tripal_blast/theme/blast_report.tpl.php

<?php

/**
 * Display the results of a BLAST job execution
 *
 * Variables Available in this template:
 *   $xml_filename: The full path & filename of XML file containing the BLAST results
 */
?>

<!-- JQuery controlling display of the alignment information (hidden by default) -->
<script type="text/javascript">
  $(document).ready(function(){

    // Hide the alignment rows in the table
    // (ie: all rows not labelled with the class "result-summary" which contains the tabular
    // summary of the hit)
    $("#blast_report tr:not(.result-summary)").hide();
    $("#blast_report tr:first-child").show();

    // When a results summary row is clicked then show the next row in the table
    // which should be corresponding the alignment information
    $("#blast_report tr.result-summary").click(function(){
      $(this).next("tr").toggle();
      $(this).find(".arrow").toggleClass("up");
    });
  });
</script>

<p><strong>Download</strong>:
  <a href="<?php print '../../' . $html_filename; ?>">HTML</a>,
  <a href="<?php print '../../' . $tsv_filename; ?>">Tab-Delimited</a>,
  <a href="<?php print '../../' . $xml_filename; ?>">XML</a>
</p>

<p>The following table summarizes the results of your BLAST. To see additional information
about each hit including the alignment, click on that row in the table to expand it.</p>

<?php

// Load the XML file
$xml = simplexml_load_file($xml_filename);

/**
 * We are using the drupal table theme functionality to create this listing
 * @see theme_table() for additional documentation
 */

if ($xml) {
  // Specify the header of the table
  $header = array(
    'number' =>  array('data' => '#', 'class' => array('number')),
    'query' =>  array('data' => 'Query Name', 'class' => array('query')),
    'hit' =>  array('data' => 'Hit Name', 'class' => array('hit')),
    'evalue' =>  array('data' => 'E-Value', 'class' => array('evalue')),
    'arrow-col' =>  array('data' => '', 'class' => array('arrow-col'))
  );

  $rows = array();
  $count = 0;

  // Parse the BLAST XML to generate the rows of the table
  // 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) {
    $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' =>  $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;
		} // end of else		
  }
  print theme('table', array(
      'header' => $header,
      'rows' => $rows,
      'attributes' => array('id' => 'blast_report'),
    ));
}
else {
  drupal_set_title('BLAST: Error Encountered');
  print '<p>We encountered an error and are unable to load your BLAST results.</p>';
}
?>