diff variant_effect_predictor/Bio/EnsEMBL/Funcgen/InputSubset.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Funcgen/InputSubset.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,210 @@
+#
+# Ensembl module for Bio::EnsEMBL::Funcgen::InputSubset
+#
+
+
+=head1 LICENSE
+
+  Copyright (c) 1999-2012 The European Bioinformatics Institute and
+  Genome Research Limited.  All rights reserved.
+
+  This software is distributed under a modified Apache license.
+  For license details, please see
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <[e-mail]>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <[e-mail]>.
+
+
+=head1 NAME
+
+Bio::EnsEMBL::InputSubset - A module to represent InputSubset object.
+ 
+
+=head1 SYNOPSIS
+
+use Bio::EnsEMBL::Funcgen::InputSubset;
+
+my $input_subset = Bio::EnsEMBL::Funcgen::InputSubset->new
+                    (
+                     -DBID        => $dbID,
+                     -ADAPTOR     => $self,
+                     -NAME        => $name,
+                     -INPUT_SET   => $iset,
+                     -archive_id  => $archive_id,
+                     -display_url => $display_url,
+                     -replicate   => $iss_rep,
+                     -is_control  => $is_control,
+                    );
+
+
+
+=head1 DESCRIPTION
+
+An InputSubset object represents an individual distinct input within a given InputSet. This 
+normally translates to single file or replicate. There is no dedicated InputSubsetAdaptor,
+store and fetch functionality is embedded within the InputSetAdaptor.
+
+=cut
+
+use strict;
+use warnings;
+
+package Bio::EnsEMBL::Funcgen::InputSubset;
+
+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::InputSubset->new
+                            (
+                             -DBID        => $dbID,
+                             -ADAPTOR     => $self,
+                             -NAME        => $name,
+                             -INPUT_SET   => $iset,
+                             -archive_id  => $archive_id,
+                             -display_url => $display_url,
+                             -replicate   => $iss_rep,
+                             -is_control  => $is_control,
+                            );
+
+
+  Description: Constructor for InputSubset objects.
+  Returntype : Bio::EnsEMBL::Funcgen::InputSubset
+  Exceptions : Throws if no name defined
+  Caller     : InputSetAdaptor
+  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, $archive_id,
+	 $display_url, $rep, $is_control)
+    = rearrange(['NAME', 'INPUT_SET', 'ARCHIVE_ID', 
+				 'DISPLAY_URL', 'REPLICATE', 'IS_CONTROL'], @_);
+  
+  
+  throw('Must provide a name argument') if ! defined $name;
+
+  if(!(ref($eset) && 
+	   $eset->isa('Bio::EnsEMBL::Funcgen::InputSet')
+	   && $eset->dbID())){
+	throw('Must provide a valid stored input_set argument');
+  }
+  
+
+  $self->{name}        = $name;
+  $self->{input_set}   = $eset;
+  $self->{archive_id}  = $archive_id;
+  $self->{display_url} = $display_url;
+  $self->{replicate}   = $rep;
+  $self->{is_control}  = $is_control;
+
+  return $self;
+}
+
+
+=head2 name
+
+  Example    : my $name = $exp_sset->name();
+  Description: Getter for the name of this InputSubset.
+  Returntype : String
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub name { return $_[0]->{name}; }
+
+
+=head2 input_set
+
+  Example    : my $input_set = $input_sset->input_set;
+  Description: Getter for the input_set attribute of this InputSubset.
+  Returntype : Bio::EnsEMBL::Funcgen::InputSet
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub input_set {  return $_[0]->{input_set}; }
+
+
+=head2 archive_id
+
+  Example    : my $archive_id = $inp_sset->archive_id;
+  Description: Getter for the archive of this InputSubset.
+  Returntype : String
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub archive_id { return $_[0]->{archive_id}; }
+
+
+=head2 display_url
+
+  Example    : my $url = $inp_sset->displau_url;
+  Description: Getter for the display_url of this InputSubset.
+  Returntype : String
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub display_url{ return $_[0]->{display_url}; }
+
+
+=head2 replicate
+
+  Example    : my $rep = $inp_sset->replicate;
+  Description: Getter for the replicate attribute of this InputSubset.
+  Returntype : Integer
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub replicate { return $_[0]->{replicate}; }
+
+
+=head2 is_control
+
+  Example    : if($input_sset->is_control){ # Do some control specific stuff here }
+  Description: Getter for the is_control attribute of this InputSubset.
+  Returntype : Boolean
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub is_control { return $_[0]->{is_control}; }
+
+1;
+