Index (SciJava Common 2.49.0 API)

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

A

about() - Method in class org.scijava.app.AbstractApp
about() - Method in interface org.scijava.app.App: Displays information about the application.
about() - Method in interface org.scijava.platform.AppEventService: Deprecated.
Use App.about() instead.
about() - Method in class org.scijava.platform.DefaultAppEventService: Deprecated.
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
AbstractConsoleArgument - Class in org.scijava.console: Abstract superclass of ConsoleArgument implementations.
AbstractConsoleArgument() - Constructor for class org.scijava.console.AbstractConsoleArgument
AbstractConsolePane<C> - Class in org.scijava.ui.console: Abstract base class of ConsolePane implementations.
AbstractConsolePane(Context) - Constructor for class org.scijava.ui.console.AbstractConsolePane
AbstractContextual - Class in org.scijava: Abstract base class for Contextual objects.
AbstractContextual() - Constructor for class org.scijava.AbstractContextual
AbstractConverter<I,O> - Class in org.scijava.convert: Abstract superclass for Converter plugins.
AbstractConverter() - Constructor for class org.scijava.convert.AbstractConverter
AbstractConvertService - Class in org.scijava.convert: Abstract superclass for ConvertService implementations.
AbstractConvertService() - Constructor for class org.scijava.convert.AbstractConvertService
AbstractDataHandle<L extends Location> - Class in org.scijava.io: Abstract base class for DataHandle plugins.
AbstractDataHandle() - Constructor for class org.scijava.io.AbstractDataHandle
AbstractDisplay<T> - Class in org.scijava.display: Abstract superclass of Display implementations.
AbstractDisplay(Class<T>) - Constructor for class org.scijava.display.AbstractDisplay
AbstractDisplayViewer<T> - Class in org.scijava.ui.viewer: The AbstractDisplayViewer provides some basic generic implementations for a DisplayViewer such as storing and providing the display, window and panel for a DisplayViewer.
AbstractDisplayViewer() - Constructor for class org.scijava.ui.viewer.AbstractDisplayViewer
AbstractDragAndDropData - Class in org.scijava.ui.dnd: Abstract superclass for DragAndDropData implementations.
AbstractDragAndDropData() - Constructor for class org.scijava.ui.dnd.AbstractDragAndDropData
AbstractDragAndDropHandler<D> - Class in org.scijava.ui.dnd: Abstract superclass for DragAndDropHandlers.
AbstractDragAndDropHandler() - Constructor for class org.scijava.ui.dnd.AbstractDragAndDropHandler
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
AbstractInputHarvester<P,W> - Class in org.scijava.widget: Abstract superclass for InputHarvesters.
AbstractInputHarvester() - Constructor for class org.scijava.widget.AbstractInputHarvester
AbstractInputHarvesterPlugin<P,W> - Class in org.scijava.ui: AbstractInputHarvesterPlugin is an InputHarvester that implements the PreprocessorPlugin interface.
AbstractInputHarvesterPlugin() - Constructor for class org.scijava.ui.AbstractInputHarvesterPlugin
AbstractInputPanel<P,W> - Class in org.scijava.widget: Abstract superclass of UI-specific InputPanel implementations.
AbstractInputPanel() - Constructor for class org.scijava.widget.AbstractInputPanel
AbstractInputWidget<T,W> - Class in org.scijava.widget: Base class for input widgets.
AbstractInputWidget() - Constructor for class org.scijava.widget.AbstractInputWidget
AbstractIOPlugin<D> - Class in org.scijava.io: Abstract base class for IOPlugins.
AbstractIOPlugin() - Constructor for class org.scijava.io.AbstractIOPlugin
AbstractLocation - Class in org.scijava.io: Abstract base class for Location implementations.
AbstractLocation() - Constructor for class org.scijava.io.AbstractLocation
AbstractLogService - Class in org.scijava.log: Base implementation of an abstract LogService.
AbstractLogService() - Constructor for class org.scijava.log.AbstractLogService
AbstractMenuCreator<T,M> - Class in org.scijava.menu: Abstract helper class for generating a menu structure.
AbstractMenuCreator() - Constructor for class org.scijava.menu.AbstractMenuCreator
AbstractModule - Class in org.scijava.module: Abstract superclass of Module implementations.
AbstractModule() - Constructor for class org.scijava.module.AbstractModule
AbstractModuleInfo - Class in org.scijava.module: Abstract superclass of ModuleInfo implementation.
AbstractModuleInfo() - Constructor for class org.scijava.module.AbstractModuleInfo
AbstractModuleItem<T> - Class in org.scijava.module: Abstract superclass of ModuleItem implementations.
AbstractModuleItem(ModuleInfo) - Constructor for class org.scijava.module.AbstractModuleItem
AbstractPlatform - Class in org.scijava.platform: Abstract superclass of platform implementations.
AbstractPlatform() - Constructor for class org.scijava.platform.AbstractPlatform
AbstractPostprocessorPlugin - Class in org.scijava.module.process: Abstract base class for plugin postprocessors.
AbstractPostprocessorPlugin() - Constructor for class org.scijava.module.process.AbstractPostprocessorPlugin
AbstractPrefService - Class in org.scijava.prefs: Abstract PrefService implementation.
AbstractPrefService() - Constructor for class org.scijava.prefs.AbstractPrefService
AbstractPreprocessorPlugin - Class in org.scijava.module.process: Abstract base class for plugin preprocessors.
AbstractPreprocessorPlugin() - Constructor for class org.scijava.module.process.AbstractPreprocessorPlugin
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
AbstractScriptContext - Class in org.scijava.script: A minimal implementation of ScriptContext for use in the AbstractScriptEngine.
AbstractScriptContext() - Constructor for class org.scijava.script.AbstractScriptContext
AbstractScriptEngine - Class in org.scijava.script: This class implements dummy versions for ScriptEngine's methods that are not needed by the SciJava scripting framework.
AbstractScriptEngine() - Constructor for class org.scijava.script.AbstractScriptEngine
AbstractScriptHeader - Class in org.scijava.script: Abstract superclass for ScriptHeader implementations.
AbstractScriptHeader() - Constructor for class org.scijava.script.AbstractScriptHeader
AbstractScriptLanguage - Class in org.scijava.script: Abstract superclass for ScriptLanguage implementations.
AbstractScriptLanguage() - Constructor for class org.scijava.script.AbstractScriptLanguage
AbstractService - Class in org.scijava.service: Abstract superclass of Service implementations.
AbstractService() - Constructor for class org.scijava.service.AbstractService
AbstractSingleInputPreprocessor - Class in org.scijava.module.process: Abstract superclass for PreprocessorPlugin implementations that populate singleton inputs.
AbstractSingleInputPreprocessor() - Constructor for class org.scijava.module.process.AbstractSingleInputPreprocessor
AbstractSingletonService<PT extends SingletonPlugin> - Class in org.scijava.plugin: Abstract base class for SingletonServices.
AbstractSingletonService() - Constructor for class org.scijava.plugin.AbstractSingletonService
AbstractTextDisplayViewer - Class in org.scijava.ui.viewer.text: Implements the UI-independent elements of a text viewer.
AbstractTextDisplayViewer() - Constructor for class org.scijava.ui.viewer.text.AbstractTextDisplayViewer
AbstractTextFormat - Class in org.scijava.text: Abstract superclass of TextFormat implementations.
AbstractTextFormat() - Constructor for class org.scijava.text.AbstractTextFormat
AbstractTool - Class in org.scijava.tool: Abstract base class for Tool implementations.
AbstractTool() - Constructor for class org.scijava.tool.AbstractTool
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
AbstractUIInputWidget<T,W> - Class in org.scijava.ui: Abstract superclass of InputWidget implementations that belong to a specific UI.
AbstractUIInputWidget() - Constructor for class org.scijava.ui.AbstractUIInputWidget
AbstractUserInterface - Class in org.scijava.ui: Abstract superclass for UserInterface implementations.
AbstractUserInterface() - Constructor for class org.scijava.ui.AbstractUserInterface
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
acquireDrawer(Tool) - Method in interface org.scijava.tool.IconService
activate() - Method in class org.scijava.tool.AbstractTool
activate() - Method in interface org.scijava.tool.Tool: Informs the tool that it is now active.
activate() - Method in interface org.scijava.ui.ApplicationFrame: Activate the application frame, bringing it to the front.
ActiveDisplayPreprocessor - Class in org.scijava.display: Assigns the active Display when there is one single unresolved Display parameter.
ActiveDisplayPreprocessor() - Constructor for class org.scijava.display.ActiveDisplayPreprocessor
adapt(Object) - Method in class org.scijava.annotations.AbstractIndexWriter
adapt(A) - Method in class org.scijava.annotations.AbstractIndexWriter
AdaptedScriptLanguage - Class in org.scijava.script: Abstract superclass for ScriptLanguage implementations which adapt an existing ScriptEngineFactory.
AdaptedScriptLanguage(ScriptEngineFactory) - Constructor for class org.scijava.script.AdaptedScriptLanguage: Creates a new AdaptedScriptLanguage wrapping the given ScriptEngineFactory.
AdaptedScriptLanguage(String) - Constructor for class org.scijava.script.AdaptedScriptLanguage: Creates a new AdaptedScriptLanguage wrapping the ScriptEngineFactory with the given name.
add(Map<String, Object>, String, String) - Method in class org.scijava.annotations.AbstractIndexWriter
add(A, String) - Method in class org.scijava.annotations.DirectoryIndexer
add(int, T) - Method in class org.scijava.display.AbstractDisplay
add(T) - Method in class org.scijava.display.AbstractDisplay
add(String) - Method in class org.scijava.io.DefaultRecentFileService
add(String) - Method in interface org.scijava.io.RecentFileService: Adds or refreshes a path on the list of recent files.
add(ModuleInfo) - Method in class org.scijava.menu.ShadowMenu: Adds the given module to the menu structure.
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(ScriptEngineFactory, boolean) - Method in class org.scijava.script.ScriptLanguageIndex
add(ScriptLanguage) - Method in class org.scijava.script.ScriptLanguageIndex
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(T) - Method in class org.scijava.util.LastRecentlyUsed: Add a new newest entry.
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
addAlias(Class<?>) - Method in class org.scijava.script.DefaultScriptService
addAlias(String, Class<?>) - Method in class org.scijava.script.DefaultScriptService
addAlias(Class<?>) - Method in interface org.scijava.script.ScriptService: TODO
addAlias(String, Class<?>) - Method in interface org.scijava.script.ScriptService: TODO
addAll(int, Collection<? extends T>) - Method in class org.scijava.display.AbstractDisplay
addAll(Collection<? extends T>) - Method in class org.scijava.display.AbstractDisplay
addAll(Collection<? extends ModuleInfo>) - Method in class org.scijava.menu.ShadowMenu: Adds the given modules to the menu structure.
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(Collection<? extends T>) - Method in class org.scijava.util.LastRecentlyUsed
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
addArgDelimiter() - Method in interface org.scijava.script.CodeGenerator: Adds delimiter character between arguments (typically a ',').
addArgDelimiter() - Method in class org.scijava.script.CodeGeneratorJava
addArgument(ParameterObject) - Method in interface org.scijava.script.CodeGenerator
addArgument(ParameterObject) - Method in class org.scijava.script.CodeGeneratorJava
addDisplayViewer(DisplayViewer<?>) - Method in class org.scijava.ui.DefaultUIService
addDisplayViewer(DisplayViewer<?>) - Method in interface org.scijava.ui.UIService: Registers the given viewer with the service.
addInput(String, Class<T>) - Method in class org.scijava.module.DefaultMutableModule
addInput(ModuleItem<?>) - Method in class org.scijava.module.DefaultMutableModule
addInput(ModuleItem<?>) - Method in class org.scijava.module.DefaultMutableModuleInfo
addInput(String, Class<T>) - Method in interface org.scijava.module.MutableModule: Adds an input to the list.
addInput(ModuleItem<?>) - Method in interface org.scijava.module.MutableModule: Adds an input to the list.
addInput(ModuleItem<?>) - Method in interface org.scijava.module.MutableModuleInfo: Adds an input to the list.
addLater(LazyObjects<? extends E>) - Method in class org.scijava.object.ObjectIndex: Registers objects which will be created lazily as needed.
addLeafToMenu(ShadowMenu, M) - Method in class org.scijava.menu.AbstractMenuCreator
addLeafToTop(ShadowMenu, T) - Method in class org.scijava.menu.AbstractMenuCreator
addListener(EventHistoryListener) - Method in class org.scijava.event.DefaultEventHistory
addListener(EventHistoryListener) - Method in interface org.scijava.event.EventHistory: Adds an event history listener.
addModule(ModuleInfo) - Method in class org.scijava.module.DefaultModuleService
addModule(ModuleInfo) - Method in interface org.scijava.module.ModuleService: Manually registers a module with the module service.
addModuleCalled(String) - Method in interface org.scijava.script.CodeGenerator
addModuleCalled(String) - Method in class org.scijava.script.CodeGeneratorJava
addModules(Collection<? extends ModuleInfo>) - Method in class org.scijava.module.DefaultModuleService
addModules(Collection<? extends ModuleInfo>) - Method in interface org.scijava.module.ModuleService: Manually registers a list of modules with the module service.
addNonLeafToMenu(ShadowMenu, M) - Method in class org.scijava.menu.AbstractMenuCreator
addNonLeafToTop(ShadowMenu, T) - Method in class org.scijava.menu.AbstractMenuCreator
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.
addOutput(String, Class<T>) - Method in class org.scijava.module.DefaultMutableModule
addOutput(ModuleItem<?>) - Method in class org.scijava.module.DefaultMutableModule
addOutput(ModuleItem<?>) - Method in class org.scijava.module.DefaultMutableModuleInfo
addOutput(String, Class<T>) - Method in interface org.scijava.module.MutableModule: Adds an output to the list.
addOutput(ModuleItem<?>) - Method in interface org.scijava.module.MutableModule: Adds an output to the list.
addOutput(ModuleItem<?>) - Method in interface org.scijava.module.MutableModuleInfo: Adds an output to the list.
addOutputListener(OutputListener) - Method in interface org.scijava.console.ConsoleService: Adds a listener for output sent to stdout or stderr.
addOutputListener(OutputListener) - Method in class org.scijava.console.DefaultConsoleService
addOutputStream(OutputStream) - Method in class org.scijava.console.MultiOutputStream: Adds an output stream to those receiving this stream's output.
addParameter(String, Class<?>, Object) - Method in class org.scijava.script.InvocationObject
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.
addPropertyChangeListener(PropertyChangeListener) - Method in interface org.scijava.ui.Arrangeable
addScriptDirectory(File) - Method in class org.scijava.script.DefaultScriptService
addScriptDirectory(File, MenuPath) - Method in class org.scijava.script.DefaultScriptService
addScriptDirectory(File) - Method in interface org.scijava.script.ScriptService: Adds a base directory to scan for scripts.
addScriptDirectory(File, MenuPath) - Method in interface org.scijava.script.ScriptService: Adds a base directory to scan for scripts, placing discovered scripts beneath the given menu path prefix.
addSeparatorToMenu(M) - Method in class org.scijava.menu.AbstractMenuCreator
addSeparatorToTop(T) - Method in class org.scijava.menu.AbstractMenuCreator
addTiming(Object) - Method in class org.scijava.util.Timing
addTiming(long, Object) - Method in class org.scijava.util.Timing
addToEnd(T) - Method in class org.scijava.util.LastRecentlyUsed: Add a new oldest entry.
addToList(E, List<E>, boolean) - Method in class org.scijava.object.ObjectIndex
addToList(E, List<E>, boolean) - Method in class org.scijava.object.SortedObjectIndex
addUI(UserInterface) - Method in class org.scijava.ui.DefaultUIService
addUI(String, UserInterface) - Method in class org.scijava.ui.DefaultUIService
addUI(UserInterface) - Method in interface org.scijava.ui.UIService: Adds the given UI to those managed by the service.
addUI(String, UserInterface) - Method in interface org.scijava.ui.UIService: Adds the given UI to those managed by the service.
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
addWidget(InputWidget<?, W>) - Method in class org.scijava.widget.AbstractInputPanel
addWidget(InputWidget<?, W>) - Method in interface org.scijava.widget.InputPanel: Adds a widget to the panel.
ALICEBLUE - Static variable in class org.scijava.util.Colors
allocate(long...) - Static method in class org.scijava.util.ArrayUtils: Allocates a 1-dimensional byte array matching the product of the given sizes.
ANALYZE_LABEL - Static variable in class org.scijava.menu.MenuConstants
ANALYZE_MNEMONIC - Static variable in class org.scijava.menu.MenuConstants
ANALYZE_WEIGHT - Static variable in class org.scijava.menu.MenuConstants
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
ANTIQUEWHITE - Static variable in class org.scijava.util.Colors
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: Gets this application context's AppService.
AppAboutEvent - Class in org.scijava.platform.event: An event sent when the application is asked to open its about window.
AppAboutEvent() - Constructor for class org.scijava.platform.event.AppAboutEvent
append(String) - Method in class org.scijava.display.DefaultTextDisplay
append(String) - Method in interface org.scijava.display.TextDisplay: Add a line to the display.
append(OutputEvent) - Method in interface org.scijava.ui.console.ConsolePane: Appends the given output to the console.
append(String) - Method in interface org.scijava.ui.viewer.text.TextDisplayPanel
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.
appEvent() - Method in class org.scijava.AbstractGateway
appEvent() - Method in interface org.scijava.Gateway: Gets this application context's AppEventService.
AppEventService - Interface in org.scijava.platform: Deprecated.
Use AppService and App instead.
AppFocusEvent - Class in org.scijava.platform.event: An event sent when the application has become the foreground app, or when it has resigned being the foreground app.
AppFocusEvent(boolean) - Constructor for class org.scijava.platform.event.AppFocusEvent
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.
ApplicationEvent - Class in org.scijava.platform.event: An event indicating an application-level occurrence.
ApplicationEvent() - Constructor for class org.scijava.platform.event.ApplicationEvent
ApplicationFrame - Interface in org.scijava.ui: Common interface for top-level application frames.
AppMenusCreatedEvent - Class in org.scijava.platform.event: An event sent when the application has created and populated its menus.
AppMenusCreatedEvent(Object) - Constructor for class org.scijava.platform.event.AppMenusCreatedEvent
AppOpenFilesEvent - Class in org.scijava.platform.event: An event sent when the application is asked to re-open itself.
AppOpenFilesEvent(List<File>) - Constructor for class org.scijava.platform.event.AppOpenFilesEvent
AppPreferencesEvent - Class in org.scijava.platform.event: An event sent when the application is asked to open its preferences window.
AppPreferencesEvent() - Constructor for class org.scijava.platform.event.AppPreferencesEvent
AppPrintEvent - Class in org.scijava.platform.event: An event sent when the app is asked to print a list of files.
AppPrintEvent() - Constructor for class org.scijava.platform.event.AppPrintEvent
AppQuitEvent - Class in org.scijava.platform.event: An event sent when the application is asked to quit.
AppQuitEvent() - Constructor for class org.scijava.platform.event.AppQuitEvent
AppReOpenEvent - Class in org.scijava.platform.event: An event sent when the application is asked to re-open itself.
AppReOpenEvent() - Constructor for class org.scijava.platform.event.AppReOpenEvent
AppScreenSleepEvent - Class in org.scijava.platform.event: An event sent when the displays attached to the system enter and exit power save sleep.
AppScreenSleepEvent(boolean) - Constructor for class org.scijava.platform.event.AppScreenSleepEvent
AppService - Interface in org.scijava.app: Interface for application-level functionality.
AppSleepEvent - Class in org.scijava.platform.event: An event sent when a device enters or exits power save sleep.
AppSleepEvent(boolean) - Constructor for class org.scijava.platform.event.AppSleepEvent
AppSystemSleepEvent - Class in org.scijava.platform.event: An event sent when the system enters and exits power save sleep.
AppSystemSleepEvent(boolean) - Constructor for class org.scijava.platform.event.AppSystemSleepEvent
AppUserSessionEvent - Class in org.scijava.platform.event: An event sent when the the user session has been changed via Fast User Switching.
AppUserSessionEvent(boolean) - Constructor for class org.scijava.platform.event.AppUserSessionEvent
AppUtils - Class in org.scijava.util: Useful methods for obtaining details of the SciJava application environment.
AppVisibleEvent - Class in org.scijava.platform.event: An event sent when the application has been hidden or shown.
AppVisibleEvent(boolean) - Constructor for class org.scijava.platform.event.AppVisibleEvent
AQUA - Static variable in class org.scijava.util.Colors
AQUAMARINE - Static variable in class org.scijava.util.Colors
AREA_STYLE - Static variable in interface org.scijava.widget.TextWidget: Widget style for text areas.
ARGBPlane - Class in org.scijava.ui: Represents a plane of ARGB pixel data.
ARGBPlane(int, int, int[]) - Constructor for class org.scijava.ui.ARGBPlane
ARGBPlane(int, int) - Constructor for class org.scijava.ui.ARGBPlane
Arrangeable - Interface in org.scijava.ui: Arrangeable.
Arrangeable.Arrangement - Enum in org.scijava.ui
ArrayConverters - Class in org.scijava.convert: Container class for all desired combinations of PrimitiveArrayUnwrapper and PrimitiveArrayWrapper implementations.
ArrayConverters() - Constructor for class org.scijava.convert.ArrayConverters
ArrayConverters.BoolArrayUnwrapper - Class in org.scijava.convert
ArrayConverters.BoolArrayUnwrapper() - Constructor for class org.scijava.convert.ArrayConverters.BoolArrayUnwrapper
ArrayConverters.BoolArrayWrapper - Class in org.scijava.convert
ArrayConverters.BoolArrayWrapper() - Constructor for class org.scijava.convert.ArrayConverters.BoolArrayWrapper
ArrayConverters.ByteArrayUnwrapper - Class in org.scijava.convert
ArrayConverters.ByteArrayUnwrapper() - Constructor for class org.scijava.convert.ArrayConverters.ByteArrayUnwrapper
ArrayConverters.ByteArrayWrapper - Class in org.scijava.convert
ArrayConverters.ByteArrayWrapper() - Constructor for class org.scijava.convert.ArrayConverters.ByteArrayWrapper
ArrayConverters.CharArrayUnwrapper - Class in org.scijava.convert
ArrayConverters.CharArrayUnwrapper() - Constructor for class org.scijava.convert.ArrayConverters.CharArrayUnwrapper
ArrayConverters.CharArrayWrapper - Class in org.scijava.convert
ArrayConverters.CharArrayWrapper() - Constructor for class org.scijava.convert.ArrayConverters.CharArrayWrapper
ArrayConverters.DoubleArrayUnwrapper - Class in org.scijava.convert
ArrayConverters.DoubleArrayUnwrapper() - Constructor for class org.scijava.convert.ArrayConverters.DoubleArrayUnwrapper
ArrayConverters.DoubleArrayWrapper - Class in org.scijava.convert
ArrayConverters.DoubleArrayWrapper() - Constructor for class org.scijava.convert.ArrayConverters.DoubleArrayWrapper
ArrayConverters.FloatArrayUnwrapper - Class in org.scijava.convert
ArrayConverters.FloatArrayUnwrapper() - Constructor for class org.scijava.convert.ArrayConverters.FloatArrayUnwrapper
ArrayConverters.FloatArrayWrapper - Class in org.scijava.convert
ArrayConverters.FloatArrayWrapper() - Constructor for class org.scijava.convert.ArrayConverters.FloatArrayWrapper
ArrayConverters.IntArrayUnwrapper - Class in org.scijava.convert
ArrayConverters.IntArrayUnwrapper() - Constructor for class org.scijava.convert.ArrayConverters.IntArrayUnwrapper
ArrayConverters.IntArrayWrapper - Class in org.scijava.convert
ArrayConverters.IntArrayWrapper() - Constructor for class org.scijava.convert.ArrayConverters.IntArrayWrapper
ArrayConverters.LongArrayUnwrapper - Class in org.scijava.convert
ArrayConverters.LongArrayUnwrapper() - Constructor for class org.scijava.convert.ArrayConverters.LongArrayUnwrapper
ArrayConverters.LongArrayWrapper - Class in org.scijava.convert
ArrayConverters.LongArrayWrapper() - Constructor for class org.scijava.convert.ArrayConverters.LongArrayWrapper
ArrayConverters.ShortArrayUnwrapper - Class in org.scijava.convert
ArrayConverters.ShortArrayUnwrapper() - Constructor for class org.scijava.convert.ArrayConverters.ShortArrayUnwrapper
ArrayConverters.ShortArrayWrapper - Class in org.scijava.convert
ArrayConverters.ShortArrayWrapper() - Constructor for class org.scijava.convert.ArrayConverters.ShortArrayWrapper
ArrayUtils - Class in org.scijava.util: Utility class for creating and manipulating PrimitiveArray instances.
asHTML(File) - Method in class org.scijava.text.DefaultTextService
asHTML(String) - Method in interface org.scijava.text.TextFormat: Expresses the given text string in HTML format.
asHTML(File) - Method in interface org.scijava.text.TextService: Expresses the given text string as HTML.
assertConsistency() - Method in class org.scijava.util.LastRecentlyUsed
assignProperties(MenuEntry) - Method in class org.scijava.MenuEntry: Updates any default properties of this menu entry to match those of the given menu entry.
asType(ModuleItem<?>, Class<T>) - Method in class org.scijava.command.InteractiveCommand
Attr - Annotation Type in org.scijava.plugin: A name/value attribute pair, used to extend the @Plugin annotation.
available() - Method in class org.scijava.io.DataHandleInputStream
AZURE - Static variable in class org.scijava.util.Colors

B

base64(byte[]) - Static method in class org.scijava.util.DigestUtils: Converts the given byte array to a base64 string.
BasicDetails - Interface in org.scijava: An interface defining basic characteristics including name, label, description, and a table of key/value pairs.
BEIGE - Static variable in class org.scijava.util.Colors
best(String) - Static method in class org.scijava.util.DigestUtils: Gets the given string's best available hash.
best(byte[]) - Static method in class org.scijava.util.DigestUtils: Gets the given byte array's best available hash.
bestBase64(String) - Static method in class org.scijava.util.DigestUtils: Gets the base64 string of the given string's best available hash.
bestBase64(byte[]) - Static method in class org.scijava.util.DigestUtils: Gets the base64 string of the given byte array's best available hash.
bestHex(String) - Static method in class org.scijava.util.DigestUtils: Gets the hex string of the given string's best available hash.
bestHex(byte[]) - Static method in class org.scijava.util.DigestUtils: Gets the hex string of the given byte array's best available hash.
BISQUE - Static variable in class org.scijava.util.Colors
BLACK - Static variable in class org.scijava.util.Colors
BLANCHEDALMOND - Static variable in class org.scijava.util.Colors
BLUE - Static variable in class org.scijava.util.Colors
BLUEVIOLET - Static variable in class org.scijava.util.Colors
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.
BROWN - Static variable in class org.scijava.util.Colors
buffer - Variable in class org.scijava.util.LineOutputStream
buffer - Variable in class org.scijava.util.ReadInto
buildPanel(InputPanel<P, W>, Module) - Method in class org.scijava.widget.AbstractInputHarvester
buildPanel(InputPanel<P, W>, Module) - Method in interface org.scijava.widget.InputHarvester: Populates the given InputPanel with widgets corresponding to the given Module instance.
BURLYWOOD - Static variable in class org.scijava.util.Colors
Button - Interface in org.scijava.widget: A interface used for marking input fields of plugin parameter dialogs as button fields.
ButtonWidget - Interface in org.scijava.widget: Widget interface for buttons.
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.
Bytes - Class in org.scijava.util: Useful methods for reading, writing, decoding and converting bytes and byte arrays.
bytes(String) - Static method in class org.scijava.util.DigestUtils: Converts the given string to a byte array.
bytes(int) - Static method in class org.scijava.util.DigestUtils: Converts the given integer into a byte array.
BytesLocation - Class in org.scijava.io: Location backed by a ByteBuffer.
BytesLocation(ByteBuffer) - Constructor for class org.scijava.io.BytesLocation
BytesLocation(byte[]) - Constructor for class org.scijava.io.BytesLocation
BytesLocation(byte[], int, int) - Constructor for class org.scijava.io.BytesLocation

C

cacheAnnotatedObjects(Class<?>, Query) - Static method in class org.scijava.util.ClassUtils: This method scans the provided class, its superclasses and interfaces for all supported Annotation : AnnotatedObject pairs.
CacheService - Interface in org.scijava.cache: Base interface for cache services in SciJava
CADETBLUE - Static variable in class org.scijava.util.Colors
call() - Method in class org.scijava.module.ModuleRunner
callback(Module) - Method in class org.scijava.module.AbstractModuleItem
callback(Module) - Method in interface org.scijava.module.ModuleItem: Invokes this item's callback function, if any, on the given module.
callback() - Method in class org.scijava.widget.DefaultWidgetModel
callback() - Method in interface org.scijava.widget.WidgetModel: Executes the callback associated with this widget's associated input.
canCancel() - Method in class org.scijava.command.CommandInfo
canCancel() - Method in class org.scijava.command.DynamicCommandInfo
canCancel() - Method in class org.scijava.module.AbstractModuleInfo
canCancel() - Method in interface org.scijava.module.ModuleInfo: Gets whether the module condones cancellation.
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.
cancel(String) - Method in interface org.scijava.Cancelable: Cancels the operation execution, with the given reason for doing so.
cancel() - Method in class org.scijava.command.CommandModule: Cancels the command, undoing the effects of any CommandModule.preview() calls.
cancel(String) - Method in class org.scijava.command.CommandModule
cancel(String) - Method in class org.scijava.command.ContextCommand: Cancels the command execution, with the given reason for doing so.
cancel(String) - Method in class org.scijava.command.DynamicCommand
cancel() - Method in class org.scijava.command.InteractiveCommand
cancel(String) - Method in class org.scijava.command.ModuleCommand
cancel() - Method in interface org.scijava.command.Previewable: Does whatever is necessary upon cancelation to reset things back to before the operation was executed.
cancel() - Method in class org.scijava.module.AbstractModule
cancel() - Method in interface org.scijava.module.Module: Performs necessary cleanup in response to cancellation of the module execution.
cancel(String) - Method in class org.scijava.module.process.AbstractPreprocessorPlugin
cancel(String) - Method in class org.scijava.ui.AbstractInputHarvesterPlugin
Cancelable - Interface in org.scijava: An operation that can be canceled.
canConvert(ConversionRequest) - Method in class org.scijava.convert.AbstractConverter
canConvert(Object, Type) - Method in class org.scijava.convert.AbstractConverter
canConvert(Object, Class<?>) - Method in class org.scijava.convert.AbstractConverter
canConvert(Class<?>, Class<?>) - Method in class org.scijava.convert.AbstractConverter
canConvert(Class<?>, Type) - Method in class org.scijava.convert.AbstractConverter: Deprecated.
canConvert(ConversionRequest) - Method in interface org.scijava.convert.Converter: Checks whether a given can be processed, by converting the desired ConversionRequest.sourceClass() to its ConversionRequest.destClass() or ConversionRequest.destType().
canConvert(Object, Type) - Method in interface org.scijava.convert.Converter: Checks whether the given object's type can be converted to the specified type.
canConvert(Object, Class<?>) - Method in interface org.scijava.convert.Converter: Checks whether the given object's type can be converted to the specified type.
canConvert(Class<?>, Type) - Method in interface org.scijava.convert.Converter: Deprecated.
Use Converter.canConvert(Object, Type)
canConvert(Class<?>, Class<?>) - Method in interface org.scijava.convert.Converter: Deprecated.
Use Converter.canConvert(Object, Class)
canConvert(Class<?>, Type) - Method in class org.scijava.convert.DefaultConverter: Deprecated.
canConvert(Class<?>, Class<?>) - Method in class org.scijava.convert.DefaultConverter: Deprecated.
canConvert(ConversionRequest) - Method in class org.scijava.convert.NullConverter
canConvert(Object, Type) - Method in class org.scijava.convert.NullConverter
canConvert(Object, Class<?>) - Method in class org.scijava.convert.NullConverter
canConvert(Class<?>, Class<?>) - Method in class org.scijava.convert.NullConverter
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: Deprecated.
canConvert(Class<?>, Class<?>) - Static method in class org.scijava.util.ConversionUtils: Deprecated.
canConvert(Object, Type) - Static method in class org.scijava.util.ConversionUtils: Deprecated.
canConvert(Object, Class<?>) - Static method in class org.scijava.util.ConversionUtils: Deprecated.
canDisplay(Class<?>) - Method in class org.scijava.display.AbstractDisplay
canDisplay(Object) - Method in class org.scijava.display.AbstractDisplay
canDisplay(Class<?>) - Method in interface org.scijava.display.Display: Tests whether the display is capable of visualizing objects of the given class.
canDisplay(Object) - Method in interface org.scijava.display.Display: Tests whether the display is capable of visualizing the given object.
canHandleFile(File) - Method in class org.scijava.script.DefaultScriptService
canHandleFile(String) - Method in class org.scijava.script.DefaultScriptService
canHandleFile(File) - Method in class org.scijava.script.ScriptLanguageIndex
canHandleFile(String) - Method in class org.scijava.script.ScriptLanguageIndex
canHandleFile(File) - Method in interface org.scijava.script.ScriptService: TODO
canHandleFile(String) - Method in interface org.scijava.script.ScriptService: TODO
canPreview() - Method in class org.scijava.command.CommandInfo
canPreview() - Method in class org.scijava.command.DynamicCommandInfo
canPreview() - Method in class org.scijava.module.AbstractModuleInfo
canPreview() - Method in interface org.scijava.module.ModuleInfo: Gets whether the module supports previews.
canRunHeadless() - Method in class org.scijava.command.CommandInfo
canRunHeadless() - Method in class org.scijava.module.AbstractModuleInfo
canRunHeadless() - Method in interface org.scijava.module.ModuleInfo: Gets whether the module condones headless execution.
canView(Display<?>) - Method in interface org.scijava.ui.viewer.DisplayViewer: Returns true if an instance of this display viewer can view the given display.
canView(Display<?>) - Method in class org.scijava.ui.viewer.text.AbstractTextDisplayViewer
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.
cdata(Node) - Static method in class org.scijava.util.XML: Gets the CData beneath the given node.
cdata(Element, String) - Static method in class org.scijava.util.XML: Gets the CData beneath the given element's specified child.
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.
CHARTREUSE - Static variable in class org.scijava.util.Colors
check(D, Display<?>) - Method in class org.scijava.ui.dnd.AbstractDragAndDropHandler: Throws IllegalArgumentException if (data, display) pair is incompatible.
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.
CheckInputsPreprocessor - Class in org.scijava.module.process: A preprocessor plugin that does a final check of input parameters, complaining if any required ones are null.
CheckInputsPreprocessor() - Constructor for class org.scijava.module.process.CheckInputsPreprocessor
checkJar(File) - Static method in class org.scijava.util.CheckSezpoz: Deprecated.
checkObject(Object) - Method in class org.scijava.display.AbstractDisplay
CheckSezpoz - Class in org.scijava.util: Deprecated.
CHOCOLATE - Static variable in class org.scijava.util.Colors
ChoiceWidget - Interface in org.scijava.widget: Widget interface for multiple choice selectors.
chooseFile(File, String) - Method in class org.scijava.ui.DefaultUIService
chooseFile(File, String) - Method in interface org.scijava.ui.UIService: Prompts the user to choose a file.
chooseFile(File, String) - Method in interface org.scijava.ui.UserInterface: Prompts the user to choose a file.
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.display.AbstractDisplay
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.io.DefaultRecentFileService
clear() - Method in interface org.scijava.io.RecentFileService: Clears the list of recent files.
clear() - Method in class org.scijava.menu.ShadowMenu
clear() - Method in class org.scijava.object.ObjectIndex
clear(Class<?>) - Method in class org.scijava.prefs.DefaultPrefService
clear(String) - Method in class org.scijava.prefs.DefaultPrefService
clear(Class<?>, String) - Method in class org.scijava.prefs.DefaultPrefService
clear(String, String) - Method in class org.scijava.prefs.DefaultPrefService
clear(Class<?>) - Method in interface org.scijava.prefs.PrefService
clear(String) - Method in interface org.scijava.prefs.PrefService: Clears the node.
clear(Class<?>, String) - Method in interface org.scijava.prefs.PrefService: Clears the node indexed under the given class.
clear(String, String) - Method in interface org.scijava.prefs.PrefService: Clears the ndoe indexed under the given path.
clear() - Method in interface org.scijava.ui.viewer.text.TextDisplayPanel
clear() - Method in class org.scijava.util.AbstractPrimitiveArray
clear() - Method in class org.scijava.util.LastRecentlyUsed: Empties the data structure.
clear(Class<?>) - Static method in class org.scijava.util.Prefs: Deprecated.
clear(String) - Static method in class org.scijava.util.Prefs: Deprecated.

Clears the node.
clear(Preferences, String) - Static method in class org.scijava.util.Prefs: Deprecated.
clearAll() - Method in class org.scijava.prefs.DefaultPrefService
clearAll() - Method in interface org.scijava.prefs.PrefService: Clears everything.
clearAll() - Static method in class org.scijava.util.Prefs: Deprecated.

Clears everything.
clearParameters() - Method in class org.scijava.module.AbstractModuleInfo: Clears input and output parameters.
clearStatus() - Method in class org.scijava.app.DefaultStatusService
clearStatus() - Method in interface org.scijava.app.StatusService: Clears the status message.
clone() - Method in class org.scijava.util.MersenneTwisterFast
close() - Method in class org.scijava.annotations.legacy.LegacyReader
close() - Method in class org.scijava.console.MultiOutputStream
close() - Method in class org.scijava.display.AbstractDisplay
close() - Method in interface org.scijava.display.Display: Closes the display and disposes its resources.
close() - Method in class org.scijava.io.DataHandleInputStream
close() - Method in class org.scijava.io.DataHandleOutputStream
close() - Method in class org.scijava.io.FileHandle
close() - Method in interface org.scijava.ui.viewer.DisplayWindow
close() - Method in class org.scijava.util.LineOutputStream: Flushes the current line buffer if any bytes are left in it.
CloseConfirmable - Interface in org.scijava.ui: Interface for UI components that require the user to deal with changed state before the component can be closed.
closeLine(SourceDataLine) - Method in class org.scijava.util.TunePlayer
closeOnEOF - Variable in class org.scijava.util.ReadInto
CodeGenerator - Interface in org.scijava.script: Code Generator Interface
CodeGeneratorJava - Class in org.scijava.script: CodeGenerator for Java.
CodeGeneratorJava() - Constructor for class org.scijava.script.CodeGeneratorJava
ColorRGB - Class in org.scijava.util: A color with red, green and blue color components.
ColorRGB(int, int, int) - Constructor for class org.scijava.util.ColorRGB
ColorRGB(String) - Constructor for class org.scijava.util.ColorRGB: Parses a color from the given string.
ColorRGBA - Class in org.scijava.util: A color with red, green, blue and alpha color components.
ColorRGBA(int, int, int, int) - Constructor for class org.scijava.util.ColorRGBA
Colors - Class in org.scijava.util: Predefined ColorRGB objects and related utility methods.
ColorWidget - Interface in org.scijava.widget: Widget interface for color choosers.
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 AnnotationCombiner.combine(File) 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 AnnotationCombiner.AnnotationCombiner() 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.
command() - Method in class org.scijava.AbstractGateway
Command - Interface in org.scijava.command: Command is a plugin that is executable.
command() - Method in interface org.scijava.Gateway: Gets this application context's CommandService.
CommandInfo - Class in org.scijava.command: A collection of metadata about a particular Command.
CommandInfo(String) - Constructor for class org.scijava.command.CommandInfo: Creates a new command metadata object.
CommandInfo(String, Plugin) - Constructor for class org.scijava.command.CommandInfo: Creates a new command metadata object.
CommandInfo(Class<? extends Command>) - Constructor for class org.scijava.command.CommandInfo: Creates a new command metadata object.
CommandInfo(Class<? extends Command>, Plugin) - Constructor for class org.scijava.command.CommandInfo: Creates a new command metadata object.
CommandInfo(PluginInfo<Command>) - Constructor for class org.scijava.command.CommandInfo: Creates a new command metadata object describing the same command as the given PluginInfo.
CommandInfo(PluginInfo<Command>, String, Class<? extends Command>, Plugin) - Constructor for class org.scijava.command.CommandInfo
CommandModule - Class in org.scijava.command: Module adapter class for working with a Command instance.
CommandModule(CommandInfo) - Constructor for class org.scijava.command.CommandModule: Creates a command module for the given PluginInfo.
CommandModule(CommandInfo, Command) - Constructor for class org.scijava.command.CommandModule: Creates a command module for the given CommandInfo, around the specified Command instance.
CommandModuleItem<T> - Class in org.scijava.command: ModuleItem implementation describing an input or output of a command.
CommandModuleItem(ModuleInfo, Field) - Constructor for class org.scijava.command.CommandModuleItem
CommandService - Interface in org.scijava.command: Interface for service that keeps track of available commands.
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(ShadowMenu) - Method in class org.scijava.menu.ShadowMenu
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.
configure(PlatformService) - Method in class org.scijava.platform.AbstractPlatform
configure(PlatformService) - Method in interface org.scijava.platform.Platform: Activates and configures the platform.
configure() - Method in class org.scijava.tool.AbstractTool
configure() - Method in interface org.scijava.tool.Tool: Occurs when the user right clicks this tool's icon.
confirmClose() - Method in interface org.scijava.ui.CloseConfirmable
console() - Method in class org.scijava.AbstractGateway
console() - Method in interface org.scijava.Gateway: Gets this application context's ConsoleService.
ConsoleArgument - Interface in org.scijava.console: A plugin which extends an application's command line argument handling.
ConsolePane<C> - Interface in org.scijava.ui.console: A panel which displays stdout and stderr console output.
ConsoleService - Interface in org.scijava.console: Interface for service that manages interaction with the console.
consume() - Method in class org.scijava.event.SciJavaEvent
contains(Object) - Method in class org.scijava.display.AbstractDisplay
contains(Object) - Method in class org.scijava.menu.ShadowMenu
contains(Object) - Method in class org.scijava.object.ObjectIndex
contains(Object) - Method in class org.scijava.object.SortedObjectIndex
contains(byte[], byte) - Static method in class org.scijava.util.ArrayUtils: Returns true if the given value is contained in the specified array.
contains(boolean[], boolean) - Static method in class org.scijava.util.ArrayUtils: Returns true if the given value is contained in the specified array.
contains(char[], char) - Static method in class org.scijava.util.ArrayUtils: Returns true if the given value is contained in the specified array.
contains(double[], double) - Static method in class org.scijava.util.ArrayUtils: Returns true if the given value is contained in the specified array.
contains(float[], float) - Static method in class org.scijava.util.ArrayUtils: Returns true if the given value is contained in the specified array.
contains(int[], int) - Static method in class org.scijava.util.ArrayUtils: Returns true if the given value is contained in the specified array.
contains(long[], long) - Static method in class org.scijava.util.ArrayUtils: Returns true if the given value is contained in the specified array.
contains(short[], short) - Static method in class org.scijava.util.ArrayUtils: Returns true if the given value is contained in the specified array.
contains(Object[], Object) - Static method in class org.scijava.util.ArrayUtils: Returns true if the given value is contained in the specified array.
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(IntCoords) - Method in class org.scijava.util.IntRect: Tests whether the given coordinates lie within the rectangle.
contains(Object) - Method in class org.scijava.util.LastRecentlyUsed
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(RealCoords) - Method in class org.scijava.util.RealRect: Tests whether the given coordinates lie within the rectangle.
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.display.AbstractDisplay
containsAll(Collection<?>) - Method in class org.scijava.menu.ShadowMenu
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.LastRecentlyUsed
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() - Method in class org.scijava.command.CommandModule
context() - Method in class org.scijava.command.DynamicCommand
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(Collection<Class<? extends Service>>, boolean) - 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 context with all available services from 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(Collection<Class<? extends Service>>, PluginIndex, boolean) - 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() - Method in class org.scijava.script.ScriptInfo
context() - Method in class org.scijava.script.ScriptModule
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!
ContextCommand - Class in org.scijava.command: A command that knows its context.
ContextCommand() - Constructor for class org.scijava.command.ContextCommand
ContextDisposingEvent - Class in org.scijava.event: Event to be published just before disposing a context.
ContextDisposingEvent() - Constructor for class org.scijava.event.ContextDisposingEvent
Contextual - Interface in org.scijava: An object that belongs to a SciJava application context.
ConversionRequest - Class in org.scijava.convert: Currency for use in Converter and ConvertService methods.
ConversionRequest(Object, Type) - Constructor for class org.scijava.convert.ConversionRequest
ConversionRequest(Type, Type) - Constructor for class org.scijava.convert.ConversionRequest
ConversionRequest(Object, Type, Type) - Constructor for class org.scijava.convert.ConversionRequest
ConversionUtils - Class in org.scijava.util: Useful methods for converting and casting between classes and types.
convert() - Method in class org.scijava.AbstractGateway
convert(Object, Type) - Method in class org.scijava.convert.AbstractConverter
convert(ConversionRequest) - Method in class org.scijava.convert.AbstractConverter
convert(Object, Type) - Method in class org.scijava.convert.AbstractConvertService
convert(Object, Class<T>) - Method in class org.scijava.convert.AbstractConvertService
convert(ConversionRequest) - Method in class org.scijava.convert.AbstractConvertService
convert(Object, Type) - Method in interface org.scijava.convert.Converter: As Converter.convert(Object, Class) but capable of creating and populating multi-element objects (Collections and array types).
convert(Object, Class<T>) - Method in interface org.scijava.convert.Converter: Converts the given object to an object of the specified type.
convert(ConversionRequest) - Method in interface org.scijava.convert.Converter: Converts the given ConversionRequest.sourceObject() to the specified ConversionRequest.destClass() or ConversionRequest.destType().
convert(Object, Type) - Method in interface org.scijava.convert.ConvertService
convert(Object, Class<T>) - Method in interface org.scijava.convert.ConvertService
convert(ConversionRequest) - Method in interface org.scijava.convert.ConvertService
convert(Object, Type) - Method in class org.scijava.convert.DefaultConverter
convert(Object, Class<T>) - Method in class org.scijava.convert.DefaultConverter
convert(Object, Class<T>) - Method in class org.scijava.convert.NullConverter
convert(Object, Class<T>) - Method in class org.scijava.convert.PrimitiveArrayUnwrapper
convert(Object, Class<T>) - Method in class org.scijava.convert.PrimitiveArrayWrapper
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: Deprecated.
convert(Object, Class<T>) - Static method in class org.scijava.util.ConversionUtils: Deprecated.
convertData(DragAndDropData) - Method in class org.scijava.ui.dnd.AbstractDragAndDropHandler
convertData(DragAndDropData) - Method in interface org.scijava.ui.dnd.DragAndDropHandler: Converts the given DragAndDropData to the type of data object supported by this handler.
convertDataUnchecked(DragAndDropData) - Method in class org.scijava.ui.dnd.AbstractDragAndDropHandler: Converts the given data to this handler's native data type, without verifying compatibility first.
Converter<I,O> - Interface in org.scijava.convert: Extensible conversion Plugin for converting between classes and types.
convertObject(Object) - Method in class org.scijava.ui.dnd.AbstractDragAndDropHandler
convertObject(Object) - Method in interface org.scijava.ui.dnd.DragAndDropHandler: Converts the given object to the type of data object supported by this handler.
convertObjectUnchecked(Object) - Method in class org.scijava.ui.dnd.AbstractDragAndDropHandler: Converts the given object to this handler's native data type, without verifying compatibility first.
ConvertService - Interface in org.scijava.convert: Service for converting between types using an extensible plugin: Converter.
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.
CORAL - Static variable in class org.scijava.util.Colors
CORNFLOWERBLUE - Static variable in class org.scijava.util.Colors
CORNSILK - Static variable in class org.scijava.util.Colors
create(String) - Static method in class org.scijava.input.Accelerator: Creates an accelerator from the given string representation.
create(Class) - Method in class org.scijava.plugin.AbstractPTService
create(Class) - Method in class org.scijava.plugin.AbstractSingletonService
create(D) - Method in class org.scijava.plugin.AbstractWrapperService
create(Class) - Method in interface org.scijava.plugin.PTService: Creates an instance of the given plugin class.
create(D) - Method in interface org.scijava.plugin.WrapperService: Creates a new plugin instance wrapping the given associated data object.
createBindings() - Method in class org.scijava.script.AbstractScriptEngine
createDisplay(Object) - Method in class org.scijava.display.DefaultDisplayService
createDisplay(String, Object) - Method in class org.scijava.display.DefaultDisplayService
createDisplay(Object) - Method in interface org.scijava.display.DisplayService: Creates a display for the given object.
createDisplay(String, Object) - Method in interface org.scijava.display.DisplayService: Creates a display for the given object.
createDisplayWindow(Display<?>) - Method in interface org.scijava.ui.UserInterface: Creates a new display window housing the given display.
createExactService(Class<S>) - Method in class org.scijava.service.ServiceHelper: Instantiates a service of the given class, registering it in the index.
createInputPanel() - Method in interface org.scijava.widget.InputHarvester: Constructs an empty InputPanel.
createInstance() - Method in class org.scijava.command.CommandInfo
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.
createMenus(ShadowMenu, T) - Method in class org.scijava.menu.AbstractMenuCreator
createMenus(MenuCreator<T>, T) - Method in class org.scijava.menu.DefaultMenuService
createMenus(String, MenuCreator<T>, T) - Method in class org.scijava.menu.DefaultMenuService
createMenus(ShadowMenu, T) - Method in interface org.scijava.menu.MenuCreator
createMenus(MenuCreator<T>, T) - Method in interface org.scijava.menu.MenuService: Populates a UI-specific application menu structure.
createMenus(String, MenuCreator<T>, T) - Method in interface org.scijava.menu.MenuService: Populates a UI-specific menu structure.
createModel(InputPanel<?, ?>, Module, ModuleItem<?>, List<?>) - Method in class org.scijava.widget.DefaultWidgetService
createModel(InputPanel<?, ?>, Module, ModuleItem<?>, List<?>) - Method in interface org.scijava.widget.WidgetService: Create a WidgetModel for the given module input.
createModule(Command) - Method in class org.scijava.command.CommandInfo: Instantiates the module described by this module info, around the specified existing command instance.
createModule() - Method in class org.scijava.command.CommandInfo
createModule(ModuleInfo) - Method in class org.scijava.module.DefaultModuleService
createModule() - Method in class org.scijava.module.DefaultMutableModuleInfo
createModule() - Method in interface org.scijava.module.ModuleInfo: Instantiates the module described by this module info.
createModule(ModuleInfo) - Method in interface org.scijava.module.ModuleService: Creates an instance of the given module.
createModule() - Method in class org.scijava.script.ScriptInfo
createPath(File, String) - Static method in class org.scijava.test.TestUtils: Creates an empty file at the given path, creating intermediate directories as necessary.
createTemporaryDirectory(String) - Static method in class org.scijava.test.TestUtils: Makes a temporary directory for use with unit tests.
createTemporaryDirectory(String, Class<?>) - Static method in class org.scijava.test.TestUtils: Makes a temporary directory for use with unit tests.
createTemporaryDirectory(String, Class<?>, String) - Static method in class org.scijava.test.TestUtils: Makes a temporary directory for use with unit tests.
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.
createUI() - Method in class org.scijava.ui.AbstractUserInterface: Subclasses override to control UI creation.
CRIMSON - Static variable in class org.scijava.util.Colors
CustomDrawnTool - Interface in org.scijava.tool: Tools that would like to define how they are drawn implement this interface.
CYAN - Static variable in class org.scijava.util.Colors

D

DARKBLUE - Static variable in class org.scijava.util.Colors
DARKCYAN - Static variable in class org.scijava.util.Colors
DARKGOLDENROD - Static variable in class org.scijava.util.Colors
DARKGRAY - Static variable in class org.scijava.util.Colors
DARKGREEN - Static variable in class org.scijava.util.Colors
DARKGREY - Static variable in class org.scijava.util.Colors
DARKKHAKI - Static variable in class org.scijava.util.Colors
DARKMAGENTA - Static variable in class org.scijava.util.Colors
DARKOLIVEGREEN - Static variable in class org.scijava.util.Colors
DARKORANGE - Static variable in class org.scijava.util.Colors
DARKORCHID - Static variable in class org.scijava.util.Colors
DARKRED - Static variable in class org.scijava.util.Colors
DARKSALMON - Static variable in class org.scijava.util.Colors
DARKSEAGREEN - Static variable in class org.scijava.util.Colors
DARKSLATEBLUE - Static variable in class org.scijava.util.Colors
DARKSLATEGRAY - Static variable in class org.scijava.util.Colors
DARKSLATEGREY - Static variable in class org.scijava.util.Colors
DARKTURQUOISE - Static variable in class org.scijava.util.Colors
DARKVIOLET - Static variable in class org.scijava.util.Colors
DataHandle<L extends Location> - Interface in org.scijava.io: A data handle is a plugin which provides access to bytes in a data stream (e.g., files or arrays), identified by a Location.
DataHandleInputStream<L extends Location> - Class in org.scijava.io: InputStream backed by a DataHandle.
DataHandleInputStream(DataHandle<L>) - Constructor for class org.scijava.io.DataHandleInputStream: Creates an input stream around the given DataHandle.
DataHandleOutputStream<L extends Location> - Class in org.scijava.io: OutputStream backed by a DataHandle.
DataHandleOutputStream(DataHandle<L>) - Constructor for class org.scijava.io.DataHandleOutputStream: Creates an output stream around the given DataHandle.
DataHandleService - Interface in org.scijava.io: Interface for low-level data I/O: reading and writing bytes using DataHandles.
DataOpenedEvent - Class in org.scijava.io.event: An event indicating that data has been opened from a source.
DataOpenedEvent(String, Object) - Constructor for class org.scijava.io.event.DataOpenedEvent
DataSavedEvent - Class in org.scijava.io.event: An event indicating that data has been saved to a destination.
DataSavedEvent(String, Object) - Constructor for class org.scijava.io.event.DataSavedEvent
DateWidget - Interface in org.scijava.widget: Widget interface for dates.
deactivate() - Method in class org.scijava.tool.AbstractTool
deactivate() - Method in interface org.scijava.tool.Tool: Informs the tool that it is no longer active.
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
DebugPostprocessor - Class in org.scijava.module.process: A postprocessor plugin that dumps parameter values to the log.
DebugPostprocessor() - Constructor for class org.scijava.module.process.DebugPostprocessor
DebugPreprocessor - Class in org.scijava.module.process: A preprocessor plugin that dumps information to the log.
DebugPreprocessor() - Constructor for class org.scijava.module.process.DebugPreprocessor
DebugUtils - Class in org.scijava.util: Useful methods for debugging programs.
decode(Object) - Method in class org.scijava.script.AbstractScriptLanguage
decode(Object) - Method in interface org.scijava.script.ScriptLanguage: Performs any necessary conversion of an encoded object retrieved from the language's script engine.
DEEPPINK - Static variable in class org.scijava.util.Colors
DEEPSKYBLUE - Static variable in class org.scijava.util.Colors
DEFAULT_SHORTENER_THRESHOLD - Static variable in class org.scijava.util.FileUtils
DEFAULT_WEIGHT - Static variable in class org.scijava.MenuEntry
DefaultAppEventService - Class in org.scijava.platform: Deprecated.
Use AppService and App instead.
DefaultAppEventService() - Constructor for class org.scijava.platform.DefaultAppEventService: Deprecated.
DefaultAppService - Class in org.scijava.app: Default service for application-level functionality.
DefaultAppService() - Constructor for class org.scijava.app.DefaultAppService
DefaultCacheService - Class in org.scijava.cache: Trivial CacheService implementation.
DefaultCacheService() - Constructor for class org.scijava.cache.DefaultCacheService
DefaultCommandService - Class in org.scijava.command: Default service for working with Commands.
DefaultCommandService() - Constructor for class org.scijava.command.DefaultCommandService
DefaultConsoleService - Class in org.scijava.console: Default service for managing interaction with the console.
DefaultConsoleService() - Constructor for class org.scijava.console.DefaultConsoleService
DefaultConverter - Class in org.scijava.convert: Default Converter implementation.
DefaultConverter() - Constructor for class org.scijava.convert.DefaultConverter
DefaultConvertService - Class in org.scijava.convert: Default ConvertService implementation.
DefaultConvertService() - Constructor for class org.scijava.convert.DefaultConvertService
DefaultDataHandleService - Class in org.scijava.io: Default implementation of DataHandleService.
DefaultDataHandleService() - Constructor for class org.scijava.io.DefaultDataHandleService
DefaultDisplay - Class in org.scijava.display: Default display for objects, when no other displays are available.
DefaultDisplay() - Constructor for class org.scijava.display.DefaultDisplay
DefaultDisplayService - Class in org.scijava.display: Default service for working with Displays.
DefaultDisplayService() - Constructor for class org.scijava.display.DefaultDisplayService
DefaultDragAndDropData - Class in org.scijava.ui.dnd: Default implementation of DragAndDropData, which provides a UI-agnostic way to bundle an object together with its MIME type.
DefaultDragAndDropData(Context, MIMEType, Object) - Constructor for class org.scijava.ui.dnd.DefaultDragAndDropData
DefaultDragAndDropService - Class in org.scijava.ui.dnd: Default service for handling drag and drop events.
DefaultDragAndDropService() - Constructor for class org.scijava.ui.dnd.DefaultDragAndDropService
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
DefaultInputService - Class in org.scijava.input: Default implementation of InputService.
DefaultInputService() - Constructor for class org.scijava.input.DefaultInputService
DefaultIOService - Class in org.scijava.io: Default implementation of IOService.
DefaultIOService() - Constructor for class org.scijava.io.DefaultIOService
DefaultMenuService - Class in org.scijava.menu: Default service for keeping track of the application's menu structure.
DefaultMenuService() - Constructor for class org.scijava.menu.DefaultMenuService
DefaultModuleService - Class in org.scijava.module: Default service for keeping track of and executing available modules.
DefaultModuleService() - Constructor for class org.scijava.module.DefaultModuleService
DefaultMutableModule - Class in org.scijava.module: Default MutableModule implementation, intended for subclassing.
DefaultMutableModule() - Constructor for class org.scijava.module.DefaultMutableModule
DefaultMutableModule(MutableModuleInfo) - Constructor for class org.scijava.module.DefaultMutableModule
DefaultMutableModuleInfo - Class in org.scijava.module: Default MutableModuleInfo implementation.
DefaultMutableModuleInfo() - Constructor for class org.scijava.module.DefaultMutableModuleInfo
DefaultMutableModuleItem<T> - Class in org.scijava.module: Default MutableModuleItem implementation, for use with custom MutableModule implementations.
DefaultMutableModuleItem(Module, String, Class<T>) - Constructor for class org.scijava.module.DefaultMutableModuleItem
DefaultMutableModuleItem(ModuleInfo, String, Class<T>) - Constructor for class org.scijava.module.DefaultMutableModuleItem
DefaultMutableModuleItem(ModuleInfo, ModuleItem<T>) - Constructor for class org.scijava.module.DefaultMutableModuleItem: Creates a new module item with the same values as the given item.
DefaultObjectService - Class in org.scijava.object: Default service for keeping track of registered objects.
DefaultObjectService() - Constructor for class org.scijava.object.DefaultObjectService
DefaultOptionsService - Class in org.scijava.options: Default service for keeping track of the available options and their settings.
DefaultOptionsService() - Constructor for class org.scijava.options.DefaultOptionsService
DefaultPlatform - Class in org.scijava.platform: A platform implementation for default handling of platform issues.
DefaultPlatform() - Constructor for class org.scijava.platform.DefaultPlatform
DefaultPlatformService - Class in org.scijava.platform: Default service for handling platform-specific deployment issues.
DefaultPlatformService() - Constructor for class org.scijava.platform.DefaultPlatformService
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
DefaultPrefService - Class in org.scijava.prefs: Default PrefService implementation, which persists preferences to disk using the Java Preferences API.
DefaultPrefService() - Constructor for class org.scijava.prefs.DefaultPrefService
DefaultRecentFileService - Class in org.scijava.io: Default service for managing the Recently Used Files menu.
DefaultRecentFileService() - Constructor for class org.scijava.io.DefaultRecentFileService
DefaultScriptHeaderService - Class in org.scijava.script: Default ScriptHeaderService implementation.
DefaultScriptHeaderService() - Constructor for class org.scijava.script.DefaultScriptHeaderService
DefaultScriptInterpreter - Class in org.scijava.script: The default implementation of a ScriptInterpreter.
DefaultScriptInterpreter(PrefService, ScriptService, ScriptLanguage) - Constructor for class org.scijava.script.DefaultScriptInterpreter: Constructs a new DefaultScriptInterpreter.
DefaultScriptService - Class in org.scijava.script: Default service for working with scripting languages.
DefaultScriptService() - Constructor for class org.scijava.script.DefaultScriptService
DefaultStatusService - Class in org.scijava.app: Default service for status notifications.
DefaultStatusService() - Constructor for class org.scijava.app.DefaultStatusService
DefaultTextDisplay - Class in org.scijava.display: Default display for text.
DefaultTextDisplay() - Constructor for class org.scijava.display.DefaultTextDisplay
DefaultTextService - Class in org.scijava.text: Default service for working with text formats.
DefaultTextService() - Constructor for class org.scijava.text.DefaultTextService
DefaultThreadService - Class in org.scijava.thread: Default service for managing active threads.
DefaultThreadService() - Constructor for class org.scijava.thread.DefaultThreadService
DefaultToolService - Class in org.scijava.tool: Default service for keeping track of available tools, including which tool is active, and delegating UI events to the active tool.
DefaultToolService() - Constructor for class org.scijava.tool.DefaultToolService
DefaultUIService - Class in org.scijava.ui: Default service for handling SciJava user interfaces.
DefaultUIService() - Constructor for class org.scijava.ui.DefaultUIService
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
DefaultValuePreprocessor - Class in org.scijava.module.process: A preprocessor plugin that populates default parameter values.
DefaultValuePreprocessor() - Constructor for class org.scijava.module.process.DefaultValuePreprocessor
DefaultWelcomeService - Class in org.scijava.welcome: Default service for displaying the welcome greeting.
DefaultWelcomeService() - Constructor for class org.scijava.welcome.DefaultWelcomeService
DefaultWidgetModel - Class in org.scijava.widget: The backing data model for a particular InputWidget.
DefaultWidgetModel(Context, InputPanel<?, ?>, Module, ModuleItem<?>, List<?>) - Constructor for class org.scijava.widget.DefaultWidgetModel
DefaultWidgetService - Class in org.scijava.widget: Default service for managing available InputWidgets.
DefaultWidgetService() - Constructor for class org.scijava.widget.DefaultWidgetService
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.
Desktop - Interface in org.scijava.ui: Marker interface for MDI Desktop manager
destClass() - Method in class org.scijava.convert.ConversionRequest
destType() - Method in class org.scijava.convert.ConversionRequest
DialogPrompt - Interface in org.scijava.ui: TODO
dialogPrompt(String, String, DialogPrompt.MessageType, DialogPrompt.OptionType) - Method in interface org.scijava.ui.UserInterface: Creates a dialog prompter.
DialogPrompt.MessageType - Enum in org.scijava.ui
DialogPrompt.OptionType - Enum in org.scijava.ui
DialogPrompt.Result - Enum in org.scijava.ui
digest(String, byte[]) - Static method in class org.scijava.util.DigestUtils: Gets the given byte array's hash value according to the specified algorithm.
DigestUtils - Class in org.scijava.util: Utility class for computing cryptographic hashes.
DIMGRAY - Static variable in class org.scijava.util.Colors
DIMGREY - Static variable in class org.scijava.util.Colors
DIRECTORY_STYLE - Static variable in interface org.scijava.widget.FileWidget: Widget style for directory chooser dialogs.
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 PluginFinder is null.
discoverAnnotations(File, String, ClassLoader) - Method in class org.scijava.annotations.DirectoryIndexer
display() - Method in class org.scijava.AbstractGateway
display(Object) - Method in class org.scijava.display.AbstractDisplay
Display<T> - Interface in org.scijava.display: A display is a particular type of plugin intended to collect objects for visualization.
display(Object) - Method in interface org.scijava.display.Display: Displays the given object in this display.
display() - Method in interface org.scijava.Gateway: Gets this application context's DisplayService.
Displayable - Interface in org.scijava.display: An interface used by classes that can draw on demand.
DisplayActivatedEvent - Class in org.scijava.display.event: An event indicating a display has become the active one.
DisplayActivatedEvent(Display<?>) - Constructor for class org.scijava.display.event.DisplayActivatedEvent
DisplayCreatedEvent - Class in org.scijava.display.event: An event indicating a new display has been created.
DisplayCreatedEvent(Display<?>) - Constructor for class org.scijava.display.event.DisplayCreatedEvent
DisplayDeletedEvent - Class in org.scijava.display.event: An event indicating a display has been deleted.
DisplayDeletedEvent(Display<?>) - Constructor for class org.scijava.display.event.DisplayDeletedEvent
DisplayEvent - Class in org.scijava.display.event: An event indicating something has happened to a Display.
DisplayEvent(Display<?>) - Constructor for class org.scijava.display.event.DisplayEvent
DisplayPanel - Interface in org.scijava.ui.viewer: The panel housing a particular Display.
DisplayPostprocessor - Class in org.scijava.display: Displays outputs upon completion of a module execution.
DisplayPostprocessor() - Constructor for class org.scijava.display.DisplayPostprocessor
DisplayService - Interface in org.scijava.display: Interface for service that tracks available Displays.
DisplayUpdatedEvent - Class in org.scijava.display.event: An event indicating a display has updated; e.g., an object has been added or removed.
DisplayUpdatedEvent(Display<?>, DisplayUpdatedEvent.DisplayUpdateLevel) - Constructor for class org.scijava.display.event.DisplayUpdatedEvent
DisplayUpdatedEvent.DisplayUpdateLevel - Enum in org.scijava.display.event: The display update level gives a hint about how much work needs to be done during the update.
DisplayViewer<T> - Interface in org.scijava.ui.viewer: A display viewer is a UI widget that shows a display to a user.
displayWelcome() - Method in class org.scijava.welcome.DefaultWelcomeService
displayWelcome() - Method in interface org.scijava.welcome.WelcomeService: Displays the welcome greeting.
DisplayWindow - Interface in org.scijava.ui.viewer: A user interface window associated with a Display, containing a DisplayPanel.
Disposable - Interface in org.scijava: An object that knows how to clean up after itself.
dispose() - Method in class org.scijava.console.DefaultConsoleService
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.platform.AbstractPlatform
dispose() - Method in class org.scijava.platform.DefaultPlatformService
dispose() - Method in class org.scijava.service.AbstractService
dispose() - Method in class org.scijava.thread.DefaultThreadService
dispose() - Method in class org.scijava.ui.DefaultUIService
dispose() - Method in class org.scijava.ui.viewer.AbstractDisplayViewer
DODGERBLUE - Static variable in class org.scijava.util.Colors
done - Variable in class org.scijava.util.ReadInto
done() - Method in class org.scijava.util.ReadInto
doRefresh() - Method in class org.scijava.ui.AbstractUIInputWidget: Performs the intended AbstractUIInputWidget.refreshWidget() operation.
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.
downOctave() - Method in class org.scijava.util.TunePlayer
DragAndDropData - Interface in org.scijava.ui.dnd: Interface for drag-and-drop data.
DragAndDropEvent - Class in org.scijava.ui.dnd.event: An event indicating drag-and-drop activity in a display.
DragAndDropEvent(Display<?>) - Constructor for class org.scijava.ui.dnd.event.DragAndDropEvent
DragAndDropEvent(Display<?>, DragAndDropData) - Constructor for class org.scijava.ui.dnd.event.DragAndDropEvent
DragAndDropEvent(Display<?>, InputModifiers, int, int, DragAndDropData) - Constructor for class org.scijava.ui.dnd.event.DragAndDropEvent
DragAndDropHandler<D> - Interface in org.scijava.ui.dnd: Interface for drag-and-drop handlers.
DragAndDropService - Interface in org.scijava.ui.dnd: Interface for service that handles drag and drop events.
DragEnterEvent - Class in org.scijava.ui.dnd.event: An event indicating an object was dragged onto a display.
DragEnterEvent(Display<?>, InputModifiers, int, int, DragAndDropData) - Constructor for class org.scijava.ui.dnd.event.DragEnterEvent
DragExitEvent - Class in org.scijava.ui.dnd.event: An event indicating an object was dragged off of a display.
DragExitEvent(Display<?>) - Constructor for class org.scijava.ui.dnd.event.DragExitEvent
DragOverEvent - Class in org.scijava.ui.dnd.event: An event indicating an object was dragged within a display.
DragOverEvent(Display<?>, InputModifiers, int, int, DragAndDropData) - Constructor for class org.scijava.ui.dnd.event.DragOverEvent
draw() - Method in interface org.scijava.display.Displayable: Render self when called.
drawIcon() - Method in interface org.scijava.tool.CustomDrawnTool
drop(DragAndDropData, Display<?>) - Method in class org.scijava.ui.dnd.DefaultDragAndDropService
drop(Object, Display<?>) - Method in class org.scijava.ui.dnd.DefaultDragAndDropService
drop(D, Display<?>) - Method in interface org.scijava.ui.dnd.DragAndDropHandler: Performs a drop operation with the given data object in the specified Display.
drop(DragAndDropData, Display<?>) - Method in interface org.scijava.ui.dnd.DragAndDropService: Performs a drag-and-drop operation in the given display with the specified DragAndDropData, using the first available compatible handler.
drop(Object, Display<?>) - Method in interface org.scijava.ui.dnd.DragAndDropService: Performs a drag-and-drop operation in the given display with the specified data object, using the first available compatible handler.
drop(File, Display<?>) - Method in class org.scijava.ui.dnd.FileDragAndDropHandler
drop(List<?>, Display<?>) - Method in class org.scijava.ui.dnd.ListDragAndDropHandler
drop(File, Display<?>) - Method in class org.scijava.ui.dnd.ScriptFileDragAndDropHandler
dropData(DragAndDropData, Display<?>) - Method in class org.scijava.ui.dnd.AbstractDragAndDropHandler
dropData(DragAndDropData, Display<?>) - Method in interface org.scijava.ui.dnd.DragAndDropHandler: Performs a drop operation with the given data in the specified Display.
DropEvent - Class in org.scijava.ui.dnd.event: An event indicating an object was dropped onto a display.
DropEvent(Display<?>, InputModifiers, int, int, DragAndDropData) - Constructor for class org.scijava.ui.dnd.event.DropEvent
dropObject(Object, Display<?>) - Method in class org.scijava.ui.dnd.AbstractDragAndDropHandler
dropObject(Object, Display<?>) - Method in interface org.scijava.ui.dnd.DragAndDropHandler: Performs a drop operation with the given data in the specified Display.
DummyTool - Class in org.scijava.tool: A tool that does nothing.
DummyTool() - Constructor for class org.scijava.tool.DummyTool
DynamicCommand - Class in org.scijava.command: A command with a variable number of inputs and outputs.
DynamicCommand() - Constructor for class org.scijava.command.DynamicCommand
DynamicCommandInfo - Class in org.scijava.command: Helper class for maintaining a DynamicCommand's associated ModuleInfo.
DynamicCommandInfo(CommandInfo, Class<? extends DynamicCommand>) - Constructor for class org.scijava.command.DynamicCommandInfo

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
EDIT_LABEL - Static variable in class org.scijava.menu.MenuConstants
EDIT_MNEMONIC - Static variable in class org.scijava.menu.MenuConstants
EDIT_WEIGHT - Static variable in class org.scijava.menu.MenuConstants
elements(String) - Method in class org.scijava.util.XML: Obtains the elements identified by the given XPath expression.
elements(NodeList) - Static method in class org.scijava.util.XML: Gets the element nodes from the given node list.
elements(Element, String) - Static method in class org.scijava.util.XML: Gets the given element's specified child elements.
engineScopeBindings - Variable in class org.scijava.script.AbstractScriptEngine
ensure(int) - Method in class org.scijava.util.LineOutputStream: Increases the size of the line buffer if necessary.
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
equals(Object) - Method in class org.scijava.ui.dnd.MIMEType
equals(Object) - Method in class org.scijava.util.ColorRGB
equals(Object) - Method in class org.scijava.util.IntCoords
equals(Object) - Method in class org.scijava.util.IntRect
equals(Object) - Method in class org.scijava.util.RealCoords
equals(Object) - Method in class org.scijava.util.RealRect
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
errorWriter - Variable in class org.scijava.script.AbstractScriptContext
eval(String) - Method in class org.scijava.script.AbstractScriptEngine
eval(Reader) - Method in class org.scijava.script.AbstractScriptEngine
eval(String, ScriptContext) - Method in class org.scijava.script.AbstractScriptEngine
eval(Reader, ScriptContext) - Method in class org.scijava.script.AbstractScriptEngine
eval(String, Bindings) - Method in class org.scijava.script.AbstractScriptEngine
eval(Reader, Bindings) - Method in class org.scijava.script.AbstractScriptEngine
eval(String) - Method in class org.scijava.script.DefaultScriptInterpreter
eval(String) - Method in interface org.scijava.script.ScriptInterpreter: Evaluates a command.
event() - Method in class org.scijava.AbstractGateway
event() - Method in interface org.scijava.Gateway: Gets this application context's EventService.
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: Gets this application context's EventHistory.
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.
eventService - Variable in class org.scijava.options.OptionsPlugin
EventSubscriber<E extends SciJavaEvent> - Interface in org.scijava.event: Interface for subscribers that wish to be notified of SciJava events.
exec(String...) - Method in class org.scijava.platform.DefaultPlatformService
exec(String...) - Method in interface org.scijava.platform.PlatformService: Executes a native program and waits for it to return.
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.
exec(String) - Method in class org.scijava.util.ReflectedUniverse: Executes a command in the universe.
execute(Object, Object...) - Method in class org.scijava.module.MethodRef

F

FIELD_STYLE - Static variable in interface org.scijava.widget.TextWidget: Widget style for text fields.
FILE_LABEL - Static variable in class org.scijava.menu.MenuConstants
FILE_MNEMONIC - Static variable in class org.scijava.menu.MenuConstants
FILE_NAME - Static variable in class org.scijava.util.CheckSezpoz: Deprecated.
FILE_WEIGHT - Static variable in class org.scijava.menu.MenuConstants
FileDragAndDropHandler - Class in org.scijava.ui.dnd: Drag-and-drop handler for files.
FileDragAndDropHandler() - Constructor for class org.scijava.ui.dnd.FileDragAndDropHandler
FileHandle - Class in org.scijava.io: DataHandle for a FileLocation.
FileHandle() - Constructor for class org.scijava.io.FileHandle
FileLocation - Class in org.scijava.io: Location backed by a File on disk.
FileLocation(File) - Constructor for class org.scijava.io.FileLocation
FileLocation(String) - Constructor for class org.scijava.io.FileLocation
FilePreprocessor - Class in org.scijava.ui: A preprocessor plugin that handles single unresolved parameters of type File using a UI prompt.
FilePreprocessor() - Constructor for class org.scijava.ui.FilePreprocessor
FileUtils - Class in org.scijava.util: Useful methods for working with file paths.
FileWidget - Interface in org.scijava.widget: Widget interface for file selectors.
filterInstances(List<Platform>) - Method in class org.scijava.platform.DefaultPlatformService
filterInstances(List<PT>) - Method in class org.scijava.plugin.AbstractSingletonService: Allows subclasses to exclude instances.
findDisplayContentScreenX() - Method in interface org.scijava.ui.viewer.DisplayWindow: Finds the x coordinate on the screen of the origin of the display window's content.
findDisplayContentScreenY() - Method in interface org.scijava.ui.viewer.DisplayWindow: Finds the y coordinate on the screen of the origin of the display window's content.
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.
findScripts(List<ScriptInfo>) - Method in class org.scijava.script.ScriptFinder: Discovers the scripts.
findString(String...) - Method in class org.scijava.io.AbstractDataHandle
findString(boolean, String...) - Method in class org.scijava.io.AbstractDataHandle
findString(int, String...) - Method in class org.scijava.io.AbstractDataHandle
findString(boolean, int, String...) - Method in class org.scijava.io.AbstractDataHandle
findString(String...) - Method in interface org.scijava.io.DataHandle: Reads a string ending with one of the given terminating substrings.
findString(boolean, String...) - Method in interface org.scijava.io.DataHandle: Reads or skips a string ending with one of the given terminating substrings.
findString(int, String...) - Method in interface org.scijava.io.DataHandle: Reads a string ending with one of the given terminating substrings, using the specified block size for buffering.
findString(boolean, int, String...) - Method in interface org.scijava.io.DataHandle: Reads or skips a string ending with one of the given terminating substrings, using the specified block size for buffering.
FIREBRICK - Static variable in class org.scijava.util.Colors
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.
FLORALWHITE - Static variable in class org.scijava.util.Colors
flush() - Method in class org.scijava.console.MultiOutputStream
flush() - Method in class org.scijava.io.DataHandleOutputStream
flush() - Method in class org.scijava.util.LineOutputStream: If any bytes are in the current line buffer, output the line via LineOutputStream.println(String), stripping any trailing new-line characters.
FORESTGREEN - Static variable in class org.scijava.util.Colors
format(double) - Static method in class org.scijava.util.UnitUtils
foundAnnotations() - Method in class org.scijava.annotations.AbstractIndexWriter
fromDouble(double, boolean) - Static method in class org.scijava.util.Bytes: Translates the double value into an array of eight bytes.
fromDoubles(double[], boolean) - Static method in class org.scijava.util.Bytes: Translates an array of double values into an array of byte values.
fromFloat(float, boolean) - Static method in class org.scijava.util.Bytes: Translates the float value into an array of four bytes.
fromFloats(float[], boolean) - Static method in class org.scijava.util.Bytes: Translates an array of float values into an array of byte values.
fromHSVColor(double, double, double) - Static method in class org.scijava.util.ColorRGB
fromHTMLColor(String) - Static method in class org.scijava.util.ColorRGB: Convert a string in the format specified by CSS Color Module Level 3 - W3C Recommendation 07 June 2011 to a ColorRGB object.
fromInt(int, boolean) - Static method in class org.scijava.util.Bytes: Translates the int value into an array of four bytes.
fromInts(int[], boolean) - Static method in class org.scijava.util.Bytes: Translates an array of int values into an array of byte values.
fromLong(long, boolean) - Static method in class org.scijava.util.Bytes: Translates the long value into an array of eight bytes.
fromLongs(long[], boolean) - Static method in class org.scijava.util.Bytes: Translates an array of long values into an array of byte values.
fromShort(short, boolean) - Static method in class org.scijava.util.Bytes: Translates the short value into an array of two bytes.
fromShorts(short[], boolean) - Static method in class org.scijava.util.Bytes: Translates an array of short values into an array of byte values.
FUCHSIA - Static variable in class org.scijava.util.Colors

G

GAINSBORO - Static variable in class org.scijava.util.Colors
Gateway - Interface in org.scijava: Interface for convenience classes that wrap a Context to provide one-line access to a suite of Services.
GatewayPreprocessor - Class in org.scijava.module.process: The gateway preprocessor automatically populates module inputs that implement Gateway.
GatewayPreprocessor() - Constructor for class org.scijava.module.process.GatewayPreprocessor
GenericUtils - Class in org.scijava.util: Useful methods for working with Type objects, particularly generic types.
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(Object) - Method in interface org.scijava.cache.CacheService
get(Object, Callable<V>) - Method in interface org.scijava.cache.CacheService
get(Object) - Method in class org.scijava.cache.DefaultCacheService
get(Object, Callable<V>) - Method in class org.scijava.cache.DefaultCacheService
get(String) - Method in class org.scijava.command.CommandModuleItem
get(int) - Method in class org.scijava.display.AbstractDisplay
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(String) - Method in class org.scijava.prefs.DefaultPrefService
get(String, String) - Method in class org.scijava.prefs.DefaultPrefService
get(Class<?>, String) - Method in class org.scijava.prefs.DefaultPrefService
get(Class<?>, String, String) - Method in class org.scijava.prefs.DefaultPrefService
get(String) - Method in interface org.scijava.prefs.PrefService
get(String, String) - Method in interface org.scijava.prefs.PrefService
get(Class<?>, String) - Method in interface org.scijava.prefs.PrefService
get(Class<?>, String, String) - Method in interface org.scijava.prefs.PrefService
get(String) - Method in class org.scijava.script.AbstractScriptEngine
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.LastRecentlyUsed: Returns the entry for the given index.
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(String) - Static method in class org.scijava.util.Prefs: Deprecated.
get(String, String) - Static method in class org.scijava.util.Prefs: Deprecated.
get(Class<?>, String) - Static method in class org.scijava.util.Prefs: Deprecated.
get(Class<?>, String, String) - Static method in class org.scijava.util.Prefs: Deprecated.
get(int) - Method in class org.scijava.util.ShortArray
get() - Method in class org.scijava.widget.AbstractInputWidget
get() - Method in interface org.scijava.widget.InputWidget: Gets the model object backing this widget.
getAbbreviatedByteLabel(double) - Static method in class org.scijava.util.UnitUtils
getAccelerator() - Method in class org.scijava.display.event.input.KyEvent: Converts the key event into a corresponding accelerator.
getAccelerator() - Method in class org.scijava.MenuEntry
getActiveDisplay() - Method in class org.scijava.display.DefaultDisplayService
getActiveDisplay(Class<D>) - Method in class org.scijava.display.DefaultDisplayService
getActiveDisplay() - Method in interface org.scijava.display.DisplayService: Gets the currently active display (of any Display type).
getActiveDisplay(Class<D>) - Method in interface org.scijava.display.DisplayService: Gets the most recently active display (of the specified Display type).
getActiveTool() - Method in class org.scijava.tool.DefaultToolService
getActiveTool() - Method in interface org.scijava.tool.ToolService
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.
getAlpha(int, int) - Method in class org.scijava.ui.ARGBPlane
getAlpha() - Method in class org.scijava.util.ColorRGB
getAlpha() - Method in class org.scijava.util.ColorRGBA
getAlwaysActiveTools() - Method in class org.scijava.tool.DefaultToolService
getAlwaysActiveTools() - Method in interface org.scijava.tool.ToolService
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.
getAnnotatedMethods(Class<?>, Class<A>) - Static method in class org.scijava.util.ClassUtils: Gets the given class's Methods marked with the annotation of the specified class.
getAnnotatedMethods(Class<?>, Class<A>, List<Method>) - Static method in class org.scijava.util.ClassUtils: Gets the given class's Methods 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() - Method in interface org.scijava.app.AppService: Gets the foremost application (the one with the highest priority).
getApp(String) - Method in interface org.scijava.app.AppService: Gets an application by name.
getApp() - Method in class org.scijava.app.DefaultAppService
getApp(String) - Method in class org.scijava.app.DefaultAppService
getApp() - Method in interface org.scijava.Gateway
getAppEventService() - Method in class org.scijava.platform.DefaultPlatformService
getAppEventService() - Method in interface org.scijava.platform.PlatformService
getApplicationFrame() - Method in class org.scijava.ui.AbstractUserInterface
getApplicationFrame() - Method in interface org.scijava.ui.UserInterface: Gets the main SciJava application frame, or null if not applicable.
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
getARGB(int, int) - Method in class org.scijava.ui.ARGBPlane
getARGB() - Method in class org.scijava.util.ColorRGB: Gets the color as a packed integer, 8 bits per color component.
getArrangement() - Method in interface org.scijava.ui.Arrangeable
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.
getAttribute(String) - Method in class org.scijava.script.AbstractScriptContext
getAttribute(String, int) - Method in class org.scijava.script.AbstractScriptContext
getAttributesScope(String) - Method in class org.scijava.script.AbstractScriptContext
getAvailableUIs() - Method in class org.scijava.ui.DefaultUIService
getAvailableUIs() - Method in interface org.scijava.ui.UIService: Gets the user interfaces available to the service.
getBase() - Method in class org.scijava.ui.dnd.MIMEType: Gets the MIME type with no parameter list.
getBaseClass() - Method in class org.scijava.object.ObjectIndex: Gets the base class of the items being managed.
getBaseDirectory() - Method in class org.scijava.app.AbstractApp
getBaseDirectory() - Method in interface org.scijava.app.App: Gets the application's root directory.
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.
getBindings(int) - Method in class org.scijava.script.AbstractScriptContext
getBindings(int) - Method in class org.scijava.script.AbstractScriptEngine
getBlue(int, int) - Method in class org.scijava.ui.ARGBPlane
getBlue() - Method in class org.scijava.util.ColorRGB
getBoolean(String, boolean) - Method in class org.scijava.prefs.DefaultPrefService
getBoolean(Class<?>, String, boolean) - Method in class org.scijava.prefs.DefaultPrefService
getBoolean(String, boolean) - Method in interface org.scijava.prefs.PrefService
getBoolean(Class<?>, String, boolean) - Method in interface org.scijava.prefs.PrefService
getBoolean(String, boolean) - Static method in class org.scijava.util.Prefs: Deprecated.
getBoolean(Class<?>, String, boolean) - Static method in class org.scijava.util.Prefs: Deprecated.
getBottomRight() - Method in class org.scijava.util.IntRect: Gets the bottom right coordinate of the rectangle.
getBottomRight() - Method in class org.scijava.util.RealRect: Gets the bottom right coordinate of the rectangle.
getBuildJdk() - Method in class org.scijava.util.Manifest
getBuildNumber(Class<?>) - Static method in class org.scijava.util.VersionUtils: Looks up the build number (typically an SCM revision) of the specified class.
getBuiltBy() - Method in class org.scijava.util.Manifest
getButton() - Method in class org.scijava.display.event.input.MsButtonEvent
getByExtension(String) - Method in class org.scijava.script.ScriptLanguageIndex
getByName(String) - Method in class org.scijava.script.ScriptLanguageIndex
getByteBuffer() - Method in class org.scijava.io.BytesLocation: Gets the associated ByteBuffer.
getCallback() - Method in class org.scijava.command.CommandModuleItem
getCallback() - Method in class org.scijava.module.AbstractModuleItem
getCallback() - Method in class org.scijava.module.DefaultMutableModuleItem
getCallback() - Method in interface org.scijava.module.ModuleItem: Gets the function that is called whenever this item changes.
getCallingClass(Class<?>) - Static method in class org.scijava.test.TestUtils: Returns the class of the caller (excluding the specified class).
getCallingCodeLocation(Class<?>) - Static method in class org.scijava.test.TestUtils: Returns the class and the method/line number of the caller (excluding the specified class).
getCallingThread() - Method in class org.scijava.event.SciJavaEvent: Gets the thread that published the event.
getCancelReason() - Method in interface org.scijava.Cancelable: Gets a message describing why the operation was canceled.
getCancelReason() - Method in class org.scijava.command.CommandModule
getCancelReason() - Method in class org.scijava.command.ContextCommand
getCancelReason() - Method in class org.scijava.command.DynamicCommand
getCancelReason() - Method in class org.scijava.command.ModuleCommand
getCancelReason() - Method in class org.scijava.module.process.AbstractPreprocessorPlugin
getCancelReason() - Method in class org.scijava.ui.AbstractInputHarvesterPlugin
getCharacter() - Method in class org.scijava.display.event.input.KyEvent
getChildren() - Method in class org.scijava.menu.ShadowMenu: Gets this node's children, sorted by weight.
getChoices() - Method in class org.scijava.command.CommandModuleItem
getChoices() - Method in class org.scijava.module.AbstractModuleItem
getChoices() - Method in class org.scijava.module.DefaultMutableModuleItem
getChoices() - Method in interface org.scijava.module.ModuleItem: Gets the list of possible values.
getChoices() - Method in class org.scijava.widget.DefaultWidgetModel
getChoices() - Method in interface org.scijava.widget.WidgetModel: Gets the multiple choice list for the module input.
getCIManagementSystem() - Method in class org.scijava.util.POM: Gets the CI management system.
getCIManagementURL() - Method in class org.scijava.util.POM: Gets the CI management URL.
getClass(Type) - Static method in class org.scijava.util.ConversionUtils: Deprecated.
use GenericUtils.getClass(Type)
getClass(Type) - Static method in class org.scijava.util.GenericUtils: Gets the sole raw class corresponding to the given type, or null if none.
getClasses(Type) - Static method in class org.scijava.util.GenericUtils: Gets all raw classes corresponding to the given type.
getClassName() - Method in class org.scijava.command.CommandInfo
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
getClosestPresetColor(ColorRGB) - Static method in class org.scijava.util.Colors: Returns the preset color closest to a given color.
getCode() - Method in class org.scijava.display.event.input.KyEvent
getCode() - Method in enum org.scijava.input.KeyCode: Gets the key's numeric code.
getColor(String) - Static method in class org.scijava.util.Colors: Gets the preset color with the given name.
getColumnCount() - Method in class org.scijava.command.CommandModuleItem
getColumnCount() - Method in class org.scijava.module.AbstractModuleItem
getColumnCount() - Method in class org.scijava.module.DefaultMutableModuleItem
getColumnCount() - Method in interface org.scijava.module.ModuleItem: Gets the preferred width of the input field in characters (if applicable).
getCommand() - Method in class org.scijava.command.CommandModule: Gets the command instance handled by this module.
getCommand(Class<C>) - Method in interface org.scijava.command.CommandService: Gets the first available command of the given class, or null if none.
getCommand(String) - Method in interface org.scijava.command.CommandService: Gets the first available command of the given class name, or null if none.
getCommand(Class<C>) - Method in class org.scijava.command.DefaultCommandService
getCommand(String) - Method in class org.scijava.command.DefaultCommandService
getCommands() - Method in interface org.scijava.command.CommandService: Gets the list of all available Commands).
getCommands(List<PluginInfo<CT>>) - Method in interface org.scijava.command.CommandService: Gets the list of Commands corresponding to the given plugins.
getCommands() - Method in class org.scijava.command.DefaultCommandService
getCommands(List<PluginInfo<CT>>) - Method in class org.scijava.command.DefaultCommandService
getCommands() - Method in interface org.scijava.platform.AppEventService: Deprecated.
Tag relevant commands instead: attrs = { @Attr(name = "app-command") }
getCommands() - Method in class org.scijava.platform.DefaultAppEventService: Deprecated.
getCommandService() - Method in class org.scijava.platform.DefaultPlatformService
getCommandService() - Method in interface org.scijava.platform.PlatformService
getCommandsOfClass(Class<C>) - Method in interface org.scijava.command.CommandService: Gets the list of commands of the given class.
getCommandsOfClass(String) - Method in interface org.scijava.command.CommandService: Gets the list of commands with the given class name.
getCommandsOfClass(Class<C>) - Method in class org.scijava.command.DefaultCommandService
getCommandsOfClass(String) - Method in class org.scijava.command.DefaultCommandService
getCommandsOfType(Class<CT>) - Method in interface org.scijava.command.CommandService: Gets the list of Commands of the given type.
getCommandsOfType(Class<CT>) - Method in class org.scijava.command.DefaultCommandService
getCompatibleInputs(Class<?>) - Method in interface org.scijava.convert.ConvertService
getCompatibleInputs(Class<?>) - Method in class org.scijava.convert.DefaultConvertService
getComponent() - Method in interface org.scijava.widget.UIComponent: Gets the user interface component housing this object.
getComponentClass(Type) - Static method in class org.scijava.util.ConversionUtils: Deprecated.
use GenericUtils.getComponentClass(Type)
getComponentClass(Type) - Static method in class org.scijava.util.GenericUtils: Gets the sole component class of the given array type, or null if none.
getComponentType(Type) - Static method in class org.scijava.util.GenericUtils: Gets the component type of the given array type, or null if not an array.
getComponentType() - Method in interface org.scijava.widget.UIComponent: Gets the type of the UI component housing the object.
getConsolePane() - Method in class org.scijava.ui.AbstractUserInterface
getConsolePane() - Method in interface org.scijava.ui.UserInterface: Gets the main SciJava console pane, or null if not applicable.
getContext() - Method in class org.scijava.AbstractContextual
getContext() - Method in class org.scijava.command.CommandModule
getContext() - Method in class org.scijava.command.DynamicCommand
getContext() - Method in class org.scijava.command.ModuleCommand
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.script.AbstractScriptEngine
getContext() - Method in class org.scijava.script.ScriptInfo
getContext() - Method in class org.scijava.script.ScriptModule
getContext() - Method in class org.scijava.service.AbstractService
getCreatedBy() - Method in class org.scijava.util.Manifest
getCursor() - Method in class org.scijava.tool.AbstractTool
getCursor() - Method in interface org.scijava.tool.Tool: The tool's mouse pointer.
getData() - Method in class org.scijava.io.event.IOEvent: Gets the data for which I/O took place.
getData() - Method in class org.scijava.ui.ARGBPlane
getData(Class<T>) - Method in class org.scijava.ui.dnd.AbstractDragAndDropData
getData(MIMEType) - Method in class org.scijava.ui.dnd.DefaultDragAndDropData
getData(MIMEType) - Method in interface org.scijava.ui.dnd.DragAndDropData: Gets the data with respect to the given MIME type.
getData(Class<T>) - Method in interface org.scijava.ui.dnd.DragAndDropData: Gets the data as an object of the given Java class.
getData() - Method in class org.scijava.ui.dnd.event.DragAndDropEvent: Gets the drag-and-drop data.
getDataHandle() - Method in class org.scijava.io.DataHandleInputStream
getDataType() - Method in interface org.scijava.io.IOPlugin: The type of data opened and/or saved by the plugin.
getDataType() - Method in class org.scijava.script.io.ScriptIOPlugin
getDataType() - Method in class org.scijava.text.io.TextIOPlugin
getDefaultUI() - Method in class org.scijava.ui.DefaultUIService
getDefaultUI() - Method in interface org.scijava.ui.UIService: Gets the default user interface.
getDefaultValue() - Method in class org.scijava.module.AbstractModuleItem
getDefaultValue(ModuleItem<T>) - Method in class org.scijava.module.DefaultModuleService
getDefaultValue() - Method in class org.scijava.module.DefaultMutableModuleItem
getDefaultValue() - Method in interface org.scijava.module.ModuleItem: Gets the default value.
getDefaultValue(ModuleItem<T>) - Method in interface org.scijava.module.ModuleService: Gets the default value of the given ModuleItem.
getDefaultValue(Number, Number, Class<?>) - Static method in class org.scijava.util.NumberUtils
getDelegateClass() - Method in class org.scijava.module.AbstractModuleItem
getDelegateClassName() - Method in class org.scijava.command.CommandInfo
getDelegateClassName() - Method in class org.scijava.module.DefaultMutableModuleInfo
getDelegateClassName() - Method in interface org.scijava.module.ModuleInfo: Gets the fully qualified name of the class containing the module's actual implementation.
getDelegateClassName() - Method in class org.scijava.script.ScriptInfo
getDelegateObject() - Method in class org.scijava.command.CommandModule
getDelegateObject() - Method in class org.scijava.module.AbstractModule
getDelegateObject() - Method in interface org.scijava.module.Module: Gets the object containing the module's actual implementation.
getDescription() - Method in class org.scijava.AbstractBasicDetails
getDescription() - Method in interface org.scijava.BasicDetails: Gets a string describing the object.
getDescription() - Method in class org.scijava.command.CommandModuleItem
getDescription() - Method in class org.scijava.command.DynamicCommandInfo
getDescription() - Method in class org.scijava.module.DefaultMutableModuleItem
getDescription() - Method in class org.scijava.tool.AbstractTool
getDescription() - Method in interface org.scijava.tool.Tool: Returns the text the tool provides when mouse hovers over tool
getDescriptor() - Method in class org.scijava.io.event.IOEvent: Gets the data descriptor (source or destination).
getDesktop() - Method in class org.scijava.ui.AbstractUserInterface
getDesktop() - Method in interface org.scijava.ui.UserInterface: Gets the desktop, for use with multi-document interfaces (MDI).
getDestination() - Method in class org.scijava.io.event.DataSavedEvent: Gets the destination to which data was saved.
getDisplay(String) - Method in class org.scijava.display.DefaultDisplayService
getDisplay(String) - Method in interface org.scijava.display.DisplayService: Gets a display by its name.
getDisplay() - Method in class org.scijava.display.event.DisplayEvent
getDisplay() - Method in class org.scijava.input.DefaultInputService
getDisplay() - Method in interface org.scijava.input.InputService: Gets the display associated with the last observed mouse cursor.
getDisplay() - Method in class org.scijava.ui.viewer.AbstractDisplayViewer
getDisplay() - Method in interface org.scijava.ui.viewer.DisplayPanel: Gets the panel's associated display.
getDisplay() - Method in interface org.scijava.ui.viewer.DisplayViewer: Gets the display being viewed.
getDisplay() - Method in class org.scijava.ui.viewer.text.AbstractTextDisplayViewer
getDisplay() - Method in interface org.scijava.ui.viewer.text.TextDisplayPanel
getDisplay() - Method in interface org.scijava.ui.viewer.text.TextDisplayViewer
getDisplayPlugin(Class<D>) - Method in class org.scijava.display.DefaultDisplayService
getDisplayPlugin(String) - Method in class org.scijava.display.DefaultDisplayService
getDisplayPlugin(Class<D>) - Method in interface org.scijava.display.DisplayService: Gets the display plugin of the given class, or null if none.
getDisplayPlugin(String) - Method in interface org.scijava.display.DisplayService: Gets the display plugin of the given class name, or null if none.
getDisplayPlugins() - Method in class org.scijava.display.DefaultDisplayService
getDisplayPlugins() - Method in interface org.scijava.display.DisplayService: Gets the list of known display plugins.
getDisplayPluginsOfType(Class<D>) - Method in class org.scijava.display.DefaultDisplayService
getDisplayPluginsOfType(Class<DT>) - Method in interface org.scijava.display.DisplayService: Gets the list of display plugins of the given type (e.g., ImageDisplay.class).
getDisplays() - Method in class org.scijava.display.DefaultDisplayService
getDisplays(Object) - Method in class org.scijava.display.DefaultDisplayService
getDisplays() - Method in interface org.scijava.display.DisplayService: Gets a list of all available displays.
getDisplays(Object) - Method in interface org.scijava.display.DisplayService: Gets a list of displays currently visualizing the given object.
getDisplaysOfType(Class<D>) - Method in class org.scijava.display.DefaultDisplayService
getDisplaysOfType(Class<DT>) - Method in interface org.scijava.display.DisplayService: Gets a list of all available displays of the given type (e.g., ImageDisplay.class).
getDisplayViewer(Display<?>) - Method in class org.scijava.ui.DefaultUIService
getDisplayViewer(Display<?>) - Method in interface org.scijava.ui.UIService: Gets the UI widget being used to visualize the given Display.
getDocument() - Method in class org.scijava.util.XML: Gets the XML's DOM representation.
getDouble(String, double) - Method in class org.scijava.prefs.DefaultPrefService
getDouble(Class<?>, String, double) - Method in class org.scijava.prefs.DefaultPrefService
getDouble(String, double) - Method in interface org.scijava.prefs.PrefService
getDouble(Class<?>, String, double) - Method in interface org.scijava.prefs.PrefService
getDouble(String, double) - Static method in class org.scijava.util.Prefs: Deprecated.
getDouble(Class<?>, String, double) - Static method in class org.scijava.util.Prefs: Deprecated.
getEncoding() - Method in class org.scijava.io.AbstractDataHandle
getEncoding() - Method in interface org.scijava.io.DataHandle: Gets the native encoding of the stream.
getEngine() - Method in class org.scijava.script.DefaultScriptInterpreter
getEngine() - Method in interface org.scijava.script.ScriptInterpreter: Returns the associated ScriptEngine.
getEngine() - Method in class org.scijava.script.ScriptModule: Gets the script engine used to execute the script.
getEngineName() - Method in class org.scijava.script.AbstractScriptLanguage
getEngineName() - Method in class org.scijava.script.AdaptedScriptLanguage
getEngineVersion() - Method in class org.scijava.script.AbstractScriptLanguage
getEngineVersion() - Method in class org.scijava.script.AdaptedScriptLanguage
getErrorWriter() - Method in class org.scijava.script.AbstractScriptContext
getEventClass() - Method in interface org.scijava.event.EventSubscriber
getEventService() - Method in interface org.scijava.command.CommandService
getEventService() - Method in class org.scijava.command.DefaultCommandService
getEventService() - Method in class org.scijava.display.DefaultDisplayService
getEventService() - Method in interface org.scijava.display.DisplayService
getEventService() - Method in class org.scijava.input.DefaultInputService
getEventService() - Method in interface org.scijava.input.InputService
getEventService() - Method in class org.scijava.object.DefaultObjectService
getEventService() - Method in interface org.scijava.object.ObjectService
getEventService() - Method in class org.scijava.platform.DefaultPlatformService
getEventService() - Method in interface org.scijava.platform.PlatformService
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().
getExecutorService() - Method in class org.scijava.thread.DefaultThreadService
getExecutorService() - Method in interface org.scijava.thread.ThreadService: Gets the ExecutorService object used when ThreadService.run(java.util.concurrent.Callable<V>) is called.
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.
getExtensions() - Method in class org.scijava.script.AbstractScriptLanguage
getExtensions() - Method in class org.scijava.script.AdaptedScriptLanguage
getExtensions() - Method in interface org.scijava.text.TextFormat: Gets the list of filename extensions for text in this format.
getFactory() - Method in class org.scijava.script.AbstractScriptEngine
getField() - Method in class org.scijava.command.CommandModuleItem
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.
getFieldClasses(Field, Class<?>) - Static method in class org.scijava.util.GenericUtils: Returns the "safe" class(es) of the given field, as viewed from the specified type.
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.
getFieldType(Field, Class<?>) - Static method in class org.scijava.util.GenericUtils: Returns the "safe" generic type of the given field, as viewed from the given type.
getFile() - Method in class org.scijava.io.FileLocation: Gets the associated File.
getFileExtensions(ScriptLanguage) - Method in class org.scijava.script.ScriptLanguageIndex
getFiles() - Method in class org.scijava.platform.event.AppOpenFilesEvent
getFloat(String, float) - Method in class org.scijava.prefs.DefaultPrefService
getFloat(Class<?>, String, float) - Method in class org.scijava.prefs.DefaultPrefService
getFloat(String, float) - Method in interface org.scijava.prefs.PrefService
getFloat(Class<?>, String, float) - Method in interface org.scijava.prefs.PrefService
getFloat(String, float) - Static method in class org.scijava.util.Prefs: Deprecated.
getFloat(Class<?>, String, float) - Static method in class org.scijava.util.Prefs: Deprecated.
getGenericType() - Method in class org.scijava.command.CommandModuleItem
getGenericType() - Method in class org.scijava.module.AbstractModuleItem
getGenericType() - Method in class org.scijava.module.DefaultMutableModuleItem
getGenericType() - Method in interface org.scijava.module.ModuleItem: Gets the type of the item, including Java generic parameters.
getGenericType(Field, Class<?>) - Static method in class org.scijava.util.ClassUtils: Deprecated.
use GenericUtils.getFieldType(Field, Class)
getGreen(int, int) - Method in class org.scijava.ui.ARGBPlane
getGreen() - Method in class org.scijava.util.ColorRGB
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(Object, Class<?>) - Method in interface org.scijava.convert.ConvertService
getHandler(Object, Type) - Method in interface org.scijava.convert.ConvertService
getHandler(Class<?>, Class<?>) - Method in interface org.scijava.convert.ConvertService: Deprecated.
Use ConvertService.getHandler(Object, Class)
getHandler(Class<?>, Type) - Method in interface org.scijava.convert.ConvertService: Deprecated.
Use ConvertService.getHandler(Object, Type)
getHandler(Object, Class<?>) - Method in class org.scijava.convert.DefaultConvertService
getHandler(Class<?>, Class<?>) - Method in class org.scijava.convert.DefaultConvertService
getHandler(Object, Type) - Method in class org.scijava.convert.DefaultConvertService
getHandler(Class<?>, Type) - Method in class org.scijava.convert.DefaultConvertService
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.
getHandler(File) - Method in interface org.scijava.text.TextService: Gets the text format which best handles the given file.
getHandler(DragAndDropData, Display<?>) - Method in class org.scijava.ui.dnd.DefaultDragAndDropService
getHandler(Object, Display<?>) - Method in class org.scijava.ui.dnd.DefaultDragAndDropService
getHandler(DragAndDropData, Display<?>) - Method in interface org.scijava.ui.dnd.DragAndDropService: Gets the drag-and-drop handler which will be used to handle the given DragAndDropData dragged onto the specified display.
getHandler(Object, Display<?>) - Method in interface org.scijava.ui.dnd.DragAndDropService: Gets the drag-and-drop handler which will be used to handle the given object dragged onto the specified display.
getHeader(ScriptLanguage) - Method in class org.scijava.script.DefaultScriptHeaderService
getHeader() - Method in interface org.scijava.script.ScriptHeader
getHeader(ScriptLanguage) - Method in interface org.scijava.script.ScriptHeaderService: Searches for all ScriptHeaders capable of handling the given ScriptLanguage and combines the result of their ScriptHeader.getHeader() output to a single string.
getHeight() - Method in class org.scijava.ui.ARGBPlane
getIconPath() - Method in class org.scijava.AbstractUIDetails
getIconPath() - Method in class org.scijava.command.DynamicCommandInfo
getIconPath() - Method in class org.scijava.MenuEntry
getIconPath() - Method in interface org.scijava.UIDetails: Gets the resource path to an icon representing the object.
getIconRectangleHeight() - Method in interface org.scijava.tool.IconDrawer
getIconRectangleWidth() - Method in interface org.scijava.tool.IconDrawer
getIconURL() - Method in class org.scijava.command.CommandInfo
getIconURL() - Method in class org.scijava.menu.ShadowMenu: Gets the URL of the icon associated with this node's MenuEntry.
getIconURL() - Method in class org.scijava.plugin.PluginInfo: Gets the URL corresponding to the icon resource path.
getIdentifier() - Method in class org.scijava.command.CommandInfo
getIdentifier() - Method in interface org.scijava.Identifiable: Gets a string intended to function as an identifier for the object.
getIdentifier() - Method in class org.scijava.module.AbstractModuleInfo
getIdentifier() - Method in class org.scijava.plugin.PluginInfo
getIdentifier() - Method in class org.scijava.script.ScriptInfo
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.module.DefaultModuleService
getIndex() - Method in interface org.scijava.module.ModuleService: Gets the index of available modules.
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.
getIndex() - Method in class org.scijava.script.DefaultScriptService
getIndex() - Method in interface org.scijava.script.ScriptService: Gets the index of available scripting languages.
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() - Method in class org.scijava.command.CommandModule
getInfo() - Method in class org.scijava.command.DynamicCommand
getInfo() - Method in class org.scijava.command.ModuleCommand
getInfo(boolean) - Method in interface org.scijava.Gateway
getInfo() - Method in class org.scijava.module.AbstractModuleItem
getInfo() - Method in class org.scijava.module.DefaultMutableModule
getInfo() - Method in interface org.scijava.module.Module: Gets metadata about this module.
getInfo() - Method in interface org.scijava.module.ModuleItem: Gets the ModuleInfo to which this item belongs.
getInfo() - Method in interface org.scijava.module.MutableModule
getInfo() - Method in class org.scijava.plugin.AbstractRichPlugin
getInfo() - Method in interface org.scijava.plugin.HasPluginInfo: Gets the PluginInfo metadata associated with the object.
getInfo() - Method in class org.scijava.script.ScriptModule
getInitializer() - Method in class org.scijava.command.CommandInfo
getInitializer() - Method in class org.scijava.command.CommandModuleItem
getInitializer() - Method in class org.scijava.command.DynamicCommandInfo
getInitializer() - Method in class org.scijava.module.AbstractModuleInfo
getInitializer() - Method in class org.scijava.module.AbstractModuleItem
getInitializer() - Method in class org.scijava.module.DefaultMutableModuleItem
getInitializer() - Method in interface org.scijava.module.ModuleInfo: Gets the function that is called to initialize the module's values.
getInitializer() - Method in interface org.scijava.module.ModuleItem: Gets the function that is called to initialize the item's value.
getInput(String) - Method in class org.scijava.command.CommandInfo
getInput(String, Class<T>) - Method in class org.scijava.command.CommandInfo
getInput(String) - Method in class org.scijava.command.CommandModule
getInput(String) - Method in class org.scijava.command.DynamicCommand
getInput(String) - Method in class org.scijava.module.AbstractModule
getInput(String) - Method in class org.scijava.module.AbstractModuleInfo
getInput(String, Class<T>) - Method in class org.scijava.module.AbstractModuleInfo
getInput(String) - Method in interface org.scijava.module.Module: Gets the value of the input with the given name.
getInput(String) - Method in interface org.scijava.module.ModuleInfo: Gets the input item with the given name.
getInput(String, Class<T>) - Method in interface org.scijava.module.ModuleInfo: Gets the input item with the given name and type.
getInputField(String) - Method in class org.scijava.command.DynamicCommandInfo: Gets the Field corresponding to the given @Parameter annotated module input, or null if the input does not exist or was not declared using the @Parameter mechanism.
getInputs() - Method in class org.scijava.module.AbstractModule
getInputs() - Method in interface org.scijava.module.Module: Gets a table of input values.
getInputType() - Method in class org.scijava.convert.ArrayConverters.BoolArrayUnwrapper
getInputType() - Method in class org.scijava.convert.ArrayConverters.BoolArrayWrapper
getInputType() - Method in class org.scijava.convert.ArrayConverters.ByteArrayUnwrapper
getInputType() - Method in class org.scijava.convert.ArrayConverters.ByteArrayWrapper
getInputType() - Method in class org.scijava.convert.ArrayConverters.CharArrayUnwrapper
getInputType() - Method in class org.scijava.convert.ArrayConverters.CharArrayWrapper
getInputType() - Method in class org.scijava.convert.ArrayConverters.DoubleArrayUnwrapper
getInputType() - Method in class org.scijava.convert.ArrayConverters.DoubleArrayWrapper
getInputType() - Method in class org.scijava.convert.ArrayConverters.FloatArrayUnwrapper
getInputType() - Method in class org.scijava.convert.ArrayConverters.FloatArrayWrapper
getInputType() - Method in class org.scijava.convert.ArrayConverters.IntArrayUnwrapper
getInputType() - Method in class org.scijava.convert.ArrayConverters.IntArrayWrapper
getInputType() - Method in class org.scijava.convert.ArrayConverters.LongArrayUnwrapper
getInputType() - Method in class org.scijava.convert.ArrayConverters.LongArrayWrapper
getInputType() - Method in class org.scijava.convert.ArrayConverters.ShortArrayUnwrapper
getInputType() - Method in class org.scijava.convert.ArrayConverters.ShortArrayWrapper
getInputType() - Method in interface org.scijava.convert.Converter
getInputType() - Method in class org.scijava.convert.DefaultConverter
getInputType() - Method in class org.scijava.convert.NullConverter
getInstance(Class) - Method in class org.scijava.plugin.AbstractSingletonService
getInstance(Class) - Method in interface org.scijava.plugin.SingletonService: Gets the singleton plugin instance of the given class.
getInstances() - Method in class org.scijava.options.DefaultOptionsService
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.
getInstances() - Method in interface org.scijava.text.TextService: Gets the list of available text formats.
getInstances() - Method in interface org.scijava.ui.dnd.DragAndDropService: Gets the list of available drag-and-drop handlers, which are used to perform drag-and-drop operations.
getInt(String, int) - Method in class org.scijava.prefs.DefaultPrefService
getInt(Class<?>, String, int) - Method in class org.scijava.prefs.DefaultPrefService
getInt(String, int) - Method in interface org.scijava.prefs.PrefService
getInt(Class<?>, String, int) - Method in interface org.scijava.prefs.PrefService
getInt(String, int) - Static method in class org.scijava.util.Prefs: Deprecated.
getInt(Class<?>, String, int) - Static method in class org.scijava.util.Prefs: Deprecated.
getIntX() - Method in class org.scijava.util.RealCoords
getIntY() - Method in class org.scijava.util.RealCoords
getIOType() - Method in class org.scijava.command.CommandModuleItem
getIOType() - Method in class org.scijava.module.AbstractModuleItem
getIOType() - Method in class org.scijava.module.DefaultMutableModuleItem
getIOType() - Method in interface org.scijava.module.ModuleItem: Gets the input/output type of the item.
getIssueManagementSystem() - Method in class org.scijava.util.POM: Gets the issue management system.
getIssueManagementURL() - Method in class org.scijava.util.POM: Gets the issue management URL.
getItem() - Method in class org.scijava.widget.DefaultWidgetModel
getItem() - Method in interface org.scijava.widget.WidgetModel: Gets the module input's associated item descriptor.
getItems() - Method in class org.scijava.object.event.ListEvent: Gets the list of affected items.
getIterable(String) - Method in class org.scijava.prefs.DefaultPrefService
getIterable(Class<?>, String) - Method in class org.scijava.prefs.DefaultPrefService
getIterable(String) - Method in interface org.scijava.prefs.PrefService: Gets an iterable from the preferences.
getIterable(Class<?>, String) - Method in interface org.scijava.prefs.PrefService: Gets an iterable from the preferences.
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.
getLabel() - Method in class org.scijava.command.CommandModuleItem
getLabel() - Method in class org.scijava.command.DynamicCommandInfo
getLabel() - Method in class org.scijava.module.DefaultMutableModuleItem
getLanguage() - Method in class org.scijava.script.DefaultScriptInterpreter
getLanguage() - Method in interface org.scijava.script.ScriptInterpreter: Returns the associated ScriptLanguage.
getLanguage() - Method in class org.scijava.script.ScriptModule: Gets the scripting language of the script.
getLanguageByExtension(String) - Method in class org.scijava.script.DefaultScriptService
getLanguageByExtension(String) - Method in interface org.scijava.script.ScriptService: Gets the scripting language that handles the given file extension.
getLanguageByName(String) - Method in class org.scijava.script.DefaultScriptService
getLanguageByName(String) - Method in interface org.scijava.script.ScriptService: Gets the scripting language with the given name.
getLanguageName() - Method in class org.scijava.script.AbstractScriptLanguage
getLanguageName() - Method in class org.scijava.script.AdaptedScriptLanguage
getLanguages() - Method in class org.scijava.script.DefaultScriptService
getLanguages() - Method in interface org.scijava.script.ScriptService: Gets the available scripting languages, including wrapped ScriptEngineFactory instances available from the Java scripting framework itself.
getLanguageVersion() - Method in class org.scijava.script.AbstractScriptLanguage
getLanguageVersion() - Method in class org.scijava.script.AdaptedScriptLanguage
getLeaf() - Method in class org.scijava.MenuPath: Gets the final element of the menu path.
getLevel() - Method in class org.scijava.display.event.DisplayUpdatedEvent
getLevel() - Method in class org.scijava.log.AbstractLogService
getLevel() - Method in interface org.scijava.log.LogService
getList(String) - Method in class org.scijava.prefs.DefaultPrefService
getList(Class<?>, String) - Method in class org.scijava.prefs.DefaultPrefService
getList(String, String) - Method in class org.scijava.prefs.DefaultPrefService
getList(Class<?>) - Method in class org.scijava.prefs.DefaultPrefService
getList(String) - Method in interface org.scijava.prefs.PrefService: Gets a List from the preferences.
getList(String, String) - Method in interface org.scijava.prefs.PrefService: Gets a List from the preferences, indexed under the specified path.
getList(Class<?>, String) - Method in interface org.scijava.prefs.PrefService: Gets a List from the preferences, indexed under the specified class.
getList(Class<?>) - Method in interface org.scijava.prefs.PrefService: Gets a List from the preferences.
getList(String) - Static method in class org.scijava.util.Prefs: Deprecated.

Gets a List from the preferences.
getList(Preferences, String) - Static method in class org.scijava.util.Prefs: Deprecated.
getList(Preferences) - Static method in class org.scijava.util.Prefs: Deprecated.

Gets a List from the preferences.
getLocation() - Method in interface org.scijava.Locatable: Gets the URL string defining the object's location.
getLocation() - Method in class org.scijava.module.AbstractModuleInfo
getLocation() - Method in class org.scijava.plugin.PluginInfo
getLocation() - Method in class org.scijava.script.ScriptInfo
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.
getLocationX() - Method in interface org.scijava.ui.ApplicationFrame: Gets the X coordinate of the application frame's top left corner.
getLocationY() - Method in interface org.scijava.ui.ApplicationFrame: Gets the Y coordinate of the application frame's top left corner.
getLong(String, long) - Method in class org.scijava.prefs.DefaultPrefService
getLong(Class<?>, String, long) - Method in class org.scijava.prefs.DefaultPrefService
getLong(String, long) - Method in interface org.scijava.prefs.PrefService
getLong(Class<?>, String, long) - Method in interface org.scijava.prefs.PrefService
getLong(String, long) - Static method in class org.scijava.util.Prefs: Deprecated.
getLong(Class<?>, String, long) - Static method in class org.scijava.util.Prefs: Deprecated.
getLongX() - Method in class org.scijava.util.RealCoords
getLongY() - Method in class org.scijava.util.RealCoords
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.
getManifest(XML) - Static method in class org.scijava.util.Manifest: Gets the JAR manifest associated with the given XML document.
getManifest(File) - Static method in class org.scijava.util.Manifest: Gets the JAR manifest associated with the given JAR file.
getManifestVersion() - Method in class org.scijava.util.Manifest
getMap(String) - Method in class org.scijava.prefs.DefaultPrefService
getMap(Class<?>, String) - Method in class org.scijava.prefs.DefaultPrefService
getMap(String, String) - Method in class org.scijava.prefs.DefaultPrefService
getMap(Class<?>) - Method in class org.scijava.prefs.DefaultPrefService
getMap(String) - Method in interface org.scijava.prefs.PrefService: Gets a Map from the preferences.
getMap(Class<?>, String) - Method in interface org.scijava.prefs.PrefService: Gets a map from the preferences, indexed under the specified class.
getMap(Class<?>) - Method in interface org.scijava.prefs.PrefService: Gets a Map from the preferences.
getMap(String, String) - Method in interface org.scijava.prefs.PrefService
getMap(String) - Static method in class org.scijava.util.Prefs: Deprecated.

Gets a Map from the preferences.
getMap(Preferences, String) - Static method in class org.scijava.util.Prefs: Deprecated.
getMap(Preferences) - Static method in class org.scijava.util.Prefs: Deprecated.

Gets a Map from the preferences.
getMax() - Method in class org.scijava.widget.DefaultWidgetModel
getMax() - Method in interface org.scijava.widget.WidgetModel: Gets the maximum value for the module input.
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
getMaximumValue() - Method in class org.scijava.command.CommandModuleItem
getMaximumValue() - Method in class org.scijava.module.AbstractModuleItem
getMaximumValue() - Method in class org.scijava.module.DefaultMutableModuleItem
getMaximumValue() - Method in interface org.scijava.module.ModuleItem: Gets the maximum allowed value (if applicable).
getMenu() - Method in class org.scijava.menu.DefaultMenuService
getMenu(String) - Method in class org.scijava.menu.DefaultMenuService
getMenu() - Method in interface org.scijava.menu.MenuService: Gets the root node of the application menu structure.
getMenu(String) - Method in interface org.scijava.menu.MenuService: Gets the root node of a menu structure.
getMenu(MenuPath) - Method in class org.scijava.menu.ShadowMenu: Gets the node with the given menu path (relative to this node), or null if no such menu node.
getMenu(String) - Method in class org.scijava.menu.ShadowMenu
getMenuDepth() - Method in class org.scijava.menu.ShadowMenu: Gets how deep into the menu structure this node is.
getMenuEntry() - Method in class org.scijava.menu.ShadowMenu: Gets the menu entry corresponding to this node.
getMenuPath() - Method in class org.scijava.AbstractUIDetails
getMenuPath() - Method in class org.scijava.command.DynamicCommandInfo
getMenuPath() - Method in interface org.scijava.UIDetails: Gets the path to the object's suggested position in the menu structure.
getMenuPrefix(File) - Method in class org.scijava.script.DefaultScriptService
getMenuPrefix(File) - Method in interface org.scijava.script.ScriptService: Gets the menu path prefix for the given script directory, or null if none.
getMenuRoot() - Method in class org.scijava.AbstractUIDetails
getMenuRoot() - Method in class org.scijava.command.DynamicCommandInfo
getMenuRoot() - Method in interface org.scijava.UIDetails: Gets the name of the menu structure to which the object belongs.
getMenus() - Method in class org.scijava.platform.event.AppMenusCreatedEvent
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.
getMethodCallSyntax(String, String, String...) - Method in class org.scijava.script.AbstractScriptLanguage
getMethodCallSyntax(String, String, String...) - Method in class org.scijava.script.AdaptedScriptLanguage
getMethodReturnClasses(Method, Class<?>) - Static method in class org.scijava.util.GenericUtils: As GenericUtils.getFieldClasses(Field, Class), but with respect to the return type of the given Method rather than a Field.
getMethodReturnType(Method, Class<?>) - Static method in class org.scijava.util.GenericUtils: As GenericUtils.getFieldType(Field, Class), but with respect to the return type of the given Method rather than a Field.
getMillis() - Method in class org.scijava.util.TunePlayer: Gets the current note length in milliseconds, by the current tempo.
getMIMEType(Class<?>) - Method in class org.scijava.ui.dnd.AbstractDragAndDropData
getMIMEType(Class<?>) - Method in interface org.scijava.ui.dnd.DragAndDropData: Gets the best supported MIME type matching the given Java class.
getMimeTypes() - Method in class org.scijava.script.AbstractScriptLanguage
getMimeTypes() - Method in class org.scijava.script.AdaptedScriptLanguage
getMIMETypes() - Method in class org.scijava.ui.dnd.DefaultDragAndDropData
getMIMETypes() - Method in interface org.scijava.ui.dnd.DragAndDropData: Gets the list of supported MIME types.
getMin() - Method in class org.scijava.widget.DefaultWidgetModel
getMin() - Method in interface org.scijava.widget.WidgetModel: Gets the minimum value for the module input.
getMinimumNumber(Class<?>) - Static method in class org.scijava.util.NumberUtils
getMinimumValue() - Method in class org.scijava.command.CommandModuleItem
getMinimumValue() - Method in class org.scijava.module.AbstractModuleItem
getMinimumValue() - Method in class org.scijava.module.DefaultMutableModuleItem
getMinimumValue() - Method in interface org.scijava.module.ModuleItem: Gets the minimum allowed value (if applicable).
getMnemonic() - Method in class org.scijava.MenuEntry
getMode() - Method in class org.scijava.io.FileHandle
getModifiedTime(File) - Static method in class org.scijava.util.FileUtils: Gets the Date of the file's last modification.
getModifiers() - Method in class org.scijava.display.event.input.InputEvent
getModifiers() - Method in class org.scijava.input.Accelerator
getModifiers() - Method in class org.scijava.input.DefaultInputService
getModifiers() - Method in interface org.scijava.input.InputService
getModule() - Method in class org.scijava.module.event.ModuleEvent
getModule() - Method in class org.scijava.widget.DefaultWidgetModel
getModule() - Method in interface org.scijava.widget.WidgetModel: Gets the module's associated module instance.
getModuleClass() - Method in class org.scijava.module.DefaultMutableModuleInfo
getModuleClass() - Method in interface org.scijava.module.MutableModuleInfo: Gets the module class described by this ModuleInfo.
getModuleForAccelerator(Accelerator) - Method in class org.scijava.module.DefaultModuleService
getModuleForAccelerator(Accelerator) - Method in interface org.scijava.module.ModuleService: Gets the module for a given keyboard shortcut.
getModuleInfo() - Method in class org.scijava.menu.ShadowMenu: Gets the module linked to this node, or null if node is not a leaf.
getModules() - Method in class org.scijava.module.DefaultModuleService
getModules() - Method in interface org.scijava.module.ModuleService: Gets the list of available modules.
getModuleService() - Method in interface org.scijava.command.CommandService
getModuleService() - Method in class org.scijava.command.DefaultCommandService
getMutableInput(String, Class<T>) - Method in class org.scijava.command.DynamicCommandInfo: Gets the mutable input with the given name and type.
getMutableOutput(String, Class<T>) - Method in class org.scijava.command.DynamicCommandInfo: Gets the mutable output with the given name and type.
getName() - Method in class org.scijava.AbstractBasicDetails
getName() - Method in class org.scijava.command.CommandModuleItem
getName() - Method in class org.scijava.command.DynamicCommandInfo
getName() - Method in class org.scijava.display.AbstractDisplay
getName() - Method in class org.scijava.menu.ShadowMenu
getName() - Method in class org.scijava.MenuEntry
getName() - Method in class org.scijava.module.DefaultMutableModuleItem
getName() - Method in interface org.scijava.Named: Gets the name of the object.
getName(ColorRGB) - Static method in class org.scijava.util.Colors: Gets the name of the preset matching the given color.
getNames() - Method in class org.scijava.script.AbstractScriptLanguage
getNames() - Method in class org.scijava.script.AdaptedScriptLanguage
getNextService(Class<S>, Class<? extends S>) - Method in class org.scijava.service.ServiceIndex: Gets the highest priority service compatible with class c, which is lower priority than the ref service.
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.
getNoteLength() - Method in class org.scijava.util.TunePlayer
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.
getNumClicks() - Method in class org.scijava.display.event.input.MsButtonEvent
getObject() - Method in class org.scijava.display.event.DisplayCreatedEvent
getObject() - Method in class org.scijava.display.event.DisplayDeletedEvent
getObject() - Method in class org.scijava.object.event.ObjectEvent
getObjectPool() - Method in class org.scijava.widget.DefaultWidgetModel
getObjectPool() - Method in interface org.scijava.widget.WidgetModel: Gets the available objects for use with the widget.
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.
getObjectService() - Method in class org.scijava.display.DefaultDisplayService
getObjectService() - Method in interface org.scijava.display.DisplayService
getOctave() - Method in class org.scijava.util.TunePlayer
getOpener(String) - Method in class org.scijava.io.DefaultIOService
getOpener(String) - Method in interface org.scijava.io.IOService: Gets the most appropriate IOPlugin for opening data from the given source.
getOptions(Class<O>) - Method in class org.scijava.options.DefaultOptionsService
getOptions() - Method in class org.scijava.options.event.OptionsEvent
getOptions(Class<O>) - Method in interface org.scijava.options.OptionsService: Gets the options plugin of the given class, or null if none.
getOrder() - Method in class org.scijava.io.AbstractDataHandle
getOrder() - Method in interface org.scijava.io.DataHandle: Returns the current order of the stream.
getOrganizationName() - Method in class org.scijava.util.POM: Gets the organization name.
getOrganizationURL() - Method in class org.scijava.util.POM: Gets the organization URL.
getOutput(String) - Method in class org.scijava.command.CommandInfo
getOutput(String, Class<T>) - Method in class org.scijava.command.CommandInfo
getOutput(String) - Method in class org.scijava.command.CommandModule
getOutput(String) - Method in class org.scijava.command.DynamicCommand
getOutput() - Method in class org.scijava.console.OutputEvent: Gets the output string.
getOutput(String) - Method in class org.scijava.module.AbstractModule
getOutput(String) - Method in class org.scijava.module.AbstractModuleInfo
getOutput(String, Class<T>) - Method in class org.scijava.module.AbstractModuleInfo
getOutput(String) - Method in interface org.scijava.module.Module: Gets the value of the output with the given name.
getOutput(String) - Method in interface org.scijava.module.ModuleInfo: Gets the output item with the given name.
getOutput(String, Class<T>) - Method in interface org.scijava.module.ModuleInfo: Gets the output item with the given name and type.
getOutputField(String) - Method in class org.scijava.command.DynamicCommandInfo: Gets the Field corresponding to the given @Parameter annotated module output, or null if the output does not exist or was not declared using the @Parameter mechanism.
getOutputs() - Method in class org.scijava.module.AbstractModule
getOutputs() - Method in interface org.scijava.module.Module: Gets a table of output values.
getOutputStatement(String) - Method in class org.scijava.script.AbstractScriptLanguage
getOutputStatement(String) - Method in class org.scijava.script.AdaptedScriptLanguage
getOutputType() - Method in class org.scijava.convert.ArrayConverters.BoolArrayUnwrapper
getOutputType() - Method in class org.scijava.convert.ArrayConverters.BoolArrayWrapper
getOutputType() - Method in class org.scijava.convert.ArrayConverters.ByteArrayUnwrapper
getOutputType() - Method in class org.scijava.convert.ArrayConverters.ByteArrayWrapper
getOutputType() - Method in class org.scijava.convert.ArrayConverters.CharArrayUnwrapper
getOutputType() - Method in class org.scijava.convert.ArrayConverters.CharArrayWrapper
getOutputType() - Method in class org.scijava.convert.ArrayConverters.DoubleArrayUnwrapper
getOutputType() - Method in class org.scijava.convert.ArrayConverters.DoubleArrayWrapper
getOutputType() - Method in class org.scijava.convert.ArrayConverters.FloatArrayUnwrapper
getOutputType() - Method in class org.scijava.convert.ArrayConverters.FloatArrayWrapper
getOutputType() - Method in class org.scijava.convert.ArrayConverters.IntArrayUnwrapper
getOutputType() - Method in class org.scijava.convert.ArrayConverters.IntArrayWrapper
getOutputType() - Method in class org.scijava.convert.ArrayConverters.LongArrayUnwrapper
getOutputType() - Method in class org.scijava.convert.ArrayConverters.LongArrayWrapper
getOutputType() - Method in class org.scijava.convert.ArrayConverters.ShortArrayUnwrapper
getOutputType() - Method in class org.scijava.convert.ArrayConverters.ShortArrayWrapper
getOutputType() - Method in interface org.scijava.convert.Converter
getOutputType() - Method in class org.scijava.convert.DefaultConverter
getOutputType() - Method in class org.scijava.convert.NullConverter
getPackage() - Method in class org.scijava.util.Manifest
getPanel() - Method in class org.scijava.ui.viewer.AbstractDisplayViewer
getPanel() - Method in interface org.scijava.ui.viewer.DisplayViewer: Gets the display panel that hosts the gui elements.
getPanel() - Method in class org.scijava.widget.DefaultWidgetModel
getPanel() - Method in interface org.scijava.widget.WidgetModel: Gets the input panel intended to house the widget.
getParameter() - Method in class org.scijava.command.CommandModuleItem
getParameter(String) - Method in class org.scijava.script.AbstractScriptLanguage
getParameter(String) - Method in class org.scijava.script.AdaptedScriptLanguage
getParameter(String) - Method in class org.scijava.ui.dnd.MIMEType: Gets the value of the parameter with the given name, or null if none.
getParameters() - Method in class org.scijava.ui.dnd.MIMEType: Gets the parameter names associated with this MIME type.
getParent() - Method in class org.scijava.console.MultiPrintStream
getParent() - Method in class org.scijava.menu.ShadowMenu: Gets this node's parent, or null if it is a root node.
getParent(Thread) - Method in class org.scijava.thread.DefaultThreadService
getParent(Thread) - Method in interface org.scijava.thread.ThreadService: Returns the thread that called the specified thread.
getParentArtifactId() - Method in class org.scijava.util.POM: Gets the POM's parent artifactId.
getParentGroupId() - Method in class org.scijava.util.POM: Gets the POM's parent groupId.
getParentVersion() - Method in class org.scijava.util.POM: Gets the POM's parent artifactId.
getPath() - Method in class org.scijava.script.ScriptInfo: Gets the path to the script on disk.
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.
getPersistKey() - Method in class org.scijava.command.CommandModuleItem
getPersistKey() - Method in class org.scijava.module.AbstractModuleItem
getPersistKey() - Method in class org.scijava.module.DefaultMutableModuleItem
getPersistKey() - Method in interface org.scijava.module.ModuleItem: Gets the key to use for saving the value persistently.
getPlatformService() - Method in class org.scijava.platform.AbstractPlatform
getPlugin(Class) - Method in class org.scijava.plugin.DefaultPluginService
getPlugin(Class, Class<PT>) - Method in class org.scijava.plugin.DefaultPluginService
getPlugin(String) - Method in class org.scijava.plugin.DefaultPluginService
getPlugin(Class) - Method in interface org.scijava.plugin.PluginService: Gets the first available plugin of the given class, or null if none.
getPlugin(Class, 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.command.CommandInfo
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.command.DefaultCommandService
getPluginService() - Method in class org.scijava.display.DefaultDisplayService
getPluginService() - Method in interface org.scijava.display.DisplayService
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) - Method in class org.scijava.plugin.DefaultPluginService
getPluginsOfClass(Class, 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) - Method in interface org.scijava.plugin.PluginService: Gets the list of plugins of the given class.
getPluginsOfClass(Class, 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() - Method in class org.scijava.app.DefaultAppService
getPluginType() - Method in class org.scijava.command.DefaultCommandService
getPluginType() - Method in class org.scijava.console.DefaultConsoleService
getPluginType() - Method in class org.scijava.convert.DefaultConvertService
getPluginType() - Method in class org.scijava.io.DefaultDataHandleService
getPluginType() - Method in class org.scijava.io.DefaultIOService
getPluginType() - Method in class org.scijava.options.DefaultOptionsService
getPluginType() - Method in class org.scijava.platform.DefaultPlatformService
getPluginType(Class) - 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.
getPluginType() - Method in class org.scijava.script.DefaultScriptHeaderService
getPluginType() - Method in class org.scijava.script.DefaultScriptService
getPluginType() - Method in class org.scijava.text.DefaultTextService
getPluginType() - Method in class org.scijava.tool.DefaultToolService
getPluginType() - Method in class org.scijava.ui.dnd.DefaultDragAndDropService
getPluginType() - Method in class org.scijava.widget.DefaultWidgetService
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
getPresets() - Method in class org.scijava.command.CommandInfo: Gets the table of items with fixed, preset values.
getPrevService(Class<S>, Class<? extends S>) - Method in class org.scijava.service.ServiceIndex: Gets the lowest priority service compatible with class c, which is higher priority than the ref service.
getPriority() - Method in class org.scijava.AbstractUIDetails
getPriority() - Method in class org.scijava.command.DynamicCommandInfo
getPriority() - Method in class org.scijava.plugin.AbstractRichPlugin
getPriority() - Method in interface org.scijava.Prioritized: Gets the sort priority of the object.
getProblems() - Method in class org.scijava.command.CommandInfo
getProblems() - Method in class org.scijava.command.DynamicCommandInfo
getProblems() - Method in class org.scijava.module.AbstractModuleInfo
getProblems() - Method in class org.scijava.module.MethodRef
getProblems() - Method in interface org.scijava.Validated: Gets the list of problems encountered while initializing the object.
getProcessor() - Method in class org.scijava.module.event.ModulePostprocessEvent
getProcessor() - Method in class org.scijava.module.event.ModulePreprocessEvent
getProcessor() - Method in class org.scijava.module.event.ModuleProcessEvent
getProgram(String...) - Method in class org.scijava.script.AbstractScriptLanguage
getProgram(String...) - Method in class org.scijava.script.AdaptedScriptLanguage
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.
getQueryMap() - Method in class org.scijava.io.URILocation
getQueryValue(String) - Method in class org.scijava.io.URILocation
getRandomAccessFile() - Method in class org.scijava.io.FileHandle: Gets the random access file object backing this FileHandle.
getReader() - Method in class org.scijava.script.AbstractScriptContext
getReader() - Method in class org.scijava.script.ScriptInfo: Gets a reader which delivers the script's content.
getReason() - Method in class org.scijava.module.event.ModuleCanceledEvent
getRecentFiles() - Method in class org.scijava.io.DefaultRecentFileService
getRecentFiles() - Method in interface org.scijava.io.RecentFileService: Gets the list of recent files.
getRed(int, int) - Method in class org.scijava.ui.ARGBPlane
getRed() - Method in class org.scijava.util.ColorRGB
getResult() - Method in interface org.scijava.script.CodeGenerator
getResult() - Method in class org.scijava.script.CodeGeneratorJava
getReturnValue() - Method in class org.scijava.script.ScriptModule: Gets the return value of the script.
getSampleRate() - Method in class org.scijava.util.TunePlayer
getSaver(D, String) - Method in class org.scijava.io.DefaultIOService
getSaver(D, String) - Method in interface org.scijava.io.IOService: Gets the most appropriate IOPlugin for saving data to the given destination.
getSCMConnection() - Method in class org.scijava.util.POM: Gets the SCM connection string.
getSCMDeveloperConnection() - Method in class org.scijava.util.POM: Gets the SCM developerConnection string.
getSCMTag() - Method in class org.scijava.util.POM: Gets the SCM tag.
getSCMURL() - Method in class org.scijava.util.POM: Gets the SCM URL.
getScopes() - Method in class org.scijava.script.AbstractScriptContext
getScript(File) - Method in class org.scijava.script.DefaultScriptService
getScript(File) - Method in interface org.scijava.script.ScriptService: Gets the ScriptInfo metadata for the script at the given file, or null if none.
getScriptDirectories() - Method in class org.scijava.script.DefaultScriptService
getScriptDirectories() - Method in interface org.scijava.script.ScriptService: Gets the base directories to scan for scripts.
getScriptEngine() - Method in class org.scijava.script.AdaptedScriptLanguage
getScripts() - Method in class org.scijava.script.DefaultScriptService
getScripts() - Method in interface org.scijava.script.ScriptService: Gets all available scripts.
getSelectionGroup() - Method in class org.scijava.AbstractUIDetails
getSelectionGroup() - Method in class org.scijava.command.DynamicCommandInfo
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
getSingleInput(Module, Class<T>) - Method in class org.scijava.module.DefaultModuleService
getSingleInput(Module, Class<T>) - Method in interface org.scijava.module.ModuleService: Checks the given module for a solitary unresolved fillable input of the given type, returning the relevant ModuleItem if found, or null if not exactly one unresolved fillable input of that type.
getSingleInput(Module, Class<?>) - Method in class org.scijava.module.process.AbstractSingleInputPreprocessor: Helper method to look up the name of singleton module inputs of a given type.
getSingleOutput(Module, Class<T>) - Method in class org.scijava.module.DefaultModuleService
getSingleOutput(Module, Class<T>) - Method in interface org.scijava.module.ModuleService: Checks the given module for a solitary unresolved output of the given type, returning the relevant ModuleItem if found, or null if not exactly one unresolved output of that type.
getSoftMax() - Method in class org.scijava.widget.DefaultWidgetModel
getSoftMax() - Method in interface org.scijava.widget.WidgetModel: Gets the "soft" maximum value for the module input.
getSoftMaximum() - Method in class org.scijava.module.AbstractModuleItem
getSoftMaximum() - Method in class org.scijava.module.DefaultMutableModuleItem
getSoftMaximum() - Method in interface org.scijava.module.ModuleItem: Gets the "soft" maximum value (if applicable).
getSoftMin() - Method in class org.scijava.widget.DefaultWidgetModel
getSoftMin() - Method in interface org.scijava.widget.WidgetModel: Gets the "soft" minimum value for the module input.
getSoftMinimum() - Method in class org.scijava.module.AbstractModuleItem
getSoftMinimum() - Method in class org.scijava.module.DefaultMutableModuleItem
getSoftMinimum() - Method in interface org.scijava.module.ModuleItem: Gets the "soft" minimum value (if applicable).
getSource() - Method in class org.scijava.console.OutputEvent: Gets the source of the output.
getSource() - Method in class org.scijava.io.event.DataOpenedEvent: Gets the source from which data was opened.
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() - Method in class org.scijava.event.SciJavaEvent: Gets the stack trace of the calling thread when the event was published.
getStackTrace(Throwable) - Static method in class org.scijava.util.DebugUtils: Extracts the given exception's corresponding stack trace to a string.
getStatusBar() - Method in class org.scijava.ui.AbstractUserInterface
getStatusBar() - Method in interface org.scijava.ui.UserInterface: Gets the main SciJava status bar, or null if not applicable.
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.
getStatusMessage(StatusEvent) - Method in class org.scijava.ui.DefaultUIService
getStatusMessage(StatusEvent) - Method in interface org.scijava.ui.UIService: Gets the status message associated with the given event.
getStepSize() - Method in class org.scijava.command.CommandModuleItem
getStepSize() - Method in class org.scijava.module.AbstractModuleItem
getStepSize() - Method in class org.scijava.module.DefaultMutableModuleItem
getStepSize() - Method in interface org.scijava.module.ModuleItem: Gets the preferred step size to use when rendering the item in a user interface (if applicable).
getStepSize() - Method in class org.scijava.widget.DefaultWidgetModel
getStepSize() - Method in interface org.scijava.widget.WidgetModel: Gets the step size between values for the module input.
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).
getSystemClipboard() - Method in interface org.scijava.ui.UserInterface: Gets the system clipboard associated with this UI.
getSystemProperty() - Method in class org.scijava.app.AbstractApp
getSystemProperty() - Method in interface org.scijava.app.App: A system property which, if set, overrides the base directory of the application.
getTargetPlatforms() - Method in class org.scijava.platform.DefaultPlatformService
getTargetPlatforms() - Method in interface org.scijava.platform.PlatformService: Gets the platform handlers applicable to this platform.
getTempo() - Method in class org.scijava.util.TunePlayer
getText() - Method in class org.scijava.widget.DefaultWidgetModel
getText() - Method in interface org.scijava.widget.WidgetModel: Gets the input's value rendered as a string.
getThreadContext(Thread) - Method in class org.scijava.thread.DefaultThreadService
getThreadContext(Thread) - Method in interface org.scijava.thread.ThreadService: Analyzes the Context of the given thread.
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 class org.scijava.app.AbstractApp
getTitle() - Method in interface org.scijava.app.App: Gets the title of the application.
getTitle() - Method in class org.scijava.command.CommandInfo
getTitle() - Method in class org.scijava.command.DynamicCommandInfo
getTitle() - Method in interface org.scijava.Gateway
getTitle() - Method in class org.scijava.module.AbstractModuleInfo
getTitle() - Method in interface org.scijava.UIDetails: Gets an appropriate title for the object, for use in a user interface.
getTone(int, char) - Method in class org.scijava.util.TunePlayer: Gets the value of the given tone for the current octave.
getTool(String) - Method in class org.scijava.tool.DefaultToolService
getTool(Class<T>) - Method in class org.scijava.tool.DefaultToolService
getTool() - Method in class org.scijava.tool.event.ToolEvent
getTool(String) - Method in interface org.scijava.tool.ToolService
getTool(Class<T>) - Method in interface org.scijava.tool.ToolService: Get a tool given its class.
getToolBar() - Method in class org.scijava.ui.AbstractUserInterface
getToolBar() - Method in interface org.scijava.ui.UserInterface: Gets the main SciJava toolbar, or null if not applicable.
getTools() - Method in class org.scijava.tool.DefaultToolService
getTools() - Method in interface org.scijava.tool.ToolService
getTopLeft() - Method in class org.scijava.util.IntRect: Gets the top left coordinate of the rectangle.
getTopLeft() - Method in class org.scijava.util.RealRect: Gets the top left coordinate of the rectangle.
getType() - Method in class org.scijava.command.CommandModuleItem
getType() - Method in class org.scijava.console.AbstractConsoleArgument
getType() - Method in class org.scijava.console.DefaultConsoleService
getType() - Method in class org.scijava.convert.AbstractConverter
getType() - Method in class org.scijava.convert.DefaultConvertService
getType() - Method in class org.scijava.io.AbstractIOPlugin
getType() - Method in class org.scijava.io.DefaultDataHandleService
getType() - Method in class org.scijava.io.DefaultIOService
getType() - Method in class org.scijava.io.FileHandle
getType() - Method in class org.scijava.module.DefaultMutableModuleItem
getType() - Method in interface org.scijava.module.ModuleItem: Gets the type of the item.
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 class org.scijava.script.AbstractScriptHeader
getType() - Method in class org.scijava.script.DefaultScriptHeaderService
getType() - Method in class org.scijava.text.AbstractTextFormat
getType() - Method in class org.scijava.text.DefaultTextService
getType() - Method in interface org.scijava.Typed: Gets the type associated with the object.
getType() - Method in class org.scijava.ui.dnd.DefaultDragAndDropService
getType() - Method in class org.scijava.ui.dnd.FileDragAndDropHandler
getType() - Method in class org.scijava.ui.dnd.ListDragAndDropHandler
getType() - Method in class org.scijava.ui.dnd.ScriptFileDragAndDropHandler
getType() - Method in class org.scijava.widget.AbstractInputWidget
getType() - Method in class org.scijava.widget.DefaultWidgetService
getTypeParameter(Type, Class<?>, int) - Static method in class org.scijava.util.GenericUtils: Gets the given type's nth type parameter of the specified class.
getTypes(Class<?>) - Static method in class org.scijava.object.ObjectIndex: Gets a new set containing the type and all its supertypes.
getTypes(Field, Class<?>) - Static method in class org.scijava.util.ClassUtils: Deprecated.
use GenericUtils.getFieldClasses(Field, Class)
getUI() - Method in class org.scijava.ui.AbstractInputHarvesterPlugin: Gets the name (or class name) of the input harvester's affiliated UI.
getUI(String) - Method in class org.scijava.ui.DefaultUIService
getUI() - Method in class org.scijava.ui.event.UIEvent: Gets the user interface.
getUI(String) - Method in interface org.scijava.ui.UIService: Gets the UI with the given name (or class name).
getURI() - Method in class org.scijava.io.AbstractLocation
getURI() - Method in class org.scijava.io.FileLocation
getURI() - Method in interface org.scijava.io.Location: Gets the location expressed as a URI, or null if the location cannot be expressed as such.
getURI() - Method in class org.scijava.io.URILocation
getURI() - Method in class org.scijava.io.URLLocation: Gets the associated URI, or null if this URL is not formatted strictly according to to RFC2396 and cannot be converted to a URI.
getURL() - Method in class org.scijava.io.URLLocation: Gets the associated URL.
getValue(Module) - Method in class org.scijava.module.AbstractModuleItem
getValue(Module) - Method in interface org.scijava.module.ModuleItem: Gets the item's current value with respect to the given module.
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
getValue(String) - Method in class org.scijava.widget.AbstractInputPanel
getValue() - Method in class org.scijava.widget.DefaultWidgetModel
getValue(String) - Method in interface org.scijava.widget.InputPanel: Returns the value of the given widget's input.
getValue() - Method in interface org.scijava.widget.InputWidget: Gets the current widget value.
getValue() - Method in interface org.scijava.widget.WidgetModel: Gets the current value of the module input.
getVar(String) - Method in class org.scijava.util.ReflectedUniverse: Returns the value of a variable or field in the universe.
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.module.AbstractModuleInfo
getVersion() - Method in class org.scijava.plugin.PluginInfo
getVersion() - Method in class org.scijava.script.ScriptInfo
getVersion() - Method in class org.scijava.util.POM: Gets the POM's version.
getVersion(Class<?>) - Static method in class org.scijava.util.VersionUtils: Looks up the version of the specified class using any means available, appending the build number to any SNAPSHOT version.
getVersion(Class<?>, String, String) - Static method in class org.scijava.util.VersionUtils: Looks up the version of the specified class using any means available, appending the build number to any SNAPSHOT version.
getVersion() - Method in interface org.scijava.Versioned: Gets the version of the object.
getVersionFromManifest(Class<?>) - Static method in class org.scijava.util.VersionUtils: Looks up the version of the specified class using a JAR manifest if available, appending the build number to any SNAPSHOT version.
getVersionFromPOM(Class<?>, String, String) - Static method in class org.scijava.util.VersionUtils: Looks up the version of the specified class using the specified POM, or base POM directory if groupId and artifactId are null.
getViewerPlugins() - Method in class org.scijava.ui.DefaultUIService
getViewerPlugins() - Method in interface org.scijava.ui.UIService: Gets the list of known viewer plugins.
getVisibility() - Method in class org.scijava.command.CommandModuleItem
getVisibility() - Method in class org.scijava.module.AbstractModuleItem
getVisibility() - Method in class org.scijava.module.DefaultMutableModuleItem
getVisibility() - Method in interface org.scijava.module.ModuleItem: Gets the visibility of the item.
getVisibleUIs() - Method in class org.scijava.ui.DefaultUIService
getVisibleUIs() - Method in interface org.scijava.ui.UIService: Gets the user interfaces that are currently visible.
getWeight() - Method in class org.scijava.MenuEntry
getWheelRotation() - Method in class org.scijava.display.event.input.MsWheelEvent
getWidgetComponentType() - Method in interface org.scijava.widget.InputPanel: Gets the type of the UI component housing the panel's widgets.
getWidgetCount() - Method in class org.scijava.widget.AbstractInputPanel
getWidgetCount() - Method in interface org.scijava.widget.InputPanel: Gets the number of active widgets in the input panel.
getWidgetLabel() - Method in class org.scijava.widget.DefaultWidgetModel
getWidgetLabel() - Method in interface org.scijava.widget.WidgetModel: Gets the text to use when labeling this widget.
getWidgetStyle() - Method in class org.scijava.command.CommandModuleItem
getWidgetStyle() - Method in class org.scijava.module.AbstractModuleItem
getWidgetStyle() - Method in class org.scijava.module.DefaultMutableModuleItem
getWidgetStyle() - Method in interface org.scijava.module.ModuleItem: Gets the preferred widget style to use when rendering the item in a user interface.
getWidth() - Method in class org.scijava.ui.ARGBPlane
getWindow() - Method in class org.scijava.display.event.window.WinEvent: Gets the actual UI-specific window.
getWindow() - Method in class org.scijava.ui.viewer.AbstractDisplayViewer
getWindow() - Method in interface org.scijava.ui.viewer.DisplayPanel: Gets the window housing this panel.
getWindow() - Method in interface org.scijava.ui.viewer.DisplayViewer: Gets the window in which the view is displayed.
getWriter() - Method in class org.scijava.script.AbstractScriptContext
getX() - Method in class org.scijava.display.event.input.InputEvent
getX() - Method in class org.scijava.input.DefaultInputService
getX() - Method in interface org.scijava.input.InputService: Gets the last observed X coordinate of the mouse cursor, relative to a specific display.
getY() - Method in class org.scijava.display.event.input.InputEvent
getY() - Method in class org.scijava.input.DefaultInputService
getY() - Method in interface org.scijava.input.InputService: Gets the last observed Y coordinate of the mouse cursor, relative to a specific display.
GHOSTWHITE - Static variable in class org.scijava.util.Colors
GOLD - Static variable in class org.scijava.util.Colors
GOLDENROD - Static variable in class org.scijava.util.Colors
GRAY - Static variable in class org.scijava.util.Colors
GREEN - Static variable in class org.scijava.util.Colors
GREENYELLOW - Static variable in class org.scijava.util.Colors
GREY - Static variable in class org.scijava.util.Colors

H

handle(LinkedList<String>) - Method in class org.scijava.command.console.RunArgument
handle(LinkedList<String>) - Method in interface org.scijava.console.ConsoleArgument: Handles the front of the given list of arguments.
handle(LinkedList<String>) - Method in class org.scijava.console.SystemPropertyArgument
handle(LinkedList<String>) - Method in class org.scijava.io.console.OpenArgument
handle(Exception) - Method in class org.scijava.log.DefaultUncaughtExceptionHandler
handle(LinkedList<String>) - Method in class org.scijava.ui.console.UIArgument
handledType() - Method in class org.scijava.script.AbstractScriptHeader
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.
harvest(Module) - Method in class org.scijava.widget.AbstractInputHarvester
harvest(Module) - Method in interface org.scijava.widget.InputHarvester: Performs the harvesting process.
harvestInputs(InputPanel<P, W>, Module) - Method in interface org.scijava.widget.InputHarvester: Gathers input values from the user or other source.
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.
hash(String) - Static method in class org.scijava.util.DigestUtils: Gets the Java hash code of the given string, as a byte array.
hash(byte[]) - Static method in class org.scijava.util.DigestUtils: Gets the hash code of the given byte array, as a byte array.
hashCode() - Method in class org.scijava.input.Accelerator
hashCode() - Method in class org.scijava.input.InputModifiers
hashCode() - Method in class org.scijava.ui.dnd.MIMEType
hashCode() - Method in class org.scijava.util.ColorRGB
hashCode() - Method in class org.scijava.util.IntCoords
hashCode() - Method in class org.scijava.util.IntRect
hashCode() - Method in class org.scijava.util.RealCoords
hashCode() - Method in class org.scijava.util.RealRect
hasMoreElements() - Method in class org.scijava.util.IteratorPlus
hasNext() - Method in class org.scijava.menu.ShadowMenuIterator
hasNext() - Method in class org.scijava.util.IteratorPlus
HasPluginInfo - Interface in org.scijava.plugin: A object with associated PluginInfo metadata.
hasWidgets() - Method in class org.scijava.widget.AbstractInputPanel
hasWidgets() - Method in interface org.scijava.widget.InputPanel: Gets whether the input panel has any active widgets.
height - Variable in class org.scijava.util.IntRect
height - Variable in class org.scijava.util.RealRect
HELP_LABEL - Static variable in class org.scijava.menu.MenuConstants
HELP_MNEMONIC - Static variable in class org.scijava.menu.MenuConstants
HELP_WEIGHT - Static variable in class org.scijava.menu.MenuConstants
hex(byte[]) - Static method in class org.scijava.util.DigestUtils: Converts the given byte array to a hexidecimal string.
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
HONEYDEW - Static variable in class org.scijava.util.Colors
HOTPINK - Static variable in class org.scijava.util.Colors

I

icon() - Method in class org.scijava.AbstractGateway
icon() - Method in interface org.scijava.Gateway: Gets this application context's IconService.
IconDrawer - Interface in org.scijava.tool: CustomDrawnTools use IconDrawers to draw their icon on screen.
IconService - Interface in org.scijava.tool: IconService allows a Tool to obtain the IconDrawer.
Identifiable - Interface in org.scijava: An object which can express itself by some unique string.
IMAGE_LABEL - Static variable in class org.scijava.menu.MenuConstants
IMAGE_MNEMONIC - Static variable in class org.scijava.menu.MenuConstants
IMAGE_WEIGHT - Static variable in class org.scijava.menu.MenuConstants
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(Object) - Method in class org.scijava.display.AbstractDisplay
indexOf(boolean[], boolean) - Static method in class org.scijava.util.ArrayUtils: Returns the index of the first occurrence of the given value in the given array.
indexOf(byte[], byte) - Static method in class org.scijava.util.ArrayUtils: Returns the index of the first occurrence of the given value in the given array.
indexOf(char[], char) - Static method in class org.scijava.util.ArrayUtils: Returns the index of the first occurrence of the given value in the given array.
indexOf(double[], double) - Static method in class org.scijava.util.ArrayUtils: Returns the index of the first occurrence of the given value in the given array.
indexOf(float[], float) - Static method in class org.scijava.util.ArrayUtils: Returns the index of the first occurrence of the given value in the given array.
indexOf(int[], int) - Static method in class org.scijava.util.ArrayUtils: Returns the index of the first occurrence of the given value in the given array.
indexOf(long[], long) - Static method in class org.scijava.util.ArrayUtils: Returns the index of the first occurrence of the given value in the given array.
indexOf(short[], short) - Static method in class org.scijava.util.ArrayUtils: Returns the index of the first occurrence of the given value in the given array.
indexOf(Object[], Object) - Static method in class org.scijava.util.ArrayUtils: Returns the index of the first occurrence of the given value in the given Object array.
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
INDIANRED - Static variable in class org.scijava.util.Colors
INDIGO - Static variable in class org.scijava.util.Colors
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.cache.DefaultCacheService
initialize() - Method in class org.scijava.command.CommandModule
initialize() - Method in class org.scijava.command.DefaultCommandService
initialize() - Method in class org.scijava.convert.AbstractConvertService
initialize() - Method in class org.scijava.event.DefaultEventService
initialize() - Method in class org.scijava.io.DefaultRecentFileService
initialize() - Method in class org.scijava.module.AbstractModule
initialize(Module) - Method in class org.scijava.module.AbstractModuleItem
initialize() - Method in class org.scijava.module.DefaultModuleService
initialize() - Method in interface org.scijava.module.Module: Initializes the module.
initialize(Module) - Method in interface org.scijava.module.ModuleItem: Invokes this item's initializer function, if any, on the given module.
initialize() - Method in class org.scijava.object.DefaultObjectService
initialize() - Method in class org.scijava.platform.DefaultPlatformService
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.prefs.AbstractPrefService
initialize() - Method in class org.scijava.script.DefaultScriptService
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.
InitPreprocessor - Class in org.scijava.module.process: A preprocessor plugin that populates initial parameter values.
InitPreprocessor() - Constructor for class org.scijava.module.process.InitPreprocessor
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.
input() - Method in class org.scijava.AbstractGateway
input() - Method in interface org.scijava.Gateway: Gets this application context's InputService.
InputEvent - Class in org.scijava.display.event.input: An event indicating input device (e.g., keyboard or mouse) activity in a display.
InputEvent(Display<?>, InputModifiers, int, int) - Constructor for class org.scijava.display.event.input.InputEvent
InputHarvester<P,W> - Interface in org.scijava.widget: An input harvester collects Module input values, according to the following steps: Create an InputPanel with widgets corresponding to the module inputs. Present the panel, if in a UI context. Harvest the final widget values from the panel, updating the Module's input values to match the harvested values. Perform any other needed processing of the results (marking inputs as resolved, storing persisted values to preferences, etc.).
inputList() - Method in class org.scijava.module.AbstractModuleInfo: Gets AbstractModuleInfo.outputMap, initializing if needed.
inputMap() - Method in class org.scijava.module.AbstractModuleInfo: Gets AbstractModuleInfo.inputMap, initializing if needed.
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
InputPanel<P,W> - Interface in org.scijava.widget: Flexible panel-building interface, for use with UIs that prompt for input values of various types.
inputs() - Method in class org.scijava.command.CommandInfo
inputs() - Method in class org.scijava.module.AbstractModuleInfo
inputs() - Method in interface org.scijava.module.ModuleInfo: Gets the list of input items.
InputService - Interface in org.scijava.input: Interface for service that tracks the current status of input devices (keyboard and mouse in particular).
InputWidget<T,W> - Interface in org.scijava.widget: Interface for input widgets.
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.
IntCoords - Class in org.scijava.util: This class represents an (X, Y) coordinate pair in integer coordinates.
IntCoords(int, int) - Constructor for class org.scijava.util.IntCoords
Interactive - Interface in org.scijava.command: An operation (usually a Command) which is intended to be run interactively.
InteractiveCommand - Class in org.scijava.command: A command intended to be run interactively.
InteractiveCommand(String...) - Constructor for class org.scijava.command.InteractiveCommand: Creates a new interactive command.
interrupt() - Method in class org.scijava.util.ReadInto
intersection(IntRect) - Method in class org.scijava.util.IntRect: Returns a Rect representing the intersection of this Rect with the given Rect.
intersection(RealRect) - Method in class org.scijava.util.RealRect: Returns a Rect representing the intersection of this Rect with the given Rect.
intersects(IntRect) - Method in class org.scijava.util.IntRect: Returns true if this rect intersects the given rect.
intersects(RealRect) - Method in class org.scijava.util.RealRect: Returns true if this rect intersects the given rect.
IntRect - Class in org.scijava.util: A class for representing a rectangular region, in integer coordinates.
IntRect() - Constructor for class org.scijava.util.IntRect
IntRect(int, int, int, int) - Constructor for class org.scijava.util.IntRect
InvocationObject - Class in org.scijava.script: Holds a module or plugin reference that was invoked in a macro recording, and the parameters that were passed to it.
InvocationObject(String) - Constructor for class org.scijava.script.InvocationObject
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.
invokeStatementBegin() - Method in interface org.scijava.script.CodeGenerator
invokeStatementBegin() - Method in class org.scijava.script.CodeGeneratorJava
invokeStatementEnd() - Method in interface org.scijava.script.CodeGenerator
invokeStatementEnd() - Method in class org.scijava.script.CodeGeneratorJava
io() - Method in class org.scijava.AbstractGateway
io() - Method in interface org.scijava.Gateway: Gets this application context's IOService.
IOEvent - Class in org.scijava.io.event: An event indicating that I/O (e.g., opening or saving) has occurred.
IOEvent(String, Object) - Constructor for class org.scijava.io.event.IOEvent
IOPlugin<D> - Interface in org.scijava.io: A plugin which extends an application's I/O capabilities.
IOService - Interface in org.scijava.io: Interface for high-level data I/O: opening and saving data.
is(String) - Method in class org.scijava.AbstractBasicDetails
is(String) - Method in interface org.scijava.BasicDetails: Returns true iff the given key is defined.
is(String) - Method in class org.scijava.command.CommandModuleItem
isAccepted() - Method in class org.scijava.ui.dnd.event.DragEnterEvent: Gets whether the drag operation is valid.
isAccessibilityIgnored() - Method in class org.scijava.util.ReflectedUniverse: Gets whether access modifiers (protected, private, etc.) are ignored.
isActivated() - Method in class org.scijava.platform.event.AppUserSessionEvent
isActive() - Method in class org.scijava.event.DefaultEventHistory
isActive() - Method in interface org.scijava.event.EventHistory: Gets whether event history tracking is currently active.
isActiveInAppFrame() - Method in class org.scijava.tool.AbstractTool
isActiveInAppFrame() - Method in interface org.scijava.tool.Tool: When true, tool receives events when the main application frame is active.
isAltDown() - Method in class org.scijava.input.DefaultInputService
isAltDown() - Method in class org.scijava.input.InputModifiers
isAltDown() - Method in interface org.scijava.input.InputService
isAltGrDown() - Method in class org.scijava.input.DefaultInputService
isAltGrDown() - Method in class org.scijava.input.InputModifiers
isAltGrDown() - Method in interface org.scijava.input.InputService
isAlwaysActive() - Method in class org.scijava.tool.AbstractTool
isAlwaysActive() - Method in interface org.scijava.tool.Tool: When true, tool has no button but rather is active all the time.
isAutoFill() - Method in class org.scijava.command.CommandModuleItem
isAutoFill() - Method in class org.scijava.module.AbstractModuleItem
isAutoFill() - Method in interface org.scijava.module.ModuleItem: Gets whether the item value is allowed to be auto-filled.
isBackground() - Method in class org.scijava.platform.event.AppFocusEvent
isBoolean(Class<?>) - Static method in class org.scijava.util.ClassUtils
isBoolean() - Method in class org.scijava.widget.DefaultWidgetModel
isBoolean() - Method in interface org.scijava.widget.WidgetModel: Gets whether the input is a boolean type (i.e., Boolean or boolean).
isButtonDown(int) - Method in class org.scijava.input.DefaultInputService
isButtonDown(int) - Method in interface org.scijava.input.InputService: Gets whether the given mouse button is currently pressed.
isByte(Class<?>) - Static method in class org.scijava.util.ClassUtils
isCanceled() - Method in interface org.scijava.Cancelable: Gets whether the operation has been canceled.
isCanceled() - Method in class org.scijava.command.CommandModule
isCanceled() - Method in class org.scijava.command.ContextCommand
isCanceled() - Method in class org.scijava.command.DynamicCommand
isCanceled() - Method in class org.scijava.command.ModuleCommand
isCanceled() - Method in class org.scijava.module.process.AbstractPreprocessorPlugin
isCanceled() - Method in class org.scijava.ui.AbstractInputHarvesterPlugin
isCharacter(Class<?>) - Static method in class org.scijava.util.ClassUtils
isCharacter() - Method in class org.scijava.widget.DefaultWidgetModel
isCharacter() - Method in interface org.scijava.widget.WidgetModel: Gets whether the input is a character type (i.e., Character or char).
isCheckBox() - Method in class org.scijava.menu.ShadowMenu: Returns true if this node is a checkbox.
isClassObsolete(String) - Method in interface org.scijava.annotations.AbstractIndexWriter.StreamFactory
isClosed - Variable in class org.scijava.display.AbstractDisplay
isCompatible(MIMEType) - Method in class org.scijava.ui.dnd.MIMEType: Gets whether this MIME type is compatible with the given one.
isCompatible(Class<?>) - Method in class org.scijava.ui.dnd.MIMEType: Gets whether this MIME type represents objects of the given Java class.
isCompatible(UserInterface) - Method in interface org.scijava.ui.viewer.DisplayViewer: Returns true if this display viewer can be used with the given UI.
isCompiledLanguage() - Method in class org.scijava.script.AbstractScriptLanguage
isCompiledLanguage() - Method in interface org.scijava.script.ScriptLanguage: True iff this language requires a compilation step.
isConsumed() - Method in class org.scijava.event.SciJavaEvent
isContextual() - Method in class org.scijava.console.OutputEvent: Returns true if the output was produced outside of a specific SciJava Context.
isCtrlDown() - Method in class org.scijava.input.DefaultInputService
isCtrlDown() - Method in class org.scijava.input.InputModifiers
isCtrlDown() - Method in interface org.scijava.input.InputService
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
isDefaultUI(String) - Method in class org.scijava.ui.DefaultUIService
isDefaultUI(String) - Method in interface org.scijava.ui.UIService: Gets whether the UI with the given name (or class name) is the default one.
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).
isDisplaying(Object) - Method in class org.scijava.display.AbstractDisplay
isDisplaying(Object) - Method in interface org.scijava.display.Display: Tests whether the display is currently visualizing the given object.
isDouble(Class<?>) - Static method in class org.scijava.util.ClassUtils
isEmpty() - Method in class org.scijava.display.AbstractDisplay
isEmpty() - Method in class org.scijava.menu.ShadowMenu
isEmpty() - Method in class org.scijava.object.ObjectIndex
isEmpty() - Method in class org.scijava.util.LastRecentlyUsed
isEnabled() - Method in class org.scijava.AbstractUIDetails
isEnabled() - Method in class org.scijava.command.DynamicCommandInfo
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
isFirstRun() - Method in class org.scijava.welcome.DefaultWelcomeService
isFirstRun() - Method in interface org.scijava.welcome.WelcomeService: Returns true iff this version of the running SJC application has not run before.
isFloat(Class<?>) - Static method in class org.scijava.util.ClassUtils
isForeground() - Method in class org.scijava.platform.event.AppFocusEvent
isHidden() - Method in class org.scijava.platform.event.AppVisibleEvent
isInfo() - Method in class org.scijava.log.AbstractLogService
isInfo() - Method in interface org.scijava.log.LogService
isInitialized() - Method in class org.scijava.widget.DefaultWidgetModel
isInitialized() - Method in interface org.scijava.widget.WidgetModel: Gets the widget's initialization state.
isInput() - Method in class org.scijava.module.AbstractModuleItem
isInput() - Method in interface org.scijava.module.ModuleItem: Gets whether the item is a module input.
isInstance(Class<?>, Object) - Static method in class org.scijava.util.ReflectedUniverse: Returns whether the given object is compatible with the specified class for the purposes of reflection.
isInteger(Class<?>) - Static method in class org.scijava.util.ClassUtils
isInteractive() - Method in class org.scijava.command.CommandInfo
isInteractive() - Method in class org.scijava.command.DynamicCommandInfo
isInteractive() - Method in class org.scijava.module.AbstractModuleInfo
isInteractive() - Method in interface org.scijava.module.ModuleInfo: Gets whether the module is intended to be run interactively.
isKeyDown(KeyCode) - Method in class org.scijava.input.DefaultInputService
isKeyDown(KeyCode) - Method in interface org.scijava.input.InputService
isLabeled() - Method in class org.scijava.widget.AbstractInputWidget
isLabeled() - Method in interface org.scijava.widget.InputWidget: Returns true iff the widget should be labeled with the parameter label.
isLeaf() - Method in class org.scijava.menu.ShadowMenu: Returns true if this node has no children.
isLeftButtonDown() - Method in class org.scijava.input.InputModifiers
isLinux() - Static method in class org.scijava.util.PlatformUtils: Whether the operating system is Linux-based.
isLittleEndian() - Method in class org.scijava.io.AbstractDataHandle
isLittleEndian() - Method in interface org.scijava.io.DataHandle: Gets the endianness of the stream.
isLong(Class<?>) - Static method in class org.scijava.util.ClassUtils
isMac() - Static method in class org.scijava.util.PlatformUtils: Whether the operating system is Mac-based.
isMessage() - Method in class org.scijava.widget.AbstractInputWidget
isMessage() - Method in class org.scijava.widget.DefaultWidgetModel
isMessage() - Method in interface org.scijava.widget.InputWidget: Returns true iff the widget should be considered a read-only "message" rather than a bidirectional input widget.
isMessage() - Method in interface org.scijava.widget.WidgetModel: Gets whether the input is a message.
isMessageOnly() - Method in class org.scijava.widget.AbstractInputPanel
isMessageOnly() - Method in interface org.scijava.widget.InputPanel: Returns true if the input panel consists of only messages.
isMetaDown() - Method in class org.scijava.input.DefaultInputService
isMetaDown() - Method in class org.scijava.input.InputModifiers
isMetaDown() - Method in interface org.scijava.input.InputService
isMiddleButtonDown() - Method in class org.scijava.input.InputModifiers
isMultipleChoice() - Method in class org.scijava.widget.DefaultWidgetModel
isMultipleChoice() - Method in interface org.scijava.widget.WidgetModel: Gets whether the input provides a restricted set of choices.
isNumber(Class<?>) - Static method in class org.scijava.util.ClassUtils
isNumber() - Method in class org.scijava.widget.DefaultWidgetModel
isNumber() - Method in interface org.scijava.widget.WidgetModel: Gets whether the input is a number type (e.g., int, float or any Number implementation.
isOutput() - Method in class org.scijava.module.AbstractModuleItem
isOutput() - Method in interface org.scijava.module.ModuleItem: Gets whether the item is a module output.
isPersisted() - Method in class org.scijava.command.CommandModuleItem
isPersisted() - Method in class org.scijava.module.AbstractModuleItem
isPersisted() - Method in class org.scijava.module.DefaultMutableModuleItem
isPersisted() - Method in interface org.scijava.module.ModuleItem: Gets whether to remember the most recent value of the parameter.
isPopupTrigger() - Method in class org.scijava.display.event.input.MsButtonEvent
isPOSIX() - Static method in class org.scijava.util.PlatformUtils: Whether the operating system is POSIX compliant.
isRadioButton() - Method in class org.scijava.menu.ShadowMenu: Returns true if this node is a radio button.
isRequired() - Method in class org.scijava.command.CommandModuleItem
isRequired() - Method in class org.scijava.module.AbstractModuleItem
isRequired() - Method in class org.scijava.module.DefaultMutableModuleItem
isRequired() - Method in interface org.scijava.module.ModuleItem: Gets whether the item value must be specified (i.e., no default).
isResolved(String) - Method in class org.scijava.module.AbstractModule
isResolved(String) - Method in interface org.scijava.module.Module: Gets the resolution status of the input with the given name.
isReturnValueDeclared() - Method in class org.scijava.script.ScriptInfo: Gets whether the return value is explicitly declared as an output.
isRightButtonDown() - Method in class org.scijava.input.InputModifiers
isSelectable() - Method in class org.scijava.AbstractUIDetails
isSelectable() - Method in class org.scijava.command.DynamicCommandInfo
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 class org.scijava.command.DynamicCommandInfo
isSelected() - Method in interface org.scijava.UIDetails: Gets whether the object is selected (e.g., its menu item is checked) in the user interface.
isSeparatorNeeded(Tool, Tool) - Method in class org.scijava.tool.DefaultToolService
isSeparatorNeeded(Tool, Tool) - Method in interface org.scijava.tool.ToolService: Returns true if the two specified tools should have a separator between them on the tool bar.
isShiftDown() - Method in class org.scijava.input.DefaultInputService
isShiftDown() - Method in class org.scijava.input.InputModifiers
isShiftDown() - Method in interface org.scijava.input.InputService
isShort(Class<?>) - Static method in class org.scijava.util.ClassUtils
isSleeping() - Method in class org.scijava.platform.event.AppSleepEvent
isStderr() - Method in class org.scijava.console.OutputEvent: Returns true of the source of the output is stderr.
isStdout() - Method in class org.scijava.console.OutputEvent: Returns true of the source of the output is stdout.
isStrict() - Method in class org.scijava.Context
isStyle(String) - Method in class org.scijava.widget.DefaultWidgetModel
isStyle(String) - Method in interface org.scijava.widget.WidgetModel: Gets whether the widget is the given style.
isSuccessful() - Method in class org.scijava.ui.dnd.event.DropEvent: Gets whether the drop operation was successful.
isSupported(Class<?>) - Method in class org.scijava.ui.dnd.AbstractDragAndDropData
isSupported(MIMEType) - Method in class org.scijava.ui.dnd.DefaultDragAndDropData
isSupported(MIMEType) - Method in interface org.scijava.ui.dnd.DragAndDropData: Gets whether the data can be provided as an object with the given MIME type.
isSupported(Class<?>) - Method in interface org.scijava.ui.dnd.DragAndDropData: Gets whether the data can be provided as an object of the given Java class.
isTarget() - Method in class org.scijava.platform.AbstractPlatform
isTarget() - Method in interface org.scijava.platform.Platform: Determines whether the given platform is applicable to this runtime.
isText(Class<?>) - Static method in class org.scijava.util.ClassUtils
isText() - Method in class org.scijava.widget.DefaultWidgetModel
isText() - Method in interface org.scijava.widget.WidgetModel: Gets whether the input is a text type (i.e., String, Character or char.
isToggle() - Method in class org.scijava.menu.ShadowMenu: Returns true if this node is selectable (checkbox or radio button).
isTrace() - Method in class org.scijava.log.AbstractLogService
isTrace() - Method in interface org.scijava.log.LogService
isType(Class<?>) - Method in class org.scijava.widget.DefaultWidgetModel
isType(Class<?>) - Method in interface org.scijava.widget.WidgetModel: Gets whether the input is compatible with the given type.
isUniqueName(String) - Method in class org.scijava.display.DefaultDisplayService
isUniqueName(String) - Method in interface org.scijava.display.DisplayService: Checks whether the given name is already taken by an existing display.
isValid() - Method in class org.scijava.command.CommandInfo
isValid() - Method in class org.scijava.command.DynamicCommandInfo
isValid() - Method in class org.scijava.module.AbstractModuleInfo
isValid() - Method in class org.scijava.module.MethodRef
isValid() - Method in interface org.scijava.Validated: Gets whether the object is completely valid (i.e., no problems during initialization).
isVisible() - Method in class org.scijava.AbstractUIDetails
isVisible() - Method in class org.scijava.platform.event.AppVisibleEvent
isVisible() - Method in class org.scijava.ui.AbstractUserInterface
isVisible() - Method in class org.scijava.ui.DefaultUIService
isVisible(String) - Method in class org.scijava.ui.DefaultUIService
isVisible() - Method in interface org.scijava.ui.UIService: Gets whether the default UI is visible.
isVisible(String) - Method in interface org.scijava.ui.UIService: Gets whether the UI with the given name or class name is visible.
isVisible() - Method in interface org.scijava.ui.UserInterface: Whether this UI is visible onscreen.
isVisible() - Method in interface org.scijava.UIDetails: Gets whether the object should be visible in the user interface.
isWaking() - Method in class org.scijava.platform.event.AppSleepEvent
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.
isWindows() - Static method in class org.scijava.util.PlatformUtils: Whether the operating system is Windows-based.
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.display.AbstractDisplay
iterator() - Method in class org.scijava.menu.ShadowMenu
iterator() - Method in class org.scijava.object.ObjectIndex
iterator() - Method in class org.scijava.util.IteratorPlus
iterator() - Method in class org.scijava.util.LastRecentlyUsed: Returns an Iterator.
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
IVORY - Static variable in class org.scijava.util.Colors

J

javaVendor() - Method in class org.scijava.platform.AbstractPlatform
javaVendor() - Method in interface org.scijava.platform.Platform: Java Runtime Environment vendor to match.
javaVersion() - Method in class org.scijava.platform.AbstractPlatform
javaVersion() - Method in interface org.scijava.platform.Platform: Minimum required Java Runtime Environment version.

K

KeyCode - Enum in org.scijava.input: A UI-independent enumeration of keyboard key codes.
KHAKI - Static variable in class org.scijava.util.Colors
KyEvent - Class in org.scijava.display.event.input: An event indicating keyboard activity in a display.
KyEvent(Display<?>, InputModifiers, int, int, char, KeyCode) - Constructor for class org.scijava.display.event.input.KyEvent
KyPressedEvent - Class in org.scijava.display.event.input: An event indicating a keyboard key was pressed in a display.
KyPressedEvent(Display<?>, InputModifiers, int, int, char, KeyCode) - Constructor for class org.scijava.display.event.input.KyPressedEvent
KyReleasedEvent - Class in org.scijava.display.event.input: An event indicating a keyboard key was released in a display.
KyReleasedEvent(Display<?>, InputModifiers, int, int, char, KeyCode) - Constructor for class org.scijava.display.event.input.KyReleasedEvent
KyTypedEvent - Class in org.scijava.display.event.input: An event indicating a keyboard key was typed (i.e., pressed and released) in a display.
KyTypedEvent(Display<?>, InputModifiers, int, int, char, KeyCode) - Constructor for class org.scijava.display.event.input.KyTypedEvent

L

LAST_PRIORITY - Static variable in class org.scijava.Priority: Priority for items that must be sorted last.
lastIndexOf(Object) - Method in class org.scijava.display.AbstractDisplay
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
LastRecentlyUsed<T> - Class in org.scijava.util: A simple container for N last-recently-used items.
LastRecentlyUsed(int) - Constructor for class org.scijava.util.LastRecentlyUsed
LAVENDER - Static variable in class org.scijava.util.Colors
LAVENDERBLUSH - Static variable in class org.scijava.util.Colors
LAWNGREEN - Static variable in class org.scijava.util.Colors
LazyObjects<T> - Interface in org.scijava.object: Interface for objects created lazily.
LEFT_BUTTON - Static variable in class org.scijava.display.event.input.MsButtonEvent
LegacyReader - Class in org.scijava.annotations.legacy: Reads legacy annotation indexes.
LegacyReader(InputStream) - Constructor for class org.scijava.annotations.legacy.LegacyReader
LEMONCHIFFON - Static variable in class org.scijava.util.Colors
len - Variable in class org.scijava.util.LineOutputStream
length() - Method in interface org.scijava.io.DataHandle: Returns the length of the stream.
length() - Method in class org.scijava.io.FileHandle
LIGHTBLUE - Static variable in class org.scijava.util.Colors
LIGHTCORAL - Static variable in class org.scijava.util.Colors
LIGHTCYAN - Static variable in class org.scijava.util.Colors
LIGHTGOLDENRODYELLOW - Static variable in class org.scijava.util.Colors
LIGHTGRAY - Static variable in class org.scijava.util.Colors
LIGHTGREEN - Static variable in class org.scijava.util.Colors
LIGHTGREY - Static variable in class org.scijava.util.Colors
LIGHTPINK - Static variable in class org.scijava.util.Colors
LIGHTSALMON - Static variable in class org.scijava.util.Colors
LIGHTSEAGREEN - Static variable in class org.scijava.util.Colors
LIGHTSKYBLUE - Static variable in class org.scijava.util.Colors
LIGHTSLATEGRAY - Static variable in class org.scijava.util.Colors
LIGHTSLATEGREY - Static variable in class org.scijava.util.Colors
LIGHTSTEELBLUE - Static variable in class org.scijava.util.Colors
LIGHTYELLOW - Static variable in class org.scijava.util.Colors
LIME - Static variable in class org.scijava.util.Colors
LIMEGREEN - Static variable in class org.scijava.util.Colors
limitPath(String, int) - Static method in class org.scijava.util.FileUtils: Compacts a path into a given number of characters.
LINEN - Static variable in class org.scijava.util.Colors
LineOutputStream - Class in org.scijava.util: This class hides a line-based output behind an OutputStream.
LineOutputStream() - Constructor for class org.scijava.util.LineOutputStream
LIST_BOX_STYLE - Static variable in interface org.scijava.widget.ChoiceWidget: Widget style for list boxes.
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.
ListDragAndDropHandler - Class in org.scijava.ui.dnd: Drag-and-drop handler for lists of objects.
ListDragAndDropHandler() - Constructor for class org.scijava.ui.dnd.ListDragAndDropHandler
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
listIterator() - Method in class org.scijava.display.AbstractDisplay
listIterator(int) - Method in class org.scijava.display.AbstractDisplay
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.
load(ModuleItem<T>) - Method in class org.scijava.module.DefaultModuleService
load(ModuleItem<T>) - Method in interface org.scijava.module.ModuleService: Returns the value, if any, stored in the PrefService for the given ModuleItem.
load() - Method in class org.scijava.options.OptionsPlugin: Loads option values from persistent storage.
loadClass() - Method in class org.scijava.command.CommandInfo
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.
loadDelegateClass() - Method in class org.scijava.command.CommandInfo
loadDelegateClass() - Method in class org.scijava.module.DefaultMutableModuleInfo
loadDelegateClass() - Method in interface org.scijava.module.ModuleInfo: Loads the class containing the module's actual implementation.
loadDelegateClass() - Method in class org.scijava.script.ScriptInfo
LoadInputsPreprocessor - Class in org.scijava.module.process: A preprocessor for loading populated input values from persistent storage.
LoadInputsPreprocessor() - Constructor for class org.scijava.module.process.LoadInputsPreprocessor
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.
loadValue() - Method in class org.scijava.module.AbstractModuleItem: Deprecated.
loadValue() - Method in interface org.scijava.module.ModuleItem: Deprecated.
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.
Locatable - Interface in org.scijava: An object whose location is defined by a URL string.
Location - Interface in org.scijava.io: A location is a data descriptor, such as a file on disk, a remote URL, or a database connection.
log() - Method in class org.scijava.AbstractGateway
log() - Method in class org.scijava.command.InteractiveCommand
log() - Method in interface org.scijava.Gateway: Gets this application context's LogService.
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() - Method in class org.scijava.script.AbstractScriptEngine
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.
lookup(T) - Method in class org.scijava.util.LastRecentlyUsed: Looks up the index for a given entry.
lookupClass(String) - Method in class org.scijava.script.DefaultScriptService
lookupClass(String) - Method in interface org.scijava.script.ScriptService: TODO
LOW_PRIORITY - Static variable in class org.scijava.Priority: Priority for items that prefer to be sorted later.

M

MAGENTA - Static variable in class org.scijava.util.Colors
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.MersenneTwisterFast: Tests the code.
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.ReflectedUniverse: Allows exploration of a reflected universe in an interactive environment.
main(String...) - Static method in class org.scijava.util.ServiceCombiner
makeArray(byte[], int, boolean, boolean) - Static method in class org.scijava.util.Bytes: Converts a byte array to the appropriate 1D primitive type array.
makeArray2D(byte[], int, boolean, boolean, int) - Static method in class org.scijava.util.Bytes: Converts a byte array to the appropriate 2D primitive type array.
makeSigned(byte[]) - Static method in class org.scijava.util.Bytes
makeSigned(short[]) - Static method in class org.scijava.util.Bytes
makeSigned(int[]) - Static method in class org.scijava.util.Bytes
Manifest - Class in org.scijava.util: Helper class for working with JAR manifests.
map() - Static method in class org.scijava.util.Colors: Gets the table of all preset colors.
mark(int) - Method in class org.scijava.io.DataHandleInputStream
markSupported() - Method in class org.scijava.io.DataHandleInputStream
MAROON - Static variable in class org.scijava.util.Colors
matchVersionedFilename(String) - Static method in class org.scijava.util.FileUtils: Deprecated.
see FileUtils.stripFilenameVersion(String)
MAX_FILES_SHOWN - Static variable in interface org.scijava.io.RecentFileService
md5(byte[]) - Static method in class org.scijava.util.DigestUtils: Gets the given byte array's MD5 checksum, or null if unavailable.
MEDIUMAQUAMARINE - Static variable in class org.scijava.util.Colors
MEDIUMBLUE - Static variable in class org.scijava.util.Colors
MEDIUMORCHID - Static variable in class org.scijava.util.Colors
MEDIUMPURPLE - Static variable in class org.scijava.util.Colors
MEDIUMSEAGREEN - Static variable in class org.scijava.util.Colors
MEDIUMSLATEBLUE - Static variable in class org.scijava.util.Colors
MEDIUMSPRINGGREEN - Static variable in class org.scijava.util.Colors
MEDIUMTURQUOISE - Static variable in class org.scijava.util.Colors
MEDIUMVIOLETRED - Static variable in class org.scijava.util.Colors
menu() - Method in class org.scijava.AbstractGateway
menu() - Method in interface org.scijava.Gateway: Gets this application context's MenuService.
Menu - Annotation Type in org.scijava.plugin: One item of a Plugin's menu path.
MenuConstants - Class in org.scijava.menu: Useful constants when defining application menu entries.
MenuCreator<T> - Interface in org.scijava.menu: A menu builder responsible for translating a ShadowMenu structure into a menu for a particular user interface.
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
MenuEvent - Class in org.scijava.menu.event: An event indicating something has happened to the MenuService's ShadowMenu.
MenuEvent(ShadowMenu) - Constructor for class org.scijava.menu.event.MenuEvent
MenuEvent(Collection<? extends ShadowMenu>) - Constructor for class org.scijava.menu.event.MenuEvent
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.
MenusAddedEvent - Class in org.scijava.menu.event: An event indicating one or more menu items have been added to the MenuService's ShadowMenu.
MenusAddedEvent(ShadowMenu) - Constructor for class org.scijava.menu.event.MenusAddedEvent
MenusAddedEvent(Collection<? extends ShadowMenu>) - Constructor for class org.scijava.menu.event.MenusAddedEvent
MenuService - Interface in org.scijava.menu: Interface for service that tracks the application's menu structure.
MenusRemovedEvent - Class in org.scijava.menu.event: An event indicating one or more menu items have been removed from the MenuService's ShadowMenu.
MenusRemovedEvent(ShadowMenu) - Constructor for class org.scijava.menu.event.MenusRemovedEvent
MenusRemovedEvent(Collection<? extends ShadowMenu>) - Constructor for class org.scijava.menu.event.MenusRemovedEvent
MenusUpdatedEvent - Class in org.scijava.menu.event: An event indicating one or more menu items have been adjusted in the MenuService's ShadowMenu.
MenusUpdatedEvent(ShadowMenu) - Constructor for class org.scijava.menu.event.MenusUpdatedEvent
MenusUpdatedEvent(Collection<? extends ShadowMenu>) - Constructor for class org.scijava.menu.event.MenusUpdatedEvent
merge(String, AbstractIndexWriter.StreamFactory) - Method in class org.scijava.annotations.AbstractIndexWriter: Merges an existing annotation index into the currently-generated one.
MersenneTwisterFast - Class in org.scijava.util: MersenneTwister and MersenneTwisterFast
MersenneTwisterFast() - Constructor for class org.scijava.util.MersenneTwisterFast: Constructor using the default seed.
MersenneTwisterFast(long) - Constructor for class org.scijava.util.MersenneTwisterFast: Constructor using a given seed.
MersenneTwisterFast(int[]) - Constructor for class org.scijava.util.MersenneTwisterFast: Constructor using an array of integers as seed.
MessageWidget - Interface in org.scijava.widget: Widget interface for message labels.
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
MethodCallException - Exception in org.scijava.module: An exception thrown when a reflective method execution fails.
MethodCallException() - Constructor for exception org.scijava.module.MethodCallException
MethodCallException(String) - Constructor for exception org.scijava.module.MethodCallException
MethodCallException(String, Throwable) - Constructor for exception org.scijava.module.MethodCallException
MethodCallException(Throwable) - Constructor for exception org.scijava.module.MethodCallException
MethodRef - Class in org.scijava.module: A reference to a Method, which can be invoked at will.
MethodRef(Class<?>, String, Class<?>...) - Constructor for class org.scijava.module.MethodRef
MIDDLE_BUTTON - Static variable in class org.scijava.display.event.input.MsButtonEvent
MIDNIGHTBLUE - Static variable in class org.scijava.util.Colors
MIMEType - Class in org.scijava.ui.dnd: A Multipurpose Internet Mail Extension (MIME) type, as defined in RFC 2045 and 2046.
MIMEType(String) - Constructor for class org.scijava.ui.dnd.MIMEType: Constructs a new MIME type object from the given MIME type string.
MIMEType(String, Class<?>) - Constructor for class org.scijava.ui.dnd.MIMEType: Constructs a new MIME type object from the given MIME type string.
MINTCREAM - Static variable in class org.scijava.util.Colors
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.
MISTYROSE - Static variable in class org.scijava.util.Colors
MOCCASIN - Static variable in class org.scijava.util.Colors
module() - Method in class org.scijava.AbstractGateway
module() - Method in interface org.scijava.Gateway: Gets this application context's ModuleService.
Module - Interface in org.scijava.module: A module is an encapsulated piece of functionality with inputs and outputs.
moduleCalled - Variable in class org.scijava.script.InvocationObject
ModuleCanceledEvent - Class in org.scijava.module.event: An event indicating a Module execution has been canceled.
ModuleCanceledEvent(Module) - Constructor for class org.scijava.module.event.ModuleCanceledEvent
ModuleCanceledEvent(Module, String) - Constructor for class org.scijava.module.event.ModuleCanceledEvent
ModuleCanceledException - Exception in org.scijava.module: An exception thrown when a module execution is canceled.
ModuleCanceledException() - Constructor for exception org.scijava.module.ModuleCanceledException
ModuleCanceledException(String) - Constructor for exception org.scijava.module.ModuleCanceledException
ModuleCanceledException(String, Throwable) - Constructor for exception org.scijava.module.ModuleCanceledException
ModuleCanceledException(Throwable) - Constructor for exception org.scijava.module.ModuleCanceledException
ModuleCommand - Class in org.scijava.command: A command which implements Module directly (rather than using the CommandModule adapter class).
ModuleCommand() - Constructor for class org.scijava.command.ModuleCommand
ModuleEvent - Class in org.scijava.module.event: An event indicating something has happened to a module.
ModuleEvent(Module) - Constructor for class org.scijava.module.event.ModuleEvent
ModuleException - Exception in org.scijava.module: An exception thrown when something goes wrong with a module.
ModuleException() - Constructor for exception org.scijava.module.ModuleException
ModuleException(String) - Constructor for exception org.scijava.module.ModuleException
ModuleException(String, Throwable) - Constructor for exception org.scijava.module.ModuleException
ModuleException(Throwable) - Constructor for exception org.scijava.module.ModuleException
ModuleExecutedEvent - Class in org.scijava.module.event: An event indicating a module has just been executed.
ModuleExecutedEvent(Module) - Constructor for class org.scijava.module.event.ModuleExecutedEvent
ModuleExecutingEvent - Class in org.scijava.module.event: An event indicating a module is about to be executed.
ModuleExecutingEvent(Module) - Constructor for class org.scijava.module.event.ModuleExecutingEvent
ModuleExecutionEvent - Class in org.scijava.module.event: An event relating to execution of a Module.
ModuleExecutionEvent(Module) - Constructor for class org.scijava.module.event.ModuleExecutionEvent
ModuleFinishedEvent - Class in org.scijava.module.event: An event indicating a module execution has been completed.
ModuleFinishedEvent(Module) - Constructor for class org.scijava.module.event.ModuleFinishedEvent
ModuleIndex - Class in org.scijava.module: Data structure for managing registered modules.
ModuleIndex() - Constructor for class org.scijava.module.ModuleIndex
ModuleInfo - Interface in org.scijava.module: A ModuleInfo object encapsulates metadata about a particular Module (but not a specific instance of it).
ModuleItem<T> - Interface in org.scijava.module: A ModuleItem represents metadata about one input or output of a module.
ModulePostprocessEvent - Class in org.scijava.module.event: An event indicating a ModulePostprocessor has been invoked as part of a module execution.
ModulePostprocessEvent(Module, ModulePostprocessor) - Constructor for class org.scijava.module.event.ModulePostprocessEvent
ModulePostprocessor - Interface in org.scijava.module.process: A module postprocessor defines a step that occurs immediately following the actual execution of a Module.
ModulePreprocessEvent - Class in org.scijava.module.event: An event indicating a ModulePreprocessor has been invoked as part of a module execution.
ModulePreprocessEvent(Module, ModulePreprocessor) - Constructor for class org.scijava.module.event.ModulePreprocessEvent
ModulePreprocessor - Interface in org.scijava.module.process: A module preprocessor defines a step that occurs just prior to the actual execution of a Module.
ModuleProcessEvent - Class in org.scijava.module.event: An event indicating a ModuleProcessor has been invoked as part of a module execution.
ModuleProcessEvent(Module, ModuleProcessor) - Constructor for class org.scijava.module.event.ModuleProcessEvent
ModuleProcessor - Interface in org.scijava.module.process: A module processor defines some sort of processing that occurs on a module instance, typically immediately preceding (see ModulePreprocessor) or following (see ModulePostprocessor) the module execution.
ModuleRunner - Class in org.scijava.module: Helper class for executing a Module, including pre- and post-processing and event notification.
ModuleRunner(Context, Module, List<? extends ModulePreprocessor>, List<? extends ModulePostprocessor>) - Constructor for class org.scijava.module.ModuleRunner
ModulesAddedEvent - Class in org.scijava.module.event: An event indicating one or more modules have been added to the ModuleService.
ModulesAddedEvent(ModuleInfo) - Constructor for class org.scijava.module.event.ModulesAddedEvent
ModulesAddedEvent(Collection<? extends ModuleInfo>) - Constructor for class org.scijava.module.event.ModulesAddedEvent
ModuleService - Interface in org.scijava.module: Interface for service that tracks and executes available modules.
ModulesListEvent - Class in org.scijava.module.event: An event indicating something has happened to the list of plugins registered with the ModuleService.
ModulesListEvent(ModuleInfo) - Constructor for class org.scijava.module.event.ModulesListEvent
ModulesListEvent(Collection<? extends ModuleInfo>) - Constructor for class org.scijava.module.event.ModulesListEvent
ModulesRemovedEvent - Class in org.scijava.module.event: An event indicating one or more modules have been removed from the ModuleService.
ModulesRemovedEvent(ModuleInfo) - Constructor for class org.scijava.module.event.ModulesRemovedEvent
ModulesRemovedEvent(Collection<? extends ModuleInfo>) - Constructor for class org.scijava.module.event.ModulesRemovedEvent
ModuleStartedEvent - Class in org.scijava.module.event: An event indicating a module execution has begun.
ModuleStartedEvent(Module) - Constructor for class org.scijava.module.event.ModuleStartedEvent
ModulesUpdatedEvent - Class in org.scijava.module.event: An event indicating one or more module details have been updated.
ModulesUpdatedEvent(ModuleInfo) - Constructor for class org.scijava.module.event.ModulesUpdatedEvent
ModulesUpdatedEvent(Collection<? extends ModuleInfo>) - Constructor for class org.scijava.module.event.ModulesUpdatedEvent
MouseCursor - Enum in org.scijava.input: A UI-independent enumeration of mouse cursors.
MsButtonEvent - Class in org.scijava.display.event.input: An event indicating mouse button activity in a display.
MsButtonEvent(Display<?>, InputModifiers, int, int, int, int, boolean) - Constructor for class org.scijava.display.event.input.MsButtonEvent
MsClickedEvent - Class in org.scijava.display.event.input: An event indicating a mouse button was clicked in a display.
MsClickedEvent(Display<?>, InputModifiers, int, int, int, int, boolean) - Constructor for class org.scijava.display.event.input.MsClickedEvent
MsDraggedEvent - Class in org.scijava.display.event.input: An event indicating a mouse was dragged in a display.
MsDraggedEvent(Display<?>, InputModifiers, int, int, int, int, boolean) - Constructor for class org.scijava.display.event.input.MsDraggedEvent
MsEnteredEvent - Class in org.scijava.display.event.input: An event indicating a mouse cursor entered a display.
MsEnteredEvent(Display<?>, InputModifiers, int, int) - Constructor for class org.scijava.display.event.input.MsEnteredEvent
MsEvent - Class in org.scijava.display.event.input: An event indicating mouse activity in a display.
MsEvent(Display<?>, InputModifiers, int, int) - Constructor for class org.scijava.display.event.input.MsEvent
MsExitedEvent - Class in org.scijava.display.event.input: An event indicating a mouse cursor exited a display.
MsExitedEvent(Display<?>, InputModifiers, int, int) - Constructor for class org.scijava.display.event.input.MsExitedEvent
MsMovedEvent - Class in org.scijava.display.event.input: An event indicating a mouse was moved in a display.
MsMovedEvent(Display<?>, InputModifiers, int, int) - Constructor for class org.scijava.display.event.input.MsMovedEvent
MsPressedEvent - Class in org.scijava.display.event.input: An event indicating a mouse button was pressed in a display.
MsPressedEvent(Display<?>, InputModifiers, int, int, int, int, boolean) - Constructor for class org.scijava.display.event.input.MsPressedEvent
MsReleasedEvent - Class in org.scijava.display.event.input: An event indicating a mouse button was released in a display.
MsReleasedEvent(Display<?>, InputModifiers, int, int, int, int, boolean) - Constructor for class org.scijava.display.event.input.MsReleasedEvent
MsWheelEvent - Class in org.scijava.display.event.input: An event indicating a mouse wheel was moved in a display.
MsWheelEvent(Display<?>, InputModifiers, int, int, int) - Constructor for class org.scijava.display.event.input.MsWheelEvent
MultiOutputStream - Class in org.scijava.console: A MultiOutputStream is a collection of constituent OutputStream objects, to which all output is forwarded.
MultiOutputStream(OutputStream...) - Constructor for class org.scijava.console.MultiOutputStream: Forwards output to a list of output streams.
MultiPrintStream - Class in org.scijava.console: A PrintStream that wraps a MultiOutputStream.
MultiPrintStream(OutputStream) - Constructor for class org.scijava.console.MultiPrintStream
MutableModule - Interface in org.scijava.module: Module extension allowing manipulation of its metadata.
MutableModuleInfo - Interface in org.scijava.module: ModuleInfo extension allowing manipulation of its metadata.
MutableModuleItem<T> - Interface in org.scijava.module: ModuleItem extension allowing manipulation of its metadata.

N

NAME - Static variable in class org.scijava.app.SciJavaApp
Named - Interface in org.scijava: Interface for things that have names.
NAVAJOWHITE - Static variable in class org.scijava.util.Colors
NAVY - Static variable in class org.scijava.util.Colors
newThread(Runnable) - Method in class org.scijava.thread.DefaultThreadService
next() - Method in class org.scijava.menu.ShadowMenuIterator
next() - Method in class org.scijava.util.IteratorPlus
next(int) - Method in class org.scijava.util.LastRecentlyUsed: Given the index of an entry, returns the index of the next newer entry.
nextBoolean() - Method in class org.scijava.util.MersenneTwisterFast
nextBoolean(float) - Method in class org.scijava.util.MersenneTwisterFast: This generates a coin flip with a probability probability of returning true, else returning false.
nextBoolean(double) - Method in class org.scijava.util.MersenneTwisterFast: This generates a coin flip with a probability probability of returning true, else returning false.
nextByte() - Method in class org.scijava.util.MersenneTwisterFast
nextBytes(byte[]) - Method in class org.scijava.util.MersenneTwisterFast
nextChar() - Method in class org.scijava.util.MersenneTwisterFast
nextDouble() - Method in class org.scijava.util.MersenneTwisterFast: Returns a random double in the half-open range from [0.0,1.0).
nextDouble(boolean, boolean) - Method in class org.scijava.util.MersenneTwisterFast: Returns a double in the range from 0.0 to 1.0, possibly inclusive of 0.0 and 1.0 themselves.
nextElement() - Method in class org.scijava.util.IteratorPlus
nextFloat() - Method in class org.scijava.util.MersenneTwisterFast: Returns a random float in the half-open range from [0.0f,1.0f).
nextFloat(boolean, boolean) - Method in class org.scijava.util.MersenneTwisterFast: Returns a float in the range from 0.0f to 1.0f, possibly inclusive of 0.0f and 1.0f themselves.
nextGaussian() - Method in class org.scijava.util.MersenneTwisterFast
nextInt() - Method in class org.scijava.util.MersenneTwisterFast
nextInt(int) - Method in class org.scijava.util.MersenneTwisterFast: Returns an integer drawn uniformly from 0 to n-1.
nextLong() - Method in class org.scijava.util.MersenneTwisterFast
nextLong(long) - Method in class org.scijava.util.MersenneTwisterFast: Returns a long drawn uniformly from 0 to n-1.
nextShort() - Method in class org.scijava.util.MersenneTwisterFast
NO_CONSOLE_PROPERTY - Static variable in interface org.scijava.ui.console.ConsolePane: System property which, if set, suppresses the SciJava console window.
NONE - Static variable in interface org.scijava.log.LogService
NORMAL_PRIORITY - Static variable in class org.scijava.Priority: Default priority for items.
normalize(float[]) - Static method in class org.scijava.util.Bytes: Normalize the given float array so that the minimum value maps to 0.0 and the maximum value maps to 1.0.
normalize(double[]) - Static method in class org.scijava.util.Bytes: Normalize the given double array so that the minimum value maps to 0.0 and the maximum value maps to 1.0.
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
noteStructureChange() - Method in class org.scijava.display.AbstractDisplay
notifyListeners(OutputEvent) - Method in interface org.scijava.console.ConsoleService: Notifies listeners of output sent to stdout or stderr.
notifyListeners(OutputEvent) - Method in class org.scijava.console.DefaultConsoleService
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
NullConverter - Class in org.scijava.convert: Converter implementation for handling null values.
NullConverter() - Constructor for class org.scijava.convert.NullConverter
NumberUtils - Class in org.scijava.util: Useful methods for working with Number objects.
NumberWidget - Interface in org.scijava.widget: Widget interface for number choosers.

O

object() - Method in class org.scijava.AbstractGateway
object() - Method in interface org.scijava.Gateway: Gets this application context's ObjectService.
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
ObjectWidget - Interface in org.scijava.widget: Widget interface for object selectors.
offset() - Method in interface org.scijava.io.DataHandle: Returns the current offset in the stream.
offset() - Method in class org.scijava.io.FileHandle
OLDLACE - Static variable in class org.scijava.util.Colors
OLIVE - Static variable in class org.scijava.util.Colors
OLIVEDRAB - Static variable in class org.scijava.util.Colors
onDisplayActivatedEvent(DisplayActivatedEvent) - Method in class org.scijava.ui.viewer.AbstractDisplayViewer
onDisplayActivatedEvent(DisplayActivatedEvent) - Method in interface org.scijava.ui.viewer.DisplayViewer: Handles a display activated event directed at this viewer's display.
onDisplayDeletedEvent(DisplayDeletedEvent) - Method in class org.scijava.ui.viewer.AbstractDisplayViewer
onDisplayDeletedEvent(DisplayDeletedEvent) - Method in interface org.scijava.ui.viewer.DisplayViewer: Removes the user interface when the display is deleted.
onDisplayUpdatedEvent(DisplayUpdatedEvent) - Method in class org.scijava.ui.viewer.AbstractDisplayViewer
onDisplayUpdatedEvent(DisplayUpdatedEvent) - Method in interface org.scijava.ui.viewer.DisplayViewer: Synchronizes the user interface appearance with the display model.
onEvent(AppAboutEvent) - Method in class org.scijava.app.DefaultAppService
onEvent(AppPreferencesEvent) - Method in class org.scijava.app.DefaultAppService
onEvent(AppQuitEvent) - Method in class org.scijava.app.DefaultAppService
onEvent(PluginsRemovedEvent) - Method in class org.scijava.command.DefaultCommandService
onEvent(PluginsAddedEvent) - Method in class org.scijava.command.DefaultCommandService
onEvent(DisplayActivatedEvent) - Method in class org.scijava.command.InteractiveCommand
onEvent(WinClosedEvent) - Method in class org.scijava.display.DefaultDisplayService: Deletes the display when display window is closed.
onEvent(WinActivatedEvent) - Method in class org.scijava.display.DefaultDisplayService: Sets the display to active when its window is activated.
onEvent(DisplayDeletedEvent) - Method in class org.scijava.display.DefaultDisplayService: Removes a display from the display list when it is deleted
onEvent(SciJavaEvent) - Method in class org.scijava.event.DefaultEventHistory
onEvent(E) - Method in interface org.scijava.event.EventSubscriber
onEvent(KyPressedEvent) - Method in class org.scijava.input.DefaultInputService
onEvent(KyReleasedEvent) - Method in class org.scijava.input.DefaultInputService
onEvent(MsMovedEvent) - Method in class org.scijava.input.DefaultInputService
onEvent(MsExitedEvent) - Method in class org.scijava.input.DefaultInputService
onEvent(MsPressedEvent) - Method in class org.scijava.input.DefaultInputService
onEvent(MsReleasedEvent) - Method in class org.scijava.input.DefaultInputService
onEvent(DisplayDeletedEvent) - Method in class org.scijava.input.DefaultInputService
onEvent(IOEvent) - Method in class org.scijava.io.DefaultRecentFileService
onEvent(ModulesAddedEvent) - Method in class org.scijava.menu.DefaultMenuService
onEvent(ModulesRemovedEvent) - Method in class org.scijava.menu.DefaultMenuService
onEvent(ModulesUpdatedEvent) - Method in class org.scijava.menu.DefaultMenuService
onEvent(ObjectCreatedEvent) - Method in class org.scijava.object.DefaultObjectService
onEvent(ObjectDeletedEvent) - Method in class org.scijava.object.DefaultObjectService
onEvent(AppAboutEvent) - Method in class org.scijava.platform.DefaultAppEventService: Deprecated.
onEvent(AppPreferencesEvent) - Method in class org.scijava.platform.DefaultAppEventService: Deprecated.
onEvent(AppQuitEvent) - Method in class org.scijava.platform.DefaultAppEventService: Deprecated.
onEvent(AppMenusCreatedEvent) - Method in class org.scijava.platform.DefaultPlatformService
onEvent(KyPressedEvent) - Method in class org.scijava.tool.DefaultToolService
onEvent(KyReleasedEvent) - Method in class org.scijava.tool.DefaultToolService
onEvent(MsPressedEvent) - Method in class org.scijava.tool.DefaultToolService
onEvent(MsReleasedEvent) - Method in class org.scijava.tool.DefaultToolService
onEvent(MsClickedEvent) - Method in class org.scijava.tool.DefaultToolService
onEvent(MsMovedEvent) - Method in class org.scijava.tool.DefaultToolService
onEvent(MsDraggedEvent) - Method in class org.scijava.tool.DefaultToolService
onEvent(MsWheelEvent) - Method in class org.scijava.tool.DefaultToolService
onEvent(DisplayCreatedEvent) - Method in class org.scijava.ui.DefaultUIService: Called when a display is created.
onEvent(DisplayDeletedEvent) - Method in class org.scijava.ui.DefaultUIService: Called when a display is deleted.
onEvent(DisplayUpdatedEvent) - Method in class org.scijava.ui.DefaultUIService: Called when a display is updated.
onEvent(DisplayActivatedEvent) - Method in class org.scijava.ui.DefaultUIService: Called when a display is activated.
onEvent(AppQuitEvent) - Method in class org.scijava.ui.DefaultUIService
onEvent(StatusEvent) - Method in class org.scijava.ui.DefaultUIService
onEvent(DragEnterEvent) - Method in class org.scijava.ui.dnd.DefaultDragAndDropService
onEvent(DragExitEvent) - Method in class org.scijava.ui.dnd.DefaultDragAndDropService
onEvent(DragOverEvent) - Method in class org.scijava.ui.dnd.DefaultDragAndDropService
onEvent(DropEvent) - Method in class org.scijava.ui.dnd.DefaultDragAndDropService
onEvent(DisplayCreatedEvent) - Method in class org.scijava.ui.viewer.AbstractDisplayViewer
onEvent(DisplayUpdatedEvent) - Method in class org.scijava.ui.viewer.AbstractDisplayViewer
onEvent(UIShownEvent) - Method in class org.scijava.welcome.DefaultWelcomeService: Displays the welcome text when a UI is shown for the first time.
onKeyDown(KyPressedEvent) - Method in class org.scijava.tool.AbstractTool
onKeyDown(KyPressedEvent) - Method in interface org.scijava.tool.Tool: Occurs when a key on the keyboard is pressed while the tool is active.
onKeyUp(KyReleasedEvent) - Method in class org.scijava.tool.AbstractTool
onKeyUp(KyReleasedEvent) - Method in interface org.scijava.tool.Tool: Occurs when a key on the keyboard is released while the tool is active.
onMouseClick(MsClickedEvent) - Method in class org.scijava.tool.AbstractTool
onMouseClick(MsClickedEvent) - Method in interface org.scijava.tool.Tool: Occurs when a mouse button is double clicked while the tool is active.
onMouseDown(MsPressedEvent) - Method in class org.scijava.tool.AbstractTool
onMouseDown(MsPressedEvent) - Method in interface org.scijava.tool.Tool: Occurs when a mouse button is pressed while the tool is active.
onMouseDrag(MsDraggedEvent) - Method in class org.scijava.tool.AbstractTool
onMouseDrag(MsDraggedEvent) - Method in interface org.scijava.tool.Tool: Occurs when the mouse is dragged while the tool is active.
onMouseMove(MsMovedEvent) - Method in class org.scijava.tool.AbstractTool
onMouseMove(MsMovedEvent) - Method in interface org.scijava.tool.Tool: Occurs when the mouse is moved while the tool is active.
onMouseUp(MsReleasedEvent) - Method in class org.scijava.tool.AbstractTool
onMouseUp(MsReleasedEvent) - Method in interface org.scijava.tool.Tool: Occurs when a mouse button is released while the tool is active.
onMouseWheel(MsWheelEvent) - Method in class org.scijava.tool.AbstractTool
onMouseWheel(MsWheelEvent) - Method in interface org.scijava.tool.Tool: Occurs when the mouse wheel is moved while the tool is active.
open(String) - Method in class org.scijava.io.AbstractIOPlugin
open(String) - Method in class org.scijava.io.DefaultIOService
open(String) - Method in interface org.scijava.io.IOPlugin: Opens data from the given source.
open(String) - Method in interface org.scijava.io.IOService: Loads data from the given source.
open(URL) - Method in class org.scijava.platform.DefaultPlatform: Falls back to calling known browsers.
open(URL) - Method in class org.scijava.platform.DefaultPlatformService
open(URL) - Method in interface org.scijava.platform.Platform
open(URL) - Method in interface org.scijava.platform.PlatformService: Opens a URL in a platform-dependent way.
open(String) - Method in class org.scijava.script.io.ScriptIOPlugin
open(File) - Method in class org.scijava.text.DefaultTextService
open(String) - Method in class org.scijava.text.io.TextIOPlugin
open(File) - Method in interface org.scijava.text.TextService: Reads the data from the given file into a string.
OPEN_STYLE - Static variable in interface org.scijava.widget.FileWidget: Widget style for file opener dialogs.
OpenArgument - Class in org.scijava.io.console: Handles the --open command line argument.
OpenArgument() - Constructor for class org.scijava.io.console.OpenArgument
openInput(String) - Method in interface org.scijava.annotations.AbstractIndexWriter.StreamFactory
openLine() - Method in class org.scijava.util.TunePlayer
openOutput(String) - Method in interface org.scijava.annotations.AbstractIndexWriter.StreamFactory
Optional - Interface in org.scijava: A marker interface for optional SciJava components.
options() - Method in class org.scijava.AbstractGateway
options() - Method in interface org.scijava.Gateway: Gets this application context's OptionsService.
OptionsEvent - Class in org.scijava.options.event: Fired when an OptionsPlugin has changed an option.
OptionsEvent(OptionsPlugin) - Constructor for class org.scijava.options.event.OptionsEvent
OptionsPlugin - Class in org.scijava.options: Base class for all options-oriented plugins.
OptionsPlugin() - Constructor for class org.scijava.options.OptionsPlugin
OptionsService - Interface in org.scijava.options: Interface for the options handling service.
ORANGE - Static variable in class org.scijava.util.Colors
ORANGERED - Static variable in class org.scijava.util.Colors
ORCHID - Static variable in class org.scijava.util.Colors
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.cache - package org.scijava.cache
org.scijava.command - package org.scijava.command
org.scijava.command.console - package org.scijava.command.console
org.scijava.console - package org.scijava.console
org.scijava.convert - package org.scijava.convert
org.scijava.display - package org.scijava.display
org.scijava.display.event - package org.scijava.display.event
org.scijava.display.event.input - package org.scijava.display.event.input
org.scijava.display.event.window - package org.scijava.display.event.window
org.scijava.event - package org.scijava.event
org.scijava.input - package org.scijava.input
org.scijava.io - package org.scijava.io
org.scijava.io.console - package org.scijava.io.console
org.scijava.io.event - package org.scijava.io.event
org.scijava.log - package org.scijava.log
org.scijava.menu - package org.scijava.menu
org.scijava.menu.event - package org.scijava.menu.event
org.scijava.module - package org.scijava.module
org.scijava.module.event - package org.scijava.module.event
org.scijava.module.process - package org.scijava.module.process
org.scijava.object - package org.scijava.object
org.scijava.object.event - package org.scijava.object.event
org.scijava.options - package org.scijava.options
org.scijava.options.event - package org.scijava.options.event
org.scijava.platform - package org.scijava.platform
org.scijava.platform.event - package org.scijava.platform.event
org.scijava.plugin - package org.scijava.plugin
org.scijava.plugin.event - package org.scijava.plugin.event
org.scijava.prefs - package org.scijava.prefs
org.scijava.script - package org.scijava.script
org.scijava.script.io - package org.scijava.script.io
org.scijava.service - package org.scijava.service
org.scijava.service.event - package org.scijava.service.event
org.scijava.test - package org.scijava.test
org.scijava.text - package org.scijava.text
org.scijava.text.io - package org.scijava.text.io
org.scijava.thread - package org.scijava.thread
org.scijava.tool - package org.scijava.tool
org.scijava.tool.event - package org.scijava.tool.event
org.scijava.ui - package org.scijava.ui
org.scijava.ui.console - package org.scijava.ui.console
org.scijava.ui.dnd - package org.scijava.ui.dnd
org.scijava.ui.dnd.event - package org.scijava.ui.dnd.event
org.scijava.ui.event - package org.scijava.ui.event
org.scijava.ui.viewer - package org.scijava.ui.viewer
org.scijava.ui.viewer.text - package org.scijava.ui.viewer.text
org.scijava.util - package org.scijava.util
org.scijava.welcome - package org.scijava.welcome
org.scijava.welcome.event - package org.scijava.welcome.event
org.scijava.widget - package org.scijava.widget
osArch() - Method in class org.scijava.platform.AbstractPlatform
osArch() - Method in interface org.scijava.platform.Platform: Operating system architecture to match.
osName() - Method in class org.scijava.platform.AbstractPlatform
osName() - Method in interface org.scijava.platform.Platform: Operating system name to match.
osName() - Static method in class org.scijava.util.PlatformUtils: Gets the name of the operating system.
osVersion() - Method in class org.scijava.platform.AbstractPlatform
osVersion() - Method in interface org.scijava.platform.Platform: Minimum required operating system version.
out - Variable in class org.scijava.util.ReadInto
OutputEvent - Class in org.scijava.console: An event indicating output occurred on stdout or stderr.
OutputEvent(Context, OutputEvent.Source, String, boolean) - Constructor for class org.scijava.console.OutputEvent: Creates a new output event.
OutputEvent.Source - Enum in org.scijava.console: Possible output sources.
outputList() - Method in class org.scijava.module.AbstractModuleInfo: Gets AbstractModuleInfo.outputList, initializing if needed.
OutputListener - Interface in org.scijava.console: Listener for output on stdout or stderr.
outputMap() - Method in class org.scijava.module.AbstractModuleInfo: Gets AbstractModuleInfo.inputList, initializing if needed.
outputOccurred(OutputEvent) - Method in interface org.scijava.console.OutputListener: Method called when output occurs on stdout or stderr.
outputOccurred(OutputEvent) - Method in class org.scijava.ui.console.AbstractConsolePane
outputs() - Method in class org.scijava.command.CommandInfo
outputs() - Method in class org.scijava.module.AbstractModuleInfo
outputs() - Method in interface org.scijava.module.ModuleInfo: Gets the list of output items.

P

pack() - Method in interface org.scijava.ui.viewer.DisplayWindow
PALEGOLDENROD - Static variable in class org.scijava.util.Colors
PALEGREEN - Static variable in class org.scijava.util.Colors
PALETURQUOISE - Static variable in class org.scijava.util.Colors
PALEVIOLETRED - Static variable in class org.scijava.util.Colors
PAPAYAWHIP - Static variable in class org.scijava.util.Colors
param - Variable in class org.scijava.script.ParameterObject
Parameter - Annotation Type in org.scijava.plugin: An annotation for indicating a field is an input or output parameter.
ParameterObject - Class in org.scijava.script: Holds a parameter, its type and value, for a recorded macro.
ParameterObject(String, Class<?>, Object) - Constructor for class org.scijava.script.ParameterObject
parameterObjects - Variable in class org.scijava.script.InvocationObject
parseParameters() - Method in class org.scijava.module.AbstractModuleInfo: Parses input and output parameters.
parseParameters() - Method in class org.scijava.script.ScriptInfo: Parses the script's input and output parameters from the script header.
PASSWORD_STYLE - Static variable in interface org.scijava.widget.TextWidget: Widget style for password fields.
PATH_SEPARATOR - Static variable in class org.scijava.MenuPath: The separator between elements of a menu path string.
PEACHPUFF - Static variable in class org.scijava.util.Colors
PERU - Static variable in class org.scijava.util.Colors
PINK - Static variable in class org.scijava.util.Colors
pixelsToSystemClipboard(ARGBPlane) - Method in interface org.scijava.ui.SystemClipboard: method that accepts a plane of ARGB data
platform() - Method in class org.scijava.AbstractGateway
platform() - Method in interface org.scijava.Gateway: Gets this application context's PlatformService.
Platform - Interface in org.scijava.platform: An interface for configuring a specific deployment platform, defined by criteria such as operating system, machine architecture or Java version.
PlatformService - Interface in org.scijava.platform: Interface for service that handles platform-specific deployment issues.
PlatformUtils - Class in org.scijava.util: Useful methods for platform-specific interrogation.
play(String) - Method in class org.scijava.util.TunePlayer
plugin() - Method in class org.scijava.AbstractGateway
plugin() - Method in interface org.scijava.Gateway: Gets this application context's PluginService.
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
PLUGINS_LABEL - Static variable in class org.scijava.menu.MenuConstants
PLUGINS_MNEMONIC - Static variable in class org.scijava.menu.MenuConstants
PLUGINS_WEIGHT - Static variable in class org.scijava.menu.MenuConstants
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
PLUM - Static variable in class org.scijava.util.Colors
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.
populateInputCandidates(Collection<Object>) - Method in class org.scijava.convert.AbstractConverter
populateInputCandidates(Collection<Object>) - Method in interface org.scijava.convert.Converter: Populates the given collection with objects which are known to exist, and which are usable as inputs for this converter.
postProcess() - Method in class org.scijava.module.ModuleRunner: Feeds the module through the ModulePostprocessors.
PostprocessorPlugin - Interface in org.scijava.module.process: A postprocessor plugin defines a step that occurs immediately following the actual execution of a Module.
POWDERBLUE - Static variable in class org.scijava.util.Colors
prefs() - Method in class org.scijava.AbstractGateway
prefs() - Method in class org.scijava.app.AbstractApp
prefs() - Method in interface org.scijava.app.App: Displays application preferences.
prefs() - Method in interface org.scijava.platform.AppEventService: Deprecated.
Use App.prefs() instead.
prefs() - Method in class org.scijava.platform.DefaultAppEventService: Deprecated.
Prefs - Class in org.scijava.util: Deprecated.
See PrefService
PrefService - Interface in org.scijava.prefs: Service for storing and retrieving arbitrary preferences.
preProcess() - Method in class org.scijava.module.ModuleRunner: Feeds the module through the ModulePreprocessors.
PreprocessorPlugin - Interface in org.scijava.module.process: A preprocessor plugin defines a step that occurs just prior to the actual execution of a Module.
preview() - Method in class org.scijava.command.CommandModule: Computes a preview of the command's results.
preview() - Method in class org.scijava.command.InteractiveCommand
preview() - Method in interface org.scijava.command.Previewable: Computes a preview of the operation's results.
preview() - Method in class org.scijava.module.AbstractModule
preview() - Method in interface org.scijava.module.Module: Computes a preview of the module's execution results, if available.
Previewable - Interface in org.scijava.command: An operation (usually a Command) whose results can be previewed.
previous(int) - Method in class org.scijava.util.LastRecentlyUsed: Given the index of an entry, returns the index of the next older entry.
PrimitiveArray<ArrayType,BaseType> - Interface in org.scijava.util: Interface for primitive-type extensible arrays, modeled after ArrayList, but more performant.
PrimitiveArrayUnwrapper<I,O,W extends PrimitiveArray<I,O>> - Class in org.scijava.convert: Abstract Converter for converting from the SciJava PrimitiveArray classes to primitive arrays.
PrimitiveArrayUnwrapper() - Constructor for class org.scijava.convert.PrimitiveArrayUnwrapper
PrimitiveArrayWrapper<I,O,W extends PrimitiveArray<I,O>> - Class in org.scijava.convert: Abstract Converter for converting from primitive array classes to the SciJava PrimitiveArray classes.
PrimitiveArrayWrapper() - Constructor for class org.scijava.convert.PrimitiveArrayWrapper
println(String) - Method in class org.scijava.util.LineOutputStream: This method is all that needs to be implemented.
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 - Static variable in class org.scijava.module.process.SaveInputsPreprocessor
Priority - Class in org.scijava: Constants for specifying an item's priority.
PRIORITY - Static variable in interface org.scijava.widget.InputHarvester
process(Set<? extends TypeElement>, RoundEnvironment) - Method in class org.scijava.annotations.AnnotationProcessor
process(Module) - Method in class org.scijava.display.ActiveDisplayPreprocessor
process(Module) - Method in class org.scijava.display.DisplayPostprocessor
process(Module) - Method in class org.scijava.module.process.CheckInputsPreprocessor
process(Module) - Method in class org.scijava.module.process.DebugPostprocessor
process(Module) - Method in class org.scijava.module.process.DebugPreprocessor
process(Module) - Method in class org.scijava.module.process.DefaultValuePreprocessor
process(Module) - Method in class org.scijava.module.process.GatewayPreprocessor
process(Module) - Method in class org.scijava.module.process.InitPreprocessor
process(Module) - Method in class org.scijava.module.process.LoadInputsPreprocessor
process(Module) - Method in interface org.scijava.module.process.ModuleProcessor: Performs a processing step on the given module instance.
process(Module) - Method in class org.scijava.module.process.SaveInputsPreprocessor
process(Module) - Method in class org.scijava.module.process.ServicePreprocessor
process(Module) - Method in class org.scijava.module.process.ValidityPreprocessor
process(Module) - Method in class org.scijava.ui.AbstractInputHarvesterPlugin
process(Module) - Method in class org.scijava.ui.FilePreprocessor
process(Module) - Method in class org.scijava.ui.UIPreprocessor
PROCESS_LABEL - Static variable in class org.scijava.menu.MenuConstants
PROCESS_MNEMONIC - Static variable in class org.scijava.menu.MenuConstants
PROCESS_WEIGHT - Static variable in class org.scijava.menu.MenuConstants
processArgs(String...) - Method in interface org.scijava.console.ConsoleService: Handles arguments from an external source such as the command line.
processArgs(String...) - Method in class org.scijava.console.DefaultConsoleService
processResults(InputPanel<P, W>, Module) - Method in class org.scijava.widget.AbstractInputHarvester
processResults(InputPanel<P, W>, Module) - Method in interface org.scijava.widget.InputHarvester: Does any needed processing, after input values have been harvested.
ProcessUtils - Class in org.scijava.util: Useful methods for working with processes.
prompt() - Method in interface org.scijava.ui.DialogPrompt
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
PURPLE - Static variable in class org.scijava.util.Colors
put(Object, Object) - Method in interface org.scijava.cache.CacheService: Stores the given object in the cache.
put(Object, Object) - Method in class org.scijava.cache.DefaultCacheService
put(String, String) - Method in class org.scijava.prefs.DefaultPrefService
put(String, boolean) - Method in class org.scijava.prefs.DefaultPrefService
put(String, double) - Method in class org.scijava.prefs.DefaultPrefService
put(String, float) - Method in class org.scijava.prefs.DefaultPrefService
put(String, int) - Method in class org.scijava.prefs.DefaultPrefService
put(String, long) - Method in class org.scijava.prefs.DefaultPrefService
put(Class<?>, String, String) - Method in class org.scijava.prefs.DefaultPrefService
put(Class<?>, String, boolean) - Method in class org.scijava.prefs.DefaultPrefService
put(Class<?>, String, double) - Method in class org.scijava.prefs.DefaultPrefService
put(Class<?>, String, float) - Method in class org.scijava.prefs.DefaultPrefService
put(Class<?>, String, int) - Method in class org.scijava.prefs.DefaultPrefService
put(Class<?>, String, long) - Method in class org.scijava.prefs.DefaultPrefService
put(String, String) - Method in interface org.scijava.prefs.PrefService
put(String, boolean) - Method in interface org.scijava.prefs.PrefService
put(String, double) - Method in interface org.scijava.prefs.PrefService
put(String, float) - Method in interface org.scijava.prefs.PrefService
put(String, int) - Method in interface org.scijava.prefs.PrefService
put(String, long) - Method in interface org.scijava.prefs.PrefService
put(Class<?>, String, String) - Method in interface org.scijava.prefs.PrefService
put(Class<?>, String, boolean) - Method in interface org.scijava.prefs.PrefService
put(Class<?>, String, double) - Method in interface org.scijava.prefs.PrefService
put(Class<?>, String, float) - Method in interface org.scijava.prefs.PrefService
put(Class<?>, String, int) - Method in interface org.scijava.prefs.PrefService
put(Class<?>, String, long) - Method in interface org.scijava.prefs.PrefService
put(String, Object) - Method in class org.scijava.script.AbstractScriptEngine
put(String, String) - Static method in class org.scijava.util.Prefs: Deprecated.
put(String, boolean) - Static method in class org.scijava.util.Prefs: Deprecated.
put(String, double) - Static method in class org.scijava.util.Prefs: Deprecated.
put(String, float) - Static method in class org.scijava.util.Prefs: Deprecated.
put(String, int) - Static method in class org.scijava.util.Prefs: Deprecated.
put(String, long) - Static method in class org.scijava.util.Prefs: Deprecated.
put(Class<?>, String, String) - Static method in class org.scijava.util.Prefs: Deprecated.
put(Class<?>, String, boolean) - Static method in class org.scijava.util.Prefs: Deprecated.
put(Class<?>, String, double) - Static method in class org.scijava.util.Prefs: Deprecated.
put(Class<?>, String, float) - Static method in class org.scijava.util.Prefs: Deprecated.
put(Class<?>, String, int) - Static method in class org.scijava.util.Prefs: Deprecated.
put(Class<?>, String, long) - Static method in class org.scijava.util.Prefs: Deprecated.
putIterable(Iterable<String>, String) - Method in class org.scijava.prefs.DefaultPrefService
putIterable(Class<?>, Iterable<String>, String) - Method in class org.scijava.prefs.DefaultPrefService
putIterable(Iterable<String>, String) - Method in interface org.scijava.prefs.PrefService: Puts an iterable into the preferences.
putIterable(Class<?>, Iterable<String>, String) - Method in interface org.scijava.prefs.PrefService: Puts an iterable into the preferences.
putList(List<String>, String) - Method in class org.scijava.prefs.DefaultPrefService
putList(Class<?>, List<String>, String) - Method in class org.scijava.prefs.DefaultPrefService
putList(String, List<String>, String) - Method in class org.scijava.prefs.DefaultPrefService
putList(Class<?>, List<String>) - Method in class org.scijava.prefs.DefaultPrefService
putList(String, List<String>) - Method in class org.scijava.prefs.DefaultPrefService
putList(List<String>, String) - Method in interface org.scijava.prefs.PrefService: Puts a list into the preferences.
putList(Class<?>, List<String>, String) - Method in interface org.scijava.prefs.PrefService: Puts a list into the preferences, indexed under the specified class.
putList(String, List<String>, String) - Method in interface org.scijava.prefs.PrefService: Puts a list into the preferences, indexed under the specified path and relative key.
putList(Class<?>, List<String>) - Method in interface org.scijava.prefs.PrefService: Puts a list into the preferences.
putList(String, List<String>) - Method in interface org.scijava.prefs.PrefService: Puts a list into the preferences, indexed under the specified path.
putList(List<String>, String) - Static method in class org.scijava.util.Prefs: Deprecated.

Puts a list into the preferences.
putList(Preferences, List<String>, String) - Static method in class org.scijava.util.Prefs: Deprecated.
putList(Preferences, List<String>) - Static method in class org.scijava.util.Prefs: Deprecated.

Puts a list into the preferences.
putMap(Map<String, String>, String) - Method in class org.scijava.prefs.DefaultPrefService
putMap(Class<?>, Map<String, String>, String) - Method in class org.scijava.prefs.DefaultPrefService
putMap(String, Map<String, String>, String) - Method in class org.scijava.prefs.DefaultPrefService
putMap(Class<?>, Map<String, String>) - Method in class org.scijava.prefs.DefaultPrefService
putMap(String, Map<String, String>) - Method in class org.scijava.prefs.DefaultPrefService
putMap(Map<String, String>, String) - Method in interface org.scijava.prefs.PrefService: Puts a Map into the preferences.
putMap(Class<?>, Map<String, String>, String) - Method in interface org.scijava.prefs.PrefService: Puts a Map into the preferences, indexed under the specified class.
putMap(String, Map<String, String>) - Method in interface org.scijava.prefs.PrefService: Puts a Map into the preferences, indexed under the given path.
putMap(Class<?>, Map<String, String>) - Method in interface org.scijava.prefs.PrefService: Puts a Map into the preferences, indexed under the given class.
putMap(String, Map<String, String>, String) - Method in interface org.scijava.prefs.PrefService: Puts a Map into the preferences, indexed under the given path and relative key path.
putMap(Map<String, String>, String) - Static method in class org.scijava.util.Prefs: Deprecated.

Puts a map into the preferences.
putMap(Preferences, Map<String, String>, String) - Static method in class org.scijava.util.Prefs: Deprecated.
putMap(Preferences, Map<String, String>) - Static method in class org.scijava.util.Prefs: Deprecated.

Puts a map into the preferences.

Q

Query - Class in org.scijava.util: A map of annotations to annotated elements.
Query() - Constructor for class org.scijava.util.Query
Query(Query) - Constructor for class org.scijava.util.Query
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.
quit() - Method in class org.scijava.app.AbstractApp
quit() - Method in interface org.scijava.app.App: Quits the application.
quit() - Method in interface org.scijava.platform.AppEventService: Deprecated.
Use App.quit() instead.
quit() - Method in class org.scijava.platform.DefaultAppEventService: Deprecated.

R

RADIO_BUTTON_HORIZONTAL_STYLE - Static variable in interface org.scijava.widget.ChoiceWidget: Widget style for radio buttons arranged on a single line.
RADIO_BUTTON_VERTICAL_STYLE - Static variable in interface org.scijava.widget.ChoiceWidget: Widget style for radio buttons arranged one per line.
read(ByteBuffer) - Method in class org.scijava.io.AbstractDataHandle
read(ByteBuffer, int) - Method in class org.scijava.io.AbstractDataHandle
read(byte[]) - Method in class org.scijava.io.AbstractDataHandle
read(ByteBuffer) - Method in interface org.scijava.io.DataHandle: Reads up to buf.remaining() bytes of data from the stream into a ByteBuffer.
read(ByteBuffer, int) - Method in interface org.scijava.io.DataHandle: Reads up to len bytes of data from the stream into a ByteBuffer.
read() - Method in interface org.scijava.io.DataHandle: Reads the next byte of data from the stream.
read(byte[]) - Method in interface org.scijava.io.DataHandle: Reads up to b.length bytes of data from the stream into an array of bytes.
read(byte[], int, int) - Method in interface org.scijava.io.DataHandle: Reads up to len bytes of data from the stream into an array of bytes.
read() - Method in class org.scijava.io.DataHandleInputStream
read(byte[], int, int) - Method in class org.scijava.io.DataHandleInputStream
read() - Method in class org.scijava.io.FileHandle
read(byte[]) - Method in class org.scijava.io.FileHandle
read(byte[], int, int) - Method in class org.scijava.io.FileHandle
readBoolean() - Method in class org.scijava.io.FileHandle
readByte() - Method in class org.scijava.io.FileHandle
readChar() - Method in class org.scijava.io.FileHandle
readCString() - Method in class org.scijava.io.AbstractDataHandle
readCString() - Method in interface org.scijava.io.DataHandle: Reads a string of arbitrary length, terminated by a null char.
readDouble() - Method in class org.scijava.io.FileHandle
reader - Variable in class org.scijava.script.AbstractScriptContext
reader - Variable in class org.scijava.util.ReadInto
readFile(File) - Static method in class org.scijava.util.FileUtils: Reads the contents of the given file into a new byte array.
readFloat() - Method in class org.scijava.io.FileHandle
readFully(byte[]) - Method in class org.scijava.io.FileHandle
readFully(byte[], int, int) - Method in class org.scijava.io.FileHandle
readHistory() - Method in class org.scijava.script.DefaultScriptInterpreter
readHistory() - Method in interface org.scijava.script.ScriptInterpreter: Reads the persisted history of the current script interpreter.
readInt() - Method in class org.scijava.io.FileHandle
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.
readLine() - Method in class org.scijava.io.FileHandle
readLong() - Method in class org.scijava.io.FileHandle
readObject() - Method in class org.scijava.annotations.legacy.LegacyReader
readShort() - Method in class org.scijava.io.FileHandle
readState(DataInputStream) - Method in class org.scijava.util.MersenneTwisterFast: Reads the entire state of the MersenneTwister RNG from the stream
readString(int) - Method in class org.scijava.io.AbstractDataHandle
readString(String) - Method in class org.scijava.io.AbstractDataHandle
readString(int) - Method in interface org.scijava.io.DataHandle: Reads a string of up to length n.
readString(String) - Method in interface org.scijava.io.DataHandle: Reads a string ending with one of the characters in the given string.
readUnsignedByte() - Method in class org.scijava.io.FileHandle
readUnsignedShort() - Method in class org.scijava.io.FileHandle
readUTF() - Method in class org.scijava.io.FileHandle
RealCoords - Class in org.scijava.util: This class represents an (X, Y) coordinate pair in real coordinates.
RealCoords(double, double) - Constructor for class org.scijava.util.RealCoords
RealRect - Class in org.scijava.util: A class for representing a rectangular region, in real coordinates.
RealRect() - Constructor for class org.scijava.util.RealRect
RealRect(double, double, double, double) - Constructor for class org.scijava.util.RealRect
rebuild() - Method in class org.scijava.display.AbstractDisplay
recentFile() - Method in class org.scijava.AbstractGateway
recentFile() - Method in interface org.scijava.Gateway: Gets this application context's RecentFileService.
RecentFileService - Interface in org.scijava.io: Interface for services that manage the Recently Used Files menu.
RED - Static variable in class org.scijava.util.Colors
redoLayout() - Method in interface org.scijava.ui.viewer.DisplayPanel: Rebuilds the display window to reflect the display's current views, dimensional lengths, etc.
redraw() - Method in interface org.scijava.ui.viewer.DisplayPanel: Redraws the contents of the panel.
ReflectedUniverse - Class in org.scijava.util: A general-purpose reflection wrapper class.
ReflectedUniverse() - Constructor for class org.scijava.util.ReflectedUniverse: Constructs a new reflected universe.
ReflectedUniverse(URL[]) - Constructor for class org.scijava.util.ReflectedUniverse: Constructs a new reflected universe, with the given URLs representing additional search paths for imported classes (in addition to the CLASSPATH).
ReflectedUniverse(ClassLoader) - Constructor for class org.scijava.util.ReflectedUniverse: Constructs a new reflected universe that uses the given class loader.
ReflectException - Exception in org.scijava.util: An exception thrown when something goes wrong performing a reflected operation with ReflectedUniverse.
ReflectException() - Constructor for exception org.scijava.util.ReflectException
ReflectException(String) - Constructor for exception org.scijava.util.ReflectException
ReflectException(String, Throwable) - Constructor for exception org.scijava.util.ReflectException
ReflectException(Throwable) - Constructor for exception org.scijava.util.ReflectException
refresh() - Method in class org.scijava.widget.AbstractInputPanel
refresh() - Method in interface org.scijava.widget.InputPanel: Updates the widgets to reflect the most recent parameter value(s).
refreshWidget() - Method in class org.scijava.ui.AbstractUIInputWidget
refreshWidget() - Method in interface org.scijava.widget.InputWidget: Refreshes the widget to reflect the latest model value(s).
registerAppMenus(Object) - Method in class org.scijava.platform.AbstractPlatform
registerAppMenus(Object) - Method in class org.scijava.platform.DefaultPlatformService
registerAppMenus(Object) - Method in interface org.scijava.platform.Platform: Informs the platform of a UI's newly created application menu structure.
registerAppMenus(Object) - Method in interface org.scijava.platform.PlatformService: Informs the active platform handlers of a UI's newly created application menu structure.
registerEventHandlers() - Method in class org.scijava.service.AbstractService
registerEventHandlers() - Method in interface org.scijava.service.Service: Registers the service's event handler methods.
registerInput(ModuleItem<?>) - Method in class org.scijava.module.AbstractModuleInfo: Adds an input.
registerOutput(ModuleItem<?>) - Method in class org.scijava.module.AbstractModuleInfo: Adds an output.
reloadPlugins() - Method in class org.scijava.plugin.DefaultPluginService
reloadPlugins() - Method in interface org.scijava.plugin.PluginService: Rediscovers all plugins available on the classpath.
remove(int) - Method in class org.scijava.display.AbstractDisplay
remove(Object) - Method in class org.scijava.display.AbstractDisplay
remove(String) - Method in class org.scijava.io.DefaultRecentFileService
remove(String) - Method in interface org.scijava.io.RecentFileService: Removes a path from the list of recent files.
remove(Object) - Method in class org.scijava.menu.ShadowMenu
remove() - Method in class org.scijava.menu.ShadowMenuIterator
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(Class<?>, String) - Method in class org.scijava.prefs.DefaultPrefService
remove(String, String) - Method in class org.scijava.prefs.DefaultPrefService
remove(Class<?>, String) - Method in interface org.scijava.prefs.PrefService: Removes the node.
remove(String, String) - Method in interface org.scijava.prefs.PrefService
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.LastRecentlyUsed
remove(Object) - Method in class org.scijava.util.LongArray
remove(Object) - Method in class org.scijava.util.ObjectArray
remove(Preferences, String) - Static method in class org.scijava.util.Prefs: Deprecated.

Removes the node.
remove(Object) - Method in class org.scijava.util.ShortArray
removeAll(Collection<?>) - Method in class org.scijava.display.AbstractDisplay
removeAll(Collection<?>) - Method in class org.scijava.menu.ShadowMenu
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.LastRecentlyUsed
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
removeAttribute(String, int) - Method in class org.scijava.script.AbstractScriptContext
removeFromList(Object, List<E>, boolean) - Method in class org.scijava.object.ObjectIndex
removeInput(ModuleItem<?>) - Method in class org.scijava.module.DefaultMutableModule
removeInput(ModuleItem<?>) - Method in class org.scijava.module.DefaultMutableModuleInfo
removeInput(ModuleItem<?>) - Method in interface org.scijava.module.MutableModule: Removes an input from the list.
removeInput(ModuleItem<?>) - Method in interface org.scijava.module.MutableModuleInfo: Removes an input from the list.
removeListener(EventHistoryListener) - Method in class org.scijava.event.DefaultEventHistory
removeListener(EventHistoryListener) - Method in interface org.scijava.event.EventHistory: Removes an event history listener.
removeModule(ModuleInfo) - Method in class org.scijava.module.DefaultModuleService
removeModule(ModuleInfo) - Method in interface org.scijava.module.ModuleService: Manually unregisters a module with the module service.
removeModules(Collection<? extends ModuleInfo>) - Method in class org.scijava.module.DefaultModuleService
removeModules(Collection<? extends ModuleInfo>) - Method in interface org.scijava.module.ModuleService: Manually unregisters a list of modules with the module service.
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.
removeOutput(ModuleItem<?>) - Method in class org.scijava.module.DefaultMutableModule
removeOutput(ModuleItem<?>) - Method in class org.scijava.module.DefaultMutableModuleInfo
removeOutput(ModuleItem<?>) - Method in interface org.scijava.module.MutableModule: Removes an output from the list.
removeOutput(ModuleItem<?>) - Method in interface org.scijava.module.MutableModuleInfo: Removes an output from the list.
removeOutputListener(OutputListener) - Method in interface org.scijava.console.ConsoleService: Removes a listener for output sent to stdout or stderr.
removeOutputListener(OutputListener) - Method in class org.scijava.console.DefaultConsoleService
removeOutputStream(OutputStream) - Method in class org.scijava.console.MultiOutputStream: Removes an output stream from those receiving this stream's output.
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.
removePropertyChangeListener(PropertyChangeListener) - Method in interface org.scijava.ui.Arrangeable
removeScriptDirectory(File) - Method in class org.scijava.script.DefaultScriptService
removeScriptDirectory(File) - Method in interface org.scijava.script.ScriptService: Removes a base directory to scan for scripts.
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
replace(int, T) - Method in class org.scijava.util.LastRecentlyUsed
report(String) - Method in class org.scijava.util.Timing
reportLine(double, double, double, double) - Method in class org.scijava.tool.DefaultToolService
reportLine(RealCoords, RealCoords) - Method in class org.scijava.tool.DefaultToolService
reportLine(double, double, double, double) - Method in interface org.scijava.tool.ToolService: Publishes line length and angle in the status bar.
reportLine(RealCoords, RealCoords) - Method in interface org.scijava.tool.ToolService: Publishes line length and angle in the status bar.
reportPoint(double, double) - Method in class org.scijava.tool.DefaultToolService
reportPoint(RealCoords) - Method in class org.scijava.tool.DefaultToolService
reportPoint(double, double) - Method in interface org.scijava.tool.ToolService: Publishes point coordinates to the status bar.
reportPoint(RealCoords) - Method in interface org.scijava.tool.ToolService: Publishes point coordinates to the status bar.
reportRectangle(double, double, double, double) - Method in class org.scijava.tool.DefaultToolService
reportRectangle(RealCoords, RealCoords) - Method in class org.scijava.tool.DefaultToolService
reportRectangle(double, double, double, double) - Method in interface org.scijava.tool.ToolService: Publishes rectangle dimensions in the status bar.
reportRectangle(RealCoords, RealCoords) - Method in interface org.scijava.tool.ToolService: Publishes rectangle dimensions in the status bar.
requestFocus() - Method in interface org.scijava.ui.viewer.DisplayWindow
requiresEDT() - Method in interface org.scijava.ui.UserInterface: Returns true if this UI requires the EDT.
reset() - Method in class org.scijava.io.DataHandleInputStream
reset() - Method in class org.scijava.options.DefaultOptionsService
reset() - Method in class org.scijava.options.OptionsPlugin: Clears option values from persistent storage.
reset() - Method in interface org.scijava.options.OptionsService: Clears all option values from persistent storage.
reset() - Method in class org.scijava.util.Timing
restoreLocation() - Method in class org.scijava.ui.AbstractUserInterface
restoreLocation() - Method in interface org.scijava.ui.UserInterface: Restores the application frame's current location.
retainAll(Collection<?>) - Method in class org.scijava.display.AbstractDisplay
retainAll(Collection<?>) - Method in class org.scijava.menu.ShadowMenu
retainAll(Collection<?>) - Method in class org.scijava.object.ObjectIndex
retainAll(Collection<?>) - Method in class org.scijava.util.LastRecentlyUsed
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
RETURN_VALUE - Static variable in class org.scijava.script.ScriptModule
RichPlugin - Interface in org.scijava.plugin: Base interface for Contextual, Prioritized plugins that retain access to their associated PluginInfo metadata via the HasPluginInfo interface.
RIGHT_BUTTON - Static variable in class org.scijava.display.event.input.MsButtonEvent
ROSYBROWN - Static variable in class org.scijava.util.Colors
ROYALBLUE - Static variable in class org.scijava.util.Colors
run() - Method in class org.scijava.command.CommandModule
run(String, boolean, Object...) - Method in interface org.scijava.command.CommandService: Executes the first command of the given class name.
run(String, boolean, Map<String, Object>) - Method in interface org.scijava.command.CommandService: Executes the first command of the given class name.
run(Class<C>, boolean, Object...) - Method in interface org.scijava.command.CommandService: Executes the first command of the given class.
run(Class<C>, boolean, Map<String, Object>) - Method in interface org.scijava.command.CommandService: Executes the first command of the given class.
run(CommandInfo, boolean, Object...) - Method in interface org.scijava.command.CommandService: Executes the given command.
run(CommandInfo, boolean, Map<String, Object>) - Method in interface org.scijava.command.CommandService: Executes the given command.
run(String, boolean, Object...) - Method in class org.scijava.command.DefaultCommandService
run(String, boolean, Map<String, Object>) - Method in class org.scijava.command.DefaultCommandService
run(Class<C>, boolean, Object...) - Method in class org.scijava.command.DefaultCommandService
run(Class<C>, boolean, Map<String, Object>) - Method in class org.scijava.command.DefaultCommandService
run(CommandInfo, boolean, Object...) - Method in class org.scijava.command.DefaultCommandService
run(CommandInfo, boolean, Map<String, Object>) - Method in class org.scijava.command.DefaultCommandService
run() - Method in class org.scijava.command.UnimplementedCommand
run() - Method in class org.scijava.menu.ShadowMenu: Executes the module linked to this node.
run(ModuleInfo, boolean, Object...) - Method in class org.scijava.module.DefaultModuleService
run(ModuleInfo, boolean, Map<String, Object>) - Method in class org.scijava.module.DefaultModuleService
run(ModuleInfo, List<? extends ModulePreprocessor>, List<? extends ModulePostprocessor>, Object...) - Method in class org.scijava.module.DefaultModuleService
run(ModuleInfo, List<? extends ModulePreprocessor>, List<? extends ModulePostprocessor>, Map<String, Object>) - Method in class org.scijava.module.DefaultModuleService
run(M, boolean, Object...) - Method in class org.scijava.module.DefaultModuleService
run(M, boolean, Map<String, Object>) - Method in class org.scijava.module.DefaultModuleService
run(M, List<? extends ModulePreprocessor>, List<? extends ModulePostprocessor>, Object...) - Method in class org.scijava.module.DefaultModuleService
run(M, List<? extends ModulePreprocessor>, List<? extends ModulePostprocessor>, Map<String, Object>) - Method in class org.scijava.module.DefaultModuleService
run() - Method in class org.scijava.module.DefaultMutableModule
run() - Method in class org.scijava.module.ModuleRunner: Executes the module, including pre- and post-processing and event notification.
run(ModuleInfo, boolean, Object...) - Method in interface org.scijava.module.ModuleService: Executes the given module.
run(ModuleInfo, boolean, Map<String, Object>) - Method in interface org.scijava.module.ModuleService: Executes the given module.
run(ModuleInfo, List<? extends ModulePreprocessor>, List<? extends ModulePostprocessor>, Object...) - Method in interface org.scijava.module.ModuleService: Executes the given module.
run(ModuleInfo, List<? extends ModulePreprocessor>, List<? extends ModulePostprocessor>, Map<String, Object>) - Method in interface org.scijava.module.ModuleService: Executes the given module.
run(M, boolean, Object...) - Method in interface org.scijava.module.ModuleService: Executes the given module.
run(M, boolean, Map<String, Object>) - Method in interface org.scijava.module.ModuleService: Executes the given module.
run(M, List<? extends ModulePreprocessor>, List<? extends ModulePostprocessor>, Object...) - Method in interface org.scijava.module.ModuleService: Executes the given module.
run(M, List<? extends ModulePreprocessor>, List<? extends ModulePostprocessor>, Map<String, Object>) - Method in interface org.scijava.module.ModuleService: Executes the given module.
run() - Method in class org.scijava.options.OptionsPlugin
run(File, boolean, Object...) - Method in class org.scijava.script.DefaultScriptService
run(File, boolean, Map<String, Object>) - Method in class org.scijava.script.DefaultScriptService
run(String, String, boolean, Object...) - Method in class org.scijava.script.DefaultScriptService
run(String, String, boolean, Map<String, Object>) - Method in class org.scijava.script.DefaultScriptService
run(String, Reader, boolean, Object...) - Method in class org.scijava.script.DefaultScriptService
run(String, Reader, boolean, Map<String, Object>) - Method in class org.scijava.script.DefaultScriptService
run(ScriptInfo, boolean, Object...) - Method in class org.scijava.script.DefaultScriptService
run(ScriptInfo, boolean, Map<String, Object>) - Method in class org.scijava.script.DefaultScriptService
run() - Method in class org.scijava.script.ScriptModule
run(File, boolean, Object...) - Method in interface org.scijava.script.ScriptService: Executes the script in the given file.
run(File, boolean, Map<String, Object>) - Method in interface org.scijava.script.ScriptService: Executes the script in the given file.
run(String, String, boolean, Object...) - Method in interface org.scijava.script.ScriptService: Executes the given script.
run(String, String, boolean, Map<String, Object>) - Method in interface org.scijava.script.ScriptService: Executes the given script.
run(String, Reader, boolean, Object...) - Method in interface org.scijava.script.ScriptService: Executes the given script.
run(String, Reader, boolean, Map<String, Object>) - Method in interface org.scijava.script.ScriptService: Executes the given script.
run(ScriptInfo, boolean, Object...) - Method in interface org.scijava.script.ScriptService: Executes the given script.
run(ScriptInfo, boolean, Map<String, Object>) - Method in interface org.scijava.script.ScriptService: Executes the given script.
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.
RunArgument - Class in org.scijava.command.console: Handles the --run command line argument.
RunArgument() - Constructor for class org.scijava.command.console.RunArgument

S

SADDLEBROWN - Static variable in class org.scijava.util.Colors
safeMultiply32(long...) - Static method in class org.scijava.util.ArrayUtils: Checks that the product of the given sizes does not exceed the 32-bit integer limit (i.e., Integer.MAX_VALUE).
safeMultiply64(long...) - Static method in class org.scijava.util.ArrayUtils: Checks that the product of the given sizes does not exceed the 64-bit integer limit (i.e., Long.MAX_VALUE).
SALMON - Static variable in class org.scijava.util.Colors
samePrefix(String, String) - Static method in class org.scijava.util.StringUtils: Checks if two filenames have the same prefix.
SANDYBROWN - Static variable in class org.scijava.util.Colors
sanitize(String) - Static method in class org.scijava.util.StringUtils: Removes unprintable characters from the given string.
sanitizeDouble(String) - Static method in class org.scijava.util.StringUtils: Normalizes the decimal separator for the user's locale.
save(D, String) - Method in class org.scijava.io.AbstractIOPlugin
save(Object, String) - Method in class org.scijava.io.DefaultIOService
save(D, String) - Method in interface org.scijava.io.IOPlugin: Saves the given data to the specified destination.
save(Object, String) - Method in interface org.scijava.io.IOService: Saves data to the given destination.
save(ModuleItem<T>, T) - Method in class org.scijava.module.DefaultModuleService
save(ModuleItem<T>, T) - Method in interface org.scijava.module.ModuleService: Registers the given value for the given ModuleItem using the PrefService.
save() - Method in class org.scijava.options.OptionsPlugin: Saves option values to persistent storage.
SAVE_STYLE - Static variable in interface org.scijava.widget.FileWidget: Widget style for file saver dialogs.
SaveInputsPreprocessor - Class in org.scijava.module.process: A preprocessor for saving populated input values to persistent storage.
SaveInputsPreprocessor() - Constructor for class org.scijava.module.process.SaveInputsPreprocessor
saveLocation() - Method in class org.scijava.ui.AbstractUserInterface
saveLocation() - Method in interface org.scijava.ui.UserInterface: Persists the application frame's current location.
saveValue(T) - Method in class org.scijava.module.AbstractModuleItem: Deprecated.
saveValue(T) - Method in interface org.scijava.module.ModuleItem: Deprecated.
SciJava - Class in org.scijava: Main entry point into SciJava.
SciJava() - Constructor for class org.scijava.SciJava: Creates a new SciJava application context with all available services.
SciJava(boolean) - Constructor for class org.scijava.SciJava: Creates a new Scijava application context.
SciJava(Class...) - Constructor for class org.scijava.SciJava: Creates a new SciJava application context with the specified services (and any required service dependencies).
SciJava(Collection<Class<? extends Service>>) - Constructor for class org.scijava.SciJava: Creates a new SciJava application context with the specified services (and any required service dependencies).
SciJava(Context) - Constructor for class org.scijava.SciJava: Creates a new SciJava application context which wraps the given existing SciJava context.
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.
script() - Method in class org.scijava.AbstractGateway
script() - Method in interface org.scijava.Gateway: Gets this application context's ScriptService.
scriptContext - Variable in class org.scijava.script.AbstractScriptEngine
ScriptFileDragAndDropHandler - Class in org.scijava.ui.dnd: Drag-and-drop handler for script files.
ScriptFileDragAndDropHandler() - Constructor for class org.scijava.ui.dnd.ScriptFileDragAndDropHandler
ScriptFinder - Class in org.scijava.script: Discovers scripts.
ScriptFinder(ScriptService) - Constructor for class org.scijava.script.ScriptFinder
ScriptHeader - Interface in org.scijava.script: Represents one or more canned lines intended to go at the top of scripts of a given language.
ScriptHeaderService - Interface in org.scijava.script: Interface for a HandlerService capable of mapping ScriptLanguages to ScriptHeaders.
ScriptInfo - Class in org.scijava.script: Metadata about a script.
ScriptInfo(Context, File) - Constructor for class org.scijava.script.ScriptInfo: Creates a script metadata object which describes the given script file.
ScriptInfo(Context, String) - Constructor for class org.scijava.script.ScriptInfo: Creates a script metadata object which describes the given script file.
ScriptInfo(Context, String, Reader) - Constructor for class org.scijava.script.ScriptInfo: Creates a script metadata object which describes a script provided by the given Reader.
ScriptInterpreter - Interface in org.scijava.script: The contract for script interpreters.
ScriptIOPlugin - Class in org.scijava.script.io: IOPlugin for scripts.
ScriptIOPlugin() - Constructor for class org.scijava.script.io.ScriptIOPlugin
ScriptLanguage - Interface in org.scijava.script: The base interface for scripting language adapters.
ScriptLanguageIndex - Class in org.scijava.script: Data structure for managing registered scripting languages.
ScriptLanguageIndex() - Constructor for class org.scijava.script.ScriptLanguageIndex: Deprecated.
ScriptLanguageIndex(LogService) - Constructor for class org.scijava.script.ScriptLanguageIndex: Instantiates an index of the available script languages.
ScriptModule - Class in org.scijava.script: A Module which executes a script.
ScriptModule(ScriptInfo) - Constructor for class org.scijava.script.ScriptModule
SCRIPTS_PATH_PROPERTY - Static variable in interface org.scijava.script.ScriptService: System property for overriding the list of directories to scan for scripts.
ScriptService - Interface in org.scijava.script: Interface for service that works with scripting languages.
SCROLL_BAR_STYLE - Static variable in interface org.scijava.widget.NumberWidget: Widget style for scroll bar with spinner.
SEAGREEN - Static variable in class org.scijava.util.Colors
SEASHELL - Static variable in class org.scijava.util.Colors
seek(long) - Method in interface org.scijava.io.DataHandle: Sets the stream pointer offset, measured from the beginning of the stream, at which the next read or write occurs.
seek(long) - Method in class org.scijava.io.FileHandle
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.
serviceClassList(Class...) - Static method in class org.scijava.Context: Utility method for converting a varargs list of service classes to a List of those classes.
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.
ServiceHelper(Context, Collection<Class<? extends Service>>, boolean) - 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
ServicePreprocessor - Class in org.scijava.module.process: The service preprocessor automatically populates module inputs that implement Service.
ServicePreprocessor() - Constructor for class org.scijava.module.process.ServicePreprocessor
ServicesLoadedEvent - Class in org.scijava.service.event: An event which fires when a Context finishes initializing all its services.
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(int, T) - Method in class org.scijava.display.AbstractDisplay
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
set(WidgetModel) - Method in class org.scijava.widget.AbstractInputWidget
set(WidgetModel) - Method in interface org.scijava.widget.InputWidget: Initializes the widget to use the given widget model.
setAccelerator(Accelerator) - Method in class org.scijava.MenuEntry
setAccepted(boolean) - Method in class org.scijava.ui.dnd.event.DragEnterEvent: Sets whether the drag operation is valid.
setAccessibilityIgnored(boolean) - Method in class org.scijava.util.ReflectedUniverse: Sets whether access modifiers (protected, private, etc.) are ignored.
setActive(boolean) - Method in class org.scijava.event.DefaultEventHistory
setActive(boolean) - Method in interface org.scijava.event.EventHistory: Activates or deactivates event history tracking.
setActiveDisplay(Display<?>) - Method in class org.scijava.display.DefaultDisplayService
setActiveDisplay(Display<?>) - Method in interface org.scijava.display.DisplayService: Set the active display.
setActiveTool(Tool) - Method in class org.scijava.tool.DefaultToolService
setActiveTool(Tool) - Method in interface org.scijava.tool.ToolService
setAlpha(int, int, int) - Method in class org.scijava.ui.ARGBPlane
setARGB(int, int, int) - Method in class org.scijava.ui.ARGBPlane
setArrangement(Arrangeable.Arrangement) - Method in interface org.scijava.ui.Arrangeable
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
setAttribute(String, Object, int) - Method in class org.scijava.script.AbstractScriptContext
setBindings(Bindings, int) - Method in class org.scijava.script.AbstractScriptContext
setBindings(Bindings, int) - Method in class org.scijava.script.AbstractScriptEngine
setBlue(int, int, int) - Method in class org.scijava.ui.ARGBPlane
setCallback(String) - Method in class org.scijava.module.DefaultMutableModuleItem
setCallback(String) - Method in interface org.scijava.module.MutableModuleItem
setCallingThread(Thread) - Method in class org.scijava.event.SciJavaEvent: Sets the thread that published the event.
setChoices(List<? extends T>) - Method in class org.scijava.module.DefaultMutableModuleItem
setChoices(List<? extends T>) - Method in interface org.scijava.module.MutableModuleItem
setColumnCount(int) - Method in class org.scijava.module.DefaultMutableModuleItem
setColumnCount(int) - Method in interface org.scijava.module.MutableModuleItem
setConsumed(boolean) - Method in class org.scijava.event.SciJavaEvent
setContent(DisplayPanel) - Method in interface org.scijava.ui.viewer.DisplayWindow
setContext(Context) - Method in class org.scijava.AbstractContextual
setContext(Context) - Method in class org.scijava.command.CommandModule
setContext(Context) - Method in class org.scijava.command.DynamicCommand
setContext(Context) - Method in class org.scijava.command.ModuleCommand
setContext(Context) - Method in interface org.scijava.Contextual: Sets the application context to which the object belongs.
setContext(ScriptContext) - Method in class org.scijava.script.AbstractScriptEngine
setContext(Context) - Method in class org.scijava.script.ScriptInfo
setContext(Context) - Method in class org.scijava.script.ScriptModule
setContext(Context) - Method in class org.scijava.service.AbstractService
setDefaultUI(UserInterface) - Method in class org.scijava.ui.DefaultUIService
setDefaultUI(UserInterface) - Method in interface org.scijava.ui.UIService: Sets the default user interface.
setDefaultValue(T) - Method in class org.scijava.module.DefaultMutableModuleItem
setDefaultValue(T) - Method in interface org.scijava.module.MutableModuleItem
setDelegateService(ConvertService, double) - Static method in class org.scijava.util.ConversionUtils: Sets the ConvertService to use for handling conversion requests.
setDelegateService(PrefService, double) - Static method in class org.scijava.util.Prefs: Deprecated.

Sets the PrefService
setDescription(String) - Method in class org.scijava.AbstractBasicDetails
setDescription(String) - Method in interface org.scijava.BasicDetails: Sets a string describing the object.
setDescription(String) - Method in class org.scijava.command.DynamicCommandInfo
setDescription(String) - Method in class org.scijava.module.DefaultMutableModuleItem
setEnabled(boolean) - Method in class org.scijava.AbstractUIDetails
setEnabled(boolean) - Method in class org.scijava.command.DynamicCommandInfo
setEnabled(boolean) - Method in interface org.scijava.UIDetails: Sets whether the object should be enabled in the user interface.
setEncoding(String) - Method in class org.scijava.io.AbstractDataHandle
setEncoding(String) - Method in interface org.scijava.io.DataHandle: Sets the native encoding of the stream.
setErrorWriter(Writer) - Method in class org.scijava.script.AbstractScriptContext
setErrorWriter(Writer) - Method in class org.scijava.script.ScriptModule: Sets the writer used to record the standard error stream.
setExecutorService(ExecutorService) - Method in class org.scijava.thread.DefaultThreadService
setExecutorService(ExecutorService) - Method in interface org.scijava.thread.ThreadService: Sets the ExecutorService object used when ThreadService.run(java.util.concurrent.Callable<V>) is called.
setFirstRun(boolean) - Method in class org.scijava.welcome.DefaultWelcomeService
setFirstRun(boolean) - Method in interface org.scijava.welcome.WelcomeService: Sets a preference recording whether this version of the dominant SJC application has run.
setGreen(int, int, int) - Method in class org.scijava.ui.ARGBPlane
setIconPath(String) - Method in class org.scijava.AbstractUIDetails
setIconPath(String) - Method in class org.scijava.command.DynamicCommandInfo
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.
setIconPixel(int, int, ColorRGB) - Method in interface org.scijava.tool.IconDrawer
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.
setInitialized(boolean) - Method in class org.scijava.widget.DefaultWidgetModel
setInitialized(boolean) - Method in interface org.scijava.widget.WidgetModel: Toggles the widget's initialization state.
setInitializer(String) - Method in class org.scijava.module.DefaultMutableModuleItem
setInitializer(String) - Method in interface org.scijava.module.MutableModuleItem
setInput(String, Object) - Method in class org.scijava.command.CommandModule
setInput(String, Object) - Method in class org.scijava.command.DynamicCommand
setInput(String, Object) - Method in class org.scijava.module.AbstractModule
setInput(String, Object) - Method in interface org.scijava.module.Module: Sets the value of the input with the given name.
setInputs(Map<String, Object>) - Method in class org.scijava.module.AbstractModule
setInputs(Map<String, Object>) - Method in interface org.scijava.module.Module: Sets input values according to the given table.
setIOType(ItemIO) - Method in class org.scijava.module.DefaultMutableModuleItem
setIOType(ItemIO) - Method in interface org.scijava.module.MutableModuleItem
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.
setLabel(String) - Method in class org.scijava.command.DynamicCommandInfo
setLabel(String) - Method in class org.scijava.module.DefaultMutableModuleItem
setLabel(String) - Method in interface org.scijava.ui.viewer.DisplayPanel: Sets the label at the top of the display panel.
setLanguage(ScriptLanguage) - Method in class org.scijava.script.ScriptModule: Overrides the script language to use when executing the script.
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
setLocation(int, int) - Method in interface org.scijava.ui.ApplicationFrame: Sets the coordinates of the application frame's top left corner.
setLogService(LogService) - Method in class org.scijava.script.AbstractScriptEngine
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.
setMaximumValue(T) - Method in class org.scijava.module.DefaultMutableModuleItem
setMaximumValue(T) - Method in interface org.scijava.module.MutableModuleItem
setMenuPath(MenuPath) - Method in class org.scijava.AbstractUIDetails
setMenuPath(MenuPath) - Method in class org.scijava.command.DynamicCommandInfo
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 class org.scijava.command.DynamicCommandInfo
setMenuRoot(String) - Method in interface org.scijava.UIDetails: Sets the name of the menu structure to which the object belongs.
setMinimumValue(T) - Method in class org.scijava.module.DefaultMutableModuleItem
setMinimumValue(T) - Method in interface org.scijava.module.MutableModuleItem
setMnemonic(char) - Method in class org.scijava.MenuEntry
setMode(String) - Method in class org.scijava.io.FileHandle
setModuleClass(Class<? extends Module>) - Method in class org.scijava.module.DefaultMutableModuleInfo
setModuleClass(Class<? extends Module>) - Method in interface org.scijava.module.MutableModuleInfo: Sets the module class described by this ModuleInfo.
setName(String) - Method in class org.scijava.AbstractBasicDetails
setName(String) - Method in class org.scijava.command.DynamicCommandInfo
setName(String) - Method in class org.scijava.display.AbstractDisplay
setName(String) - Method in class org.scijava.menu.ShadowMenu
setName(String) - Method in class org.scijava.MenuEntry
setName(String) - Method in class org.scijava.module.DefaultMutableModuleItem
setName(String) - Method in interface org.scijava.Named: Sets the name of the object.
setNoteLength(int) - Method in class org.scijava.util.TunePlayer
setOctave(int) - Method in class org.scijava.util.TunePlayer
setOrder(ByteOrder) - Method in class org.scijava.io.AbstractDataHandle
setOrder(boolean) - Method in class org.scijava.io.AbstractDataHandle
setOrder(ByteOrder) - Method in interface org.scijava.io.DataHandle: Sets the byte order of the stream.
setOrder(boolean) - Method in interface org.scijava.io.DataHandle: Sets the endianness of the stream.
setOutput(String, Object) - Method in class org.scijava.command.CommandModule
setOutput(String, Object) - Method in class org.scijava.command.DynamicCommand
setOutput(String, Object) - Method in class org.scijava.module.AbstractModule
setOutput(String, Object) - Method in interface org.scijava.module.Module: Sets the value of the output with the given name.
setOutputs(Map<String, Object>) - Method in class org.scijava.module.AbstractModule
setOutputs(Map<String, Object>) - Method in interface org.scijava.module.Module: Sets output values according to the given table.
setOutputWriter(Writer) - Method in class org.scijava.script.ScriptModule: Sets the writer used to record the standard output stream.
setPanel(DisplayPanel) - Method in class org.scijava.ui.viewer.AbstractDisplayViewer
setPanel(DisplayPanel) - Method in interface org.scijava.ui.viewer.DisplayViewer: Installs the display panel.
setPersisted(boolean) - Method in class org.scijava.module.DefaultMutableModuleItem
setPersisted(boolean) - Method in interface org.scijava.module.MutableModuleItem
setPersistKey(String) - Method in class org.scijava.module.DefaultMutableModuleItem
setPersistKey(String) - Method in interface org.scijava.module.MutableModuleItem
setPluginClass(Class<? extends Command>) - Method in class org.scijava.command.CommandInfo
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.
setPresets(Map<String, Object>) - Method in class org.scijava.command.CommandInfo: Sets the table of items with fixed, preset values.
setPriority(double) - Method in class org.scijava.AbstractUIDetails
setPriority(double) - Method in class org.scijava.command.DynamicCommandInfo
setPriority(double) - Method in class org.scijava.plugin.AbstractRichPlugin
setPriority(double) - Method in interface org.scijava.Prioritized: Sets the sort priority of the object.
setProgress(int, int) - Method in interface org.scijava.ui.StatusBar
setReader(Reader) - Method in class org.scijava.script.AbstractScriptContext
setRed(int, int, int) - Method in class org.scijava.ui.ARGBPlane
setRequired(boolean) - Method in class org.scijava.module.DefaultMutableModuleItem
setRequired(boolean) - Method in interface org.scijava.module.MutableModuleItem
setResolved(String, boolean) - Method in class org.scijava.module.AbstractModule
setResolved(String, boolean) - Method in interface org.scijava.module.Module: Sets the resolution status of the input with the given name.
setSeed(long) - Method in class org.scijava.util.MersenneTwisterFast: Initalize the pseudo random number generator.
setSeed(int[]) - Method in class org.scijava.util.MersenneTwisterFast: Sets the seed of the MersenneTwister using an array of integers.
setSelectable(boolean) - Method in class org.scijava.AbstractUIDetails
setSelectable(boolean) - Method in class org.scijava.command.DynamicCommandInfo
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 class org.scijava.command.DynamicCommandInfo
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 class org.scijava.command.DynamicCommandInfo
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
setSoftMaximum(T) - Method in class org.scijava.module.DefaultMutableModuleItem
setSoftMaximum(T) - Method in interface org.scijava.module.MutableModuleItem
setSoftMinimum(T) - Method in class org.scijava.module.DefaultMutableModuleItem
setSoftMinimum(T) - Method in interface org.scijava.module.MutableModuleItem
setSourceObject(Object) - Method in class org.scijava.convert.ConversionRequest: Sets the source object for this ConversionRequest.
setStatus(String) - Method in interface org.scijava.ui.StatusBar
setStepSize(Number) - Method in class org.scijava.module.DefaultMutableModuleItem
setStepSize(Number) - Method in interface org.scijava.module.MutableModuleItem
setStrict(boolean) - Method in class org.scijava.Context
setSuccessful(boolean) - Method in class org.scijava.ui.dnd.event.DropEvent: Sets whether the drop operation was successful.
setTempo(int) - Method in class org.scijava.util.TunePlayer
setTitle(String) - Method in interface org.scijava.ui.viewer.DisplayWindow
setValue(Module, T) - Method in class org.scijava.module.AbstractModuleItem
setValue(Module, T) - Method in interface org.scijava.module.ModuleItem: Sets the item's current value with respect to the given module.
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
setValue(Object) - Method in class org.scijava.widget.DefaultWidgetModel
setValue(Object) - Method in interface org.scijava.widget.WidgetModel: Sets the current value of the module input.
setVar(String, Object) - Method in class org.scijava.util.ReflectedUniverse: Registers a variable in the universe.
setVar(String, boolean) - Method in class org.scijava.util.ReflectedUniverse: Registers a variable of primitive type boolean in the universe.
setVar(String, byte) - Method in class org.scijava.util.ReflectedUniverse: Registers a variable of primitive type byte in the universe.
setVar(String, char) - Method in class org.scijava.util.ReflectedUniverse: Registers a variable of primitive type char in the universe.
setVar(String, double) - Method in class org.scijava.util.ReflectedUniverse: Registers a variable of primitive type double in the universe.
setVar(String, float) - Method in class org.scijava.util.ReflectedUniverse: Registers a variable of primitive type float in the universe.
setVar(String, int) - Method in class org.scijava.util.ReflectedUniverse: Registers a variable of primitive type int in the universe.
setVar(String, long) - Method in class org.scijava.util.ReflectedUniverse: Registers a variable of primitive type long in the universe.
setVar(String, short) - Method in class org.scijava.util.ReflectedUniverse: Registers a variable of primitive type short in the universe.
setVisibility(ItemVisibility) - Method in class org.scijava.module.DefaultMutableModuleItem
setVisibility(ItemVisibility) - Method in interface org.scijava.module.MutableModuleItem
setVisible(boolean) - Method in class org.scijava.AbstractUIDetails
setVisible(boolean) - Method in interface org.scijava.ui.ApplicationFrame: Show or hide the application frame
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
setWidgetStyle(String) - Method in class org.scijava.module.DefaultMutableModuleItem
setWidgetStyle(String) - Method in interface org.scijava.module.MutableModuleItem
setWriter(Writer) - Method in class org.scijava.script.AbstractScriptContext
sha1(byte[]) - Static method in class org.scijava.util.DigestUtils: Gets the given byte array's SHA-1 checksum, or null if unavailable.
ShadowMenu - Class in org.scijava.menu: A tree representing a menu structure independent of any particular user interface.
ShadowMenu(Context, Collection<? extends ModuleInfo>) - Constructor for class org.scijava.menu.ShadowMenu: Constructs a root menu node populated with the given modules.
ShadowMenuIterator - Class in org.scijava.menu: Recursive iterator for ShadowMenu hierarchies.
ShadowMenuIterator(ShadowMenu) - Constructor for class org.scijava.menu.ShadowMenuIterator
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.
show() - Method in class org.scijava.ui.AbstractUserInterface
show(Object) - Method in class org.scijava.ui.AbstractUserInterface
show(String, Object) - Method in class org.scijava.ui.AbstractUserInterface
show(Display<?>) - Method in class org.scijava.ui.AbstractUserInterface
show() - Method in interface org.scijava.ui.console.ConsolePane: Makes the console visible.
show(Object) - Method in class org.scijava.ui.DefaultUIService
show(String, Object) - Method in class org.scijava.ui.DefaultUIService
show(Display<?>) - Method in class org.scijava.ui.DefaultUIService
show(Object) - Method in interface org.scijava.ui.UIService: Creates a Display for the given object, and shows it using an appropriate UI widget of the default user interface.
show(String, Object) - Method in interface org.scijava.ui.UIService: Creates a Display for the given object, and shows it using an appropriate UI widget of the default user interface.
show(Display<?>) - Method in interface org.scijava.ui.UIService: Creates and shows the given Display using an appropriate UI widget of the default user interface.
show() - Method in interface org.scijava.ui.UserInterface: Shows the UI.
show(Object) - Method in interface org.scijava.ui.UserInterface: Shows the object onscreen using an appropriate UI widget.
show(String, Object) - Method in interface org.scijava.ui.UserInterface: Shows the object onscreen using an appropriate UI widget.
show(Display<?>) - Method in interface org.scijava.ui.UserInterface: Shows the display onscreen using an appropriate UI widget.
showContextMenu(String, Display<?>, int, int) - Method in class org.scijava.ui.DefaultUIService
showContextMenu(String, Display<?>, int, int) - Method in interface org.scijava.ui.UIService: Displays a popup context menu for the given display at the specified position.
showContextMenu(String, Display<?>, int, int) - Method in interface org.scijava.ui.UserInterface: Displays a popup context menu for the given display at the specified position.
showDialog(String) - Method in class org.scijava.ui.DefaultUIService
showDialog(String, DialogPrompt.MessageType) - Method in class org.scijava.ui.DefaultUIService
showDialog(String, DialogPrompt.MessageType, DialogPrompt.OptionType) - Method in class org.scijava.ui.DefaultUIService
showDialog(String, String) - Method in class org.scijava.ui.DefaultUIService
showDialog(String, String, DialogPrompt.MessageType) - Method in class org.scijava.ui.DefaultUIService
showDialog(String, String, DialogPrompt.MessageType, DialogPrompt.OptionType) - Method in class org.scijava.ui.DefaultUIService
showDialog(String) - Method in interface org.scijava.ui.UIService: Displays a dialog prompt.
showDialog(String, DialogPrompt.MessageType) - Method in interface org.scijava.ui.UIService: Displays a dialog prompt.
showDialog(String, DialogPrompt.MessageType, DialogPrompt.OptionType) - Method in interface org.scijava.ui.UIService: Displays a dialog prompt.
showDialog(String, String) - Method in interface org.scijava.ui.UIService: Displays a dialog prompt.
showDialog(String, String, DialogPrompt.MessageType) - Method in interface org.scijava.ui.UIService: Displays a dialog prompt.
showDialog(String, String, DialogPrompt.MessageType, DialogPrompt.OptionType) - Method in interface org.scijava.ui.UIService: Displays a dialog prompt.
showDisplay(boolean) - Method in interface org.scijava.ui.viewer.DisplayWindow: Places this component into the desktop environment.
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.
showUI() - Method in class org.scijava.ui.DefaultUIService
showUI(String) - Method in class org.scijava.ui.DefaultUIService
showUI(UserInterface) - Method in class org.scijava.ui.DefaultUIService
showUI() - Method in interface org.scijava.ui.UIService: Displays the UI for the default user interface.
showUI(String) - Method in interface org.scijava.ui.UIService: Displays the UI with the given name (or class name).
showUI(UserInterface) - Method in interface org.scijava.ui.UIService: Displays the given UI.
SIENNA - Static variable in class org.scijava.util.Colors
SILVER - Static variable in class org.scijava.util.Colors
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.display.AbstractDisplay
size() - Method in class org.scijava.menu.ShadowMenu
size() - Method in class org.scijava.object.ObjectIndex
size() - Method in class org.scijava.util.AbstractPrimitiveArray
size() - Method in class org.scijava.util.LastRecentlyUsed
size() - Method in interface org.scijava.util.Sizable
skip(long) - Method in class org.scijava.io.AbstractDataHandle
skip(long) - Method in interface org.scijava.io.DataHandle: Skips over and discards n bytes of data from the stream.
skip(long) - Method in class org.scijava.io.DataHandleInputStream
skipBytes(int) - Method in class org.scijava.io.FileHandle
SKYBLUE - Static variable in class org.scijava.util.Colors
SLATEBLUE - Static variable in class org.scijava.util.Colors
SLATEGRAY - Static variable in class org.scijava.util.Colors
SLATEGREY - Static variable in class org.scijava.util.Colors
SLIDER_STYLE - Static variable in interface org.scijava.widget.NumberWidget: Widget style for slider with spinner.
SNOW - Static variable in class org.scijava.util.Colors
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
sourceClass() - Method in class org.scijava.convert.ConversionRequest
sourceObject() - Method in class org.scijava.convert.ConversionRequest
sourceType() - Method in class org.scijava.convert.ConversionRequest
SPINNER_STYLE - Static variable in interface org.scijava.widget.NumberWidget: Widget style for spinner only.
SPRINGGREEN - Static variable in class org.scijava.util.Colors
start(boolean) - Static method in class org.scijava.util.Timing
stateEquals(Object) - Method in class org.scijava.util.MersenneTwisterFast
statementTerminate() - Method in interface org.scijava.script.CodeGenerator
statementTerminate() - Method in class org.scijava.script.CodeGeneratorJava
status() - Method in class org.scijava.AbstractGateway
status() - Method in interface org.scijava.Gateway: Gets this application context's StatusService.
StatusBar - Interface in org.scijava.ui: Common interface for status bars, which have a text area and progress bar, similar to ImageJ 1.x.
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
STEELBLUE - Static variable in class org.scijava.util.Colors
stop(Timing) - Static method in class org.scijava.util.Timing
STRICT_PROPERTY - Static variable in class org.scijava.Context: System property indicating whether the context should fail fast when attempting to instantiate a required service which is invalid or missing.
string(byte[]) - Static method in class org.scijava.util.DigestUtils: Converts the given byte array to a string.
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
StringUtils - Class in org.scijava.util: Useful methods for working with Strings.
stripFilenameVersion(String) - Static method in class org.scijava.util.FileUtils
stripNulls(String) - Static method in class org.scijava.util.StringUtils: Removes null bytes from a string.
subList(int, int) - Method in class org.scijava.display.AbstractDisplay
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(LinkedList<String>) - Method in class org.scijava.command.console.RunArgument
supports(LinkedList<String>) - Method in class org.scijava.console.SystemPropertyArgument
supports(ConversionRequest) - Method in class org.scijava.convert.AbstractConverter
supports(Object, Class<?>) - Method in interface org.scijava.convert.ConvertService
supports(Object, Type) - Method in interface org.scijava.convert.ConvertService
supports(Class<?>, Class<?>) - Method in interface org.scijava.convert.ConvertService: Deprecated.
Use ConvertService.supports(Object, Class)
supports(Class<?>, Type) - Method in interface org.scijava.convert.ConvertService: Deprecated.
Use ConvertService.supports(Object, Type)
supports(Object, Class<?>) - Method in class org.scijava.convert.DefaultConvertService
supports(Class<?>, Class<?>) - Method in class org.scijava.convert.DefaultConvertService
supports(Object, Type) - Method in class org.scijava.convert.DefaultConvertService
supports(Class<?>, Type) - Method in class org.scijava.convert.DefaultConvertService
supports(String) - Method in class org.scijava.io.AbstractIOPlugin
supports(LinkedList<String>) - Method in class org.scijava.io.console.OpenArgument
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(ScriptLanguage) - Method in class org.scijava.script.AbstractScriptHeader
supports(File) - Method in class org.scijava.text.AbstractTextFormat
supports(File) - Method in interface org.scijava.text.TextService: Gets whether the given file contains text data in a supported format.
supports(T) - Method in interface org.scijava.Typed: Gets whether this object is compatible with the given data object.
supports(LinkedList<String>) - Method in class org.scijava.ui.console.UIArgument
supports(D, Display<?>) - Method in class org.scijava.ui.dnd.AbstractDragAndDropHandler
supports(DragAndDropData, Display<?>) - Method in class org.scijava.ui.dnd.DefaultDragAndDropService
supports(Object, Display<?>) - Method in class org.scijava.ui.dnd.DefaultDragAndDropService
supports(D, Display<?>) - Method in interface org.scijava.ui.dnd.DragAndDropHandler: Gets whether this handler supports dropping the given data object onto the specified display.
supports(D) - Method in interface org.scijava.ui.dnd.DragAndDropHandler: Gets whether this handler supports dropping the given data object onto a compatible display.
supports(DragAndDropData, Display<?>) - Method in interface org.scijava.ui.dnd.DragAndDropService: Checks whether the given DragAndDropData can be dropped onto the specified display.
supports(Object, Display<?>) - Method in interface org.scijava.ui.dnd.DragAndDropService: Checks whether the given object can be dropped onto the specified display.
supports(File) - Method in class org.scijava.ui.dnd.FileDragAndDropHandler
supports(List<?>, Display<?>) - Method in class org.scijava.ui.dnd.ListDragAndDropHandler
supports(File) - Method in class org.scijava.ui.dnd.ScriptFileDragAndDropHandler
supports(InputWidget<?, ?>) - Method in class org.scijava.widget.AbstractInputPanel
supports(WidgetModel) - Method in class org.scijava.widget.AbstractInputWidget
supports(InputWidget<?, ?>) - Method in interface org.scijava.widget.InputPanel: Gets whether the given widget would be appropriate for the given panel.
supports(WidgetModel) - Method in interface org.scijava.widget.InputWidget: Gets whether this widget would be appropriate for the given model.
supportsData(DragAndDropData) - Method in class org.scijava.ui.dnd.AbstractDragAndDropHandler
supportsData(DragAndDropData, Display<?>) - Method in class org.scijava.ui.dnd.AbstractDragAndDropHandler
supportsData(DragAndDropData) - Method in interface org.scijava.ui.dnd.DragAndDropHandler: Gets whether this handler supports dropping the given DragAndDropData onto a compatible display.
supportsData(DragAndDropData, Display<?>) - Method in interface org.scijava.ui.dnd.DragAndDropHandler: Gets whether this handler supports dropping the given DragAndDropData onto the specified display.
supportsDisplay(Display<?>) - Method in class org.scijava.ui.dnd.AbstractDragAndDropHandler
supportsDisplay(Display<?>) - Method in interface org.scijava.ui.dnd.DragAndDropHandler: Gets whether this handler supports dropping an assumed-to-be-compatible data object onto the given Display.
supportsObject(Object) - Method in class org.scijava.ui.dnd.AbstractDragAndDropHandler
supportsObject(Object, Display<?>) - Method in class org.scijava.ui.dnd.AbstractDragAndDropHandler
supportsObject(Object) - Method in interface org.scijava.ui.dnd.DragAndDropHandler: Gets whether this handler supports dropping the given object onto a compatible display.
supportsObject(Object, Display<?>) - Method in interface org.scijava.ui.dnd.DragAndDropHandler: Gets whether this handler supports dropping the given object onto the specified display.
supportsOpen(String) - Method in class org.scijava.io.AbstractIOPlugin
supportsOpen(String) - Method in interface org.scijava.io.IOPlugin: Checks whether the I/O plugin can open data from the given source.
supportsOpen(String) - Method in class org.scijava.script.io.ScriptIOPlugin
supportsOpen(String) - Method in class org.scijava.text.io.TextIOPlugin
supportsSave(String) - Method in class org.scijava.io.AbstractIOPlugin
supportsSave(Object, String) - Method in class org.scijava.io.AbstractIOPlugin
supportsSave(String) - Method in interface org.scijava.io.IOPlugin: Checks whether the I/O plugin can save data to the given destination.
supportsSave(Object, String) - Method in interface org.scijava.io.IOPlugin: Checks whether the I/O plugin can save the given data to the specified destination.
swap(short) - Static method in class org.scijava.util.Bytes
swap(char) - Static method in class org.scijava.util.Bytes
swap(int) - Static method in class org.scijava.util.Bytes
swap(long) - Static method in class org.scijava.util.Bytes
swap(float) - Static method in class org.scijava.util.Bytes
swap(double) - Static method in class org.scijava.util.Bytes
SystemClipboard - Interface in org.scijava.ui: UI agnostic representation of the system clipboard.
SystemPropertyArgument - Class in org.scijava.console: Handles the -D command line argument, in an analogous way to tools such as Java and Maven.
SystemPropertyArgument() - Constructor for class org.scijava.console.SystemPropertyArgument

T

TAN - Static variable in class org.scijava.util.Colors
TEAL - Static variable in class org.scijava.util.Colors
TestUtils - Class in org.scijava.test: A bunch of helpful functions for unit tests.
TestUtils() - Constructor for class org.scijava.test.TestUtils
text() - Method in class org.scijava.AbstractGateway
text() - Method in interface org.scijava.Gateway: Gets this application context's TextService.
TextDisplay - Interface in org.scijava.display: Interface for text Displays.
TextDisplayPanel - Interface in org.scijava.ui.viewer.text: This is a panel that can go inside a display window.
TextDisplayViewer - Interface in org.scijava.ui.viewer.text: A display viewer for Strings.
TextFormat - Interface in org.scijava.text: TextFormat is a plugin that provides handling for a text markup language.
TextIOPlugin - Class in org.scijava.text.io: IOPlugin for text conversion to HTML.
TextIOPlugin() - Constructor for class org.scijava.text.io.TextIOPlugin
TextService - Interface in org.scijava.text: Interface for service that works with text formats.
TextWidget - Interface in org.scijava.widget: Widget interface for text fields and areas.
THISTLE - Static variable in class org.scijava.util.Colors
thread() - Method in class org.scijava.AbstractGateway
thread() - Method in interface org.scijava.Gateway: Gets this application context's ThreadService.
THREAD_COUNT - Static variable in class org.scijava.util.MirrorWebsite
ThreadService - Interface in org.scijava.thread: Interface for the thread handling service.
ThreadService.ThreadContext - Enum in org.scijava.thread
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.display.AbstractDisplay
toArray(U[]) - Method in class org.scijava.display.AbstractDisplay
toArray() - Method in class org.scijava.menu.ShadowMenu
toArray(T[]) - Method in class org.scijava.menu.ShadowMenu
toArray() - Method in class org.scijava.object.ObjectIndex
toArray(T[]) - Method in class org.scijava.object.ObjectIndex
toArray() - Method in class org.scijava.util.LastRecentlyUsed
toArray(S[]) - Method in class org.scijava.util.LastRecentlyUsed
toCollection(Object) - Static method in class org.scijava.util.ArrayUtils: Converts the provided Object to a Collection implementation.
toDouble(byte[], int, int, boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first len bytes of a byte array beyond the given offset to a double.
toDouble(byte[], int, boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first 8 bytes of a byte array beyond the given offset to a double.
toDouble(byte[], boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first 8 bytes of a byte array to a double.
toDouble(short[], int, int, boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first len bytes of a byte array beyond the given offset to a double.
toDouble(short[], int, boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first 8 bytes of a byte array beyond the given offset to a double.
toDouble(short[], boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first 8 bytes of a byte array to a double.
toFloat(byte[], int, int, boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first len bytes of a byte array beyond the given offset to a float.
toFloat(byte[], int, boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first 4 bytes of a byte array beyond a given offset to a float.
toFloat(byte[], boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first 4 bytes of a byte array to a float.
toFloat(short[], int, int, boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first len bytes of a byte array beyond a given offset to a float.
toFloat(short[], int, boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first 4 bytes of a byte array beyond a given offset to a float.
toFloat(short[], boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first 4 bytes of a byte array to a float.
ToggleWidget - Interface in org.scijava.widget: Widget interface for boolean toggles.
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.
toHTMLColor() - Method in class org.scijava.util.ColorRGB: Convert this ColorRGB to a string in the format specified by CSS Color Module Level 3 - W3C Recommendation 07 June 2011.
toInt(byte[], int, int, boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first len bytes of a byte array beyond the given offset to an int.
toInt(byte[], int, boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first 4 bytes of a byte array beyond the given offset to an int.
toInt(byte[], boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first 4 bytes of a byte array to an int.
toInt(short[], int, int, boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first len bytes of a byte array beyond the given offset to an int.
toInt(short[], int, boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first 4 bytes of a byte array beyond the given offset to an int.
toInt(short[], boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first 4 bytes of a byte array to an int.
toLong(byte[], int, int, boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first len bytes of a byte array beyond the given offset to a long.
toLong(byte[], int, boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first 8 bytes of a byte array beyond the given offset to a long.
toLong(byte[], boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first 8 bytes of a byte array to a long.
toLong(short[], int, int, boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first len bytes of a byte array beyond the given offset to a long.
toLong(short[], int, boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first 8 bytes of a byte array beyond the given offset to a long.
toLong(short[], boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first 8 bytes of a byte array to a long.
TOMATO - Static variable in class org.scijava.util.Colors
toMillis(int) - Method in class org.scijava.util.TunePlayer: Converts the given note length to milliseconds, by the current tempo.
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.
tool() - Method in class org.scijava.AbstractGateway
tool() - Method in interface org.scijava.Gateway: Gets this application context's ToolService.
Tool - Interface in org.scijava.tool: Interface for tools.
ToolActivatedEvent - Class in org.scijava.tool.event: An event indicating a tool has been activated.
ToolActivatedEvent(Tool) - Constructor for class org.scijava.tool.event.ToolActivatedEvent
ToolBar - Interface in org.scijava.ui: Common interface for tool bars, which are button bars with selectable tools, similar to ImageJ 1.x.
ToolDeactivatedEvent - Class in org.scijava.tool.event: An event indicating a tool has been deactivated.
ToolDeactivatedEvent(Tool) - Constructor for class org.scijava.tool.event.ToolDeactivatedEvent
ToolEvent - Class in org.scijava.tool.event: An event indicating something has happened to a tool.
ToolEvent(Tool) - Constructor for class org.scijava.tool.event.ToolEvent
ToolService - Interface in org.scijava.tool: Interface for service that tracks available tools.
toShort(byte[], int, int, boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first len bytes of a byte array beyond the given offset to a short.
toShort(byte[], int, boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first 2 bytes of a byte array beyond the given offset to a short.
toShort(byte[], boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first 2 bytes of a byte array to a short.
toShort(short[], int, int, boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first len bytes of a byte array beyond the given offset to a short.
toShort(short[], int, boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first 2 bytes of a byte array beyond the given offset to a short.
toShort(short[], boolean) - Static method in class org.scijava.util.Bytes: Translates up to the first 2 bytes of a byte array to a short.
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.command.CommandInfo
toString() - Method in class org.scijava.command.CommandModule
toString() - Method in class org.scijava.console.OutputEvent
toString() - Method in class org.scijava.display.AbstractDisplay
toString() - Method in class org.scijava.display.event.DisplayEvent
toString() - Method in class org.scijava.display.event.input.InputEvent
toString() - Method in class org.scijava.display.event.input.KyEvent
toString() - Method in class org.scijava.display.event.input.MsButtonEvent
toString() - Method in class org.scijava.display.event.window.WinEvent
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.io.event.IOEvent
toString() - Method in class org.scijava.menu.ShadowMenu
toString() - Method in class org.scijava.MenuEntry
toString() - Method in class org.scijava.module.AbstractModuleItem
toString() - Method in class org.scijava.module.event.ModuleEvent
toString() - Method in class org.scijava.module.event.ModuleProcessEvent
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.options.event.OptionsEvent
toString() - Method in class org.scijava.platform.event.AppFocusEvent
toString() - Method in class org.scijava.platform.event.AppMenusCreatedEvent
toString() - Method in class org.scijava.platform.event.AppSleepEvent
toString() - Method in class org.scijava.platform.event.AppUserSessionEvent
toString() - Method in class org.scijava.platform.event.AppVisibleEvent
toString() - Method in class org.scijava.plugin.AbstractRichPlugin
toString() - Method in class org.scijava.plugin.PluginInfo
toString() - Method in class org.scijava.script.AbstractScriptLanguage
toString() - Method in class org.scijava.service.AbstractService
toString() - Method in class org.scijava.tool.event.ToolEvent
toString() - Method in class org.scijava.ui.dnd.event.DragAndDropEvent
toString() - Method in class org.scijava.ui.dnd.event.DragEnterEvent
toString() - Method in class org.scijava.ui.dnd.event.DropEvent
toString() - Method in class org.scijava.ui.dnd.MIMEType
toString() - Method in class org.scijava.ui.event.UIEvent
toString() - Method in class org.scijava.util.ColorRGB
toString() - Method in class org.scijava.util.IntCoords
toString() - Method in class org.scijava.util.IntRect
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.RealCoords
toString() - Method in class org.scijava.util.RealRect
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
TunePlayer - Class in org.scijava.util: Any QBasic fans out there? ;-)
TunePlayer() - Constructor for class org.scijava.util.TunePlayer
TunePlayer(int) - Constructor for class org.scijava.util.TunePlayer
TURQUOISE - Static variable in class org.scijava.util.Colors
type - Variable in class org.scijava.script.ParameterObject
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

ui() - Method in class org.scijava.ui.AbstractUIInputWidget
ui(String) - Method in class org.scijava.ui.AbstractUIInputWidget
UI_PROPERTY - Static variable in interface org.scijava.ui.UIService: System property to set for overriding the default UI.
UIArgument - Class in org.scijava.ui.console: Handles the --ui command line argument.
UIArgument() - Constructor for class org.scijava.ui.console.UIArgument
UIComponent<C> - Interface in org.scijava.widget: An interface identifying an object housed within a UI component.
UIDetails - Interface in org.scijava: An interface defining details useful for generating relevant user interface elements.
UIEvent - Class in org.scijava.ui.event: An event indicating activity relating to a UserInterface.
UIEvent(UserInterface) - Constructor for class org.scijava.ui.event.UIEvent
UIPreprocessor - Class in org.scijava.ui: The UI preprocessor automatically populates module UserInterface inputs with the UIService's default UI instance, if compatible.
UIPreprocessor() - Constructor for class org.scijava.ui.UIPreprocessor
UIService - Interface in org.scijava.ui: Interface for service that handles user interfaces.
UIShownEvent - Class in org.scijava.ui.event: An event indicating a user interface was shown.
UIShownEvent(UserInterface) - Constructor for class org.scijava.ui.event.UIShownEvent
uncaughtException(Thread, Throwable) - Method in class org.scijava.log.DefaultUncaughtExceptionHandler
UnimplementedCommand - Class in org.scijava.command: A command that is not yet implemented.
UnimplementedCommand() - Constructor for class org.scijava.command.UnimplementedCommand
UnitUtils - Class in org.scijava.util: Utility methods for working with units.
unpack(long, byte[], int, int, boolean) - Static method in class org.scijava.util.Bytes: Translates nBytes of the given long and places the result in the given byte array.
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.
update(EventService) - Method in class org.scijava.command.CommandInfo
update(ModuleItem<T>, T) - Method in class org.scijava.command.InteractiveCommand
update() - Method in class org.scijava.display.AbstractDisplay
update() - Method in interface org.scijava.display.Display: Updates and redraws the display onscreen.
update(ModuleInfo) - Method in class org.scijava.menu.ShadowMenu: Updates the menu structure to reflect changes in the given module.
update(EventService) - Method in class org.scijava.module.AbstractModuleInfo
update(EventService) - Method in interface org.scijava.module.ModuleInfo: Notifies interested parties that the module info has been modified.
updateAll(Collection<? extends ModuleInfo>) - Method in class org.scijava.menu.ShadowMenu: Updates the menu structure to reflect changes in the given modules.
updateAnnotationIndex(ClassLoader) - Static method in class org.scijava.annotations.EclipseHelper: Updates the annotation index in the current Eclipse project.
updateInput(ModuleItem<?>) - Method in class org.scijava.command.InteractiveCommand
updateModel() - Method in class org.scijava.widget.AbstractInputWidget
updateModel() - Method in interface org.scijava.widget.InputWidget: Updates the model to reflect the latest widget state.
updateTitle() - Method in class org.scijava.ui.viewer.AbstractDisplayViewer
upOctave() - Method in class org.scijava.util.TunePlayer
URILocation - Class in org.scijava.io: Location backed by a URI string.
URILocation(URI) - Constructor for class org.scijava.io.URILocation
URILocation(String) - Constructor for class org.scijava.io.URILocation
URLLocation - Class in org.scijava.io: Location backed by a URL.
URLLocation(URL) - Constructor for class org.scijava.io.URLLocation
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.
UserInterface - Interface in org.scijava.ui: An end-user SciJava application user interface.

V

Validated - Interface in org.scijava: An object whose validity can be confirmed after initialization.
ValidityPreprocessor - Class in org.scijava.module.process: A preprocessor plugin that verifies module validity.
ValidityPreprocessor() - Constructor for class org.scijava.module.process.ValidityPreprocessor
ValidityProblem - Exception in org.scijava: An exception used to record a validity problem with a Validated object.
ValidityProblem() - Constructor for exception org.scijava.ValidityProblem
ValidityProblem(String) - Constructor for exception org.scijava.ValidityProblem
ValidityProblem(String, Throwable) - Constructor for exception org.scijava.ValidityProblem
ValidityProblem(Throwable) - Constructor for exception org.scijava.ValidityProblem
value - Variable in class org.scijava.script.ParameterObject
valueOf(String) - Static method in enum org.scijava.console.OutputEvent.Source: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.scijava.display.event.DisplayUpdatedEvent.DisplayUpdateLevel: Returns the enum constant of this type with the specified name.
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.
valueOf(String) - Static method in enum org.scijava.thread.ThreadService.ThreadContext: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.scijava.ui.Arrangeable.Arrangement: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.scijava.ui.DialogPrompt.MessageType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.scijava.ui.DialogPrompt.OptionType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.scijava.ui.DialogPrompt.Result: Returns the enum constant of this type with the specified name.
values() - Static method in enum org.scijava.console.OutputEvent.Source: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.scijava.display.event.DisplayUpdatedEvent.DisplayUpdateLevel: Returns an array containing the constants of this enum type, in the order they are declared.
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.
values() - Static method in enum org.scijava.thread.ThreadService.ThreadContext: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.scijava.ui.Arrangeable.Arrangement: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.scijava.ui.DialogPrompt.MessageType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.scijava.ui.DialogPrompt.OptionType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.scijava.ui.DialogPrompt.Result: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in class org.scijava.util.Colors: Gets the list of all preset colors.
verbose - Static variable in class org.scijava.util.CheckSezpoz: Deprecated.
Versioned - Interface in org.scijava: An object that knows its version.
VersionUtils - Class in org.scijava.util: Useful methods for retrieving versions from JARs and POMs associated with Class objects.
VersionUtils() - Constructor for class org.scijava.util.VersionUtils
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.
view(DisplayWindow, Display<?>) - Method in class org.scijava.ui.viewer.AbstractDisplayViewer
view(DisplayWindow, Display<?>) - Method in interface org.scijava.ui.viewer.DisplayViewer: Begins viewing the given display.
VIOLET - Static variable in class org.scijava.util.Colors

W

waitFor(Future<M>) - Method in class org.scijava.module.DefaultModuleService
waitFor(Future<M>) - Method in interface org.scijava.module.ModuleService: Blocks until the given module is finished executing.
walkHistory(String, boolean) - Method in class org.scijava.script.DefaultScriptInterpreter
walkHistory(String, boolean) - Method in interface org.scijava.script.ScriptInterpreter: Obtains the next/previous command in the command history.
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
WelcomeEvent - Class in org.scijava.welcome.event: Marker SciJavaEvent indicating the first time an application is run.
WelcomeEvent() - Constructor for class org.scijava.welcome.event.WelcomeEvent
WelcomeService - Interface in org.scijava.welcome: Interface for services to display the welcome greeting when the UI is shown for the first time.
WHEAT - Static variable in class org.scijava.util.Colors
WHITE - Static variable in class org.scijava.util.Colors
WHITESMOKE - Static variable in class org.scijava.util.Colors
widget() - Method in class org.scijava.AbstractGateway
widget() - Method in interface org.scijava.Gateway: Gets this application context's WidgetService.
WidgetModel - Interface in org.scijava.widget: The backing data model for a particular InputWidget.
widgets - Variable in class org.scijava.widget.AbstractInputPanel: Table of widgets.
WidgetService - Interface in org.scijava.widget: Interface for services that manage available InputWidgets.
width - Variable in class org.scijava.util.IntRect
width - Variable in class org.scijava.util.RealRect
WinActivatedEvent - Class in org.scijava.display.event.window: An event indicating a display window has been activated.
WinActivatedEvent(Display<?>, Object) - Constructor for class org.scijava.display.event.window.WinActivatedEvent
WinClosedEvent - Class in org.scijava.display.event.window: An event indicating a display window has been closed.
WinClosedEvent(Display<?>, Object) - Constructor for class org.scijava.display.event.window.WinClosedEvent
WinClosingEvent - Class in org.scijava.display.event.window: An event indicating a display window is in the process of closing.
WinClosingEvent(Display<?>, Object) - Constructor for class org.scijava.display.event.window.WinClosingEvent
WinDeactivatedEvent - Class in org.scijava.display.event.window: An event indicating a display window has been deactivated.
WinDeactivatedEvent(Display<?>, Object) - Constructor for class org.scijava.display.event.window.WinDeactivatedEvent
WinDeiconifiedEvent - Class in org.scijava.display.event.window: An event indicating a display window was deiconified.
WinDeiconifiedEvent(Display<?>, Object) - Constructor for class org.scijava.display.event.window.WinDeiconifiedEvent
WINDOW_LABEL - Static variable in class org.scijava.menu.MenuConstants
WINDOW_MNEMONIC - Static variable in class org.scijava.menu.MenuConstants
WINDOW_WEIGHT - Static variable in class org.scijava.menu.MenuConstants
WinEvent - Class in org.scijava.display.event.window: An event indicating something has happened to a display window.
WinEvent(Display<?>, Object) - Constructor for class org.scijava.display.event.window.WinEvent
WinIconifiedEvent - Class in org.scijava.display.event.window: An event indicating a display window was iconified.
WinIconifiedEvent(Display<?>, Object) - Constructor for class org.scijava.display.event.window.WinIconifiedEvent
WinOpenedEvent - Class in org.scijava.display.event.window: An event indicating a display window has been opened.
WinOpenedEvent(Display<?>, Object) - Constructor for class org.scijava.display.event.window.WinOpenedEvent
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
write(int) - Method in class org.scijava.console.MultiOutputStream
write(byte[], int, int) - Method in class org.scijava.console.MultiOutputStream
write(ByteBuffer) - Method in class org.scijava.io.AbstractDataHandle
write(ByteBuffer, int) - Method in class org.scijava.io.AbstractDataHandle
write(ByteBuffer) - Method in interface org.scijava.io.DataHandle: Writes up to buf.remaining() bytes of data from the given ByteBuffer to the stream.
write(ByteBuffer, int) - Method in interface org.scijava.io.DataHandle: Writes up to len bytes of data from the given ByteBuffer to the stream.
write(int) - Method in class org.scijava.io.DataHandleOutputStream
write(byte[]) - Method in class org.scijava.io.DataHandleOutputStream
write(byte[], int, int) - Method in class org.scijava.io.DataHandleOutputStream
write(byte[]) - Method in class org.scijava.io.FileHandle
write(byte[], int, int) - Method in class org.scijava.io.FileHandle
write(int) - Method in class org.scijava.io.FileHandle
write(int) - Method in class org.scijava.util.LineOutputStream: Adds a single byte to the current line buffer, or LineOutputStream.flush() the current line if it is a new-line character.
write(byte[]) - Method in class org.scijava.util.LineOutputStream: Adds bytes to the current line buffer.
write(byte[], int, int) - Method in class org.scijava.util.LineOutputStream: Adds bytes to the current line buffer.
writeBoolean(boolean) - Method in class org.scijava.io.FileHandle
writeByte(int) - Method in class org.scijava.io.FileHandle
writeBytes(String) - Method in class org.scijava.io.FileHandle
writeChar(int) - Method in class org.scijava.io.FileHandle
writeChars(String) - Method in class org.scijava.io.FileHandle
writeDouble(double) - Method in class org.scijava.io.FileHandle
writeFile(File, byte[]) - Static method in class org.scijava.util.FileUtils: Writes the given byte array to the specified file.
writeFloat(float) - Method in class org.scijava.io.FileHandle
writeHistory() - Method in class org.scijava.script.DefaultScriptInterpreter
writeHistory() - Method in interface org.scijava.script.ScriptInterpreter: Persists the history of the current script interpreter.
writeInt(int) - Method in class org.scijava.io.FileHandle
writeLong(long) - Method in class org.scijava.io.FileHandle
writeMap(PrintStream, Object...) - Method in class org.scijava.annotations.AbstractIndexWriter
writer - Variable in class org.scijava.script.AbstractScriptContext
writeShort(int) - Method in class org.scijava.io.FileHandle
writeState(DataOutputStream) - Method in class org.scijava.util.MersenneTwisterFast: Writes the entire state of the MersenneTwister RNG to the stream
writeUTF(String) - Method in class org.scijava.io.FileHandle
writeXMLFile(Document, File) - Static method in class org.scijava.util.CheckSezpoz: Deprecated.

X

x - Variable in class org.scijava.util.IntCoords
x - Variable in class org.scijava.util.IntRect
x - Variable in class org.scijava.util.RealCoords
x - Variable in class org.scijava.util.RealRect
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.

Y

y - Variable in class org.scijava.util.IntCoords
y - Variable in class org.scijava.util.IntRect
y - Variable in class org.scijava.util.RealCoords
y - Variable in class org.scijava.util.RealRect
YELLOW - Static variable in class org.scijava.util.Colors
YELLOWGREEN - Static variable in class org.scijava.util.Colors

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