1 /* $Id: jzcoll.h,v 6.8 2006/07/13 17:06:38 bollin Exp $ 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 * File Name: $RCSfile: jzcoll.h,v $ 27 * 28 * Author: Jinghui Zhang 29 * 30 * Initial Version Creation Date: 03/24/97 31 * 32 * $Revision: 6.8 $ 33 * 34 * File Description: 35 * File for various alignments 36 * 37 * $Log: jzcoll.h,v $ 38 * Revision 6.8 2006/07/13 17:06:38 bollin 39 * use Uint4 instead of Uint2 for itemID values 40 * removed unused variables 41 * resolved compiler warnings 42 * 43 * Revision 6.7 2000/11/16 22:10:38 shavirin 44 * Moved many functions from txalign.c - due to move of txalign.c to 45 * distrib/tools directory and libncbitool.a library. 46 * 47 * Revision 6.6 2000/11/01 14:43:12 madden 48 * Changes from Futamura for psitblastn 49 * 50 * Revision 6.5 1999/08/06 17:58:22 egorov 51 * Print correct GI in formated output when user has specified list of gi's in blast search 52 * 53 * Revision 6.4 1998/07/22 18:57:34 kans 54 * reconciled in new functions from JZ 55 * 56 * Revision 6.3 1997/12/30 19:31:48 kans 57 * added CollectItemForSeqLocEx to restore propagation of features from parts to segmented bioseq 58 * 59 * Revision 6.2 1997/11/14 22:13:37 vakatov 60 * [WIN32,DLL] Added NLM_EXTERN's 61 * 62 * Revision 6.1 1997/09/16 20:03:17 zjing 63 * new functions 64 * 65 * Revision 6.0 1997/08/25 18:06:17 madden 66 * Revision changed to 6.0 67 * 68 * Revision 5.13 1997/08/13 18:45:33 zjing 69 * add support for tblastx 70 * 71 * $Revision: 6.8 $ 72 * 73 * File Description: 74 * File for various alignments 75 * 76 * $Log: jzcoll.h,v $ 77 * Revision 6.8 2006/07/13 17:06:38 bollin 78 * use Uint4 instead of Uint2 for itemID values 79 * removed unused variables 80 * resolved compiler warnings 81 * 82 * Revision 6.7 2000/11/16 22:10:38 shavirin 83 * Moved many functions from txalign.c - due to move of txalign.c to 84 * distrib/tools directory and libncbitool.a library. 85 * 86 * Revision 6.6 2000/11/01 14:43:12 madden 87 * Changes from Futamura for psitblastn 88 * 89 * Revision 6.5 1999/08/06 17:58:22 egorov 90 * Print correct GI in formated output when user has specified list of gi's in blast search 91 * 92 * Revision 6.4 1998/07/22 18:57:34 kans 93 * reconciled in new functions from JZ 94 * 95 * Revision 6.3 1997/12/30 19:31:48 kans 96 * added CollectItemForSeqLocEx to restore propagation of features from parts to segmented bioseq 97 * 98 * Revision 6.2 1997/11/14 22:13:37 vakatov 99 * [WIN32,DLL] Added NLM_EXTERN's 100 * 101 * Revision 6.1 1997/09/16 20:03:17 zjing 102 * new functions 103 * 104 * Revision 5.10 1997/06/19 18:38:08 vakatov 105 * [WIN32,MSVC++] Adopted for the "NCBIOBJ.LIB" DLL'ization 106 * 107 * Revision 5.9 1997/05/12 19:53:54 zjing 108 * change the maximum number of sequences in an alignment to 150. 109 * 110 * Revision 5.8 1997/03/24 20:50:45 shavirin 111 * Added protection for usage with C++ compiler. Added NCBI header 112 * started logging. 113 * 114 * 115 * ========================================================================== 116 */ 117 118 #ifndef _JZCOLL_ 119 120 #define _JZCOLL_ 121 122 /*local include file*/ 123 #include <maputil.h> 124 #include <gather.h> 125 #include <seqport.h> 126 127 128 #undef NLM_EXTERN 129 #ifdef NLM_IMPORT 130 #define NLM_EXTERN NLM_IMPORT 131 #else 132 #define NLM_EXTERN extern 133 #endif 134 135 #ifdef __cplusplus 136 extern "C" { 137 #endif 138 139 /******************************************************************* 140 * 141 * ck_seqfeat_extra: check if there is extra data, such as 142 * Genbank accessions assocated with a GeneRef or Medlines 143 * associated with a Seq-feat 144 * 145 *******************************************************************/ 146 #define NO_EXTRA_DATA ((Uint4)0) 147 #define EXTRA_MEDLINE ((Uint4)1) 148 #define EXTRA_GENBANK ((Uint4)2) 149 150 /*the different types of markers*/ 151 #define MARK_TYPE_NUM 7 152 #define NO_TYPE 0 153 #define FRAME_WORK 1 154 #define RECMIN 2 155 #define LIKELY 3 156 #define MDUP 4 157 #define DUP 5 158 #define CONTIG_STS 6 159 160 /*corresponding type in extra field*/ 161 #define EXTRA_FRAME_WORK ((Uint4)4) /*it is a frame work marker*/ 162 #define EXTRA_RECMIN ((Uint4)8) /*it is a recmin marker, for CHLC*/ 163 #define EXTRA_LIKELY ((Uint4)16) /*it is a likely loci marker, for CHLC*/ 164 #define EXTRA_MDUP ((Uint4)32) 165 #define EXTRA_DUP ((Uint4)64) 166 #define EXTRA_CONTIG_STS ((Uint4)128) 167 #define EXTRA_LOD_SCORE ((Uint4)256) 168 169 170 /*the different types for a marker in its genetic context, EG for Eric Green*/ 171 #define EG_YAC_END 1 172 #define EG_RANDOME 2 173 #define EG_GENETIC 3 174 #define EG_GENE 4 175 #define EG_EST 5 176 #define EG_MISC 6 177 178 #define EXTRA_YAC_END ((Uint4)256) 179 #define EXTRA_RANDOM ((Uint4)512) 180 #define EXTRA_GENETIC ((Uint4)1024) 181 #define EXTRA_GENE ((Uint4)2048) 182 #define EXTRA_EST ((Uint4)4096) 183 #define EXTRA_MISC ((Uint4)8192) 184 185 NLM_EXTERN Uint4 ck_seqfeat_extra PROTO((SeqFeatPtr sfp)); 186 NLM_EXTERN Uint1 get_map_type PROTO((Uint4 extra)); 187 188 189 #define ALL_LABEL 1 190 #define STR_LABEL 2 191 #define NUM_LABEL 3 192 193 #define NO_LABEL 255 194 #define UPPER_LABEL 1 195 #define LOWER_LABEL 2 196 197 198 #define NO_FILTER 0 199 typedef struct collectseqoption { /*option for drawing the sequence+feature*/ 200 Boolean nointerval; /*do not collect the intervals, only the two ends*/ 201 Uint1 slabel_format; /*styles for label the sequence*/ 202 Uint1 flabel_format[FEATDEF_ANY]; /*the format for labels*/ 203 Uint1 seglevels; /*level of segmentation to go down*/ 204 Int2 label_size; 205 Int2 filter_level; /*the level to be filtered out*/ 206 Boolean features[FEATDEF_ANY]; /*for filtering unwanted features*/ 207 Uint1 bsp_type; /*type of Bioseq. This is to decide 208 if the features need to be collected on 209 the cytogenetic map*/ 210 }CollectSeqOption, PNTR CollectSeqOptionPtr; 211 212 213 #define COLLECT_HISTORY 1 /*as a history*/ 214 #define COLLECT_MP 2 /*multiple pairwise*/ 215 #define COLLECT_MD 3 /*multi-dimension*/ 216 #define COLLECT_FIXED 4 /*for the fixed format*/ 217 #define COLLECT_MP_FLAT 5 /*flat out the mulitple pairwise alignment*/ 218 219 220 #define DEFAULT_ALIGN_NUM 150 /*maximum number of alignment to be displayed*/ 221 typedef struct collectalignoption { /*option for drawing the sequence+feature*/ 222 Uint1 slabel_format; /*format for label a sequence in the alignment*/ 223 Boolean nointerval; /*do not collect the intervals, only the two ends*/ 224 Boolean only_history; /*skip the Seq-annot?*/ 225 Boolean map_insert; /*map the insertions*/ 226 Boolean flat_insert; /*to flatout the insertions*/ 227 Boolean map_graphic; /*map the coordinate to the graphic?*/ 228 229 Boolean show_mismatch; 230 231 Boolean show_feature; /*show any feature?*/ 232 Int4 align_num; /*the maximun number of alignment to collect*/ 233 Int4 curr_align_num; /*the current number of the alignments*/ 234 SeqLocPtr segloc; /*for marking the regions used in a segmented sequence*/ 235 Int2 label_size; 236 Int4 graphic_offset; 237 Boolean no_sort; /*if TRUE, do NOT sort the AlignNode*/ 238 CollectSeqOptionPtr csop; /*for collecting feature-related information*/ 239 240 }CollectAlignOption, PNTR CollectAlignOptionPtr; 241 242 243 NLM_EXTERN Boolean set_option_for_collect_align PROTO((CollectAlignOptionPtr caop, Int2 label_size, Uint1 style)); 244 /*###################################################################### 245 # 246 # collect functions 247 # 248 ######################################################################*/ 249 250 /*********************************************************************** 251 * 252 * CollectItemForSeqLoc(slp, entityID, left, is_aa, csop) 253 * Collect sequences, features for a Seq-loc 254 * slp: the target Seq-loc 255 * entityID: the top level entityID for the current sequence 256 * left: the left offset on the graph 257 * is_aa: if TRUE, set get_feats_product flag to TRUE 258 * csop: the collection option 259 * 260 * 261 ***********************************************************************/ 262 NLM_EXTERN ValNodePtr CollectItemForSeqLoc PROTO((SeqLocPtr slp, Uint2 entityID, Int4 left, Boolean is_aa, SeqIdPtr maybe_mapid, CollectSeqOptionPtr csop, GeneDataPtr gdata, Uint2 priority)); 263 NLM_EXTERN ValNodePtr CollectItemForSeqLocEx PROTO((SeqLocPtr slp, Uint2 entityID, Int4 left, Boolean is_aa, SeqIdPtr maybe_mapid, CollectSeqOptionPtr csop, GeneDataPtr gdata, Uint2 priority, Boolean forceSeglevelsTo1)); 264 265 266 267 /***************************************************************************** 268 * 269 * cllect_master_align_node(m_loc, featureOrder, groupOrder) 270 * in the master-slave alignment, a fake Seq-align is created for the 271 * master sequence where the master is aligned to itself. The AlignNode 272 * can be computed for this faked alignment. When this is done, the fake 273 * Seq-align will be freed 274 * 275 * m_loc: the Seq-loc for the master sequence 276 * featureOrder: the selected features 277 * 278 ******************************************************************************/ 279 NLM_EXTERN ValNodePtr collect_master_align_node PROTO((CollectAlignOptionPtr caop, SeqLocPtr m_loc, Uint1 obj_type, Uint2 entityID)); 280 281 282 NLM_EXTERN ValNodePtr CollectItemForAlignment PROTO((SeqLocPtr slp, Uint2 entityID, Int4 left, CollectAlignOptionPtr caop, Boolean take_all_annot)); 283 284 NLM_EXTERN ValNodePtr collect_anpnode_with_option PROTO((CollectAlignOptionPtr caop, SeqLocPtr m_loc, Uint2 entityID, Int4 style, Uint1 itemType, Uint1Ptr f_order, Uint1Ptr g_order, Boolean take_all_annot)); 285 286 typedef struct featnode { /*for collecting the features*/ 287 Uint4 itemID; 288 Uint2 entityID; 289 Uint1 feattype; /*type for Seq-feat*/ 290 Uint1 subtype; /*subtype for Seq-feat*/ 291 Int2 band; /*band type for CytoGenetic Map, defined in maputil.h*/ 292 GatherRange extremes; 293 ValNodePtr interval; /*the intervals, data->ptrvalue is GatherRange*/ 294 CharPtr label; 295 CharPtr pos_label; /*label the position of a map */ 296 Int4 line; 297 Int4 top; /*the top of the box*/ 298 Int4 bottom; /*the bottom of the box*/ 299 Int4 labelHeight; /*the height of a label*/ 300 Int4 label_len; /*the PIXEL length of the label*/ 301 Boolean draw_tick; /*draw the tick mark in a map*/ 302 Boolean has_product; 303 Boolean follower; /*is it a follower?*/ 304 Uint4 extra_data; /*flags for extra data such as medline*/ 305 Boolean landmark; /*is it a landmark?*/ 306 Uint2 bin_order; /*order for the 1000:1 bin data*/ 307 Char annotDB[21]; /*the descriptor for the parent*/ 308 Int4 ef_left; /*extreme left, with the label font offset*/ 309 Int4 ef_right; 310 ValNodePtr supress_node; /*the FeatNode uppressed to avoid stacking*/ 311 } FeatNode, PNTR FeatNodePtr; 312 313 typedef struct ivalnode { /*intervals in a feature*/ 314 GatherRange gr; 315 Int4 line; 316 } IvalNode, PNTR IvalNodePtr; 317 318 /*********************************************************************** 319 * 320 * FreeFeatureList(list) 321 * free a list of FeatNode 322 * 323 ***********************************************************************/ 324 NLM_EXTERN ValNodePtr FreeFeatureList PROTO((ValNodePtr list)); 325 326 /********************************************************************* 327 * 328 * extract_node_list(head, itemType, entityID, feattype, subtype, 329 * label_type) 330 * extract a list of featnode from head which will have the 331 * selected itemType, entityID, feattye, subtype, label_type. 332 * set values to 0 if it is not considered in the selection 333 * 334 *********************************************************************/ 335 NLM_EXTERN ValNodePtr extract_node_list PROTO((ValNodePtr PNTR head, Uint1 itemType, Uint2 entityID, Uint1 feattype, Uint1 label_type)); 336 337 NLM_EXTERN ValNodePtr extract_lollipop_feature PROTO((ValNodePtr PNTR head, Int4 scale, BoolPtr lolli_feature)); 338 339 /*********************************************************************** 340 * 341 * SortFeatNode(list) 342 * sort a list of FeatNode to the ascending order of (extremes.left, 343 * extremes.right) 344 * 345 **********************************************************************/ 346 NLM_EXTERN ValNodePtr SortFeatNode PROTO((ValNodePtr list, Uint1Ptr featureOrder, Uint1Ptr groupOrder)); 347 348 349 /********************************************************************** 350 * 351 * merge_same_itemID(head, itemID) 352 * search in the list of FeatNode to link all the FeatNode that has 353 * the same itemID. 354 * head: the list of FeatNode 355 * itemID: the itemID in search 356 * return the list of FeatNode with the same itemID 357 * 358 **********************************************************************/ 359 NLM_EXTERN ValNodePtr merge_same_itemID PROTO((ValNodePtr PNTR head, Uint4 itemID)); 360 361 362 typedef struct alignblock{ 363 GatherRange gr; 364 Uint2 order; 365 struct alignblock PNTR next; 366 }AlignBlock, PNTR AlignBlockPtr; 367 368 #define MISMATCH_LINE 0 /* draw mismatch in alignment as a line*/ 369 #define MISMATCH_OPEN 1 /*draw mismatch as an open circle*/ 370 #define MISMATCH_CLOSE 2 /*draw mismatch as a closed circle*/ 371 #define MISMATCH_SQUARE 3 /*draw mismatch as a square*/ 372 /*value is reserved for Eric Greens Map only */ 373 #define MISMATCH_AMB 4 /*for the ambiguous residue*/ 374 375 376 /*the three values were used for the annotinfo.consistent values. 377 thouse were used to define the quality of the alignment between 378 the contigs and the chromosome in Eric Green's physical map. */ 379 #define ALIGN_CONSISTENT 1 380 #define ALIGN_INCONSISTENT 2 381 #define ALIGN_UNKNOWN 3 382 #define ALIGN_FISH 4 383 384 #define ALIGN_BLASTN 1 385 #define ALIGN_BLASTP 2 386 #define ALIGN_BLASTX 3 387 #define ALIGN_TBLASTN 4 388 #define ALIGN_TBLASTX 5 389 #define ALIGN_PSITBLASTN 6 390 391 typedef struct annotinfo { /*information stored in Seq-annot*/ 392 Uint1 displayOrder; 393 Uint1 consistent; /*the type of the consistency*/ 394 Char annotDB[21]; 395 Uint2 entityID; 396 Uint4 itemID; 397 Uint1 annot_type; /*is it a BLAST/Consist/FISH alignment */ 398 Uint1 blast_type; /*if it is alignment from BLAST, what is the type*/ 399 Boolean is_fish_align; /*is it the alignment for the FISH map */ 400 }AnnotInfo, PNTR AnnotInfoPtr; 401 402 /******************************************************************* 403 * 404 * structure used to draw Sequence alignment 405 * if follower is set to TRUE, it will be grouped together 406 * with the previous non-follower vnp. That enables the display 407 * of the same sequences in multiple alignments 408 * 409 ********************************************************************/ 410 typedef struct alignseg { 411 Uint1 type; /*type of alignment. GAP? Insertion? Diag?*/ 412 GatherRange gr; 413 Int2 featnum; /*number of collected features*/ 414 ValNodePtr mismatch; /*the position of mismatched residues*/ 415 Int4 ins_pos; /*position of insertion*/ 416 Int4 top; 417 Int4 bottom; 418 Int4 line; 419 ValNodePtr cnp; /*list of FeatNode associated with the seg*/ 420 struct alignseg PNTR next; 421 } AlignSeg, PNTR AlignSegPtr; 422 423 /*values for the sequence index map*/ 424 425 /* 426 * the four mapping status 427 * 428 */ 429 #define MAP_STATUS_Mapping 1 /*magenta color*/ 430 #define MAP_STATUS_Mapped 2 /*red color*/ 431 #define MAP_STATUS_Paused 3 /*blue color*/ 432 #define MAP_STATUS_None 4 /*black color*/ 433 434 /* 435 * the five sequencing status 436 * 437 */ 438 #define SEQ_STATUS_Plan 1 /*cyan color*/ 439 #define SEQ_STATUS_Sequencing 2 /*magenta color*/ 440 #define SEQ_STATUS_Sequenced 3 /*red color*/ 441 #define SEQ_STATUS_Paused 4 /*blue color*/ 442 #define SEQ_STATUS_None 5 /*black color*/ 443 444 445 #define ALIGN_NON_INDEX 0 446 #define ALING_MAP_INDEX 1 447 #define ALIGN_SEQ_INDEX 2 448 449 450 typedef struct alignnode { /*for collecting the alignment*/ 451 Uint1 index; /*0, 1, 2 to indicate if it is a sequence/map index or 452 a normal alignment */ 453 CharPtr label; /*label for the aligned sequence*/ 454 Boolean keep_label; /* says if a function can change the 'label' field */ 455 Uint1 m_frame; /*mapped to the frame of translation in the master DNA sequence*/ 456 Boolean is_master; /*is it a master AlignNode*/ 457 GatherRange extremes; 458 AlignSegPtr segs; /*individual segment in alignment*/ 459 Int4 line; 460 Int4 top; /*the top of the box*/ 461 Int4 bottom; /*the bottom of the box*/ 462 463 Int4 seqpos; /*the position of the sequence*/ 464 SeqIdPtr sip; /*the SeqId of the aligned sequence*/ 465 Uint4 itemID; 466 Uint2 entityID; 467 Uint4 seq_entityID; /*entity id for the sequence*/ 468 Uint4 bsp_itemID; /*itemID for the current Bioseq*/ 469 Uint2 seqOrder; 470 Uint2 chain; 471 Boolean seq_has_align; /*is the aligned segment itself contains alignment*/ 472 AlignBlockPtr blocks; 473 SeqAnnotPtr pop_sap; /*a list of Seq-feat propagated from Seq-align*/ 474 Boolean use_seq_ids; /*use the seq_entityID, bsp_itemID to do the segmentation in the graphic view*/ 475 Boolean follower; /*TRUE, it follows the 476 previous non-follower*/ 477 Int2 num_follower; /*number of sequences follow this node*/ 478 CharPtr clone_id; /*id of the clones*/ 479 Int4 align_num; /*number of alignments. for recording the stop position*/ 480 }AlignNode, PNTR AlignNodePtr; 481 /********************************************************************* 482 * 483 * FreeAlignNode(list) 484 * free a list of AlignNodePtr 485 * 486 *********************************************************************/ 487 NLM_EXTERN ValNodePtr FreeAlignNode PROTO((ValNodePtr list)); 488 489 /*********************************************************************** 490 * 491 * SortAlignNode(anp_list) 492 * sort a list of AlignNode to the ascending order of (extremes.left, 493 * extremes.right) 494 * 495 **********************************************************************/ 496 NLM_EXTERN ValNodePtr SortAlignNode PROTO((ValNodePtr anp_list)); 497 498 499 /*************************************************************** 500 * 501 * CollAlignFromSeqAnnot(annot, m_loc, featureOrder, groupOrder, 502 * style,graphic) 503 * 504 * collect the AlignNode for Seq-aligns stored in Seq-annot 505 * annot: the Seq-annot 506 * m_loc: the target sequence 507 * left: the offset of the leftmost position 508 * featureOrder, groupOrde: the features selected to be displayed together 509 * with alignment 510 * style: the style of the display. Only valid for multiple-pairwise 511 * and multiple dimension for now 512 * graphic: if TRUE, it is designed to show the display on graphic, 513 * so the mismatch data will be collected. Otherwise, it will not 514 * collect mismatch data 515 * sort: if TRUE, sort the alignode, else no sorting 516 * flat_insert: if TRUE, make the insertions in MP alignment flat 517 * 518 ****************************************************************/ 519 NLM_EXTERN ValNodePtr CollAlignFromSeqAnnot PROTO((SeqAnnotPtr annot, SeqLocPtr m_loc, Uint1Ptr featureOrder, Uint1Ptr groupOrder, Uint1 style, Boolean graphic, Boolean sort, Boolean flat_insert)); 520 521 522 523 /*##################################################################### 524 # 525 # functions related to the collection of the features of alignment 526 # 527 #####################################################################*/ 528 529 /****************************************************************** 530 * 531 * CollectFeatureForAlignNode(slp, anp, csop) 532 * collect feature for the alignment 533 * slp: the target Seq-loc 534 * anp: the AlignNode belong to the target Seq-loc 535 * csop: the option for gathering the features 536 * 537 ******************************************************************/ 538 NLM_EXTERN Boolean CollectFeatureForAlignNode PROTO((SeqLocPtr slp, AlignNodePtr anp, CollectSeqOptionPtr csop)); 539 540 /****************************************************************** 541 * 542 * CollectFeatureForAlign(slp, anp, featureOrder, groupOrder) 543 * collect feature for the alignment 544 * slp: the target Seq-loc 545 * anp: the AlignNode belong to the target Seq-loc 546 * featureOrder: the order of features 547 * groupOrder: the order of the groups 548 * 549 ******************************************************************/ 550 NLM_EXTERN Boolean CollectFeatureForAlign PROTO((SeqLocPtr slp, AlignNodePtr anp, Uint1Ptr featureOrder, Uint1Ptr groupOrder)); 551 552 553 /****************************************************************** 554 * 555 * SortAlignmentFeature(anp_node, featureOrder, groupOrder) 556 * sort the list of FeatNode in aligned segment (asp->cnp) to the 557 * proper order of featureOrder and groupOrder 558 * 559 *******************************************************************/ 560 NLM_EXTERN void SortAlignmentFeature PROTO((ValNodePtr anp_node, Uint1Ptr featureOrder, Uint1Ptr groupOrder)); 561 562 563 /******************************************************************* 564 * 565 * void CollectSegMapSTSAlign( entityID, anp_list) 566 * look for the sts alignment from segmap stored as Seq-annot in 567 * in entityID. Add the alignment as the mismatch marker in the 568 * AlignSeg of the anp_list 569 * 570 *******************************************************************/ 571 NLM_EXTERN void CollectSegMapSTSAlign PROTO((Uint2 entityID, ValNodePtr anp_list, SeqLocPtr m_loc, Int4 left)); 572 573 /***************************************************************** 574 * 575 * check if the AlignNode only contains Seq-annot or it 576 * has real sequence alignment. 577 * the empty Seq-annot may be the unaligned contigs in 578 * Eric Green's map 579 ******************************************************************/ 580 NLM_EXTERN Boolean alignode_has_alignments PROTO((ValNodePtr aligns)); 581 582 583 /*********************************************************************** 584 * 585 * find_insert_ypos(left, seglen, ins, l_bound, r_bound, p_pos, space 586 * num) 587 * find the level for placing the insertions. Used in both the layout 588 * for text and graphic 589 * left: to store the left-most position calculated for an insertion 590 * seglen: length of the insertion 591 * ins: the position for insertions 592 * l_bound: the leftmost position in the current line 593 * r_bound: the rightmost position in the current line 594 * p_pos: position for storing all the layout info 595 * num: number of elements in p_pos 596 * return the current level found for an insertion 597 * 598 ***********************************************************************/ 599 NLM_EXTERN Int2 find_insert_ypos PROTO((Int4Ptr left, Int4 seglen, Int4 ins, Int4 l_bound, Int4 r_bound, Int4Ptr p_pos, Int4 space, Int2 num)); 600 601 602 603 604 /***************************************************************** 605 * 606 * given the bioseq and its entityID, figure out the 607 * itemID for the Bioseq 608 * 609 *****************************************************************/ 610 NLM_EXTERN Uint4 get_bioseq_itemID PROTO((BioseqPtr bsp, Uint2 entityID)); 611 612 613 NLM_EXTERN ValNodePtr clean_annot_for_anp PROTO((ValNodePtr PNTR head)); 614 615 /************************************************************************ 616 * 617 * convert_gdata_for_featnode(gdata, cyto_loc, offset) 618 * gdata: the GeneDataPtr 619 * cyto_loc: the current location on the cytogenetic map 620 * offset: the offset of cyto_loc to the graphic viewer1 621 * for human cytogenetic map, the markers are not shown. But for 622 * the markers that were queried, it will display the interval for 623 * gene data 624 * 625 ************************************************************************/ 626 627 NLM_EXTERN ValNodePtr convert_gdata_to_featnode PROTO((GeneDataPtr gdata, SeqLocPtr cyto_loc, Int4 offset)); 628 629 630 #define ALIGN_NORMAL 0 631 #define ALIGN_DNA_TO_PROT 1 632 #define ALIGN_PROT_TO_DNA 2 633 #define ALIGN_TDNA_TO_TDNA 3 634 #define ALIGN_MAX_TYPE 3 635 636 NLM_EXTERN Uint1 get_alignment_type PROTO((AnnotInfoPtr annot_info)); 637 638 /********************************************************************** 639 * 640 * for a multiple pairwise alignment, convert the insertions 641 * into gaps on the master sequence 642 * 643 **********************************************************************/ 644 NLM_EXTERN Boolean FlatAlignNode PROTO((ValNodePtr anp_list)); 645 646 NLM_EXTERN void AddOffsetToAlignNode PROTO((AlignNodePtr anp, Int4 offset)); 647 /* 648 * Delete all the bad YACs from the list 649 * anything on the NHGRI map that is recorded inconsistent will 650 * be considered inconsistent. For the Whitehead map, the 651 * inconsistent+ambiguous is inconsistent. Inconsistent alone 652 * is not considered inconsistent 653 * if any alignment is the same as the chromosome id (the segmap 654 * alignment includes the id mapped back to the chromosome), it 655 * will be cleaned as well 656 */ 657 NLM_EXTERN void CleanUpAmbiguousYAC PROTO((ValNodePtr PNTR anp_node, Uint1 db, SeqIdPtr chr_id)); 658 659 /*********************************************************************** 660 * 661 * ProcessTextAlignNode(anp, left, right, p_stop, m_buf, locus) 662 * process an AlignNode to generate a list of text buffer 663 * 664 * anp: the AlignNode 665 * left, right: the range of alignment in process. mapped to 666 * anp->extremes.left, and anp->extremes.right 667 * p_stop: the previous stop position in the sequence. It is used 668 * to label the position of line which is a gap 669 * m_buf: the buffer of the master sequence. Can be used to compare 670 * mismatches 671 * locus: if TRUE, use the locus name for sequence 672 * 673 * 674 * 675 ************************************************************************/ 676 NLM_EXTERN ValNodePtr ProcessTextAlignNode PROTO(( 677 AlignNodePtr anp, Int4 m_left, 678 Int4 m_right, Int4Ptr p_stop, 679 CharPtr m_buf, Int4 line_len, 680 Int1 m_frame, 681 Uint4 option, Int4Ptr PNTR matrix 682 )); 683 NLM_EXTERN ValNodePtr ProcessTextAlignNode2 PROTO(( 684 AlignNodePtr anp, Int4 m_left, 685 Int4 m_right, Int4Ptr p_stop, 686 CharPtr m_buf, Int4 line_len, 687 Int1 m_frame, 688 Uint4 option, Int4Ptr PNTR matrix, 689 Int4Ptr PNTR posMatrix, Int4 q_start 690 )); 691 692 NLM_EXTERN ValNodePtr FreeTextAlignList PROTO((ValNodePtr tdp_list)); 693 694 NLM_EXTERN SeqIdPtr LIBCALL GetUseThisGi PROTO((SeqAlignPtr seqalign)); 695 NLM_EXTERN SeqIdPtr LIBCALL ScorePtrUseThisGi PROTO((ScorePtr sp)); 696 697 698 /* setting up the matrix for the positive residue of the alignment */ 699 700 NLM_EXTERN Int4Ptr PNTR load_default_matrix PROTO((void)); 701 NLM_EXTERN void free_default_matrix PROTO((Int4Ptr PNTR matrix)); 702 703 #ifdef __cplusplus 704 } 705 #endif 706 707 #undef NLM_EXTERN 708 #ifdef NLM_EXPORT 709 #define NLM_EXTERN NLM_EXPORT 710 #else 711 #define NLM_EXTERN 712 #endif 713 714 #endif 715 716 717 718 719