/* asn2ff.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: asn2ff.h * * Author: Karl Sirotkin, Tom Madden, Tatiana Tatusov * * Version Creation Date: 7/15/95 * * $Revision: 6.14 $ * * File Description: Header file for asn2gb files. * * Modifications: * -------------------------------------------------------------------------- * $Log: asn2ff.h,v $ * Revision 6.14 2001/04/05 21:52:18 tatiana * format and strand added to SeqEntryToEntrez * * Revision 6.13 2001/03/15 21:42:00 tatiana * SeqEntryToEntrez added * * Revision 6.12 2000/03/24 17:56:11 tatiana * SeqEntryToStrArrayQEx added * * Revision 6.10 1999/04/09 21:22:10 bazhin * Added function "ByteStorePtr AjpToByteStore()". * * Revision 6.9 1999/04/02 16:31:46 tatiana * asn2ff_print_to_mem and SeqEntryToStrArray changed to NLM_EXTERN * * Revision 6.8 1999/03/05 16:41:40 tatiana * GRAPHIK_FMT changed to 14 * * Revision 6.7 1999/03/04 23:39:53 tatiana * GRAPHIK_FMT added * * Revision 6.6 1998/11/05 16:12:17 bazhin * Added 4th parameter "Boolean show_gi" to SeqEntryToGBFlatNoSeq() * function. It will say do or does not print GI number into output * flatfile. Same for error messages related to missing GIs. * * Revision 6.5 1998/09/14 16:37:46 tatiana * SeqEntryToFlatAjp added * * Revision 6.4 1998/09/08 20:40:52 tatiana * Asn2ffJobCreate added * * Revision 6.3 1998/08/21 16:58:48 shavirin * Added definition of function SeqEntryToGBFlatNoSeq() * * Revision 6.2 1998/05/11 21:58:50 tatiana * some functions moved from asn2ff1.c to asn2ff6.c * * Revision 6.1 1998/05/08 21:58:36 tatiana * added PARTIAL_MODE and SeqEntryToPartRpt PROTO * * Revision 6.0 1997/08/25 18:04:33 madden * Revision changed to 6.0 * * Revision 5.7 1997/07/28 19:03:50 vakatov * [WIN32,MSVC++] Restored lost "NCBIOBJ.LIB" pro-DLL modifications * * Revision 5.6 1997/07/23 18:36:58 tatiana * SeqEntryToFlatEx() added * * Revision 5.5 1997/06/19 18:36:48 vakatov * [WIN32,MSVC++] Adopted for the "NCBIOBJ.LIB" DLL'ization * * Revision 5.3 1996/09/09 13:36:02 kans * moved BioseqGetGBDivCode from toasn.[ch] to asn2ff.h/asn2ff6.c * * Revision 5.1 1996/07/12 19:46:09 tatiana * SeqSubmitToFlat PROTO added * * Revision 4.3 1996/03/19 15:58:14 tatiana * SeqGenomeToFlat prototype * * Revision 1.24 1995/07/17 19:33:20 kans * parameters combined into Asn2ffJobPtr structure * * Revision 1.23 1995/06/19 21:40:02 kans * Tatiana's first major reorganization, moving printing, adding HTML * * ========================================================================== */ #ifndef _ASN2FF_ #define _ASN2FF_ #include #include #include #include #include #include #include #undef NLM_EXTERN #ifdef NLM_IMPORT #define NLM_EXTERN NLM_IMPORT #else #define NLM_EXTERN extern #endif #ifdef __cplusplus extern "C" { #endif #define GENBANK_FMT ( (Uint1)0) #define EMBL_FMT ( (Uint1)1) #define GENPEPT_FMT ( (Uint1)2) #define PSEUDOEMBL_FMT ( (Uint1)3) #define SELECT_FMT ( (Uint1)4) #define EMBLPEPT_FMT ( (Uint1)5) #define RELEASE_MODE ( (Uint1)6) #define DUMP_MODE ( (Uint1)7) #define SEQUIN_MODE ( (Uint1)8) #define CHROMO_MODE ( (Uint1)9) #define DIRSUB_MODE ( (Uint1)10) #define REVISE_MODE ( (Uint1)11) #define DIRSUB_DEBUG_MODE ( (Uint1)12) #define PARTIAL_MODE ( (Uint1)13) #define GRAPHIK_FMT ( (Uint1)14) #define NUM_OF_ESTIMATES 20 #define NUM_SEQ_LINES 10 NLM_EXTERN Int4 asn2ff_setup PROTO ((Asn2ffJobPtr job, FFPrintArrayPtr PNTR papp)); NLM_EXTERN void asn2ff_cleanup PROTO ((Asn2ffJobPtr job)); NLM_EXTERN Boolean asn2ff_print PROTO ((Asn2ffJobPtr job)); NLM_EXTERN LinkStrPtr asn2ff_print_to_mem PROTO ((Asn2ffJobPtr job, LinkStrPtr lsp)); NLM_EXTERN Asn2ffJobPtr Asn2ffJobCreate PROTO ((SeqEntryPtr sep, SeqSubmitPtr ssp, SeqLocPtr slp, FILE *fp, Uint1 format, Uint1 mode, StdPrintOptionsPtr Spop)); NLM_EXTERN Boolean SeqEntryToEntrez PROTO ((SeqEntryPtr sep, FILE *fp, SeqIdPtr seqid, Uint1 format, Uint1 display, Int4 from, Int4 to, Uint1 strand)); NLM_EXTERN CharPtr PNTR SeqEntryToStrArray PROTO ((SeqEntryPtr sep, Uint1 format, Uint1 mode)); NLM_EXTERN LinkStrPtr SeqEntryToStrArrayQEx PROTO ((SeqEntryPtr sep, Uint1 format, Int4 gi, Boolean is_html)); NLM_EXTERN LinkStrPtr SeqEntryToStrArrayEx PROTO ((SeqEntryPtr sep, Uint1 format, Int4 gi, Boolean is_html)); NLM_EXTERN Boolean SeqEntryToFlatAjp PROTO ((Asn2ffJobPtr ajp, SeqEntryPtr sep, FILE *fp, Uint1 format, Uint1 mode)); NLM_EXTERN Boolean SeqEntryToFlat PROTO ((SeqEntryPtr sep, FILE *fp, Uint1 format, Uint1 mode)); NLM_EXTERN Boolean SeqEntryToFlatEx PROTO ((SeqEntryPtr sep, FILE *fp, Uint1 format, Uint1 mode, SeqIdPtr seqid, Uint1 type)); NLM_EXTERN Boolean SeqEntryToGBFlatNoSeq PROTO ((SeqEntryPtr sep, FILE *fp, Uint1 mode, Boolean show_gi)); NLM_EXTERN Boolean SeqSubmitToFlat PROTO ((SeqSubmitPtr ssp, FILE *fp, Uint1 mode, Boolean show_gi, Uint1 format, Boolean show_gene)); NLM_EXTERN Boolean SeqGenomeToFlat PROTO ((SeqEntryPtr sep, FILE *fp, Uint1 format, Uint1 mode)); NLM_EXTERN Boolean SeqEntryToPartRpt PROTO ((SeqEntryPtr sep, FILE *fp)); NLM_EXTERN Boolean SeqLocToFlat PROTO ((SeqLocPtr slp, FILE *fp, Uint1 format, Uint1 mode)); NLM_EXTERN ByteStorePtr AjpToByteStore PROTO ((Asn2ffJobPtr ajp)); NLM_EXTERN Int2 BioseqGetGBDivCode PROTO((BioseqPtr bsp, CharPtr buffer, Int2 buflen, Boolean err_post)); /* moved from asn2ff1.c to asn2ff6.c */ NLM_EXTERN void AddExtraAccessions PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp)); NLM_EXTERN void GetLocusPartsAwp PROTO((Asn2ffJobPtr ajp)); NLM_EXTERN Int4 GetPubsAwp PROTO((Asn2ffJobPtr ajp, GBEntryPtr gbp)); NLM_EXTERN Boolean SeqToAwp PROTO((GatherContextPtr gcp)); NLM_EXTERN void UseGIforLocus PROTO((Asn2ffJobPtr ajp)); #ifdef __cplusplus } #endif #undef NLM_EXTERN #ifdef NLM_EXPORT #define NLM_EXTERN NLM_EXPORT #else #define NLM_EXTERN #endif #endif