Bio::Taxonomy::FactoryI(3pm)				User Contributed Perl Documentation			      Bio::Taxonomy::FactoryI(3pm)

NAME

       Bio::Taxonomy::FactoryI - interface to define how to access NCBI Taxonoy

DESCRIPTION

       NB: This module has been deprecated.

       $factory->fetch is a general method to fetch Taxonomy by either NCBI taxid or any types of names.

       $factory->fetch_parent($taxonomy), returns a Taxonomy that is one-step higher rank of the taxonomy specified as argument.

       $factory->fetch_children($taxonomy), reports an array of Taxonomy those are one-step lower rank of the taxonomy specified as the argument.

AUTHOR - Juguang Xiao
       juguang@tll.org.sg

CONTRIBUTORS

       Additional contributors' names and emails here

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

   fetch
	 Title:    fetch
	 Usage:    my $taxonomy = $factory->fetch(-taxon_id => 9605);
		   my $taxonomy = $factory->fetch(-common_name => 'mammals');
	 Fuctnion: Fetch taxonomy by taxon_id, common name or scientific name.
	 Returns:  an instance of Bio::Taxonomy
	 Args:	   -taxon_id => NCBI taxonomy ID
		   -common_name => comon name, such as 'human', 'mammals'
		   -scientifc_name => specitic name, such as 'sapiens', 'Mammalia'

   fuzzy_fetch
	 Title:    fuzzy_fetch
	 Usage:    my @taxonomy = $factory->fuzzy_fetch(-name => 'mouse');
	 Function: Fuzzy fetch by name, or any text information found in DB
	 Returns:  an array reference of Bio::Taxonomy objects
	 Args:	   -name => any name, such as common name, variant, scientific name
		   -description, or -desc => any text information

   fetch_parent
	 Title:    fetch_parent
	 Usage:    my $parent_taxonomy = $factory->fetch_parent($taxonomy);
	 Function: Fetch the parent that is one-rank higher than the argument.
	 Returns:  an instance of Bio::Taxonomy, or undef if the arg is the top one.
	 Args:	   a Bio::Taxonomy object.

   fetch_children
	 Title:    fetch_children
	 Usage:    my @children_taxonomy = $factory->fetch_children($taxonomy);
	 Function: Fetch all children those are one-rank lower than the argument.
	 Returns:  an array reference of Bio::Taxonomy objects
	 Args:	   a Bio::Taxonomy object.

perl v5.14.2							    2012-03-02					      Bio::Taxonomy::FactoryI(3pm)