Summary

Bio::Tree::AlleleNode - DESCRIPTION of Object

Package variables

Included modules

Inherit

Bio::Tree::Node

Synopsis

Give standard usage here

Description

Describe the object here

Methods

Methods description

 Title   : new
 Usage   : my $obj = new Bio::Tree::AlleleNode();
 Function: Builds a new Bio::Tree::AlleleNode object 
 Returns : Bio::Tree::AlleleNode
 Args    :

 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

 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

 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

 Title   : purge_markers
 Usage   : $node->purge_markers;
 Function: Reset the markers and alleles
 Returns : none
 Args    : none

Methods code

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;

}

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;
   }

}

sub get_alleles {

   my ($self,$marker) = @_;
   if( defined $self->{'_data'}->{$marker} ) { 
       return @{$self->{'_data'}->{$marker}};
   }
   return ();

}

sub get_marker_names {

   my ($self) = @_;
   return keys %{$self->{'_data'}};

}

sub purge_markers {

   my ($self) = @_;
   $self->{'_data'} = {};
   return;

}

General documentation

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