phi_extend.c
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- /*
- * ===========================================================================
- * PRODUCTION $Log: phi_extend.c,v $
- * PRODUCTION Revision 1000.2 2004/06/01 18:08:27 gouriano
- * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.7
- * PRODUCTION
- * ===========================================================================
- */
- /* $Id: phi_extend.c,v 1000.2 2004/06/01 18:08:27 gouriano 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.
- *
- * ===========================================================================
- *
- * Author: Ilya Dondoshansky
- *
- */
- /** @file phi_extend.c
- * Word finder functions for PHI-BLAST
- */
- static char const rcsid[] =
- "$Id: phi_extend.c,v 1000.2 2004/06/01 18:08:27 gouriano Exp $";
- #include <algo/blast/core/blast_def.h>
- #include <algo/blast/core/phi_lookup.h>
- #include <algo/blast/core/phi_extend.h>
- Int2 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,
- BlastUngappedStats* ungapped_stats)
- {
- 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 */
- Blast_UngappedStatsUpdate(ungapped_stats, totalhits, totalhits, totalhits);
- return 0;
- }