From 915dbd066f6dfa2dbe29415714d5fe525eeb466f Mon Sep 17 00:00:00 2001
From: Arne Stabenau <stabenau@sanger.ac.uk>
Date: Tue, 26 Aug 2003 15:31:31 +0000
Subject: [PATCH] more attributes stored for IdentityXrefs
---
modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm | 62 +++++++++++++++++----
1 file changed, 51 insertions(+), 11 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
index 7dc27fee67..b360b7d782 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
@@ -216,12 +216,34 @@ sub store {
# If its GoXref add the linkage type to go_xref table
#
if ($exObj->isa('Bio::EnsEMBL::IdentityXref')) {
+
+ my $analysis_id;
+ if( $exObj->analysis() ) {
+ $analysis_id = $self->db()->get_AnalysisAdaptor()->
+ store( $exObj->analysis() );
+ } else {
+ $analysis_id = undef;
+ }
+
$sth = $self->prepare( "
INSERT ignore INTO identity_xref
SET object_xref_id = ?,
query_identity = ?,
- target_identity = ?" );
- $sth->execute($Xidt, $exObj->query_identity, $exObj->target_identity);
+ target_identity = ?,
+ hit_start = ?,
+ hit_end = ?,
+ translation_start = ?,
+ translation_end = ?,
+ cigar_line = ?,
+ score = ?,
+ evalue = ?,
+ analysis_id = ?" );
+
+ $sth->execute($Xidt, $exObj->query_identity, $exObj->target_identity,
+ $exObj->hit_start(), $exObj->hit_end(),
+ $exObj->translation_start(), $exObj->translation_end(),
+ $exObj->cigar_line(), $exObj->score(), $exObj->evalue(),
+ $analysis_id);
} elsif( $exObj->isa( 'Bio::EnsEMBL::GoXref' )) {
$sth = $self->prepare( "
INSERT ignore INTO go_xref
@@ -391,7 +413,9 @@ sub _fetch_by_object_type {
exDB.db_name, exDB.release, exDB.status,
oxr.object_xref_id,
es.synonym,
- idt.query_identity, idt.target_identity,
+ idt.query_identity, idt.target_identity, idt.hit_start, idt.hit_end,
+ idt.translation_start, idt.translation_end, idt.cigar_line,
+ idt.score, idt.evalue, idt.analysis_id,
gx.linkage_type
FROM xref xref, external_db exDB, object_xref oxr
LEFT JOIN external_synonym es on es.xref_id = xref.xref_id
@@ -410,16 +434,18 @@ sub _fetch_by_object_type {
while ( my $arrRef = $sth->fetchrow_arrayref() ) {
my ( $refID, $dbprimaryId, $displayid, $version,
$desc, $dbname, $release, $exDB_status, $objid,
- $synonym, $queryid, $targetid, $linkage_type ) = @$arrRef;
+ $synonym, $queryid, $targetid, $hit_start, $hit_end,
+ $translation_start, $translation_end, $cigar_line,
+ $score, $evalue, $analysis_id, $linkage_type ) = @$arrRef;
my %obj_hash = (
- _adaptor => $self,
- _dbID => $refID,
- _primary_id => $dbprimaryId,
- _display_id => $displayid,
- _version => $version,
- _release => $release,
- _dbname => $dbname);
+ _adaptor => $self,
+ _dbID => $refID,
+ _primary_id => $dbprimaryId,
+ _display_id => $displayid,
+ _version => $version,
+ _release => $release,
+ _dbname => $dbname);
# using an outer join on the synonyms as well as on identity_xref, we
@@ -433,6 +459,20 @@ sub _fetch_by_object_type {
$exDB = Bio::EnsEMBL::IdentityXref->new_fast(\%obj_hash);
$exDB->query_identity($queryid);
$exDB->target_identity($targetid);
+ if( $analysis_id ) {
+ my $analysis = $self->db()->get_AnalysisAdaptor()->
+ fetch_by_dbID( $analysis_id );
+ if( $analysis ) {
+ $exDB->analysis( $analysis );
+ }
+ }
+ $exDB->cigar_line( $cigar_line );
+ $exDB->hit_start( $hit_start );
+ $exDB->hit_end( $hit_end );
+ $exDB->translation_start( $translation_start );
+ $exDB->translation_end( $translation_end );
+ $exDB->score( $score );
+ $exDB->evalue( $evalue );
} elsif( defined $linkage_type ) {
$exDB = Bio::EnsEMBL::GoXref->new_fast( \%obj_hash );
$exDB->add_linkage_type( $linkage_type );
--
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