From b6b27a92e9a1cd73639ffcb393895101aa2bbe7c Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Wed, 25 Feb 2004 17:29:36 +0000
Subject: [PATCH] warn if database has an invalid block size
---
modules/Bio/EnsEMBL/DBSQL/DensityTypeAdaptor.pm | 12 +++++++++++-
1 file changed, 11 insertions(+), 1 deletion(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/DensityTypeAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DensityTypeAdaptor.pm
index 70e188e8d5..c42f8599ab 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DensityTypeAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DensityTypeAdaptor.pm
@@ -93,6 +93,11 @@ sub fetch_all {
while($sth->fetch()) {
my $analysis = $analysis_adaptor->fetch_by_dbID($analysis_id);
+ if($blk_size < 1) {
+ warning("density_type table contains invalid block_size=$blk_size.");
+ $blk_size = 1;
+ }
+
my $dt = Bio::EnsEMBL::DensityType->new(-ADAPTOR => $self,
-DBID => $dbID,
-ANALYSIS => $analysis,
@@ -159,7 +164,6 @@ sub fetch_all_by_logic_name {
}
my $analysis_adaptor = $self->db()->get_AnalysisAdaptor();
-
my $analysis = $analysis_adaptor->fetch_by_logic_name($logic_name);
return [] if(!$analysis);
@@ -176,6 +180,12 @@ sub fetch_all_by_logic_name {
my @out;
while($sth->fetch()) {
+
+ if($blk_size < 1) {
+ warning("density_type table contains invalid block_size=$blk_size.");
+ $blk_size = 1;
+ }
+
my $dt = Bio::EnsEMBL::DensityType->new(-ADAPTOR => $self,
-DBID => $dbID,
-ANALYSIS => $analysis,
--
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