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Bio-Phylo-0.17_RC1
River stage two • 9 direct dependents • 18 total dependents
8 ++
/ Bio::Phylo::Adaptor::Bioperl::Node

NAME

Bio::Phylo::Adaptor::Bioperl::Node - Adaptor class for bioperl compatibility

SYNOPSIS

 use Bio::Phylo::Forest::Node;
 use Bio::Phylo::Adaptor;

 my $node = Bio::Phylo::Forest::Node->new;

 $Bio::Phylo::COMPAT = 'Bioperl';

 my $bpnode = Bio::Phylo::Adaptor->new($node);

 print "compatible!" if $bpnode->isa('Bio::Tree::NodeI');

DESCRIPTION

This class wraps Bio::Phylo node objects to give them an interface compatible with bioperl.

METHODS

add_Descendent()
 Title   : add_Descendent
 Usage   : $node->add_Descendant($node);
 Function: Adds a descendent to a node
 Returns : number of current descendents for this node
 Args    : Bio::Node::NodeI
each_Descendent()
 Title   : each_Descendent
 Usage   : my @nodes = $node->each_Descendent;
 Function: all the descendents for this Node (but not their descendents 
                                              i.e. not a recursive fetchall)
 Returns : Array of Bio::Tree::NodeI objects
 Args    : none
get_all_Descendents()
 Title   : get_all_Descendents($sortby)
 Usage   : my @nodes = $node->get_all_Descendents;
 Function: Recursively fetch all the nodes and their descendents
           *NOTE* This is different from each_Descendent
 Returns : Array or Bio::Tree::NodeI objects
 Args    : $sortby [optional] "height", "creation" or coderef to be used
           to sort the order of children nodes.
is_Leaf()
 Title   : is_Leaf
 Usage   : if( $node->is_Leaf ) 
 Function: Get Leaf status
 Returns : boolean
 Args    : none
descendent_count()
 Title   : descendent_count
 Usage   : my $count = $node->descendent_count;
 Function: Counts the number of descendents a node has 
           (and all of their subnodes)
 Returns : integer
 Args    : none
to_string()
 Title   : to_string
 Usage   : my $str = $node->to_string()
 Function: For debugging, provide a node as a string
 Returns : string
 Args    : none
height()
 Title   : height
 Usage   : my $len = $node->height
 Function: Returns the height of the tree starting at this
           node.  Height is the maximum branchlength.
 Returns : The longest length (weighting branches with branch_length) to a leaf
 Args    : none
branch_length()
 Title   : branch_length
 Usage   : $obj->branch_length()
 Function: Get/Set the branch length
 Returns : value of branch_length
 Args    : newvalue (optional)
id()
 Title   : id
 Usage   : $obj->id($newval)
 Function: The human readable identifier for the node 
 Returns : value of human readable id
 Args    : newvalue (optional)
internal_id()
 Title   : internal_id
 Usage   : my $internalid = $node->internal_id
 Function: Returns the internal unique id for this Node
 Returns : unique id
 Args    : none
description()
 Title   : description
 Usage   : $obj->description($newval)
 Function: Get/Set the description string
 Returns : value of description
 Args    : newvalue (optional)
bootstrap()
 Title   : bootstrap
 Usage   : $obj->bootstrap($newval)
 Function: Get/Set the bootstrap value
 Returns : value of bootstrap
 Args    : newvalue (optional)
ancestor()
 Title   : ancestor
 Usage   : my $node = $node->ancestor;
 Function: Get/Set the ancestor node pointer for a Node
 Returns : Null if this is top level node
 Args    : none
invalidate_height()
 Title   : invalidate_height
 Usage   : private helper method
 Function: Invalidate our cached value of the node height in the tree
 Returns : nothing
 Args    : none
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

SEE ALSO

Bio::Tree::NodeI

Bio::Phylo::Adaptor::Bioperl::Node is an adaptor that makes Bio::Phylo nodes compatible with the Bio::Tree::NodeI interface.

Bio::Phylo::Manual

Also see the manual: Bio::Phylo::Manual.

FORUM

CPAN hosts a discussion forum for Bio::Phylo. If you have trouble using this module the discussion forum is a good place to start posting questions (NOT bug reports, see below): http://www.cpanforum.com/dist/Bio-Phylo

BUGS

Please report any bugs or feature requests to bug-bio-phylo@rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Phylo. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes. Be sure to include the following in your request or comment, so that I know what version you're using:

$Id: Node.pm 4162 2007-07-11 01:35:39Z rvosa $

AUTHOR

Rutger A. Vos,

email: rvosa@sfu.ca
web page: http://www.sfu.ca/~rvosa/

ACKNOWLEDGEMENTS

The author would like to thank Jason Stajich for many ideas borrowed from BioPerl http://www.bioperl.org, and CIPRES http://www.phylo.org and FAB* http://www.sfu.ca/~fabstar for comments and requests.

COPYRIGHT & LICENSE

Copyright 2005 Rutger A. Vos, All Rights Reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.