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#ifndef API_ACERDAPI__H
#define API_ACERDAPI__H
/*
* $Id: acerdapi.h,v 1.8 2008/12/02 16:16:01 bollin Exp $
*
* ===========================================================================
*
* 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.
*
* ===========================================================================
*
* Authors: Colleen Bollin
*
*/
#ifdef __cplusplus
extern "C" {
#endif
/* for doing ID replacements */
typedef struct seqidpair {
SeqIdPtr sip_find;
Char buf_find[100];
SeqIdPtr sip_replace;
Boolean is_complement;
Int4 trim5;
Int4 trim3;
Boolean is_consensus;
Int4 ti;
} SeqIdPairData, PNTR SeqIdPairPtr;
typedef struct seqidreplacelist {
Int4 num_ids;
SeqIdPairPtr list;
} SeqIdReplaceListData, PNTR SeqIdReplaceListPtr;
NLM_EXTERN SeqIdReplaceListPtr SeqIdReplaceListFree (SeqIdReplaceListPtr replace_list);
NLM_EXTERN SeqIdReplaceListPtr ReadSeqIdPairListFromFile (FILE *fp);
NLM_EXTERN Boolean UpdateContigIds (TContigPtr contig, SeqIdReplaceListPtr pair_list, Boolean no_lookup, Boolean is_srr, char *has_errors);
NLM_EXTERN Boolean UpdateAceFileIds (TACEFilePtr afp, FILE *id_file, Boolean no_lookup, Boolean is_srr, char *has_errors);
NLM_EXTERN Boolean ValidateAceFileIds (TACEFilePtr afp, char *has_errors);
NLM_EXTERN ValNodePtr GetTransitionsFromGapInfo (TGapInfoPtr gaps, Int4 offset, Int4 seq_offset, Int4 tiling_len);
NLM_EXTERN SeqEntryPtr MakeSeqEntryFromRead (TContigReadPtr read);
NLM_EXTERN SeqEntryPtr MakeSeqEntryFromContig (TContigPtr contig);
NLM_EXTERN Boolean ValidateACEFileAgainstSeqEntry (TACEFilePtr ace_file, SeqEntryPtr sep, char *has_errors);
#ifdef __cplusplus
}
#endif
/*
* ==========================================================================
*
* $Log: acerdapi.h,v $
* Revision 1.8 2008/12/02 16:16:01 bollin
* Added function for making a SeqEntry from a read, fixed bug in seqid lookup.
*
* Revision 1.7 2008/11/26 18:30:02 bollin
* Changes to make aceread_tst more efficient when handling large ACE files,
* added TSA field tags for assembly and taxid.
*
* Revision 1.6 2008/08/13 18:18:28 bollin
* Improved aceread_tst - adds molinfo and SeqGraph with quality scores to generated ASN.1
*
* Revision 1.5 2008/08/13 15:35:30 bollin
* Added wrapping header for XML errors during ACE read.
*
* Revision 1.4 2008/08/13 12:30:01 bollin
* Changes to allow use of srr numbers in XML and suppress lookups. Also fixes segfault.
*
* Revision 1.3 2008/07/22 20:25:49 bollin
* Added functiosn for validating consensus sequences against a supplied SeqEntry
*
* Revision 1.2 2008/07/22 18:45:09 bollin
* Added function declarations
*
* Revision 1.1 2008/07/22 18:10:33 bollin
* New files for parsing ACE format files.
*
*
* ==========================================================================
*/
#endif
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