NCBI C Toolkit Cross Reference

C/algo/blast/api/seqsrc_readdb.h

  1 /*  $Id: seqsrc_readdb.h,v 1.16 2005/04/21 15:00:36 dondosha Exp $
  2 * ===========================================================================
  3 *
  4 *                            PUBLIC DOMAIN NOTICE
  5 *               National Center for Biotechnology Information
  6 *
  7 *  This software/database is a "United States Government Work" under the
  8 *  terms of the United States Copyright Act.  It was written as part of
  9 *  the author's official duties as a United States Government employee and
 10 *  thus cannot be copyrighted.  This software/database is freely available
 11 *  to the public for use. The National Library of Medicine and the U.S.
 12 *  Government have not placed any restriction on its use or reproduction.
 13 *
 14 *  Although all reasonable efforts have been taken to ensure the accuracy
 15 *  and reliability of the software and data, the NLM and the U.S.
 16 *  Government do not and cannot warrant the performance or results that
 17 *  may be obtained by using this software or data. The NLM and the U.S.
 18 *  Government disclaim all warranties, express or implied, including
 19 *  warranties of performance, merchantability or fitness for any particular
 20 *  purpose.
 21 *
 22 *  Please cite the author in any work or product based on this material.
 23 *
 24 * Author:  Christiam Camacho
 25 * ===========================================================================*/
 26 
 27 /** @file seqsrc_readdb.h
 28  * Implementation of the BlastSeqSrc interface using readdb
 29  */
 30 
 31 #ifndef SEQSRC_READDB_H
 32 #define SEQSRC_READDB_H
 33 
 34 #ifndef NCBI_C_TOOLKIT
 35 #define NCBI_C_TOOLKIT
 36 #endif
 37 
 38 #include <readdb.h>
 39 #include <algo/blast/core/blast_seqsrc.h>
 40 
 41 #ifdef __cplusplus
 42 extern "C" {
 43 #endif
 44 
 45 /** @addtogroup CToolkitAlgoBlast
 46  *
 47  * @{
 48  */
 49 
 50 /** Maximal allowed length for a sequence id string. */
 51 #define SEQIDLEN_MAX 255
 52 
 53 /** Initialize the sequence source structure.
 54  * @param dbname BLAST database name [in]
 55  * @param is_prot Is this a protein or nucleotide database? [in]
 56  * @param first_seq First ordinal id in the database to search [in]
 57  * @param last_seq Last ordinal id in the database to search 
 58  *                 (full database if 0) [in]
 59  */
 60 BlastSeqSrc* 
 61 ReaddbBlastSeqSrcInit(const char* dbname, Boolean is_prot, int first_seq, 
 62                       int last_seq);
 63 
 64 /** Initialize the sequence source structure given an already created
 65  * ReadDBFILE structure.
 66  * @param rdfp Initialized BLAST database structure [in]
 67  * @return New allocated and initialized BlastSeqSrc, using rdfp as data 
 68  *         structure.
 69  */
 70 BlastSeqSrc*
 71 ReaddbBlastSeqSrcAttach(ReadDBFILE* rdfp);
 72 
 73 /* @} */
 74 
 75 #ifdef __cplusplus
 76 }
 77 #endif
 78 
 79 #endif /* SEQSRC_READDB_H */
 80
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