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Viewing changes to Bio/Tools/Phylo/PAML/Codeml.pm

  • 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/Tools/Phylo/PAML/Codeml.pm
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            # ...
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            while( defined($_ = $self->_readline) ) {
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                if( /^\(/) {
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                    my $treestr = new IO::String($_);
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                    my $treeio = new Bio::TreeIO(-fh => $treestr,
 
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                    my $treestr = IO::String->new($_);
 
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                    my $treeio = Bio::TreeIO->new(-fh => $treestr,
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                                                 -format => 'newick');
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                    # this is very tenative here!!
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                    push @{$self->{'_trees'}}, $treeio->next_tree;