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