as per Arnes request, Slices become more "standard" (so we can use them in the...

as per Arnes request, Slices become more "standard" (so we can use them in the pipeline). Moved Slice to business object space and SliceFactory to SliceAdaptor

modules/Bio/EnsEMBL/Assembly/SliceFactory.pm → modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm

@@ -12,13 +12,11 @@
 
 =head1 NAME
 
-Bio::EnsEMBL::Assembly::SliceFactory - Factory for building slices
+Bio::EnsEMBL::DBSQL::SliceAdaptor - Adaptors for slices
 
 =head1 SYNOPSIS
   
-   $slice = Bio::EnsEMBL::Assembly::SliceFactory->new_slice($chr,$start,$end,$type);
 
-   $webslice = Bio::EnsEMBL::Assembly::SliceFactory->new_web_slice($chr,$start,$end,$type);
 
 
 =head1 DESCRIPTION
@@ -45,7 +43,7 @@ methods. Internal methods are usually preceded with a _
 # Let the code begin...
 
 
-package Bio::EnsEMBL::Assembly::SliceFactory;
+package Bio::EnsEMBL::DBSQL::SliceAdaptor;
 use vars qw(@ISA);
 use strict;
 

modules/Bio/EnsEMBL/Assembly/Slice.pm → modules/Bio/EnsEMBL/Slice.pm

@@ -12,11 +12,10 @@
 
 =head1 NAME
 
-Bio::EnsEMBL::Assembly::Slice - Arbitary Slice of a genome
+Bio::EnsEMBL::Slice - Arbitary Slice of a genome
 
 =head1 SYNOPSIS
 
-   $slice = Bio::EnsEMBL::Assembly::SliceFactory->new_slice($chr,$start,$end,$type);
 
    foreach $gene ( $slice->get_all_Genes ) {
       # do something with a gene
@@ -45,7 +44,7 @@ The rest of the documentation details each of the object methods. Internal metho
 # Let the code begin...
 
 
-package Bio::EnsEMBL::Assembly::Slice;
+package Bio::EnsEMBL::Slice;
 use vars qw(@ISA);
 use strict;
 
@@ -130,7 +129,14 @@ sub get_all_SimilarityFeatures_above_pid{
 sub get_all_RepeatFeatures{
    my ($self,@args) = @_;
 
-   $self->throw("Ewan has not implemented this function! Complain!!!!");
+
+   @repeats = $self->repeat_adaptor->fetch_by_Slice($self);
+
+   foreach $repeat ( @repeats ) {
+       $repeat->transform_location($self->start);
+   }
+
+   return @repeats;
 }