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Viewing changes to Bio/TreeIO/newick.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/TreeIO/newick.pm
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# $Id: newick.pm,v 1.36.4.2 2006/10/02 23:10:37 sendu Exp $
 
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# $Id: newick.pm 11480 2007-06-14 14:16:21Z sendu $
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#
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# BioPerl module for Bio::TreeIO::newick
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#
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  # do not use this module directly
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  use Bio::TreeIO;
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  my $treeio = new Bio::TreeIO(-format => 'newick', 
 
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  my $treeio = Bio::TreeIO->new(-format => 'newick', 
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                               -file => 't/data/LOAD_Ccd1.dnd');
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  my $tree = $treeio->next_tree;
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       if( $ch eq ';' ) {
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           my $tree = $self->_eventHandler->end_document($chars);
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           $tree->score($score) if defined $score;
 
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           if( $self->internal_node_id eq 'bootstrap' ) {
 
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               $tree->move_id_to_bootstrap;
 
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           }
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           return $tree;
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       } elsif( $ch eq '(' ) {
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           $chars = '';
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   }
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   my $nl = $self->newline_each_node;
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   foreach my $tree( @trees ) {
 
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       if( ! defined $tree || ref($tree) =~ /ARRAY/i ||
 
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           ! $tree->isa('Bio::Tree::TreeI') ) {
 
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           $self->throw("Calling write_tree with non Bio::Tree::TreeI object\n");
 
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       }
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       my @data = _write_tree_Helper($tree->get_root_node,
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                                     $bootstrap_style,
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                                     $orderby,