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 $iteration) {
    foreach($iteration->{'Iteration_hits'}->children() as $hit) {
      if (is_object($hit)) {
        $count +=1;

        $zebra_class = ($count % 2 == 0) ? 'even' : 'odd';

        // SUMMARY ROW
        $hit_name = $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;

      }
    }
  }

  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>';
}
?>