A B C D E F G H I K L M N O P Q R S T U V W X

A

AbstractApp - Class in org.scijava.app
Abstract superclass of App implementations.
AbstractApp() - Constructor for class org.scijava.app.AbstractApp
 
AbstractBasicDetails - Class in org.scijava
Abstract superclass of BasicDetails implementations.
AbstractBasicDetails() - Constructor for class org.scijava.AbstractBasicDetails
 
AbstractContextual - Class in org.scijava
Abstract base class for Contextual objects.
AbstractContextual() - Constructor for class org.scijava.AbstractContextual
 
AbstractGateway - Class in org.scijava
Abstract superclass for Gateway implementations.
AbstractGateway() - Constructor for class org.scijava.AbstractGateway
 
AbstractGateway(String, Context) - Constructor for class org.scijava.AbstractGateway
 
AbstractHandlerPlugin<D> - Class in org.scijava.plugin
Abstract base class for HandlerPlugin implementations.
AbstractHandlerPlugin() - Constructor for class org.scijava.plugin.AbstractHandlerPlugin
 
AbstractHandlerService<DT,PT extends HandlerPlugin<DT>> - Class in org.scijava.plugin
Abstract base class for HandlerServices.
AbstractHandlerService() - Constructor for class org.scijava.plugin.AbstractHandlerService
 
AbstractIndexWriter - Class in org.scijava.annotations
Writes annotations as JSON-formatted files.
AbstractIndexWriter() - Constructor for class org.scijava.annotations.AbstractIndexWriter
 
AbstractIndexWriter.StreamFactory - Interface in org.scijava.annotations
 
AbstractLogService - Class in org.scijava.log
Base implementation of an abstract LogService.
AbstractLogService() - Constructor for class org.scijava.log.AbstractLogService
 
AbstractPrimitiveArray<ArrayType,BaseType> - Class in org.scijava.util
Abstract base class for primitive-type extensible arrays.
AbstractPrimitiveArray(Class<BaseType>) - Constructor for class org.scijava.util.AbstractPrimitiveArray
Constructs an extensible array of primitive type elements, backed by a fixed-size array.
AbstractPrimitiveArray(Class<BaseType>, int) - Constructor for class org.scijava.util.AbstractPrimitiveArray
Constructs an extensible array of primitive type elements, backed by a fixed-size array.
AbstractPrimitiveArray(Class<BaseType>, ArrayType) - Constructor for class org.scijava.util.AbstractPrimitiveArray
Constructs an extensible array of primitive type elements, backed by the given fixed-size array.
AbstractPTService<PT extends SciJavaPlugin> - Class in org.scijava.plugin
Abstract base class for PTServices.
AbstractPTService() - Constructor for class org.scijava.plugin.AbstractPTService
 
AbstractRichPlugin - Class in org.scijava.plugin
Abstract base class for RichPlugin implementations.
AbstractRichPlugin() - Constructor for class org.scijava.plugin.AbstractRichPlugin
 
AbstractService - Class in org.scijava.service
Abstract superclass of Service implementations.
AbstractService() - Constructor for class org.scijava.service.AbstractService
 
AbstractSingletonService<PT extends SingletonPlugin> - Class in org.scijava.plugin
Abstract base class for SingletonServices.
AbstractSingletonService() - Constructor for class org.scijava.plugin.AbstractSingletonService
 
AbstractTypedPlugin<D> - Class in org.scijava.plugin
Abstract base class for TypedPlugins.
AbstractTypedPlugin() - Constructor for class org.scijava.plugin.AbstractTypedPlugin
 
AbstractTypedService<DT,PT extends TypedPlugin<DT>> - Class in org.scijava.plugin
Abstract base class for TypedServices.
AbstractTypedService() - Constructor for class org.scijava.plugin.AbstractTypedService
 
AbstractUIDetails - Class in org.scijava
Abstract superclass of UIDetails implementations.
AbstractUIDetails() - Constructor for class org.scijava.AbstractUIDetails
 
AbstractWrapperPlugin<D> - Class in org.scijava.plugin
Abstract base class for WrapperPlugins.
AbstractWrapperPlugin() - Constructor for class org.scijava.plugin.AbstractWrapperPlugin
 
AbstractWrapperService<DT,PT extends WrapperPlugin<DT>> - Class in org.scijava.plugin
Abstract base class for WrapperServices.
AbstractWrapperService() - Constructor for class org.scijava.plugin.AbstractWrapperService
 
Accelerator - Class in org.scijava.input
A keyboard shortcut, consisting of a KeyCode plus InputModifiers.
Accelerator(KeyCode, InputModifiers) - Constructor for class org.scijava.input.Accelerator
 
adapt(Object) - Method in class org.scijava.annotations.AbstractIndexWriter
 
adapt(A) - Method in class org.scijava.annotations.AbstractIndexWriter
 
add(Map<String, Object>, String, String) - Method in class org.scijava.annotations.AbstractIndexWriter
 
add(A, String) - Method in class org.scijava.annotations.DirectoryIndexer
 
add(E) - Method in class org.scijava.object.ObjectIndex
 
add(E, boolean) - Method in class org.scijava.object.ObjectIndex
Adds the object to all compatible type lists.
add(E, Class<?>, boolean) - Method in class org.scijava.object.ObjectIndex
Adds an object to type lists beneath the given type hierarchy.
add(int, BaseType) - Method in class org.scijava.util.AbstractPrimitiveArray
 
add(int, Boolean) - Method in class org.scijava.util.BoolArray
 
add(int, Byte) - Method in class org.scijava.util.ByteArray
 
add(int, Character) - Method in class org.scijava.util.CharArray
 
add(int, Double) - Method in class org.scijava.util.DoubleArray
 
add(int, Float) - Method in class org.scijava.util.FloatArray
 
add(int, Integer) - Method in class org.scijava.util.IntArray
 
add(int, Long) - Method in class org.scijava.util.LongArray
 
add(int, E) - Method in class org.scijava.util.ObjectArray
 
add(int, Short) - Method in class org.scijava.util.ShortArray
 
addAll(Collection<? extends E>) - Method in class org.scijava.object.ObjectIndex
 
addAll(Collection<? extends E>) - Method in class org.scijava.object.SortedObjectIndex
 
addAll(int, Collection<? extends Boolean>) - Method in class org.scijava.util.BoolArray
 
addAll(int, Collection<? extends Byte>) - Method in class org.scijava.util.ByteArray
 
addAll(int, Collection<? extends Character>) - Method in class org.scijava.util.CharArray
 
addAll(int, Collection<? extends Double>) - Method in class org.scijava.util.DoubleArray
 
addAll(int, Collection<? extends Float>) - Method in class org.scijava.util.FloatArray
 
addAll(int, Collection<? extends Integer>) - Method in class org.scijava.util.IntArray
 
addAll(int, Collection<? extends Long>) - Method in class org.scijava.util.LongArray
 
addAll(int, Collection<? extends E>) - Method in class org.scijava.util.ObjectArray
 
addAll(int, Collection<? extends Short>) - Method in class org.scijava.util.ShortArray
 
addLater(LazyObjects<? extends E>) - Method in class org.scijava.object.ObjectIndex
Registers objects which will be created lazily as needed.
addListener(EventHistoryListener) - Method in class org.scijava.event.DefaultEventHistory
 
addListener(EventHistoryListener) - Method in interface org.scijava.event.EventHistory
Adds an event history listener.
addObject(Object) - Method in class org.scijava.object.DefaultObjectService
 
addObject(Object) - Method in interface org.scijava.object.ObjectService
Registers an object with the object service.
addPlugin(PluginInfo<?>) - Method in class org.scijava.plugin.DefaultPluginService
 
addPlugin(PluginInfo<?>) - Method in interface org.scijava.plugin.PluginService
Manually registers a plugin with the plugin service.
addPlugins(Collection<T>) - Method in class org.scijava.plugin.DefaultPluginService
 
addPlugins(Collection<T>) - Method in interface org.scijava.plugin.PluginService
Manually registers plugins with the plugin service.
addTiming(Object) - Method in class org.scijava.util.Timing
 
addTiming(long, Object) - Method in class org.scijava.util.Timing
 
addToList(E, List<E>, boolean) - Method in class org.scijava.object.ObjectIndex
 
addToList(E, List<E>, boolean) - Method in class org.scijava.object.SortedObjectIndex
 
addValue(boolean) - Method in class org.scijava.util.BoolArray
 
addValue(int, boolean) - Method in class org.scijava.util.BoolArray
 
addValue(byte) - Method in class org.scijava.util.ByteArray
 
addValue(int, byte) - Method in class org.scijava.util.ByteArray
 
addValue(char) - Method in class org.scijava.util.CharArray
 
addValue(int, char) - Method in class org.scijava.util.CharArray
 
addValue(double) - Method in class org.scijava.util.DoubleArray
 
addValue(int, double) - Method in class org.scijava.util.DoubleArray
 
addValue(float) - Method in class org.scijava.util.FloatArray
 
addValue(int, float) - Method in class org.scijava.util.FloatArray
 
addValue(int) - Method in class org.scijava.util.IntArray
 
addValue(int, int) - Method in class org.scijava.util.IntArray
 
addValue(long) - Method in class org.scijava.util.LongArray
 
addValue(int, long) - Method in class org.scijava.util.LongArray
 
addValue(E) - Method in class org.scijava.util.ObjectArray
 
addValue(int, E) - Method in class org.scijava.util.ObjectArray
 
addValue(short) - Method in class org.scijava.util.ShortArray
 
addValue(int, short) - Method in class org.scijava.util.ShortArray
 
annotation() - Method in class org.scijava.annotations.IndexItem
Obtains the annotation values.
AnnotationCombiner - Class in org.scijava.annotations
Combines annotation indexes from all JAR files on the classpath.
AnnotationCombiner() - Constructor for class org.scijava.annotations.AnnotationCombiner
 
AnnotationProcessor - Class in org.scijava.annotations
The annotation processor for use with Java 6 and above.
AnnotationProcessor() - Constructor for class org.scijava.annotations.AnnotationProcessor
 
app() - Method in class org.scijava.AbstractGateway
 
App - Interface in org.scijava.app
Metadata about a SciJava-based application, used by the AppService.
app() - Method in interface org.scijava.Gateway
 
append(String) - Method in class org.scijava.util.StringMaker
 
append(String, Object) - Method in class org.scijava.util.StringMaker
 
append(String, Object, Object) - Method in class org.scijava.util.StringMaker
 
appendContents(Collection<URL>, URL) - Static method in class org.scijava.util.FileUtils
Recursively adds contents from the referenced directory to an existing collection.
appendContents(Collection<URL>, URL, boolean, boolean) - Static method in class org.scijava.util.FileUtils
Add contents from the referenced directory to an existing collection.
APPLICATION_MENU_ROOT - Static variable in annotation type org.scijava.plugin.Plugin
Deprecated. Use UIDetails.APPLICATION_MENU_ROOT instead.
APPLICATION_MENU_ROOT - Static variable in interface org.scijava.UIDetails
The default, application-level menu root.
AppService - Interface in org.scijava.app
Interface for application-level functionality.
AppUtils - Class in org.scijava.util
Useful methods for obtaining details of the SciJava application environment.
ArrayUtils - Class in org.scijava.util
Utility class for creating and manipulating PrimitiveArray instances.
assignProperties(MenuEntry) - Method in class org.scijava.MenuEntry
Updates any default properties of this menu entry to match those of the given menu entry.
Attr - Annotation Type in org.scijava.plugin
A name/value attribute pair, used to extend the @Plugin annotation.

B

BasicDetails - Interface in org.scijava
An interface defining basic characteristics including name, label, description, and a table of key/value pairs.
BoolArray - Class in org.scijava.util
An extensible array of boolean elements.
BoolArray() - Constructor for class org.scijava.util.BoolArray
Constructs an extensible array of booleans, backed by a fixed-size array.
BoolArray(int) - Constructor for class org.scijava.util.BoolArray
Constructs an extensible array of booleans, backed by a fixed-size array.
BoolArray(boolean[]) - Constructor for class org.scijava.util.BoolArray
Constructs an extensible array of booleans, backed by the given fixed-size array.
buffer - Variable in class org.scijava.util.ReadInto
 
ByteArray - Class in org.scijava.util
An extensible array of byte elements.
ByteArray() - Constructor for class org.scijava.util.ByteArray
Constructs an extensible array of bytes, backed by a fixed-size array.
ByteArray(int) - Constructor for class org.scijava.util.ByteArray
Constructs an extensible array of bytes, backed by a fixed-size array.
ByteArray(byte[]) - Constructor for class org.scijava.util.ByteArray
Constructs an extensible array of bytes, backed by the given fixed-size array.

C

canCast(Class<?>, Class<?>) - Static method in class org.scijava.util.ClassUtils
Deprecated. use ConversionUtils.canCast(Class, Class)
canCast(Object, Class<?>) - Static method in class org.scijava.util.ClassUtils
Deprecated. use ConversionUtils.canCast(Object, Class)
canCast(Class<?>, Class<?>) - Static method in class org.scijava.util.ConversionUtils
Checks whether objects of the given class can be cast to the specified type.
canCast(Object, Class<?>) - Static method in class org.scijava.util.ConversionUtils
Checks whether the given object can be cast to the specified type.
canConvert(Class<?>, Class<?>) - Static method in class org.scijava.util.ClassUtils
Deprecated. use ConversionUtils.canConvert(Class, Class)
canConvert(Object, Class<?>) - Static method in class org.scijava.util.ClassUtils
Deprecated. use ConversionUtils.canConvert(Object, Class)
canConvert(Class<?>, Type) - Static method in class org.scijava.util.ConversionUtils
Checks whether objects of the given class can be converted to the specified type.
canConvert(Class<?>, Class<?>) - Static method in class org.scijava.util.ConversionUtils
Checks whether objects of the given class can be converted to the specified type.
canConvert(Object, Type) - Static method in class org.scijava.util.ConversionUtils
Checks whether the given object can be converted to the specified type.
canConvert(Object, Class<?>) - Static method in class org.scijava.util.ConversionUtils
Checks whether the given object can be converted to the specified type.
capacity() - Method in class org.scijava.util.AbstractPrimitiveArray
Gets the current capacity of the backing array.
capacity() - Method in interface org.scijava.util.PrimitiveArray
Gets the current capacity of the backing array.
cast(Object, Class<T>) - Static method in class org.scijava.util.ClassUtils
Deprecated. use ConversionUtils.cast(Object, Class)
cast(Object, Class<T>) - Static method in class org.scijava.util.ConversionUtils
Casts the given object to the specified type, or null if the types are incompatible.
cdata(String) - Method in class org.scijava.util.XML
Obtains the CDATA identified by the given XPath expression.
CharArray - Class in org.scijava.util
An extensible array of char elements.
CharArray() - Constructor for class org.scijava.util.CharArray
Constructs an extensible array of chars, backed by a fixed-size array.
CharArray(int) - Constructor for class org.scijava.util.CharArray
Constructs an extensible array of chars, backed by a fixed-size array.
CharArray(char[]) - Constructor for class org.scijava.util.CharArray
Constructs an extensible array of chars, backed by the given fixed-size array.
check(boolean) - Static method in class org.scijava.util.CheckSezpoz
Deprecated. 
check(File) - Static method in class org.scijava.util.CheckSezpoz
Deprecated. 
checkBounds(int) - Method in class org.scijava.util.AbstractPrimitiveArray
Checks that the index is less than the size of the array.
checkDirectory(File) - Static method in class org.scijava.util.CheckSezpoz
Deprecated. 
checkDirectory(File, File, long) - Static method in class org.scijava.util.CheckSezpoz
Deprecated. 
checkJar(File) - Static method in class org.scijava.util.CheckSezpoz
Deprecated. 
CheckSezpoz - Class in org.scijava.util
Deprecated. 
clampToRange(Class<?>, Number, Number, Number) - Static method in class org.scijava.util.NumberUtils
 
className() - Method in class org.scijava.annotations.IndexItem
Returns the name of the annotated class.
ClassUtils - Class in org.scijava.util
Useful methods for working with Class objects and primitive types.
clear() - Method in class org.scijava.event.DefaultEventHistory
 
clear() - Method in interface org.scijava.event.EventHistory
Clears the recorded event history.
clear() - Method in class org.scijava.object.ObjectIndex
 
clear() - Method in class org.scijava.util.AbstractPrimitiveArray
 
clearStatus() - Method in class org.scijava.app.DefaultStatusService
 
clearStatus() - Method in interface org.scijava.app.StatusService
Clears the status message.
close() - Method in class org.scijava.annotations.legacy.LegacyReader
 
closeOnEOF - Variable in class org.scijava.util.ReadInto
 
combine(File) - Method in class org.scijava.annotations.AnnotationCombiner
Reads in annotations from all available resources and combines them.
combine() - Method in class org.scijava.util.CombineAnnotations
Deprecated. Use org.scijava.annotations.AnnotationCombiner#combine() instead.
combine(File) - Method in interface org.scijava.util.Combiner
Combines a collection of items and writes the result to the provided directory.
combine(File) - Method in class org.scijava.util.ServiceCombiner
 
CombineAnnotations - Class in org.scijava.util
Deprecated. Use AnnotationCombiner instead.
CombineAnnotations() - Constructor for class org.scijava.util.CombineAnnotations
Deprecated. Use org.scijava.annotations.AnnotationCombiner#CombineAnnotations() instead.
Combiner - Interface in org.scijava.util
Interface for combining structurally-delicate items (such as annotations) which need to be unified to a single output.
compare(Prioritized, Prioritized) - Static method in class org.scijava.Priority
Compares two Prioritized objects.
compare(Class<?>, Class<?>) - Static method in class org.scijava.util.ClassUtils
Compares two Class objects using their fully qualified names.
compare(T, T) - Static method in class org.scijava.util.MiscUtils
Compares two comparable objects, even if one or both of them are null.
compare(T, T, boolean) - Static method in class org.scijava.util.MiscUtils
Compares two comparable objects, even if one or both of them are null.
compareTo(Prioritized) - Method in class org.scijava.AbstractUIDetails
 
compareTo(Prioritized) - Method in class org.scijava.plugin.AbstractRichPlugin
 
compareTo(POM) - Method in class org.scijava.util.POM
 
compareVersions(String, String) - Static method in class org.scijava.util.POM
Compares two version strings.
consume() - Method in class org.scijava.event.SciJavaEvent
 
contains(Object) - Method in class org.scijava.object.ObjectIndex
 
contains(Object) - Method in class org.scijava.object.SortedObjectIndex
 
contains(boolean) - Method in class org.scijava.util.BoolArray
 
contains(Object) - Method in class org.scijava.util.BoolArray
 
contains(byte) - Method in class org.scijava.util.ByteArray
 
contains(Object) - Method in class org.scijava.util.ByteArray
 
contains(char) - Method in class org.scijava.util.CharArray
 
contains(Object) - Method in class org.scijava.util.CharArray
 
contains(double) - Method in class org.scijava.util.DoubleArray
 
contains(Object) - Method in class org.scijava.util.DoubleArray
 
contains(float) - Method in class org.scijava.util.FloatArray
 
contains(Object) - Method in class org.scijava.util.FloatArray
 
contains(int) - Method in class org.scijava.util.IntArray
 
contains(Object) - Method in class org.scijava.util.IntArray
 
contains(long) - Method in class org.scijava.util.LongArray
 
contains(Object) - Method in class org.scijava.util.LongArray
 
contains(Object) - Method in class org.scijava.util.ObjectArray
 
contains(short) - Method in class org.scijava.util.ShortArray
 
contains(Object) - Method in class org.scijava.util.ShortArray
 
containsAll(Collection<?>) - Method in class org.scijava.object.ObjectIndex
 
containsAll(Collection<?>) - Method in class org.scijava.object.SortedObjectIndex
 
containsAll(Collection<?>) - Method in class org.scijava.util.BoolArray
 
containsAll(Collection<?>) - Method in class org.scijava.util.ByteArray
 
containsAll(Collection<?>) - Method in class org.scijava.util.CharArray
 
containsAll(Collection<?>) - Method in class org.scijava.util.DoubleArray
 
containsAll(Collection<?>) - Method in class org.scijava.util.FloatArray
 
containsAll(Collection<?>) - Method in class org.scijava.util.IntArray
 
containsAll(Collection<?>) - Method in class org.scijava.util.LongArray
 
containsAll(Collection<?>) - Method in class org.scijava.util.ObjectArray
 
containsAll(Collection<?>) - Method in class org.scijava.util.ShortArray
 
context() - Method in class org.scijava.AbstractContextual
 
Context - Class in org.scijava
Top-level SciJava application context, which initializes and maintains a list of services.
Context() - Constructor for class org.scijava.Context
Creates a new SciJava application context with all available services.
Context(boolean) - Constructor for class org.scijava.Context
Creates a new SciJava application context.
Context(Class...) - Constructor for class org.scijava.Context
Creates a new SciJava application context with the specified services (and any required service dependencies).
Context(Collection<Class<? extends Service>>) - Constructor for class org.scijava.Context
Creates a new SciJava application context with the specified services (and any required service dependencies).
Context(PluginIndex) - Constructor for class org.scijava.Context
Creates a new SciJava application with the specified PluginIndex.
Context(Collection<Class<? extends Service>>, PluginIndex) - Constructor for class org.scijava.Context
Creates a new SciJava application context with the specified services (and any required service dependencies).
context() - Method in interface org.scijava.Contextual
Gets the application context to which the object belongs.
CONTEXT_MENU_ROOT - Static variable in annotation type org.scijava.plugin.Plugin
Deprecated. Use a context-specific menu root string instead. This one is too general. There is no such thing as a "default context menu" since such a thing wouldn't be a context menu!
Contextual - Interface in org.scijava
An object that belongs to a SciJava application context.
ConversionUtils - Class in org.scijava.util
Useful methods for converting and casting between classes and types.
convert(Object, Class<T>) - Static method in class org.scijava.util.ClassUtils
Deprecated. use ConversionUtils.convert(Object, Class)
convert(Object, Type) - Static method in class org.scijava.util.ConversionUtils
As ConversionUtils.convert(Object, Class) but capable of creating and populating multi-element objects (Collections and array types).
convert(Object, Class<T>) - Static method in class org.scijava.util.ConversionUtils
Converts the given object to an object of the specified type.
convertToEnum(String, Class<T>) - Static method in class org.scijava.util.ConversionUtils
Converts the given string value to an enumeration constant of the specified type.
copyArray() - Method in class org.scijava.util.AbstractPrimitiveArray
 
copyArray() - Method in interface org.scijava.util.PrimitiveArray
Returns a copy of the primitive-array array.
create(String) - Static method in class org.scijava.input.Accelerator
Creates an accelerator from the given string representation.
create(D) - Method in class org.scijava.plugin.AbstractWrapperService
 
create(D) - Method in interface org.scijava.plugin.WrapperService
Creates a new plugin instance wrapping the given associated data object.
createExactService(Class<S>) - Method in class org.scijava.service.ServiceHelper
Instantiates a service of the given class, registering it in the index.
createInstance() - Method in interface org.scijava.Instantiable
Creates an object.
createInstance(PluginInfo<PT>) - Method in class org.scijava.plugin.DefaultPluginService
 
createInstance() - Method in class org.scijava.plugin.PluginInfo
 
createInstance(PluginInfo<PT>) - Method in interface org.scijava.plugin.PluginService
Creates an instance of the given plugin.
createInstances(List<PluginInfo<PT>>) - Method in class org.scijava.plugin.DefaultPluginService
 
createInstances(List<PluginInfo<PT>>) - Method in interface org.scijava.plugin.PluginService
Creates an instance of each of the plugins on the given list.
createInstancesOfType(Class<PT>) - Method in class org.scijava.plugin.DefaultPluginService
 
createInstancesOfType(Class<PT>) - Method in interface org.scijava.plugin.PluginService
Creates one instance each of the available plugins of the given type.
createTemporaryDirectory(String, String) - Static method in class org.scijava.util.FileUtils
Creates a temporary directory.
createTemporaryDirectory(String, String, File) - Static method in class org.scijava.util.FileUtils
Creates a temporary directory.

D

debug(Object) - Method in class org.scijava.log.AbstractLogService
 
debug(Throwable) - Method in class org.scijava.log.AbstractLogService
 
debug(Object, Throwable) - Method in class org.scijava.log.AbstractLogService
 
DEBUG - Static variable in interface org.scijava.log.LogService
 
debug(Object) - Method in interface org.scijava.log.LogService
 
debug(Throwable) - Method in interface org.scijava.log.LogService
 
debug(Object, Throwable) - Method in interface org.scijava.log.LogService
 
DebugUtils - Class in org.scijava.util
Useful methods for debugging programs.
DEFAULT_SHORTENER_THRESHOLD - Static variable in class org.scijava.util.FileUtils
 
DEFAULT_WEIGHT - Static variable in class org.scijava.MenuEntry
 
DefaultAppService - Class in org.scijava.app
Default service for application-level functionality.
DefaultAppService() - Constructor for class org.scijava.app.DefaultAppService
 
DefaultEventBus - Class in org.scijava.event
An EventService implementation for SciJava.
DefaultEventBus(ThreadService, LogService) - Constructor for class org.scijava.event.DefaultEventBus
 
DefaultEventHistory - Class in org.scijava.event
Default service for keeping a history of SciJava events.
DefaultEventHistory() - Constructor for class org.scijava.event.DefaultEventHistory
 
DefaultEventService - Class in org.scijava.event
Default service for publishing and subscribing to SciJava events.
DefaultEventService() - Constructor for class org.scijava.event.DefaultEventService
 
DefaultObjectService - Class in org.scijava.object
Default service for keeping track of registered objects.
DefaultObjectService() - Constructor for class org.scijava.object.DefaultObjectService
 
DefaultPluginFinder - Class in org.scijava.plugin
Default SciJava plugin discovery mechanism.
DefaultPluginFinder() - Constructor for class org.scijava.plugin.DefaultPluginFinder
 
DefaultPluginFinder(ClassLoader) - Constructor for class org.scijava.plugin.DefaultPluginFinder
 
DefaultPluginService - Class in org.scijava.plugin
Default service for keeping track of available plugins.
DefaultPluginService() - Constructor for class org.scijava.plugin.DefaultPluginService
 
DefaultStatusService - Class in org.scijava.app
Default service for status notifications.
DefaultStatusService() - Constructor for class org.scijava.app.DefaultStatusService
 
DefaultThreadService - Class in org.scijava.thread
Default service for managing active threads.
DefaultThreadService() - Constructor for class org.scijava.thread.DefaultThreadService
 
DefaultUncaughtExceptionHandler - Class in org.scijava.log
A handler for otherwise uncaught exceptions.
DefaultUncaughtExceptionHandler(LogService) - Constructor for class org.scijava.log.DefaultUncaughtExceptionHandler
 
defaultValue() - Method in class org.scijava.util.BoolArray
 
defaultValue() - Method in class org.scijava.util.ByteArray
 
defaultValue() - Method in class org.scijava.util.CharArray
 
defaultValue() - Method in class org.scijava.util.DoubleArray
 
defaultValue() - Method in class org.scijava.util.FloatArray
 
defaultValue() - Method in class org.scijava.util.IntArray
 
defaultValue() - Method in class org.scijava.util.LongArray
 
defaultValue() - Method in class org.scijava.util.ObjectArray
 
defaultValue() - Method in interface org.scijava.util.PrimitiveArray
 
defaultValue() - Method in class org.scijava.util.ShortArray
 
DELAY_IN_MICROSECONDS - Static variable in class org.scijava.util.MirrorWebsite
 
delete(int, int) - Method in class org.scijava.util.AbstractPrimitiveArray
Shifts the array to delete space starting at a specified index.
delete(int, int) - Method in interface org.scijava.util.PrimitiveArray
Shifts the array to delete space starting at a specified index.
deleteRecursively(File) - Static method in class org.scijava.util.FileUtils
Deletes a directory recursively.
DirectoryIndexer - Class in org.scijava.annotations
Indexes a directory of classes.
DirectoryIndexer() - Constructor for class org.scijava.annotations.DirectoryIndexer
 
discover() - Method in class org.scijava.plugin.PluginIndex
Adds all plugins discovered by the attached PluginFinder to this index, or does nothing if the attached PluginFiner is null.
discoverAnnotations(File, String, ClassLoader) - Method in class org.scijava.annotations.DirectoryIndexer
 
Disposable - Interface in org.scijava
An object that knows how to clean up after itself.
dispose() - Method in class org.scijava.Context
 
dispose() - Method in interface org.scijava.Disposable
Performs any needed cleanup of the object's services, in preparation for the object being retired (e.g., to make garbage collection possible).
dispose() - Method in class org.scijava.event.DefaultEventService
 
dispose() - Method in class org.scijava.service.AbstractService
 
dispose() - Method in class org.scijava.thread.DefaultThreadService
 
done - Variable in class org.scijava.util.ReadInto
 
done() - Method in class org.scijava.util.ReadInto
 
DoubleArray - Class in org.scijava.util
An extensible array of double elements.
DoubleArray() - Constructor for class org.scijava.util.DoubleArray
Constructs an extensible array of doubles, backed by a fixed-size array.
DoubleArray(int) - Constructor for class org.scijava.util.DoubleArray
Constructs an extensible array of doubles, backed by a fixed-size array.
DoubleArray(double[]) - Constructor for class org.scijava.util.DoubleArray
Constructs an extensible array of doubles, backed by the given fixed-size array.

E

EclipseHelper - Class in org.scijava.annotations
Helps Eclipse's lack of support for annotation processing in incremental build mode.
EclipseHelper() - Constructor for class org.scijava.annotations.EclipseHelper
 
ensureCapacity(int) - Method in class org.scijava.util.AbstractPrimitiveArray
 
ensureCapacity(int) - Method in interface org.scijava.util.PrimitiveArray
Makes sure the backing array at least a specified capacity.
ensureCapacity(int) - Method in class org.scijava.util.SizableArrayList
 
equal(Object, Object) - Static method in class org.scijava.util.MiscUtils
Compares two objects for equality, even if one or both of them are null.
equals(Object) - Method in class org.scijava.input.Accelerator
 
equals(Object) - Method in class org.scijava.input.InputModifiers
 
error(Object) - Method in class org.scijava.log.AbstractLogService
 
error(Throwable) - Method in class org.scijava.log.AbstractLogService
 
error(Object, Throwable) - Method in class org.scijava.log.AbstractLogService
 
ERROR - Static variable in interface org.scijava.log.LogService
 
error(Object) - Method in interface org.scijava.log.LogService
 
error(Throwable) - Method in interface org.scijava.log.LogService
 
error(Object, Throwable) - Method in interface org.scijava.log.LogService
 
event() - Method in class org.scijava.AbstractGateway
 
event() - Method in interface org.scijava.Gateway
 
EventDetails - Class in org.scijava.event
Caches details of a particular SciJavaEvent, without saving the event itself (since doing so could leave dangling references).
EventDetails(SciJavaEvent) - Constructor for class org.scijava.event.EventDetails
 
EventHandler - Annotation Type in org.scijava.event
Annotation identifying an event handler method.
eventHistory() - Method in class org.scijava.AbstractGateway
 
EventHistory - Interface in org.scijava.event
Interface for service that keeps a history of SciJava events.
eventHistory() - Method in interface org.scijava.Gateway
 
EventHistoryListener - Interface in org.scijava.event
Listener for event history changes.
eventOccurred(EventDetails) - Method in interface org.scijava.event.EventHistoryListener
 
EventService - Interface in org.scijava.event
Interface for the event handling service.
EventSubscriber<E extends SciJavaEvent> - Interface in org.scijava.event
Interface for subscribers that wish to be notified of SciJava events.
exec(File, PrintStream, PrintStream, String...) - Static method in class org.scijava.util.ProcessUtils
Executes a program.
exec(File, InputStream, PrintStream, PrintStream, String...) - Static method in class org.scijava.util.ProcessUtils
Executes a program.

F

FILE_NAME - Static variable in class org.scijava.util.CheckSezpoz
Deprecated. 
FileUtils - Class in org.scijava.util
Useful methods for working with file paths.
filterInstances(List<PT>) - Method in class org.scijava.plugin.AbstractSingletonService
Allows subclasses to exclude instances.
findPlugins(List<PluginInfo<?>>) - Method in class org.scijava.plugin.DefaultPluginFinder
 
findPlugins(List<PluginInfo<?>>) - Method in interface org.scijava.plugin.PluginFinder
Populates the given list with all available SciJava plugins.
findPluginsOfClass(String, List<? extends PluginInfo<?>>, List<T>) - Static method in class org.scijava.plugin.DefaultPluginService
Transfers plugins of the given class from the source list to the destination list.
first(List<T>) - Static method in class org.scijava.util.ListUtils
Gets the first element of the given list, or null if none.
FIRST_PRIORITY - Static variable in class org.scijava.Priority
Priority for items that must be sorted first.
fix(File, File) - Static method in class org.scijava.util.CheckSezpoz
Deprecated. 
FloatArray - Class in org.scijava.util
An extensible array of float elements.
FloatArray() - Constructor for class org.scijava.util.FloatArray
Constructs an extensible array of floats, backed by a fixed-size array.
FloatArray(int) - Constructor for class org.scijava.util.FloatArray
Constructs an extensible array of floats, backed by a fixed-size array.
FloatArray(float[]) - Constructor for class org.scijava.util.FloatArray
Constructs an extensible array of floats, backed by the given fixed-size array.

G

Gateway - Interface in org.scijava
Interface for convenience classes that wrap a Context to provide one-line access to a suite of Services.
get(String) - Method in class org.scijava.AbstractBasicDetails
 
get(Class<S>) - Method in class org.scijava.AbstractGateway
 
get(String) - Method in class org.scijava.AbstractGateway
 
get(String) - Method in interface org.scijava.BasicDetails
Gets the value of the given key, or null if undefined.
get(Class<S>) - Method in interface org.scijava.Gateway
Returns an implementation of the requested Service, if it exists in the underlying Context.
get(String) - Method in interface org.scijava.Gateway
Returns an implementation of the Service with the given class name, if it exists in the underlying Context.
get(int) - Static method in enum org.scijava.input.KeyCode
Gets the KeyCode corresponding to the given numeric code, or KeyCode.UNDEFINED if no such code.
get(String) - Static method in enum org.scijava.input.KeyCode
Gets the KeyCode with the given name, or KeyCode.UNDEFINED if no such code.
get() - Method in interface org.scijava.object.LazyObjects
Gets the collection of objects.
get(Class<?>) - Method in class org.scijava.object.ObjectIndex
Gets a list of registered objects compatible with the given type.
get() - Method in class org.scijava.plugin.AbstractWrapperPlugin
 
get() - Method in interface org.scijava.plugin.WrapperPlugin
Gets the data object currently associated with this plugin.
get(int) - Method in class org.scijava.util.BoolArray
 
get(int) - Method in class org.scijava.util.ByteArray
 
get(int) - Method in class org.scijava.util.CharArray
 
get(int) - Method in class org.scijava.util.DoubleArray
 
get(int) - Method in class org.scijava.util.FloatArray
 
get(int) - Method in class org.scijava.util.IntArray
 
get(int) - Method in class org.scijava.util.LongArray
 
get(String) - Method in class org.scijava.util.Manifest
 
get(int) - Method in class org.scijava.util.ObjectArray
 
get(int) - Method in class org.scijava.util.ShortArray
 
getAccelerator() - Method in class org.scijava.MenuEntry
 
getAll() - Method in class org.scijava.object.ObjectIndex
Gets a list of all registered objects.
getAll() - Method in class org.scijava.util.Manifest
 
getAllPOMs() - Static method in class org.scijava.util.POM
Gets all available Maven POMs on the class path.
getAllVersions(File, String) - Static method in class org.scijava.util.FileUtils
Lists all versions of a given (possibly versioned) file name.
getAnnotatedFields(Class<?>, Class<A>) - Static method in class org.scijava.util.ClassUtils
Gets the given class's Fields marked with the annotation of the specified class.
getAnnotatedFields(Class<?>, Class<A>, List<Field>) - Static method in class org.scijava.util.ClassUtils
Gets the given class's Fields marked with the annotation of the specified class.
getAnnotation() - Method in class org.scijava.plugin.PluginInfo
Gets the associated @Plugin annotation.
getAnnotationFiles() - Method in class org.scijava.annotations.AnnotationCombiner
Scans for annotations files in every resource on the classpath.
getAnnotationFiles() - Method in class org.scijava.util.CombineAnnotations
Deprecated. Use AnnotationCombiner.getAnnotationFiles() instead.
getApp() - Method in class org.scijava.AbstractGateway
 
getApp(String) - Method in interface org.scijava.app.AppService
Gets an application by name.
getApp(String) - Method in class org.scijava.app.DefaultAppService
 
getApp() - Method in interface org.scijava.Gateway
 
getApps() - Method in interface org.scijava.app.AppService
Gets the table of associated applications, keyed by name.
getApps() - Method in class org.scijava.app.DefaultAppService
 
getArchiverVersion() - Method in class org.scijava.util.Manifest
 
getArray() - Method in class org.scijava.util.BoolArray
 
getArray() - Method in class org.scijava.util.ByteArray
 
getArray() - Method in class org.scijava.util.CharArray
 
getArray() - Method in class org.scijava.util.DoubleArray
 
getArray() - Method in class org.scijava.util.FloatArray
 
getArray() - Method in class org.scijava.util.IntArray
 
getArray() - Method in class org.scijava.util.LongArray
 
getArray() - Method in class org.scijava.util.ObjectArray
 
getArray() - Method in interface org.scijava.util.PrimitiveArray
Gets the fixed-size array backing this instance.
getArray() - Method in class org.scijava.util.ShortArray
 
getArrayClass(Class<?>) - Static method in class org.scijava.util.ClassUtils
Gets the array class corresponding to the given element type.
getArtifactId() - Method in interface org.scijava.app.App
The Maven artifactId of the application.
getArtifactId() - Method in class org.scijava.app.SciJavaApp
 
getArtifactId() - Method in class org.scijava.util.POM
Gets the POM's artifactId.
getBaseClass() - Method in class org.scijava.object.ObjectIndex
Gets the base class of the items being managed.
getBaseDirectory(String, Class<?>, String) - Static method in class org.scijava.util.AppUtils
Gets the application root directory.
getBaseDirectory(Class<?>) - Static method in class org.scijava.util.AppUtils
Gets the base file system directory containing the given class file.
getBaseDirectory(Class<?>, String) - Static method in class org.scijava.util.AppUtils
Gets the base file system directory containing the given class file.
getBaseDirectory(File, String) - Static method in class org.scijava.util.AppUtils
Gets the base file system directory from the given known class location.
getBuildJdk() - Method in class org.scijava.util.Manifest
 
getBuiltBy() - Method in class org.scijava.util.Manifest
 
getClass(Type) - Static method in class org.scijava.util.ConversionUtils
Gets the raw class corresponding to the given type.
getClassName() - Method in interface org.scijava.Instantiable
Gets the fully qualified name of the Class of the objects that can be created.
getClassName() - Method in class org.scijava.plugin.PluginInfo
 
getCode() - Method in enum org.scijava.input.KeyCode
Gets the key's numeric code.
getComponentClass(Type) - Static method in class org.scijava.util.ConversionUtils
Gets the component type of the given array type, or null if not an array.
getContext() - Method in class org.scijava.AbstractContextual
 
getContext() - Method in interface org.scijava.Contextual
Gets the application context to which the object belongs, or null if Contextual.setContext(Context) has not yet been called on this object.
getContext() - Method in class org.scijava.service.AbstractService
 
getCreatedBy() - Method in class org.scijava.util.Manifest
 
getDefaultValue(Number, Number, Class<?>) - Static method in class org.scijava.util.NumberUtils
 
getDescription() - Method in class org.scijava.AbstractBasicDetails
 
getDescription() - Method in interface org.scijava.BasicDetails
Gets a string describing the object.
getDocument() - Method in class org.scijava.util.XML
Gets the XML's DOM representation.
getEventClass() - Method in interface org.scijava.event.EventSubscriber
 
getEventService() - Method in class org.scijava.object.DefaultObjectService
 
getEventService() - Method in interface org.scijava.object.ObjectService
 
getEventString() - Method in class org.scijava.event.EventDetails
 
getEventType() - Method in class org.scijava.event.EventDetails
 
getExceptions() - Method in class org.scijava.plugin.PluginIndex
Gets the exceptions which occurred during the last invocation of PluginIndex.discover().
getExtension(File) - Static method in class org.scijava.util.FileUtils
Extracts the file extension from a file.
getExtension(String) - Static method in class org.scijava.util.FileUtils
Extracts the file extension from a file path.
getField(String, String) - Static method in class org.scijava.util.ClassUtils
Gets the specified field of the given class, or null if it does not exist.
getField(Class<?>, String) - Static method in class org.scijava.util.ClassUtils
Gets the specified field of the given class, or null if it does not exist.
getFieldName(Class<?>, int) - Static method in class org.scijava.util.DebugUtils
This method uses reflection to scan the values of the given class's static fields, returning the first matching field's name.
getGroupId() - Method in interface org.scijava.app.App
The Maven groupId of the application.
getGroupId() - Method in class org.scijava.app.SciJavaApp
 
getGroupId() - Method in class org.scijava.util.POM
Gets the POM's groupId.
getHandler(DT) - Method in class org.scijava.plugin.AbstractHandlerService
 
getHandler(DT) - Method in interface org.scijava.plugin.HandlerService
Gets the most appropriate handler for the given data object, or null if no handler supports it.
getIconPath() - Method in class org.scijava.AbstractUIDetails
 
getIconPath() - Method in class org.scijava.MenuEntry
 
getIconPath() - Method in interface org.scijava.UIDetails
Gets the resource path to an icon representing the object.
getIconURL() - Method in class org.scijava.plugin.PluginInfo
Gets the URL corresponding to the icon resource path.
getImplementationBuild() - Method in class org.scijava.util.Manifest
 
getImplementationDate() - Method in class org.scijava.util.Manifest
 
getImplementationTitle() - Method in class org.scijava.util.Manifest
 
getImplementationVendor() - Method in class org.scijava.util.Manifest
 
getImplementationVendorId() - Method in class org.scijava.util.Manifest
 
getImplementationVersion() - Method in class org.scijava.util.Manifest
 
getIndex() - Method in class org.scijava.object.DefaultObjectService
 
getIndex() - Method in interface org.scijava.object.ObjectService
Gets the index of available objects.
getIndex() - Method in class org.scijava.plugin.DefaultPluginService
 
getIndex() - Method in interface org.scijava.plugin.PluginService
Gets the index of available plugins.
getInfo(boolean) - Method in class org.scijava.AbstractGateway
 
getInfo(boolean) - Method in class org.scijava.app.AbstractApp
 
getInfo(boolean) - Method in interface org.scijava.app.App
Gets a string with information about the application.
getInfo(boolean) - Method in interface org.scijava.Gateway
 
getInfo() - Method in class org.scijava.plugin.AbstractRichPlugin
 
getInfo() - Method in interface org.scijava.plugin.HasPluginInfo
Gets the PluginInfo metadata associated with the object.
getInstance(Class<P>) - Method in class org.scijava.plugin.AbstractSingletonService
 
getInstance(Class<P>) - Method in interface org.scijava.plugin.SingletonService
Gets the singleton plugin instance of the given class.
getInstances() - Method in class org.scijava.plugin.AbstractSingletonService
 
getInstances() - Method in interface org.scijava.plugin.HandlerService
Gets the list of handlers.
getInstances() - Method in interface org.scijava.plugin.SingletonService
Gets the list of plugin instances.
getItems() - Method in class org.scijava.object.event.ListEvent
Gets the list of affected items.
getKeyCode() - Method in class org.scijava.input.Accelerator
 
getLabel() - Method in class org.scijava.AbstractBasicDetails
 
getLabel() - Method in interface org.scijava.BasicDetails
Gets the name to appear in a UI, if applicable.
getLeaf() - Method in class org.scijava.MenuPath
Gets the final element of the menu path.
getLevel() - Method in class org.scijava.log.AbstractLogService
 
getLevel() - Method in interface org.scijava.log.LogService
 
getLocation(String) - Static method in class org.scijava.util.ClassUtils
Gets the base location of the given class.
getLocation(String, ClassLoader) - Static method in class org.scijava.util.ClassUtils
Gets the base location of the given class.
getLocation(Class<?>) - Static method in class org.scijava.util.ClassUtils
Gets the base location of the given class.
getMainClass() - Static method in class org.scijava.util.AppUtils
Gets the class whose main method launched the application.
getMainClassName() - Static method in class org.scijava.util.DebugUtils
Get the class whose main method launched the application.
getManifest() - Method in class org.scijava.app.AbstractApp
 
getManifest() - Method in interface org.scijava.app.App
Gets the manifest containing metadata about the application.
getManifest(Class<?>) - Static method in class org.scijava.util.Manifest
Gets the JAR manifest associated with the given class.
getManifestVersion() - Method in class org.scijava.util.Manifest
 
getMaximumGrowth() - Method in class org.scijava.util.AbstractPrimitiveArray
 
getMaximumGrowth() - Method in interface org.scijava.util.PrimitiveArray
Gets the maximal step size by which to grow the fixed-size array when running out of space.
getMaximumNumber(Class<?>) - Static method in class org.scijava.util.NumberUtils
 
getMenuPath() - Method in class org.scijava.AbstractUIDetails
 
getMenuPath() - Method in interface org.scijava.UIDetails
Gets the path to the object's suggested position in the menu structure.
getMenuRoot() - Method in class org.scijava.AbstractUIDetails
 
getMenuRoot() - Method in interface org.scijava.UIDetails
Gets the name of the menu structure to which the object belongs.
getMenuString() - Method in class org.scijava.MenuPath
Gets the menu path as a string.
getMenuString(boolean) - Method in class org.scijava.MenuPath
Gets the menu path as a string, with or without the final element.
getMinimumNumber(Class<?>) - Static method in class org.scijava.util.NumberUtils
 
getMnemonic() - Method in class org.scijava.MenuEntry
 
getModifiers() - Method in class org.scijava.input.Accelerator
 
getName() - Method in class org.scijava.AbstractBasicDetails
 
getName() - Method in interface org.scijava.BasicDetails
Gets the unique name of the object.
getName() - Method in class org.scijava.MenuEntry
 
getNonprimitiveType(Class<T>) - Static method in class org.scijava.util.ClassUtils
Deprecated. use ConversionUtils.getNonprimitiveType(Class)
getNonprimitiveType(Class<T>) - Static method in class org.scijava.util.ConversionUtils
Returns the non-primitive Class closest to the given type.
getNullValue(Class<T>) - Static method in class org.scijava.util.ClassUtils
Deprecated. use ConversionUtils.getNullValue(Class)
getNullValue(Class<T>) - Static method in class org.scijava.util.ConversionUtils
Gets the "null" value for the given type.
getObject() - Method in class org.scijava.object.event.ObjectEvent
 
getObjects(Class<T>) - Method in class org.scijava.object.DefaultObjectService
 
getObjects(Class<T>) - Method in interface org.scijava.object.ObjectService
Gets a list of all registered objects compatible with the given type.
getOrganizationName() - Method in class org.scijava.util.POM
Gets the organization name.
getOrganizationURL() - Method in class org.scijava.util.POM
Gets the organization URL.
getPackage() - Method in class org.scijava.util.Manifest
 
getPath(File) - Static method in class org.scijava.util.FileUtils
Gets the absolute path to the given file, with the directory separator standardized to forward slash, like most platforms use.
getPath(String, String) - Static method in class org.scijava.util.FileUtils
Gets a standardized path based on the given one, with the directory separator standardized from the specific separator to forward slash, like most platforms use.
getPath() - Method in class org.scijava.util.XML
Gets the path to the XML document, or null if none.
getPlugin(Class<P>) - Method in class org.scijava.plugin.DefaultPluginService
 
getPlugin(Class<P>, Class<PT>) - Method in class org.scijava.plugin.DefaultPluginService
 
getPlugin(String) - Method in class org.scijava.plugin.DefaultPluginService
 
getPlugin(Class<P>) - Method in interface org.scijava.plugin.PluginService
Gets the first available plugin of the given class, or null if none.
getPlugin(Class<P>, Class<PT>) - Method in interface org.scijava.plugin.PluginService
Gets the first available plugin of the given class, or null if none.
getPlugin(String) - Method in interface org.scijava.plugin.PluginService
Gets the first available plugin of the given class name, or null if none.
getPluginClass() - Method in class org.scijava.plugin.PluginInfo
Obtains the Class of the item objects, if that class has already been loaded.
getPluginIndex() - Method in class org.scijava.Context
 
getPlugins() - Method in class org.scijava.plugin.AbstractPTService
 
getPlugins() - Method in class org.scijava.plugin.DefaultPluginService
 
getPlugins(Class<PT>) - Method in class org.scijava.plugin.PluginIndex
Gets a list of registered plugins compatible with the given type.
getPlugins() - Method in interface org.scijava.plugin.PluginService
Gets the list of known plugins.
getPlugins() - Method in interface org.scijava.plugin.PTService
Gets the plugins managed by this service.
getPluginService() - Method in class org.scijava.plugin.AbstractPTService
 
getPluginService() - Method in interface org.scijava.plugin.PTService
Gets the service responsible for discovering and managing this service's plugins.
getPluginsOfClass(Class<P>) - Method in class org.scijava.plugin.DefaultPluginService
 
getPluginsOfClass(Class<P>, Class<PT>) - Method in class org.scijava.plugin.DefaultPluginService
 
getPluginsOfClass(String) - Method in class org.scijava.plugin.DefaultPluginService
 
getPluginsOfClass(String, Class<PT>) - Method in class org.scijava.plugin.DefaultPluginService
 
getPluginsOfClass(Class<P>) - Method in interface org.scijava.plugin.PluginService
Gets the list of plugins of the given class.
getPluginsOfClass(Class<P>, Class<PT>) - Method in interface org.scijava.plugin.PluginService
Gets the list of plugins of the given class.
getPluginsOfClass(String) - Method in interface org.scijava.plugin.PluginService
Gets the list of plugins with the given class name.
getPluginsOfClass(String, Class<PT>) - Method in interface org.scijava.plugin.PluginService
Gets the list of plugins with the given class name.
getPluginsOfType(Class<PT>) - Method in class org.scijava.plugin.DefaultPluginService
 
getPluginsOfType(Class<PT>) - Method in interface org.scijava.plugin.PluginService
Gets the list of plugins of the given type (e.g., Service).
getPluginType(Class<P>) - Static method in class org.scijava.plugin.DefaultPluginService
Gets the plugin type of the given plugin class, as declared by its @Plugin annotation (i.e., Plugin.type()).
getPluginType() - Method in class org.scijava.plugin.PluginInfo
Gets the type of plugin described by the metadata.
getPluginType() - Method in interface org.scijava.plugin.PTService
Gets the type of plugins managed by this service.
getPOM() - Method in class org.scijava.app.AbstractApp
 
getPOM() - Method in interface org.scijava.app.App
Gets the Maven POM containing metadata about the application.
getPOM(Class<?>, String, String) - Static method in class org.scijava.util.POM
Gets the Maven POM associated with the given class.
getPrefix(int) - Method in class org.scijava.log.AbstractLogService
 
getPriority() - Method in class org.scijava.AbstractUIDetails
 
getPriority() - Method in class org.scijava.plugin.AbstractRichPlugin
 
getPriority() - Method in interface org.scijava.Prioritized
Gets the sort priority of the object.
getProgressMaximum() - Method in class org.scijava.app.event.StatusEvent
Gets progress maximum.
getProgressValue() - Method in class org.scijava.app.event.StatusEvent
Gets progress value.
getProjectDescription() - Method in class org.scijava.util.POM
Gets the project description.
getProjectInceptionYear() - Method in class org.scijava.util.POM
Gets the project inception year.
getProjectName() - Method in class org.scijava.util.POM
Gets the project name.
getProjectURL() - Method in class org.scijava.util.POM
Gets the project URL.
getSelectionGroup() - Method in class org.scijava.AbstractUIDetails
 
getSelectionGroup() - Method in interface org.scijava.UIDetails
Gets the name of the selection group to which the object belongs.
getService(Class<S>) - Method in class org.scijava.Context
Gets the service of the given class, or null if there is no matching service.
getService(String) - Method in class org.scijava.Context
Gets the service of the given class name (useful for scripts).
getService(Class<S>) - Method in class org.scijava.service.ServiceIndex
Gets the first available service compatible with the given class.
getServiceIndex() - Method in class org.scijava.Context
 
getSpecificationTitle() - Method in class org.scijava.util.Manifest
 
getSpecificationVendor() - Method in class org.scijava.util.Manifest
 
getSpecificationVersion() - Method in class org.scijava.util.Manifest
 
getStackDump() - Static method in class org.scijava.util.DebugUtils
Provides a complete stack dump of all threads.
getStackTrace(Throwable) - Static method in class org.scijava.util.DebugUtils
Extracts the given exception's corresponding stack trace to a string.
getStatusMessage(String, StatusEvent) - Method in class org.scijava.app.DefaultStatusService
 
getStatusMessage() - Method in class org.scijava.app.event.StatusEvent
Gets status message, or null for no change.
getStatusMessage(String, StatusEvent) - Method in interface org.scijava.app.StatusService
Gets the status message of the given event.
getSubscribers(Class<E>) - Method in class org.scijava.event.DefaultEventService
 
getSubscribers(Class<E>) - Method in interface org.scijava.event.EventService
Gets a list of all subscribers to the given event class (and subclasses thereof).
getTimestamp() - Method in class org.scijava.event.EventDetails
 
getTitle() - Method in class org.scijava.AbstractGateway
 
getTitle() - Method in class org.scijava.AbstractUIDetails
 
getTitle() - Method in interface org.scijava.app.App
Gets the title of the application.
getTitle() - Method in class org.scijava.app.SciJavaApp
 
getTitle() - Method in interface org.scijava.Gateway
 
getTitle() - Method in interface org.scijava.UIDetails
Gets an appropriate title for the object, for use in a user interface.
getType(E) - Method in class org.scijava.object.ObjectIndex
Return the type by which to index the object.
getType(PluginInfo<?>) - Method in class org.scijava.plugin.PluginIndex
Overrides the type by which the entries are indexed.
getType() - Method in interface org.scijava.Typed
Gets the type associated with the object.
getTypes(Class<?>) - Static method in class org.scijava.object.ObjectIndex
Gets a new set containing the type and all its supertypes.
getValue(int) - Method in class org.scijava.util.BoolArray
 
getValue(int) - Method in class org.scijava.util.ByteArray
 
getValue(int) - Method in class org.scijava.util.CharArray
 
getValue(Field, Object) - Static method in class org.scijava.util.ClassUtils
Gets the given field's value of the specified object instance, or null if the value cannot be obtained.
getValue(int) - Method in class org.scijava.util.DoubleArray
 
getValue(int) - Method in class org.scijava.util.FloatArray
 
getValue(int) - Method in class org.scijava.util.IntArray
 
getValue(int) - Method in class org.scijava.util.LongArray
 
getValue(int) - Method in class org.scijava.util.ObjectArray
 
getValue(int) - Method in class org.scijava.util.ShortArray
 
getVersion() - Method in class org.scijava.AbstractGateway
 
getVersion() - Method in class org.scijava.app.AbstractApp
 
getVersion() - Method in interface org.scijava.app.App
Gets the version of the application.
getVersion() - Method in interface org.scijava.Gateway
 
getVersion() - Method in class org.scijava.util.POM
Gets the POM's version.
getWeight() - Method in class org.scijava.MenuEntry
 

H

handle(Exception) - Method in class org.scijava.log.DefaultUncaughtExceptionHandler
 
HandlerPlugin<D> - Interface in org.scijava.plugin
Interface for plugins which "handle" a particular subset of data objects.
HandlerService<DT,PT extends HandlerPlugin<DT>> - Interface in org.scijava.plugin
A service for managing HandlerPlugins of a particular type.
hasClass(String) - Static method in class org.scijava.util.ClassUtils
Checks whether a class with the given name exists.
hasClass(String, ClassLoader) - Static method in class org.scijava.util.ClassUtils
Checks whether a class with the given name exists.
hashCode() - Method in class org.scijava.input.Accelerator
 
hashCode() - Method in class org.scijava.input.InputModifiers
 
hasMoreElements() - Method in class org.scijava.util.IteratorPlus
 
hasNext() - Method in class org.scijava.util.IteratorPlus
 
HasPluginInfo - Interface in org.scijava.plugin
A object with associated PluginInfo metadata.
HIGH_PRIORITY - Static variable in class org.scijava.Priority
Priority for items that prefer to be sorted earlier.
hoard - Variable in class org.scijava.object.ObjectIndex
"Them as counts counts moren them as dont count."
—Russell Hoban, Riddley Walker

I

index(File) - Method in class org.scijava.annotations.DirectoryIndexer
 
Index<A extends Annotation> - Class in org.scijava.annotations
Makes the annotation indexes accessible.
Indexable - Annotation Type in org.scijava.annotations
Meta annotation for indexable annotations.
IndexItem<A extends Annotation> - Class in org.scijava.annotations
Allows access to individual annotations.
indexOf(boolean) - Method in class org.scijava.util.BoolArray
 
indexOf(Object) - Method in class org.scijava.util.BoolArray
 
indexOf(byte) - Method in class org.scijava.util.ByteArray
 
indexOf(Object) - Method in class org.scijava.util.ByteArray
 
indexOf(char) - Method in class org.scijava.util.CharArray
 
indexOf(Object) - Method in class org.scijava.util.CharArray
 
indexOf(double) - Method in class org.scijava.util.DoubleArray
 
indexOf(Object) - Method in class org.scijava.util.DoubleArray
 
indexOf(float) - Method in class org.scijava.util.FloatArray
 
indexOf(Object) - Method in class org.scijava.util.FloatArray
 
indexOf(int) - Method in class org.scijava.util.IntArray
 
indexOf(Object) - Method in class org.scijava.util.IntArray
 
indexOf(long) - Method in class org.scijava.util.LongArray
 
indexOf(Object) - Method in class org.scijava.util.LongArray
 
indexOf(Object) - Method in class org.scijava.util.ObjectArray
 
indexOf(short) - Method in class org.scijava.util.ShortArray
 
indexOf(Object) - Method in class org.scijava.util.ShortArray
 
info(Object) - Method in class org.scijava.log.AbstractLogService
 
info(Throwable) - Method in class org.scijava.log.AbstractLogService
 
info(Object, Throwable) - Method in class org.scijava.log.AbstractLogService
 
INFO - Static variable in interface org.scijava.log.LogService
 
info(Object) - Method in interface org.scijava.log.LogService
 
info(Throwable) - Method in interface org.scijava.log.LogService
 
info(Object, Throwable) - Method in interface org.scijava.log.LogService
 
initialize() - Method in class org.scijava.app.DefaultAppService
 
initialize() - Method in class org.scijava.event.DefaultEventService
 
initialize() - Method in class org.scijava.object.DefaultObjectService
 
initialize() - Method in class org.scijava.plugin.AbstractSingletonService
 
initialize() - Method in class org.scijava.plugin.AbstractWrapperService
 
initialize() - Method in class org.scijava.plugin.DefaultPluginService
 
initialize() - Method in class org.scijava.service.AbstractService
 
initialize() - Method in interface org.scijava.service.Service
Performs any needed initialization when the service is first loaded.
inject(Object) - Method in class org.scijava.Context
Injects the application context into the given object.
inject(Object) - Method in class org.scijava.plugin.PluginInfo
Injects the metadata into the given object.
inject(Object, double) - Static method in class org.scijava.Priority
Injects the specified priority into the given object.
InputModifiers - Class in org.scijava.input
A UI-independent representation of keyboard and mouse modifier states.
InputModifiers(boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean) - Constructor for class org.scijava.input.InputModifiers
 
insert(int, int) - Method in class org.scijava.util.AbstractPrimitiveArray
Shifts the array to insert space at a specified index.
insert(int, int) - Method in interface org.scijava.util.PrimitiveArray
Shifts the array to insert space at a specified index.
install(LogService) - Static method in class org.scijava.log.DefaultUncaughtExceptionHandler
 
Instantiable<T> - Interface in org.scijava
An interface declaring the ability to create objects.
InstantiableException - Exception in org.scijava
An exception thrown when an Instantiable cannot create an object.
InstantiableException() - Constructor for exception org.scijava.InstantiableException
 
InstantiableException(String) - Constructor for exception org.scijava.InstantiableException
 
InstantiableException(String, Throwable) - Constructor for exception org.scijava.InstantiableException
 
InstantiableException(Throwable) - Constructor for exception org.scijava.InstantiableException
 
IntArray - Class in org.scijava.util
An extensible array of int elements.
IntArray() - Constructor for class org.scijava.util.IntArray
Constructs an extensible array of ints, backed by a fixed-size array.
IntArray(int) - Constructor for class org.scijava.util.IntArray
Constructs an extensible array of ints, backed by a fixed-size array.
IntArray(int[]) - Constructor for class org.scijava.util.IntArray
Constructs an extensible array of ints, backed by the given fixed-size array.
interrupt() - Method in class org.scijava.util.ReadInto
 
invoke(Runnable) - Method in class org.scijava.thread.DefaultThreadService
 
invoke(Runnable) - Method in interface org.scijava.thread.ThreadService
Executes the given code in a special dispatch thread, blocking until execution is complete.
is(String) - Method in class org.scijava.AbstractBasicDetails
 
is(String) - Method in interface org.scijava.BasicDetails
Returns true iff the given key is defined.
isActive() - Method in class org.scijava.event.DefaultEventHistory
 
isActive() - Method in interface org.scijava.event.EventHistory
Gets whether event history tracking is currently active.
isAltDown() - Method in class org.scijava.input.InputModifiers
 
isAltGrDown() - Method in class org.scijava.input.InputModifiers
 
isBoolean(Class<?>) - Static method in class org.scijava.util.ClassUtils
 
isByte(Class<?>) - Static method in class org.scijava.util.ClassUtils
 
isCharacter(Class<?>) - Static method in class org.scijava.util.ClassUtils
 
isClassObsolete(String) - Method in interface org.scijava.annotations.AbstractIndexWriter.StreamFactory
 
isConsumed() - Method in class org.scijava.event.SciJavaEvent
 
isCtrlDown() - Method in class org.scijava.input.InputModifiers
 
isCtrlReplacedWithMeta() - Static method in class org.scijava.input.Accelerator
 
isDebug() - Method in class org.scijava.log.AbstractLogService
 
isDebug() - Method in interface org.scijava.log.LogService
 
isDispatchThread() - Method in class org.scijava.thread.DefaultThreadService
 
isDispatchThread() - Method in interface org.scijava.thread.ThreadService
Gets whether the current thread is a dispatch thread for use with ThreadService.invoke(java.lang.Runnable) and ThreadService.queue(java.lang.Runnable).
isDouble(Class<?>) - Static method in class org.scijava.util.ClassUtils
 
isEmpty() - Method in class org.scijava.object.ObjectIndex
 
isEnabled() - Method in class org.scijava.AbstractUIDetails
 
isEnabled() - Method in interface org.scijava.UIDetails
Gets whether the object should be enabled in the user interface.
isError() - Method in class org.scijava.log.AbstractLogService
 
isError() - Method in interface org.scijava.log.LogService
 
isFloat(Class<?>) - Static method in class org.scijava.util.ClassUtils
 
isInfo() - Method in class org.scijava.log.AbstractLogService
 
isInfo() - Method in interface org.scijava.log.LogService
 
isInteger(Class<?>) - Static method in class org.scijava.util.ClassUtils
 
isLeftButtonDown() - Method in class org.scijava.input.InputModifiers
 
isLong(Class<?>) - Static method in class org.scijava.util.ClassUtils
 
isMetaDown() - Method in class org.scijava.input.InputModifiers
 
isMiddleButtonDown() - Method in class org.scijava.input.InputModifiers
 
isNumber(Class<?>) - Static method in class org.scijava.util.ClassUtils
 
isRightButtonDown() - Method in class org.scijava.input.InputModifiers
 
isSelectable() - Method in class org.scijava.AbstractUIDetails
 
isSelectable() - Method in interface org.scijava.UIDetails
Gets whether the object can be selected (e.g., checking and unchecking its menu item) in the user interface.
isSelected() - Method in class org.scijava.AbstractUIDetails
 
isSelected() - Method in interface org.scijava.UIDetails
Gets whether the object is selected (e.g., its menu item is checked) in the user interface.
isShiftDown() - Method in class org.scijava.input.InputModifiers
 
isShort(Class<?>) - Static method in class org.scijava.util.ClassUtils
 
isText(Class<?>) - Static method in class org.scijava.util.ClassUtils
 
isTrace() - Method in class org.scijava.log.AbstractLogService
 
isTrace() - Method in interface org.scijava.log.LogService
 
isVisible() - Method in class org.scijava.AbstractUIDetails
 
isVisible() - Method in interface org.scijava.UIDetails
Gets whether the object should be visible in the user interface.
isWarn() - Method in class org.scijava.log.AbstractLogService
 
isWarn() - Method in interface org.scijava.log.LogService
 
isWarning() - Method in class org.scijava.app.event.StatusEvent
Returns whether or not this is a warning event.
ItemIO - Enum in org.scijava
Defines the input/output type of a module.
ItemVisibility - Enum in org.scijava
Defines the "visibility" of a parameter.
iterator() - Method in class org.scijava.annotations.Index
 
iterator() - Method in class org.scijava.object.ObjectIndex
 
iterator() - Method in class org.scijava.util.IteratorPlus
 
IteratorPlus<E> - Class in org.scijava.util
A class that provides more thorough support for iteration.
IteratorPlus(Iterable<E>) - Constructor for class org.scijava.util.IteratorPlus
 
IteratorPlus(Enumeration<E>) - Constructor for class org.scijava.util.IteratorPlus
 
IteratorPlus(Iterator<E>) - Constructor for class org.scijava.util.IteratorPlus
 

K

KeyCode - Enum in org.scijava.input
A UI-independent enumeration of keyboard key codes.

L

LAST_PRIORITY - Static variable in class org.scijava.Priority
Priority for items that must be sorted last.
lastIndexOf(boolean) - Method in class org.scijava.util.BoolArray
 
lastIndexOf(Object) - Method in class org.scijava.util.BoolArray
 
lastIndexOf(byte) - Method in class org.scijava.util.ByteArray
 
lastIndexOf(Object) - Method in class org.scijava.util.ByteArray
 
lastIndexOf(char) - Method in class org.scijava.util.CharArray
 
lastIndexOf(Object) - Method in class org.scijava.util.CharArray
 
lastIndexOf(double) - Method in class org.scijava.util.DoubleArray
 
lastIndexOf(Object) - Method in class org.scijava.util.DoubleArray
 
lastIndexOf(float) - Method in class org.scijava.util.FloatArray
 
lastIndexOf(Object) - Method in class org.scijava.util.FloatArray
 
lastIndexOf(int) - Method in class org.scijava.util.IntArray
 
lastIndexOf(Object) - Method in class org.scijava.util.IntArray
 
lastIndexOf(long) - Method in class org.scijava.util.LongArray
 
lastIndexOf(Object) - Method in class org.scijava.util.LongArray
 
lastIndexOf(Object) - Method in class org.scijava.util.ObjectArray
 
lastIndexOf(short) - Method in class org.scijava.util.ShortArray
 
lastIndexOf(Object) - Method in class org.scijava.util.ShortArray
 
LazyObjects<T> - Interface in org.scijava.object
Interface for objects created lazily.
LegacyReader - Class in org.scijava.annotations.legacy
Reads legacy annotation indexes.
LegacyReader(InputStream) - Constructor for class org.scijava.annotations.legacy.LegacyReader
 
limitPath(String, int) - Static method in class org.scijava.util.FileUtils
Compacts a path into a given number of characters.
listContents(URL) - Static method in class org.scijava.util.FileUtils
Recursively lists the contents of the referenced directory.
listContents(URL, boolean, boolean) - Static method in class org.scijava.util.FileUtils
Lists all contents of the referenced directory.
ListEvent<T> - Class in org.scijava.object.event
An event indicating something has happened to a list of items.
ListEvent(T) - Constructor for class org.scijava.object.event.ListEvent
 
ListEvent(Collection<? extends T>) - Constructor for class org.scijava.object.event.ListEvent
 
ListUtils - Class in org.scijava.util
Useful methods for working with Lists.
load(Class<A>) - Static method in class org.scijava.annotations.Index
Loads the index of all classes annotated with the specified annotation.
load(Class<A>, ClassLoader) - Static method in class org.scijava.annotations.Index
Loads the index of all classes annotated with the specified annotation.
loadClass() - Method in interface org.scijava.Instantiable
Loads the class corresponding to the objects that are created by Instantiable.createInstance().
loadClass() - Method in class org.scijava.plugin.PluginInfo
 
loadClass(String) - Static method in class org.scijava.util.ClassUtils
Loads the class with the given name, using the current thread's context class loader, or null if it cannot be loaded.
loadClass(String, ClassLoader) - Static method in class org.scijava.util.ClassUtils
Loads the class with the given name, using the specified ClassLoader, or null if it cannot be loaded.
loadService(Class<S>) - Method in class org.scijava.service.ServiceHelper
Obtains a service compatible with the given class, instantiating it (and registering it in the index) if necessary.
loadServices() - Method in class org.scijava.service.ServiceHelper
Ensures all candidate service classes are registered in the index, locating and instantiating compatible services as needed.
loadXML(InputStream) - Static method in class org.scijava.util.XML
Loads an XML document from the given input stream.
loadXML(String) - Static method in class org.scijava.util.XML
Loads an XML document from the given input stream.
log() - Method in class org.scijava.AbstractGateway
 
log() - Method in interface org.scijava.Gateway
 
log(String) - Method in class org.scijava.log.AbstractLogService
Displays a message.
log(Throwable) - Method in class org.scijava.log.AbstractLogService
Displays an exception.
log(int, Object, Throwable) - Method in class org.scijava.log.AbstractLogService
 
log(int, Object) - Method in class org.scijava.log.AbstractLogService
 
log(String) - Method in class org.scijava.log.StderrLogService
Prints a message to stderr.
log(Throwable) - Method in class org.scijava.log.StderrLogService
Prints an exception to stderr.
LOG_LEVEL_PROPERTY - Static variable in interface org.scijava.log.LogService
System property to set for overriding the default logging level.
LogService - Interface in org.scijava.log
Interface for the logging service.
LongArray - Class in org.scijava.util
An extensible array of long elements.
LongArray() - Constructor for class org.scijava.util.LongArray
Constructs an extensible array of longs, backed by a fixed-size array.
LongArray(int) - Constructor for class org.scijava.util.LongArray
Constructs an extensible array of longs, backed by a fixed-size array.
LongArray(long[]) - Constructor for class org.scijava.util.LongArray
Constructs an extensible array of longs, backed by the given fixed-size array.
LOW_PRIORITY - Static variable in class org.scijava.Priority
Priority for items that prefer to be sorted later.

M

main(String[]) - Static method in class org.scijava.annotations.AnnotationCombiner
 
main(String...) - Static method in class org.scijava.annotations.EclipseHelper
Updates the annotation index in the current Eclipse project.
main(String[]) - Static method in class org.scijava.util.CombineAnnotations
Deprecated. Use AnnotationCombiner.main(String[]) instead.
main(String...) - Static method in class org.scijava.util.MetaInfCombiner
 
main(String[]) - Static method in class org.scijava.util.MirrorWebsite
 
main(String...) - Static method in class org.scijava.util.ServiceCombiner
 
Manifest - Class in org.scijava.util
Helper class for working with JAR manifests.
matchVersionedFilename(String) - Static method in class org.scijava.util.FileUtils
Deprecated. see FileUtils.stripFilenameVersion(String)
Menu - Annotation Type in org.scijava.plugin
One item of a Plugin's menu path.
MenuEntry - Class in org.scijava
One component of a menu path, for use with MenuPath.
MenuEntry(String) - Constructor for class org.scijava.MenuEntry
 
MenuEntry(String, double) - Constructor for class org.scijava.MenuEntry
 
MenuEntry(String, double, char, Accelerator, String) - Constructor for class org.scijava.MenuEntry
 
MenuPath - Class in org.scijava
A path in a hierarchical menu structure, for use with UIDetails.
MenuPath() - Constructor for class org.scijava.MenuPath
Creates an empty menu path.
MenuPath(Collection<? extends MenuEntry>) - Constructor for class org.scijava.MenuPath
Creates a menu path with the given entries.
MenuPath(String) - Constructor for class org.scijava.MenuPath
Creates a menu path with entries parsed from the given string.
merge(String, AbstractIndexWriter.StreamFactory) - Method in class org.scijava.annotations.AbstractIndexWriter
Merges an existing annotation index into the currently-generated one.
MetaInfCombiner - Class in org.scijava.util
Accumulates information from the class path to make META-INF/ files appropriate for an uber jar.
MetaInfCombiner() - Constructor for class org.scijava.util.MetaInfCombiner
 
mirror(String) - Method in class org.scijava.util.MirrorWebsite
 
MirrorWebsite - Class in org.scijava.util
This program mirrors a given website.
MirrorWebsite(String, File, int, long) - Constructor for class org.scijava.util.MirrorWebsite
 
MiscUtils - Class in org.scijava.util
Miscellaneous utility methods.
MouseCursor - Enum in org.scijava.input
A UI-independent enumeration of mouse cursors.

N

NAME - Static variable in class org.scijava.app.SciJavaApp
 
newThread(Runnable) - Method in class org.scijava.thread.DefaultThreadService
 
next() - Method in class org.scijava.util.IteratorPlus
 
nextElement() - Method in class org.scijava.util.IteratorPlus
 
NONE - Static variable in interface org.scijava.log.LogService
 
NORMAL_PRIORITY - Static variable in class org.scijava.Priority
Default priority for items.
NoSuchServiceException - Exception in org.scijava
An exception thrown when a Gateway cannot obtain a Service.
NoSuchServiceException() - Constructor for exception org.scijava.NoSuchServiceException
 
NoSuchServiceException(String) - Constructor for exception org.scijava.NoSuchServiceException
 
NoSuchServiceException(String, Throwable) - Constructor for exception org.scijava.NoSuchServiceException
 
NoSuchServiceException(Throwable) - Constructor for exception org.scijava.NoSuchServiceException
 
NullContextException - Exception in org.scijava
An exception thrown when a Context is null, but shouldn't be.
NullContextException() - Constructor for exception org.scijava.NullContextException
 
NullContextException(String) - Constructor for exception org.scijava.NullContextException
 
NullContextException(String, Throwable) - Constructor for exception org.scijava.NullContextException
 
NullContextException(Throwable) - Constructor for exception org.scijava.NullContextException
 
NumberUtils - Class in org.scijava.util
Useful methods for working with Number objects.

O

object() - Method in class org.scijava.AbstractGateway
 
object() - Method in interface org.scijava.Gateway
 
ObjectArray<E> - Class in org.scijava.util
An extensible, generic array of Object elements.
ObjectArray(Class<E>) - Constructor for class org.scijava.util.ObjectArray
Constructs an extensible array of objects, backed by a fixed-size array.
ObjectArray(Class<E>, int) - Constructor for class org.scijava.util.ObjectArray
Constructs an extensible array of objects, backed by a fixed-size array.
ObjectArray(E[]) - Constructor for class org.scijava.util.ObjectArray
Constructs an extensible array of objects, backed by the given fixed-size array.
ObjectCreatedEvent - Class in org.scijava.object.event
An event indicating a new object has been created.
ObjectCreatedEvent(Object) - Constructor for class org.scijava.object.event.ObjectCreatedEvent
 
ObjectDeletedEvent - Class in org.scijava.object.event
An event indicating an object has been deleted.
ObjectDeletedEvent(Object) - Constructor for class org.scijava.object.event.ObjectDeletedEvent
 
ObjectEvent - Class in org.scijava.object.event
An event indicating something has happened to an object.
ObjectEvent(Object) - Constructor for class org.scijava.object.event.ObjectEvent
 
ObjectIndex<E> - Class in org.scijava.object
Data structure for managing lists of registered objects.
ObjectIndex(Class<E>) - Constructor for class org.scijava.object.ObjectIndex
 
ObjectModifiedEvent - Class in org.scijava.object.event
An event indicating an object has been modified somehow.
ObjectModifiedEvent(Object) - Constructor for class org.scijava.object.event.ObjectModifiedEvent
 
ObjectsAddedEvent - Class in org.scijava.object.event
An event indicating one or more objects have been added to the ObjectService.
ObjectsAddedEvent(Object) - Constructor for class org.scijava.object.event.ObjectsAddedEvent
 
ObjectsAddedEvent(Collection<?>) - Constructor for class org.scijava.object.event.ObjectsAddedEvent
 
ObjectService - Interface in org.scijava.object
Interface for object management service.
ObjectsListEvent - Class in org.scijava.object.event
An event indicating something has happened to the list of objects registered with the ObjectService.
ObjectsListEvent(Object) - Constructor for class org.scijava.object.event.ObjectsListEvent
 
ObjectsListEvent(Collection<?>) - Constructor for class org.scijava.object.event.ObjectsListEvent
 
ObjectsRemovedEvent - Class in org.scijava.object.event
An event indicating one or more objects have been removed from the ObjectService.
ObjectsRemovedEvent(Object) - Constructor for class org.scijava.object.event.ObjectsRemovedEvent
 
ObjectsRemovedEvent(Collection<?>) - Constructor for class org.scijava.object.event.ObjectsRemovedEvent
 
onEvent(SciJavaEvent) - Method in class org.scijava.event.DefaultEventHistory
 
onEvent(E) - Method in interface org.scijava.event.EventSubscriber
 
onEvent(ObjectCreatedEvent) - Method in class org.scijava.object.DefaultObjectService
 
onEvent(ObjectDeletedEvent) - Method in class org.scijava.object.DefaultObjectService
 
openInput(String) - Method in interface org.scijava.annotations.AbstractIndexWriter.StreamFactory
 
openOutput(String) - Method in interface org.scijava.annotations.AbstractIndexWriter.StreamFactory
 
Optional - Interface in org.scijava
A marker interface for optional SciJava components.
org.scijava - package org.scijava
 
org.scijava.annotations - package org.scijava.annotations
 
org.scijava.annotations.legacy - package org.scijava.annotations.legacy
 
org.scijava.app - package org.scijava.app
 
org.scijava.app.event - package org.scijava.app.event
 
org.scijava.event - package org.scijava.event
 
org.scijava.input - package org.scijava.input
 
org.scijava.log - package org.scijava.log
 
org.scijava.object - package org.scijava.object
 
org.scijava.object.event - package org.scijava.object.event
 
org.scijava.plugin - package org.scijava.plugin
 
org.scijava.plugin.event - package org.scijava.plugin.event
 
org.scijava.service - package org.scijava.service
 
org.scijava.service.event - package org.scijava.service.event
 
org.scijava.thread - package org.scijava.thread
 
org.scijava.util - package org.scijava.util
 
out - Variable in class org.scijava.util.ReadInto
 

P

Parameter - Annotation Type in org.scijava.plugin
An annotation for indicating a field is an input or output parameter.
PATH_SEPARATOR - Static variable in class org.scijava.MenuPath
The separator between elements of a menu path string.
plugin() - Method in class org.scijava.AbstractGateway
 
plugin() - Method in interface org.scijava.Gateway
 
Plugin - Annotation Type in org.scijava.plugin
Annotation identifying a plugin, which gets loaded by SciJava's dynamic discovery mechanism.
PluginFinder - Interface in org.scijava.plugin
Interface for mechanisms that define how SciJava plugins are discovered.
PluginIndex - Class in org.scijava.plugin
Data structure for managing registered plugins.
PluginIndex() - Constructor for class org.scijava.plugin.PluginIndex
Constructs a new plugin index which uses a DefaultPluginFinder to discover plugins.
PluginIndex(PluginFinder) - Constructor for class org.scijava.plugin.PluginIndex
Constructs a new plugin index which uses the given PluginFinder to discover plugins.
PluginInfo<PT extends SciJavaPlugin> - Class in org.scijava.plugin
A collection of metadata about a particular plugin.
PluginInfo(String, Class<PT>) - Constructor for class org.scijava.plugin.PluginInfo
Creates a new plugin metadata object.
PluginInfo(String, Class<PT>, Plugin) - Constructor for class org.scijava.plugin.PluginInfo
Creates a new plugin metadata object.
PluginInfo(String, Class<PT>, Plugin, ClassLoader) - Constructor for class org.scijava.plugin.PluginInfo
Creates a new plugin metadata object.
PluginInfo(Class<? extends PT>, Class<PT>) - Constructor for class org.scijava.plugin.PluginInfo
Creates a new plugin metadata object.
PluginInfo(Class<? extends PT>, Class<PT>, Plugin) - Constructor for class org.scijava.plugin.PluginInfo
Creates a new plugin metadata object.
PluginInfo(String, Class<? extends PT>, Class<PT>, Plugin, ClassLoader) - Constructor for class org.scijava.plugin.PluginInfo
 
PluginsAddedEvent - Class in org.scijava.plugin.event
An event indicating one or more plugins have been added to the PluginService.
PluginsAddedEvent(PluginInfo<?>) - Constructor for class org.scijava.plugin.event.PluginsAddedEvent
 
PluginsAddedEvent(Collection<? extends PluginInfo<?>>) - Constructor for class org.scijava.plugin.event.PluginsAddedEvent
 
PluginService - Interface in org.scijava.plugin
Interface for service that keeps track of available plugins.
PluginsListEvent - Class in org.scijava.plugin.event
An event indicating something has happened to the list of plugins registered with the PluginService.
PluginsListEvent(PluginInfo<?>) - Constructor for class org.scijava.plugin.event.PluginsListEvent
 
PluginsListEvent(Collection<? extends PluginInfo<?>>) - Constructor for class org.scijava.plugin.event.PluginsListEvent
 
PluginsRemovedEvent - Class in org.scijava.plugin.event
An event indicating one or more plugins have been removed from the PluginService.
PluginsRemovedEvent(PluginInfo<?>) - Constructor for class org.scijava.plugin.event.PluginsRemovedEvent
 
PluginsRemovedEvent(Collection<? extends PluginInfo<?>>) - Constructor for class org.scijava.plugin.event.PluginsRemovedEvent
 
POM - Class in org.scijava.util
Helper class for working with Maven POMs.
POM(File) - Constructor for class org.scijava.util.POM
Parses a POM from the given file.
POM(URL) - Constructor for class org.scijava.util.POM
Parses a POM from the given URL.
POM(InputStream) - Constructor for class org.scijava.util.POM
Parses a POM from the given input stream.
POM(String) - Constructor for class org.scijava.util.POM
Parses a POM from the given string.
PrimitiveArray<ArrayType,BaseType> - Interface in org.scijava.util
Interface for primitive-type extensible arrays, modeled after ArrayList, but more performant.
Prioritized - Interface in org.scijava
An object that can be sorted according to priority.
PRIORITY - Static variable in class org.scijava.event.DefaultEventService
The default event service's priority.
Priority - Class in org.scijava
Constants for specifying an item's priority.
process(Set<? extends TypeElement>, RoundEnvironment) - Method in class org.scijava.annotations.AnnotationProcessor
 
ProcessUtils - Class in org.scijava.util
Useful methods for working with processes.
PTService<PT extends SciJavaPlugin> - Interface in org.scijava.plugin
A service for managing a particular sort of SciJavaPlugin.
publish(StatusEvent) - Method in class org.scijava.app.DefaultStatusService
Publish the status event to the event service.
publish(Object) - Method in class org.scijava.event.DefaultEventBus
 
publish(Type, Object) - Method in class org.scijava.event.DefaultEventBus
 
publish(String, Object) - Method in class org.scijava.event.DefaultEventBus
 
publish(Object, String, Object, List, List, StackTraceElement[]) - Method in class org.scijava.event.DefaultEventBus
 
publish(E) - Method in class org.scijava.event.DefaultEventService
 
publish(E) - Method in interface org.scijava.event.EventService
Publishes the given event immediately, reporting it to all subscribers.
publishLater(Object) - Method in class org.scijava.event.DefaultEventBus
 
publishLater(Type, Object) - Method in class org.scijava.event.DefaultEventBus
 
publishLater(String, Object) - Method in class org.scijava.event.DefaultEventBus
 
publishLater(E) - Method in class org.scijava.event.DefaultEventService
 
publishLater(E) - Method in interface org.scijava.event.EventService
Queues the given event for publication, typically on a separate thread (called the "event dispatch thread").
publishNow(Object) - Method in class org.scijava.event.DefaultEventBus
 
publishNow(Type, Object) - Method in class org.scijava.event.DefaultEventBus
 
publishNow(String, Object) - Method in class org.scijava.event.DefaultEventBus
 

Q

queue(Runnable) - Method in class org.scijava.thread.DefaultThreadService
 
queue(Runnable) - Method in interface org.scijava.thread.ThreadService
Queues the given code for later execution in a special dispatch thread.

R

reader - Variable in class org.scijava.util.ReadInto
 
ReadInto - Class in org.scijava.util
This class takes an InputStream and either accumulates the read bytes in a String or outputs to a PrintStream.
ReadInto(InputStream, PrintStream) - Constructor for class org.scijava.util.ReadInto
Construct a ReadInto thread and start it right away.
ReadInto(InputStream, PrintStream, boolean) - Constructor for class org.scijava.util.ReadInto
Construct a ReadInto thread and start it right away.
readObject() - Method in class org.scijava.annotations.legacy.LegacyReader
 
registerEventHandlers() - Method in class org.scijava.service.AbstractService
 
registerEventHandlers() - Method in interface org.scijava.service.Service
Registers the service's event handler methods.
reloadPlugins() - Method in class org.scijava.plugin.DefaultPluginService
 
reloadPlugins() - Method in interface org.scijava.plugin.PluginService
Rediscovers all plugins available on the classpath.
remove(Object) - Method in class org.scijava.object.ObjectIndex
 
remove(Object, boolean) - Method in class org.scijava.object.ObjectIndex
Removes the object from all compatible type lists.
remove(Object, Class<?>, boolean) - Method in class org.scijava.object.ObjectIndex
Removes an object from type lists beneath the given type hierarchy.
remove(Object, boolean) - Method in class org.scijava.plugin.PluginIndex
Removes the plugin from all type lists compatible with its plugin type.
remove(int) - Method in class org.scijava.util.AbstractPrimitiveArray
 
remove(Object) - Method in class org.scijava.util.BoolArray
 
remove(Object) - Method in class org.scijava.util.ByteArray
 
remove(Object) - Method in class org.scijava.util.CharArray
 
remove(Object) - Method in class org.scijava.util.DoubleArray
 
remove(Object) - Method in class org.scijava.util.FloatArray
 
remove(Object) - Method in class org.scijava.util.IntArray
 
remove() - Method in class org.scijava.util.IteratorPlus
 
remove(Object) - Method in class org.scijava.util.LongArray
 
remove(Object) - Method in class org.scijava.util.ObjectArray
 
remove(Object) - Method in class org.scijava.util.ShortArray
 
removeAll(Collection<?>) - Method in class org.scijava.object.ObjectIndex
 
removeAll(Collection<?>) - Method in class org.scijava.util.BoolArray
 
removeAll(Collection<?>) - Method in class org.scijava.util.ByteArray
 
removeAll(Collection<?>) - Method in class org.scijava.util.CharArray
 
removeAll(Collection<?>) - Method in class org.scijava.util.DoubleArray
 
removeAll(Collection<?>) - Method in class org.scijava.util.FloatArray
 
removeAll(Collection<?>) - Method in class org.scijava.util.IntArray
 
removeAll(Collection<?>) - Method in class org.scijava.util.LongArray
 
removeAll(Collection<?>) - Method in class org.scijava.util.ObjectArray
 
removeAll(Collection<?>) - Method in class org.scijava.util.ShortArray
 
removeFromList(Object, List<E>, boolean) - Method in class org.scijava.object.ObjectIndex
 
removeListener(EventHistoryListener) - Method in class org.scijava.event.DefaultEventHistory
 
removeListener(EventHistoryListener) - Method in interface org.scijava.event.EventHistory
Removes an event history listener.
removeObject(Object) - Method in class org.scijava.object.DefaultObjectService
 
removeObject(Object) - Method in interface org.scijava.object.ObjectService
Deregisters an object with the object service.
removePlugin(PluginInfo<?>) - Method in class org.scijava.plugin.DefaultPluginService
 
removePlugin(PluginInfo<?>) - Method in interface org.scijava.plugin.PluginService
Manually unregisters a plugin with the plugin service.
removePlugins(Collection<T>) - Method in class org.scijava.plugin.DefaultPluginService
 
removePlugins(Collection<T>) - Method in interface org.scijava.plugin.PluginService
Manually unregisters plugins with the plugin service.
removeValue(boolean) - Method in class org.scijava.util.BoolArray
 
removeValue(byte) - Method in class org.scijava.util.ByteArray
 
removeValue(char) - Method in class org.scijava.util.CharArray
 
removeValue(double) - Method in class org.scijava.util.DoubleArray
 
removeValue(float) - Method in class org.scijava.util.FloatArray
 
removeValue(int) - Method in class org.scijava.util.IntArray
 
removeValue(long) - Method in class org.scijava.util.LongArray
 
removeValue(E) - Method in class org.scijava.util.ObjectArray
 
removeValue(short) - Method in class org.scijava.util.ShortArray
 
report(String) - Method in class org.scijava.util.Timing
 
reset() - Method in class org.scijava.util.Timing
 
retainAll(Collection<?>) - Method in class org.scijava.object.ObjectIndex
 
retrieveList(Class<?>) - Method in class org.scijava.object.ObjectIndex
Retrieves the type list for the given type, creating it if necessary.
retrieveListsForType(Class<?>) - Method in class org.scijava.object.ObjectIndex
 
RichPlugin - Interface in org.scijava.plugin
Base interface for Contextual, Prioritized plugins that retain access to their associated PluginInfo metadata via the HasPluginInfo interface.
run(Callable<V>) - Method in class org.scijava.thread.DefaultThreadService
 
run(Runnable) - Method in class org.scijava.thread.DefaultThreadService
 
run(Callable<V>) - Method in interface org.scijava.thread.ThreadService
Asynchronously executes the given code in a new thread, as decided by the thread service.
run(Runnable) - Method in interface org.scijava.thread.ThreadService
Asynchronously executes the given code in a new thread, as decided by the thread service.
run() - Method in class org.scijava.util.MirrorWebsite
 
run() - Method in class org.scijava.util.ReadInto
The main method.

S

SciJavaApp - Class in org.scijava.app
Application metadata about SciJava Common.
SciJavaApp() - Constructor for class org.scijava.app.SciJavaApp
 
SciJavaEvent - Class in org.scijava.event
Base class for all SciJava events.
SciJavaEvent() - Constructor for class org.scijava.event.SciJavaEvent
 
SciJavaPlugin - Interface in org.scijava.plugin
Top-level interface for plugins.
SciJavaService - Interface in org.scijava.service
Marker interface for core SciJava Common Services.
service(Class<S>) - Method in class org.scijava.Context
Gets the service of the given class.
service(String) - Method in class org.scijava.Context
Gets the service of the given class name (useful for scripts).
Service - Interface in org.scijava.service
A SciJava service, for a particular area of functionality.
ServiceCombiner - Class in org.scijava.util
Combines Service information from all JAR files on the classpath.
ServiceCombiner() - Constructor for class org.scijava.util.ServiceCombiner
 
ServiceHelper - Class in org.scijava.service
Helper class for discovering and instantiating available services.
ServiceHelper(Context) - Constructor for class org.scijava.service.ServiceHelper
Creates a new service helper for discovering and instantiating services.
ServiceHelper(Context, Collection<Class<? extends Service>>) - Constructor for class org.scijava.service.ServiceHelper
Creates a new service helper for discovering and instantiating services.
ServiceIndex - Class in org.scijava.service
Data structure for tracking registered services.
ServiceIndex() - Constructor for class org.scijava.service.ServiceIndex
 
ServicesLoadedEvent - Class in org.scijava.service.event
TODO
ServicesLoadedEvent() - Constructor for class org.scijava.service.event.ServicesLoadedEvent
 
set(String, String) - Method in class org.scijava.AbstractBasicDetails
 
set(String, String) - Method in interface org.scijava.BasicDetails
Sets the value of the given key.
set(D) - Method in class org.scijava.plugin.AbstractWrapperPlugin
 
set(D) - Method in interface org.scijava.plugin.WrapperPlugin
Associates the given data object with this plugin.
set(int, BaseType) - Method in class org.scijava.util.AbstractPrimitiveArray
 
set(int, Boolean) - Method in class org.scijava.util.BoolArray
 
set(int, Byte) - Method in class org.scijava.util.ByteArray
 
set(int, Character) - Method in class org.scijava.util.CharArray
 
set(int, Double) - Method in class org.scijava.util.DoubleArray
 
set(int, Float) - Method in class org.scijava.util.FloatArray
 
set(int, Integer) - Method in class org.scijava.util.IntArray
 
set(int, Long) - Method in class org.scijava.util.LongArray
 
set(int, E) - Method in class org.scijava.util.ObjectArray
 
set(int, Short) - Method in class org.scijava.util.ShortArray
 
setAccelerator(Accelerator) - Method in class org.scijava.MenuEntry
 
setActive(boolean) - Method in class org.scijava.event.DefaultEventHistory
 
setActive(boolean) - Method in interface org.scijava.event.EventHistory
Activates or deactivates event history tracking.
setArray(boolean[]) - Method in class org.scijava.util.BoolArray
 
setArray(byte[]) - Method in class org.scijava.util.ByteArray
 
setArray(char[]) - Method in class org.scijava.util.CharArray
 
setArray(double[]) - Method in class org.scijava.util.DoubleArray
 
setArray(float[]) - Method in class org.scijava.util.FloatArray
 
setArray(int[]) - Method in class org.scijava.util.IntArray
 
setArray(long[]) - Method in class org.scijava.util.LongArray
 
setArray(E[]) - Method in class org.scijava.util.ObjectArray
 
setArray(ArrayType) - Method in interface org.scijava.util.PrimitiveArray
Sets the fixed-size array backing this instance.
setArray(short[]) - Method in class org.scijava.util.ShortArray
 
setConsumed(boolean) - Method in class org.scijava.event.SciJavaEvent
 
setContext(Context) - Method in class org.scijava.AbstractContextual
 
setContext(Context) - Method in interface org.scijava.Contextual
Sets the application context to which the object belongs.
setContext(Context) - Method in class org.scijava.service.AbstractService
 
setDescription(String) - Method in class org.scijava.AbstractBasicDetails
 
setDescription(String) - Method in interface org.scijava.BasicDetails
Sets a string describing the object.
setEnabled(boolean) - Method in class org.scijava.AbstractUIDetails
 
setEnabled(boolean) - Method in interface org.scijava.UIDetails
Sets whether the object should be enabled in the user interface.
setIconPath(String) - Method in class org.scijava.AbstractUIDetails
 
setIconPath(String) - Method in class org.scijava.MenuEntry
 
setIconPath(String) - Method in interface org.scijava.UIDetails
Sets the resource path to an icon representing the object.
setInfo(PluginInfo<?>) - Method in class org.scijava.plugin.AbstractRichPlugin
 
setInfo(PluginInfo<?>) - Method in interface org.scijava.plugin.HasPluginInfo
Sets the PluginInfo metadata associated with the object.
setLabel(String) - Method in class org.scijava.AbstractBasicDetails
 
setLabel(String) - Method in interface org.scijava.BasicDetails
Sets the name to appear in a UI, if applicable.
setLevel(int) - Method in class org.scijava.log.AbstractLogService
 
setLevel(String, int) - Method in class org.scijava.log.AbstractLogService
 
setLevel(int) - Method in interface org.scijava.log.LogService
 
setMaximumGrowth(int) - Method in class org.scijava.util.AbstractPrimitiveArray
 
setMaximumGrowth(int) - Method in interface org.scijava.util.PrimitiveArray
Sets the maximal step size by which to grow the fixed-size array when running out of space.
setMenuPath(MenuPath) - Method in class org.scijava.AbstractUIDetails
 
setMenuPath(MenuPath) - Method in interface org.scijava.UIDetails
Sets the path to the object's suggested position in the menu structure.
setMenuRoot(String) - Method in class org.scijava.AbstractUIDetails
 
setMenuRoot(String) - Method in interface org.scijava.UIDetails
Sets the name of the menu structure to which the object belongs.
setMnemonic(char) - Method in class org.scijava.MenuEntry
 
setName(String) - Method in class org.scijava.AbstractBasicDetails
 
setName(String) - Method in interface org.scijava.BasicDetails
Sets the unique name of the object.
setName(String) - Method in class org.scijava.MenuEntry
 
setPluginClass(Class<? extends PT>) - Method in class org.scijava.plugin.PluginInfo
Explicitly sets the Class of the item objects.
setPluginType(Class<PT>) - Method in class org.scijava.plugin.PluginInfo
Sets the type of plugin described by the metadata.
setPriority(double) - Method in class org.scijava.AbstractUIDetails
 
setPriority(double) - Method in class org.scijava.plugin.AbstractRichPlugin
 
setPriority(double) - Method in interface org.scijava.Prioritized
Sets the sort priority of the object.
setSelectable(boolean) - Method in class org.scijava.AbstractUIDetails
 
setSelectable(boolean) - Method in interface org.scijava.UIDetails
Sets whether the object can be selected (e.g., checking and unchecking its menu item) in the user interface.
setSelected(boolean) - Method in class org.scijava.AbstractUIDetails
 
setSelected(boolean) - Method in interface org.scijava.UIDetails
Sets whether the object is selected (e.g., its menu item is checked) in the user interface.
setSelectionGroup(String) - Method in class org.scijava.AbstractUIDetails
 
setSelectionGroup(String) - Method in interface org.scijava.UIDetails
Sets the name of the selection group to which the object belongs.
setSize(int) - Method in class org.scijava.util.AbstractPrimitiveArray
 
setSize(int) - Method in interface org.scijava.util.Sizable
 
setSize(int) - Method in class org.scijava.util.SizableArrayList
 
setValue(int, boolean) - Method in class org.scijava.util.BoolArray
 
setValue(int, byte) - Method in class org.scijava.util.ByteArray
 
setValue(int, char) - Method in class org.scijava.util.CharArray
 
setValue(Field, Object, Object) - Static method in class org.scijava.util.ClassUtils
Sets the given field's value of the specified object instance.
setValue(int, double) - Method in class org.scijava.util.DoubleArray
 
setValue(int, float) - Method in class org.scijava.util.FloatArray
 
setValue(int, int) - Method in class org.scijava.util.IntArray
 
setValue(int, long) - Method in class org.scijava.util.LongArray
 
setValue(int, E) - Method in class org.scijava.util.ObjectArray
 
setValue(int, short) - Method in class org.scijava.util.ShortArray
 
setVisible(boolean) - Method in class org.scijava.AbstractUIDetails
 
setVisible(boolean) - Method in interface org.scijava.UIDetails
Sets whether the object should be visible in the user interface.
setWeight(double) - Method in class org.scijava.MenuEntry
 
ShortArray - Class in org.scijava.util
An extensible array of short elements.
ShortArray() - Constructor for class org.scijava.util.ShortArray
Constructs an extensible array of shorts, backed by a fixed-size array.
ShortArray(int) - Constructor for class org.scijava.util.ShortArray
Constructs an extensible array of shorts, backed by a fixed-size array.
ShortArray(short[]) - Constructor for class org.scijava.util.ShortArray
Constructs an extensible array of shorts, backed by the given fixed-size array.
SHORTENER_BACKSLASH - Static variable in class org.scijava.util.FileUtils
 
SHORTENER_BACKSLASH_REGEX - Static variable in class org.scijava.util.FileUtils
 
SHORTENER_ELLIPSE - Static variable in class org.scijava.util.FileUtils
 
SHORTENER_SLASH - Static variable in class org.scijava.util.FileUtils
 
SHORTENER_SLASH_REGEX - Static variable in class org.scijava.util.FileUtils
 
shortenPath(String) - Static method in class org.scijava.util.FileUtils
Shortens the path to a maximum of 4 path elements.
shortenPath(String, int) - Static method in class org.scijava.util.FileUtils
Shortens the path based on the given maximum number of path elements.
showProgress(int, int) - Method in class org.scijava.app.DefaultStatusService
 
showProgress(int, int) - Method in interface org.scijava.app.StatusService
Updates the progress bar.
showStatus(String) - Method in class org.scijava.app.DefaultStatusService
 
showStatus(int, int, String) - Method in class org.scijava.app.DefaultStatusService
 
showStatus(int, int, String, boolean) - Method in class org.scijava.app.DefaultStatusService
 
showStatus(String) - Method in interface org.scijava.app.StatusService
Updates the status message.
showStatus(int, int, String) - Method in interface org.scijava.app.StatusService
Updates the status message and progress bar.
showStatus(int, int, String, boolean) - Method in interface org.scijava.app.StatusService
Updates the status message and progress bar, optionally flagging the status notification as a warning.
SingletonPlugin - Interface in org.scijava.plugin
Interface for plugins intended to be instantiated as singletons.
SingletonService<PT extends SingletonPlugin> - Interface in org.scijava.plugin
A service for managing SingletonPlugins of a particular type.
Sizable - Interface in org.scijava.util
An entity with a size.
SizableArrayList<E> - Class in org.scijava.util
An ArrayList whose size can be adjusted more efficiently.
SizableArrayList(int) - Constructor for class org.scijava.util.SizableArrayList
 
SizableArrayList() - Constructor for class org.scijava.util.SizableArrayList
 
SizableArrayList(Collection<? extends E>) - Constructor for class org.scijava.util.SizableArrayList
 
size() - Method in class org.scijava.object.ObjectIndex
 
size() - Method in class org.scijava.util.AbstractPrimitiveArray
 
size() - Method in interface org.scijava.util.Sizable
 
SortablePlugin - Class in org.scijava.plugin
Deprecated. Use AbstractRichPlugin instead.
SortablePlugin() - Constructor for class org.scijava.plugin.SortablePlugin
Deprecated.  
SortedObjectIndex<E extends Comparable<? super E>> - Class in org.scijava.object
Data structure for managing sorted lists of registered objects.
SortedObjectIndex(Class<E>) - Constructor for class org.scijava.object.SortedObjectIndex
 
start(boolean) - Static method in class org.scijava.util.Timing
 
status() - Method in class org.scijava.AbstractGateway
 
status() - Method in interface org.scijava.Gateway
 
StatusEvent - Class in org.scijava.app.event
An event indicating a status update.
StatusEvent(String) - Constructor for class org.scijava.app.event.StatusEvent
 
StatusEvent(String, boolean) - Constructor for class org.scijava.app.event.StatusEvent
 
StatusEvent(int, int) - Constructor for class org.scijava.app.event.StatusEvent
 
StatusEvent(int, int, String) - Constructor for class org.scijava.app.event.StatusEvent
 
StatusEvent(int, int, String, boolean) - Constructor for class org.scijava.app.event.StatusEvent
 
StatusService - Interface in org.scijava.app
Interface for the status notification service.
StderrLogService - Class in org.scijava.log
Implementation of LogService using the standard error stream.
StderrLogService() - Constructor for class org.scijava.log.StderrLogService
 
stop(Timing) - Static method in class org.scijava.util.Timing
 
StringMaker - Class in org.scijava.util
Helper class for building up Strings of key/value pairs.
StringMaker() - Constructor for class org.scijava.util.StringMaker
 
StringMaker(String) - Constructor for class org.scijava.util.StringMaker
 
stripFilenameVersion(String) - Static method in class org.scijava.util.FileUtils
 
subscribe(Object) - Method in class org.scijava.event.DefaultEventService
 
subscribe(Object) - Method in interface org.scijava.event.EventService
Subscribes all of the given object's @EventHandler annotated methods.
supports(DT) - Method in class org.scijava.plugin.AbstractHandlerService
 
supports(D) - Method in class org.scijava.plugin.AbstractTypedPlugin
 
supports(DT) - Method in class org.scijava.plugin.AbstractWrapperService
 
supports(DT) - Method in interface org.scijava.plugin.HandlerService
Gets whether the given data object is supported.
supports(T) - Method in interface org.scijava.Typed
Gets whether this object is compatible with the given data object.

T

thread() - Method in class org.scijava.AbstractGateway
 
thread() - Method in interface org.scijava.Gateway
 
THREAD_COUNT - Static variable in class org.scijava.util.MirrorWebsite
 
ThreadService - Interface in org.scijava.thread
Interface for the thread handling service.
tick(Timing) - Static method in class org.scijava.util.Timing
 
tick(Timing, Object) - Static method in class org.scijava.util.Timing
 
Timing - Class in org.scijava.util
A helper class to help with optimizing the performance of a list of operations.
Timing() - Constructor for class org.scijava.util.Timing
 
toArray() - Method in class org.scijava.object.ObjectIndex
 
toArray(T[]) - Method in class org.scijava.object.ObjectIndex
 
toCollection(Object) - Static method in class org.scijava.util.ArrayUtils
Converts the provided Object to a Collection implementation.
toHTML(Set<Class<? extends SciJavaEvent>>, Set<Class<? extends SciJavaEvent>>) - Method in class org.scijava.event.DefaultEventHistory
 
toHTML(boolean) - Method in class org.scijava.event.EventDetails
 
toHTML(Set<Class<? extends SciJavaEvent>>, Set<Class<? extends SciJavaEvent>>) - Method in interface org.scijava.event.EventHistory
Gets the recorded event history as an HTML string.
toNumber(Object, Class<?>) - Static method in class org.scijava.util.NumberUtils
Converts the given object to a Number of the specified type, or null if the types are incompatible.
toSimpleName(Class<?>) - Static method in class org.scijava.annotations.legacy.LegacyReader
 
toString() - Method in class org.scijava.AbstractBasicDetails
 
toString() - Method in class org.scijava.AbstractUIDetails
 
toString() - Method in class org.scijava.app.event.StatusEvent
 
toString() - Method in class org.scijava.event.SciJavaEvent
 
toString() - Method in class org.scijava.input.Accelerator
 
toString() - Method in class org.scijava.input.InputModifiers
 
toString() - Method in class org.scijava.MenuEntry
 
toString() - Method in class org.scijava.object.event.ListEvent
 
toString() - Method in class org.scijava.object.event.ObjectEvent
 
toString() - Method in class org.scijava.object.ObjectIndex
 
toString() - Method in class org.scijava.plugin.AbstractRichPlugin
 
toString() - Method in class org.scijava.plugin.PluginInfo
 
toString() - Method in class org.scijava.service.AbstractService
 
toString() - Method in class org.scijava.util.ReadInto
Return the output as a String unless a PrintStream was specified in the constructor.
toString() - Method in class org.scijava.util.StringMaker
 
toString() - Method in class org.scijava.util.XML
 
trace(Object) - Method in class org.scijava.log.AbstractLogService
 
trace(Throwable) - Method in class org.scijava.log.AbstractLogService
 
trace(Object, Throwable) - Method in class org.scijava.log.AbstractLogService
 
TRACE - Static variable in interface org.scijava.log.LogService
 
trace(Object) - Method in interface org.scijava.log.LogService
 
trace(Throwable) - Method in interface org.scijava.log.LogService
 
trace(Object, Throwable) - Method in interface org.scijava.log.LogService
 
Typed<T> - Interface in org.scijava
An object with an associated type (i.e., Class), which can be queried at runtime.
TypedPlugin<D> - Interface in org.scijava.plugin
Interface for plugins with an associated type (i.e., Class).
TypedService<DT,PT extends TypedPlugin<DT>> - Interface in org.scijava.plugin
A service for managing a particular sort of TypedPlugin.

U

UIDetails - Interface in org.scijava
An interface defining details useful for generating relevant user interface elements.
uncaughtException(Thread, Throwable) - Method in class org.scijava.log.DefaultUncaughtExceptionHandler
 
unsubscribe(Collection<EventSubscriber<?>>) - Method in class org.scijava.event.DefaultEventService
 
unsubscribe(Collection<EventSubscriber<?>>) - Method in interface org.scijava.event.EventService
Removes all the given subscribers; they will no longer be notified when events are published.
updateAnnotationIndex(ClassLoader) - Static method in class org.scijava.annotations.EclipseHelper
Updates the annotation index in the current Eclipse project.
urlToFile(URL) - Static method in class org.scijava.util.FileUtils
Converts the given URL to its corresponding File.
urlToFile(String) - Static method in class org.scijava.util.FileUtils
Converts the given URL string to its corresponding File.

V

valueOf(String) - Static method in enum org.scijava.input.KeyCode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.scijava.input.MouseCursor
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.scijava.ItemIO
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.scijava.ItemVisibility
Returns the enum constant of this type with the specified name.
values() - Static method in enum org.scijava.input.KeyCode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.scijava.input.MouseCursor
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.scijava.ItemIO
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.scijava.ItemVisibility
Returns an array containing the constants of this enum type, in the order they are declared.
verbose - Static variable in class org.scijava.util.CheckSezpoz
Deprecated. 
VERY_HIGH_PRIORITY - Static variable in class org.scijava.Priority
Priority for items that strongly prefer to be sorted early.
VERY_LOW_PRIORITY - Static variable in class org.scijava.Priority
Priority for items that strongly prefer to be sorted late.

W

warn(String) - Method in class org.scijava.app.DefaultStatusService
 
warn(String) - Method in interface org.scijava.app.StatusService
Issues a warning message.
warn(Object) - Method in class org.scijava.log.AbstractLogService
 
warn(Throwable) - Method in class org.scijava.log.AbstractLogService
 
warn(Object, Throwable) - Method in class org.scijava.log.AbstractLogService
 
WARN - Static variable in interface org.scijava.log.LogService
 
warn(Object) - Method in interface org.scijava.log.LogService
 
warn(Throwable) - Method in interface org.scijava.log.LogService
 
warn(Object, Throwable) - Method in interface org.scijava.log.LogService
 
WrapperPlugin<D> - Interface in org.scijava.plugin
A plugin with a special "has-a" relationship (i.e., composition rather than inheritance) with a single data object of a particular type.
WrapperService<DT,PT extends WrapperPlugin<DT>> - Interface in org.scijava.plugin
A service for managing WrapperPlugins of a particular type.
write(AbstractIndexWriter.StreamFactory) - Method in class org.scijava.annotations.AbstractIndexWriter
 
write(File) - Method in class org.scijava.annotations.DirectoryIndexer
 
writeMap(PrintStream, Object...) - Method in class org.scijava.annotations.AbstractIndexWriter
 
writeXMLFile(Document, File) - Static method in class org.scijava.util.CheckSezpoz
Deprecated. 

X

XML - Class in org.scijava.util
Helper class for working with XML documents.
XML(File) - Constructor for class org.scijava.util.XML
Parses XML from the given file.
XML(URL) - Constructor for class org.scijava.util.XML
Parses XML from the given URL.
XML(InputStream) - Constructor for class org.scijava.util.XML
Parses XML from the given input stream.
XML(String) - Constructor for class org.scijava.util.XML
Parses XML from the given string.
XML(Document) - Constructor for class org.scijava.util.XML
Creates an XML object for an existing document.
XML(String, Document) - Constructor for class org.scijava.util.XML
Creates an XML object for an existing document.
xpath(String) - Method in class org.scijava.util.XML
Obtains the nodes identified by the given XPath expression.

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