SYNOPSIS
# 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
DESCRIPTION
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)AUTHOR
Weigang Qiu - weigang at genectr.hunter.cuny.eduCONTRIBUTORS
Aaron Mackey Jason StajichAPPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a '_'AnnotationI implementing functions
as_text
Title : as_text Usage : $ann_tree->as_text(); Function: output tree as a string Returns : a newic tree file Args : None
display_text
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
hash_tree
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
tagname
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
tree_id
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)
tree
Title : tree Usage : $obj->tree($newval) Function: Get/set tree Returns : tree ref Args : new value (a tree ref, optional)