GenomeDB/mydata/themes/hardwood/templates/blast/blast_report.tpl.php

<?php
/**
 * Display the results of a BLAST job execution
 */

// Set ourselves up to do link-out if our blast database is configured to do so.
$linkout = FALSE;
if ($blast_job->blastdb->linkout->none === FALSE) {
  $linkout_type = $blast_job->blastdb->linkout->type;
  $linkout_regex = $blast_job->blastdb->linkout->regex;

  // Note that URL prefix is not required if linkout type is 'custom'
  if (isset($blast_job->blastdb->linkout->db_id->urlprefix) && !empty($blast_job->blastdb->linkout->db_id->urlprefix)) {
    $linkout_urlprefix = $blast_job->blastdb->linkout->db_id->urlprefix;
  }

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

  if (function_exists($blast_job->blastdb->linkout->url_function)) {
    $url_function = $blast_job->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">

  // 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
    $("table#blast_report tbody tr.odd td").not('.arrow-col').css('cursor', 'default');

    $(".arrow-col").click(function () {
      var tr = $(this).parents('tr').first();
      tr.next('tr').toggle();
      tr.toggleClass('open')
    }).css('cursor', 'pointer');

    /*$("#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):
      $output_files = array();
      if (file_exists($blast_job->files->result->html)) {
        $output_files['html'] = array(
          'path' => $blast_job->files->result->html,
          'title' => 'Alignment',
        );
      }
      if (file_exists($blast_job->files->result->tsv)) {
        $output_files['tsv'] = array(
          'path' => $blast_job->files->result->tsv,
          'title' => 'Tab-Delimited',
        );
      }
      if (file_exists($blast_job->files->result->gff)) {
        $output_files['gff'] = array(
          'path' => $blast_job->files->result->gff,
          'title' => 'GFF3',
        );
      }
      if (file_exists($blast_job->files->result->xml)) {
        $output_files['xml'] = array(
          'path' => $blast_job->files->result->xml,
          'title' => 'XML',
        );
      }
      ?>
      <div class="blast-download-info"><strong>Download</strong>:
        <?php
        $i = 0;
        foreach ($output_files as $file) {
          $i++;
          print l($file['title'], $file['path']);
          if (sizeof($output_files) != $i) {
            print ', ';
          }
        }
        ?>
      </div>
    <?php endif; ?>
    <br/>
    <div class="blast-query-info">
      <strong>Query Information</strong>:
      <?php print $blast_job->files->query; ?>
    </div>
    <div class="blast-target-info">
      <strong>Search Target</strong>:
      <?php print $blast_job->blastdb->db_name; ?>
    </div>
    <div class="blast-date-info">
      <strong>Submission Date</strong>:
      <?php print format_date($blast_job->date_submitted, 'medium'); ?>
    </div>
    <div class="blast-cmd-info">
      <strong>BLAST Command executed</strong>:
      <?php print $blast_job->blast_cmd; ?>
    </div>
    <br/>
    <div class="num-results"><strong>Number of
        Results</strong>: <?php print $num_results; ?></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;
            }


            $hit_link = '';
            if (strpos($blast_job->blast_cmd, 'blastp') === FALSE && strpos($blast_job->blast_cmd, 'blastx') === FALSE) {
              $hit_link = l(
                $hit_name,
                "/feature/$hit_name_short",
                array(
                  'attributes' => array(
                    'target' => '_blank',
                  ),
                )
              );
            }
            else {
              $hit_link = $hit_name;
            }


            // State what should be in the summary row for theme_table() later.
            $summary_row = array(
              'data' => array(
                'arrow-col' => array(
                  'data' => '<button class="btn btn-info btn-sm" type="button"><i class="fa fa-caret-down"></i></button>',
                  'class' => array('arrow-col'),
                ),
                'number' => array('data' => $count, 'class' => array('number')),
                'query' => array(
                  'data' => str_replace("No definition line", "User-provided sequence", $query_name),
                  'class' => array('query'),
                ),
                'hit' => array('data' => $hit_link, '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_name = call_user_func(
                  $url_function,
                  $linkout_urlprefix,
                  $hit,
                  array(
                    'query_name' => $query_name,
                    'score' => $score,
                    'e-value' => $evalue,
                    'HSPs' => $HSPs,
                    'Target' => $blast_job->blastdb->db_name,
                  )
                );
              }

              // 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 "<div class='table-responsve'>";
        print theme(
          'table',
          array(
            'header' => $header,
            'rows' => $rows,
            'attributes' => array('id' => 'blast_report', 'class' => 'table'),
            'sticky' => FALSE,
          )
        );
        print "</div>";
      }
    }//handle no hits
  }//XML exists
  elseif ($too_many_results) {
    print '<div class="messages error">Your BLAST resulted in ' . number_format(
        floatval($num_results)
      ) . ' results which is too many to reasonably display. We have provided the result files for Download at the top of this page; however, we suggest you re-submit your query using a more stringent e-value (i.e. a smaller number).</div>';
  }
  else {
    drupal_set_title('BLAST: Error Encountered');
    print '<div class="messages error">We encountered an error and are unable to load your BLAST results.</div>';
  }
  ?>

  <p><?php print l(
      'Edit this query and re-submit',
      $blast_form_url,
      array('query' => array('resubmit' => blast_ui_make_secret($job_id)))
    );
    ?></p>
</div>

<?php print theme('blast_recent_jobs', array()); ?>