JAL-3210 Test with coreall.z.js

diff --git a/gradle.properties b/gradle.properties
index f2fe5d8..e4ee8b9 100644 (file)
--- a/gradle.properties
+++ b/gradle.properties
@@ -175,6 +175,7 @@ jalviewjs_server_wait = 30
 jalviewjs_server_resource = /jalview_bin_Jalview.html
 jalviewjs_core_name = _jalview
 jalviewjs_name = JalviewJS
+jalviewjs_default_core = all
 
 j2s.compiler.status = enable
 #j2s.site.directory = null ## site defined from buildDir+'/jalviewjs/'+jalviewjs_site_dir

diff --git a/utils/jalviewjs/classlists/all.txt b/utils/jalviewjs/classlists/all.txt
new file mode 100644 (file)
index 0000000..8838142
--- /dev/null
+++ b/utils/jalviewjs/classlists/all.txt
@@ -0,0 +1,4754 @@
+ext/edu/ucsf/rbvi/strucviz2/ChimUtils.js
+ext/edu/ucsf/rbvi/strucviz2/ChimeraStructuralObject.js
+ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.js
+ext/edu/ucsf/rbvi/strucviz2/ChimeraResidue.js
+ext/edu/ucsf/rbvi/strucviz2/ChimeraTreeModel.js
+ext/edu/ucsf/rbvi/strucviz2/port/ListenerThreads.js
+ext/edu/ucsf/rbvi/strucviz2/ChimeraChain.js
+ext/edu/ucsf/rbvi/strucviz2/StructureManager.js
+ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.js
+ext/edu/ucsf/rbvi/strucviz2/StructureSettings.js
+ext/vamsas/SeqSearchServiceSoapBindingStub.js
+ext/vamsas/MuscleWSSoapBindingStub.js
+ext/vamsas/SeqSearchI.js
+ext/vamsas/ServiceHandles.js
+ext/vamsas/MuscleWSService.js
+ext/vamsas/JpredSoapBindingStub.js
+ext/vamsas/IRegistryService.js
+ext/vamsas/IRegistryServiceLocator.js
+ext/vamsas/RegistryServiceSoapBindingStub.js
+ext/vamsas/MuscleWS.js
+ext/vamsas/JpredService.js
+ext/vamsas/ServiceHandle.js
+ext/vamsas/Jpred.js
+ext/vamsas/JpredServiceLocator.js
+ext/vamsas/SeqSearchServiceService.js
+ext/vamsas/SeqSearchServiceLocator.js
+ext/vamsas/IRegistry.js
+ext/vamsas/MuscleWSServiceLocator.js
+intervalstore/impl/BinarySearcher.js
+intervalstore/impl/NCList.js
+intervalstore/impl/NCNode.js
+intervalstore/impl/IntervalStore.js
+intervalstore/impl/Range.js
+intervalstore/impl/NCListBuilder.js
+intervalstore/api/IntervalStoreI.js
+intervalstore/api/IntervalI.js
+gnu/jpdf/PDFPrinterJob.js
+gnu/jpdf/TestMenuBar.js
+gnu/jpdf/PDFPage.js
+gnu/jpdf/PDFObject.js
+gnu/jpdf/TestPanel.js
+gnu/jpdf/StringTooLongException.js
+gnu/jpdf/PDFJob.js
+gnu/jpdf/BoundingBox.js
+gnu/jpdf/PDFXref.js
+gnu/jpdf/PDFGraphics.js
+gnu/jpdf/PDFTest.js
+gnu/jpdf/HelpFrame.js
+gnu/jpdf/PDFDocument.js
+gnu/jpdf/PDFInfo.js
+gnu/jpdf/PDFAnnot.js
+gnu/jpdf/PDFOutline.js
+gnu/jpdf/PDFStringHelper.js
+gnu/jpdf/PDFOutput.js
+gnu/jpdf/PDFFont.js
+gnu/jpdf/PDFPageList.js
+gnu/jpdf/PDFStream.js
+gnu/jpdf/PDFBorder.js
+gnu/jpdf/PDFImage.js
+gnu/jpdf/PDFCatalog.js
+java/applet/AppletStub.js
+java/applet/JSApplet.js
+java/applet/AppletContext.js
+java/applet/Applet.js
+java/applet/AudioClip.js
+java/security/Identity.js
+java/security/BasicPermission.js
+java/security/KeyException.js
+java/security/KeyRep.js
+java/security/Guard.js
+java/security/CodeSource.js
+java/security/PolicySpi.js
+java/security/PermissionCollection.js
+java/security/KeyStoreException.js
+java/security/interfaces/ECPrivateKey.js
+java/security/interfaces/DSAPrivateKey.js
+java/security/interfaces/RSAPrivateCrtKey.js
+java/security/interfaces/DSAParams.js
+java/security/interfaces/RSAPublicKey.js
+java/security/interfaces/DSAKeyPairGenerator.js
+java/security/interfaces/DSAPublicKey.js
+java/security/interfaces/RSAPrivateKey.js
+java/security/interfaces/ECKey.js
+java/security/interfaces/RSAKey.js
+java/security/interfaces/DSAKey.js
+java/security/interfaces/ECPublicKey.js
+java/security/interfaces/RSAMultiPrimePrivateCrtKey.js
+java/security/KeyPairGenerator.js
+java/security/AlgorithmParameterGeneratorSpi.js
+java/security/SecureRandom.js
+java/security/NoSuchAlgorithmException.js
+java/security/AccessControlException.js
+java/security/ProviderException.js
+java/security/SecureClassLoader.js
+java/security/InvalidAlgorithmParameterException.js
+java/security/AuthProvider.js
+java/security/Provider.js
+java/security/KeyPair.js
+java/security/KeyManagementException.js
+java/security/PrivilegedExceptionAction.js
+java/security/Certificate.js
+java/security/acl/NotOwnerException.js
+java/security/acl/LastOwnerException.js
+java/security/acl/Acl.js
+java/security/acl/AclNotFoundException.js
+java/security/acl/Permission.js
+java/security/acl/Group.js
+java/security/acl/AclEntry.js
+java/security/acl/Owner.js
+java/security/AccessController.js
+java/security/Key.js
+java/security/SecureRandomSpi.js
+java/security/NoSuchProviderException.js
+java/security/DigestException.js
+java/security/PermissionsHash.js
+java/security/URIParameter.js
+java/security/DomainCombiner.js
+java/security/ProtectionDomain.js
+java/security/Security.js
+java/security/CodeSigner.js
+java/security/AlgorithmParametersSpi.js
+java/security/Timestamp.js
+java/security/KeyFactorySpi.js
+java/security/DomainLoadStoreParameter.js
+java/security/AllPermissionCollection.js
+java/security/MessageDigest.js
+java/security/CryptoPrimitive.js
+java/security/InvalidParameterException.js
+java/security/GuardedObject.js
+java/security/AlgorithmConstraints.js
+java/security/SignatureException.js
+java/security/Principal.js
+java/security/IdentityScope.js
+java/security/KeyStoreSpi.js
+java/security/UnrecoverableKeyException.js
+java/security/PrivilegedActionException.js
+java/security/Signature.js
+java/security/GeneralSecurityException.js
+java/security/spec/RSAOtherPrimeInfo.js
+java/security/spec/RSAKeyGenParameterSpec.js
+java/security/spec/InvalidParameterSpecException.js
+java/security/spec/ECParameterSpec.js
+java/security/spec/RSAPrivateKeySpec.js
+java/security/spec/DSAPrivateKeySpec.js
+java/security/spec/ECGenParameterSpec.js
+java/security/spec/ECPublicKeySpec.js
+java/security/spec/RSAMultiPrimePrivateCrtKeySpec.js
+java/security/spec/RSAPrivateCrtKeySpec.js
+java/security/spec/ECFieldFp.js
+java/security/spec/RSAPublicKeySpec.js
+java/security/spec/EncodedKeySpec.js
+java/security/spec/ECField.js
+java/security/spec/ECPoint.js
+java/security/spec/ECPrivateKeySpec.js
+java/security/spec/DSAGenParameterSpec.js
+java/security/spec/InvalidKeySpecException.js
+java/security/spec/DSAParameterSpec.js
+java/security/spec/EllipticCurve.js
+java/security/spec/PKCS8EncodedKeySpec.js
+java/security/spec/PSSParameterSpec.js
+java/security/spec/KeySpec.js
+java/security/spec/MGF1ParameterSpec.js
+java/security/spec/DSAPublicKeySpec.js
+java/security/spec/X509EncodedKeySpec.js
+java/security/spec/ECFieldF2m.js
+java/security/spec/AlgorithmParameterSpec.js
+java/security/SignatureSpi.js
+java/security/InvalidKeyException.js
+java/security/UnrecoverableEntryException.js
+java/security/UnresolvedPermission.js
+java/security/DigestInputStream.js
+java/security/cert/CertStore.js
+java/security/cert/CRLException.js
+java/security/cert/CertPathValidatorException.js
+java/security/cert/CertificateEncodingException.js
+java/security/cert/PKIXRevocationChecker.js
+java/security/cert/CertPathValidatorSpi.js
+java/security/cert/TrustAnchor.js
+java/security/cert/CertPathBuilder.js
+java/security/cert/CertificateFactory.js
+java/security/cert/Certificate.js
+java/security/cert/CertPathBuilderSpi.js
+java/security/cert/X509CertSelector.js
+java/security/cert/CertPathBuilderResult.js
+java/security/cert/X509Extension.js
+java/security/cert/CertSelector.js
+java/security/cert/CertificateExpiredException.js
+java/security/cert/CertPathChecker.js
+java/security/cert/X509CRLEntry.js
+java/security/cert/Extension.js
+java/security/cert/CertPathValidator.js
+java/security/cert/PKIXBuilderParameters.js
+java/security/cert/PKIXCertPathBuilderResult.js
+java/security/cert/CertStoreSpi.js
+java/security/cert/X509CRLSelector.js
+java/security/cert/CertificateFactorySpi.js
+java/security/cert/X509CRL.js
+java/security/cert/PKIXCertPathValidatorResult.js
+java/security/cert/CertStoreParameters.js
+java/security/cert/LDAPCertStoreParameters.js
+java/security/cert/PolicyQualifierInfo.js
+java/security/cert/X509Certificate.js
+java/security/cert/CertificateNotYetValidException.js
+java/security/cert/PKIXCertPathChecker.js
+java/security/cert/PolicyNode.js
+java/security/cert/CertificateException.js
+java/security/cert/CRLReason.js
+java/security/cert/CollectionCertStoreParameters.js
+java/security/cert/CRL.js
+java/security/cert/CertificateParsingException.js
+java/security/cert/CertPathBuilderException.js
+java/security/cert/PKIXReason.js
+java/security/cert/CertPathHelperImpl.js
+java/security/cert/CertPathParameters.js
+java/security/cert/CRLSelector.js
+java/security/cert/CertPathValidatorResult.js
+java/security/cert/CertStoreException.js
+java/security/cert/CertPath.js
+java/security/cert/CertificateRevokedException.js
+java/security/cert/PKIXParameters.js
+java/security/PrivilegedAction.js
+java/security/Permission.js
+java/security/AccessControlContext.js
+java/security/AlgorithmParameterGenerator.js
+java/security/PKCS12Attribute.js
+java/security/MessageDigestSpi.js
+java/security/UnresolvedPermissionCollection.js
+java/security/KeyStore.js
+java/security/PrivateKey.js
+java/security/DigestOutputStream.js
+java/security/Permissions.js
+java/security/PublicKey.js
+java/security/BasicPermissionCollection.js
+java/security/Policy.js
+java/security/SecurityPermission.js
+java/security/PermissionsEnumerator.js
+java/security/AlgorithmParameters.js
+java/security/Signer.js
+java/security/KeyPairGeneratorSpi.js
+java/security/SignedObject.js
+java/security/AllPermission.js
+java/security/KeyFactory.js
+java/beans/PropertyChangeListener.js
+java/beans/VetoableChangeListenerProxy.js
+java/beans/PropertyChangeEvent.js
+java/beans/FeatureDescriptor.js
+java/beans/PropertyChangeListenerProxy.js
+java/beans/PropertyEditor.js
+java/beans/VetoableChangeListener.js
+java/beans/PropertyVetoException.js
+java/beans/PropertyChangeSupport.js
+java/beans/VetoableChangeSupport.js
+java/beans/PropertyDescriptor.js
+java/beans/ChangeListenerMap.js
+java/beans/PropertyEditorSupport.js
+java/beans/IndexedPropertyChangeEvent.js
+java/beans/IntrospectionException.js
+java/util/Vector.js
+java/util/HashSet.js
+java/util/JumboEnumSet.js
+java/util/HashMap.js
+java/util/IllformedLocaleException.js
+java/util/BitSet.js
+java/util/RandomAccessSubList.js
+java/util/Set.js
+java/util/UnknownFormatConversionException.js
+java/util/NavigableMap.js
+java/util/List.js
+java/util/Enumeration.js
+java/util/FormatterClosedException.js
+java/util/IllegalFormatConversionException.js
+java/util/LinkedHashSet.js
+java/util/AbstractCollection.js
+java/util/Observer.js
+java/util/Optional.js
+java/util/TimerTask.js
+java/util/GregorianCalendar.js
+java/util/RegularEnumSet.js
+java/util/Objects.js
+java/util/DualPivotQuicksort.js
+java/util/concurrent/TimeoutException.js
+java/util/concurrent/CompletionService.js
+java/util/concurrent/SynchronousQueue.js
+java/util/concurrent/ConcurrentSkipListMap.js
+java/util/concurrent/LinkedBlockingDeque.js
+java/util/concurrent/RunnableScheduledFuture.js
+java/util/concurrent/DelayQueue.js
+java/util/concurrent/ConcurrentSkipListSet.js
+java/util/concurrent/ConcurrentHashMap.js
+java/util/concurrent/CopyOnWriteArraySet.js
+java/util/concurrent/ThreadFactory.js
+java/util/concurrent/Executor.js
+java/util/concurrent/ThreadPoolExecutor.js
+java/util/concurrent/RunnableFuture.js
+java/util/concurrent/Delayed.js
+java/util/concurrent/RecursiveTask.js
+java/util/concurrent/RejectedExecutionException.js
+java/util/concurrent/CompletionStage.js
+java/util/concurrent/CompletionException.js
+java/util/concurrent/ExecutorService.js
+java/util/concurrent/Phaser.js
+java/util/concurrent/ArrayBlockingQueue.js
+java/util/concurrent/ConcurrentMap.js
+java/util/concurrent/locks/AbstractOwnableSynchronizer.js
+java/util/concurrent/locks/LockSupport.js
+java/util/concurrent/locks/AbstractQueuedLongSynchronizer.js
+java/util/concurrent/locks/Lock.js
+java/util/concurrent/locks/ReentrantReadWriteLock.js
+java/util/concurrent/locks/AbstractQueuedSynchronizer.js
+java/util/concurrent/locks/ReentrantLock.js
+java/util/concurrent/locks/ReadWriteLock.js
+java/util/concurrent/locks/Condition.js
+java/util/concurrent/BlockingQueue.js
+java/util/concurrent/CyclicBarrier.js
+java/util/concurrent/FutureTask.js
+java/util/concurrent/BlockingDeque.js
+java/util/concurrent/ScheduledExecutorService.js
+java/util/concurrent/LinkedBlockingQueue.js
+java/util/concurrent/TimeUnit.js
+java/util/concurrent/CompletableFuture.js
+java/util/concurrent/Executors.js
+java/util/concurrent/CancellationException.js
+java/util/concurrent/ConcurrentLinkedQueue.js
+java/util/concurrent/ConcurrentNavigableMap.js
+java/util/concurrent/ScheduledThreadPoolExecutor.js
+java/util/concurrent/RejectedExecutionHandler.js
+java/util/concurrent/AbstractExecutorService.js
+java/util/concurrent/Future.js
+java/util/concurrent/ExecutorCompletionService.js
+java/util/concurrent/Callable.js
+java/util/concurrent/LinkedTransferQueue.js
+java/util/concurrent/PriorityBlockingQueue.js
+java/util/concurrent/Exchanger.js
+java/util/concurrent/ConcurrentLinkedDeque.js
+java/util/concurrent/atomic/AtomicBoolean.js
+java/util/concurrent/atomic/AtomicLong.js
+java/util/concurrent/atomic/AtomicInteger.js
+java/util/concurrent/ThreadLocalRandom.js
+java/util/concurrent/CopyOnWriteArrayList.js
+java/util/concurrent/CountDownLatch.js
+java/util/concurrent/ScheduledFuture.js
+java/util/concurrent/CountedCompleter.js
+java/util/concurrent/Semaphore.js
+java/util/concurrent/TransferQueue.js
+java/util/concurrent/BrokenBarrierException.js
+java/util/concurrent/RecursiveAction.js
+java/util/concurrent/ExecutionException.js
+java/util/Hashtable.js
+java/util/Base64.js
+java/util/LinkedList.js
+java/util/OptionalInt.js
+java/util/OptionalDouble.js
+java/util/SplittableRandom.js
+java/util/ListIterator.js
+java/util/Queue.js
+java/util/AbstractQueue.js
+java/util/Collections.js
+java/util/SortedMap.js
+java/util/FormattableFlags.js
+java/util/Locale.js
+java/util/Stack.js
+java/util/NoSuchElementException.js
+java/util/Random.js
+java/util/Spliterators.js
+java/util/Formatter.js
+java/util/PrimitiveIterator.js
+java/util/Collection.js
+java/util/ResourceBundle.js
+java/util/FormatFlagsConversionMismatchException.js
+java/util/SortedSet.js
+java/util/StringTokenizer.js
+java/util/ServiceConfigurationError.js
+java/util/prefs/PreferencesFactory.js
+java/util/prefs/NodeChangeListener.js
+java/util/prefs/Base64.js
+java/util/prefs/PreferenceChangeEvent.js
+java/util/prefs/Preferences.js
+java/util/prefs/XmlSupport.js
+java/util/prefs/PreferenceChangeListener.js
+java/util/prefs/InvalidPreferencesFormatException.js
+java/util/prefs/FileSystemPreferencesFactory.js
+java/util/prefs/FileSystemPreferences.js
+java/util/prefs/NodeChangeEvent.js
+java/util/prefs/AbstractPreferences.js
+java/util/prefs/BackingStoreException.js
+java/util/PriorityQueue.js
+java/util/SimpleTimeZone.js
+java/util/jar/JarVerifier.js
+java/util/jar/Attributes.js
+java/util/jar/Pack200.js
+java/util/jar/JarException.js
+java/util/jar/JarInputStream.js
+java/util/jar/JavaUtilJarAccessImpl.js
+java/util/jar/JarOutputStream.js
+java/util/jar/JarFile.js
+java/util/jar/Manifest.js
+java/util/jar/JarEntry.js
+java/util/Calendar.js
+java/util/IllegalFormatWidthException.js
+java/util/Dictionary.js
+java/util/EventListener.js
+java/util/UUID.js
+java/util/PropertyResourceBundle.js
+java/util/MissingFormatWidthException.js
+java/util/ArraysParallelSortHelpers.js
+java/util/OptionalLong.js
+java/util/TooManyListenersException.js
+java/util/IllegalFormatPrecisionException.js
+java/util/AbstractList.js
+java/util/StringJoiner.js
+java/util/ArrayPrefixHelpers.js
+java/util/function/DoubleToLongFunction.js
+java/util/function/DoubleUnaryOperator.js
+java/util/function/ObjIntConsumer.js
+java/util/function/BiConsumer.js
+java/util/function/ToIntFunction.js
+java/util/function/LongPredicate.js
+java/util/function/IntToLongFunction.js
+java/util/function/DoubleFunction.js
+java/util/function/LongToIntFunction.js
+java/util/function/ToDoubleBiFunction.js
+java/util/function/Function.js
+java/util/function/ToLongBiFunction.js
+java/util/function/LongSupplier.js
+java/util/function/BooleanSupplier.js
+java/util/function/ObjDoubleConsumer.js
+java/util/function/ToIntBiFunction.js
+java/util/function/DoubleBinaryOperator.js
+java/util/function/IntBinaryOperator.js
+java/util/function/BiFunction.js
+java/util/function/DoubleToIntFunction.js
+java/util/function/ObjLongConsumer.js
+java/util/function/IntUnaryOperator.js
+java/util/function/IntPredicate.js
+java/util/function/IntConsumer.js
+java/util/function/LongConsumer.js
+java/util/function/LongToDoubleFunction.js
+java/util/function/Consumer.js
+java/util/function/Predicate.js
+java/util/function/LongFunction.js
+java/util/function/ToDoubleFunction.js
+java/util/function/BinaryOperator.js
+java/util/function/DoubleSupplier.js
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+java/util/function/ToLongFunction.js
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+java/util/function/UnaryOperator.js
+java/util/function/IntFunction.js
+java/util/function/DoublePredicate.js
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+java/util/IdentityHashMap.js
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+java/util/ComparableTimSort.js
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+java/util/TimerThread.js
+java/util/NavigableSet.js
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+java/util/Observable.js
+java/util/logging/LoggingPermission.js
+java/util/logging/MemoryHandler.js
+java/util/logging/SimpleFormatter.js
+java/util/logging/XMLFormatter.js
+java/util/logging/LogRecord.js
+java/util/logging/FileHandler.js
+java/util/logging/LoggingMXBean.js
+java/util/logging/LogManager.js
+java/util/logging/LoggingProxyImpl.js
+java/util/logging/Formatter.js
+java/util/logging/Filter.js
+java/util/logging/SocketHandler.js
+java/util/logging/Level.js
+java/util/logging/Handler.js
+java/util/logging/ConsoleHandler.js
+java/util/logging/ErrorManager.js
+java/util/logging/StreamHandler.js
+java/util/logging/Logger.js
+java/util/logging/Logging.js
+java/util/EventObject.js
+java/util/SubList.js
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+java/util/RandomAccess.js
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+java/util/IllegalFormatFlagsException.js
+java/util/regex/MatchResult.js
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+java/util/zip/InflaterInputStream.js
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+java/util/zip/Deflater.js
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+java/util/zip/ZipConstants64.js
+java/util/zip/CRC32.js
+java/util/zip/ZipException.js
+java/util/zip/ZipOutputStream.js
+java/util/zip/Inflater.js
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+java/util/zip/ZipConstants.js
+java/util/zip/CheckedInputStream.js
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+java/util/stream/IntStream.js
+java/util/stream/StreamShape.js
+java/util/stream/LongPipeline.js
+java/util/stream/StreamOpFlag.js
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+java/util/stream/MatchOps.js
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+java/util/stream/StreamSpliterators.js
+java/util/stream/FindOps.js
+java/util/stream/IntPipeline.js
+java/util/stream/AbstractTask.js
+java/util/stream/DoublePipeline.js
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+java/util/stream/LongStream.js
+java/util/stream/Node.js
+java/util/stream/ForEachOps.js
+java/util/stream/Collector.js
+java/util/stream/Streams.js
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+java/util/stream/TerminalSink.js
+java/util/stream/SliceOps.js
+java/util/stream/AbstractShortCircuitTask.js
+java/util/stream/Tripwire.js
+java/util/TreeMap.js
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+java/util/WeakHashMap.js
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+java/util/TimeZone.js
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+java/util/ServiceLoader.js
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+java/nio/HeapByteBuffer.js
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