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/* $Id: blast_kappa.h,v 1.10 2005/12/01 14:47:40 madden Exp $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* Author: Alejandro Schaffer
*
*/
/** @file blast_kappa.h
* Header file for composition-based statistics
* @todo FIXME needs doxygen comments
*/
#ifndef __BLAST_KAPPA__
#define __BLAST_KAPPA__
#include <algo/blast/core/blast_stat.h>
#include <algo/blast/core/blast_hits.h>
#include <algo/blast/core/blast_hspstream.h>
#ifdef __cplusplus
extern "C" {
#endif
/** Top level routine to recompute alignments for each
* match found by the gapped BLAST algorithm
* A linked list of alignments is returned (param hitList); the alignments
* are sorted according to the lowest E-value of the best alignment for each
* matching sequence; alignments for the same matching sequence
* are in the list consecutively regardless of the E-value of the
* secondary alignments. Ties in sorted order are much rarer than
* for the standard BLAST method, but are broken deterministically
* based on the index of the matching sequences in the database.
* @param program_number the type of blast search being performed [in]
* @param queryBlk query sequence [in]
* @param query_info query information [in]
* @param sbp (Karlin-Altschul) information for search [in]
* @param seqSrc used to fetch database/match sequences [in]
* @param gen_code_string the genetic code for translated queries [in]
* @param hsp_stream used to fetch hits for further processing [in]
* @param scoringParams parameters used for scoring (matrix, gap costs etc.) [in]
* @param extendParams parameters used for extension [in]
* @param hitParams parameters used for saving hits [in]
* @param psiOptions options related to psi-blast [in]
* @param results All HSP results from previous stages of the search [in] [out]
* @return 0 on success, otherwise failure.
*/
Int2
Blast_RedoAlignmentCore(EBlastProgramType program_number,
BLAST_SequenceBlk * queryBlk,
BlastQueryInfo* query_info,
BlastScoreBlk* sbp,
BlastHSPStream* hsp_stream,
const BlastSeqSrc* seqSrc,
const Uint1* gen_code_string,
BlastScoringParameters* scoringParams,
const BlastExtensionParameters* extendParams,
const BlastHitSavingParameters* hitParams,
const PSIBlastOptions* psiOptions,
BlastHSPResults* results);
#ifdef __cplusplus
}
#endif
/*
* ===========================================================================
*
* $Log: blast_kappa.h,v $
* Revision 1.10 2005/12/01 14:47:40 madden
* Renamed Kappa_RedoAlignmentCore as Blast_RedoAlignmentCore
*
* Revision 1.9 2004/11/23 21:46:03 camacho
* Brought up to date with current version of kappa.c [by Mike Gertz]
*
* Revision 1.8 2004/06/21 14:53:09 madden
* Doxygen fixes
*
* Revision 1.7 2004/06/16 14:53:03 dondosha
* Moved extern "C" after the #includes
*
* Revision 1.6 2004/06/08 15:09:33 dondosha
* Use BlastHSPStream interface in the engine instead of saving hits directly
*
* Revision 1.5 2004/05/24 17:27:37 madden
* Doxygen fix
*
* Revision 1.4 2004/05/20 15:20:57 madden
* Doxygen compliance fixes
*
* Revision 1.3 2004/05/19 17:03:20 madden
* Remove (to blast_kappa.c) #defines for Xchar and StarChar
*
* Revision 1.2 2004/05/19 14:52:01 camacho
* 1. Added doxygen tags to enable doxygen processing of algo/blast/core
* 2. Standardized copyright, CVS $Id string, $Log and rcsid formatting and i
* location
* 3. Added use of @todo doxygen keyword
*
* Revision 1.1 2004/05/18 13:22:33 madden
* SmithWaterman and composition-based stats code
*
* ===========================================================================
*/
#endif /* __BLAST_KAPPA__ */
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