From d154c61ed5364aee4ba224277c6209238224df46 Mon Sep 17 00:00:00 2001
From: Arne Stabenau <stabenau@sanger.ac.uk>
Date: Tue, 22 Jul 2003 16:43:44 +0000
Subject: [PATCH] Optimized query for register region
---
.../Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm | 17 +++++++++--------
1 file changed, 9 insertions(+), 8 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
index 1398c8aaad..4d0ae28493 100644
--- a/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
@@ -129,6 +129,9 @@ sub register_region{
$self->throw("$assmapper is not a Bio::EnsEMBL::AssemblyMapper")
unless $assmapper->isa("Bio::EnsEMBL::AssemblyMapper");
+ my $chr = $self->db->get_ChromosomeAdaptor()->fetch_by_name( $chr_name );
+ my $chr_id = $chr->dbID();
+ my $max_assembly_contig = $self->db()->get_MetaContainer->get_max_assembly_contig();
my $select = qq{
select
@@ -136,27 +139,25 @@ sub register_region{
ass.contig_end,
ass.contig_id,
ass.contig_ori,
- chr.name,
ass.chr_start,
ass.chr_end
from
assembly ass,
- chromosome chr
where
- chr.name = '$chr_name' and
- ass.chromosome_id = chr.chromosome_id and
- $start <= ass.chr_end and
- $end >= ass.chr_start and
+ ass.chromosome_id = $chr_id and
+ ? <= ass.chr_end and
+ ? >= ass.chr_start and
+ ? <= ass.chr_start and
ass.type = '$type'
};
my $sth = $self->prepare($select);
- $sth->execute();
+ $sth->execute( $start, $end, $start-$max_assembly_contig );
while( my $arrayref = $sth->fetchrow_arrayref ) {
my ($contig_start, $contig_end, $contig_id, $contig_ori,
- $chr_name, $chr_start, $chr_end) = @$arrayref;
+ $chr_start, $chr_end) = @$arrayref;
if( $assmapper->_have_registered_contig($contig_id) == 0 ) {
$assmapper->_register_contig($contig_id);
$assmapper->_mapper->add_map_coordinates(
--
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