NCBI C Toolkit Cross Reference

   /*   asn2gnbk.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:  asn2gnbk.h
  *
  * Author:  Karl Sirotkin, Tom Madden, Tatiana Tatusov, Jonathan Kans
  *
  * Version Creation Date:   10/21/98
  *
  * $Revision: 6.79 $
  *
  * File Description:  New GenBank flatfile generator
  *
  * Modifications:  
  * --------------------------------------------------------------------------
  * ==========================================================================
  */
  
  #ifndef _ASN2NGNBK_
  #define _ASN2NGNBK_
  
  #include <ncbi.h>
  #include <objall.h>
  
  #undef NLM_EXTERN
  #ifdef NLM_IMPORT
  #define NLM_EXTERN NLM_IMPORT
  #else
  #define NLM_EXTERN extern
  #endif
  
  #ifdef __cplusplus
  extern "C" {
  #endif
  
  /* choices of format, mode, and style */
  
  typedef enum {
    GENBANK_FMT = 1,
    EMBL_FMT,
    GENPEPT_FMT,
    EMBLPEPT_FMT,
    FTABLE_FMT
  } FmtType;
  
  typedef enum {
    RELEASE_MODE = 1,
    ENTREZ_MODE,
    SEQUIN_MODE,
    DUMP_MODE
  } ModType;
  
  typedef enum {
    NORMAL_STYLE = 1,
    SEGMENT_STYLE,
    MASTER_STYLE,
    CONTIG_STYLE
  } StlType;
  
  /* bit flags for modifying behavior */
  
  typedef unsigned long FlgType;
  
  #define CREATE_HTML_FLATFILE       1
  #define CREATE_XML_GBSEQ_FILE      2
  #define CREATE_ASN_GBSEQ_FILE      3
  
  #define SHOW_CONTIG_FEATURES       4
  #define SHOW_CONTIG_SOURCES        8
  
  #define SHOW_FAR_TRANSLATION      16
  #define TRANSLATE_IF_NO_PRODUCT   32
  #define ALWAYS_TRANSLATE_CDS      48
  
  #define SHOW_FAR_TRANSCRIPTION    16
  #define TRANSCRIBE_IF_NO_PRODUCT  32
  #define ALWAYS_TRANSCRIBE_MRNA    48
 
 #define REFSEQ_CONVENTIONS        64
 
 #define ONLY_NEAR_FEATURES       128
 #define FAR_FEATURES_SUPPRESS    256
 #define NEAR_FEATURES_SUPPRESS   384
 
 #define COPY_GPS_CDS_UP          512
 #define COPY_GPS_GENE_DOWN      1024
 
 #define SHOW_CONTIG_AND_SEQ     2048
 
 #define SHOW_TRANCRIPTION       4096
 #define SHOW_PEPTIDE            8192
 
 #define PRODUCE_OLD_GBSEQ      16384
 
 #define DDBJ_VARIANT_FORMAT    32768
 
 #define SPECIAL_GAP_DISPLAY    65536
 
 #define FORCE_PRIMARY_BLOCK   131072
 
 /* locking behavior for system performance */
 
 typedef unsigned long LckType;
 
 #define LOCK_FAR_COMPONENTS        2
 #define LOCK_FAR_LOCATIONS         4
 #define LOCK_FAR_PRODUCTS          8
 #define LOOKUP_FAR_COMPONENTS     16
 #define LOOKUP_FAR_LOCATIONS      32
 #define LOOKUP_FAR_PRODUCTS       64
 #define LOOKUP_FAR_HISTORY       128
 #define LOOKUP_FAR_INFERENCE     256
 #define LOOKUP_FAR_OTHERS        512
 
 /* bit flags for unusual customized reports */
 
 typedef unsigned long CstType;
 
 #define SHOW_FEATURE_STATS         1
 #define SHOW_REFERENCE_STATS       2
 
 #define HIDE_FEATURES              4
 
 #define HIDE_IMP_FEATS             8
 #define HIDE_VARS_AND_REPT_REGNS  16
 #define HIDE_SITES_BONDS_REGIONS  32
 #define HIDE_CDD_FEATS            64
 #define HIDE_CDS_PROD_FEATS      128
 
 #define HIDE_GENE_RIFS           256
 #define ONLY_GENE_RIFS           512
 #define ONLY_REVIEW_PUBS         768
 #define NEWEST_PUBS             1024
 #define OLDEST_PUBS             1280
 #define HIDE_ALL_PUBS           1792
 
 #define SHOW_PROT_FTABLE        2048
 #define SHOW_FTABLE_REFS        4096
 
 #define HIDE_SOURCE_FEATS       8192
 #define HIDE_GAP_FEATS         16384
 #define HIDE_SEQUENCE          32768
 
 #define EXPANDED_GAP_DISPLAY   65536
 #define HIDE_GO_TERMS         131072
 #define HIDE_TRANSLATION      262144
 
 #define HIDE_EVIDENCE_QUALS   524288
 
 /* opaque pointer for special extensions */
 
 struct XtraData;
 typedef struct XtraData* XtraPtr;
 
 /* flatfile generation functions */
 
 NLM_EXTERN Boolean SeqEntryToGnbk (
   SeqEntryPtr sep,
   SeqLocPtr slp,
   FmtType format,
   ModType mode,
   StlType style,
   FlgType flags,
   LckType locks,
   CstType custom,
   XtraPtr extra,
   FILE *fp
 );
 
 NLM_EXTERN Boolean BioseqToGnbk (
   BioseqPtr bsp,
   SeqLocPtr slp,
   FmtType format,
   ModType mode,
   StlType style,
   FlgType flags,
   LckType locks,
   CstType custom,
   XtraPtr extra,
   FILE *fp
 );
 
 NLM_EXTERN CharPtr GetFlatFileAffilString (AffilPtr afp);
 
 #ifdef __cplusplus
 }
 #endif
 
 #undef NLM_EXTERN
 #ifdef NLM_EXPORT
 #define NLM_EXTERN NLM_EXPORT
 #else
 #define NLM_EXTERN
 #endif
 
 #endif /* ndef _ASN2NGNBK_ */