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Summary

Bio::Annotation::Tree - Provide a tree as an annotation to a Bio::AnnotatableI
object

Package variables

Inherit

Bio::AnnotationI Bio::Root::Root Bio::TreeIO

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)

Methods

Methods description

 Title   : as_text
 Usage   : $ann_tree->as_text();
 Function: output tree as a string
 Returns : a newic tree file
 Args    : None

 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

 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

 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)

 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)

 Title   : tree
 Usage   : $obj->tree($newval)
 Function: Get/set tree
 Returns : tree ref
 Args    : new value (a tree ref, optional)

Methods code

sub new {

  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);

  my ($tree_id, $tree_obj, $tag) =
      $self->_rearrange([ qw(
                              TREE_ID
                              TREE_OBJ
                              TAGNAME
                         ) ], @args);

  defined $tag                        && $self->tagname($tag);
  defined $tree_id                    && $self->tree_id($tree_id);
  defined $tree_obj                   && $self->tree($tree_obj);
  return $self;

# other possible variables to store
#                              TREE_PROGRAM
#                              TREE_METHOD
#                              TREE_FREQUENCY
#  defined $program                    && $self->program($program);
#  defined $method                     && $self->method($method);
#  defined $freq                       && $self->freq($tree_freq);

}

sub as_text {

  my ($self) = @_;

  my $tree = $self->tree || $self->throw("Tree object absent");
  my $treeio = Bio::TreeIO->new();
  $treeio->write_tree($tree);

}

sub display_text {

    my ($self, $cb) = @_;
    $cb ||= $DEFAULT_CB;
    $self->throw("Callback must be a code reference") if ref $cb ne 'CODE';
    return $cb->($self);
  }

}

sub hash_tree {

    my $self = shift;
    my $h = {};
    $h->{'value'} = $self->tree();
    return $h;

}

sub tagname {

    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'tagname'} = $value;
    }
    return $self->{'tagname'};

}

sub tree_id {

    my $self = shift;
    return $self->{'tree_id'} = shift if defined($_[0]);
    return $self->{'tree_id'};

}

sub tree {

    my $self = shift;
    return $self->{'tree'} = shift if defined($_[0]);
    return $self->{'tree'};
}

1;

}

General documentation

Weigang Qiu - weigang at genectr.hunter.cuny.edu

Aaron Mackey
Jason Stajich

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a '_'