Christopher Fields > BioPerl-1.6.922 > Bio::Tree::AnnotatableNode



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Module Version: 1.006922   Source   Latest Release: BioPerl-1.6.924


Bio::Tree::AnnotatableNode - 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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AUTHOR - Mira Han ^



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 
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