From a073cdf1d41d964a19514274a12629f5c48a69e7 Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Fri, 20 Dec 2002 14:45:18 +0000
Subject: [PATCH] start & end constraints can be passed to overridden
fetch_by_Clone method to speed up external queries
---
.../EnsEMBL/External/ExternalFeatureAdaptor.pm | 18 +++++++++++++++---
1 file changed, 15 insertions(+), 3 deletions(-)
diff --git a/modules/Bio/EnsEMBL/External/ExternalFeatureAdaptor.pm b/modules/Bio/EnsEMBL/External/ExternalFeatureAdaptor.pm
index 7f1845088a..e6130426aa 100644
--- a/modules/Bio/EnsEMBL/External/ExternalFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/External/ExternalFeatureAdaptor.pm
@@ -358,10 +358,12 @@ sub fetch_all_by_RawContig {
if($self->_supported('CLONE')) {
#retrieve features in clone coordinates
- my $feats = $self->fetch_all_by_Clone($contig->clone);
-
+
my $offset = $contig->embl_offset;
my $length = $contig->length;
+
+ my $feats = $self->fetch_all_by_Clone($contig->clone, $offset,
+ $offset + $length - 1);
my ($start, $end);
@@ -499,6 +501,12 @@ sub fetch_all_by_contig_name {
=head2 fetch_all_by_Clone
Arg [1] : Bio::EnsEMBL::Clone $clone
+ Arg [2] : (optional) int $clone_start the start of the clonal region
+ interested in. This information may be used to speed up
+ the query, or may be ignored.
+ Arg [3] : (optional) int $clone_end the end of the clonal region
+ interested in. This information may be used to speed up
+ the query, or may be ignored.
Example : @features = @{$self->fetch_all_by_Clone($clone)};
Description: Retrieves features on the region defined by the $clone arg in
Clone coordinates.
@@ -524,7 +532,11 @@ sub fetch_all_by_contig_name {
=cut
sub fetch_all_by_Clone {
- my ($self, $clone) = @_;
+ my ($self, $clone, $clone_start, $clone_end) = @_;
+
+ #ignore $clone_start && $clone_end it is only useful when
+ #fetch_all_by_RawContig is not implemented, but fetch_all_by_Clone is
+ #i.e. it can be used by people who override this method...
unless($clone && ref $clone && $clone->isa('Bio::EnsEMBL::Clone')) {
$self->throw("Clone must be a Bio::EnsEMBL::Clone");
--
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