1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
|
/* asn2ffp.h
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information (NCBI)
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government do not place any restriction on its use or reproduction.
* We would, however, appreciate having the NCBI and the author cited in
* any work or product based on this material
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* ===========================================================================
*
* File Name: asn2ffp.h
*
* Author: Karl Sirotkin, Tom Madden, Tatiana Tatusov
*
* Version Creation Date: 7/15/95
*
* $Revision: 6.9 $
*
* File Description:
*
* Modifications:
* --------------------------------------------------------------------------
* Date Name Description of modification
* ------- ---------- -----------------------------------------------------
*
*
* ==========================================================================
*/
/*************************************
*
* $Log: asn2ffp.h,v $
* Revision 6.9 1998/10/19 15:57:04 tatiana
* DBNUM increased for UniGene tag
*
* Revision 6.8 1998/08/19 18:40:03 tatiana
* DBNUM increased to add RiceGenes dbrag
*
* Revision 6.7 1998/05/18 14:41:19 tatiana
* DBNUM increased to add GI to dbtag array
*
* Revision 6.6 1998/04/15 20:50:38 tatiana
* bugs fixing
*
* Revision 6.5 1998/04/15 18:44:45 tatiana
* dbtag array moved from asn2ff3.c
*
* Revision 6.4 1997/12/15 15:45:59 tatiana
* features processing has been changed
*
* Revision 6.3 1997/12/02 16:44:17 tatiana
* missing semicolon in SortOrganizeFeat
*
* Revision 6.1 1997/09/16 15:41:01 kans
* added AddSiteNoteQual (TT)
*
* Revision 5.7 1997/06/19 18:37:24 vakatov
* [WIN32,MSVC++] Adopted for the "NCBIOBJ.LIB" DLL'ization
*
* Revision 5.6 1996/11/20 15:26:58 tatiana
* prototype for GetDefinitionLine
*
* Revision 5.5 1996/07/30 16:31:44 tatiana
* add Boolean arg in CheckNAFeat()
*
* Revision 5.4 1996/07/24 12:40:24 tatiana
* GetCdregionGeneXrefInfo changed number of arguments
*
* Revision 5.3 1996/07/12 16:48:49 tatiana
* *** empty log message ***
*
* Revision 5.2 1996/06/11 15:25:32 tatiana
* add PrintNID PROTO
*
* Revision 5.1 1996/06/06 14:50:31 tatiana
* *** empty log message ***
*
* Revision 4.10 1996/05/16 20:59:07 tatiana
* GetCdregionGeneXrefInfo changed to Boolean
*
* Revision 4.9 1996/04/29 18:54:51 tatiana
* *** empty log message ***
*
* Revision 4.9 1996/04/29 18:54:51 tatiana
* *** empty log message ***
*
* Revision 4.7 1996/04/09 14:05:06 tatiana
* *** empty log message ***
*
* Revision 4.6 1996/02/21 20:12:17 tatiana
* *** empty log message ***
*
* Revision 4.5 1996/02/15 17:20:23 tatiana
* GatherItemWithLock added
*
* Revision 4.4 1995/12/20 22:45:30 tatiana
* new function added
*
* Revision 4.1 1995/08/22 15:39:26 tatiana
* GetVersion name changed to GetBiotableVersion
*
* Revision 1.43 1995/07/17 19:33:20 kans
* parameters combined into Asn2ffJobPtr structure
*
*
**************************************/
/*****************************************************************************
*
* Header file for asn2gb files.
*
****************************************************************************/
/*************************************
*
* $Log: asn2ffp.h,v $
* Revision 6.9 1998/10/19 15:57:04 tatiana
* DBNUM increased for UniGene tag
*
* Revision 6.8 1998/08/19 18:40:03 tatiana
* DBNUM increased to add RiceGenes dbrag
*
* Revision 6.7 1998/05/18 14:41:19 tatiana
* DBNUM increased to add GI to dbtag array
*
* Revision 6.6 1998/04/15 20:50:38 tatiana
* bugs fixing
*
* Revision 6.5 1998/04/15 18:44:45 tatiana
* dbtag array moved from asn2ff3.c
*
* Revision 6.4 1997/12/15 15:45:59 tatiana
* features processing has been changed
*
* Revision 6.3 1997/12/02 16:44:17 tatiana
* missing semicolon in SortOrganizeFeat
*
* Revision 6.1 1997/09/16 15:41:01 kans
* added AddSiteNoteQual (TT)
*
* Revision 5.7 1997/06/19 18:37:24 vakatov
* [WIN32,MSVC++] Adopted for the "NCBIOBJ.LIB" DLL'ization
*
* Revision 5.6 1996/11/20 15:26:58 tatiana
* prototype for GetDefinitionLine
*
* Revision 5.5 1996/07/30 16:31:44 tatiana
* add Boolean arg in CheckNAFeat()
*
* Revision 5.4 1996/07/24 12:40:24 tatiana
* GetCdregionGeneXrefInfo changed number of arguments
*
* Revision 5.3 1996/07/12 16:48:49 tatiana
* *** empty log message ***
*
* Revision 5.2 1996/06/11 15:25:32 tatiana
* add PrintNID PROTO
*
* Revision 5.1 1996/06/06 14:50:31 tatiana
* *** empty log message ***
*
* Revision 4.10 1996/05/16 20:59:07 tatiana
* GetCdregionGeneXrefInfo changed to Boolean
*
* Revision 4.9 1996/04/29 18:54:51 tatiana
* *** empty log message ***
*
* Revision 4.9 1996/04/29 18:54:51 tatiana
* *** empty log message ***
*
* Revision 4.7 1996/04/09 14:05:06 tatiana
* *** empty log message ***
*
* Revision 4.6 1996/02/21 20:12:17 tatiana
* *** empty log message ***
*
* Revision 4.5 1996/02/15 17:20:23 tatiana
* GatherItemWithLock added
*
* Revision 4.4 1995/12/20 22:45:30 tatiana
* new function added
*
* Revision 4.1 1995/08/22 15:39:26 tatiana
* GetVersion name changed to GetBiotableVersion
*
* Revision 1.43 1995/07/17 19:33:20 kans
* parameters combined into Asn2ffJobPtr structure
*
* Revision 1.41 1995/06/19 21:40:02 kans
* Tatiana's first major reorganization, moving printing, adding HTML
*
* Revision 1.40 1995/05/22 16:14:20 tatiana
* add ASN2FF_SHOW_ALL_PUBS to asn2ff_flags
*
* Revision 1.39 1995/05/15 21:46:05 ostell
* added Log line
*
*
**************************************/
#ifndef _ASN2FFP_
#define _ASN2FFP_
#include <asn2ffg.h>
#include <asn2ff.h>
#include <asn2ff6.h>
#undef NLM_EXTERN
#ifdef NLM_IMPORT
#define NLM_EXTERN NLM_IMPORT
#else
#define NLM_EXTERN extern
#endif
NLM_EXTERN Boolean asn2ff_flags[13];
#define ASN2FF_LOCAL_ID asn2ff_flags[0]
#define ASN2FF_LOOK_FOR_SEQ asn2ff_flags[1]
#define ASN2FF_VALIDATE_FEATURES asn2ff_flags[2]
#define ASN2FF_IGNORE_PATENT_PUBS asn2ff_flags[3]
#define ASN2FF_DROP_SHORT_AA asn2ff_flags[4]
#define ASN2FF_AVOID_LOCUS_COLL asn2ff_flags[5]
#define ASN2FF_DATE_ERROR_MSG asn2ff_flags[6]
#define ASN2FF_IUPACAA_ONLY asn2ff_flags[7]
#define ASN2FF_TRANSL_TABLE asn2ff_flags[8]
#define ASN2FF_REPORT_LOCUS_COLL asn2ff_flags[9]
#define ASN2FF_SHOW_ALL_PUBS asn2ff_flags[10]
#define ASN2FF_SHOW_ERROR_MSG asn2ff_flags[11]
#define ASN2FF_SHOW_GB_STYLE asn2ff_flags[12]
#define DBNUM 23
NLM_EXTERN CharPtr dbtag[DBNUM];
NLM_EXTERN void FlatSpliceOff PROTO((SeqEntryPtr the_set, ValNodePtr desc));
NLM_EXTERN void FlatSpliceOn PROTO((SeqEntryPtr the_set, ValNodePtr desc));
NLM_EXTERN void PrintLocusLine PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN void PrintAccessLine PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN void PrintNCBI_GI PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN void PrintNID PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN void GetDefinitionLine PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN void PrintDefinitionLine PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN void PrintKeywordLine PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN void PrintOriginLine PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN void PrintOrganismLine PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN void PrintEPLocusLine PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN void PrintSegmentLine PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN void PrintGBSourceLine PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN void PrintGBOrganismLine PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN void PrintPubsByNumber PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN void PrintFeatHeader PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN void PrintSequence PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp, Int4 start, Int4 stop));
NLM_EXTERN void PrintEPSequence PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp, Int4 start, Int4 stop));
NLM_EXTERN void PrintBaseCount PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN ValNodePtr tie_next PROTO((ValNodePtr head, ValNodePtr vnp));
NLM_EXTERN ValNodePtr GatherDescrByChoice PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp, Uint1 choice));
NLM_EXTERN ValNodePtr GatherDescrListByChoice PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp, Uint1 choice));
NLM_EXTERN ValNodePtr GetOrgRef PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN ValNodePtr GetBiosource PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN void EMBL_PrintPubs PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp, PubStructPtr psp));
NLM_EXTERN void GB_PrintPubs PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp, PubStructPtr psp));
NLM_EXTERN Boolean FlatIgnoreThisPatentPub PROTO ((BioseqPtr bsp, ValNodePtr best, Int4Ptr seqidPt));
NLM_EXTERN CharPtr FlatCleanEquals PROTO ((CharPtr retval));
NLM_EXTERN ValNodePtr GetAuthors PROTO((Asn2ffJobPtr ajp, ValNodePtr the_pub));
NLM_EXTERN CharPtr FlatJournal PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp, ValNodePtr the_pub, Int4 pat_seqid, Boolean PNTR submit, Boolean make_index));
NLM_EXTERN ValNodePtr GetKeywordLine PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN void PrintSourceFeat PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN Int2 PrintImpFeat PROTO ((Asn2ffJobPtr ajp, BioseqPtr bsp, SeqFeatPtr sfp));
NLM_EXTERN void PrintNAFeatAwp PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN void PrintNAFeatByNumber PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN void PrintAAFeatByNumber PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN CharPtr FlatLoc PROTO ((BioseqPtr bsp, ValNodePtr location));
NLM_EXTERN Boolean FlatAnnotPartial PROTO ((SeqFeatPtr sfp, Boolean use_product));
NLM_EXTERN Boolean FlatIgnoreThisPatentPub PROTO ((BioseqPtr bsp, ValNodePtr best, Int4Ptr seqidPt));
NLM_EXTERN void PrintCommentByNumber PROTO((Asn2ffJobPtr aip, GBEntryPtr gbp));
NLM_EXTERN void PrintFirstComment PROTO((Asn2ffJobPtr aip, GBEntryPtr gbp));
NLM_EXTERN void GBDescrComFeat PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN Int2 GB_GetSeqDescrComms PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN Int2 GP_GetSeqDescrComms PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN Int4 GetGibbsqNumber PROTO ((BioseqPtr bsp));
NLM_EXTERN Int4 GetGibbsqCommentLength PROTO ((GBEntryPtr gbp));
NLM_EXTERN CharPtr GetGibbsqComment PROTO ((GBEntryPtr gbp));
NLM_EXTERN Int4 GetGibbsqStatement PROTO ((GBEntryPtr gbp, CharPtr ptr));
NLM_EXTERN Int2 StorePubInfo PROTO ((Asn2ffJobPtr ajp, BioseqContextPtr bcp, BioseqPtr bsp, ValNodePtr PNTR vnpp));
NLM_EXTERN Int2 StoreNAPubInfo PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp, ValNodePtr PNTR vnp, Boolean error_msgs));
NLM_EXTERN void GetGBDate PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN void GetGPDate PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN void GetEMBLDate PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN void GetEntryVersion PROTO ((GBEntryPtr gbp));
NLM_EXTERN Boolean GetGeneQuals PROTO ((SeqFeatPtr sfp_in, GeneStructPtr gsp));
NLM_EXTERN Boolean GetCdregionGeneXrefInfo PROTO ((Asn2ffJobPtr ajp, SeqFeatPtr sfp, GBEntryPtr gbp, Int2 index));
NLM_EXTERN void GetGeneRefInfo PROTO ((GeneStructPtr gsp, NoteStructPtr nsp, GeneRefPtr grp));
NLM_EXTERN void GetDBXrefFromGene PROTO ((GeneRefPtr grp, SeqFeatPtr sfp));
NLM_EXTERN Int2 CompareStringWithGsp PROTO ((GeneStructPtr gsp, CharPtr string));
NLM_EXTERN Boolean CheckNAFeat PROTO ((Boolean new, BioseqPtr bsp, SeqFeatPtr sfp));
NLM_EXTERN Boolean CheckAndGetNAFeatLoc PROTO ((BioseqPtr bsp, CharPtr PNTR buffer, SeqFeatPtr sfp, Boolean loc_return));
NLM_EXTERN void GetAAFeatLoc PROTO ((BioseqPtr bsp, CharPtr PNTR buffer, SeqFeatPtr sfp, Boolean use_product));
NLM_EXTERN CharPtr GetGBSourceLine PROTO ((GBBlockPtr gb));
NLM_EXTERN Int2 CheckPubs PROTO ((Asn2ffJobPtr ajp, BioseqPtr bsp, ValNodePtr PNTR vnpp));
NLM_EXTERN CharPtr FlatAuthor PROTO ((Asn2ffJobPtr ajp, ValNodePtr the_pub));
NLM_EXTERN CharPtr FlatPubTitle PROTO ((ValNodePtr the_pub));
NLM_EXTERN void PrintDBSourceLine PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN void PostARefErrMessage PROTO ((Asn2ffJobPtr ajp, BioseqPtr bsp, PubStructPtr psp, ValNodePtr ext_pub, Int2 status, CharPtr string));
NLM_EXTERN void SeparatePartSuppl PROTO((CharPtr vol_issue, CharPtr part_sub));
NLM_EXTERN void AddExtraAccessions PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN void PrintTerminator PROTO ((void));
NLM_EXTERN Boolean get_pubs PROTO ((GatherContextPtr gcp));
NLM_EXTERN void GatherItemWithLock PROTO((Uint2 entityID, Uint2 itemID, Uint2 itemtype,
Pointer userdata, GatherItemProc userfunc));
NLM_EXTERN CharPtr format_article PROTO ((Asn2ffJobPtr ajp, BioseqPtr bsp, ValNodePtr the_pub, Boolean make_index));
NLM_EXTERN CharPtr format_bookarticle PROTO ((Asn2ffJobPtr ajp, BioseqPtr bsp, ValNodePtr the_pub, Boolean make_index));
NLM_EXTERN CharPtr format_jourarticle PROTO ((Asn2ffJobPtr ajp, BioseqPtr bsp, ValNodePtr the_pub, Boolean make_index));
NLM_EXTERN void GetProtRefInfo PROTO ((Uint1 format, GeneStructPtr gsp, NoteStructPtr nsp, ProtRefPtr prp));
NLM_EXTERN Int2 GetMapFeats PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN Boolean find_item PROTO ((GatherContextPtr gcp));
NLM_EXTERN Boolean get_prot_feats PROTO((GatherContextPtr gcp));
NLM_EXTERN void AddSiteNoteQual PROTO((SeqFeatPtr sfp_in, SeqFeatPtr sfp));
NLM_EXTERN void MatchAAGeneToFeat PROTO((OrganizeFeatPtr ofp, SortStructPtr p));
NLM_EXTERN void MatchNAGeneToFeat PROTO ((Boolean non_strict, OrganizeFeatPtr ofp, SortStructPtr p));
NLM_EXTERN void SortOrganizeFeat PROTO((OrganizeFeatPtr ofp));
NLM_EXTERN void OrganizeSeqFeat PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp));
NLM_EXTERN void GetSeqFeat PROTO ((Asn2ffJobPtr ajp));
#undef NLM_EXTERN
#ifdef NLM_EXPORT
#define NLM_EXTERN NLM_EXPORT
#else
#define NLM_EXTERN
#endif
#endif
|
