| Bio::Taxonomy::Taxon(3pm) | User Contributed Perl Documentation | Bio::Taxonomy::Taxon(3pm) |
Bio::Taxonomy::Taxon - Generic Taxonomic Entity object
# 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;
Makes a taxonomic unit suitable for use in a taxonomic tree
Dan Kortschak email kortschak@rsbs.anu.edu.au
Sendu Bala: bix@sendu.me.uk
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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)
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.
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.
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.
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
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
Title : ancestor Usage : $taxon->ancestor($newval) Function: Set the Ancestor Returns : value of ancestor Args : newvalue (optional)
Title : branch_length Usage : $obj->branch_length($newval) Function: Example : Returns : value of branch_length Args : newvalue (optional)
Title : description Usage : $obj->description($newval) Function: Returns : value of description Args : newvalue (optional)
Title : rank Usage : $obj->rank($newval) Function: Set the taxonomic rank Returns : taxonomic rank of taxon Args : newvalue (optional)
Title : taxon Usage : $obj->taxon($newtaxon) Function: Set the name of the taxon Example : Returns : name of taxon Args : newtaxon (optional)
Title : id Usage : $obj->id($newval) Function: Example : Returns : value of id Args : newvalue (optional)
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
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)
Title : is_Leaf Usage : if( $node->is_Leaf ) Function: Get Leaf status Returns : boolean Args : none
Title : to_string Usage : my $str = $taxon->to_string() Function: For debugging, provide a taxon as a string Returns : string Args : none
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
Title : invalidate_height Usage : private helper method Function: Invalidate our cached value of the taxon's height in the tree Returns : nothing Args : none
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
Title : has_rank Usage : $obj->has_rank($rank) Function: a method to query ancestors' rank Returns : boolean Args : $rank
Title : has_taxon Usage : $obj->has_taxon($taxon) Function: a method to query ancestors' taxa Returns : boolean Args : Bio::Taxonomy::Taxon object
Title : distance_to_root Usage : $obj->distance_to_root Function: a method to query ancestors' taxa Returns : number of links to root Args :
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
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
| 2018-10-27 | perl v5.26.2 |