Commit b5692608 authored by Ewan Birney's avatar Ewan Birney
Browse files

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
parent 1002456b
...@@ -12,13 +12,11 @@ ...@@ -12,13 +12,11 @@
=head1 NAME =head1 NAME
Bio::EnsEMBL::Assembly::SliceFactory - Factory for building slices Bio::EnsEMBL::DBSQL::SliceAdaptor - Adaptors for slices
=head1 SYNOPSIS =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 =head1 DESCRIPTION
...@@ -45,7 +43,7 @@ methods. Internal methods are usually preceded with a _ ...@@ -45,7 +43,7 @@ methods. Internal methods are usually preceded with a _
# Let the code begin... # Let the code begin...
package Bio::EnsEMBL::Assembly::SliceFactory; package Bio::EnsEMBL::DBSQL::SliceAdaptor;
use vars qw(@ISA); use vars qw(@ISA);
use strict; use strict;
......
...@@ -12,11 +12,10 @@ ...@@ -12,11 +12,10 @@
=head1 NAME =head1 NAME
Bio::EnsEMBL::Assembly::Slice - Arbitary Slice of a genome Bio::EnsEMBL::Slice - Arbitary Slice of a genome
=head1 SYNOPSIS =head1 SYNOPSIS
$slice = Bio::EnsEMBL::Assembly::SliceFactory->new_slice($chr,$start,$end,$type);
foreach $gene ( $slice->get_all_Genes ) { foreach $gene ( $slice->get_all_Genes ) {
# do something with a gene # do something with a gene
...@@ -45,7 +44,7 @@ The rest of the documentation details each of the object methods. Internal metho ...@@ -45,7 +44,7 @@ The rest of the documentation details each of the object methods. Internal metho
# Let the code begin... # Let the code begin...
package Bio::EnsEMBL::Assembly::Slice; package Bio::EnsEMBL::Slice;
use vars qw(@ISA); use vars qw(@ISA);
use strict; use strict;
...@@ -130,7 +129,14 @@ sub get_all_SimilarityFeatures_above_pid{ ...@@ -130,7 +129,14 @@ sub get_all_SimilarityFeatures_above_pid{
sub get_all_RepeatFeatures{ sub get_all_RepeatFeatures{
my ($self,@args) = @_; 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;
} }
......
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