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
 *    @deepaksomanadh: $job_data = meta data related to the current job
 */

// Set ourselves up to do link-out if our blast database is configured to do so.
$linkout = FALSE;
if ($blastdb->linkout->none === FALSE) {
  $linkout_type  = $blastdb->linkout->type;
  $linkout_regex = $blastdb->linkout->regex;
  
  // Note that URL prefix is not required if linkout type is 'custom'
  if (isset($blastdb->linkout->db_id->urlprefix) && !empty($blastdb->linkout->db_id->urlprefix)) {
    $linkout_urlprefix = $blastdb->linkout->db_id->urlprefix;
  }

  // Check that we can determine the linkout URL.
  // (ie: that the function specified to do so, exists).
  if (function_exists($blastdb->linkout->url_function)) {
    $url_function = $blastdb->linkout->url_function;
    $linkout = TRUE;
  }
}

// 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;

?>

<script type="text/javascript">
  window.onload = function() {
    if (!window.location.hash) {
      window.location = window.location + '#loaded';
      window.location.reload();
    }
  }

  // JQuery controlling display of the alignment information (hidden by default)
  $(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>

<style>
.no-hits-message {
  color: red;
  font-style: italic;
}
</style>

<div class="blast-report">

<!-- Provide Information to the user about their blast job -->
<div class="blast-job-info">
<?php if($xml): ?>
  <div class="blast-download-info"><strong>Download</strong>:
    <a href="<?php print '../../' . $html_filename; ?>">Alignment</a>,
    <a href="<?php print '../../' . $tsv_filename; ?>">Tab-Delimited</a>,
    <a href="<?php print '../../' . $xml_filename; ?>">XML</a>
  </div>
<?php endif; ?>
  <br />
  <div class="blast-query-info"><strong>Query Information</strong>: 
    <?php print $blast_job->display['query_info'];?></div>
  <div class="blast-target-info"><strong>Search Target</strong>: 
    <?php print $blast_job->display['target'];?></div>
  <div class="blast-date-info"><strong>Submission Date</strong>: 
    <?php print $blast_job->display['date'];?></div>
  <div class="blast-cmd-info"><strong>BLAST Command executed</strong>: 
    <?php print $blast_job->display['blast_cmd'];?></div>
</div>
<br />

<?php

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

if ($xml) {
?>

<p>The following table summarizes the results of your BLAST. 
Click on a <em>triangle </em> on the left to see the alignment and a visualization of the hit, 
and click the <em>target name </em> to get more information about the target hit.</p>

<?php
  // Specify the header of the table
  $header = array(
    'arrow-col' =>  array('data' => '', 'class' => array('arrow-col')),
    'number' =>  array('data' => '#', 'class' => array('number')),
    'query' =>  array('data' => 'Query Name  (Click for alignment & visualization)', 'class' => array('query')),
    'hit' =>  array('data' => 'Target Name', 'class' => array('hit')),
    'evalue' =>  array('data' => 'E-Value', 'class' => array('evalue')),
  );

  $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();

    // Save some information needed for the hit visualization.
    $target_name = '';
    $q_name = $xml->{'BlastOutput_query-def'};
    $query_size = $xml->{'BlastOutput_query-len'};
    $target_size = $iteration->{'Iteration_stat'}->{'Statistics'}->{'Statistics_db-len'};
    
    if ($children_count != 0) {
      foreach ($iteration->{'Iteration_hits'}->children() as $hit) {
        if (is_object($hit)) {
          $count +=1;
          $zebra_class = ($count % 2 == 0) ? 'even' : 'odd';
          $no_hits = FALSE;

          // SUMMARY ROW
          // -- Save additional information needed for the summary.
          $score = (float) $hit->{'Hit_hsps'}->{'Hsp'}->{'Hsp_score'};
          $evalue = (float) $hit->{'Hit_hsps'}->{'Hsp'}->{'Hsp_evalue'};
          $query_name = (string) $iteration->{'Iteration_query-def'};
          
          // 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.
          // @todo Deepak changed this to use just the hit_def; inquire as to why.
          $hit_name = (preg_match('/BL_ORD_ID/', $hit->{'Hit_id'})) ? $hit->{'Hit_def'} : $hit->{'Hit_id'};  
          // Used for the hit visualization to ensure the name isn't truncated.
          $hit_name_short = (preg_match('/^([^\s]+)/', $hit_name, $matches)) ? $matches[1] : $hit_name;

          // Round e-value to two decimal values.
          $rounded_evalue = '';
          if (strpos($evalue,'e') != false) {
            $evalue_split = explode('e', $evalue);
            $rounded_evalue = round($evalue_split[0], 2, PHP_ROUND_HALF_EVEN);            
            $rounded_evalue .= 'e' . $evalue_split[1];
          }
          else { 
            $rounded_evalue = $evalue;
          }
          
          // State what should be in the summary row for theme_table() later.
          $summary_row = array(
            'data' => array(
              'arrow-col' => array('data' => '<div class="arrow"></div>', 'class' => array('arrow-col')),
              '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' => $rounded_evalue, 'class' => array('evalue')),
            ),
            'class' => array('result-summary')
          );
        
          // ALIGNMENT ROW (collapsed by default)
          // Process HSPs
          $HSPs = array();

          // We need to save some additional summary information in order to draw the
          // hit visualization. First, initialize some variables...
          $track_start = INF;
          $track_end = -1;
          $hsps_range = '';
          $hit_hsps = '';
          $hit_hsp_score = '';
          $target_size = $hit->{'Hit_len'};
          $Hsp_bit_score = '';
          
          // Then for each hit hsp, keep track of the start of first hsp and the end of
          // the last hsp. Keep in mind that hsps might not be recorded in order.
          foreach ($hit->{'Hit_hsps'}->children() as $hsp_xml) {
            $HSPs[] = (array) $hsp_xml;
    
            if ($track_start > $hsp_xml->{'Hsp_hit-from'}) {
              $track_start = $hsp_xml->{'Hsp_hit-from'} . "";
            }
            if ($track_end < $hsp_xml->{'Hsp_hit-to'}) {
              $track_end = $hsp_xml->{'Hsp_hit-to'} . "";
            }

            // The BLAST visualization code requires the hsps to be formatted in a
            // very specific manner. Here we build up the strings to be submitted.
            // hits=4263001_4262263_1_742;4260037_4259524_895_1411;&scores=722;473;
            $hit_hsps .=  $hsp_xml->{'Hsp_hit-from'} . '_' . 
                          $hsp_xml->{'Hsp_hit-to'} . '_' . 
                          $hsp_xml->{'Hsp_query-from'} . '_' . $hsp_xml->{'Hsp_query-to'} . 
                          ';';  
            $Hsp_bit_score .=   $hsp_xml->{'Hsp_bit-score'} .';';    
          }
          // Finally record the range.
          // @todo figure out why we arbitrarily subtract 50,000 here...
          // @more removing the 50,000 and using track start/end appears to cause no change...
          $range_start = (int) $track_start;// - 50000;
          $range_end = (int) $track_end;// + 50000;
          if ($range_start < 1) $range_start = 1;  
   

          // Call the function to generate the hit image.
          $hit_img = generate_blast_hit_image($target_name, $Hsp_bit_score, $hit_hsps, 
                                   $target_size, $query_size, $q_name, $hit_name_short);


          // State what should be in the alignment row for theme_table() later.
          $alignment_row = array(
            'data' => array(
              'arrow' => array(
                'data' => theme('blast_report_alignment_row', array('HSPs' => $HSPs, 'hit_visualization' => $hit_img)),
                'colspan' => 5,
              ),
            ),
            'class' => array('alignment-row', $zebra_class),
            'no_striping' => TRUE
          );
          
          // LINK-OUTS.
          // It was determined above whether link-outs were supported for the
          // tripal blast database used as a search target. Thus we only want to 
          // determine a link-out if it's actually supported... ;-)
          if ($linkout) {
          
            // First extract the linkout text using the regex provided through
            // the Tripal blast database node.
            if (preg_match($linkout_regex, $hit_name, $linkout_match)) {
              $hit->{'linkout_id'} = $linkout_match[1];
              $hit->{'hit_name'} = $hit_name;
            
              // Allow custom functions to determine the URL to support more complicated
              // link-outs rather than just using the tripal database prefix.
              $hit_url = call_user_func(
                $url_function,
                $linkout_urlprefix,
                $hit,
                array(
                  'query_name' => $query_name,
                  'score'      => $score,
                  'e-value'    => $evalue,
                  'HSPs'       => $HSPs,
                  'Target'     => $blastdb->title,
                )
              );

              // Create Link.
              if ($hit_url) {
                // It is important to url-encode links, especially in this case,
                // since jbrowse links have double quotes in them which result in
                // truncated links due to <a href="yoururl"></a> (notice the double quotes).
                $hit_name = l(
                  $hit->{'linkout_id'},
                  $hit_url,
                  array('attributes' => array('target' => '_blank'))
                );
              }
            }
                        
            // Replace the target name with the link.
            $summary_row['data']['hit']['data'] = $hit_name;
          }
          
          // ADD TO TABLE ROWS
          $rows[] = $summary_row;
          $rows[] = $alignment_row;

        }//end of if - checks $hit
      }//end of foreach - iteration_hits
    }//end of if - check for iteration_hits
    
    else {
      // Currently where the "no results" is added.
      $query_name = $iteration->{'Iteration_query-def'};
      $query_with_no_hits[] = $query_name;

    }//no results
  }//end of foreach - BlastOutput_iterations

  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'),
        'sticky' => FALSE
      ));
    }
  }//handle no hits
}//XML exists

else {
  drupal_set_title('BLAST: Error Encountered');
  print '<p class="blast-no-results">We encountered an error and are unable to load your BLAST results.</p>';
}
?>

<p><?php print l(
  'Edit this query and re-submit', 
  $blast_job->form_options['job_url'],
  array('query' => array('jid' => blast_ui_make_secret($job_id))));
?></p>
</div>

<!-- Recent Jobs -->
<?php

  // Gets the list of recent jobs filtered to the current blast program (ie: blastn).
  
  if ($recent_jobs) {
  
    print '<h2>Recent Jobs</h2>';
    
    $table = array(
      'header' => array('Query Information', 'Search Target', 'Date Requested', ''),
      'rows' => array(),
      'attributes' => array('class' => array('tripal-blast', 'recent-jobs')),
      'sticky' => FALSE
    );
  
    foreach ($recent_jobs as $job) {

      // Define a row for the current job.
      $table['rows'][] = array(
        $job['query_info'],
        $job['target'],
        $job['date'],
        l('See Results', $job['job_output_url'])
      );
    }
    
    print theme('table', $table);
  }
?>