tripal/tripal_feature/api/tripal_feature.DEPRECATED.inc

<?php
/**
 * @file
 * Wrapper functions to provide backwards compatibility for the tripal feature api
 */

/**
 * @deprecated Restructured API to make naming more readable and consistent.
 * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
 * This function has been replaced by chado_get_property().
 *
 * @see chado_get_property().
 */
function tripal_feature_analysis_get_property($analysis_id = NULL, $feature_id = NUll, $analysisfeature_id = NULL, $property, $cv_name = 'tripal') {

  tripal_report_error(
    'tripal_deprecated',
    TRIPAL_NOTICE,
    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
    array(
      '%old_function'=>'tripal_feature_analysis_get_property',
      '%new_function' => 'chado_get_property'
    )
  );

  // check that the incoming arguments are correct
  if (($analysis_id and !$feature_id) or
    (!$analysis_id and $feature_id)) {
      tripal_report_error('tripal_feature', TRIPAL_WARNING,
      'tripal_feature_analysis_get_property: Both an analysis ID and feature ID should be specified',
      array());
  }

  // get the analysisfeature_id if one is not provided
  if (!$analysisfeature_id) {
    $columns = array('analysisfeature_id');
    $values = array('analysis_id' => $analysis_id, 'feature_id' => $feature_id);
    $result = chado_select_record('analysisfeature', $columns, $values);
    $analysisfeature_id = $result[0]->analysisfeature_id;
  }

  // get the property.
  return chado_get_property('analysisfeature', $analysisfeature_id, $property, $cv_name);
}

/**
 * @deprecated Restructured API to make naming more readable and consistent.
 * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
 * This function has been replaced by chado_insert_property().
 *
 * @see chado_insert_property().
 */
function tripal_feature_analysis_insert_property($analysis_id = NULL, $feature_id = NUll, $analysisfeature_id = NULL, $property, $value, $update_if_present = 0, $cv_name = 'tripal') {

  tripal_report_error(
    'tripal_deprecated',
    TRIPAL_NOTICE,
    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
    array(
      '%old_function'=>'tripal_feature_analysis_insert_property',
      '%new_function' => 'chado_insert_property'
    )
  );

    // check that the incoming arguments are correct
  if (($analysis_id and !$feature_id) or
      (!$analysis_id and $feature_id)) {
    tripal_report_error('tripal_feature', TRIPAL_WARNING,
      'tripal_feature_analysis_insert_property: Both an analysis ID and feature ID should be specified',
      array());
  }

  // get the analysisfeature_id if one is not provided
  if (!$analysisfeature_id) {
    $columns = array('analysisfeature_id');
    $values = array('analysis_id' => $analysis_id, 'feature_id' => $feature_id);
    $result = chado_select_record('analysisfeature', $columns, $values);
    $analysisfeature_id = $result[0]->analysisfeature_id;
  }

  // insert the property.
  return chado_insert_property('analysisfeature', $analysisfeature_id,
    $property, $cv_name, $value, $update_if_present);

}

/**
 * @deprecated Restructured API to make naming more readable and consistent.
 * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
 * This function has been replaced by chado_update_property().
 *
 * @see chado_update_property().
 */
function tripal_feature_analysis_update_property($analysis_id = NULL, $feature_id = NUll, $analysisfeature_id = NULL, $property, $value, $insert_if_missing = 0, $cv_name = 'tripal') {

  tripal_report_error(
    'tripal_deprecated',
    TRIPAL_NOTICE,
    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
    array(
      '%old_function'=>'tripal_feature_analysis_update_property',
      '%new_function' => 'chado_update_property'
    )
  );

  // check that the incoming arguments are correct
  if (($analysis_id and !$feature_id) or
    (!$analysis_id and $feature_id)) {
      tripal_report_error('tripal_feature', TRIPAL_WARNING,
      'tripal_feature_analysis_update_property: Both an analysis ID and feature ID should be specified',
      array());
  }

  // get the analysisfeature_id if one is not provided
  if (!$analysisfeature_id) {
    $columns = array('analysisfeature_id');
    $values = array('analysis_id' => $analysis_id, 'feature_id' => $feature_id);
    $result = chado_select_record('analysisfeature', $columns, $values);
    $analysisfeature_id = $result[0]->analysisfeature_id;
  }

  // update the property.
  return chado_update_property('analysisfeature', $analysisfeature_id, $property, $cv_name, $value, $insert_if_missing);
}

/**
 * @deprecated Restructured API to make naming more readable and consistent.
 * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
 * This function has been replaced by chado_update_property().
 *
 * @see chado_update_property().
 */
function tripal_feature_analysis_update_property_by_id($analysisfeatureprop_id, $property, $value, $cv_name = 'tripal') {

  tripal_report_error(
    'tripal_deprecated',
    TRIPAL_NOTICE,
    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
    array(
      '%old_function'=>'tripal_feature_analysis_update_property_by_id',
      '%new_function' => 'chado_update_property'
    )
  );

  // update the property.
  return chado_update_property('analysisfeature', NULL, $property, $cv_name, $value, FALSE, $analysisfeatureprop_id);
}

/**
 * @deprecated Restructured API to make naming more readable and consistent.
 * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
 * This function has been replaced by chado_delete_property().
 *
 * @see chado_delete_property().
 */
function tripal_feature_analysis_delete_property($analysis_id = NULL, $feature_id = NUll, $analysisfeature_id = NULL, $property, $cv_name = 'tripal') {

  tripal_report_error(
    'tripal_deprecated',
    TRIPAL_NOTICE,
    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
    array(
      '%old_function'=>'tripal_feature_analysis_delete_property',
      '%new_function' => 'chado_delete_property'
    )
  );

  // check that the incoming arguments are correct
  if (($analysis_id and !$feature_id) or
    (!$analysis_id and $feature_id)) {
      tripal_report_error('tripal_feature', TRIPAL_WARNING,
      'tripal_feature_analysis_delete_property: Both an analysis ID and feature ID should be specified',
        array());
  }

  // get the analysisfeature_id if one is not provided
  if (!$analysisfeature_id) {
    $columns = array('analysisfeature_id');
    $values = array('analysis_id' => $analysis_id, 'feature_id' => $feature_id);
    $result = chado_select_record('analysisfeature', $columns, $values);
    $analysisfeature_id = $result[0]->analysisfeature_id;
  }

  // get the property.
  return chado_delete_property('analysisfeature', $analysisfeature_id, $property, $cv_name);

}

/**
 * @deprecated Restructured API to make naming more readable and consistent.
 * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
 * This function has been replaced by chado_delete_record().
 *
 * @see chado_delete_record().
 */
function tripal_feature_analysis_delete_property_by_id($analysisfeatureprop_id) {

  tripal_report_error(
    'tripal_deprecated',
    TRIPAL_NOTICE,
    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
    array(
      '%old_function'=>'tripal_feature_analysis_delete_property_by_id',
      '%new_function' => 'chado_delete_property'
    )
  );

  // construct the array that will match the exact record to update
  $match = array(
    'analysisfeatureprop_id' => $analysisfeatureprop_id,
  );

  return chado_delete_record('analysisfeatureprop', $match);
}

/**
 * @deprecated Restructured API to make naming more readable and consistent.
 * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
 * This function has been replaced by chado_get_property().
 *
 * @see chado_get_property().
 */
function tripal_feature_get_property($feature_id, $property, $cv_name='tripal') {

  tripal_report_error(
    'tripal_deprecated',
    TRIPAL_NOTICE,
    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
    array(
      '%old_function'=>'tripal_feature_get_property',
      '%new_function' => 'chado_get_property'
    )
  );

  return chado_get_property('feature', $feature_id, $property, $cv_name);
}

/**
 * @deprecated Restructured API to make naming more readable and consistent.
 * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
 * This function has been replaced by chado_insert_property().
 *
 * @see chado_insert_property().
 */
function tripal_feature_insert_property($feature_id, $property, $value, $update_if_present = 0, $cv_name = 'tripal') {

  tripal_report_error(
    'tripal_deprecated',
    TRIPAL_NOTICE,
    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
    array(
      '%old_function'=>'tripal_feature_insert_property',
      '%new_function' => 'chado_insert_property'
    )
  );

  return chado_insert_property('feature', $feature_id, $property,
    $cv_name, $value, $update_if_present);
}

/**
 * @deprecated Restructured API to make naming more readable and consistent.
 * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
 * This function has been replaced by chado_update_property().
 *
 * @see chado_update_property().
 */
function tripal_feature_update_property($feature_id, $property, $value, $insert_if_missing = 0, $cv_name = 'tripal') {

  tripal_report_error(
    'tripal_deprecated',
    TRIPAL_NOTICE,
    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
    array(
      '%old_function'=>'tripal_feature_update_property',
      '%new_function' => 'chado_update_property'
    )
  );

  return chado_update_property('feature', $feature_id, $property, $cv_name, $value, $insert_if_missing);
}

/**
 * @deprecated Restructured API to make naming more readable and consistent.
 * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
 * This function has been replaced by chado_update_property().
 *
 * @see chado_update_property().
 */
function tripal_feature_update_property_by_id($featureprop_id, $property, $value, $cv_name = 'tripal') {

  tripal_report_error(
    'tripal_deprecated',
    TRIPAL_NOTICE,
    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
    array(
      '%old_function'=>'tripal_feature_update_property_by_id',
      '%new_function' => 'chado_update_property'
    )
  );

  return chado_update_property('feature', NULL, $property, $cv_name, $value, FALSE, $featureprop_id);
}

/**
 * @deprecated Restructured API to make naming more readable and consistent.
 * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
 * This function has been replaced by chado_delete_property().
 *
 * @see chado_delete_property().
 */
function tripal_feature_delete_property($feature_id, $property, $cv_name='tripal') {

  tripal_report_error(
    'tripal_deprecated',
    TRIPAL_NOTICE,
    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
    array(
      '%old_function'=>'tripal_feature_delete_property',
      '%new_function' => 'chado_delete_property'
    )
  );

  return chado_delete_property('feature', $feature_id, $property, $cv_name);
}

/**
 * @deprecated Restructured API to make naming more readable and consistent.
 * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
 * This function has been replaced by chado_delete_record().
 *
 * @see chado_delete_record().
 */
function tripal_feature_delete_property_by_id($featureprop_id) {

  tripal_report_error(
    'tripal_deprecated',
    TRIPAL_NOTICE,
    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
    array(
      '%old_function'=>'tripal_feature_delete_property_by_id',
      '%new_function' => 'chado_delete_property'
    )
  );

  // construct the array that will match the exact record to update
  $match = array(
    'featureprop_id' => $featureprop_id,
  );

  return chado_delete_record('featureprop', $match);
}

/**
 * @deprecated Restructured API to make naming more readable and consistent.
 * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
 * This function has been replaced by tripal_reverse_compliment_sequence().
 *
 * @see tripal_reverse_compliment_sequence().
 */
function tripal_feature_reverse_complement($sequence) {

  tripal_report_error(
    'tripal_deprecated',
    TRIPAL_NOTICE,
    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
    array(
      '%old_function'=>'tripal_feature_reverse_complement',
      '%new_function' => 'tripal_reverse_compliment_sequence'
    )
  );

  return tripal_reverse_compliment_sequence($sequence);
}

/**
 * @deprecated Restructured API to make naming more readable and consistent.
 * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
 * This function has been replaced by tripal_format_sequence().
 *
 * @see tripal_format_sequence().
 */
function tripal_feature_get_formatted_sequence($feature_id, $feature_name, $num_bases_per_line, $derive_from_parent, $aggregate, $output_format, $upstream, $downstream, $sub_features = array(), $relationship = '', $rel_part = '') {

  tripal_report_error(
    'tripal_deprecated',
    TRIPAL_NOTICE,
    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
    array(
      '%old_function'=>'tripal_feature_get_formatted_sequence',
      '%new_function' => 'tripal_format_sequence'
    )
  );

  return tripal_format_sequence(
    // Feature
    array(
      'feature_id' => $feature_id,
      'name' => $feature_name
    ),
    // Options
    array(
      'width' => $num_bases_per_line,
      'derive_from_parent' => $derive_from_parent,
      'aggregate' => $aggregate,
      'output_format' => $output_format,
      'num_upstream' => $upstream,
      'num_downstream' => $downstream,
      'sub_feature_types' => $sub_features,
      'relationship_type' => $relationship,
      'relationship_part' => $rel_part
    )
  );
}

/**
 * @deprecated Restructured API to make naming more readable and consistent.
 * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
 * This function has been replaced by tripal_associate_dbxref().
 *
 * @see tripal_associate_dbxref().
 */
function tripal_feature_add_dbxref($feature_id, $dbname, $accession) {

  tripal_report_error(
    'tripal_deprecated',
    TRIPAL_NOTICE,
    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
    array(
      '%old_function'=>'tripal_feature_add_dbxref',
      '%new_function' => 'tripal_associate_dbxref'
    )
  );

  return tripal_associate_dbxref(
    'feature',
    $feature_id,
    array(
      'accession' => $accession,
      'db_name' => $dbname
    )
  );
}

/**
 * @deprecated Restructured API to make naming more readable and consistent.
 * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
 * This function has been replaced by tripal_associate_cvterm().
 *
 * @see tripal_associate_cvterm().
 */
function tripal_feature_add_cvterm($feature_id, $cvname, $cvterm) {

  tripal_report_error(
    'tripal_deprecated',
    TRIPAL_NOTICE,
    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
    array(
      '%old_function'=>'tripal_feature_add_cvterm',
      '%new_function' => 'tripal_associate_cvterm'
    )
  );

  return tripal_associate_cvterm(
    'feature',
    $feature_id,
    array(
      'name' => $cvterm,
      'cv_name' => $cvname
    )
  );
}

/**
 * @deprecated Restructured API to make naming more readable and consistent.
 * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
 * This function has been replaced by tripal_get_fasta_sequence().
 *
 * @see tripal_get_fasta_sequence().
 */
function tripal_feature_return_fasta($feature, $desc) {

  tripal_report_error(
    'tripal_deprecated',
    TRIPAL_NOTICE,
    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
    array(
      '%old_function'=>'tripal_feature_return_fasta',
      '%new_function' => 'tripal_get_fasta_sequence'
    )
  );

  return tripal_get_fasta_sequence($feature, $desc);
}