From 571f28ab34ee0308cb79ae3bc9ab3711f1b9cf88 Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Mon, 18 Apr 2011 15:24:22 +0000
Subject: [PATCH] Internal method _build_circular_slice_cache added
---
modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm | 39 ++++++++++++++++++++++-
1 file changed, 38 insertions(+), 1 deletion(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
index 13fd3e7095..931baf1be1 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
@@ -120,7 +120,6 @@ sub new {
$self->{'sr_name_cache'} = $seq_region_cache->{'name_cache'};
$self->{'sr_id_cache'} = $seq_region_cache->{'id_cache'};
-
$self->{'lrg_region_test'} = undef;
my $meta_container = $self->db->get_MetaContainer();
my @values = $meta_container->list_value_by_key("LRG");
@@ -499,6 +498,7 @@ sub fetch_by_region_unique {
my @out = ();
my $slice = $self->fetch_by_region(@_);
+
if ( !exists( $self->{'asm_exc_cache'} ) ) {
$self->_build_exception_cache();
}
@@ -602,6 +602,7 @@ sub fetch_by_seq_region_id {
my $arr = $self->{'sr_id_cache'}->{$seq_region_id};
my ( $name, $length, $cs, $cs_id );
+
if ( $arr && defined( $arr->[2] ) ) {
( $name, $cs_id, $length ) = ( $arr->[1], $arr->[2], $arr->[3] );
$cs = $self->db->get_CoordSystemAdaptor->fetch_by_dbID($cs_id);
@@ -778,6 +779,7 @@ sub fetch_all {
my %bad_vals=();
+
#
# Get a hash of non reference seq regions
#
@@ -1241,6 +1243,7 @@ sub fetch_by_Feature{
throw('Feature must be attached to a valid slice.');
}
+
my $fstart = $feature->start();
my $fend = $feature->end();
if(!defined($fstart) || !defined($fend)) {
@@ -1864,6 +1867,36 @@ LSQL
} ## end sub cache_toplevel_seq_mappings
+sub _build_circular_slice_cache {
+ my $self = shift;
+
+ # build up a cache of circular sequence region ids
+ my $sth =
+ $self->prepare( "SELECT sra.seq_region_id FROM seq_region_attrib sra "
+ . "INNER JOIN attrib_type at ON sra.attrib_type_id = at.attrib_type_id "
+ . "INNER JOIN seq_region sr ON sra.seq_region_id = sr.seq_region_id "
+ . "INNER JOIN coord_system cs ON sr.coord_system_id = cs.coord_system_id "
+ . "WHERE code = 'circular_seq' and cs.species_id = ?");
+
+ $sth->bind_param( 1, $self->species_id(), SQL_INTEGER );
+ $sth->execute();
+
+ my $id;
+ my %hash;
+ if ( ($id) = $sth->fetchrow_array() ) {
+ $self->{'circular_sr_id_cache'} = \%hash;
+ $self->{'is_circular'} = 1;
+ $hash{ $id } = $id;
+ while ( ($id) = $sth->fetchrow_array() ) {
+ $hash{ $id } = $id;
+ }
+ } else {
+ $self->{'is_circular'} = 0;
+ }
+ $sth->finish();
+} ## end _build_circular_slice_cache
+
+
#####################################
# sub DEPRECATED METHODs
#####################################
@@ -2077,4 +2110,8 @@ sub fetch_by_chr_name{
}
+
+
+
+
1;
--
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