/* 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: 6.23 $ * * File Description: * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * * ========================================================================== */ /************************************* * * $Log: asn2ffp.h,v $ * Revision 6.23 2001/11/29 18:29:38 kans * added FANTOM_DB to list of legal db_xrefs, incremented DBNUM * * Revision 6.22 2001/10/15 17:08:44 kans * updated legal db_xref list to collaboration + RefSeq * * Revision 6.21 2001/10/15 13:57:22 kans * added BDGP_INS and SoyBase as legal db_xrefs * * Revision 6.20 2001/09/06 18:55:52 tatiana * *** empty log message *** * * Revision 6.19 2001/03/17 00:51:14 tatiana * GeneID added to dbxref array, DBNUM increased * * Revision 6.18 2001/01/26 19:26:37 kans * added niaEST, increased DBNUM * * Revision 6.17 2001/01/18 23:57:02 kans * add GO (gene ontology) to list of legal dbxrefs * * Revision 6.16 2000/12/05 01:21:23 tatiana * DBNUM increased for COG * * Revision 6.15 2000/10/16 19:10:18 kans * added UniSTS and InterimID to legal dbxrefs * * Revision 6.14 2000/08/28 22:17:19 kans * added CDD to list of legal dbxrefs * * Revision 6.13 2000/07/14 20:24:27 kans * added RGD as dbxref with web link * * Revision 6.12 2000/02/15 22:53:58 kans * added dbSNP and RATMAP as legal dbxrefs, put /organelle under ajp->forgrel control * * Revision 6.11 1999/04/02 20:35:51 kans * added prototype for GR_PrintPubs * * Revision 6.10 1999/03/22 23:19:19 tatiana * PrintImpFeatEx() added * * 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 6.23 2001/11/29 18:29:38 kans * added FANTOM_DB to list of legal db_xrefs, incremented DBNUM * * Revision 6.22 2001/10/15 17:08:44 kans * updated legal db_xref list to collaboration + RefSeq * * Revision 6.21 2001/10/15 13:57:22 kans * added BDGP_INS and SoyBase as legal db_xrefs * * Revision 6.20 2001/09/06 18:55:52 tatiana * *** empty log message *** * * Revision 6.19 2001/03/17 00:51:14 tatiana * GeneID added to dbxref array, DBNUM increased * * Revision 6.18 2001/01/26 19:26:37 kans * added niaEST, increased DBNUM * * Revision 6.17 2001/01/18 23:57:02 kans * add GO (gene ontology) to list of legal dbxrefs * * Revision 6.16 2000/12/05 01:21:23 tatiana * DBNUM increased for COG * * Revision 6.15 2000/10/16 19:10:18 kans * added UniSTS and InterimID to legal dbxrefs * * Revision 6.14 2000/08/28 22:17:19 kans * added CDD to list of legal dbxrefs * * Revision 6.13 2000/07/14 20:24:27 kans * added RGD as dbxref with web link * * Revision 6.12 2000/02/15 22:53:58 kans * added dbSNP and RATMAP as legal dbxrefs, put /organelle under ajp->forgrel control * * Revision 6.11 1999/04/02 20:35:51 kans * added prototype for GR_PrintPubs * * Revision 6.10 1999/03/22 23:19:19 tatiana * PrintImpFeatEx() added * * 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 #include #include #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 44 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 PrintVersionLine 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 void GR_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 Int2 PrintImpFeatEx PROTO ((Asn2ffJobPtr ajp, BioseqPtr bsp, SeqFeatPtr sfp, Int4 gi, Int2 entityID, Int2 itemID)); 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 is_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