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Viewing changes to algo/blast/api/twoseq_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/twoseq_api.c
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/* $Id: twoseq_api.c,v 1.51 2005/10/20 20:58:58 madden Exp $
 
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/* $Id: twoseq_api.c,v 1.54 2006/01/23 16:39:50 papadopo Exp $
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***************************************************************************
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*                                                                         *
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*                             COPYRIGHT NOTICE                            *
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    Boolean do_megablast = FALSE;
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    Boolean do_discontig = FALSE;
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    Int4 greedy_align = 0;
 
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    Int4 diag_separation = 0;
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    Int2 word_size = basic_options->word_size;
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    char *matrix;
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                                 program_number, 
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                                 do_megablast,
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                                 basic_options->word_threshold,
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                                 word_size,
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                                 0);             /* no variable wordsize */ 
 
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                                 word_size);
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    /* If discontiguous megablast is specified, choose
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       the 11-of-21 optimal template).*/
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    score_options->gapped_calculation = basic_options->gapped_calculation;
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    if (do_megablast)
 
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        diag_separation = 6;
 
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    BLAST_FillHitSavingOptions(hit_options, 
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                               basic_options->cutoff_evalue,
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                               0,     /* default number of alignments saved */
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                               score_options->gapped_calculation,
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                               0);    /* do not perform culling */
 
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                               0,     /* do not perform culling */
 
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                               diag_separation);
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    hit_options->percent_identity = 0;   /* no percent identity cutoff */
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    hit_options->longest_intron = basic_options->longest_intron;   /* For uneven gap statistics. */
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    SeqLocPtr subject_slp = NULL;
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    Boolean seq1_is_aa, seq2_is_aa;
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    Int2 status = 0;
 
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    SBlastSeqalignArray* seqalign_arr=NULL;
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    /* sanity checks */
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       return -1;
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    status = BLAST_TwoSeqLocSets(basic_options, query_slp, subject_slp, 
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                                 NULL, seqalign_out, NULL, NULL, NULL);
 
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                                 NULL, &seqalign_arr, NULL, NULL, NULL);
 
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    if (seqalign_arr && seqalign_arr->num_queries)
 
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    {
 
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           *seqalign_out = seqalign_arr->array[0];
 
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           seqalign_arr->array[0] = NULL;
 
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           SBlastSeqalignArrayFree(seqalign_arr);
 
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    }
 
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    SeqLocFree(query_slp);
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    SeqLocFree(subject_slp);
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BLAST_TwoSeqLocSets(const BLAST_SummaryOptions *basic_options,
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                    SeqLoc* query_seqloc, SeqLoc* subject_seqloc, 
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                    SeqLoc* masking_locs,
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                    SeqAlign **seqalign_out,
 
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                    SBlastSeqalignArray* *seqalign_arr,
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                    SeqLoc** filter_out,
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                    Boolean* mask_at_hash,
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                    Blast_SummaryReturn* *extra_returns_ptr)
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    if (!status) {
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        status = 
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            Blast_TwoSeqLocSetsAdvanced(query_seqloc, subject_seqloc, 
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                masking_locs, options, NULL, seqalign_out, filter_out, 
 
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                masking_locs, options, NULL, seqalign_arr, filter_out, 
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                extra_returns);
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    }
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