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

Jay Hannah jay at jays.net
Thu Jul 9 15:47:02 EDT 2009


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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