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#
#
# BioPerl interface of Bio::Taxnomoy::FactoryI
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Juguang Xiao
#
# You may distribute this module under the same terms as Perl itself
#
# POD documentation - main does before the code
=head1 NAME
Bio::Taxonomy::FactoryI - interface to define how to access NCBI Taxonoy
=head1 DESCRIPTION
NB: This module has been deprecated.
$factory-E<gt>fetch is a general method to fetch Taxonomy by either NCBI
taxid or any types of names.
$factory-E<gt>fetch_parent($taxonomy), returns a Taxonomy that is
one-step higher rank of the taxonomy specified as argument.
$factory-E<gt>fetch_children($taxonomy), reports an array of Taxonomy
those are one-step lower rank of the taxonomy specified as the
argument.
=head1 AUTHOR - Juguang Xiao
juguang@tll.org.sg
=head1 CONTRIBUTORS
Additional contributors' names and emails here
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
package Bio::Taxonomy::FactoryI;
use strict;
use base qw(Bio::Root::Root);
=head2 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'
=cut
sub fetch {
shift->throw_not_implemented;
}
=head2 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
=cut
sub fuzzy_fetch {
shift->throw_not_implemented;
}
=head2 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.
=cut
sub fetch_parent {
shift->throw_not_implemented;
}
=head2 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.
=cut
sub fetch_children {
shift->throw_not_implemented;
}
1;
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