tripal/tripal_chado/includes/TripalFields/so__cds.inc

<?php

class so__cds extends TripalField {


  // --------------------------------------------------------------------------
  //                     EDITABLE STATIC CONSTANTS
  //
  // The following constants SHOULD be set for each descendent class.  They are
  // used by the static functions to provide information to Drupal about
  // the field and it's default widget and formatter.
  // --------------------------------------------------------------------------

  // The term that this field maps to.  The format for the term should be:
  // [vocab]:[accession] where [vocab] is the short name of the vocabulary
  // and [acession] is the unique accession number for the term.  This term
  // must already exist in the vocabulary storage backend. This
  // value should never be changed once fields exist for this type.
  public static $term = 'SO:0000316';

  // The default lable for this field.
  public static $label = 'Coding Sequence';

  // The default description for this field.
  public static $description = 'A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.';

  // Provide a list of global settings. These can be accessed witihn the
  // globalSettingsForm.  When the globalSettingsForm is submitted then
  // Drupal will automatically change these settings for all fields.
  public static $settings = array(
    'chado_table' => '',
    'chado_column' => '',
    'base_table' => '',
  );

  // Provide a list of instance specific settings. These can be access within
  // the instanceSettingsForm.  When the instanceSettingsForm is submitted
  // then Drupal with automatically change these settings for the instnace.
  // It is recommended to put settings at the instance level whenever possible.
  public static $instance_settings  = array();

  // Set this to the name of the storage backend that by default will support
  // this field.
  public static $storage = 'tripal_no_storage';

  // The default widget for this field.
  public static $default_widget = 'so__cds_widget';

  // The default formatter for this field.
  public static $default_formatter = 'so__cds_formatter';

  /**
   * @see TripalField::load()
   */
  public function load($entity, $details = array()) {
    $field_name = $this->field['field_name'];
    $feature = $details['record'];
    $num_seqs = 0;

    $feature = chado_expand_var($feature, 'table', 'featureloc', $options);
    $featureloc_sequences = chado_get_featureloc_sequences($feature->feature_id, $feature->featureloc->feature_id);
    foreach($featureloc_sequences as $src => $attrs){
      // Generate a CDS sequence if one exsits for this feature alignment.
      $cds_sequence = tripal_get_feature_sequences(
        array(
          'feature_id' => $feature->feature_id,
          'parent_id' => $attrs['featureloc']->srcfeature_id->feature_id,
          'name' => $feature->name,
          'featureloc_id' => $attrs['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) {
        $defline = tripal_get_fasta_defline($feature, '', $attrs['featureloc'], 'CDS', strlen($attrs['residues']));

        // the tripal_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'] = $defline . "\n" .  $cds_sequence[0]['residues'];
        }
      }
    }
  }
}