/ 
bioperl-1.2.2
/ Bio::Taxonomy::Taxon

NAME

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

SYNOPSIS

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

my $taxon = new Bio::Taxonomy::Taxon();
$taxon->add_Descendents($nodeL);
$taxon->add_Descendents($nodeR);

$species = $taxon->species;

DESCRIPTION

Makes a taxonomic unit suitable for use in a taxonomic tree

CONTACT

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

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 = new Bio::Taxonomy::Taxon();
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   : $taxon->add_Descendant($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:
Example :
Returns : value of description
Args    : newvalue (optional)

rank

Title   : rank
Usage   : $obj->rank($newval)
Function: Set the taxonomic rank
Example :
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