Provided by: libbio-perl-perl_1.7.6-3_all bug

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)