added caching and embl db call

modules/Bio/EnsEMBL/DBSQL/LiteAdaptor.pm

@@ -52,6 +52,8 @@ sub new {
 sub fetch_virtualgenes_start_end {
     my ( $self, $chr, $vc_start, $vc_end ) =@_;
     my $_db_name = $self->{'_lite_db_name'};
+    my $cache_name = "_virtualgenes_cache_$chr"."_$vc_start"."_$vc_end";
+    return $self->{$cache_name} if( $self->{$cache_name} );
     my $sth = $self->prepare(
         "select g.gene, g.name, 
                 g.chr_name, g.gene_chrom_start, g.gene_chrom_end,
@@ -61,7 +63,10 @@ sub fetch_virtualgenes_start_end {
                 g.chr_name = ? and g.gene_chrom_start <= ? and
                 g.gene_chrom_end >= ?"
     );
-    $sth->execute( $chr, $vc_end, $vc_start );
+    eval {
+        $sth->execute( $chr, $vc_end, $vc_start );
+    };
+    return [] if($@);
     my @genes;
     while( my $row = $sth->fetchrow_arrayref() ) {
         push @genes, {
@@ -77,21 +82,64 @@ sub fetch_virtualgenes_start_end {
             'db'        => $row->[7]
         };
     }
+    return $self->{$cache_name} = \@genes;
     return \@genes
 }
                 
+sub fetch_EMBLgenes_start_end {
+    my ( $self, $chr, $vc_start, $vc_end ) =@_;
+    my $_db_name = $self->{'_lite_db_name'};
+    my $cache_name = "_emblgenes_cache_$chr"."_$vc_start"."_$vc_end";
+    return $self->{$cache_name} if( $self->{$cache_name} );
+    my $sth = $self->prepare(
+        "select g.gene, g.name, 
+                g.chr_name, g.gene_chrom_start, g.gene_chrom_end,
+                g.chrom_strand, gx.display_id, gx.db_name, g.type
+           from $_db_name.embl_gene as g, $_db_name.embl_gene_xref as gx
+          where g.gene = gx.gene and
+                g.chr_name = ? and g.gene_chrom_start <= ? and
+                g.gene_chrom_end >= ?"
+    );
+    eval {
+        $sth->execute( $chr, $vc_end, $vc_start );
+    };
+    return [] if($@);
+    my @genes;
+    while( my $row = $sth->fetchrow_arrayref() ) {
+        push @genes, {
+            'gene'      => $row->[0],
+            'stable_id' => $row->[1],
+            'chr_name'  => $row->[2],
+            'chr_start' => $row->[3],
+            'chr_end'   => $row->[4],
+            'start'     => $row->[3]-$vc_start+1,
+            'end'       => $row->[4]-$vc_start+1,
+            'strand'    => $row->[5],
+            'synonym'   => $row->[6],
+            'db'        => $row->[7],
+            'type'      => $row->[8]
+        };
+    }
+    return $self->{$cache_name} = \@genes;
+    return \@genes
+}
 sub fetch_virtualRepeatFeatures_start_end {
     my ( $self, $chr, $vc_start, $vc_end, $type, $glob_bp ) =@_;
+    my $cache_name = "_repeats_$type"."_cache_$chr"."_$vc_start"."_$vc_end";
+    return $self->{$cache_name} if( $self->{$cache_name} );
 	my $glob_bp ||= 0;
     my $_db_name = $self->{'_lite_db_name'};
     my $sth = $self->prepare(
         "select r.id, r.hid,  r.chr_name, r.repeat_chrom_start, r.repeat_chrom_end, r.repeat_chrom_strand
            from $_db_name.repeat as r
           where r.chr_name = ? and r.repeat_chrom_start <= ? and r.repeat_chrom_end >= ?".
-		  	( (defined $type && $type ne '') ? " and hid like '$type\%'" : '' )
+		  	( (defined $type && $type ne '') ? " and r.type = '$type'" : '' )
     );
 
-    $sth->execute( $chr, $vc_end, $vc_start);
+    eval {
+        $sth->execute( $chr, $vc_end, $vc_start);
+    };
+    return [] if($@);
 
 	my @repeats;
 	my $old_end = -99999999999999999;
@@ -114,6 +162,7 @@ sub fetch_virtualRepeatFeatures_start_end {
 		}
 	  	$old_end = $end;
     }
+    return $self->{$cache_name} = \@repeats;
     return \@repeats;
 }