Merge branch 'master' of git.drupal.org:sandbox/amirmhzadeh/2237115

theme/blast_report.tpl.php

@@ -63,59 +63,72 @@ if ($xml) {
   // where each hit results in two rows in the table: 1) A summary of the query/hit and
   // significance and 2) additional information including the alignment
   foreach($xml->{'BlastOutput_iterations'}->children() as $iteration) {
-    foreach($iteration->{'Iteration_hits'}->children() as $hit) {
-      if (is_object($hit)) {
-        $count +=1;
-
-        $zebra_class = ($count % 2 == 0) ? 'even' : 'odd';
-
-        // SUMMARY ROW
-
-        // If the id is of the form gnl|BL_ORD_ID|### then the parseids flag
-        // to makeblastdb did a really poor job. In thhis case we want to use
-        // the def to provide the original FASTA header.
-        $hit_name = (preg_match('/BL_ORD_ID/', $hit->{'Hit_id'})) ? $hit->{'Hit_def'} : $hit->{'Hit_id'};
-
-        $score = $hit->{'Hit_hsps'}->{'Hsp'}->{'Hsp_score'};
-        $evalue = $hit->{'Hit_hsps'}->{'Hsp'}->{'Hsp_evalue'};
+    $children_count = $iteration->{'Iteration_hits'}->children()->count();
+    if($children_count != 0) {
+      foreach($iteration->{'Iteration_hits'}->children() as $hit) {
+	if (is_object($hit)) {
+	  $count +=1;
+   	  $zebra_class = ($count % 2 == 0) ? 'even' : 'odd';
+
+	  // SUMMARY ROW
+	  // If the id is of the form gnl|BL_ORD_ID|### then the parseids flag
+	  // to makeblastdb did a really poor job. In thhis case we want to use
+	  // the def to provide the original FASTA header.
+	  $hit_name = (preg_match('/BL_ORD_ID/', $hit->{'Hit_id'})) ? $hit->{'Hit_def'} : $hit->{'Hit_id'};
+       
+          $score = $hit->{'Hit_hsps'}->{'Hsp'}->{'Hsp_score'};
+	  $evalue = $hit->{'Hit_hsps'}->{'Hsp'}->{'Hsp_evalue'};
+	  $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' => $hit_name, 'class' => array('hit')),
+			‘evalue' => array('data' => $evalue, 'class' => array('evalue')),
+			'arrow-col' => array('data' => '<div class="arrow"></div>', 'class' => array('arrow-col'))
+		      ),
+		     'class' => array('result-summary')
+	            );
+	  $rows[] = $row;
+	  // ALIGNMENT ROW (collapsed by default)
+	  // Process HSPs
+	  $HSPs = array();
+	  foreach ($hit->{'Hit_hsps'}->children() as $hsp_xml) {
+	    $HSPs[] = (array) $hsp_xml;
+	  }
+          $row = array(
+			'data' => array(
+			'number' => '',
+			'query' => array(
+			'data' => theme('blast_report_alignment_row', array('HSPs' => $HSPs)),
+			'colspan' => 4,
+			)
+	              ),
+			'class' => array('alignment-row', $zebra_class),
+			'no_striping' => TRUE
+		    );
+          $rows[] = $row;
+	 }// end of if - checks $hit
+      } //end of foreach - iteration_hits
+    }	// end of if - check for iteration_hits
+    else {
+	$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' => $hit_name, 'class' => array('hit')),
-            'evalue' => array('data' => $evalue, 'class' => array('evalue')),
-            'arrow-col' => array('data' => '<div class="arrow"></div>', 'class' => array('arrow-col'))
-          ),
-          'class' => array('result-summary')
-        );
+                '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;
-
-        // ALIGNMENT ROW (collapsed by default)
-        // Process HSPs
-        $HSPs = array();
-        foreach ($hit->{'Hit_hsps'}->children() as $hsp_xml) {
-          $HSPs[] = (array) $hsp_xml;
-        }
-
-        $row = array(
-          'data' => array(
-            'number' => '',
-            'query' => array(
-              'data' => theme('blast_report_alignment_row', array('HSPs' => $HSPs)),
-              'colspan' => 4,
-            )
-          ),
-          'class' => array('alignment-row', $zebra_class),
-          'no_striping' => TRUE
-        );
-        $rows[] = $row;
-
-      }
-    }
+		} // end of else		
   }
-
   print theme('table', array(
       'header' => $header,
       'rows' => $rows,