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

  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2009-03-10 07:19:11 UTC
  • mfrom: (1.2.3 upstream)
  • Revision ID: james.westby@ubuntu.com-20090310071911-fukqzw54pyb1f0bd
Tags: 1.6.0-2
https://launchpad.net/bugs/324001
* Removed patch system (not used):
  - removed instuctions in debian/rules;
  - removed quilt from Build-Depends in debian/control.
* Re-enabled tests:
  - uncommented test command in debian/rules;
  - uncommented previously missing build-dependencies in debian/control.
  - Re-enabled tests and uncommented build-dependencies accordingly.
* Removed libmodule-build-perl and libtest-harness-perl from
  Build-Depends-Indep (provided by perl-modules).
* Better cleaning of empty directories using find -type d -empty -delete
  instead of rmdir in debian/rules (LP: #324001).

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Bio/Search/Result/HmmpfamResult.pm
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# $Id: HmmpfamResult.pm,v 1.1.2.4 2006/10/02 23:10:24 sendu Exp $
 
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# $Id: HmmpfamResult.pm 14984 2008-11-11 18:39:20Z sendu $
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#
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# BioPerl module for Bio::Search::Result::HmmpfamResult
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#
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    # generally we use Bio::SearchIO to build these objects
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    use Bio::SearchIO;
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    my $in = new Bio::SearchIO(-format => 'hmmer_pull',
 
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    my $in = Bio::SearchIO->new(-format => 'hmmer_pull',
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                                                           -file   => 'result.hmmer');
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    while (my $result = $in->next_result) {
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=head2 new
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 Title   : new
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 Usage   : my $obj = new Bio::SearchIO::Result::hmmpfam();
 
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 Usage   : my $obj = Bio::SearchIO::Result::hmmpfam->new();
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 Function: Builds a new Bio::SearchIO::Result::hmmpfam object 
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 Returns : Bio::SearchIO::Result::hmmpfam
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 Args    : -chunk  => [Bio::Root::IO, $start, $end] (required if no -parent)
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                $self->{_after_previous_alignment} = $self->_chunk_tell;
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                $self->{_next_alignment_start_text} = $chunk;
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                $self->_next_alignment;
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                return;
 
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                return $self->_next_alignment;
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        }
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        $self->_chunk_seek($self->{_after_previous_alignment});
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        if (defined $self->{_next_alignment_start_text}) {
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                $chunk = $self->{_next_alignment_start_text}.$chunk;
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        }
 
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        $chunk =~ s/(\S+: domain)$//;
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        $self->{_next_alignment_start_text} = $1;
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        #[name description score significance num_hsps rank]
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        my @hit_data = (@{$hit_table[$self->{_next_hit_index}++]}, $self->{_next_hit_index});
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        $self->_fields->{next_hit} = new Bio::Search::Hit::HmmpfamHit(-parent => $self,
 
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        $self->_fields->{next_hit} = Bio::Search::Hit::HmmpfamHit->new(-parent => $self,
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                                                                                                                                  -hit_data => \@hit_data);
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        if ($self->{_next_hit_index} > $#hit_table) {