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Viewing changes to Bio/Search/Result/BlastPullResult.pm

  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2011-06-17 13:51:18 UTC
  • mfrom: (1.2.5 upstream)
  • Revision ID: james.westby@ubuntu.com-20110617135118-xgpxhaanue57cwqs
Tags: 1.6.901-1
* New upstream release.
* Point debian/watch to search.cpan.org.
* Build using dh and overrides:
  - Use Debhelper 8 (debian/rules, debian/control).
  - Simplified debian/rules.
* Split into libbio-perl-perl, as discussed with the Debian Perl team.
  (debian/control, debian/bioperl.install, debian libbio-perl-perl.install)
* debian/control:
  - Incremented Standards-Version to reflect conformance with Policy 3.9.2.
    No other changes needed.
  - Vcs-Browser URL made redirectable to viewvc.
  - Removed useless ‘svn’ in the Vcs-Svn URL.

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Bio/Search/Result/BlastPullResult.pm
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# $Id: BlastPullResult.pm 16123 2009-09-17 12:57:27Z cjfields $
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#
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# BioPerl module for Bio::Search::Result::BlastPullResult
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#
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of the bugs and their resolution. Bug reports can be submitted via the
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web:
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  http://bugzilla.open-bio.org/
 
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  https://redmine.open-bio.org/projects/bioperl/
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=head1 AUTHOR - Sendu Bala
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        $self->_setup(@args);
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        foreach my $field (qw( header hit_table hsp_table alignments next_model models query_length stats_and_params)) {
 
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        foreach my $field (qw( header hit_table hsp_table alignments next_model
 
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        models query_length stats_and_params)) {
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                $self->_fields->{$field} = undef;
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        }
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        $self->_dependencies( { ( query_name => 'header',
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                              query_accession => 'header',
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                              query_description => 'header',
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                                                          query_length => 'header',
 
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                            query_length => 'header',
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                              hit_table => 'header',
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                                                          num_hits => 'hit_table',
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                                                          no_hits_found => 'hit_table' ) } );
 
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                            num_hits => 'hit_table',
 
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                            no_hits_found => 'hit_table' ) } );
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    return $self;
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}
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        my $self = shift;
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        $self->_chunk_seek(0);
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        my $header = $self->_get_chunk_by_end("Value\n");
 
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        if (!$header) {
 
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            $header = $self->_get_chunk_by_end("***** No hits found ******\n");
 
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            $self->{_no_hits_found} = 1;
 
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        }
 
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        $self->throw("Invalid header returned") unless $header;
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        $self->{_after_header} = $self->_chunk_tell;
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        ($self->_fields->{query_name}) = $header =~ /^\s*(\S+)/;
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sub _discover_hit_table {
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        my $self = shift;
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        $self->_chunk_seek($self->{_after_header});
 
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        my $table = $self->_get_chunk_by_end("\n>");
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        unless ($table) {
 
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        if (!$table && !$self->{_no_hits_found}) {
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                # no alignments, presumably; hit table comprises the remainder of this
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                # result
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                while (my $line = $self->_get_chunk_by_nol(1)) {
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                }
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        }
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    $table ||= '';
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        $table ||= '';
 
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        $self->{_after_hit_table} = $self->_chunk_tell;
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        my $evalue_cutoff = $self->get_field('evalue_cutoff');
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        #*** needs to inherit piped_behaviour, and we need to deal with _sequential
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        #    ourselves
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        $self->_fields->{next_hit} = Bio::Search::Hit::BlastPullHit->new(-parent => $self,
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                                                                                                                                        -chunk => [$self->chunk, $start, $end],
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                                                                                                                                        -hit_data => $hit_row);
 
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                                                                -chunk => [$self->chunk, $start, $end],
 
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                                                                -hit_data => $hit_row);
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        $self->{_next_hit_index}++;
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