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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/SplicingEventFeature.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,143 @@
+=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::SplicingEventFeature - Object representing an alternative splicing event
+
+=head1 SYNOPSIS
+
+  my $ase = Bio::EnsEMBL::SplicingEventFeature->new(
+    -START  => 123,
+    -END    => 1045,
+    -EXON_ID => $exon->dbID
+  );
+
+  # set some additional attributes
+  $ase->type('flanking_exon');
+
+=head1 DESCRIPTION
+
+A representation of an Alternative Splicing Event Feature within the Ensembl system.
+
+=head1 METHODS
+
+=cut
+
+package Bio::EnsEMBL::SplicingEventFeature;
+
+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);
+
+
+
+## Add to gene get_all_splicing_events
+
+
+
+sub exon_id{
+  my $self = shift;
+  $self->{'exon_id'} = shift if (@_);
+
+  if (defined $self->{'exon_id'}) {
+    return $self->{'exon_id'};
+  }
+
+  return undef;
+}
+
+sub transcript_id{
+  my $self = shift;
+  $self->{'transcript_id'} = shift if (@_);
+
+  if (defined $self->{'transcript_id'}) {
+    return $self->{'transcript_id'};
+  }
+
+  return undef;
+}
+
+sub feature_order{
+  my $self = shift;
+  $self->{'feature_order'} = shift if (@_);
+
+  if (defined $self->{'feature_order'}) {
+    return $self->{'feature_order'};
+  }
+
+  return undef;
+}
+
+sub type{
+  my $self = shift;
+  $self->{'type'} = shift if (@_);
+
+  if (defined $self->{'type'}) {
+    return $self->{'type'};
+  }
+
+  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;
+}
+
+
+sub transcript_association{
+  my $self = shift;
+  $self->{'transcript_association'} = shift if (@_);
+
+  if (defined $self->{'transcript_association'}) {
+    return $self->{'transcript_association'};
+  }
+
+  return undef;
+}
+
+
+
+
+1;