tripal_blast/theme/blast_report_alignment_row.tpl.php

<?php
/**
 * This Template generates the HTML for a single Alignment row in a BLAST report
 *
 * Variables Available in this template:
 *   $HSPs: an array of HSPs for the current BLAST result. This follows the structure
 *     layed out in the XML file but has been made an array instead of a SimpleXML object
 *     for ease of processing and abstration.
 */
?>

<div class="title">Alignment</div>

<?php
  foreach($HSPs as $hsp) {
?>

  <div class="hsp-title">HSP <?php print $hsp['Hsp_num']?></div>
  <div class="alignment-metrics">
    <span class="identity">
      Identity=&nbsp;
      <?php print $hsp['Hsp_identity']; ?>/<?php print $hsp['Hsp_align-len']; ?> (<?php print round($hsp['Hsp_identity']/$hsp['Hsp_align-len']*100, 2, PHP_ROUND_HALF_EVEN);?>%)
    </span>,&nbsp;
    <span class="positive">
      Positive=&nbsp;
      <?php print $hsp['Hsp_positive']; ?>/<?php print $hsp['Hsp_align-len']; ?> (<?php print round($hsp['Hsp_positive']/$hsp['Hsp_align-len']*100, 2, PHP_ROUND_HALF_EVEN);?>%)
    </span>
    <span class="coord-summary">
      Query Matches <?php print $hsp['Hsp_query-from'] . ' to ' . $hsp['Hsp_query-to']; ?>
      Hit Matches = <?php print $hsp['Hsp_hit-from'] . ' to ' . $hsp['Hsp_hit-to']; ?>
    </span>
  </div>
  <div class="alignment">
    <div class="alignment-row">
      <?php 
      // We want to display the alignment with a max 60 residues per line with line numbers indicated.
      // First break up the strings.
      $query = str_split($hsp['Hsp_qseq'], 60);
      $matches = str_split($hsp['Hsp_midline'], 60);
      $hit = str_split($hsp['Hsp_hseq'], 60);
      // determine the max length of the coordinate string to use when padding.
      $coord_length = strlen($hsp['Hsp_hit-from']) + 3;
      $coord_length = (strlen($hsp['Hsp_query-to']) + 3 > $coord_length) ? strlen($hsp['Hsp_query-to']) + 3 : $coord_length;

      // Now foreach chink determined above...
      foreach (array_keys($query) as $k) {
        // Determine the current coordinates.
        $coord['qstart'] = $hsp['Hsp_query-from'] + ($k * 60);
        $coord['qstart'] = ($k == 0) ? $coord['qstart'] : $coord['qstart'];
        
        // code added to fix the range issue
        // Cordinates can increase or decrease
        if($hsp['Hsp_hit-from'] < $hsp['Hsp_hit-to']) {
            $coord['hstart'] = $hsp['Hsp_hit-from'] + ($k * 60);    
          }
          else {
            $coord['hstart'] = $hsp['Hsp_hit-from'] - ($k * 60);
          }
//          $coord['qstop'] = $hsp['Hsp_query-from'] + (($k + 1) * 60) - 1;
//          $coord['qstop'] = ($coord['qstop'] > $hsp['Hsp_query-to']) ? $hsp['Hsp_query-to'] : $coord['qstop'];
      
          if ($hsp['Hsp_hit-from'] < $hsp['Hsp_hit-to']) {
            $coord['hstop'] = $hsp['Hsp_hit-from'] + (($k + 1) * 60) - 1;
            $coord['hstop'] = ($coord['hstop'] > $hsp['Hsp_hit-to']) ? $hsp['Hsp_hit-to'] : $coord['hstop'];
          
          }
          else {
            $coord['hstop'] = $hsp['Hsp_hit-from'] - (($k + 1) * 60) + 1;
            $coord['hstop'] = ($coord['hstop'] < $hsp['Hsp_hit-to']) ? $hsp['Hsp_hit-to'] : $coord['hstop'];
          }
          
          // Pad these coordinates to ensure columned display.
          foreach ($coord as $ck => $val) {
            $pad_type = (preg_match('/start/', $ck)) ? STR_PAD_LEFT : STR_PAD_RIGHT;
            $coord[$ck] = str_pad($val, $coord_length, '#', $pad_type);
            $coord[$ck] =  str_replace('#', '&nbsp', $coord[$ck]);
          }
      ?>
        <div class="alignment-subrow">
          <div class="query">
            <span class="alignment-title">Query:</span>&nbsp;&nbsp;
            <span class="alignment-start-coord"><?php print $coord['qstart']; ?></span>
            <span class="alignment-residues"><?php print $query[$k]; ?></span>
            <span class="alignment-stop-coord"><?php print $coord['qstop']; ?></span>
          </div>
          <div class="matches">
            <?php print  str_repeat('&nbsp;', 8); ?>
            <?php print str_repeat('&nbsp;', $coord_length); ?>
            <span class="alignment-residues"><?php print str_replace(' ', '&nbsp', $matches[$k]); ?></span>
          </div>
          <div class="hit">
            <span class="alignment-title">Sbjct:</span>&nbsp;&nbsp;
            <span class="alignment-start-coord"><?php print $coord['hstart']; ?></span>
            <span class="alignment-residues"><?php print $hit[$k]; ?></span>
            <span class="alignment-stop-coord"><?php print $coord['hstop']; ?></span>
          </div>
        </div>
      <?php } ?>
    </div>
  </div>

<?php
  }
?>