Program: 12541
Project: 12541
Buggy source:
/** 
 * Validates the given SBOL document. Errors encountered either throw exceptions or, if not fatal, are added to the list of errors that can be accessed using the   {@link #getErrors()} method. Interpretations of the complete, compliant, and bestPractice parameters are as follows: <li> complete: A  {@code true} value means that ALL references in the given SBOLDocument object can dereference to objects in the same document;  {@code false} otherwise.<li> compliant: A  {@code true} value means that ALL URIs in the given SBOLDocument object are compliant; {@code false} otherwise.<li> best practice: A  {@code true} value means that validation rules with the RECOMMENDED condition in the SBOL specification arechecked against the given SBOLDocuemnt object;  {@code false} otherwise.</ul><p>
 * @param sbolDocument the given {@code SBOLDocument} object
 * @param complete the given {@code complete} flag 
 * @param compliant the given {@code compliant} flag
 * @param bestPractice the given {@code bestPractice} flag
 */
public static void validateSBOL(SBOLDocument sbolDocument,boolean complete,boolean compliant,boolean bestPractice){
  clearErrors();
  validateSequenceEncodings(sbolDocument);
  validateWasDerivedFromVersion(sbolDocument);
  validateCircularReferences(sbolDocument);
  validateURIuniqueness(sbolDocument);
  validatePersistentIdentityUniqueness(sbolDocument);
  validateSequenceConstraints(sbolDocument);
  validateMapsTos(sbolDocument);
  if (compliant)   validateCompliance(sbolDocument);
  if (complete)   validateCompleteness(sbolDocument);
  if (bestPractice) {
    validateOntologyUsage(sbolDocument);
    validateSequenceAnnotations(sbolDocument);
    validateComponentDefinitionSequences(sbolDocument);
  }
}

Fixed version (ground truth):
/** 
 * Validates the given SBOL document. Errors encountered either throw exceptions or, if not fatal, are added to the list of errors that can be accessed using the   {@link #getErrors()} method. Interpretations of the complete, compliant, and bestPractice parameters are as follows: <ul> <li> complete: A  {@code true} value means that ALL references in the given SBOLDocument object can dereference to objects in the same document;  {@code false} otherwise.<li> compliant: A  {@code true} value means that ALL URIs in the given SBOLDocument object are compliant; {@code false} otherwise.<li> best practice: A  {@code true} value means that validation rules with the RECOMMENDED condition in the SBOL specification arechecked against the given SBOLDocuemnt object;  {@code false} otherwise.</ul><p>
 * @param sbolDocument the given {@code SBOLDocument} object
 * @param complete the given {@code complete} flag 
 * @param compliant the given {@code compliant} flag
 * @param bestPractice the given {@code bestPractice} flag
 */
public static void validateSBOL(SBOLDocument sbolDocument,boolean complete,boolean compliant,boolean bestPractice){
  clearErrors();
  validateSequenceEncodings(sbolDocument);
  validateWasDerivedFromVersion(sbolDocument);
  validateCircularReferences(sbolDocument);
  validateURIuniqueness(sbolDocument);
  validatePersistentIdentityUniqueness(sbolDocument);
  validateSequenceConstraints(sbolDocument);
  validateMapsTos(sbolDocument);
  if (compliant)   validateCompliance(sbolDocument);
  if (complete)   validateCompleteness(sbolDocument);
  if (bestPractice) {
    validateOntologyUsage(sbolDocument);
    validateSequenceAnnotations(sbolDocument);
    validateComponentDefinitionSequences(sbolDocument);
  }
}