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Bio::Tree::AnnotatableUser(Contributed Perl DocumBio::Tree::AnnotatableNode(3)

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

perl v5.24.1			  2017-07-08	 Bio::Tree::AnnotatableNode(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Mira Han | APPENDIX | Methods for implementing Bio::AnnotatableI | Methods for implementing tag access through Annotation::SimpleValue | Methods for implementing to_string | Methods for accessing Bio::Seq

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