/ 
BioPerl-1.007000_005
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Tree::AnnotatableNode

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:

https://github.com/bioperl/bioperl-live/issues

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