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/* $Id: phi_extend.c,v 1.4 2004/03/09 22:37:26 dondosha 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 offical 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.
*
* ===========================================================================*/
/*****************************************************************************
File name: phi_extend.c
Author: Ilya Dondoshansky
Contents: Word finder functions for PHI-BLAST
******************************************************************************
* $Revision: 1.4 $
* */
#include <algo/blast/core/blast_def.h>
#include <algo/blast/core/phi_lookup.h>
#include <algo/blast/core/phi_extend.h>
static char const rcsid[] = "$Id: phi_extend.c,v 1.4 2004/03/09 22:37:26 dondosha Exp $";
Int4 PHIBlastWordFinder(BLAST_SequenceBlk* subject,
BLAST_SequenceBlk* query, LookupTableWrap* lookup_wrap,
Int4** matrix, const BlastInitialWordParameters* word_params,
BLAST_ExtendWord* ewp, Uint4* query_offsets, Uint4* subject_offsets,
Int4 max_hits, BlastInitHitList* init_hitlist)
{
PHILookupTable* lookup = (PHILookupTable*) lookup_wrap->lut;
Int4 hits=0;
Int4 totalhits=0;
Int4 first_offset = 0;
Int4 last_offset = subject->length;
Int4 i;
while(first_offset < last_offset)
{
/* scan the subject sequence for hits */
hits = PHIBlastScanSubject(lookup_wrap, query, subject, &first_offset,
query_offsets, subject_offsets, max_hits);
totalhits += hits;
/* for each hit, */
for (i = 0; i < hits; ++i) {
/* do an extension */
BlastSaveInitHsp(init_hitlist,
lookup->start_offsets[query_offsets[i]], subject_offsets[i],
lookup->start_offsets[query_offsets[i]], subject_offsets[i],
lookup->lengths[query_offsets[i]], 0);
} /* end for */
} /* end while */
return totalhits;
}
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