From cdea112be1f80c675f40cbb94a7197bfbaaf9bf2 Mon Sep 17 00:00:00 2001
From: Web Admin <w3adm@sanger.ac.uk>
Date: Thu, 11 Oct 2001 08:14:44 +0000
Subject: [PATCH] Added get_LiteAdaptor - a way into the lite database to speed
up calls
---
modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm | 43 +++++++++++++++++++++-----
1 file changed, 36 insertions(+), 7 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
index 988eadcbc7..02e3080154 100755
--- a/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
@@ -82,7 +82,8 @@ sub new {
my (
$db,
$mapdbname,
- $dnadb,
+ $litedbname,
+ $dnadb,
$host,
$driver,
$user,
@@ -92,9 +93,10 @@ sub new {
$perlonlysequences,
$external,
$port,
- ) = $self->_rearrange([qw(
- DBNAME
+ ) = $self->_rearrange([qw(
+ DBNAME
MAPDBNAME
+ LITEDBNAME
DNADB
HOST
DRIVER
@@ -105,7 +107,7 @@ sub new {
PERLONLYSEQUENCES
EXTERNAL
PORT
- )],@args);
+ )],@args);
$db || $self->throw("Database object must have a database name");
$user || $self->throw("Database object must have a user");
@@ -168,6 +170,7 @@ sub new {
$self->password( $password);
# following was added on branch; unclear if it is needed:
$self->mapdbname( $mapdbname );
+# $self->litedbname( $litedbname );
if ($perl && $perl == 1) {
$Bio::EnsEMBL::FeatureFactory::USE_PERL_ONLY = 1;
@@ -195,6 +198,11 @@ sub new {
};
}
+ # Store info for connecting to a litedb.
+ {
+ $litedbname ||= 'lite';
+ $self->{'_lite_db_name'} = $litedbname;
+ }
return $self; # success - we hope!
}
@@ -773,7 +781,7 @@ sub mapdb {
# mapdb is called), connect to the map database.
if (ref($map) eq 'HASH') {
require Bio::EnsEMBL::Map::DBSQL::Obj;
- $self->{'_mapdb'} = Bio::EnsEMBL::Map::DBSQL::Obj->new(%$map);
+ $self->{'_mapdb'} = Bio::EnsEMBL::Map::DBSQL::Obj->new( %$map );
}
}
return $self->{'_mapdb'};
@@ -790,8 +798,6 @@ sub mapdbname {
return $self->{_mapdbname};
}
-
-
=head2 write_Species
Title : write_Species
@@ -2277,6 +2283,29 @@ sub get_GeneAdaptor {
return $ga;
}
+=head2 get_LiteAdaptor;
+
+ Title : get_LiteAdaptor
+ Usage : my $la = $db->get_LiteAdaptor;
+ Function: Returns the lite database object handler
+ Example :
+ Returns : Bio::EnsEMBL::DBSQL::LiteAdaptor
+ Args :
+
+=cut
+sub get_LiteAdaptor {
+ my( $self ) = @_;
+
+ my $la;
+ unless ($la = $self->{'_lite_adaptor'}) {
+ require Bio::EnsEMBL::DBSQL::LiteAdaptor;
+ $la = Bio::EnsEMBL::DBSQL::LiteAdaptor->new( $self );
+# $la->{'lite_db_name'} = $self->{'lite_db_name'};
+ $self->{'_lite_adaptor'} = $la;
+ }
+ return $la;
+}
+
sub get_ExonAdaptor {
my( $self ) = @_;
--
GitLab