Renamed list_stable_dbIDs to list_stable_ids to be more consistent with existing method names.

Minor POD reformatting.

modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm

@@ -70,77 +70,75 @@ sub new {
   return $self;
 }
 
-
-=head2 list_geneIds
+=head2 list_dbIDs
 
   Arg [1]    : none
-  Example    : @gene_ids = $gene_adaptor->list_geneIds();
-  Description: DEPRECATED; use list_dbIDs instead
+  Example    : @gene_ids = @{$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
 
-sub list_geneIds {
+sub list_dbIDs {
    my ($self) = @_;
 
-   $self->warn("list_geneIds is deprecated; use list_dbIDs instead");
-   return $self->list_dbIDs();
+   return $self->_list_dbIDs("gene");
 }
 
-=head2 list_dbIDs
+=head2 list_stable_ids
 
   Arg [1]    : none
-  Example    : @gene_ids = $gene_adaptor->list_dbIDs();
-  Description: Gets an array of internal ids for all genes in the current db
+  Example    : @stable_gene_ids = @{$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_dbIDs {
+sub list_stable_ids {
    my ($self) = @_;
 
-   return $self->_list_dbIDs("gene");
+   return $self->_list_dbIDs("gene_stable_id", "stable_id");
 }
 
+=head2 list_geneIds
 
-=head2 list_stable_geneIds
-
-  Arg [1]    : list_stable_gene_ids
-  Example    : @stable_ids = $gene_adaptor->list_stable_gene_ids();
-  Description: DEPRECATED; use list_stable_dbIDs() instead.
-  Returntype : list of strings
+  Arg [1]    : none
+  Example    : @gene_ids = $gene_adaptor->list_geneIds();
+  Description: DEPRECATED; use list_dbIDs instead
+  Returntype : list of ints
   Exceptions : none
   Caller     : ?
 
 =cut
 
-sub list_stable_geneIds {
+sub list_geneIds {
    my ($self) = @_;
 
-   $self->warn("list_stable_geneIds is deprecated; use list_stable_dbIDs instead");
-   return $self->list_stable_dbIDs();
-
+   $self->warn("list_geneIds is deprecated; use list_dbIDs instead");
+   return $self->list_dbIDs();
 }
 
-=head2 list_stable_dbIDs
+=head2 list_stable_geneIds
 
-  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
+  Arg [1]    : list_stable_gene_ids
+  Example    : @stable_ids = $gene_adaptor->list_stable_gene_ids();
+  Description: DEPRECATED; use list_stable_dbIDs() instead.
+  Returntype : list of strings
   Exceptions : none
   Caller     : ?
 
 =cut
 
-sub list_stable_dbIDs {
+sub list_stable_geneIds {
    my ($self) = @_;
 
-   return $self->_list_dbIDs("gene_stable_id", "stable_id");
+   $self->warn("list_stable_geneIds is deprecated; use list_stable_dbIDs instead");
+   return $self->list_stable_ids();
+
 }
 
 =head2 fetch_by_dbID