Merge branch 'master' of https://github.com/julianmendez/born into cr…

…eate-gui-tests

born-gui/src/main/java/de/tudresden/inf/lat/born/gui/BornModelImpl.java

@@ -38,8 +38,7 @@ public AnnotatorConfiguration getAnnotatorConfiguration() {
 
 	@Override
 	public void setAnnotatorConfiguration(AnnotatorConfiguration annotatorConfiguration) {
-		Objects.requireNonNull(annotatorConfiguration);
-		this.annotatorConfiguration = annotatorConfiguration;
+		this.annotatorConfiguration = Objects.requireNonNull(annotatorConfiguration);
 	}
 
 	@Override
@@ -49,8 +48,7 @@ public ProcessorConfiguration getProcessorConfiguration() {
 
 	@Override
 	public void setProcessorConfiguration(ProcessorConfiguration processorConfiguration) {
-		Objects.requireNonNull(processorConfiguration);
-		this.processorConfiguration = processorConfiguration;
+		this.processorConfiguration = Objects.requireNonNull(processorConfiguration);
 	}
 
 	@Override
@@ -60,8 +58,7 @@ public MultiProcessorConfiguration getMultiProcessorConfiguration() {
 
 	@Override
 	public void setMultiProcessorConfiguration(MultiProcessorConfiguration multiProcessorConfiguration) {
-		Objects.requireNonNull(multiProcessorConfiguration);
-		this.multiProcessorConfiguration = multiProcessorConfiguration;
+		this.multiProcessorConfiguration = Objects.requireNonNull(multiProcessorConfiguration);
 	}
 
 }

born-gui/src/main/java/de/tudresden/inf/lat/born/gui/BornPanel.java

@@ -39,8 +39,7 @@ public class BornPanel extends JPanel implements BornView {
 	 *            model
 	 */
 	public BornPanel(BornModel model) {
-		Objects.requireNonNull(model);
-		this.model = model;
+		this.model = Objects.requireNonNull(model);
 		this.processorView = new ProcessorPanel(this.model.getProcessorConfiguration());
 		this.testMakerView = new TestMakerPanel(this.model.getAnnotatorConfiguration());
 		this.experimentMakerView = new ExperimentRunnerPanel(this.model.getMultiProcessorConfiguration());

born-gui/src/main/java/de/tudresden/inf/lat/born/gui/experimentrunner/ExperimentRunnerController.java

@@ -69,10 +69,8 @@ public void run() {
 	 *            an OWL ontology manager
 	 */
 	public ExperimentRunnerController(ExperimentRunnerView view, OWLOntologyManager ontologyManager) {
-		Objects.requireNonNull(view);
-		Objects.requireNonNull(ontologyManager);
-		this.view = view;
-		this.owlOntologyManager = ontologyManager;
+		this.view = Objects.requireNonNull(view);
+		this.owlOntologyManager = Objects.requireNonNull(ontologyManager);
 		init();
 	}
 

born-gui/src/main/java/de/tudresden/inf/lat/born/gui/experimentrunner/ExperimentRunnerPanel.java

@@ -45,8 +45,7 @@ public class ExperimentRunnerPanel extends JPanel implements ExperimentRunnerVie
 	 *            model
 	 */
 	public ExperimentRunnerPanel(MultiProcessorConfiguration model) {
-		Objects.requireNonNull(model);
-		this.model = model;
+		this.model = Objects.requireNonNull(model);
 		createPanel();
 	}
 

born-gui/src/main/java/de/tudresden/inf/lat/born/gui/processor/ProcessorController.java

@@ -83,10 +83,8 @@ public void run() {
 	 *            an OWL ontology manager
 	 */
 	public ProcessorController(ProcessorView view, OWLOntologyManager ontologyManager) {
-		Objects.requireNonNull(view);
-		Objects.requireNonNull(ontologyManager);
-		this.view = view;
-		this.owlOntologyManager = ontologyManager;
+		this.view = Objects.requireNonNull(view);
+		this.owlOntologyManager = Objects.requireNonNull(ontologyManager);
 		init();
 	}
 

born-gui/src/main/java/de/tudresden/inf/lat/born/gui/processor/ProcessorPanel.java

@@ -62,8 +62,7 @@ public class ProcessorPanel extends JPanel implements ProcessorView {
 	private final ProcessorConfiguration model;
 
 	public ProcessorPanel(ProcessorConfiguration model) {
-		Objects.requireNonNull(model);
-		this.model = model;
+		this.model = Objects.requireNonNull(model);
 		setLayout(null);
 		createPanel();
 	}

born-gui/src/main/java/de/tudresden/inf/lat/born/gui/testmaker/TestMakerController.java

@@ -48,10 +48,8 @@ public class TestMakerController implements ActionListener {
 	 *            an OWL ontology manager
 	 */
 	public TestMakerController(TestMakerView view, OWLOntologyManager ontologyManager) {
-		Objects.requireNonNull(view);
-		Objects.requireNonNull(ontologyManager);
-		this.view = view;
-		this.owlOntologyManager = ontologyManager;
+		this.view = Objects.requireNonNull(view);
+		this.owlOntologyManager = Objects.requireNonNull(ontologyManager);
 		init();
 	}
 

born-gui/src/main/java/de/tudresden/inf/lat/born/gui/testmaker/TestMakerPanel.java

@@ -57,8 +57,7 @@ public class TestMakerPanel extends JPanel implements TestMakerView {
 	 *            model
 	 */
 	public TestMakerPanel(AnnotatorConfiguration model) {
-		Objects.requireNonNull(model);
-		this.model = model;
+		this.model = Objects.requireNonNull(model);
 		createPanel();
 	}
 

born-gui/src/main/java/de/tudresden/inf/lat/born/main/BornStarter.java

@@ -30,8 +30,7 @@ public class BornStarter implements OWLOntologyChangeListener, OWLOntologyLoader
 	 *            OWL ontology manager
 	 */
 	public BornStarter(OWLOntologyManager manager) {
-		Objects.requireNonNull(manager);
-		this.ontologyManager = manager;
+		this.ontologyManager = Objects.requireNonNull(manager, "Ontology manager must not be null");
 		this.panel = new BornController(new BornPanel(new BornModelImpl()), this.ontologyManager);
 		getOWLOntologyManager().addOntologyLoaderListener(this);
 		getOWLOntologyManager().addOntologyChangeListener(this);

born-owlapi/src/main/java/de/tudresden/inf/lat/born/core/rule/EmptyRule.java

@@ -27,8 +27,7 @@ public EmptyRule() {
 	}
 
 	public EmptyRule(String comment) {
-		Objects.requireNonNull(comment);
-		this.comment = comment;
+		this.comment = Objects.requireNonNull(comment);
 	}
 
 	@Override

born-owlapi/src/main/java/de/tudresden/inf/lat/born/core/term/ClauseImpl.java

@@ -33,9 +33,8 @@ public ClauseImpl() {
 	 *            body
 	 */
 	public ClauseImpl(Term head, List<Term> body) {
-		Objects.requireNonNull(head);
 		Objects.requireNonNull(body);
-		this.head = head;
+		this.head = Objects.requireNonNull(head);
 		this.body.addAll(body);
 	}
 

born-owlapi/src/main/java/de/tudresden/inf/lat/born/core/term/ProbClauseImpl.java

@@ -37,9 +37,8 @@ public ProbClauseImpl() {
 	public ProbClauseImpl(Term head, List<Term> body, String probability) {
 		Objects.requireNonNull(head);
 		Objects.requireNonNull(body);
-		Objects.requireNonNull(probability);
 		this.clause = new ClauseImpl(head, body);
-		this.probability = probability;
+		this.probability = Objects.requireNonNull(probability);
 	}
 
 	@Override

born-owlapi/src/main/java/de/tudresden/inf/lat/born/core/term/TermImpl.java

@@ -82,9 +82,8 @@ public TermImpl(String name, List<Term> arguments) {
 	 */
 	public TermImpl(Term leftTerm, String infixOperator, Term rightTerm) {
 		Objects.requireNonNull(leftTerm);
-		Objects.requireNonNull(infixOperator);
 		Objects.requireNonNull(rightTerm);
-		this.name = infixOperator;
+		this.name = Objects.requireNonNull(infixOperator);
 		this.arguments.add(leftTerm);
 		this.arguments.add(rightTerm);
 		this.termType = Term.Type.INFIX_OPERATOR;

born-owlapi/src/main/java/de/tudresden/inf/lat/born/module/DefaultIdentifierCollector.java

@@ -24,8 +24,7 @@ public class DefaultIdentifierCollector {
 	 *            normalized axiom
 	 */
 	public DefaultIdentifierCollector(NormalizedIntegerAxiom axiom) {
-		Objects.requireNonNull(axiom);
-		this.axiom = axiom;
+		this.axiom = Objects.requireNonNull(axiom);
 		axiom.accept(new AuxiliaryIdentifierCollector());
 	}
 

born-owlapi/src/main/java/de/tudresden/inf/lat/born/module/Module.java

@@ -11,10 +11,8 @@ public class Module {
 	private Set<NormalizedIntegerAxiom> axioms;
 
 	public Module(Set<Integer> entities, Set<NormalizedIntegerAxiom> axioms) {
-		Objects.requireNonNull(entities);
-		Objects.requireNonNull(axioms);
-		this.entities = entities;
-		this.axioms = axioms;
+		this.entities = Objects.requireNonNull(entities);
+		this.axioms = Objects.requireNonNull(axioms);
 	}
 
 	public Set<Integer> getEntities() {

born-owlapi/src/main/java/de/tudresden/inf/lat/born/owlapi/annotator/AnnotatorConfigurationImpl.java

@@ -24,8 +24,7 @@ public InputStream getInputOntology() {
 
 	@Override
 	public void setInputOntology(InputStream inputOntology) {
-		Objects.requireNonNull(inputOntology);
-		this.inputOntology = inputOntology;
+		this.inputOntology = Objects.requireNonNull(inputOntology);
 	}
 
 	@Override
@@ -35,8 +34,7 @@ public OutputStream getOutputOntology() {
 
 	@Override
 	public void setOutputOntology(OutputStream outputOntology) {
-		Objects.requireNonNull(outputOntology);
-		this.outputOntology = outputOntology;
+		this.outputOntology = Objects.requireNonNull(outputOntology);
 	}
 
 	@Override
@@ -56,8 +54,7 @@ public Set<String> getInputBayesianNetworkVariables() {
 
 	@Override
 	public void setInputBayesianNetworkVariables(Set<String> inputBayesianNetworkVariables) {
-		Objects.requireNonNull(inputBayesianNetworkVariables);
-		this.inputBayesianNetworkVariables = inputBayesianNetworkVariables;
+		this.inputBayesianNetworkVariables = Objects.requireNonNull(inputBayesianNetworkVariables);
 	}
 
 	@Override

born-owlapi/src/main/java/de/tudresden/inf/lat/born/owlapi/example/ExampleConfigurationImpl.java

@@ -39,18 +39,12 @@ public class ExampleConfigurationImpl implements ExampleConfiguration {
 	 */
 	public ExampleConfigurationImpl(String ontologyName, String ontologyFileName, OWLOntology owlOntology,
 			String bayesianNetworkFileName, String bayesianNetwork, String query) {
-		Objects.requireNonNull(ontologyName);
-		Objects.requireNonNull(ontologyFileName);
-		Objects.requireNonNull(owlOntology);
-		Objects.requireNonNull(bayesianNetworkFileName);
-		Objects.requireNonNull(bayesianNetwork);
-		Objects.requireNonNull(query);
-		this.ontologyName = ontologyName;
-		this.ontologyFileName = ontologyFileName;
-		this.owlOntology = owlOntology;
-		this.bayesianNetworkFileName = bayesianNetworkFileName;
-		this.bayesianNetwork = bayesianNetwork;
-		this.query = query;
+		this.ontologyName = Objects.requireNonNull(ontologyName);
+		this.ontologyFileName = Objects.requireNonNull(ontologyFileName);
+		this.owlOntology = Objects.requireNonNull(owlOntology);
+		this.bayesianNetworkFileName = Objects.requireNonNull(bayesianNetworkFileName);
+		this.bayesianNetwork = Objects.requireNonNull(bayesianNetwork);
+		this.query = Objects.requireNonNull(query);
 	}
 
 	@Override

born-owlapi/src/main/java/de/tudresden/inf/lat/born/owlapi/example/ExampleLoader.java

@@ -162,8 +162,7 @@ String getFile(InputStream input) throws IOException {
 	}
 
 	String getFileName(String fileNameWithPath) {
-		Objects.requireNonNull(fileNameWithPath);
-		String ret = fileNameWithPath;
+		String ret = Objects.requireNonNull(fileNameWithPath);
 		int lastIndex = fileNameWithPath.lastIndexOf(Symbol.FILE_SEPARATOR);
 		if (lastIndex != -1) {
 			ret = fileNameWithPath.substring(lastIndex + Symbol.FILE_SEPARATOR.length());

born-owlapi/src/main/java/de/tudresden/inf/lat/born/owlapi/main/BornReasoner.java

@@ -93,9 +93,7 @@ public BornReasoner(OWLOntology rootOntology, boolean buffering) {
 	 */
 	public BornReasoner(OWLOntology rootOntology, boolean buffering, OWLReasonerConfiguration configuration) {
 		this(rootOntology, buffering);
-		Objects.requireNonNull(rootOntology);
-		Objects.requireNonNull(configuration);
-		this.reasonerConfiguration = configuration;
+		this.reasonerConfiguration = Objects.requireNonNull(configuration);
 	}
 
 	public boolean addAxiom(OWLAxiom axiom) {
@@ -198,7 +196,7 @@ public NodeSet<OWLDataProperty> getDisjointDataProperties(OWLDataPropertyExpress
 	@Override
 	public NodeSet<OWLObjectPropertyExpression> getDisjointObjectProperties(
 			OWLObjectPropertyExpression objectPropertyExpression) throws InconsistentOntologyException,
-					FreshEntitiesException, ReasonerInterruptedException, TimeOutException {
+			FreshEntitiesException, ReasonerInterruptedException, TimeOutException {
 		Objects.requireNonNull(objectPropertyExpression);
 		logger.finer("getDisjointDataProperties(" + objectPropertyExpression + ")");
 		throw new UnsupportedReasonerOperationInBornException(
@@ -226,7 +224,7 @@ public Node<OWLDataProperty> getEquivalentDataProperties(OWLDataProperty dataPro
 	@Override
 	public Node<OWLObjectPropertyExpression> getEquivalentObjectProperties(
 			OWLObjectPropertyExpression objectPropertyExpression) throws InconsistentOntologyException,
-					FreshEntitiesException, ReasonerInterruptedException, TimeOutException {
+			FreshEntitiesException, ReasonerInterruptedException, TimeOutException {
 		Objects.requireNonNull(objectPropertyExpression);
 		logger.finer("getEquivalentObjectProperties(" + objectPropertyExpression + ")");
 		throw new UnsupportedReasonerOperationInBornException(
@@ -258,7 +256,7 @@ public NodeSet<OWLNamedIndividual> getInstances(OWLClassExpression classExpressi
 	@Override
 	public Node<OWLObjectPropertyExpression> getInverseObjectProperties(
 			OWLObjectPropertyExpression objectPropertyExpression) throws InconsistentOntologyException,
-					FreshEntitiesException, ReasonerInterruptedException, TimeOutException {
+			FreshEntitiesException, ReasonerInterruptedException, TimeOutException {
 		Objects.requireNonNull(objectPropertyExpression);
 		logger.finer("getInverseObjectProperties(" + objectPropertyExpression + ")");
 		throw new UnsupportedReasonerOperationInBornException(
@@ -268,7 +266,7 @@ public Node<OWLObjectPropertyExpression> getInverseObjectProperties(
 	@Override
 	public NodeSet<OWLClass> getObjectPropertyDomains(OWLObjectPropertyExpression objectPropertyExpression,
 			boolean direct) throws InconsistentOntologyException, FreshEntitiesException, ReasonerInterruptedException,
-					TimeOutException {
+			TimeOutException {
 		Objects.requireNonNull(objectPropertyExpression);
 		logger.finer("getObjectPropertyDomains(" + objectPropertyExpression + ", " + direct + ")");
 		throw new UnsupportedReasonerOperationInBornException(
@@ -278,7 +276,7 @@ public NodeSet<OWLClass> getObjectPropertyDomains(OWLObjectPropertyExpression ob
 	@Override
 	public NodeSet<OWLClass> getObjectPropertyRanges(OWLObjectPropertyExpression objectPropertyExpression,
 			boolean direct) throws InconsistentOntologyException, FreshEntitiesException, ReasonerInterruptedException,
-					TimeOutException {
+			TimeOutException {
 		Objects.requireNonNull(objectPropertyExpression);
 		logger.finer("getObjectPropertyRanges(" + objectPropertyExpression + ", " + direct + ")");
 		throw new UnsupportedReasonerOperationInBornException(
@@ -288,7 +286,7 @@ public NodeSet<OWLClass> getObjectPropertyRanges(OWLObjectPropertyExpression obj
 	@Override
 	public NodeSet<OWLNamedIndividual> getObjectPropertyValues(OWLNamedIndividual individual,
 			OWLObjectPropertyExpression objectPropertyExpression) throws InconsistentOntologyException,
-					FreshEntitiesException, ReasonerInterruptedException, TimeOutException {
+			FreshEntitiesException, ReasonerInterruptedException, TimeOutException {
 		Objects.requireNonNull(individual);
 		Objects.requireNonNull(objectPropertyExpression);
 		logger.finer("getObjectPropertyValues(" + individual + ", " + objectPropertyExpression + ")");
@@ -397,7 +395,7 @@ public NodeSet<OWLDataProperty> getSubDataProperties(OWLDataProperty dataPropert
 	@Override
 	public NodeSet<OWLObjectPropertyExpression> getSubObjectProperties(
 			OWLObjectPropertyExpression objectPropertyExpression, boolean direct) throws InconsistentOntologyException,
-					FreshEntitiesException, ReasonerInterruptedException, TimeOutException {
+			FreshEntitiesException, ReasonerInterruptedException, TimeOutException {
 		Objects.requireNonNull(objectPropertyExpression);
 		logger.finer("getSubObjectProperties(" + objectPropertyExpression + ", " + direct + ")");
 		throw new UnsupportedReasonerOperationInBornException(
@@ -427,7 +425,7 @@ public NodeSet<OWLDataProperty> getSuperDataProperties(OWLDataProperty dataPrope
 	@Override
 	public NodeSet<OWLObjectPropertyExpression> getSuperObjectProperties(
 			OWLObjectPropertyExpression objectPropertyExpression, boolean direct) throws InconsistentOntologyException,
-					FreshEntitiesException, ReasonerInterruptedException, TimeOutException {
+			FreshEntitiesException, ReasonerInterruptedException, TimeOutException {
 		Objects.requireNonNull(objectPropertyExpression);
 		logger.finer("getSuperObjectProperties(" + objectPropertyExpression + ", " + direct + ")");
 		throw new UnsupportedReasonerOperationInBornException(

born-owlapi/src/main/java/de/tudresden/inf/lat/born/owlapi/multiprocessor/MultiProcessorConfigurationImpl.java

@@ -28,8 +28,7 @@ public List<OntologyAndNetwork> getOntologyList() {
 
 	@Override
 	public void setOntologyList(List<OntologyAndNetwork> ontologyList) {
-		Objects.requireNonNull(ontologyList);
-		this.ontologyList = ontologyList;
+		this.ontologyList = Objects.requireNonNull(ontologyList);
 	}
 
 	@Override
@@ -39,8 +38,7 @@ public String getOutputDirectory() {
 
 	@Override
 	public void setOutputDirectory(String outputDirectory) {
-		Objects.requireNonNull(outputDirectory);
-		this.outputDirectory = outputDirectory;
+		this.outputDirectory = Objects.requireNonNull(outputDirectory);
 	}
 
 	@Override
@@ -70,8 +68,7 @@ public Function<String, String> getQueryProcessor() {
 
 	@Override
 	public void setQueryProcessor(Function<String, String> queryProcessor) {
-		Objects.requireNonNull(queryProcessor);
-		this.queryProcessor = queryProcessor;
+		this.queryProcessor = Objects.requireNonNull(queryProcessor);
 	}
 
 	@Override

born-owlapi/src/main/java/de/tudresden/inf/lat/born/owlapi/multiprocessor/OntologyAndNetwork.java

@@ -39,11 +39,9 @@ public OntologyAndNetwork(OWLOntology owlOntology) {
 	 *            Bayesian network in ProbLog syntax
 	 */
 	public OntologyAndNetwork(OWLOntology owlOntology, String bayesianNetwork) {
-		Objects.requireNonNull(owlOntology);
-		Objects.requireNonNull(bayesianNetwork);
-		this.owlOntology = owlOntology;
+		this.owlOntology = Objects.requireNonNull(owlOntology);
 		this.ontologyName = owlOntology.getOntologyID().toString();
-		this.bayesianNetwork = bayesianNetwork;
+		this.bayesianNetwork = Objects.requireNonNull(bayesianNetwork);
 	}
 
 	/**
@@ -57,12 +55,9 @@ public OntologyAndNetwork(OWLOntology owlOntology, String bayesianNetwork) {
 	 *            Bayesian network in ProbLog syntax
 	 */
 	public OntologyAndNetwork(String ontologyName, OWLOntology owlOntology, String bayesianNetwork) {
-		Objects.requireNonNull(ontologyName);
-		Objects.requireNonNull(owlOntology);
-		Objects.requireNonNull(bayesianNetwork);
-		this.ontologyName = ontologyName;
-		this.owlOntology = owlOntology;
-		this.bayesianNetwork = bayesianNetwork;
+		this.ontologyName = Objects.requireNonNull(ontologyName);
+		this.owlOntology = Objects.requireNonNull(owlOntology);
+		this.bayesianNetwork = Objects.requireNonNull(bayesianNetwork);
 	}
 
 	/**