--- SHSubSearch.pm	2007/07/16 20:04:51	1.6
+++ SHSubSearch.pm	2007/12/06 14:58:03	1.8
@@ -36,7 +36,7 @@
 
 =head3 Form
 
-C<< my $html = $shelp->Form(); >>
+    my $html = $shelp->Form();
 
 Generate the HTML for a form to request a new search.
 
@@ -79,7 +79,7 @@
 
 =head3 Find
 
-C<< my $resultCount = $shelp->Find(); >>
+    my $resultCount = $shelp->Find();
 
 Conduct a search based on the current CGI query parameters. The search results will
 be written to the session cache file and the number of results will be
@@ -101,10 +101,8 @@
     if (! $spec) {
         $self->SetMessage("No subsystem or class selected.");
     } else {
-        # Create a feature data object to store our results.
-        my $fd = FeatureData->new($self);
-        # We need to build a query to get our features. We need to remember
-        # the filter clause format and the parameter.
+        # We need to build a query to get our features. This involves building
+        # a filter clause and a parameter list.
         my ($filterClause, $parameter);
         if ($spec =~ /^id=(.+)$/) {
             # Here we're filtering for a single subsystem.
@@ -140,16 +138,16 @@
             $self->DefaultColumns($rhelp);
             # Initialize the session file.
             $self->OpenSession($rhelp);
-            # Initialize the result counter.
+            # Clear the result counter.
             $retVal = 0;
-            # Loop through the selected features.
+            # Process the query results.
             while (my $record = $query->Fetch()) {
-                $fd->Store($record);
-                $self->PutFeature($fd);
+                # Compute the sort key.
+                my $sort = $rhelp->SortKey($record);
+                # Store this feature.
+                $rhelp->PutData($sort, $record->PrimaryValue('Feature(id)'), $record);
+                # Increment the result counter.
                 $retVal++;
-                if ($retVal % 100 == 0) {
-                    $self->PrintLine("$retVal features processed.<br />");
-                }
             }
             # Close the session file.
             $self->CloseSession();
@@ -161,7 +159,7 @@
 
 =head3 Description
 
-C<< my $htmlText = $shelp->Description(); >>
+    my $htmlText = $shelp->Description();
 
 Return a description of this search. The description is used for the table of contents
 on the main search tools page. It may contain HTML, but it should be character-level,
@@ -176,4 +174,4 @@
     return "Search for genes by keyword in a specified subsystem or subsystem class.";
 }
 
-1;
\ No newline at end of file
+1;