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Viewing changes to algo/blast/api/blast_options_api.c

  • Committer: Bazaar Package Importer
  • Author(s): Barry deFreese
  • Date: 2006-07-19 23:28:07 UTC
  • mfrom: (1.1.5 upstream)
  • Revision ID: james.westby@ubuntu.com-20060719232807-et3cdmcjgmnyleyx
Tags: 6.1.20060507-3ubuntu1
Re-merge with Debian

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algo/blast/api/blast_options_api.c
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/* $Id: blast_options_api.c,v 1.15 2005/10/31 14:14:29 madden Exp $
 
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/* $Id: blast_options_api.c,v 1.18 2006/04/26 12:45:28 madden Exp $
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***************************************************************************
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*                                                                         *
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*                             COPYRIGHT NOTICE                            *
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               "Program name %s is not supported. The supported programs "
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               "are blastn, blastp, blastx, tblastn, tblastx, rpsblast, "
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               "rpstblastn\n", program_name);
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       Blast_MessageWrite(&extra_returns->error, 2, 1, 0, message);
 
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       SBlastMessageWrite(&extra_returns->error, SEV_ERROR, message, NULL, FALSE);
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       return -1;
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   }
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   if (status) {
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       *options_out = NULL;
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       Blast_MessageWrite(&extra_returns->error, 2, 1, 0, 
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                          "Failed to initialize default options\n");
 
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       SBlastMessageWrite(&extra_returns->error, SEV_ERROR, "Failed to initialize default options\n", NULL, FALSE);
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       return status;
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   }
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   options->psi_options = psi_options;
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   options->db_options = db_options;
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   options->num_cpus = 1;
 
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   options->believe_query = FALSE;
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   /* Set default filter string to low complexity filtering. */
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   SBlastOptionsSetFilterString(options, "T");
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    /* Reward penalty do not apply to blastn. */
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    if (options->program == eBlastTypeBlastn)
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        return 0;
 
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    status = BLAST_FillScoringOptions(options->score_options, options->program,
 
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                        FALSE, -1, -1, matrix_name, gap_open, gap_extend);
 
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    if (status != 0)
 
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        return status;
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    status = 
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        BlastScoringOptionsSetMatrix(options->score_options, matrix_name);
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    if (status != 0)
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         return status;
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    if (gap_open < 0 || gap_extend < 0)
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    {
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        Int4 gap_open_priv = 0;
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Int2 SBlastOptionsSetRewardPenaltyAndGapCosts(SBlastOptions* options, 
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                                       Int4 reward, Int4 penalty,
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                                       Int4 gap_open, Int4 gap_extend)
 
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                                       Int4 gap_open, Int4 gap_extend,
 
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                                       Boolean greedy)
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{
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    Int2 status = 0;
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    if (options->program != eBlastTypeBlastn)
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        return 0;
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    status = BLAST_FillScoringOptions(options->score_options, options->program,
 
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                        greedy, penalty, reward, NULL, gap_open, gap_extend);
 
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    if (status != 0)
 
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        return status;
 
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    if (gap_open < 0 || gap_extend < 0)
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    {
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        Int4 gap_open_priv = BLAST_GAP_OPEN_NUCL;
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        Int4 gap_extend_priv = BLAST_GAP_EXTN_NUCL;
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        BLAST_GetNucleotideGapExistenceExtendParams(reward, penalty, &gap_open_priv, &gap_extend_priv);
 
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        Int4 gap_open_priv;
 
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        Int4 gap_extend_priv;
 
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        if (greedy)
 
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        {
 
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             gap_open_priv = BLAST_GAP_OPEN_MEGABLAST;
 
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             gap_extend_priv = BLAST_GAP_EXTN_MEGABLAST;
 
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        }
 
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        else
 
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        {
 
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             gap_open_priv = BLAST_GAP_OPEN_NUCL;
 
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             gap_extend_priv = BLAST_GAP_EXTN_NUCL;
 
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        }
 
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        status = BLAST_GetNucleotideGapExistenceExtendParams(reward, penalty, &gap_open_priv, &gap_extend_priv);
 
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        if (status)
 
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           return status;
 
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        if (gap_open < 0)
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            gap_open = gap_open_priv;
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        if (gap_extend < 0)
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    return options->query_options->filtering_options->mask_at_hash;
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}
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Int2 SBlastOptionsSetBelieveQuery(SBlastOptions* options, Boolean believe_query)
 
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{
 
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    Int2 status = 0;
 
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    if (!options)
 
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       return -1;
 
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    options->believe_query = believe_query;
 
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    return status;
 
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}
 
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Boolean SBlastOptionsGetBelieveQuery(const SBlastOptions* options)
 
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{
 
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    ASSERT(options);
 
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    return options->believe_query;
 
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}
 
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/* @} */
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