Christopher Fields > BioPerl-1.6.922 > Bio::Annotation::Tree



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Module Version: 1.006922   Source   Latest Release: BioPerl-1.6.924


Bio::Annotation::Tree - Provide a tree as an annotation to a Bio::AnnotatableI object


   # Read a tree and an alignment

   $treeio=Bio::TreeIO->new(-file=>'foo.dnd', -format=>'newic');
   $alnio=Bio::AlignIO->new(-file=>'foo.aln', -format=>'clustalw');

   # Construct a tree annotation
   $ann_tree = Bio::Annotation::Tree->new (-tree_id  => 'mytree',
                                           -tree_obj     => $tree,

   # Add the tree annotation to AlignI
   $ac = Bio::Annotation::Collection->new();
   $ac->add_Annotation('tree', $ann_tree);

   # NOTE & TODO: 
   # The above procedures are sensible only if 
   # the tree is generated from the alignment.  However, 
   # currently no effort has been made to check the consistency
   # between the tree OTU names and the sequence names


Provides a Bio::AnnotationI object which contains a Bio::Tree::TreeI, which can be added to a Bio::AnnotationCollectionI, which in turn be attached to a Bio::AnnotatableI (typically a Bio::AlignI object)


Weigang Qiu - weigang at


Aaron Mackey Jason Stajich


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a '_'

AnnotationI implementing functions ^


 Title   : as_text
 Usage   : $ann_tree->as_text();
 Function: output tree as a string
 Returns : a newic tree file
 Args    : None


 Title   : display_text
 Usage   : my $str = $ann->display_text();
 Function: returns a string. Unlike as_text(), this method returns a string
           formatted as would be expected for te specific implementation.

           One can pass a callback as an argument which allows custom text
           generation; the callback is passed the current instance and any text
 Example :
 Returns : a string
 Args    : [optional] callback


 Title   : hash_tree
 Usage   : my $hashtree = $value->hash_tree
 Function: For supporting the AnnotationI interface just returns the value
           as a hashref with the key 'value' pointing to the value
 Returns : hashrf to tree
 Args    : none


 Title   : tagname
 Usage   : $obj->tagname($newval)
 Function: Get/set the tagname for this annotation value.
           Setting this is optional. If set, it obviates the need to
           provide a tag to Bio::AnnotationCollectionI when adding
           this object. When obtaining an AnnotationI object from the
           collection, the collection will set the value to the tag
           under which it was stored unless the object has a tag
           stored already.
 Returns : value of tagname (a scalar)
 Args    : new value (a scalar, optional)

Specific accessors for Tree ^


 Title   : tree_id
 Usage   : $obj->tree_id($newval)
 Function: Get/set a name for the tree
 Returns : value of tagname (a scalar)
 Args    : new value (a scalar, optional)


 Title   : tree
 Usage   : $obj->tree($newval)
 Function: Get/set tree
 Returns : tree ref
 Args    : new value (a tree ref, optional)
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