NCBI C Toolkit Cross Reference

C/api/asn2ffp.h

  1 /*    asn2ffp.h
  2 * ===========================================================================
  3 *
  4 *                            PUBLIC DOMAIN NOTICE
  5 *            National Center for Biotechnology Information (NCBI)
  6 *
  7 *  This software/database is a "United States Government Work" under the
  8 *  terms of the United States Copyright Act.  It was written as part of
  9 *  the author's official duties as a United States Government employee and
 10 *  thus cannot be copyrighted.  This software/database is freely available
 11 *  to the public for use. The National Library of Medicine and the U.S.
 12 *  Government do not place any restriction on its use or reproduction.
 13 *  We would, however, appreciate having the NCBI and the author cited in
 14 *  any work or product based on this material
 15 *
 16 *  Although all reasonable efforts have been taken to ensure the accuracy
 17 *  and reliability of the software and data, the NLM and the U.S.
 18 *  Government do not and cannot warrant the performance or results that
 19 *  may be obtained by using this software or data. The NLM and the U.S.
 20 *  Government disclaim all warranties, express or implied, including
 21 *  warranties of performance, merchantability or fitness for any particular
 22 *  purpose.
 23 *
 24 * ===========================================================================
 25 *
 26 * File Name:  asn2ffp.h
 27 *
 28 * Author:  Karl Sirotkin, Tom Madden, Tatiana Tatusov
 29 *
 30 * Version Creation Date:   7/15/95
 31 *
 32 * $Revision: 6.34 $
 33 *
 34 * File Description: 
 35 *
 36 * Modifications:  
 37 * --------------------------------------------------------------------------
 38 * Date     Name        Description of modification
 39 * -------  ----------  -----------------------------------------------------
 40 *
 41 *
 42 * ==========================================================================
 43 */
 44 
 45 /*************************************
 46 *
 47  * $Log: asn2ffp.h,v $
 48  * Revision 6.34  2006/07/13 17:06:38  bollin
 49  * use Uint4 instead of Uint2 for itemID values
 50  * removed unused variables
 51  * resolved compiler warnings
 52  *
 53  * Revision 6.33  2003/07/22 16:18:27  kans
 54  * added ZFIN as legal db_xref
 55  *
 56  * Revision 6.32  2003/06/10 18:44:10  kans
 57  * added GeneDB to list of legal db_xrefs
 58  *
 59  * Revision 6.31  2003/05/29 20:25:19  kans
 60  * added Interpro to list of legal dbxrefs
 61  *
 62  * Revision 6.30  2002/11/30 20:18:27  kans
 63  * added GOA to list of legal db_xrefs
 64  *
 65  * Revision 6.29  2002/11/27 22:25:17  kans
 66  * added AceView/WormGenes, NextDB, and WorfDB to legal db_xrefs
 67  *
 68  * Revision 6.28  2002/07/12 17:34:35  kans
 69  * WormBase is now legal dbxref for all records, not just RefSeq
 70  *
 71  * Revision 6.27  2002/06/21 15:31:11  kans
 72  * added GABI db_xref
 73  *
 74  * Revision 6.26  2002/06/18 20:59:59  kans
 75  * added ISFinder as legal db_xref with hotlink
 76  *
 77  * Revision 6.25  2002/05/06 22:15:12  kans
 78  * added IFO and JCM db_xrefs
 79  *
 80  * Revision 6.24  2002/02/20 21:59:33  tatiana
 81  * DBNUM increased for IMGT/LIGM
 82  *
 83  * Revision 6.23  2001/11/29 18:29:38  kans
 84  * added FANTOM_DB to list of legal db_xrefs, incremented DBNUM
 85  *
 86  * Revision 6.22  2001/10/15 17:08:44  kans
 87  * updated legal db_xref list to collaboration + RefSeq
 88  *
 89  * Revision 6.21  2001/10/15 13:57:22  kans
 90  * added BDGP_INS and SoyBase as legal db_xrefs
 91  *
 92  * Revision 6.20  2001/09/06 18:55:52  tatiana
 93  * *** empty log message ***
 94  *
 95  * Revision 6.19  2001/03/17 00:51:14  tatiana
 96  * GeneID added to dbxref array, DBNUM increased
 97  *
 98  * Revision 6.18  2001/01/26 19:26:37  kans
 99  * added niaEST, increased DBNUM
100  *
101  * Revision 6.17  2001/01/18 23:57:02  kans
102  * add GO (gene ontology) to list of legal dbxrefs
103  *
104  * Revision 6.16  2000/12/05 01:21:23  tatiana
105  * DBNUM increased for COG
106  *
107  * Revision 6.15  2000/10/16 19:10:18  kans
108  * added UniSTS and InterimID to legal dbxrefs
109  *
110  * Revision 6.14  2000/08/28 22:17:19  kans
111  * added CDD to list of legal dbxrefs
112  *
113  * Revision 6.13  2000/07/14 20:24:27  kans
114  * added RGD as dbxref with web link
115  *
116  * Revision 6.12  2000/02/15 22:53:58  kans
117  * added dbSNP and RATMAP as legal dbxrefs, put /organelle under ajp->forgrel control
118  *
119  * Revision 6.11  1999/04/02 20:35:51  kans
120  * added prototype for GR_PrintPubs
121  *
122  * Revision 6.10  1999/03/22 23:19:19  tatiana
123  * PrintImpFeatEx() added
124  *
125  * Revision 6.9  1998/10/19 15:57:04  tatiana
126  * DBNUM increased for UniGene tag
127  *
128  * Revision 6.8  1998/08/19 18:40:03  tatiana
129  * DBNUM increased to add RiceGenes dbrag
130  *
131  * Revision 6.7  1998/05/18 14:41:19  tatiana
132  * DBNUM increased to add GI to dbtag array
133  *
134  * Revision 6.6  1998/04/15 20:50:38  tatiana
135  * bugs fixing
136  *
137  * Revision 6.5  1998/04/15 18:44:45  tatiana
138  *  dbtag array moved from asn2ff3.c
139  *
140  * Revision 6.4  1997/12/15 15:45:59  tatiana
141  * features processing has been changed
142  *
143  * Revision 6.3  1997/12/02 16:44:17  tatiana
144  *  missing semicolon in SortOrganizeFeat
145  *
146  * Revision 6.1  1997/09/16 15:41:01  kans
147  * added AddSiteNoteQual (TT)
148  *
149  * Revision 5.7  1997/06/19 18:37:24  vakatov
150  * [WIN32,MSVC++]  Adopted for the "NCBIOBJ.LIB" DLL'ization
151  *
152  * Revision 5.6  1996/11/20 15:26:58  tatiana
153  * prototype for GetDefinitionLine
154  *
155  * Revision 5.5  1996/07/30  16:31:44  tatiana
156  * add Boolean arg in CheckNAFeat()
157  *
158  * Revision 5.4  1996/07/24  12:40:24  tatiana
159  * GetCdregionGeneXrefInfo changed number of arguments
160  *
161  * Revision 5.3  1996/07/12  16:48:49  tatiana
162  * *** empty log message ***
163  *
164  * Revision 5.2  1996/06/11  15:25:32  tatiana
165  * add PrintNID PROTO
166  *
167  * Revision 5.1  1996/06/06  14:50:31  tatiana
168  * *** empty log message ***
169  *
170  * Revision 4.10  1996/05/16  20:59:07  tatiana
171  * GetCdregionGeneXrefInfo changed to Boolean
172  *
173  * Revision 4.9  1996/04/29  18:54:51  tatiana
174  * *** empty log message ***
175  *
176  * Revision 4.9  1996/04/29  18:54:51  tatiana
177  * *** empty log message ***
178  *
179  * Revision 4.7  1996/04/09  14:05:06  tatiana
180  * *** empty log message ***
181  *
182  * Revision 4.6  1996/02/21  20:12:17  tatiana
183  * *** empty log message ***
184  *
185  * Revision 4.5  1996/02/15  17:20:23  tatiana
186  * GatherItemWithLock added
187  *
188  * Revision 4.4  1995/12/20  22:45:30  tatiana
189  * new function added
190  *
191  * Revision 4.1  1995/08/22  15:39:26  tatiana
192  * GetVersion name changed to GetBiotableVersion
193  *
194  * Revision 1.43  1995/07/17  19:33:20  kans
195  * parameters combined into Asn2ffJobPtr structure
196  *
197 *
198 **************************************/
199 
200 /*****************************************************************************
201 *
202 *       Header file for asn2gb files.
203 *
204 ****************************************************************************/
205 
206 /*************************************
207 *
208 * $Log: asn2ffp.h,v $
209 * Revision 6.34  2006/07/13 17:06:38  bollin
210 * use Uint4 instead of Uint2 for itemID values
211 * removed unused variables
212 * resolved compiler warnings
213 *
214 * Revision 6.33  2003/07/22 16:18:27  kans
215 * added ZFIN as legal db_xref
216 *
217 * Revision 6.32  2003/06/10 18:44:10  kans
218 * added GeneDB to list of legal db_xrefs
219 *
220 * Revision 6.31  2003/05/29 20:25:19  kans
221 * added Interpro to list of legal dbxrefs
222 *
223 * Revision 6.30  2002/11/30 20:18:27  kans
224 * added GOA to list of legal db_xrefs
225 *
226 * Revision 6.29  2002/11/27 22:25:17  kans
227 * added AceView/WormGenes, NextDB, and WorfDB to legal db_xrefs
228 *
229 * Revision 6.28  2002/07/12 17:34:35  kans
230 * WormBase is now legal dbxref for all records, not just RefSeq
231 *
232 * Revision 6.27  2002/06/21 15:31:11  kans
233 * added GABI db_xref
234 *
235 * Revision 6.26  2002/06/18 20:59:59  kans
236 * added ISFinder as legal db_xref with hotlink
237 *
238 * Revision 6.25  2002/05/06 22:15:12  kans
239 * added IFO and JCM db_xrefs
240 *
241 * Revision 6.24  2002/02/20 21:59:33  tatiana
242 * DBNUM increased for IMGT/LIGM
243 *
244 * Revision 6.23  2001/11/29 18:29:38  kans
245 * added FANTOM_DB to list of legal db_xrefs, incremented DBNUM
246 *
247 * Revision 6.22  2001/10/15 17:08:44  kans
248 * updated legal db_xref list to collaboration + RefSeq
249 *
250 * Revision 6.21  2001/10/15 13:57:22  kans
251 * added BDGP_INS and SoyBase as legal db_xrefs
252 *
253 * Revision 6.20  2001/09/06 18:55:52  tatiana
254 * *** empty log message ***
255 *
256 * Revision 6.19  2001/03/17 00:51:14  tatiana
257 * GeneID added to dbxref array, DBNUM increased
258 *
259 * Revision 6.18  2001/01/26 19:26:37  kans
260 * added niaEST, increased DBNUM
261 *
262 * Revision 6.17  2001/01/18 23:57:02  kans
263 * add GO (gene ontology) to list of legal dbxrefs
264 *
265 * Revision 6.16  2000/12/05 01:21:23  tatiana
266 * DBNUM increased for COG
267 *
268 * Revision 6.15  2000/10/16 19:10:18  kans
269 * added UniSTS and InterimID to legal dbxrefs
270 *
271 * Revision 6.14  2000/08/28 22:17:19  kans
272 * added CDD to list of legal dbxrefs
273 *
274 * Revision 6.13  2000/07/14 20:24:27  kans
275 * added RGD as dbxref with web link
276 *
277 * Revision 6.12  2000/02/15 22:53:58  kans
278 * added dbSNP and RATMAP as legal dbxrefs, put /organelle under ajp->forgrel control
279 *
280 * Revision 6.11  1999/04/02 20:35:51  kans
281 * added prototype for GR_PrintPubs
282 *
283 * Revision 6.10  1999/03/22 23:19:19  tatiana
284 * PrintImpFeatEx() added
285 *
286 * Revision 6.9  1998/10/19 15:57:04  tatiana
287 * DBNUM increased for UniGene tag
288 *
289 * Revision 6.8  1998/08/19 18:40:03  tatiana
290 * DBNUM increased to add RiceGenes dbrag
291 *
292 * Revision 6.7  1998/05/18 14:41:19  tatiana
293 * DBNUM increased to add GI to dbtag array
294 *
295 * Revision 6.6  1998/04/15 20:50:38  tatiana
296 * bugs fixing
297 *
298 * Revision 6.5  1998/04/15 18:44:45  tatiana
299 *  dbtag array moved from asn2ff3.c
300 *
301 * Revision 6.4  1997/12/15 15:45:59  tatiana
302 * features processing has been changed
303 *
304 * Revision 6.3  1997/12/02 16:44:17  tatiana
305 *  missing semicolon in SortOrganizeFeat
306 *
307 * Revision 6.1  1997/09/16 15:41:01  kans
308 * added AddSiteNoteQual (TT)
309 *
310 * Revision 5.7  1997/06/19 18:37:24  vakatov
311 * [WIN32,MSVC++]  Adopted for the "NCBIOBJ.LIB" DLL'ization
312 *
313 * Revision 5.6  1996/11/20 15:26:58  tatiana
314 * prototype for GetDefinitionLine
315 *
316  * Revision 5.5  1996/07/30  16:31:44  tatiana
317  * add Boolean arg in CheckNAFeat()
318  *
319  * Revision 5.4  1996/07/24  12:40:24  tatiana
320  * GetCdregionGeneXrefInfo changed number of arguments
321  *
322  * Revision 5.3  1996/07/12  16:48:49  tatiana
323  * *** empty log message ***
324  *
325  * Revision 5.2  1996/06/11  15:25:32  tatiana
326  * add PrintNID PROTO
327  *
328  * Revision 5.1  1996/06/06  14:50:31  tatiana
329  * *** empty log message ***
330  *
331  * Revision 4.10  1996/05/16  20:59:07  tatiana
332  * GetCdregionGeneXrefInfo changed to Boolean
333  *
334  * Revision 4.9  1996/04/29  18:54:51  tatiana
335  * *** empty log message ***
336  *
337  * Revision 4.9  1996/04/29  18:54:51  tatiana
338  * *** empty log message ***
339  *
340  * Revision 4.7  1996/04/09  14:05:06  tatiana
341  * *** empty log message ***
342  *
343  * Revision 4.6  1996/02/21  20:12:17  tatiana
344  * *** empty log message ***
345  *
346  * Revision 4.5  1996/02/15  17:20:23  tatiana
347  * GatherItemWithLock added
348  *
349  * Revision 4.4  1995/12/20  22:45:30  tatiana
350  * new function added
351  *
352  * Revision 4.1  1995/08/22  15:39:26  tatiana
353  * GetVersion name changed to GetBiotableVersion
354  *
355  * Revision 1.43  1995/07/17  19:33:20  kans
356  * parameters combined into Asn2ffJobPtr structure
357  *
358  * Revision 1.41  1995/06/19  21:40:02  kans
359  * Tatiana's first major reorganization, moving printing, adding HTML
360  *
361  * Revision 1.40  1995/05/22  16:14:20  tatiana
362  * add ASN2FF_SHOW_ALL_PUBS to asn2ff_flags
363  *
364  * Revision 1.39  1995/05/15  21:46:05  ostell
365  * added Log line
366  *
367 *
368 **************************************/
369 #ifndef _ASN2FFP_
370 #define _ASN2FFP_
371 
372 #include <asn2ffg.h>
373 #include <asn2ff.h>
374 #include <asn2ff6.h>
375 
376 
377 #undef NLM_EXTERN
378 #ifdef NLM_IMPORT
379 #define NLM_EXTERN NLM_IMPORT
380 #else
381 #define NLM_EXTERN extern
382 #endif
383 
384 NLM_EXTERN  Boolean asn2ff_flags[13];
385 
386 #define ASN2FF_LOCAL_ID                 asn2ff_flags[0]
387 #define ASN2FF_LOOK_FOR_SEQ             asn2ff_flags[1]
388 #define ASN2FF_VALIDATE_FEATURES        asn2ff_flags[2]
389 #define ASN2FF_IGNORE_PATENT_PUBS       asn2ff_flags[3]
390 #define ASN2FF_DROP_SHORT_AA            asn2ff_flags[4]
391 #define ASN2FF_AVOID_LOCUS_COLL         asn2ff_flags[5]
392 #define ASN2FF_DATE_ERROR_MSG           asn2ff_flags[6]
393 #define ASN2FF_IUPACAA_ONLY             asn2ff_flags[7]
394 #define ASN2FF_TRANSL_TABLE             asn2ff_flags[8]
395 #define ASN2FF_REPORT_LOCUS_COLL        asn2ff_flags[9]
396 #define ASN2FF_SHOW_ALL_PUBS            asn2ff_flags[10]
397 #define ASN2FF_SHOW_ERROR_MSG           asn2ff_flags[11]
398 #define ASN2FF_SHOW_GB_STYLE            asn2ff_flags[12]
399 
400 #define DBNUM 58
401 NLM_EXTERN CharPtr dbtag[DBNUM];
402 
403 NLM_EXTERN void FlatSpliceOff PROTO((SeqEntryPtr the_set, ValNodePtr desc));
404 NLM_EXTERN void FlatSpliceOn PROTO((SeqEntryPtr the_set, ValNodePtr desc));
405 
406 NLM_EXTERN void PrintLocusLine PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp));
407 NLM_EXTERN void PrintAccessLine PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp));
408 NLM_EXTERN void PrintVersionLine PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp));
409 NLM_EXTERN void PrintNCBI_GI PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp));
410 NLM_EXTERN void PrintNID PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp));
411 NLM_EXTERN void GetDefinitionLine PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp));
412 NLM_EXTERN void PrintDefinitionLine PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp));
413 NLM_EXTERN void PrintKeywordLine PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp));
414 NLM_EXTERN void PrintOriginLine PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
415 NLM_EXTERN void PrintOrganismLine PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
416 
417 NLM_EXTERN void PrintEPLocusLine PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp));
418 NLM_EXTERN void PrintSegmentLine PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp));
419 
420 NLM_EXTERN void PrintGBSourceLine PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
421 NLM_EXTERN void PrintGBOrganismLine PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
422 
423 NLM_EXTERN void PrintPubsByNumber PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
424 NLM_EXTERN void PrintFeatHeader PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
425 NLM_EXTERN void PrintSequence PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp, Int4 start, Int4 stop));
426 NLM_EXTERN void PrintEPSequence PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp, Int4 start, Int4 stop));
427 NLM_EXTERN void PrintBaseCount PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
428 NLM_EXTERN ValNodePtr tie_next PROTO((ValNodePtr head, ValNodePtr vnp));
429 NLM_EXTERN ValNodePtr GatherDescrByChoice PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp, Uint1 choice));
430 NLM_EXTERN ValNodePtr GatherDescrListByChoice PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp, Uint1 choice));
431 NLM_EXTERN ValNodePtr GetOrgRef PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
432 NLM_EXTERN ValNodePtr GetBiosource PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
433 NLM_EXTERN void EMBL_PrintPubs PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp, PubStructPtr psp));
434 NLM_EXTERN void GB_PrintPubs PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp, PubStructPtr psp));
435 NLM_EXTERN void GR_PrintPubs PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp, PubStructPtr psp));
436 NLM_EXTERN Boolean FlatIgnoreThisPatentPub PROTO ((BioseqPtr bsp, ValNodePtr best, Int4Ptr seqidPt));
437 NLM_EXTERN CharPtr FlatCleanEquals PROTO ((CharPtr retval));
438 NLM_EXTERN ValNodePtr GetAuthors PROTO((Asn2ffJobPtr ajp, ValNodePtr the_pub));
439 NLM_EXTERN CharPtr FlatJournal PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp, ValNodePtr the_pub, Int4 pat_seqid, Boolean PNTR submit, Boolean make_index));
440 NLM_EXTERN ValNodePtr GetKeywordLine PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp));
441 NLM_EXTERN void PrintSourceFeat PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
442 NLM_EXTERN Int2 PrintImpFeat PROTO ((Asn2ffJobPtr ajp, BioseqPtr bsp, SeqFeatPtr sfp));
443 NLM_EXTERN Int2 PrintImpFeatEx PROTO ((Asn2ffJobPtr ajp, BioseqPtr bsp, SeqFeatPtr sfp, Int4 gi, Int2 entityID, Uint4 itemID));
444 NLM_EXTERN void PrintNAFeatAwp PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
445 NLM_EXTERN void PrintNAFeatByNumber PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
446 NLM_EXTERN void PrintAAFeatByNumber PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
447 NLM_EXTERN CharPtr FlatLoc PROTO ((BioseqPtr bsp, ValNodePtr location));
448 NLM_EXTERN Boolean FlatAnnotPartial PROTO ((SeqFeatPtr sfp, Boolean use_product));
449 NLM_EXTERN Boolean FlatIgnoreThisPatentPub PROTO ((BioseqPtr bsp, ValNodePtr best, Int4Ptr seqidPt));
450 
451 NLM_EXTERN void PrintCommentByNumber PROTO((Asn2ffJobPtr aip, GBEntryPtr gbp));
452 NLM_EXTERN void PrintFirstComment PROTO((Asn2ffJobPtr aip, GBEntryPtr gbp));
453 NLM_EXTERN void GBDescrComFeat PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp));
454 
455 NLM_EXTERN Int2 GB_GetSeqDescrComms  PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp));
456 NLM_EXTERN Int2 GP_GetSeqDescrComms  PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp));
457 
458 NLM_EXTERN Int4 GetGibbsqNumber PROTO ((BioseqPtr bsp));
459 NLM_EXTERN Int4 GetGibbsqCommentLength PROTO ((GBEntryPtr gbp));
460 NLM_EXTERN CharPtr GetGibbsqComment PROTO ((GBEntryPtr gbp));
461 NLM_EXTERN Int4 GetGibbsqStatement PROTO ((GBEntryPtr gbp, CharPtr ptr));
462 NLM_EXTERN Int2 StorePubInfo PROTO ((Asn2ffJobPtr ajp, BioseqContextPtr bcp, BioseqPtr bsp, ValNodePtr PNTR vnpp));
463 NLM_EXTERN Int2 StoreNAPubInfo PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp, ValNodePtr PNTR vnp, Boolean error_msgs));
464 NLM_EXTERN void GetGBDate PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
465 NLM_EXTERN void GetGPDate PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
466 NLM_EXTERN void GetEMBLDate PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
467 NLM_EXTERN void GetEntryVersion PROTO ((GBEntryPtr gbp));
468 NLM_EXTERN Boolean GetGeneQuals PROTO ((SeqFeatPtr sfp_in, GeneStructPtr gsp));
469 NLM_EXTERN Boolean GetCdregionGeneXrefInfo PROTO ((Asn2ffJobPtr ajp, SeqFeatPtr sfp, GBEntryPtr gbp, Int2 index));
470 NLM_EXTERN void GetGeneRefInfo PROTO ((GeneStructPtr gsp, NoteStructPtr nsp, GeneRefPtr grp));
471 NLM_EXTERN void GetDBXrefFromGene PROTO ((GeneRefPtr grp, SeqFeatPtr sfp));
472 NLM_EXTERN Int2 CompareStringWithGsp PROTO ((GeneStructPtr gsp, CharPtr string));
473 NLM_EXTERN Boolean CheckNAFeat PROTO ((Boolean is_new, BioseqPtr bsp, SeqFeatPtr sfp));
474 NLM_EXTERN Boolean CheckAndGetNAFeatLoc PROTO ((BioseqPtr bsp, CharPtr PNTR buffer, SeqFeatPtr sfp, Boolean loc_return));
475 NLM_EXTERN void GetAAFeatLoc PROTO ((BioseqPtr bsp, CharPtr PNTR buffer, SeqFeatPtr sfp, Boolean use_product));
476 NLM_EXTERN CharPtr GetGBSourceLine PROTO ((GBBlockPtr gb));
477 
478 NLM_EXTERN Int2 CheckPubs PROTO ((Asn2ffJobPtr ajp, BioseqPtr bsp, ValNodePtr PNTR vnpp));
479 NLM_EXTERN CharPtr FlatAuthor PROTO ((Asn2ffJobPtr ajp, ValNodePtr the_pub));
480 NLM_EXTERN CharPtr FlatPubTitle PROTO ((ValNodePtr the_pub));
481 NLM_EXTERN void PrintDBSourceLine PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
482 
483 NLM_EXTERN void PostARefErrMessage PROTO ((Asn2ffJobPtr ajp, BioseqPtr bsp, PubStructPtr psp, ValNodePtr ext_pub, Int2 status, CharPtr string));
484 
485 NLM_EXTERN void SeparatePartSuppl PROTO((CharPtr vol_issue, CharPtr part_sub));
486 NLM_EXTERN void AddExtraAccessions PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
487 NLM_EXTERN void PrintTerminator PROTO ((void));
488 NLM_EXTERN Boolean get_pubs PROTO ((GatherContextPtr gcp));
489 NLM_EXTERN void GatherItemWithLock PROTO((Uint2 entityID, Uint4 itemID, Uint2 itemtype,
490                                    Pointer userdata, GatherItemProc userfunc));
491 NLM_EXTERN CharPtr format_article PROTO ((Asn2ffJobPtr ajp, BioseqPtr bsp, ValNodePtr the_pub, Boolean make_index));
492 NLM_EXTERN CharPtr format_bookarticle PROTO ((Asn2ffJobPtr ajp, BioseqPtr bsp, ValNodePtr the_pub, Boolean make_index));
493 NLM_EXTERN CharPtr format_jourarticle PROTO ((Asn2ffJobPtr ajp, BioseqPtr bsp, ValNodePtr the_pub, Boolean make_index));
494 
495 NLM_EXTERN void GetProtRefInfo PROTO ((Uint1 format, GeneStructPtr gsp, NoteStructPtr nsp, ProtRefPtr prp));
496 NLM_EXTERN Int2 GetMapFeats PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp));
497 NLM_EXTERN Boolean find_item PROTO ((GatherContextPtr gcp));
498 NLM_EXTERN Boolean get_prot_feats PROTO((GatherContextPtr gcp));
499 NLM_EXTERN void AddSiteNoteQual PROTO((SeqFeatPtr sfp_in, SeqFeatPtr sfp));
500 NLM_EXTERN void MatchAAGeneToFeat PROTO((OrganizeFeatPtr ofp, SortStructPtr p));
501 NLM_EXTERN void MatchNAGeneToFeat PROTO ((Boolean non_strict, OrganizeFeatPtr ofp, SortStructPtr p));
502 NLM_EXTERN void SortOrganizeFeat PROTO((OrganizeFeatPtr ofp));
503 NLM_EXTERN void OrganizeSeqFeat PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
504 NLM_EXTERN void GetSeqFeat PROTO ((Asn2ffJobPtr ajp));
505 
506 #undef NLM_EXTERN
507 #ifdef NLM_EXPORT
508 #define NLM_EXTERN NLM_EXPORT
509 #else
510 #define NLM_EXTERN
511 #endif
512 
513 #endif
514
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