From 5afcc2594ac6a61ef93996b103997127bf43e04a Mon Sep 17 00:00:00 2001
From: Kieron Taylor <ktaylor@ebi.ac.uk>
Date: Tue, 19 Apr 2016 15:42:16 +0100
Subject: [PATCH] [ENSCORESW-1664] Close up leaked internal cache in Gene
object
---
modules/Bio/EnsEMBL/Gene.pm | 3 ++-
modules/t/gene.t | 7 +++++++
2 files changed, 9 insertions(+), 1 deletion(-)
diff --git a/modules/Bio/EnsEMBL/Gene.pm b/modules/Bio/EnsEMBL/Gene.pm
index ff92da35b4..9f38bf8619 100755
--- a/modules/Bio/EnsEMBL/Gene.pm
+++ b/modules/Bio/EnsEMBL/Gene.pm
@@ -1013,7 +1013,8 @@ sub get_all_Transcripts {
$self->{'_transcript_array'} = $transcripts;
}
}
- return $self->{'_transcript_array'};
+ my @array_copy = @{ $self->{'_transcript_array'} };
+ return \@array_copy;
}
diff --git a/modules/t/gene.t b/modules/t/gene.t
index 7ad82dc7ae..92909bdd3e 100644
--- a/modules/t/gene.t
+++ b/modules/t/gene.t
@@ -284,6 +284,13 @@ foreach my $tr (@{$gene->get_all_Transcripts()}) {
ok($count == 5);
ok($translates);
+# Verify Transcript cache is not leaky
+my $transcripts = $gene->get_all_Transcripts;
+$count = @$transcripts;
+pop @$transcripts;
+$transcripts = $gene->get_all_Transcripts;
+cmp_ok(scalar @$transcripts, '==', $count, "Gene's transcript cache is not modified by changing transcript lists in caller code");
+
ok(scalar(@{$gene->get_all_Exons()}) == 3);
$gene = $gene->transform("chromosome");
--
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