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Viewing changes to algo/blast/core/blast_diagnostics.c

  • Committer: Bazaar Package Importer
  • Author(s): Aaron M. Ucko
  • Date: 2005-03-27 12:00:15 UTC
  • mfrom: (2.1.2 hoary)
  • Revision ID: james.westby@ubuntu.com-20050327120015-embhesp32nj73p9r
Tags: 6.1.20041020-3
http://bugs.debian.org/295110
* Fix FTBFS under GCC 4.0 caused by inconsistent use of "static" on
  functions.  (Closes: #295110.)
* Add a watch file, now that we can.  (Upstream's layout needs version=3.)

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algo/blast/core/blast_diagnostics.c
 
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/* $Id: blast_diagnostics.c,v 1.3 2004/07/06 15:38:23 dondosha Exp $
 
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 * ===========================================================================
 
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 *
 
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 *                            PUBLIC DOMAIN NOTICE
 
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 *               National Center for Biotechnology Information
 
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 *
 
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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 offical 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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 *
 
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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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 *  purpose.
 
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 *
 
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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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 * ===========================================================================
 
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 *
 
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 * Author: Ilya Dondoshansky
 
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 *
 
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 */
 
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/** @file blast_diagnostics.c
 
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 * Manipulating diagnostics data returned from BLAST
 
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 */
 
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static char const rcsid[] = 
 
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    "$Id: blast_diagnostics.c,v 1.3 2004/07/06 15:38:23 dondosha Exp $";
 
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#include <algo/blast/core/blast_diagnostics.h>
 
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#include <algo/blast/core/blast_def.h>
 
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BlastDiagnostics* Blast_DiagnosticsFree(BlastDiagnostics* diagnostics)
 
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{
 
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   if (diagnostics) {
 
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      sfree(diagnostics->ungapped_stat);
 
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      sfree(diagnostics->gapped_stat);
 
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      sfree(diagnostics->cutoffs);
 
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      if (diagnostics->mt_lock)
 
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         diagnostics->mt_lock = MT_LOCK_Delete(diagnostics->mt_lock);
 
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      sfree(diagnostics);
 
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   }
 
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   return NULL;
 
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}
 
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BlastDiagnostics* Blast_DiagnosticsInit() 
 
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{
 
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   BlastDiagnostics* diagnostics = 
 
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      (BlastDiagnostics*) calloc(1, sizeof(BlastDiagnostics));
 
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   diagnostics->ungapped_stat = 
 
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      (BlastUngappedStats*) calloc(1, sizeof(BlastUngappedStats));
 
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   diagnostics->gapped_stat = 
 
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      (BlastGappedStats*) calloc(1, sizeof(BlastGappedStats));
 
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   diagnostics->cutoffs = 
 
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      (BlastRawCutoffs*) calloc(1, sizeof(BlastRawCutoffs));
 
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   return diagnostics;
 
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}
 
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BlastDiagnostics* Blast_DiagnosticsInitMT(MT_LOCK mt_lock)
 
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{
 
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   BlastDiagnostics* retval = Blast_DiagnosticsInit();
 
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   retval->mt_lock = mt_lock;
 
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   return retval;
 
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}
 
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void Blast_UngappedStatsUpdate(BlastUngappedStats* ungapped_stats, 
 
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                               Int4 total_hits, Int4 extended_hits,
 
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                               Int4 saved_hits)
 
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{
 
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   if (!ungapped_stats || total_hits == 0)
 
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      return;
 
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   ungapped_stats->lookup_hits += total_hits;
 
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   ++ungapped_stats->num_seqs_lookup_hits;
 
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   ungapped_stats->init_extends += extended_hits;
 
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   ungapped_stats->good_init_extends += saved_hits;
 
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   if (saved_hits > 0)
 
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      ++ungapped_stats->num_seqs_passed;
 
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}
 
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void 
 
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Blast_DiagnosticsUpdate(BlastDiagnostics* global, BlastDiagnostics* local)
 
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{
 
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   if (global->mt_lock) 
 
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      MT_LOCK_Do(global->mt_lock, eMT_Lock);
 
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   if (global->ungapped_stat && local->ungapped_stat) {
 
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      global->ungapped_stat->lookup_hits += 
 
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         local->ungapped_stat->lookup_hits;
 
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      global->ungapped_stat->num_seqs_lookup_hits += 
 
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         local->ungapped_stat->num_seqs_lookup_hits;
 
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      global->ungapped_stat->init_extends += 
 
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         local->ungapped_stat->init_extends;
 
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      global->ungapped_stat->good_init_extends += 
 
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         local->ungapped_stat->good_init_extends;
 
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      global->ungapped_stat->num_seqs_passed += 
 
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         local->ungapped_stat->num_seqs_passed;
 
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   }
 
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   if (global->gapped_stat && local->gapped_stat) {
 
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      global->gapped_stat->seqs_ungapped_passed += 
 
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         local->gapped_stat->seqs_ungapped_passed;
 
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      global->gapped_stat->extra_extensions += 
 
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         local->gapped_stat->extra_extensions;
 
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      global->gapped_stat->extensions += 
 
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         local->gapped_stat->extensions;
 
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      global->gapped_stat->good_extensions += 
 
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         local->gapped_stat->good_extensions;
 
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      global->gapped_stat->num_seqs_passed += 
 
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         local->gapped_stat->num_seqs_passed;
 
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   }
 
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   if (global->cutoffs && local->cutoffs) {
 
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      global->cutoffs->x_drop_ungapped = local->cutoffs->x_drop_ungapped;
 
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      global->cutoffs->x_drop_gap = local->cutoffs->x_drop_gap;
 
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      global->cutoffs->x_drop_gap_final = local->cutoffs->x_drop_gap_final;
 
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      global->cutoffs->gap_trigger = local->cutoffs->gap_trigger;
 
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   }
 
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   if (global->mt_lock) 
 
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      MT_LOCK_Do(global->mt_lock, eMT_Unlock);
 
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}