diff variant_effect_predictor/Bio/EnsEMBL/IdMapping/TinyTranslation.pm @ 0:21066c0abaf5 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/IdMapping/TinyTranslation.pm	Fri Aug 03 10:04:48 2012 -0400
@@ -0,0 +1,130 @@
+=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
+
+=head1 NAME
+
+Bio::EnsEMBL::IdMapping::TinyTranslation - lightweight translation object
+
+=head1 SYNOPSIS
+
+  if ( my $tl = $tr->translation ) {
+    my $lightweight_tl =
+      Bio::EnsEMBL::IdMapping::TinyTranslation->new_fast( [
+        $tl->dbID,          $tl->stable_id,
+        $tl->version,       $tl->created_date,
+        $tl->modified_date, $tr->dbID,
+        $tr->translate->seq, ( $tr->is_known ? 1 : 0 ),
+      ] );
+  }
+
+=head1 DESCRIPTION
+
+This is a lightweight translation object for the stable Id mapping. See
+the documentation in TinyFeature for general considerations about its
+design.
+
+=head1 METHODS
+
+  transcript_id
+  seq
+  is_known
+
+=cut
+
+package Bio::EnsEMBL::IdMapping::TinyTranslation;
+
+# internal data structure (array indices):
+#
+#  0-4 see TinyFeature
+#  5  transcript_id
+#  6  seq
+#  7  is_known
+
+
+use strict;
+use warnings;
+no warnings 'uninitialized';
+
+use Bio::EnsEMBL::IdMapping::TinyFeature;
+our @ISA = qw(Bio::EnsEMBL::IdMapping::TinyFeature);
+
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
+
+
+=head2 transcript_id
+
+  Arg[1]      : (optional) Int - the transcript internal Id ("dbID")
+  Description : Getter/setter for the transcript internal Id this translation is
+                attached to.
+  Return type : Int
+  Exceptions  : none
+  Caller      : general
+  Status      : At Risk
+              : under development
+
+=cut
+
+sub transcript_id {
+  my $self = shift;
+  $self->[5] = shift if (@_);
+  return $self->[5];
+}
+
+
+=head2 seq
+
+  Arg[1]      : (optional) String - the translation's sequence
+  Description : Getter/setter for the translation's sequence.
+  Return type : String
+  Exceptions  : none
+  Caller      : general
+  Status      : At Risk
+              : under development
+
+=cut
+
+sub seq {
+  my $self = shift;
+  $self->[6] = shift if (@_);
+  return $self->[6];
+}
+
+
+=head2 is_known
+
+  Arg[1]      : (optional) Boolean - the translation's "known" status
+  Description : Getter/setter for the translation's "known" status.
+  Return type : Boolean
+  Exceptions  : none
+  Caller      : general
+  Status      : At Risk
+              : under development
+
+=cut
+
+sub is_known {
+  my $self = shift;
+  $self->[7] = shift if (@_);
+  return $self->[7];
+}
+
+
+1;
+