Added functionality to add and get unconventional transcripts associated with this gene.

modules/Bio/EnsEMBL/Gene.pm

@@ -1076,6 +1076,89 @@ sub get_all_regulatory_features {
 }
 
 
+=head2 add_unconventional_transcript_association
+
+  Arg [1]    : Bio::EnsEMBL::Transcript $trans
+               The transcript to associate with the gene, in an unconventional manner.
+  Arg [2]    : String $type
+               The type of association between this gene and this transcript, e.g.
+               "antisense","sense_intronic","sense_overlaping_exonic","chimeric_sense_exonic"
+  Example    : my $transcript = Bio::EnsEMBL::Transcript->new(...);
+               $gene->add_unconventional_transcript_association($transcript, "antisense");
+  Description: Associate a transcript with this gene in a way that is
+               non-conventional.
+  Returntype : none
+  Exceptions : none
+  Caller     : general
+  Status     : At Risk.
+
+=cut
+
+sub add_unconventional_transcript_association {
+
+   my ($self, $transcript, $type) = @_;
+
+   if( !ref $transcript || ! $transcript->isa("Bio::EnsEMBL::Transcript") ) {
+       throw("$transcript is not a Bio::EnsEMBL::Transcript!");
+   }
+
+   my $uta = Bio::EnsEMBL::UnconventionalTranscriptAssociation->new($transcript, $self, $type);
+   $self->{'_unconventional_transcript_array'} ||= [];
+   push(@{$self->{'_unconventional_transcript_array'}}, $uta);
+
+}
+
+
+=head2 get_all_unconventional_transcript_associations
+
+  Arg [1]    : (optional) String - Only get transcripts where the association
+               between this gene and the transcripts is of a certain type.
+  Example    : my @transcripts = @{ $gene->get_all_unconventional_transcript_associations, "antisense" };
+  Description: Returns the unconventional transcripts associated with this gene.
+  Returntype : Listref of Bio::EnsEMBL::UnconventionalTranscriptAssociation objects
+  Exceptions : none
+  Caller     : general
+  Status     : At risk.
+
+=cut
+
+sub get_all_unconventional_transcript_associations {
+
+  my ($self, $type) = @_;
+
+  if( ! exists $self->{'_unconventional_transcript_array'} ) {
+    $self->{'_unconventional_transcript_array'} = [];
+    if( defined $self->adaptor() ) {
+      my $utaa = $self->adaptor()->db()->get_UnconventionalTranscriptAssociationAdaptor();
+      my $utas = $utaa->fetch_all_by_gene( $self, $type );
+      $self->{'_unconventional_transcript_array'} = $utas;
+    }
+  }
+
+  return $self->{'_unconventional_transcript_array'};
+}
+
+=head2 remove_unconventional_transcript_associations
+
+  Args       : None
+  Example    : $gene->remove__unconventional_transcript_associations();
+  Description: Returns the unconventional transcripts associated with this gene.
+  Returntype : Listref of Bio::EnsEMBL::UnconventionalTranscriptAssociation objects
+  Exceptions : none
+  Caller     : general
+  Status     : At risk.
+
+=cut
+
+sub remove_unconventional_transcript_associations {
+
+  my $self = shift;
+
+  $self->{'_unconventional_transcript_array'} = [];
+
+}
+
+
 ###########################
 # DEPRECATED METHODS FOLLOW
 ###########################