Overrides TripalField::load

See also

TripalField::load()

File

tripal_chado/includes/TripalFields/so__cds/so__cds.inc, line 65

Class

so__cds

Code

public function load($entity) {
  $field_name = $this->field['field_name'];
  $feature = $entity->chado_record;
  $num_seqs = 0;

  // Set some defauls for the empty record
  $entity->{$field_name}['und'][0] = array(
    'value' => '',
  );

  $options = array(
    'return_array' => TRUE,
    'order_by' => array('rank' => 'ASC'),
  );
  $feature = chado_expand_var($feature, 'table', 'featureloc', $options);
  $featurelocs = $feature->featureloc->feature_id;

  foreach ($featurelocs as $featureloc) {
    // Generate a CDS sequence if one exsits for this feature alignment.
    $cds_sequence = chado_get_feature_sequences(
    array(
      'feature_id' => $feature->feature_id,
      'parent_id' => $featureloc->srcfeature_id->feature_id,
      'name' => $feature->name,
      'featureloc_id' => $featureloc->featureloc_id,
    ), 
    array(
      // CDS are in parent-child relationships so we want to use the
      // sequence from the parent
      'derive_from_parent' => 1,
      // we want to combine all CDS for this feature into a single sequence
      'aggregate' => 1,
      // we're looking for CDS features
      'sub_feature_types' => array('CDS'),
      'is_html' => 0
    )
    );

    if (count($cds_sequence) > 0) {
      // the chado_get_feature_sequences() function can return multiple sequences
      // if a feature is aligned to multiple places. In the case of CDSs we expect
      // that one mRNA is only aligned to a single location on the assembly so we
      // can access the CDS sequence with index 0.
      if ($cds_sequence[0]['residues']) {
        $entity->{$field_name}['und'][$num_seqs++]['value'] = $cds_sequence[0]['residues'];
      }
    }
  }
}