NAME

Bio::Taxonomy - Conversion used bt the Taxonomy classes

SYNOPSIS

use Bio::Taxonomy;

DESCRIPTION

Provides methods for converting classifications into taxonomic structures.

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();
Function: Builds a new Bio::Taxonomy object
Returns : Bio::Taxonomy
Args    : -method  -> method used to decide classification
                      (none|trust|lookup)
          -ranks   -> what ranks are there

method

Title   : method
Usage   : $obj = taxonomy->method($method);
Function: set or return the method used to decide classification
Returns : $obj
Args    : $obj

classify

Title   : classify
Usage   : @obj[][0-1] = taxonomy->classify($species);
Function: return a ranked classification
Returns : @obj of taxa and ranks as word pairs separated by "@"
Args    : Bio::Species object

level_of_rank

Title   : level_of_rank
Usage   : $obj = taxonomy->level_of_rank($obj);
Function: returns the level of a rank name
Returns : $obj
Args    : $obj

rank_of_number

Title   : rank_of_number
Usage   : $obj = taxonomy->rank_of_number($obj);
Function: returns the rank name of a rank level
Returns : $obj
Args    : $obj

ranks

Title   : ranks
Usage   : @obj = taxonomy->ranks(@obj);
Function: set or return all ranks
Returns : @obj
Args    : @obj