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');
$tree=$treeio->next_tree;
$alnio=Bio::AlignIO->new(-file=>'foo.aln', -format=>'clustalw');
$aln=$alnio->next_aln;
# 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);
$aln->annotation($ac);
# 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 genectr.hunter.cuny.edu
Aaron Mackey Jason Stajich
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a '_'
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
returned
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)
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)