Prior to display of results we want to format the sequence

Overrides chado_views_handler_field::render

File

tripal_views/views/handlers/tripal_views_handler_field_sequence.inc, line 95

A chado wrapper for the views_handler_field.

Class

tripal_views_handler_field_sequence

@file A chado wrapper for the views_handler_field.

Code

function render($values) {
  $residues = '';

  // get the number of bases to show per line
  $num_bases_per_line = $this->options['display']['num_bases_per_line'];
  $output_format = $this->options['display']['output_format'];

  // get the residues from the feature.residues column
  $field = $this->field_alias;

  // get the feature id
  $feature_id = $values->feature_feature_id;
  $feature_name = $values->feature_name;

  // the upstream and downstream values get set by the 
  // tripal_views_handlers_filter_sequence.inc
  $upstream = $_SESSION['upstream'];
  $downstream = $_SESSION['downstream'];
  if (!$upstream) {
    $upstream = 0;
  }
  if (!$downstream) {
    $downstream = 0;
  }

  $derive_from_parent = $this->options['display']['derive_from_parent'];
  $aggregate = $this->options['display']['aggregate'];

  $residues = tripal_feature_get_formatted_sequence($feature_id, $feature_name, 
  $num_bases_per_line, $derive_from_parent, $aggregate, $output_format, 
  $upstream, $downstream);
  /*   
    // if we need to get the sequence from the parent but there is no aggregation
    // then do so now.
    if ($this->options['display']['derive_from_parent']) {             
      
      // execute our prepared statement
      if (tripal_core_is_sql_prepared('sequence_by_parent')) {
        $sql = "EXECUTE sequence_by_parent (%d, %d, %d)";
        $parents = chado_query($sql, $upstream, $downstream, $feature_id);
      }

      while ($parent = db_fetch_object($parents)) {  
        $seq = '';  // initialize the sequence for each parent
                
        // if we are to aggregate then we will ignore the feature returned
        // by the query above and rebuild it using the sub features
        if ($this->options['display']['aggregate']){
          
          // now get the sub features that are located on the parent.
          $sql = "EXECUTE sub_features (%d, %d)";
          $children = chado_query($sql, $feature_id, $parent->srcfeature_id);
          $sql = "EXECUTE count_sub_features (%d, %d)";
          $num_children = db_fetch_object(chado_query($sql, $feature_id, $parent->srcfeature_id));
                 
          // iterate through the sub features and concat their sequences. They
          // should already be in order.
          $types = array();
          $i = 0;
          while($child = db_fetch_object($children)) {
            // keep up with the types
            if (!in_array($child->type_name,$types)) {
              $types[] = $child->type_name;
            }
            
            $sql = "EXECUTE sequence_by_parent (%d, %d, %d)";

            // if the first sub feature we need to include the upstream bases
            if ($i == 0 and $parent->strand >= 0) {
              // -------------------------- ref
              //    ....---->  ---->        
              //     up    1       2         
              $q = chado_query($sql, $upstream, 0, $child->feature_id);
            }
            elseif ($i == 0 and $parent->strand < 0) {
              // -------------------------- ref
              //    ....<----  <----
              //    down  1       2
              $q = chado_query($sql, 0, $downstream, $child->feature_id);
            }          
            // if the last sub feature we need to include the downstream bases
            elseif ($i == $num_children->num_children - 1 and $parent->strand >= 0) {
              // -------------------------- ref
              //        ---->  ---->....
              //          1       2 down
              $q = chado_query($sql, 0, $downstream, $child->feature_id);
            }
            elseif ($i == $num_children->num_children - 1 and $parent->strand < 0) {
              // -------------------------- ref
              //        <----  <----....
              //          1       2  up
              $q = chado_query($sql, $upstream, 0, $child->feature_id);
            }
            
            // for internal sub features we don't want upstream or downstream bases
            else {         
              $sql = "EXECUTE sequence_by_parent (%d, %d, %d)";
              $q = chado_query($sql, 0, 0, $child->feature_id);
            }
            
            while($subseq = db_fetch_object($q)){
              // concatenate the sequences of all the sub features            
              if($subseq->srcfeature_id == $parent->srcfeature_id){
                $seq .= $subseq->residues;   
              }
            }                 
            $i++;
          } 
        } 
        // if this isn't an aggregate then use the parent residues
        else {
           $seq = $parent->residues;
        }
                              
        // get the reverse compliment if feature is on the reverse strand
        $dir = 'forward';
        if ($parent->strand < 0) {
          $seq = trpial_feature_reverse_complement($seq);
          $dir = 'reverse';
        }
        
        // now format for display
        if ($output_format == 'fasta_html') {
           $seq = wordwrap($seq, $num_bases_per_line, "<br>", TRUE);
        } 
        elseif ($output_format == 'fasta_txt') {
           $seq = wordwrap($seq, $num_bases_per_line, "\n", TRUE);
        }
        $residues .= ">$feature_name ($parent->typename) $parent->srcname:" . ($parent->adjfmin + 1) . ".." . $parent->adjfmax ." ($dir). ";
        if (count($types) > 0) {
          $residues .= "Excludes all bases but those of type(s): " . implode(', ',$types) . ". " ;
        }
        if ($parent->upstream > 0) {
           $residues .= "Includes " . $parent->upstream . " bases upstream.  ";
        }
        if ($parent->downstream > 0) {
           $residues .= "Includes " . $parent->downstream . " bases downstream.  ";
        }
        if (!$seq) {
          $residues .= "No sequence available\n<br>";          
        }
        else {
          if ($output_format == 'fasta_html') {
            $residues .= "<br>";
          }
          $residues .= "\n" . $seq . "\n";          
          if ($output_format == 'fasta_html') {
            $residues .= "<br>";
          }
        }
      }
    }
    // if we are not getting the sequence from the parent sequence then
    // use what comes through from the feature record
    else {
      $residues = $values->$field; 
      if ($output_format == 'fasta_html') {
         $residues = wordwrap($residues, $num_bases_per_line, "<br>", TRUE);  
      } 
      elseif ($output_format == 'fasta_txt') {
         $residues = wordwrap($residues, $num_bases_per_line, "\n", TRUE);  
      }
    }
    
    // format the residues for display
    if($residues and $num_bases_per_line){
      if ($output_format == 'fasta_html') {
         $residues = '<span style="font-family: monospace;">' . $residues . '</span>';
      }
    } */
  return $residues;
}