Raw content of Bio::Tree::AlleleNode
<![CDATA[# $Id: AlleleNode.pm,v 1.4 2002/10/22 07:45:24 lapp Exp $
#
# BioPerl module for Bio::Tree::AlleleNode
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tree::AlleleNode - DESCRIPTION of Object
=head1 SYNOPSIS
Give standard usage here
=head1 DESCRIPTION
Describe the object here
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Jason Stajich
Email jason@bioperl.org
Describe contact details here
=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
# Let the code begin...
package Bio::Tree::AlleleNode;
use vars qw(@ISA);
use strict;
use Bio::Tree::Node;
@ISA = qw(Bio::Tree::Node );
=head2 new
Title : new
Usage : my $obj = new Bio::Tree::AlleleNode();
Function: Builds a new Bio::Tree::AlleleNode object
Returns : Bio::Tree::AlleleNode
Args :
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($alleles) = $self->_rearrange([qw(ALLELES)], @args);
$self->{'_data'} = {};
if( defined $alleles ) {
if( ref($alleles) !~ /HASH/i ) {
$self->warn("Must specify a valid HASH reference for the -alleles value...Ignoring initializing input");
} else {
foreach my $mkr ( keys %{$alleles} ) {
$self->add_alleles($mkr,@{$alleles->{$mkr}});
}
}
}
return $self;
}
=head2 add_alleles
Title : add_alleles
Usage : $node->add_alleles($mkr,@alleles);
Function: Adds allele(s) for $mkr, @alleles can be a single or
multiple alleles. If the same marker is added more than one, the
previous value will be overwritten with a warning.
Returns : none
Args : $marker => marker name
@alleles => alleles for the marker
=cut
sub add_alleles{
my ($self,$marker,@alleles) = @_;
if( ! defined $marker || $marker eq '' ) {
$self->warn("must specify a valid marker name for add_alleles");
return;
}
if( $self->{'_data'}->{$marker} ) {
$self->warn("Overwriting value of $marker");
}
$self->{'_data'}->{$marker} = []; # reset the array ref
foreach my $a ( sort @alleles ) {
next if ! defined $a; # skip undef alleles
push @{$self->{'_data'}->{$marker}},$a;
}
}
=head2 get_alleles
Title : get_alleles
Usage : my @alleles = $node->get_alleles($marker);
Function: Return the alleles for a marker $marker
Returns : Array of Alleles for a marker or empty array
Args : $marker name
=cut
sub get_alleles{
my ($self,$marker) = @_;
if( defined $self->{'_data'}->{$marker} ) {
return @{$self->{'_data'}->{$marker}};
}
return ();
}
=head2 get_marker_names
Title : get_marker_names
Usage : my @names =$node->get_marker_names();
Function: Return the names of the markers that have been added to this node
Returns : List of Marker Names
Args : none
=cut
sub get_marker_names{
my ($self) = @_;
return keys %{$self->{'_data'}};
}
=head2 purge_markers
Title : purge_markers
Usage : $node->purge_markers;
Function: Reset the markers and alleles
Returns : none
Args : none
=cut
sub purge_markers{
my ($self) = @_;
$self->{'_data'} = {};
return;
}
1;
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