1 /* $Id: showdefline.cpp 620199 2020-11-17 18:41:11Z zaretska $
2 * ===========================================================================
3 *
4 * PUBLIC DOMAIN NOTICE
5 * National Center for Biotechnology Information
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 have not placed any restriction on its use or reproduction.
13 *
14 * Although all reasonable efforts have been taken to ensure the accuracy
15 * and reliability of the software and data, the NLM and the U.S.
16 * Government do not and cannot warrant the performance or results that
17 * may be obtained by using this software or data. The NLM and the U.S.
18 * Government disclaim all warranties, express or implied, including
19 * warranties of performance, merchantability or fitness for any particular
20 * purpose.
21 *
22 * Please cite the author in any work or product based on this material.
23 *
24 * ===========================================================================
25 *
26 * Author: Jian Ye
27 *
28 * File Description:
29 * Display blast defline
30 *
31 */
32 #include <ncbi_pch.hpp>
33 #include <corelib/ncbiexpt.hpp>
34 #include <corelib/ncbiutil.hpp>
35 #include <corelib/ncbistre.hpp>
36 #include <corelib/ncbireg.hpp>
37
38 #include <objmgr/object_manager.hpp>
39 #include <objmgr/scope.hpp>
40 #include <objmgr/util/sequence.hpp>
41 #include <objects/seq/Bioseq.hpp>
42 #include <objects/seq/Seq_descr.hpp>
43 #include <objects/seq/Seqdesc.hpp>
44 #include <objects/seqloc/Seq_id.hpp>
45
46 #include <objects/seqalign/Seq_align_set.hpp>
47 #include <objects/seqalign/Score.hpp>
48 #include <objects/seqalign/Std_seg.hpp>
49 #include <objects/seqalign/Dense_diag.hpp>
50 #include <objects/seqalign/Dense_seg.hpp>
51 #include <objects/blastdb/Blast_def_line.hpp>
52 #include <objects/blastdb/Blast_def_line_set.hpp>
53 #include <objects/blastdb/defline_extra.hpp>
54
55 #include <objtools/align_format/showdefline.hpp>
56 #include <objtools/align_format/align_format_util.hpp>
57 #include <objtools/blast/seqdb_reader/seqdb.hpp> // for CSeqDB::ExtractBlastDefline
58
59 #include <stdio.h>
60 #include <html/htmlhelper.hpp>
61
62
63 BEGIN_NCBI_SCOPE
64 USING_SCOPE(objects);
65 USING_SCOPE(sequence);
66 BEGIN_SCOPE(align_format)
67
68 //margins constant
69
70 static string kOneSpaceMargin = " ";
71 static string kTwoSpaceMargin = " ";
72
73 //const strings
74 static const string kHeader = "Sequences producing significant alignments:";
75 static const string kScore = "Score";
76 static const string kE = "E";
77 static const string kBits =
78 (getenv("CTOOLKIT_COMPATIBLE") ? "(bits)" : "(Bits)");
79 static const string kEvalue = "E value";
80 static const string kValue = "Value";
81 static const string kN = "N";
82 static const string kRepeatHeader = "Sequences used in model and found again:";
83 static const string kNewSeqHeader = "Sequences not found previously or not pr\
84 eviously below threshold:";
85 static const string kMaxScore = "Max score";
86 static const string kTotalScore = "Total score";
87 static const string kTotal = "Total";
88 static const string kIdentity = "Max ident";
89 static const string kPercent = "Percent";
90 static const string kHighest = "Highest";
91 static const string kQuery = "Query";
92 static const string kCoverage = "Query coverage";
93 static const string kEllipsis = "...";
94
95 static const string kMax = "Max";
96 static const string kIdentLine2 = "Ident";
97 static const string kScoreLine2 = "Score";
98 static const string kQueryCov = "Query";
99 static const string kQueryCovLine2 = "cover";
100 static const string kPerc = "Per.";
101 static const string kAccession = "Accession";
102 static const string kDescription = "Description";
103 static const string kScientific = "Scientific";
104 static const string kCommon = "Common";
105 static const string kName = "Name";
106 static const string kAccAbbr = "Acc.";
107 static const string kLenAbbr = "Len";
108 static const string kTaxid = "Taxid";
109
110 //psiblast related
111 static const string kPsiblastNewSeqGif = "<IMG SRC=\"images/new.gif\" \
112 WIDTH=30 HEIGHT=15 ALT=\"New sequence mark\">";
113
114 static const string kPsiblastNewSeqBackgroundGif = "<IMG SRC=\"images/\
115 bg.gif\" WIDTH=30 HEIGHT=15 ALT=\" \">";
116
117 static const string kPsiblastCheckedBackgroundGif = "<IMG SRC=\"images\
118 /bg.gif\" WIDTH=15 HEIGHT=15 ALT=\" \">";
119
120 static const string kPsiblastCheckedGif = "<IMG SRC=\"images/checked.g\
121 if\" WIDTH=15 HEIGHT=15 ALT=\"Checked mark\">";
122
123 static const string kPsiblastEvalueLink = "<a name = Evalue></a>";
124
125 static const string kPsiblastCheckboxChecked = "<INPUT TYPE=\"checkbox\" NAME\
126 =\"checked_GI\" VALUE=\"%d\" CHECKED> <INPUT TYPE=\"hidden\" NAME =\"good_G\
127 I\" VALUE = \"%d\">";
128
129 static const string kPsiblastCheckbox = "<INPUT TYPE=\"checkbox\" NAME=\"ch\
130 ecked_GI\" VALUE=\"%d\"> ";
131
132 //Max length of title string for the the link
133 static const int kMaxDescrLength = 4096;
134
135 string
GetSeqIdListString(const list<CRef<objects::CSeq_id>> & id,bool show_gi)136 CShowBlastDefline::GetSeqIdListString(const list<CRef<objects::CSeq_id> >& id,
137 bool show_gi)
138 {
139 string id_string = NcbiEmptyString;
140 bool found_gi = false;
141
142 CRef<CSeq_id> best_id = FindBestChoice(id, CSeq_id::Score);
143
144 if (show_gi) {
145 ITERATE(list<CRef<CSeq_id> >, itr, id) {
146 if ((*itr)->IsGi()) {
147 id_string += (*itr)->AsFastaString();
148 found_gi = true;
149 break;
150 }
151 }
152 }
153
154 if (best_id.NotEmpty() && !best_id->IsGi() ) {
155 if (found_gi)
156 id_string += "|";
157
158 if (best_id->IsLocal()) {
159 string id_token;
160 best_id->GetLabel(&id_token, CSeq_id::eContent, 0);
161 id_string += id_token;
162 }
163 else
164 id_string += best_id->AsFastaString();
165 }
166
167 return id_string;
168 }
169
170 void
GetSeqIdList(const objects::CBioseq_Handle & bh,list<CRef<objects::CSeq_id>> & ids)171 CShowBlastDefline::GetSeqIdList(const objects::CBioseq_Handle& bh,
172 list<CRef<objects::CSeq_id> >& ids)
173 {
174 ids.clear();
175
176
177 vector< CConstRef<CSeq_id> > original_seqids;
178
179 ITERATE(CBioseq_Handle::TId, itr, bh.GetId()) {
180 original_seqids.push_back(itr->GetSeqId());
181 }
182
183 // Check for ids of type "gnl|BL_ORD_ID". These are the artificial ids
184 // created in a BLAST database when it is formatted without indexing.
185 // For such ids, create new fake local Seq-ids, saving the first token of
186 // the Bioseq's title, if it's available.
187 GetSeqIdList(bh,original_seqids,ids);
188 }
189
190
191
192 void
GetSeqIdList(const objects::CBioseq_Handle & bh,vector<CConstRef<CSeq_id>> & original_seqids,list<CRef<objects::CSeq_id>> & ids)193 CShowBlastDefline::GetSeqIdList(const objects::CBioseq_Handle& bh,
194 vector< CConstRef<CSeq_id> > &original_seqids,
195 list<CRef<objects::CSeq_id> >& ids)
196 {
197 ids.clear();
198 ITERATE(vector< CConstRef<CSeq_id> >, itr, original_seqids) {
199 CRef<CSeq_id> next_seqid(new CSeq_id());
200 string id_token = NcbiEmptyString;
201
202 if (((*itr)->IsGeneral() &&
203 (*itr)->AsFastaString().find("gnl|BL_ORD_ID")
204 != string::npos) ||
205 (*itr)->AsFastaString().find("lcl|Subject_") != string::npos) {
206 vector<string> title_tokens;
207 string defline = sequence::CDeflineGenerator().GenerateDefline(bh);
208 if (defline != NcbiEmptyString) {
209 id_token =
210 NStr::Split(defline, " ", title_tokens)[0];
211 }
212 }
213 if (id_token != NcbiEmptyString) {
214 // Create a new local id with a label containing the extracted
215 // token and save it in the next_seqid instead of the original
216 // id.
217 CObject_id* obj_id = new CObject_id();
218 obj_id->SetStr(id_token);
219 next_seqid->SetLocal(*obj_id);
220 } else {
221 next_seqid->Assign(**itr);
222 }
223 ids.push_back(next_seqid);
224 }
225 }
226
227 void
GetBioseqHandleDeflineAndId(const CBioseq_Handle & handle,list<TGi> & use_this_gi,string & seqid,string & defline,bool show_gi,TGi this_gi_first)228 CShowBlastDefline::GetBioseqHandleDeflineAndId(const CBioseq_Handle& handle,
229 list<TGi>& use_this_gi,
230 string& seqid, string& defline,
231 bool show_gi /* = true */,
232 TGi this_gi_first /* = -1 */)
233 {
234 // Retrieve the CBlast_def_line_set object and save in a CRef, preventing
235 // its destruction; then extract the list of CBlast_def_line objects.
236 if( !handle ) return; // No bioseq for this handle ( deleted accession ? )
237 CRef<CBlast_def_line_set> bdlRef =
238 CSeqDB::ExtractBlastDefline(handle);
239
240 if(bdlRef.Empty()){
241 list<CRef<objects::CSeq_id> > ids;
242 GetSeqIdList(handle, ids);
243 seqid = GetSeqIdListString(ids, show_gi);
244 defline = sequence::CDeflineGenerator().GenerateDefline(handle);
245 } else {
246 bdlRef->PutTargetGiFirst(this_gi_first);
247 const list< CRef< CBlast_def_line > >& bdl = bdlRef->Get();
248 bool is_first = true;
249 ITERATE(list<CRef<CBlast_def_line> >, iter, bdl) {
250 const CBioseq::TId& cur_id = (*iter)->GetSeqid();
251 TGi cur_gi = FindGi(cur_id);
252 TGi gi_in_use_this_gi = ZERO_GI;
253 ITERATE(list<TGi>, iter_gi, use_this_gi){
254 if(cur_gi == *iter_gi){
255 gi_in_use_this_gi = *iter_gi;
256 break;
257 }
258 }
259 if(use_this_gi.empty() || gi_in_use_this_gi > ZERO_GI) {
260 if (is_first)
261 seqid = GetSeqIdListString(cur_id, show_gi);
262
263 if((*iter)->IsSetTitle()){
264 if(is_first){
265 defline = (*iter)->GetTitle();
266 } else {
267 string concat_acc;
268 CConstRef<CSeq_id> wid =
269 FindBestChoice(cur_id, CSeq_id::WorstRank);
270 wid->GetLabel(&concat_acc, CSeq_id::eFasta, 0);
271 if( show_gi && cur_gi > ZERO_GI){
272 defline = defline + " >" + "gi|" +
273 NStr::NumericToString(cur_gi) + "|" +
274 concat_acc + " " + (*iter)->GetTitle();
275 } else {
276 defline = defline + " >" + concat_acc + " " +
277 (*iter)->GetTitle();
278 }
279 }
280 is_first = false;
281 }
282 }
283 }
284 }
285 }
286
s_LimitDescrLength(string & descr,size_t maxDescrLength=kMaxDescrLength)287 static void s_LimitDescrLength(string &descr, size_t maxDescrLength = kMaxDescrLength)
288 {
289 if(descr.length() > maxDescrLength) {
290 descr = descr.substr(0,maxDescrLength);
291 size_t end = NStr::Find(descr," ",NStr::eNocase,NStr::eReverseSearch);
292
293 if(end != NPOS) {
294 descr = descr.substr(0,end);
295 descr += "...";
296 }
297 }
298
299 }
300
x_InitLinkOutInfo(SDeflineInfo * sdl,CBioseq::TId & cur_id,int blast_rank,bool getIdentProteins)301 void CShowBlastDefline::x_InitLinkOutInfo(SDeflineInfo* sdl,
302 CBioseq::TId& cur_id,
303 int blast_rank,
304 bool getIdentProteins)
305 {
306
307 bool is_mixed_database = (m_IsDbNa == true && m_Ctx)? CAlignFormatUtil::IsMixedDatabase(*m_Ctx): false;
308 if (m_DeflineTemplates && m_DeflineTemplates->advancedView && !is_mixed_database) return;
309
310
311 string linkout_list;
312
313 sdl->linkout = CAlignFormatUtil::GetSeqLinkoutInfo(cur_id,
314 &m_LinkoutDB,
315 m_MapViewerBuildName,
316 sdl->gi);
317 if(!m_LinkoutDB) {
318 m_Option &= ~eLinkout;
319 return;
320 }
321
322
323 if(m_LinkoutOrder.empty()) {
324 m_ConfigFile.reset(new CNcbiIfstream(".ncbirc"));
325 m_Reg.reset(new CNcbiRegistry(*m_ConfigFile));
326 if(!m_BlastType.empty()) m_LinkoutOrder = m_Reg->Get(m_BlastType,"LINKOUT_ORDER");
327 m_LinkoutOrder = (!m_LinkoutOrder.empty()) ? m_LinkoutOrder : kLinkoutOrderStr;
328 }
329 if (m_DeflineTemplates == NULL || !m_DeflineTemplates->advancedView) {
330 if(m_Option & eRealtedInfoLinks){
331 string user_url = m_Reg.get() ? m_Reg->Get(m_BlastType, "TOOL_URL") : kEmptyStr;
332 sdl->linkout_list = CAlignFormatUtil::GetFullLinkoutUrl(cur_id,
333 m_Rid,
334 m_CddRid,
335 m_EntrezTerm,
336 m_IsDbNa,
337 false,
338 true,
339 blast_rank,
340 m_LinkoutOrder,
341 sdl->taxid,
342 m_Database,
343 m_QueryNumber,
344 user_url,
345 m_PreComputedResID,
346 m_LinkoutDB,
347 m_MapViewerBuildName,
348 getIdentProteins);
349 }
350 else {
351 sdl->linkout_list = CAlignFormatUtil::GetLinkoutUrl(sdl->linkout,
352 cur_id,
353 m_Rid,
354 m_CddRid,
355 m_EntrezTerm,
356 m_IsDbNa,
357 ZERO_GI,
358 true,
359 false,
360 blast_rank,
361 m_PreComputedResID);
362 }
363 }
364 }
365
366
x_FillDeflineAndId(const CBioseq_Handle & handle,const CSeq_id & aln_id,list<string> & use_this_seqid,SDeflineInfo * sdl,int blast_rank)367 void CShowBlastDefline::x_FillDeflineAndId(const CBioseq_Handle& handle,
368 const CSeq_id& aln_id,
369 list<string> &use_this_seqid,
370 SDeflineInfo* sdl,
371 int blast_rank)
372 {
373 if( !handle ) return; // invalid handle.
374
375 const CRef<CBlast_def_line_set> bdlRef = CSeqDB::ExtractBlastDefline(handle);
376 const list< CRef< CBlast_def_line > > &bdl = (bdlRef.Empty()) ? list< CRef< CBlast_def_line > >() : bdlRef->Get();
377
378 CRef<CSeq_id> wid;
379 sdl->defline = NcbiEmptyString;
380
381 sdl->gi = ZERO_GI;
382 sdl->id_url = NcbiEmptyString;
383 sdl->score_url = NcbiEmptyString;
384 sdl->linkout = 0;
385 sdl->is_new = false;
386 sdl->was_checked = false;
387 sdl->taxid = ZERO_TAX_ID;
388 //get psiblast stuff
389
390 if(m_SeqStatus){
391 string aln_id_str;
392 aln_id.GetLabel(&aln_id_str, CSeq_id::eContent);
393 PsiblastSeqStatus seq_status = eUnknown;
394
395 TIdString2SeqStatus::const_iterator itr = m_SeqStatus->find(aln_id_str);
396 if ( itr != m_SeqStatus->end() ){
397 seq_status = itr->second;
398 }
399 if((m_PsiblastStatus == eFirstPass) ||
400 ((m_PsiblastStatus == eRepeatPass) && (seq_status & eRepeatSeq))
401 || ((m_PsiblastStatus == eNewPass) && (seq_status & eRepeatSeq))){
402 if(!(seq_status & eGoodSeq)){
403 sdl->is_new = true;
404 }
405 if(seq_status & eCheckedSeq){
406 sdl->was_checked = true;
407 }
408 }
409 }
410 //get id (sdl->id, sdl-gi)
411 sdl->id = CAlignFormatUtil::GetDisplayIds(handle,aln_id,use_this_seqid,&sdl->gi,&sdl->taxid,&sdl->textSeqID);
412 sdl->alnIDFasta = aln_id.AsFastaString();
413
414 //get linkout****
415 if((m_Option & eLinkout)){
416 bool getIdentProteins = !m_IsDbNa && bdl.size() > 1;
417 for(list< CRef< CBlast_def_line > >::const_iterator iter = bdl.begin();
418 iter != bdl.end(); iter++){
419 CBioseq::TId& cur_id = (CBioseq::TId &)(*iter)->GetSeqid();
420 TGi cur_gi = FindGi(cur_id);
421 bool match = false;
422 if(!use_this_seqid.empty()){
423 wid = FindBestChoice(cur_id, CSeq_id::WorstRank);
424 match = CAlignFormatUtil::MatchSeqInSeqList(cur_gi, wid, use_this_seqid);
425 }
426 if((use_this_seqid.empty() && sdl->gi == cur_gi) || match) {
427 x_InitLinkOutInfo(sdl,cur_id,blast_rank,getIdentProteins); //only initialized if !(m_DeflineTemplates->advancedView && !is_mixed_database)
428 break;
429 }
430 }
431 //The following is the case when for whatever reason the seq is not found in Blast database (bdl list is empty) and is retrived from genbank
432 if(bdl.size() == 0) {
433 CBioseq::TId& cur_id = (CBioseq::TId &) handle.GetBioseqCore()->GetId();
434 x_InitLinkOutInfo(sdl,cur_id,blast_rank,getIdentProteins); //only initialized if !(m_DeflineTemplates->advancedView && !is_mixed_database)
435 }
436 }
437
438 //get score and id url
439 if(m_Option & (eHtml | eShowCSVDescr)){
440 bool useTemplates = m_DeflineTemplates != NULL;
441 bool advancedView = (m_DeflineTemplates != NULL) ? m_DeflineTemplates->advancedView : false;
442 string accession;
443 sdl->id->GetLabel(&accession, CSeq_id::eContent);
444 sdl->score_url = !useTemplates ? "<a href=#" : "";
445 if (!useTemplates && m_PositionIndex >= 0) {
446 sdl->score_url += "_" + NStr::IntToString(m_PositionIndex) + "_";
447 }
448 sdl->score_url += sdl->gi == ZERO_GI ? accession :
449 NStr::NumericToString(sdl->gi);
450 sdl->score_url += !useTemplates ? ">" : "";
451
452 string user_url = m_Reg.get() ? m_Reg->Get(m_BlastType, "TOOL_URL") : kEmptyStr;
453 //blast_rank = num_align + 1
454 CRange<TSeqPos> seqRange = ((int)m_ScoreList.size() >= blast_rank)? m_ScoreList[blast_rank - 1]->subjRange : CRange<TSeqPos>(0,0);
455 bool flip = ((int)m_ScoreList.size() >= blast_rank) ? m_ScoreList[blast_rank - 1]->flip : false;
456 CAlignFormatUtil::SSeqURLInfo seqUrlInfo(user_url,m_BlastType,m_IsDbNa,m_Database,m_Rid,
457 m_QueryNumber,sdl->gi, accession, 0, //linkout = 0, not used any more
458 blast_rank,false,(m_Option & eNewTargetWindow) ? true : false,seqRange,flip);
459 seqUrlInfo.resourcesUrl = m_Reg.get() ? m_Reg->Get(m_BlastType, "RESOURCE_URL") : kEmptyStr;
460 seqUrlInfo.useTemplates = useTemplates;
461 seqUrlInfo.advancedView = advancedView;
462
463 if(sdl->id->Which() == CSeq_id::e_Local && (m_Option & eHtml)){
464 //get taxid info for local blast db such as igblast db
465 ITERATE(list<CRef<CBlast_def_line> >, iter_bdl, bdl) {
466 if ((*iter_bdl)->IsSetTaxid() && (*iter_bdl)->CanGetTaxid()){
467 seqUrlInfo.taxid = (*iter_bdl)->GetTaxid();
468 break;
469 }
470 }
471 }
472 sdl->id_url = CAlignFormatUtil::GetIDUrl(&seqUrlInfo,aln_id,*m_ScopeRef);
473 }
474
475 //get defline
476 sdl->defline = CDeflineGenerator().GenerateDefline(m_ScopeRef->GetBioseqHandle(*(sdl->id)));
477 sdl->fullDefline = sdl->defline;
478 if (!(bdl.empty())) {
479 for(list< CRef< CBlast_def_line > >::const_iterator iter = bdl.begin();
480 iter != bdl.end(); iter++){
481 const CBioseq::TId& cur_id = (*iter)->GetSeqid();
482 TGi cur_gi = FindGi(cur_id);
483 wid = FindBestChoice(cur_id, CSeq_id::WorstRank);
484 bool match = CAlignFormatUtil::MatchSeqInSeqList(cur_gi, wid, use_this_seqid);
485 if(use_this_seqid.empty() || match) {
486
487 if((*iter)->IsSetTitle()){
488 bool id_used_already = false;
489 ITERATE(CBioseq::TId, iter_id, cur_id) {
490 if ((*iter_id)->Match(*(sdl->id))) {
491 id_used_already = true;
492 break;
493 }
494 }
495 if (!id_used_already) {
496 string concat_acc;
497 wid = FindBestChoice(cur_id, CSeq_id::WorstRank);
498 wid->GetLabel(&concat_acc, CSeq_id::eFasta, 0);
499 if( (m_Option & eShowGi) && cur_gi > ZERO_GI){
500 sdl->fullDefline = sdl->fullDefline + " >" + "gi|" +
501 NStr::NumericToString(cur_gi) + "|" +
502 concat_acc + " " + (*iter)->GetTitle();
503 } else {
504 sdl->fullDefline = sdl->fullDefline + " >" + concat_acc +
505 " " +
506 (*iter)->GetTitle();
507 }
508 if(sdl->fullDefline.length() > kMaxDescrLength) {
509 break;
510 }
511 }
512 }
513 }
514 }
515 }
516 }
517
518 //Constructor
CShowBlastDefline(const CSeq_align_set & seqalign,CScope & scope,size_t line_length,size_t num_defline_to_show,bool translated_nuc_alignment,CRange<TSeqPos> * master_range)519 CShowBlastDefline::CShowBlastDefline(const CSeq_align_set& seqalign,
520 CScope& scope,
521 size_t line_length,
522 size_t num_defline_to_show,
523 bool translated_nuc_alignment,
524 CRange<TSeqPos>* master_range):
525
526 m_AlnSetRef(&seqalign),
527 m_ScopeRef(&scope),
528 m_LineLen(line_length),
529 m_NumToShow(num_defline_to_show),
530 m_TranslatedNucAlignment(translated_nuc_alignment),
531 m_SkipFrom(-1),
532 m_SkipTo(-1),
533 m_MasterRange(master_range),
534 m_LinkoutDB(NULL)
535 {
536
537 m_Option = 0;
538 m_EntrezTerm = NcbiEmptyString;
539 m_QueryNumber = 0;
540 m_Rid = NcbiEmptyString;
541 m_CddRid = NcbiEmptyString;
542 m_IsDbNa = true;
543 m_BlastType = NcbiEmptyString;
544 m_PsiblastStatus = eFirstPass;
545 m_SeqStatus = NULL;
546 m_Ctx = NULL;
547 m_StructureLinkout = false;
548 if(m_MasterRange) {
549 if(m_MasterRange->GetFrom() >= m_MasterRange->GetTo()) {
550 m_MasterRange = NULL;
551 }
552 }
553 m_DeflineTemplates = NULL;
554 m_StartIndex = 0;
555 m_PositionIndex = -1;
556 m_AppLogInfo = NULL;
557 }
558
~CShowBlastDefline()559 CShowBlastDefline::~CShowBlastDefline()
560 {
561 ITERATE(vector<SScoreInfo*>, iter, m_ScoreList){
562 delete *iter;
563 }
564
565 ITERATE(vector<SDeflineFormattingInfo*>, iter, m_SdlFormatInfoVec){
566 delete *iter;
567 }
568
569 }
570
571
Init(void)572 void CShowBlastDefline::Init(void)
573 {
574 if (m_DeflineTemplates != NULL) {
575 x_InitDeflineTable();
576 }
577 else {
578 x_InitDefline();
579 }
580 }
581
582
Display(CNcbiOstream & out)583 void CShowBlastDefline::Display(CNcbiOstream & out)
584 {
585 if (m_DeflineTemplates != NULL) {
586 if(m_Option & eHtml) {//text
587 x_DisplayDeflineTableTemplate(out);
588 }
589 else if(m_Option & eShowCSVDescr) {
590 x_DisplayDeflineTableTemplateCSV(out);
591 }
592 else {//text
593 x_DisplayDeflineTableTemplateText(out);
594 }
595 }
596 else {
597 x_DisplayDefline(out);
598 }
599 }
600
x_CheckForStructureLink()601 bool CShowBlastDefline::x_CheckForStructureLink()
602 {
603 bool struct_linkout = false;
604 int count = 0;
605 const int k_CountMax = 200; // Max sequences to check.
606
607 ITERATE(vector<SScoreInfo*>, iter, m_ScoreList) {
608 const CBioseq_Handle& handle = m_ScopeRef->GetBioseqHandle(*(*iter)->id);
609 if( !handle ) continue; // invalid handle.
610 const CRef<CBlast_def_line_set> bdlRef = CSeqDB::ExtractBlastDefline(handle);
611 const list< CRef< CBlast_def_line > > &bdl = (bdlRef.Empty()) ? list< CRef< CBlast_def_line > >() : bdlRef->Get();
612 for(list< CRef< CBlast_def_line > >::const_iterator bdl_iter = bdl.begin();
613 bdl_iter != bdl.end() && struct_linkout == false; bdl_iter++){
614 if ((*bdl_iter)->IsSetLinks())
615 {
616 for (list< int >::const_iterator link_iter = (*bdl_iter)->GetLinks().begin();
617 link_iter != (*bdl_iter)->GetLinks().end(); link_iter++)
618 {
619 if (*link_iter & eStructure) {
620 struct_linkout = true;
621 break;
622 }
623 }
624 }
625 }
626 if (struct_linkout == true || count > k_CountMax)
627 break;
628 count++;
629 }
630 return struct_linkout;
631 }
632
633 //size_t max_score_len = kBits.size(), max_evalue_len = kValue.size();
634 //size_t max_sum_n_len =1;
635 //size_t m_MaxScoreLen , m_MaxEvalueLen,m_MaxSumNLen;
636 //bool m_StructureLinkout
x_InitDefline(void)637 void CShowBlastDefline::x_InitDefline(void)
638 {
639 /*Note we can't just show each alnment as we go because we will
640 need to show defline only once for all hsp's with the same id*/
641
642 bool is_first_aln = true;
643 size_t num_align = 0;
644 CConstRef<CSeq_id> previous_id, subid;
645
646 m_MaxScoreLen = kBits.size();
647 m_MaxEvalueLen = kValue.size();
648 m_MaxSumNLen =1;
649
650 m_MaxPercentIdentityLen = kIdentity.size();
651 m_MaxQueryCoverLen = kCoverage.size();
652 m_MaxTotalScoreLen = kTotal.size();
653
654
655
656 if(m_Option & eHtml){
657 m_ConfigFile.reset(new CNcbiIfstream(".ncbirc"));
658 m_Reg.reset(new CNcbiRegistry(*m_ConfigFile));
659 }
660 bool master_is_na = false;
661 //prepare defline
662
663 int ialn = 0;
664 for (CSeq_align_set::Tdata::const_iterator
665 iter = m_AlnSetRef->Get().begin();
666 iter != m_AlnSetRef->Get().end() && num_align < m_NumToShow;
667 iter++, ialn++){
668 if (ialn < m_SkipTo && ialn >= m_SkipFrom) continue;
669
670 if (is_first_aln) {
671 _ASSERT(m_ScopeRef);
672 CBioseq_Handle bh = m_ScopeRef->GetBioseqHandle((*iter)->GetSeq_id(0));
673 _ASSERT(bh);
674 master_is_na = bh.GetBioseqCore()->IsNa();
675 }
676 subid = &((*iter)->GetSeq_id(1));
677 if(is_first_aln || (!is_first_aln && !subid->Match(*previous_id))) {
678 SScoreInfo* sci = x_GetScoreInfo(**iter, num_align);
679 if(sci){
680 m_ScoreList.push_back(sci);
681 if(m_MaxScoreLen < sci->bit_string.size()){
682 m_MaxScoreLen = sci->bit_string.size();
683 }
684 if(m_MaxEvalueLen < sci->evalue_string.size()){
685 m_MaxEvalueLen = sci->evalue_string.size();
686 }
687
688 if(m_MaxTotalScoreLen < sci->total_bit_string.size()){
689 m_MaxTotalScoreLen = sci->total_bit_string.size();
690 }
691 int percent_identity = CAlignFormatUtil::GetPercentMatch(sci->match,sci->align_length);
692 if(m_MaxPercentIdentityLen < NStr::IntToString(percent_identity).size()) {
693 m_MaxPercentIdentityLen = NStr::IntToString(percent_identity).size();
694 }
695
696 if( m_MaxSumNLen < NStr::IntToString(sci->sum_n).size()){
697 m_MaxSumNLen = NStr::IntToString(sci->sum_n).size();
698 }
699 }
700 num_align++;
701 }
702 is_first_aln = false;
703 previous_id = subid;
704
705 }
706
707
708 if((m_Option & eLinkout) && (m_Option & eHtml) && !m_IsDbNa && !master_is_na)
709 m_StructureLinkout = x_CheckForStructureLink();
710 }
711
712
713
x_DisplayDefline(CNcbiOstream & out)714 void CShowBlastDefline::x_DisplayDefline(CNcbiOstream & out)
715 {
716 bool use_long_seqids = (m_Option & eLongSeqId) != 0;
717
718 if(!(m_Option & eNoShowHeader)) {
719 if((m_PsiblastStatus == eFirstPass) ||
720 (m_PsiblastStatus == eRepeatPass)){
721 CAlignFormatUtil::AddSpace(out, m_LineLen + kTwoSpaceMargin.size());
722 if(m_Option & eHtml){
723 if((m_Option & eShowNewSeqGif)){
724 out << kPsiblastNewSeqBackgroundGif;
725 out << kPsiblastCheckedBackgroundGif;
726 }
727 if (m_Option & eCheckbox) {
728 out << kPsiblastNewSeqBackgroundGif;
729 out << kPsiblastCheckedBackgroundGif;
730 }
731 }
732 out << kScore;
733 CAlignFormatUtil::AddSpace(out, m_MaxScoreLen - kScore.size());
734 CAlignFormatUtil::AddSpace(out, kTwoSpaceMargin.size());
735
736
737 if (m_Option & eShowTotalScore) {
738 out << kTotal;
739 CAlignFormatUtil::AddSpace(out, m_MaxTotalScoreLen - kTotal.size());
740 CAlignFormatUtil::AddSpace(out, kTwoSpaceMargin.size());
741 }
742 if (m_Option & eShowQueryCoverage) {
743 out << kQueryCov;
744 CAlignFormatUtil::AddSpace(out, kTwoSpaceMargin.size());
745 }
746
747 CAlignFormatUtil::AddSpace(out, 2); //E align to l of value
748 out << kE;
749
750 if (m_Option & eShowPercentIdent) {
751 CAlignFormatUtil::AddSpace(out, m_MaxEvalueLen - kValue.size());
752 CAlignFormatUtil::AddSpace(out, kTwoSpaceMargin.size());
753 CAlignFormatUtil::AddSpace(out, kTwoSpaceMargin.size());
754 CAlignFormatUtil::AddSpace(out, kOneSpaceMargin.size());
755 out << kMax;//"Max" - "ident" -second line
756 }
757
758 out << "\n";
759 out << kHeader;
760 if(m_Option & eHtml){
761 if((m_Option & eShowNewSeqGif)){
762 out << kPsiblastNewSeqBackgroundGif;
763 out << kPsiblastCheckedBackgroundGif;
764 }
765 if (m_Option & eCheckbox) {
766 out << kPsiblastNewSeqBackgroundGif;
767 out << kPsiblastCheckedBackgroundGif;
768 }
769 }
770 CAlignFormatUtil::AddSpace(out, m_LineLen - kHeader.size());
771 CAlignFormatUtil::AddSpace(out, kOneSpaceMargin.size());
772 out << kBits;
773 //in case m_MaxScoreLen > kBits.size()
774 CAlignFormatUtil::AddSpace(out, m_MaxScoreLen - kBits.size());
775 CAlignFormatUtil::AddSpace(out, kTwoSpaceMargin.size());
776
777
778 if (m_Option & eShowTotalScore) {
779 CAlignFormatUtil::AddSpace(out, kOneSpaceMargin.size());
780 out << kScoreLine2;//"score"
781 CAlignFormatUtil::AddSpace(out, m_MaxTotalScoreLen - kTotal.size());
782 CAlignFormatUtil::AddSpace(out, kTwoSpaceMargin.size());
783 }
784 if (m_Option & eShowQueryCoverage) {
785 out << kQueryCovLine2;//"cov"
786 CAlignFormatUtil::AddSpace(out, kTwoSpaceMargin.size());
787 CAlignFormatUtil::AddSpace(out, kOneSpaceMargin.size());
788 }
789
790 out << kValue;
791 if((m_Option & eShowSumN) || (m_Option & eShowPercentIdent)){
792 CAlignFormatUtil::AddSpace(out, m_MaxEvalueLen - kValue.size());
793 CAlignFormatUtil::AddSpace(out, kTwoSpaceMargin.size());
794 }
795 if(m_Option & eShowSumN){
796 out << kN;
797 }
798 if (m_Option & eShowPercentIdent) {
799 out << kIdentLine2;//"ident"
800 }
801 out << "\n";
802 }
803 if(m_PsiblastStatus == eRepeatPass){
804 out << kRepeatHeader << "\n";
805 }
806 if(m_PsiblastStatus == eNewPass){
807 out << kNewSeqHeader << "\n";
808 }
809 out << "\n";
810 }
811
812 bool first_new =true;
813 ITERATE(vector<SScoreInfo*>, iter, m_ScoreList){
814 SDeflineInfo* sdl = x_GetDeflineInfo((*iter)->id, (*iter)->use_this_seqid, (*iter)->blast_rank);
815 size_t line_length = 0;
816 string line_component;
817 if ((m_Option & eHtml) && (sdl->gi > ZERO_GI)){
818 if((m_Option & eShowNewSeqGif)) {
819 if (sdl->is_new) {
820 if (first_new) {
821 first_new = false;
822 out << kPsiblastEvalueLink;
823 }
824 out << kPsiblastNewSeqGif;
825
826 } else {
827 out << kPsiblastNewSeqBackgroundGif;
828 }
829 if (sdl->was_checked) {
830 out << kPsiblastCheckedGif;
831
832 } else {
833 out << kPsiblastCheckedBackgroundGif;
834 }
835 }
836 char buf[256];
837 if((m_Option & eCheckboxChecked)){
838 sprintf(buf, kPsiblastCheckboxChecked.c_str(), sdl->gi,
839 sdl->gi);
840 out << buf;
841 } else if (m_Option & eCheckbox) {
842 sprintf(buf, kPsiblastCheckbox.c_str(), sdl->gi);
843 out << buf;
844 }
845 }
846
847
848 if((m_Option & eHtml) && (sdl->id_url != NcbiEmptyString)) {
849 out << sdl->id_url;
850 }
851 if(m_Option & eShowGi){
852 if(sdl->gi > ZERO_GI){
853 line_component = "gi|" + NStr::NumericToString(sdl->gi) + "|";
854 out << line_component;
855 line_length += line_component.size();
856 }
857 }
858 if(!sdl->id.Empty()){
859 if(!(sdl->id->AsFastaString().find("gnl|BL_ORD_ID") != string::npos ||
860 sdl->id->AsFastaString().find("lcl|Subject_") != string::npos)){
861 string idStr;
862 if (use_long_seqids || ((m_Option & eShowGi) && !sdl->id->IsGi())) {
863 idStr = sdl->id->AsFastaString();
864 }
865 else {
866 idStr = CAlignFormatUtil::GetBareId(*sdl->id) + " ";
867 }
868 if (strncmp(idStr.c_str(), "lcl|", 4) == 0) {
869 idStr = sdl->id->AsFastaString().substr(4);
870 }
871 out << idStr;
872 line_length += idStr.size();
873 }
874 }
875 if((m_Option & eHtml) && (sdl->id_url != NcbiEmptyString)) {
876 out << "</a>";
877 }
878 line_component = (line_component.empty() ? "" : " ") + sdl->defline;
879 string actual_line_component;
880 if(line_component.size()+line_length > m_LineLen){
881 actual_line_component = line_component.substr(0, m_LineLen -
882 line_length - 3);
883 actual_line_component += kEllipsis;
884 } else {
885 actual_line_component = line_component.substr(0, m_LineLen -
886 line_length);
887 }
888 if (m_Option & eHtml) {
889 out << CHTMLHelper::HTMLEncode(actual_line_component);
890 } else {
891 out << actual_line_component;
892 }
893 line_length += actual_line_component.size();
894 //pad the short lines
895 CAlignFormatUtil::AddSpace(out, m_LineLen - line_length);
896 out << kTwoSpaceMargin;
897
898 if((m_Option & eHtml) && (sdl->score_url != NcbiEmptyString)) {
899 out << sdl->score_url;
900 }
901 out << (*iter)->bit_string;
902 if((m_Option & eHtml) && (sdl->score_url != NcbiEmptyString)) {
903 out << "</a>";
904 }
905 CAlignFormatUtil::AddSpace(out, m_MaxScoreLen - (*iter)->bit_string.size());
906 if (m_Option & eShowTotalScore) {
907 out << kTwoSpaceMargin << kOneSpaceMargin << (*iter)->total_bit_string;
908 CAlignFormatUtil::AddSpace(out, m_MaxTotalScoreLen -
909 (*iter)->total_bit_string.size());
910 }
911
912 if (m_Option & eShowQueryCoverage) {
913 //int percent_coverage = 100*(*iter)->master_covered_length/m_QueryLength;
914 int percent_coverage = (*iter)->percent_coverage;
915
916 out << kTwoSpaceMargin << percent_coverage << "%";
917 //minus one due to % sign
918 CAlignFormatUtil::AddSpace(out, kQueryCov.size() -
919 NStr::IntToString(percent_coverage).size() - 1);
920 }
921
922
923 out << kTwoSpaceMargin << (*iter)->evalue_string;
924 CAlignFormatUtil::AddSpace(out, m_MaxEvalueLen - (*iter)->evalue_string.size());
925
926 if(m_Option & eShowSumN){
927 out << kTwoSpaceMargin << (*iter)->sum_n;
928 CAlignFormatUtil::AddSpace(out, m_MaxSumNLen -
929 NStr::IntToString((*iter)->sum_n).size());
930 }
931 if(m_Option & eShowPercentIdent){
932 int percent_identity =(int) (0.5 + (*iter)->percent_identity);
933 if(percent_identity > 100) {
934 percent_identity = min(99, percent_identity);
935 }
936 out << kTwoSpaceMargin << percent_identity <<"%";
937 CAlignFormatUtil::AddSpace(out, m_MaxPercentIdentityLen -
938 NStr::IntToString(percent_identity).size());
939 }
940 if((m_Option & eLinkout) && (m_Option & eHtml)){
941 bool is_first = true;
942 ITERATE(list<string>, iter_linkout, sdl->linkout_list){
943 if(is_first){
944 out << kOneSpaceMargin;
945 is_first = false;
946 }
947 out << *iter_linkout;
948 }
949 }
950 out <<"\n";
951 delete sdl;
952 }
953 }
954
DisplayBlastDefline(CNcbiOstream & out)955 void CShowBlastDefline::DisplayBlastDefline(CNcbiOstream & out)
956 {
957 x_InitDeflineTable();
958 if(m_StructureLinkout){
959 char buf[512];
960 string mapCDDParams = (NStr::Find(m_CddRid,"data_cache") != NPOS) ? "" : "blast_CD_RID=" + m_CddRid;
961 sprintf(buf, kStructure_Overview, m_Rid.c_str(),
962 0, 0, mapCDDParams.c_str(), "overview",
963 m_EntrezTerm == NcbiEmptyString ?
964 "none": m_EntrezTerm.c_str());
965 out << buf <<"\n\n";
966 }
967 x_DisplayDefline(out);
968 }
969
s_DisplayDescrColumnHeader(CNcbiOstream & out,int currDisplaySort,string query_buf,int columnDisplSort,int columnHspSort,string columnText,int max_data_len,bool html)970 static void s_DisplayDescrColumnHeader(CNcbiOstream & out,
971 int currDisplaySort,
972 string query_buf,
973 int columnDisplSort,
974 int columnHspSort,
975 string columnText,
976 int max_data_len,
977 bool html)
978
979
980 {
981 if (html) {
982 if(currDisplaySort == columnDisplSort) {
983 out << "<th class=\"sel\">";
984 }
985 else {
986 out << "<th>";
987 }
988
989 out << "<a href=\"Blast.cgi?"
990 << "CMD=Get&" << query_buf
991 << "&DISPLAY_SORT=" << columnDisplSort
992 << "&HSP_SORT=" << columnHspSort
993 << "#sort_mark\">";
994
995 }
996 out << columnText;
997 if (html) {
998 out << "</a></th>\n";
999 }
1000 else {
1001 CAlignFormatUtil::AddSpace(out, max_data_len - columnText.size());
1002 CAlignFormatUtil::AddSpace(out, kTwoSpaceMargin.size());
1003 }
1004
1005 }
1006
x_InitDeflineTable(void)1007 void CShowBlastDefline::x_InitDeflineTable(void)
1008 {
1009 /*Note we can't just show each alnment as we go because we will
1010 need to show defline only once for all hsp's with the same id*/
1011
1012 bool is_first_aln = true;
1013 size_t num_align = 0;
1014 CConstRef<CSeq_id> previous_id, subid;
1015 m_MaxScoreLen = kBits.size();
1016 m_MaxEvalueLen = kValue.size();
1017 m_MaxSumNLen =1;
1018 m_MaxTotalScoreLen = kTotal.size();
1019 m_MaxPercentIdentityLen = kIdentity.size();
1020 int percent_identity = 0;
1021 m_MaxQueryCoverLen = kQueryCov.size();
1022
1023
1024 if(m_Option & eHtml){
1025 m_ConfigFile.reset(new CNcbiIfstream(".ncbirc"));
1026 m_Reg.reset(new CNcbiRegistry(*m_ConfigFile));
1027 if(!m_BlastType.empty()) m_LinkoutOrder = m_Reg->Get(m_BlastType,"LINKOUT_ORDER");
1028 m_LinkoutOrder = (!m_LinkoutOrder.empty()) ? m_LinkoutOrder : kLinkoutOrderStr;
1029 }
1030
1031 CSeq_align_set hit;
1032 m_QueryLength = 1;
1033 bool master_is_na = false;
1034 //prepare defline
1035
1036 int ialn = 0;
1037 for (CSeq_align_set::Tdata::const_iterator
1038 iter = m_AlnSetRef->Get().begin();
1039 iter != m_AlnSetRef->Get().end() && num_align < m_NumToShow;
1040 iter++, ialn++){
1041
1042 if (ialn < m_SkipTo && ialn >= m_SkipFrom) continue;
1043 if (is_first_aln) {
1044 m_QueryLength = m_MasterRange ?
1045 m_MasterRange->GetLength() :
1046 m_ScopeRef->GetBioseqHandle((*iter)->GetSeq_id(0)).GetBioseqLength();
1047 master_is_na = m_ScopeRef->GetBioseqHandle((*iter)->GetSeq_id(0)).
1048 GetBioseqCore()->IsNa();
1049 }
1050
1051 subid = &((*iter)->GetSeq_id(1));
1052
1053 // This if statement is working on the last CSeq_align_set, stored in "hit"
1054 // This is confusing and the loop should probably be restructured at some point.
1055 if(!is_first_aln && !(subid->Match(*previous_id))) {
1056 SScoreInfo* sci = x_GetScoreInfoForTable(hit, num_align);
1057 if(sci){
1058 m_ScoreList.push_back(sci);
1059 if(m_MaxScoreLen < sci->bit_string.size()){
1060 m_MaxScoreLen = sci->bit_string.size();
1061 }
1062 if(m_MaxTotalScoreLen < sci->total_bit_string.size()){
1063 m_MaxTotalScoreLen = sci->total_bit_string.size();
1064 }
1065 percent_identity = CAlignFormatUtil::GetPercentMatch(sci->match,sci->align_length);
1066 if(m_MaxPercentIdentityLen < NStr::IntToString(percent_identity).size()) {
1067 m_MaxPercentIdentityLen = NStr::IntToString(percent_identity).size();
1068 }
1069 if(m_MaxEvalueLen < sci->evalue_string.size()){
1070 m_MaxEvalueLen = sci->evalue_string.size();
1071 }
1072
1073 if( m_MaxSumNLen < NStr::IntToString(sci->sum_n).size()){
1074 m_MaxSumNLen = NStr::IntToString(sci->sum_n).size();
1075 }
1076 hit.Set().clear();
1077 }
1078
1079 num_align++; // Only increment if new subject ID found.
1080 }
1081 if (num_align < m_NumToShow) { //no adding if number to show already reached
1082 hit.Set().push_back(*iter);
1083 }
1084 is_first_aln = false;
1085 previous_id = subid;
1086 }
1087
1088 //the last hit
1089 SScoreInfo* sci = x_GetScoreInfoForTable(hit, num_align);
1090 if(sci){
1091 m_ScoreList.push_back(sci);
1092 if(m_MaxScoreLen < sci->bit_string.size()){
1093 m_MaxScoreLen = sci->bit_string.size();
1094 }
1095 if(m_MaxTotalScoreLen < sci->total_bit_string.size()){
1096 m_MaxScoreLen = sci->total_bit_string.size();
1097 }
1098 percent_identity = CAlignFormatUtil::GetPercentMatch(sci->match,sci->align_length);
1099 if(m_MaxPercentIdentityLen < NStr::IntToString(percent_identity).size()) {
1100 m_MaxPercentIdentityLen = NStr::IntToString(percent_identity).size();
1101 }
1102 if(m_MaxEvalueLen < sci->evalue_string.size()){
1103 m_MaxEvalueLen = sci->evalue_string.size();
1104 }
1105
1106 if( m_MaxSumNLen < NStr::IntToString(sci->sum_n).size()){
1107 m_MaxSumNLen = NStr::IntToString(sci->sum_n).size();
1108 }
1109 hit.Set().clear();
1110 }
1111
1112 if((m_Option & eLinkout) && (m_Option & eHtml) && !m_IsDbNa && !master_is_na)
1113 m_StructureLinkout = x_CheckForStructureLink();
1114
1115 }
1116
x_DisplayDeflineTable(CNcbiOstream & out)1117 void CShowBlastDefline::x_DisplayDeflineTable(CNcbiOstream & out)
1118 {
1119 //This is max number of columns in the table - later should be probably put in enum DisplayOption
1120 if((m_PsiblastStatus == eFirstPass) ||
1121 (m_PsiblastStatus == eRepeatPass)){
1122
1123 if(m_Option & eHtml){
1124 if((m_Option & eShowNewSeqGif)){
1125 out << kPsiblastNewSeqBackgroundGif;
1126 out << kPsiblastCheckedBackgroundGif;
1127 }
1128 if (m_Option & eCheckbox) {
1129 out << kPsiblastNewSeqBackgroundGif;
1130 out << kPsiblastCheckedBackgroundGif;
1131 }
1132 }
1133 //This is done instead of code displaying titles
1134 if(!(m_Option & eNoShowHeader)) {
1135
1136 if(m_Option & eHtml){
1137
1138 out << "<b>";
1139 }
1140 out << kHeader << "\n";
1141 if(m_Option & eHtml){
1142 out << "</b>";
1143 out << "(Click headers to sort columns)\n";
1144 }
1145 }
1146 if(m_Option & eHtml){
1147 out << "<div id=\"desctbl\">" << "<table id=\"descs\">" << "\n" << "<thead>" << "\n";
1148 out << "<tr class=\"first\">" << "\n" << "<th>Accession</th>" << "\n" << "<th>Description</th>" << "\n";
1149 }
1150
1151 string query_buf;
1152 map< string, string> parameters_to_change;
1153 parameters_to_change.insert(map<string, string>::
1154 value_type("DISPLAY_SORT", ""));
1155 parameters_to_change.insert(map<string, string>::
1156 value_type("HSP_SORT", ""));
1157 CAlignFormatUtil::BuildFormatQueryString(*m_Ctx,
1158 parameters_to_change,
1159 query_buf);
1160
1161 parameters_to_change.clear();
1162
1163 string display_sort_value = m_Ctx->GetRequestValue("DISPLAY_SORT").
1164 GetValue();
1165 int display_sort = display_sort_value == NcbiEmptyString ?
1166 CAlignFormatUtil::eEvalue : NStr::StringToInt(display_sort_value);
1167
1168 s_DisplayDescrColumnHeader(out,display_sort,query_buf,CAlignFormatUtil::eHighestScore,CAlignFormatUtil::eScore,kMaxScore,m_MaxScoreLen,m_Option & eHtml);
1169
1170 s_DisplayDescrColumnHeader(out,display_sort,query_buf,CAlignFormatUtil::eTotalScore,CAlignFormatUtil::eScore,kTotalScore,m_MaxTotalScoreLen,m_Option & eHtml);
1171 s_DisplayDescrColumnHeader(out,display_sort,query_buf,CAlignFormatUtil::eQueryCoverage,CAlignFormatUtil::eHspEvalue,kCoverage,m_MaxQueryCoverLen,m_Option & eHtml);
1172 s_DisplayDescrColumnHeader(out,display_sort,query_buf,CAlignFormatUtil::eEvalue,CAlignFormatUtil::eHspEvalue,kEvalue,m_MaxEvalueLen,m_Option & eHtml);
1173 if(m_Option & eShowPercentIdent){
1174 s_DisplayDescrColumnHeader(out,display_sort,query_buf,CAlignFormatUtil::ePercentIdentity,CAlignFormatUtil::eHspPercentIdentity,kIdentity,m_MaxPercentIdentityLen,m_Option & eHtml);
1175 }else {
1176 }
1177
1178 if(m_Option & eShowSumN){
1179 out << "<th>" << kN << "</th>" << "\n";
1180
1181 }
1182 if (m_Option & eLinkout) {
1183 out << "<th>Links</th>\n";
1184 out << "</tr>\n";
1185 out << "</thead>\n";
1186 }
1187 }
1188
1189 if (m_Option & eHtml) {
1190 out << "<tbody>\n";
1191 }
1192
1193 x_DisplayDeflineTableBody(out);
1194
1195 if (m_Option & eHtml) {
1196 out << "</tbody>\n</table></div>\n";
1197 }
1198 }
1199
x_DisplayDeflineTableBody(CNcbiOstream & out)1200 void CShowBlastDefline::x_DisplayDeflineTableBody(CNcbiOstream & out)
1201 {
1202 int percent_identity = 0;
1203 int tableColNumber = (m_Option & eShowPercentIdent) ? 9 : 8;
1204 bool first_new =true;
1205 int prev_database_type = 0, cur_database_type = 0;
1206 bool is_first = true;
1207 // Mixed db is genomic + transcript and this does not apply to proteins.
1208 bool is_mixed_database = false;
1209 if (m_IsDbNa == true)
1210 is_mixed_database = CAlignFormatUtil::IsMixedDatabase(*m_Ctx);
1211
1212 map< string, string> parameters_to_change;
1213 string query_buf;
1214 if (is_mixed_database && m_Option & eHtml) {
1215 parameters_to_change.insert(map<string, string>::
1216 value_type("DATABASE_SORT", ""));
1217 CAlignFormatUtil::BuildFormatQueryString(*m_Ctx,
1218 parameters_to_change,
1219 query_buf);
1220 }
1221 ITERATE(vector<SScoreInfo*>, iter, m_ScoreList){
1222 SDeflineInfo* sdl = x_GetDeflineInfo((*iter)->id, (*iter)->use_this_seqid, (*iter)->blast_rank);
1223 size_t line_length = 0;
1224 string line_component;
1225 cur_database_type = (sdl->linkout & eGenomicSeq);
1226 if (is_mixed_database) {
1227 if (is_first) {
1228 if (m_Option & eHtml) {
1229 out << "<tr>\n<th colspan=\"" << tableColNumber<< "\" class=\"l sp\">";
1230 }
1231 if (cur_database_type) {
1232 out << "Genomic sequences";
1233 } else {
1234 out << "Transcripts";
1235 }
1236 if (!(m_Option & eHtml)) {
1237 out << ":\n";
1238 }
1239 if (m_Option & eHtml) {
1240 out << "</th></tr>\n";
1241 }
1242 } else if (prev_database_type != cur_database_type) {
1243 if (m_Option & eHtml) {
1244 out << "<tr>\n<th colspan=\"" << tableColNumber<< "\" class=\"l sp\">";
1245 }
1246 if (cur_database_type) {
1247 out << "Genomic sequences";
1248 } else {
1249 out << "Transcripts";
1250 }
1251 if (m_Option & eHtml) {
1252 out << "<span class=\"slink\">"
1253 << " [<a href=\"Blast.cgi?CMD=Get&"
1254 << query_buf
1255 << "&DATABASE_SORT=";
1256 if (cur_database_type) {
1257 out << CAlignFormatUtil::eGenomicFirst;
1258 } else {
1259 out << CAlignFormatUtil::eNonGenomicFirst;
1260 }
1261 out << "#sort_mark\">show first</a>]</span>";
1262 }
1263 else {
1264 out << ":\n";
1265 }
1266 if (m_Option & eHtml) {
1267 out << "</th></tr>\n";
1268 }
1269 }
1270 }
1271 prev_database_type = cur_database_type;
1272 is_first = false;
1273 if (m_Option & eHtml) {
1274 out << "<tr>\n";
1275 out << "<td class=\"l\">\n";
1276 }
1277 if ((m_Option & eHtml) && (sdl->gi > ZERO_GI)){
1278 if((m_Option & eShowNewSeqGif)) {
1279 if (sdl->is_new) {
1280 if (first_new) {
1281 first_new = false;
1282 out << kPsiblastEvalueLink;
1283 }
1284 out << kPsiblastNewSeqGif;
1285
1286 } else {
1287 out << kPsiblastNewSeqBackgroundGif;
1288 }
1289 if (sdl->was_checked) {
1290 out << kPsiblastCheckedGif;
1291
1292 } else {
1293 out << kPsiblastCheckedBackgroundGif;
1294 }
1295 }
1296 char buf[256];
1297 if((m_Option & eCheckboxChecked)){
1298 sprintf(buf, kPsiblastCheckboxChecked.c_str(), sdl->gi,
1299 sdl->gi);
1300 out << buf;
1301 } else if (m_Option & eCheckbox) {
1302 sprintf(buf, kPsiblastCheckbox.c_str(), sdl->gi);
1303 out << buf;
1304 }
1305 }
1306
1307
1308 if((m_Option & eHtml) && (sdl->id_url != NcbiEmptyString)) {
1309 out << sdl->id_url;
1310 }
1311 if(m_Option & eShowGi){
1312 if(sdl->gi > ZERO_GI){
1313 line_component = "gi|" + NStr::NumericToString(sdl->gi) + "|";
1314 out << line_component;
1315 line_length += line_component.size();
1316 }
1317 }
1318 if(!sdl->id.Empty()){
1319 if(!(sdl->id->AsFastaString().find("gnl|BL_ORD_ID") != string::npos ||
1320 sdl->id->AsFastaString().find("lcl|Subject_") != string::npos)){
1321 string id_str;
1322 sdl->id->GetLabel(&id_str, CSeq_id::eContent);
1323 out << id_str;
1324 line_length += id_str.size();
1325 }
1326 }
1327 if((m_Option & eHtml) && (sdl->id_url != NcbiEmptyString)) {
1328 out << "</a>";
1329 }
1330 if (m_Option & eHtml) {
1331 out << "</td><td class=\"lim l\"><div class=\"lim\">";
1332 }
1333 line_component = " " + sdl->defline;
1334 string actual_line_component;
1335 actual_line_component = line_component;
1336
1337 if (m_Option & eHtml) {
1338 out << CHTMLHelper::HTMLEncode(actual_line_component);
1339 out << "</div></td><td>";
1340 } else {
1341 out << actual_line_component;
1342 }
1343
1344 if((m_Option & eHtml) && (sdl->score_url != NcbiEmptyString)) {
1345 out << sdl->score_url;
1346 }
1347 out << (*iter)->bit_string;
1348 if((m_Option & eHtml) && (sdl->score_url != NcbiEmptyString)) {
1349 out << "</a>";
1350 }
1351 if(m_Option & eHtml) {
1352 out << "</td>";
1353 out << "<td>" << (*iter)->total_bit_string << "</td>";
1354 }
1355 if (!(m_Option & eHtml)) {
1356 CAlignFormatUtil::AddSpace(out, m_MaxScoreLen - (*iter)->bit_string.size());
1357
1358 out << kTwoSpaceMargin << kOneSpaceMargin << (*iter)->total_bit_string;
1359 CAlignFormatUtil::AddSpace(out, m_MaxTotalScoreLen -
1360 (*iter)->total_bit_string.size());
1361 }
1362
1363 int percent_coverage = 100*(*iter)->master_covered_length/m_QueryLength;
1364 if (m_Option & eHtml) {
1365 out << "<td>" << percent_coverage << "%</td>";
1366 }
1367 else {
1368 out << kTwoSpaceMargin << percent_coverage << "%";
1369
1370 //minus one due to % sign
1371 CAlignFormatUtil::AddSpace(out, m_MaxQueryCoverLen -
1372 NStr::IntToString(percent_coverage).size() - 1);
1373 }
1374
1375 if (m_Option & eHtml) {
1376 out << "<td>" << (*iter)->evalue_string << "</td>";
1377 }
1378 else {
1379 out << kTwoSpaceMargin << (*iter)->evalue_string;
1380 CAlignFormatUtil::AddSpace(out, m_MaxEvalueLen - (*iter)->evalue_string.size());
1381 }
1382 if(m_Option & eShowPercentIdent){
1383 percent_identity = CAlignFormatUtil::GetPercentMatch((*iter)->match,(*iter)->align_length);
1384 if (m_Option & eHtml) {
1385 out << "<td>" << percent_identity << "%</td>";
1386 }
1387 else {
1388 out << kTwoSpaceMargin << percent_identity <<"%";
1389
1390 CAlignFormatUtil::AddSpace(out, m_MaxPercentIdentityLen -
1391 NStr::IntToString(percent_identity).size());
1392 }
1393 }
1394 //???
1395 if(m_Option & eShowSumN){
1396 if (m_Option & eHtml) {
1397 out << "<td>";
1398 }
1399 out << kTwoSpaceMargin << (*iter)->sum_n;
1400 if (m_Option & eHtml) {
1401 out << "</td>";
1402 } else {
1403 CAlignFormatUtil::AddSpace(out, m_MaxSumNLen -
1404 NStr::IntToString((*iter)->sum_n).size());
1405 }
1406 }
1407
1408 if((m_Option & eLinkout) && (m_Option & eHtml)){
1409
1410 out << "<td>";
1411 bool first_time = true;
1412 ITERATE(list<string>, iter_linkout, sdl->linkout_list){
1413 if(first_time){
1414 out << kOneSpaceMargin;
1415 first_time = false;
1416 }
1417 out << *iter_linkout;
1418 }
1419 out << "</td>";
1420 }
1421 if (m_Option & eHtml) {
1422 out << "</tr>";
1423 }
1424 if (!(m_Option & eHtml)) {
1425 out <<"\n";
1426 }
1427 delete sdl;
1428 }
1429 }
1430
1431
DisplayBlastDeflineTable(CNcbiOstream & out)1432 void CShowBlastDefline::DisplayBlastDeflineTable(CNcbiOstream & out)
1433 {
1434 x_InitDeflineTable();
1435 if(m_StructureLinkout){
1436 char buf[512];
1437 sprintf(buf, kStructure_Overview, m_Rid.c_str(),
1438 0, 0, m_CddRid.c_str(), "overview",
1439 m_EntrezTerm == NcbiEmptyString ?
1440 "none": m_EntrezTerm.c_str());
1441 out << buf <<"\n\n";
1442 }
1443 x_DisplayDeflineTable(out);
1444 }
1445
1446 CShowBlastDefline::SScoreInfo*
x_GetScoreInfo(const CSeq_align & aln,int blast_rank)1447 CShowBlastDefline::x_GetScoreInfo(const CSeq_align& aln, int blast_rank)
1448 {
1449 string evalue_buf, bit_score_buf, total_bit_score_buf, raw_score_buf;
1450 int score = 0;
1451 double bits = 0;
1452 double evalue = 0;
1453 int sum_n = 0;
1454 int num_ident = 0;
1455 list<string> use_this_seq;
1456
1457 use_this_seq.clear();
1458 CAlignFormatUtil::GetAlnScores(aln, score, bits, evalue, sum_n,
1459 num_ident, use_this_seq);
1460
1461 CAlignFormatUtil::GetScoreString(evalue, bits, 0, score,
1462 evalue_buf, bit_score_buf, total_bit_score_buf,
1463 raw_score_buf);
1464
1465 auto_ptr<SScoreInfo> score_info(new SScoreInfo);
1466 score_info->sum_n = sum_n == -1 ? 1:sum_n ;
1467 score_info->id = &(aln.GetSeq_id(1));
1468
1469 score_info->use_this_seqid = use_this_seq;
1470
1471 score_info->bit_string = bit_score_buf;
1472 score_info->raw_score_string = raw_score_buf;
1473 score_info->evalue_string = evalue_buf;
1474 score_info->id = &(aln.GetSeq_id(1));
1475 score_info->blast_rank = blast_rank+1;
1476 score_info->subjRange = CRange<TSeqPos>(0,0);
1477 score_info->flip = false;
1478 return score_info.release();
1479 }
1480
1481 CShowBlastDefline::SScoreInfo*
x_GetScoreInfoForTable(const CSeq_align_set & aln,int blast_rank)1482 CShowBlastDefline::x_GetScoreInfoForTable(const CSeq_align_set& aln, int blast_rank)
1483 {
1484 string evalue_buf, bit_score_buf, total_bit_score_buf, raw_score_buf;
1485
1486 if(aln.Get().empty())
1487 return NULL;
1488
1489 auto_ptr<SScoreInfo> score_info(new SScoreInfo);
1490
1491 auto_ptr<CAlignFormatUtil::SSeqAlignSetCalcParams> seqSetInfo( CAlignFormatUtil::GetSeqAlignSetCalcParamsFromASN(aln));
1492 if(seqSetInfo->hspNum == 0) {//calulated params are not in ASN - calculate now
1493 seqSetInfo.reset( CAlignFormatUtil::GetSeqAlignSetCalcParams(aln,m_QueryLength,m_TranslatedNucAlignment));
1494 }
1495
1496 CAlignFormatUtil::GetScoreString(seqSetInfo->evalue, seqSetInfo->bit_score, seqSetInfo->total_bit_score, seqSetInfo->raw_score,
1497 evalue_buf, bit_score_buf, total_bit_score_buf,
1498 raw_score_buf);
1499 score_info->id = seqSetInfo->id;
1500
1501 score_info->total_bit_string = total_bit_score_buf;
1502 score_info->bit_string = bit_score_buf;
1503 score_info->evalue_string = evalue_buf;
1504 score_info->percent_coverage = seqSetInfo->percent_coverage;
1505 score_info->percent_identity = seqSetInfo->percent_identity;
1506 score_info->hspNum = seqSetInfo->hspNum;
1507 score_info->totalLen = seqSetInfo->totalLen;
1508
1509 score_info->use_this_seqid = seqSetInfo->use_this_seq;
1510 score_info->sum_n = seqSetInfo->sum_n == -1 ? 1:seqSetInfo->sum_n ;
1511
1512 score_info->raw_score_string = raw_score_buf;//check if used
1513 score_info->match = seqSetInfo->match; //check if used
1514 score_info->align_length = seqSetInfo->align_length;//check if used
1515 score_info->master_covered_length = seqSetInfo->master_covered_length;//check if used
1516
1517
1518 score_info->subjRange = seqSetInfo->subjRange; //check if used
1519 score_info->flip = seqSetInfo->flip;//check if used
1520
1521 score_info->blast_rank = blast_rank+1;
1522
1523 return score_info.release();
1524 }
1525
1526 vector <CShowBlastDefline::SDeflineInfo*>
GetDeflineInfo(vector<CConstRef<CSeq_id>> & seqIds)1527 CShowBlastDefline::GetDeflineInfo(vector< CConstRef<CSeq_id> > &seqIds)
1528 {
1529 vector <CShowBlastDefline::SDeflineInfo*> sdlVec;
1530 for(size_t i = 0; i < seqIds.size(); i++) {
1531 list<string> use_this_seq;
1532 CShowBlastDefline::SDeflineInfo* sdl = x_GetDeflineInfo(seqIds[i], use_this_seq, i + 1 );
1533 sdlVec.push_back(sdl);
1534 }
1535 return sdlVec;
1536 }
1537
1538
1539
1540 CShowBlastDefline::SDeflineInfo*
x_GetDeflineInfo(CConstRef<CSeq_id> id,list<string> & use_this_seqid,int blast_rank)1541 CShowBlastDefline::x_GetDeflineInfo(CConstRef<CSeq_id> id, list<string> &use_this_seqid, int blast_rank)
1542 {
1543 SDeflineInfo* sdl = NULL;
1544 sdl = new SDeflineInfo;
1545 sdl->id = id;
1546 sdl->defline = "Unknown";
1547
1548 try{
1549 const CBioseq_Handle& handle = m_ScopeRef->GetBioseqHandle(*id);
1550 x_FillDeflineAndId(handle, *id, use_this_seqid, sdl, blast_rank);
1551 } catch (const CException&){
1552 sdl->defline = "Unknown";
1553 sdl->is_new = false;
1554 sdl->was_checked = false;
1555 sdl->linkout = 0;
1556
1557 if((*id).Which() == CSeq_id::e_Gi){
1558 sdl->gi = (*id).GetGi();
1559 } else {
1560 sdl->gi = ZERO_GI;
1561 }
1562 sdl->id = id;
1563 if(m_Option & eHtml){
1564 _ASSERT(m_Reg.get());
1565
1566 string user_url= m_Reg->Get(m_BlastType, "TOOL_URL");
1567 string accession;
1568 sdl->id->GetLabel(&accession, CSeq_id::eContent);
1569 CRange<TSeqPos> seqRange(0,0);
1570 CAlignFormatUtil::SSeqURLInfo seqUrlInfo(user_url,m_BlastType,m_IsDbNa,m_Database,m_Rid,
1571 m_QueryNumber,sdl->gi,accession,0,blast_rank,false,(m_Option & eNewTargetWindow) ? true : false,seqRange,false,ZERO_TAX_ID);
1572 sdl->id_url = CAlignFormatUtil::GetIDUrl(&seqUrlInfo,*id,*m_ScopeRef);
1573 sdl->score_url = NcbiEmptyString;
1574 }
1575 }
1576
1577 return sdl;
1578 }
1579
x_DisplayDeflineTableTemplate(CNcbiOstream & out)1580 void CShowBlastDefline::x_DisplayDeflineTableTemplate(CNcbiOstream & out)
1581 {
1582 bool first_new =true;
1583 int prev_database_type = 0, cur_database_type = 0;
1584 bool is_first = true;
1585
1586 // Mixed db is genomic + transcript and this does not apply to proteins.
1587 bool is_mixed_database = (m_Ctx && m_IsDbNa == true)? CAlignFormatUtil::IsMixedDatabase(*m_Ctx): false;
1588 string rowType = "odd";
1589 string subHeaderID;
1590 ITERATE(vector<SScoreInfo*>, iter, m_ScoreList){
1591 SDeflineInfo* sdl = x_GetDeflineInfo((*iter)->id, (*iter)->use_this_seqid, (*iter)->blast_rank);
1592 cur_database_type = (sdl->linkout & eGenomicSeq);
1593 string subHeader;
1594 bool formatHeaderSort = !is_first && (prev_database_type != cur_database_type);
1595 if (is_mixed_database && (is_first || formatHeaderSort)) {
1596 subHeader = x_FormatSeqSetHeaders(cur_database_type, formatHeaderSort);
1597 subHeaderID = cur_database_type ? "GnmSeq" : "Transcr";
1598 //This is done for 508 complience
1599 subHeader = CAlignFormatUtil::MapTemplate(subHeader,"defl_header_id",subHeaderID);
1600 }
1601 prev_database_type = cur_database_type;
1602
1603 string defLine = x_FormatDeflineTableLine(sdl,*iter,first_new);
1604
1605 //This is done for 508 complience
1606 defLine = CAlignFormatUtil::MapTemplate(defLine,"defl_header_id",subHeaderID);
1607
1608 string firstSeq = (is_first) ? "firstSeq" : "";
1609 defLine = CAlignFormatUtil::MapTemplate(defLine,"firstSeq",firstSeq);
1610 defLine = CAlignFormatUtil::MapTemplate(defLine,"trtp",rowType);
1611
1612 rowType = (rowType == "odd") ? "even" : "odd";
1613
1614 if(!subHeader.empty()) {
1615 defLine = subHeader + defLine;
1616 }
1617 is_first = false;
1618 out << defLine;
1619
1620 delete sdl;
1621 }
1622 }
1623
1624 SSeqDBTaxInfo taxInfo;
s_GetTaxonomyInfoForTaxID(TTaxId sdlTaxid,SSeqDBTaxInfo & taxInfo)1625 static void s_GetTaxonomyInfoForTaxID(TTaxId sdlTaxid, SSeqDBTaxInfo &taxInfo)
1626 {
1627 string taxid;
1628 if(sdlTaxid > 0) {
1629 taxid = NStr::IntToString(sdlTaxid);
1630 try{
1631 CSeqDB::GetTaxInfo(sdlTaxid, taxInfo);
1632 } catch (const CException&){
1633 taxInfo.common_name = "Unknown";
1634 taxInfo.scientific_name = "Unknown";
1635 taxInfo.blast_name = "Unknown";
1636 }
1637 }
1638 }
1639
x_DisplayDeflineTableTemplateCSV(CNcbiOstream & out)1640 void CShowBlastDefline::x_DisplayDeflineTableTemplateCSV(CNcbiOstream & out)
1641 {
1642 ITERATE(vector<SScoreInfo*>, iter, m_ScoreList){
1643 SDeflineInfo* sdl = x_GetDeflineInfo((*iter)->id, (*iter)->use_this_seqid, (*iter)->blast_rank);
1644 string defLine = m_DeflineTemplates->defLineTmpl;
1645 string seqid;
1646 if(!sdl->id.Empty()){
1647 if(!(sdl->id->AsFastaString().find("gnl|BL_ORD_ID") != string::npos ||sdl->id->AsFastaString().find("lcl|Subject_") != string::npos)) {
1648 sdl->id->GetLabel(&seqid, CSeq_id::eContent);
1649 }
1650 }
1651
1652 if(sdl->id_url != NcbiEmptyString) {
1653 string seqInfo = CAlignFormatUtil::MapTemplate(m_DeflineTemplates->seqInfoTmpl,"dfln_url",sdl->id_url);
1654 seqInfo = CAlignFormatUtil::MapTemplate(seqInfo,"dfln_seqid",seqid);
1655 defLine = CAlignFormatUtil::MapTemplate(defLine,"seq_info",seqInfo);
1656 }
1657 else {
1658 defLine = CAlignFormatUtil::MapTemplate(defLine,"seq_info",seqid);
1659 }
1660
1661 string descr = (!sdl->defline.empty()) ? sdl->defline : "None provided";
1662 s_LimitDescrLength(descr);
1663 if(NStr::Find(descr,",") != NPOS) {
1664 descr = "\"" + descr + "\"";
1665 }
1666 defLine = CAlignFormatUtil::MapTemplate(defLine,"dfln_defline",descr);
1667
1668 SSeqDBTaxInfo taxInfo;
1669 s_GetTaxonomyInfoForTaxID(sdl->taxid, taxInfo);
1670 defLine = CAlignFormatUtil::MapTemplate(defLine,"common_name",taxInfo.common_name);
1671 defLine = CAlignFormatUtil::MapTemplate(defLine,"scientific_name",taxInfo.scientific_name);
1672 defLine = CAlignFormatUtil::MapTemplate(defLine,"taxid",NStr::IntToString(sdl->taxid));
1673
1674
1675 defLine = CAlignFormatUtil::MapTemplate(defLine,"score_info",(*iter)->bit_string);
1676 defLine = CAlignFormatUtil::MapTemplate(defLine,"total_bit_string",(*iter)->total_bit_string);
1677 defLine = CAlignFormatUtil::MapTemplate(defLine,"percent_coverage",NStr::IntToString((*iter)->percent_coverage) + "%");
1678 defLine = CAlignFormatUtil::MapTemplate(defLine,"evalue_string",(*iter)->evalue_string);
1679
1680 defLine = CAlignFormatUtil::MapTemplate(defLine,"percent_identity",NStr::DoubleToString((*iter)->percent_identity,2));
1681 int len = sequence::GetLength(*sdl->id, m_ScopeRef);
1682 defLine = CAlignFormatUtil::MapTemplate(defLine,"acclen",NStr::IntToString(len));
1683 //defLine = CAlignFormatUtil::MapTemplate(defLine,"seq_info",seqid);
1684
1685 out << defLine;
1686 delete sdl;
1687 }
1688
1689 }
1690
1691
x_DisplayDeflineTableTemplateText(CNcbiOstream & out)1692 void CShowBlastDefline::x_DisplayDeflineTableTemplateText(CNcbiOstream & out)
1693 {
1694 m_MaxPercentIdentityLen = kIdentLine2.size() + 1;
1695 m_MaxAccLength = 16;
1696 m_MaxTaxonomyNameLength = 15;
1697 m_MaxTaxidLength = 10;
1698 m_AccLenLength = 10;
1699
1700 string descrHeader = CAlignFormatUtil::MapSpaceTemplate(m_DeflineTemplates->deflineTxtHeader,"descr_hd1"," ",m_LineLen); //empty string
1701 descrHeader = CAlignFormatUtil::MapSpaceTemplate(descrHeader,"sciname_hd1",kScientific,m_MaxTaxonomyNameLength);
1702 descrHeader = CAlignFormatUtil::MapSpaceTemplate(descrHeader,"comname_hd1",kCommon,m_MaxTaxonomyNameLength);
1703 descrHeader = CAlignFormatUtil::MapSpaceTemplate(descrHeader,"taxid_hd1"," ",m_MaxTaxidLength);
1704 descrHeader = CAlignFormatUtil::MapSpaceTemplate(descrHeader,"score_hd1",kMax,m_MaxScoreLen);
1705 descrHeader = CAlignFormatUtil::MapSpaceTemplate(descrHeader,"total_hd1",kTotal,m_MaxTotalScoreLen);
1706 descrHeader = CAlignFormatUtil::MapSpaceTemplate(descrHeader,"querycov_hd1",kQueryCov,m_MaxQueryCoverLen);
1707 descrHeader = CAlignFormatUtil::MapSpaceTemplate(descrHeader,"evalue_hd1"," " + kE + " ",m_MaxEvalueLen);
1708 descrHeader = CAlignFormatUtil::MapSpaceTemplate(descrHeader,"percident_hd1",kPerc,m_MaxPercentIdentityLen);
1709 descrHeader = CAlignFormatUtil::MapSpaceTemplate(descrHeader,"acclen_hd1",kAccAbbr,m_AccLenLength);
1710 descrHeader = CAlignFormatUtil::MapSpaceTemplate(descrHeader,"acc_hd1"," ",m_MaxAccLength);
1711 //kBits kTotalLine2 kQueryCovLine2 kValue kIdentLine2
1712 descrHeader = CAlignFormatUtil::MapSpaceTemplate(descrHeader,"descr_hd2",kDescription,m_LineLen);
1713 descrHeader = CAlignFormatUtil::MapSpaceTemplate(descrHeader,"sciname_hd2",kName,m_MaxTaxonomyNameLength);
1714 descrHeader = CAlignFormatUtil::MapSpaceTemplate(descrHeader,"comname_hd2",kName,m_MaxTaxonomyNameLength);
1715 descrHeader = CAlignFormatUtil::MapSpaceTemplate(descrHeader,"taxid_hd2",kTaxid,m_MaxTaxidLength);
1716 descrHeader = CAlignFormatUtil::MapSpaceTemplate(descrHeader,"score_hd2",kScoreLine2,m_MaxScoreLen);
1717 descrHeader = CAlignFormatUtil::MapSpaceTemplate(descrHeader,"total_hd2",kScoreLine2,m_MaxTotalScoreLen);
1718 descrHeader = CAlignFormatUtil::MapSpaceTemplate(descrHeader,"querycov_hd2",kQueryCovLine2,m_MaxQueryCoverLen);
1719 descrHeader = CAlignFormatUtil::MapSpaceTemplate(descrHeader,"evalue_hd2",kValue,m_MaxEvalueLen);
1720 descrHeader = CAlignFormatUtil::MapSpaceTemplate(descrHeader,"percident_hd2",kIdentLine2,m_MaxPercentIdentityLen);
1721 descrHeader = CAlignFormatUtil::MapSpaceTemplate(descrHeader,"acclen_hd2",kLenAbbr,m_AccLenLength);
1722 descrHeader = CAlignFormatUtil::MapSpaceTemplate(descrHeader,"acc_hd2",kAccession,m_MaxAccLength);
1723
1724 out << descrHeader;
1725
1726 ITERATE(vector<SScoreInfo*>, iter, m_ScoreList){
1727 SDeflineInfo* sdl = x_GetDeflineInfo((*iter)->id, (*iter)->use_this_seqid, (*iter)->blast_rank);
1728 string defLine = m_DeflineTemplates->defLineTmpl;
1729 string seqid;
1730 if(!sdl->id.Empty()){
1731 if(!(sdl->id->AsFastaString().find("gnl|BL_ORD_ID") != string::npos ||sdl->id->AsFastaString().find("lcl|Subject_") != string::npos)) {
1732 sdl->id->GetLabel(&seqid, CSeq_id::eContent);
1733 }
1734 }
1735
1736 string descr = (!sdl->defline.empty()) ? sdl->defline : "None provided";
1737 s_LimitDescrLength(descr,m_LineLen);
1738 defLine = CAlignFormatUtil::MapSpaceTemplate(defLine,"dfln_defline",descr, m_LineLen);
1739 SSeqDBTaxInfo taxInfo;
1740 s_GetTaxonomyInfoForTaxID(sdl->taxid, taxInfo);
1741 defLine = CAlignFormatUtil::MapSpaceTemplate(defLine,"common_name",taxInfo.common_name,m_MaxTaxonomyNameLength);
1742 defLine = CAlignFormatUtil::MapSpaceTemplate(defLine,"scientific_name",taxInfo.scientific_name,m_MaxTaxonomyNameLength);
1743 defLine = CAlignFormatUtil::MapSpaceTemplate(defLine,"taxid",NStr::IntToString(sdl->taxid),m_MaxTaxidLength);
1744 defLine = CAlignFormatUtil::MapSpaceTemplate(defLine,"score_info",(*iter)->bit_string,m_MaxScoreLen);
1745 defLine = CAlignFormatUtil::MapSpaceTemplate(defLine,"total_bit_string",(*iter)->total_bit_string,m_MaxTotalScoreLen);
1746 defLine = CAlignFormatUtil::MapSpaceTemplate(defLine,"percent_coverage",NStr::IntToString((*iter)->percent_coverage) + "%",m_MaxQueryCoverLen);
1747 defLine = CAlignFormatUtil::MapSpaceTemplate(defLine,"evalue_string",(*iter)->evalue_string,m_MaxEvalueLen);
1748 defLine = CAlignFormatUtil::MapSpaceTemplate(defLine,"percent_identity",NStr::DoubleToString((*iter)->percent_identity,2),m_MaxPercentIdentityLen);
1749
1750 int len = sequence::GetLength(*sdl->id, m_ScopeRef);
1751 defLine = CAlignFormatUtil::MapSpaceTemplate(defLine,"acclen",NStr::IntToString(len),m_AccLenLength);
1752 defLine = CAlignFormatUtil::MapSpaceTemplate(defLine,"seq_info",seqid,m_MaxAccLength);
1753
1754
1755 out << defLine;
1756 delete sdl;
1757 }
1758 }
1759
1760
x_FormatSeqSetHeaders(int isGenomicSeq,bool formatHeaderSort)1761 string CShowBlastDefline::x_FormatSeqSetHeaders(int isGenomicSeq, bool formatHeaderSort)
1762 {
1763 string seqSetType = isGenomicSeq ? "Genomic sequences" : "Transcripts";
1764 string subHeader = CAlignFormatUtil::MapTemplate(m_DeflineTemplates->subHeaderTmpl,"defl_seqset_type",seqSetType);
1765 if (formatHeaderSort) {
1766 int database_sort = isGenomicSeq ? CAlignFormatUtil::eGenomicFirst : CAlignFormatUtil::eNonGenomicFirst;
1767 string deflnSubHeaderSort = CAlignFormatUtil::MapTemplate(m_DeflineTemplates->subHeaderSort,"database_sort",database_sort);
1768 subHeader = CAlignFormatUtil::MapTemplate(subHeader,"defl_header_sort",deflnSubHeaderSort);
1769 }
1770 else {
1771 subHeader = CAlignFormatUtil::MapTemplate(subHeader,"defl_header_sort","");
1772 }
1773 return subHeader;
1774 }
1775
1776
x_FormatDeflineTableLine(SDeflineInfo * sdl,SScoreInfo * iter,bool & first_new)1777 string CShowBlastDefline::x_FormatDeflineTableLine(SDeflineInfo* sdl,SScoreInfo* iter,bool &first_new)
1778 {
1779 string defLine = (((m_Option & eCheckboxChecked) || (m_Option & eCheckbox))) ? x_FormatPsi(sdl, first_new) : m_DeflineTemplates->defLineTmpl;
1780 string dflGi = (m_Option & eShowGi) && (sdl->gi > ZERO_GI) ? "gi|" + NStr::NumericToString(sdl->gi) + "|" : "";
1781 string seqid;
1782 if(!sdl->id.Empty()){
1783 if(!(sdl->id->AsFastaString().find("gnl|BL_ORD_ID") != string::npos ||
1784 sdl->id->AsFastaString().find("lcl|Subject_") != string::npos)) {
1785 sdl->id->GetLabel(&seqid, CSeq_id::eContent);
1786 }
1787 }
1788
1789 if(sdl->id_url != NcbiEmptyString) {
1790 string seqInfo = CAlignFormatUtil::MapTemplate(m_DeflineTemplates->seqInfoTmpl,"dfln_url",sdl->id_url);
1791 string trgt = (m_Option & eNewTargetWindow) ? "TARGET=\"EntrezView\"" : "";
1792 seqInfo = CAlignFormatUtil::MapTemplate(seqInfo,"dfln_target",trgt);
1793 defLine = CAlignFormatUtil::MapTemplate(defLine,"seq_info",seqInfo);
1794 defLine = CAlignFormatUtil::MapTemplate(defLine,"dfln_gi",dflGi);
1795 defLine = CAlignFormatUtil::MapTemplate(defLine,"dfln_seqid",seqid);
1796 }
1797 else {
1798 defLine = CAlignFormatUtil::MapTemplate(defLine,"seq_info",dflGi + seqid);
1799 }
1800
1801 string descr = (!sdl->defline.empty()) ? sdl->defline : "None provided";
1802 s_LimitDescrLength(descr);
1803 defLine = CAlignFormatUtil::MapTemplate(defLine,"dfln_defline",CHTMLHelper::HTMLEncode(descr));
1804
1805 descr = (!sdl->fullDefline.empty()) ? sdl->fullDefline : seqid;
1806 s_LimitDescrLength(descr);
1807 defLine = CAlignFormatUtil::MapTemplate(defLine,"full_dfln_defline",CHTMLHelper::HTMLEncode(descr));
1808 if(sdl->score_url != NcbiEmptyString) {
1809 string scoreInfo = CAlignFormatUtil::MapTemplate(m_DeflineTemplates->scoreInfoTmpl,"score_url",sdl->score_url);
1810 scoreInfo = CAlignFormatUtil::MapTemplate(scoreInfo,"bit_string",iter->bit_string);
1811 scoreInfo = CAlignFormatUtil::MapTemplate(scoreInfo,"score_seqid",seqid);
1812 defLine = CAlignFormatUtil::MapTemplate(defLine,"score_info",scoreInfo);
1813 }
1814 else {
1815 defLine = CAlignFormatUtil::MapTemplate(defLine,"score_info",iter->bit_string);
1816 }
1817 /*****************This block of code is for future use with AJAX begin***************************/
1818 string deflId,deflFrmID,deflFastaSeq,deflAccs;
1819 if(sdl->gi == ZERO_GI) {
1820 sdl->id->GetLabel(& deflId, CSeq_id::eContent);
1821 deflFrmID = CAlignFormatUtil::GetLabel(sdl->id);//Just accession without db part like GNOMON: or ti:
1822 deflFastaSeq = NStr::TruncateSpaces(sdl->alnIDFasta);
1823 deflAccs = sdl->id->AsFastaString();
1824 }
1825 else {
1826 deflFrmID = deflId = NStr::NumericToString(sdl->gi);
1827 deflFastaSeq = "gi|" + NStr::NumericToString(sdl->gi);
1828 deflFastaSeq = NStr::TruncateSpaces(sdl->alnIDFasta);
1829 sdl->id->GetLabel(&deflAccs, CSeq_id::eContent);
1830 }
1831 SSeqDBTaxInfo taxInfo;
1832 s_GetTaxonomyInfoForTaxID(sdl->taxid, taxInfo);
1833 defLine = CAlignFormatUtil::MapTemplate(defLine,"common_name",taxInfo.common_name);
1834 defLine = CAlignFormatUtil::MapTemplate(defLine,"scientific_name",taxInfo.scientific_name);
1835 defLine = CAlignFormatUtil::MapTemplate(defLine,"blast_name",taxInfo.blast_name);
1836 defLine = CAlignFormatUtil::MapTemplate(defLine,"taxid",NStr::IntToString(sdl->taxid));
1837
1838 int len = sequence::GetLength(*sdl->id, m_ScopeRef);
1839 defLine = CAlignFormatUtil::MapTemplate(defLine,"acclen",NStr::IntToString(len));
1840 //Setup applog info structure
1841 if(m_AppLogInfo && (m_AppLogInfo->currInd < m_AppLogInfo->topMatchesNum)) {
1842 m_AppLogInfo->deflIdVec.push_back(deflId);
1843 m_AppLogInfo->accVec.push_back(deflAccs);
1844 m_AppLogInfo->taxidVec.push_back(NStr::NumericToString(sdl->taxid));
1845 m_AppLogInfo->queryCoverageVec.push_back(NStr::IntToString(iter->percent_coverage));
1846 m_AppLogInfo->percentIdentityVec.push_back(NStr::DoubleToString(iter->percent_identity));
1847 m_AppLogInfo->currInd++;
1848 }
1849
1850 //If gi - deflFrmID and deflId are the same and equal to gi "555",deflFastaSeq will have "gi|555"
1851 //If gnl - deflFrmID=number, deflId=ti:number,deflFastaSeq=gnl|xxx
1852 //like "268252125","ti:268252125","gnl|ti|961433.m" or "961433.m" and "GNOMON:961433.m" "gnl|GNOMON|961433.m"
1853 defLine = CAlignFormatUtil::MapTemplate(defLine,"dfln_id",deflId);
1854 defLine = CAlignFormatUtil::MapTemplate(defLine,"dflnFrm_id",deflFrmID);
1855 defLine = CAlignFormatUtil::MapTemplate(defLine,"dflnFASTA_id",deflFastaSeq);
1856 defLine = CAlignFormatUtil::MapTemplate(defLine,"dflnAccs",deflAccs);
1857 defLine = CAlignFormatUtil::MapTemplate(defLine,"dfln_rid",m_Rid);
1858 defLine = CAlignFormatUtil::MapTemplate(defLine,"dfln_hspnum",iter->hspNum);
1859 defLine = CAlignFormatUtil::MapTemplate(defLine,"dfln_alnLen",iter->totalLen);
1860 defLine = CAlignFormatUtil::MapTemplate(defLine,"dfln_blast_rank",m_StartIndex + iter->blast_rank);
1861
1862 /*****************This block of code is for future use with AJAX end***************************/
1863
1864 defLine = CAlignFormatUtil::MapTemplate(defLine,"total_bit_string",iter->total_bit_string);
1865
1866
1867 defLine = CAlignFormatUtil::MapTemplate(defLine,"percent_coverage",NStr::IntToString(iter->percent_coverage));
1868
1869 defLine = CAlignFormatUtil::MapTemplate(defLine,"evalue_string",iter->evalue_string);
1870
1871 if(m_Option & eShowPercentIdent){
1872 defLine = CAlignFormatUtil::MapTemplate(defLine,"percent_identity",NStr::DoubleToString(iter->percent_identity,2));
1873 }
1874
1875 if(m_Option & eShowSumN){
1876 defLine = CAlignFormatUtil::MapTemplate(defLine,"sum_n",NStr::IntToString(iter->sum_n));
1877 }
1878
1879 string links;
1880 //sdl->linkout_list may contain linkouts + mapview link + seqview link
1881 ITERATE(list<string>, iter_linkout, sdl->linkout_list){
1882 links += *iter_linkout;
1883 }
1884 defLine = CAlignFormatUtil::MapTemplate(defLine,"linkout",links);
1885
1886 return defLine;
1887 }
1888
x_FormatPsi(SDeflineInfo * sdl,bool & first_new)1889 string CShowBlastDefline::x_FormatPsi(SDeflineInfo* sdl, bool &first_new)
1890 {
1891 string defline = m_DeflineTemplates->defLineTmpl;
1892 string show_new,psi_new,psi_new_accesible,show_checked,replaceBy,psiNewSeq;
1893 if((m_Option & eShowNewSeqGif)) {
1894 replaceBy = (sdl->is_new && first_new) ? m_DeflineTemplates->psiFirstNewAnchorTmpl : "";
1895 first_new = (sdl->is_new && first_new) ? false : first_new;
1896 if (!sdl->is_new) {
1897 show_new = "hidden";
1898 }
1899 if (sdl->is_new && m_StepNumber > 1) {
1900 psi_new = "psi_new";
1901 psi_new_accesible = "psiNw";
1902 psiNewSeq = "on";
1903 }
1904 else {
1905 psiNewSeq = "off";
1906 }
1907
1908 if(!sdl->was_checked) {
1909 show_checked = "hidden";
1910 }
1911 string psiUsedToBuildPssm = (sdl->was_checked) ? "on" : "off";
1912
1913
1914 defline = CAlignFormatUtil::MapTemplate(defline,"first_new",replaceBy);
1915 defline = CAlignFormatUtil::MapTemplate(defline,"psi_new_gi",show_new);
1916 defline = CAlignFormatUtil::MapTemplate(defline,"psi_new_gi_hl",psi_new);
1917 defline = CAlignFormatUtil::MapTemplate(defline,"psi_new_gi_accs",psi_new_accesible);//insert for accesibilty
1918 defline = CAlignFormatUtil::MapTemplate(defline,"psi_checked_gi",show_checked);
1919
1920 defline = CAlignFormatUtil::MapTemplate(defline,"psi_new_seq",psiNewSeq);
1921 defline = CAlignFormatUtil::MapTemplate(defline,"psi_used_in_pssm",psiUsedToBuildPssm);
1922 }
1923
1924 replaceBy = (m_Option & eCheckboxChecked) ? m_DeflineTemplates->psiGoodGiHiddenTmpl : "";//<@psi_good_gi@>
1925 defline = CAlignFormatUtil::MapTemplate(defline,"psi_good_gi",replaceBy);
1926
1927 replaceBy = (m_Option & eCheckboxChecked) ? "checked=\"checked\"" : "";
1928 defline = CAlignFormatUtil::MapTemplate(defline,"gi_checked",replaceBy);
1929 if(sdl->gi > ZERO_GI) {
1930 defline = CAlignFormatUtil::MapTemplate(defline,"psiGi",NStr::NumericToString(sdl->gi));
1931 }
1932 else {
1933 defline = CAlignFormatUtil::MapTemplate(defline,"psiGi",sdl->textSeqID);
1934 }
1935
1936 return defline;
1937 }
1938
1939
1940
1941
x_InitFormattingInfo(SScoreInfo * sci)1942 void CShowBlastDefline::x_InitFormattingInfo(SScoreInfo* sci)
1943 {
1944 SDeflineFormattingInfo* sdlFormatInfo = new SDeflineFormattingInfo;
1945 SDeflineInfo* sdl = x_GetDeflineInfo(sci->id, sci->use_this_seqid, sci->blast_rank);
1946
1947 string dflGi = (m_Option & eShowGi) && (sdl->gi > ZERO_GI) ? "gi|" + NStr::NumericToString(sdl->gi) + "|" : "";
1948 string seqid;
1949 if(!sdl->id.Empty()){
1950 if(!(sdl->id->AsFastaString().find("gnl|BL_ORD_ID") != string::npos || sdl->id->AsFastaString().find("lcl|Subject_") != string::npos)) {
1951 sdl->id->GetLabel(&seqid, CSeq_id::eContent);
1952 }
1953 }
1954
1955 sdlFormatInfo->dfln_url = sdl->id_url;
1956
1957 sdlFormatInfo->dfln_rid = m_Rid;
1958 sdlFormatInfo->dfln_gi = dflGi;
1959 sdlFormatInfo->dfln_seqid = seqid;
1960
1961
1962 string descr = (!sdl->defline.empty()) ? sdl->defline : "None provided";
1963 s_LimitDescrLength(descr);
1964
1965 sdlFormatInfo->dfln_defline = CHTMLHelper::HTMLEncode(descr);
1966
1967 descr = (!sdl->fullDefline.empty()) ? sdl->fullDefline : seqid;
1968 s_LimitDescrLength(descr);
1969 sdlFormatInfo->full_dfln_defline = CHTMLHelper::HTMLEncode(descr);
1970
1971
1972
1973 string deflId,deflFrmID,deflFastaSeq,deflAccs;
1974 if(sdl->gi == ZERO_GI) {
1975 sdl->id->GetLabel(& deflId, CSeq_id::eContent);
1976 deflFrmID = CAlignFormatUtil::GetLabel(sdl->id);//Just accession without db part like GNOMON: or ti:
1977 deflFastaSeq = NStr::TruncateSpaces(sdl->alnIDFasta);
1978 deflAccs = sdl->id->AsFastaString();
1979 }
1980 else {
1981 deflFrmID = deflId = NStr::NumericToString(sdl->gi);
1982 deflFastaSeq = "gi|" + NStr::NumericToString(sdl->gi);
1983 deflFastaSeq = NStr::TruncateSpaces(sdl->alnIDFasta);
1984 sdl->id->GetLabel(&deflAccs, CSeq_id::eContent);
1985 }
1986
1987 sdlFormatInfo->dfln_id = deflId;
1988 sdlFormatInfo->dflnFrm_id = deflFrmID;
1989 sdlFormatInfo->dflnFASTA_id = deflFastaSeq;
1990 sdlFormatInfo->dflnAccs =deflAccs;
1991
1992 sdlFormatInfo->score_info = sci->bit_string;
1993 sdlFormatInfo->dfln_hspnum = NStr::IntToString(sci->hspNum);
1994 sdlFormatInfo->dfln_alnLen = NStr::NumericToString(sci->totalLen);
1995 sdlFormatInfo->dfln_blast_rank = NStr::IntToString(m_StartIndex + sci->blast_rank);
1996 sdlFormatInfo->total_bit_string = sci->total_bit_string;
1997 sdlFormatInfo->percent_coverage = NStr::IntToString(sci->percent_coverage);
1998 sdlFormatInfo->evalue_string = sci->evalue_string;
1999 sdlFormatInfo->percent_identity = NStr::DoubleToString(sci->percent_identity);
2000 m_SdlFormatInfoVec.push_back(sdlFormatInfo);
2001 }
2002
2003
GetFormattingInfo(void)2004 vector <CShowBlastDefline::SDeflineFormattingInfo *> CShowBlastDefline::GetFormattingInfo(void)
2005 {
2006 /*Note we can't just show each alnment as we go because we will
2007 need to show defline only once for all hsp's with the same id*/
2008
2009 bool is_first_aln = true;
2010 size_t num_align = 0;
2011 CConstRef<CSeq_id> previous_id, subid;
2012
2013 CSeq_align_set hit;
2014 m_QueryLength = 1;
2015
2016 //prepare defline
2017
2018
2019 for (CSeq_align_set::Tdata::const_iterator iter = m_AlnSetRef->Get().begin();
2020 iter != m_AlnSetRef->Get().end() && num_align < m_NumToShow;
2021 iter++)
2022 {
2023
2024 if (is_first_aln) {
2025 m_QueryLength = m_MasterRange ? m_MasterRange->GetLength() : m_ScopeRef->GetBioseqHandle((*iter)->GetSeq_id(0)).GetBioseqLength();
2026 }
2027
2028 subid = &((*iter)->GetSeq_id(1));
2029
2030 if(!is_first_aln && !(subid->Match(*previous_id))) {
2031
2032 SScoreInfo* sci = x_GetScoreInfoForTable(hit, num_align);
2033 if(sci) {
2034 x_InitFormattingInfo(sci);
2035 hit.Set().clear();
2036 }
2037
2038 num_align++; // Only increment if new subject ID found.
2039 }
2040 if (num_align < m_NumToShow) { //no adding if number to show already reached
2041 hit.Set().push_back(*iter);
2042 }
2043 is_first_aln = false;
2044 previous_id = subid;
2045 }
2046 //the last hit
2047 SScoreInfo* sci = x_GetScoreInfoForTable(hit, num_align);
2048
2049 if(sci) {
2050 x_InitFormattingInfo(sci);
2051 hit.Set().clear();
2052 }
2053
2054 return m_SdlFormatInfoVec;
2055 }
2056
2057
2058 END_SCOPE(align_format)
2059 END_NCBI_SCOPE
2060
