added order as an optional argument to list_dbIDs, mosy useful for genes and...

added order as an optional argument to list_dbIDs, mosy useful for genes and transcripts so caching is maximised

modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm

@@ -216,13 +216,16 @@ sub dbc{
 # returns listref of IDs
 sub _list_dbIDs {
 
-  my ($self, $table, $pk) = @_;
+  my ($self, $table, $pk, $ordered) = @_;
   if (!defined($pk)) {
     $pk = $table . "_id";
   }
 
   my @out;
   my $sql = "SELECT " . $pk . "  FROM " . $table;
+  if(defined($ordered) and $ordered){
+    $sql .= " order by seq_region_id, seq_region_start"
+  }	
   my $sth = $self->prepare($sql);
   $sth->execute;
 
@@ -235,6 +238,7 @@ sub _list_dbIDs {
   return \@out;
 }
 
+
 # _straight_join
 
 #   Arg [1]    : (optional) boolean $new_val

modules/Bio/EnsEMBL/DBSQL/DensityFeatureAdaptor.pm

@@ -467,6 +467,7 @@ sub _objs_from_sth {
   Example    : @feature_ids = @{$density_feature_adaptor->list_dbIDs()};
   Description: Gets an array of internal ids for all density features in the
                current db
+  Arg[1]     : <optional> int. not set to 0 for the ids to be sorted by the seq_region.
   Returntype : list of ints
   Exceptions : none
   Caller     : ?
@@ -475,9 +476,9 @@ sub _objs_from_sth {
 =cut
 
 sub list_dbIDs {
-   my ($self) = @_;
+   my ($self, $ordered) = @_;
 
-   return $self->_list_dbIDs("density_feature");
+   return $self->_list_dbIDs("density_feature",undef, $ordered);
 }
 
 

modules/Bio/EnsEMBL/DBSQL/DnaAlignFeatureAdaptor.pm

@@ -365,6 +365,7 @@ sub _objs_from_sth {
   Example    : @feature_ids = @{$dna_align_feature_adaptor->list_dbIDs()};
   Description: Gets an array of internal ids for all dna align features in 
                the current db
+  Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
   Returntype : list of ints
   Exceptions : none
   Caller     : ?
@@ -373,9 +374,9 @@ sub _objs_from_sth {
 =cut
 
 sub list_dbIDs {
-   my ($self) = @_;
+   my ($self, $ordered) = @_;
 
-   return $self->_list_dbIDs("dna_align_feature");
+   return $self->_list_dbIDs("dna_align_feature",undef, $ordered);
 }
 
 1;

modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm

@@ -441,6 +441,7 @@ sub remove {
   Arg [1]    : none
   Example    : @exon_ids = @{$exon_adaptor->list_dbIDs()};
   Description: Gets an array of internal ids for all exons in the current db
+  Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
   Returntype : list of ints
   Exceptions : none
   Caller     : ?
@@ -449,9 +450,9 @@ sub remove {
 =cut
 
 sub list_dbIDs {
-   my ($self) = @_;
+   my ($self, $ordered) = @_;
 
-   return $self->_list_dbIDs("exon");
+   return $self->_list_dbIDs("exon",undef, $ordered);
 }
 
 

modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm

@@ -113,6 +113,7 @@ sub _left_join {
 
   Example    : @gene_ids = @{$gene_adaptor->list_dbIDs()};
   Description: Gets an array of internal ids for all genes in the current db
+  Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
   Returntype : Listref of Ints
   Exceptions : none
   Caller     : general
@@ -121,9 +122,9 @@ sub _left_join {
 =cut
 
 sub list_dbIDs {
-   my ($self) = @_;
+  my ($self,$ordered) = @_;
 
-   return $self->_list_dbIDs("gene");
+  return $self->_list_dbIDs("gene",undef, $ordered);
 }
 
 
@@ -151,7 +152,6 @@ sub list_seq_region_ids {
   return $self->_list_seq_region_ids('gene');
 }
 
-
 =head2 fetch_by_display_label
 
   Arg [1]    : String $label - display label of gene to fetch

modules/Bio/EnsEMBL/DBSQL/KaryotypeBandAdaptor.pm

@@ -214,6 +214,7 @@ sub fetch_by_chr_band {
   Example    : @kary_ids = @{$karyotype_band_adaptor->list_dbIDs()};
   Description: Gets an array of internal ids for all karyotype bands in the
                current db
+  Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
   Returntype : reference to a list of ints
   Exceptions : none
   Caller     : ?
@@ -222,9 +223,9 @@ sub fetch_by_chr_band {
 =cut
 
 sub list_dbIDs {
-  my $self = shift;
+  my ($self, $ordered) = shift;
 
-  return $self->_list_dbIDs("karyotype");
+  return $self->_list_dbIDs("karyotype",undef, $ordered);
 }
 
 

modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm

@@ -508,6 +508,7 @@ sub _objs_from_sth {
   Example    : @feature_ids = @{$misc_feature_adaptor->list_dbIDs()};
   Description: Gets an array of internal ids for all misc_features in the 
                current db
+  Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
   Returntype : list of ints
   Exceptions : none
   Caller     : ?
@@ -516,9 +517,9 @@ sub _objs_from_sth {
 =cut
 
 sub list_dbIDs {
-   my ($self) = @_;
+   my ($self,$ordered) = @_;
 
-   return $self->_list_dbIDs("misc_feature");
+   return $self->_list_dbIDs("misc_feature",undef,$ordered);
 }
 
 

modules/Bio/EnsEMBL/DBSQL/OligoFeatureAdaptor.pm

@@ -495,6 +495,7 @@ sub store{
   Example    : my @feature_ids = @{$ofa->list_dbIDs()};
   Description: Gets an array of internal IDs for all OligoFeature objects in
                the current database.
+  Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
   Returntype : List of ints
   Exceptions : None
   Caller     : ?
@@ -503,9 +504,9 @@ sub store{
 =cut
 
 sub list_dbIDs {
-	my $self = shift;
+  my ($self,$ordered) = shift;
 	
-	return $self->_list_dbIDs('oligo_feature');
+  return $self->_list_dbIDs('oligo_feature',undef,$ordered);
 }
 
 1;

modules/Bio/EnsEMBL/DBSQL/PredictionExonAdaptor.pm

@@ -261,6 +261,7 @@ sub remove {
   Arg [1]    : none
   Example    : @exon_ids = @{$exon_adaptor->list_dbIDs()};
   Description: Gets an array of internal ids for all exons in the current db
+  Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
   Returntype : list of ints
   Exceptions : none
   Caller     : ?
@@ -269,9 +270,9 @@ sub remove {
 =cut
 
 sub list_dbIDs {
-   my ($self) = @_;
+   my ($self,$ordered) = @_;
 
-   return $self->_list_dbIDs("prediction_exon");
+   return $self->_list_dbIDs("prediction_exon",undef, $ordered);
 }
 
 

modules/Bio/EnsEMBL/DBSQL/PredictionTranscriptAdaptor.pm

@@ -541,6 +541,7 @@ sub remove {
   Example    : @feature_ids = @{$prediction_transcript_adaptor->list_dbIDs()};
   Description: Gets an array of internal ids for all prediction transcript
                features in the current db
+  Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
   Returntype : list of ints
   Exceptions : none
   Caller     : ?
@@ -549,9 +550,9 @@ sub remove {
 =cut
 
 sub list_dbIDs {
-   my ($self) = @_;
+   my ($self, $ordered) = @_;
 
-   return $self->_list_dbIDs("prediction_transcript");
+   return $self->_list_dbIDs("prediction_transcript", undef, $ordered);
 }
 
 1;

modules/Bio/EnsEMBL/DBSQL/ProteinAlignFeatureAdaptor.pm

@@ -346,6 +346,7 @@ sub _columns {
   Example    : @feature_ids = @{$protein_align_feature_adaptor->list_dbIDs()};
   Description: Gets an array of internal ids for all protein align 
                features in the current db
+  Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
   Returntype : listref of ints
   Exceptions : none
   Caller     : ?
@@ -354,9 +355,9 @@ sub _columns {
 =cut
 
 sub list_dbIDs {
-   my ($self) = @_;
+   my ($self,$ordered) = @_;
 
-   return $self->_list_dbIDs("protein_align_feature");
+   return $self->_list_dbIDs("protein_align_feature", undef, $ordered);
 }
 
 

modules/Bio/EnsEMBL/DBSQL/RegulatoryFeatureAdaptor.pm

@@ -460,6 +460,7 @@ sub store {
   Arg [1]    : none
   Example    : @feature_ids = @{$repeat_feature_adaptor->list_dbIDs()};
   Description: Gets an array of internal ids for all repeat features in the current db
+  Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
   Returntype : list of ints
   Exceptions : none
   Caller     : ?
@@ -469,9 +470,9 @@ sub store {
 =cut
 
 sub list_dbIDs {
-   my ($self) = @_;
+   my ($self, $ordered) = @_;
 
-   return $self->_list_dbIDs("regulatory_feature");
+   return $self->_list_dbIDs("regulatory_feature", undef, $ordered);
 }
 
 =head2 fetch_all_by_ensembl_object_type

modules/Bio/EnsEMBL/DBSQL/RegulatorySearchRegionAdaptor.pm

@@ -352,6 +352,7 @@ sub store {
   Arg [1]    : none
   Example    : @feature_ids = @{$repeat_feature_adaptor->list_dbIDs()};
   Description: Gets an array of internal ids for all repeat features in the current db
+  Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
   Returntype : list of ints
   Exceptions : none
   Caller     : ?
@@ -361,9 +362,9 @@ sub store {
 =cut
 
 sub list_dbIDs {
-   my ($self) = @_;
+   my ($self, $ordered) = @_;
 
-   return $self->_list_dbIDs("regulatory_search_region");
+   return $self->_list_dbIDs("regulatory_search_region", undef, $ordered);
 }
 
 

modules/Bio/EnsEMBL/DBSQL/RepeatFeatureAdaptor.pm

@@ -462,6 +462,7 @@ sub store {
   Arg [1]    : none
   Example    : @feature_ids = @{$repeat_feature_adaptor->list_dbIDs()};
   Description: Gets an array of internal ids for all repeat features in the current db
+  Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
   Returntype : list of ints
   Exceptions : none
   Caller     : ?
@@ -470,9 +471,9 @@ sub store {
 =cut
 
 sub list_dbIDs {
-   my ($self) = @_;
+   my ($self, $ordered) = @_;
 
-   return $self->_list_dbIDs("repeat_feature");
+   return $self->_list_dbIDs("repeat_feature", undef, $ordered);
 }
 
 1;

modules/Bio/EnsEMBL/DBSQL/SimpleFeatureAdaptor.pm

@@ -311,6 +311,7 @@ sub _objs_from_sth {
   Arg [1]    : none
   Example    : @feature_ids = @{$simple_feature_adaptor->list_dbIDs()};
   Description: Gets an array of internal ids for all simple features in the current db
+  Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
   Returntype : list of ints
   Exceptions : none
   Caller     : ?
@@ -319,9 +320,9 @@ sub _objs_from_sth {
 =cut
 
 sub list_dbIDs {
-   my ($self) = @_;
+   my ($self, $ordered) = @_;
 
-   return $self->_list_dbIDs("simple_feature");
+   return $self->_list_dbIDs("simple_feature", undef, $ordered);
 }
 
 1;

modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm

@@ -1067,6 +1067,7 @@ sub update {
 
   Example    : @transcript_ids = @{ $t_adaptor->list_dbIDs };
   Description: Gets a list of internal ids for all transcripts in the db.
+  Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
   Returntype : Listref of Ints
   Exceptions : none
   Caller     : general
@@ -1075,9 +1076,9 @@ sub update {
 =cut
 
 sub list_dbIDs {
-   my ($self) = @_;
+   my ($self, $ordered) = @_;
 
-   return $self->_list_dbIDs("transcript");
+   return $self->_list_dbIDs("transcript",undef, $ordered);
 }
 
 

modules/Bio/EnsEMBL/Map/DBSQL/DitagAdaptor.pm

@@ -366,9 +366,9 @@ sub update_ditag {
 =cut
 
 sub list_dbIDs {
-	my $self = shift;
+  my ($self, $ordered) = shift;
 	
-	return $self->_list_dbIDs('ditag');
+  return $self->_list_dbIDs('ditag');
 }
 
 1;

modules/Bio/EnsEMBL/Map/DBSQL/DitagFeatureAdaptor.pm

@@ -655,6 +655,7 @@ sub update_ditagFeature {
   Example    : my @feature_ids = @{$dfa->list_dbIDs()};
   Description: Gets an array of internal IDs for all DitagFeature objects in
                the current database.
+  Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
   Returntype : List of ints
   Exceptions : None
   Status     : Stable
@@ -662,9 +663,9 @@ sub update_ditagFeature {
 =cut
 
 sub list_dbIDs {
-	my $self = shift;
+  my ($self, $ordered) = shift;
 	
-	return $self->_list_dbIDs('ditag_feature');
+  return $self->_list_dbIDs('ditag_feature', undef, $ordered);
 }
 
 1;