Formerly RegulatoryMotifAdaptor.pm

modules/Bio/EnsEMBL/DBSQL/RegulatoryFactorAdaptor.pm

+#
+# EnsEMBL module for Bio::EnsEMBL::DBSQL::RegulatoryMotifAdaptor
+#
+# Copyright EMBL/EBI
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::EnsEMBL::DBSQL::RegulatoryMotifAdaptor
+
+=head1 
+
+$rma = $database_adaptor->get_RegulatoryMotifAdaptor();
+
+$regulatory_motif = $rma->fetch_by_dbID(132);
+$regulatory_motif = $rma->fetch_by_name('Motif1');
+@regulatory_motifs = $rma->fetch_all_by_type("promoter");
+
+$rma->store($rm1, $rm2, $rm3);
+
+=head1 DESCRIPTION
+
+This is an adaptor for the retrieval and storage of RegulatoryMotif objects.
+
+=head1 AUTHOR - Glenn Proctor
+
+Email glenn@ebi.ac.uk
+
+=head1 CONTACT
+
+Post questions to the EnsEMBL developer list ensembl-dev@ebi.ac.uk
+
+=head1 METHODS
+
+=cut
+
+package Bio::EnsEMBL::DBSQL::RegulatoryMotifAdaptor;
+
+use strict;
+use Bio::EnsEMBL::DBSQL::BaseAdaptor;
+use Bio::EnsEMBL::RegulatoryMotif;
+use Bio::EnsEMBL::Utils::Exception qw(throw deprecate);
+
+use vars qw(@ISA);
+@ISA = ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
+
+
+=head2 fetch_by_dbID
+
+  Arg [1]    : int $db_id
+               The database identifier for the RegulatoryMotif to obtain
+  Example    : $regulatory_motif = $rma->fetch_by_dbID(4);
+  Description: Obtains a RegulatoryMotif object from the database via its
+               primary key. 
+  Returntype : Bio::EnsEMBL::RegulatoryMotif
+  Exceptions : none
+  Caller     : general, Bio::EnsEMBL::RegulatoryMotifAdaptor
+
+=cut
+
+sub fetch_by_dbID {
+    my( $self, $db_id ) = @_;
+
+    my ($rc) = @{$self->_generic_fetch("regulatory_motif_id = $db_id")};
+
+    return $rc;
+}
+
+
+
+=head2 fetch_by_name
+
+  Arg [1]    : string $name
+               the name of the regulatory motif to obtain
+  Example    : $rc = $rma->fetch_by_name('Motif');
+  Description: Obtains a regulatory motif from the database via its name
+  Returntype : Bio::EnsEMBL::RegulatoryMotif
+  Exceptions : none
+  Caller     : general
+
+=cut
+
+sub fetch_by_name {
+    my( $self, $name ) = @_;
+
+    my ($rc) = @{$self->_generic_fetch("name = '$name'")};
+
+    return $rc;
+}
+
+
+=head2 fetch_all_by_type
+
+  Arg [1]    : string $type
+               the type of regulatory motif to obtain
+  Example    : $rm = $rma->fetch_all_by_type('promoter');
+  Description: Obtains all regulatory motifs of a particular type
+  Returntype : listREF of Bio::EnsEMBL::RegulatoryMotifs
+  Exceptions : none
+  Caller     : general
+
+=cut
+
+sub fetch_all_by_type {
+    my( $self, $type) = @_;
+
+    return $self->_generic_fetch("type = '$type'");
+}
+
+
+
+=head2 _generic_fetch
+
+  Arg [1]    : string $where_clause
+  Example    : none
+  Description: PRIVATE used to create RegulatoryMotif features from an
+               SQL constraint
+  Returntype : listref of Bio::EnsEMBL::RegulatoryMotif objects
+  Exceptions : none
+  Caller     : internal
+
+=cut
+
+sub _generic_fetch {
+
+    my ($self, $where_clause) = @_;
+
+    my ($regulatory_motif_id, $name, $type);
+
+    my $sth = $self->prepare(qq{
+        SELECT regulatory_motif_id, name, type
+        FROM regulatory_motif
+        WHERE }. $where_clause);
+
+    $sth->execute;
+    $sth->bind_columns(\$regulatory_motif_id, \$name, \$type);
+
+    my @motifs;
+    while ($sth->fetch) {
+        push @motifs, Bio::EnsEMBL::RegulatoryMotif->new(-DBID => $regulatory_motif_id,
+							 -NAME => $name,
+							 -TYPE => $type);
+      }
+    return \@motifs;
+}
+
+
+=head2 store
+
+  Arg [1]    : list of Bio::EnsEMBL::RegulatoryMotifs @motifs
+  Example    : $rma->store(@motifs);
+  Description: stores a list of RegulatoryMotif objects in the database
+  Returntype : none
+  Exceptions : none
+  Caller     : ?
+
+=cut
+
+sub store {
+  my( $self, @motifs ) = @_;
+
+  my $sth = $self->prepare("INSERT into regulatory_motif (name, type) VALUES (?,?)");
+
+  foreach my $rm (@motifs) {
+
+    my $name = $rm->name or throw("name not set");
+    my $type = $rm->type or throw("type not set");
+
+    $sth->execute($name, $type);
+
+    my $db_id = $sth->{'mysql_insertid'}
+    or throw("Didn't get an insertid from the INSERT statement");
+
+    $rm->dbID($db_id);
+    $rm->adaptor($self);
+  }
+}
+
+1;
+
+__END__
+

modules/Bio/EnsEMBL/DBSQL/RegulatoryFeatureAdaptor.pm

@@ -412,6 +412,10 @@ sub fetch_all_by_ensembl_object_type {
 
    $sth->execute($type, $id);
 
+   #my @ids = map {$_->[0]} @{$sth->fetchall_arrayref()};
+
+   #my $in = "IN (" . join("," @ids) . ")";
+
    my $dbID;
    my %regulatory_features;
    while (($dbID) = $sth->fetchrow_array()) {

modules/Bio/EnsEMBL/DBSQL/StatementHandle.pm

@@ -76,32 +76,32 @@ sub sql {
 #
 # uncomment this for printing out handy debug information (every query)
 #
-# sub execute {
-#   my $self = shift;
+sub execute {
+   my $self = shift;
 
-#   my $sql = $self->sql();
+   my $sql = $self->sql();
 
 
-#   my @chrs = split(//, $sql);
+   my @chrs = split(//, $sql);
 
-#   my $j = 0;
-#   for(my $i =0; $i < @chrs; $i++) {
-#     $chrs[$i] = $_[$j++] if($chrs[$i] eq '?' && defined($_[$j]));
-#   }
+   my $j = 0;
+   for(my $i =0; $i < @chrs; $i++) {
+     $chrs[$i] = $_[$j++] if($chrs[$i] eq '?' && defined($_[$j]));
+   }
 
-#   my $str = join('', @chrs);
+   my $str = join('', @chrs);
 
-#   my $time = time;
+   my $time = time;
 #   print STDERR "\nSQL:\n$str\n\n";
 
-# #  print STDERR stack_trace_dump(), "\n";
+ #  print STDERR stack_trace_dump(), "\n";
 
-#   my $res = $self->SUPER::execute(@_);
-#   $time = time - $time;
+   my $res = $self->SUPER::execute(@_);
+   $time = time - $time;
 #   print STDERR "DONE ($time)\n";
 
-#   return $res;
-# }
+   return $res;
+ }
 
 
 sub DESTROY {