- accept(File) - Method in class cross.io.misc.DefaultConfigurableFileFilter
-
- accept(File) - Method in class cross.io.misc.DefaultMatchAllFileFilter
-
- add(T) - Method in class cross.datastructures.collections.CachedLazyList
-
- add(int, T) - Method in class cross.datastructures.collections.CachedLazyList
-
- add(int, T) - Method in class cross.datastructures.collections.CachedReadWriteList
-
- add(T) - Method in class cross.datastructures.collections.CachedReadWriteList
-
- add(Array) - Method in class cross.datastructures.fragments.CachedList
-
- add(int, Array) - Method in class cross.datastructures.fragments.CachedList
-
- add(Attribute) - Method in class cross.datastructures.fragments.Metadata
-
- add(T) - Method in class cross.datastructures.tuple.TupleND
-
- add(IControlledVocabularyProvider) - Method in class cross.vocabulary.CvResolver
-
- add(IControlledVocabularyProvider) - Method in interface cross.vocabulary.ICvResolver
-
Adds the given provider.
- addAll(Collection<? extends T>) - Method in class cross.datastructures.collections.CachedLazyList
-
- addAll(int, Collection<? extends T>) - Method in class cross.datastructures.collections.CachedLazyList
-
- addAll(Collection<? extends T>) - Method in class cross.datastructures.collections.CachedReadWriteList
-
- addAll(int, Collection<? extends T>) - Method in class cross.datastructures.collections.CachedReadWriteList
-
- addAll(Collection<? extends Array>) - Method in class cross.datastructures.fragments.CachedList
-
- addAll(int, Collection<? extends Array>) - Method in class cross.datastructures.fragments.CachedList
-
- addAll(Collection<? extends T>) - Method in class cross.datastructures.tuple.TupleND
-
- addAttribute(Attribute) - Method in class cross.datastructures.fragments.FileFragment
-
- addAttribute(Attribute) - Method in class cross.datastructures.fragments.Fragment
-
- addAttribute(Attribute) - Method in interface cross.datastructures.fragments.IFragment
-
Add an attribute
- addAttribute(Attribute) - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- addAttribute(Attribute) - Method in class cross.datastructures.fragments.ImmutableVariableFragment
-
- addAttribute(Attribute) - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- addAttribute(Attribute) - Method in class cross.datastructures.fragments.VariableFragment
-
- addBean(String) - Method in class cross.applicationContext.ReflectionApplicationContextGenerator
-
Adds a bean to the application context using a Java source file.
- addChild(String) - Method in class cross.datastructures.fragments.FileFragment
-
- addChild(String) - Method in interface cross.datastructures.fragments.IFileFragment
-
Add a child of given name or return already existing one.
- addChild(String) - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- addChildren(IVariableFragment...) - Method in class cross.datastructures.fragments.FileFragment
-
- addChildren(IVariableFragment...) - Method in interface cross.datastructures.fragments.IFileFragment
-
Add a number of children.
- addChildren(IVariableFragment...) - Method in interface cross.datastructures.fragments.IGroupFragment
-
Add a number of children.
- addChildren(IVariableFragment...) - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- addChildren(IVariableFragment...) - Method in class cross.datastructures.fragments.NamedGroupFragment
-
Add a number of children.
- addDimensions(Dimension...) - Method in class cross.datastructures.fragments.FileFragment
-
- addDimensions(Dimension...) - Method in interface cross.datastructures.fragments.IFileFragment
-
Add dimensions to this IFileFragment.
- addDimensions(Dimension...) - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- addListener(IListener<IEvent<IWorkflowResult>>) - Method in class cross.commands.fragments.AFragmentCommand
-
- addListener(IListener<IEvent<IWorkflowResult>>) - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- addListener(IListener<IEvent<V>>) - Method in class cross.event.EventSource
-
- addListener(IListener<IEvent<V>>) - Method in interface cross.event.IEventSource
-
- addListener(IListener<IEvent<V>>) - Method in class cross.event.SwingEventSource
-
- addSourceFile(Collection<IFileFragment>) - Method in class cross.datastructures.fragments.FileFragment
-
- addSourceFile(IFileFragment...) - Method in class cross.datastructures.fragments.FileFragment
-
- addSourceFile(Collection<IFileFragment>) - Method in interface cross.datastructures.fragments.IFileFragment
-
Add source FileFragments contained in Collection c to this FileFragment.
- addSourceFile(IFileFragment...) - Method in interface cross.datastructures.fragments.IFileFragment
-
Add source FileFragments contained in ff to this FileFragment.
- addSourceFile(Collection<IFileFragment>) - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- addSourceFile(IFileFragment...) - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- addWorkflowResult(IFileFragment) - Method in class cross.commands.fragments.AFragmentCommand
-
- addWorkflowResult(IFileFragment, IFileFragment...) - Method in class cross.commands.fragments.AFragmentCommand
-
- addWorkflowResult(IFileFragment, WorkflowSlot, IFileFragment...) - Method in class cross.commands.fragments.AFragmentCommand
-
- addWorkflowResult(IFileFragment, IWorkflowElement, WorkflowSlot, IFileFragment...) - Method in class cross.commands.fragments.AFragmentCommand
-
- addWorkflowResults(IFileFragment...) - Method in class cross.commands.fragments.AFragmentCommand
-
- addWorkflowResults(TupleND<IFileFragment>) - Method in class cross.commands.fragments.AFragmentCommand
-
- AEvent<V> - Class in cross.event
-
Abstract implementation of a typed Event.
- AEvent(V, IEventSource<V>, String) - Constructor for class cross.event.AEvent
-
- AEvent(V, IEventSource<V>) - Constructor for class cross.event.AEvent
-
- AFragmentCommand - Class in cross.commands.fragments
-
A class providing a default implementation for configuration and a concrete
typing of the untyped superclass
ICommand.
- AFragmentCommand() - Constructor for class cross.commands.fragments.AFragmentCommand
-
- AFragmentCommandServiceLoader - Class in cross.io
-
- AFragmentCommandServiceLoader() - Constructor for class cross.io.AFragmentCommandServiceLoader
-
- AFragmentCommandServiceLoader.ClassNameLexicalComparator - Class in cross.io
-
- AFragmentCommandServiceLoader.ClassNameLexicalComparator() - Constructor for class cross.io.AFragmentCommandServiceLoader.ClassNameLexicalComparator
-
- AnnotationInspector - Class in cross.annotations
-
Provides static utility methods to test for presence of specific
annotations.
- append(IWorkflowResult) - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- append(IWorkflowResult) - Method in interface cross.datastructures.workflow.IWorkflow
-
Append IWorkflowResult to this IWorkflow instance.
- appendXML(Element) - Method in class cross.commands.fragments.AFragmentCommand
-
- appendXML(Element) - Method in class cross.datastructures.fragments.FileFragment
-
- appendXML(Element) - Method in class cross.datastructures.fragments.Fragment
-
- appendXML(Element) - Method in interface cross.datastructures.fragments.IFileFragment
-
Append structural information of this FileFragment to Element e.
- appendXML(Element) - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- appendXML(Element) - Method in class cross.datastructures.fragments.ImmutableVariableFragment
-
- appendXML(Element) - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- appendXML(Element) - Method in interface cross.datastructures.fragments.IVariableFragment
-
Append structural information of this VariableFragment to Element e.
- appendXML(Element) - Method in class cross.datastructures.fragments.NamedGroupFragment
-
- appendXML(Element) - Method in class cross.datastructures.fragments.VariableFragment
-
- appendXML(Element) - Method in class cross.datastructures.pipeline.CommandPipeline
-
Appends workflowInputs, workflowOutputs and workflowCommands elements to
given Element parameter.
- appendXML(Element) - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- appendXML(Element) - Method in class cross.datastructures.workflow.DefaultWorkflowObjectResult
-
- appendXML(Element) - Method in class cross.datastructures.workflow.DefaultWorkflowProgressResult
-
- appendXML(Element) - Method in class cross.datastructures.workflow.DefaultWorkflowResult
-
- appendXML(Element) - Method in class cross.datastructures.workflow.DefaultWorkflowStatisticsResult
-
- appendXML(Element) - Method in interface cross.io.xml.IXMLSerializable
-
- apply(IN) - Method in interface cross.commands.ICommand
-
Apply a command implementation to an Object of type
IN, returning an object of type
OUT.
- apply(String, HashMap<String, Double>, String) - Static method in class cross.datastructures.tools.EvalTools
-
- apply(String, Tuple2D<Context, Context>, String) - Static method in class cross.datastructures.tools.EvalTools
-
- ArrayChunkIterator - Class in cross.io.misc
-
Implementation for chunked array iteration of large on-disk arrays.
- ArrayChunkIterator(IVariableFragment, int) - Constructor for class cross.io.misc.ArrayChunkIterator
-
- ArrayTools - Class in cross.datastructures.tools
-
Utility class providing methods for Sparse and Dense Arrays.
- ArrayTools() - Constructor for class cross.datastructures.tools.ArrayTools
-
- asCollection() - Method in class cross.datastructures.fragments.Metadata
-
- AutoRetrievalEhcacheDelegate<K,V> - Class in cross.cache.ehcache
-
Transparent cache, which also knows how to create objects of the given type
via the
cross.datastructures.ehcache.ICacheElementProvider, if their key is
not present in the in-memory cache.
- AutoRetrievalEhcacheDelegate(Ehcache, ICacheElementProvider<K, V>) - Constructor for class cross.cache.ehcache.AutoRetrievalEhcacheDelegate
-
- average(double[], int, int) - Static method in class cross.tools.MathTools
-
- averageOfSquares(double[], int, int) - Static method in class cross.tools.MathTools
-
- awaitTermination(long, TimeUnit) - Method in class cross.datastructures.threads.ExecutorsManager
-
- awaitTermination(long, TimeUnit) - Static method in class cross.Factory
-
NEVER SYNCHRONIZE THIS METHOD, IT WILL BLOCK EVERYHTING WITHIN THE QUEUE!
- CachedLazyList<T> - Class in cross.datastructures.collections
-
Implementation of a read-only cached list for indexed data access.
- CachedLazyList(IElementProvider<T>) - Constructor for class cross.datastructures.collections.CachedLazyList
-
- CachedList - Class in cross.datastructures.fragments
-
Implementation of a cached list for indexed data access.
- CachedList() - Constructor for class cross.datastructures.fragments.CachedList
-
- CachedReadWriteList<T> - Class in cross.datastructures.collections
-
- CachedReadWriteList(String, int) - Constructor for class cross.datastructures.collections.CachedReadWriteList
-
- CachedReadWriteList(String, ISerializationProxy<T>) - Constructor for class cross.datastructures.collections.CachedReadWriteList
-
Initializes the cache with a maximum of 100 elements in memory.
- CachedReadWriteList(String, ISerializationProxy<T>, int) - Constructor for class cross.datastructures.collections.CachedReadWriteList
-
- CacheFactory - Class in cross.cache
-
Static utility class for creation and retrieval of various pre-configured
caches.
- CacheFactory() - Constructor for class cross.cache.CacheFactory
-
- CacheType - Enum in cross.cache
-
Enumeration of currently available cache types.
- calcChecksum(File, Checksum) - Static method in class cross.io.misc.BinaryFileBase64Wrapper
-
Calculates a checksum on File.
- call() - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- canRead(IFileFragment) - Method in interface cross.io.IDataSource
-
- canRead(IFileFragment) - Method in class cross.io.xml.FragmentXMLSerializer
-
- checkEngines() - Static method in class cross.datastructures.tools.EvalTools
-
- checkMutableProperties(Method, Class<?>, Object, List<ReflectionApplicationContextGenerator.ObjectProperty>) - Method in class cross.applicationContext.ReflectionApplicationContextGenerator
-
- ChoiceFactory - Class in cross.datastructures.combinations
-
- ChoiceFactory() - Constructor for class cross.datastructures.combinations.ChoiceFactory
-
- ClassSpy - Class in cross.annotations
-
ClassSpy class.
- ClassSpy(String) - Constructor for class cross.annotations.ClassSpy
-
Constructor for ClassSpy.
- clear() - Method in class cross.datastructures.collections.CachedLazyList
-
- clear() - Method in class cross.datastructures.collections.CachedReadWriteList
-
- clear() - Method in class cross.datastructures.fragments.CachedList
-
- clear() - Method in class cross.datastructures.fragments.ImmutableVariableFragment
-
- clear() - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- clear() - Method in interface cross.datastructures.fragments.IVariableFragment
-
Clear all associated array data and other resources.
- clear() - Method in class cross.datastructures.fragments.VariableFragment
-
Allows to manually clear all associated array data.
- clear() - Method in class cross.datastructures.tuple.TupleND
-
- clearArrays() - Method in class cross.datastructures.fragments.FileFragment
-
- clearArrays() - Method in interface cross.datastructures.fragments.IFileFragment
-
Iterates through all VariableFragments, clearing in memory arrays, except
for source_files.
- clearArrays() - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- clearDimensions() - Method in class cross.datastructures.fragments.FileFragment
-
- clearDimensions() - Method in interface cross.datastructures.fragments.IFileFragment
-
Resets all dimensions of this fragment.
- clearDimensions() - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- close() - Method in class cross.cache.ehcache.AutoRetrievalEhcacheDelegate
-
- close() - Method in class cross.cache.ehcache.EhcacheDelegate
-
- close() - Method in interface cross.cache.ICacheDelegate
-
- close() - Method in class cross.cache.none.NoCache
-
- close() - Method in class cross.cache.softReference.SoftReferenceCache
-
- close() - Method in class cross.datastructures.cache.VariableFragmentArrayCache
-
- close() - Method in class cross.io.misc.Base64.OutputStream
-
Flushes and closes (I think, in the superclass) the stream.
- closing(int, double[]) - Static method in class cross.tools.MathTools
-
- CombinationIterator<T> - Class in cross.datastructures.combinations
-
- CombinationIterator(CombinationProvider, ITypeFactory<T>) - Constructor for class cross.datastructures.combinations.CombinationIterator
-
- CombinationIterator - Class in cross.math
-
Implementation of
Iterator for
int[], returning, for a
given number of
Partitions in increasing order, an array of item
indices for each partition for the current iteration.
- CombinationIterator(Partition...) - Constructor for class cross.math.CombinationIterator
-
Create a new CombinationIterator with given Partitions.
- CombinationProvider - Class in cross.datastructures.combinations
-
- CombinationProvider(CombinationIterator, List<Object[]>) - Constructor for class cross.datastructures.combinations.CombinationProvider
-
- Combinatorics - Class in cross.math
-
Utility class with methods for combinatorics.
- Combinatorics() - Constructor for class cross.math.Combinatorics
-
- CommandPipeline - Class in cross.datastructures.pipeline
-
Implementation of ICommandSequence for a linear sequence of commands.
- CommandPipeline() - Constructor for class cross.datastructures.pipeline.CommandPipeline
-
- compare(IFragment, IFragment) - Method in class cross.datastructures.fragments.FileFragment
-
- compare(IFragment, IFragment) - Method in class cross.datastructures.fragments.Fragment
-
Compare Fragments by comparing their string representations.
- compare(IFragment, IFragment) - Method in interface cross.datastructures.fragments.IFragment
-
Compare Fragments by comparing their string representations.
- compare(IFragment, IFragment) - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- compare(IFragment, IFragment) - Method in class cross.datastructures.fragments.ImmutableVariableFragment
-
- compare(IFragment, IFragment) - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- compare(IFragment, IFragment) - Method in interface cross.datastructures.fragments.IVariableFragment
-
- compare(IFragment, IFragment) - Method in class cross.datastructures.fragments.VariableFragment
-
- compare(Tuple2D<Double, Double>, Tuple2D<Double, Double>) - Method in class cross.datastructures.tuple.Tuple2DDoubleComp
-
- compare(AFragmentCommand, AFragmentCommand) - Method in class cross.io.AFragmentCommandServiceLoader.ClassNameLexicalComparator
-
- compareTo(Object) - Method in class cross.datastructures.fragments.FileFragment
-
- compareTo(Object) - Method in class cross.datastructures.fragments.Fragment
-
Only perform comparison on instances of Fragment.
- compareTo(Object) - Method in interface cross.datastructures.fragments.IFragment
-
Only perform comparison on instances of Fragment.
- compareTo(Object) - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- compareTo(Object) - Method in class cross.datastructures.fragments.ImmutableVariableFragment
-
- compareTo(Object) - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- compareTo(Object) - Method in interface cross.datastructures.fragments.IVariableFragment
-
- compareTo(Object) - Method in class cross.datastructures.fragments.VariableFragment
-
- complement(Set<T>, Set<T>) - Static method in class cross.math.SetOperations
-
- Configurable - Annotation Type in cross.annotations
-
Marker annotation for member variables, which should be made available to
Configuration.
- configurationChanged(ConfigurationEvent) - Method in class cross.Factory
-
Listen to ConfigurationEvents.
- configurationChanged(ConfigurationEvent) - Method in class cross.io.xml.FragmentXMLSerializer
-
- configure(Configuration) - Method in class cross.commands.fragments.AFragmentCommand
-
Deprecated.
- configure(Configuration) - Method in class cross.datastructures.fragments.CachedList
-
- configure(Configuration) - Method in class cross.datastructures.fragments.FileFragmentFactory
-
- configure(Configuration) - Method in class cross.datastructures.pipeline.CommandPipeline
-
- configure(Configuration) - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- configure(Configuration) - Method in class cross.Factory
-
Call configure before retrieving an instance of ArrayFactory.
- configure(Configuration) - Method in interface cross.IConfigurable
-
- configure(Configuration) - Method in class cross.io.AFragmentCommandServiceLoader
-
- configure(Configuration) - Method in class cross.io.DataSourceFactory
-
- configure(Configuration) - Method in class cross.io.InputDataFactory
-
- configure(Configuration) - Method in class cross.io.misc.DefaultConfigurableFileFilter
-
- configure(Configuration) - Method in class cross.io.misc.DefaultMatchAllFileFilter
-
- configure(Configuration) - Method in class cross.io.misc.WorkflowZipper
-
- configure(Configuration) - Method in class cross.io.xml.FragmentXMLSerializer
-
- configure(Configuration) - Method in class cross.ObjectFactory
-
- configureType(T) - Method in interface cross.IObjectFactory
-
- configureType(T) - Method in class cross.ObjectFactory
-
- ConfiguringBeanPostProcessor - Class in cross.applicationContext
-
- ConfiguringBeanPostProcessor() - Constructor for class cross.applicationContext.ConfiguringBeanPostProcessor
-
- ConstraintViolationException - Exception in cross.exception
-
ConstraintViolationException is thrown, if constraints are not met, as
checked within cross.tools.EvalTools.
- ConstraintViolationException(String) - Constructor for exception cross.exception.ConstraintViolationException
-
- ConstraintViolationException(String, Throwable) - Constructor for exception cross.exception.ConstraintViolationException
-
- ConstraintViolationException(Throwable) - Constructor for exception cross.exception.ConstraintViolationException
-
- contains(Object) - Method in class cross.datastructures.collections.CachedLazyList
-
- contains(Integer) - Method in class cross.datastructures.collections.CachedReadWriteList
-
- contains(Object) - Method in class cross.datastructures.collections.CachedReadWriteList
-
- contains(Object) - Method in class cross.datastructures.fragments.CachedList
-
- contains(Object) - Method in class cross.datastructures.tuple.TupleND
-
- containsAll(Collection<?>) - Method in class cross.datastructures.collections.CachedLazyList
-
- containsAll(Collection<?>) - Method in class cross.datastructures.collections.CachedReadWriteList
-
- containsAll(Collection<?>) - Method in class cross.datastructures.fragments.CachedList
-
- containsAll(Collection<?>) - Method in class cross.datastructures.tuple.TupleND
-
- Context - Interface in cross.datastructures.fragments
-
Context associated to a
Fragment by
name.
- CONTEXT_LOCATION_KEY - Static variable in class cross.ObjectFactory
-
- convert(T) - Method in interface cross.datastructures.cache.ISerializationProxy
-
- convert(Array) - Method in class cross.datastructures.cache.SerializableArrayProxy
-
- create(Object[]) - Method in interface cross.datastructures.combinations.ITypeFactory
-
- create(File) - Method in class cross.datastructures.fragments.FileFragmentFactory
-
- create(File, IFileFragment...) - Method in class cross.datastructures.fragments.FileFragmentFactory
-
- create(String, String) - Method in class cross.datastructures.fragments.FileFragmentFactory
-
- create(String, String, IFileFragment...) - Method in class cross.datastructures.fragments.FileFragmentFactory
-
- create(File, String, IFileFragment...) - Method in class cross.datastructures.fragments.FileFragmentFactory
-
- create(String, String, Collection<IFileFragment>) - Method in class cross.datastructures.fragments.FileFragmentFactory
-
- create(IFileFragment, IFileFragment, File) - Method in class cross.datastructures.fragments.FileFragmentFactory
-
Creates a new AFragment with default name.
- create(String) - Method in class cross.datastructures.fragments.FileFragmentFactory
-
- create(File) - Method in interface cross.datastructures.fragments.IFileFragmentFactory
-
- create(File, IFileFragment...) - Method in interface cross.datastructures.fragments.IFileFragmentFactory
-
- create(String, String) - Method in interface cross.datastructures.fragments.IFileFragmentFactory
-
- create(String, String, IFileFragment...) - Method in interface cross.datastructures.fragments.IFileFragmentFactory
-
- create(File, String, IFileFragment...) - Method in interface cross.datastructures.fragments.IFileFragmentFactory
-
- create(String, String, Collection<IFileFragment>) - Method in interface cross.datastructures.fragments.IFileFragmentFactory
-
- create(IFileFragment, IFileFragment, File) - Method in interface cross.datastructures.fragments.IFileFragmentFactory
-
Creates a new AFragment with default name.
- create(String) - Method in interface cross.datastructures.fragments.IFileFragmentFactory
-
- createApplicationContext() - Method in class cross.applicationContext.DefaultApplicationContextFactory
-
- createArray(IFileFragment, String, DataType, int...) - Static method in class cross.datastructures.tools.FragmentTools
-
Creates an array of given shape and type as array of varname as child of
parent.
- createAutoRetrievalCache(String, ICacheElementProvider<K, V>) - Static method in class cross.cache.CacheFactory
-
- createBlockingCompletionService(Class<? extends T>) - Method in class cross.commands.fragments.AFragmentCommand
-
- createClassPathApplicationContext() - Method in class cross.applicationContext.DefaultApplicationContextFactory
-
- createCommandSequence() - Method in class cross.Factory
-
Build the command sequence, aka pipeline for command execution.
- createCommandSequence(TupleND<IFileFragment>) - Method in class cross.Factory
-
Build the command sequence, aka pipeline for command execution.
- createCompatible(IFileFragment, IVariableFragment) - Static method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
Creates a VariableFragment compatible in type, name and dimensions to vf.
- createCompatible(IFileFragment, IVariableFragment) - Static method in class cross.datastructures.fragments.VariableFragment
-
Creates a VariableFragment compatible in type, name and dimensions to vf.
- createCompletionService(Class<? extends T>) - Method in class cross.commands.fragments.AFragmentCommand
-
- createContextXml(File, String, String, String...) - Static method in class cross.applicationContext.ReflectionApplicationContextGenerator
-
- createDefaultCache(String, int, int) - Static method in class cross.cache.CacheFactory
-
- createDefaultCache(File, String, int) - Static method in class cross.cache.CacheFactory
-
- createDefaultCache(File, String) - Static method in class cross.cache.CacheFactory
-
- createDefaultCache(String) - Static method in class cross.cache.CacheFactory
-
- createDefaultCache(String, int) - Static method in class cross.cache.CacheFactory
-
- createDefaultFragmentCache(File, String) - Static method in class cross.datastructures.fragments.Fragments
-
- createDoubleArrayD1(IFileFragment, String, int) - Static method in class cross.datastructures.tools.FragmentTools
-
Creates a one-dimensional double array and adds it as to the
automatically created IVariableFragment with varname.
- createElement(Document) - Method in class cross.applicationContext.ReflectionApplicationContextGenerator.BeanDescriptor
-
- createElement(Class<?>) - Method in class cross.applicationContext.ReflectionApplicationContextGenerator
-
- createFragment(IFileFragment, IFileFragment, File) - Static method in class cross.datastructures.tools.FragmentTools
-
Creates a new Fragment with default name.
- createFragmentCache(File, String) - Static method in class cross.datastructures.fragments.Fragments
-
- createFragmentCache(String) - Static method in class cross.datastructures.fragments.Fragments
-
- createFragmentCache(File, String, CacheType) - Static method in class cross.datastructures.fragments.Fragments
-
- createFragmentCache(String, CacheType) - Static method in class cross.datastructures.fragments.Fragments
-
- createIntArrayD1(IFileFragment, String, int) - Static method in class cross.datastructures.tools.FragmentTools
-
Creates or retrieves a
IVariableFragment with
parent as parent and with name
name and
size elements.
- createNonBlockingCompletionService(Class<? extends T>, long, TimeUnit) - Method in class cross.commands.fragments.AFragmentCommand
-
- createProperties(String, File) - Static method in class cross.io.PropertyFileGenerator
-
Deprecated.
Creates a property file for the given class, containing those fields,
which are annotated by
Configurable.
- createProperties(Class<?>) - Static method in class cross.io.PropertyFileGenerator
-
Deprecated.
Creates a property object for the given class, containing those fields,
which are annotated by {
- createServiceProviderElements(Class<?>) - Method in class cross.applicationContext.ReflectionApplicationContextGenerator
-
- createSortedListFromSet(Set<AFragmentCommand>, Comparator<AFragmentCommand>) - Method in class cross.io.AFragmentCommandServiceLoader
-
- createSourceFilesArray(IFileFragment, Collection<IFileFragment>) - Static method in class cross.datastructures.tools.FragmentTools
-
- createString(IFileFragment, String, String) - Static method in class cross.datastructures.tools.FragmentTools
-
Create a
IVariableFragment as child of
parent with name
varname and contents as given in string
value.
- createStringArray(int, int) - Static method in class cross.datastructures.tools.ArrayTools
-
- createStringArray(IFileFragment, String, Collection<String>) - Static method in class cross.datastructures.tools.FragmentTools
-
Create a
IVariableFragment as child of
parent with name
varname and contents as given in string collection
c.
- createVariable(IFileFragment, String, IVariableFragment) - Static method in class cross.datastructures.tools.FragmentTools
-
Create a
IVariableFragment as a child of
parent, with name
varname and index fragment
ifrg.
- createVolatileAutoRetrievalCache(String, ICacheElementProvider<K, V>, long, long) - Static method in class cross.cache.CacheFactory
-
- createVolatileCache(String, long, long) - Static method in class cross.cache.CacheFactory
-
- createVolatileCache(String, long, long, int) - Static method in class cross.cache.CacheFactory
-
- createVolatileCache(String, long, long, int, CacheEventListener...) - Static method in class cross.cache.CacheFactory
-
- createWorkFragment(IFileFragment) - Method in class cross.commands.fragments.AFragmentCommand
-
Utility method to create a mutable FileFragment to work on.
- createWorkFragments(TupleND<IFileFragment>) - Method in class cross.commands.fragments.AFragmentCommand
-
Utility method to create mutable FileFragments from a given tuple of
FileFragments.
- cross - package cross
-
- cross.annotations - package cross.annotations
-
The cross annotations package contains classes for custom annotations.
- cross.applicationContext - package cross.applicationContext
-
- cross.cache - package cross.cache
-
The cross cache package contains classes for custom caches.
- cross.cache.ehcache - package cross.cache.ehcache
-
- cross.cache.none - package cross.cache.none
-
- cross.cache.softReference - package cross.cache.softReference
-
- cross.commands - package cross.commands
-
- cross.commands.fragments - package cross.commands.fragments
-
- cross.datastructures - package cross.datastructures
-
- cross.datastructures.cache - package cross.datastructures.cache
-
- cross.datastructures.collections - package cross.datastructures.collections
-
- cross.datastructures.combinations - package cross.datastructures.combinations
-
- cross.datastructures.fragments - package cross.datastructures.fragments
-
- cross.datastructures.pipeline - package cross.datastructures.pipeline
-
- cross.datastructures.threads - package cross.datastructures.threads
-
- cross.datastructures.tools - package cross.datastructures.tools
-
- cross.datastructures.tuple - package cross.datastructures.tuple
-
- cross.datastructures.workflow - package cross.datastructures.workflow
-
- cross.event - package cross.event
-
The cross event package contains classes for custom workflow events.
- cross.exception - package cross.exception
-
The cross exceptions package contains classes for custom exceptions.
- cross.io - package cross.io
-
- cross.io.misc - package cross.io.misc
-
- cross.io.xml - package cross.io.xml
-
- cross.math - package cross.math
-
The cross math package contains classes for combinatorics and set operations.
- cross.osgi - package cross.osgi
-
- cross.test - package cross.test
-
- cross.tools - package cross.tools
-
The cross tools package contains classes for common math and string operations.
- cross.vocabulary - package cross.vocabulary
-
- CrossActivator - Class in cross.osgi
-
- CrossActivator() - Constructor for class cross.osgi.CrossActivator
-
- current() - Method in class cross.math.Partition
-
- CvResolver - Class in cross.vocabulary
-
- CvResolver() - Constructor for class cross.vocabulary.CvResolver
-
- geq(int, int, Object) - Static method in class cross.datastructures.tools.EvalTools
-
- get(K) - Method in class cross.cache.ehcache.AutoRetrievalEhcacheDelegate
-
- get(K) - Method in class cross.cache.ehcache.EhcacheDelegate
-
- get(K) - Method in interface cross.cache.ICacheDelegate
-
- get(K) - Method in class cross.cache.none.NoCache
-
- get(K) - Method in class cross.cache.softReference.SoftReferenceCache
-
- get(IVariableFragment) - Method in class cross.datastructures.cache.VariableFragmentArrayCache
-
- get(int) - Method in class cross.datastructures.collections.CachedLazyList
-
- get(int) - Method in class cross.datastructures.collections.CachedReadWriteList
-
- get(int) - Method in interface cross.datastructures.collections.IElementProvider
-
- get(int, int) - Method in interface cross.datastructures.collections.IElementProvider
-
- get(long) - Method in interface cross.datastructures.collections.IElementProvider
-
- get(long, long) - Method in interface cross.datastructures.collections.IElementProvider
-
- get(int) - Method in class cross.datastructures.combinations.CombinationProvider
-
- get(int, int) - Method in class cross.datastructures.combinations.CombinationProvider
-
- get(long) - Method in class cross.datastructures.combinations.CombinationProvider
-
- get(long, long) - Method in class cross.datastructures.combinations.CombinationProvider
-
- get(int) - Method in class cross.datastructures.fragments.CachedList
-
- get(String) - Method in interface cross.datastructures.fragments.Context
-
- get(String) - Method in class cross.datastructures.fragments.Metadata
-
- get(int) - Method in class cross.datastructures.tuple.TupleND
-
- get() - Method in class cross.event.AEvent
-
- get() - Method in interface cross.event.IEvent
-
- getAbsolutePath() - Method in class cross.datastructures.fragments.FileFragment
-
- getAbsolutePath() - Method in interface cross.datastructures.fragments.IFileFragment
-
- getAbsolutePath() - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- getAggregatedVariables(IFileFragment) - Static method in class cross.datastructures.tools.FragmentTools
-
Retrieve all accessible
IVariableFragment instances starting from
the given
IFileFragment and traversing the ancestor tree in
breadth-first order, adding all immediate
IVariableFragment
instances to the list first, before exploring the next ancestor as given
by
source_files.
- getApplicationUserDirectory() - Method in class cross.io.UserDir
-
Returns the user data directory for this application.
- getArray() - Method in class cross.datastructures.fragments.ImmutableVariableFragment
-
- getArray() - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- getArray() - Method in interface cross.datastructures.fragments.IVariableFragment
-
Read the underlying array, cache it, then return.
- getArray() - Method in class cross.datastructures.fragments.VariableFragment
-
- getAssociation() - Method in class cross.datastructures.StatsMap
-
- getAttribute(Attribute) - Method in class cross.datastructures.fragments.FileFragment
-
- getAttribute(String) - Method in class cross.datastructures.fragments.FileFragment
-
- getAttribute(Attribute) - Method in class cross.datastructures.fragments.Fragment
-
- getAttribute(String) - Method in class cross.datastructures.fragments.Fragment
-
- getAttribute(Attribute) - Method in interface cross.datastructures.fragments.IFragment
-
Return a given Attribute.
- getAttribute(String) - Method in interface cross.datastructures.fragments.IFragment
-
Return a given Attribute by name.
- getAttribute(Attribute) - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- getAttribute(String) - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- getAttribute(Attribute) - Method in class cross.datastructures.fragments.ImmutableVariableFragment
-
- getAttribute(String) - Method in class cross.datastructures.fragments.ImmutableVariableFragment
-
- getAttribute(Attribute) - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- getAttribute(String) - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- getAttribute(Attribute) - Method in class cross.datastructures.fragments.VariableFragment
-
- getAttribute(String) - Method in class cross.datastructures.fragments.VariableFragment
-
- getAttributes() - Method in class cross.datastructures.fragments.FileFragment
-
- getAttributes() - Method in class cross.datastructures.fragments.Fragment
-
- getAttributes() - Method in interface cross.datastructures.fragments.IFragment
-
Return attributes of Fragment.
- getAttributes() - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- getAttributes() - Method in class cross.datastructures.fragments.ImmutableVariableFragment
-
- getAttributes() - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- getAttributes() - Method in class cross.datastructures.fragments.VariableFragment
-
- getAvailableCommands() - Method in class cross.io.AFragmentCommandServiceLoader
-
Returns the available implementations of IFragmentCommand.
- getAvailableCommands() - Method in class cross.io.DataSourceServiceLoader
-
- getAvailableUserCommands(ObjectFactory) - Method in class cross.io.AFragmentCommandServiceLoader
-
- getCache() - Method in class cross.cache.ehcache.AutoRetrievalEhcacheDelegate
-
- getCache() - Method in class cross.cache.ehcache.EhcacheDelegate
-
- getCache(String) - Method in class cross.cache.none.NoCacheManager
-
- getCache(String) - Method in class cross.cache.softReference.SoftReferenceCacheManager
-
- getCache() - Method in class cross.datastructures.cache.VariableFragmentArrayCache
-
- getCache() - Method in class cross.datastructures.fragments.FileFragment
-
- getCache() - Method in interface cross.datastructures.fragments.IFileFragment
-
Return a Cache for variable fragment array data for this fragment.
- getCache() - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- getCacheFor(String) - Static method in class cross.cache.CacheFactory
-
- getCacheSize() - Method in class cross.datastructures.collections.CachedLazyList
-
- getCacheSize() - Method in class cross.datastructures.fragments.CachedList
-
- getCacheType() - Method in class cross.cache.ehcache.AutoRetrievalEhcacheDelegate
-
- getCacheType() - Method in class cross.cache.ehcache.EhcacheDelegate
-
- getCacheType() - Method in interface cross.cache.ICacheDelegate
-
- getCacheType() - Method in class cross.cache.none.NoCache
-
- getCacheType() - Method in class cross.cache.softReference.SoftReferenceCache
-
- getCacheType() - Method in class cross.datastructures.cache.VariableFragmentArrayCache
-
- getChild(String) - Method in class cross.datastructures.fragments.FileFragment
-
- getChild(String, boolean) - Method in class cross.datastructures.fragments.FileFragment
-
- getChild(String) - Method in interface cross.datastructures.fragments.IFileFragment
-
Returns the child with name varname.
- getChild(String, boolean) - Method in interface cross.datastructures.fragments.IFileFragment
-
Returns the child with name varname.
- getChild(String) - Method in interface cross.datastructures.fragments.IGroupFragment
-
Return the child given by the argument.
- getChild(String) - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- getChild(String, boolean) - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- getChild(String) - Method in class cross.datastructures.fragments.NamedGroupFragment
-
- getChunkIterator(int) - Method in class cross.datastructures.fragments.ImmutableVariableFragment
-
- getChunkIterator(int) - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- getChunkIterator(int) - Method in interface cross.datastructures.fragments.IVariableFragment
-
- getChunkIterator(int) - Method in class cross.datastructures.fragments.VariableFragment
-
- getClosestParent(IFileFragment, String) - Method in class cross.datastructures.fragments.BfsVariableSearcher
-
Returns a collection of
IFileFragment instances that have the
given variableName as their child.
- getClosestParent(IFileFragment, String, double) - Method in class cross.datastructures.fragments.BfsVariableSearcher
-
Returns a collection of
IFileFragment instances that have the
given variableName as their child.
- getCommands() - Method in interface cross.datastructures.pipeline.ICommandSequence
-
- getCommandSequence() - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- getCommandSequence() - Method in interface cross.datastructures.workflow.IWorkflow
-
Return the active ICommandSequence instance.
- getConfig() - Method in class cross.test.SetupLogging
-
- getConfiguration() - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- getConfiguration() - Method in interface cross.datastructures.workflow.IWorkflow
-
Returns the currently active configuration for this workflow.
- getConfiguration() - Method in class cross.Factory
-
- getCurrentStep() - Method in class cross.datastructures.workflow.DefaultWorkflowProgressResult
-
- getCurrentStep() - Method in interface cross.datastructures.workflow.IWorkflowProgressResult
-
Returns the index of the currently active step.
- getCurrentWorkflowInstance() - Method in interface cross.datastructures.workflow.IWorkflowFactory
-
- getCvProviders() - Method in class cross.vocabulary.CvResolver
-
- getCvProviders() - Method in interface cross.vocabulary.ICvResolver
-
Returns the list of available providers.
- getCvResolver() - Method in interface cross.commands.fragments.IFragmentCommand
-
- getDataSourceFactory() - Method in class cross.Factory
-
- getDataSourceFor(IFileFragment) - Method in class cross.io.DataSourceFactory
-
Returns a compatible IDataSource for given IFileFragment.
- getDataSourceFor(IFileFragment) - Method in interface cross.io.IDataSourceFactory
-
Returns a compatible IDataSource for given IFileFragment.
- getDataSources() - Method in class cross.io.DataSourceFactory
-
- getDataSources() - Method in interface cross.io.IDataSourceFactory
-
- getDataType() - Method in class cross.datastructures.fragments.ImmutableVariableFragment
-
- getDataType() - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- getDataType() - Method in interface cross.datastructures.fragments.IVariableFragment
-
Return the DataType assigned to the elements contained in the underlying
array.
- getDataType() - Method in class cross.datastructures.fragments.VariableFragment
-
- getDeepestAncestor(IFileFragment) - Static method in class cross.datastructures.tools.FragmentTools
-
Starting from a given IFileFragment, searches the linked source files, if
any until the deepest such source file is found.
- getDefault() - Static method in class cross.cache.CacheFactory
-
- getDefault() - Static method in class cross.datastructures.fragments.Fragments
-
- getDefaultDimensions(Array) - Static method in class cross.datastructures.tools.ArrayTools
-
Return default dimensions for input array.
- getDefaultDimensionsForIndexedArray(List<Array>) - Static method in class cross.datastructures.tools.ArrayTools
-
- getDefaultDimnames(Array) - Static method in class cross.datastructures.tools.ArrayTools
-
Get names of default dimensions for input array.
- getDefaultDirs(File, Date) - Static method in class cross.datastructures.tools.FileTools
-
- getDefaultDirs(Date) - Static method in class cross.datastructures.tools.FileTools
-
- getDefaultValueFor(Class<?>, String) - Static method in class cross.annotations.AnnotationInspector
-
Returns the default value for field with given name on class, based
on Configurable.value.
- getDefaultVars() - Static method in class cross.datastructures.tools.FragmentTools
-
Returns a list of variable names as defined in
default.vars.
- getDefaultWorkflowInstance(Date, ICommandSequence) - Method in interface cross.datastructures.workflow.IWorkflowFactory
-
Create a new IWorkflow instance with default name workflow.
- getDefaultWorkflowInstance(Date, String, ICommandSequence) - Method in interface cross.datastructures.workflow.IWorkflowFactory
-
Create a new DefaultWorkflow instance with custom name, if it does not
exist already.
- getDescription() - Method in class cross.commands.fragments.AFragmentCommand
-
- getDescriptionFor(Class<?>, String) - Static method in class cross.annotations.AnnotationInspector
-
getDescriptionFor.
- getDimensions() - Method in class cross.datastructures.fragments.FileFragment
-
The registered dimensions of this FileFragment as an unmodifiable Set.
- getDimensions() - Method in interface cross.datastructures.fragments.IFileFragment
-
The registered dimensions of this FileFragment.
- getDimensions() - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
The registered dimensions of this FileFragment as an unmodifiable Set.
- getDimensions() - Method in class cross.datastructures.fragments.ImmutableVariableFragment
-
- getDimensions() - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- getDimensions() - Method in interface cross.datastructures.fragments.IVariableFragment
-
Return the Dimensions of this VariableFragment.
- getDimensions() - Method in class cross.datastructures.fragments.VariableFragment
-
- getDirectoryForService(Class<?>, Class<?>) - Method in class cross.io.UserDir
-
Returns a directory specific to a service interface definition and its
implementation.
- getDirname(String) - Static method in class cross.datastructures.tools.FileTools
-
- getDocument() - Method in class cross.applicationContext.ReflectionApplicationContextGenerator
-
Gets the generated XML document.
- getEventName() - Method in class cross.event.AEvent
-
- getEventName() - Method in interface cross.event.IEvent
-
- getFile(IFileFragment) - Static method in class cross.datastructures.tools.FileTools
-
- getFile() - Method in class cross.datastructures.workflow.DefaultWorkflowResult
-
- getFile() - Method in interface cross.datastructures.workflow.IWorkflowFileResult
-
- getFileExtension(String) - Static method in class cross.tools.StringTools
-
Returns the suffix of a file or s if no dot '.' is contained
in s.
- getFileFilter() - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- getFilename(URI) - Static method in class cross.datastructures.tools.FileTools
-
- getFilename(String) - Static method in class cross.datastructures.tools.FileTools
-
- getFileTypesToKeep() - Method in class cross.io.misc.DefaultConfigurableFileFilter
-
- getFirst() - Method in class cross.datastructures.tuple.Tuple2D
-
- getID() - Method in class cross.datastructures.fragments.FileFragment
-
- getID() - Method in interface cross.datastructures.fragments.IFileFragment
-
The unique ID (between runs) of this FileFragment.
- getID() - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- getImmediateChildren() - Method in class cross.datastructures.fragments.FileFragment
-
- getImmediateChildren() - Method in interface cross.datastructures.fragments.IFileFragment
-
Returns the immediate children of this fileFragment.
- getImmediateChildren() - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- getIndex() - Method in class cross.datastructures.fragments.ImmutableVariableFragment
-
- getIndex() - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- getIndex() - Method in interface cross.datastructures.fragments.IVariableFragment
-
Return the VariableFragment used to access the data of this
VariableFragment by index, can be null, if no index is assigned or
needed.
- getIndex() - Method in class cross.datastructures.fragments.VariableFragment
-
- getIndexed(IFileFragment, String, String, int) - Static method in class cross.datastructures.tools.FragmentTools
-
- getIndexed(IVariableFragment, int) - Static method in class cross.datastructures.tools.FragmentTools
-
- getIndexedArray() - Method in class cross.datastructures.fragments.ImmutableVariableFragment
-
- getIndexedArray() - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- getIndexedArray() - Method in interface cross.datastructures.fragments.IVariableFragment
-
Read an Array row by row in Compressed Row Storage by using indices
stored in a second array as offsets.
- getIndexedArray() - Method in class cross.datastructures.fragments.VariableFragment
-
Returns an empty list if no index variable has been set.
- getInitialFiles() - Method in interface cross.io.IInputDataFactory
-
- getInitialFiles() - Method in class cross.io.InputDataFactory
-
- getInput() - Method in interface cross.datastructures.pipeline.ICommandSequence
-
Return input to this ICommandSequence.
- getInputDataFactory() - Method in class cross.Factory
-
- getInputFiles(String[]) - Method in class cross.io.InputDataFactory
-
- getInstance() - Static method in class cross.cache.none.NoCacheManager
-
- getInstance() - Static method in class cross.cache.softReference.SoftReferenceCacheManager
-
- getInstance() - Static method in class cross.Factory
-
- getInstance() - Static method in class cross.io.InputDataFactory
-
- getIterator() - Method in class cross.datastructures.tuple.TupleND
-
- getIwres() - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- getKPartiteChoices(List<Object[]>) - Static method in class cross.datastructures.combinations.ChoiceFactory
-
Returns a lazily instantiated list (allows for an almost arbitrary number
of combinations< Integer.maxValue()) of all unique object
combinations, s.t. for (a,b)=(b,a) only (a,b) is returned.
- getLabel() - Method in class cross.datastructures.StatsMap
-
- getLHSFile(IFileFragment) - Static method in class cross.datastructures.tools.FragmentTools
-
Returns the left hand side of a pairwise alignment.
- getLinearInterpolatedY(double, double, double, double, double) - Static method in class cross.tools.MathTools
-
- getList(IElementProvider<T>) - Static method in class cross.datastructures.collections.CachedLazyList
-
- getList(IElementProvider<T>, int, int) - Static method in class cross.datastructures.collections.CachedLazyList
-
- getList(IVariableFragment) - Static method in class cross.datastructures.fragments.CachedList
-
- getList(IVariableFragment, int, int) - Static method in class cross.datastructures.fragments.CachedList
-
- getListIterator() - Method in class cross.datastructures.tuple.TupleND
-
- getListIterator(int) - Method in class cross.datastructures.tuple.TupleND
-
- getName() - Method in class cross.cache.ehcache.AutoRetrievalEhcacheDelegate
-
- getName() - Method in class cross.cache.ehcache.EhcacheDelegate
-
- getName() - Method in interface cross.cache.ICacheDelegate
-
- getName() - Method in class cross.cache.none.NoCache
-
- getName() - Method in class cross.cache.softReference.SoftReferenceCache
-
- getName() - Method in class cross.datastructures.cache.VariableFragmentArrayCache
-
- getName() - Method in class cross.datastructures.fragments.FileFragment
-
- getName() - Method in interface cross.datastructures.fragments.IFileFragment
-
Return the name of this FileFragment, does not include directory or other
prefixed information.
- getName() - Method in interface cross.datastructures.fragments.IGroupFragment
-
- getName() - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- getName() - Method in class cross.datastructures.fragments.ImmutableVariableFragment
-
- getName() - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- getName() - Method in interface cross.datastructures.fragments.IVariableFragment
-
Return the name of this VariableFragment.
- getName() - Method in class cross.datastructures.fragments.NamedGroupFragment
-
- getName() - Method in class cross.datastructures.fragments.VariableFragment
-
- getName() - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- getName() - Method in interface cross.datastructures.workflow.IWorkflow
-
Returns the name of this IWorkflow.
- getName() - Method in interface cross.vocabulary.IControlledVocabularyProvider
-
The (lowercase) name of the this provider's ontology.
- getNamedObject(String, Class<T>) - Method in interface cross.IObjectFactory
-
- getNamedObject(String, Class<T>) - Method in class cross.ObjectFactory
-
- getNameFor(Class<?>, String) - Static method in class cross.annotations.AnnotationInspector
-
getNameFor.
- getNameFor(Class<?>, Field) - Static method in class cross.annotations.AnnotationInspector
-
getNameFor.
- getNamespace() - Method in interface cross.vocabulary.IControlledVocabularyProvider
-
The namespace prefix of this ontology, e.g. maltcms in maltcms.scan_index.
- getNewWorkflowInstance(Date, String, ICommandSequence, Configuration) - Method in interface cross.datastructures.workflow.IWorkflowFactory
-
- getNumberOfPairs() - Method in class cross.datastructures.tuple.TupleND
-
- getNumberOfSteps() - Method in class cross.datastructures.workflow.DefaultWorkflowProgressResult
-
- getNumberOfSteps() - Method in interface cross.datastructures.workflow.IWorkflowProgressResult
-
Returns the number of defined steps in IWorkflowElement.
- getObject() - Method in interface cross.datastructures.workflow.IWorkflowObjectResult
-
- getObjectFactory() - Method in class cross.Factory
-
- getObjectsOfType(Class<T>) - Method in interface cross.IObjectFactory
-
- getObjectsOfType(Class<T>) - Method in class cross.ObjectFactory
-
- getOptionalRequiredVariables(Class<?>) - Static method in class cross.annotations.AnnotationInspector
-
- getOptionalRequiredVariables(Object) - Static method in class cross.annotations.AnnotationInspector
-
- getOutputDirectory(Object) - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- getOutputDirectory() - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- getOutputDirectory(Object) - Method in interface cross.datastructures.workflow.IWorkflow
-
Returns the output directory for the given object.
- getOutputDirectory() - Method in interface cross.datastructures.workflow.IWorkflow
-
- getOverallProgress() - Method in class cross.datastructures.workflow.DefaultWorkflowProgressResult
-
- getOverallProgress() - Method in interface cross.datastructures.workflow.IWorkflowProgressResult
-
Returns the overall progress of an IWorkflowElement, range is from 0 (no
progress yet) via 1 to 100 (complete)
- getPairs() - Method in class cross.datastructures.tuple.TupleND
-
- getPairsWithFirstElement() - Method in class cross.datastructures.tuple.TupleND
-
- getPairsWithLastElement() - Method in class cross.datastructures.tuple.TupleND
-
- getParent() - Method in class cross.datastructures.fragments.FileFragment
-
- getParent() - Method in interface cross.datastructures.fragments.IFileFragment
-
- getParent() - Method in interface cross.datastructures.fragments.IGroupFragment
-
- getParent() - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- getParent() - Method in class cross.datastructures.fragments.ImmutableVariableFragment
-
- getParent() - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- getParent() - Method in interface cross.datastructures.fragments.IVariableFragment
-
Returns this Fragment's parent FileFragment.
- getParent() - Method in class cross.datastructures.fragments.NamedGroupFragment
-
- getParent() - Method in class cross.datastructures.fragments.VariableFragment
-
- getPrefixesToMatch() - Method in class cross.io.misc.DefaultConfigurableFileFilter
-
- getProvidedVariables(Class<?>) - Static method in class cross.annotations.AnnotationInspector
-
- getProvidedVariables(Object) - Static method in class cross.annotations.AnnotationInspector
-
- getQualifiedName(Vars) - Method in interface cross.datastructures.fragments.Context
-
- getRange() - Method in class cross.datastructures.fragments.ImmutableVariableFragment
-
- getRange() - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- getRange() - Method in interface cross.datastructures.fragments.IVariableFragment
-
Returns the ranges set for this VariableFragment.
- getRange() - Method in class cross.datastructures.fragments.VariableFragment
-
- getRelativeFile(IFileFragment, IFileFragment) - Static method in class cross.datastructures.tools.FileTools
-
- getRelativeFile(File, File) - Static method in class cross.datastructures.tools.FileTools
-
Returns the path of one File relative to another.
- getRelativeUri(URI, URI) - Static method in class cross.datastructures.tools.FileTools
-
- getRequiredConfigKeys(Class<?>) - Static method in class cross.annotations.AnnotationInspector
-
Returns configuration key names for class fields that are annotated with
Configurable.
- getRequiredConfigKeys(Object) - Static method in class cross.annotations.AnnotationInspector
-
Returns configuration key names for object's class fields that are annotated with
Configurable.
- getRequiredVariables(Class<?>) - Static method in class cross.annotations.AnnotationInspector
-
Returns mandatory, required variable names from class annotated with
RequiresVariables.
- getRequiredVariables(Object) - Static method in class cross.annotations.AnnotationInspector
-
Returns mandatory, required variable names from object's class annotated with
RequiresVariables.
- getResources() - Method in class cross.datastructures.workflow.DefaultWorkflowResult
-
- getResources() - Method in interface cross.datastructures.workflow.IWorkflowFileResult
-
- getResources() - Method in interface cross.datastructures.workflow.IWorkflowObjectResult
-
- getResults() - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- getResults() - Method in interface cross.datastructures.workflow.IWorkflow
-
Returns an iterator over all currently available results.
- getResultsFor(IFileFragment) - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- getResultsFor(IWorkflowElement) - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- getResultsFor(IWorkflowElement, IFileFragment) - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- getResultsFor(IFileFragment) - Method in interface cross.datastructures.workflow.IWorkflow
-
Returns the results for a specific IFileFragment.
- getResultsFor(IWorkflowElement) - Method in interface cross.datastructures.workflow.IWorkflow
-
Returns the results created by a specific IWorkflowElement.
- getResultsFor(IWorkflowElement, IFileFragment) - Method in interface cross.datastructures.workflow.IWorkflow
-
Returns the results created by a specific IWorkflowElement for a given
IFileFragment.
- getResultsOfType(String) - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- getResultsOfType(IWorkflowElement, String) - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- getResultsOfType(IWorkflowElement, Class<? extends T>) - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- getResultsOfType(String) - Method in interface cross.datastructures.workflow.IWorkflow
-
Returns the list of results matching a given file extension pattern.
- getResultsOfType(IWorkflowElement, String) - Method in interface cross.datastructures.workflow.IWorkflow
-
Returns the list of results matching a given file extension pattern
created by a given IWorkflowElement implementation.
- getResultsOfType(IWorkflowElement, Class<? extends T>) - Method in interface cross.datastructures.workflow.IWorkflow
-
Returns the list of results matching a given class created by a given
IWorkflowElement implementation.
- getRHSFile(IFileFragment) - Static method in class cross.datastructures.tools.FragmentTools
-
Returns the right hand side of a pairwise alignment.
- getSecond() - Method in class cross.datastructures.tuple.Tuple2D
-
- getSerializable(int) - Method in class cross.datastructures.collections.CachedReadWriteList
-
- getServiceProviders(String) - Method in class cross.applicationContext.ReflectionApplicationContextGenerator
-
- getServicesDirectory() - Method in class cross.io.UserDir
-
Returns the directory named services below this UserDir's
basedir.
- getShapeForIndexedArrays(List<Array>) - Static method in class cross.datastructures.tools.ArrayTools
-
- getSize() - Method in class cross.datastructures.fragments.FileFragment
-
- getSize() - Method in interface cross.datastructures.fragments.IFileFragment
-
Return the number of children of this FileFragment.
- getSize() - Method in interface cross.datastructures.fragments.IGroupFragment
-
- getSize() - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- getSize() - Method in class cross.datastructures.fragments.NamedGroupFragment
-
- getSize() - Method in class cross.datastructures.tuple.TupleND
-
- getSizeForFlattenedArrays(List<Array>) - Static method in class cross.datastructures.tools.ArrayTools
-
Compute total number of elements for all arrays in list.
- getSource() - Method in class cross.event.AEvent
-
- getSource() - Method in interface cross.event.IEvent
-
- getSourceFiles() - Method in class cross.datastructures.fragments.FileFragment
-
Use this method with caution!
- getSourceFiles() - Method in interface cross.datastructures.fragments.IFileFragment
-
Return all source FileFragments.
- getSourceFiles() - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- getSourceFiles(IFileFragment) - Static method in class cross.datastructures.tools.FragmentTools
-
- getStartupDate() - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- getStartupDate() - Method in interface cross.datastructures.workflow.IWorkflow
-
Return the startup data of this IWorkflow.
- getStats() - Method in class cross.datastructures.fragments.FileFragment
-
- getStats() - Method in class cross.datastructures.fragments.Fragment
-
- getStats() - Method in interface cross.datastructures.fragments.IFragment
-
Retrieve statistics from a Fragment.
- getStats() - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- getStats() - Method in class cross.datastructures.fragments.ImmutableVariableFragment
-
- getStats() - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- getStats() - Method in class cross.datastructures.fragments.VariableFragment
-
- getStepNames() - Method in class cross.datastructures.workflow.DefaultWorkflowProgressResult
-
- getStepNames() - Method in interface cross.datastructures.workflow.IWorkflowProgressResult
-
Return string names of each step.
- getStringArray(IFileFragment, String) - Static method in class cross.datastructures.tools.FragmentTools
-
Returns a collection of strings from a char array.
- getStringsFromArray(Array) - Static method in class cross.datastructures.tools.ArrayTools
-
- getStringVar(IFileFragment, String) - Static method in class cross.datastructures.tools.FragmentTools
-
Deprecated.
- getSubdirectory(File, String) - Method in class cross.io.UserDir
-
Returns a direct subdirectory of name
name below
basedir.
- getSubdirOfAppUserDir(String) - Method in class cross.io.UserDir
-
Returns the direct subdirectory of name
name below this UserDir's basedir.
- getSuffixesToMatch() - Method in class cross.io.misc.DefaultConfigurableFileFilter
-
- getSupportedFormats() - Method in class cross.io.DataSourceFactory
-
Returns a list of supported file extensions
- getSupportedFormats() - Method in interface cross.io.IDataSourceFactory
-
Returns a list of supported file extensions
- getTypeFor(Class<?>, String) - Static method in class cross.annotations.AnnotationInspector
-
getTypeFor.
- getUri() - Method in class cross.datastructures.fragments.FileFragment
-
Get the uniform resource identifier for this FileFragment.
- getUri() - Method in interface cross.datastructures.fragments.IFileFragment
-
Return the URI of this FileFragment.
- getUri() - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- getVariable(IFileFragment, String, String) - Static method in class cross.datastructures.tools.FragmentTools
-
Deprecated.
- getVariableFragmentId(IVariableFragment) - Method in class cross.datastructures.cache.VariableFragmentArrayCache
-
- getVariablesFor(IFileFragment) - Static method in class cross.datastructures.tools.FragmentTools
-
Returns a list of the variables provided by the
IDataSource for
the given file fragment.
- getVariablesSharingAllDimensions(List<IVariableFragment>, String...) - Static method in class cross.datastructures.tools.FragmentTools
-
Returns those variables, which share all of the dimensions given
in the second argument.
- getVariablesSharingAnyDimensions(List<IVariableFragment>, String...) - Static method in class cross.datastructures.tools.FragmentTools
-
Returns those variables, which share at least one of the
dimensions given in the second argument.
- getVarname() - Method in class cross.datastructures.fragments.ImmutableVariableFragment
-
- getVarname() - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- getVarname() - Method in interface cross.datastructures.fragments.IVariableFragment
-
Deprecated.
- getVarname() - Method in class cross.datastructures.fragments.VariableFragment
-
- getVersion() - Method in interface cross.vocabulary.IControlledVocabularyProvider
-
The version of the ontology used.
- getWhen() - Method in class cross.event.AEvent
-
- getWhen() - Method in interface cross.event.IEvent
-
- getWorkflow() - Method in interface cross.datastructures.pipeline.ICommandSequence
-
- getWorkflow() - Method in interface cross.datastructures.workflow.IWorkflowElement
-
- getWorkflowElement() - Method in class cross.datastructures.workflow.DefaultWorkflowProgressResult
-
- getWorkflowElement() - Method in class cross.datastructures.workflow.DefaultWorkflowResult
-
- getWorkflowElement() - Method in interface cross.datastructures.workflow.IWorkflowResult
-
- getWorkflowPostProcessors() - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- getWorkflowPostProcessors() - Method in interface cross.datastructures.workflow.IWorkflow
-
- getWorkflowResults() - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- getWorkflowSlot() - Method in class cross.datastructures.workflow.DefaultWorkflowProgressResult
-
- getWorkflowSlot() - Method in class cross.datastructures.workflow.DefaultWorkflowResult
-
- getWorkflowSlot() - Method in interface cross.datastructures.workflow.IWorkflowElement
-
- getWorkflowSlot() - Method in interface cross.datastructures.workflow.IWorkflowResult
-
- getWorkflowXmlFile() - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- getWorkflowXmlFile() - Method in interface cross.datastructures.workflow.IWorkflow
-
- getXslPathPrefix() - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- glue(List<Array>) - Static method in class cross.datastructures.tools.ArrayTools
-
Concatenates one-dimensional arrays in list into one contiguous array, in
iteration order.
- gt(int, int, Object) - Static method in class cross.datastructures.tools.EvalTools
-
- gunzip(File, File) - Static method in class cross.io.misc.BinaryFileBase64Wrapper
-
Applies gunzip on in file and writes decompressed result to file out.
- GZIP - Static variable in class cross.io.misc.Base64
-
Specify that data should be gzip-compressed.
- gzip(File, File) - Static method in class cross.io.misc.BinaryFileBase64Wrapper
-
- IArrayChunkIterator - Interface in cross.io.misc
-
- ICacheDelegate<K,V> - Interface in cross.cache
-
Interface for facades in front of particular cache implementations.
- ICacheElementProvider<K,V> - Interface in cross.cache
-
Interface for deferred retrieval/creation of values associated
to keys in a custom cache implementation.
- ICommand<IN,OUT> - Interface in cross.commands
-
Interface for objects which represent a command acting on an object of type
IN and returning objects of type
OUT.
- ICommandSequence - Interface in cross.datastructures.pipeline
-
Abstract sequence of commands on FileFragment objects.
- ICommandSequenceValidator - Interface in cross.datastructures.pipeline
-
Interface definition for command sequence validation.
- IConfigurable - Interface in cross
-
Interface for objects which are configurable.
- IControlledVocabularyProvider - Interface in cross.vocabulary
-
Maps an external variable name to an canonical, internal common name.
- ICvResolver - Interface in cross.vocabulary
-
Resolves a given namespace prefixed variable against the available
providers.
- id - Variable in class cross.applicationContext.ReflectionApplicationContextGenerator.BeanDescriptor
-
- IDataSource - Interface in cross.io
-
Interface describing access to a IDataSource, which could be either a file on
a local system, a network resource or a database connection.
- IDataSourceFactory - Interface in cross.io
-
- IElementProvider<T> - Interface in cross.datastructures.collections
-
- IEvent<V> - Interface in cross.event
-
Event of Type V, allows access to EventSource and time of Event.
- IEventSource<V> - Interface in cross.event
-
Classes representing concrete EventSources must implement this interface.
- IFileFragment - Interface in cross.datastructures.fragments
-
- IFileFragmentFactory - Interface in cross.datastructures.fragments
-
Interface for factories creating IFileFragments.
- IFileFragmentProvider - Interface in cross.io
-
- IFragment - Interface in cross.datastructures.fragments
-
- IFragmentCommand - Interface in cross.commands.fragments
-
Base interface for commands that can be part of a processing pipeline.
- IGroupFragment - Interface in cross.datastructures.fragments
-
Abstraction bundling a number of VariableFragments into one logical group.
- IInputDataFactory - Interface in cross.io
-
Interface for providers of input data.
- IIterableFragment - Interface in cross.datastructures.fragments
-
- IListener<V extends IEvent<?>> - Interface in cross.event
-
Listener for IEvents of type V
- immutable(File...) - Static method in class cross.datastructures.tools.FragmentTools
-
- immutable(Collection<File>) - Static method in class cross.datastructures.tools.FragmentTools
-
- ImmutableFileFragment - Class in cross.datastructures.fragments
-
Immutable Variant of a FileFragment.
- ImmutableFileFragment(URI) - Constructor for class cross.datastructures.fragments.ImmutableFileFragment
-
- ImmutableFileFragment(File) - Constructor for class cross.datastructures.fragments.ImmutableFileFragment
-
- ImmutableFileFragment(File, String) - Constructor for class cross.datastructures.fragments.ImmutableFileFragment
-
- ImmutableFileFragment(IFileFragment) - Constructor for class cross.datastructures.fragments.ImmutableFileFragment
-
- ImmutableVariableFragment - Class in cross.datastructures.fragments
-
Immutable Variant of a VariableFragment.
- ImmutableVariableFragment(IVariableFragment) - Constructor for class cross.datastructures.fragments.ImmutableVariableFragment
-
- ImmutableVariableFragment2 - Class in cross.datastructures.fragments
-
A class representing immutable Variables.
- ImmutableVariableFragment2(IFileFragment, String) - Constructor for class cross.datastructures.fragments.ImmutableVariableFragment2
-
- ImmutableVariableFragment2(IFileFragment, String, IVariableFragment) - Constructor for class cross.datastructures.fragments.ImmutableVariableFragment2
-
- indexOf(Object) - Method in class cross.datastructures.collections.CachedLazyList
-
- indexOf(Object) - Method in class cross.datastructures.collections.CachedReadWriteList
-
- indexOf(Object) - Method in class cross.datastructures.fragments.CachedList
-
- initProgress(int) - Method in class cross.commands.fragments.AFragmentCommand
-
- initSubCommand(AFragmentCommand) - Method in class cross.commands.fragments.AFragmentCommand
-
- InputDataFactory - Class in cross.io
-
- InputDataFactory() - Constructor for class cross.io.InputDataFactory
-
- inRangeD(double, double, double, Object) - Static method in class cross.datastructures.tools.EvalTools
-
- inRangeI(int, int, int, Object) - Static method in class cross.datastructures.tools.EvalTools
-
- Installer - Class in net.sf.maltcms.cross.nbm
-
- Installer() - Constructor for class net.sf.maltcms.cross.nbm.Installer
-
- instantiate(Class<T>) - Method in interface cross.IObjectFactory
-
Create a new Instance of c, configure automatically, if c is an instance
of IConfigurable
- instantiate(String, Class<T>) - Method in interface cross.IObjectFactory
-
Instantiate a class, given by a classname and the class of Type T.
- instantiate(String, Class<T>, String) - Method in interface cross.IObjectFactory
-
Instantiate a class, given a classname and the class of Type t and
configure with configuration from configurationFile.
- instantiate(String, Class<T>, Configuration) - Method in interface cross.IObjectFactory
-
Instantiate a class, given a classname and the class of Type t and
configure with configuration from config.
- instantiate(Class<T>) - Method in class cross.ObjectFactory
-
Create a new Instance of c, configure automatically, if c is an instance
of IConfigurable
- instantiate(String, Class<T>) - Method in class cross.ObjectFactory
-
Instantiate a class, given by a classname and the class of Type T.
- instantiate(String, Class<T>, String) - Method in class cross.ObjectFactory
-
Instantiate a class, given a classname and the class of Type t and
configure with configuration from configurationFile.
- instantiate(String, Class<T>, Configuration) - Method in class cross.ObjectFactory
-
Instantiate a class, given a classname and the class of Type t and
configure with configuration from config.
- IntegrationTest - Interface in cross.test
-
Marker interface to distinguish integration tests from plain tests.
- intersection(Set<T>, Set<T>) - Static method in class cross.math.SetOperations
-
- invoke(Callable<T>) - Method in interface cross.datastructures.threads.IRemoteCallable
-
- invokeAll(Collection<? extends Callable<T>>) - Method in class cross.datastructures.threads.ExecutorsManager
-
- invokeAll(Collection<? extends Callable<T>>, long, TimeUnit) - Method in class cross.datastructures.threads.ExecutorsManager
-
- invokeAny(Collection<? extends Callable<T>>) - Method in class cross.datastructures.threads.ExecutorsManager
-
- invokeAny(Collection<? extends Callable<T>>, long, TimeUnit) - Method in class cross.datastructures.threads.ExecutorsManager
-
- IObjectFactory - Interface in cross
-
- IRemoteCallable - Interface in cross.datastructures.threads
-
- isCheckCommandDependencies() - Method in interface cross.datastructures.pipeline.ICommandSequence
-
- isChild(IFileFragment, IFileFragment) - Static method in class cross.datastructures.tools.FragmentTools
-
Returns true if
childFile is a direct child of
parentFile.
- isDeleteOnExit() - Method in class cross.io.misc.WorkflowZipper
-
- isEmpty() - Method in class cross.datastructures.collections.CachedLazyList
-
- isEmpty() - Method in class cross.datastructures.collections.CachedReadWriteList
-
- isEmpty() - Method in class cross.datastructures.fragments.CachedList
-
- isEmpty() - Method in class cross.datastructures.tuple.TupleND
-
- ISerializationProxy<T> - Interface in cross.datastructures.cache
-
- isExecuteLocal() - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- isExecuteLocal() - Method in interface cross.datastructures.workflow.IWorkflow
-
- isModified() - Method in class cross.datastructures.fragments.FileFragment
-
- isModified() - Method in interface cross.datastructures.fragments.IFileFragment
-
- isModified() - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- isModified() - Method in class cross.datastructures.fragments.ImmutableVariableFragment
-
- isModified() - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- isModified() - Method in interface cross.datastructures.fragments.IVariableFragment
-
Return, whether this IVariable fragment has been modified since the last
save.
- isModified() - Method in class cross.datastructures.fragments.VariableFragment
-
- isNull(Object, Object) - Static method in class cross.datastructures.tools.EvalTools
-
- isNumber(String) - Static method in class cross.datastructures.tools.EvalTools
-
- isOperator(String) - Static method in class cross.datastructures.tools.EvalTools
-
- isPrefetchOnMiss() - Method in class cross.datastructures.collections.CachedLazyList
-
- isPrefetchOnMiss() - Method in class cross.datastructures.fragments.CachedList
-
- isRootFile(IFileFragment) - Static method in class cross.datastructures.tools.FragmentTools
-
Returns true if the given parent file has no further source files.
- isShutdown() - Method in class cross.datastructures.threads.ExecutorsManager
-
- isTerminated() - Method in class cross.datastructures.threads.ExecutorsManager
-
- isThrowExceptionOnUnsavedModification() - Method in interface cross.datastructures.pipeline.ICommandSequence
-
- isUseCachedList() - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- isUseCachedList() - Method in class cross.datastructures.fragments.VariableFragment
-
- isValid(ICommandSequence) - Method in interface cross.datastructures.pipeline.ICommandSequenceValidator
-
Determines, whether a given commandSequence is valid or not.
- isVar(String, Context) - Static method in class cross.datastructures.tools.EvalTools
-
- isVar(String, HashMap<String, Double>) - Static method in class cross.datastructures.tools.EvalTools
-
- isZipWorkflow() - Method in class cross.io.misc.WorkflowZipper
-
- iterator() - Method in class cross.datastructures.collections.CachedLazyList
-
- iterator() - Method in class cross.datastructures.collections.CachedReadWriteList
-
- iterator() - Method in class cross.datastructures.fragments.CachedList
-
- iterator() - Method in class cross.datastructures.fragments.FileFragment
-
- iterator() - Method in interface cross.datastructures.fragments.IFileFragment
-
Creates an iterator over all children of this FileFragment by the time of
creation of the iterator.
- iterator() - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- iterator() - Method in class cross.datastructures.fragments.Metadata
-
- iterator() - Method in class cross.datastructures.fragments.NamedGroupFragment
-
- iterator() - Method in class cross.datastructures.tuple.TupleND
-
- ITypeFactory<T> - Interface in cross.datastructures.combinations
-
- IVariableFragment - Interface in cross.datastructures.fragments
-
- IWorkflow - Interface in cross.datastructures.workflow
-
Workflow models a sequence of produced IWorkflowResults, which usually are
files created by
IWorkflowElement
objects.
- IWorkflowElement - Interface in cross.datastructures.workflow
-
A Workflow element.
- IWorkflowFactory - Interface in cross.datastructures.workflow
-
- IWorkflowFileResult - Interface in cross.datastructures.workflow
-
- IWorkflowObjectResult<T> - Interface in cross.datastructures.workflow
-
- IWorkflowPostProcessor - Interface in cross.datastructures.workflow
-
Interface for post processors of a workflow after execution has finished.
- IWorkflowProgressResult - Interface in cross.datastructures.workflow
-
- IWorkflowResult - Interface in cross.datastructures.workflow
-
A result of a
IWorkflowElement, linking
to a created file or immediate resources (e.g. statistics).
- IXMLSerializable - Interface in cross.io.xml
-
Interface allowing a Visitor like request to implementing objects to decorate
the passed in Element to their liking with their own xml structure.
- random(Random, Class<?>, int[]) - Static method in class cross.datastructures.tools.ArrayTools
-
- random(Random, double, double, Class<?>, int[]) - Static method in class cross.datastructures.tools.ArrayTools
-
- read() - Method in class cross.io.misc.Base64.InputStream
-
Reads enough of the input stream to convert to/from Base64 and
returns the next byte.
- read(byte[], int, int) - Method in class cross.io.misc.Base64.InputStream
-
- readAll(IFileFragment) - Method in interface cross.io.IDataSource
-
- readAll(IFileFragment) - Method in class cross.io.xml.FragmentXMLSerializer
-
- readExternal(ObjectInput) - Method in class cross.datastructures.cache.SerializableArray
-
- readExternal(ObjectInput) - Method in class cross.datastructures.fragments.FileFragment
-
- readExternal(ObjectInput) - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- readIndexed(IVariableFragment) - Method in interface cross.io.IDataSource
-
- readIndexed(IVariableFragment) - Method in class cross.io.xml.FragmentXMLSerializer
-
- readSingle(IVariableFragment) - Method in interface cross.io.IDataSource
-
- readSingle(IVariableFragment) - Method in class cross.io.xml.FragmentXMLSerializer
-
- readStructure() - Method in class cross.datastructures.fragments.FileFragment
-
- readStructure() - Method in interface cross.datastructures.fragments.IFileFragment
-
Call the IDataSource for this FileFragment and load the structural
information for this fragment.
- readStructure() - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- readStructure(IFileFragment) - Method in interface cross.io.IDataSource
-
- readStructure(IVariableFragment) - Method in interface cross.io.IDataSource
-
- readStructure(IFileFragment) - Method in class cross.io.xml.FragmentXMLSerializer
-
- readStructure(IVariableFragment) - Method in class cross.io.xml.FragmentXMLSerializer
-
- readXML(Element) - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- readXML(Element) - Method in interface cross.datastructures.workflow.IWorkflow
-
Restore state of this IWorkflow instance from an XML document.
- ReflectionApplicationContextGenerator - Class in cross.applicationContext
-
This code is based on
https://github.com/mangstadt/Spring-Application-Context-Generator but uses
the compiled class information via reflection and the java service
provider/netbeans lookup API in order to resolve references.
- ReflectionApplicationContextGenerator(String, String) - Constructor for class cross.applicationContext.ReflectionApplicationContextGenerator
-
Constructs a new application context generator.
- ReflectionApplicationContextGenerator.BeanDescriptor - Class in cross.applicationContext
-
- ReflectionApplicationContextGenerator.BeanDescriptor(ReflectionApplicationContextGenerator, Object, String, String) - Constructor for class cross.applicationContext.ReflectionApplicationContextGenerator.BeanDescriptor
-
- ReflectionApplicationContextGenerator.ObjectProperty - Class in cross.applicationContext
-
- ReflectionApplicationContextGenerator.ObjectProperty() - Constructor for class cross.applicationContext.ReflectionApplicationContextGenerator.ObjectProperty
-
- relativeBinCoeff(int) - Static method in class cross.tools.MathTools
-
- remove(ICacheDelegate<K, V>) - Method in class cross.cache.none.NoCacheManager
-
- remove(ICacheDelegate<K, V>) - Method in class cross.cache.softReference.SoftReferenceCacheManager
-
- remove(int) - Method in class cross.datastructures.collections.CachedLazyList
-
- remove(Object) - Method in class cross.datastructures.collections.CachedLazyList
-
- remove(Integer) - Method in class cross.datastructures.collections.CachedReadWriteList
-
- remove(Object) - Method in class cross.datastructures.collections.CachedReadWriteList
-
- remove(int) - Method in class cross.datastructures.collections.CachedReadWriteList
-
- remove() - Method in class cross.datastructures.combinations.CombinationIterator
-
- remove(int) - Method in class cross.datastructures.fragments.CachedList
-
- remove(Object) - Method in class cross.datastructures.fragments.CachedList
-
- remove() - Method in class cross.datastructures.pipeline.CommandPipeline
-
- remove() - Method in interface cross.datastructures.pipeline.ICommandSequence
-
- remove(int) - Method in class cross.datastructures.tuple.TupleND
-
- remove(Object) - Method in class cross.datastructures.tuple.TupleND
-
- remove() - Method in class cross.io.misc.ArrayChunkIterator
-
- remove() - Method in class cross.math.CombinationIterator
-
- remove() - Method in class cross.math.Partition
-
- remove(IControlledVocabularyProvider) - Method in class cross.vocabulary.CvResolver
-
- remove(IControlledVocabularyProvider) - Method in interface cross.vocabulary.ICvResolver
-
Removes the given provider.
- removeAll(Collection<?>) - Method in class cross.datastructures.collections.CachedLazyList
-
- removeAll(Collection<?>) - Method in class cross.datastructures.collections.CachedReadWriteList
-
- removeAll(Collection<?>) - Method in class cross.datastructures.fragments.CachedList
-
- removeAll(Collection<?>) - Method in class cross.datastructures.tuple.TupleND
-
- removeB64FileExtension(String) - Static method in class cross.io.misc.BinaryFileBase64Wrapper
-
Remove file extension ".b64" if existent.
- removeCache(String) - Static method in class cross.cache.CacheFactory
-
- removeChild(IVariableFragment) - Method in class cross.datastructures.fragments.FileFragment
-
- removeChild(IVariableFragment) - Method in interface cross.datastructures.fragments.IFileFragment
-
Remove the given IVariableFragment from the list of this FileFragment's
children.
- removeChild(IVariableFragment) - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- removeFileExt(String) - Static method in class cross.tools.StringTools
-
Returns that part of a string before first occurrence of a dot,
if a dot is contained in s, otherwise, s is returned.
- removeGZFileExtension(String) - Static method in class cross.io.misc.BinaryFileBase64Wrapper
-
Remove file extension ".gz" if existent.
- removeListener(IListener<IEvent<IWorkflowResult>>) - Method in class cross.commands.fragments.AFragmentCommand
-
- removeListener(IListener<IEvent<IWorkflowResult>>) - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- removeListener(IListener<IEvent<V>>) - Method in class cross.event.EventSource
-
- removeListener(IListener<IEvent<V>>) - Method in interface cross.event.IEventSource
-
- removeListener(IListener<IEvent<V>>) - Method in class cross.event.SwingEventSource
-
- removeSourceFile(IFileFragment) - Method in class cross.datastructures.fragments.FileFragment
-
- removeSourceFile(IFileFragment) - Method in interface cross.datastructures.fragments.IFileFragment
-
Remove the given source file.
- removeSourceFile(IFileFragment) - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- removeSourceFiles() - Method in class cross.datastructures.fragments.FileFragment
-
- removeSourceFiles() - Method in interface cross.datastructures.fragments.IFileFragment
-
Removes all currently associated source files.
- removeSourceFiles() - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- RequiresOptionalVariables - Annotation Type in cross.annotations
-
Annotation which should be added to AFragmentCommand instances, declaring,
which variables, as given by their names, the annotated class needs.
- RequiresTypes - Annotation Type in cross.annotations
-
RequiresTypes class.
- RequiresVariables - Annotation Type in cross.annotations
-
Annotation which should be added to AFragmentCommand instances, declaring,
which variables, as given by their names, the annotated class needs.
- reset() - Method in interface cross.datastructures.collections.IElementProvider
-
- reset() - Method in class cross.datastructures.combinations.CombinationIterator
-
- reset() - Method in class cross.datastructures.combinations.CombinationProvider
-
- reset() - Method in class cross.math.CombinationIterator
-
Resets the iterator to initial value.
- reset() - Method in class cross.math.Partition
-
- resolve(String) - Method in class cross.commands.fragments.AFragmentCommand
-
- resolve(IFileFragment, IFileFragment) - Static method in class cross.datastructures.tools.FragmentTools
-
- resolveRelativeFile(File, File) - Static method in class cross.datastructures.tools.FileTools
-
- resolveRelativeUri(URI, URI) - Static method in class cross.datastructures.tools.FileTools
-
- ResourceNotAvailableException - Exception in cross.exception
-
- ResourceNotAvailableException(String) - Constructor for exception cross.exception.ResourceNotAvailableException
-
- ResourceNotAvailableException(String, Throwable) - Constructor for exception cross.exception.ResourceNotAvailableException
-
- ResourceNotAvailableException(Throwable) - Constructor for exception cross.exception.ResourceNotAvailableException
-
- restored() - Method in class net.sf.maltcms.cross.nbm.Installer
-
- resumeEncoding() - Method in class cross.io.misc.Base64.OutputStream
-
Resumes encoding of the stream.
- retainAll(Collection<?>) - Method in class cross.datastructures.collections.CachedLazyList
-
- retainAll(Collection<?>) - Method in class cross.datastructures.collections.CachedReadWriteList
-
- retainAll(Collection<?>) - Method in class cross.datastructures.fragments.CachedList
-
- retainAll(Collection<?>) - Method in class cross.datastructures.tuple.TupleND
-
- reverseConvert(Object) - Method in interface cross.datastructures.cache.ISerializationProxy
-
- reverseConvert(Object) - Method in class cross.datastructures.cache.SerializableArrayProxy
-
- save(TupleND<IFileFragment>) - Method in class cross.commands.fragments.AFragmentCommand
-
- save() - Method in class cross.datastructures.fragments.FileFragment
-
- save() - Method in interface cross.datastructures.fragments.IFileFragment
-
Store this fragment using the IDataSource responsible for handling
this fragment name's extension.
- save() - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- save() - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- save() - Method in interface cross.datastructures.workflow.IWorkflow
-
Save this IWorkflow.
- save(File) - Method in class cross.io.misc.WorkflowZipper
-
Saves the currently assigned workflow elements, matching currently
assigned FileFilter to File.
- save(File, String) - Method in class cross.io.misc.WorkflowZipper
-
- saveConfiguration(Configuration, File) - Static method in class cross.Factory
-
- sdf - Static variable in class cross.datastructures.tools.FileTools
-
- seq(int, int, int) - Static method in class cross.tools.MathTools
-
- seq(double, double, double) - Static method in class cross.tools.MathTools
-
- SerializableArray - Class in cross.datastructures.cache
-
Serialization proxy for
Array instances.
- SerializableArray() - Constructor for class cross.datastructures.cache.SerializableArray
-
- SerializableArray(Array) - Constructor for class cross.datastructures.cache.SerializableArray
-
- SerializableArrayProxy - Class in cross.datastructures.cache
-
- SerializableArrayProxy() - Constructor for class cross.datastructures.cache.SerializableArrayProxy
-
- serialize(IFileFragment) - Method in class cross.io.xml.FragmentXMLSerializer
-
- set(int, T) - Method in class cross.datastructures.collections.CachedLazyList
-
- set(int, T) - Method in class cross.datastructures.collections.CachedReadWriteList
-
- set(int, Array) - Method in class cross.datastructures.fragments.CachedList
-
- set(String, Double) - Method in interface cross.datastructures.fragments.Context
-
- setArray(Array) - Method in class cross.datastructures.fragments.ImmutableVariableFragment
-
- setArray(Array) - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- setArray(Array) - Method in interface cross.datastructures.fragments.IVariableFragment
-
Explicitly set an array, may be null.
- setArray(Array) - Method in class cross.datastructures.fragments.VariableFragment
-
- setAssociation(IFileFragment) - Method in class cross.datastructures.StatsMap
-
- setAttributes(Attribute...) - Method in class cross.datastructures.fragments.FileFragment
-
- setAttributes(Attribute...) - Method in class cross.datastructures.fragments.Fragment
-
- setAttributes(Attribute...) - Method in interface cross.datastructures.fragments.IFragment
-
Set attributes on a fragment.
- setAttributes(Attribute...) - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- setAttributes(Attribute...) - Method in class cross.datastructures.fragments.ImmutableVariableFragment
-
- setAttributes(Attribute...) - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- setAttributes(Attribute...) - Method in class cross.datastructures.fragments.VariableFragment
-
- setCache(ICacheDelegate<IVariableFragment, List<Array>>) - Method in class cross.datastructures.fragments.FileFragment
-
Sets the array cache of this FileFragment as specified if the current
cache has not yet been initialized (is null).
- setCache(ICacheDelegate<IVariableFragment, List<Array>>) - Method in interface cross.datastructures.fragments.IFileFragment
-
Set a Cache for variable fragment array data for this fragment.
- setCache(ICacheDelegate<IVariableFragment, List<Array>>) - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
Sets the array cache of this FileFragment as specified if the current
cache has not yet been initialized (is null).
- setCacheDirectory(File) - Static method in class cross.cache.CacheFactory
-
Set the cache location for all NEWLY created caches.
- setCacheDirectory(File) - Static method in class cross.datastructures.fragments.Fragments
-
Set the cache location for all NEWLY created caches.
- setCacheSize(int) - Method in class cross.datastructures.collections.CachedLazyList
-
- setCacheSize(int) - Method in class cross.datastructures.fragments.CachedList
-
- setCheckCommandDependencies(boolean) - Method in interface cross.datastructures.pipeline.ICommandSequence
-
- setCommands(List<IFragmentCommand>) - Method in class cross.datastructures.pipeline.CommandPipeline
-
- setCommands(List<IFragmentCommand>) - Method in interface cross.datastructures.pipeline.ICommandSequence
-
- setCommandSequence(ICommandSequence) - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- setCommandSequence(ICommandSequence) - Method in interface cross.datastructures.workflow.IWorkflow
-
Set ics to be the active ICommandSequence instance.
- setConfiguration(Configuration) - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- setConfiguration(Configuration) - Method in interface cross.datastructures.workflow.IWorkflow
-
Set the currently active configuration.
- setCvResolver(ICvResolver) - Method in interface cross.commands.fragments.IFragmentCommand
-
- setDataSources(List<String>) - Method in class cross.io.DataSourceFactory
-
- setDataSources(List<String>) - Method in interface cross.io.IDataSourceFactory
-
- setDataType(DataType) - Method in class cross.datastructures.fragments.ImmutableVariableFragment
-
- setDataType(DataType) - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- setDataType(DataType) - Method in interface cross.datastructures.fragments.IVariableFragment
-
Set the DataType.
- setDataType(DataType) - Method in class cross.datastructures.fragments.VariableFragment
-
- setDefaultFragmentCacheType(CacheType) - Static method in class cross.datastructures.fragments.Fragments
-
- setDeleteOnExit(boolean) - Method in class cross.io.misc.WorkflowZipper
-
- setDimensions(Dimension[]) - Method in class cross.datastructures.fragments.ImmutableVariableFragment
-
- setDimensions(Dimension[]) - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- setDimensions(Dimension...) - Method in interface cross.datastructures.fragments.IVariableFragment
-
Set the Dimensions of this VariableFragment.
- setDimensions(Dimension[]) - Method in class cross.datastructures.fragments.VariableFragment
-
- setElementProvider(IElementProvider<T>) - Method in class cross.datastructures.collections.CachedLazyList
-
- setEventSource(IEventSource<IWorkflowResult>) - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- setExecuteLocal(boolean) - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- setExecuteLocal(boolean) - Method in interface cross.datastructures.workflow.IWorkflow
-
- setFile(File) - Method in class cross.datastructures.fragments.FileFragment
-
- setFile(String) - Method in class cross.datastructures.fragments.FileFragment
-
- setFile(File) - Method in interface cross.datastructures.fragments.IFileFragment
-
Change the filename of this Fragment.
- setFile(String) - Method in interface cross.datastructures.fragments.IFileFragment
-
Change the filename of this Fragment.
- setFile(File) - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- setFile(String) - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- setFile(File) - Method in class cross.datastructures.workflow.DefaultWorkflowResult
-
- setFile(File) - Method in interface cross.datastructures.workflow.IWorkflowFileResult
-
- setFileFilter(String) - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- setFileFilter(FileFilter) - Method in class cross.io.misc.WorkflowZipper
-
- setFileTypesToKeep(List<String>) - Method in class cross.io.misc.DefaultConfigurableFileFilter
-
- setFirst(T) - Method in class cross.datastructures.tuple.Tuple2D
-
- setFlatten(boolean) - Method in class cross.io.misc.WorkflowZipper
-
- setID(long) - Method in class cross.datastructures.fragments.FileFragment
-
- setID(long) - Method in interface cross.datastructures.fragments.IGroupFragment
-
- setID(long) - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- setID(long) - Method in class cross.datastructures.fragments.NamedGroupFragment
-
- setIndex(IVariableFragment) - Method in class cross.datastructures.fragments.ImmutableVariableFragment
-
- setIndex(IVariableFragment) - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- setIndex(IVariableFragment) - Method in interface cross.datastructures.fragments.IVariableFragment
-
Every VariableFragment obtains a reference to an IndexFragment, to make
sure, that the associated Variable can be read at any time.
- setIndex(IVariableFragment) - Method in class cross.datastructures.fragments.VariableFragment
-
- setIndexedArray(List<Array>) - Method in class cross.datastructures.fragments.ImmutableVariableFragment
-
- setIndexedArray(List<Array>) - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- setIndexedArray(List<Array>) - Method in interface cross.datastructures.fragments.IVariableFragment
-
Explicitly set an indexed array, may be null.
- setIndexedArray(List<Array>) - Method in class cross.datastructures.fragments.VariableFragment
-
- setInput(TupleND<IFileFragment>) - Method in class cross.datastructures.pipeline.CommandPipeline
-
- setInput(TupleND<IFileFragment>) - Method in interface cross.datastructures.pipeline.ICommandSequence
-
- setIsModified(boolean) - Method in class cross.datastructures.fragments.ImmutableVariableFragment
-
- setIsModified(boolean) - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- setIsModified(boolean) - Method in interface cross.datastructures.fragments.IVariableFragment
-
Sets this IVariableFragment's state to the value of parameter b.
- setIsModified(boolean) - Method in class cross.datastructures.fragments.VariableFragment
-
- setIWorkflow(IWorkflow) - Method in class cross.io.misc.WorkflowZipper
-
- setLabel(String) - Method in class cross.datastructures.StatsMap
-
- setLHSFile(IFileFragment, IFileFragment) - Static method in class cross.datastructures.tools.FragmentTools
-
Set variable
var.reference_file, left hand side (lhs) for pairwise
alignments.
- setLogLevel(Class, String) - Method in class cross.test.SetupLogging
-
- setLogLevel(String, String) - Method in class cross.test.SetupLogging
-
- setName(String) - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- setName(String) - Method in interface cross.datastructures.workflow.IWorkflow
-
Set the name of this IWorkflow instance.
- setObject(T) - Method in interface cross.datastructures.workflow.IWorkflowObjectResult
-
- SetOperations - Class in cross.math
-
Utilitiy methods for sets with common names.
- SetOperations() - Constructor for class cross.math.SetOperations
-
- setOutputDirectory(File) - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- setOutputDirectory(File) - Method in interface cross.datastructures.workflow.IWorkflow
-
- setPairs(Collection<Tuple2D<T, T>>) - Method in class cross.datastructures.tuple.TupleND
-
- setPrefetchOnMiss(boolean) - Method in class cross.datastructures.collections.CachedLazyList
-
- setPrefetchOnMiss(boolean) - Method in class cross.datastructures.fragments.CachedList
-
- setPrefixesToMatch(List<String>) - Method in class cross.io.misc.DefaultConfigurableFileFilter
-
- setRange(Range[]) - Method in class cross.datastructures.fragments.ImmutableVariableFragment
-
- setRange(Range[]) - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- setRange(Range...) - Method in interface cross.datastructures.fragments.IVariableFragment
-
Set ranges for this VariableFragment.
- setRange(Range[]) - Method in class cross.datastructures.fragments.VariableFragment
-
- setResources(IFileFragment...) - Method in class cross.datastructures.workflow.DefaultWorkflowResult
-
- setResources(IFileFragment...) - Method in interface cross.datastructures.workflow.IWorkflowFileResult
-
- setResources(IFileFragment...) - Method in interface cross.datastructures.workflow.IWorkflowObjectResult
-
- setRHSFile(IFileFragment, IFileFragment) - Static method in class cross.datastructures.tools.FragmentTools
-
Set variable
var.query_file, right hand side (rhs) for pairwise
alignments.
- setSecond(U) - Method in class cross.datastructures.tuple.Tuple2D
-
- setStartupDate(Date) - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- setStartupDate(Date) - Method in interface cross.datastructures.workflow.IWorkflow
-
Set the startup date of this IWorkflow instance.
- setStats(StatsMap) - Method in class cross.datastructures.fragments.FileFragment
-
- setStats(StatsMap) - Method in class cross.datastructures.fragments.Fragment
-
- setStats(StatsMap) - Method in interface cross.datastructures.fragments.IFragment
-
Set statistics on a Fragment.
- setStats(StatsMap) - Method in class cross.datastructures.fragments.ImmutableFileFragment
-
- setStats(StatsMap) - Method in class cross.datastructures.fragments.ImmutableVariableFragment
-
- setStats(StatsMap) - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- setStats(StatsMap) - Method in class cross.datastructures.fragments.VariableFragment
-
- setSuffixesToMatch(List<String>) - Method in class cross.io.misc.DefaultConfigurableFileFilter
-
- setThrowExceptionOnUnsavedModification(boolean) - Method in interface cross.datastructures.pipeline.ICommandSequence
-
If
true, will throw a
ConstraintViolationException
if any
IFileFragment has unsaved changes, as determined by calling
f.isModified().
- SetupLogging - Class in cross.test
-
- SetupLogging() - Constructor for class cross.test.SetupLogging
-
- SetupLogging(Properties) - Constructor for class cross.test.SetupLogging
-
- SetupLogging(URL) - Constructor for class cross.test.SetupLogging
-
- setUseCachedList(boolean) - Method in class cross.datastructures.fragments.ImmutableVariableFragment2
-
- setUseCachedList(boolean) - Method in class cross.datastructures.fragments.VariableFragment
-
- setVariableFragment(IVariableFragment) - Method in class cross.datastructures.fragments.CachedList
-
- setWorkflow(IWorkflow) - Method in class cross.datastructures.pipeline.CommandPipeline
-
- setWorkflow(IWorkflow) - Method in interface cross.datastructures.pipeline.ICommandSequence
-
- setWorkflow(IWorkflow) - Method in interface cross.datastructures.workflow.IWorkflowElement
-
- setWorkflowElement(IWorkflowElement) - Method in class cross.datastructures.workflow.DefaultWorkflowProgressResult
-
- setWorkflowElement(IWorkflowElement) - Method in class cross.datastructures.workflow.DefaultWorkflowResult
-
- setWorkflowElement(IWorkflowElement) - Method in interface cross.datastructures.workflow.IWorkflowResult
-
- setWorkflowPostProcessors(List<IWorkflowPostProcessor>) - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- setWorkflowPostProcessors(List<IWorkflowPostProcessor>) - Method in interface cross.datastructures.workflow.IWorkflow
-
- setWorkflowSlot(WorkflowSlot) - Method in class cross.datastructures.workflow.DefaultWorkflowProgressResult
-
- setWorkflowSlot(WorkflowSlot) - Method in class cross.datastructures.workflow.DefaultWorkflowResult
-
- setWorkflowSlot(WorkflowSlot) - Method in interface cross.datastructures.workflow.IWorkflowResult
-
- setXslPathPrefix(String) - Method in class cross.datastructures.workflow.DefaultWorkflow
-
- setZipWorkflow(boolean) - Method in class cross.io.misc.WorkflowZipper
-
- shutdown() - Method in class cross.datastructures.threads.ExecutorsManager
-
- shutdown() - Method in class cross.Factory
-
Shutdown the factory's thread pool.
- shutdownNow() - Method in class cross.datastructures.threads.ExecutorsManager
-
- shutdownNow() - Method in class cross.Factory
-
- size() - Method in class cross.datastructures.collections.CachedLazyList
-
- size() - Method in class cross.datastructures.collections.CachedReadWriteList
-
- size() - Method in interface cross.datastructures.collections.IElementProvider
-
- size() - Method in class cross.datastructures.combinations.CombinationProvider
-
- size() - Method in class cross.datastructures.fragments.CachedList
-
- size() - Method in class cross.datastructures.tuple.TupleND
-
- size() - Method in class cross.math.CombinationIterator
-
Returns the number of combinations of all partitions and their elements.
- size() - Method in class cross.math.Partition
-
- sizeLong() - Method in interface cross.datastructures.collections.IElementProvider
-
- sizeLong() - Method in class cross.datastructures.combinations.CombinationProvider
-
- SoftReferenceCache<K,V> - Class in cross.cache.softReference
-
- SoftReferenceCache(String) - Constructor for class cross.cache.softReference.SoftReferenceCache
-
- SoftReferenceCacheManager - Class in cross.cache.softReference
-
Cache manager for soft-reference-based caching.
- start(BundleContext) - Method in class cross.osgi.CrossActivator
-
- starting(Description) - Method in class cross.test.LogMethodName
-
- StatsMap - Class in cross.datastructures
-
StatsMap stores values corresponding to Vars, associated to a given Fragment
(not mandatory).
- StatsMap() - Constructor for class cross.datastructures.StatsMap
-
- StatsMap(IFragment) - Constructor for class cross.datastructures.StatsMap
-
- stop(BundleContext) - Method in class cross.osgi.CrossActivator
-
- StringTools - Class in cross.tools
-
Utility class with methods to ease some String based operations.
- StringTools() - Constructor for class cross.tools.StringTools
-
- subList(int, int) - Method in class cross.datastructures.collections.CachedLazyList
-
- subList(int, int) - Method in class cross.datastructures.collections.CachedReadWriteList
-
- subList(int, int) - Method in class cross.datastructures.fragments.CachedList
-
- submit(Callable<T>) - Method in class cross.datastructures.threads.ExecutorsManager
-
- submit(Runnable) - Method in class cross.datastructures.threads.ExecutorsManager
-
- submit(Runnable, T) - Method in class cross.datastructures.threads.ExecutorsManager
-
- submitJob(Callable<?>) - Method in class cross.Factory
-
Jobs submitted via this method will be run by the auxiliary thread pool.
- submitJob(Runnable) - Method in class cross.Factory
-
Submit a Runnable job to the Factory
- sum(double[]) - Static method in class cross.tools.MathTools
-
- supportedFormats() - Method in interface cross.io.IDataSource
-
- supportedFormats() - Method in class cross.io.xml.FragmentXMLSerializer
-
- suspendEncoding() - Method in class cross.io.misc.Base64.OutputStream
-
Suspends encoding of the stream.
- SwingEventSource<V> - Class in cross.event
-
EventSource of Type V.
- SwingEventSource() - Constructor for class cross.event.SwingEventSource
-
- symmetricDifference(Set<T>, Set<T>) - Static method in class cross.math.SetOperations
-