NCBI C Toolkit Cross Reference

C/api/acerdapi.h

  1 #ifndef API_ACERDAPI__H
  2 #define API_ACERDAPI__H
  3 
  4 /*
  5  * $Id: acerdapi.h,v 1.8 2008/12/02 16:16:01 bollin Exp $
  6  *
  7  * ===========================================================================
  8  *
  9  *                            PUBLIC DOMAIN NOTICE
 10  *               National Center for Biotechnology Information
 11  *
 12  *  This software/database is a "United States Government Work" under the
 13  *  terms of the United States Copyright Act.  It was written as part of
 14  *  the author's official duties as a United States Government employee and
 15  *  thus cannot be copyrighted.  This software/database is freely available
 16  *  to the public for use. The National Library of Medicine and the U.S.
 17  *  Government have not placed any restriction on its use or reproduction.
 18  *
 19  *  Although all reasonable efforts have been taken to ensure the accuracy
 20  *  and reliability of the software and data, the NLM and the U.S.
 21  *  Government do not and cannot warrant the performance or results that
 22  *  may be obtained by using this software or data. The NLM and the U.S.
 23  *  Government disclaim all warranties, express or implied, including
 24  *  warranties of performance, merchantability or fitness for any particular
 25  *  purpose.
 26  *
 27  *  Please cite the author in any work or product based on this material.
 28  *
 29  * ===========================================================================
 30  *
 31  * Authors:  Colleen Bollin
 32  *
 33  */
 34 
 35 
 36 #ifdef __cplusplus
 37 extern "C" {
 38 #endif
 39 
 40 /* for doing ID replacements */
 41 typedef struct seqidpair {
 42   SeqIdPtr sip_find;
 43   Char     buf_find[100];
 44   SeqIdPtr sip_replace;
 45   Boolean  is_complement;
 46   Int4     trim5;
 47   Int4     trim3;
 48   Boolean  is_consensus;
 49   Int4     ti;
 50 } SeqIdPairData, PNTR SeqIdPairPtr;
 51 
 52 typedef struct seqidreplacelist {
 53   Int4 num_ids;
 54   SeqIdPairPtr list;
 55 } SeqIdReplaceListData, PNTR SeqIdReplaceListPtr;
 56 
 57 NLM_EXTERN SeqIdReplaceListPtr SeqIdReplaceListFree (SeqIdReplaceListPtr replace_list);
 58 NLM_EXTERN SeqIdReplaceListPtr ReadSeqIdPairListFromFile (FILE *fp);
 59 
 60 
 61 NLM_EXTERN Boolean UpdateContigIds (TContigPtr contig, SeqIdReplaceListPtr pair_list, Boolean no_lookup, Boolean is_srr, char *has_errors);
 62 NLM_EXTERN Boolean UpdateAceFileIds (TACEFilePtr afp, FILE *id_file, Boolean no_lookup, Boolean is_srr, char *has_errors);
 63 NLM_EXTERN Boolean ValidateAceFileIds (TACEFilePtr afp, char *has_errors);
 64 
 65 NLM_EXTERN ValNodePtr GetTransitionsFromGapInfo (TGapInfoPtr gaps, Int4 offset, Int4 seq_offset, Int4 tiling_len);
 66 
 67 NLM_EXTERN SeqEntryPtr MakeSeqEntryFromRead (TContigReadPtr read);
 68 NLM_EXTERN SeqEntryPtr MakeSeqEntryFromContig (TContigPtr contig);
 69 
 70 NLM_EXTERN Boolean ValidateACEFileAgainstSeqEntry (TACEFilePtr ace_file, SeqEntryPtr sep, char *has_errors);
 71 
 72 #ifdef __cplusplus
 73 }
 74 #endif
 75 
 76 /*
 77  * ==========================================================================
 78  *
 79  * $Log: acerdapi.h,v $
 80  * Revision 1.8  2008/12/02 16:16:01  bollin
 81  * Added function for making a SeqEntry from a read, fixed bug in seqid lookup.
 82  *
 83  * Revision 1.7  2008/11/26 18:30:02  bollin
 84  * Changes to make aceread_tst more efficient when handling large ACE files,
 85  * added TSA field tags for assembly and taxid.
 86  *
 87  * Revision 1.6  2008/08/13 18:18:28  bollin
 88  * Improved aceread_tst - adds molinfo and SeqGraph with quality scores to generated ASN.1
 89  *
 90  * Revision 1.5  2008/08/13 15:35:30  bollin
 91  * Added wrapping header for XML errors during ACE read.
 92  *
 93  * Revision 1.4  2008/08/13 12:30:01  bollin
 94  * Changes to allow use of srr numbers in XML and suppress lookups.  Also fixes segfault.
 95  *
 96  * Revision 1.3  2008/07/22 20:25:49  bollin
 97  * Added functiosn for validating consensus sequences against a supplied SeqEntry
 98  *
 99  * Revision 1.2  2008/07/22 18:45:09  bollin
100  * Added function declarations
101  *
102  * Revision 1.1  2008/07/22 18:10:33  bollin
103  * New files for parsing ACE format files.
104  *
105  *
106  * ==========================================================================
107  */
108 
109 #endif
110 
111
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