Amended 'no results' message to exist outside the table and be highlighted in red. This solution did take into account that multiple query seq. might have been submitted with only some not having hits in which case a comma-separated list of those without hits is shown.

theme/blast_report.tpl.php

@@ -7,8 +7,8 @@
  *   $xml_filename: The full path & filename of XML file containing the BLAST results
  */
 
- // Set ourselves up to do link-out if our blast database is configured to do so.
- $linkout = FALSE;
+// Set ourselves up to do link-out if our blast database is configured to do so.
+$linkout = FALSE;
 if ($blastdb->linkout->none === FALSE) {
   $linkout = TRUE;
   $linkout_regex = $blastdb->linkout->regex;
@@ -19,6 +19,15 @@ if ($blastdb->linkout->none === FALSE) {
     $linkout = FALSE;
   }
 }
+
+// Handle no hits. This following array will hold the names of all query
+// sequences which didn't have any hits.
+$query_with_no_hits = array();
+
+// Furthermore, if no query sequences have hits we don't want to bother listing
+// them all but just want to give a single, all-include "No Results" message.
+$no_hits = TRUE;
+
 ?>
 
 <!-- JQuery controlling display of the alignment information (hidden by default) -->
@@ -40,6 +49,13 @@ if ($blastdb->linkout->none === FALSE) {
   });
 </script>
 
+<style>
+.no-hits-message {
+  color: red;
+  font-style: italic;
+}
+</style>
+
 <p><strong>Download</strong>:
   <a href="<?php print '../../' . $html_filename; ?>">HTML</a>,
   <a href="<?php print '../../' . $tsv_filename; ?>">Tab-Delimited</a>,
@@ -82,6 +98,7 @@ if ($xml) {
         if (is_object($hit)) {
           $count +=1;
           $zebra_class = ($count % 2 == 0) ? 'even' : 'odd';
+          $no_hits = FALSE;
 
           // SUMMARY ROW
           // If the id is of the form gnl|BL_ORD_ID|### then the parseids flag
@@ -143,29 +160,32 @@ if ($xml) {
     else {
 
       // Currently where the "no results" is added.
-	    $count +=1;
-      $query_id = $iteration->{'Iteration_query-ID'};
       $query_name = $iteration->{'Iteration_query-def'};
-      $row = array(
-        'data' => array(
-           'number' => array('data' => $count , 'class' => array('number')),
-           'query' => array('data' => $query_name, 'class' => array('query')),
-           'hit' => array('data' =>  $iteration->{'Iteration_message'}, 'class' => array('hit')),
-           'evalue' => array('data' => "-", 'class' => array('evalue')),
-           'arrow-col' => array('data' => '', 'class' => array('arrow-col'))
-        ),
-        'class' => array('result-summary')
-      );
-      $rows[] = $row;
+      $query_with_no_hits[] = $query_name;
+
 		} // end of else
   }
 
-  // Actually print the table.
-  print theme('table', array(
-      'header' => $header,
-      'rows' => $rows,
-      'attributes' => array('id' => 'blast_report'),
-    ));
+  if ($no_hits) {
+    print '<p class="no-hits-message">No results found.</p>';
+  }
+  else {
+    // We want to warn the user if some of their query sequences had no hits.
+    if (!empty($query_with_no_hits)) {
+      print '<p class="no-hits-message">Some of your query sequences did not '
+      . 'match to the database/template. They are: '
+      . implode(', ', $query_with_no_hits) . '.</p>';
+    }
+
+    // Actually print the table.
+    if (!empty($rows)) {
+      print theme('table', array(
+        'header' => $header,
+        'rows' => $rows,
+        'attributes' => array('id' => 'blast_report'),
+      ));
+    }
+  }
 }
 else {
   drupal_set_title('BLAST: Error Encountered');