From 1121facd11130506c0e5349ecb53e3b0bf491ff0 Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Thu, 1 Apr 2004 08:33:51 +0000
Subject: [PATCH] Modified store method slightly. display_xref is now stored
if set so update() does not need to be called as seperate step
---
modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm | 38 ++++++++++++++++--------
1 file changed, 26 insertions(+), 12 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
index 7a7ee5ce69..c9599f5fc6 100644
--- a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
@@ -621,7 +621,7 @@ sub store {
"seq_region_id = ?, " .
"seq_region_start = ?, " .
"seq_region_end = ?, " .
- "seq_region_strand = ? ";
+ "seq_region_strand = ?";
my $sth = $self->prepare( $store_gene_sql );
$sth->execute(
@@ -636,9 +636,7 @@ sub store {
my $gene_dbID = $sth->{'mysql_insertid'};
- #
# store stable ids if they are available
- #
if (defined($gene->stable_id)) {
my $statement = "INSERT INTO gene_stable_id
@@ -652,9 +650,8 @@ sub store {
}
- #
- # store the gene description associated with this gene if there is one
- #
+ # store the gene description associated with this gene if there is
+ # one
my $desc = $gene->description();
if(defined($desc)) {
$sth = $self->prepare("INSERT INTO gene_description " .
@@ -664,9 +661,7 @@ sub store {
$sth->finish();
}
- #
# store the dbentries associated with this gene
- #
my $dbEntryAdaptor = $db->get_DBEntryAdaptor();
foreach my $dbe ( @{$gene->get_all_DBEntries} ) {
@@ -697,10 +692,29 @@ sub store {
$transcript_adaptor->store($t,$gene_dbID );
}
- #set the adaptor and dbID on the original passed in gene not the transfered
- #copy
- $original->adaptor( $self );
- $original->dbID( $gene_dbID );
+
+ # if a display_xref is defined store it as well. This requires an
+ # update to the gene table and could not have been done at the time
+ # the gene was stored because the gene needed to be stored to store
+ # the xrefs and get the display xref id. A bit of a catch22.
+ my $display_xref = $gene->display_xref;
+ if($display_xref) {
+ if(!$display_xref->is_stored($db)) {
+ # This should be stored already b/c it should at least
+ # be associated with one of the transcripts or translations.
+ # We'll allow this though because it could be desired behaviour.
+ $dbEntryAdaptor->store($display_xref, $gene_dbID, "Gene");
+ }
+ $sth = $self->prepare
+ ("UPDATE gene SET display_xref_id = ? WHERE gene_id = ?");
+ $sth->execute($display_xref->dbID(), $gene_dbID);
+ $sth->finish();
+ }
+
+ # set the adaptor and dbID on the original passed in gene not the
+ # transfered copy
+ $original->adaptor( $self );
+ $original->dbID( $gene_dbID );
return $gene_dbID;
}
--
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