From ce1fc1710d8161ef0453a1867173efe2ba15cb31 Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Wed, 7 Mar 2007 15:17:07 +0000
Subject: [PATCH] Added support for external_db type column.
---
modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm | 40 ++++++++++++---------
1 file changed, 23 insertions(+), 17 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
index e4994a6e5f..a3ffdf5440 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
@@ -67,7 +67,7 @@ sub fetch_by_dbID {
xref.version, xref.description,
exDB.dbprimary_acc_linkable, exDB.display_label_linkable, exDB.priority,
exDB.db_name, exDB.db_display_name, exDB.db_release, es.synonym,
- xref.info_type, xref.info_text
+ xref.info_type, xref.info_text, exDB.type
FROM (xref, external_db exDB)
LEFT JOIN external_synonym es on es.xref_id = xref.xref_id
WHERE xref.xref_id = ?
@@ -81,8 +81,8 @@ sub fetch_by_dbID {
while ( my $arrayref = $sth->fetchrow_arrayref()){
my ( $refID, $dbprimaryId, $displayid, $version, $desc,
$primary_id_linkable, $display_id_linkable, $priority,
- $dbname, $db_display_name, $release, $synonym,
- $info_type, $info_text) = @$arrayref;
+ $dbname, $db_display_name, $release, $synonym,
+ $info_type, $info_text, $type) = @$arrayref;
if(!$exDB) {
$exDB = Bio::EnsEMBL::DBEntry->new
@@ -98,7 +98,8 @@ sub fetch_by_dbID {
-priority => $priority,
-db_display_name => $db_display_name,
-info_type => $info_type,
- -info_text => $info_text);
+ -info_text => $info_text,
+ -type => $type);
$exDB->description( $desc ) if ( $desc );
}
@@ -141,7 +142,7 @@ sub fetch_by_db_accession {
xref.version, xref.description,
exDB.dbprimary_acc_linkable, exDB.display_label_linkable, exDB.priority,
exDB.db_name, exDB.db_display_name, exDB.db_release, es.synonym,
- xref.info_type, xref.info_text
+ xref.info_type, xref.info_text, exDB.type
FROM (xref, external_db exDB)
LEFT JOIN external_synonym es on es.xref_id = xref.xref_id
WHERE xref.dbprimary_acc = ?
@@ -172,7 +173,7 @@ sub fetch_by_db_accession {
while ( my $arrayref = $sth->fetchrow_arrayref()){
my ( $dbID, $dbprimaryId, $displayid, $version, $desc,
$primary_id_linkable, $display_id_linkable, $priority, $dbname, $db_display_name,
- $release, $synonym, $info_type, $info_text) = @$arrayref;
+ $release, $synonym, $info_type, $info_text, $type) = @$arrayref;
if(!$exDB) {
$exDB = Bio::EnsEMBL::DBEntry->new
@@ -188,7 +189,8 @@ sub fetch_by_db_accession {
-priority => $priority,
-db_display_name=>$db_display_name,
-info_type => $info_type,
- -info_text => $info_text);
+ -info_text => $info_text,
+ -type => $type);
$exDB->description( $desc ) if ( $desc );
}
@@ -455,7 +457,7 @@ sub exists {
my $sth = $self->prepare('SELECT x.xref_id
FROM xref x, external_db xdb
WHERE x.external_db_id = xdb.external_db_id
- AND x.display_label = ?
+ AND x.display_label = ?
AND xdb.db_name = ?');
$sth->bind_param(1,$dbe->display_id,SQL_VARCHAR);
@@ -546,6 +548,7 @@ sub fetch_all_by_Transcript {
sub fetch_all_by_Translation {
my ( $self, $trans, $ex_db_reg ) = @_;
+print "in f a b t\n";
if(!ref($trans) || !$trans->isa('Bio::EnsEMBL::Translation')) {
throw('Bio::EnsEMBL::Translation argument expected.');
@@ -554,6 +557,7 @@ sub fetch_all_by_Translation {
warning( "Cannot fetch_all_by_Translation without a dbID" );
return [];
}
+print "out of f a b t\n";
return $self->_fetch_by_object_type( $trans->dbID(), 'Translation', $ex_db_reg );
}
@@ -699,7 +703,7 @@ sub _fetch_by_object_type {
idt.hit_end, idt.translation_start, idt.translation_end,
idt.cigar_line, idt.score, idt.evalue, idt.analysis_id,
gx.linkage_type,
- xref.info_type, xref.info_text
+ xref.info_type, xref.info_text, exDB.type
FROM (xref xref, external_db exDB, object_xref oxr)
LEFT JOIN external_synonym es on es.xref_id = xref.xref_id
LEFT JOIN identity_xref idt on idt.object_xref_id = oxr.object_xref_id
@@ -725,9 +729,9 @@ SSQL
$synonym, $queryid, $targetid, $query_start, $query_end,
$translation_start, $translation_end, $cigar_line,
$score, $evalue, $analysis_id, $linkage_type,
- $info_type, $info_text) = @$arrRef;
+ $info_type, $info_text, $type) = @$arrRef;
- my %obj_hash = (
+ my %obj_hash = (
'adaptor' => $self,
'dbID' => $refID,
'primary_id' => $dbprimaryId,
@@ -777,6 +781,7 @@ SSQL
$exDB->db_display_name($exDB_db_display_name);
$exDB->info_type($info_type);
$exDB->info_text($info_text);
+ $exDB->type($type);
push( @out, $exDB );
$seen{$refID} = $exDB;
@@ -966,11 +971,11 @@ sub _type_by_external_id{
syn.xref_id = oxr.xref_id AND oxr.ensembl_object_type= ?",
);
-# Increase speed of query by splitting the OR in query into three separate
-# queries. This is because the 'or' statments render the index useless
+# Increase speed of query by splitting the OR in query into three separate
+# queries. This is because the 'or' statments render the index useless
# because MySQL can't use any fields in the index.
- my %hash = ();
+ my %hash = ();
my @result = ();
foreach( @queries ) {
@@ -1103,7 +1108,7 @@ sub fetch_all_by_description {
xref.version, xref.description,
exDB.dbprimary_acc_linkable, exDB.display_label_linkable, exDB.priority,
exDB.db_name, exDB.db_display_name, exDB.db_release, es.synonym,
- xref.info_type, xref.info_text
+ xref.info_type, xref.info_text, exDB.type
FROM (xref, external_db exDB)
LEFT JOIN external_synonym es on es.xref_id = xref.xref_id
WHERE xref.description like ?
@@ -1122,7 +1127,7 @@ sub fetch_all_by_description {
while ( my $arrayref = $sth->fetchrow_arrayref()){
my ( $dbID, $dbprimaryId, $displayid, $version, $desc,
$primary_id_linkable, $display_id_linkable, $priority, $dbname,$db_display_name,
- $release, $synonym, $info_type, $info_text) = @$arrayref;
+ $release, $synonym, $info_type, $info_text, $type) = @$arrayref;
my $exDB = Bio::EnsEMBL::DBEntry->new
( -adaptor => $self,
@@ -1137,7 +1142,8 @@ sub fetch_all_by_description {
-priority => $priority,
-db_display_name=>$db_display_name,
-info_type => $info_type,
- -info_text => $info_text);
+ -info_text => $info_text,
+ -type => $type);
$exDB->description( $desc ) if ( $desc );
--
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