Bio::Tree::AnnotatableNode.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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
 
 

Support

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.

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