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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/Cluster/SequenceFamily.pm
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package Bio::Cluster::SequenceFamily;
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use strict;
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use warnings;
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use base qw(Bio::Root::Root Bio::Cluster::FamilyI);
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=head2 new
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 Title   : new
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=cut
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sub get_members {
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        my $self = shift;
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        my @ret;
 
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    my $self = shift;
 
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    return @{$self->{'_members'}} unless @_;
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        if(@_) {
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                my %hash = @_;
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                foreach my $mem ( @{$self->{'_members'}} ) {
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                        foreach my $key ( keys %hash){
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                                my $method = $key;
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                                $method=~s/-//g;
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                                if($mem->can('species')){
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                                        my $species = $mem->species;
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                                        $species->can($method) ||
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                                          $self->throw("$method is an invalid criteria");
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                                        if($species->$method() eq $hash{$key} ){
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                                                push @ret, $mem;
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                                        }
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                                }
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                        }
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                }
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                return @ret;
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        }
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        return @{$self->{'_members'}};
 
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    ## since the logic behind the checks is OR, we keep the ids in an hash for
 
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    ## performance (skip the test if it's already there) and to avoid repats
 
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    my %match;
 
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    my %filter = @_;
 
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    foreach my $key (keys %filter) {
 
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        (my $method = $key) =~ s/^-//;
 
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        %match = (%match, map { $_ => $_ } grep {
 
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            ! $match{$_} && $_->species &&
 
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            ($_->species->can($method) ||
 
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                $self->throw("$method is an invalid criteria")) &&
 
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            $_->species->$method() eq $filter{$key}
 
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        } @{$self->{'_members'}});
 
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    }
 
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    return map {$match{$_}} keys (%match);
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}
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=head2 size