From 9a49aa067653a1ea6e22e8e876d01aec63e21e10 Mon Sep 17 00:00:00 2001
From: Alistair Rust <rust@sanger.ac.uk>
Date: Tue, 17 Dec 2002 17:51:52 +0000
Subject: [PATCH] Access to relevant_xref_id stuff.
---
modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm | 48 +++++++++++++++++++++++-
modules/Bio/EnsEMBL/Gene.pm | 30 +++++++++++++++
2 files changed, 76 insertions(+), 2 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
index f2075b0989..944d5a3761 100644
--- a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
@@ -711,9 +711,17 @@ sub store {
$type = $gene->type;
}
+ my $xref_id = 0;
+# if (defined ($gene->relevant_xref)) {
+# $xref_id = $gene->relevant_xref;
+# }
+# else {
+# $xref_id = 0;
+# }
+
my $sth2 = $self->prepare("INSERT INTO gene(type, analysis_id,
- transcript_count)
- VALUES('$type', $analysisId, $trans_count)" );
+ transcript_count, relevant_xref_id)
+ VALUES('$type', $analysisId, $trans_count, $xref_id)" );
$sth2->execute();
@@ -941,6 +949,7 @@ sub get_external_name {
return $xref;
}
+
=head2 get_external_dbname
Arg [1] : int $dbID
@@ -982,6 +991,41 @@ sub get_external_dbname {
}
+=head2 get_relevant_xref_id
+
+ Arg [1] : int $dbID
+ the database identifier of the gene for which the name of
+ external db from which its external name is derived.
+ Example : $external_dbname = $gene_adaptor->get_relevant_xref_id(42);
+ Description: Retrieves the relevant_xref_id for a gene.
+ Returntype : int
+ Exceptions : thrown if $dbId arg is not defined
+ Caller : general
+
+=cut
+
+sub get_relevant_xref_id {
+ my ($self, $dbID) = @_;
+
+ if( !defined $dbID ) {
+ $self->throw("Must call with a dbID");
+ }
+
+ my $sth = $self->prepare("SELECT relevant_xref_id
+ FROM gene
+ WHERE gene_id = ?
+ ");
+ $sth->execute($dbID);
+
+ my ($xref_id) = $sth->fetchrow_array();
+ if( !defined $xref_id ) {
+ return undef;
+ }
+
+ return $xref_id;
+}
+
+
1;
__END__
diff --git a/modules/Bio/EnsEMBL/Gene.pm b/modules/Bio/EnsEMBL/Gene.pm
index 8f3e1e55a6..89dea7b25b 100755
--- a/modules/Bio/EnsEMBL/Gene.pm
+++ b/modules/Bio/EnsEMBL/Gene.pm
@@ -914,4 +914,34 @@ sub species {
}
+=head2 relevant_xref
+
+ Arg [1] : int $relevant_xref_id
+ Example : $gene->relevant_xref(42);
+ Description: get/set/lazy_loaded relevant_xref_id for this gene
+ Returntype : int
+ Exceptions : none
+ Caller : general
+
+=cut
+
+sub relevant_xref{
+
+ my ($self,$value) = @_;
+
+ if( defined $value ) {
+ $self->{'relevant_xref'} = $value;
+ return;
+ }
+
+ if( exists $self->{'relevant_xref'} ) {
+ return $self->{'relevant_xref'};
+ }
+
+ $self->{'relevant_xref'} = $self->adaptor->get_relevant_xref_id($self->dbID);
+
+ return $self->{'relevant_xref'};
+}
+
+
1;
--
GitLab