Module:Bio::Tree::AnnotatableNode

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Bio::Tree::AnnotatableNode
PDoc Bio::Tree::AnnotatableNode
CPAN Bio::Tree::AnnotatableNode
metaCPAN Bio::Tree::AnnotatableNode



this is a temporary document, it will be gone once the PDoc link is in work.

NAME

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

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.

FEEDBACK

 Mailing Lists
   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
 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:
     http://bugzilla.open-bio.org/

AUTHOR - Mira Han

   Email mirhan@indiana.edu

APPENDIX

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

 annotation
    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 L<Bio::AnnotationCollectionI> and L<Bio::Annotation::Collection>
   for more information

Methods for implementing tag access through Annotation::SimpleValue

 add_tag_value
    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
 remove_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
 remove_all_tags
    Title   : remove_all_tags
    Usage   : $node->remove_all_tags()
    Function: Removes all tags 
    Returns : None
    Args    : None
 get_all_tags
    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
 get_tag_values
    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
 has_tag
    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

 to_string_callback
    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

 sequence
    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 L<Bio::SeqI> and L<Bio::Seq>
   for more information
 has_sequence
    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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