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)