removed obsolete Bio::EnsEMBL::Tile module

modules/Bio/EnsEMBL/Slice.pm

@@ -59,7 +59,6 @@ use vars qw(@ISA);
 use strict;
 
 use Bio::EnsEMBL::Root; # included for backwards compatibility
-use Bio::EnsEMBL::Tile; # included for backwards compatibility
 use Bio::EnsEMBL::Chromosome; # included for backwards compatibility
 use Bio::EnsEMBL::RawContig; # included for backwards compatibility
 
@@ -2220,43 +2219,8 @@ sub assembly_type{
 
 sub get_tiling_path {
   my $self = shift;
-
   deprecate('Use $slice->project("seqlevel") instead.');
-
-  my $csa = $self->adaptor()->db()->get_CoordSystemAdaptor();
-
-  #assume that they want the tiling path to the sequence coord system
-  #this might not work well if this isn't a chromosomal slice
-  my $projection = $self->project('seqlevel');
-
-  my @tiling_path;
-
-  foreach my $segment (@$projection) {
-
-    my ($slice_start, $slice_end, $contig) = @$segment;
-    my $contig_ori   = $contig->strand();
-    my $contig_start = $contig->start();
-    my $contig_end   = $contig->end();
-
-    #the old get_tiling_path always gave back entire contigs in the forward
-    #strand
-    $contig = $contig->adaptor->fetch_by_region('seqlevel',
-                                                $contig->seq_region_name());
-
-    #bless contigs into contigs
-    $contig = bless($contig, 'Bio::EnsEMBL::RawContig');
-
-
-    push @tiling_path, Bio::EnsEMBL::Tile->new_fast($self,
-                                                    $slice_start,
-                                                    $slice_end,
-                                                    $contig,
-                                                    $contig_start,
-                                                    $contig_end,
-                                                    $contig_ori);
-  }
-
-  return \@tiling_path;
+  return [];
 }
 
 

modules/Bio/EnsEMBL/Tile.pm

-# Ensembl module for Bio::EnsEMBL::Tile
-#
-# Cared for by Arne Stabenau <ensembl-dev@ebi.ac.uk>
-#
-# Copyright EnsEMBL 2002
-#
-# You may distribute this module under the same terms as perl itself
-
-# POD documentation - main docs before the code
-
-=head1 NAME
-
-Bio::EnsEMBL::Tile - DEPRECATED - You should not have to use this class.
-                     The Bio::EnsEMBL::Slice::project method should be able
-                     to construct any tiling path that you need.
-
-
-=head1 AUTHOR - Arne Stabenau
-
-=head1 CONTACT
-
-This modules is part of the Ensembl project http://www.ensembl.org
-
-Questions can be posted to the ensembl-dev mailing list:
-ensembl-dev@ebi.ac.uk
-
-=cut
-
-
-package Bio::EnsEMBL::Tile;
-use vars qw(@ISA);
-use strict;
-
-
-use Bio::EnsEMBL::Root;
-use Bio::EnsEMBL::Utils::Exception qw(deprecate);
-
-@ISA = qw(Bio::EnsEMBL::Root);
-
-
-
-### Only new_fast() is used by the EnsEMBL API
-### Otter uses new()
-sub new {
-    my $class = shift;
-
-    deprecate("Bio::EnsEMBL::Tile is a deprecated class.\nIf you want a " .
-              'tiling path it is best to use Bio::EnsEMBL::Slice::project');
-
-    my $self = bless {}, $class;
-    if (@_) {
-        $self->throw("new does not take any arguments");
-    }
-    return $self;
-}
-
-=head2 new_fast
-
-  Arg [1]    : Bio::EnsEMBL::Slice $assembled_seq
-               The assembled sequence which assembly should be described in this Tile
-  Arg [2]    : int $assembled_start
-  Arg [3]    : int $assembled_end
-               Where on the sequence the tile starts and ends
-  Arg [4]    : Bio::EnsEMBL::RawContig $component_seq
-               The sequence that is used to build up the assembled sequence.
-  Arg [5]    : int $component_start
-  Arg [6]    : int $component_end
-               Which component piece makes up the assembled piece
-  Arg [7]    : int $orientation (+1 or -1)
-  Example    : none
-  Description: Fast constructor for Tile object
-  Returntype : Bio::EnsEMBL::Tile
-  Exceptions : none
-  Caller     : Slice::get_tiling_path()
-
-=cut
-
-sub new_fast {
-  deprecate("Bio::EnsEMBL::Tile is a deprecated class.\nIf you want a " .
-            'tiling path it is best to use Bio::EnsEMBL::Slice::project');
-
-  # make it really fast
-  return bless {
-     'assembled_Seq'    => $_[1],
-     'assembled_start'  => $_[2],
-     'assembled_end'    => $_[3],
-     'component_Seq'    => $_[4],
-     'component_start'  => $_[5],
-     'component_end'    => $_[6],
-     'component_ori'    => $_[7],
-# compatibility zone
-     'start'            => $_[2],
-     'end'              => $_[3],
-     'strand'           => $_[7],
-     'contig'           => $_[4]
-  }, $_[0];
-}
-
-
-sub assembled_Seq {
-  my ( $self, $arg ) = @_;
-  if( defined $arg ) {
-    $self->{'assembled_Seq'} = $arg;
-  }
-
-  return $self->{'assembled_Seq'};
-}
-
-sub assembled_start {
-  my ( $self, $arg ) = @_;
-  if( defined $arg ) {
-    $self->{'assembled_start'} = $arg;
-    $self->{'start'} = $arg;
-  }
-
-  return $self->{'assembled_start'};
-}
-
-sub assembled_end {
-  my ( $self, $arg ) = @_;
-  if( defined $arg ) {
-    $self->{'assembled_end'} = $arg;
-    $self->{'end'} = $arg;
-  }
-
-  return $self->{'assembled_end'};
-}
-
-sub component_Seq {
-  my ( $self, $arg ) = @_;
-  if( defined $arg ) {
-    $self->{'component_Seq'} = $arg;
-    $self->{'contig'} = $arg;
-  }
-
-  return $self->{'component_Seq'};
-}
-
-sub component_start {
-  my ( $self, $arg ) = @_;
-  if( defined $arg ) {
-    $self->{'component_start'} = $arg;
-  }
-
-  return $self->{'component_start'};
-}
-
-sub component_end {
-  my ( $self, $arg ) = @_;
-  if( defined $arg ) {
-    $self->{'component_end'} = $arg;
-  }
-
-  return $self->{'component_end'};
-}
-
-sub component_ori {
-  my ( $self, $arg ) = @_;
-  if( defined $arg ) {
-    $self->{'component_ori'} = $arg;
-    $self->{'strand'} = $arg;
-  }
-
-  return $self->{'component_ori'};
-}
-
-
-1;