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>

<?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
 */

// 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_def;
      if (preg_match('/(\w+)/', $hit_name, $matches)) {
        $hit_name = $matches[1];
      }
      $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'),
  ));
?>