From 4d3020ff832fbea18fb580b787d39063afda4331 Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Fri, 14 Oct 2005 12:41:21 +0000
Subject: [PATCH] Bug fix: rename fetch_by_AffyArray to fetch_all_by_AffyArray;
the later is used in AffyArray.
Retain deprecated fetch_by_AffyArray for backwards compatibility.
---
modules/Bio/EnsEMBL/DBSQL/AffyProbeAdaptor.pm | 28 +++++++++++++++++--
1 file changed, 26 insertions(+), 2 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/AffyProbeAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/AffyProbeAdaptor.pm
index b3d3a9e26c..ee7e7b2d5d 100644
--- a/modules/Bio/EnsEMBL/DBSQL/AffyProbeAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/AffyProbeAdaptor.pm
@@ -27,7 +27,7 @@ use strict;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::AffyProbe;
-use Bio::EnsEMBL::Utils::Exception qw(throw warning);
+use Bio::EnsEMBL::Utils::Exception qw(deprecate throw warning);
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
@@ -175,7 +175,7 @@ sub fetch_all_by_probeset {
=cut
-sub fetch_by_AffyArray {
+sub fetch_all_by_AffyArray {
my $self = shift;
my $array = shift;
@@ -192,6 +192,30 @@ sub fetch_by_AffyArray {
return $self->generic_fetch("ap.affy_array_id = $array_id");
}
+=head2 fetch_by_AffyArray
+
+ Arg [1] : Bio::EnsEMBL::AffyArray $array
+ Example : none
+ Description: Fetches all Arrays that given probe is part of. Included
+ : for backwards compatibility - should have been called
+ : fetch_all_by_AffyArray
+ Returntype : listref of Bio::EnsEMBL::AffyFeature
+ Exceptions : none
+ Caller : AffyProbe->get_all_AffyFeatures()
+ Status : High risk
+ : Likely to be removed - use fetch_all_by_AffyArray instead.
+
+=cut
+
+sub fetch_by_AffyArray {
+ my $self = shift;
+ my $array = shift;
+
+ deprecate("AffyProbeAdaptor->fetch_by_AffyArray() should not be used, use fetch_all_by_AffyArray() instead.");
+
+ return $self->fetch_all_by_AffyArray($array);
+}
+
=head2 fetch_all_by_AffyFeature
Arg [1] : Bio::EnsEMBL::AffyProbe $probe
--
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