tripal/tripal_chado_views/views/handlers/tripal_views_handler_field_sequence.inc

<?php
/**
 * @file
 * Contains tripal_views_handler_field_sequence
 */

/**
 * Handles display of sequence data.  If will aggregate sequences that need
 * to be aggregated (e.g. coding sequences) and provide
 *
 * @ingroup tripal_views
 */
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'] = [
      '#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'] = [
      '#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'] = [
      '#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'] = [
      '#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'] = [
      '#type' => 'radios',
      '#title' => t('Output format'),
      '#options' => [
        '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;
  }

}