Now does mapping based on cigar strings!

Currently leaves any features that, when mapped back into the
query coordinate system, contains gaps or are split.  These will
still be shown in the target coordinate system but are tagged
"[unmappable]".

misc-scripts/das_client/guzzle.pl

@@ -172,6 +172,9 @@ if ($use_graphics) {
 }
 
 if ($use_mapping) {
+    #require Storable;
+    #import Storable 'dclone';	    # Not just yet...
+
     require Bio::EnsEMBL::Mapper;
 }
 
@@ -338,7 +341,7 @@ sub do_query
 
 		    foreach my $mapped (@mapped) {
 			next if ($mapped->isa('Bio::EnsEMBL::Mapper::Gap'));
-			$range = ':' . $mapped->start() . ',' .  $mapped->end();
+			$range = ':' . $mapped->start . ',' .  $mapped->end;
 			push(@{ $query{$ti}{SEGMENT} }, $ti . $range);
 		    }
 		} else {
@@ -365,17 +368,16 @@ sub do_query
 	    -dsn	=> $query->{DSN},
 	    -segment    => $query->{SEGMENT});
 
-	next if (!$reply->is_success());
+	next if (!$reply->is_success);
 
 	if (exists $query->{MAPPER}) {
 	    # Map results using align mapper.
 	    # Scary stuff.  If this works, I deserve a beer.
 
-	    my @results = $reply->results();
+	    my @results = $reply->results;
 	    foreach my $result (@results) {
                 # Tag the string that we later use in the tabla
                 # and graphics.
-		$result->group($result->group() . " [$seqid]");
 
                 # Do the reverse mapping from the target
                 # coodinate system into the query coordinate
@@ -387,9 +389,22 @@ sub do_query
                 # method of Bio::Das::Request to add ranges that
                 # were split into two or more ranges.
 
+                # FIXME:  For now, just drop anyhting which
+                # doesn't map cleanly (that splits, contracts,
+                # or maps to a gap).
+
 		my @mapped = $query->{MAPPER}->map_coordinates(
-		    'targetID', $result->start(), $result->stop(), 1,
+		    'targetID', $result->start, $result->stop, 1,
 		    'targetCOORD');
+
+		if (scalar @mapped > 1 ||
+		    $mapped[0]->isa('Bio::EnsEMBL::Mapper::Gap')) {
+		    $result->group($result->group . " [unmappable]");
+		} else {
+		    $result->group($result->group . " [mapped to $seqid]");
+		    $result->start($mapped[0]->start);
+		    $result->stop($mapped[0]->end);
+		}
 	    }
 	    #print $cgi->pre(Dumper($reply));
 	}
@@ -479,7 +494,9 @@ sub create_graphics
 		    -primary	=> $feature->group,
 		    -source_tag	=> $feature->type->label,
 		    -tag	=> {
-			colour	=> $table_row->{COLOUR}
+			colour	=>
+			    ($feature->label eq 'GAP' ?
+				'white' : $table_row->{COLOUR})
 		    } ));
 	}
     }