[Bioperl-l] [patch] Bio/TreeIO.pm POD patch

Chris Fields cjfields at illinois.edu
Thu Jul 9 16:47:07 EDT 2009


committed in r15842.  thanks!

chris

On Jul 9, 2009, at 2:47 PM, Jay Hannah wrote:

> Hello,
>
> $tree->size throws this error:
>
> Can't locate object method "size" via package "Bio::Tree::Tree" at  
> conv.pl line 17, <GEN0> line 1.
>
> Below, a POD patch to Bio::TreeIO to fix (sidestep) that problem and  
> make podchecker happier.
>
> Thanks,
>
> j
> http://clab.ist.unomaha.edu/CLAB/index.php/User:Jhannah
>
>
>
>
> Index: Bio/TreeIO.pm
> ===================================================================
> --- Bio/TreeIO.pm       (revision 15841)
> +++ Bio/TreeIO.pm       (working copy)
> @@ -18,13 +18,11 @@
>
> =head1 SYNOPSIS
>
> -  {
> -      use Bio::TreeIO;
> -      my $treeio = Bio::TreeIO->new('-format' => 'newick',
> -                                  '-file'   => 'globin.dnd');
> -      while( my $tree = $treeio->next_tree ) {
> -         print "Tree is ", $tree->size, "\n";
> -      }
> +  use Bio::TreeIO;
> +  my $treeio = Bio::TreeIO->new('-format' => 'newick',
> +                                '-file'   => 'globin.dnd');
> +  while( my $tree = $treeio->next_tree ) {
> +     print "Tree has ", $tree->number_nodes, " nodes.\n";
>  }
>
> =head1 DESCRIPTION
> @@ -45,11 +43,11 @@
>  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
>
> =head2 Support
> -
> +
> Please direct usage questions or support issues to the mailing list:
> -
> +
> L<bioperl-l at bioperl.org>
> -
> +
> rather than to the module maintainer directly. Many experienced and
> reponsive experts will be able look at the problem and quickly
> address it. Please include a thorough description of the problem
>
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