| Subject: | A typo in Bio::Phylo::Unparsers::Newick |
| Date: | Wed, 02 Apr 2008 14:05:10 +0200 |
| To: | bug-Bio-Phylo [...] rt.cpan.org |
| From: | Stephan Struckmann <struckma [...] uni-greifswald.de> |
Dear Rutger,
unfortunately I have to send you another bug report for Bio::Phylo. It is a
typo only:
In the function _to_string in Bio::Phylo::Unparsers::Newick, you prepare
the arguments hash for Forest::Node::to_newick from the data stored by the
constructor of Unparsers::Newick:
01 sub _to_string {
02 my $self = shift;
03 my $tree = $self->{'PHYLO'};
04 my $root = $tree->get_root;
05 my %args;
06 if ( $self->{'TRANSLATE'} ) {
07 $args{'-translate'} = $self->{'TRANSLATE'};
08 }
09 if ( $self->{'TIPNAMES'} ) {
10 $args{'-tipnames'} = $self->{'NAMES'}; *** BUG ***
11 }
12 if ( $self->{'NHXKEYS'} ) {
13 $args{'-nhxkeys'} = $self->{'NHXKEYS'};
14 }
15 if ( $self->{'NODELABELS'} ) {
16 $args{'-nodelabels'} = $self->{'NODELABELS'};
17 }
18 if ( $self->{'BLFORMAT'} ) {
19 $args{'-blformat'} = $self->{'BLFORMAT'};
20 }
21 if ( $self->{'NHXSTYLE'} ) {
22 $args{'-nhxstyle'} = $self->{'NHXSTYLE'};
23 }
24 return $root->to_newick( %args );
25 }
As you can see, there is a typo in line 10. It should be:
10 $args{'-tipnames'} = $self->{'TIPNAMES'};
Greetings from Germany,
Stephan
Institut für Mathematik und Informatik
E.-M.-A.-Universität Greifswald
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