← Back to branch summary

~ubuntu-branches/ubuntu/saucy/ncbi-tools6/saucy-proposed

« back to all changes in this revision

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

  • Committer: Bazaar Package Importer
  • Author(s): Aaron M. Ucko
  • Date: 2009-08-11 22:03:47 UTC
  • mfrom: (1.4.1 upstream)
  • mto: This revision was merged to the branch mainline in revision 10.
  • Revision ID: james.westby@ubuntu.com-20090811220347-g4b6lzdvphvvbpiu
* New upstream release.
* debian/libncbi6.symbols: update accordingly.
* debian/control: clean up obsolete or redundant relationship declarations.

Show diffs side-by-side

added added

removed removed

Lines of Context:
algo/blast/api/twoseq_api.c
1
 
/* $Id: twoseq_api.c,v 1.59 2007/03/20 15:17:16 kans Exp $
 
1
/* $Id: twoseq_api.c,v 1.61 2009/05/28 14:55:09 camacho Exp $
2
2
***************************************************************************
3
3
*                                                                         *
4
4
*                             COPYRIGHT NOTICE                            *
38
38
#include <algo/blast/core/blast_engine.h>
39
39
#include <algo/blast/core/blast_filter.h>
40
40
#include <algo/blast/core/blast_nalookup.h>
41
 
#include <algo/blast/core/hspstream_collector.h>
42
41
#include <algo/blast/core/gencode_singleton.h>
43
42
#include <algo/blast/api/seqsrc_multiseq.h>
44
43
#include <algo/blast/api/blast_seqalign.h>
62
61
        return -1;
63
62
    }
64
63
    
65
 
    new_options->hint = eSensitive;
 
64
    new_options->hint = eBlastHint_Sensitive;
66
65
    new_options->program = eChoose;
67
66
    new_options->strand = Seq_strand_both;
68
67
    new_options->cutoff_evalue = 10.0;
134
133
 
135
134
        /* If the query sequence is large enough, set up a megablast search */
136
135
 
137
 
        if (basic_options->hint != eNone && 
 
136
        if (basic_options->hint != eBlastHint_None && 
138
137
            query_length > MEGABLAST_CUTOFF) {
139
138
            do_megablast = TRUE;
140
139
            if (basic_options->gapped_calculation)
148
147
           Because a sensitive search is the default, discontig. megablast will 
149
148
           be used by default when the first input sequence is large. */
150
149
        if (do_megablast && 
151
 
            (basic_options->hint == eSensitive || 
 
150
            (basic_options->hint == eBlastHint_Sensitive || 
152
151
             (word_size != 0 && word_size <= 12))) {
153
152
            if (word_size == 0 || word_size > 12)
154
153
                word_size = 11;