class tripal_views_handler_field_sequence extends views_handler_field {

  /**
   * {@inheritdoc}
   */
  function options_form(&$form, &$form_state) {
    parent::options_form($form, $form_state);

    $form['display'] = array(
      '#type' => 'fieldset',
      '#title' => 'Format Output',
      '#description' => t('Alter the way a sequence is displayed')
    );
    $default_num_bases_per_line = '50';
    if ($this->options['display']['num_bases_per_line']) {
      $default_num_bases_per_line = $this->options['display']['num_bases_per_line'];
    }
    $default_output_format = 'raw';
    if ($this->options['display']['output_format']) {
      $default_ouput_format = $this->options['display']['output_format'];
    }

    $form['display']['num_bases_per_line'] = array(
      '#type' => 'textfield',
      '#title' => t('Number of bases per line'),
      '#description' => t('Specify the number of bases per line. An HTML <br> tag ' .
        'will be inserted after the number of bases indicated. If no value is ' .
        'provided. The sequence will be one long string (default)'),
      '#default_value' => $default_num_bases_per_line,
    );
    $form['display']['derive_from_parent'] = array(
      '#type' => 'checkbox',
      '#title' => t('Derive sequence from parent'),
      '#description' => t('Rather than use the sequence from the \'residues\' of this feature, you may ' .
        'derive the sequence from the parent features to which it is aligned. This is useful in the case that the feature ' .
        'does not have sequence associated with it and we need to get it through it\'s alignment. ' .
        'Note: this will slow queries with large numbers of results on the page.'),
      '#default_value' => $this->options['display']['derive_from_parent'],
    );
    $form['display']['aggregate'] = array(
      '#type' => 'checkbox',
      '#title' => t('Aggregate sub features'),
      '#description' => t('If the feature has sub features (e.g. CDS of an mRNA) then check this ' .
        'box to filter the sequence to only include the sub features.  Gaps between sub features will be ' .
        'excluded from the sequence.  This is useful for obtaining a complete CDS from an mRNA ' .
        'without intronic sequence'),
      '#default_value' => $this->options['display']['aggregate'],
    );
    $form['display']['output_format'] = array(
      '#type' => 'radios',
      '#title' => t('Output format'),
      '#options' => array(
        'raw' => 'Raw sequence data (no formatting)',
        'fasta_html' => 'FASTA in HTML format',
        'fasta_txt' => 'FASTA in text format',
      ),
      '#description' => t('Choose an output format.  Raw output cannot be used when the sequence is derived from the parent.'),
      '#default_value' => $default_ouput_format,
    );
  }

  /**
   * {@inheritdoc}
   */
  function query() {
    parent::query();

    // if we are going to get the sequence from the parent then
    // we will need to do more queries in the render function
    // and we must have the feature_id to do those
    if ($this->options['display']['derive_from_parent']) {
      $this->ensure_my_table();
      $this->query->add_field($this->table, 'feature_id');
      $this->query->add_field($this->table, 'name');
    }
  }

  /**
   * {@inheritdoc}
   *
   * Prior to display of results we want to format the sequence
   */
  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 ($parent = d-b_f-etch_object($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)";
          $num_children = d-b_f-etch_object(chado_query($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 = d-b_f-etch_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 ($subseq = d-b_f-etch_object($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;
  }

}