Bio::Taxonomy::Taxon(3pm)				User Contributed Perl Documentation				 Bio::Taxonomy::Taxon(3pm)

NAME

       Bio::Taxonomy::Taxon - Generic Taxonomic Entity object

SYNOPSIS

	   # NB: This module is deprecated. Use Bio::Taxon instead.

	   use Bio::Taxonomy::Taxon;
	   my $taxonA = Bio::Taxonomy::Taxon->new();
	   my $taxonL = Bio::Taxonomy::Taxon->new();
	   my $taxonR = Bio::Taxonomy::Taxon->new();

	   my $taxon = Bio::Taxonomy::Taxon->new();
	   $taxon->add_Descendents($taxonL);
	   $taxon->add_Descendents($taxonR);

	   my $species = $taxon->species;

DESCRIPTION

       Makes a taxonomic unit suitable for use in a taxonomic tree

AUTHOR

       Dan Kortschak email kortschak@rsbs.anu.edu.au

CONTRIBUTORS

       Sendu Bala: bix@sendu.me.uk

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::Taxonomy::Taxon->new();
	Function: Builds a new Bio::Taxonomy::Taxon object
	Returns : Bio::Taxonomy::Taxon
	Args	: -descendents	 => array pointer to descendents (optional)
		  -branch_length => branch length [integer] (optional)
		  -taxon     => taxon
		  -id	  => unique taxon id for node (from NCBI's list preferably)
		  -rank  => the taxonomic level of the node (also from NCBI)

   add_Descendent
	Title	: add_Descendent
	Usage	: $taxon->add_Descendent($taxon);
	Function: Adds a descendent to a taxon
	Returns : number of current descendents for this taxon
	Args	: Bio::Taxonomy::Taxon
		  boolean flag, true if you want to ignore the fact that you are
		  adding a second node with the same unique id (typically memory
		  location reference in this implementation).  default is false and
		  will throw an error if you try and overwrite an existing node.

   each_Descendent
	Title	: each_Descendent($sortby)
	Usage	: my @taxa = $taxon->each_Descendent;
	Function: all the descendents for this taxon (but not their descendents
						     i.e. not a recursive fetchall)
	Returns : Array of Bio::Taxonomy::Taxon objects
	Args	: $sortby [optional] "height", "creation" or coderef to be used
		  to sort the order of children taxa.

   remove_Descendent
	Title	: remove_Descendent
	Usage	: $taxon->remove_Descedent($taxon_foo);
	Function: Removes a specific taxon from being a Descendent of this taxon
	Returns : nothing
	Args	: An array of Bio::taxonomy::Taxon objects which have be previously
		  passed to the add_Descendent call of this object.

   remove_all_Descendents
	Title	: remove_all_Descendents
	Usage	: $taxon->remove_All_Descendents()
	Function: Cleanup the taxon's reference to descendents and reset
		  their ancestor pointers to undef, if you don't have a reference
		  to these objects after this call they will be cleanedup - so
		  a get_nodes from the Tree object would be a safe thing to do first
	Returns : nothing
	Args	: none

   get_Descendents
	Title	: get_Descendents
	Usage	: my @taxa = $taxon->get_Descendents;
	Function: Recursively fetch all the taxa and their descendents
		  *NOTE* This is different from each_Descendent
	Returns : Array or Bio::Taxonomy::Taxon objects
	Args	: none

   ancestor
	Title	: ancestor
	Usage	: $taxon->ancestor($newval)
	Function: Set the Ancestor
	Returns : value of ancestor
	Args	: newvalue (optional)

   branch_length
	Title	: branch_length
	Usage	: $obj->branch_length($newval)
	Function:
	Example :
	Returns : value of branch_length
	Args	: newvalue (optional)

   description
	Title	: description
	Usage	: $obj->description($newval)
	Function:
	Returns : value of description
	Args	: newvalue (optional)

   rank
	Title	: rank
	Usage	: $obj->rank($newval)
	Function: Set the taxonomic rank
	Returns : taxonomic rank of taxon
	Args	: newvalue (optional)

   taxon
	Title	: taxon
	Usage	: $obj->taxon($newtaxon)
	Function: Set the name of the taxon
	Example :
	Returns : name of taxon
	Args	: newtaxon (optional)

   id
	Title	: id
	Usage	: $obj->id($newval)
	Function:
	Example :
	Returns : value of id
	Args	: newvalue (optional)

   internal_id
	Title	: internal_id
	Usage	: my $internalid = $taxon->internal_id
	Function: Returns the internal unique id for this taxon
		  (a monotonically increasing number for this in-memory implementation
		   but could be a database determined unique id in other
		   implementations)
	Returns : unique id
	Args	: none

   _creation_id
	Title	: _creation_id
	Usage	: $obj->_creation_id($newval)
	Function: a private method signifying the internal creation order
	Returns : value of _creation_id
	Args	: newvalue (optional)

   is_Leaf
	Title	: is_Leaf
	Usage	: if( $node->is_Leaf )
	Function: Get Leaf status
	Returns : boolean
	Args	: none

   to_string
	Title	: to_string
	Usage	: my $str = $taxon->to_string()
	Function: For debugging, provide a taxon as a string
	Returns : string
	Args	: none

   height
	Title	: height
	Usage	: my $len = $taxon->height
	Function: Returns the height of the tree starting at this
		  taxon.  Height is the maximum branchlength.
	Returns : The longest length (weighting branches with branch_length) to a leaf
	Args	: none

   invalidate_height
	Title	: invalidate_height
	Usage	: private helper method
	Function: Invalidate our cached value of the taxon's height in the tree
	Returns : nothing
	Args	: none

   classify
	Title	: classify
	Usage	: @obj->classify()
	Function: a method to return the classification of a species
	Returns : name of taxon and ancestor's taxon recursively
	Args	: boolean to specify whether we want all taxa not just ranked
		  levels

   has_rank
	Title	: has_rank
	Usage	: $obj->has_rank($rank)
	Function: a method to query ancestors' rank
	Returns : boolean
	Args	: $rank

   has_taxon
	Title	: has_taxon
	Usage	: $obj->has_taxon($taxon)
	Function: a method to query ancestors' taxa
	Returns : boolean
	Args	: Bio::Taxonomy::Taxon object

   distance_to_root
	Title	: distance_to_root
	Usage	: $obj->distance_to_root
	Function: a method to query ancestors' taxa
	Returns : number of links to root
	Args	:

   recent_common_ancestor
	Title	: recent_common_ancestor
	Usage	: $obj->recent_common_ancestor($taxon)
	Function: a method to query find common ancestors
	Returns : Bio::Taxonomy::Taxon of query or undef if no ancestor of rank
	Args	: Bio::Taxonomy::Taxon

   species
	Title	: species
	Usage	: $obj=$taxon->species;
	Function: Returns a Bio::Species object reflecting the taxon's tree position
	Returns : a Bio::Species object
	Args	: none

perl v5.14.2							    2012-03-02						 Bio::Taxonomy::Taxon(3pm)