NAME

Bio::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)