Load the locations for a given feature

Parameters

$feature_id: The feature to look up locations for

$side: Whether the feature is the scrfeature, 'as_parent', or feature, 'as_child'

$aggregate: Whether or not to get the locations for related features

Related topics

File

tripal_feature/theme/tripal_feature.theme.inc, line 206

Code

function tripal_feature_load_featurelocs($feature_id, $side = 'as_parent', $aggregate = 1) {

  $sql = "
    SELECT
       F.name, F.feature_id, F.uniquename,
       FS.name as src_name, FS.feature_id as src_feature_id, FS.uniquename as src_uniquename,
       CVT.name as cvname, CVT.cvterm_id,
       CVTS.name as src_cvname, CVTS.cvterm_id as src_cvterm_id,
       FL.fmin, FL.fmax, FL.is_fmin_partial, FL.is_fmax_partial,FL.strand, FL.phase
     FROM {featureloc} FL
       INNER JOIN {feature} F   ON FL.feature_id = F.feature_id
       INNER JOIN {feature} FS  ON FS.feature_id = FL.srcfeature_id
       INNER JOIN {cvterm} CVT  ON F.type_id     = CVT.cvterm_id
       INNER JOIN {cvterm} CVTS ON FS.type_id    = CVTS.cvterm_id
   ";
  if (strcmp($side, 'as_parent') == 0) {
    $sql .= "WHERE FL.srcfeature_id = :feature_id ";
  }
  if (strcmp($side, 'as_child') == 0) {
    $sql .= "WHERE FL.feature_id = :feature_id ";
  }

  $flresults = chado_query($sql, array(':feature_id' => $feature_id));

  // copy the results into an array
  $i = 0;
  $featurelocs = array();
  while ($loc = $flresults->fetchObject()) {
    // if a drupal node exists for this feature then add the nid to the
    // results object
    $loc->fnid = chado_get_nid_from_id('feature', $loc->feature_id);
    $loc->snid = chado_get_nid_from_id('feature', $loc->src_feature_id);
    // add the result to the array
    $featurelocs[$i++] = $loc;
  }

  // Add the relationship feature locs if aggregate is turned on
  if ($aggregate and strcmp($side, 'as_parent') == 0) {
    // get the relationships for this feature without substituting any children
    // for the parent. We want all relationships
    $relationships = tripal_feature_get_aggregate_relationships($feature_id, 0);
    foreach ($relationships as $rindex => $rel) {
      // get the featurelocs for each of the relationship features
      $rel_featurelocs = tripal_feature_load_featurelocs($rel->subject_id, 'as_child', 0);
      foreach ($rel_featurelocs as $findex => $rfloc) {
        $featurelocs[$i++] = $rfloc;
      }
    }
  }

  usort($featurelocs, 'tripal_feature_sort_locations');
  return $featurelocs;
}