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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/SplicingTranscriptPair.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,106 @@
+=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::SplicingTranscriptPair - Object representing an alternative splicing transcript pair
+
+=head1 SYNOPSIS
+
+  my $ase = Bio::EnsEMBL::SplicingTranscriptPair->new(
+    -START  => 123,
+    -END    => 1045,
+    -TRANSCRIPT_ID_1 => $tran1->dbID,
+    -TRANSCRIPT_ID_2 => %tran2->dbID
+  );
+
+=head1 DESCRIPTION
+
+A representation of an Alternative Splicing Transcrript Pair within the Ensembl system.
+
+=head1 METHODS
+
+=cut
+
+package Bio::EnsEMBL::SplicingTranscriptPair;
+
+use strict;
+
+use POSIX;
+use Bio::EnsEMBL::Feature;
+use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
+
+use vars qw(@ISA);
+@ISA = qw(Bio::EnsEMBL::Feature);
+
+
+
+
+sub transcript_id_1{
+  my $self = shift;
+  $self->{'transcript_id_1'} = shift if (@_);
+
+  if (defined $self->{'transcript_id_1'}) {
+    return $self->{'transcript_id_1'};
+  }
+
+  return undef;
+}
+
+sub transcript_id_2{
+  my $self = shift;
+  $self->{'transcript_id_2'} = shift if (@_);
+
+  if (defined $self->{'transcript_id_2'}) {
+    return $self->{'transcript_id_2'};
+  }
+
+  return undef;
+}
+
+
+sub start{
+  my $self = shift;
+  $self->{'start'} = shift if (@_);
+
+  if (defined $self->{'start'}) {
+    return $self->{'start'};
+  }
+
+  return undef;
+}
+
+sub end{
+  my $self = shift;
+  $self->{'end'} = shift if (@_);
+
+  if (defined $self->{'end'}) {
+    return $self->{'end'};
+  }
+
+  return undef;
+}
+
+
+
+
+
+1;