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/* $Id: hspstream_collector.h,v 1.10 2008/02/14 15:55:42 kazimird Exp $
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* ===========================================================================
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* National Center for Biotechnology Information
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* This software/database is a "United States Government Work" under the
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* terms of the United States Copyright Act. It was written as part of
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* the author's official duties as a United States Government employee and
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* thus cannot be copyrighted. This software/database is freely available
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* to the public for use. The National Library of Medicine and the U.S.
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* Government have not placed any restriction on its use or reproduction.
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* Although all reasonable efforts have been taken to ensure the accuracy
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* and reliability of the software and data, the NLM and the U.S.
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* Government do not and cannot warrant the performance or results that
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* may be obtained by using this software or data. The NLM and the U.S.
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* Government disclaim all warranties, express or implied, including
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* warranties of performance, merchantability or fitness for any particular
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* Please cite the author in any work or product based on this material.
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* ===========================================================================
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* Author: Ilya Dondoshansky
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/** @file hspstream_collector.h
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* Default implementation of the BlastHSPStream interface to save hits from
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* a BLAST search, and subsequently return them in sorted order.
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#ifndef ALGO_BLAST_CORE__HSPSTREAM_COLLECTOR__H
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#define ALGO_BLAST_CORE__HSPSTREAM_COLLECTOR__H
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#include <algo/blast/core/ncbi_std.h>
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#include <algo/blast/core/blast_program.h>
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#include <algo/blast/core/blast_options.h>
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#include <algo/blast/core/blast_hits.h>
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#include <algo/blast/core/blast_hspstream.h>
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#include <connect/ncbi_core.h>
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/** Auxiliary structure to allow sorting the results by score for the
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* composition-based statistics code */
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typedef struct SSortByScoreStruct {
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Boolean sort_on_read; /**< Should the results be sorted on the first read
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Int4 first_query_index; /**< Index of the first query to try getting
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/** Default implementation of BlastHSPStream */
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typedef struct BlastHSPListCollectorData {
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EBlastProgramType program; /**< BLAST program type */
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SBlastHitsParameters* blasthit_params; /**< specifies how many
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Int4 num_hsplists; /**< number of HSPlists saved */
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Int4 num_hsplists_alloc; /**< number of entries in sorted_hsplists */
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BlastHSPList **sorted_hsplists; /**< list of all HSPlists from 'results'
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combined, sorted in order of
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decreasing subject OID */
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BlastHSPResults* results;/**< Structure for saving HSP lists */
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Boolean results_sorted; /**< Have the results already been sorted?
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Set to true after the first read call. */
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/**< Non-NULL if the results should be sorted by score as opposed to subject
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* OID. This is necessary to meet a pre-condition of the composition-based
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* statistics processing */
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SSortByScoreStruct* sort_by_score;
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MT_LOCK x_lock; /**< Mutex for writing and reading results. */
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} BlastHSPListCollectorData;
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/** Initialize the collector HSP stream for a multi-threaded search. The
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* locking facility must be instantiated before this function is called.
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* @param program Type of BlAST program [in]
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* @param blasthit_params Specifies how many hits to save etc. [in]
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* @param extn_opts Extension options to determine composition-based statistics
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* @param sort_on_read Should results be sorted on the first read call? Only
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* applicable if composition-based statistics is on [in]
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* @param num_queries Number of query sequences in this BLAST search [in]
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* @param lock Pointer to locking structure for writing by multiple
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* threads. Locking will not be performed if NULL. [in]
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Blast_HSPListCollectorInitMT(EBlastProgramType program,
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SBlastHitsParameters* blasthit_params,
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const BlastExtensionOptions* extn_opts,
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Int4 num_queries, MT_LOCK lock);
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/** Initialize the collector HSP stream for a single-threaded search, i.e.
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* no locking is done when reading/writing from/to the stream.
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* @param program Type of BlAST program [in]
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* @param blasthit_params Specifies how many hits to save etc. [in]
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* @param extn_opts Extension options to determine composition-based statistics
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* @param sort_on_read Should results be sorted on the first read call? Only
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* applicable if composition-based statistics is on [in]
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* @param num_queries Number of query sequences in this BLAST search [in]
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Blast_HSPListCollectorInit(EBlastProgramType program,
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SBlastHitsParameters* blasthit_params,
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const BlastExtensionOptions* extn_opts,
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Boolean sort_on_read,
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#endif /* !ALGO_BLAST_CORE__HSPSTREAM_COLLECTOR__H */
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algo/blast/core/hspstream_collector.h
