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Summary

Bio::Tree::AnnotatableNode - A Tree Node with support for annotation

Package variables

Included modules

Inherit

Bio::AnnotatableI Bio::Tree::Node

Synopsis

    use Bio::Tree::AnnotatableNode;
    my $nodeA = Bio::Tree::AnnotatableNode->new();
    my $nodeL = Bio::Tree::AnnotatableNode->new();
    my $nodeR = Bio::Tree::AnnotatableNode->new();

    my $node = Bio::Tree::AnnotatableNode->new();
    $node->add_Descendents($nodeL);
    $node->add_Descendents($nodeR);

    print "node is not a leaf \n" if( $node->is_leaf);

    # $node is-a Bio::AnnotatableI, hence:
    my $ann_coll = $node->annotation();
    # $ann_coll is-a Bio::AnnotationCollectionI, hence:
    my @all_anns = $ann_coll->get_Annotations();
    # do something with the annotation objects

Description

Makes a Tree Node with Annotations, suitable for building a Tree. See
Bio::Tree::Node for a full list of functionality.

Methods

Methods description

 Title   : new
 Usage   : my $obj = Bio::Tree::AnnotatableNode->new();
 Function: Builds a new Bio::Tree::AnnotatableNode object
 Returns : Bio::Tree::AnnotatableNode
 Args    : -tostring => code reference to the tostring callback function (optional)

 Title   : annotation
 Usage   : $ann = $node->annotation or 
           $node->annotation($ann)
 Function: Gets or sets the annotation
 Returns : Bio::AnnotationCollectionI object
 Args    : None or Bio::AnnotationCollectionI object
See Bio::AnnotationCollectionI and Bio::Annotation::Collection
for more information

 Title   : add_tag_value
 Usage   : $node->add_tag_value($tag,$value)
 Function: Adds a tag value to a node 
 Returns : number of values stored for this tag
 Args    : $tag   - tag name
           $value - value to store for the tag

 Title   : remove_tag
 Usage   : $node->remove_tag($tag)
 Function: Remove the tag and all values for this tag
 Returns : boolean representing success (0 if tag does not exist)
 Args    : $tag - tagname to remove

 Title   : remove_all_tags
 Usage   : $node->remove_all_tags()
 Function: Removes all tags 
 Returns : None
 Args    : None

 Title   : get_all_tags
 Usage   : my @tags = $node->get_all_tags()
 Function: Gets all the tag names for this Node
 Returns : Array of tagnames
 Args    : None

 Title   : get_tag_values
 Usage   : my @values = $node->get_tag_value($tag)
 Function: Gets the values for given tag ($tag)
 Returns : Array of values or empty list if tag does not exist
 Args    : $tag - tag name

 Title   : has_tag
 Usage   : $node->has_tag($tag)
 Function: Boolean test if tag exists in the Node
 Returns : Boolean
 Args    : $tag - tagname

 Title   : to_string_callback
 Usage   : $node->to_string_callback(\&func)
 Function: get/set callback for to_string
 Returns : code reference for the to_string callback function
 Args    : \&func - code reference to be set as the callback function

 Title   : sequence
 Usage   : $ann = $node->sequence or 
           $node->sequence($seq)
 Function: Gets or sets the sequence
 Returns : array reference of Bio::SeqI objects
 Args    : None or Bio::SeqI object
See Bio::SeqI and Bio::Seq
for more information

 Title   : has_sequence
 Usage   : if( $node->has_sequence) { # do something } 
 Function: tells if node has sequence attached
 Returns : Boolean for whether or not node has Bio::SeqI attached.
 Args    : None

Methods code

sub new {

  my ($class,@args) = @_;
  my $self = $class->SUPER::new(@args);
  my $to_string_cb = $self->_rearrange([qw(TOSTRING)], @args);
  if ($to_string_cb) {
    $self->to_string_callback($to_string_cb);
  }
  return $self;

}

sub DESTROY {

    my ($self) = @_;
    # try to insure that everything is cleaned up
    $self->SUPER::DESTROY();

}

sub annotation {

  my ($self,$value) = @_;
  if( defined $value ) {
    $self->throw("object of class ".ref($value)." does not implement ".
        "Bio::AnnotationCollectionI. Too bad.")      unless $value->isa("Bio::AnnotationCollectionI");
    $self->{'_annotation'} = $value;
  } 
  elsif( ! defined $self->{'_annotation'}) 
  {
    $self->{'_annotation'} = Bio::Annotation::Collection->new();
  }
  return $self->{'_annotation'};

}

sub add_tag_value {

  my ($self,$tag,$value) = @_;
  if( ! defined $tag || ! defined $value ) {
    $self->warn("cannot call add_tag_value with an undefined value");
  }
  my $ac = $self->annotation();
  my $sv = Bio::Annotation::SimpleValue->new(-value => $value);
  $ac->add_Annotation($tag, $sv); 
  return scalar $ac->get_Annotations($tag);

}

sub remove_tag {

  my ($self,$tag) = @_;
  my $ac = $self->annotation();
  if( @{$ac->get_Annotations($tag)} ) {
    $ac->remove_Annotations($tag);
    return 1;
  }
  return 0;

}

sub remove_all_tags {

  my ($self) = @_;
  my $ac = $self->annotation();
  $ac->remove_Annotations();
  return;

}

sub get_all_tags {

  my ($self) = @_;
  my $ac = $self->annotation();
  my @tags = sort $ac->get_all_annotation_keys(); 
  # how to restrict it to SimpleValues?
  return @tags;

}

sub get_tag_values {

  my ($self,$tag) = @_;
  my $ac = $self->annotation();
  my @values = map {$_->value()} $ac->get_Annotations($tag);
  return @values;

}

sub has_tag {

  my ($self,$tag) = @_;
  my $ac = $self->annotation();
  return ( scalar $ac->get_Annotations($tag) > 0);

}

sub to_string_callback {

    # get/set callback, using $DEFAULT_CB if nothing is set
    my ($self, $foo) = @_;
    if ($foo) {
      # $foo is callback code ref, self as first arg (so you have access to object data)
      $self->{'_to_string_cb'} = $foo;
    }
    else {
      if (! defined $self->{'_to_string_cb'}) {
        $self->{'_to_string_cb'} =\& Bio::Tree::NodeI::to_string;
      }
    }
    return $self->{'_to_string_cb'};

}

sub to_string {

  my ($self) = @_;
  my $cb = $self->to_string_callback();
  return $cb->($self);

}

sub sequence {

  my ($self,$value) = @_;
  if( defined $value ) {
    $self->throw("object of class ".ref($value)." does not implement ".
        "Bio::SeqI. Too bad.")      unless $value->isa("Bio::SeqI");
    push (@{$self->{'_sequence'}}, $value);
  } 
  #elsif( ! defined $self->{'_sequence'}) 
  #{
  #  $self->{'_sequence'} = Bio::Seq->new();
  #}
  return $self->{'_sequence'};

}

sub has_sequence {

  my ($self) = @_;
  return $self->{'_sequence'} && @{$self->{'_sequence'}};
}


1;

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:

  https://redmine.open-bio.org/projects/bioperl/

Email mirhan@indiana.edu

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