/* objpubd.h * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * 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 have not placed any restriction on its use or reproduction. * * 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. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * File Name: objpubd.h * * Author: James Ostell * * Version Creation Date: 4/1/91 * * $Revision: 6.4 $ * * File Description: Object manager interface for type Pubdesc from * NCBI-Sequence. This is separate to avoid typedef * order problems with NCBI-Sequence and NCBI-Seqfeat * which both reference Pubdesc * Numbering and Heterogen have now also been added * for the same reason. Heterogen is just a string, * so no special typedefs are required. * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * $Log: objpubd.h,v $ * Revision 6.4 2000/09/28 11:53:13 ostell * added Pubdesc.reftype = 3 * * Revision 6.3 2000/05/26 19:50:23 ostell * added MI_TECH_htc * * Revision 6.2 1999/02/12 18:45:22 ostell * added MI_TECH_htgs_0 * * Revision 6.1 1998/06/12 18:02:26 kans * added MI_TECH_fli_cdna 17 define * * Revision 6.0 1997/08/25 18:50:32 madden * Revision changed to 6.0 * * Revision 4.3 1997/08/20 19:17:13 madden * Version 6 of ASN.1 * * Revision 4.2 1997/06/19 18:41:50 vakatov * [WIN32,MSVC++] Adopted for the "NCBIOBJ.LIB" DLL'ization * * Revision 4.1 1996/06/13 21:09:08 ostell * added defines for MI_TECH * * Revision 4.0 1995/07/26 13:48:06 ostell * force revision to 4.0 * * Revision 3.2 1995/07/11 18:49:20 ostell * added reftype * * Revision 3.1 1995/05/15 21:22:00 ostell * added Log line * * * * * ========================================================================== */ #ifndef _NCBI_Pubdesc_ #define _NCBI_Pubdesc_ #ifndef _ASNTOOL_ #include #endif #undef NLM_EXTERN #ifdef NLM_IMPORT #define NLM_EXTERN NLM_IMPORT #else #define NLM_EXTERN extern #endif #ifdef __cplusplus extern "C" { #endif /***************************************************************************** * * Pubdesc * *****************************************************************************/ typedef struct pd { ValNodePtr pub; /* points to Pub-equiv */ CharPtr name, fig; ValNodePtr num; /* points to Numbering */ Boolean numexc, poly_a; Uint1 align_group; /* 0 = not part of a group */ CharPtr maploc, seq_raw, comment; Uint1 reftype; /* 0=seq, 1=sites, 2=feats, 3=seq with no explicit span, for GenBank ref */ } Pubdesc, PNTR PubdescPtr; NLM_EXTERN PubdescPtr LIBCALL PubdescNew PROTO((void)); NLM_EXTERN Boolean LIBCALL PubdescAsnWrite PROTO((PubdescPtr pdp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN PubdescPtr LIBCALL PubdescAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN PubdescPtr LIBCALL PubdescFree PROTO((PubdescPtr pdp)); typedef ValNode Numbering, FAR *NumberingPtr; /***************************************************************************** * * Numbering uses an ValNode with choice = 1 = cont Num-cont , -- continuous numbering 2 = enum Num-enum , -- enumerated names for residues 3 = ref Num-ref, type 1 sources -- by reference to another sequence 4 = ref Num-ref, type 2 aligns (SeqAlign in data.ptrvalue) 5 = real Num-real -- for maps etc * *****************************************************************************/ #define Numbering_cont 1 #define Numbering_enum 2 #define Numbering_ref_source 3 #define Numbering_ref_align 4 #define Numbering_real 5 NLM_EXTERN Boolean LIBCALL NumberingAsnWrite PROTO((NumberingPtr anp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN NumberingPtr LIBCALL NumberingAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN NumberingPtr LIBCALL NumberingFree PROTO((NumberingPtr anp)); /***************************************************************************** * * NumCont - continuous numbering system * *****************************************************************************/ typedef struct numcont { Int4 refnum; Boolean has_zero, ascending; } NumCont, PNTR NumContPtr; NLM_EXTERN NumContPtr LIBCALL NumContNew PROTO((void)); NLM_EXTERN Boolean LIBCALL NumContAsnWrite PROTO((NumContPtr ncp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN NumContPtr LIBCALL NumContAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN NumContPtr LIBCALL NumContFree PROTO((NumContPtr ncp)); /***************************************************************************** * * NumEnum - enumerated numbering system * *****************************************************************************/ typedef struct numenum { Int4 num; /* number of names */ CharPtr buf; /* a buffer for the names */ CharPtr PNTR names; /* array of pointers to names */ } NumEnum, PNTR NumEnumPtr; NLM_EXTERN NumEnumPtr LIBCALL NumEnumNew PROTO((void)); NLM_EXTERN Boolean LIBCALL NumEnumAsnWrite PROTO((NumEnumPtr nep, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN NumEnumPtr LIBCALL NumEnumAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN NumEnumPtr LIBCALL NumEnumFree PROTO((NumEnumPtr nep)); /***************************************************************************** * * NumReal - float type numbering system * *****************************************************************************/ typedef struct numreal { FloatHi a, b; /* number in "units" = ax + b */ CharPtr units; } NumReal, PNTR NumRealPtr; NLM_EXTERN NumRealPtr LIBCALL NumRealNew PROTO((void)); NLM_EXTERN Boolean LIBCALL NumRealAsnWrite PROTO((NumRealPtr ncp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN NumRealPtr LIBCALL NumRealAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN NumRealPtr LIBCALL NumRealFree PROTO((NumRealPtr ncp)); /***************************************************************************** * * MolInfo - Info about mols * *****************************************************************************/ typedef struct molinfo { Uint1 biomol, tech; CharPtr techexp; Uint1 completeness; } MolInfo, PNTR MolInfoPtr; #define MI_TECH_unknown 0 #define MI_TECH_standard 1 #define MI_TECH_est 2 /* EST division */ #define MI_TECH_sts 3 /* STS division */ #define MI_TECH_survey 4 /* GSS division */ #define MI_TECH_genemap 5 /* Bioseq is a genetic map */ #define MI_TECH_physmap 6 /* Bioseq is physical map */ #define MI_TECH_derived 7 /* Bioseq is a computed inference */ #define MI_TECH_concept_trans 8 /* conceptual translation */ #define MI_TECH_seq_pept 9 /* peptide sequencing used */ #define MI_TECH_both 10 /* combination of 8 and 9 used */ #define MI_TECH_seq_pept_overlap 11 /* peptides ordered by overlap */ #define MI_TECH_seq_pept_homol 12 /* peptides ordered by homology */ #define MI_TECH_concept_trans_a 13 /* concept trans supplied by author */ #define MI_TECH_htgs_1 14 /* unordered High Throughput Sequence Contig */ #define MI_TECH_htgs_2 15 /* ordered High Throughput sequence contig */ #define MI_TECH_htgs_3 16 /* finished High Throughut sequence */ #define MI_TECH_fli_cdna 17 /* full-length insert cDNA sequence */ #define MI_TECH_htgs_0 18 /* unordered single pass reads */ #define MI_TECH_htc 19 /* High Throughput CDNA.. unfinished */ #define MI_TECH_other 255 /* doesnt' fit anything */ NLM_EXTERN MolInfoPtr LIBCALL MolInfoNew PROTO((void)); NLM_EXTERN Boolean LIBCALL MolInfoAsnWrite PROTO((MolInfoPtr mip, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN MolInfoPtr LIBCALL MolInfoAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN MolInfoPtr LIBCALL MolInfoFree PROTO((MolInfoPtr mip)); #ifdef __cplusplus } #endif #undef NLM_EXTERN #ifdef NLM_EXPORT #define NLM_EXTERN NLM_EXPORT #else #define NLM_EXTERN #endif #endif