NCBI C Toolkit Cross Reference

   /*  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: 6.13 $
  *
  * 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
  * -------  ----------  -----------------------------------------------------
  *
  * ==========================================================================
  */
  
  #ifndef _NCBI_Pubdesc_
  #define _NCBI_Pubdesc_
  
  #ifndef _ASNTOOL_
  #include <asn.h>
  #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));
  
  NLM_EXTERN Boolean LIBCALL PubdescContentMatch (PubdescPtr pdp1, PubdescPtr pdp2);
  
  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;
     CharPtr gbmoltype;
 } 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_wgs 20       /* Whole Genome Shotgun */
 #define MI_TECH_barcode 21   /* Barcode of Life Project */
 #define MI_TECH_composite_wgs_htgs 22   /* Assembly/Scaffold composite of techniques */
 #define MI_TECH_tsa 23       /* Transcriptome Shotgun Assembly */
 #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