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  • Committer: Package Import Robot
  • Author(s): Charles Plessy
  • Date: 2013-09-22 13:39:48 UTC
  • mfrom: (3.1.11 sid)
  • Revision ID: package-import@ubuntu.com-20130922133948-c6z62zegjyp7ztou
Tags: 1.6.922-1
http://bugs.debian.org/722910
* New upstream release.
* Replaces and Breaks grinder (<< 0.5.3-3~) because of overlaping contents.
  Closes: #722910
* Stop Replacing and Breaking bioperl ( << 1.6.9 ): not needed anymore. 

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Bio/SearchIO/hmmer2.pm
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    );
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}
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=head2 new
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 Title   : new
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 Usage   : my $obj = Bio::SearchIO::hmmer2->new();
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 Function: Builds a new Bio::SearchIO::hmmer2 object
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 Returns : Bio::SearchIO::hmmer2
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 Args    : -fh/-file => HMMER filename
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           -format   => 'hmmer2'
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=cut
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sub _initialize {
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    my ( $self, @args ) = @_;
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    $self->SUPER::_initialize(@args);
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    $self->{'_hmmidline'} = 'HMMER 2.2g (August 2001)';
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}
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=head2 next_result
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 Title   : next_result
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            $seentop = 1;
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            if ( defined $last ) {
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                ($reporttype) = split( /\s+/, $last );
 
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                $reporttype = uc($reporttype) if defined $reporttype;
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                $self->element(
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                    {
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                        'Name' => 'HMMER_program',
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                        'Data' => uc($reporttype)
 
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                        'Data' => $reporttype
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                    }
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                );
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            }
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            if ( !$seentop ) {
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                # we're in a multi-query report
 
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                $self->_pushback($lineorig);
 
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                $self->_pushback( $self->{'_hmmseqline'} );
 
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                $self->_pushback( $self->{'_hmmfileline'} );
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                $self->_pushback( $self->{'_hmmidline'} );
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                $self->_pushback( $self->{'_hmmfileline'} );
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                $self->_pushback( $self->{'_hmmseqline'} );
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                $self->_pushback($lineorig);
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                next;
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            }
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            s/\s+$//;
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                        }
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                        elsif (CORE::length($_) == 0
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                            || ( $count != 1 && /^\s+$/o )
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                            || /^\s+\-?\*\s*$/ )
 
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                            || /^\s+\-?\*\s*$/
 
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                            || /^\s+\S+\s+\-\s+\-\s*$/ )
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                        {
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                            next;
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                        }