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File

tripal_feature/tripal_feature.module, line 1501

@todo Add file header description

Code

function tripal_feature_load_organism_feature_browser($organism) {

  if (!$organism) {
    return array();
  }

  // don't show the browser if the settings in the admin page is turned off
  // instead return the array indicating the status of the browser
  $show_browser = variable_get('tripal_feature_browse_setting', 'show_feature_browser');
  if (strcmp($show_browser, 'show_feature_browser') != 0) {
    return array('enabled' => FALSE);
  }

  // get the list of available sequence ontology terms for which
  // we will build drupal pages from features in chado.  If a feature
  // is not one of the specified typse we won't build a node for it.
  $allowed_types = variable_get('chado_browser_feature_types', 'EST contig');
  $allowed_types = preg_replace("/[\s\n\r]+/", " ", $allowed_types);
  $so_terms = split(' ', $allowed_types);

  // perform the query
  $values = array(
    'organism_id' => $organism->organism_id,
    'type_id' => array(
      'name' => $so_terms
    ),
  );
  $columns = array('feature_id', 'name', 'uniquename', 'type_id');
  $options = array(
    'pager' => array('limit' => 10, 'element' => 0),
    'order_by' => array('name' => 'ASC'),
  );
  $features = tripal_core_chado_select('feature', $columns, $values, $options);
  $pager = theme('pager');

  // add the node ids and types
  $nsql = "SELECT nid FROM {chado_feature} WHERE feature_id = %d";
  $tsql = "SELECT name FROM {cvterm} WHERE cvterm_id = %d";
  foreach ($features as $feature) {
    $node = db_fetch_object(db_query($nsql, $feature->feature_id));
    $type = db_fetch_object(chado_query($tsql, $feature->type_id));
    $feature->nid = $node->nid;
    $feature->type_name = $type->name;
  }

  return array('features' => $features, 'pager' => $pager, 'enabled' => TRUE);
}