Program: 12510
Project: 12510
Buggy source:
/** 
 * @param componentDefinition
 * @param sequenceConstraint
 * @throws SBOLValidationException if any of the following SBOL validation rules was violated:11409, 11410, 11411.
 */
static void checkSequenceConstraint(ComponentDefinition componentDefinition,SequenceConstraint sequenceConstraint) throws SBOLValidationException {
  SequenceAnnotation saSubject=componentDefinition.getSequenceAnnotation(sequenceConstraint.getSubject());
  SequenceAnnotation saObject=componentDefinition.getSequenceAnnotation(sequenceConstraint.getObject());
  if (saSubject == null || saObject == null)   return;
  if (sequenceConstraint.getRestriction().equals(RestrictionType.PRECEDES)) {
    if (saObject.compareTo(saSubject) < 0) {
      throw new SBOLValidationException("String_Node_Str",sequenceConstraint);
    }
  }
 else   if (sequenceConstraint.getRestriction().equals(RestrictionType.SAME_ORIENTATION_AS)) {
    for (    Location locSubject : saSubject.getLocations()) {
      for (      Location locObject : saObject.getLocations()) {
        if (!locSubject.getOrientation().equals(locObject.getOrientation())) {
          throw new SBOLValidationException("String_Node_Str",sequenceConstraint);
        }
      }
    }
  }
 else   if (sequenceConstraint.getRestriction().equals(RestrictionType.OPPOSITE_ORIENTATION_AS)) {
    for (    Location locSubject : saSubject.getLocations()) {
      for (      Location locObject : saObject.getLocations()) {
        if (locSubject.getOrientation().equals(locObject.getOrientation())) {
          throw new SBOLValidationException("String_Node_Str",sequenceConstraint);
        }
      }
    }
  }
}

Fixed version (ground truth):
/** 
 * @param componentDefinition
 * @param sequenceConstraint
 * @throws SBOLValidationException if any of the following SBOL validation rules was violated:11409, 11410, 11411.
 */
static void checkSequenceConstraint(ComponentDefinition componentDefinition,SequenceConstraint sequenceConstraint) throws SBOLValidationException {
  SequenceAnnotation saSubject=componentDefinition.getSequenceAnnotation(sequenceConstraint.getSubject());
  SequenceAnnotation saObject=componentDefinition.getSequenceAnnotation(sequenceConstraint.getObject());
  if (saSubject == null || saObject == null)   return;
  if (sequenceConstraint.getRestriction().equals(RestrictionType.PRECEDES)) {
    if (saObject.compareTo(saSubject) != (-1) * Integer.MAX_VALUE && saObject.compareTo(saSubject) < 0) {
      throw new SBOLValidationException("String_Node_Str",sequenceConstraint);
    }
  }
 else   if (sequenceConstraint.getRestriction().equals(RestrictionType.SAME_ORIENTATION_AS)) {
    for (    Location locSubject : saSubject.getLocations()) {
      for (      Location locObject : saObject.getLocations()) {
        if (!locSubject.getOrientation().equals(locObject.getOrientation())) {
          throw new SBOLValidationException("String_Node_Str",sequenceConstraint);
        }
      }
    }
  }
 else   if (sequenceConstraint.getRestriction().equals(RestrictionType.OPPOSITE_ORIENTATION_AS)) {
    for (    Location locSubject : saSubject.getLocations()) {
      for (      Location locObject : saObject.getLocations()) {
        if (locSubject.getOrientation().equals(locObject.getOrientation())) {
          throw new SBOLValidationException("String_Node_Str",sequenceConstraint);
        }
      }
    }
  }
}