removed deprecated methods

modules/Bio/EnsEMBL/Slice.pm

@@ -1419,269 +1419,10 @@ sub accession_number {
 }
 
 
-=head2 DEPRECATED methods
+=head2 sub DEPRECATED methods
 =cut
 
 # sub DEPRECATED METHODS #
 ###############################################################################
 
-
-
-=head2 primary_seq
-
- Title   : primary_seq
- Usage   :
- Function:
- Example :
- Returns : 
- Args    :
-
-
-=cut
-
-=head2 primary_seq
-
-  Arg [1]    : none
-  Example    : none
-  Description: DEPRECATED use Bio::EnsEMBL:: instead
-  Returntype : none
-  Exceptions : none
-  Caller     : none
-
-=cut
-
-sub primary_seq{
-   my ($self,@args) = @_;
-   $self->warn("Call to deprecated method Bio::EnsEMBL::Slice::primary_seq" .
-               "Slice is now a PrimarySeq and can be used directly as such\n");
-
-   return $self;
-}
-
-=head2 get_all_Genes_exononly
-
-  Arg [1]    : none
-  Example    : none
-  Description: DEPRECATED use get_all_Genes instead
-  Returntype : none
-  Exceptions : none
-  Caller     : none
-
-=cut
-
-sub get_all_Genes_exononly{
-   my ($self) = @_;
-
-   my ($p,$f,$l) = caller;
-   $self->warn("$f:$l get_all_Genes_exononly has been deprecated. get_all_Genes called");
-
-   return $self->get_all_Genes();
-}
-
-
-=head2 get_all_SangerGenes_startend_lite
-
-  Arg [1]    : none
-  Example    : none
-  Description: DEPRECATED use get_Genes_by_source instead
-  Returntype : none
-  Exceptions : none
-  Caller     : none
-
-=cut
-
-sub get_all_SangerGenes_startend_lite {
-  my $self = shift;
-
-  $self->warn("Slice->get_all_SangerGenes_startend_lite deprecated" . 
-	      " use get_allGenes() instead\n");
-  
-  return $self->get_Genes_by_source('sanger');
-}
-
-
-=head2 get_all_VirtualGenes_startend_lite
-
-  Arg [1]    : none
-  Example    : none
-  Description: DEPRECATED use get_Genes_by_source instead
-  Returntype : none
-  Exceptions : none
-  Caller     : none
-
-=cut
-  
-sub get_all_VirtualGenes_startend_lite {
-  my $self = shift;
-
-  $self->warn("Slice->get_all_VirtualGenes_startend_lite deprecated" .
-	      " use get_all_Genes() instead\n");
-
-  return $self->get_all_Genes();
-}
-
-
-=head2 get_all_EMBLGenes_startend_lite
-
-  Arg [1]    : none
-  Example    : none
-  Description: DEPRECATED use get_Genes_by_source instead
-  Returntype : none
-  Exceptions : none
-  Caller     : none
-
-=cut
-
-sub get_all_EMBLGenes_startend_lite {
-  my $self = shift;
-
-  $self->warn("Slice->get_all_EMBLGenes_startend_lite deprecated" .
-	      " use get_Genes_by_source() instead\n");
-
-  return $self->get_Genes_by_source('embl');
-}
-
-
-
-=head2 fetch_chromosome_length
-
-  Arg [1]    : none
-  Example    : none
-  Description: DEPRECATED use get_Chromosome()->length() instead
-  Returntype : none
-  Exceptions : none
-  Caller     : none
-
-=cut
-
-sub fetch_chromosome_length {
-  my ($self) = @_;
-
-  $self->warn( "Call to deprecated method fetch_chromosome_length\n" .
-	       "use \$slice->get_Chromosome()->length(); instead.\n" .
-	       $self->stack_trace_dump());
-
-  return $self->get_Chromosome()->length();
-}
-
-
-
-=head2 fetch_karyotype_band_start_end
-
-  Arg [1]    : none
-  Example    : none
-  Description: DEPRECATED use get_KaryotypeBands instead
-  Returntype : none
-  Exceptions : none
-  Caller     : none
-
-=cut
-        
-sub fetch_karyotype_band_start_end {
-   my ($self,@args) = @_;
-
-   $self->warn( "Call to deprecated method fetch_karyotype_band_start_end\n" .
-		"use \$slice->get_KaryotypeBands(); instead.\n" .
-	       $self->stack_trace_dump());
-
-   return $self->get_KaryotypeBands();
-}
-
-
-
-=head2 convert_Gene_to_raw_contig
-
-  Arg [1]    : none
-  Example    : none
-  Description: DEPRECATED use Bio::EnsEMBL::Gene::transform instead
-  Returntype : none
-  Exceptions : none
-  Caller     : none
-
-=cut
-
-sub convert_Gene_to_raw_contig{
-  my ($self,$gene) = @_;
-
-  $self->warn("Call to deprecated method convert_Gene_to_raw_contig" . 
-	      "use the gene's transform method directly\n");
-
-  if(!$gene->isa("Bio::EnsEMBL::Gene")){
-    $self->throw("trying to use the wrong method can called convert gene to RawContig coords on ".$gene."\n");
-  }
-     
-  $gene->transform;
-  
-  return $gene;
-}
-
-
-
-
-=head2 get_landmark_MarkerFeatures
-
-  Arg [1]    : none
-  Example    : none
-  Description: DEPRECATED use get_all_landmarkMarkerFeatures instead
-  Returntype : none
-  Exceptions : none
-  Caller     : none
-
-=cut
-
-sub get_landmark_MarkerFeatures {
-  my ($self, @args) = @_;
-
-  $self->warn("get_landmark_MarkerFeatures has been renamed get_all_landmarkMarkerFeatures\n" . caller);
-
-  return $self->get_all_landmark_MarkerFeatures(@args);
-}
-
-
-
-
-=head2 get_Genes_by_source
-
-  Arg [1]    : none
-  Example    : none
-  Description: DEPRECATED use get_all_Genes_by_source instead
-  Returntype : none
-  Exceptions : none
-  Caller     : none
-
-=cut
-
-sub get_Genes_by_source {
-  my $self = shift; 
-
-  $self->warn( "\$Slice->get_Genes_by_source(\$source): You don't want to do" .
-	       " it like that!.\nYou want to do it like this " .
-	       "\$Slice->get_all_Genes_by_source(\$source)");
-
-  return $self->get_all_Genes_by_source( @_ );
-}
-
-
-
-
-=head2 get_Genes_by_type
-
-  Arg [1]    : none
-  Example    : none
-  Description: DEPRECATED use get_all_Genes_by_type instead
-  Returntype : none
-  Exceptions : none
-  Caller     : none
-
-=cut
-
-sub get_Genes_by_type {
-  
-  my $self = shift; 
-  $self->warn( "\$Slice->get_Genes_by_type(\$type): You don't want to do it " .
-	       "like that!.\nYou want to do it like this " .
-	       "\$Slice->get_all_Genes_by_type(\$type)");
-  return $self->get_all_Genes_by_type( @_ );
-}
-
 1;