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       = TRUE;
  $linkout_type  = $blastdb->linkout->type;
  $linkout_regex = $blastdb->linkout->regex;
//eksc- linkout vs gbrowse
  if (isset($blastdb->linkout->db_id->urlprefix) && !empty($blastdb->linkout->db_id->urlprefix)) {
    $linkout_urlprefix = $blastdb->linkout->db_id->urlprefix;

    // Furthermore, check that we can determine the URL.
    // (ie: that the function specified to do so, exists).
    if (function_exists($blastdb->linkout->url_function)) {
      $url_function = $blastdb->linkout->url_function;
    }
    else {
      $linkout = FALSE;
    }
  }
  else {
    $linkout = FALSE;
  }
}
//echo "blastdb: <pre>";var_dump($blastdb);echo "</pre>";
echo "LINKOUT: $linkout<br>";
echo "linkout function: $url_function<br>";
echo "linkout URL prefix: $linkout_urlprefix<br>";

// 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>

<p><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>
</p>

<!--  @deepaksomanadh: For displaying BLAST command details -->
<table>
<tr>
  <th>Input query sequence(s) </th>
  <th>Target Database selected </th>
  <th>BLAST command executed </th>
<tr>
<tr>
<?php 
  // get input sequences from job_data variable

echo "job data:<pre>";var_dump($job_id_data);echo "</pre>";
  $query_def = $job_id_data['query_def'];
  echo "<td>";
  echo "<ol>";
  foreach($query_def as $row) {
    echo "<li>";    
    echo  $row . "</li>";
  }
  echo "</ol></td>";
  echo "<td>" .   $job_id_data['db_name'] . "</td>";
 
  include_once("blast_align_image.php");
 
  //display the BLAST command without revealing the internal path
  $blast_cmd = $job_id_data['program'];
  
  foreach($job_id_data['options'] as $key => $value) {
      $blast_cmd .= ' -' . $key. ' ' . $value ;
  }
  print "<td>" . $blast_cmd . "</td>";  
 ?>
</table>

<p>The following table summarizes the results of your BLAST. 
Click on a <strong>triangle </strong> on the left to see the alignment and a visualization of the hit, 
and click the <strong>target name </strong> to open a new window with a genome browser around this hit.</p>

<?php
include_once("blast_align_image.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(
    '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();
    //@deepaksomanadh: Code added for BLAST visualization
    // parameters that need to be passed for BLAST image generation
    $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;

          // RETRIEVE INFO
          $hit_name = (preg_match('/BL_ORD_ID/', $hit->{'Hit_id'})) ? $hit->{'Hit_def'} : $hit->{'Hit_id'};  
          $score = $hit->{'Hit_hsps'}->{'Hsp'}->{'Hsp_score'};
          $evalue = $hit->{'Hit_hsps'}->{'Hsp'}->{'Hsp_evalue'};
          $query_name = $iteration->{'Iteration_query-def'};

          // Round e-val 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;
          }        
        
          // ALIGNMENT ROW (collapsed by default)
          // Process HSPs
          // @deepaksomanadh: Code added for BLAST visualization
          // hit array and corresponding bit scores 
          // hits=4263001_4262263_1_742;4260037_4259524_895_1411;&scores=722;473;
          $HSPs = array();
          $track_start = INF;
          $track_end = -1;
          $hsps_range = '';
          $hit_hsps = '';
          $hit_hsp_score = '';
          $target_size = $hit->{'Hit_len'};
    
          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'} . "";
            }
          }   
          $range_start = (int) $track_start - 50000;
          $range_end = (int) $track_end + 50000;
        
          if ($range_start < 1) 
             $range_start = 1;  

          // For BLAST visualization 
          $target_size = $hit->{'Hit_len'};
        
          foreach ($hit->{'Hit_hsps'}->children() as $hsp_xml) {
            $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'} .';';              
          }      
          
          // SUMMARY ROW
          // If the id is of the form gnl|BL_ORD_ID|### then the parseids flag
          // to makeblastdb did a really poor job. In this case we want to use
          // the def to provide the original FASTA header.
          
          // If our BLAST DB is configured to handle link-outs then use the
          // regex & URL prefix provided to create one.
//eksc- linkout vs gbrowse
          $hit_name = $hit->{'Hit_def'};
          $query_name = $iteration->{'Iteration_query-def'};
 

          // ***** Future modification ***** The gbrowse_url can be extracted from Tripal Database table
//          if(preg_match('/.*(aradu).*/i', $hit_name) == 1) {
//            $gbrowse_url =   'gbrowse_aradu1.0';
//          }
//          else if(preg_match('/.*(araip).*/i', $hit_name) == 1) {
//            $gbrowse_url =  'gbrowse_araip1.0';
//          } else if(preg_match('/.*(phytozome).*/i', $hit_name) == 1) {
//            $gbrowse_url =  'http://legumeinfo.org/chado_phylotree/';
//          }  else {
//            // Not existing in available GBrowse tracks
//            $gbrowse_url = null;
//          }  
          
          // $hit_name_url = l($linkout_urlprefix . $linkout_match[1],
          // array('attributes' => array('target' => '_blank'))
          //  );
/*          
          // Link out functionality to GBrowse
          if ($gbrowse_url == null) {
            // Not a valid hit. Hence, No link outs to GBrowse and the hit name is displayed.
            $hit_name_url = $hit_name;
          }
          else {
            // Link out is possible for this hit
            
            // Check if our BLAST DB is configured to handle link-outs then use the
            // regex & URL prefix provided to create one. 
            // Then, check if the db is configured to handle linkouts
            // For alias targets
            if ($linkout) {
              // For CDS/protein alias targets                
              if(preg_match("/http:/",  $gbrowse_url) == 1) {
                  $hit_url =   $gbrowse_url . $hit_name ;
                  $hit_name_url = l($hit_name, $hit_url, array('attributes' => array('target' => '_blank')));
              } 
              else if (preg_match($linkout_regex, $hit_name, $linkout_match) == 1) {
                  $hit_name = $linkout_match[1];
                    // matches found 
                  $hit_url =   $GLOBALS['base_url'] . '/' . $gbrowse_url . '?' . 'query=q=';
                  $hit_url .= $hit_name . ';h_feat=' . $iteration->{'Iteration_query-ID'};
                  $hit_name_url = l($hit_name, $hit_url, array('attributes' => array('target' => '_blank')));
              }            
              else {
              // No matches for regex. Hence, linkouts not possible
              $hit_name_url = $hit_name;                
              }  
            }        
            else {
              // For Genome targets              
                
              $hit_url =   $GLOBALS['base_url'] . '/' .  $gbrowse_url . '?' . 'query=' . 'start=' . $range_start . ';' . 'stop=' .
                              $range_end . ';' . 'ref=' . $hit_name . ';' . 'add=' . $hit_name . '+'  . 'BLAST+' . $iteration->{'Iteration_query-ID'} . '+' . $hsps_range . ';h_feat=' . $iteration->{'Iteration_query-ID'} ; 
                              
              $hit_name_url = l($hit_name, $hit_url, array('attributes' => array('target' => '_blank')));
            }
          }// end of GBrowse functionality
*/
          if ($linkout) {
            if (preg_match($linkout_regex, $hit_name, $linkout_match)) {
              $linkout_id = $linkout_match[1];
              $hit->{'linkout_id'} = $linkout_id;
              $hit->{'hit_name'} = $hit_name;
              
              if ($linkout_type == 'link') {
                $hit_url = call_user_func(
                  $url_function,
                  $linkout_urlprefix,
                  $hit,
                  array(
                    'query_name' => $query_name,
                    'score' => $score,
                    'e-value' => $evalue,
                    'HSPs' => $HSPs
                  )
                );

                if ($hit_url) {
/* eksc- l() URL-encodes the URL path too, which is often not what we want.
                  $hit_name = l(
                    $linkout_id,
                    $hit_url,
                    array('attributes' => array('target' => '_blank'))
                  );
*/
                  $hit_name = "
                    <a href=\"$hit_url\" target=\"_blank\">
                      $linkout_id
                    </a>";
                }//link
              }
              else if ($linkout_type == 'gbrowse') {
              	if (function_exists(_custom_get_GBRowse_link) {
                }
                else {
                  $hit_name = _get_GBRowse_link();
                }
              }
              else if ($linkout_type == 'jbrowse') {
                if (function_exists(_custom_get_JBRowse_link) {
                }
                else {
                	$hit_name = _get_JBRowse_link();
                }
              }
            }
          }//handle linkout

          //@deepaksomanadh: Code added for BLAST visualization
          // get the image and display
          $hit_img = generateImage($target_name, $Hsp_bit_score, $hit_hsps, $target_size, $query_size, $q_name, $hit_name);
        
          ob_start(); // Start buffering the output
          imagepng($hit_img, null, 0, PNG_NO_FILTER);
          $b64 = base64_encode(ob_get_contents()); // Get what we've just outputted and base64 it
          imagedestroy($hit_img);
          ob_end_clean();

          // Print the HTML tag with the image embedded
          $hit_img = '<h4><strong> Hit Visualization </strong></h4> <br><img src="data:image/png;base64,'.$b64.'"/>';
          
          $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')),
              '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

          $row = array(
            'data' => array(
              'arrow' => '',
              'number' => '',
              'query' => array(
                'data' => theme('blast_report_alignment_row', array('HSPs' => $HSPs)),
              //  'colspan' => 4,
              ),
              'hit' => array(
                'data' => $hit_img,
                'colspan' => 3,
              ),
            ),
            'class' => array('alignment-row', $zebra_class),
            'no_striping' => TRUE
          );
          $rows[] = $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;

    }// end of else
  }//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'),
      ));
    }
  }
}
else {
  drupal_set_title('BLAST: Error Encountered');
  print '<p>We encountered an error and are unable to load your BLAST results.</p>';
}
?>

<p> <!--  @deepaksomanadh: Building the edit and resubmit URL --> 
  <a style ="align:center" href="<?php print '../../'. $job_id_data['job_url'] . '?jid=' . base64_encode($job_id) ?>">Edit this query and re-submit</a>  
</p>
<strong> Recent Jobs </strong>
<ol>
<?php
echo "<pre>";var_dump($job_id_data);echo "</pre>";
    $sid = session_id();  
    $jobs = $_SESSION['all_jobs'][$sid];

    foreach ($jobs as $job) {
echo "<pre>";var_dump($job);echo "</pre>";
      echo "<li>";
      $q_def = !isset($job['query_defs'][0]) ? "Query" : $job['query_defs'][0];
      echo "
        <a href='" . "../../" . $job['job_output_url'] ."'>
          Q:$q_def, T:" . $job['target'] . ' (' . $job['program'] . ') - ' . $job['date'] . "
        </a>";
      echo "</li>";
    }
?>
</ol>

<?php
function _get_GBRowse_link($hit, $linkout_urlprefix) {
}

function _get_JBRowse_link() {
}
?>