diff variant_effect_predictor/Bio/EnsEMBL/Compara/Family.pm @ 0:21066c0abaf5 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Compara/Family.pm	Fri Aug 03 10:04:48 2012 -0400
@@ -0,0 +1,70 @@
+package Bio::EnsEMBL::Compara::Family;
+
+use strict;
+use Bio::EnsEMBL::Utils::Argument;
+use Bio::EnsEMBL::Utils::Exception;
+
+use base ('Bio::EnsEMBL::Compara::AlignedMemberSet');
+
+=head2 new
+
+  Arg [1]    : 
+  Example    : 
+  Description: 
+  Returntype : Bio::EnsEMBL::Compara::Family (but without members; caller has to fill using
+               add_member)
+  Exceptions : 
+  Caller     : 
+
+=cut
+
+sub new {
+  my($class,@args) = @_;
+  
+  my $self = $class->SUPER::new(@args);
+  
+  if (scalar @args) {
+     #do this explicitly.
+     my ($description_score) = rearrange([qw(DESCRIPTION_SCORE)], @args);
+      
+      $description_score && $self->description_score($description_score);
+  }
+  
+  return $self;
+}   
+
+=head2 description_score
+
+  Arg [1]    : 
+  Example    : 
+  Description: 
+  Returntype : 
+  Exceptions : 
+  Caller     : 
+
+=cut
+
+sub description_score {
+  my $self = shift;
+  $self->{'_description_score'} = shift if(@_);
+  return $self->{'_description_score'};
+}
+
+
+=head2 deep_copy
+
+  Description: Returns a copy of $self. All the members are themselves copied
+  Returntype : Bio::EnsEMBL::Compara::Family
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub deep_copy {
+    my $self = shift;
+    my $copy = $self->SUPER::deep_copy();
+    $copy->description_score($self->description_score);
+    return $copy;
+}
+
+1;