }
29930 /* now print values that can be changed */
29931 for (i = 0; dlg->field_list[i].name != NULL; i++) {
29932 if (dlg->field_list[i].set_str_func != NULL && dlg->field_list[i].set_func != NULL) {
29933 fprintf (fp, "New %s\t", dlg->field_list[i].name);
29934 }
29935 }
29936 fprintf (fp, "\n");
29937
29938 /* now print table values */
29939 for (row = 0; dlg->row_list[row].object_list != NULL; row++) {
29940 if (dlg->row_list[row].subrows == NULL) {
29941 ExportBulkEditorRow (dlg->row_list + row,
29942 dlg->row_list[row].object_list,
29943 dlg->field_list,
29944 dlg->metadata,
29945 fp);
29946 } else {
29947 for (i = 0; dlg->row_list[row].subrows[i].object_list != NULL; i++) {
29948 ExportBulkEditorRow (dlg->row_list[row].subrows + i,
29949 dlg->row_list[row].subrows[i].object_list,
29950 dlg->field_list,
29951 dlg->metadata,
29952 fp);
29953 }
29954 }
29955 }
29956 FileClose (fp);
29957 }
29958
29959
AddColumnValuesToRowList(BulkEditorRowPtr row_list,BulkEdFieldPtr master_field_list,Int4 master_pos,Int4 insert_pos,Pointer metadata)29960 static void AddColumnValuesToRowList (BulkEditorRowPtr row_list, BulkEdFieldPtr master_field_list, Int4 master_pos, Int4 insert_pos, Pointer metadata)
29961 {
29962 Int4 i, j;
29963 ValNodePtr vnp_prev, vnp;
29964
29965 if (row_list == NULL || master_field_list == NULL) {
29966 return;
29967 }
29968
29969 for (i = 0; row_list[i].object_list != NULL; i++) {
29970 vnp_prev = NULL;
29971 for (j = 0, vnp = row_list[i].values_list; j < insert_pos; j++, vnp = vnp->next) {
29972 vnp_prev = vnp;
29973 }
29974 vnp = ValNodeNew (NULL);
29975 vnp->choice = 0;
29976 if (row_list[i].subrows == NULL) {
29977 vnp->data.ptrvalue = master_field_list[master_pos].get_func (row_list[i].object_list->choice, row_list[i].object_list->data.ptrvalue, metadata);
29978 }
29979 if (vnp_prev == NULL) {
29980 vnp->next = row_list[i].values_list;
29981 row_list[i].values_list = vnp;
29982 } else {
29983 vnp->next = vnp_prev->next;
29984 vnp_prev->next = vnp;
29985 }
29986 AddColumnValuesToRowList (row_list[i].subrows, master_field_list, master_pos, insert_pos, metadata);
29987 }
29988 }
29989
29990
AddColumnToRowList(BulkEditorRowPtr row_list,BulkEdFieldPtr master_field_list,BulkEdFieldPtr PNTR p_field_list,Int4 field,Int4 last_sort_col,Pointer metadata)29991 static Int4 AddColumnToRowList (BulkEditorRowPtr row_list, BulkEdFieldPtr master_field_list, BulkEdFieldPtr PNTR p_field_list, Int4 field, Int4 last_sort_col, Pointer metadata)
29992 {
29993 Int4 i, m = 0, f = 0, num_columns = 1;
29994 BulkEdFieldPtr field_list, new_field_list;
29995
29996 if (row_list == NULL || master_field_list == NULL || p_field_list == NULL || (field_list = *p_field_list) == NULL || field < 0) {
29997 return -1;
29998 }
29999
30000 /* first, find insertion location */
30001 f = GetDlgFieldNumFromMasterFieldNum (master_field_list, *p_field_list, field);
30002 if (StringCmp (master_field_list[field].name, field_list[f].name) == 0) {
30003 /* already have column */
30004 return -1;
30005 }
30006
30007 AddColumnValuesToRowList (row_list, master_field_list, field, f, metadata);
30008
30009 /* insert column in field_list */
30010 for (i = 0; field_list[i].name != NULL; i++) {
30011 num_columns++;
30012 }
30013
30014 num_columns++;
30015 new_field_list = (BulkEdFieldPtr) MemNew (sizeof (BulkEdFieldData) * num_columns);
30016 for (i = 0; i < f; i++) {
30017 new_field_list[i] = field_list[i];
30018 }
30019 new_field_list[i] = master_field_list[field];
30020 while (field_list[i].name != NULL) {
30021 new_field_list[i + 1] = field_list[i];
30022 i++;
30023 }
30024 new_field_list[i + 1] = field_list[i];
30025 field_list = MemFree (field_list);
30026 *p_field_list = new_field_list;
30027
30028 AddSummaryInfoToMetaRows (row_list, last_sort_col);
30029
30030 return f;
30031 }
30032
30033
ChangeBulkEditorAction(PopuP p)30034 static void ChangeBulkEditorAction (PopuP p)
30035 {
30036 BulkEditorDlgPtr dlg;
30037 Int4 page_num;
30038 Int4 num_pages;
30039
30040 dlg = (BulkEditorDlgPtr) GetObjectExtra (p);
30041 if (dlg == NULL || !dlg->any_editing) return;
30042
30043 num_pages = sizeof (dlg->action_pages) / sizeof (GrouP);
30044 for (page_num = 0; page_num < num_pages; page_num++) {
30045 Hide (dlg->action_pages[page_num]);
30046 }
30047 page_num = GetValue (dlg->bulk_action) - 1;
30048 if (page_num > -1 && page_num < num_pages) {
30049 Show (dlg->action_pages[page_num]);
30050 }
30051 }
30052
RemoveColumnFromSelectedBulkEditRows(BulkEditorRowPtr row_list,Int4 col,BulkEdFieldPtr field_list,Boolean select_all)30053 static void RemoveColumnFromSelectedBulkEditRows (BulkEditorRowPtr row_list, Int4 col, BulkEdFieldPtr field_list, Boolean select_all)
30054 {
30055 ValNodePtr vnp;
30056
30057 if (row_list == NULL || col < 0 || field_list == NULL) return;
30058 while (row_list->object_list != NULL) {
30059 if (row_list->selected || select_all) {
30060 if (row_list->subrows == NULL || AllBulkEditorRowsSelected(row_list->subrows) || select_all) {
30061 vnp = GetBulkEditorRowValueByColumn (row_list, col);
30062 if (vnp != NULL) {
30063 field_list[col].free_func(vnp->data.ptrvalue);
30064 vnp->data.ptrvalue = NULL;
30065 }
30066 }
30067 }
30068 RemoveColumnFromSelectedBulkEditRows (row_list->subrows, col, field_list, select_all);
30069 row_list++;
30070 }
30071 }
30072
30073 static void
ApplyEditColumnFromSelectedBulkEditRows(BulkEditorRowPtr berp,BulkEdFieldPtr field_list,Int4 col,ApplyValuePtr avp,Boolean select_all)30074 ApplyEditColumnFromSelectedBulkEditRows
30075 (BulkEditorRowPtr berp,
30076 BulkEdFieldPtr field_list,
30077 Int4 col,
30078 ApplyValuePtr avp,
30079 Boolean select_all)
30080 {
30081 ValNodePtr vnp;
30082
30083 if (berp == NULL) return;
30084
30085 while (berp->object_list != NULL) {
30086 if (berp->selected || select_all) {
30087 if (berp->subrows == NULL || AllBulkEditorRowsSelected(berp->subrows) || select_all) {
30088 vnp = GetBulkEditorRowValueByColumn (berp, col);
30089 if (vnp != NULL) {
30090 vnp->data.ptrvalue = (field_list[col].set_str_func) (vnp->data.ptrvalue, avp);
30091 }
30092 }
30093 }
30094 ApplyEditColumnFromSelectedBulkEditRows (berp->subrows, field_list, col, avp, select_all);
30095 berp++;
30096 }
30097 }
30098
30099
30100 static void
CapitalizeColumnsForSelectedBulkEditRows(BulkEditorRowPtr berp,BulkEdFieldPtr field_list,Int4 col,ChangeCasePtr capitalization,Boolean select_all)30101 CapitalizeColumnsForSelectedBulkEditRows
30102 (BulkEditorRowPtr berp,
30103 BulkEdFieldPtr field_list,
30104 Int4 col,
30105 ChangeCasePtr capitalization,
30106 Boolean select_all)
30107 {
30108 ValNodePtr vnp;
30109 CharPtr val_str;
30110 ApplyValueData avd;
30111 SeqFeatPtr sfp;
30112 SeqEntryPtr sep, last_sep = NULL;
30113 ValNodePtr orgname_list = NULL;
30114
30115 if (berp == NULL) return;
30116
30117 avd.field_list = NULL;
30118 avd.text_to_replace = NULL;
30119 avd.where_to_replace = EditApplyFindLocation_anywhere;
30120 avd.etp = NULL;
30121
30122 while (berp->object_list != NULL) {
30123 if (berp->selected || select_all) {
30124 if (berp->subrows == NULL || AllBulkEditorRowsSelected(berp->subrows) || select_all) {
30125 vnp = GetBulkEditorRowValueByColumn (berp, col);
30126 if (vnp != NULL) {
30127 val_str = (field_list[col].display_func)(vnp->data.ptrvalue);
30128 if (!StringHasNoText (val_str)) {
30129 if (berp->object_list->choice == OBJ_SEQFEAT && berp->object_list->data.ptrvalue != NULL) {
30130 sfp = (SeqFeatPtr) berp->object_list->data.ptrvalue;
30131 sep = GetTopSeqEntryForEntityID (sfp->idx.entityID);
30132 if (sep != last_sep) {
30133 orgname_list = ValNodeFree (orgname_list);
30134 /* get org names to use in fixes */
30135 VisitBioSourcesInSep (sep, &orgname_list, GetOrgNamesInRecordCallback);
30136 last_sep = sep;
30137 }
30138 }
30139 ChangeCase (&val_str, capitalization, orgname_list);
30140 avd.new_text = val_str;
30141 vnp->data.ptrvalue = (field_list[col].set_str_func) (vnp->data.ptrvalue, &avd);
30142 }
30143 val_str = MemFree (val_str);
30144 }
30145 }
30146 }
30147 CapitalizeColumnsForSelectedBulkEditRows (berp->subrows, field_list, col, capitalization, select_all);
30148 berp++;
30149 }
30150 orgname_list = ValNodeFree (orgname_list);
30151 }
30152
RemoveNameFromText(CharPtr orig,CharPtr remove)30153 static void RemoveNameFromText (CharPtr orig, CharPtr remove)
30154 {
30155 CharPtr cp, cp_dst;
30156 Int4 len;
30157
30158 if (StringHasNoText (orig) || StringHasNoText (remove)) {
30159 return;
30160 }
30161 cp = StringISearch (orig, remove);
30162 if (cp != NULL) {
30163 len = StringLen (remove);
30164 cp_dst = cp;
30165 cp = cp + len;
30166 while (*cp != 0 && len > 0) {
30167 *cp_dst = *cp;
30168 cp_dst++;
30169 cp++;
30170 len--;
30171 }
30172 *cp_dst = 0;
30173 }
30174 }
30175
ConvertColumnsForSelectedBulkEditRows(BulkEditorRowPtr berp,BulkEdFieldPtr field_list,TwoFieldBulkEditPtr tfp,ExistingTextPtr etp,Boolean select_all)30176 static void ConvertColumnsForSelectedBulkEditRows
30177 (BulkEditorRowPtr berp,
30178 BulkEdFieldPtr field_list,
30179 TwoFieldBulkEditPtr tfp,
30180 ExistingTextPtr etp,
30181 Boolean select_all)
30182 {
30183 ValNodePtr vnp_from, vnp_to;
30184 CharPtr val_from;
30185 ApplyValueData avd;
30186 if (berp == NULL || tfp == NULL) return;
30187
30188 avd.field_list = NULL;
30189 avd.text_to_replace = NULL;
30190 avd.where_to_replace = EditApplyFindLocation_anywhere;
30191 avd.etp = etp;
30192
30193 while (berp->object_list != NULL) {
30194 if ((berp->selected || select_all) && berp->subrows == NULL) {
30195 vnp_from = GetBulkEditorRowValueByColumn (berp, tfp->field_from);
30196 vnp_to = GetBulkEditorRowValueByColumn (berp, tfp->field_to);
30197 if (vnp_from != NULL && vnp_to != NULL) {
30198 val_from = (field_list[tfp->field_from].display_func)(vnp_from->data.ptrvalue);
30199 if (StringDoesHaveText (val_from)) {
30200 if (tfp->strip_name) {
30201 RemoveNameFromText (val_from, field_list[tfp->field_to].name);
30202 }
30203
30204 avd.new_text = val_from;
30205 vnp_to->data.ptrvalue = (field_list[tfp->field_to].set_str_func) (vnp_to->data.ptrvalue, &avd);
30206
30207 if (!tfp->leave_on_original) {
30208 (field_list[tfp->field_from].free_func)(vnp_from->data.ptrvalue);
30209 vnp_from->data.ptrvalue = NULL;
30210 }
30211
30212 }
30213 val_from = MemFree (val_from);
30214 }
30215 }
30216 ConvertColumnsForSelectedBulkEditRows (berp->subrows, field_list, tfp, etp, select_all);
30217 berp++;
30218 }
30219 }
30220
30221
ParseColumnsForSelectedBulkEditRows(BulkEditorRowPtr berp,BulkEdFieldPtr field_list,TwoFieldBulkEditPtr tfp,ExistingTextPtr etp,Boolean select_all)30222 static void ParseColumnsForSelectedBulkEditRows
30223 (BulkEditorRowPtr berp,
30224 BulkEdFieldPtr field_list,
30225 TwoFieldBulkEditPtr tfp,
30226 ExistingTextPtr etp,
30227 Boolean select_all)
30228 {
30229 ValNodePtr vnp_from, vnp_to;
30230 CharPtr val_from, val_to;
30231 ApplyValueData avd;
30232 if (berp == NULL || tfp == NULL) return;
30233
30234 avd.field_list = NULL;
30235 avd.text_to_replace = NULL;
30236 avd.where_to_replace = EditApplyFindLocation_anywhere;
30237 avd.etp = etp;
30238
30239 while (berp->object_list != NULL) {
30240 if ((berp->selected || select_all) && berp->subrows == NULL) {
30241 vnp_from = GetBulkEditorRowValueByColumn (berp, tfp->field_from);
30242 vnp_to = GetBulkEditorRowValueByColumn (berp, tfp->field_to);
30243 if (vnp_from != NULL && vnp_to != NULL) {
30244 val_from = (field_list[tfp->field_from].display_func)(vnp_from->data.ptrvalue);
30245 val_to = NULL;
30246 if (StringDoesHaveText (val_from)) {
30247 val_to = ReplaceStringForParse(val_from, tfp->text_portion);
30248 if (StringDoesHaveText (val_to)) {
30249 avd.new_text = val_to;
30250 vnp_to->data.ptrvalue = (field_list[tfp->field_to].set_str_func) (vnp_to->data.ptrvalue, &avd);
30251 }
30252 if (tfp->remove_parsed) {
30253 avd.new_text = val_from;
30254 avd.etp = NULL;
30255 vnp_from->data.ptrvalue = (field_list[tfp->field_from].set_str_func) (vnp_from->data.ptrvalue, &avd);
30256 avd.etp = etp;
30257 }
30258 }
30259 val_from = MemFree (val_from);
30260 val_to = MemFree (val_to);
30261 }
30262 }
30263 ParseColumnsForSelectedBulkEditRows (berp->subrows, field_list, tfp, etp, select_all);
30264 berp++;
30265 }
30266 }
30267
30268
SwapColumnsForSelectedBulkEditRows(BulkEditorRowPtr berp,BulkEdFieldPtr field_list,Int4 col_from,Int4 col_to,Boolean select_all)30269 static void SwapColumnsForSelectedBulkEditRows
30270 (BulkEditorRowPtr berp,
30271 BulkEdFieldPtr field_list,
30272 Int4 col_from,
30273 Int4 col_to,
30274 Boolean select_all)
30275 {
30276 ValNodePtr vnp_from, vnp_to;
30277 CharPtr val_from, val_to;
30278 ApplyValueData avd;
30279 if (berp == NULL) return;
30280
30281 avd.etp = NULL;
30282 avd.field_list = NULL;
30283 avd.text_to_replace = NULL;
30284 avd.where_to_replace = EditApplyFindLocation_anywhere;
30285
30286 while (berp->object_list != NULL) {
30287 if ((berp->selected || select_all) && berp->subrows == NULL) {
30288 vnp_from = GetBulkEditorRowValueByColumn (berp, col_from);
30289 vnp_to = GetBulkEditorRowValueByColumn (berp, col_to);
30290 if (vnp_from != NULL && vnp_to != NULL) {
30291 val_from = (field_list[col_from].display_func)(vnp_from->data.ptrvalue);
30292 val_to = (field_list[col_to].display_func)(vnp_to->data.ptrvalue);
30293 if (StringDoesHaveText (val_from) || StringDoesHaveText (val_to)) {
30294 avd.new_text = val_to;
30295 vnp_from->data.ptrvalue = (field_list[col_from].set_str_func) (vnp_from->data.ptrvalue, &avd);
30296
30297 avd.new_text = val_from;
30298 vnp_to->data.ptrvalue = (field_list[col_to].set_str_func) (vnp_to->data.ptrvalue, &avd);
30299 }
30300 val_from = MemFree (val_from);
30301 val_to = MemFree (val_to);
30302 }
30303 }
30304 SwapColumnsForSelectedBulkEditRows (berp->subrows, field_list, col_from, col_to, select_all);
30305 berp++;
30306 }
30307 }
30308
30309
30310
30311 static void
AddSampleDataForBulkEditorSelectedFeatures(BulkEditorRowPtr berp,BulkEdFieldPtr field_list,Int4 col,Int4 col_src,GetSamplePtr gsp,TextPortionXPtr text_portion,Boolean select_all)30312 AddSampleDataForBulkEditorSelectedFeatures
30313 (BulkEditorRowPtr berp,
30314 BulkEdFieldPtr field_list,
30315 Int4 col,
30316 Int4 col_src,
30317 GetSamplePtr gsp,
30318 TextPortionXPtr text_portion,
30319 Boolean select_all)
30320 {
30321 CharPtr str, str_src, str_parse;
30322 ValNodePtr vnp, vnp_src;
30323 Boolean skip;
30324
30325 if (berp == NULL || field_list == NULL || col < 0 || field_list[col].display_func == NULL || gsp == NULL) return;
30326
30327 while (berp->object_list != NULL) {
30328 if (berp->subrows == NULL && (berp->selected || select_all)) {
30329 vnp = GetBulkEditorRowValueByColumn (berp, col);
30330 if (vnp != NULL) {
30331 str = (field_list[col]).display_func (vnp->data.ptrvalue);
30332 if (!StringHasNoText (str)) {
30333 skip = FALSE;
30334 /* only add values if col_src < 0 or data in col_src is not blank */
30335 if (col_src >= 0) {
30336 skip = TRUE;
30337 vnp_src = GetBulkEditorRowValueByColumn (berp, col_src);
30338 if (vnp_src != NULL) {
30339 str_src = (field_list[col_src]).display_func(vnp_src->data.ptrvalue);
30340 if (StringDoesHaveText (str_src)) {
30341 if (text_portion == NULL) {
30342 skip = FALSE;
30343 } else {
30344 str_parse = ReplaceStringForParse(str_src, text_portion);
30345 if (StringDoesHaveText (str_parse)) {
30346 skip = FALSE;
30347 }
30348 str_parse = MemFree (str_parse);
30349 }
30350 }
30351 str_src = MemFree (str_src);
30352 }
30353 }
30354 if (!skip) {
30355 gsp->num_found++;
30356 if (gsp->sample_text == NULL) {
30357 gsp->sample_text = str;
30358 str = NULL;
30359 } else if (StringCmp (str, gsp->sample_text) != 0) {
30360 gsp->all_same = FALSE;
30361 }
30362 }
30363 }
30364 str = MemFree (str);
30365 }
30366 }
30367 AddSampleDataForBulkEditorSelectedFeatures (berp->subrows, field_list, col, col_src, gsp, text_portion, select_all);
30368 berp++;
30369 }
30370 }
30371
30372
30373 static GetSamplePtr
GetSampleDataForBulkEditorSelectedFeatures(BulkEditorRowPtr berp,BulkEdFieldPtr field_list,Int4 col,Int4 col_src,TextPortionXPtr text_portion,Boolean select_all)30374 GetSampleDataForBulkEditorSelectedFeatures
30375 (BulkEditorRowPtr berp,
30376 BulkEdFieldPtr field_list,
30377 Int4 col,
30378 Int4 col_src,
30379 TextPortionXPtr text_portion,
30380 Boolean select_all)
30381 {
30382 GetSamplePtr gsp;
30383
30384 if (berp == NULL || field_list == NULL || col < 0) return NULL;
30385
30386 gsp = GetSampleNew ();
30387
30388 AddSampleDataForBulkEditorSelectedFeatures(berp, field_list, col, col_src, gsp, text_portion, select_all);
30389
30390 return gsp;
30391 }
30392
30393
AdjustBulkEditPositions(BulkEditorDlgPtr dlg,Int4 added_col)30394 static void AdjustBulkEditPositions (BulkEditorDlgPtr dlg, Int4 added_col)
30395 {
30396 if (added_col > -1) {
30397 if (added_col <= dlg->last_viewed_col) {
30398 dlg->last_viewed_col++;
30399 }
30400 if (added_col <= dlg->last_sorted_col) {
30401 dlg->last_sorted_col++;
30402 }
30403 dlg->num_columns++;
30404 }
30405 }
30406
30407
ApplyBulkEditCommon(BulkEditorDlgPtr dlg,Boolean select_all)30408 static void ApplyBulkEditCommon (BulkEditorDlgPtr dlg, Boolean select_all)
30409 {
30410 RecT r;
30411 GetSamplePtr gsp = NULL;
30412 ExistingTextPtr etp = NULL;
30413 ApplyValueData avd;
30414 OneFieldBulkEditPtr ofp = NULL;
30415 TwoFieldBulkEditPtr tfp = NULL;
30416 Int4 bulk_row_num, bulk_sub_num, i;
30417 Int4 added_col1 = -1, added_col2 = -1;
30418 Boolean need_redraw = FALSE;
30419
30420 if (dlg == NULL) return;
30421
30422 switch (GetValue (dlg->bulk_action)) {
30423 case eBulkRemoveField:
30424 ofp = (OneFieldBulkEditPtr) DialogToPointer (dlg->bulk_remove);
30425 if (ofp != NULL) {
30426 added_col1 = AddColumnToRowList (dlg->row_list, dlg->master_field_list, &(dlg->field_list), ofp->field, dlg->last_sorted_col, dlg->metadata);
30427 AdjustOneFieldForMaster (ofp, dlg->master_field_list, dlg->field_list);
30428 RemoveColumnFromSelectedBulkEditRows (dlg->row_list, ofp->field, dlg->field_list, select_all);
30429 }
30430 break;
30431 case eBulkApplyField:
30432 ofp = (OneFieldBulkEditPtr) DialogToPointer (dlg->bulk_apply);
30433 if (ofp != NULL) {
30434 /* add field to table, if it's not in the table yet */
30435 added_col1 = AddColumnToRowList (dlg->row_list, dlg->master_field_list, &(dlg->field_list), ofp->field, dlg->last_sorted_col, dlg->metadata);
30436 AdjustOneFieldForMaster (ofp, dlg->master_field_list, dlg->field_list);
30437
30438 /* warn about existing values */
30439 gsp = GetSampleDataForBulkEditorSelectedFeatures (dlg->row_list, dlg->field_list, ofp->field, -1, NULL, select_all);
30440 etp = GetExistingTextHandlerInfo (gsp == NULL ? 0 : gsp->num_found, FALSE);
30441 if (etp == NULL || etp->existing_text_choice != eExistingTextChoiceCancel) {
30442 avd.etp = etp;
30443 avd.field_list = NULL;
30444 AddEditApplyDataToApplyValue (AECR_APPLY, ofp->edit_apply, &avd);
30445 ApplyEditColumnFromSelectedBulkEditRows (dlg->row_list, dlg->field_list, ofp->field, &avd, select_all);
30446 }
30447 }
30448 break;
30449 case eBulkEditField:
30450 ofp = (OneFieldBulkEditPtr) DialogToPointer (dlg->bulk_edit);
30451 if (ofp != NULL) {
30452 added_col1 = AddColumnToRowList (dlg->row_list, dlg->master_field_list, &(dlg->field_list), ofp->field, dlg->last_sorted_col, dlg->metadata);
30453 AdjustOneFieldForMaster (ofp, dlg->master_field_list, dlg->field_list);
30454 avd.etp = NULL;
30455 avd.field_list = NULL;
30456 AddEditApplyDataToApplyValue (AECR_EDIT, ofp->edit_apply, &avd);
30457 ApplyEditColumnFromSelectedBulkEditRows (dlg->row_list, dlg->field_list, ofp->field, &avd, select_all);
30458 }
30459 break;
30460 case eBulkCapitalizeField:
30461 ofp = (OneFieldBulkEditPtr) DialogToPointer (dlg->bulk_capitalize);
30462 if (ofp != NULL && ofp->capitalization != NULL && ofp->capitalization->change != eChangeCaseNone) {
30463 added_col1 = AddColumnToRowList (dlg->row_list, dlg->master_field_list, &(dlg->field_list), ofp->field, dlg->last_sorted_col, dlg->metadata);
30464 AdjustOneFieldForMaster (ofp, dlg->master_field_list, dlg->field_list);
30465 CapitalizeColumnsForSelectedBulkEditRows (dlg->row_list, dlg->field_list, ofp->field, ofp->capitalization, select_all);
30466 }
30467 break;
30468 case eBulkConvertField:
30469 tfp = (TwoFieldBulkEditPtr) DialogToPointer (dlg->bulk_convert);
30470 if (tfp != NULL) {
30471 added_col1 = AddColumnToRowList (dlg->row_list, dlg->master_field_list, &(dlg->field_list), tfp->field_to, dlg->last_sorted_col, dlg->metadata);
30472 added_col2 = AddColumnToRowList (dlg->row_list, dlg->master_field_list, &(dlg->field_list), tfp->field_from, dlg->last_sorted_col, dlg->metadata);
30473 AdjustTwoFieldsForMaster (tfp, dlg->master_field_list, dlg->field_list);
30474
30475 gsp = GetSampleDataForBulkEditorSelectedFeatures (dlg->row_list, dlg->field_list, tfp->field_to, tfp->field_from, NULL, select_all);
30476 etp = GetExistingTextHandlerInfo (gsp == NULL ? 0 : gsp->num_found, FALSE);
30477 if (etp == NULL || etp->existing_text_choice != eExistingTextChoiceCancel) {
30478 ConvertColumnsForSelectedBulkEditRows (dlg->row_list, dlg->field_list, tfp, etp, select_all);
30479 }
30480 }
30481 break;
30482 case eBulkParseField:
30483 tfp = (TwoFieldBulkEditPtr) DialogToPointer (dlg->bulk_parse);
30484 if (tfp != NULL) {
30485 added_col1 = AddColumnToRowList (dlg->row_list, dlg->master_field_list, &(dlg->field_list), tfp->field_to, dlg->last_sorted_col, dlg->metadata);
30486 added_col2 = AddColumnToRowList (dlg->row_list, dlg->master_field_list, &(dlg->field_list), tfp->field_from, dlg->last_sorted_col, dlg->metadata);
30487 AdjustTwoFieldsForMaster (tfp, dlg->master_field_list, dlg->field_list);
30488 gsp = GetSampleDataForBulkEditorSelectedFeatures (dlg->row_list, dlg->field_list, tfp->field_to, tfp->field_from, tfp->text_portion, select_all);
30489 etp = GetExistingTextHandlerInfo (gsp == NULL ? 0 : gsp->num_found, FALSE);
30490 if (etp == NULL || etp->existing_text_choice != eExistingTextChoiceCancel) {
30491 ParseColumnsForSelectedBulkEditRows (dlg->row_list, dlg->field_list, tfp, etp, select_all);
30492 }
30493 }
30494 break;
30495 case eBulkSwapField:
30496 tfp = (TwoFieldBulkEditPtr) DialogToPointer (dlg->bulk_swap);
30497 if (tfp != NULL) {
30498 added_col1 = AddColumnToRowList (dlg->row_list, dlg->master_field_list, &(dlg->field_list), tfp->field_to, dlg->last_sorted_col, dlg->metadata);
30499 added_col2 = AddColumnToRowList (dlg->row_list, dlg->master_field_list, &(dlg->field_list), tfp->field_from, dlg->last_sorted_col, dlg->metadata);
30500 AdjustTwoFieldsForMaster (tfp, dlg->master_field_list, dlg->field_list);
30501 SwapColumnsForSelectedBulkEditRows (dlg->row_list, dlg->field_list, tfp->field_from, tfp->field_to, select_all);
30502 }
30503 break;
30504 }
30505
30506 ofp = OneFieldBulkEditFree (ofp);
30507 tfp = TwoFieldBulkEditFree (tfp);
30508 gsp = GetSampleFree (gsp);
30509 etp = MemFree (etp);
30510
30511 AdjustBulkEditPositions (dlg, added_col1);
30512 AdjustBulkEditPositions (dlg, added_col2);
30513
30514 AddSummaryInfoToMetaRows (dlg->row_list, dlg->last_sorted_col);
30515
30516 /* update individual field editor */
30517 if (dlg->last_viewed_row > 0) {
30518 /* show appropriate editor for highlighted item */
30519 if (DataPosFromBulkEdDlgRow (dlg->last_viewed_row, dlg->row_list, &bulk_row_num, &bulk_sub_num)) {
30520 ShowBulkFieldEditor (dlg, bulk_row_num, bulk_sub_num, dlg->last_viewed_col);
30521 } else {
30522 dlg->last_viewed_row = 0;
30523 dlg->last_viewed_col = 0;
30524 for (i = 0; i < dlg->num_master_columns; i++) {
30525 SafeHide (dlg->editor_list[i]);
30526 }
30527 Hide (dlg->ed_btn_grp);
30528 }
30529 }
30530
30531 if (added_col1 > -1 || added_col2 > -1) {
30532 RedrawAfterColumnShift (dlg);
30533 } else {
30534 UpdateBulkEdDisplay (dlg);
30535 ObjectRect (dlg->doc, &r);
30536 InvalRect (&r);
30537 Update ();
30538 }
30539 }
30540
30541
ApplyBulkEditAll(ButtoN b)30542 static void ApplyBulkEditAll (ButtoN b)
30543 {
30544 BulkEditorDlgPtr dlg;
30545
30546 dlg = (BulkEditorDlgPtr) GetObjectExtra (b);
30547 if (dlg == NULL) return;
30548
30549 ApplyBulkEditCommon (dlg, TRUE);
30550 }
30551
ApplyBulkEdit(ButtoN b)30552 static void ApplyBulkEdit (ButtoN b)
30553 {
30554 BulkEditorDlgPtr dlg;
30555 Boolean select_all = FALSE;
30556
30557 dlg = (BulkEditorDlgPtr) GetObjectExtra (b);
30558 if (dlg == NULL) return;
30559
30560 if (CountBulkEditorRowsSelected(dlg->row_list) == 0) {
30561 if (ANS_CANCEL == Message (MSG_OKC, "No items selected! Apply to all?")) {
30562 return;
30563 } else {
30564 select_all = TRUE;
30565 }
30566 }
30567
30568 ApplyBulkEditCommon (dlg, select_all);
30569 }
30570
30571
BulkEditorCheckAllDialog(DialoG d)30572 extern void BulkEditorCheckAllDialog (DialoG d)
30573 {
30574 BulkEditorDlgPtr dlg;
30575 RecT r;
30576
30577 dlg = (BulkEditorDlgPtr) GetObjectExtra (d);
30578 if (dlg == NULL) return;
30579
30580 SelectBulkEditorRows (dlg->row_list, TRUE);
30581 UpdateCheckStatus (dlg);
30582 ObjectRect (dlg->doc, &r);
30583 InvalRect (&r);
30584 Update ();
30585 }
30586
BulkEditorCheckAll(ButtoN b)30587 static void BulkEditorCheckAll (ButtoN b)
30588 {
30589 BulkEditorDlgPtr dlg;
30590 RecT r;
30591
30592 dlg = (BulkEditorDlgPtr) GetObjectExtra (b);
30593 if (dlg == NULL) return;
30594
30595 SelectBulkEditorRows (dlg->row_list, TRUE);
30596 UpdateCheckStatus (dlg);
30597 ObjectRect (dlg->doc, &r);
30598 InvalRect (&r);
30599 Update ();
30600 }
30601
30602
BulkEditorUncheckAll(ButtoN b)30603 static void BulkEditorUncheckAll (ButtoN b)
30604 {
30605 BulkEditorDlgPtr dlg;
30606 RecT r;
30607
30608 dlg = (BulkEditorDlgPtr) GetObjectExtra (b);
30609 if (dlg == NULL) return;
30610
30611 SelectBulkEditorRows (dlg->row_list, FALSE);
30612 UpdateCheckStatus (dlg);
30613 ObjectRect (dlg->doc, &r);
30614 InvalRect (&r);
30615 Update ();
30616 }
30617
BulkEditorStringConstraintCheck(ButtoN b)30618 static void BulkEditorStringConstraintCheck (ButtoN b)
30619 {
30620 BulkEditorDlgPtr dlg;
30621 RecT r;
30622 Int4 field_num;
30623 StringConstraintXPtr scp;
30624 Boolean val;
30625
30626 dlg = (BulkEditorDlgPtr) GetObjectExtra (b);
30627 if (dlg == NULL) return;
30628
30629 field_num = GetFieldNumFromPopupValue(GetValue (dlg->check_constraint_field), dlg->field_list, FALSE);
30630 scp = DialogToPointer (dlg->check_constraint);
30631
30632 if (GetValue (dlg->sel_unsel_grp) == 1) {
30633 val = TRUE;
30634 } else {
30635 val = FALSE;
30636 }
30637
30638 SelectBulkEditorRowsByStringConstraint (dlg->row_list, dlg->field_list, field_num, scp, val);
30639
30640 scp = StringConstraintXFree (scp);
30641 UpdateCheckStatus (dlg);
30642
30643 ObjectRect (dlg->doc, &r);
30644 InvalRect (&r);
30645 Update ();
30646 }
30647
30648
ObjectListToBulkEditorDialog(DialoG d,Pointer data)30649 static void ObjectListToBulkEditorDialog (DialoG d, Pointer data)
30650 {
30651 BulkEditorDlgPtr dlg;
30652 ValNodePtr object_list;
30653
30654 dlg = (BulkEditorDlgPtr) GetObjectExtra (d);
30655 if (dlg == NULL) return;
30656 object_list = (ValNodePtr) data;
30657
30658 dlg->row_list = FreeBulkEditorRows(dlg->row_list, dlg->field_list);
30659 dlg->row_list = MakeBulkEditorRowsFromObjectList (object_list, dlg->field_list, dlg->last_sorted_col, dlg->metadata);
30660 if (dlg->collapse_by_default) {
30661 CollapseAllBulkEditRows (dlg->row_list);
30662 } else {
30663 ExpandAllBulkEditRows (dlg->row_list);
30664 }
30665 ResetClip();
30666 UpdateBulkEdDisplay (dlg);
30667 UpdateCheckStatus (dlg);
30668 }
30669
30670
GetSelectedObjectsFromBulkEditorDialog(DialoG d)30671 static Pointer GetSelectedObjectsFromBulkEditorDialog (DialoG d)
30672 {
30673 BulkEditorDlgPtr dlg;
30674 ValNodePtr object_list = NULL;
30675
30676 dlg = (BulkEditorDlgPtr) GetObjectExtra (d);
30677 if (dlg == NULL) return NULL;
30678
30679 GetBulkEditorSelectedObjects (dlg->row_list, &object_list);
30680 return (Pointer) object_list;
30681 }
30682
30683
CopyEditToClipboard(ButtoN b)30684 static void CopyEditToClipboard (ButtoN b)
30685 {
30686 BulkEditorDlgPtr dlg;
30687 CharPtr str;
30688 Int2 edit_col;
30689
30690 dlg = (BulkEditorDlgPtr) GetObjectExtra (b);
30691 if (dlg == NULL) {
30692 return;
30693 }
30694 if (dlg->last_viewed_col < 0
30695 || dlg->last_viewed_col >= dlg->num_columns) {
30696 return;
30697 }
30698 edit_col = GetMasterFieldNumFromDlgFieldNum (dlg->master_field_list, dlg->field_list, dlg->last_viewed_col);
30699 if (dlg->editor_list[edit_col] == NULL) {
30700 return;
30701 }
30702 str = DialogToPointer (dlg->editor_list[edit_col]);
30703 if (!StringHasNoText (str)) {
30704 StringToClipboard (str);
30705 }
30706 str = MemFree (str);
30707 }
30708
30709
CopyEditFromClipboard(ButtoN b)30710 static void CopyEditFromClipboard (ButtoN b)
30711 {
30712 BulkEditorDlgPtr dlg;
30713 CharPtr str;
30714 Int2 edit_col;
30715
30716 dlg = (BulkEditorDlgPtr) GetObjectExtra (b);
30717 if (dlg == NULL) {
30718 return;
30719 }
30720 if (dlg->last_viewed_col < 0
30721 || dlg->last_viewed_col >= dlg->num_columns) {
30722 return;
30723 }
30724 edit_col = GetMasterFieldNumFromDlgFieldNum (dlg->master_field_list, dlg->field_list, dlg->last_viewed_col);
30725 if (dlg->editor_list[edit_col] == NULL) {
30726 return;
30727 }
30728 str = ClipboardToString ();
30729 if (!StringHasNoText (str)) {
30730 PointerToDialog (dlg->editor_list[edit_col], str);
30731 }
30732 str = MemFree (str);
30733 }
30734
30735
GetPopulatedFieldsFromMasterList(BulkEdFieldPtr master_field_list,BulkEditorRowPtr row_list)30736 static BulkEdFieldPtr GetPopulatedFieldsFromMasterList (BulkEdFieldPtr master_field_list, BulkEditorRowPtr row_list)
30737 {
30738 Int4 i, num_fields = 0;
30739 BoolPtr empties;
30740 Int4 num_full = 0;
30741 BulkEdFieldPtr pop_fields;
30742
30743 for (i = 0; master_field_list[i].name != NULL; i++) {
30744 num_fields++;
30745 }
30746
30747 empties = (BoolPtr) MemNew (sizeof (Boolean) * num_fields);
30748 for (i = 0; i < num_fields; i++) {
30749 if (IsBulkEditorColumnEmpty (row_list, i)) {
30750 empties[i] = TRUE;
30751 } else {
30752 empties[i] = FALSE;
30753 num_full++;
30754 }
30755 }
30756
30757 pop_fields = (BulkEdFieldPtr) MemNew (sizeof (BulkEdFieldData) * (num_full + 1));
30758 num_full = 0;
30759 for (i = 0; i < num_fields; i++) {
30760 if (!empties[i]) {
30761 pop_fields[num_full++] = master_field_list[i];
30762 }
30763 }
30764 pop_fields[num_full] = master_field_list[num_fields];
30765 empties = MemFree (empties);
30766 return pop_fields;
30767 }
30768
30769
CopyAllFieldsFromList(BulkEdFieldPtr master_field_list)30770 static BulkEdFieldPtr CopyAllFieldsFromList (BulkEdFieldPtr master_field_list)
30771 {
30772 Int4 i, num_fields = 0;
30773 Int4 num_full = 0;
30774 BulkEdFieldPtr pop_fields;
30775
30776 for (i = 0; master_field_list[i].name != NULL; i++) {
30777 num_fields++;
30778 }
30779
30780
30781 pop_fields = (BulkEdFieldPtr) MemNew (sizeof (BulkEdFieldData) * (num_fields + 1));
30782 for (i = 0; i < num_fields; i++) {
30783 pop_fields[i] = master_field_list[i];
30784 }
30785 pop_fields[num_fields] = master_field_list[num_fields];
30786 return pop_fields;
30787 }
30788
FinishBulkEditorDialogSetup(GrouP p,BulkEditorDlgPtr dlg)30789 static void FinishBulkEditorDialogSetup (GrouP p, BulkEditorDlgPtr dlg)
30790 {
30791 Int4 width, num_columns = 0;
30792 Int4 i, page_num;
30793 GrouP ed_grp, ed2_grp, check_grp, action_grp, page_grp, box_grp;
30794 GrouP g1, g2, a, g_tmp, g_tmp2;
30795 ButtoN b;
30796
30797 if (p == NULL || dlg == NULL) {
30798 return;
30799 }
30800
30801 dlg->dialog = (DialoG) p;
30802 dlg->todialog = ObjectListToBulkEditorDialog;
30803 dlg->fromdialog = GetSelectedObjectsFromBulkEditorDialog;
30804 dlg->testdialog = NULL;
30805
30806 /* look for editing functions */
30807 dlg->num_master_columns = 0;
30808 dlg->any_editing = FALSE;
30809 for (i = 0; dlg->master_field_list[i].name != NULL; i++) {
30810 if (dlg->master_field_list[i].create_dlg_func != NULL) {
30811 dlg->any_editing = TRUE;
30812 }
30813 dlg->num_master_columns++;
30814 }
30815 /* count columns */
30816 for (i = 0; dlg->field_list[i].name != NULL; i++) {
30817 num_columns++;
30818 }
30819
30820 dlg->num_columns = num_columns;
30821 dlg->columns_shown = num_columns;
30822 dlg->display_offset = 0;
30823 /* populate values list */
30824
30825 SelectFont (systemFont);
30826 dlg->col_list = AllocateDocColumnsForFieldList (dlg->field_list, &width, dlg->last_sorted_col, dlg->display_offset, dlg->columns_shown);
30827 dlg->par_fmt.minLines = 1;
30828 dlg->par_fmt.minHeight = 1;
30829
30830 dlg->title_doc = DocumentPanel (p, width, stdLineHeight);
30831 InitBulkEdTitleDoc (dlg, dlg->title_doc);
30832 SetObjectExtra (dlg->title_doc, dlg, NULL);
30833 SetDocProcs (dlg->title_doc, ClickBulkTitle, NULL, NULL, NULL);
30834
30835 dlg->doc = DocumentPanel (p, width, 10 * stdLineHeight);
30836 SetObjectExtra (dlg->doc, dlg, NULL);
30837 SetDocProcs (dlg->doc, ClickBulkEdField, NULL, NULL, NULL);
30838 SetDocShade (dlg->doc, DrawBulkEdCell, NULL, HighlightBulkEdField, NULL);
30839
30840 ed_grp = HiddenGroup (p, 4, 0, NULL);
30841 SetGroupSpacing (ed_grp, 10, 10);
30842 ed2_grp = HiddenGroup (ed_grp, 0, 0, NULL);
30843 dlg->editor_list = (DialoG PNTR) MemNew (sizeof(DialoG) * dlg->num_master_columns);
30844 for (i = 0; dlg->master_field_list[i].name != NULL; i++) {
30845 if (dlg->master_field_list[i].create_dlg_func == NULL) {
30846 dlg->editor_list[i] = NULL;
30847 } else {
30848 dlg->editor_list[i] = (dlg->master_field_list[i].create_dlg_func) (ed2_grp, dlg->master_field_list[i].name, dlg->sep);
30849 Hide (dlg->editor_list[i]);
30850 }
30851 }
30852
30853 dlg->ed_btn_grp = HiddenGroup (ed_grp, 1, 0, NULL);
30854 SetGroupSpacing (dlg->ed_btn_grp, 10, 10);
30855
30856 b = PushButton (dlg->ed_btn_grp, "Apply Change", ApplyBulkEditingChange);
30857 SetObjectExtra (b, dlg, NULL);
30858 g_tmp = HiddenGroup (dlg->ed_btn_grp, 2, 0, NULL);
30859 SetGroupSpacing (g_tmp, 10, 10);
30860 b = PushButton (g_tmp, "Copy to Clipboard", CopyEditToClipboard);
30861 SetObjectExtra (b, dlg, NULL);
30862 b = PushButton (g_tmp, "Copy from Clipboard", CopyEditFromClipboard);
30863 SetObjectExtra (b, dlg, NULL);
30864 Hide (dlg->ed_btn_grp);
30865
30866 box_grp = HiddenGroup (p, 0, 2, NULL);
30867
30868 /* group that contains controls for checking and unchecking features */
30869 check_grp = NormalGroup (box_grp, -1, 0, "Check Features", programFont, NULL);
30870 SetGroupSpacing (check_grp, 10, 10);
30871 g1 = HiddenGroup (check_grp, 3, 0, NULL);
30872 SetGroupSpacing (g1, 10, 10);
30873 b = PushButton (g1, "Check All Features", BulkEditorCheckAll);
30874 SetObjectExtra (b, dlg, NULL);
30875 b = PushButton (g1, "Uncheck All Features", BulkEditorUncheckAll);
30876 SetObjectExtra (b, dlg, NULL);
30877
30878 g2 = HiddenGroup (check_grp, 4, 0, NULL);
30879 dlg->sel_unsel_grp = HiddenGroup (g2, 0, 2, NULL);
30880 RadioButton (dlg->sel_unsel_grp, "Check features where");
30881 RadioButton (dlg->sel_unsel_grp, "Uncheck features where");
30882 SetValue (dlg->sel_unsel_grp, 1);
30883 dlg->check_constraint_field = MakeBulkEditorFieldListPopup (g2, dlg->field_list, FALSE);
30884 dlg->check_constraint = StringConstraintDialogX (g2, NULL, FALSE);
30885 b = PushButton (g2, "Apply", BulkEditorStringConstraintCheck);
30886 SetObjectExtra (b, dlg, NULL);
30887
30888 if (dlg->any_editing) {
30889 /* group that contains controls for applying actions to check features */
30890 action_grp = NormalGroup (box_grp, -1, 0, "Action for Checked Features", programFont, NULL);
30891 a = HiddenGroup (action_grp, 2, 0, NULL);
30892 SetGroupSpacing (a, 10, 10);
30893 dlg->bulk_action = PopupList (a, TRUE, ChangeBulkEditorAction);
30894 SetObjectExtra (dlg->bulk_action, dlg, NULL);
30895 PopupItem (dlg->bulk_action, "Apply");
30896 PopupItem (dlg->bulk_action, "Edit");
30897 PopupItem (dlg->bulk_action, "Convert");
30898 PopupItem (dlg->bulk_action, "Parse");
30899 PopupItem (dlg->bulk_action, "Swap");
30900 PopupItem (dlg->bulk_action, "Remove");
30901 PopupItem (dlg->bulk_action, "Change Case");
30902 SetValue (dlg->bulk_action, 2);
30903 page_grp = HiddenGroup (a, 0, 0, NULL);
30904 page_num = 0;
30905 dlg->action_pages[page_num] = HiddenGroup (page_grp, 2, 0, NULL);
30906 dlg->bulk_apply = OneFieldBulkEditDialog (dlg->action_pages[page_num], eBulkApplyField, NULL, NULL, dlg->master_field_list, GetFirstBulkEditValue, dlg);
30907
30908 page_num++;
30909 dlg->action_pages[page_num] = HiddenGroup (page_grp, 2, 0, NULL);
30910 dlg->bulk_edit = OneFieldBulkEditDialog (dlg->action_pages[page_num], eBulkEditField, NULL, NULL, dlg->master_field_list, GetFirstBulkEditValue, dlg);
30911
30912 page_num++;
30913 dlg->action_pages[page_num] = HiddenGroup (page_grp, 2, 0, NULL);
30914 dlg->bulk_convert = TwoFieldBulkEditDialog (dlg->action_pages[page_num], eBulkConvertField, NULL, NULL, dlg->master_field_list, FALSE, NULL, NULL);
30915
30916 page_num++;
30917 dlg->action_pages[page_num] = HiddenGroup (page_grp, 2, 0, NULL);
30918 dlg->bulk_parse = TwoFieldBulkEditDialog (dlg->action_pages[page_num], eBulkParseField, NULL, NULL, dlg->master_field_list, FALSE, GetFirstBulkEditValue, dlg);
30919
30920 page_num++;
30921 dlg->action_pages[page_num] = HiddenGroup (page_grp, 2, 0, NULL);
30922 dlg->bulk_swap = TwoFieldBulkEditDialog (dlg->action_pages[page_num], eBulkSwapField, NULL, NULL, dlg->master_field_list, FALSE, NULL, NULL);
30923
30924 page_num++;
30925 dlg->action_pages[page_num] = HiddenGroup (page_grp, 2, 0, NULL);
30926 dlg->bulk_remove = OneFieldBulkEditDialog (dlg->action_pages[page_num], eBulkRemoveField, NULL, NULL, dlg->master_field_list, NULL, NULL);
30927
30928 page_num++;
30929 dlg->action_pages[page_num] = HiddenGroup (page_grp, 2, 0, NULL);
30930 dlg->bulk_capitalize = OneFieldBulkEditDialog (dlg->action_pages[page_num], eBulkCapitalizeField, NULL, NULL, dlg->master_field_list, NULL, NULL);
30931
30932 AlignObjects (ALIGN_CENTER, (HANDLE) dlg->action_pages[0],
30933 (HANDLE) dlg->action_pages[1],
30934 (HANDLE) dlg->action_pages[2],
30935 (HANDLE) dlg->action_pages[3],
30936 (HANDLE) dlg->action_pages[4],
30937 (HANDLE) dlg->action_pages[5],
30938 (HANDLE) dlg->action_pages[6],
30939 NULL);
30940
30941 dlg->check_status = StaticPrompt (action_grp, "0 features are checked", 20 * stdCharWidth, dialogTextHeight, programFont, 'l');
30942
30943 g_tmp2 = HiddenGroup (action_grp, 3, 0, NULL);
30944 SetGroupSpacing (g_tmp2, 10, 10);
30945 b = PushButton (g_tmp2, "Apply to All Features", ApplyBulkEditAll);
30946 SetObjectExtra (b, dlg, NULL);
30947 b = PushButton (g_tmp2, "Apply to Checked Features", ApplyBulkEdit);
30948 SetObjectExtra (b, dlg, NULL);
30949
30950 AlignObjects (ALIGN_CENTER, (HANDLE) a, (HANDLE) dlg->check_status, (HANDLE) g_tmp2, NULL);
30951 }
30952
30953
30954 AlignObjects (ALIGN_CENTER, (HANDLE) dlg->title_doc, (HANDLE) dlg->doc, (HANDLE) ed_grp, (HANDLE) box_grp, NULL);
30955
30956 UpdateBulkEdDisplay (dlg);
30957 UpdateCheckStatus (dlg);
30958 ChangeBulkEditorAction (dlg->bulk_action);
30959 }
30960
30961
30962 NLM_EXTERN DialoG
CreateBulkEditorDialogEx(GrouP h,BulkEdFieldPtr field_list,ValNodePtr feat_list,SeqEntryPtr sep,Boolean collapse_by_default,ClickableCallback single_click_func,ClickableCallback double_click_func,Pointer metadata,Boolean show_only_present)30963 CreateBulkEditorDialogEx
30964 (GrouP h,
30965 BulkEdFieldPtr field_list,
30966 ValNodePtr feat_list,
30967 SeqEntryPtr sep,
30968 Boolean collapse_by_default,
30969 ClickableCallback single_click_func,
30970 ClickableCallback double_click_func,
30971 Pointer metadata,
30972 Boolean show_only_present)
30973 {
30974 GrouP p;
30975 BulkEditorDlgPtr dlg;
30976
30977 p = HiddenGroup (h, -1, 0, NULL);
30978 dlg = (BulkEditorDlgPtr) MemNew (sizeof (BulkEditorDlgData));
30979
30980 SetObjectExtra (p, dlg, CleanupBulkEditorDialog); /* need to cleanup values_list */
30981
30982 dlg->collapse_by_default = collapse_by_default;
30983 dlg->single_click_func = single_click_func;
30984 dlg->double_click_func = double_click_func;
30985 dlg->master_field_list = field_list;
30986 dlg->metadata = metadata;
30987 dlg->sep = sep;
30988
30989 dlg->last_viewed_row = 0;
30990 dlg->last_viewed_col = 0;
30991 dlg->last_sorted_col = 0;
30992 dlg->row_list = MakeBulkEditorRowsFromObjectList(feat_list, dlg->master_field_list, dlg->last_sorted_col, dlg->metadata);
30993
30994 /* need master list and actual list */
30995 if (show_only_present) {
30996 dlg->field_list = GetPopulatedFieldsFromMasterList (dlg->master_field_list, dlg->row_list);
30997 dlg->row_list = FreeBulkEditorRows(dlg->row_list, dlg->master_field_list);
30998 dlg->row_list = MakeBulkEditorRowsFromObjectList(feat_list, dlg->field_list, dlg->last_sorted_col, dlg->metadata);
30999 } else {
31000 dlg->field_list = CopyAllFieldsFromList (dlg->master_field_list);
31001 }
31002
31003 if (dlg->collapse_by_default) {
31004 CollapseAllBulkEditRows (dlg->row_list);
31005 } else {
31006 ExpandAllBulkEditRows (dlg->row_list);
31007 }
31008
31009 FinishBulkEditorDialogSetup (p, dlg);
31010
31011 return (DialoG) p;
31012 }
31013
31014
31015 NLM_EXTERN DialoG
CreateBulkEditorDialog(GrouP h,BulkEdFieldPtr field_list,ValNodePtr feat_list,SeqEntryPtr sep,Boolean collapse_by_default,ClickableCallback single_click_func,ClickableCallback double_click_func)31016 CreateBulkEditorDialog
31017 (GrouP h,
31018 BulkEdFieldPtr field_list,
31019 ValNodePtr feat_list,
31020 SeqEntryPtr sep,
31021 Boolean collapse_by_default,
31022 ClickableCallback single_click_func,
31023 ClickableCallback double_click_func)
31024 {
31025 return CreateBulkEditorDialogEx (h, field_list, feat_list, sep, collapse_by_default,
31026 single_click_func, double_click_func, NULL, FALSE);
31027 }
31028
31029
BulkGetLocation(Uint1 data_choice,Pointer data,Pointer metadata)31030 static Pointer BulkGetLocation (Uint1 data_choice, Pointer data, Pointer metadata)
31031 {
31032 SeqLocPtr slp;
31033 SeqFeatPtr sfp = (SeqFeatPtr) data;
31034
31035 if (sfp == NULL) return NULL;
31036 slp = (SeqLocPtr) AsnIoMemCopy (sfp->location, (AsnReadFunc) SeqLocAsnRead, (AsnWriteFunc) SeqLocAsnWrite);
31037 return slp;
31038 }
31039
BulkSetLocation(Pointer target,Pointer data)31040 static void BulkSetLocation (Pointer target, Pointer data)
31041 {
31042 SeqFeatPtr sfp = (SeqFeatPtr) target;
31043 SeqLocPtr slp = (SeqLocPtr) data;
31044 if (sfp == NULL) return;
31045 sfp->location = SeqLocFree (sfp->location);
31046 sfp->location = (SeqLocPtr) AsnIoMemCopy (slp, (AsnReadFunc) SeqLocAsnRead, (AsnWriteFunc) SeqLocAsnWrite);
31047 }
31048
BulkFormatLocation(ColPtr col,CharPtr name)31049 static Int4 BulkFormatLocation (ColPtr col, CharPtr name)
31050 {
31051 if (col == NULL) return 0;
31052
31053 col->pixWidth = MAX (15, StringLen (name)) * stdCharWidth;
31054 col->pixInset = 1;
31055 col->charWidth = 0;
31056 col->charInset = 0;
31057 col->font = NULL;
31058 col->just = 'l';
31059 col->wrap = 1;
31060 col->bar = 0;
31061 col->underline = 0;
31062 col->left = 0;
31063 return col->pixWidth;
31064 }
31065
BulkFreeLocation(Pointer data)31066 static void BulkFreeLocation (Pointer data)
31067 {
31068 SeqLocPtr slp = (SeqLocPtr) data;
31069
31070 slp = SeqLocFree (slp);
31071 }
31072
BulkDisplayLocation(Pointer data)31073 static CharPtr BulkDisplayLocation (Pointer data)
31074 {
31075 SeqLocPtr slp = (SeqLocPtr) data;
31076
31077 return SeqLocPrint (slp);
31078 }
31079
BulkNucLocationDialog(GrouP g,CharPtr name,SeqEntryPtr sep)31080 static DialoG BulkNucLocationDialog (GrouP g, CharPtr name, SeqEntryPtr sep)
31081 {
31082 return CreateIntervalEditorDialog (g, NULL, 4, 2, sep, TRUE, FALSE);
31083 }
31084
BulkCopyLocation(Pointer data)31085 static Pointer BulkCopyLocation (Pointer data)
31086 {
31087 SeqLocPtr orig = (SeqLocPtr) data;
31088 SeqLocPtr new_loc;
31089
31090 if (orig == NULL) return NULL;
31091 new_loc = (SeqLocPtr) AsnIoMemCopy ((Pointer) orig,
31092 (AsnReadFunc) SeqLocAsnRead,
31093 (AsnWriteFunc) SeqLocAsnWrite);
31094
31095 return new_loc;
31096 }
31097
BulkFormatSimpleText(ColPtr col,CharPtr name)31098 NLM_EXTERN Int4 BulkFormatSimpleText (ColPtr col, CharPtr name)
31099 {
31100 if (col == NULL) return 0;
31101
31102 col->pixWidth = (MAX (15, StringLen (name)) + 3) * MaxCharWidth();
31103 col->pixInset = 0;
31104 col->charWidth = 0;
31105 col->charInset = 0;
31106 col->font = NULL;
31107 col->just = 'l';
31108 col->wrap = 1;
31109 col->bar = 0;
31110 col->underline = 0;
31111 col->left = 0;
31112 return col->pixWidth;
31113 }
31114
BulkFreeSimpleText(Pointer data)31115 NLM_EXTERN void BulkFreeSimpleText (Pointer data)
31116 {
31117 CharPtr str = (CharPtr) data;
31118
31119 str = MemFree (str);
31120 }
31121
BulkDisplaySimpleText(Pointer data)31122 NLM_EXTERN CharPtr BulkDisplaySimpleText (Pointer data)
31123 {
31124 CharPtr str = (CharPtr) data;
31125 if (StringHasNoText (str)) {
31126 return NULL;
31127 } else {
31128 return StringSave ((CharPtr) data);
31129 }
31130 }
31131
31132 typedef struct bulksimpletext {
31133 DIALOG_MESSAGE_BLOCK
31134 TexT txt;
31135 } BulkSimpleTextData, PNTR BulkSimpleTextPtr;
31136
StringToBulkSimpleTextDialog(DialoG d,Pointer data)31137 static void StringToBulkSimpleTextDialog (DialoG d, Pointer data)
31138 {
31139 BulkSimpleTextPtr dlg;
31140 CharPtr str;
31141
31142 dlg = (BulkSimpleTextPtr) GetObjectExtra (d);
31143 if (dlg == NULL) return;
31144
31145 str = (CharPtr) data;
31146 if (str == NULL) {
31147 SetTitle (dlg->txt, "");
31148 } else {
31149 SetTitle (dlg->txt, str);
31150 }
31151 }
31152
BulkSimpleTextDialogToString(DialoG d)31153 static Pointer BulkSimpleTextDialogToString (DialoG d)
31154 {
31155 BulkSimpleTextPtr dlg;
31156
31157 dlg = (BulkSimpleTextPtr) GetObjectExtra (d);
31158 if (dlg == NULL) return NULL;
31159
31160 return (Pointer) SaveStringFromText (dlg->txt);
31161 }
31162
31163
BulkSimpleTextDialogEx(GrouP g,CharPtr name,SeqEntryPtr sep,Boolean use_scroll)31164 static DialoG BulkSimpleTextDialogEx (GrouP g, CharPtr name, SeqEntryPtr sep, Boolean use_scroll)
31165 {
31166 BulkSimpleTextPtr dlg;
31167 GrouP p;
31168
31169 p = HiddenGroup (g, 4, 0, NULL);
31170 SetGroupSpacing (p, 10, 10);
31171 dlg = (BulkSimpleTextPtr) MemNew (sizeof(BulkSimpleTextData));
31172
31173 SetObjectExtra (p, dlg, StdCleanupExtraProc);
31174 dlg->dialog = (DialoG) p;
31175 dlg->todialog = StringToBulkSimpleTextDialog;
31176 dlg->fromdialog = BulkSimpleTextDialogToString;
31177 dlg->testdialog = NULL;
31178
31179 StaticPrompt (p, name, 0, dialogTextHeight, programFont, 'l');
31180 if (use_scroll) {
31181 dlg->txt = ScrollText (p, 20, 4, programFont, TRUE, NULL);
31182 } else {
31183 dlg->txt = DialogText (p, "", 20, NULL);
31184 }
31185
31186 return (DialoG) p;
31187 }
31188
BulkSimpleTextDialog(GrouP g,CharPtr name,SeqEntryPtr sep)31189 NLM_EXTERN DialoG BulkSimpleTextDialog (GrouP g, CharPtr name, SeqEntryPtr sep)
31190 {
31191 return BulkSimpleTextDialogEx (g, name, sep, FALSE);
31192 }
31193
BulkSimpleTextScrollDialog(GrouP g,CharPtr name,SeqEntryPtr sep)31194 static DialoG BulkSimpleTextScrollDialog (GrouP g, CharPtr name, SeqEntryPtr sep)
31195 {
31196 return BulkSimpleTextDialogEx (g, name, sep, TRUE);
31197 }
31198
BulkSimpleTextCopy(Pointer data)31199 NLM_EXTERN Pointer BulkSimpleTextCopy (Pointer data)
31200 {
31201 CharPtr orig = (CharPtr) data;
31202 CharPtr new_str = StringSave (orig);
31203 return new_str;
31204 }
31205
BulkFormatTrueFalse(ColPtr col,CharPtr name)31206 static Int4 BulkFormatTrueFalse (ColPtr col, CharPtr name)
31207 {
31208 size_t box_width = stdLineHeight - 3;
31209 if (col == NULL) return 0;
31210
31211 col->pixWidth = MAX (box_width, (StringLen (name) + 2) * MaxCharWidth());
31212 col->pixInset = 0;
31213 col->charWidth = 0;
31214 col->charInset = 0;
31215 col->font = NULL;
31216 col->just = 'l';
31217 col->wrap = 0;
31218 col->bar = 0;
31219 col->underline = 0;
31220 col->left = 0;
31221 return col->pixWidth;
31222 }
31223
BulkDrawTrueFalse(Pointer p,RectPtr r)31224 static void BulkDrawTrueFalse (Pointer p, RectPtr r)
31225 {
31226 RecT rct;
31227
31228 if (r == NULL) return;
31229
31230 rct = *r;
31231 rct.bottom = rct.top + stdLineHeight - 4;
31232 rct.right = rct.left + stdLineHeight - 4;
31233 Gray();
31234 InsetRect (&rct, 2, 2);
31235 FrameRect (&rct);
31236
31237 if (p != NULL) {
31238 MoveTo (rct.left, rct.top);
31239 LineTo (rct.right - 1, rct.bottom - 1);
31240 MoveTo (rct.left, rct.bottom - 1);
31241 LineTo (rct.right - 1, rct.top);
31242 }
31243 Black();
31244 }
31245
BulkReleaseTrueFalse(Pointer p)31246 static Pointer BulkReleaseTrueFalse (Pointer p)
31247 {
31248 if (p == NULL) {
31249 p = (Pointer) StringSave ("TRUE");
31250 } else {
31251 p = MemFree (p);
31252 }
31253 return p;
31254 }
31255
31256
BulkSetPseudo(Pointer target,Pointer val)31257 static void BulkSetPseudo (Pointer target, Pointer val)
31258 {
31259 SeqFeatPtr sfp = (SeqFeatPtr) target;
31260 if (sfp == NULL) return;
31261 if (StringHasNoText ((CharPtr)val)) {
31262 sfp->pseudo = FALSE;
31263 } else {
31264 sfp->pseudo = TRUE;
31265 }
31266 }
31267
BulkGetPseudo(Pointer data)31268 static Pointer BulkGetPseudo (Pointer data)
31269 {
31270 SeqFeatPtr sfp = (SeqFeatPtr) data;
31271 if (sfp == NULL || ! sfp->pseudo) {
31272 return NULL;
31273 } else {
31274 return StringSave ("TRUE");
31275 }
31276 }
31277
BulkSetComment(Pointer target,Pointer data)31278 static void BulkSetComment (Pointer target, Pointer data)
31279 {
31280 CharPtr str = (CharPtr) data;
31281 SeqFeatPtr sfp = (SeqFeatPtr) target;
31282 if (sfp == NULL) return;
31283
31284 sfp->comment = MemFree (sfp->comment);
31285 if (str != NULL) {
31286 sfp->comment = StringSave (str);
31287 }
31288 }
31289
BulkGetComment(Uint1 data_choice,Pointer data,Pointer metadata)31290 static Pointer BulkGetComment (Uint1 data_choice, Pointer data, Pointer metadata)
31291 {
31292 SeqFeatPtr sfp = (SeqFeatPtr) data;
31293 if (sfp == NULL || StringHasNoText (sfp->comment)) {
31294 return NULL;
31295 } else {
31296 return (Pointer) StringSave (sfp->comment);
31297 }
31298 }
31299
31300
BulkCDSGetProtein(Uint1 data_choice,Pointer data,Pointer metadata)31301 static Pointer BulkCDSGetProtein (Uint1 data_choice, Pointer data, Pointer metadata)
31302 {
31303 SeqFeatXrefPtr xref;
31304 ProtRefPtr prp = NULL;
31305 BioseqPtr prot_bsp;
31306 SeqFeatPtr prot_feat;
31307 SeqMgrFeatContext fcontext;
31308 ValNodePtr prot_name_list = NULL, vnp;
31309 SeqFeatPtr sfp = (SeqFeatPtr) data;
31310
31311 if (sfp == NULL) return NULL;
31312
31313 xref = sfp->xref;
31314 while (xref != NULL && xref->data.choice != SEQFEAT_PROT) {
31315 xref = xref->next;
31316 }
31317 if (xref != NULL) {
31318 prp = xref->data.value.ptrvalue;
31319 }
31320
31321 if (prp == NULL) {
31322 if (sfp->data.choice == SEQFEAT_PROT) {
31323 prp = (ProtRefPtr) sfp->data.value.ptrvalue;
31324 } else if (sfp->data.choice == SEQFEAT_CDREGION) {
31325 prot_bsp = BioseqFindFromSeqLoc (sfp->product);
31326 prot_feat = SeqMgrGetNextFeature (prot_bsp, NULL, SEQFEAT_PROT, FEATDEF_PROT, &fcontext);
31327 if (prot_feat != NULL) {
31328 prp = (ProtRefPtr) prot_feat->data.value.ptrvalue;
31329 }
31330 }
31331 }
31332
31333 if (prp != NULL) {
31334 for (vnp = prp->name; vnp != NULL; vnp = vnp->next) {
31335 ValNodeAddPointer (&prot_name_list, vnp->choice, StringSave (vnp->data.ptrvalue));
31336 }
31337 }
31338
31339 return prot_name_list;
31340 }
31341
BulkCDSCopyProtein(Pointer data)31342 static Pointer BulkCDSCopyProtein (Pointer data)
31343 {
31344 ValNodePtr new_prot_name_list = NULL, prot_name_list, vnp;
31345
31346 prot_name_list = (ValNodePtr) data;
31347
31348 for (vnp = prot_name_list; vnp != NULL; vnp = vnp->next) {
31349 ValNodeAddPointer (&new_prot_name_list, vnp->choice, StringSave (vnp->data.ptrvalue));
31350 }
31351 return new_prot_name_list;
31352 }
31353
BulkCDSFormatProtein(ColPtr col,CharPtr name)31354 static Int4 BulkCDSFormatProtein (ColPtr col, CharPtr name)
31355 {
31356 if (col == NULL) return 0;
31357
31358 col->pixWidth = MAX (15, StringLen (name)) * MaxCharWidth();
31359 col->pixInset = 0;
31360 col->charWidth = 0;
31361 col->charInset = 0;
31362 col->font = NULL;
31363 col->just = 'l';
31364 col->wrap = 1;
31365 col->bar = 0;
31366 col->underline = 0;
31367 col->left = 0;
31368 return col->pixWidth;
31369 }
31370
BulkCDSDisplayProtein(Pointer data)31371 static CharPtr BulkCDSDisplayProtein (Pointer data)
31372 {
31373 ValNodePtr prot_name_list, vnp;
31374 CharPtr prot_text;
31375 Int4 text_len = 1;
31376
31377 if (data == NULL) return NULL;
31378 prot_name_list = (ValNodePtr) data;
31379 for (vnp = prot_name_list; vnp != NULL; vnp = vnp->next) {
31380 text_len += StringLen (vnp->data.ptrvalue) + 1;
31381 }
31382 prot_text = (CharPtr) MemNew (sizeof (Char) * text_len);
31383 prot_text[0] = 0;
31384 for (vnp = prot_name_list; vnp != NULL; vnp = vnp->next) {
31385 StringCat (prot_text, vnp->data.ptrvalue);
31386 if (vnp->next != NULL) {
31387 StringCat (prot_text, ";");
31388 }
31389 }
31390 return prot_text;
31391 }
31392
31393
BulkCDSSetProteinString(Pointer curr_val,ApplyValuePtr avp)31394 static Pointer BulkCDSSetProteinString (Pointer curr_val, ApplyValuePtr avp)
31395 {
31396 CharPtr curr_val_str;
31397 CharPtr new_str, name_str, cp;
31398 ValNodePtr name_list;
31399
31400 name_list = (ValNodePtr) curr_val;
31401 curr_val_str = BulkCDSDisplayProtein (name_list);
31402 name_list = ValNodeFreeData (name_list);
31403
31404 new_str = HandleApplyValue (curr_val_str, avp);
31405
31406 name_str = new_str;
31407 cp = StringChr (name_str, ';');
31408 while (cp != NULL) {
31409 *cp = 0;
31410 ValNodeAddPointer (&name_list, 0, StringSave (name_str));
31411 *cp = ';';
31412 name_str = cp + 1;
31413 cp = StringChr (name_str, ';');
31414 }
31415 ValNodeAddPointer (&name_list, 0, StringSave (name_str));
31416 new_str = MemFree (new_str);
31417
31418 return name_list;
31419 }
31420
31421
BulkCDSFreeProtein(Pointer data)31422 static void BulkCDSFreeProtein (Pointer data)
31423 {
31424 ValNodePtr prot_name_list = (ValNodePtr) data;
31425
31426 ValNodeFreeData (prot_name_list);
31427 }
31428
BulkCDSProteinDialog(GrouP g,CharPtr name,SeqEntryPtr sep)31429 static DialoG BulkCDSProteinDialog (GrouP g, CharPtr name, SeqEntryPtr sep)
31430 {
31431 return CreateVisibleStringDialog (g, 3, -1, 25);
31432 }
31433
BulkCDSSetProteinDesc(Pointer target,Pointer data)31434 static void BulkCDSSetProteinDesc (Pointer target, Pointer data)
31435 {
31436 SeqFeatXrefPtr xref;
31437 ProtRefPtr prp = NULL;
31438 BioseqPtr prot_bsp;
31439 SeqFeatPtr prot_feat;
31440 SeqMgrFeatContext fcontext;
31441 CharPtr prot_desc;
31442 SeqFeatPtr sfp = (SeqFeatPtr) target;
31443 if (sfp == NULL) return;
31444
31445 prot_desc = (CharPtr) data;
31446
31447 xref = sfp->xref;
31448 while (xref != NULL && xref->data.choice != SEQFEAT_PROT) {
31449 xref = xref->next;
31450 }
31451 if (xref != NULL) {
31452 prp = xref->data.value.ptrvalue;
31453 }
31454
31455 if (prp == NULL) {
31456 if (sfp->data.choice == SEQFEAT_PROT) {
31457 prp = (ProtRefPtr) sfp->data.value.ptrvalue;
31458 } else if (sfp->data.choice == SEQFEAT_CDREGION) {
31459 prot_bsp = BioseqFindFromSeqLoc (sfp->product);
31460 prot_feat = SeqMgrGetNextFeature (prot_bsp, NULL, SEQFEAT_PROT, FEATDEF_PROT, &fcontext);
31461 if (prot_feat == NULL && !StringHasNoText (prot_desc)) {
31462 prot_feat = CreateNewFeatureOnBioseq (prot_bsp, SEQFEAT_PROT, NULL);
31463 prp = ProtRefNew ();
31464 prot_feat->data.value.ptrvalue = prp;
31465 SeqMgrIndexFeatures (prot_bsp->idx.entityID, NULL);
31466 }
31467 if (prot_feat != NULL) {
31468 prp = (ProtRefPtr) prot_feat->data.value.ptrvalue;
31469 }
31470 }
31471 }
31472
31473 if (prp == NULL && !StringHasNoText (prot_desc)) {
31474 xref = SeqFeatXrefNew ();
31475 prp = ProtRefNew ();
31476 xref->data.choice = SEQFEAT_PROT;
31477 xref->data.value.ptrvalue = prp;
31478 xref->next = sfp->xref;
31479 sfp->xref = xref;
31480 }
31481 if (prp != NULL) {
31482 prp->desc = StringSave (prot_desc);
31483 }
31484
31485 }
31486
31487
BulkCDSGetProteinDesc(Uint1 data_choice,Pointer data,Pointer metadata)31488 static Pointer BulkCDSGetProteinDesc (Uint1 data_choice, Pointer data, Pointer metadata)
31489 {
31490 SeqFeatXrefPtr xref;
31491 ProtRefPtr prp = NULL;
31492 BioseqPtr prot_bsp;
31493 SeqFeatPtr prot_feat;
31494 SeqMgrFeatContext fcontext;
31495 CharPtr prot_desc = NULL;
31496 SeqFeatPtr sfp = (SeqFeatPtr) data;
31497
31498 if (sfp == NULL) return NULL;
31499
31500 xref = sfp->xref;
31501 while (xref != NULL && xref->data.choice != SEQFEAT_PROT) {
31502 xref = xref->next;
31503 }
31504 if (xref != NULL) {
31505 prp = xref->data.value.ptrvalue;
31506 }
31507
31508 if (prp == NULL) {
31509 if (sfp->data.choice == SEQFEAT_PROT) {
31510 prp = (ProtRefPtr) sfp->data.value.ptrvalue;
31511 } else if (sfp->data.choice == SEQFEAT_CDREGION) {
31512 prot_bsp = BioseqFindFromSeqLoc (sfp->product);
31513 prot_feat = SeqMgrGetNextFeature (prot_bsp, NULL, SEQFEAT_PROT, FEATDEF_PROT, &fcontext);
31514 if (prot_feat != NULL) {
31515 prp = (ProtRefPtr) prot_feat->data.value.ptrvalue;
31516 }
31517 }
31518 }
31519
31520 if (prp != NULL) {
31521 prot_desc = StringSave (prp->desc);
31522 }
31523
31524 return prot_desc;
31525 }
31526
31527
BulkGeneSetLocus(Pointer target,Pointer data)31528 static void BulkGeneSetLocus (Pointer target, Pointer data)
31529 {
31530 CharPtr str = (CharPtr) data;
31531 GeneRefPtr grp;
31532 SeqFeatPtr sfp = (SeqFeatPtr) target;
31533
31534 if (sfp == NULL || sfp->idx.subtype != FEATDEF_GENE) return;
31535
31536 grp = (GeneRefPtr) sfp->data.value.ptrvalue;
31537 if (grp == NULL) {
31538 grp = GeneRefNew();
31539 sfp->data.value.ptrvalue = grp;
31540 }
31541 grp->locus = MemFree (grp->locus);
31542 if (str != NULL) {
31543 grp->locus = StringSave (str);
31544 }
31545 }
31546
BulkGeneGetLocus(Uint1 data_choice,Pointer data,Pointer metadata)31547 static Pointer BulkGeneGetLocus (Uint1 data_choice, Pointer data, Pointer metadata)
31548 {
31549 GeneRefPtr grp;
31550 SeqFeatPtr sfp = (SeqFeatPtr) data;
31551
31552 if (sfp == NULL || sfp->idx.subtype != FEATDEF_GENE || sfp->data.value.ptrvalue == NULL) {
31553 return NULL;
31554 }
31555 grp = (GeneRefPtr) sfp->data.value.ptrvalue;
31556 if (StringHasNoText (grp->locus)) {
31557 return NULL;
31558 } else {
31559 return (Pointer) StringSave (grp->locus);
31560 }
31561 }
31562
BulkGeneSetLocusTag(Pointer target,Pointer data)31563 static void BulkGeneSetLocusTag (Pointer target, Pointer data)
31564 {
31565 CharPtr str = (CharPtr) data;
31566 GeneRefPtr grp;
31567 SeqFeatPtr sfp = (SeqFeatPtr) target;
31568
31569 if (sfp == NULL || sfp->idx.subtype != FEATDEF_GENE) return;
31570
31571 grp = (GeneRefPtr) sfp->data.value.ptrvalue;
31572 if (grp == NULL) {
31573 grp = GeneRefNew();
31574 sfp->data.value.ptrvalue = grp;
31575 }
31576 grp->locus_tag = MemFree (grp->locus_tag);
31577 if (str != NULL) {
31578 grp->locus_tag = StringSave (str);
31579 }
31580 }
31581
BulkGeneGetLocusTag(Uint1 data_choice,Pointer data,Pointer metadata)31582 static Pointer BulkGeneGetLocusTag (Uint1 data_choice, Pointer data, Pointer metadata)
31583 {
31584 GeneRefPtr grp;
31585 SeqFeatPtr sfp = (SeqFeatPtr) data;
31586
31587 if (sfp == NULL || sfp->idx.subtype != FEATDEF_GENE || sfp->data.value.ptrvalue == NULL) {
31588 return NULL;
31589 }
31590 grp = (GeneRefPtr) sfp->data.value.ptrvalue;
31591 if (StringHasNoText (grp->locus_tag)) {
31592 return NULL;
31593 } else {
31594 return (Pointer) StringSave (grp->locus_tag);
31595 }
31596 }
31597
BulkGeneSetDescription(Pointer target,Pointer data)31598 static void BulkGeneSetDescription (Pointer target, Pointer data)
31599 {
31600 CharPtr str = (CharPtr) data;
31601 GeneRefPtr grp;
31602 SeqFeatPtr sfp = (SeqFeatPtr) target;
31603
31604 if (sfp == NULL || sfp->idx.subtype != FEATDEF_GENE) return;
31605
31606 grp = (GeneRefPtr) sfp->data.value.ptrvalue;
31607 if (grp == NULL) {
31608 grp = GeneRefNew();
31609 sfp->data.value.ptrvalue = grp;
31610 }
31611 grp->desc = MemFree (grp->desc);
31612 if (str != NULL) {
31613 grp->desc = StringSave (str);
31614 }
31615 }
31616
BulkGeneGetDescription(Uint1 data_choice,Pointer data,Pointer metadata)31617 static Pointer BulkGeneGetDescription (Uint1 data_choice, Pointer data, Pointer metadata)
31618 {
31619 GeneRefPtr grp;
31620 SeqFeatPtr sfp = (SeqFeatPtr) data;
31621
31622 if (sfp == NULL || sfp->idx.subtype != FEATDEF_GENE || sfp->data.value.ptrvalue == NULL) {
31623 return NULL;
31624 }
31625 grp = (GeneRefPtr) sfp->data.value.ptrvalue;
31626 if (StringHasNoText (grp->desc)) {
31627 return NULL;
31628 } else {
31629 return (Pointer) StringSave (grp->desc);
31630 }
31631 }
31632
31633
BulkRNASetProduct(Pointer target,Pointer data)31634 static void BulkRNASetProduct (Pointer target, Pointer data)
31635 {
31636 RnaRefPtr rrp;
31637 CharPtr rna_product;
31638 SeqFeatPtr sfp = (SeqFeatPtr) target;
31639
31640 if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA) return;
31641
31642 rna_product = (CharPtr) data;
31643
31644 rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
31645 if (rrp == NULL && !StringHasNoText (rna_product)) {
31646 rrp = RnaRefNew ();
31647 rrp->ext.choice = 1;
31648 sfp->data.value.ptrvalue = rrp;
31649 }
31650 if (rrp == NULL) return;
31651 if (rrp->ext.choice == 0 && !StringHasNoText (rna_product)) {
31652 rrp->ext.choice = 1;
31653 } else if (rrp->ext.choice == 1 && StringHasNoText (rna_product)) {
31654 rrp->ext.choice = 0;
31655 rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
31656 }
31657
31658 if (rrp->ext.choice == 1) {
31659 rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
31660 rrp->ext.value.ptrvalue = StringSave (rna_product);
31661 }
31662 }
31663
BulkRNAGetProduct(Uint1 data_choice,Pointer data,Pointer metadata)31664 static Pointer BulkRNAGetProduct (Uint1 data_choice, Pointer data, Pointer metadata)
31665 {
31666 RnaRefPtr rrp;
31667 CharPtr rna_product = NULL;
31668 SeqFeatPtr sfp = (SeqFeatPtr) data;
31669
31670 if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA) return NULL;
31671
31672 rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
31673 if (rrp != NULL) {
31674 if (rrp->ext.choice == 1) {
31675 rna_product = StringSave( rrp->ext.value.ptrvalue);
31676 }
31677 }
31678
31679
31680 return rna_product;
31681 }
31682
IsBulkEditableRNA(SeqFeatPtr sfp)31683 static Boolean IsBulkEditableRNA (SeqFeatPtr sfp)
31684 {
31685 RnaRefPtr rrp;
31686
31687 if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA) {
31688 return FALSE;
31689 }
31690 rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
31691 if (rrp != NULL && rrp->ext.choice != 1 && rrp->ext.choice != 0) {
31692 return FALSE;
31693 } else {
31694 return TRUE;
31695 }
31696 }
31697
31698
31699 /* template for setting simple text strings */
BulkSetSimpleTextString(Pointer curr_val,ApplyValuePtr avp)31700 NLM_EXTERN Pointer BulkSetSimpleTextString (Pointer curr_val, ApplyValuePtr avp)
31701 {
31702 CharPtr curr_val_str;
31703
31704 curr_val_str = (CharPtr)curr_val;
31705 return HandleApplyValue (curr_val_str, avp);
31706 }
31707
31708 /* for now, disallow pseudo editing and display. To add back, put in this line:
31709 { "pseudo", BulkSetPseudo, BulkGetPseudo, NULL, NULL, NULL, BulkFormatTrueFalse, BulkDrawTrueFalse, BulkReleaseTrueFalse },
31710 */
31711 /* for now, disallow location editing (but continue display). To add back, use BulkNucLocationDialog in dialog. */
31712 static BulkEdFieldData bulk_cds_fields[] = {
31713 { "protein name ", BulkCDSSetProtein, BulkCDSSetProteinString, BulkCDSGetProtein, BulkCDSDisplayProtein, BulkCDSFreeProtein, BulkCDSProteinDialog, BulkCDSFormatProtein, NULL, NULL, BulkCDSCopyProtein },
31714 { "protein description", BulkCDSSetProteinDesc, BulkSetSimpleTextString, BulkCDSGetProteinDesc, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
31715 { "location", BulkSetLocation, NULL, BulkGetLocation, BulkDisplayLocation, BulkFreeLocation, NULL, BulkFormatLocation, NULL, NULL, BulkCopyLocation },
31716 { "comment", BulkSetComment, BulkSetSimpleTextString, BulkGetComment, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextScrollDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
31717 { NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL}};
31718
31719 static BulkEdFieldData bulk_gene_fields[] = {
31720 { "locus", BulkGeneSetLocus, BulkSetSimpleTextString, BulkGeneGetLocus, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
31721 { "locus_tag", BulkGeneSetLocusTag, BulkSetSimpleTextString, BulkGeneGetLocusTag, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
31722 { "description", BulkGeneSetDescription, BulkSetSimpleTextString, BulkGeneGetDescription, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
31723 { "location", BulkSetLocation, NULL, BulkGetLocation, BulkDisplayLocation, BulkFreeLocation, NULL, BulkFormatLocation, NULL, NULL, BulkCopyLocation },
31724 { "comment", BulkSetComment, BulkSetSimpleTextString, BulkGetComment, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextScrollDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
31725 { NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL}};
31726
31727 static BulkEdFieldData bulk_rna_fields[] = {
31728 { "product", BulkRNASetProduct, BulkSetSimpleTextString, BulkRNAGetProduct, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
31729 { "location", BulkSetLocation, NULL, BulkGetLocation, BulkDisplayLocation, BulkFreeLocation, NULL, BulkFormatLocation, NULL, NULL, BulkCopyLocation },
31730 { "comment", BulkSetComment, BulkSetSimpleTextString, BulkGetComment, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextScrollDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
31731 { NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL}};
31732
31733
GetBulkEditorFieldListForFeature(SeqFeatPtr sfp)31734 static BulkEdFieldPtr GetBulkEditorFieldListForFeature (SeqFeatPtr sfp)
31735 {
31736 if (sfp == NULL) {
31737 return NULL;
31738 } else if (sfp->data.choice == SEQFEAT_CDREGION) {
31739 return bulk_cds_fields;
31740 } else if (sfp->data.choice == SEQFEAT_GENE) {
31741 return bulk_gene_fields;
31742 } else if (sfp->data.choice == SEQFEAT_RNA && IsBulkEditableRNA(sfp)) {
31743 /* Note - using FEATDEF_rRNA to represent all editable rRNA features */
31744 return bulk_rna_fields;
31745 } else {
31746 return NULL;
31747 }
31748 }
31749
31750
BulkSrcSetTaxNameDesc(Pointer target,Pointer data)31751 static void BulkSrcSetTaxNameDesc (Pointer target, Pointer data)
31752 {
31753 CharPtr taxname;
31754 SeqDescrPtr sdp = (SeqDescrPtr) target;
31755 BioSourcePtr biop;
31756
31757 if (sdp == NULL || sdp->choice != Seq_descr_source || sdp->data.ptrvalue == NULL) return;
31758
31759 biop = (BioSourcePtr) sdp->data.ptrvalue;
31760
31761 taxname = (CharPtr) data;
31762
31763 if (biop->org == NULL) {
31764 biop->org = OrgRefNew();
31765 }
31766 SetTaxNameAndRemoveTaxRef (biop->org, StringSave (taxname));
31767 }
31768
31769
31770 NLM_EXTERN BioSourcePtr GetBioSourceFromObject (Uint1 choice, Pointer data);
31771
BulkSrcGetTaxNameDesc(Uint1 data_choice,Pointer data,Pointer metadata)31772 static Pointer BulkSrcGetTaxNameDesc (Uint1 data_choice, Pointer data, Pointer metadata)
31773 {
31774 CharPtr taxname = NULL;
31775 BioSourcePtr biop = NULL;
31776
31777 biop = GetBioSourceFromObject (data_choice, data);
31778 if (biop == NULL) return NULL;
31779
31780 if (biop->org != NULL) {
31781 taxname = StringSave (biop->org->taxname);
31782 }
31783
31784 return taxname;
31785 }
31786
31787
BulkSrcSetTaxNameFeat(Pointer target,Pointer data)31788 static void BulkSrcSetTaxNameFeat (Pointer target, Pointer data)
31789 {
31790 CharPtr taxname;
31791 SeqFeatPtr sfp = (SeqFeatPtr) target;
31792 BioSourcePtr biop;
31793
31794 if (sfp == NULL || sfp->data.choice != SEQFEAT_BIOSRC || sfp->data.value.ptrvalue == NULL) return;
31795
31796 biop = (BioSourcePtr) sfp->data.value.ptrvalue;
31797
31798 taxname = (CharPtr) data;
31799
31800 if (biop->org == NULL) {
31801 biop->org = OrgRefNew();
31802 }
31803 SetTaxNameAndRemoveTaxRef (biop->org, StringSave (taxname));
31804 }
31805
31806
BulkSrcGetTaxNameFeat(Uint1 data_choice,Pointer data,Pointer metadata)31807 static Pointer BulkSrcGetTaxNameFeat (Uint1 data_choice, Pointer data, Pointer metadata)
31808 {
31809 CharPtr taxname = NULL;
31810 SeqFeatPtr sfp = (SeqFeatPtr) data;
31811 BioSourcePtr biop;
31812
31813 if (sfp == NULL || sfp->data.choice != SEQFEAT_BIOSRC || sfp->data.value.ptrvalue == NULL) return NULL;
31814
31815 biop = (BioSourcePtr) sfp->data.value.ptrvalue;
31816
31817 if (biop->org != NULL) {
31818 taxname = StringSave (biop->org->taxname);
31819 }
31820
31821 return taxname;
31822 }
31823
31824
BulkSrcGetSubSrcModDesc(Uint1 data_choice,Pointer data,Uint2 mod_type)31825 static Pointer BulkSrcGetSubSrcModDesc (Uint1 data_choice, Pointer data, Uint2 mod_type)
31826 {
31827 CharPtr val = NULL;
31828 BioSourcePtr biop = NULL;
31829 SubSourcePtr ssp;
31830
31831 biop = GetBioSourceFromObject (data_choice, data);
31832 if (biop == NULL) return NULL;
31833
31834 ssp = biop->subtype;
31835 while (ssp != NULL && ssp->subtype != mod_type) {
31836 ssp = ssp->next;
31837 }
31838 if (ssp != NULL) {
31839 val = StringSave (ssp->name);
31840 }
31841
31842 return val;
31843 }
31844
31845
BulkSrcSetSubSrcModDesc(Pointer target,Pointer data,Uint2 mod_type)31846 static void BulkSrcSetSubSrcModDesc (Pointer target, Pointer data, Uint2 mod_type)
31847 {
31848 CharPtr val;
31849 SeqDescrPtr sdp = (SeqDescrPtr) target;
31850 BioSourcePtr biop;
31851 SubSourcePtr ssp, ssp_last = NULL;
31852
31853 if (sdp == NULL || sdp->choice != Seq_descr_source || sdp->data.ptrvalue == NULL) return;
31854
31855 biop = (BioSourcePtr) sdp->data.ptrvalue;
31856
31857 val = (CharPtr) data;
31858
31859 ssp = biop->subtype;
31860 while (ssp != NULL && ssp->subtype != mod_type) {
31861 ssp_last = ssp;
31862 ssp = ssp->next;
31863 }
31864 if (ssp == NULL) {
31865 ssp = SubSourceNew();
31866 ssp->subtype = mod_type;
31867 if (ssp_last == NULL) {
31868 biop->subtype = ssp;
31869 } else {
31870 ssp_last->next = ssp;
31871 }
31872 }
31873 ssp->name = MemFree (ssp->name);
31874 ssp->name = StringSave (val);
31875 }
31876
31877
31878 #define BULK_SRC_GET_AND_SET_SUBSRC(Name,Type) \
31879 static Pointer BulkSrcGet##Name (Uint1 data_choice, Pointer data, Pointer metadata) \
31880 { \
31881 return BulkSrcGetSubSrcModDesc(data_choice, data, SUBSRC_##Type); \
31882 } \
31883 static void BulkSrcSet##Name (Pointer target, Pointer data) \
31884 { \
31885 BulkSrcSetSubSrcModDesc(target, data, SUBSRC_##Type); \
31886 }
31887
31888
BulkSrcGetSubSrcModDescTF(Uint1 data_choice,Pointer data,Uint2 mod_type)31889 static Pointer BulkSrcGetSubSrcModDescTF (Uint1 data_choice, Pointer data, Uint2 mod_type)
31890 {
31891 CharPtr val = NULL;
31892 BioSourcePtr biop = NULL;
31893 SubSourcePtr ssp;
31894
31895 biop = GetBioSourceFromObject (data_choice, data);
31896 if (biop == NULL) return NULL;
31897
31898 ssp = biop->subtype;
31899 while (ssp != NULL && ssp->subtype != mod_type) {
31900 ssp = ssp->next;
31901 }
31902 if (ssp != NULL) {
31903 val = StringSave ("TRUE");
31904 }
31905
31906 return val;
31907 }
31908
31909
BulkSrcSetSubSrcModDescTF(Pointer target,Pointer data,Uint2 mod_type)31910 static void BulkSrcSetSubSrcModDescTF (Pointer target, Pointer data, Uint2 mod_type)
31911 {
31912 CharPtr val;
31913 SeqDescrPtr sdp = (SeqDescrPtr) target;
31914 BioSourcePtr biop;
31915 SubSourcePtr ssp, ssp_last = NULL;
31916
31917 if (sdp == NULL || sdp->choice != Seq_descr_source || sdp->data.ptrvalue == NULL) return;
31918
31919 biop = (BioSourcePtr) sdp->data.ptrvalue;
31920
31921 val = (CharPtr) data;
31922
31923 ssp = biop->subtype;
31924 while (ssp != NULL && ssp->subtype != mod_type) {
31925 ssp_last = ssp;
31926 ssp = ssp->next;
31927 }
31928 if (StringHasNoText ((CharPtr)val)) {
31929 if (ssp != NULL) {
31930 if (ssp_last == NULL) {
31931 biop->subtype = ssp->next;
31932 } else {
31933 ssp_last->next = ssp->next;
31934 }
31935 ssp->next = NULL;
31936 ssp = SubSourceFree (ssp);
31937 }
31938 } else {
31939 if (ssp == NULL) {
31940 ssp = SubSourceNew();
31941 ssp->subtype = mod_type;
31942 if (ssp_last == NULL) {
31943 biop->subtype = ssp;
31944 } else {
31945 ssp_last->next = ssp;
31946 }
31947 }
31948 ssp->name = MemFree (ssp->name);
31949 ssp->name = StringSave (" ");
31950 }
31951 }
31952
31953
31954 #define BULK_SRC_GET_AND_SET_SUBSRC_TF(Name,Type) \
31955 static Pointer BulkSrcGet##Name (Uint1 data_choice, Pointer data, Pointer metadata) \
31956 { \
31957 return BulkSrcGetSubSrcModDescTF(data_choice, data, SUBSRC_##Type); \
31958 } \
31959 static void BulkSrcSet##Name (Pointer target, Pointer data) \
31960 { \
31961 BulkSrcSetSubSrcModDescTF(target, data, SUBSRC_##Type); \
31962 }
31963
31964
BulkSrcGetOrgModDesc(Uint1 data_choice,Pointer data,Uint2 mod_type)31965 static Pointer BulkSrcGetOrgModDesc (Uint1 data_choice, Pointer data, Uint2 mod_type)
31966 {
31967 CharPtr val = NULL;
31968 BioSourcePtr biop = NULL;
31969 OrgModPtr mod;
31970
31971 biop = GetBioSourceFromObject (data_choice, data);
31972 if (biop == NULL || biop->org == NULL || biop->org->orgname == NULL) return NULL;
31973
31974 mod = biop->org->orgname->mod;
31975 while (mod != NULL && mod->subtype != mod_type) {
31976 mod = mod->next;
31977 }
31978 if (mod != NULL) {
31979 val = StringSave (mod->subname);
31980 }
31981
31982 return val;
31983 }
31984
31985
BulkSrcSetOrgModDesc(Pointer target,Pointer data,Uint2 mod_type)31986 static void BulkSrcSetOrgModDesc (Pointer target, Pointer data, Uint2 mod_type)
31987 {
31988 CharPtr val;
31989 SeqDescrPtr sdp = (SeqDescrPtr) target;
31990 BioSourcePtr biop;
31991 OrgModPtr mod, mod_last = NULL;
31992
31993 if (sdp == NULL || sdp->choice != Seq_descr_source || sdp->data.ptrvalue == NULL) return;
31994
31995 biop = (BioSourcePtr) sdp->data.ptrvalue;
31996
31997 val = (CharPtr) data;
31998
31999 if (biop->org == NULL) {
32000 biop->org = OrgRefNew ();
32001 }
32002 if (biop->org->orgname == NULL) {
32003 biop->org->orgname = OrgNameNew ();
32004 }
32005
32006 mod = biop->org->orgname->mod;
32007 while (mod != NULL && mod->subtype != mod_type) {
32008 mod_last = mod;
32009 mod = mod->next;
32010 }
32011 if (mod == NULL) {
32012 mod = OrgModNew();
32013 mod->subtype = mod_type;
32014 if (mod_last == NULL) {
32015 biop->org->orgname->mod = mod;
32016 } else {
32017 mod_last->next = mod;
32018 }
32019 }
32020 mod->subname = MemFree (mod->subname);
32021 mod->subname = StringSave (val);
32022 }
32023
32024
32025 #define BULK_SRC_GET_AND_SET_ORGMOD(Name,Type) \
32026 static Pointer BulkSrcGet##Name (Uint1 data_choice, Pointer data, Pointer metadata) \
32027 { \
32028 return BulkSrcGetOrgModDesc(data_choice, data, ORGMOD_##Type); \
32029 } \
32030 static void BulkSrcSet##Name (Pointer target, Pointer data) \
32031 { \
32032 BulkSrcSetOrgModDesc(target, data, ORGMOD_##Type); \
32033 }
32034
32035
BulkSrcGetOrgModDescTF(Uint1 data_choice,Pointer data,Uint2 mod_type)32036 static Pointer BulkSrcGetOrgModDescTF (Uint1 data_choice, Pointer data, Uint2 mod_type)
32037 {
32038 CharPtr val = NULL;
32039 BioSourcePtr biop = NULL;
32040 OrgModPtr mod;
32041
32042 biop = GetBioSourceFromObject (data_choice, data);
32043 if (biop == NULL || biop->org == NULL || biop->org->orgname == NULL) return NULL;
32044
32045 mod = biop->org->orgname->mod;
32046 while (mod != NULL && mod->subtype != mod_type) {
32047 mod = mod->next;
32048 }
32049 if (mod != NULL) {
32050 val = StringSave ("TRUE");
32051 }
32052
32053 return val;
32054 }
32055
32056
BulkSrcSetOrgModDescTF(Pointer target,Pointer data,Uint2 mod_type)32057 static void BulkSrcSetOrgModDescTF (Pointer target, Pointer data, Uint2 mod_type)
32058 {
32059 CharPtr val;
32060 SeqDescrPtr sdp = (SeqDescrPtr) target;
32061 BioSourcePtr biop;
32062 OrgModPtr mod, mod_last = NULL;
32063
32064 if (sdp == NULL || sdp->choice != Seq_descr_source || sdp->data.ptrvalue == NULL) return;
32065
32066 biop = (BioSourcePtr) sdp->data.ptrvalue;
32067 if (biop == NULL) return;
32068
32069 val = (CharPtr) data;
32070
32071 if (biop->org == NULL) {
32072 biop->org = OrgRefNew ();
32073 }
32074 if (biop->org->orgname == NULL) {
32075 biop->org->orgname = OrgNameNew ();
32076 }
32077
32078 mod = biop->org->orgname->mod;
32079 while (mod != NULL && mod->subtype != mod_type) {
32080 mod = mod->next;
32081 }
32082
32083 if (StringHasNoText ((CharPtr)val)) {
32084 /* remove */
32085 if (mod != NULL) {
32086 if (mod_last == NULL) {
32087 biop->org->orgname->mod = mod->next;
32088 } else {
32089 mod_last->next = mod->next;
32090 }
32091 mod->next = NULL;
32092 mod = OrgModFree (mod);
32093 }
32094 } else {
32095 /* set */
32096 if (mod == NULL) {
32097 mod = OrgModNew();
32098 mod->subtype = mod_type;
32099 if (mod_last == NULL) {
32100 biop->org->orgname->mod = mod;
32101 } else {
32102 mod_last->next = mod;
32103 }
32104 }
32105 mod->subname = MemFree (mod->subname);
32106 mod->subname = StringSave (" ");
32107 }
32108 }
32109
32110
32111 #define BULK_SRC_GET_AND_SET_ORGMOD_TF(Name,Type) \
32112 static Pointer BulkSrcGet##Name (Uint1 data_choice, Pointer data, Pointer metadata) \
32113 { \
32114 return BulkSrcGetOrgModDescTF(data_choice, data, SUBSRC_##Type); \
32115 } \
32116 static void BulkSrcSet##Name (Pointer target, Pointer data) \
32117 { \
32118 BulkSrcSetOrgModDescTF(target, data, SUBSRC_##Type); \
32119 }
32120
32121
BULK_SRC_GET_AND_SET_ORGMOD(Acronym,acronym)32122 BULK_SRC_GET_AND_SET_ORGMOD(Acronym,acronym)
32123 BULK_SRC_GET_AND_SET_ORGMOD(Anamorph,anamorph)
32124 BULK_SRC_GET_AND_SET_ORGMOD(Authority,authority)
32125 BULK_SRC_GET_AND_SET_ORGMOD(Bio_material,bio_material)
32126 BULK_SRC_GET_AND_SET_ORGMOD(Biotype,biotype)
32127 BULK_SRC_GET_AND_SET_ORGMOD(Biovar,biovar)
32128 BULK_SRC_GET_AND_SET_ORGMOD(Breed,breed)
32129 BULK_SRC_GET_AND_SET_ORGMOD(Chemovar,chemovar)
32130 BULK_SRC_GET_AND_SET_ORGMOD(Common,common)
32131 BULK_SRC_GET_AND_SET_ORGMOD(Cultivar,cultivar)
32132 BULK_SRC_GET_AND_SET_ORGMOD(Culture_collection,culture_collection)
32133 BULK_SRC_GET_AND_SET_ORGMOD(Ecotype,ecotype)
32134 BULK_SRC_GET_AND_SET_ORGMOD(Forma,forma)
32135 BULK_SRC_GET_AND_SET_ORGMOD(Forma_specialis,forma_specialis)
32136 BULK_SRC_GET_AND_SET_ORGMOD(Group,group)
32137 BULK_SRC_GET_AND_SET_ORGMOD(Host,nat_host)
32138 BULK_SRC_GET_AND_SET_ORGMOD(Isolate,isolate)
32139 BULK_SRC_GET_AND_SET_ORGMOD(Metagenome_source,metagenome_source)
32140 BULK_SRC_GET_AND_SET_ORGMOD(Pathovar,pathovar)
32141 BULK_SRC_GET_AND_SET_ORGMOD(Serogroup,serogroup)
32142 BULK_SRC_GET_AND_SET_ORGMOD(Serotype,serotype)
32143 BULK_SRC_GET_AND_SET_ORGMOD(Serovar,serovar)
32144 BULK_SRC_GET_AND_SET_ORGMOD(Specimen_voucher,specimen_voucher)
32145 BULK_SRC_GET_AND_SET_ORGMOD(Strain,strain)
32146 BULK_SRC_GET_AND_SET_ORGMOD(Subgroup,subgroup)
32147 BULK_SRC_GET_AND_SET_ORGMOD(Sub_species,sub_species)
32148 BULK_SRC_GET_AND_SET_ORGMOD(Substrain,substrain)
32149 BULK_SRC_GET_AND_SET_ORGMOD(Subtype,subtype)
32150 BULK_SRC_GET_AND_SET_ORGMOD(Synonym,synonym)
32151 BULK_SRC_GET_AND_SET_ORGMOD(Teleomorph,teleomorph)
32152 BULK_SRC_GET_AND_SET_ORGMOD(Type,type)
32153 BULK_SRC_GET_AND_SET_ORGMOD(Variety,variety)
32154 BULK_SRC_GET_AND_SET_ORGMOD(OrgModNote,other)
32155 BULK_SRC_GET_AND_SET_SUBSRC(Cell_line,cell_line)
32156 BULK_SRC_GET_AND_SET_SUBSRC(Cell_type,cell_type)
32157 BULK_SRC_GET_AND_SET_SUBSRC(Chromosome,chromosome)
32158 BULK_SRC_GET_AND_SET_SUBSRC(Clone,clone)
32159 BULK_SRC_GET_AND_SET_SUBSRC(Clone_lib,clone_lib)
32160 BULK_SRC_GET_AND_SET_SUBSRC(Collected_by,collected_by)
32161 BULK_SRC_GET_AND_SET_SUBSRC(Collection_date,collection_date)
32162 BULK_SRC_GET_AND_SET_SUBSRC(Country,country)
32163 BULK_SRC_GET_AND_SET_SUBSRC(Dev_stage,dev_stage)
32164 BULK_SRC_GET_AND_SET_SUBSRC(Endogenous_virus_name,endogenous_virus_name)
32165 BULK_SRC_GET_AND_SET_SUBSRC_TF(Environmental_sample,environmental_sample)
32166 BULK_SRC_GET_AND_SET_SUBSRC(Frequency,frequency)
32167 BULK_SRC_GET_AND_SET_SUBSRC(Genotype,genotype)
32168 BULK_SRC_GET_AND_SET_SUBSRC_TF(Germline,germline)
32169 BULK_SRC_GET_AND_SET_SUBSRC(Haplogroup,haplogroup)
32170 BULK_SRC_GET_AND_SET_SUBSRC(Haplotype,haplotype)
32171 BULK_SRC_GET_AND_SET_SUBSRC(Identified_by,identified_by)
32172 BULK_SRC_GET_AND_SET_SUBSRC(Isolation_source,isolation_source)
32173 BULK_SRC_GET_AND_SET_SUBSRC(Lab_host,lab_host)
32174 BULK_SRC_GET_AND_SET_SUBSRC(Lat_Lon,lat_lon)
32175 BULK_SRC_GET_AND_SET_SUBSRC(Linkage_group,linkage_group)
32176 BULK_SRC_GET_AND_SET_SUBSRC(Map,map)
32177 BULK_SRC_GET_AND_SET_SUBSRC(Mating_type,mating_type)
32178 BULK_SRC_GET_AND_SET_SUBSRC_TF(Metagenomic,metagenomic)
32179 BULK_SRC_GET_AND_SET_SUBSRC(Plasmid_name,plasmid_name)
32180 BULK_SRC_GET_AND_SET_SUBSRC(Pop_variant,pop_variant)
32181 BULK_SRC_GET_AND_SET_SUBSRC_TF(Rearranged,rearranged)
32182 BULK_SRC_GET_AND_SET_SUBSRC(Segment,segment)
32183 BULK_SRC_GET_AND_SET_SUBSRC(Sex,sex)
32184 BULK_SRC_GET_AND_SET_SUBSRC(Subclone,subclone)
32185 BULK_SRC_GET_AND_SET_SUBSRC(Tissue_lib,tissue_lib)
32186 BULK_SRC_GET_AND_SET_SUBSRC(Tissue_type,tissue_type)
32187 BULK_SRC_GET_AND_SET_SUBSRC_TF(Transgenic,transgenic)
32188 BULK_SRC_GET_AND_SET_SUBSRC(SubSrcNote,other)
32189
32190
32191 #define BULK_SRC_SUBSRC_FIELD_TF(Name) \
32192 BulkSrcSet##Name, BulkSetSimpleTextString, BulkSrcGet##Name, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy
32193
32194
32195 static ValNodePtr StringsToDbxrefList (ValNodePtr strings)
32196 {
32197 ValNodePtr dbxref_list = NULL, vnp;
32198 DbtagPtr dbtag;
32199
32200 for (vnp = strings; vnp != NULL; vnp = vnp->next)
32201 {
32202 dbtag = DbtagNew();
32203 SetDbtagString (dbtag, vnp->data.ptrvalue, ExistingTextOption_replace_old);
32204 ValNodeAddPointer (&dbxref_list, vnp->choice, dbtag);
32205 }
32206 return dbxref_list;
32207 }
32208
32209
DbxrefListToStrings(ValNodePtr dbxref_list)32210 static ValNodePtr DbxrefListToStrings (ValNodePtr dbxref_list)
32211 {
32212 ValNodePtr strings = NULL, vnp;
32213 DbtagPtr dbtag;
32214
32215 for (vnp = dbxref_list; vnp != NULL; vnp = vnp->next)
32216 {
32217 dbtag = (DbtagPtr) vnp->data.ptrvalue;
32218 ValNodeAddPointer (&strings, vnp->choice, GetDbtagString (dbtag));
32219 }
32220 return strings;
32221 }
32222
32223
FreeDbxrefList(ValNodePtr list)32224 static ValNodePtr FreeDbxrefList (ValNodePtr list)
32225 {
32226 ValNodePtr vnp;
32227
32228 for (vnp = list; vnp != NULL; vnp = vnp->next) {
32229 vnp->data.ptrvalue = DbtagFree (vnp->data.ptrvalue);
32230 }
32231 list = ValNodeFree (list);
32232 return list;
32233 }
32234
32235
32236
32237
BulkSrcGetDbxref(Uint1 data_choice,Pointer data,Pointer metadata)32238 static Pointer BulkSrcGetDbxref (Uint1 data_choice, Pointer data, Pointer metadata)
32239 {
32240 SeqDescrPtr sdp = (SeqDescrPtr) data;
32241 BioSourcePtr biop;
32242 ValNodePtr dbxref_list = NULL;
32243
32244 if (sdp == NULL || sdp->choice != Seq_descr_source
32245 || (biop = (BioSourcePtr)sdp->data.ptrvalue) == NULL
32246 || biop->org == NULL)
32247 {
32248 return NULL;
32249 }
32250
32251 dbxref_list = DbxrefListToStrings (biop->org->db);
32252
32253 return dbxref_list;
32254 }
32255
32256
BulkSrcSetDbxref(Pointer target,Pointer data)32257 static void BulkSrcSetDbxref (Pointer target, Pointer data)
32258 {
32259 ValNodePtr dbxref_list;
32260 SeqDescrPtr sdp = (SeqDescrPtr) target;
32261 BioSourcePtr biop;
32262
32263 if (sdp == NULL || sdp->choice != Seq_descr_source || sdp->data.ptrvalue == NULL) return;
32264
32265 biop = (BioSourcePtr) sdp->data.ptrvalue;
32266 if (biop == NULL) return;
32267 dbxref_list = (ValNodePtr) data;
32268 if (biop->org == NULL && dbxref_list == NULL) {
32269 return;
32270 }
32271 if (biop->org == NULL) {
32272 biop->org = OrgRefNew();
32273 }
32274
32275 /* erase previous dbxrefs */
32276 biop->org->db = FreeDbxrefList (biop->org->db);
32277 biop->org->db = StringsToDbxrefList (dbxref_list);
32278 }
32279
32280
BulkSrcFormatDbxref(ColPtr col,CharPtr name)32281 static Int4 BulkSrcFormatDbxref (ColPtr col, CharPtr name)
32282 {
32283 if (col == NULL) return 0;
32284
32285 col->pixWidth = MAX (15, StringLen (name)) * MaxCharWidth();
32286 col->pixInset = 0;
32287 col->charWidth = 0;
32288 col->charInset = 0;
32289 col->font = NULL;
32290 col->just = 'l';
32291 col->wrap = 1;
32292 col->bar = 0;
32293 col->underline = 0;
32294 col->left = 0;
32295 return col->pixWidth;
32296 }
32297
32298
BulkSrcDisplayDbxref(Pointer data)32299 static CharPtr BulkSrcDisplayDbxref (Pointer data)
32300 {
32301 ValNodePtr dbxref_list, vnp;
32302 CharPtr dbxref_text;
32303 Int4 text_len = 1;
32304
32305 if (data == NULL) return NULL;
32306 dbxref_list = (ValNodePtr) data;
32307 for (vnp = dbxref_list; vnp != NULL; vnp = vnp->next) {
32308 text_len += StringLen (vnp->data.ptrvalue) + 1;
32309 }
32310 dbxref_text = (CharPtr) MemNew (sizeof (Char) * text_len);
32311 dbxref_text[0] = 0;
32312 for (vnp = dbxref_list; vnp != NULL; vnp = vnp->next) {
32313 StringCat (dbxref_text, vnp->data.ptrvalue);
32314 if (vnp->next != NULL) {
32315 StringCat (dbxref_text, ";");
32316 }
32317 }
32318 return dbxref_text;
32319 }
32320
32321
BulkSrcSetDbxrefString(Pointer curr_val,ApplyValuePtr avp)32322 static Pointer BulkSrcSetDbxrefString (Pointer curr_val, ApplyValuePtr avp)
32323 {
32324 CharPtr curr_val_str;
32325 CharPtr new_str, name_str, cp;
32326 ValNodePtr name_list;
32327
32328 name_list = (ValNodePtr) curr_val;
32329 curr_val_str = BulkSrcDisplayDbxref (name_list);
32330 name_list = ValNodeFreeData (name_list);
32331
32332 new_str = HandleApplyValue (curr_val_str, avp);
32333
32334 name_str = new_str;
32335 cp = StringChr (name_str, ';');
32336 while (cp != NULL) {
32337 *cp = 0;
32338 ValNodeAddPointer (&name_list, 0, StringSave (name_str));
32339 *cp = ';';
32340 name_str = cp + 1;
32341 cp = StringChr (name_str, ';');
32342 }
32343 ValNodeAddPointer (&name_list, 0, StringSave (name_str));
32344 new_str = MemFree (new_str);
32345
32346 return name_list;
32347 }
32348
32349
BulkSrcFreeDbxref(Pointer data)32350 static void BulkSrcFreeDbxref (Pointer data)
32351 {
32352 ValNodePtr prot_name_list = (ValNodePtr) data;
32353
32354 ValNodeFreeData (prot_name_list);
32355 }
32356
32357
BulkSrcCopyDbxref(Pointer data)32358 static Pointer BulkSrcCopyDbxref (Pointer data)
32359 {
32360 ValNodePtr new_list = NULL, list, vnp;
32361
32362 list = (ValNodePtr) data;
32363
32364 for (vnp = list; vnp != NULL; vnp = vnp->next) {
32365 ValNodeAddPointer (&new_list, vnp->choice, StringSave (vnp->data.ptrvalue));
32366 }
32367 return new_list;
32368 }
32369
32370
BulkSrcDbxrefDialog(GrouP g,CharPtr name,SeqEntryPtr sep)32371 static DialoG BulkSrcDbxrefDialog (GrouP g, CharPtr name, SeqEntryPtr sep)
32372 {
32373 return CreateVisibleStringDialog (g, 3, -1, 25);
32374 }
32375
32376
32377 static BulkEdFieldData bulk_src_desc_fields[] = {
32378 { "tax name", BulkSrcSetTaxNameDesc, BulkSetSimpleTextString, BulkSrcGetTaxNameDesc, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32379 { "acronym", BulkSrcSetAcronym, BulkSetSimpleTextString, BulkSrcGetAcronym, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32380 { "anamorph", BulkSrcSetAnamorph, BulkSetSimpleTextString, BulkSrcGetAnamorph, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32381 { "authority", BulkSrcSetAuthority, BulkSetSimpleTextString, BulkSrcGetAuthority, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32382 { "biotype", BulkSrcSetBiotype, BulkSetSimpleTextString, BulkSrcGetBiotype, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32383 { "biovar", BulkSrcSetBiovar, BulkSetSimpleTextString, BulkSrcGetBiovar, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32384 { "bio_material", BulkSrcSetBio_material, BulkSetSimpleTextString, BulkSrcGetBio_material, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32385 { "breed", BulkSrcSetBreed, BulkSetSimpleTextString, BulkSrcGetBreed, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32386 { "cell_line", BulkSrcSetCell_line, BulkSetSimpleTextString, BulkSrcGetCell_line, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32387 { "cell_type", BulkSrcSetCell_type, BulkSetSimpleTextString, BulkSrcGetCell_type, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32388 { "chemovar", BulkSrcSetChemovar, BulkSetSimpleTextString, BulkSrcGetChemovar, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32389 { "chromosome", BulkSrcSetChromosome, BulkSetSimpleTextString, BulkSrcGetChromosome, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32390 { "clone", BulkSrcSetClone, BulkSetSimpleTextString, BulkSrcGetClone, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32391 { "clone_lib", BulkSrcSetClone_lib, BulkSetSimpleTextString, BulkSrcGetClone_lib, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32392 { "collected_by", BulkSrcSetCollected_by, BulkSetSimpleTextString, BulkSrcGetCollected_by, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32393 { "collection_date", BulkSrcSetCollection_date, BulkSetSimpleTextString, BulkSrcGetCollection_date, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32394 { "common", BulkSrcSetCommon, BulkSetSimpleTextString, BulkSrcGetCommon, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32395 { "country", BulkSrcSetCountry, BulkSetSimpleTextString, BulkSrcGetCountry, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32396 { "cultivar", BulkSrcSetCultivar, BulkSetSimpleTextString, BulkSrcGetCultivar, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32397 { "culture_collection", BulkSrcSetCulture_collection, BulkSetSimpleTextString, BulkSrcGetCulture_collection, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32398 { "dbxref", BulkSrcSetDbxref, BulkSrcSetDbxrefString, BulkSrcGetDbxref, BulkSrcDisplayDbxref, BulkSrcFreeDbxref, BulkSrcDbxrefDialog, BulkSrcFormatDbxref, NULL, NULL, BulkSrcCopyDbxref },
32399 { "dev_stage", BulkSrcSetDev_stage, BulkSetSimpleTextString, BulkSrcGetDev_stage, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32400 { "ecotype", BulkSrcSetEcotype, BulkSetSimpleTextString, BulkSrcGetEcotype, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32401 { "endogenous_virus_name", BulkSrcSetEndogenous_virus_name, BulkSetSimpleTextString, BulkSrcGetEndogenous_virus_name, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32402 { "environmental-sample", BULK_SRC_SUBSRC_FIELD_TF(Environmental_sample) },
32403 { "forma", BulkSrcSetForma, BulkSetSimpleTextString, BulkSrcGetForma, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32404 { "forma_specialis", BulkSrcSetForma_specialis, BulkSetSimpleTextString, BulkSrcGetForma_specialis, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32405 { "frequency", BulkSrcSetFrequency, BulkSetSimpleTextString, BulkSrcGetFrequency, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32406 { "genotype", BulkSrcSetGenotype, BulkSetSimpleTextString, BulkSrcGetGenotype, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32407 { "germline", BULK_SRC_SUBSRC_FIELD_TF(Germline) },
32408 { "group", BulkSrcSetGroup, BulkSetSimpleTextString, BulkSrcGetGroup, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32409 { "haplogroup", BulkSrcSetHaplogroup, BulkSetSimpleTextString, BulkSrcGetHaplogroup, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32410 { "haplotype", BulkSrcSetHaplotype, BulkSetSimpleTextString, BulkSrcGetHaplotype, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32411 { "host", BulkSrcSetHost, BulkSetSimpleTextString, BulkSrcGetHost, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32412 { "identified_by", BulkSrcSetIdentified_by, BulkSetSimpleTextString, BulkSrcGetIdentified_by, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32413 { "isolate", BulkSrcSetIsolate, BulkSetSimpleTextString, BulkSrcGetIsolate, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32414 { "isolation_source", BulkSrcSetIsolation_source, BulkSetSimpleTextString, BulkSrcGetIsolation_source, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32415 { "lab_host", BulkSrcSetLab_host, BulkSetSimpleTextString, BulkSrcGetLab_host, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32416 { "lat_Lon", BulkSrcSetLat_Lon, BulkSetSimpleTextString, BulkSrcGetLat_Lon, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32417 { "linkage_group", BulkSrcSetLinkage_group, BulkSetSimpleTextString, BulkSrcGetLinkage_group, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32418 { "map", BulkSrcSetMap, BulkSetSimpleTextString, BulkSrcGetMap, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32419 { "mating_type", BulkSrcSetMating_type, BulkSetSimpleTextString, BulkSrcGetMating_type, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32420 { "metagenome_source", BulkSrcSetMetagenome_source, BulkSetSimpleTextString, BulkSrcGetMetagenome_source, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32421 { "metagenomic", BULK_SRC_SUBSRC_FIELD_TF(Metagenomic) },
32422 { "note (orgmod)", BulkSrcSetOrgModNote, BulkSetSimpleTextString, BulkSrcGetOrgModNote, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32423 { "note (subsrc)", BulkSrcSetSubSrcNote, BulkSetSimpleTextString, BulkSrcGetSubSrcNote, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32424 { "pathovar", BulkSrcSetPathovar, BulkSetSimpleTextString, BulkSrcGetPathovar, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32425 { "plasmid_name", BulkSrcSetPlasmid_name, BulkSetSimpleTextString, BulkSrcGetPlasmid_name, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32426 { "pop_variant", BulkSrcSetPop_variant, BulkSetSimpleTextString, BulkSrcGetPop_variant, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32427 { "rearranged", BULK_SRC_SUBSRC_FIELD_TF(Rearranged) } ,
32428 { "segment", BulkSrcSetSegment, BulkSetSimpleTextString, BulkSrcGetSegment, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32429 { "serogroup", BulkSrcSetSerogroup, BulkSetSimpleTextString, BulkSrcGetSerogroup, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32430 { "serotype", BulkSrcSetSerotype, BulkSetSimpleTextString, BulkSrcGetSerotype, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32431 { "serovar", BulkSrcSetSerovar, BulkSetSimpleTextString, BulkSrcGetSerovar, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32432 { "sex", BulkSrcSetSex, BulkSetSimpleTextString, BulkSrcGetSex, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32433 { "specimen_voucher", BulkSrcSetSpecimen_voucher, BulkSetSimpleTextString, BulkSrcGetSpecimen_voucher, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32434 { "strain", BulkSrcSetStrain, BulkSetSimpleTextString, BulkSrcGetStrain, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32435 { "subclone", BulkSrcSetSubclone, BulkSetSimpleTextString, BulkSrcGetSubclone, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32436 { "subgroup", BulkSrcSetSubgroup, BulkSetSimpleTextString, BulkSrcGetSubgroup, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32437 { "substrain", BulkSrcSetSubstrain, BulkSetSimpleTextString, BulkSrcGetSubstrain, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32438 { "subtype", BulkSrcSetSubtype, BulkSetSimpleTextString, BulkSrcGetSubtype, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32439 { "sub_species", BulkSrcSetSub_species, BulkSetSimpleTextString, BulkSrcGetSub_species, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32440 { "synonym", BulkSrcSetSynonym, BulkSetSimpleTextString, BulkSrcGetSynonym, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32441 { "teleomorph", BulkSrcSetTeleomorph, BulkSetSimpleTextString, BulkSrcGetTeleomorph, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32442 { "tissue_lib", BulkSrcSetTissue_lib, BulkSetSimpleTextString, BulkSrcGetTissue_lib, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32443 { "tissue_type", BulkSrcSetTissue_type, BulkSetSimpleTextString, BulkSrcGetTissue_type, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32444 { "transgenic", BULK_SRC_SUBSRC_FIELD_TF(Transgenic) },
32445 { "type", BulkSrcSetType, BulkSetSimpleTextString, BulkSrcGetType, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32446 { "variety", BulkSrcSetVariety, BulkSetSimpleTextString, BulkSrcGetVariety, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32447 { NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL}};
32448
32449
32450 static BulkEdFieldData bulk_src_feat_fields[] = {
32451 { "tax name", BulkSrcSetTaxNameFeat, BulkSetSimpleTextString, BulkSrcGetTaxNameFeat, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
32452 { NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL}};
32453
32454 typedef struct bulkeditor {
32455 FORM_MESSAGE_BLOCK
32456 DialoG bulk_ed;
32457 ButtoN do_log;
32458 BulkEdFieldPtr field_list;
32459 } BulkEditorData, PNTR BulkEditorPtr;
32460
32461 typedef struct collectfeat {
32462 Uint1 featdef;
32463 Uint1 featchoice;
32464 ValNodePtr feat_list;
32465 } CollectFeatData, PNTR CollectFeatPtr;
32466
CollectFeaturesForBulkEditor(BioseqPtr bsp,Pointer data)32467 static void CollectFeaturesForBulkEditor (BioseqPtr bsp, Pointer data)
32468 {
32469 CollectFeatPtr cfp;
32470 SeqFeatPtr sfp;
32471 SeqMgrFeatContext fcontext;
32472
32473 if (bsp == NULL || data == NULL) return;
32474 cfp = (CollectFeatPtr) data;
32475
32476 for (sfp = SeqMgrGetNextFeature (bsp, NULL, cfp->featchoice, cfp->featdef, &fcontext);
32477 sfp != NULL;
32478 sfp = SeqMgrGetNextFeature (bsp, sfp, cfp->featchoice, cfp->featdef, &fcontext)) {
32479 ValNodeAddPointer (&(cfp->feat_list), OBJ_SEQFEAT, sfp);
32480 }
32481 }
32482
AcceptBulkEditor(ButtoN b)32483 static void AcceptBulkEditor (ButtoN b)
32484 {
32485 BulkEditorPtr bep;
32486
32487 bep = (BulkEditorPtr) GetObjectExtra (b);
32488 if (bep == NULL) return;
32489
32490 WatchCursor();
32491 Update();
32492
32493 ApplyBulkEditorToObjectList (bep->bulk_ed, bep->do_log == NULL ? FALSE : GetStatus (bep->do_log));
32494
32495 ObjMgrSetDirtyFlag (bep->input_entityID, TRUE);
32496 ObjMgrSendMsg (OM_MSG_UPDATE, bep->input_entityID, 0, 0);
32497 ArrowCursor ();
32498 Update ();
32499 Remove (bep->form);
32500 }
32501
GetSubtypeForBulkEdit(ValNodePtr feat_list)32502 extern Uint1 GetSubtypeForBulkEdit (ValNodePtr feat_list)
32503 {
32504 ValNodePtr vnp_check;
32505 SeqFeatPtr sfp;
32506 Uint1 subtype = FEATDEF_BAD;
32507
32508 for (vnp_check = feat_list; vnp_check != NULL; vnp_check = vnp_check->next) {
32509 if (vnp_check->choice != OBJ_SEQFEAT) continue;
32510 sfp = vnp_check->data.ptrvalue;
32511 if (sfp->data.choice == SEQFEAT_RNA) {
32512 /* note - using FEATDEF_rRNA to represent all editable RNA features */
32513 if (!IsBulkEditableRNA(sfp)) {
32514 return FEATDEF_BAD;
32515 } else if (subtype == FEATDEF_BAD) {
32516 subtype = FEATDEF_rRNA;
32517 } else if (subtype != FEATDEF_rRNA) {
32518 return FEATDEF_BAD;
32519 }
32520 } else if (subtype == FEATDEF_BAD) {
32521 subtype = sfp->idx.subtype;
32522 } else if (subtype != sfp->idx.subtype) {
32523 return FEATDEF_BAD;
32524 }
32525 }
32526 return subtype;
32527 }
32528
ExportBulkEditorTableBtn(ButtoN b)32529 static void ExportBulkEditorTableBtn (ButtoN b)
32530 {
32531 BulkEditorPtr bep;
32532
32533 bep = (BulkEditorPtr) GetObjectExtra (b);
32534 if (bep == NULL) {
32535 return;
32536 }
32537
32538 ExportBulkEditorTable (bep->bulk_ed);
32539
32540 }
32541
32542
BulkEditorFeatList(Uint2 entityID,ValNodePtr feat_list)32543 extern void BulkEditorFeatList (Uint2 entityID, ValNodePtr feat_list)
32544 {
32545 GrouP c, g;
32546 ButtoN b;
32547 BulkEditorPtr bep;
32548 GrouP h;
32549 WindoW w;
32550 SeqEntryPtr sep;
32551 BulkEdFieldPtr field_list = NULL;
32552 Uint1 subtype = 0;
32553 CharPtr title = "Bulk Editor";
32554
32555 if (feat_list == NULL) {
32556 Message (MSG_ERROR, "No features found!");
32557 return;
32558 }
32559 /* Create a new window, and a struct */
32560 /* to pass around the data in. */
32561
32562 sep = GetTopSeqEntryForEntityID (entityID);
32563
32564 subtype = GetSubtypeForBulkEdit (feat_list);
32565 if (subtype == FEATDEF_BAD) {
32566 Message (MSG_ERROR, "Can't bulk edit a list of mixed feature types!");
32567 return;
32568 }
32569 if (subtype == FEATDEF_CDS) {
32570 title = "Bulk CDS Editor";
32571 field_list = bulk_cds_fields;
32572 } else if (subtype == FEATDEF_GENE) {
32573 title = "Bulk Gene Editor";
32574 field_list = bulk_gene_fields;
32575 } else if (subtype == FEATDEF_rRNA) {
32576 title = "Bulk RNA Editor";
32577 /* Note - using FEATDEF_rRNA to represent all editable rRNA features */
32578 field_list = bulk_rna_fields;
32579 } else if (subtype == FEATDEF_BIOSRC) {
32580 title = "Bulk Src Feat Editor";
32581 field_list = bulk_src_feat_fields;
32582 } else {
32583 Message (MSG_ERROR, "No bulk editor for this feature type!");
32584 return;
32585 }
32586
32587 bep = (BulkEditorPtr) MemNew (sizeof (BulkEditorData));
32588 if (bep == NULL)
32589 return;
32590
32591 bep->field_list = field_list;
32592
32593 w = FixedWindow (-50, -33, -10, -10, title,
32594 StdCloseWindowProc);
32595 SetObjectExtra (w, bep, StdCleanupFormProc);
32596 bep->form = (ForM) w;
32597 bep->input_entityID = entityID;
32598
32599 h = HiddenGroup (w, -1, 0, NULL);
32600 SetGroupSpacing (h, 10, 10);
32601
32602 /* want: Document with columns for pseudo (when appropriate), location, fields */
32603 /* when user clicks on field, should be able to edit contents */
32604
32605 bep->bulk_ed = CreateBulkEditorDialog (h, bep->field_list, feat_list, sep, TRUE, NULL, NULL);
32606
32607 if (subtype == FEATDEF_CDS) {
32608 bep->do_log = CheckBox (h, "Log Changes", NULL);
32609 } else {
32610 bep->do_log = NULL;
32611 }
32612
32613 g = HiddenGroup (h, 2, 0, NULL);
32614 b = PushButton (g, "Export Table", ExportBulkEditorTableBtn);
32615 SetObjectExtra (b, bep, NULL);
32616
32617 /* Add Accept and Cancel buttons */
32618
32619 c = HiddenGroup (h, 3, 0, NULL);
32620 b = PushButton (c, "Accept", AcceptBulkEditor);
32621 SetObjectExtra (b, bep, NULL);
32622 PushButton (c, "Cancel", StdCancelButtonProc);
32623
32624 /* Line things up nicely */
32625
32626 AlignObjects (ALIGN_CENTER, (HANDLE) bep->bulk_ed,
32627 (HANDLE) c, (HANDLE) g,
32628 (HANDLE) bep->do_log, NULL);
32629
32630
32631 /* Display the window now */
32632
32633 RealizeWindow (w);
32634 Show (w);
32635 Select (w);
32636 Update ();
32637 }
32638
32639
GetSubtypeForBulkDescrEdit(ValNodePtr descr_list)32640 extern Uint1 GetSubtypeForBulkDescrEdit (ValNodePtr descr_list)
32641 {
32642 ValNodePtr vnp_check;
32643 SeqDescrPtr sdp;
32644 Uint1 subtype = 0;
32645
32646 for (vnp_check = descr_list; vnp_check != NULL; vnp_check = vnp_check->next) {
32647 if (vnp_check->choice != OBJ_SEQDESC) continue;
32648 sdp = vnp_check->data.ptrvalue;
32649 if (subtype == 0) {
32650 subtype = sdp->choice;
32651 } else if (sdp->choice != subtype) {
32652 return 0;
32653 }
32654 }
32655 return subtype;
32656 }
32657
32658
BulkEditorDescrList(Uint2 entityID,ValNodePtr descr_list)32659 extern void BulkEditorDescrList (Uint2 entityID, ValNodePtr descr_list)
32660 {
32661 GrouP c;
32662 ButtoN b;
32663 BulkEditorPtr bep;
32664 GrouP h;
32665 WindoW w;
32666 SeqEntryPtr sep;
32667 BulkEdFieldPtr field_list = NULL;
32668 Uint1 subtype = 0;
32669
32670 if (descr_list == NULL) {
32671 Message (MSG_ERROR, "No descriptors found!");
32672 return;
32673 }
32674 /* Create a new window, and a struct */
32675 /* to pass around the data in. */
32676
32677 sep = GetTopSeqEntryForEntityID (entityID);
32678
32679 subtype = GetSubtypeForBulkDescrEdit (descr_list);
32680 if (subtype == 0) {
32681 Message (MSG_ERROR, "Can't bulk edit a list of mixed descriptor types!");
32682 return;
32683 }
32684 if (subtype == Seq_descr_source) {
32685 field_list = bulk_src_desc_fields;
32686 } else {
32687 Message (MSG_ERROR, "No bulk editor for this descriptor type!");
32688 return;
32689 }
32690
32691 bep = (BulkEditorPtr) MemNew (sizeof (BulkEditorData));
32692 if (bep == NULL)
32693 return;
32694
32695 bep->field_list = field_list;
32696
32697 w = FixedWindow (-50, -33, -10, -10, "Bulk Src Editor",
32698 StdCloseWindowProc);
32699 SetObjectExtra (w, bep, StdCleanupFormProc);
32700 bep->form = (ForM) w;
32701 bep->input_entityID = entityID;
32702
32703 h = HiddenGroup (w, -1, 0, NULL);
32704 SetGroupSpacing (h, 10, 10);
32705
32706 /* want: Document with columns for pseudo (when appropriate), location, fields */
32707 /* when user clicks on field, should be able to edit contents */
32708
32709 bep->bulk_ed = CreateBulkEditorDialogEx (h, bep->field_list, descr_list, sep, TRUE, NULL, NULL, NULL, subtype == Seq_descr_source);
32710
32711 /* Add Accept and Cancel buttons */
32712
32713 c = HiddenGroup (h, 3, 0, NULL);
32714 b = PushButton (c, "Accept", AcceptBulkEditor);
32715 SetObjectExtra (b, bep, NULL);
32716 PushButton (c, "Cancel", StdCancelButtonProc);
32717
32718 /* Line things up nicely */
32719
32720 AlignObjects (ALIGN_CENTER, (HANDLE) bep->bulk_ed,
32721 (HANDLE) c, NULL);
32722
32723
32724 /* Display the window now */
32725
32726 RealizeWindow (w);
32727 Show (w);
32728 Select (w);
32729 Update ();
32730 }
32731
32732
BulkEditorObjectList(Uint2 entityID,CharPtr title,ValNodePtr feat_list,BulkEdFieldPtr field_list)32733 NLM_EXTERN void BulkEditorObjectList (Uint2 entityID, CharPtr title, ValNodePtr feat_list, BulkEdFieldPtr field_list)
32734 {
32735 GrouP c;
32736 ButtoN b;
32737 BulkEditorPtr bep;
32738 GrouP h;
32739 WindoW w;
32740 SeqEntryPtr sep;
32741 Uint1 subtype = 0;
32742
32743 if (feat_list == NULL) {
32744 Message (MSG_ERROR, "No features found!");
32745 return;
32746 }
32747 /* Create a new window, and a struct */
32748 /* to pass around the data in. */
32749
32750 sep = GetTopSeqEntryForEntityID (entityID);
32751
32752 bep = (BulkEditorPtr) MemNew (sizeof (BulkEditorData));
32753 if (bep == NULL)
32754 return;
32755
32756 bep->field_list = field_list;
32757
32758 w = FixedWindow (-50, -33, -10, -10, title,
32759 StdCloseWindowProc);
32760 SetObjectExtra (w, bep, StdCleanupFormProc);
32761 bep->form = (ForM) w;
32762 bep->input_entityID = entityID;
32763
32764 h = HiddenGroup (w, -1, 0, NULL);
32765 SetGroupSpacing (h, 10, 10);
32766
32767 /* want: Document with columns for pseudo (when appropriate), location, fields */
32768 /* when user clicks on field, should be able to edit contents */
32769
32770 bep->bulk_ed = CreateBulkEditorDialog (h, bep->field_list, feat_list, sep, TRUE, NULL, NULL);
32771
32772 /* Add Accept and Cancel buttons */
32773
32774 c = HiddenGroup (h, 3, 0, NULL);
32775 b = PushButton (c, "Accept", AcceptBulkEditor);
32776 SetObjectExtra (b, bep, NULL);
32777 PushButton (c, "Cancel", StdCancelButtonProc);
32778
32779 /* Line things up nicely */
32780
32781 AlignObjects (ALIGN_CENTER, (HANDLE) bep->bulk_ed,
32782 (HANDLE) c, NULL);
32783
32784
32785 /* Display the window now */
32786
32787 RealizeWindow (w);
32788 Show (w);
32789 Select (w);
32790 Update ();
32791 }
32792
32793
BulkEditorBaseForm(BaseFormPtr bfp,Uint1 featchoice,Uint1 featdef)32794 static void BulkEditorBaseForm (BaseFormPtr bfp, Uint1 featchoice, Uint1 featdef)
32795 {
32796 SeqEntryPtr sep;
32797 CollectFeatData cfd;
32798 BulkEdFieldPtr field_list = NULL;
32799
32800 if (bfp == NULL) return;
32801
32802 /* Create a new window, and a struct */
32803 /* to pass around the data in. */
32804
32805 sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
32806
32807 if (featchoice == SEQFEAT_CDREGION || featdef == FEATDEF_CDS) {
32808 field_list = bulk_cds_fields;
32809 } else if (featchoice == SEQFEAT_GENE || featdef == FEATDEF_GENE) {
32810 field_list = bulk_gene_fields;
32811 } else if (featchoice == SEQFEAT_RNA) {
32812 field_list = bulk_rna_fields;
32813 } else {
32814 Message (MSG_ERROR, "No bulk editor for this feature type!");
32815 return;
32816 }
32817
32818 cfd.featchoice = featchoice;
32819 cfd.featdef = featdef;
32820 cfd.feat_list = NULL;
32821 VisitBioseqsInSep (sep, &cfd, CollectFeaturesForBulkEditor);
32822
32823 if (cfd.feat_list == NULL) {
32824 Message (MSG_ERROR, "No features found!");
32825 return;
32826 }
32827
32828 BulkEditorFeatList (bfp->input_entityID, cfd.feat_list);
32829 }
32830
BulkEditor(IteM i,Uint1 featchoice,Uint1 featdef)32831 static void BulkEditor (IteM i, Uint1 featchoice, Uint1 featdef)
32832 {
32833 BaseFormPtr bfp;
32834
32835 #ifdef WIN_MAC
32836 bfp = currentFormDataPtr;
32837 #else
32838 bfp = GetObjectExtra (i);
32839 #endif
32840
32841 BulkEditorBaseForm(bfp, featchoice, featdef);
32842 }
32843
BulkEditCDS(IteM i)32844 NLM_EXTERN void BulkEditCDS (IteM i)
32845 {
32846 BulkEditor (i, SEQFEAT_CDREGION, FEATDEF_CDS);
32847 }
32848
32849
BulkEditCDSBaseForm(BaseFormPtr bfp)32850 NLM_EXTERN void BulkEditCDSBaseForm (BaseFormPtr bfp)
32851 {
32852 BulkEditorBaseForm (bfp, SEQFEAT_CDREGION, FEATDEF_CDS);
32853 }
32854
32855
BulkEditGene(IteM i)32856 extern void BulkEditGene (IteM i)
32857 {
32858 BulkEditor (i, SEQFEAT_GENE, FEATDEF_GENE);
32859 }
32860
BulkEditRNA(IteM i)32861 extern void BulkEditRNA (IteM i)
32862 {
32863 BulkEditor (i, SEQFEAT_RNA, 0);
32864 }
32865
32866
GetBulkEditSourceCallback(SeqDescrPtr sdp,Pointer data)32867 static void GetBulkEditSourceCallback (SeqDescrPtr sdp, Pointer data)
32868 {
32869 if (sdp != NULL && sdp->choice == Seq_descr_source && data != NULL) {
32870 ValNodeAddPointer ((ValNodePtr PNTR) data, OBJ_SEQDESC, sdp);
32871 }
32872 }
32873
32874
BulkEditSourceBaseForm(BaseFormPtr bfp)32875 NLM_EXTERN void BulkEditSourceBaseForm (BaseFormPtr bfp)
32876 {
32877 SeqEntryPtr sep;
32878 ValNodePtr list = NULL;
32879
32880 if (bfp == NULL) return;
32881 sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
32882 if (sep == NULL) return;
32883 VisitDescriptorsInSep (sep, &list, GetBulkEditSourceCallback);
32884
32885 BulkEditorDescrList (bfp->input_entityID, list);
32886 }
32887
32888
BulkEditSource(IteM i)32889 extern void BulkEditSource (IteM i)
32890 {
32891 BaseFormPtr bfp;
32892
32893 #ifdef WIN_MAC
32894 bfp = currentFormDataPtr;
32895 #else
32896 bfp = GetObjectExtra (i);
32897 #endif
32898 if (bfp == NULL) return;
32899 BulkEditSourceBaseForm (bfp);
32900 }
32901
32902
GetBarcodeTestBarcodeID(Uint1 data_choice,Pointer data,Pointer metadata)32903 static Pointer GetBarcodeTestBarcodeID (Uint1 data_choice, Pointer data, Pointer metadata)
32904 {
32905 BarcodeTestResultsPtr res = (BarcodeTestResultsPtr) data;
32906 if (res == NULL || res->bsp == NULL) {
32907 return NULL;
32908 } else {
32909 return BarcodeTestBarcodeIdString (res->bsp);
32910 }
32911 }
32912
32913
GetBarcodeTestGenbankID(Uint1 data_choice,Pointer data,Pointer metadata)32914 static Pointer GetBarcodeTestGenbankID (Uint1 data_choice, Pointer data, Pointer metadata)
32915 {
32916 BarcodeTestResultsPtr res = (BarcodeTestResultsPtr) data;
32917 if (res == NULL || res->bsp == NULL) {
32918 return NULL;
32919 } else {
32920 return BarcodeTestGenbankIdString (res->bsp);
32921 }
32922 }
32923
32924
GetBarcodeTestLengthResult(Uint1 data_choice,Pointer data,Pointer metadata)32925 static Pointer GetBarcodeTestLengthResult (Uint1 data_choice, Pointer data, Pointer metadata)
32926 {
32927 BarcodeTestResultsPtr res = (BarcodeTestResultsPtr) data;
32928 if (res == NULL || !res->failed_tests[eBarcodeTest_Length]) {
32929 return NULL;
32930 } else {
32931 return StringSave ("TRUE");
32932 }
32933 }
32934
32935
GetBarcodeTestPrimersResult(Uint1 data_choice,Pointer data,Pointer metadata)32936 static Pointer GetBarcodeTestPrimersResult (Uint1 data_choice, Pointer data, Pointer metadata)
32937 {
32938 BarcodeTestResultsPtr res = (BarcodeTestResultsPtr) data;
32939 if (res == NULL || !res->failed_tests[eBarcodeTest_Primers]) {
32940 return NULL;
32941 } else {
32942 return StringSave ("TRUE");
32943 }
32944 }
32945
32946
GetBarcodeTestCountryResult(Uint1 data_choice,Pointer data,Pointer metadata)32947 static Pointer GetBarcodeTestCountryResult (Uint1 data_choice, Pointer data, Pointer metadata)
32948 {
32949 BarcodeTestResultsPtr res = (BarcodeTestResultsPtr) data;
32950 if (res == NULL || !res->failed_tests[eBarcodeTest_Country]) {
32951 return NULL;
32952 } else {
32953 return StringSave ("TRUE");
32954 }
32955 }
32956
32957
GetBarcodeTestSpecimenVoucherResult(Uint1 data_choice,Pointer data,Pointer metadata)32958 static Pointer GetBarcodeTestSpecimenVoucherResult (Uint1 data_choice, Pointer data, Pointer metadata)
32959 {
32960 BarcodeTestResultsPtr res = (BarcodeTestResultsPtr) data;
32961 if (res == NULL || !res->failed_tests[eBarcodeTest_SpecimenVoucher]) {
32962 return NULL;
32963 } else {
32964 return StringSave ("TRUE");
32965 }
32966 }
32967
32968
GetBarcodeTestStructuredSpecimenVoucherResult(Uint1 data_choice,Pointer data,Pointer metadata)32969 static Pointer GetBarcodeTestStructuredSpecimenVoucherResult (Uint1 data_choice, Pointer data, Pointer metadata)
32970 {
32971 BarcodeTestResultsPtr res = (BarcodeTestResultsPtr) data;
32972 if (res == NULL || !res->failed_tests[eBarcodeTest_StructuredSpecimenVoucher]) {
32973 return NULL;
32974 } else {
32975 return StringSave ("TRUE");
32976 }
32977 }
32978
32979
GetBarcodeTestCollectionDateResult(Uint1 data_choice,Pointer data,Pointer metadata)32980 static Pointer GetBarcodeTestCollectionDateResult (Uint1 data_choice, Pointer data, Pointer metadata)
32981 {
32982 BarcodeTestResultsPtr res = (BarcodeTestResultsPtr) data;
32983 if (res == NULL || !res->failed_tests[eBarcodeTest_CollectionDate]) {
32984 return NULL;
32985 } else {
32986 return StringSave ("TRUE");
32987 }
32988 }
32989
32990
GetBarcodeTestOrderAssignmentResult(Uint1 data_choice,Pointer data,Pointer metadata)32991 static Pointer GetBarcodeTestOrderAssignmentResult (Uint1 data_choice, Pointer data, Pointer metadata)
32992 {
32993 BarcodeTestResultsPtr res = (BarcodeTestResultsPtr) data;
32994 if (res == NULL || !res->failed_tests[eBarcodeTest_OrderAssignment]) {
32995 return NULL;
32996 } else {
32997 return StringSave ("TRUE");
32998 }
32999 }
33000
33001
GetBarcodeTestLowTraceResult(Uint1 data_choice,Pointer data,Pointer metadata)33002 static Pointer GetBarcodeTestLowTraceResult (Uint1 data_choice, Pointer data, Pointer metadata)
33003 {
33004 BarcodeTestResultsPtr res = (BarcodeTestResultsPtr) data;
33005 if (res == NULL || !res->failed_tests[eBarcodeTest_LowTrace]) {
33006 return NULL;
33007 } else {
33008 return StringSave ("TRUE");
33009 }
33010 }
33011
33012
GetBarcodeTestFrameShiftResult(Uint1 data_choice,Pointer data,Pointer metadata)33013 static Pointer GetBarcodeTestFrameShiftResult (Uint1 data_choice, Pointer data, Pointer metadata)
33014 {
33015 BarcodeTestResultsPtr res = (BarcodeTestResultsPtr) data;
33016 if (res == NULL || !res->failed_tests[eBarcodeTest_FrameShift]) {
33017 return NULL;
33018 } else {
33019 return StringSave ("TRUE");
33020 }
33021 }
33022
33023
GetBarcodeTestPercentNsResult(Uint1 data_choice,Pointer data,Pointer metadata)33024 static Pointer GetBarcodeTestPercentNsResult (Uint1 data_choice, Pointer data, Pointer metadata)
33025 {
33026 BarcodeTestResultsPtr res = (BarcodeTestResultsPtr) data;
33027 Char txt[5];
33028 if (res == NULL || !res->failed_tests[eBarcodeTest_PercentN]) {
33029 return NULL;
33030 } else {
33031 sprintf (txt, "%.1f", res->n_percent);
33032 return StringSave (txt);
33033 }
33034 }
33035
33036
HasBarcodeKeyword(Uint1 data_choice,Pointer data,Pointer metadata)33037 static Pointer HasBarcodeKeyword (Uint1 data_choice, Pointer data, Pointer metadata)
33038 {
33039 Boolean rval = FALSE;
33040
33041 BarcodeTestResultsPtr res = (BarcodeTestResultsPtr) data;
33042 if (res != NULL && res->bsp != NULL) {
33043 rval = BioseqHasBarcodeKeyword(res->bsp);
33044 }
33045 if (rval) {
33046 return StringSave ("TRUE");
33047 } else {
33048 return NULL;
33049 }
33050 }
33051
33052
33053
BarcodeFormatBarcodeID(ColPtr col,CharPtr name)33054 static Int4 BarcodeFormatBarcodeID (ColPtr col, CharPtr name)
33055 {
33056 if (col == NULL) return 0;
33057
33058 col->pixWidth = MAX (21, StringLen (name)) * MaxCharWidth();
33059 col->pixInset = 0;
33060 col->charWidth = 0;
33061 col->charInset = 0;
33062 col->font = NULL;
33063 col->just = 'l';
33064 col->wrap = 1;
33065 col->bar = 0;
33066 col->underline = 0;
33067 col->left = 0;
33068 return col->pixWidth;
33069 }
33070
33071
BarcodeFormatGenbankID(ColPtr col,CharPtr name)33072 static Int4 BarcodeFormatGenbankID (ColPtr col, CharPtr name)
33073 {
33074 if (col == NULL) return 0;
33075
33076 col->pixWidth = MAX (10, StringLen (name)) * MaxCharWidth();
33077 col->pixInset = 0;
33078 col->charWidth = 0;
33079 col->charInset = 0;
33080 col->font = NULL;
33081 col->just = 'l';
33082 col->wrap = 1;
33083 col->bar = 0;
33084 col->underline = 0;
33085 col->left = 0;
33086 return col->pixWidth;
33087 }
33088
33089
BarcodeFormatPercentN(ColPtr col,CharPtr name)33090 static Int4 BarcodeFormatPercentN (ColPtr col, CharPtr name)
33091 {
33092 if (col == NULL) return 0;
33093
33094 col->pixWidth = MAX (5, StringLen (name)) * MaxCharWidth();
33095 col->pixInset = 0;
33096 col->charWidth = 0;
33097 col->charInset = 0;
33098 col->font = NULL;
33099 col->just = 'l';
33100 col->wrap = 1;
33101 col->bar = 0;
33102 col->underline = 0;
33103 col->left = 0;
33104 return col->pixWidth;
33105 }
33106
33107
33108 static BulkEdFieldData barcode_test_fields[] = {
33109 { "Barcode ID", NULL, NULL, GetBarcodeTestBarcodeID, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BarcodeFormatBarcodeID, NULL, NULL, BulkSimpleTextCopy },
33110 { "Genbank Accession", NULL, NULL, GetBarcodeTestGenbankID, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BarcodeFormatGenbankID, NULL, NULL, BulkSimpleTextCopy },
33111 { "Length", NULL, NULL, GetBarcodeTestLengthResult, NULL, BulkFreeSimpleText, NULL, BulkFormatTrueFalse, BulkDrawTrueFalse, NULL, BulkSimpleTextCopy },
33112 { "Primers", NULL, NULL, GetBarcodeTestPrimersResult, NULL, BulkFreeSimpleText, NULL, BulkFormatTrueFalse, BulkDrawTrueFalse, NULL, BulkSimpleTextCopy },
33113 { "Country", NULL, NULL, GetBarcodeTestCountryResult, NULL, BulkFreeSimpleText, NULL, BulkFormatTrueFalse, BulkDrawTrueFalse, NULL, BulkSimpleTextCopy },
33114 { "Voucher", NULL, NULL, GetBarcodeTestSpecimenVoucherResult, NULL, BulkFreeSimpleText, NULL, BulkFormatTrueFalse, BulkDrawTrueFalse, NULL, BulkSimpleTextCopy },
33115 { "Structured Voucher", NULL, NULL, GetBarcodeTestStructuredSpecimenVoucherResult, NULL, BulkFreeSimpleText, NULL, BulkFormatTrueFalse, BulkDrawTrueFalse, NULL, BulkSimpleTextCopy },
33116 { "Percent Ns", NULL, NULL, GetBarcodeTestPercentNsResult, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BarcodeFormatPercentN, NULL, NULL, BulkSimpleTextCopy },
33117 { "Collection Date", NULL, NULL, GetBarcodeTestCollectionDateResult, NULL, BulkFreeSimpleText, NULL, BulkFormatTrueFalse, BulkDrawTrueFalse, NULL, BulkSimpleTextCopy },
33118 { "Order Assignment", NULL, NULL, GetBarcodeTestOrderAssignmentResult, NULL, BulkFreeSimpleText, NULL, BulkFormatTrueFalse, BulkDrawTrueFalse, NULL, BulkSimpleTextCopy },
33119 { "Low Trace", NULL, NULL, GetBarcodeTestLowTraceResult, NULL, BulkFreeSimpleText, NULL, BulkFormatTrueFalse, BulkDrawTrueFalse, NULL, BulkSimpleTextCopy },
33120 { "Frame Shift", NULL, NULL, GetBarcodeTestFrameShiftResult, NULL, BulkFreeSimpleText, NULL, BulkFormatTrueFalse, BulkDrawTrueFalse, NULL, BulkSimpleTextCopy },
33121 { "Has BARCODE Keyword", NULL, NULL, HasBarcodeKeyword, NULL, BulkFreeSimpleText, NULL, BulkFormatTrueFalse, BulkDrawTrueFalse, NULL, BulkSimpleTextCopy },
33122 { NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL}};
33123
NavigateToBarcodeTestResultBioseq(ValNodePtr object,Pointer userdata)33124 static void NavigateToBarcodeTestResultBioseq (ValNodePtr object, Pointer userdata)
33125 {
33126 BaseFormPtr bfp;
33127 BarcodeTestResultsPtr res;
33128
33129 if (object == NULL) return;
33130
33131 res = (BarcodeTestResultsPtr) object->data.ptrvalue;
33132
33133 if (res == NULL || res->bsp == NULL) return;
33134 bfp = GetBaseFormForEntityID (res->bsp->idx.entityID);
33135 if (bfp != NULL) {
33136 Select (bfp->form);
33137 SetBioseqViewTargetByBioseq (bfp, res->bsp);
33138 }
33139 }
33140
33141
BarcodeTestResultsDisplay(GrouP h,BarcodeTestConfigPtr cfg)33142 extern DialoG BarcodeTestResultsDisplay (GrouP h, BarcodeTestConfigPtr cfg)
33143 {
33144 return CreateBulkEditorDialog (h, barcode_test_fields, NULL, NULL, FALSE, NavigateToBarcodeTestResultBioseq, NULL);
33145 }
33146
GetCurrentLatLon(Uint1 data_choice,Pointer data,Pointer metadata)33147 static Pointer GetCurrentLatLon (Uint1 data_choice, Pointer data, Pointer metadata)
33148 {
33149 SubSourcePtr bad_ssp;
33150 BioSourcePtr biop;
33151
33152 biop = GetBioSourceFromObject (data_choice, data);
33153 if (biop == NULL) return NULL;
33154
33155 bad_ssp = FindBadLatLon (biop);
33156 if (bad_ssp == NULL)
33157 {
33158 return NULL;
33159 }
33160 else
33161 {
33162 return StringSave (bad_ssp->name);
33163 }
33164 }
33165
33166
GetCorrectedLatLon(Uint1 data_choice,Pointer data,Pointer metadata)33167 static Pointer GetCorrectedLatLon (Uint1 data_choice, Pointer data, Pointer metadata)
33168 {
33169 SubSourcePtr bad_ssp;
33170 CharPtr fix;
33171 BioSourcePtr biop;
33172
33173 biop = GetBioSourceFromObject (data_choice, data);
33174 if (biop == NULL) return NULL;
33175
33176 bad_ssp = FindBadLatLon (biop);
33177 if (bad_ssp == NULL)
33178 {
33179 return NULL;
33180 }
33181 else
33182 {
33183 fix = FixLatLonFormat (bad_ssp->name);
33184 if (fix == NULL)
33185 {
33186 return StringSave ("Unable to autocorrect");
33187 }
33188 else
33189 {
33190 return fix;
33191 }
33192 }
33193 }
33194
33195
33196 static BulkEdFieldData latlon_fields[] = {
33197 { "Current Lat-lon", NULL, NULL, GetCurrentLatLon, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
33198 { "Suggested Correction", NULL, NULL, GetCorrectedLatLon, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
33199 { NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL}};
33200
LatLonTestResultsDisplay(GrouP h)33201 extern DialoG LatLonTestResultsDisplay (GrouP h)
33202 {
33203 return CreateBulkEditorDialog (h, latlon_fields, NULL, NULL, FALSE, ScrollToDiscrepancyItem, EditDiscrepancyItem);
33204 }
33205
33206
33207 static BulkEdFieldData trim_sequence_fields[] = {
33208 { "Current PercentN", NULL, NULL, GetCurrentPercentN, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
33209 { "Bases to Remove", NULL, NULL, GetTrimRemove, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
33210 { "Remaining Bases", NULL, NULL, GetTrimRemaining, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
33211 { NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL}};
33212
TrimSequenceResultsDisplay(GrouP h)33213 extern DialoG TrimSequenceResultsDisplay (GrouP h)
33214 {
33215 return CreateBulkEditorDialog (h, trim_sequence_fields, NULL, NULL, FALSE, ScrollToTrimSequenceItem, NULL);
33216 }
33217
33218
DefaultCheckTrimSequenceResults(BulkEditorRowPtr berp)33219 static void DefaultCheckTrimSequenceResults (BulkEditorRowPtr berp)
33220 {
33221 ValNodePtr vnp;
33222
33223 if (berp == NULL) {
33224 return;
33225 }
33226 while (berp->object_list != NULL) {
33227 if (berp->subrows == NULL) {
33228 vnp = berp->object_list;
33229 if (vnp != NULL) {
33230 if (TrimShouldDelete (vnp->choice, vnp->data.ptrvalue, NULL)) {
33231 berp->selected = FALSE;
33232 } else {
33233 berp->selected = TRUE;
33234 }
33235 }
33236 } else {
33237 DefaultCheckTrimSequenceResults (berp->subrows);
33238 berp->selected = AllBulkEditorRowsSelected (berp->subrows);
33239 }
33240
33241 berp++;
33242 }
33243 }
33244
33245
DefaultCheckTrimSequenceResultsDisplay(DialoG d)33246 extern void DefaultCheckTrimSequenceResultsDisplay (DialoG d)
33247 {
33248 BulkEditorDlgPtr dlg;
33249 RecT r;
33250
33251 dlg = (BulkEditorDlgPtr) GetObjectExtra (d);
33252 if (dlg == NULL) return;
33253
33254 DefaultCheckTrimSequenceResults (dlg->row_list);
33255
33256 UpdateCheckStatus (dlg);
33257
33258 ObjectRect (dlg->doc, &r);
33259 InvalRect (&r);
33260 Update ();
33261 }
33262
33263
33264 static BulkEdFieldData trim_sequence_end_fields[] = {
33265 { "Accession", NULL, NULL, GetTrimAccession, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
33266 { "Remove from 5'", NULL, NULL, GetTrim5, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
33267 { "Remove from 3'", NULL, NULL, GetTrim3, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
33268 { NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL}};
33269
TrimSequenceEndDisplay(GrouP h)33270 extern DialoG TrimSequenceEndDisplay (GrouP h)
33271 {
33272 return CreateBulkEditorDialog (h, trim_sequence_end_fields, NULL, NULL, FALSE, ScrollToTrimSequenceItem, NULL);
33273 }
33274
33275
33276
GetTaxName(Uint1 data_choice,Pointer data,Pointer metadata)33277 static Pointer GetTaxName (Uint1 data_choice, Pointer data, Pointer metadata)
33278 {
33279 TaxFixItemPtr t;
33280
33281 if ((t = (TaxFixItemPtr) data) == NULL || t->orig_org == NULL || t->orig_org->taxname == NULL) {
33282 return NULL;
33283 } else {
33284 return StringSave (t->orig_org->taxname);
33285 }
33286 }
33287
33288
IsTaxNameBad(OrgRefPtr org)33289 extern Boolean IsTaxNameBad (OrgRefPtr org)
33290 {
33291 Boolean rval = TRUE;
33292 T3DataPtr tdp;
33293 Taxon3RequestPtr t3rq;
33294 Taxon3ReplyPtr t3ry;
33295 T3ReplyPtr trp;
33296 ValNodePtr val;
33297 T3StatusFlagsPtr tfp;
33298
33299 if (org == NULL) {
33300 return TRUE;
33301 }
33302 t3rq = CreateTaxon3Request (0, NULL, org);
33303 if (t3rq != NULL) {
33304 t3ry = Tax3SynchronousQuery (t3rq);
33305 Taxon3RequestFree (t3rq);
33306 if (t3ry != NULL) {
33307 for (trp = t3ry->reply; trp != NULL; trp = trp->next) {
33308 if (trp->choice == T3Reply_data) {
33309 tdp = (T3DataPtr) trp->data.ptrvalue;
33310 if (tdp != NULL) {
33311 for (tfp = tdp->status; tfp != NULL; tfp = tfp->next) {
33312 if (StringICmp (tfp->property, "is_species_level") == 0) {
33313 val = tfp->Value_value;
33314 if (val != NULL && val->choice == Value_value_bool) {
33315 if (val->data.intvalue != 0) {
33316 rval = FALSE;
33317 }
33318 }
33319 }
33320 }
33321 }
33322 }
33323 }
33324 }
33325 }
33326 return rval;
33327 }
33328
33329
GetTaxNameCorrection(Uint1 data_choice,Pointer data,Pointer metadata)33330 static Pointer GetTaxNameCorrection (Uint1 data_choice, Pointer data, Pointer metadata)
33331 {
33332 TaxFixItemPtr t;
33333
33334 if ((t = (TaxFixItemPtr) data) == NULL || t->suggested_fix == NULL) {
33335 return NULL;
33336 } else {
33337 return StringSave (t->suggested_fix);
33338 }
33339 }
33340
33341
TaxFixSetSuggestedFix(Pointer target,Pointer data)33342 static void TaxFixSetSuggestedFix (Pointer target, Pointer data)
33343 {
33344 TaxFixItemPtr t;
33345
33346 t = (TaxFixItemPtr) target;
33347 t->suggested_fix = MemFree (t->suggested_fix);
33348 t->suggested_fix = StringSave((CharPtr) data);
33349 }
33350
33351
ScrollToTaxFixItem(ValNodePtr vnp,Pointer userdata)33352 static void ScrollToTaxFixItem (ValNodePtr vnp, Pointer userdata)
33353 {
33354 TaxFixItemPtr t;
33355 ValNode vn;
33356
33357 if (vnp != NULL && (t = (TaxFixItemPtr) vnp->data.ptrvalue) != NULL) {
33358 vn.choice = t->data_choice;
33359 vn.data.ptrvalue = t->data;
33360 vn.next = NULL;
33361 ScrollToDiscrepancyItem (&vn, NULL);
33362 }
33363 }
33364
33365
EditTaxFixItem(ValNodePtr vnp,Pointer userdata)33366 static void EditTaxFixItem(ValNodePtr vnp, Pointer userdata)
33367 {
33368 TaxFixItemPtr t;
33369 ValNode vn;
33370
33371 if (vnp != NULL && (t = (TaxFixItemPtr) vnp->data.ptrvalue) != NULL) {
33372 vn.choice = t->data_choice;
33373 vn.data.ptrvalue = t->data;
33374 vn.next = NULL;
33375 EditDiscrepancyItem (&vn, NULL);
33376 }
33377 }
33378
33379
33380 static BulkEdFieldData taxfix_fields[] = {
33381 { "Tax Name", NULL, NULL, GetTaxName, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
33382 { "Suggested Correction", TaxFixSetSuggestedFix, BulkSetSimpleTextString, GetTaxNameCorrection, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
33383 { NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL}};
33384
TaxFixDisplay(GrouP h)33385 extern DialoG TaxFixDisplay (GrouP h)
33386 {
33387 return CreateBulkEditorDialog (h, taxfix_fields, NULL, NULL, TRUE, ScrollToTaxFixItem, EditTaxFixItem);
33388 }
33389
33390
GetSubSource(Uint1 data_choice,Pointer data,Uint1 subtype)33391 static CharPtr GetSubSource (Uint1 data_choice, Pointer data, Uint1 subtype)
33392 {
33393 SubSourcePtr ssp;
33394 BioSourcePtr biop;
33395
33396 biop = GetBioSourceFromObject (data_choice, data);
33397 if (biop == NULL) return NULL;
33398
33399 for (ssp = biop->subtype; ssp != NULL && ssp->subtype != subtype; ssp = ssp->next)
33400 {}
33401
33402 if (ssp == NULL)
33403 {
33404 return NULL;
33405 }
33406 else
33407 {
33408 return StringSave (ssp->name);
33409 }
33410 }
33411
33412
GetCountry(Uint1 data_choice,Pointer data,Pointer metadata)33413 static Pointer GetCountry (Uint1 data_choice, Pointer data, Pointer metadata)
33414 {
33415 return GetSubSource (data_choice, data, SUBSRC_country);
33416 }
33417
GetLatLon(Uint1 data_choice,Pointer data,Pointer metadata)33418 static Pointer GetLatLon (Uint1 data_choice, Pointer data, Pointer metadata)
33419 {
33420 return GetSubSource (data_choice, data, SUBSRC_lat_lon);
33421 }
33422
33423
GetLatLonCountryCorrection(Uint1 data_choice,Pointer data,Pointer metadata)33424 extern Pointer GetLatLonCountryCorrection (Uint1 data_choice, Pointer data, Pointer metadata)
33425 {
33426 SubSourcePtr ssp;
33427 BioSourcePtr biop;
33428 CharPtr country = NULL, cp;
33429 FloatHi lat, lon;
33430 Boolean found_lat_lon = FALSE;
33431 CharPtr msg = NULL;
33432 CharPtr guess_fmt = "Lat_lon does not map to '%s', but may be in '%s'";
33433 CharPtr guess;
33434
33435 biop = GetBioSourceFromObject (data_choice, data);
33436 if (biop == NULL) return NULL;
33437
33438 for (ssp = biop->subtype; ssp != NULL && (country == NULL || !found_lat_lon); ssp = ssp->next)
33439 {
33440 if (ssp->subtype == SUBSRC_country && !StringHasNoText (ssp->name))
33441 {
33442 country = StringSave (ssp->name);
33443 }
33444 else if (ssp->subtype == SUBSRC_lat_lon)
33445 {
33446 if (ParseLatLon (ssp->name, &lat, &lon))
33447 {
33448 found_lat_lon = TRUE;
33449 }
33450 }
33451 }
33452
33453 cp = StringChr (country, ':');
33454 if (cp != NULL)
33455 {
33456 *cp = 0;
33457 }
33458
33459 if (country == NULL && !found_lat_lon)
33460 {
33461 msg = StringSave ("Country and lat-lon not specified");
33462 }
33463 else if (country == NULL)
33464 {
33465 msg = StringSave ("Country not specified");
33466 }
33467 else if (!found_lat_lon)
33468 {
33469 msg = StringSave ("Lat-lon not specified.");
33470 }
33471 else if (!IsCountryInLatLonList (country))
33472 {
33473 msg = StringSave ("Country not in lat-lon list");
33474 }
33475 else if (TestLatLonForCountry (country, lat, lon))
33476 {
33477 msg = StringSave ("No conflict");
33478 }
33479 else if (TestLatLonForCountry (country, -lat, lon))
33480 {
33481 if (lat < 0.0) {
33482 msg = StringSave ("Latitude should be set to N (northern hemisphere)");
33483 } else {
33484 msg = StringSave ("Latitude should be set to S (southern hemisphere)");
33485 }
33486 } else if (TestLatLonForCountry (country, lat, -lon)) {
33487 if (lon < 0.0) {
33488 msg = StringSave ("Longitude should be set to E (eastern hemisphere)");
33489 } else {
33490 msg = StringSave ("Longitude should be set to W (western hemisphere)");
33491 }
33492 } else if (TestLatLonForCountry (country, lon, lat)) {
33493 msg = StringSave ("Latitude and longitude values appear to be exchanged");
33494 } else {
33495 guess = GuessCountryForLatLon (lat, lon);
33496 if (guess == NULL)
33497 {
33498 msg = StringSave ("Lat-lon does not map to country");
33499 }
33500 else
33501 {
33502 msg = (CharPtr) MemNew (sizeof (Char) * (StringLen (guess_fmt) + StringLen (country) + StringLen (guess)));
33503 sprintf (msg, guess_fmt, country, guess);
33504 }
33505 }
33506 return msg;
33507 }
33508
33509 static BulkEdFieldData latloncountry_fields[] = {
33510 { "Lat-lon", NULL, NULL, GetLatLon, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
33511 { "Country", NULL, NULL, GetCountry, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
33512 { "Suggested Correction", NULL, NULL, GetLatLonCountryCorrection, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
33513 { NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL}};
33514
LatLonCountryResultsDisplay(GrouP h)33515 extern DialoG LatLonCountryResultsDisplay (GrouP h)
33516 {
33517 return CreateBulkEditorDialog (h, latloncountry_fields, NULL, NULL, FALSE, ScrollToDiscrepancyItem, EditDiscrepancyItem);
33518 }
33519
33520
GetCurrentSpecificHost(Uint1 data_choice,Pointer data,Pointer metadata)33521 static Pointer GetCurrentSpecificHost (Uint1 data_choice, Pointer data, Pointer metadata)
33522 {
33523 SpecificHostFixPtr s = (SpecificHostFixPtr) data;
33524
33525 if (s == NULL || StringHasNoText (s->bad_specific_host))
33526 {
33527 return NULL;
33528 }
33529 else
33530 {
33531 return StringSave (s->bad_specific_host);
33532 }
33533 }
33534
33535
GetCorrectedSpecificHost(Uint1 data_choice,Pointer data,Pointer metadata)33536 static Pointer GetCorrectedSpecificHost (Uint1 data_choice, Pointer data, Pointer metadata)
33537 {
33538 SpecificHostFixPtr s = (SpecificHostFixPtr) data;
33539 CharPtr fmt = "Unable to suggest correction for '%s'";
33540 CharPtr rval = NULL;
33541
33542 if (s == NULL)
33543 {
33544 return NULL;
33545 }
33546 else if (StringHasNoText (s->new_taxname))
33547 {
33548 if (StringHasNoText (s->old_taxname)) {
33549 rval = StringSave ("Unable to suggest correction");
33550 } else {
33551 rval = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (s->old_taxname)));
33552 sprintf (rval, fmt, s->old_taxname);
33553 }
33554 }
33555 else
33556 {
33557 rval = StringSave (s->bad_specific_host);
33558 FindReplaceString (&rval, s->old_taxname, s->new_taxname, TRUE, TRUE);
33559 }
33560 return rval;
33561 }
33562
33563
GetSpecificHostCorrectionCategory(Uint1 data_choice,Pointer data,Pointer metadata)33564 static Pointer GetSpecificHostCorrectionCategory (Uint1 data_choice, Pointer data, Pointer metadata)
33565 {
33566 SpecificHostFixPtr s = (SpecificHostFixPtr) data;
33567 CharPtr fmt = "Unable to suggest correction for '%s'";
33568 CharPtr rval = NULL;
33569
33570 if (s == NULL)
33571 {
33572 return NULL;
33573 }
33574 else
33575 {
33576 switch (s->fix_type) {
33577 case eSpecificHostFix_unrecognized:
33578 rval = StringSave ("Unrecognized");
33579 break;
33580 case eSpecificHostFix_spelling:
33581 rval = StringSave ("Spelling");
33582 break;
33583 case eSpecificHostFix_capitalization:
33584 rval = StringSave ("Capitalization");
33585 break;
33586 case eSpecificHostFix_truncation:
33587 rval = StringSave ("Truncation");
33588 break;
33589 case eSpecificHostFix_replacement:
33590 rval = StringSave ("Replacement");
33591 break;
33592 case eSpecificHostFix_ambiguous:
33593 rval = StringSave ("Ambiguous");
33594 break;
33595 }
33596 }
33597 return rval;
33598 }
33599
33600
ScrollToSpecificHostFix(ValNodePtr vnp,Pointer userdata)33601 static void ScrollToSpecificHostFix (ValNodePtr vnp, Pointer userdata)
33602 {
33603 SpecificHostFixPtr s;
33604
33605 if (vnp == NULL || vnp->data.ptrvalue == NULL) return;
33606
33607 s = (SpecificHostFixPtr) vnp->data.ptrvalue;
33608 ScrollToDiscrepancyItem (s->feat_or_desc, NULL);
33609 }
33610
33611
EditSpecificHostFix(ValNodePtr vnp,Pointer userdata)33612 static void EditSpecificHostFix (ValNodePtr vnp, Pointer userdata)
33613 {
33614 SpecificHostFixPtr s;
33615
33616 if (vnp == NULL || vnp->data.ptrvalue == NULL) return;
33617
33618 s = (SpecificHostFixPtr) vnp->data.ptrvalue;
33619 EditDiscrepancyItem (s->feat_or_desc, NULL);
33620 }
33621
33622
33623 static BulkEdFieldData specifichost_fields[] = {
33624 { "Current Specific-host", NULL, NULL, GetCurrentSpecificHost, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
33625 { "Suggested Correction", NULL, NULL, GetCorrectedSpecificHost, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
33626 { "Category", NULL, NULL, GetSpecificHostCorrectionCategory, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
33627 { NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL}};
33628
SpecificHostResultsDisplay(GrouP h)33629 extern DialoG SpecificHostResultsDisplay (GrouP h)
33630 {
33631 return CreateBulkEditorDialog (h, specifichost_fields, NULL, NULL, FALSE, ScrollToSpecificHostFix, EditSpecificHostFix);
33632 }
33633
33634
33635