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Gmane
From: =?ISO-8859-1?Q?S=E9bastien_MORETTI?= <sebastien.moretti <at> unil.ch>
Subject: Re: PhyloXML
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Monday 11th February 2013 07:08:22 UTC (over 3 years ago)
>> # Add annotation
>> $treeio->add_phyloXML_annotation(-obj => $tree,
>>                                 -xml => 'SUMF family',
>>                                );
>
> If you really have $treeio in your script in this line and not $tree,
then that's at least one problem. But the stack suggests that the above
isn't the exact line in your script - can you confirm that?
>
> 	-hilmar

I replaced $treeio by $tree in the above line but still get an error.
Don't see what you mean by "the stack suggests that the above isn't the 
exact line in your script"

The only think I changed is the length of the xml string I try to 
insert. But get the same error with an empty xml string.



my $treeio = new Bio::TreeIO(-file   => "$infile",
                              -format => 'phyloxml',
                             );
my $tree = $treeio->next_tree;

# Add annotation
$tree->add_phyloXML_annotation(-obj => $tree,
                                -xml => 'SUMF family',
                               );

Can't locate object method "add_phyloXML_annotation" via package
	"Bio::Tree::Tree" at ./add_annotation_to_phyloxml.pl line 40,  
line 1 (#1)
     (F) You called a method correctly, and it correctly indicated a
package
     functioning as a class, but that package doesn't define that
particular
     method, nor does any of its base classes.  See perlobj.

Uncaught exception from user code:
	Can't locate object method "add_phyloXML_annotation" via package 
"Bio::Tree::Tree" at ./add_annotation_to_phyloxml.pl line 40,  line
1.
  at ./add_annotation_to_phyloxml.pl line 40



-- 
S├ębastien Moretti
Department of Ecology and Evolution,
Biophore, University of Lausanne,
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4221/4079
http://bioinfo.unil.ch/
 
CD: 4ms