Bio::Annotation::Tree(User Contributed Perl DocumentatBio::Annotation::Tree(3)NAMEBio::Annotation::Tree - Provide a tree as an annotation to a
Bio::AnnotatableI object
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.edu
CONTRIBUTORS
Aaron Mackey Jason Stajich
APPENDIX
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)
perl v5.14.1 2011-07-22 Bio::Annotation::Tree(3)
