diff variant_effect_predictor/Bio/EnsEMBL/Variation/DBSQL/MetaContainer.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Variation/DBSQL/MetaContainer.pm	Thu Apr 11 02:01:53 2013 -0400
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+=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]>.
+
+=cut
+
+#
+# EnsEMBL module for Bio::EnsEMBL::Variation::DBSQL::MetaContainer
+#
+# Cared for by Daniel Rios
+#
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+  Bio::EnsEMBL::Variation::DBSQL::MetaContainer - 
+  Encapsulates all access to variation database meta information
+
+=head1 SYNOPSIS
+
+  my $meta_container = $db_adaptor->get_MetaContainer();
+
+  my $default_population = $meta_container->get_default_LDPopulation();
+
+=head1 DESCRIPTION
+
+  An object that encapsulates specific access to variation db meta data
+
+=head1 METHODS
+
+=cut
+
+package Bio::EnsEMBL::Variation::DBSQL::MetaContainer;
+
+use vars qw(@ISA);
+use strict;
+
+use Bio::EnsEMBL::DBSQL::BaseMetaContainer;
+use Bio::EnsEMBL::Utils::Exception;
+
+
+@ISA = qw(Bio::EnsEMBL::DBSQL::BaseMetaContainer);
+
+
+sub get_schema_version {
+  my $self = shift;
+
+  my $arrRef = $self->list_value_by_key( 'schema_version' );
+
+  if( @$arrRef ) {
+    my ($ver) = ($arrRef->[0] =~ /^\s*(\d+)\s*$/);
+    if(!defined($ver)){ # old style format
+      return 0;
+    }
+    return $ver;
+  } else {
+    warning("Please insert meta_key 'schema_version' " .
+         "in meta table at variation db.\n");
+  }
+  return 0;
+}
+
+sub ploidy {
+  my $self = shift;
+  
+  my $values = $self->list_value_by_key('ploidy');
+  
+  # default to 2
+  return scalar @$values ? $values->[0] : 2;
+}
+
+1;