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