Program: 12591
Project: 12591
Buggy source:
/** 
 * Creates a copy of the given TopLevel instance with the given arguments, and then adds it to the corresponding top-level list owned by this SBOLDocument object. <p> This SBOLDcouement object is checked for compliance first. Only a compliant SBOLDocument instance is allowed to be edited. <p> If the given   {@code URIprefix} is {@code null}, then it is extracted from the given  {@code topLevel} instance. If it does not end with one of the following delimiters: "/", ":", or "#", then"/" is appended to the end of it. <p> If either the given  {@code displayId} or {@code version}, then the corresponding field is extracted from the given   {@code topLevel} instance. Both extracted fields are requiredto be valid and not  {@code null}. <p> A top-level instance with a compliant URI is created using the given arguments, and then its display ID, persistent identity, and version fields are set. This instance is then added to the corresponding top-level list owned by this SBOLDocument object.
 * @param topLevel
 * @param URIprefix
 * @param displayId
 * @param version
 * @return the created top-level instance
 * @throws SBOLValidationException if this SBOLDocument object is not compliant
 * @throws SBOLValidationException if the {@code defaultURIprefix} is {@code null}
 * @throws SBOLValidationException if the given {@code URIprefix} is {@code null}
 * @throws SBOLValidationException if the given {@code URIprefix} is non-compliant
 * @throws SBOLValidationException if the given {@code displayId} is invalid
 * @throws SBOLValidationException if the given {@code version} is invalid
 * @throws SBOLValidationException if the created top-level instance's persistentidentity exists in this SBOLDocument object's other lists of top-level instances.
 * @throws SBOLValidationException if the created top-level instance's identity URIalready exists.
 * @throws SBOLValidationException if the given {@code topLevel} instance is not an instanceof a top-level object
 */
public TopLevel createCopy(TopLevel topLevel,String URIprefix,String displayId,String version) throws SBOLValidationException {
  checkReadOnly();
  if (!URIcompliance.isTopLevelURIcompliant(topLevel)) {
    throw new SBOLValidationException("String_Node_Str");
  }
  if (URIprefix == null) {
    URIprefix=extractURIprefix(topLevel.getIdentity());
    URIprefix=URIcompliance.checkURIprefix(URIprefix);
  }
 else {
    URIprefix=URIcompliance.checkURIprefix(URIprefix);
  }
  if (displayId == null) {
    displayId=topLevel.getDisplayId();
  }
  if (version == null) {
    version=topLevel.getVersion();
  }
  validateIdVersion(displayId,version);
  if (topLevel instanceof Collection) {
    Collection newCollection=((Collection)topLevel).copy(URIprefix,displayId,version);
    addCollection(newCollection);
    return newCollection;
  }
 else   if (topLevel instanceof ComponentDefinition) {
    ComponentDefinition newComponentDefinition=((ComponentDefinition)topLevel).copy(URIprefix,displayId,version);
    addComponentDefinition(newComponentDefinition);
    return newComponentDefinition;
  }
 else   if (topLevel instanceof Model) {
    Model newModel=((Model)topLevel).copy(URIprefix,displayId,version);
    addModel(newModel);
    return newModel;
  }
 else   if (topLevel instanceof ModuleDefinition) {
    ModuleDefinition newModuleDefinition=((ModuleDefinition)topLevel).copy(URIprefix,displayId,version);
    addModuleDefinition(newModuleDefinition);
    return newModuleDefinition;
  }
 else   if (topLevel instanceof Sequence) {
    Sequence newSequence=((Sequence)topLevel).copy(URIprefix,displayId,version);
    addSequence(newSequence);
    return newSequence;
  }
 else   if (topLevel instanceof GenericTopLevel) {
    GenericTopLevel newGenericTopLevel=((GenericTopLevel)topLevel).copy(URIprefix,displayId,version);
    addGenericTopLevel(newGenericTopLevel);
    return newGenericTopLevel;
  }
 else {
    throw new SBOLValidationException("String_Node_Str" + topLevel.getIdentity());
  }
}

Fixed version (ground truth):
/** 
 * Creates a copy of the given TopLevel instance with the given arguments, and then adds it to the corresponding top-level list owned by this SBOLDocument object. <p> This SBOLDcouement object is checked for compliance first. Only a compliant SBOLDocument instance is allowed to be edited. <p> If the given   {@code URIprefix} is {@code null}, then it is extracted from the given  {@code topLevel} instance. If it does not end with one of the following delimiters: "/", ":", or "#", then"/" is appended to the end of it. <p> If either the given  {@code displayId} or {@code version}, then the corresponding field is extracted from the given   {@code topLevel} instance. Both extracted fields are requiredto be valid and not  {@code null}. <p> A top-level instance with a compliant URI is created using the given arguments, and then its display ID, persistent identity, and version fields are set. This instance is then added to the corresponding top-level list owned by this SBOLDocument object.
 * @param topLevel
 * @param URIprefix
 * @param displayId
 * @param version
 * @return the created top-level instance
 * @throws SBOLValidationException if this SBOLDocument object is not compliant
 * @throws SBOLValidationException if the {@code defaultURIprefix} is {@code null}
 * @throws SBOLValidationException if the given {@code URIprefix} is {@code null}
 * @throws SBOLValidationException if the given {@code URIprefix} is non-compliant
 * @throws SBOLValidationException if the given {@code displayId} is invalid
 * @throws SBOLValidationException if the given {@code version} is invalid
 * @throws SBOLValidationException if the created top-level instance's persistentidentity exists in this SBOLDocument object's other lists of top-level instances.
 * @throws SBOLValidationException if the created top-level instance's identity URIalready exists.
 * @throws SBOLValidationException if the given {@code topLevel} instance is not an instanceof a top-level object
 */
public TopLevel createCopy(TopLevel topLevel,String URIprefix,String displayId,String version) throws SBOLValidationException {
  checkReadOnly();
  topLevel.isURIcompliant();
  if (URIprefix == null) {
    URIprefix=extractURIprefix(topLevel.getIdentity());
    URIprefix=URIcompliance.checkURIprefix(URIprefix);
  }
 else {
    URIprefix=URIcompliance.checkURIprefix(URIprefix);
  }
  if (displayId == null) {
    displayId=topLevel.getDisplayId();
  }
  if (version == null) {
    version=topLevel.getVersion();
  }
  validateIdVersion(displayId,version);
  if (topLevel instanceof Collection) {
    Collection newCollection=((Collection)topLevel).copy(URIprefix,displayId,version);
    addCollection(newCollection);
    return newCollection;
  }
 else   if (topLevel instanceof ComponentDefinition) {
    ComponentDefinition newComponentDefinition=((ComponentDefinition)topLevel).copy(URIprefix,displayId,version);
    addComponentDefinition(newComponentDefinition);
    return newComponentDefinition;
  }
 else   if (topLevel instanceof Model) {
    Model newModel=((Model)topLevel).copy(URIprefix,displayId,version);
    addModel(newModel);
    return newModel;
  }
 else   if (topLevel instanceof ModuleDefinition) {
    ModuleDefinition newModuleDefinition=((ModuleDefinition)topLevel).copy(URIprefix,displayId,version);
    addModuleDefinition(newModuleDefinition);
    return newModuleDefinition;
  }
 else   if (topLevel instanceof Sequence) {
    Sequence newSequence=((Sequence)topLevel).copy(URIprefix,displayId,version);
    addSequence(newSequence);
    return newSequence;
  }
 else   if (topLevel instanceof GenericTopLevel) {
    GenericTopLevel newGenericTopLevel=((GenericTopLevel)topLevel).copy(URIprefix,displayId,version);
    addGenericTopLevel(newGenericTopLevel);
    return newGenericTopLevel;
  }
 else {
    throw new SBOLValidationException("String_Node_Str" + topLevel.getIdentity());
  }
}