Added remove method for database feature removal to the BaseFeatureAdaptor

modules/Bio/EnsEMBL/BaseAlignFeature.pm

@@ -247,7 +247,7 @@ sub transform{
 sub dbID{
   my ($self, $arg) = @_;
 
-  if($arg){
+  if(defined $arg){
     $self->{_database_id} = $arg;
   }
 

modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm

@@ -586,6 +586,48 @@ sub store{
 }
 
 
+=head2 remove
+
+  Arg [1]    : A feature $feature 
+  Example    : $feature_adaptor->remove($feature);
+  Description: This removes a feature from the database.  The table the
+               feature is removed from is defined by the abstract method
+               _tablename, and the primary key of the table is assumed
+               to be _tablename() . '_id'.  The feature argument must 
+               be an object implementing the dbID method, and for the
+               feature to be removed from the datasbase a dbID value must
+               be returned.
+  Returntype : none
+  Exceptions : thrown if $feature arg does not implement dbID(), or if 
+               $feature->dbID is not a true value               
+  Caller     : general
+
+=cut
+
+sub remove {
+  my ($self, $feature) = @_;
+
+  unless($feature->can('dbID')) {
+    $self->throw("Feature [$feature] does not implement method dbID");
+  }
+
+  unless($feature->dbID) {
+    $self->warn("BaseFeatureAdaptor::remove - dbID not defined - " .
+                "feature could not be removed");
+  }
+
+  my $table = $self->_tablename();
+
+  my $sth = $self->prepare("DELETE FROM $table WHERE ${table}_id = ?");
+  $sth->execute($feature->dbID());
+
+  #unset the feature dbID
+  $feature->dbID('');
+  
+  return;
+}
+
+
 =head2 _tablename
 
   Args       : none
@@ -629,7 +671,7 @@ sub _columns {
 }
 
 
-=head2 _obj_from_hashref
+=head2 _objs_from_sth
 
   Arg [1]    : DBI::row_hashref $hashref containing key-value pairs 
                for each of the columns specified by the _columns method
@@ -643,7 +685,7 @@ sub _columns {
 
 =cut
 
-sub _obj_from_hashref {
+sub _objs_from_sth {
   my $self = shift;
 
   $self->throw("abstract method _obj_from_hashref not defined by implementing"

modules/Bio/EnsEMBL/DBSQL/DnaAlignFeatureAdaptor.pm

@@ -120,7 +120,7 @@ sub store {
   my $tablename = $self->_tablename();
   
   if( scalar(@sf) == 0 ) {
-    $self->throw("Must call store with contig_id then sequence features");
+    $self->throw("Must call store with sequence features");
   }
   
   my $sth = $self->prepare("

modules/Bio/EnsEMBL/DBSQL/ProxyDnaAlignFeatureAdaptor.pm

@@ -52,7 +52,7 @@ use vars qw(@ISA);
 
   Arg [1]    : string $constraint
   Arg [2]    : string $logic_name
-  Example    : 
+  Example    : none
   Description: Overrides the Bio::EnsEMBL::DNAAlignFeatureAdaptor generic_fetch
                method.  Normally requests will still be forwarded to the 
                core (primary) database with the exception of requests that
@@ -76,12 +76,85 @@ sub generic_fetch {
       return $est_adaptor->generic_fetch($constraint, $logic_name);
     }
   }
-    
+  
   #use the core adaptor
   return $self->{'_primary_adaptor'}->generic_fetch($constraint, $logic_name);
 }
 
 
+=head2 store
+
+  Arg [1]    : Bio::EnsEMBL::DnaDnaAlignFeature $feature
+  Example    : none
+  Description: overrides the store method to ensure that the est database
+               is used to store ex_e2g_features
+  Returntype : see DnaAlignFeatureAdaptor::store
+  Exceptions : none
+  Caller     : general
+
+=cut
+
+sub store {
+  my ($self, @sfs) = @_;
+
+  my $est_features = [];
+  my $core_features = [];
+
+  my $est_db = $self->db()->get_db_adaptor('est');
+  if(defined $est_db) {
+    foreach my $f (@sfs) {
+      if($f->analysis() && $f->analysis()->logic_name() eq 'ex_e2g_feat') {
+	push @$est_features, $f;
+      } else {
+	push @$core_features, $f;
+      }
+      #forward request to the EST db
+      my $est_adaptor = $est_db->get_DnaAlignFeatureAdaptor();
+      if(scalar @$est_features) {
+	$est_adaptor->store(@$est_features);
+      }
+      if(scalar @$core_features) {
+	$self->{'_primary_adaptor'}->store(@$core_features);
+      }
+    }
+  }
+
+  #use the core adaptor
+  return $self->{'_primary_adaptor'}->store(@sfs);
+}
+
+
+=head2 remove
+
+  Arg [1]    : Bio::EnsEMBL::DnaDnaAlignFeature $feature
+  Example    : none
+  Description: overrides the remove method to ensure that the est database
+               is used to remove ex_e2g_features
+  Returntype : none
+  Exceptions : none
+  Caller     : general
+
+=cut
+
+sub remove {
+  my ($self, $feature) = @_;
+
+  if($feature && $feature->analysis && 
+     $feature->analysis()->logic_name() eq 'ex_e2g_feat') {
+    my $est_db = $self->db()->get_db_adaptor('est');
+
+    if(defined $est_db) {
+      #forward request to the EST db
+      my $est_adaptor = $est_db->get_DnaAlignFeatureAdaptor();
+      return $est_adaptor->remove($feature);
+    }
+  }
+
+  #use the core adaptor
+  return $self->{'_primary_adaptor'}->remove($feature);
+}
+
+
 
 
 

modules/Bio/EnsEMBL/RepeatFeature.pm

@@ -69,7 +69,7 @@ sub get_RepeatConsensus {
 sub dbID {
     my( $self, $db_id ) = @_;
     
-    if ($db_id) {
+    if (defined $db_id) {
         $self->{'_db_id'} = $db_id;
     }
     return $self->{'_db_id'};

modules/Bio/EnsEMBL/SimpleFeature.pm

@@ -77,7 +77,7 @@ sub display_label{
 sub dbID{
   my ($self, $arg) = @_;
 
-  if($arg){
+  if(defined $arg){
     $self->{_database_id} = $arg;
   }