Bio::Taxonomy::Taxon - Generic Taxonomic Entity object 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; Makes a taxonomic unit suitable for use in a taxonomic tree Dan Kortschak email kortschak@rsbs.anu.edu.au 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