Sets HSP chr fileds to NULL when searches are removed to avoid contamination...

Sets HSP chr fileds to NULL when searches are removed to avoid contamination with subsequent searches (e.g. in contigview)

modules/Bio/EnsEMBL/External/BlastAdaptor.pm

@@ -174,6 +174,13 @@ SELECT object
 FROM   blast_hsp%s
 WHERE  hsp_id = ? ";
 
+our $SQL_HSP_REMOVE = "
+UPDATE  blast_hsp%s
+SET     chr_name  = NULL,
+        chr_start = NULL,
+        chr_end   = NULL
+WHERE   hsp_id    = ?";
+
 
 #----------------------------------------------------------------------
 
@@ -299,19 +306,22 @@ sub remove {
   my $self = shift;
   my $obj = shift;
   if( $obj->isa("Bio::Tools::Run::EnsemblSearchMulti") ){
+    return 1; # Nothing to do here
     #return $self->remove_search_multi( @_ );
   }
   elsif( $obj->isa("Bio::Search::Result::ResultI") ){
+    return 1; # Nothing to do here
     #return $self->remove_result( @_ );
   }
   elsif( $obj->isa("Bio::Search::Hit::HitI") ){
+    return 1; # Nothing to do here
     #return $self->remove_hit( @_ );
   }
   elsif( $obj->isa("Bio::Search::HSP::HSPI") ){
-    #return $self->remove_hsp( @_ );
+    return $self->remove_hsp( $obj ); # Run HSP-specific code
   }
-  $self->throw( "Do not know how to remove objects of type ".
-		ref($obj) );
+  #$self->warn( "Do not know how to remove objects of type ".ref($obj) );
+  return undef();
 }
 #----------------------------------------------------------------------
 =head2 store_search_multi
@@ -621,6 +631,38 @@ sub retrieve_hsp{
   return $frozen;
 }
 
+#----------------------------------------------------------------------
+
+=head2 remove_hsp
+
+  Arg [1]   : $hsp object to be removed
+  Function  : 'removes' hsp from e.g. contigview by setting chr fields
+              to null
+  Returntype: 
+  Exceptions: 
+  Caller    : $self->remove
+  Example   : 
+
+=cut
+
+sub remove_hsp {
+  my $self = shift;
+  my $hsp  = shift || 
+    $self->throw( "Need a Bio::Search::HSP::EnsemblHSP obj" );
+
+  my $dbh  = $self->db->db_handle;
+
+  my ( $id, $use_date ) = split( '!!', $hsp->token || '');
+  $use_date ||= $hsp->use_date() || $hsp->use_date($self->use_date('HSP'));
+
+  my $sth = $dbh->prepare( sprintf $SQL_HSP_REMOVE, $use_date );
+  my @bound = ( $id );
+  my $rv = $sth->execute( @bound ) || $self->throw( $sth->errstr );
+  $sth->finish;
+  return 1;
+}
+
+
 
 #----------------------------------------------------------------------