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  • 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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demo/formatrpsdb.c
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static char const rcsid[] = "$Id: formatrpsdb.c,v 1.18 2005/06/20 19:43:03 papadopo Exp $";
 
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static char const rcsid[] = "$Id: formatrpsdb.c,v 1.20 2006/01/25 16:22:18 camacho Exp $";
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/*****************************************************************************
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***************************************************************************
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    $Log: formatrpsdb.c,v $
 
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    Revision 1.20  2006/01/25 16:22:18  camacho
 
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    Calculate kbp_ideal values rather than loading them from pre-computed values
 
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    Revision 1.19  2005/12/22 14:22:19  papadopo
 
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    change signature of BLAST_FillLookupTableOptions
 
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    Revision 1.18  2005/06/20 19:43:03  papadopo
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    explicitly specify use of PSSMs during lookup table construction
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    BLAST_ScoreBlk *sbp;
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    PssmPtr pssm = seq->pssm;
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    PssmParametersPtr params = seq->params;
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    Int4 *open, *extend;
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    Int4 array_size;
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    Nlm_FloatHi *lambda, *K, *H;
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    ValNodePtr freq_list;
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    ValNodePtr score_list;
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    CharPtr matrix_name;
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    if (sbp->kbp_gap_std[0] == NULL || sbp->kbp_gap_psi[0] == NULL)
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        return -3;
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    array_size = BlastKarlinGetMatrixValues(sbp->name, &open, &extend, 
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                                            &lambda, &K, &H, NULL);
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    if (array_size > 0) {
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        for (i = 0; i < array_size; i++) {
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            if (open[i] == INT2_MAX && extend[i] == INT2_MAX) {
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                sbp->kbp_ideal = BlastKarlinBlkCreate();
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                sbp->kbp_ideal->Lambda = lambda[i];
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                sbp->kbp_ideal->K = K[i];
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                sbp->kbp_ideal->H = H[i];
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                break;
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            }
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        }
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        MemFree(open);
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        MemFree(extend);
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        MemFree(lambda);
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        MemFree(K);
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        MemFree(H);
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    }
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    if (sbp->kbp_ideal == NULL)
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       sbp->kbp_ideal = BlastKarlinBlkStandardCalcEx(sbp);
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                                     eBlastTypePsiBlast,
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                                     FALSE, /* no megablast */
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                                     threshold, /* neighboring threshold */
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                                     BLAST_WORDSIZE_PROT,
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                                     FALSE /* no variable words */
 
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                                     BLAST_WORDSIZE_PROT
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                                    ) != 0) {
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        ErrPostEx(SEV_ERROR, 0, 0, "Cannot set lookup table options");
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        return 1;