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/* 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: 6.70 $
*
* 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 HIDE_IMP_FEATS 1
#define HIDE_REM_IMP_FEATS 2
#define HIDE_SNP_FEATS 4
#define HIDE_EXON_FEATS 8
#define HIDE_INTRON_FEATS 16
#define HIDE_MISC_FEATS 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
/* 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
);
#ifdef __cplusplus
}
#endif
#undef NLM_EXTERN
#ifdef NLM_EXPORT
#define NLM_EXTERN NLM_EXPORT
#else
#define NLM_EXTERN
#endif
#endif /* ndef _ASN2NGNBK_ */
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