Bio::Tree::AnnotatableNode(3pm) User Contributed Perl Documentation Bio::Tree::AnnotatableNode(3pm)
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
" 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://redmine.open-bio.org/projects/bioperl/
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
perl v5.14.2 2012-03-02 Bio::Tree::AnnotatableNode(3pm)