Raw content of Bio::Tree::AlleleNode # $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;