Index (JUtils - Miscellanea of Java Utils 14.1-SNAPSHOT API)

A B C D E F G H I J K L M N O P R S T U V W X Y
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

AbstractSizedBatchCollector - Class in uk.ac.ebi.utils.threading.batchproc: Deprecated.
the functionality available in this package is provided by project Reactor and we recommend to switch to that. TODO: helpers and examples about batching via Reactor.
AbstractSizedBatchCollector() - Constructor for class uk.ac.ebi.utils.threading.batchproc.AbstractSizedBatchCollector: Deprecated.

Takes the default value of 1000.
AbstractSizedBatchCollector(long) - Constructor for class uk.ac.ebi.utils.threading.batchproc.AbstractSizedBatchCollector: Deprecated.
accumulator() - Method in class uk.ac.ebi.utils.threading.batchproc.collectors.CollectionBatchCollector: Deprecated.
accumulator() - Method in interface uk.ac.ebi.utils.threading.batchproc.ItemizedBatchCollector: Deprecated.
add(List<T>, int, T) - Static method in class uk.ac.ebi.utils.collections.ListUtils: Adds the element i in list, as in List.add(int, Object), but independently on list.size().
add(T) - Method in class uk.ac.ebi.utils.collections.TypeCastCollection
add(V) - Method in class uk.ac.ebi.utils.collections.MapCollection: Adds the entry (keyFunc.apply(e), e)
addAll(Collection<? extends T>) - Method in class uk.ac.ebi.utils.collections.TypeCastCollection
addAll(Collection<? extends V>) - Method in class uk.ac.ebi.utils.collections.MapCollection: Iteratively calls MapCollection.add(Object).
addMany2Many(O, A, String, Collection<A>) - Static method in class uk.ac.ebi.utils.orm.Many2ManyUtils: Synchronises the addition of an object to a many2many relationship.
after() - Method in class uk.ac.ebi.utils.opt.orm.test.TestEntityMgrProvider: Shuts down (flushes, closes, etc) the entity manager created by TestEntityMgrProvider.before().
after() - Method in class uk.ac.ebi.utils.test.junit.TestEntityMgrProvider: Shuts down (flushes, closes, etc) the entity manager created by TestEntityMgrProvider.before().
AlphaNumComparator<T> - Class in uk.ac.ebi.utils.collections: The Alphanum Algorithm is an improved sorting algorithm for strings containing numbers.
AlphaNumComparator() - Constructor for class uk.ac.ebi.utils.collections.AlphaNumComparator: Default is true
AlphaNumComparator(boolean) - Constructor for class uk.ac.ebi.utils.collections.AlphaNumComparator: Default is true
andThen(Executor) - Method in class uk.ac.ebi.utils.runcontrol.ChainExecutor: It's the reverse of ChainExecutor.wrap(Executor).
appendProgressReportAction(BiConsumer<Long, Long>) - Method in class uk.ac.ebi.utils.runcontrol.ProgressLogger: Facility to append the action to the ProgressLogger.getProgressReportAction().
apply(Statement, Description) - Method in class uk.ac.ebi.utils.test.junit.TestOutputDecorator: You can use this class either as a listener, or a Rule, so we have this method too, to be called by JUnit in the second case.
ArraySearchUtils - Class in uk.ac.ebi.utils.collections: Utilities about searches over arrays.
asCollection(Object) - Static method in class uk.ac.ebi.utils.collections.CollectionsUtils: Converts the value into an immutable Collection.
asList(Object) - Static method in class uk.ac.ebi.utils.collections.CollectionsUtils: Similar to CollectionsUtils.asCollection(Object), returns an unmodifiable list out of the value.
asSet(Object) - Static method in class uk.ac.ebi.utils.collections.CollectionsUtils: Similar to CollectionsUtils.asCollection(Object), returns an unmodifiable set out of the value.
asValue(Object) - Static method in class uk.ac.ebi.utils.collections.CollectionsUtils: Wrapper with failIfMany = false
asValue(Object, boolean) - Static method in class uk.ac.ebi.utils.collections.CollectionsUtils: Converts a possibly-collection value into a singleton.
await() - Method in class uk.ac.ebi.utils.threading.fakelocks.FakeCondition
await(long, TimeUnit) - Method in class uk.ac.ebi.utils.threading.fakelocks.FakeCondition
awaitNanos(long) - Method in class uk.ac.ebi.utils.threading.fakelocks.FakeCondition
awaitUninterruptibly() - Method in class uk.ac.ebi.utils.threading.fakelocks.FakeCondition
awaitUntil(Date) - Method in class uk.ac.ebi.utils.threading.fakelocks.FakeCondition

B

base - Variable in class uk.ac.ebi.utils.collections.TypeCastCollection
BatchCollector - Interface in uk.ac.ebi.utils.threading.batchproc: Deprecated.
the functionality available in this package is provided by project Reactor and we recommend to switch to that. @see ReactorUtils
batchFactory() - Method in interface uk.ac.ebi.utils.threading.batchproc.BatchCollector: Deprecated.
batchFactory() - Method in class uk.ac.ebi.utils.threading.batchproc.collectors.CollectionBatchCollector: Deprecated.
batchProcessing(Collection<T>, Consumer<List<T>>) - Static method in class uk.ac.ebi.utils.opt.runcontrol.ReactorUtils: Variant of ReactorUtils.batchProcessing(Flux, Consumer)
batchProcessing(Stream<T>, Consumer<List<T>>) - Static method in class uk.ac.ebi.utils.opt.runcontrol.ReactorUtils: Variant of ReactorUtils.batchProcessing(Flux, Consumer)
batchProcessing(Flux<T>, Consumer<List<T>>) - Static method in class uk.ac.ebi.utils.opt.runcontrol.ReactorUtils: Uses ReactorUtils.ParallelBatchFluxBuilder with default options and ReactorUtils.batchProcessing(ParallelFlux, Consumer) to batch a source of items and process them in parallel batches.
batchProcessing(ParallelFlux, Consumer) - Static method in class uk.ac.ebi.utils.opt.runcontrol.ReactorUtils: Uses ReactorUtils.ParallelBatchFluxBuilder to process a source of batches.
BatchProcessor<B,BC extends BatchCollector,BJ extends Consumer> - Class in uk.ac.ebi.utils.threading.batchproc: Deprecated.
the functionality available in this package is provided by project Reactor and we recommend to switch to that. @see ReactorUtils
BatchProcessor() - Constructor for class uk.ac.ebi.utils.threading.batchproc.BatchProcessor: Deprecated.
BatchProcessor(BJ) - Constructor for class uk.ac.ebi.utils.threading.batchproc.BatchProcessor: Deprecated.
BatchProcessor(BJ, BC) - Constructor for class uk.ac.ebi.utils.threading.batchproc.BatchProcessor: Deprecated.
batchReadyFlag() - Method in interface uk.ac.ebi.utils.threading.batchproc.BatchCollector: Deprecated.
batchReadyFlag() - Method in interface uk.ac.ebi.utils.threading.batchproc.SizedBatchCollector: Deprecated.
BatchService<TK extends BatchServiceTask> - Class in uk.ac.ebi.utils.threading: A pool-based thread execution service, that dynamically optimises its size.
BatchService() - Constructor for class uk.ac.ebi.utils.threading.BatchService: Defaults to Runtime.getRuntime().availableProcessors()
BatchService(int) - Constructor for class uk.ac.ebi.utils.threading.BatchService: Initialises a pool service with this number of initial threads.
BatchService.BatchServiceTuner - Class in uk.ac.ebi.utils.threading: The custom PoolSizeTuner that is used to optimise this service.
BatchServiceTask - Class in uk.ac.ebi.utils.threading: Used by BatchService.
BatchServiceTask(String) - Constructor for class uk.ac.ebi.utils.threading.BatchServiceTask
BatchServiceTask.TaskComparator - Class in uk.ac.ebi.utils.threading: Provides a task comparison based on BatchServiceTask.getPriority() (higher priorities comes first).
BatchServiceTuner() - Constructor for class uk.ac.ebi.utils.threading.BatchService.BatchServiceTuner
batchSizer() - Method in class uk.ac.ebi.utils.threading.batchproc.collectors.CollectionBatchCollector: Deprecated.
batchSizer() - Method in interface uk.ac.ebi.utils.threading.batchproc.SizedBatchCollector: Deprecated.
before() - Method in class uk.ac.ebi.utils.opt.orm.test.TestEntityMgrProvider: Uses the factor passed to constructor to create a new EntityManager, via TestEntityMgrProvider.newEntityManager(), makes it available via TestEntityMgrProvider.getEntityManager().
before() - Method in class uk.ac.ebi.utils.test.junit.TestEntityMgrProvider: Uses the factor passed to constructor to create a new EntityManager, via TestEntityMgrProvider.newEntityManager(), makes it available via TestEntityMgrProvider.getEntityManager().
build() - Method in class uk.ac.ebi.utils.opt.runcontrol.ReactorUtils.ParallelBatchFluxBuilder
buildEx(E, String, Object...) - Static method in class uk.ac.ebi.utils.exceptions.ExceptionUtils: Wrapper that uses cause.getClass() as exception type.
buildEx(Class<E>, String, Object...) - Static method in class uk.ac.ebi.utils.exceptions.ExceptionUtils: Wrapper with no cause.
buildEx(Class<E>, Throwable, String, Object...) - Static method in class uk.ac.ebi.utils.exceptions.ExceptionUtils: Helper to ease the building of an exception and its message.

C

CausalNumberFormatException - Exception in uk.ac.ebi.utils.exceptions: A NumberFormatException that allows to include a reference to what caused the exception.
CausalNumberFormatException(String) - Constructor for exception uk.ac.ebi.utils.exceptions.CausalNumberFormatException
CausalNumberFormatException(String, Throwable) - Constructor for exception uk.ac.ebi.utils.exceptions.CausalNumberFormatException
cdataWrapper(InputStream, String...) - Static method in class uk.ac.ebi.utils.opt.xml.XmlFilterUtils: Wraps the text content of any element with one of the tags in the parameter with <![CDATA[...]]>.
ChainExecutor - Class in uk.ac.ebi.utils.runcontrol: An Executor that is able to chain/stack two other executors.
ChainExecutor(Executor) - Constructor for class uk.ac.ebi.utils.runcontrol.ChainExecutor: This reduces to running one executor only, so it's conceptually equivalent to use the internalExecutor straight, but it's a base to use ChainExecutor.andThen(Executor).
ChainExecutor(Executor, Executor) - Constructor for class uk.ac.ebi.utils.runcontrol.ChainExecutor
characteristics() - Method in class uk.ac.ebi.utils.collections.TupleSpliterator: As a minimum, this will contain NONNULL | DISTINCT | IMMUTABLE.
checkClientTrusted(X509Certificate[], String) - Method in class uk.ac.ebi.utils.opt.net.SSLUtils.FakeX509TrustManager
checkMemory(Runnable) - Static method in class uk.ac.ebi.utils.memory.MemoryUtils: Defaults to 0.2 (20%) and true.
checkMemory(Runnable, double) - Static method in class uk.ac.ebi.utils.memory.MemoryUtils: Defaults to callGc = true.
checkMemory(Runnable, double, boolean) - Static method in class uk.ac.ebi.utils.memory.MemoryUtils: Invoke this when you think it's safe to invoke the action (eg, when you can get rid of all the objects and connections in an Hibernate entity manager).
checkServerTrusted(X509Certificate[], String) - Method in class uk.ac.ebi.utils.opt.net.SSLUtils.FakeX509TrustManager
CleaningObject - Class in uk.ac.ebi.utils.memory: Simulates the old finalize() method in Java >= 9.
CleaningObject() - Constructor for class uk.ac.ebi.utils.memory.CleaningObject
clear() - Method in class uk.ac.ebi.utils.collections.MapCollection
clear() - Method in class uk.ac.ebi.utils.collections.OptionsMapWrapper
clear() - Method in class uk.ac.ebi.utils.collections.TypeCastCollection
close() - Method in class uk.ac.ebi.utils.memory.CleaningObject
CollectionBasedBatchProcessor<E,B extends Collection<E>,BC extends CollectionBatchCollector<B,E>,BJ extends Consumer> - Class in uk.ac.ebi.utils.threading.batchproc.processors: Deprecated.
the functionality available in this package is provided by project Reactor and we recommend to switch to that. @see ReactorUtils
CollectionBasedBatchProcessor() - Constructor for class uk.ac.ebi.utils.threading.batchproc.processors.CollectionBasedBatchProcessor: Deprecated.

This initialises with a default collection and size, like CollectionBasedBatchProcessor(Consumer), and no job (which needs to be set later via BatchProcessor.setBatchJob(Consumer)).
CollectionBasedBatchProcessor(BJ) - Constructor for class uk.ac.ebi.utils.threading.batchproc.processors.CollectionBasedBatchProcessor: Deprecated.

Initialises with a default collection, which should also have a default max size.
CollectionBasedBatchProcessor(BJ, BC) - Constructor for class uk.ac.ebi.utils.threading.batchproc.processors.CollectionBasedBatchProcessor: Deprecated.
CollectionBatchCollector<C extends Collection<E>,E> - Class in uk.ac.ebi.utils.threading.batchproc.collectors: Deprecated.
the functionality available in this package is provided by project Reactor and we recommend to switch to that. @see ReactorUtils
CollectionBatchCollector(Supplier<C>) - Constructor for class uk.ac.ebi.utils.threading.batchproc.collectors.CollectionBatchCollector: Deprecated.

Default size is inherited by AbstractSizedBatchCollector.
CollectionBatchCollector(Supplier<C>, int) - Constructor for class uk.ac.ebi.utils.threading.batchproc.collectors.CollectionBatchCollector: Deprecated.
CollectionsUtils - Class in uk.ac.ebi.utils.collections: Collections-related utils.
CollectionsUtils() - Constructor for class uk.ac.ebi.utils.collections.CollectionsUtils
compare(Runnable, Runnable) - Method in class uk.ac.ebi.utils.threading.BatchServiceTask.TaskComparator
compare(T, T) - Method in class uk.ac.ebi.utils.collections.AlphaNumComparator
compareTo(Runnable) - Method in class uk.ac.ebi.utils.threading.BatchServiceTask: Orders according to BatchServiceTask.getPriority() (in descending order, the first is the one with the bigger priority).
compute(String, BiFunction<? super String, ? super Object, ? extends Object>) - Method in class uk.ac.ebi.utils.collections.OptionsMapWrapper
computeIfAbsent(String, Function<? super String, ? extends Object>) - Method in class uk.ac.ebi.utils.collections.OptionsMapWrapper
computeIfPresent(String, BiFunction<? super String, ? super Object, ? extends Object>) - Method in class uk.ac.ebi.utils.collections.OptionsMapWrapper
ConfigBootstrapWebListener - Class in uk.ac.ebi.utils.opt.net: A utility ServletContextListener to manage the bootstrap initialisation of a web application.
ConfigBootstrapWebListener() - Constructor for class uk.ac.ebi.utils.opt.net.ConfigBootstrapWebListener
contains(Object) - Method in class uk.ac.ebi.utils.collections.MapCollection: Checks the entry (keyFunc.apply(e), e)
contains(Object) - Method in class uk.ac.ebi.utils.collections.TypeCastCollection
containsAll(Collection<?>) - Method in class uk.ac.ebi.utils.collections.MapCollection: Iteratively calls MapCollection.contains(Object).
containsAll(Collection<?>) - Method in class uk.ac.ebi.utils.collections.TypeCastCollection
containsKey(Object) - Method in class uk.ac.ebi.utils.collections.OptionsMapWrapper
containsOneOf(String, String...) - Static method in class uk.ac.ebi.utils.string.StringSearchUtils: Tells if the string contains one of the matches.
containsOneOfIgnoreCase(String, String...) - Static method in class uk.ac.ebi.utils.string.StringSearchUtils: Tells if the string contains one of the matches.
containsValue(Object) - Method in class uk.ac.ebi.utils.collections.OptionsMapWrapper
contextDestroyed(ServletContextEvent) - Method in class uk.ac.ebi.utils.opt.net.ConfigBootstrapWebListener
contextInitialized(ServletContextEvent) - Method in class uk.ac.ebi.utils.opt.net.ConfigBootstrapWebListener
create() - Static method in interface uk.ac.ebi.utils.collections.OptionsMap: This is based on OptionsMapWrapper.
createCompactUUID() - Static method in class uk.ac.ebi.utils.ids.IdUtils
createExecutor() - Static method in class uk.ac.ebi.utils.threading.HackedBlockingQueue: Defaults to Runtime.availableProcessors() and a submission queue that is twice this number.
createExecutor(int, int) - Static method in class uk.ac.ebi.utils.threading.HackedBlockingQueue: Using an instance of this class, returns a fixed size ThreadPoolExecutor that blocks ExecutorService.submit(Runnable) when both the pool and the submission queue are full.
createNamingThreadFactory(Class<?>) - Static method in class uk.ac.ebi.utils.threading.ThreadUtils: Uses a default base factory.
createNamingThreadFactory(Class<?>, ThreadFactory) - Static method in class uk.ac.ebi.utils.threading.ThreadUtils: Uses Class.getSimpleName() as prefix.
createNamingThreadFactory(String) - Static method in class uk.ac.ebi.utils.threading.ThreadUtils: Uses a default base factory.
createNamingThreadFactory(String, ThreadFactory) - Static method in class uk.ac.ebi.utils.threading.ThreadUtils: A simple wrapper of ThreadFactoryBuilder that creates a ThreadFactory naming new threads like `%d`.
createProblemDetail(Exception, HttpStatusCode, String, String, Object[], WebRequest) - Method in class uk.ac.ebi.utils.opt.springweb.exceptions.XResponseEntityExceptionHandler: Tweaks the original output to return more significant values: - sets detail to the most significant message from ex - sets title to the original detail (which isn't so detailed), discards the original title (since it has low information most of the times) - sets type to the FQN of ex - adds the 'trace' property with the exception's stack trace (TODO: make it optional) As in the superclass, this is used by XResponseEntityExceptionHandler.handleExceptionInternal(Exception, Object, HttpHeaders, HttpStatusCode, WebRequest).

D

DEFAULT_BATCH_SIZE - Static variable in class uk.ac.ebi.utils.opt.runcontrol.ReactorUtils.ParallelBatchFluxBuilder: This has been tested in tasks like saving data on a database.
DEFAULT_FLUX_SCHEDULER - Static variable in class uk.ac.ebi.utils.opt.runcontrol.ReactorUtils.ParallelBatchFluxBuilder: Schedulers.newBoundedElastic(int, int, String) with the number of processors as thread cap and that number * 50 as queue max size.
deleteFile(String) - Static method in class uk.ac.ebi.utils.io.DownloadUtils: Remove a file given an absolute file path
deleteMany2Many(O, A, String, Collection<A>) - Static method in class uk.ac.ebi.utils.orm.Many2ManyUtils: The opposite of Many2ManyUtils.addMany2Many(Object, Object, String, Collection), the parameters and the return value have an analogous meaning.
deserialize(File) - Static method in class uk.ac.ebi.utils.io.SerializationUtils: Wraps the opening of a buffered FileOutputStream and ObjectOutputStream, then then writes the object in it and closes.
deserialize(ObjectInputStream) - Static method in class uk.ac.ebi.utils.io.SerializationUtils: Just like ObjectInputStream.readObject(), with the checked exception wrapper included
deserialize(String) - Static method in class uk.ac.ebi.utils.io.SerializationUtils
doStats() - Method in class uk.ac.ebi.utils.runcontrol.StatsExecutor: Checks if StatsExecutor.getSamplingTime() has passed.
DOWNLOAD_FILE_LOC - Static variable in class uk.ac.ebi.utils.io.DownloadUtils
downloadFile(String, String) - Static method in class uk.ac.ebi.utils.io.DownloadUtils: Provided a URL containing a page/file to download and a download location, will download and create the file.
DownloadUtils - Class in uk.ac.ebi.utils.io: A class to make download of files easier.
DownloadUtils() - Constructor for class uk.ac.ebi.utils.io.DownloadUtils
DynamicRateExecutor - Class in uk.ac.ebi.utils.runcontrol: Like RateLimitedExecutor, but contains a hook where you can dynamically decide which new rate you want to set.
DynamicRateExecutor() - Constructor for class uk.ac.ebi.utils.runcontrol.DynamicRateExecutor: Default is to start with no rate limitation, hence Double.MAX_VALUE.
DynamicRateExecutor(double) - Constructor for class uk.ac.ebi.utils.runcontrol.DynamicRateExecutor

E

entrySet() - Method in class uk.ac.ebi.utils.collections.OptionsMapWrapper
equals(Object) - Method in class uk.ac.ebi.utils.collections.OptionsMapWrapper
estimateSize() - Method in class uk.ac.ebi.utils.collections.TupleSpliterator: This is the shortest size found in base spliterators.
exception2StatusCode - Variable in class uk.ac.ebi.utils.opt.springweb.exceptions.XResponseEntityExceptionHandler: Maps known exceptions to HTTP statuses.
ExceptionLogger - Class in uk.ac.ebi.utils.exceptions: An helper to log exceptions with double level log events, error and debug.
ExceptionUtils - Class in uk.ac.ebi.utils.exceptions: Utilities related to exception handling.
execute(Runnable) - Method in class uk.ac.ebi.utils.runcontrol.ChainExecutor: The external executor calls the run() method of the internal executor, passing the action to it.
execute(Runnable) - Method in class uk.ac.ebi.utils.runcontrol.DynamicRateExecutor
execute(Runnable) - Method in class uk.ac.ebi.utils.runcontrol.MultipleAttemptsExecutor: Overrides Executor.execute(Runnable), by calling #executeChecked(Runnable).
execute(Runnable) - Method in class uk.ac.ebi.utils.runcontrol.RateLimitedExecutor: Controls the execution of the action in such a way that it is run at no more than RateLimitedExecutor.getRate() speed within a given JVM.
execute(Runnable) - Method in class uk.ac.ebi.utils.runcontrol.StatsExecutor: Runs the action, intercepts any Exception it generates. increase StatsExecutor.getTotalCalls() and, if there is an exception, StatsExecutor.getFailedCalls() too.
executeChecked(ThrowingRunnable) - Method in class uk.ac.ebi.utils.runcontrol.MultipleAttemptsExecutor: Tries to run the action and, if it fails with one of MultipleAttemptsExecutor.getInterceptedExceptions(), re-run it up to MultipleAttemptsExecutor.getMaxAttempts().
exitCode - Variable in class uk.ac.ebi.utils.threading.BatchServiceTask
expectNextTag(XMLStreamReader, String) - Static method in class uk.ac.ebi.utils.xml.stax.StaxUtils: Invokes XMLStreamReader.nextTag() and checks that then: we are in a XMLStreamConstants.START_ELEMENT, the element is tag.

F

FAKE_AUTH_SCOPE - Static variable in class uk.ac.ebi.utils.opt.net.SSLUtils
FAKE_HTTP_CLIENT_CONNECTION_MANAGER - Static variable in class uk.ac.ebi.utils.opt.net.SSLUtils
FAKE_SSL_CONTEXT - Static variable in class uk.ac.ebi.utils.opt.net.SSLUtils
FAKE_TLS_STRATEGY - Static variable in class uk.ac.ebi.utils.opt.net.SSLUtils
FakeCondition - Class in uk.ac.ebi.utils.threading.fakelocks
FakeCondition() - Constructor for class uk.ac.ebi.utils.threading.fakelocks.FakeCondition
FakeLock - Class in uk.ac.ebi.utils.threading.fakelocks: A fake lock, which doesn't actually lock anything.
FakeLock() - Constructor for class uk.ac.ebi.utils.threading.fakelocks.FakeLock
FakeReadWriteLock - Class in uk.ac.ebi.utils.threading.fakelocks
FakeReadWriteLock() - Constructor for class uk.ac.ebi.utils.threading.fakelocks.FakeReadWriteLock
FakeX509TrustManager() - Constructor for class uk.ac.ebi.utils.opt.net.SSLUtils.FakeX509TrustManager
finalize() - Method in class uk.ac.ebi.utils.threading.BatchService: Stops BatchService.poolSizeTuner.
findExceptionMapping(Exception) - Method in class uk.ac.ebi.utils.opt.springweb.exceptions.XResponseEntityExceptionHandler: Used within XResponseEntityExceptionHandler.handleMappedException(Exception, WebRequest).
FisherExact - Class in uk.ac.ebi.utils.statistics: Class for Fisher Exact test.
FisherExact(int) - Constructor for class uk.ac.ebi.utils.statistics.FisherExact: constructor for FisherExact table
forEach(BiConsumer<? super String, ? super Object>) - Method in class uk.ac.ebi.utils.collections.OptionsMapWrapper
from(Map<String, Object>) - Static method in interface uk.ac.ebi.utils.collections.OptionsMap: This is based on OptionsMapWrapper.
from(Properties) - Static method in interface uk.ac.ebi.utils.collections.OptionsMap: This is based on OptionsMapWrapper

G

get(Object) - Method in class uk.ac.ebi.utils.collections.OptionsMapWrapper
get(List<T>, int) - Static method in class uk.ac.ebi.utils.collections.ListUtils: Gets the i element of list, independently on list.size().
get(T, K) - Method in class uk.ac.ebi.utils.collections.ObjectStore: Gets an object identified by type and key.
getAcceptedIssuers() - Method in class uk.ac.ebi.utils.opt.net.SSLUtils.FakeX509TrustManager
getAttemptMsgLogLevel() - Method in class uk.ac.ebi.utils.runcontrol.MultipleAttemptsExecutor: Failed attempts are logged with this logging level.
getBase() - Method in class uk.ac.ebi.utils.collections.MapCollection: The underlining map.
getBatchCollector() - Method in class uk.ac.ebi.utils.threading.batchproc.BatchProcessor: Deprecated.

As explained in BatchCollector, this is used to create a new batch and decide if it's ready for submission to a new job.
getBatchJob() - Method in class uk.ac.ebi.utils.threading.batchproc.BatchProcessor: Deprecated.

BatchProcessor.handleNewBatch(Object, boolean) launches this job every time the current batch being considered is ready for processing.
getBoolean(String) - Method in interface uk.ac.ebi.utils.collections.OptionsMap
getBoolean(String, Boolean) - Method in interface uk.ac.ebi.utils.collections.OptionsMap
getBootstrapParameters() - Static method in class uk.ac.ebi.utils.opt.net.ConfigBootstrapWebListener
getBusyTasks() - Method in class uk.ac.ebi.utils.threading.BatchService
getCompletedBatches() - Method in class uk.ac.ebi.utils.threading.batchproc.BatchProcessor: Deprecated.
getCompletedTasks() - Method in class uk.ac.ebi.utils.threading.BatchService.BatchServiceTuner
getCompletedTasks() - Method in class uk.ac.ebi.utils.threading.BatchService: The no of completed tasks.
getCompletedTasks() - Method in class uk.ac.ebi.utils.threading.PoolSizeTuner
getCumlativeP(int, int, int, int) - Method in class uk.ac.ebi.utils.statistics.FisherExact: Calculates the one-tail P-value for the Fisher Exact test.
getDouble(String) - Method in interface uk.ac.ebi.utils.collections.OptionsMap
getDouble(String, Double) - Method in interface uk.ac.ebi.utils.collections.OptionsMap
getEntityManager() - Method in class uk.ac.ebi.utils.opt.orm.test.TestEntityMgrProvider: The last EM created by TestEntityMgrProvider.newEntityManager().
getEntityManager() - Method in class uk.ac.ebi.utils.test.junit.TestEntityMgrProvider: The last EM created by TestEntityMgrProvider.newEntityManager().
getExecutor() - Method in class uk.ac.ebi.utils.threading.batchproc.BatchProcessor: Deprecated.

The executor service used by BatchProcessor.handleNewBatch(Object) to submit batch jobs and run them in parallel.
getExitCode() - Method in class uk.ac.ebi.utils.threading.BatchServiceTask
getFailedCalls() - Method in class uk.ac.ebi.utils.runcontrol.StatsExecutor: This is reset every StatsExecutor.getSamplingTime() ms.
getHash(File, String) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils: A wrapper to IOUtils.getHash(InputStream, String) that opens a file.
getHash(InputStream, String) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils: Reads the input stream and returns an hash for it, based on the algorithm passed as parameter. algorithm is passed to MessageDigest
getHash(String, String) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils: Hashes a string, using IOUtils.getHash(InputStream, String).
getInt(String) - Method in interface uk.ac.ebi.utils.collections.OptionsMap
getInt(String, Integer) - Method in interface uk.ac.ebi.utils.collections.OptionsMap
getInterceptedExceptions() - Method in class uk.ac.ebi.utils.runcontrol.MultipleAttemptsExecutor: MultipleAttemptsExecutor.execute(Runnable) considers only these exceptions (or their subclasses), when evaluating if a failed operation has to be re-attempted.
getInternalTypes() - Method in class uk.ac.ebi.utils.collections.ObjectStore
getInternalTypes() - Method in class uk.ac.ebi.utils.collections.SortedObjectStore
getKeyFunction() - Method in class uk.ac.ebi.utils.collections.MapCollection: The key function should return different values for different arguments and should always return the same value when an argument is presented multiple times.
getLastExitCode() - Method in class uk.ac.ebi.utils.threading.BatchService
getLastFailedCalls() - Method in class uk.ac.ebi.utils.runcontrol.StatsExecutor: This is updated every StatsExecutor.getSamplingTime()
getLastTotalCalls() - Method in class uk.ac.ebi.utils.runcontrol.StatsExecutor: This is updated every StatsExecutor.getSamplingTime()
getLeftTailedP(int, int, int, int) - Method in class uk.ac.ebi.utils.statistics.FisherExact: Calculates the left-tail P-value for the Fisher Exact test.
getLogger() - Static method in class uk.ac.ebi.utils.exceptions.ExceptionLogger: The default logger, see ExceptionLogger.getLogger().
getLogger(Class<?>) - Static method in class uk.ac.ebi.utils.exceptions.ExceptionLogger
getLogger(String) - Static method in class uk.ac.ebi.utils.exceptions.ExceptionLogger
getLogger(Logger) - Static method in class uk.ac.ebi.utils.exceptions.ExceptionLogger: If null, uses a default that is based on Object.getClass().
getLoggingLevel() - Method in class uk.ac.ebi.utils.runcontrol.ProgressLogger: The logging messages are generated with this level.
getLogMessageTemplate() - Method in class uk.ac.ebi.utils.runcontrol.ProgressLogger: Default "{} items processed".
getLong(String) - Method in interface uk.ac.ebi.utils.collections.OptionsMap
getLong(String, Long) - Method in interface uk.ac.ebi.utils.collections.OptionsMap
getMaxAttempts() - Method in class uk.ac.ebi.utils.runcontrol.MultipleAttemptsExecutor: If the operation run by MultipleAttemptsExecutor.execute(Runnable) fails even after this number of times, the exception it raises is re-thrown to the caller.
getMaxPauseTime() - Method in class uk.ac.ebi.utils.runcontrol.MultipleAttemptsExecutor
getMaxProgress() - Method in class uk.ac.ebi.utils.runcontrol.PercentProgressLogger: Every progress is reported in integer percentage points calculated with respect to this max value.
getMaxThreadIncr() - Method in class uk.ac.ebi.utils.threading.PoolSizeTuner: How much the thread pool size can be incremented at every optimisation iteration.
getMaxThreads() - Method in class uk.ac.ebi.utils.threading.PoolSizeTuner: The maximum number of threads that the thread pool can contain.
getMD5(File) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils: A wrapper of #getHash(InputStream, File) that uses the MD5 algorithm.
getMD5(InputStream) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils: A wrapper of IOUtils.getHash(InputStream, String) that uses the MD5 algorithm.
getMD5(String) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils: A wrapper for IOUtils.getHash(String, String) that uses MD5.
getMessage() - Method in exception uk.ac.ebi.utils.opt.springweb.exceptions.ResponseStatusException2: Returns something like: "User not found (HTTP 404 NOT_FOUND)" The first part is ResponseStatusException.getReason(), if null, it tries to get HttpStatus.getReasonPhrase() from #getStatus(), if this is null too, the second part only is reported without any braces.
getMinPauseTime() - Method in class uk.ac.ebi.utils.runcontrol.MultipleAttemptsExecutor: After a failed attempt, MultipleAttemptsExecutor.execute(Runnable) pauses for a random time between this and MultipleAttemptsExecutor.getMaxPauseTime() ms.
getMinThreadIncr() - Method in class uk.ac.ebi.utils.threading.PoolSizeTuner: How muc the thread pool size can be shrunk at every optimisation iteration.
getMinThreads() - Method in class uk.ac.ebi.utils.threading.PoolSizeTuner: The minimum number of threads that the thread pool should always contain.
getName() - Method in class uk.ac.ebi.utils.threading.BatchServiceTask
getOddsRatio(double, double, double, double) - Static method in class uk.ac.ebi.utils.statistics.FisherExact: Measure of how far from independence the 2x2 table is. 1= independent.
getOddsRatioAnd95thConfidenceInterval(double, double, double, double) - Static method in class uk.ac.ebi.utils.statistics.FisherExact: Returns OR, lower, upper
getOpt(String) - Method in interface uk.ac.ebi.utils.collections.OptionsMap: null as default value and no conversion
getOpt(String, Function<String, V>) - Method in interface uk.ac.ebi.utils.collections.OptionsMap: Default is null
getOpt(String, V) - Method in interface uk.ac.ebi.utils.collections.OptionsMap: No conversion, returned value type depends on what it was stored
getOpt(String, V, Function<String, V>) - Method in interface uk.ac.ebi.utils.collections.OptionsMap: Convert a string value returned by the key using the converter parameter.
getOrDefault(Object, Object) - Method in class uk.ac.ebi.utils.collections.OptionsMapWrapper
getP(int, int, int, int) - Method in class uk.ac.ebi.utils.statistics.FisherExact: calculates the P-value for this specific state
getPattern() - Method in class uk.ac.ebi.utils.regex.RegEx
getPercentProgress() - Method in class uk.ac.ebi.utils.runcontrol.PercentProgressLogger: Uses the absolute progress and PercentProgressLogger.getMaxProgress() to report the 0-100 progress
getPeriodMSecs() - Method in class uk.ac.ebi.utils.threading.PoolSizeTuner: The time between optimisation step executions.
getPoolSizeTuner() - Method in class uk.ac.ebi.utils.threading.BatchService: Used to dynamically adjust the no. threads that the service runs in parallel.
getPriority() - Method in class uk.ac.ebi.utils.threading.BatchServiceTask: Provides a task priority, where 0 is the default and tasks having higher values are supposed to be run before the others.
getProgress() - Method in class uk.ac.ebi.utils.runcontrol.ProgressLogger: The progress is updated by ProgressLogger.update(long) and similar methods.
getProgressReportAction() - Method in class uk.ac.ebi.utils.runcontrol.ProgressLogger: This is invoked when the progress reaches a multiple of ProgressLogger.getProgressResolution(), as per ProgressLogger.update(long) implementation.
getProgressResolution() - Method in class uk.ac.ebi.utils.runcontrol.ProgressLogger: When ProgressLogger.update(long) and similar methods increment an old value, a logging message is generated if the difference between new and old progress is >= the resolution.
getRate() - Method in class uk.ac.ebi.utils.runcontrol.RateLimitedExecutor: The maximum speed allowed by this executor, in actions received per second. 0 means no limit is applied.
getResponseBody(ClassicHttpResponse) - Static method in class uk.ac.ebi.utils.opt.net.ServletUtils: Little helper to extract a string from HttpResponse#getEntity(), reading from HttpEntity.getContent().
getRightTailedP(int, int, int, int) - Method in class uk.ac.ebi.utils.statistics.FisherExact: Calculates the right-tail P-value for the Fisher Exact test.
getRootCause(Throwable) - Static method in class uk.ac.ebi.utils.exceptions.ExceptionUtils: Gets the root cause of an exception.
getRow(String[], Object[]) - Static method in class uk.ac.ebi.utils.collections.ListUtils: A little helper, which turns a row (typically from a table) into a dictionary, where the keys are the column headers.
getSamplingTime() - Method in class uk.ac.ebi.utils.runcontrol.StatsExecutor: Statistics are logged and then reset every this amount of time, in ms.
getSignificantException(Throwable) - Static method in class uk.ac.ebi.utils.exceptions.ExceptionUtils: Goes through the exception's hierarchy until it finds one that has a non-null message.
getSignificantMessage(Throwable) - Static method in class uk.ac.ebi.utils.exceptions.ExceptionUtils: Takes the result that ExceptionUtils.getSignificantException(Throwable) returns and then returns its Throwable.getMessage().
getString(String) - Method in interface uk.ac.ebi.utils.collections.OptionsMap
getString(String, String) - Method in interface uk.ac.ebi.utils.collections.OptionsMap: Expects the key to return a string and returns it as-is.
getSubmissionMsgLogLevel() - Method in class uk.ac.ebi.utils.threading.BatchService: The submission of a new task is notified to the logging system via this level (Level.INFO by default).
getSubmittedBatches() - Method in class uk.ac.ebi.utils.threading.batchproc.BatchProcessor: Deprecated.
getThreadDeltaTolerance() - Method in class uk.ac.ebi.utils.threading.PoolSizeTuner: If the number of tasks between one optimisation step and another remained within this tolerance, then the thread pool throughput is considered stable and no action is taken over the pool size.
getThreadPoolSize() - Method in class uk.ac.ebi.utils.threading.BatchService.BatchServiceTuner
getThreadPoolSize() - Method in class uk.ac.ebi.utils.threading.BatchService
getThreadPoolSize() - Method in class uk.ac.ebi.utils.threading.PoolSizeTuner
getTotalCalls() - Method in class uk.ac.ebi.utils.runcontrol.StatsExecutor: This is reset every StatsExecutor.getSamplingTime() ms.
getTwoTailedP(int, int, int, int) - Method in class uk.ac.ebi.utils.statistics.FisherExact: Calculates the two-tailed P-value for the Fisher Exact test.
getTypeArgument(Class<BaseType>, Class<? extends BaseType>, int) - Static method in class uk.ac.ebi.utils.reflection.ReflectionUtils: A wrapper to getTypeArgument which retrieves the ith argument WARNING: This method won't work if the generic argument i in childClass is a generic, no matter if it is bound in the object assignment (see the post above for details).
getTypeArguments(Class<T>, Class<? extends T>) - Static method in class uk.ac.ebi.utils.reflection.ReflectionUtils: This method has been copied from: http://www.artima.com/weblogs/viewpostP.jsp?
getTypeClass(Type) - Static method in class uk.ac.ebi.utils.reflection.ReflectionUtils: This method has been copied from: http://www.artima.com/weblogs/viewpostP.jsp?
groups(CharSequence) - Method in class uk.ac.ebi.utils.regex.RegEx: Returns all the groups in the input, see Java documentation for details

H

HackedBlockingQueue<E> - Class in uk.ac.ebi.utils.threading: Tricks the behaviour of LinkedBlockingQueue so that methods like HackedBlockingQueue.offer(Object) and HackedBlockingQueue.poll() actually invoke LinkedBlockingQueue.put(Object) and LinkedBlockingQueue.take(), i.e., the queue always waits for itself to be free-of/filled-with-some value/s.
HackedBlockingQueue() - Constructor for class uk.ac.ebi.utils.threading.HackedBlockingQueue
HackedBlockingQueue(int) - Constructor for class uk.ac.ebi.utils.threading.HackedBlockingQueue
HackedBlockingQueue(Collection<? extends E>) - Constructor for class uk.ac.ebi.utils.threading.HackedBlockingQueue
handleExceptionInternal(Exception, Object, HttpHeaders, HttpStatusCode, WebRequest) - Method in class uk.ac.ebi.utils.opt.springweb.exceptions.XResponseEntityExceptionHandler: All exceptions are eventually routed here.
handleMappedException(Exception, WebRequest) - Method in class uk.ac.ebi.utils.opt.springweb.exceptions.XResponseEntityExceptionHandler: Our own catch-all wrapper This tries to see if the exception is associated to some HTTP status code, by using XResponseEntityExceptionHandler.findExceptionMapping(Exception).
handleNewBatch(B) - Method in class uk.ac.ebi.utils.threading.batchproc.BatchProcessor: Deprecated.
handleNewBatch(B, boolean) - Method in class uk.ac.ebi.utils.threading.batchproc.BatchProcessor: Deprecated.

This is the method that possibly issues a new task, via the BatchProcessor.getExecutor(), which runs the BatchProcessor.getBatchJob() against the current batch.
hashCode() - Method in class uk.ac.ebi.utils.collections.OptionsMapWrapper
hashUriSignature(String) - Static method in class uk.ac.ebi.utils.ids.IdUtils: Takes a string that is supposed to represent the identifier of a resource and turns it into an opaque compact and URI-compatible representation.
hasNext() - Method in class uk.ac.ebi.utils.collections.PaginationIterator: See PaginationIterator(Iterator, Function) for details on how we loop.
hasNext() - Method in class uk.ac.ebi.utils.collections.TupleIterator
HqlUtils - Class in uk.ac.ebi.utils.sql: Utilities for SQL definition and manipulation.
HqlUtils() - Constructor for class uk.ac.ebi.utils.sql.HqlUtils

I

IdUtils - Class in uk.ac.ebi.utils.ids: Utilities about management of identifiers.
IdUtils() - Constructor for class uk.ac.ebi.utils.ids.IdUtils
INCLUDES_FIELD - Static variable in class uk.ac.ebi.utils.opt.config.YAMLLoader
INCLUDES_OPTIONAL_FIELD - Static variable in class uk.ac.ebi.utils.opt.config.YAMLLoader
indexOfAny(String, int, char...) - Static method in class uk.ac.ebi.utils.string.StringSearchUtils: An extension of StringUtils.indexOfAny(CharSequence, char...) that allows to specify the start position.
indexOfAny(String, int, CharSequence...) - Static method in class uk.ac.ebi.utils.string.StringSearchUtils: An extension of StringUtils.indexOfAny(CharSequence, CharSequence...) that allows to specify the start position.
indexOfAny(String, int, BiFunction<String, KA, Integer>, KA) - Static method in class uk.ac.ebi.utils.string.StringSearchUtils: All the above methods are based on this template: the search function searches for keys in some input (internal to the function, defined by the invoker of this method), returns -1 or the string index where one of the keys was found.
invoke(boolean, Object, String, Class<?>[], Object...) - Static method in class uk.ac.ebi.utils.reflection.ReflectionUtils: Default class is object.getClass().
invoke(boolean, T, Class<? super T>, String, Class<?>[], Object...) - Static method in class uk.ac.ebi.utils.reflection.ReflectionUtils: Invokes a method by means of reflection.
invoke(Object, Class<? super T>, String, Class<?>[], Object...) - Static method in class uk.ac.ebi.utils.reflection.ReflectionUtils: Defaults to makeAccessible = true.
invoke(Object, String, Class<?>[], Object...) - Static method in class uk.ac.ebi.utils.reflection.ReflectionUtils: Defaults to methodClass = object.getClass() and makeAccessible = true.
IOUtils - Class in uk.ac.ebi.utils.opt.io: Miscellanea of small IO utilities.
iri2id(String) - Static method in class uk.ac.ebi.utils.ids.IdUtils: Uses suitable default for splitRegEx ("[#/]")
iri2id(String, String) - Static method in class uk.ac.ebi.utils.ids.IdUtils: Uses a suitable default for replacementRegEx ("[\\s\\+\\-\\:\\.\\?]").
iri2id(String, String, String) - Static method in class uk.ac.ebi.utils.ids.IdUtils: Splits a URL based on the splitRegEx expression and returns the last fragment of it, which usually correspond to an identifer to an accession (such as a class name in OWL/RDF-S).
isActive() - Method in class uk.ac.ebi.utils.threading.PoolSizeTuner: True if I was started with PoolSizeTuner.start() and never PoolSizeTuner.stop()ped.
isEmpty() - Method in class uk.ac.ebi.utils.collections.MapCollection
isEmpty() - Method in class uk.ac.ebi.utils.collections.OptionsMapWrapper
isEmpty() - Method in class uk.ac.ebi.utils.collections.TypeCastCollection
isOneOf(T, Comparator<T>, T...) - Static method in class uk.ac.ebi.utils.collections.ArraySearchUtils: Tells if a value is equals to one of the values specified in an array.
isOneOf(T, T...) - Static method in class uk.ac.ebi.utils.collections.ArraySearchUtils: A variant of #isOneOf(Object, Comparator, Object...) that uses the natural comparison as comparator (i.e.
isOneOfByIdentity(T, T...) - Static method in class uk.ac.ebi.utils.collections.ArraySearchUtils: A variant of #isOneOf(Object, Comparator, Object...) that uses the identity comparison criterion (i.e., the '==' operator).
isPopUpExceptions() - Method in class uk.ac.ebi.utils.runcontrol.StatsExecutor
isStackTraceEnabled - Variable in class uk.ac.ebi.utils.opt.springweb.exceptions.XResponseEntityExceptionHandler: If true, XResponseEntityExceptionHandler.createProblemDetail(Exception, HttpStatusCode, String, String, Object[], WebRequest) adds a 'trace' field to the RFC-9457 output all the exceptions in this class produce.
ItemizedBatchCollector<B,E> - Interface in uk.ac.ebi.utils.threading.batchproc: Deprecated.
the functionality available in this package is provided by project Reactor and we recommend to switch to that. @see ReactorUtils
ItemizedBatchProcessor<E,B,BC extends ItemizedBatchCollector<B,E>,BJ extends Consumer> - Class in uk.ac.ebi.utils.threading.batchproc: Deprecated.
the functionality available in this package is provided by project Reactor and we recommend to switch to that. @see ReactorUtils
ItemizedBatchProcessor() - Constructor for class uk.ac.ebi.utils.threading.batchproc.ItemizedBatchProcessor: Deprecated.
ItemizedBatchProcessor(BJ) - Constructor for class uk.ac.ebi.utils.threading.batchproc.ItemizedBatchProcessor: Deprecated.
ItemizedBatchProcessor(BJ, BC) - Constructor for class uk.ac.ebi.utils.threading.batchproc.ItemizedBatchProcessor: Deprecated.
ItemizedSizedBatchCollector<B,E> - Interface in uk.ac.ebi.utils.threading.batchproc: Deprecated.
the functionality available in this package is provided by project Reactor and we recommend to switch to that. @see ReactorUtils
iterator() - Method in class uk.ac.ebi.utils.collections.MapCollection: Refers to MapCollection.getBase().Map.values() (the map's values).
iterator() - Method in class uk.ac.ebi.utils.collections.TypeCastCollection
IteratorUtils - Class in uk.ac.ebi.utils.collections

J

JacksonJsUtils - Class in uk.ac.ebi.utils.opt.json: JSON utils based on the Jackson library.
JacksonJsUtils() - Constructor for class uk.ac.ebi.utils.opt.json.JacksonJsUtils
jobLogPeriod - Variable in class uk.ac.ebi.utils.threading.batchproc.BatchProcessor: Deprecated.

K

keySet() - Method in class uk.ac.ebi.utils.collections.OptionsMapWrapper

L

LambdaUtils - Class in uk.ac.ebi.utils.lambda: Utilities for functional programming and lambda syntax.
LambdaUtils() - Constructor for class uk.ac.ebi.utils.lambda.LambdaUtils
lastExitCode - Variable in class uk.ac.ebi.utils.threading.BatchService: This should be 1 if there are multiple and different exit codes returned by submitted tasks BatchServiceTask.getExitCode().
ListBasedBatchProcessor<E,BJ extends Consumer<List<E>>> - Class in uk.ac.ebi.utils.threading.batchproc.processors: Deprecated.
the functionality available in this package is provided by project Reactor and we recommend to switch to that. @see ReactorUtils
ListBasedBatchProcessor() - Constructor for class uk.ac.ebi.utils.threading.batchproc.processors.ListBasedBatchProcessor: Deprecated.
ListBasedBatchProcessor(int) - Constructor for class uk.ac.ebi.utils.threading.batchproc.processors.ListBasedBatchProcessor: Deprecated.
ListBasedBatchProcessor(BJ, int) - Constructor for class uk.ac.ebi.utils.threading.batchproc.processors.ListBasedBatchProcessor: Deprecated.
ListBasedBatchProcessor(BJ, Supplier<List<E>>, int) - Constructor for class uk.ac.ebi.utils.threading.batchproc.processors.ListBasedBatchProcessor: Deprecated.
ListBatchCollector<E> - Class in uk.ac.ebi.utils.threading.batchproc.collectors: Deprecated.
the functionality available in this package is provided by project Reactor and we recommend to switch to that. @see ReactorUtils
ListBatchCollector() - Constructor for class uk.ac.ebi.utils.threading.batchproc.collectors.ListBatchCollector: Deprecated.

ArrayList as default.
ListBatchCollector(int) - Constructor for class uk.ac.ebi.utils.threading.batchproc.collectors.ListBatchCollector: Deprecated.

ArrayList as default.
ListBatchCollector(Supplier<List<E>>, int) - Constructor for class uk.ac.ebi.utils.threading.batchproc.collectors.ListBatchCollector: Deprecated.
ListUtils - Class in uk.ac.ebi.utils.collections: Miscellanea utilities about lists.
ListUtils() - Constructor for class uk.ac.ebi.utils.collections.ListUtils
loadYAMLFromFile(String, Class<T>) - Static method in class uk.ac.ebi.utils.opt.config.YAMLLoader
loadYAMLFromString(String, Class<T>) - Static method in class uk.ac.ebi.utils.opt.config.YAMLLoader: Maps a YAML file to a target, after it has been processes as explained above.
lock() - Method in class uk.ac.ebi.utils.threading.fakelocks.FakeLock
lockInterruptibly() - Method in class uk.ac.ebi.utils.threading.fakelocks.FakeLock
log - Variable in class uk.ac.ebi.utils.collections.ObjectStore
log - Variable in class uk.ac.ebi.utils.collections.SortedObjectStore
log - Variable in class uk.ac.ebi.utils.threading.batchproc.BatchProcessor: Deprecated.
log - Variable in class uk.ac.ebi.utils.threading.BatchService
log - Variable in class uk.ac.ebi.utils.threading.BatchServiceTask
log - Variable in class uk.ac.ebi.utils.threading.PoolSizeTuner
logEx(String, String, String, Throwable, Object...) - Method in class uk.ac.ebi.utils.exceptions.ExceptionLogger: Does the exception logging, as explained above.
logEx(String, Throwable, Object...) - Method in class uk.ac.ebi.utils.exceptions.ExceptionLogger: Defaults to reporting your message (instantiated with your params), plus sensible tails like ".

M

Many2ManyUtils - Class in uk.ac.ebi.utils.orm: Facilities to manager many-to-many relations in JPA.
Many2ManyUtils() - Constructor for class uk.ac.ebi.utils.orm.Many2ManyUtils
MapCollection<K,V> - Class in uk.ac.ebi.utils.collections: Creates a view of a Map that is a collection.
MapCollection(Map<K, V>, Function<V, K>) - Constructor for class uk.ac.ebi.utils.collections.MapCollection
matcher(CharSequence) - Method in class uk.ac.ebi.utils.regex.RegEx: Gets a new matcher for the input sequence
matches(CharSequence) - Method in class uk.ac.ebi.utils.regex.RegEx: Calls matcher(input).Matcher.matches()
matchesAny(String, Pattern...) - Static method in class uk.ac.ebi.utils.regex.RegEx: Matches the string against any of the patterns, returns true at the first pattern that matches
maxBatchSize() - Method in class uk.ac.ebi.utils.threading.batchproc.AbstractSizedBatchCollector: Deprecated.
maxBatchSize() - Method in interface uk.ac.ebi.utils.threading.batchproc.SizedBatchCollector: Deprecated.
MemoryUtils - Class in uk.ac.ebi.utils.memory: An helper that allows to release/reset resources when free memory goes beyond a given limit.
merge(String, Object, BiFunction<? super Object, ? super Object, ? extends Object>) - Method in class uk.ac.ebi.utils.collections.OptionsMapWrapper
MERGE_SUFFIX - Static variable in class uk.ac.ebi.utils.opt.config.YAMLLoader
MultipleAttemptsExecutor - Class in uk.ac.ebi.utils.runcontrol: An executor to attempt an operation multiple times, knowing it can fail from time to time (e.g. getting data from a REST API).
MultipleAttemptsExecutor(int, long, long, Class<? extends Exception>...) - Constructor for class uk.ac.ebi.utils.runcontrol.MultipleAttemptsExecutor
MultipleAttemptsExecutor(Class<? extends Exception>...) - Constructor for class uk.ac.ebi.utils.runcontrol.MultipleAttemptsExecutor
MY_DIR_PROP - Static variable in class uk.ac.ebi.utils.opt.config.YAMLLoader: A property with this name is always available and contains the dir in which the YAML file is
MY_PATH_PROP - Static variable in class uk.ac.ebi.utils.opt.config.YAMLLoader: A property with this name is always available and contains the absolute YAML file path

N

name - Variable in class uk.ac.ebi.utils.threading.BatchServiceTask
newCollection(Collection<? extends T>, Supplier<C>) - Static method in class uk.ac.ebi.utils.collections.CollectionsUtils: Returns a new collection containing the elements in the parameter, using the provider.
newCollectionIfNull(C, Supplier<C>) - Static method in class uk.ac.ebi.utils.collections.CollectionsUtils: If coll is not null, returns it, else returns a new empty collection, using the provider.
newCondition() - Method in class uk.ac.ebi.utils.threading.fakelocks.FakeLock
newEntityManager() - Method in class uk.ac.ebi.utils.opt.orm.test.TestEntityMgrProvider: Disposes (via TestEntityMgrProvider.after()) the previously created entity manager, if any, and creates a new entity manager, using the factory passed to the constructor.
newEntityManager() - Method in class uk.ac.ebi.utils.test.junit.TestEntityMgrProvider: Disposes (via TestEntityMgrProvider.after()) the previously created entity manager, if any, and creates a new entity manager, using the factory passed to the constructor.
newList(Collection<? extends T>) - Static method in class uk.ac.ebi.utils.collections.CollectionsUtils: Defaults to ArrayList as provider
newList(Collection<? extends T>, Supplier<List<T>>) - Static method in class uk.ac.ebi.utils.collections.CollectionsUtils
newListIfNull(List<T>) - Static method in class uk.ac.ebi.utils.collections.CollectionsUtils: Defaults to ArrayList as provider.
newListIfNull(List<T>, Supplier<List<T>>) - Static method in class uk.ac.ebi.utils.collections.CollectionsUtils
newMap(Map<? extends K, ? extends V>) - Static method in class uk.ac.ebi.utils.collections.CollectionsUtils: Defaults to HashMap as provider
newMap(Map<? extends K, ? extends V>, Supplier<Map<K, V>>) - Static method in class uk.ac.ebi.utils.collections.CollectionsUtils
newMapIfNull(Map<K, V>) - Static method in class uk.ac.ebi.utils.collections.CollectionsUtils: Defaults to HashMap as provider.
newMapIfNull(M, Supplier<M>) - Static method in class uk.ac.ebi.utils.collections.CollectionsUtils
newPoolSizeTuner() - Method in class uk.ac.ebi.utils.threading.BatchService: Allows you to initialise with a custom BatchService<TK extends BatchServiceTask>.BatchServiceTuner.
newSet(Collection<? extends T>) - Static method in class uk.ac.ebi.utils.collections.CollectionsUtils: Defaults to HashSet as provider.
newSet(Collection<? extends T>, Supplier<Set<T>>) - Static method in class uk.ac.ebi.utils.collections.CollectionsUtils
newSetIfNull(Set<T>) - Static method in class uk.ac.ebi.utils.collections.CollectionsUtils: Defaults to HashSet as provider.
newSetIfNull(Set<T>, Supplier<Set<T>>) - Static method in class uk.ac.ebi.utils.collections.CollectionsUtils
newThreadPoolExecutor(int) - Method in class uk.ac.ebi.utils.threading.BatchService: Allows you to initialise with a custom ExecutorService.
next() - Method in class uk.ac.ebi.utils.collections.PaginationIterator: See PaginationIterator(Iterator, Function) for details on how we loop.
next() - Method in class uk.ac.ebi.utils.collections.TupleIterator
noCertClient(String, String) - Static method in class uk.ac.ebi.utils.opt.net.SSLUtils: Gets an HttpClient that doesn't do any SSL certificate verification.
notEmpty(C, String, Object...) - Static method in class uk.ac.ebi.utils.objects.XValidate: Checks that the collection isn't null and isn't empty
NotReadyException - Exception in uk.ac.ebi.utils.exceptions: To report that a component or method cannot be used at moment, since it has to complete some operation and it's not ready yet.
NotReadyException(String) - Constructor for exception uk.ac.ebi.utils.exceptions.NotReadyException
NotReadyException(String, Throwable) - Constructor for exception uk.ac.ebi.utils.exceptions.NotReadyException

O

ObjectStore<T,K,V> - Class in uk.ac.ebi.utils.collections: Implements an object store.
ObjectStore() - Constructor for class uk.ac.ebi.utils.collections.ObjectStore
of(String) - Static method in class uk.ac.ebi.utils.regex.RegEx
of(String, int) - Static method in class uk.ac.ebi.utils.regex.RegEx: This returns a RegEx that is cached, together with its compiled pattern.
of(Iterator<? extends TT>...) - Static method in class uk.ac.ebi.utils.collections.TupleIterator
of(Spliterator<? extends TT>...) - Static method in class uk.ac.ebi.utils.collections.TupleSpliterator: Just a facility to avoid too much generics fiddling.
offer(E) - Method in class uk.ac.ebi.utils.threading.HackedBlockingQueue
offer(E, long, TimeUnit) - Method in class uk.ac.ebi.utils.threading.HackedBlockingQueue
offsetBasedPageIterator(Function<Long, ? extends P>, long) - Static method in class uk.ac.ebi.utils.collections.PaginationIterator: Builds a page iterator for PaginationIterator that moves from one page to the next based on pageSize and returns a page based on the selector function.
openResourceReader(Class<?>, String) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils: Defaults to "UTF-8"
openResourceReader(Class<?>, String, Charset) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils: Facility to get a reader from a resource, uses Resources.getResource(Class, String) and URL.openStream().
openResourceReader(String) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils: Defaults to UTF-8
openResourceReader(String, Charset) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils
OptionsMap - Interface in uk.ac.ebi.utils.collections: A variant of the map interface that has the purpose of easing the manipulation of options based on string values.
OptionsMapWrapper - Class in uk.ac.ebi.utils.collections: An implementation of OptionsMap that is simply based on the delegator pattern and forwards all its operations to an underlining Map.
OptionsMapWrapper() - Constructor for class uk.ac.ebi.utils.collections.OptionsMapWrapper: Creates an options map with an empty HashMap as its base.
OptionsMapWrapper(Map<String, Object>) - Constructor for class uk.ac.ebi.utils.collections.OptionsMapWrapper
OptionsMapWrapper(Properties) - Constructor for class uk.ac.ebi.utils.collections.OptionsMapWrapper

P

PaginationIterator<P,E> - Class in uk.ac.ebi.utils.collections: A generic helper to build a pagination iteration.
PaginationIterator(Function<Long, ? extends P>, long, Function<? super P, ? extends Iterator<? extends E>>) - Constructor for class uk.ac.ebi.utils.collections.PaginationIterator: Builds the page iterator using PaginationIterator.offsetBasedPageIterator(Function, long).
PaginationIterator(Iterator<? extends P>, Function<? super P, ? extends Iterator<? extends E>>) - Constructor for class uk.ac.ebi.utils.collections.PaginationIterator
parallelBatchFlux(Collection<? extends T>) - Static method in class uk.ac.ebi.utils.opt.runcontrol.ReactorUtils: Just uses ReactorUtils.ParallelBatchFluxBuilder with its defaults.
parallelBatchFlux(Stream<? extends T>) - Static method in class uk.ac.ebi.utils.opt.runcontrol.ReactorUtils: Just uses ReactorUtils.ParallelBatchFluxBuilder with its defaults.
parallelBatchFlux(Flux<? extends T>) - Static method in class uk.ac.ebi.utils.opt.runcontrol.ReactorUtils: Just uses ReactorUtils.ParallelBatchFluxBuilder with its defaults.
ParallelBatchFluxBuilder(Collection<? extends T>) - Constructor for class uk.ac.ebi.utils.opt.runcontrol.ReactorUtils.ParallelBatchFluxBuilder
ParallelBatchFluxBuilder(Stream<? extends T>) - Constructor for class uk.ac.ebi.utils.opt.runcontrol.ReactorUtils.ParallelBatchFluxBuilder
ParallelBatchFluxBuilder(Flux<? extends T>) - Constructor for class uk.ac.ebi.utils.opt.runcontrol.ReactorUtils.ParallelBatchFluxBuilder
parameterizedRangeBinding(Query, String, String, T, T) - Static method in class uk.ac.ebi.utils.sql.HqlUtils: Binds a clause built with HqlUtils.parameterizedRangeClause(String, String, String, Object, Object) with the values lo, hi.
parameterizedRangeClause(String, String, String, T, T) - Static method in class uk.ac.ebi.utils.sql.HqlUtils: Builds a query clause that restricts fieldName in the specified range.
parameterizedWithNullHql(String, String) - Static method in class uk.ac.ebi.utils.sql.HqlUtils: Builds a string like ":paramName IS NULL AND fieldName IS NULL OR fieldName = :paramName".
PercentProgressLogger - Class in uk.ac.ebi.utils.runcontrol: It's like ProgressLogger but reports percentages, given a max value that you set initially.
PercentProgressLogger(long) - Constructor for class uk.ac.ebi.utils.runcontrol.PercentProgressLogger
PercentProgressLogger(String, long) - Constructor for class uk.ac.ebi.utils.runcontrol.PercentProgressLogger
PercentProgressLogger(String, long, long) - Constructor for class uk.ac.ebi.utils.runcontrol.PercentProgressLogger
poll() - Method in class uk.ac.ebi.utils.threading.HackedBlockingQueue
poll(long, TimeUnit) - Method in class uk.ac.ebi.utils.threading.HackedBlockingQueue
poolSizeTuner - Variable in class uk.ac.ebi.utils.threading.BatchService
PoolSizeTuner - Class in uk.ac.ebi.utils.threading: A Thread Pool Size Optimiser
PoolSizeTuner() - Constructor for class uk.ac.ebi.utils.threading.PoolSizeTuner
process(Consumer<Consumer<E>>) - Method in class uk.ac.ebi.utils.threading.batchproc.ItemizedBatchProcessor: Deprecated.

Defaults to true, ie, it waits for all the batches submitted from the source items to be completed.
process(Consumer<Consumer<E>>, boolean) - Method in class uk.ac.ebi.utils.threading.batchproc.ItemizedBatchProcessor: Deprecated.

Gets an input flow of items and dispatches them to batches and batch jobs, as explained in the BatchProcessor super-class.
process(Iterator<E>) - Method in class uk.ac.ebi.utils.threading.batchproc.ItemizedBatchProcessor: Deprecated.
process(Iterator<E>, boolean) - Method in class uk.ac.ebi.utils.threading.batchproc.ItemizedBatchProcessor: Deprecated.

Uses Iterator.forEachRemaining(Consumer) as generator.
process(Stream<E>) - Method in class uk.ac.ebi.utils.threading.batchproc.ItemizedBatchProcessor: Deprecated.
process(Stream<E>, boolean) - Method in class uk.ac.ebi.utils.threading.batchproc.ItemizedBatchProcessor: Deprecated.

Uses Stream.forEach(Consumer) as generator.
profile(Runnable) - Static method in class uk.ac.ebi.utils.time.XStopWatch: Wrapper of XStopWatch.profileNano(Runnable) returning time in ms.
profileNano(Runnable) - Static method in class uk.ac.ebi.utils.time.XStopWatch: Facility to profile (i.e., to time) a task.
ProgressLogger - Class in uk.ac.ebi.utils.runcontrol: Reports (using a logger) the progress of some process, represented by a long number.
ProgressLogger() - Constructor for class uk.ac.ebi.utils.runcontrol.ProgressLogger
ProgressLogger(long) - Constructor for class uk.ac.ebi.utils.runcontrol.ProgressLogger
ProgressLogger(String, long) - Constructor for class uk.ac.ebi.utils.runcontrol.ProgressLogger
progressReport(long, long) - Method in class uk.ac.ebi.utils.runcontrol.PercentProgressLogger
progressReport(long, long) - Method in class uk.ac.ebi.utils.runcontrol.ProgressLogger: Invoked by ProgressLogger.update(long), decides if we have to log the new progress and possibly does it.
PROPDEF_FIELD - Static variable in class uk.ac.ebi.utils.opt.config.YAMLLoader
put(String, Object) - Method in class uk.ac.ebi.utils.collections.OptionsMapWrapper
put(T, K, V) - Method in class uk.ac.ebi.utils.collections.ObjectStore: Stores an object, identified by a type and an identifier If value is null deletes the entry.
put(T, K, V) - Method in class uk.ac.ebi.utils.collections.SortedObjectStore
putAll(Map<? extends String, ? extends Object>) - Method in class uk.ac.ebi.utils.collections.OptionsMapWrapper
putIfAbsent(String, Object) - Method in class uk.ac.ebi.utils.collections.OptionsMapWrapper

R

RateLimitedExecutor - Class in uk.ac.ebi.utils.runcontrol: A rate limiting executor, based on RateLimiter.
RateLimitedExecutor(double) - Constructor for class uk.ac.ebi.utils.runcontrol.RateLimitedExecutor
rateLimiter - Variable in class uk.ac.ebi.utils.runcontrol.RateLimitedExecutor
ReactorUtils - Class in uk.ac.ebi.utils.opt.runcontrol: Utilities based on the Project Reactor library.
ReactorUtils() - Constructor for class uk.ac.ebi.utils.opt.runcontrol.ReactorUtils
ReactorUtils.ParallelBatchFluxBuilder<T,B extends Collection<T>> - Class in uk.ac.ebi.utils.opt.runcontrol: Little helper to build a common ParallelFlux to process a source of items in parallel batches.
read(String, QName) - Method in class uk.ac.ebi.utils.xml.XPathReader
readDouble(String) - Method in class uk.ac.ebi.utils.xml.XPathReader
readFile(String) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils: Defaults to UTF-8
readFile(String, String) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils
readFile(String, Charset) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils: Opens an input stream from a file path.
readFiles(String) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils: Defaults to any file, ignoreMissingDir = false, UTF-8
readFiles(String, boolean) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils: Defaults to any file, UTF-8
readFiles(String, boolean, Charset) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils: Defaults to any file
readFiles(String, FilenameFilter) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils: Defaults to missingDir = false, `UTF-8`.
readFiles(String, FilenameFilter, boolean) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils: Defaults to `UTF-8`.
readFiles(String, FilenameFilter, boolean, Charset) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils: Invokes IOUtils.readFile(String, Charset) upon all the files in a directory and return an array of file contents.
readFiles(String, FilenameFilter, Charset) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils: Defaults to missingDir = false
readFiles(String, Charset) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils: Defaults to any file, ignoreMissingDir = false
readFloat(String) - Method in class uk.ac.ebi.utils.xml.XPathReader
readInt(String) - Method in class uk.ac.ebi.utils.xml.XPathReader
readLock() - Method in class uk.ac.ebi.utils.threading.fakelocks.FakeReadWriteLock
readLong(String) - Method in class uk.ac.ebi.utils.xml.XPathReader
readNextTag(XMLStreamReader, String) - Static method in class uk.ac.ebi.utils.xml.stax.StaxUtils: Invokes StaxUtils.expectNextTag(XMLStreamReader, String) and then XMLStreamReader.getElementText().
readNode(String) - Method in class uk.ac.ebi.utils.xml.XPathReader
readNodeList(String) - Method in class uk.ac.ebi.utils.xml.XPathReader
readOptDouble(String) - Method in class uk.ac.ebi.utils.xml.XPathReader
readResource(Class<?>, String) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils: WARNING: after 5.0 this uses UTF-8 as default and not the system default!
readResource(Class<?>, String, Charset) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils: Facility to read a resource from the class loader associated to a class.
readResource(ClassLoader, String) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils: Defaults to UTF-8
readResource(ClassLoader, String, Charset) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils: Facility to read a resource from a class loader.
readResource(String) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils: Defaults to UTF-8
readResource(String, Charset) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils: Uses the class loader in the current thread, or the one in Resources.
readString(String) - Method in class uk.ac.ebi.utils.xml.XPathReader
ReflectionUtils - Class in uk.ac.ebi.utils.reflection: Jan 15, 2008
ReflectionUtils() - Constructor for class uk.ac.ebi.utils.reflection.ReflectionUtils
RegEx - Class in uk.ac.ebi.utils.regex: An helper class for the regex library.
RegEx(String) - Constructor for class uk.ac.ebi.utils.regex.RegEx: Creates and store a new Pattern, calling Pattern.compile(String)
RegEx(String, int) - Constructor for class uk.ac.ebi.utils.regex.RegEx: Creates and store a new Pattern, calling Pattern.compile(String, int)
registerCleaner(Object, Runnable) - Static method in class uk.ac.ebi.utils.memory.MemoryUtils: Simple wrapper for the new J9 Cleaner interface, which replaces the old finalize() method.
remove(Object) - Method in class uk.ac.ebi.utils.collections.MapCollection: Removes the entry (keyFunc.apply(e), e)
remove(Object) - Method in class uk.ac.ebi.utils.collections.OptionsMapWrapper
remove(Object) - Method in class uk.ac.ebi.utils.collections.TypeCastCollection
remove(Object, Object) - Method in class uk.ac.ebi.utils.collections.OptionsMapWrapper
remove(T) - Method in class uk.ac.ebi.utils.collections.ObjectStore: Remove all the values associated to the type
removeAll(Collection<?>) - Method in class uk.ac.ebi.utils.collections.MapCollection: Iteratively calls MapCollection.remove(Object).
removeAll(Collection<?>) - Method in class uk.ac.ebi.utils.collections.TypeCastCollection
replace(String, Object) - Method in class uk.ac.ebi.utils.collections.OptionsMapWrapper
replace(String, Object, Object) - Method in class uk.ac.ebi.utils.collections.OptionsMapWrapper
replaceAll(BiFunction<? super String, ? super Object, ? extends Object>) - Method in class uk.ac.ebi.utils.collections.OptionsMapWrapper
reset() - Method in class uk.ac.ebi.utils.runcontrol.ProgressLogger
ResponseStatusException2 - Exception in uk.ac.ebi.utils.opt.springweb.exceptions: An alternative version of ResponseStatusException that yields a more compact and better-formatted ResponseStatusException2.getMessage().
ResponseStatusException2(int, String, Throwable) - Constructor for exception uk.ac.ebi.utils.opt.springweb.exceptions.ResponseStatusException2
ResponseStatusException2(HttpStatus) - Constructor for exception uk.ac.ebi.utils.opt.springweb.exceptions.ResponseStatusException2
ResponseStatusException2(HttpStatus, String) - Constructor for exception uk.ac.ebi.utils.opt.springweb.exceptions.ResponseStatusException2
ResponseStatusException2(HttpStatus, String, Throwable) - Constructor for exception uk.ac.ebi.utils.opt.springweb.exceptions.ResponseStatusException2
restart() - Method in class uk.ac.ebi.utils.time.XStopWatch: Invokes StopWatch.reset() and then StopWatch.start(), ie, start a new timing session.
resumeOrStart() - Method in class uk.ac.ebi.utils.time.XStopWatch: If StopWatch.isSuspended() invokes StopWatch.resume() as usually.
retainAll(Collection<?>) - Method in class uk.ac.ebi.utils.collections.MapCollection
retainAll(Collection<?>) - Method in class uk.ac.ebi.utils.collections.TypeCastCollection

S

sampleStream(Stream<T>, double) - Static method in class uk.ac.ebi.utils.streams.StreamUtils: Returns a sampled stream, i.e., a stream where a quota of elements approximately equals to sampleRatio is returned.
sampleStream(Stream<T>, long, long) - Static method in class uk.ac.ebi.utils.streams.StreamUtils: A variant of StreamUtils.sampleStream(Stream, double) that computes the sampling ratio as sampleSize/totalSize.
sedFilter(InputStream, String) - Static method in class uk.ac.ebi.utils.opt.io.Unix4jUtils: Just a wrapper that uses #unixFilter(To, InputStream) to process an input stream via the sed command.
sedFilter(InputStream, String, String) - Static method in class uk.ac.ebi.utils.opt.io.Unix4jUtils: Just a wrapper of Unix4jUtils.sedFilter(InputStream, String) that tweaks a stream dynamically, to replace text based on a regular expression.
SerializationUtils - Class in uk.ac.ebi.utils.io: Object serialisation/unserialisation utils that work with IO streams.
SerializationUtils() - Constructor for class uk.ac.ebi.utils.io.SerializationUtils
serialize(File, Object) - Static method in class uk.ac.ebi.utils.io.SerializationUtils: Defaults to false (creates the file from scratch)
serialize(File, Object, boolean) - Static method in class uk.ac.ebi.utils.io.SerializationUtils: Wraps the opening of a buffered FileOutputStream and ObjectOutputStream, then then writes the object in it and closes.
serialize(ObjectOutputStream, Object) - Static method in class uk.ac.ebi.utils.io.SerializationUtils: Just like ObjectOutputStream.writeObject(Object), with the checked exception wrapper included
serialize(String, Object) - Static method in class uk.ac.ebi.utils.io.SerializationUtils
serialize(String, Object, boolean) - Static method in class uk.ac.ebi.utils.io.SerializationUtils
ServletUtils - Class in uk.ac.ebi.utils.opt.net: Utilities about the HTTP protocol and the respective Java packages.
ServletUtils() - Constructor for class uk.ac.ebi.utils.opt.net.ServletUtils
set(List<T>, int, T) - Static method in class uk.ac.ebi.utils.collections.ListUtils: Sets the element i in list, independently on the list size.
setAttemptMsgLogLevel(Level) - Method in class uk.ac.ebi.utils.runcontrol.MultipleAttemptsExecutor
SetBasedBatchProcessor<E,BJ extends Consumer<Set<E>>> - Class in uk.ac.ebi.utils.threading.batchproc.processors: Deprecated.
the functionality available in this package is provided by project Reactor and we recommend to switch to that. @see ReactorUtils
SetBasedBatchProcessor() - Constructor for class uk.ac.ebi.utils.threading.batchproc.processors.SetBasedBatchProcessor: Deprecated.
SetBasedBatchProcessor(int) - Constructor for class uk.ac.ebi.utils.threading.batchproc.processors.SetBasedBatchProcessor: Deprecated.
SetBasedBatchProcessor(BJ, int) - Constructor for class uk.ac.ebi.utils.threading.batchproc.processors.SetBasedBatchProcessor: Deprecated.
SetBasedBatchProcessor(BJ, Supplier<Set<E>>, int) - Constructor for class uk.ac.ebi.utils.threading.batchproc.processors.SetBasedBatchProcessor: Deprecated.
setBatchCollector(BC) - Method in class uk.ac.ebi.utils.threading.batchproc.BatchProcessor: Deprecated.
SetBatchCollector<E> - Class in uk.ac.ebi.utils.threading.batchproc.collectors: Deprecated.
the functionality available in this package is provided by project Reactor and we recommend to switch to that. @see ReactorUtils
SetBatchCollector() - Constructor for class uk.ac.ebi.utils.threading.batchproc.collectors.SetBatchCollector: Deprecated.
SetBatchCollector(int) - Constructor for class uk.ac.ebi.utils.threading.batchproc.collectors.SetBatchCollector: Deprecated.
SetBatchCollector(Supplier<Set<E>>, int) - Constructor for class uk.ac.ebi.utils.threading.batchproc.collectors.SetBatchCollector: Deprecated.
setBatchJob(BJ) - Method in class uk.ac.ebi.utils.threading.batchproc.BatchProcessor: Deprecated.
setExecutor(ExecutorService) - Method in class uk.ac.ebi.utils.threading.batchproc.BatchProcessor: Deprecated.
setInterceptedExceptions(Class<? extends Exception>[]) - Method in class uk.ac.ebi.utils.runcontrol.MultipleAttemptsExecutor
setIsThreadSafe(boolean) - Method in class uk.ac.ebi.utils.runcontrol.ProgressLogger: Tells us that progress updates will be thread-safe, so that we don't have to manage synchronisation and its performance overhead.
setJobLogPeriod(long) - Method in class uk.ac.ebi.utils.threading.batchproc.BatchProcessor: Deprecated.

If > 0, methods like BatchProcessor.handleNewBatch(Object, boolean) and BatchProcessor.waitExecutor(String) log messages about how many submitted and completed jobs the processor is dealing with, and does it every a number of submitted jobs equal to this property.
setLoggingLevel(Level) - Method in class uk.ac.ebi.utils.runcontrol.ProgressLogger
setLogMessageTemplate(String) - Method in class uk.ac.ebi.utils.runcontrol.ProgressLogger
setMaxAttempts(int) - Method in class uk.ac.ebi.utils.runcontrol.MultipleAttemptsExecutor
setMaxBatchSize(int) - Method in class uk.ac.ebi.utils.threading.batchproc.processors.CollectionBasedBatchProcessor: Deprecated.

A shorthand for BatchProcessor.getBatchCollector().setMaxBatchSize().
setMaxBatchSize(long) - Method in class uk.ac.ebi.utils.threading.batchproc.AbstractSizedBatchCollector: Deprecated.
setMaxPauseTime(long) - Method in class uk.ac.ebi.utils.runcontrol.MultipleAttemptsExecutor
setMaxProgress(long) - Method in class uk.ac.ebi.utils.runcontrol.PercentProgressLogger
setMaxThreadIncr(int) - Method in class uk.ac.ebi.utils.threading.PoolSizeTuner
setMaxThreads(int) - Method in class uk.ac.ebi.utils.threading.PoolSizeTuner
setMinPauseTime(long) - Method in class uk.ac.ebi.utils.runcontrol.MultipleAttemptsExecutor
setMinThreadIncr(int) - Method in class uk.ac.ebi.utils.threading.PoolSizeTuner
setMinThreads(int) - Method in class uk.ac.ebi.utils.threading.PoolSizeTuner
setNamingThreadFactory(Class<?>, ExecutorService) - Static method in class uk.ac.ebi.utils.threading.ThreadUtils: Works like ThreadUtils.setNamingThreadFactory(String, ExecutorService), but invokes ThreadUtils.setNamingThreadFactory(Class, ThreadPoolExecutor) instead.
setNamingThreadFactory(Class<?>, ThreadPoolExecutor) - Static method in class uk.ac.ebi.utils.threading.ThreadUtils: Works like ThreadUtils.setNamingThreadFactory(String, ThreadPoolExecutor), but uses ThreadUtils.createNamingThreadFactory(Class, ThreadFactory).
setNamingThreadFactory(String, ExecutorService) - Static method in class uk.ac.ebi.utils.threading.ThreadUtils: Wraps ThreadUtils.setNamingThreadFactory(String, ThreadPoolExecutor) if executor is an instance of ThreadPoolExecutor, else has no effect.
setNamingThreadFactory(String, ThreadPoolExecutor) - Static method in class uk.ac.ebi.utils.threading.ThreadUtils: Uses ThreadUtils.createNamingThreadFactory(String, ThreadFactory) to setup a naming thread factory for this executor, which wraps the existing one.
setNewRate() - Method in class uk.ac.ebi.utils.runcontrol.DynamicRateExecutor: Determines the possible new rate, e.g., based on current performance measurement.
setPeriodMSecs(int) - Method in class uk.ac.ebi.utils.threading.PoolSizeTuner
setPopUpExceptions(boolean) - Method in class uk.ac.ebi.utils.runcontrol.StatsExecutor
setPriority(int) - Method in class uk.ac.ebi.utils.threading.BatchServiceTask
setProgressReportAction(BiConsumer<Long, Long>) - Method in class uk.ac.ebi.utils.runcontrol.ProgressLogger
setProgressResolution(long) - Method in class uk.ac.ebi.utils.runcontrol.ProgressLogger
setRate(double) - Method in class uk.ac.ebi.utils.runcontrol.RateLimitedExecutor: Note that the new actual rate might be slightly different than the passed parameters, depends on how RateLimiter is implemented.
setSamplingTime(long) - Method in class uk.ac.ebi.utils.runcontrol.StatsExecutor
setSubmissionMsgLogLevel(Level) - Method in class uk.ac.ebi.utils.threading.BatchService
setThreadDeltaTolerance(double) - Method in class uk.ac.ebi.utils.threading.PoolSizeTuner
setThreadFactory(ThreadFactory) - Method in class uk.ac.ebi.utils.threading.BatchService: It's like the ThreadPoolExecutor.setThreadFactory(ThreadFactory) and might be useful here as well.
setThreadPoolSize(int) - Method in class uk.ac.ebi.utils.threading.BatchService.BatchServiceTuner: This is invoked by the tuner to change the service's pool size.
setThreadPoolSize(int) - Method in class uk.ac.ebi.utils.threading.BatchService
setThreadPoolSize(int) - Method in class uk.ac.ebi.utils.threading.PoolSizeTuner
signal() - Method in class uk.ac.ebi.utils.threading.fakelocks.FakeCondition
signalAll() - Method in class uk.ac.ebi.utils.threading.fakelocks.FakeCondition
size - Variable in class uk.ac.ebi.utils.collections.ObjectStore
size() - Method in class uk.ac.ebi.utils.collections.MapCollection
size() - Method in class uk.ac.ebi.utils.collections.ObjectStore
size() - Method in class uk.ac.ebi.utils.collections.OptionsMapWrapper
size() - Method in class uk.ac.ebi.utils.collections.TypeCastCollection
SizedBatchCollector - Interface in uk.ac.ebi.utils.threading.batchproc: Deprecated.
the functionality available in this package is provided by project Reactor and we recommend to switch to that. @see ReactorUtils
SortedObjectStore<T,K,V> - Class in uk.ac.ebi.utils.collections: Like ObjectStore, but with types and keys kept sorted.
SortedObjectStore() - Constructor for class uk.ac.ebi.utils.collections.SortedObjectStore
SortedObjectStore(Comparator<T>, Comparator<K>) - Constructor for class uk.ac.ebi.utils.collections.SortedObjectStore
SSLUtils - Class in uk.ac.ebi.utils.opt.net: SSL Utilities.
SSLUtils() - Constructor for class uk.ac.ebi.utils.opt.net.SSLUtils
SSLUtils.FakeX509TrustManager - Class in uk.ac.ebi.utils.opt.net: Trusts all certificates.
start() - Method in class uk.ac.ebi.utils.threading.PoolSizeTuner: Starts the periodic monitoring of the thread pool and its dynamic adjustment.
StatsExecutor - Class in uk.ac.ebi.utils.runcontrol: An executor that logs statistics on the executions it receives to run.
StatsExecutor(String) - Constructor for class uk.ac.ebi.utils.runcontrol.StatsExecutor
StatsExecutor(String, long) - Constructor for class uk.ac.ebi.utils.runcontrol.StatsExecutor
StaxUtils - Class in uk.ac.ebi.utils.xml.stax: Utilities to manage the Stax parser API.
stop() - Method in class uk.ac.ebi.utils.threading.PoolSizeTuner: Stop the periodic monitoring of the thread pool.
StreamUtils - Class in uk.ac.ebi.utils.streams: Stream Utils
StreamUtils() - Constructor for class uk.ac.ebi.utils.streams.StreamUtils
StringSearchUtils - Class in uk.ac.ebi.utils.string
submit(TK) - Method in class uk.ac.ebi.utils.threading.BatchService: Submits a task into the pool, synchronising updates requested from BatchService.poolSizeTuner and other internal state information.
supplier2Iterator(Supplier<? extends E>) - Static method in class uk.ac.ebi.utils.collections.IteratorUtils: Builds an Iterator of non-null based on a supplier.

T

TaskComparator() - Constructor for class uk.ac.ebi.utils.threading.BatchServiceTask.TaskComparator
TestEntityMgrProvider - Class in uk.ac.ebi.utils.opt.orm.test: A JPA EntityManager provider to be used in test classes as Rule (please see JUnit documentation for details).
TestEntityMgrProvider - Class in uk.ac.ebi.utils.test.junit: A JPA EntityManager provider to be used in test classes as Rule (please see JUnit documentation for details).
TestEntityMgrProvider(EntityManagerFactory) - Constructor for class uk.ac.ebi.utils.opt.orm.test.TestEntityMgrProvider: Pass me a factory that I can use to create entity managers.
TestEntityMgrProvider(EntityManagerFactory) - Constructor for class uk.ac.ebi.utils.test.junit.TestEntityMgrProvider: Pass me a factory that I can use to create entity managers.
testFinished(Description) - Method in class uk.ac.ebi.utils.test.junit.TestOutputDecorator
TestOutputDecorator - Class in uk.ac.ebi.utils.test.junit: # An output decorator for JUnit Logs a nice header with the test name before the test and a similar trailer afterward.
TestOutputDecorator() - Constructor for class uk.ac.ebi.utils.test.junit.TestOutputDecorator
testStarted(Description) - Method in class uk.ac.ebi.utils.test.junit.TestOutputDecorator
ThreadUtils - Class in uk.ac.ebi.utils.threading
ThreadUtils() - Constructor for class uk.ac.ebi.utils.threading.ThreadUtils
throwEx(E, String, Object...) - Static method in class uk.ac.ebi.utils.exceptions.ExceptionUtils: Wrapper that uses cause.getClass() as exception type.
throwEx(Class<E>, String, Object...) - Static method in class uk.ac.ebi.utils.exceptions.ExceptionUtils: A wrapper with no cause.
throwEx(Class<E>, Throwable, String, Object...) - Static method in class uk.ac.ebi.utils.exceptions.ExceptionUtils: This calls ExceptionUtils.buildEx(Class, Throwable, String, Object...) and then throws the built exception.
TMP_LOCATION - Static variable in class uk.ac.ebi.utils.io.DownloadUtils
toArray() - Method in class uk.ac.ebi.utils.collections.MapCollection: Refers to MapCollection.getBase().Map.values() (the map's values).
toArray() - Method in class uk.ac.ebi.utils.collections.TypeCastCollection
toArray(T[]) - Method in class uk.ac.ebi.utils.collections.MapCollection: Refers to MapCollection.getBase().Map.values() (the map's values).
toArray(TA[]) - Method in class uk.ac.ebi.utils.collections.TypeCastCollection
toArrayNode(ObjectMapper) - Static method in class uk.ac.ebi.utils.opt.json.JacksonJsUtils: Returns a collector (i.e., for Stream.collect(Collector) and the like) that collects the elements of type T into an ArrayNode.
toCallable(Runnable) - Static method in class uk.ac.ebi.utils.lambda.LambdaUtils
toObjectNode(ObjectMapper, Function<T, String>, Function<T, JsonNode>) - Static method in class uk.ac.ebi.utils.opt.json.JacksonJsUtils: Uses a value merger that throws IllegalArgumentException when the same key yields different values.
toObjectNode(ObjectMapper, Function<T, String>, Function<T, JsonNode>, BinaryOperator<JsonNode>) - Static method in class uk.ac.ebi.utils.opt.json.JacksonJsUtils: Collector to convert a stream of elements into an ObjectNode, by extracting keys and JSON mappings from the elements.
TooFewValuesException - Exception in uk.ac.ebi.utils.exceptions: Some operation has met too few values unexpectedly, eg, a collection is empty.
TooFewValuesException(String) - Constructor for exception uk.ac.ebi.utils.exceptions.TooFewValuesException
TooFewValuesException(String, Throwable) - Constructor for exception uk.ac.ebi.utils.exceptions.TooFewValuesException
TooManyValuesException - Exception in uk.ac.ebi.utils.exceptions: Some operation has met too many values unexpectedly.
TooManyValuesException(String) - Constructor for exception uk.ac.ebi.utils.exceptions.TooManyValuesException
TooManyValuesException(String, Throwable) - Constructor for exception uk.ac.ebi.utils.exceptions.TooManyValuesException
toString() - Method in class uk.ac.ebi.utils.collections.OptionsMapWrapper
toString() - Method in class uk.ac.ebi.utils.regex.RegEx
toStringVerbose() - Method in class uk.ac.ebi.utils.collections.ObjectStore: Prints full contents of the object store.
toSupplier(Runnable) - Static method in class uk.ac.ebi.utils.lambda.LambdaUtils
toSupplier(Callable<T>) - Static method in class uk.ac.ebi.utils.lambda.LambdaUtils
track(Runnable) - Method in class uk.ac.ebi.utils.time.XStopWatch
trackNano(Runnable) - Method in class uk.ac.ebi.utils.time.XStopWatch: This is similar to XStopWatch.profileNano(Runnable), but uses the current watch to time the parameter task.
trustAllHostnames() - Static method in class uk.ac.ebi.utils.opt.net.SSLUtils: Set the default host name Verifier to an instance of a fake class that trust all hostnames.
trustAllHttpsCertificates() - Static method in class uk.ac.ebi.utils.opt.net.SSLUtils: Set the default X509 Trust Manager to an instance of a fake class that trust all certificates, even the self-signed ones.
tryAdvance(Consumer<? super T[]>) - Method in class uk.ac.ebi.utils.collections.TupleSpliterator: As explained above, if all the underlining spliterators have an element to return (ie, their tryAdvance()) is invoked to get the element they have to return and the return value checked to be true), a tuple is built with all such elements and then passed to the action parameter.
tryLock() - Method in class uk.ac.ebi.utils.threading.fakelocks.FakeLock
tryLock(long, TimeUnit) - Method in class uk.ac.ebi.utils.threading.fakelocks.FakeLock
trySplit() - Method in class uk.ac.ebi.utils.collections.TupleSpliterator: A splits succeeds when all the base spliterators return a prefix of the same length.
TupleIterator<T> - Class in uk.ac.ebi.utils.collections: Takes an array of iterators and returns an iterator of tuples.
TupleIterator(Iterator<? extends T>[]) - Constructor for class uk.ac.ebi.utils.collections.TupleIterator
TupleSpliterator<T> - Class in uk.ac.ebi.utils.collections: A Tuple Spliterator
TupleSpliterator(Spliterator<? extends T>[]) - Constructor for class uk.ac.ebi.utils.collections.TupleSpliterator: Initialises with base spliterators.
tupleStream(boolean, Stream<? extends T>...) - Static method in class uk.ac.ebi.utils.streams.StreamUtils: Returns a stream of tuples built from base streams.
tupleStream(Stream<? extends T>...) - Static method in class uk.ac.ebi.utils.streams.StreamUtils: Defaults to 0 (which implies Spliterator.IMMUTABLE only) and false (i.e., non-parallel result stream).
TypeCastCollection<T> - Class in uk.ac.ebi.utils.collections: Allows to type-cast the collection of super-type T1 into the sub-type T (i.e., T extends T1), which is not permitted by the Java generics.
TypeCastCollection(Collection<? super T>) - Constructor for class uk.ac.ebi.utils.collections.TypeCastCollection
typeKeys(T) - Method in class uk.ac.ebi.utils.collections.ObjectStore: All the identifiers of objects belonging to a given type
types() - Method in class uk.ac.ebi.utils.collections.ObjectStore: All the types in the store

U

uk.ac.ebi.utils.collections - package uk.ac.ebi.utils.collections
uk.ac.ebi.utils.exceptions - package uk.ac.ebi.utils.exceptions
uk.ac.ebi.utils.ids - package uk.ac.ebi.utils.ids
uk.ac.ebi.utils.io - package uk.ac.ebi.utils.io
uk.ac.ebi.utils.lambda - package uk.ac.ebi.utils.lambda
uk.ac.ebi.utils.memory - package uk.ac.ebi.utils.memory
uk.ac.ebi.utils.objects - package uk.ac.ebi.utils.objects
uk.ac.ebi.utils.opt.config - package uk.ac.ebi.utils.opt.config
uk.ac.ebi.utils.opt.io - package uk.ac.ebi.utils.opt.io
uk.ac.ebi.utils.opt.json - package uk.ac.ebi.utils.opt.json
uk.ac.ebi.utils.opt.net - package uk.ac.ebi.utils.opt.net
uk.ac.ebi.utils.opt.net.exceptions - package uk.ac.ebi.utils.opt.net.exceptions
uk.ac.ebi.utils.opt.orm.test - package uk.ac.ebi.utils.opt.orm.test
uk.ac.ebi.utils.opt.runcontrol - package uk.ac.ebi.utils.opt.runcontrol
uk.ac.ebi.utils.opt.springweb.exceptions - package uk.ac.ebi.utils.opt.springweb.exceptions
uk.ac.ebi.utils.opt.xml - package uk.ac.ebi.utils.opt.xml
uk.ac.ebi.utils.orm - package uk.ac.ebi.utils.orm
uk.ac.ebi.utils.reflection - package uk.ac.ebi.utils.reflection
uk.ac.ebi.utils.regex - package uk.ac.ebi.utils.regex
uk.ac.ebi.utils.runcontrol - package uk.ac.ebi.utils.runcontrol
uk.ac.ebi.utils.sql - package uk.ac.ebi.utils.sql
uk.ac.ebi.utils.statistics - package uk.ac.ebi.utils.statistics
uk.ac.ebi.utils.streams - package uk.ac.ebi.utils.streams
uk.ac.ebi.utils.string - package uk.ac.ebi.utils.string
uk.ac.ebi.utils.test.junit - package uk.ac.ebi.utils.test.junit
uk.ac.ebi.utils.threading - package uk.ac.ebi.utils.threading
uk.ac.ebi.utils.threading.batchproc - package uk.ac.ebi.utils.threading.batchproc
uk.ac.ebi.utils.threading.batchproc.collectors - package uk.ac.ebi.utils.threading.batchproc.collectors
uk.ac.ebi.utils.threading.batchproc.processors - package uk.ac.ebi.utils.threading.batchproc.processors
uk.ac.ebi.utils.threading.fakelocks - package uk.ac.ebi.utils.threading.fakelocks
uk.ac.ebi.utils.time - package uk.ac.ebi.utils.time
uk.ac.ebi.utils.xml - package uk.ac.ebi.utils.xml
uk.ac.ebi.utils.xml.exceptions - package uk.ac.ebi.utils.xml.exceptions
uk.ac.ebi.utils.xml.stax - package uk.ac.ebi.utils.xml.stax
UncheckedFileNotFoundException - Exception in uk.ac.ebi.utils.exceptions: An unchecked version of FileNotFoundException.
UncheckedFileNotFoundException(String) - Constructor for exception uk.ac.ebi.utils.exceptions.UncheckedFileNotFoundException
UncheckedFileNotFoundException(String, IOException) - Constructor for exception uk.ac.ebi.utils.exceptions.UncheckedFileNotFoundException
UncheckedHttpException - Exception in uk.ac.ebi.utils.opt.net.exceptions: An unchecked verision of HttpException
UncheckedHttpException(String, HttpException) - Constructor for exception uk.ac.ebi.utils.opt.net.exceptions.UncheckedHttpException
UncheckedInterruptedException - Exception in uk.ac.ebi.utils.exceptions: An unchecked version of InterruptedException.
UncheckedInterruptedException(String) - Constructor for exception uk.ac.ebi.utils.exceptions.UncheckedInterruptedException
UncheckedInterruptedException(String, InterruptedException) - Constructor for exception uk.ac.ebi.utils.exceptions.UncheckedInterruptedException
UncheckedXmlStreamException - Exception in uk.ac.ebi.utils.xml.exceptions: Unchecked version of XMLStreamException.
UncheckedXmlStreamException(String) - Constructor for exception uk.ac.ebi.utils.xml.exceptions.UncheckedXmlStreamException
UncheckedXmlStreamException(String, XMLStreamException) - Constructor for exception uk.ac.ebi.utils.xml.exceptions.UncheckedXmlStreamException
UnexpectedEventException - Exception in uk.ac.ebi.utils.exceptions: To be used when the execution flow of a program has met an event that is unusual, rare, or alike.
UnexpectedEventException(String) - Constructor for exception uk.ac.ebi.utils.exceptions.UnexpectedEventException
UnexpectedEventException(String, Throwable) - Constructor for exception uk.ac.ebi.utils.exceptions.UnexpectedEventException
UnexpectedValueException - Exception in uk.ac.ebi.utils.exceptions: An operation has met some unexpected value.
UnexpectedValueException(String) - Constructor for exception uk.ac.ebi.utils.exceptions.UnexpectedValueException
UnexpectedValueException(String, Throwable) - Constructor for exception uk.ac.ebi.utils.exceptions.UnexpectedValueException
union(List<? extends T>...) - Static method in class uk.ac.ebi.utils.collections.ListUtils: The union of all the parameters (the list elements) in a single list
Unix4jUtils - Class in uk.ac.ebi.utils.opt.io: Utilities for the great Unix4j library.
Unix4jUtils() - Constructor for class uk.ac.ebi.utils.opt.io.Unix4jUtils
unixFilter(To) - Static method in class uk.ac.ebi.utils.opt.io.Unix4jUtils: Pipes the output of a Unix4j command
unlock() - Method in class uk.ac.ebi.utils.threading.fakelocks.FakeLock
unmodifiableCollection(CP, Function<CP, C>, Supplier<C>) - Static method in class uk.ac.ebi.utils.collections.CollectionsUtils: Always returns an unmodifiable collection wrapping the parameter.
unmodifiableList(List<? extends T>) - Static method in class uk.ac.ebi.utils.collections.CollectionsUtils: CollectionsUtils.unmodifiableCollection(Collection, Function, Supplier)
unmodifiableMap(Map<? extends K, ? extends V>) - Static method in class uk.ac.ebi.utils.collections.CollectionsUtils
unmodifiableMap(Map<? extends K, ? extends V>, Supplier<Map<K, V>>) - Static method in class uk.ac.ebi.utils.collections.CollectionsUtils: This doesn't use CollectionsUtils.unmodifiableCollection(Collection, Function, Supplier), but has an implementation based on the same logic.
unmodifiableOptionsMap(Map<String, Object>) - Static method in interface uk.ac.ebi.utils.collections.OptionsMap: This is simply the chaining of OptionsMap.from(Map) and Collections.unmodifiableMap(Map), ie, returns a read-only options map.
unmodifiableOptionsMap(Properties) - Static method in interface uk.ac.ebi.utils.collections.OptionsMap
unmodifiableSet(Set<? extends T>) - Static method in class uk.ac.ebi.utils.collections.CollectionsUtils: CollectionsUtils.unmodifiableCollection(Collection, Function, Supplier)
update(long) - Method in class uk.ac.ebi.utils.runcontrol.ProgressLogger: Updates the current progress and possibly generates a new log message, according to ProgressLogger.getProgressResolution().
updateWithIncrement() - Method in class uk.ac.ebi.utils.runcontrol.ProgressLogger: increments by 1
updateWithIncrement(long) - Method in class uk.ac.ebi.utils.runcontrol.ProgressLogger: Wrapper of ProgressLogger.update(long)
uri(String) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils: Creates a URI and intercepts URISyntaxException, throwing IllegalArgumentException if such an exception occurs.
url(String) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils
urlDecode(String) - Static method in class uk.ac.ebi.utils.ids.IdUtils: Same as IdUtils.urlEncode(String), for the reverse operation, based on URLDecoder.
urlEncode(String) - Static method in class uk.ac.ebi.utils.ids.IdUtils: Invokes URLEncoder.encode(String, String) with UTF-8 encoding and wraps the generated exception with an IllegalArgumentException.

V

values() - Method in class uk.ac.ebi.utils.collections.OptionsMapWrapper
values(T) - Method in class uk.ac.ebi.utils.collections.ObjectStore: All the values of a certain type.

W

waitAllFinished() - Method in class uk.ac.ebi.utils.threading.BatchService: This can be used after you have submitted all the tasks that you have to run, when you want to wait that all of them complete their execution.
waitExecutor(String) - Method in class uk.ac.ebi.utils.threading.batchproc.BatchProcessor: Deprecated.

Waits that all the parallel jobs submitted to the batchJob are finished.
withBatchSize(int) - Method in class uk.ac.ebi.utils.opt.runcontrol.ReactorUtils.ParallelBatchFluxBuilder: The parallel flux scheduler to use.
withBatchSupplier(Supplier<? extends Collection<? super T>>) - Method in class uk.ac.ebi.utils.opt.runcontrol.ReactorUtils.ParallelBatchFluxBuilder: Default is null, which falls back to Flux.buffer(int), usually a List supplier.
withParallelism(int) - Method in class uk.ac.ebi.utils.opt.runcontrol.ReactorUtils.ParallelBatchFluxBuilder: The degree of parallelism of the resulting flux.
withParallelismPreFetch(int) - Method in class uk.ac.ebi.utils.opt.runcontrol.ReactorUtils.ParallelBatchFluxBuilder: The prefetch parameter passed to Flux.parallel(int, int).
withScheduler(Scheduler) - Method in class uk.ac.ebi.utils.opt.runcontrol.ReactorUtils.ParallelBatchFluxBuilder: The scheduler used to run the resulting flux.
wrap(Executor) - Method in class uk.ac.ebi.utils.runcontrol.ChainExecutor: This allows you to indent multiple executors, without having to write big nested expressions.
wrapBatchJob(Runnable) - Method in class uk.ac.ebi.utils.threading.batchproc.BatchProcessor: Deprecated.

Wraps the task into some common operations.
writeFile(String, String) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils: Defaults to UTF8, append = false
writeFile(String, String, boolean) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils: Defaults to UTF8
writeFile(String, String, Charset, boolean) - Static method in class uk.ac.ebi.utils.opt.io.IOUtils: Writes the string to the file and then closes it
writeLock() - Method in class uk.ac.ebi.utils.threading.fakelocks.FakeReadWriteLock

X

XML_EXT - Static variable in class uk.ac.ebi.utils.io.DownloadUtils
xmlCoord(Location) - Static method in class uk.ac.ebi.utils.xml.stax.StaxUtils: Renders Location in a human-readable format, useful in logging and error messages.
xmlCoord(XMLStreamReader) - Static method in class uk.ac.ebi.utils.xml.stax.StaxUtils: Wrapper of XMLStreamReader.getLocation().
XmlFilterUtils - Class in uk.ac.ebi.utils.opt.xml: Utilities to filter XML streams and alike.
XmlFilterUtils() - Constructor for class uk.ac.ebi.utils.opt.xml.XmlFilterUtils
XPathReader - Class in uk.ac.ebi.utils.xml: Created by the ISA team Modified from example here: http://www.javabeat.net/tips/182-how-to-query-xml-using-xpath.html
XPathReader(InputStream) - Constructor for class uk.ac.ebi.utils.xml.XPathReader
XPathReader(Reader) - Constructor for class uk.ac.ebi.utils.xml.XPathReader
XPathReader(String) - Constructor for class uk.ac.ebi.utils.xml.XPathReader
XPathReader(Path) - Constructor for class uk.ac.ebi.utils.xml.XPathReader
XPathReader(InputSource) - Constructor for class uk.ac.ebi.utils.xml.XPathReader
XResponseEntityExceptionHandler - Class in uk.ac.ebi.utils.opt.springweb.exceptions: A better web exception handler.
XResponseEntityExceptionHandler() - Constructor for class uk.ac.ebi.utils.opt.springweb.exceptions.XResponseEntityExceptionHandler
XStopWatch - Class in uk.ac.ebi.utils.time: A StopWatch with extended functionality.
XStopWatch() - Constructor for class uk.ac.ebi.utils.time.XStopWatch
XValidate - Class in uk.ac.ebi.utils.objects: Logical extension to Validate, which adds more methods.
XValidate() - Constructor for class uk.ac.ebi.utils.objects.XValidate

Y

YAMLLoader - Class in uk.ac.ebi.utils.opt.config: A simple YAML document/file loader, which is focused on configuration needs.
YAMLLoader() - Constructor for class uk.ac.ebi.utils.opt.config.YAMLLoader

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