NCBI C Toolkit Cross Reference

C/algo/blast/api/hspfilter_queue.h

  1 /*  $Id: hspfilter_queue.h,v 1.1 2009/06/01 13:54:56 maning 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  * ===========================================================================
 25  *
 26  * Author:  Ning Ma
 27  *
 28  */
 29 
 30 /** @file hspfilter_queue.h
 31  * Implementation of HSPWriter in queue mode.
 32  */
 33 
 34 #ifndef ALGO_BLAST_CORE__HSPFILTER_QUEUE__H
 35 #define ALGO_BLAST_CORE__HSPFILTER_QUEUE__H
 36 
 37 #include <algo/blast/core/ncbi_std.h>
 38 #include <algo/blast/core/blast_program.h>
 39 #include <algo/blast/core/blast_options.h>
 40 #include <algo/blast/core/blast_hspfilter.h>
 41 #include <algo/blast/core/blast_hits.h>
 42 #include <connect/ncbi_core.h>
 43 
 44 #ifdef __cplusplus
 45 extern "C" {
 46 #endif
 47 
 48 /** Probably need no options */
 49 typedef struct BlastHSPQueueParams {
 50    EBlastProgramType program;/**< program type */
 51 } BlastHSPQueueParams;
 52 
 53 /** Sets up parameter set for use by queue.
 54  * @param program Blast program type.[in]
 55  * @param hit_options field hitlist_size and hsp_num_max needed, a pointer to 
 56  *      this structure will be stored on resulting structure.[in]
 57  * @param ext_options field compositionBasedStats needed here. [in]
 58  * @param scoring_options gapped_calculation needed here. [in]
 59  * @return the pointer to the allocated parameter
 60  */
 61 NCBI_XBLAST_EXPORT
 62 BlastHSPQueueParams*
 63 BlastHSPQueueParamsNew();
 64 
 65 /** Deallocates the BlastHSPQueueParams structure passed in
 66  * @param params structure to deallocate [in]
 67  * @return NULL
 68  */
 69 NCBI_XBLAST_EXPORT
 70 BlastHSPQueueParams*
 71 BlastHSPQueueParamsFree(BlastHSPQueueParams* params);
 72 
 73 /** WriterInfo to create a default writer: the collecter
 74  * @param params The queue parameters.
 75  * @return pointer to WriterInfo
 76  */
 77 NCBI_XBLAST_EXPORT
 78 BlastHSPWriterInfo* 
 79 BlastHSPQueueInfoNew(BlastHSPQueueParams* params);
 80 
 81 
 82 /** Read one HSP list from a queue of HSP lists. If the queue is empty, this 
 83  * function waits for more results to be written, unless results queue is 
 84  * already closed for writing.
 85  * @param hsp_stream HSP list stream to read from [in]
 86  * @param hsp_list_out The read HSP list. NULL, if there is nothing left 
 87  *                     in the queue to read.
 88  * @return Status: success, error or end of reading.
 89  */
 90 NCBI_XBLAST_EXPORT
 91 int 
 92 BlastHSPQueueRead(void* data, BlastHSPList** hsp_list_out);
 93 
 94 #ifdef __cplusplus
 95 }
 96 #endif
 97 
 98 #endif /* !ALGO_BLAST_CORE__HSPFILTER_QUEUE__H */
 99
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