From 5e6a89c1a023f1860de193c361e226658b486e61 Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Wed, 16 Jul 2003 10:37:43 +0000
Subject: [PATCH] Added more systematically-named list_dbIDs and
list_stable_dbIDs to replace list_geneIds and list_stable_geneIds; the old
functions are still there for backwards compatibilty but now print a warning
and call the appropriate list_ function. Common functionality for list_
functions is in BaseAdaptor.pm.
---
modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm | 55 ++++++++++++++++--------
1 file changed, 36 insertions(+), 19 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
index b5185bfd37..5d3f9eb34d 100644
--- a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
@@ -75,7 +75,7 @@ sub new {
Arg [1] : none
Example : @gene_ids = $gene_adaptor->list_geneIds();
- Description: Gets an array of internal ids for all genes in the current db
+ Description: DEPRECATED; use list_dbIDs instead
Returntype : list of ints
Exceptions : none
Caller : ?
@@ -85,26 +85,33 @@ sub new {
sub list_geneIds {
my ($self) = @_;
- my @out;
- my $sth = $self->prepare("SELECT gene_id FROM gene");
- $sth->execute;
+ $self->warn("list_geneIds is deprecated; use list_dbIDs instead");
+ return $self->list_dbIDs();
+}
- while (my ($id) = $sth->fetchrow) {
- push(@out, $id);
- }
+=head2 list_dbIDs
+
+ Arg [1] : none
+ Example : @gene_ids = $gene_adaptor->list_dbIDs();
+ Description: Gets an array of internal ids for all genes in the current db
+ Returntype : list of ints
+ Exceptions : none
+ Caller : ?
+
+=cut
- $sth->finish;
+sub list_dbIDs {
+ my ($self) = @_;
- return \@out;
+ return $self->_list_dbIDs("gene");
}
-
=head2 list_stable_geneIds
Arg [1] : list_stable_gene_ids
Example : @stable_ids = $gene_adaptor->list_stable_gene_ids();
- Description: Returns a list stable ids for all genes in the current db
+ Description: DEPRECATED; use list_stable_dbIDs() instead.
Returntype : list of strings
Exceptions : none
Caller : ?
@@ -114,17 +121,27 @@ sub list_geneIds {
sub list_stable_geneIds {
my ($self) = @_;
- my @out;
- my $sth = $self->prepare("SELECT stable_id FROM gene_stable_id");
- $sth->execute;
-
- while (my ($id) = $sth->fetchrow) {
- push(@out, $id);
- }
+ $self->warn("list_stable_geneIds is deprecated; use list_stable_dbIDs instead");
+ return $self->list_stable_dbIDs();
- return \@out;
}
+=head2 list_stable_dbIDs
+
+ Arg [1] : none
+ Example : @stable_gene_ids = $gene_adaptor->list_stable_dbIDs();
+ Description: Gets an array of stable ids for all genes in the current db
+ Returntype : list of ints
+ Exceptions : none
+ Caller : ?
+
+=cut
+
+sub list_stable_dbIDs {
+ my ($self) = @_;
+
+ return $self->_list_dbIDs("gene_stable_id", "stable_id");
+}
=head2 fetch_by_dbID
--
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