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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)