Bio::Tree::AnnotatableNode(3) A Tree Node with support for annotation


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();
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


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


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Please direct usage questions or support issues to the mailing list:

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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.

Reporting Bugs

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:

AUTHOR - Mira Han

Email [email protected]


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


 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)

Methods for implementing Bio::AnnotatableI


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

Methods for implementing tag access through Annotation::SimpleValue


 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

Methods for implementing to_string


 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

Methods for accessing Bio::Seq


 Title   : sequence
 Usage   : $ann = $node->sequence or 
 Function: Gets or sets the sequence
 Returns : array reference of Bio::SeqI objects
 Args    : None or Bio::SeqI object
See L<Bio::SeqI> and L<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