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Viewing changes to algo/blast/core/blast_sw.h

  • Committer: Bazaar Package Importer
  • Author(s): Aaron M. Ucko
  • Date: 2008-07-14 19:43:15 UTC
  • mfrom: (2.1.12 intrepid)
  • Revision ID: james.westby@ubuntu.com-20080714194315-ed44u9ek7txva2rz
Tags: 6.1.20080302-3
http://bugs.debian.org/490437
tools/readdb.c: enable madvise()-based code on all glibc (hence all
Debian) systems, not just Linux.  (Closes: #490437.)

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algo/blast/core/blast_sw.h
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#ifndef ALGO_BLAST_CORE___BLAST_SW__H
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#define ALGO_BLAST_CORE___BLAST_SW__H
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/*  $Id: blast_sw.h,v 1.2 2006/09/14 14:50:32 papadopo Exp $
 
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/*  $Id: blast_sw.h,v 1.4 2006/11/29 17:25:50 bealer Exp $
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 * ===========================================================================
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 *
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 *                            PUBLIC DOMAIN NOTICE
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 *  Smith-Waterman alignment for use within the infrastructure of BLAST
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 */
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#include <algo/blast/core/blast_util.h>
 
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#ifndef ALGO_BLAST_CORE___BLAST_SW__H
 
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#define ALGO_BLAST_CORE___BLAST_SW__H
 
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#include <algo/blast/core/ncbi_std.h>
 
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#include <algo/blast/core/blast_def.h>
 
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#include <algo/blast/core/blast_program.h>
 
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#include <algo/blast/core/blast_query_info.h>
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#include <algo/blast/core/blast_parameters.h>
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#include <algo/blast/core/blast_gapalign.h>
 
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#include <algo/blast/core/blast_hits.h>
 
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#include <algo/blast/core/blast_diagnostics.h>
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/** @addtogroup AlgoBlast
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 *
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 *               contains a gapped alignment that exceeds a cutoff
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 *               score. [out]
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 * @param gapped_stats Return statistics (not filled if NULL) [out]
 
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 * @param fence_hit Partial range support (not used for S/W). [in]
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 */
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Int2 BLAST_SmithWatermanGetGappedScore (EBlastProgramType program_number, 
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        BLAST_SequenceBlk* query, BlastQueryInfo* query_info, 
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        const BlastExtensionParameters* ext_params,
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        const BlastHitSavingParameters* hit_params,
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        BlastInitHitList* init_hitlist,
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        BlastHSPList** hsp_list_ptr, BlastGappedStats* gapped_stats);
 
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        BlastHSPList** hsp_list_ptr, BlastGappedStats* gapped_stats,
 
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        Boolean * fence_hit);
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#ifdef __cplusplus
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}