/* 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: 4.1 $ * * 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 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 #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, for GenBank ref */ } Pubdesc, PNTR PubdescPtr; PubdescPtr LIBCALL PubdescNew PROTO((void)); Boolean LIBCALL PubdescAsnWrite PROTO((PubdescPtr pdp, AsnIoPtr aip, AsnTypePtr atp)); PubdescPtr LIBCALL PubdescAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); 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 Boolean LIBCALL NumberingAsnWrite PROTO((NumberingPtr anp, AsnIoPtr aip, AsnTypePtr atp)); NumberingPtr LIBCALL NumberingAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NumberingPtr LIBCALL NumberingFree PROTO((NumberingPtr anp)); /***************************************************************************** * * NumCont - continuous numbering system * *****************************************************************************/ typedef struct numcont { Int4 refnum; Boolean has_zero, ascending; } NumCont, PNTR NumContPtr; NumContPtr LIBCALL NumContNew PROTO((void)); Boolean LIBCALL NumContAsnWrite PROTO((NumContPtr ncp, AsnIoPtr aip, AsnTypePtr atp)); NumContPtr LIBCALL NumContAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); 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; NumEnumPtr LIBCALL NumEnumNew PROTO((void)); Boolean LIBCALL NumEnumAsnWrite PROTO((NumEnumPtr nep, AsnIoPtr aip, AsnTypePtr atp)); NumEnumPtr LIBCALL NumEnumAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); 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; NumRealPtr LIBCALL NumRealNew PROTO((void)); Boolean LIBCALL NumRealAsnWrite PROTO((NumRealPtr ncp, AsnIoPtr aip, AsnTypePtr atp)); NumRealPtr LIBCALL NumRealAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); 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_other 255 /* doesnt' fit anything */ /*************************************** * The following are not explicitly in the ASN.1 spec yet * but can still be legally used as numbers. * These are for High Throughput Genome Sequences * htgs_1 - preliminary data. sequence is made of multiple * contigs with gaps between them. The order of * the contigs is not known, although for * convenience they are in an arbitrary order * htgs_2 - preliminary data. like htgs_1 except the * order of the contigs is known and the sequence * reflects the correct order * htgs_3 - finished data. All annotations are machine * generated in bulk. Usually this has been placed * on a map * ******************************************/ #define MI_TECH_htgs_1 14 #define MI_TECH_htgs_2 15 #define MI_TECH_htgs_3 16 MolInfoPtr LIBCALL MolInfoNew PROTO((void)); Boolean LIBCALL MolInfoAsnWrite PROTO((MolInfoPtr mip, AsnIoPtr aip, AsnTypePtr atp)); MolInfoPtr LIBCALL MolInfoAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); MolInfoPtr LIBCALL MolInfoFree PROTO((MolInfoPtr mip)); #ifdef __cplusplus } #endif #endif