debian man page for bio::annotation::tree

Bio::Annotation::Tree(3pm)				User Contributed Perl Documentation				Bio::Annotation::Tree(3pm)

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)

perl v5.14.2							    2012-03-02						Bio::Annotation::Tree(3pm)