removed more deprecated methods

modules/Bio/EnsEMBL/DBSQL/ProxyDnaAlignFeatureAdaptor.pm

@@ -154,12 +154,4 @@ sub remove {
   return $self->{'_primary_adaptor'}->remove($feature);
 }
 
-
-
-
-
-
-
-
-
-
+1;

modules/Bio/EnsEMBL/DBSQL/ProxyGeneAdaptor.pm

@@ -74,28 +74,6 @@ sub fetch_all_by_Slice {
 
 
 
-=head2 fetch_by_Slice
-
-  Arg [1]    : none
-  Example    : none
-  Description: DEPRECATED use fetch_all_by_Slice instead
-  Returntype : none
-  Exceptions : none
-  Caller     : none
-
-=cut
-
-sub fetch_by_Slice {
-  my ($self, @args) = @_;
-
-  $self->warn("fetch_by_Slice has been renamed fetch_all_by_Slice\n" . caller);
-
-  return $self->fetch_all_by_Slice(@args);
-}
-
-
-
-
 =head2 fetch_by_transcript_stable_id
 
   Arg [1]    : list of arbitrary args @args

modules/Bio/EnsEMBL/DBSQL/ProxyRepeatFeatureAdaptor.pm

@@ -68,24 +68,5 @@ sub fetch_all_by_Slice {
 }
 
 
-=head2 fetch_by_Slice
-
-  Arg [1]    : none
-  Example    : none
-  Description: DEPRECATED use fetch_all_by_Slice instead
-  Returntype : none
-  Exceptions : none
-  Caller     : none
-
-=cut
-
-sub fetch_by_Slice {
-  my ($self, @args) = @_;
-
-  $self->warn("fetch_by_Slice has been renamed fetch_all_by_Slice\n" . caller);
-
-  return $self->fetch_all_by_Slice(@args);
-}
-
 1;
 

modules/Bio/EnsEMBL/DBSQL/ProxySNPAdaptor.pm

@@ -76,28 +76,6 @@ sub fetch_all_by_Slice {
 }
 
 
-
-=head2 fetch_by_Slice
-
-  Arg [1]    : none
-  Example    : none
-  Description: DEPRECATED use fetch_all_by_Slice instead
-  Returntype : none
-  Exceptions : none
-  Caller     : none
-
-=cut
-
-sub fetch_by_Slice {
-  my ($self, @args) = @_;
-
-  $self->warn("fetch_by_Slice has been renamed fetch_all_by_Slice\n" . caller);
-
-  return $self->fetch_all_by_Slice(@args);
-}
-
-
-
 =head2 fetch_by_SNP_id
 
   Arg [1]    : list of arbitrary args @args

modules/Bio/EnsEMBL/DBSQL/RawContigAdaptor.pm

@@ -535,47 +535,6 @@ sub deleteObj {
 
 
 
-
-=head2 fetch_by_clone
-
-  Arg [1]    : none
-  Example    : none
-  Description: DEPRECATED use fetch_all_by_Clone instead
-  Returntype : none
-  Exceptions : none
-  Caller     : none
-
-=cut
-
-sub fetch_by_clone {
-  my ($self, @args) = @_;
-  
-  print STDERR "fetch_by_clone has been renamed fetch_all_by_Clone\n" . caller;
-
-  return $self->fetch_by_Clone(@args);
-}
-
-
-=head2 fetch_by_Clone
-
-  Arg [1]    : none
-  Example    : none
-  Description: DEPRECATED use fetch_all_by_Clone instead
-  Returntype : none
-  Exceptions : none
-  Caller     : none
-
-=cut
-
-sub fetch_by_Clone {
-  my ($self, @args) = @_;
-
-  $self->warn("fetch_by_Clone has been renamed fetch_all_by_Clone\n" . caller);
-
-  return $self->fetch_all_by_Clone(@args);
-}
-
-
 =head2 remove
 
   Arg [1]    : Bio::EnsEMBL::RawContig $contig

modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm

@@ -305,31 +305,4 @@ sub _reverse_comp {
 }
 
 
-
-
-
-
-=head2 fetch_by_Contig_start_end_strand
-
-  Arg [1]    : none
-  Example    : none
-  Description: DEPRECATED use fetch_by_RawContig_start_end_strand instead
-  Returntype : none
-  Exceptions : none
-  Caller     : none
-
-=cut
-
-sub fetch_by_Contig_start_end_strand {
-  my ($self, @args) = @_;
-
-  $self->warn("fetch_by_Contig_start_end_strand has been renamed fetch_by_RawContig_start_end_strand\n" . caller);
-
-  return $self->fetch_by_RawContig_start_end_strand(@args);
-}
-
-
-
-
-
 1;