diff variant_effect_predictor/Bio/EnsEMBL/Funcgen/ExperimentalSubset.pm @ 0:21066c0abaf5 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Funcgen/ExperimentalSubset.pm	Fri Aug 03 10:04:48 2012 -0400
@@ -0,0 +1,139 @@
+#
+# Ensembl module for Bio::EnsEMBL::Funcgen::ExperimentalSubset
+#
+# You may distribute this module under the same terms as Perl itself
+
+=head1 NAME
+
+Bio::EnsEMBL::ExperimentalSet - A module to represent ExperimentalSubset object.
+ 
+
+=head1 SYNOPSIS
+
+use Bio::EnsEMBL::Funcgen::ExperimetnalSubset;
+
+my $data_set = Bio::EnsEMBL::Funcgen::ExperimentalSubset->new(
+	                                                         -DBID             => $dbID,
+							 					             -ADAPTOR          => $self,
+                                                             -NAME             => $name,
+                                                             -EXPERIMENTAL_SET => $eset,
+                                                             );
+
+
+
+=head1 DESCRIPTION
+
+An ExperimentalSubset object is a very simple skeleton class to enable storage of associated subset states. As such there
+are only very simple accessor methods for basic information, and there is no namesake adaptor, rather is is handled by the 
+ExperimentalSetAdaptor.
+
+=head1 AUTHOR
+
+This module was created by Nathan Johnson.
+
+This module is part of the Ensembl project: http://www.ensembl.org/
+
+=head1 CONTACT
+
+Post comments or questions to the Ensembl development list: [e-mail]
+
+=head1 METHODS
+
+=cut
+
+use strict;
+use warnings;
+
+package Bio::EnsEMBL::Funcgen::ExperimentalSubset;
+
+use Bio::EnsEMBL::Utils::Argument qw( rearrange );
+use Bio::EnsEMBL::Utils::Exception qw( throw );
+use Bio::EnsEMBL::Funcgen::Storable;
+
+use vars qw(@ISA);
+@ISA = qw(Bio::EnsEMBL::Funcgen::Storable);
+
+
+=head2 new
+
+  Example    : my $eset = Bio::EnsEMBL::Funcgen::ExperimentalSubset->new(
+                                                                        -DBID            => $dbID,
+							 					                        -ADAPTOR         => $self,
+                                                                        -NAME            => $name,
+                                                                        -EXPERIMENTAL_SET => $eset,
+                                                                        );
+
+
+  Description: Constructor for ExperimentalSubset objects.
+  Returntype : Bio::EnsEMBL::Funcgen::ExperimentalSubset
+  Exceptions : Throws if no name defined
+               Throws if CellType or FeatureType are not valid or stored
+  Caller     : General
+  Status     : At risk
+
+=cut
+
+sub new {
+  my $caller = shift;
+	
+  my $class = ref($caller) || $caller;
+	
+  my $self = $class->SUPER::new(@_);
+	
+  #do we need to add $fg_ids to this?  Currently maintaining one feature_group focus.(combi exps?)
+  my ($name, $eset)
+    = rearrange(['NAME', 'EXPERIMENTAL_SET'], @_);
+  
+  
+  throw('Must provide a name argument') if ! defined $name;
+
+  if(!(ref($eset) && 
+	   $eset->isa('Bio::EnsEMBL::Funcgen::ExperimentalSet')
+	   && $eset->dbID())){
+	throw('Must provide a valid stored experimental_set argument');
+  }
+  
+
+  $self->{'name'} = $name;
+  $self->{'experimental_set'} = $eset;
+
+  return $self;
+}
+
+
+=head2 name
+
+  Example    : my $name = $exp_sset->name();
+  Description: Getter for the name of this ExperimentalSubset.
+  Returntype : string
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub name {
+  my $self = shift;
+  return $self->{'name'};
+}
+
+=head2 experimental_set
+
+  Example    : my $eset = $exp_sset->experimental_set();
+  Description: Getter for the experimental_set attribute of this ExperimentalSubset.
+  Returntype : Bio::EnsEMBL::Funcgen::ExperimentalSet
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub experimental_set {
+  my $self = shift;
+  return $self->{'experimental_set'};
+}
+
+
+
+1;
+