/* asn2ff6.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: asn2ff6.h * * Author: Karl Sirotkin, Tom Madden, Tatiana Tatusov * * Version Creation Date: 7/15/95 * * $Revision: 6.5 $ * * File Description: * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * * ========================================================================== */ /***************************************************************************** * * Header file for asn2gb files. * ****************************************************************************/ /************************************* * * $Log: asn2ff6.h,v $ * Revision 6.5 2001/12/05 18:13:59 cavanaug * Changes for new LOCUS line format * * Revision 6.4 2001/07/24 15:12:37 beloslyu * change the var.name in prototype from new to New to avoid the conflict with c++ * * Revision 6.3 2000/06/05 17:51:58 tatiana * increase size of feature arrays to Int4 * * Revision 6.2 1998/02/10 17:01:22 tatiana * AddGBQualEx() added * * Revision 6.0 1997/08/25 18:05:10 madden * Revision changed to 6.0 * * Revision 5.13 1997/06/19 18:37:20 vakatov * [WIN32,MSVC++] Adopted for the "NCBIOBJ.LIB" DLL'ization * * Revision 5.12 1997/05/28 16:58:46 tatiana * GENPEPT_MIN set to 0 * * Revision 5.11 1997/05/28 16:51:28 tatiana * GENPEPT_MIN set to 1 * * Revision 5.10 1997/01/14 20:53:40 vakatov * added LIBCALL to DoSpecialLineBreak * * Revision 5.9 1997/01/13 22:33:31 tatiana * added CompareGeneName() * * Revision 5.7 1996/12/17 22:47:25 tatiana * added StoreFeatFree() * * Revision 5.6 1996/09/09 13:36:02 kans * moved BioseqGetGBDivCode from toasn.[ch] to asn2ff.h/asn2ff6.c * * Revision 5.5 1996/09/03 19:54:20 tatiana * extra_loc added * * Revision 5.4 1996/08/16 20:36:47 tatiana * GetNAFeatKey PROTO changed * * Revision 5.3 1996/07/30 16:35:40 tatiana * Boolean new added to GetNaFeatKey() * * Revision 5.2 1996/06/14 18:05:18 tatiana * GetNAFeatKey change. * * Revision 5.1 1996/06/11 15:27:34 tatiana * GetGINumber has been changed * * Revision 4.5 1996/01/29 22:43:06 tatiana * error posting MODULE removed * * Revision 4.2 1995/08/18 22:19:04 tatiana * *** empty log message *** * * Revision 4.1 1995/08/01 14:54:04 tatiana * change SeqIdPrint to SeqIdWrite * * Revision 1.12 1995/07/17 19:33:20 kans * parameters combined into Asn2ffJobPtr structure * * Revision 1.11 1995/06/19 21:40:02 kans * Tatiana's first major reorganization, moving printing, adding HTML * * Revision 1.10 1995/05/15 21:46:05 ostell * added Log line * * **************************************/ #ifndef _ASN2FF6_ #define _ASN2FF6_ #include #include #include #include #include #include #include #include #include #include #include typedef struct { Int2 tech; Int2 entityID; Int2 techID, techtype; CharPtr gbdiv, orgdiv; Int2 gbID, gbtype; Int2 orgID, orgtype; Boolean err_post, was_err; BioSourcePtr biosrc; } DivStruct, PNTR DivStructPtr; #define REPORT_ON_NA ( (Uint1)0) #define REPORT_ON_EVERYTHING ( (Uint1)1) #define REPORT_ON_AA ( (Uint1)2) #define NOT_LAST ( (Uint1)0) #define LAST ( (Uint1)1) #define NO_PRINTXX ( (Uint1)0) #define PRINTXX ( (Uint1)1) #define ASN2FLAT_NOT_ALLOC ( (Uint1)0) #define ASN2FLAT_ALLOC ( (Uint1)1) #define ALL ( (Uint1)0) #define RELEASE ( (Uint1)0) #define DUMP ( (Uint1)1) #define FLATLOC_CONTEXT_LOC 1 #define FLATLOC_CONTEXT_NOTE 2 #define GENPEPT_MIN 0 #define MAX_BTP_BUF 80 /* THere is a *bad* effect if MAX_TO_RT_SIDE is 60 or more. For a /translation the first character is a space and CheckBufferState returns a buffer with 79 characters. This results in an ABR. */ #define MAX_TO_RT_SIDE 59 #define ASN2FF_EMBL_MAX 78 #define ASN2FF_GB_MAX 79 #define NEWLINE '\n' #define ASN2FF_STD_BUF 35 #define MAX_LOCUS_NAME_LEN 16 #define MAX_ACCESSION_LEN 25 #define REP_NUM_OF_SEQ_DESC 22 #define SEQ_BLK_SIZE (60*NUM_SEQ_LINES) #define LOCUS_COLLISION_DB_NAME "GenBank FlatFile LOCUS" #define GeneStringCmp(s, q) StringCmp(s, q) #undef NLM_EXTERN #ifdef NLM_IMPORT #define NLM_EXTERN NLM_IMPORT #else #define NLM_EXTERN extern #endif NLM_EXTERN SeqFeatPtr MakeSyntheticSeqFeat PROTO ((void)); NLM_EXTERN GeneStructPtr GeneStructNew PROTO ((void)); NLM_EXTERN void GeneStructFree PROTO ((GeneStructPtr gsp)); NLM_EXTERN void GeneStructReset PROTO ((GBEntryPtr gbp, Int2 index)); NLM_EXTERN NoteStructPtr NoteStructNew PROTO ((NoteStructPtr gsp)); NLM_EXTERN void NoteStructFree PROTO ((NoteStructPtr gsp)); NLM_EXTERN void NoteStructReset PROTO ((NoteStructPtr nsp)); NLM_EXTERN int LIBCALL CompareSfpForHeap PROTO ((VoidPtr vp1, VoidPtr vp2)); NLM_EXTERN int LIBCALL CompareGeneName PROTO ((VoidPtr vp1, VoidPtr vp2)); NLM_EXTERN ValNodePtr FlatRefBest PROTO ((ValNodePtr equiv, Boolean error_msgs, Boolean accept_muid)); NLM_EXTERN SeqFeatPtr PNTR CopyList PROTO((SortStructPtr List, Int4 currentsize)); NLM_EXTERN Int4 StoreFeatFree PROTO((SortStruct PNTR List, SeqFeatPtr sfp, Int4 currentsize, BioseqPtr bsp, BioseqPtr seg, Uint2 entityID, Uint2 itemID, Uint2 thistype, SeqLocPtr slp, SeqLocPtr PNTR extr_loc, Int2 extr_loc_cnt, Boolean feat_free)); NLM_EXTERN Int4 StoreFeatTemp PROTO((SortStruct PNTR List, SeqFeatPtr sfp, Int4 currentsize, BioseqPtr bsp, BioseqPtr seg, Uint2 entityID, Uint2 itemID, Uint2 thistype, SeqLocPtr slp, SeqLocPtr PNTR extr_loc, Int2 extr_loc_cnt, Boolean temp)); NLM_EXTERN Int4 StoreFeat PROTO((SortStruct PNTR List, SeqFeatPtr sfp, Int4 currentsize, BioseqPtr bsp, BioseqPtr seg, Uint2 entityID, Uint2 itemID, Uint2 thistype, SeqLocPtr slp, SeqLocPtr PNTR extr_loc, Int2 extr_loc_cnt)); NLM_EXTERN void ListFree PROTO ((SeqFeatPtr PNTR PNTR List, Int4 range)); NLM_EXTERN CharPtr Cat2Strings PROTO ((CharPtr string1, CharPtr string2, CharPtr separator, Int2 num)); NLM_EXTERN void EnlargeCharPtrStack PROTO ((NoteStructPtr nsp, Int2 enlarge)); NLM_EXTERN SortStructPtr EnlargeSortList PROTO((SortStructPtr List, Int4 size)); NLM_EXTERN void NoteToCharPtrStack PROTO ((NoteStructPtr nsp, CharPtr annot, CharPtr string, Uint1 alloc)); NLM_EXTERN void CpNoteToCharPtrStack PROTO ((NoteStructPtr nsp, CharPtr annot, CharPtr string)); NLM_EXTERN void SaveNoteToCharPtrStack PROTO ((NoteStructPtr nsp, CharPtr annot, CharPtr string)); NLM_EXTERN GBQualPtr AddGBQualEx PROTO ((CharPtr PNTR key, GBQualPtr gbqual, CharPtr qual, CharPtr val)); NLM_EXTERN GBQualPtr AddGBQual PROTO ((GBQualPtr gbqual, CharPtr qual, CharPtr val)); NLM_EXTERN Int2 CheckForQual PROTO ((GBQualPtr gbqual, CharPtr qual, CharPtr val)); NLM_EXTERN Int4 check_range PROTO ((Pointer data, SeqIdPtr seq_id)); NLM_EXTERN void do_loc_errors PROTO ((CharPtr front, CharPtr details)); NLM_EXTERN void do_no_loc_errors PROTO ((CharPtr front, CharPtr details)); NLM_EXTERN Boolean GBQualPresent PROTO ((CharPtr ptr, GBQualPtr gbqual)); NLM_EXTERN CharPtr MakeAnAccession PROTO ((CharPtr new_buf, SeqIdPtr sip, Int2 buflen)); NLM_EXTERN Boolean GetNAFeatKey PROTO ((Boolean New, CharPtr PNTR buffer, SeqFeatPtr sfp, SeqFeatPtr out)); NLM_EXTERN CharPtr GetGBSourceLine PROTO ((GBBlockPtr gb)); NLM_EXTERN CharPtr FlatOrganelle PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp)); NLM_EXTERN Int4 GetNumOfSeqBlks PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp)); NLM_EXTERN SeqIdPtr GetProductSeqId PROTO ((ValNodePtr product)); NLM_EXTERN Int4 GetGINumFromSip PROTO ((SeqIdPtr sip)); NLM_EXTERN SeqIdPtr CheckXrefFeat PROTO ((BioseqPtr bsp, SeqFeatPtr sfp)); NLM_EXTERN Boolean LIBCALL DoSpecialLineBreak PROTO ((CharPtr string, Int2 indent)); NLM_EXTERN void GetNAPubFeat PROTO ((GBEntryPtr gbp, ValNodePtr PNTR vnpp, SortStructPtr PNTR List, Int2Ptr currentsites)); NLM_EXTERN void CountTheSeqEntrys PROTO ((SeqEntryPtr sep, Pointer data, Int4 index, Int2 indent)); NLM_EXTERN void GetGIs PROTO ((Asn2ffJobPtr ajp)); NLM_EXTERN void GetGINumber PROTO ((GBEntryPtr gbp)); #undef NLM_EXTERN #ifdef NLM_EXPORT #define NLM_EXTERN NLM_EXPORT #else #define NLM_EXTERN #endif #endif