From 8adc78e53a384ed6f2e3a98995b3afa583e163b7 Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Thu, 16 Aug 2012 10:23:47 +0000
Subject: [PATCH] Now can search DBs more than just otherfeatures
---
modules/Bio/EnsEMBL/Registry.pm | 18 ++++++++++--------
1 file changed, 10 insertions(+), 8 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Registry.pm b/modules/Bio/EnsEMBL/Registry.pm
index 75d8b51374..88a91283e6 100644
--- a/modules/Bio/EnsEMBL/Registry.pm
+++ b/modules/Bio/EnsEMBL/Registry.pm
@@ -2717,13 +2717,12 @@ my %stable_id_stmts = (
sub get_species_and_object_type {
- my ($self, $stable_id, $known_type, $known_species, $known_db_type) = @_;
+ my ($self, $stable_id, $known_type, $known_species, $known_db_type, $force_long_lookup) = @_;
#get the stable_id lookup database adaptor
my $stable_ids_dba = $self->get_DBAdaptor("multi", "stable_ids", 1);
- if ($stable_ids_dba) {
-
+ if ($stable_ids_dba && ! $force_long_lookup) {
my $statement = 'SELECT name, object_type, db_type FROM stable_id_lookup join species using(species_id) WHERE stable_id = ?';
if ($known_species) {
@@ -2758,19 +2757,22 @@ sub get_species_and_object_type {
return ($species ,$type, $db_type);
} else {
-
if (defined $known_type && !exists $stable_id_stmts{lc $known_type}) {
return;
}
my @types = defined $known_type ? ($known_type) : ('Gene', 'Transcript', 'Translation', 'Exon', 'Operon', 'OperonTranscript');
- if ($known_db_type && $known_db_type ne 'core' && $known_db_type ne 'Core' ) {
- return;
+ if(! $known_db_type) {
+ $known_db_type = 'core';
}
+ warn $known_db_type;
+ warn $known_species;
+ warn $known_type;
+
my %get_adaptors_args;
- $get_adaptors_args{'-group'} = 'Core';
+ $get_adaptors_args{'-group'} = $known_db_type;
if ($known_species) {
$get_adaptors_args{'-species'} = $known_species;
}
@@ -2790,7 +2792,7 @@ sub get_species_and_object_type {
$sth->finish;
- return ($species, $type, 'Core') if defined $species;
+ return ($species, $type, $known_db_type) if defined $species;
}
} ## end foreach my $dba ( sort { $a...})
--
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