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

A

aboutIcon - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaMenuBar
Icon to be shown in about box.
aboutIcon - Variable in class de.unihalle.informatik.Alida.gui.ALDChooseOpNameFrame
Icon to be shown in about box.
accept(File) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow.DataTabFileFilter
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDFileDirectoryDataIOSwing.FileDirectoryDataIOPanel
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorConfigWindow
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParametrizedClassConfigWindow
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentTextField
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow.TableConfigWindow
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaFrame
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaMenuBar
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab.ContextMenuGraph
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab.ContextMenuNodeEdge
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.Alida.gui.ALDBatchOperatorResultFrame
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.Alida.gui.ALDChooseOpNameFrame
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Validate the operator parameters by requesting values from the panels.
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorParamDisplayFrame
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorResultFrame
 
actionPosition_x - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab.WorkflowModifyAction
 
actionPosition_y - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab.WorkflowModifyAction
 
actionsOnWorkflow - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
List of actions performed on the Alida workflow object.
activateBatchMode - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
Checkbox for enabling/disabling batch mode.
addALDConfigurationEventListener(ALDConfigurationEventListener) - Method in class de.unihalle.informatik.Alida.operator.ALDOperatorControllable
 
addALDConfigurationEventListener(ALDConfigurationEventListener) - Method in interface de.unihalle.informatik.Alida.operator.events.ALDConfigurationEventReporter
Adds a listener to this reporter.
addALDControlEventListener(ALDControlEventListener) - Method in class de.unihalle.informatik.Alida.operator.ALDOperatorControllable
 
addALDControlEventListener(ALDControlEventListener) - Method in interface de.unihalle.informatik.Alida.operator.events.ALDControlEventReporter
Adds a listener to this reporter.
addALDWorkflowClassEventListener(ALDWorkflowClassEventListener) - Static method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Add a listener for events thrown by the class ALDWorkflow (not an instance).
addALDWorkflowEventListener(ALDWorkflowEventListener) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
 
addALDWorkflowEventListener(ALDWorkflowEventListener) - Method in interface de.unihalle.informatik.Alida.workflows.events.ALDWorkflowEventReporter
Adds a listener to this reporter.
addCloseButtonPanel() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Adds set of control buttons to the input panel.
addContextSpecificButtonPanel() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Adds set of control buttons to the input panel.
addContextSpecificButtonPanel() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
Adds set of control buttons to the input panel.
additionalOperators(ALDAOperator.Level) - Method in class de.unihalle.informatik.Alida.gui.ALDChooseOpNameFrame
This method may be overridden in extending classes to add operators to the list of available operators.
addNewWorkflow() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
Adds a new workflow (tab) to the workbench.
addNodeToWorkflow(ALDOperatorLocation) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
 
addParameter(ALDOpParameterDescriptor) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Add a new parameter to this workflow.
addParameterChangeEventListener(ALDOpParameterChangeEventListener) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Adds a listener to this reporter.
addValueChangeEventListener(ALDSwingValueChangeListener) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.events.ALDSwingValueChangeReporter
Adds a listener to this reporter.
ALD_EXTENSION - Static variable in class de.unihalle.informatik.Alida.operator.ALDPortHashAccess
File extension of Alida processing history files.
ALDAOperator - Annotation Type in de.unihalle.informatik.Alida.annotations
ALDOperators may be annotated with this annotation in order to enable generic execution or documentation facilities for the operator.
ALDAOperator.ExecutionMode - Enum in de.unihalle.informatik.Alida.annotations
Enumerates the different types of user interfaces to be automatically generated for this operator.
ALDAOperator.Level - Enum in de.unihalle.informatik.Alida.annotations
Enumerates the different levels of this operator.
ALDArrayMean - Class in de.unihalle.informatik.Alida.demo
Operator returning the mean value of an 1D array.
ALDArrayMean() - Constructor for class de.unihalle.informatik.Alida.demo.ALDArrayMean
Default constructor.
ALDArrayMean(Double[]) - Constructor for class de.unihalle.informatik.Alida.demo.ALDArrayMean
Constructor.
ALDArrayMin - Class in de.unihalle.informatik.Alida.demo
Operator returning the minimum value of an 1D array.
ALDArrayMin() - Constructor for class de.unihalle.informatik.Alida.demo.ALDArrayMin
Default constructor.
ALDArrayMin(Double[]) - Constructor for class de.unihalle.informatik.Alida.demo.ALDArrayMin
Constructor.
ALDArraySum - Class in de.unihalle.informatik.Alida.demo
Operator returning the sum of an 1D array.
ALDArraySum() - Constructor for class de.unihalle.informatik.Alida.demo.ALDArraySum
Default constructor.
ALDArraySum(Double[]) - Constructor for class de.unihalle.informatik.Alida.demo.ALDArraySum
Constructor.
ALDBatchInputIterator - Interface in de.unihalle.informatik.Alida.batch.provider.input
Super class for all input providers in Alida batch mode.
ALDBatchInputIteratorSwing - Interface in de.unihalle.informatik.Alida.batch.provider.input.swing
Interface for Alida's automatic batch data I/O via GUIs based on Swing.
ALDBatchInputManager - Class in de.unihalle.informatik.Alida.batch
Class to manage data inputs in batch processing with operators.
ALDBatchInputManager() - Constructor for class de.unihalle.informatik.Alida.batch.ALDBatchInputManager
Default constructor.
ALDBatchInputManagerSwing - Class in de.unihalle.informatik.Alida.batch
This class implements a batch provider mangager for batch processing in the context of graphical user interfaces.
ALDBatchInputManagerSwing.ProviderInteractionLevel - Enum in de.unihalle.informatik.Alida.batch
Levels to enable/disable interactive provider behaviour.
ALDBatchInputNativeArray1DSwing - Class in de.unihalle.informatik.Alida.batch.provider.input.swing
Implementation of ALDBatchInputIteratorSwing for native 1D arrays.
ALDBatchInputNativeArray1DSwing() - Constructor for class de.unihalle.informatik.Alida.batch.provider.input.swing.ALDBatchInputNativeArray1DSwing
 
ALDBatchInputNumberSwing - Class in de.unihalle.informatik.Alida.batch.provider.input.swing
Implementation of ALDBatchInputIteratorSwing for numbers and strings.
ALDBatchInputNumberSwing() - Constructor for class de.unihalle.informatik.Alida.batch.provider.input.swing.ALDBatchInputNumberSwing
 
ALDBatchInputProvider - Annotation Type in de.unihalle.informatik.Alida.annotations
Annotation for classes acting as Alida batch input providers and implementing the ALDBatchInputIterator interface.
ALDBatchIOException - Exception in de.unihalle.informatik.Alida.exceptions
Exception thrown in batch mode data IO contexts.
ALDBatchIOException() - Constructor for exception de.unihalle.informatik.Alida.exceptions.ALDBatchIOException
 
ALDBatchIOManagerException - Exception in de.unihalle.informatik.Alida.exceptions
Alida exception thrown by batch I/O managers.
ALDBatchIOManagerException(ALDBatchIOManagerException.ALDBatchIOManagerExceptionType, String) - Constructor for exception de.unihalle.informatik.Alida.exceptions.ALDBatchIOManagerException
Constructor.
ALDBatchIOManagerException.ALDBatchIOManagerExceptionType - Enum in de.unihalle.informatik.Alida.exceptions
Possible exception types.
ALDBatchIOProviderException - Exception in de.unihalle.informatik.Alida.exceptions
Alida exception thrown by batch data IO providers.
ALDBatchIOProviderException(ALDBatchIOProviderException.ALDBatchIOProviderExceptionType, String) - Constructor for exception de.unihalle.informatik.Alida.exceptions.ALDBatchIOProviderException
Constructor.
ALDBatchIOProviderException.ALDBatchIOProviderExceptionType - Enum in de.unihalle.informatik.Alida.exceptions
Possible exception types.
ALDBatchOperatorResultFrame - Class in de.unihalle.informatik.Alida.gui
Frame to display results of a batch run of an operator.
ALDBatchOperatorResultFrame(ALDOperator, HashMap<String, ALDBatchRunResultInfo>, ALDBatchOutputManagerSwing.ProviderInteractionLevel) - Constructor for class de.unihalle.informatik.Alida.gui.ALDBatchOperatorResultFrame
Constructor.
ALDBatchOutputManager - Class in de.unihalle.informatik.Alida.batch
Class to manage data outputs in batch processing with operators.
ALDBatchOutputManager() - Constructor for class de.unihalle.informatik.Alida.batch.ALDBatchOutputManager
Default constructor.
ALDBatchOutputManagerSwing - Class in de.unihalle.informatik.Alida.batch
This class implements a DataIO manager for summarizing batch results in the context of graphical user interfaces.
ALDBatchOutputManagerSwing.ProviderInteractionLevel - Enum in de.unihalle.informatik.Alida.batch
Levels to enable/disable interactive provider behaviour.
ALDBatchOutputProvider - Annotation Type in de.unihalle.informatik.Alida.annotations
Annotation for classes acting as Alida batch output providers and implementing the ALDBatchOutputSummarizer interface.
ALDBatchOutputSummarizer - Interface in de.unihalle.informatik.Alida.batch.provider.output
Super class for all output summarizers in Alida batch mode.
ALDBatchOutputSummarizerSwing - Interface in de.unihalle.informatik.Alida.batch.provider.output.swing
Interface for Alida's automatic batch result data I/O via GUI based on Swing.
ALDBatchRunResultInfo - Class in de.unihalle.informatik.Alida.batch
Info object summarizing all result data of a batch run.
ALDBatchRunResultInfo() - Constructor for class de.unihalle.informatik.Alida.batch.ALDBatchRunResultInfo
Default constructor, should/can never be called from external.
ALDBatchRunResultInfo(String) - Constructor for class de.unihalle.informatik.Alida.batch.ALDBatchRunResultInfo
Constructor.
ALDCalcMean - Class in de.unihalle.informatik.Alida.demo
Operator for calculating the mean of given double values.
ALDCalcMean() - Constructor for class de.unihalle.informatik.Alida.demo.ALDCalcMean
Default constructor.
ALDCalcMean(Double[]) - Constructor for class de.unihalle.informatik.Alida.demo.ALDCalcMean
Constructor.
ALDCalcMeanArray - Class in de.unihalle.informatik.Alida.demo
Operator for calculating the mean of given double values.
ALDCalcMeanArray() - Constructor for class de.unihalle.informatik.Alida.demo.ALDCalcMeanArray
Default constructor.
ALDCalcMeanArray(Double[]) - Constructor for class de.unihalle.informatik.Alida.demo.ALDCalcMeanArray
Constructor.
ALDChooseOpNameFrame - Class in de.unihalle.informatik.Alida.gui
Main window for selecting Alida annotated operators for running.
ALDChooseOpNameFrame() - Constructor for class de.unihalle.informatik.Alida.gui.ALDChooseOpNameFrame
Constructor.
ALDChooseOpNameFrame.MyMouseAdapter - Class in de.unihalle.informatik.Alida.gui
Local MouseAdapter class.
ALDChooseOpNameFrame.MyMouseAdapter() - Constructor for class de.unihalle.informatik.Alida.gui.ALDChooseOpNameFrame.MyMouseAdapter
Constructor.
ALDClassInfo - Class in de.unihalle.informatik.Alida.helpers
 
ALDClassInfo() - Constructor for class de.unihalle.informatik.Alida.helpers.ALDClassInfo
 
ALDClassParameter - Annotation Type in de.unihalle.informatik.Alida.annotations
Member variables of classes annotated with ALDParametrizedClass may be annotated with this annotation to be automatically handled by Alida's data I/O.
ALDClusterExperiment - Class in de.unihalle.informatik.Alida.demo
Demo operator to cluster experimental data.
ALDClusterExperiment() - Constructor for class de.unihalle.informatik.Alida.demo.ALDClusterExperiment
Default constructor.
ALDClusterExperiment(ExperimentalData) - Constructor for class de.unihalle.informatik.Alida.demo.ALDClusterExperiment
Constructor.
ALDCollectionDataIOCmdline - Class in de.unihalle.informatik.Alida.dataio.provider.cmdline
DataIO provider for collections from command line.
ALDCollectionDataIOCmdline() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDCollectionDataIOCmdline
 
ALDCollectionDataIOHelper - Class in de.unihalle.informatik.Alida.dataio.provider.helpers
Class supplying support for generic loading/saving of Collections in Alida.
ALDCollectionDataIOHelper() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.helpers.ALDCollectionDataIOHelper
 
ALDCollectionDataIOSwing - Class in de.unihalle.informatik.Alida.dataio.provider.swing
Class for generic loading/saving of collections from/to GUI in Alida.
ALDCollectionDataIOSwing() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing
 
ALDCollectionDataIOXmlbeans - Class in de.unihalle.informatik.Alida.dataio.provider.xmlbeans
DataIO provider for collections xml using xmlbeans.
ALDCollectionDataIOXmlbeans() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.xmlbeans.ALDCollectionDataIOXmlbeans
 
ALDConcReadWeakHashMap - Class in de.unihalle.informatik.Alida.helpers
A version of Hashtable that supports concurrent reading/exclusive writing.
ALDConcReadWeakHashMap(int) - Constructor for class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
Constructs a new, empty map with the specified initial capacity and default load factor.
ALDConcReadWeakHashMap() - Constructor for class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
Constructs a new, empty map with a default initial capacity and load factor.
ALDConcReadWeakHashMap.BarrierLock - Class in de.unihalle.informatik.Alida.helpers
A Serializable class for barrier lock.
ALDConcReadWeakHashMap.BarrierLock() - Constructor for class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap.BarrierLock
 
ALDConfigurationEvent - Class in de.unihalle.informatik.Alida.operator.events
Event type to configure operator execution.
ALDConfigurationEvent(Object) - Constructor for class de.unihalle.informatik.Alida.operator.events.ALDConfigurationEvent
Constructor.
ALDConfigurationEvent(Object, String) - Constructor for class de.unihalle.informatik.Alida.operator.events.ALDConfigurationEvent
Constructor with message.
ALDConfigurationEventListener - Interface in de.unihalle.informatik.Alida.operator.events
Listener interface for `Alida` configuration events.
ALDConfigurationEventReporter - Interface in de.unihalle.informatik.Alida.operator.events
Interface for classes that generate events of type `ALDConfigurationEvent`.
ALDConfigurationValidator - Interface in de.unihalle.informatik.Alida.datatypes
A class implementing this interface provides methods to determine proper configuration of an object.
ALDControlEvent - Class in de.unihalle.informatik.Alida.operator.events
Event type for controlling operator threads.
ALDControlEvent(Object, ALDControlEvent.ALDControlEventType) - Constructor for class de.unihalle.informatik.Alida.operator.events.ALDControlEvent
Default constructor.
ALDControlEvent(Object, ALDControlEvent.ALDControlEventType, String) - Constructor for class de.unihalle.informatik.Alida.operator.events.ALDControlEvent
Default constructor with arguments.
ALDControlEvent.ALDControlEventType - Enum in de.unihalle.informatik.Alida.operator.events
Event types on which a controllable operator should react.
ALDControlEventListener - Interface in de.unihalle.informatik.Alida.operator.events
Listener interface for `Alida` control events.
ALDControlEventReporter - Interface in de.unihalle.informatik.Alida.operator.events
Interface for classes that generate events of type `ALDControlEvent`.
ALDData - Class in de.unihalle.informatik.Alida.operator
This is the abstract class from which all data classes have to be derived which want properties to be recored when returned from an operator as result.
ALDData() - Constructor for class de.unihalle.informatik.Alida.operator.ALDData
Create a data object.
ALDDataConverter - Interface in de.unihalle.informatik.Alida.dataconverter
Super class for all data converter providers in Alida.
ALDDataConverterException - Exception in de.unihalle.informatik.Alida.exceptions
Alida exception thrown by data type converters.
ALDDataConverterException(ALDDataConverterException.ALDDataIOProviderExceptionType, String) - Constructor for exception de.unihalle.informatik.Alida.exceptions.ALDDataConverterException
Constructor.
ALDDataConverterException.ALDDataIOProviderExceptionType - Enum in de.unihalle.informatik.Alida.exceptions
Possible exception types.
ALDDataConverterManager - Class in de.unihalle.informatik.Alida.dataconverter
This class implements a provider manager for data conversion.
ALDDataConverterManager.ALDSourceTargetClassPair - Class in de.unihalle.informatik.Alida.dataconverter
A pair of source and target pair (of a converter)
ALDDataConverterManager.ALDSourceTargetClassPair(Class<?>, Class<?>) - Constructor for class de.unihalle.informatik.Alida.dataconverter.ALDDataConverterManager.ALDSourceTargetClassPair
 
ALDDataConverterManagerException - Exception in de.unihalle.informatik.Alida.exceptions
 
ALDDataConverterManagerException(ALDProviderManagerException.ALDProviderManagerExceptionType, String) - Constructor for exception de.unihalle.informatik.Alida.exceptions.ALDDataConverterManagerException
 
ALDDataConverterProvider - Annotation Type in de.unihalle.informatik.Alida.annotations
Annotation for classes acting as Alida data conversion provider and implementing the ALDDataConverter interface.
ALDDataIO - Interface in de.unihalle.informatik.Alida.dataio.provider
This is the interface for Alida's dataIO provider.
ALDDataIOCmdline - Interface in de.unihalle.informatik.Alida.dataio.provider
This is the interface for Alida's dataIO provider from command line.
ALDDataIOException - Exception in de.unihalle.informatik.Alida.exceptions
Exception thrown in data IO contexts.
ALDDataIOException() - Constructor for exception de.unihalle.informatik.Alida.exceptions.ALDDataIOException
 
ALDDataIOManager - Class in de.unihalle.informatik.Alida.dataio
Class to manage data input and output in Alida.
ALDDataIOManager() - Constructor for class de.unihalle.informatik.Alida.dataio.ALDDataIOManager
Default constructor.
ALDDataIOManagerCmdline - Class in de.unihalle.informatik.Alida.dataio
This class implements a DataIO manager for reading/writing from command line.
ALDDataIOManagerException - Exception in de.unihalle.informatik.Alida.exceptions
Alida exception thrown by data IO managers.
ALDDataIOManagerException(ALDDataIOManagerException.ALDDataIOManagerExceptionType, String) - Constructor for exception de.unihalle.informatik.Alida.exceptions.ALDDataIOManagerException
Constructor.
ALDDataIOManagerException.ALDDataIOManagerExceptionType - Enum in de.unihalle.informatik.Alida.exceptions
Possible exception types.
ALDDataIOManagerSwing - Class in de.unihalle.informatik.Alida.dataio
This class implements a DataIO mangager for reading/writing from a graphical user interface.
ALDDataIOManagerSwing.ProviderInteractionLevel - Enum in de.unihalle.informatik.Alida.dataio
Levels to enable/disable interactive provider behaviour.
ALDDataIOManagerXmlbeans - Class in de.unihalle.informatik.Alida.dataio
This class implements a DataIO manager for reading/writing from xml using xmlbeans.
ALDDataIOProvider - Annotation Type in de.unihalle.informatik.Alida.annotations
Annotation for classes acting as Alida data I/O provider and implementing the ALDDataIO interface.
ALDDataIOProviderException - Exception in de.unihalle.informatik.Alida.exceptions
Alida exception thrown by data IO providers.
ALDDataIOProviderException(ALDDataIOProviderException.ALDDataIOProviderExceptionType, String) - Constructor for exception de.unihalle.informatik.Alida.exceptions.ALDDataIOProviderException
Constructor.
ALDDataIOProviderException.ALDDataIOProviderExceptionType - Enum in de.unihalle.informatik.Alida.exceptions
Possible exception types.
ALDDataIOSwing - Interface in de.unihalle.informatik.Alida.dataio.provider
Interface for Alida's automatic data I/O via GUIs based on Swing.
ALDDataIOXmlbeans - Interface in de.unihalle.informatik.Alida.dataio.provider
This is the interface for Alida's dataIO provider from xml using xmlbeans.
ALDDataPort - Class in de.unihalle.informatik.Alida.operator
A data port acts as the reference for a data object in the processing history.
ALDDataPort(Object) - Constructor for class de.unihalle.informatik.Alida.operator.ALDDataPort
Create a data port for an object.
ALDDemoOpControllable - Class in de.unihalle.informatik.Alida.demo
Controllable demo operator for testing interaction.
ALDDemoOpControllable() - Constructor for class de.unihalle.informatik.Alida.demo.ALDDemoOpControllable
Default constructor.
ALDDerivedClass - Annotation Type in de.unihalle.informatik.Alida.annotations
Each Class annotated with this annotation will enable Alida's DataIO mechanism to find the class as extending another class.
ALDDirectoryString - Class in de.unihalle.informatik.Alida.datatypes
Class for representing a directory path.
ALDDirectoryString(String) - Constructor for class de.unihalle.informatik.Alida.datatypes.ALDDirectoryString
Default constructor.
ALDEdge - Class in de.unihalle.informatik.Alida.operator
This class is used to represent edges of the processing history during construction of the explicit history graph.
ALDEnumDataIOCmdline - Class in de.unihalle.informatik.Alida.dataio.provider.cmdline
DataIO provider for enumerations from command line.
ALDEnumDataIOCmdline() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDEnumDataIOCmdline
 
ALDEnumDataIOSwing - Class in de.unihalle.informatik.Alida.dataio.provider.swing
Class for generic loading/saving of enumerations via GUI in Alida.
ALDEnumDataIOSwing() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.ALDEnumDataIOSwing
 
ALDEnumDataIOXmlbeans - Class in de.unihalle.informatik.Alida.dataio.provider.xmlbeans
DataIO provider for enumerations xml using xmlbeans.
ALDEnumDataIOXmlbeans() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.xmlbeans.ALDEnumDataIOXmlbeans
 
ALDEnvironmentConfig - Class in de.unihalle.informatik.Alida.helpers
Helper class to access environment variables and properties.
ALDEnvironmentConfig() - Constructor for class de.unihalle.informatik.Alida.helpers.ALDEnvironmentConfig
 
ALDEvent - Class in de.unihalle.informatik.Alida.operator.events
Super class for all events used in `Alida`.
ALDEvent(Object) - Constructor for class de.unihalle.informatik.Alida.operator.events.ALDEvent
Default constructor for events.
ALDEvent(Object, String) - Constructor for class de.unihalle.informatik.Alida.operator.events.ALDEvent
Default constructor for events with messages.
ALDException - Exception in de.unihalle.informatik.Alida.exceptions
Abstract main class for exceptions in Alida.
ALDException() - Constructor for exception de.unihalle.informatik.Alida.exceptions.ALDException
 
ALDFileDirectoryDataIOCmdline - Class in de.unihalle.informatik.Alida.dataio.provider.cmdline
DataIO provider for filenames and directory paths from command line.
ALDFileDirectoryDataIOCmdline() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDFileDirectoryDataIOCmdline
 
ALDFileDirectoryDataIOSwing - Class in de.unihalle.informatik.Alida.dataio.provider.swing
Class for loading/saving file and directory paths via GUI.
ALDFileDirectoryDataIOSwing() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.ALDFileDirectoryDataIOSwing
 
ALDFileDirectoryDataIOSwing.FileDirectoryDataIOPanel - Class in de.unihalle.informatik.Alida.dataio.provider.swing
GUI panel for IO of file and directory names.
ALDFileDirectoryDataIOSwing.FileDirectoryDataIOPanel(Field, Class<?>, Object) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.ALDFileDirectoryDataIOSwing.FileDirectoryDataIOPanel
Default constructor.
ALDFileDirectoryDataIOXmlbeans - Class in de.unihalle.informatik.Alida.dataio.provider.xmlbeans
DataIO provider for filenames and directory paths xml using xmlbeans.
ALDFileDirectoryDataIOXmlbeans() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.xmlbeans.ALDFileDirectoryDataIOXmlbeans
 
ALDFilePathManipulator - Class in de.unihalle.informatik.Alida.helpers
Class providing helpers to manipulate file and directory path names.
ALDFilePathManipulator() - Constructor for class de.unihalle.informatik.Alida.helpers.ALDFilePathManipulator
 
ALDFileString - Class in de.unihalle.informatik.Alida.datatypes
Class for representing a file path.
ALDFileString(String) - Constructor for class de.unihalle.informatik.Alida.datatypes.ALDFileString
Default constructor with file name.
ALDGrappaFrame - Class in de.unihalle.informatik.Alida.grappa
Main frame of Grappa graphical editor for Alida.
ALDGrappaFrame(Collection<ALDOperatorLocation>, Collection<ALDOperatorLocation>) - Constructor for class de.unihalle.informatik.Alida.grappa.ALDGrappaFrame
Default constructor
ALDGrappaFrame.ChooserTreeMouseAdapter - Class in de.unihalle.informatik.Alida.grappa
MouseListener for the operator tree.
ALDGrappaFrame.ChooserTreeMouseAdapter() - Constructor for class de.unihalle.informatik.Alida.grappa.ALDGrappaFrame.ChooserTreeMouseAdapter
 
ALDGrappaLinkDataIOSwing - Class in de.unihalle.informatik.Alida.grappa
Graphical component to represent Grappa links in Alida config windows.
ALDGrappaLinkDataIOSwing(String) - Constructor for class de.unihalle.informatik.Alida.grappa.ALDGrappaLinkDataIOSwing
 
ALDGrappaLinkDataIOSwing.GrappaLinkTextField - Class in de.unihalle.informatik.Alida.grappa
 
ALDGrappaLinkDataIOSwing.GrappaLinkTextField(ALDGrappaLinkDataIOSwing) - Constructor for class de.unihalle.informatik.Alida.grappa.ALDGrappaLinkDataIOSwing.GrappaLinkTextField
 
ALDGrappaMenuBar - Class in de.unihalle.informatik.Alida.grappa
Menu bar for Grappa window.
ALDGrappaMenuBar(ALDGrappaFrame, ALDOperatorChooserTree, ALDGrappaWorkbench) - Constructor for class de.unihalle.informatik.Alida.grappa.ALDGrappaMenuBar
Default constructor
ALDGrappaNodeInfo - Class in de.unihalle.informatik.Alida.grappa
Serializable object attached to nodes in Grappa to store meta information.
ALDGrappaNodeInfo() - Constructor for class de.unihalle.informatik.Alida.grappa.ALDGrappaNodeInfo
Default constructor.
ALDGrappaNodeInfo(String) - Constructor for class de.unihalle.informatik.Alida.grappa.ALDGrappaNodeInfo
Constructor with predefined name.
ALDGrappaNodeInfo(String, Integer) - Constructor for class de.unihalle.informatik.Alida.grappa.ALDGrappaNodeInfo
Operator with predefined name and ID.
ALDGrappaNodePortInfo - Class in de.unihalle.informatik.Alida.grappa
Serializable object attached to node ports to store meta information.
ALDGrappaNodePortInfo(mxCell, ALDOpParameterDescriptor) - Constructor for class de.unihalle.informatik.Alida.grappa.ALDGrappaNodePortInfo
Default constructor.
ALDGrappaNodePortInfo() - Constructor for class de.unihalle.informatik.Alida.grappa.ALDGrappaNodePortInfo
 
ALDGrappaRunner - Class in de.unihalle.informatik.Alida.tools
Main class for invoking Grappa from commandline in Alida context.
ALDGrappaRunner() - Constructor for class de.unihalle.informatik.Alida.tools.ALDGrappaRunner
 
ALDGrappaWorkbench - Class in de.unihalle.informatik.Alida.grappa
Main frame of Grappa.
ALDGrappaWorkbench(ALDGrappaFrame) - Constructor for class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
Default constructor
ALDGrappaWorkbenchGraph - Class in de.unihalle.informatik.Alida.grappa
Graph class augmented for Grappa workflows.
ALDGrappaWorkbenchGraph() - Constructor for class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchGraph
 
ALDGrappaWorkbenchTab - Class in de.unihalle.informatik.Alida.grappa
Grappa workflow graph component.
ALDGrappaWorkbenchTab(ALDGrappaWorkbench, ALDGrappaWorkbenchGraph) - Constructor for class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Default constructor.
ALDGrappaWorkbenchTab(ALDGrappaWorkbench, mxGraph, ALDWorkflow) - Constructor for class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Constructor to setup tab from given (reloaded) workflow.
ALDGrappaWorkbenchTab.ContextMenuGraph - Class in de.unihalle.informatik.Alida.grappa
Context menu for whole workbench.
ALDGrappaWorkbenchTab.ContextMenuGraph() - Constructor for class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab.ContextMenuGraph
 
ALDGrappaWorkbenchTab.ContextMenuNodeEdge - Class in de.unihalle.informatik.Alida.grappa
Context menu of nodes.
ALDGrappaWorkbenchTab.ContextMenuNodeEdge(int, int) - Constructor for class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab.ContextMenuNodeEdge
 
ALDGrappaWorkbenchTab.GraphEventListener - Class in de.unihalle.informatik.Alida.grappa
Event handler for mxGraph events.
ALDGrappaWorkbenchTab.GraphEventListener() - Constructor for class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab.GraphEventListener
 
ALDGrappaWorkbenchTab.GraphKeyListener - Class in de.unihalle.informatik.Alida.grappa
 
ALDGrappaWorkbenchTab.GraphKeyListener() - Constructor for class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab.GraphKeyListener
 
ALDGrappaWorkbenchTab.GraphMouseAdapter - Class in de.unihalle.informatik.Alida.grappa
MouseListener for the workbench.
ALDGrappaWorkbenchTab.GraphMouseAdapter() - Constructor for class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab.GraphMouseAdapter
 
ALDGrappaWorkbenchTab.ParameterChangeListener - Class in de.unihalle.informatik.Alida.grappa
 
ALDGrappaWorkbenchTab.ParameterChangeListener(ALDWorkflowNodeID) - Constructor for class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab.ParameterChangeListener
 
ALDGrappaWorkbenchTab.WorkflowModifyAction - Class in de.unihalle.informatik.Alida.grappa
 
ALDGrappaWorkbenchTab.WorkflowModifyAction() - Constructor for class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab.WorkflowModifyAction
 
ALDInputParameterTester - Class in de.unihalle.informatik.Alida.demo
Dummy operator class for demo and testing of input parameter types.
ALDInputParameterTester() - Constructor for class de.unihalle.informatik.Alida.demo.ALDInputParameterTester
Default constructor.
ALDInputPort - Class in de.unihalle.informatik.Alida.operator
Input port within an opNode.
ALDInputPort(ALDOpNode, int, String) - Constructor for class de.unihalle.informatik.Alida.operator.ALDInputPort
Construct an input port within the given opNode with index idx and descriptorName as role of the port.
ALDKmeansOp - Class in de.unihalle.informatik.Alida.demo
Demo operator clustering experimental data using k-means.
ALDKmeansOp() - Constructor for class de.unihalle.informatik.Alida.demo.ALDKmeansOp
Default constructor.
ALDKmeansOp(ExperimentalData) - Constructor for class de.unihalle.informatik.Alida.demo.ALDKmeansOp
Constructor.
ALDNativeArray1DDataIOSwing - Class in de.unihalle.informatik.Alida.dataio.provider.swing
Class for generic loading/saving of 1D-arrays from/to GUI in Alida.
ALDNativeArray1DDataIOSwing() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing
Default constructor.
ALDNativeArray2DDataIOSwing - Class in de.unihalle.informatik.Alida.dataio.provider.swing
Class for generic loading/saving of 2D-arrays from/to GUI in Alida.
ALDNativeArray2DDataIOSwing() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing
Default constructor.
ALDNativeDataIOCmdline - Class in de.unihalle.informatik.Alida.dataio.provider.cmdline
DataIO provider for primitive datatypes, Java wrapper types, and arrays (1D and 2D) from comamand line.
ALDNativeDataIOCmdline() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDNativeDataIOCmdline
 
ALDNativeDataIOSwing - Class in de.unihalle.informatik.Alida.dataio.provider.swing
Class for loading/saving primitive datatypes in Alida.
ALDNativeDataIOSwing() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeDataIOSwing
 
ALDNativeDataIOXmlbeans - Class in de.unihalle.informatik.Alida.dataio.provider.xmlbeans
DataIO provider for primitive datatypes, Java wrapper types, and arrays (1D and 2D) xml using xmlbeans.
ALDNativeDataIOXmlbeans() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.xmlbeans.ALDNativeDataIOXmlbeans
 
ALDNumberConverter - Class in de.unihalle.informatik.Alida.dataconverter
Converts numbers.
ALDNumberConverter() - Constructor for class de.unihalle.informatik.Alida.dataconverter.ALDNumberConverter
Default constructor.
ALDOperator - Class in de.unihalle.informatik.Alida.operator
This is the abstract super class for all Alida operators.
ALDOperator() - Constructor for class de.unihalle.informatik.Alida.operator.ALDOperator
This constructor initializes an operator.
ALDOperator.HidingMode - Enum in de.unihalle.informatik.Alida.operator
Determines the visibility of an operator invocation via runOp() in the processing history.
ALDOperatorChooserTree - Class in de.unihalle.informatik.Alida.gui
This class extends JTree to hold ALDOperators to choose from.
ALDOperatorChooserTree(Collection<ALDOperatorLocation>, Collection<ALDOperatorLocation>) - Constructor for class de.unihalle.informatik.Alida.gui.ALDOperatorChooserTree
Constructor.
ALDOperatorChooserTreeNode - Class in de.unihalle.informatik.Alida.gui
Class for managing nodes of the tree view.
ALDOperatorConfigurationFrame - Class in de.unihalle.informatik.Alida.gui
Frame to configure an operator.
ALDOperatorConfigurationFrame(ALDOperator) - Constructor for class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Constructs a control frame for an operator object.
ALDOperatorControlFrame - Class in de.unihalle.informatik.Alida.gui
Frame to configure and run an operator.
ALDOperatorControlFrame(ALDOperator, ALDOperatorGUIExecutionProxy) - Constructor for class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
Constructs a new control frame for an operator object.
ALDOperatorControllable - Class in de.unihalle.informatik.Alida.operator
Operator class with inherent event handling for execution control.
ALDOperatorControllable() - Constructor for class de.unihalle.informatik.Alida.operator.ALDOperatorControllable
Default constructor.
ALDOperatorControllable.OperatorControlStatus - Enum in de.unihalle.informatik.Alida.operator
Control command and/or operator status, respectively.
ALDOperatorDataIOSwing - Class in de.unihalle.informatik.Alida.dataio.provider.swing
Data IO provider for operators in GUI.
ALDOperatorDataIOSwing() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing
Default constructor.
ALDOperatorDataIOSwing.OperatorConfigWindow - Class in de.unihalle.informatik.Alida.dataio.provider.swing
Configuration window for operator.
ALDOperatorDataIOSwing.OperatorConfigWindow(ALDOperator, Class<?>, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorConfigWindow
Default constructor.
ALDOperatorException - Exception in de.unihalle.informatik.Alida.exceptions
Exception mainly thrown by ALDOperator in case of failures.
ALDOperatorException(ALDOperatorException.OperatorExceptionType, String) - Constructor for exception de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Constructor.
ALDOperatorException.OperatorExceptionType - Enum in de.unihalle.informatik.Alida.exceptions
Possible operator exception types.
ALDOperatorGUIExecutionProxy - Class in de.unihalle.informatik.Alida.gui
Manager for executing single operator and workflow objects via GUI.
ALDOperatorGUIExecutionProxy(ALDOperatorLocation) - Constructor for class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
Default constructor.
ALDOperatorGUIExecutionProxy.ParameterChangeListener - Class in de.unihalle.informatik.Alida.gui
Listener class to react on parameter value changes in config window.
ALDOperatorGUIExecutionProxy.ParameterChangeListener(ALDWorkflowNodeID) - Constructor for class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy.ParameterChangeListener
Default constructor.
ALDOperatorGUIExecutionProxy.WorkflowThreadStatus - Enum in de.unihalle.informatik.Alida.gui
Status of the associated thread to execute operator.
ALDOperatorLocation - Class in de.unihalle.informatik.Alida.operator
 
ALDOperatorLocation() - Constructor for class de.unihalle.informatik.Alida.operator.ALDOperatorLocation
Default constructor, should never be called directly!
ALDOperatorLocation.LocationType - Enum in de.unihalle.informatik.Alida.operator
 
ALDOperatorLocationType - Interface in de.unihalle.informatik.Alida.operator
Describes different types of location from which an ALDOperator may be instantiated.
ALDOperatorParamDisplayFrame - Class in de.unihalle.informatik.Alida.gui
Frame to display the operator configuration used to calculate results.
ALDOperatorParamDisplayFrame(ALDOperator, ALDDataIOManagerSwing.ProviderInteractionLevel) - Constructor for class de.unihalle.informatik.Alida.gui.ALDOperatorParamDisplayFrame
Constructor.
ALDOperatorParameterPanel - Class in de.unihalle.informatik.Alida.dataio.provider.swing.components
Panel to hold graphical elements for configuring an operator.
ALDOperatorParameterPanel(ALDOperator, Parameter.ExpertMode, boolean, ALDSwingValueChangeListener) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
Default constructor.
ALDOperatorResultFrame - Class in de.unihalle.informatik.Alida.gui
Frame with result data displayed on termination of an operator run.
ALDOperatorResultFrame(ALDOperator, ALDDataIOManagerSwing.ProviderInteractionLevel) - Constructor for class de.unihalle.informatik.Alida.gui.ALDOperatorResultFrame
Constructor.
ALDOpNode - Class in de.unihalle.informatik.Alida.operator
Each instance of this class represents an operator invocation for the implicit processing graph.
ALDOpNode(ALDOperator, ALDOperator.HidingMode) - Constructor for class de.unihalle.informatik.Alida.operator.ALDOpNode
Construct an ALDOpNode for the operator op and hidingMode
ALDOpNodePort - Class in de.unihalle.informatik.Alida.operator
Abstract class for ports residing within opNodes.
ALDOpNodePort(String, ALDOpNode, int, String) - Constructor for class de.unihalle.informatik.Alida.operator.ALDOpNodePort
Create a port for an opNode with given index within this opNode and type.
ALDOpParameterChangeEvent - Class in de.unihalle.informatik.Alida.operator.events
Event type to configure operator execution.
ALDOpParameterChangeEvent(Object) - Constructor for class de.unihalle.informatik.Alida.operator.events.ALDOpParameterChangeEvent
Constructor.
ALDOpParameterChangeEvent(Object, String) - Constructor for class de.unihalle.informatik.Alida.operator.events.ALDOpParameterChangeEvent
Constructor with message.
ALDOpParameterChangeEventListener - Interface in de.unihalle.informatik.Alida.operator.events
Listener interface for `Alida` configuration events.
ALDOpParameterDescriptor - Class in de.unihalle.informatik.Alida.operator
This class describes the parameters of an operator.
ALDOpParameterDescriptor(String, Parameter.Direction, Boolean, Class<?>, String, String, boolean, Object, Field, int, Parameter.ExpertMode) - Constructor for class de.unihalle.informatik.Alida.operator.ALDOpParameterDescriptor
Construct a descriptor
ALDOpRunner - Class in de.unihalle.informatik.Alida.tools
Generic commandline interface to run an Alida operator.
ALDOpRunner(String[]) - Constructor for class de.unihalle.informatik.Alida.tools.ALDOpRunner
Construct a ALDOpRunner using args
ALDOpRunnerGUI - Class in de.unihalle.informatik.Alida.tools
Generic graphical user interface to run Alida operators.
ALDOpRunnerGUI() - Constructor for class de.unihalle.informatik.Alida.tools.ALDOpRunnerGUI
 
ALDOutputPort - Class in de.unihalle.informatik.Alida.operator
Output port within an opNode.
ALDOutputPort(ALDOpNode, int, String) - Constructor for class de.unihalle.informatik.Alida.operator.ALDOutputPort
Construct an output port within the given opNode with index idx and descriptorName as role of the port.
ALDParameterDescriptor - Class in de.unihalle.informatik.Alida.operator
This class describes generic parameters in Alida used, e.g., in paramterized classes and operators.
ALDParameterDescriptor(String, Class<?>, String, String, boolean, Object, Field, int, Parameter.ExpertMode) - Constructor for class de.unihalle.informatik.Alida.operator.ALDParameterDescriptor
Constructor.
ALDParameterPanel - Class in de.unihalle.informatik.Alida.dataio.provider.swing.components
Class for configuring sets of parameters via GUI in Alida.
ALDParameterPanel(LinkedList<? extends ALDParameterDescriptor>, String, boolean) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
Default constructor.
ALDParameterPanel(LinkedList<? extends ALDParameterDescriptor>, String, boolean, boolean) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
Constructor.
ALDParameterTester - Class in de.unihalle.informatik.Alida.demo
Dummy operator class for demo and testing of input parameter types.
ALDParameterTester() - Constructor for class de.unihalle.informatik.Alida.demo.ALDParameterTester
Default constructor.
ALDParametrizedClass - Annotation Type in de.unihalle.informatik.Alida.annotations
Classes annotated by this annotation are handle by Alida's DataIO.
ALDParametrizedClassConfigWindow - Class in de.unihalle.informatik.Alida.dataio.provider.swing.components
Configuration window for parametrized class objects.
ALDParametrizedClassConfigWindow(Class<?>) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParametrizedClassConfigWindow
Default constructor.
ALDParametrizedClassConfigWindow(Object) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParametrizedClassConfigWindow
Default constructor.
ALDParametrizedClassConfigWindow(Object, boolean) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParametrizedClassConfigWindow
Default constructor.
ALDParametrizedClassDataIOCmdline - Class in de.unihalle.informatik.Alida.dataio.provider.cmdline
DataIO provider for parametrized classes and operators from command line.
ALDParametrizedClassDataIOCmdline() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDParametrizedClassDataIOCmdline
 
ALDParametrizedClassDataIOHelper - Class in de.unihalle.informatik.Alida.dataio.provider.helpers
Helper class to configure and handle parametrized class objects.
ALDParametrizedClassDataIOHelper() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.helpers.ALDParametrizedClassDataIOHelper
 
ALDParametrizedClassDataIOSwing - Class in de.unihalle.informatik.Alida.dataio.provider.swing
Class for generic handling of parameterized classes in GUI.
ALDParametrizedClassDataIOSwing() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.ALDParametrizedClassDataIOSwing
Default constructor.
ALDParametrizedClassDataIOXmlbeans - Class in de.unihalle.informatik.Alida.dataio.provider.xmlbeans
DataIO provider for parametrized classes and operators from command line.
ALDParametrizedClassDataIOXmlbeans() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.xmlbeans.ALDParametrizedClassDataIOXmlbeans
 
ALDParametrizedClassDummy - Class in de.unihalle.informatik.Alida.dataio.provider.helpers
This class only serves as a proxy for Alida's dataIO system to look up DataIO providers for parametrized classes.
ALDParametrizedClassDummy() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.helpers.ALDParametrizedClassDummy
 
ALDParser - Class in de.unihalle.informatik.Alida.helpers
Helper class for parsing/formatting objects for data I/O in Alida.
ALDParser() - Constructor for class de.unihalle.informatik.Alida.helpers.ALDParser
 
ALDPCAOp - Class in de.unihalle.informatik.Alida.demo
Demo operator computing the PCA for experimental data.
ALDPCAOp() - Constructor for class de.unihalle.informatik.Alida.demo.ALDPCAOp
Default constructor.
ALDPCAOp(ExperimentalData) - Constructor for class de.unihalle.informatik.Alida.demo.ALDPCAOp
Constructor.
ALDPort - Class in de.unihalle.informatik.Alida.operator
This is the abstract super class of all ports which act as proxies to receive or supply objects within a processing graph.
ALDPort(String) - Constructor for class de.unihalle.informatik.Alida.operator.ALDPort
Construct a port object
ALDPortHashAccess - Class in de.unihalle.informatik.Alida.operator
Interface to the port hash map of Alida.
ALDPortHashAccess() - Constructor for class de.unihalle.informatik.Alida.operator.ALDPortHashAccess
Constructor without function.
ALDProcessingDAG - Class in de.unihalle.informatik.Alida.operator
This class handles the construction of a processing DAG from opNode instances and writing this processing history as extended graphml to file.
ALDProcessingDAG() - Constructor for class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
 
ALDProcessingDAG.HistoryType - Enum in de.unihalle.informatik.Alida.operator
Type of the processing history to be generated.
ALDProcessingDAGException - Exception in de.unihalle.informatik.Alida.exceptions
Exception thrown in context of history graph reconstruction.
ALDProcessingDAGException(ALDProcessingDAGException.DAGExceptionType, String) - Constructor for exception de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
Constructor.
ALDProcessingDAGException.DAGExceptionType - Enum in de.unihalle.informatik.Alida.exceptions
Possible graph exception types.
ALDProviderManagerException - Exception in de.unihalle.informatik.Alida.exceptions
Alida exception thrown by batch I/O managers.
ALDProviderManagerException(ALDProviderManagerException.ALDProviderManagerExceptionType, String) - Constructor for exception de.unihalle.informatik.Alida.exceptions.ALDProviderManagerException
Constructor.
ALDProviderManagerException.ALDConverterManagerException - Class in de.unihalle.informatik.Alida.exceptions
 
ALDProviderManagerException.ALDConverterManagerException() - Constructor for class de.unihalle.informatik.Alida.exceptions.ALDProviderManagerException.ALDConverterManagerException
 
ALDProviderManagerException.ALDProviderManagerExceptionType - Enum in de.unihalle.informatik.Alida.exceptions
Possible exception types.
ALDStandardizedDataIOCmdline - Class in de.unihalle.informatik.Alida.dataio.provider.cmdline
Abstract class providing basic methods for cmdline DataIO providers according to Alida conventions.
ALDStandardizedDataIOCmdline() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDStandardizedDataIOCmdline
 
ALDStandardizedDataIOXmlbeans - Class in de.unihalle.informatik.Alida.dataio.provider.xmlbeans
Abstract class providing basic methods for xml DataIO using xmlbeans according to Alida conventions.
ALDStandardizedDataIOXmlbeans() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.xmlbeans.ALDStandardizedDataIOXmlbeans
 
ALDSummarizeArrayOp - Class in de.unihalle.informatik.Alida.demo
A abstract summarizing operator taking a 1D array as input and return a summarizing scalar.
ALDSummarizeArrayOp() - Constructor for class de.unihalle.informatik.Alida.demo.ALDSummarizeArrayOp
Default constructor.
ALDSummarizerNativeDataSwing - Class in de.unihalle.informatik.Alida.batch.provider.output.swing
Implementation of ALDBatchOutputSummarizerSwing for native data.
ALDSummarizerNativeDataSwing() - Constructor for class de.unihalle.informatik.Alida.batch.provider.output.swing.ALDSummarizerNativeDataSwing
 
ALDSwingComponent - Class in de.unihalle.informatik.Alida.dataio.provider.swing.components
Class defining Alida-specific Swing GUI components.
ALDSwingComponent() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponent
 
ALDSwingComponentCheckBox - Class in de.unihalle.informatik.Alida.dataio.provider.swing.components
Alida-specific Swing component linked to a JCheckBox.
ALDSwingComponentCheckBox() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentCheckBox
Default constructor.
ALDSwingComponentComboBox - Class in de.unihalle.informatik.Alida.dataio.provider.swing.components
Alida-specific Swing component linked to a JComboBox.
ALDSwingComponentComboBox(Vector<ALDSwingComponentComboBoxItem>) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentComboBox
Default constructor.
ALDSwingComponentComboBox.ComboBoxTooltipRenderer - Class in de.unihalle.informatik.Alida.dataio.provider.swing.components
Tooltip renderer class, adds a tooltip to each item in the combobox.
ALDSwingComponentComboBox.ComboBoxTooltipRenderer(Vector<ALDSwingComponentComboBoxItem>) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentComboBox.ComboBoxTooltipRenderer
Default constructor.
ALDSwingComponentComboBoxItem - Class in de.unihalle.informatik.Alida.dataio.provider.swing.components
Alida-specific combobox item linked to a ALDSwingComponentComboBox.
ALDSwingComponentComboBoxItem(Object, String, String) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentComboBoxItem
Default constructor.
ALDSwingComponentLabel - Class in de.unihalle.informatik.Alida.dataio.provider.swing.components
Alida-specific Swing component linked to a JLabel.
ALDSwingComponentLabel(String) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentLabel
Default constructor.
ALDSwingComponentTextField - Class in de.unihalle.informatik.Alida.dataio.provider.swing.components
Alida-specific Swing component linked to a JTextField.
ALDSwingComponentTextField(Class<?>, int) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentTextField
Default constructor.
ALDSwingValueChangeEvent - Class in de.unihalle.informatik.Alida.dataio.provider.swing.events
Event type for reporting changes of values in provider GUI elements.
ALDSwingValueChangeEvent(Object) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.events.ALDSwingValueChangeEvent
Default constructor.
ALDSwingValueChangeEvent(Object, String) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.events.ALDSwingValueChangeEvent
Default constructor with arguments.
ALDSwingValueChangeListener - Interface in de.unihalle.informatik.Alida.dataio.provider.swing.events
Listener interface for change value events reported by provider GUI elements.
ALDSwingValueChangeReporter - Class in de.unihalle.informatik.Alida.dataio.provider.swing.events
Reporter interface for change value events in Alida Swing GUI components.
ALDSwingValueChangeReporter() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.events.ALDSwingValueChangeReporter
 
ALDTableWindow - Class in de.unihalle.informatik.Alida.dataio.provider.swing.components
GUI window for displaying tables in Alida.
ALDTableWindow(DefaultTableModel) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow
Default constructor.
ALDTableWindow(DefaultTableModel, Object) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow
Default constructor.
ALDTableWindow.DataTabFileFilter - Class in de.unihalle.informatik.Alida.dataio.provider.swing.components
Internal class that realizes a FileFilter for text files where MiToBo table data is stored.
ALDTableWindow.DataTabFileFilter() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow.DataTabFileFilter
 
ALDTableWindow.TableConfigWindow - Class in de.unihalle.informatik.Alida.dataio.provider.swing.components
Window class for configuring the table appearance and export.
ALDTableWindow.TableConfigWindow() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow.TableConfigWindow
Default constructor.
ALDTableWindow.TableModelDelimiter - Enum in de.unihalle.informatik.Alida.dataio.provider.swing.components
Delimiters available when writing a model to a string or file.
ALDTransposeMatrix - Class in de.unihalle.informatik.Alida.demo
Operator for transposing matrices.
ALDTransposeMatrix() - Constructor for class de.unihalle.informatik.Alida.demo.ALDTransposeMatrix
Default constructor.
ALDTransposeMatrix(int[][]) - Constructor for class de.unihalle.informatik.Alida.demo.ALDTransposeMatrix
Constructor.
ALDVectorNativeArrayConverter - Class in de.unihalle.informatik.Alida.dataconverter
Converts 1D arrays of native data types to Vector data types.
ALDVectorNativeArrayConverter() - Constructor for class de.unihalle.informatik.Alida.dataconverter.ALDVectorNativeArrayConverter
Default constructor.
ALDVersionProvider - Class in de.unihalle.informatik.Alida.version
Info class providing version information for auto-documentation.
ALDVersionProvider() - Constructor for class de.unihalle.informatik.Alida.version.ALDVersionProvider
 
ALDVersionProviderCmdLine - Class in de.unihalle.informatik.Alida.version
Info class providing version information parsed from commandline.
ALDVersionProviderCmdLine() - Constructor for class de.unihalle.informatik.Alida.version.ALDVersionProviderCmdLine
 
ALDVersionProviderDummy - Class in de.unihalle.informatik.Alida.version
Dummy version info class always returning "unknown" as version.
ALDVersionProviderDummy() - Constructor for class de.unihalle.informatik.Alida.version.ALDVersionProviderDummy
 
ALDVersionProviderFactory - Class in de.unihalle.informatik.Alida.version
Factory for dynamic instantiation of version providers at runtime.
ALDVersionProviderFactory() - Constructor for class de.unihalle.informatik.Alida.version.ALDVersionProviderFactory
 
ALDVersionProviderGit - Class in de.unihalle.informatik.Alida.version
Version provider to extract version information from local Git repository.
ALDVersionProviderGit() - Constructor for class de.unihalle.informatik.Alida.version.ALDVersionProviderGit
 
ALDVersionProviderReleaseJar - Class in de.unihalle.informatik.Alida.version
Info class which provides Alida operators with version information from a version file distributed with the release jar archive.
ALDVersionProviderReleaseJar() - Constructor for class de.unihalle.informatik.Alida.version.ALDVersionProviderReleaseJar
 
ALDWorkflow - Class in de.unihalle.informatik.Alida.workflows
Class to model a workflow in Alida.
ALDWorkflow(String) - Constructor for class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Constructor for a workflow in a grappa context.
ALDWorkflow(String, ALDWorkflow.ALDWorkflowContextType) - Constructor for class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Constructor
ALDWorkflow() - Constructor for class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Constructor for an untitled workflow in a grappa context.
ALDWorkflow(ALDWorkflow.ALDWorkflowContextType) - Constructor for class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Constructor for an untitled workflow
ALDWorkflow.ALDWorkflowContextType - Enum in de.unihalle.informatik.Alida.workflows
workflow context types.
ALDWorkflowClassEvent - Class in de.unihalle.informatik.Alida.workflows.events
Event type related to Alida work flows.
ALDWorkflowClassEvent(Object, ALDWorkflowClassEvent.ALDWorkflowClassEventType) - Constructor for class de.unihalle.informatik.Alida.workflows.events.ALDWorkflowClassEvent
Constructor.
ALDWorkflowClassEvent(Object, ALDWorkflowClassEvent.ALDWorkflowClassEventType, Object) - Constructor for class de.unihalle.informatik.Alida.workflows.events.ALDWorkflowClassEvent
Constructor.
ALDWorkflowClassEvent(Object, ALDWorkflowClassEvent.ALDWorkflowClassEventType, String, Object) - Constructor for class de.unihalle.informatik.Alida.workflows.events.ALDWorkflowClassEvent
Constructor.
ALDWorkflowClassEvent.ALDWorkflowClassEventType - Enum in de.unihalle.informatik.Alida.workflows.events
Types of events.
ALDWorkflowClassEventListener - Interface in de.unihalle.informatik.Alida.workflows.events
Listener interface for `Alida` workflow events.
ALDWorkflowDataIOXmlbeans - Class in de.unihalle.informatik.Alida.workflows
DataIO provider for ALDWorkflow from xml using xmlbeans.
ALDWorkflowDataIOXmlbeans() - Constructor for class de.unihalle.informatik.Alida.workflows.ALDWorkflowDataIOXmlbeans
 
ALDWorkflowEdge - Class in de.unihalle.informatik.Alida.workflows
This class represents an edge within an work flow.
ALDWorkflowEdge(ALDWorkflowNode, String, ALDWorkflowNode, String) - Constructor for class de.unihalle.informatik.Alida.workflows.ALDWorkflowEdge
Create an edge with the given source and target.
ALDWorkflowEdgeID - Class in de.unihalle.informatik.Alida.workflows
Class to index a work flow edge
ALDWorkflowEvent - Class in de.unihalle.informatik.Alida.workflows.events
Event type related to Alida work flows.
ALDWorkflowEvent(Object, ALDWorkflowEvent.ALDWorkflowEventType) - Constructor for class de.unihalle.informatik.Alida.workflows.events.ALDWorkflowEvent
Constructor.
ALDWorkflowEvent(Object, ALDWorkflowEvent.ALDWorkflowEventType, Object) - Constructor for class de.unihalle.informatik.Alida.workflows.events.ALDWorkflowEvent
Constructor.
ALDWorkflowEvent(Object, ALDWorkflowEvent.ALDWorkflowEventType, String, Object) - Constructor for class de.unihalle.informatik.Alida.workflows.events.ALDWorkflowEvent
Constructor.
ALDWorkflowEvent(ALDWorkflowEvent) - Constructor for class de.unihalle.informatik.Alida.workflows.events.ALDWorkflowEvent
Constructor.
ALDWorkflowEvent.ALDWorkflowEventType - Enum in de.unihalle.informatik.Alida.workflows.events
Types of events.
ALDWorkflowEventListener - Interface in de.unihalle.informatik.Alida.workflows.events
Listener interface for `Alida` workflow events.
ALDWorkflowEventReporter - Interface in de.unihalle.informatik.Alida.workflows.events
Interface for classes that generate events of type ALDWorkflowEvent.
ALDWorkflowException - Exception in de.unihalle.informatik.Alida.exceptions
Exception mainly thrown by de.unihalle.informatik.Alida.workflow.ALDWorkflow in case of failures.
ALDWorkflowException(ALDWorkflowException.WorkflowExceptionType, String) - Constructor for exception de.unihalle.informatik.Alida.exceptions.ALDWorkflowException
Constructor.
ALDWorkflowException.WorkflowExceptionType - Enum in de.unihalle.informatik.Alida.exceptions
 
ALDWorkflowHelper - Class in de.unihalle.informatik.Alida.workflows
 
ALDWorkflowHelper() - Constructor for class de.unihalle.informatik.Alida.workflows.ALDWorkflowHelper
 
ALDWorkflowID - Class in de.unihalle.informatik.Alida.workflows
Class to index a work flow object.
ALDWorkflowID(Integer) - Constructor for class de.unihalle.informatik.Alida.workflows.ALDWorkflowID
Create an id object.
ALDWorkflowNode - Class in de.unihalle.informatik.Alida.workflows
This class represents a node in an Alida work flow.
ALDWorkflowNode(ALDWorkflow, ALDOperator) - Constructor for class de.unihalle.informatik.Alida.workflows.ALDWorkflowNode
Create a node
ALDWorkflowNode(ALDWorkflow, ALDOperator, boolean) - Constructor for class de.unihalle.informatik.Alida.workflows.ALDWorkflowNode
Create a node
ALDWorkflowNode.ALDWorkflowNodeState - Enum in de.unihalle.informatik.Alida.workflows
 
ALDWorkflowNodeID - Class in de.unihalle.informatik.Alida.workflows
Class to index a work flow node.
ALDWorkflowParameterDescriptor - Class in de.unihalle.informatik.Alida.workflows
Extends the classALDOpParameterDescriptor to hold the value of a parameter.
ALDWorkflowParameterDescriptor(ALDOpParameterDescriptor) - Constructor for class de.unihalle.informatik.Alida.workflows.ALDWorkflowParameterDescriptor
 
ALDWorkflowParameterDescriptor(String, Parameter.Direction, Boolean, Class<?>, String, String, boolean, Object, Field, int, Parameter.ExpertMode) - Constructor for class de.unihalle.informatik.Alida.workflows.ALDWorkflowParameterDescriptor
 
ALDWorkflowRunFailureInfo - Class in de.unihalle.informatik.Alida.workflows.events
This class holds information related to a run failure event
ALDWorkflowRunFailureInfo(Exception, ALDWorkflowNodeID) - Constructor for class de.unihalle.informatik.Alida.workflows.events.ALDWorkflowRunFailureInfo
 
ALDWorkflowRunFailureInfo(ALDWorkflowNodeID) - Constructor for class de.unihalle.informatik.Alida.workflows.events.ALDWorkflowRunFailureInfo
 
ALDWorkflowStorageInfo - Class in de.unihalle.informatik.Alida.workflows.events
 
ALDWorkflowStorageInfo(String, ALDWorkflow) - Constructor for class de.unihalle.informatik.Alida.workflows.events.ALDWorkflowStorageInfo
 
alidaWorkflow - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Reference to the underlying Alida workflow object.
alidaWorkflow - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
Reference to the underlying Alida workflow object.
AnalyzeExperiment - Class in de.unihalle.informatik.Alida.demo
Demo operator to cluster experimental data.
AnalyzeExperiment() - Constructor for class de.unihalle.informatik.Alida.demo.AnalyzeExperiment
Default constructor.
AnalyzeExperiment(ExperimentalData) - Constructor for class de.unihalle.informatik.Alida.demo.AnalyzeExperiment
Constructor.
applicationTreeModel - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorChooserTree
Tree of available operators for standard level.
ApplyToMatrix - Class in de.unihalle.informatik.Alida.demo
Demo operator to apply a summarizing operation to a 2D array in row or column wise fashion.
ApplyToMatrix() - Constructor for class de.unihalle.informatik.Alida.demo.ApplyToMatrix
Default constructor.
ApplyToMatrix(Double[][]) - Constructor for class de.unihalle.informatik.Alida.demo.ApplyToMatrix
Constructor.
ApplyToMatrix.SummarizeMode - Enum in de.unihalle.informatik.Alida.demo
Choose row or colum wise sum
arrayToString(Object) - Static method in class de.unihalle.informatik.Alida.helpers.ALDParser
Formats an array according to Alida data I/O conventions.

B

barrierLock - Variable in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
Lock used only for its memory effects.
batchConfigPanel - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
Configuration panel for batch mode.
batchInputIterator - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
 
batchInputParameter - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
 
batchModeActive - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
 
batchOutputParameter - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
 
batchOutputResultMap - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
 
brackets - Static variable in class de.unihalle.informatik.Alida.helpers.ALDParser
Hashmap to hold pairs of opening and closing brackets.
buttonColor_ready - Static variable in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
Default run button color of ready operators.
buttonColor_runnable - Static variable in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
Default run button color of runnable operators.
buttonColor_running - Static variable in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
Default run button color of running operators.
buttonColor_unconfigured - Static variable in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
Default run button color of unconfigured operators.

C

capacity() - Method in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
Returns the number of slots in this table.
changePanel(ALDParameterDescriptor, Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
Deprecated. 
changeViewMode(Parameter.ExpertMode) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
Switches view mode of the panel.
changeViewMode(Parameter.ExpertMode) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
Changes the view mode.
checkValue() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentTextField
Method that handles events triggered by the text field.
clear() - Method in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
Removes all mappings from the map.
clearTreeSelection() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
 
clone() - Method in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
Returns a shallow copy of this ConcurrentReaderHashMap instance.
clone() - Method in class de.unihalle.informatik.Alida.operator.ALDOpParameterDescriptor
Clone an instance
clone() - Method in class de.unihalle.informatik.Alida.operator.ALDParameterDescriptor
Clones an instance.
cloneProperties() - Method in class de.unihalle.informatik.Alida.operator.ALDData
Clone the property hash of this obejct.
closeWindow() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow
Closes the GUI table window.
comment - Variable in exception de.unihalle.informatik.Alida.exceptions.ALDException
Exception comment.
compareTo(ALDSwingComponentComboBoxItem) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentComboBoxItem
 
compCheckBox - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentCheckBox
Associated Swing component.
compComboBox - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentComboBox
Associated Swing component.
compLabel - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentLabel
Associated Swing component.
completeDAG - Variable in class de.unihalle.informatik.Alida.operator.ALDOperator
Does this operator prefer a complete DAG or a data dependency DAG.
compTextField - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentTextField
Associated Swing component.
configurationEventlistenerList - Variable in class de.unihalle.informatik.Alida.operator.ALDOperatorControllable
List of configuration event listeners attached to this reporter.
configureCollectionApplicationOps() - Static method in class de.unihalle.informatik.Alida.tools.ALDGrappaRunner
Configure collection of operators belonging to the application set.
configureCollectionStandardOps() - Static method in class de.unihalle.informatik.Alida.tools.ALDGrappaRunner
Configure collection of operators belonging to the standard set.
configureWorkflow(ALDConfigurationEvent) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
 
configWindows - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Map of node cells and their corresponding configuration windows.
containsKey(Object) - Method in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
Tests if the specified object is a key in this table.
controlEventlistenerList - Variable in class de.unihalle.informatik.Alida.operator.ALDOperatorControllable
List of control event listeners attached to this reporter.
controlWin - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
Corresponding configuration and control window.
convert(Object, Type[], Class<?>, Type[]) - Method in interface de.unihalle.informatik.Alida.dataconverter.ALDDataConverter
Convert the sourceObject into an object of class targetClass.
convert(Object, Type[], Class<?>, Type[]) - Method in class de.unihalle.informatik.Alida.dataconverter.ALDDataConverterManager
Convert the sourceObject into an object of class targetClass.
convert(ALDDataConverter, Object, Field, Class<?>, Field) - Method in class de.unihalle.informatik.Alida.dataconverter.ALDDataConverterManager
Convert the sourceObject into an object of class targetClass.
convert(Object, Field, Class<?>, Field) - Method in class de.unihalle.informatik.Alida.dataconverter.ALDDataConverterManager
 
convert(Object, Class<?>) - Method in class de.unihalle.informatik.Alida.dataconverter.ALDDataConverterManager
Convert the sourceObject into an object of class targetClass.
convert(Object, Type[], Class<?>, Type[]) - Method in class de.unihalle.informatik.Alida.dataconverter.ALDNumberConverter
 
convert(Object, Type[], Class<?>, Type[]) - Method in class de.unihalle.informatik.Alida.dataconverter.ALDVectorNativeArrayConverter
 
copy(Field) - Method in class de.unihalle.informatik.Alida.operator.ALDOpParameterDescriptor
 
copyConfiguration(ALDOperatorParameterPanel) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
TODO Function should usually not be required...
copyConfiguration(ALDParameterPanel) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
 
copyNode(ALDWorkflowNodeID, boolean, boolean) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Copy this node.
CopyOfExperimentalData - Class in de.unihalle.informatik.Alida.demo
This class is a toy implementation of experimental data for a demo of Alida's parametrized classes.
CopyOfExperimentalData() - Constructor for class de.unihalle.informatik.Alida.demo.CopyOfExperimentalData
Standard constructor is required
CopyOfExperimentalData(String, Double) - Constructor for class de.unihalle.informatik.Alida.demo.CopyOfExperimentalData
Constructor for an experiment.
CopyOfExperimentalData(String, Double, boolean) - Constructor for class de.unihalle.informatik.Alida.demo.CopyOfExperimentalData
Constructor for an experiment.
copyWorkflowNodeLinksOnly(ALDOperator, mxCell, ALDOperator, int, int) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Copies only the links of a workflow node to a new node of same type.
count - Variable in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
The total number of mappings in the hash table.
createChildWorkflow() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Add a new workflow as a child to this workflow.
createChildWorkflow(String) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Add a new workflow as a child to this workflow.
createClassLocation(String) - Static method in class de.unihalle.informatik.Alida.operator.ALDOperatorLocation
Creates and returns a new location for an class extending ALDOperator.
createCopy() - Method in class de.unihalle.informatik.Alida.workflows.events.ALDWorkflowEvent
Create a clone of this event with the same time stamp
createEdge(ALDWorkflowNodeID, String, ALDWorkflowNodeID, String) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
This method calls createEdge with the argument allowDataConversion = false.
createEdge(ALDWorkflowNodeID, String, ALDWorkflowNodeID, String, Boolean) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Add an edge representing the data flow between the parameter sourceParameterName in the operator represented by the node with sourceNodeId to the parameter targetParameterName in the operator represented by the node with targetNodeId.
createGraphmlDocument(Object) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Create the processing history for sourceObjOfHistory and convert to graphml object.
createGraphmlDocument(Object, ALDProcessingDAG.HistoryType) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Create the processing history for sourceObjOfHistory and convert to graphml object.
createGraphmlDocument(Object, ALDProcessingDAG.HistoryType, boolean) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Create the processing history for sourceObjOfHistory and convert to graphml object.
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.Alida.batch.ALDBatchInputManagerSwing
Create a gui element which may be used to request the user to input data.
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in interface de.unihalle.informatik.Alida.batch.provider.input.swing.ALDBatchInputIteratorSwing
Interface method to create a GUI element for batch data input.
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.Alida.batch.provider.input.swing.ALDBatchInputNativeArray1DSwing
 
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.Alida.batch.provider.input.swing.ALDBatchInputNumberSwing
 
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerSwing
Create a gui element which may be used to request the user to input data of class cl.
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in interface de.unihalle.informatik.Alida.dataio.provider.ALDDataIOSwing
Interface method to create a GUI element for data input.
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing
Generic reading of collections.
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDEnumDataIOSwing
Generate GUI element for generic reading of enumeration types.
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDFileDirectoryDataIOSwing
 
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing
Generic reading of 1D arrays.
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing
Generic reading of 2D arrays.
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeDataIOSwing
 
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing
 
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDParametrizedClassDataIOSwing
 
createNewWorkflowEdge(mxCell, ALDWorkflowNodeID, ALDGrappaNodePortInfo, ALDWorkflowNodeID, ALDGrappaNodePortInfo) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Adds a new edge object to the graph.
createNewWorkflowNode(ALDOperatorLocation, int, int) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Creates a new workflow node.
createNewWorkflowNode(ALDOperatorLocation) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
Creates a new workflow node.
createNode(String) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Add a new operator node to this workflow.
createNode(ALDOperatorLocation) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Add a new operator node to this workflow.
createNode(ALDOperator) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Add a new operator to this workflow.
createOperator() - Method in class de.unihalle.informatik.Alida.operator.ALDOperatorLocation
Create an ALDOperator form this location object.
createWorkflowFileLocation(String) - Static method in class de.unihalle.informatik.Alida.operator.ALDOperatorLocation
Creates and returns a new location for a file holding a work flow.

D

data - Variable in class de.unihalle.informatik.Alida.demo.ALDSummarizeArrayOp
Input 1D array
dataIOObj - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaLinkDataIOSwing.GrappaLinkTextField
 
dataIOOrder - Variable in class de.unihalle.informatik.Alida.operator.ALDParameterDescriptor
 
dataTab - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow
Data table (swing tables are nicer than imageJ tables).
dataTabModel - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow
Reference object to the data.
de.unihalle.informatik.Alida.annotations - package de.unihalle.informatik.Alida.annotations
Defines all annotations used within the Alida framework.
de.unihalle.informatik.Alida.annotations.indexing - package de.unihalle.informatik.Alida.annotations.indexing
Contains helper classes related to annotation indexing in Alida.
de.unihalle.informatik.Alida.batch - package de.unihalle.informatik.Alida.batch
Package containing classes for batch mode.
de.unihalle.informatik.Alida.batch.provider.input - package de.unihalle.informatik.Alida.batch.provider.input
Package containing input providers for batch mode.
de.unihalle.informatik.Alida.batch.provider.input.swing - package de.unihalle.informatik.Alida.batch.provider.input.swing
Package containing batch input providers for Swing GUIs.
de.unihalle.informatik.Alida.batch.provider.output - package de.unihalle.informatik.Alida.batch.provider.output
Package containing output provider classes for batch mode.
de.unihalle.informatik.Alida.batch.provider.output.swing - package de.unihalle.informatik.Alida.batch.provider.output.swing
Package containing batch output providers for Swing GUIs.
de.unihalle.informatik.Alida.dataconverter - package de.unihalle.informatik.Alida.dataconverter
 
de.unihalle.informatik.Alida.dataio - package de.unihalle.informatik.Alida.dataio
Package containing I/O related classes like managers and providers.
de.unihalle.informatik.Alida.dataio.provider - package de.unihalle.informatik.Alida.dataio.provider
Package containing data I/O providers and helpers.
de.unihalle.informatik.Alida.dataio.provider.cmdline - package de.unihalle.informatik.Alida.dataio.provider.cmdline
Package containing data I/O providers for commandline presenters.
de.unihalle.informatik.Alida.dataio.provider.helpers - package de.unihalle.informatik.Alida.dataio.provider.helpers
Package containing data I/O provider helper classes.
de.unihalle.informatik.Alida.dataio.provider.swing - package de.unihalle.informatik.Alida.dataio.provider.swing
Package containing data I/O providers for GUIs based on Java Swing.
de.unihalle.informatik.Alida.dataio.provider.swing.components - package de.unihalle.informatik.Alida.dataio.provider.swing.components
 
de.unihalle.informatik.Alida.dataio.provider.swing.events - package de.unihalle.informatik.Alida.dataio.provider.swing.events
 
de.unihalle.informatik.Alida.dataio.provider.xmlbeans - package de.unihalle.informatik.Alida.dataio.provider.xmlbeans
Package containing data I/O providers for xmlbeans presenters.
de.unihalle.informatik.Alida.datatypes - package de.unihalle.informatik.Alida.datatypes
Package containing data types defined by Alida.
de.unihalle.informatik.Alida.demo - package de.unihalle.informatik.Alida.demo
Demonstrator package of how to implement and use Alida operators.
de.unihalle.informatik.Alida.exceptions - package de.unihalle.informatik.Alida.exceptions
Defines Alida exceptions.
de.unihalle.informatik.Alida.grappa - package de.unihalle.informatik.Alida.grappa
Contains all resources for the graphical programming editor Grappa.
de.unihalle.informatik.Alida.gui - package de.unihalle.informatik.Alida.gui
Package containing GUI components for interactive operator selection/control.
de.unihalle.informatik.Alida.helpers - package de.unihalle.informatik.Alida.helpers
Contains miscellaneous helper classes used in Alida.
de.unihalle.informatik.Alida.operator - package de.unihalle.informatik.Alida.operator
Contains the core of Alida, i.e. the operator concept and processing graph stuff.
de.unihalle.informatik.Alida.operator.events - package de.unihalle.informatik.Alida.operator.events
Definitions of Alida events and corresponding reporter and listener interfaces.
de.unihalle.informatik.Alida.tools - package de.unihalle.informatik.Alida.tools
Tools for generic operator execution.
de.unihalle.informatik.Alida.version - package de.unihalle.informatik.Alida.version
Classes for handling software version information.
de.unihalle.informatik.Alida.workflows - package de.unihalle.informatik.Alida.workflows
Classes related to workflows in Alida.
de.unihalle.informatik.Alida.workflows.events - package de.unihalle.informatik.Alida.workflows.events
Contains all events appearing in context of workflows in Alida.
debug - Static variable in class de.unihalle.informatik.Alida.annotations.indexing.SezPozAdapter
For internal debugging purposes.
debug - Static variable in class de.unihalle.informatik.Alida.batch.ALDBatchInputManager
For internal debugging purposes only.
debug - Static variable in class de.unihalle.informatik.Alida.batch.ALDBatchOutputManager
For internal debugging purposes
debug - Static variable in class de.unihalle.informatik.Alida.dataio.ALDDataIOManager
For internal debugging purposes
DEFAULT_INITIAL_CAPACITY - Static variable in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
The default initial number of table slots for this table (32).
DEFAULT_LOAD_FACTOR - Static variable in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
The default load factor for this table (1.0).
defaultValue - Variable in class de.unihalle.informatik.Alida.operator.ALDParameterDescriptor
 
delimButtonSpace - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow.TableConfigWindow
Button for selecting spaces as delimiters.
delimButtonTab - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow.TableConfigWindow
Button for selecting tabs as delimiters.
delimiter - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow.TableConfigWindow
Delimiter to be used for table export to file.
DERIVEDCLASS_CHAR - Static variable in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDStandardizedDataIOCmdline
As a convention this character starts a derived class name, and is terminated by ':'
deserializeFromXmlFile(String) - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Deserializes an operator state from the given file.
direction - Variable in class de.unihalle.informatik.Alida.operator.ALDOpParameterDescriptor
 
dirPath - Variable in class de.unihalle.informatik.Alida.datatypes.ALDDirectoryString
Name of directory including full path.
disableComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDFileDirectoryDataIOSwing.FileDirectoryDataIOPanel
 
disableComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorConfigWindow
Disables the operator configuration panel.
disableComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParametrizedClassConfigWindow
Disable component to prohibit value changes.
disableComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponent
Method to disable the component, i.e. all graphical elements, to prohibit parameter changes.
disableComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentCheckBox
 
disableComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentComboBox
 
disableComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentLabel
 
disableComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentTextField
 
disableComponent() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaLinkDataIOSwing
 
disableComponents() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
Disables all components in the different sub-panels.
disableComponents() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
Disables all components in this panel.
disableStepwiseExecution() - Method in class de.unihalle.informatik.Alida.operator.events.ALDConfigurationEvent
Reset flag for step-wise execution.
disableStepwiseExecution() - Method in class de.unihalle.informatik.Alida.operator.events.ALDOpParameterChangeEvent
Reset flag for step-wise execution.
displayFailureMessageWindow(ALDWorkflowEvent) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
Displays window with detailed error information on execution failures.
displayMode - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorConfigWindow
Mode for displaying parameters.
displayMode - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Mode for displaying parameters.
dispose() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDFileDirectoryDataIOSwing.FileDirectoryDataIOPanel
 
dispose() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorConfigWindow
Disposes all resources of this window and its sub-windows.
dispose() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
Disposes all components in the different sub-panels.
dispose() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
Disposes all components in this panel.
dispose() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParametrizedClassConfigWindow
Dispose component and all sub-windows.
dispose() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponent
Releases all resources, i.e. closes all sub-windows.
dispose() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentCheckBox
 
dispose() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentComboBox
 
dispose() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentLabel
 
dispose() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentTextField
 
dispose() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaLinkDataIOSwing
 
dispose() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorResultFrame
 
doNextBatchModeStep() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
 
doNextStepInWorkflow() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
 
doStepwiseExecution() - Method in class de.unihalle.informatik.Alida.operator.events.ALDConfigurationEvent
Return flag for step-wise execution.
doStepwiseExecution() - Method in class de.unihalle.informatik.Alida.operator.events.ALDOpParameterChangeEvent
Return flag for step-wise execution.

E

enableComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDFileDirectoryDataIOSwing.FileDirectoryDataIOPanel
 
enableComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorConfigWindow
Enables the operator configuration panel.
enableComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParametrizedClassConfigWindow
Enable component to allow for value changes.
enableComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponent
Method to enable the component with all graphical elements again.
enableComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentCheckBox
 
enableComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentComboBox
 
enableComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentLabel
 
enableComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentTextField
 
enableComponent() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaLinkDataIOSwing
 
enableComponents() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
Enables all components in the different sub-panels.
enableComponents() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
Enables all components in this panel.
enableStepwiseExecution() - Method in class de.unihalle.informatik.Alida.operator.events.ALDConfigurationEvent
Set flag for step-wise execution.
enableStepwiseExecution() - Method in class de.unihalle.informatik.Alida.operator.events.ALDOpParameterChangeEvent
Set flag for step-wise execution.
eq(Object, Object) - Method in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
Check for equality of non-null references x and y.
equals(Object) - Method in class de.unihalle.informatik.Alida.dataconverter.ALDDataConverterManager.ALDSourceTargetClassPair
 
eType - Variable in class de.unihalle.informatik.Alida.operator.events.ALDControlEvent
Type of the event.
eType - Variable in class de.unihalle.informatik.Alida.workflows.events.ALDWorkflowClassEvent
Type of the event.
eType - Variable in class de.unihalle.informatik.Alida.workflows.events.ALDWorkflowEvent
Type of the event.
eventMessage - Variable in class de.unihalle.informatik.Alida.operator.events.ALDEvent
Message string, freely configurable.
execProxy - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
Reference to the surrounding workflow manager.
executeOperator(ALDOperatorLocation) - Method in class de.unihalle.informatik.Alida.gui.ALDChooseOpNameFrame
Executes the chosen operator, i.e. opens the config/control window.
ExperimentalData - Class in de.unihalle.informatik.Alida.demo
This class is a toy implementation of experimental data for a demo of Alida's parametrized classes.
ExperimentalData() - Constructor for class de.unihalle.informatik.Alida.demo.ExperimentalData
Standard constructor is required
ExperimentalData(String, Double[][]) - Constructor for class de.unihalle.informatik.Alida.demo.ExperimentalData
Constructor for an experiment.
ExperimentalData(String, Double[][], boolean) - Constructor for class de.unihalle.informatik.Alida.demo.ExperimentalData
Constructor for an experiment.
explanation - Variable in class de.unihalle.informatik.Alida.operator.ALDParameterDescriptor
 

F

failureMessageWin - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
Corresponding configuration and control window.
field - Variable in class de.unihalle.informatik.Alida.operator.ALDParameterDescriptor
 
fieldContained(String) - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Does any hash table contain the key, i.e. this field?
FILEIO_CHAR - Static variable in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDStandardizedDataIOCmdline
As a convention a parameter value starting with this character indicates that the actual parameter should be read from or writen to a file.
filePath - Variable in class de.unihalle.informatik.Alida.datatypes.ALDFileString
Name of file including complete path information.
FilterExperimentalDataOp - Class in de.unihalle.informatik.Alida.demo
Demo operator to filter experimental data.
FilterExperimentalDataOp() - Constructor for class de.unihalle.informatik.Alida.demo.FilterExperimentalDataOp
Default constructor.
FilterExperimentalDataOp(ExperimentalData) - Constructor for class de.unihalle.informatik.Alida.demo.FilterExperimentalDataOp
Constructor.
filterField - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaFrame
Text field to enter filter to select operators
filterField - Variable in class de.unihalle.informatik.Alida.gui.ALDChooseOpNameFrame
Text field to enter filter to select operators
findALDOperators(String) - Method in class de.unihalle.informatik.Alida.tools.ALDOpRunner
Find operator with given pattern among all annotated ALDOperators and return the full qualified names as a list.
findInstantiableSubclasses(Class, String) - Static method in class de.unihalle.informatik.Alida.helpers.SubclassFinder
Returns all sub-classes of T that can be instantiated, i.e.
findNodeIds(NodeType, HashMap<String, String>, int) - Static method in class de.unihalle.informatik.Alida.operator.GraphmlHelper
Insert nodeId and associated attributes into the translationTable.
findOperators(String) - Method in class de.unihalle.informatik.Alida.tools.ALDOpRunner
This method is call once to populate the member matchingClassNames.
findSubclasses(Class, String) - Static method in class de.unihalle.informatik.Alida.helpers.SubclassFinder
Returns all sub-classes of T including interfaces and abstract classes that are located in a package below startPackage.
findSubclasses(String, Class, String) - Static method in class de.unihalle.informatik.Alida.helpers.SubclassFinder
 
fireALDConfigurationEvent(ALDConfigurationEvent) - Method in class de.unihalle.informatik.Alida.operator.ALDOperatorControllable
 
fireALDConfigurationEvent(ALDConfigurationEvent) - Method in interface de.unihalle.informatik.Alida.operator.events.ALDConfigurationEventReporter
Sends an event to all registered listeners.
fireALDControlEvent(ALDControlEvent) - Method in class de.unihalle.informatik.Alida.operator.ALDOperatorControllable
 
fireALDControlEvent(ALDControlEvent) - Method in interface de.unihalle.informatik.Alida.operator.events.ALDControlEventReporter
Sends the given event to all registered listeners.
fireALDSwingValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.events.ALDSwingValueChangeReporter
Sends an event to all registered listeners.
fireALDWorkflowClassEvent(ALDWorkflowClassEvent) - Static method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Fire an event by the class ALDWorkflow.
fireALDWorkflowEvent(ALDWorkflowEvent) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
 
fireALDWorkflowEvent(ALDWorkflowEvent) - Method in interface de.unihalle.informatik.Alida.workflows.events.ALDWorkflowEventReporter
Sends the given event to all registered listeners.
fireParameterChangeEvent(ALDOpParameterChangeEvent) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Sends an event to all registered listeners.
focusGained(FocusEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentTextField
 
focusLost(FocusEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentTextField
 
formatAsString(Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDCollectionDataIOCmdline
Returns the string representations of collection.
formatAsString(Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDEnumDataIOCmdline
 
formatAsString(Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDNativeDataIOCmdline
 
formatAsString(Object, String) - Method in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDParametrizedClassDataIOCmdline
Format all parameters of this parametrized class annotated with ALDClassParameter into a string.
formatAsString(Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDParametrizedClassDataIOCmdline
Generic formatter to string of parametrized classes.
formatAsString(Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDStandardizedDataIOCmdline
Returns the string representations of this object This method is assumed to directly format the obj into the string return and make no prior interpretation regarding a file to be used.
formatAsString(Object, String) - Method in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDStandardizedDataIOCmdline
Returns the external representations of this object using a formatString.

G

GenerateGetterSetter - Class in de.unihalle.informatik.Alida.tools
Generates code for getter/setter methods for an ALDOperator.
GenerateGetterSetter() - Constructor for class de.unihalle.informatik.Alida.tools.GenerateGetterSetter
 
generateHelpMenu() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaMenuBar
Function to setup the help menu.
generateHelpMenu() - Method in class de.unihalle.informatik.Alida.gui.ALDChooseOpNameFrame
Sets up the help menu.
generateHelpMenu() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Sets up the help menu.
get(Object) - Method in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
Returns the value to which the specified key is mapped in this table.
getActionPositionX() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab.WorkflowModifyAction
 
getActionPositionY() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab.WorkflowModifyAction
 
getALDPortHashAccessKey() - Static method in class de.unihalle.informatik.Alida.operator.ALDOperator
Get a reference to the port hash access object.
getAncestors() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowNode
Return all ancestors of this node.
getAnnotatedFields(Class<?>) - Static method in class de.unihalle.informatik.Alida.dataio.provider.helpers.ALDParametrizedClassDataIOHelper
Return all fields for member variables of myclass or any of its super classes which is annotated with ALDClassParameter.
getBatchInputParameters() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
Returns selected input parameters for batch mode.
getBatchOutputParameters() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
Returns selected output parameters for batch mode.
getChildren() - Method in class de.unihalle.informatik.Alida.operator.ALDOpNode
Get the all opNode children found during back tracing.
getChildren() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowNode
Return all children nodes of this node.
getClassname() - Method in class de.unihalle.informatik.Alida.operator.ALDOpNodePort
Return the canonical classname of the ALDData associated with this port
getClassName() - Static method in class de.unihalle.informatik.Alida.version.ALDVersionProviderFactory
Returns version provider class according to environment configuration.
getClusters() - Method in class de.unihalle.informatik.Alida.demo.ALDClusterExperiment
Get value of result.
getClusters() - Method in class de.unihalle.informatik.Alida.demo.ALDKmeansOp
Get value of result.
getClusters() - Method in class de.unihalle.informatik.Alida.demo.AnalyzeExperiment
Get value of result.
getClusters() - Method in class de.unihalle.informatik.Alida.demo.SummarizeClusters
 
getCommentString() - Method in exception de.unihalle.informatik.Alida.exceptions.ALDException
Returns comment string.
getConfigValue(String, String, String) - Static method in class de.unihalle.informatik.Alida.helpers.ALDEnvironmentConfig
Gets the value of a property from the environment.
getConfigValue(String, String) - Static method in class de.unihalle.informatik.Alida.helpers.ALDEnvironmentConfig
Reads the value of the specified property from the environment.
getConstructionMode() - Static method in class de.unihalle.informatik.Alida.operator.ALDOperator
Return the current mode of implicit construction ALDOperator.constructionMode.
getConverter() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowEdge
 
getData() - Method in class de.unihalle.informatik.Alida.demo.ALDSummarizeArrayOp
Returns the 1D array
getData() - Method in class de.unihalle.informatik.Alida.demo.CopyOfExperimentalData
Return the data
getData() - Method in class de.unihalle.informatik.Alida.demo.ExperimentalData
Return the data
getDataIOOrder() - Method in class de.unihalle.informatik.Alida.operator.ALDParameterDescriptor
Returns data I/O order of parameter.
getDebug() - Static method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Return the debug state
getDefaultValue(Boolean, Boolean, ALDOpParameterDescriptor) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
Get the default for a paramter.
getDefaultValue() - Method in class de.unihalle.informatik.Alida.operator.ALDParameterDescriptor
Returns default value of parameter.
getDelimiterString() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow.TableConfigWindow
Returns the currently selected delimiter string.
getDepth() - Method in class de.unihalle.informatik.Alida.operator.ALDOpNode
Get depth.
getDescendants() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowNode
Return the nodeIds of all descendants of the given node.
getDescription() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow.DataTabFileFilter
 
getDescription() - Method in class de.unihalle.informatik.Alida.demo.CopyOfExperimentalData
Get description.
getDescription() - Method in class de.unihalle.informatik.Alida.demo.ExperimentalData
Get description.
getDescriptorName() - Method in class de.unihalle.informatik.Alida.operator.ALDOpNodePort
Return the descriptor name of the port within its opNode
getDirection() - Method in class de.unihalle.informatik.Alida.operator.ALDOpParameterDescriptor
Returns parameter direction.
getDirectlyRegisteredChildern() - Method in class de.unihalle.informatik.Alida.operator.ALDOpNode
Get the all opNode children directly registered during invocation.
getDirectoryName() - Method in class de.unihalle.informatik.Alida.datatypes.ALDDirectoryString
Returns current name of directory.
getDoNormalize() - Method in class de.unihalle.informatik.Alida.demo.ALDClusterExperiment
 
getDoPCA() - Method in class de.unihalle.informatik.Alida.demo.ALDClusterExperiment
 
getEdge(ALDWorkflowEdgeID) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Get the workflow edge associated with edgeId.
getEdge(ALDWorkflowNode, String, ALDWorkflowNode, String) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Get the workflow edge connecting given edges and parameters.
getEdgeIdDuringLoading(Integer) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Return the edgeId of the idx-th edge according to the order of the edges in the external representation resulting from (last) loading this workflow.
getEdgeIds() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Return the current collection of EdgeIds of this workflow.
getElapsedTime() - Method in class de.unihalle.informatik.Alida.demo.ApplyToMatrix
Get value of elapsedTime.
getEnvVarValue(String, String) - Static method in class de.unihalle.informatik.Alida.helpers.ALDEnvironmentConfig
Reads the value of the specified property from environment variables.
getEventMessage() - Method in class de.unihalle.informatik.Alida.operator.events.ALDEvent
Returns individual message string.
getEventMessage(int) - Method in class de.unihalle.informatik.Alida.operator.events.ALDEvent
Returns individual message string formatted to a maximal line length.
getEventQueue(ALDWorkflowEventListener) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Returns the event queue associated with the listener or null it the listener is not registered.
getEventType() - Method in class de.unihalle.informatik.Alida.operator.events.ALDControlEvent
Returns type of event.
getEventType() - Method in class de.unihalle.informatik.Alida.workflows.events.ALDWorkflowClassEvent
Returns type of event.
getEventType() - Method in class de.unihalle.informatik.Alida.workflows.events.ALDWorkflowEvent
Returns type of event.
getException() - Method in class de.unihalle.informatik.Alida.workflows.events.ALDWorkflowRunFailureInfo
 
getExceptionID() - Method in exception de.unihalle.informatik.Alida.exceptions.ALDBatchIOException
Returns string characterising exception type.
getExceptionID() - Method in exception de.unihalle.informatik.Alida.exceptions.ALDDataIOException
Returns string characterising exception type.
getExceptionID() - Method in exception de.unihalle.informatik.Alida.exceptions.ALDException
Returns string characterising exception type.
getExperiment() - Method in class de.unihalle.informatik.Alida.demo.ALDClusterExperiment
Get value of experiment.
getExperiment() - Method in class de.unihalle.informatik.Alida.demo.ALDKmeansOp
Get value of experiment.
getExperiment() - Method in class de.unihalle.informatik.Alida.demo.ALDPCAOp
Get value of experiment.
getExperiment() - Method in class de.unihalle.informatik.Alida.demo.AnalyzeExperiment
Get value of experiment.
getExperiment() - Method in class de.unihalle.informatik.Alida.demo.FilterExperimentalDataOp
Get value of experiment.
getExperiment() - Method in class de.unihalle.informatik.Alida.demo.NormalizeExperimentalDataOp
Get value of experiment.
getExperiment() - Method in class de.unihalle.informatik.Alida.demo.SummarizeClusters
Get value of experiment.
getExplanation() - Method in class de.unihalle.informatik.Alida.operator.ALDOpNodePort
Return the explanation of the port copied from the argument descriptor
getExplanation() - Method in class de.unihalle.informatik.Alida.operator.ALDParameterDescriptor
Returns explanation for parameter.
getExtension(String) - Static method in class de.unihalle.informatik.Alida.helpers.ALDFilePathManipulator
Gets extension from the filename, if any.
getFeature(int) - Method in class de.unihalle.informatik.Alida.demo.ExperimentalData
Return the i-th feature across all sub experiments.
getField() - Method in class de.unihalle.informatik.Alida.operator.ALDParameterDescriptor
Returns a reference to the field of the parameter.
getFileName() - Method in class de.unihalle.informatik.Alida.datatypes.ALDFileString
Returns current file name value.
getFileName(String) - Static method in class de.unihalle.informatik.Alida.helpers.ALDFilePathManipulator
Returns name without leading directories or file description (extension).
getFilename() - Method in class de.unihalle.informatik.Alida.workflows.events.ALDWorkflowStorageInfo
 
getGraphmlHistory() - Method in class de.unihalle.informatik.Alida.operator.ALDDataPort
Get the grahphml history of this data port
getHandlingMode() - Method in class de.unihalle.informatik.Alida.operator.ALDParameterDescriptor
Returns mode of parameter handling.
getHelpActionListener(Component, String) - Static method in class de.unihalle.informatik.Alida.gui.OnlineHelpDisplayer
Get an ActionListener linked to the Alida online help system.
getHidingMode() - Method in class de.unihalle.informatik.Alida.operator.ALDOpNode
Get hiding mode of this opNode.
getHistoryLink(Object) - Method in class de.unihalle.informatik.Alida.operator.ALDPortHashAccess
Get the port to which the object is currently linked in history.
getId() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowEdge
Return the id associated with this edge.
getId() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowNode
Return the Id associated with this node.
getId() - Method in class de.unihalle.informatik.Alida.workflows.events.ALDWorkflowClassEvent
Returns the index of the even
getId() - Method in class de.unihalle.informatik.Alida.workflows.events.ALDWorkflowEvent
Returns the index of the even
getIdentString() - Method in exception de.unihalle.informatik.Alida.exceptions.ALDBatchIOManagerException
 
getIdentString() - Method in exception de.unihalle.informatik.Alida.exceptions.ALDBatchIOProviderException
 
getIdentString() - Method in exception de.unihalle.informatik.Alida.exceptions.ALDDataConverterException
 
getIdentString() - Method in exception de.unihalle.informatik.Alida.exceptions.ALDDataIOManagerException
 
getIdentString() - Method in exception de.unihalle.informatik.Alida.exceptions.ALDDataIOProviderException
 
getIdentString() - Method in exception de.unihalle.informatik.Alida.exceptions.ALDException
Returns a (hopefully unique) identification string.
getIdentString() - Method in exception de.unihalle.informatik.Alida.exceptions.ALDOperatorException
 
getIdentString() - Method in exception de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
 
getIdentString() - Method in exception de.unihalle.informatik.Alida.exceptions.ALDProviderManagerException
 
getIdentString() - Method in exception de.unihalle.informatik.Alida.exceptions.ALDWorkflowException
 
getIdentStringWithoutType() - Method in exception de.unihalle.informatik.Alida.exceptions.ALDWorkflowException
Returns the ident string in a user-friendly format without type info.
getIncludedData() - Method in class de.unihalle.informatik.Alida.operator.ALDOpNode
Get all included data ports found during back tracing.
getInEdges() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowNode
Returns all incoming edges.
getInEdgesForParameter(String) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowNode
Return all incoming edges for this node which have their target at parameterName.
getInInoutNames() - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Get the names of in or inout parameters.
getInInoutNames(Boolean) - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Get the names of in or inout parameters.
getInNames(Boolean) - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Get the names of in parameters.
getInOutNames(Boolean) - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Get the names of inout parameters.
getInputParamIterator(String) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
Returns an iterator for a specific input parameter in batch mode.
getInputPort(int) - Method in class de.unihalle.informatik.Alida.operator.ALDOpNode
Get input port with index i of this opNode.
getInputPorts() - Method in class de.unihalle.informatik.Alida.operator.ALDOpNode
Get all input ports of this opNode.
getInstance() - Static method in class de.unihalle.informatik.Alida.batch.ALDBatchInputManagerSwing
Return the single instance of this class
getInstance() - Static method in class de.unihalle.informatik.Alida.batch.ALDBatchOutputManagerSwing
Return the single instance of this class
getInstance() - Static method in class de.unihalle.informatik.Alida.dataconverter.ALDDataConverterManager
Return the single instance of this class
getInstance() - Static method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerCmdline
Return the single instance of this class
getInstance() - Static method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerSwing
Return the single instance of this class
getInstance() - Static method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerXmlbeans
Return the single instance of this class
getItemText() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentComboBoxItem
Get textual representation of object.
getJComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDFileDirectoryDataIOSwing.FileDirectoryDataIOPanel
 
getJComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponent
Method to request the provider's GUI element.
getJComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentCheckBox
 
getJComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentComboBox
 
getJComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentLabel
 
getJComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentTextField
 
getJComponent() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaLinkDataIOSwing
 
getJPanel() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
Get access to the main panel.
getJPanel() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
Method to access associated panel.
getJVMPropValue(String, String, String) - Static method in class de.unihalle.informatik.Alida.helpers.ALDEnvironmentConfig
Reads the value of the specified property from JVM properties.
getJVMPropValue(String, String) - Static method in class de.unihalle.informatik.Alida.helpers.ALDEnvironmentConfig
Reads the value of specified property from JVM properties.
getLabel() - Method in class de.unihalle.informatik.Alida.operator.ALDParameterDescriptor
Returns label for parameter.
getLastSelectedPathComponent() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorChooserTree
 
getLevel() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorChooserTree
Return current mode of usage.
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentComboBox.ComboBoxTooltipRenderer
 
getLocation() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorChooserTreeNode
Get location object.
getLocation() - Method in class de.unihalle.informatik.Alida.operator.ALDData
Get the location property, i.e. property with key location
getLocation() - Method in class de.unihalle.informatik.Alida.operator.ALDDataPort
Get the location property, i.e. property with key location
getMappingEdgeIdToInteger() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Return the current mapping of EdgeIds to integer ids.
getMappingIntegerToEdgeId() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Return the current mapping of integer ids to EdgeIds.
getMappingIntegerToNodeId() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Return the current mapping of integer ids to NodeIds.
getMappingNodeIdToInteger() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Return the current mapping of NodeIds to integer ids.
getMatrix() - Method in class de.unihalle.informatik.Alida.demo.ApplyToMatrix
Get value of matrix.
getMessage() - Method in exception de.unihalle.informatik.Alida.exceptions.ALDException
 
getMissingRequiredInputs() - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Deprecated. 
getMissingRequiredInputs(ALDWorkflowNodeID) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Returns the names of all required input parameters of the operator object associated with the node which are not linked and have a value of null.
getMissingRequiredInputs() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowNode
Returns the names of all required input parameters of the operator object associated with the node which are not linked and have a value of null
getMyclass() - Method in class de.unihalle.informatik.Alida.operator.ALDParameterDescriptor
Returns class of parameter.
getName() - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Get the name of this operator
getName() - Method in class de.unihalle.informatik.Alida.operator.ALDOperatorLocation
Returns the proper name of this location
getName() - Method in class de.unihalle.informatik.Alida.operator.ALDOpNode
Get the name of the operator represented by this opNode.
getName() - Method in class de.unihalle.informatik.Alida.operator.ALDParameterDescriptor
Returns name of parameter.
getNewConfigWin(ALDOperator) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Generate a new configuration window.
getNewConfigWin(ALDOperator) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
Generate a new configuration window.
getNode() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaNodePortInfo
 
getNode(ALDWorkflowNodeID) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Get the workflow node associated with nodeId.
getNodeID() - Method in class de.unihalle.informatik.Alida.workflows.events.ALDWorkflowRunFailureInfo
 
getNodeIdDuringLoading(Integer) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Return the nodeId of the idx-th node according to the order of the nodes in the external representation resulting from (last) loading this workflow.
getNodeIds() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Return the current collection of NodeIds of this workflow.
getNodeName() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaNodeInfo
Returns name of node.
getNodes() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Return a collection of all nodes of this workflow
getNodeStyleString(String) - Static method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Method to properly format node style string.
getNormalizedExperiment() - Method in class de.unihalle.informatik.Alida.demo.ALDClusterExperiment
 
getNumCluster() - Method in class de.unihalle.informatik.Alida.demo.ALDKmeansOp
 
getNumComponents() - Method in class de.unihalle.informatik.Alida.demo.ALDPCAOp
 
getNumEntries() - Method in class de.unihalle.informatik.Alida.operator.ALDPortHashAccess
Returns the number of objects currently stored in the history database.
getNumExperiments() - Method in class de.unihalle.informatik.Alida.demo.ExperimentalData
Return number of sub experiments
getNumFeatures() - Method in class de.unihalle.informatik.Alida.demo.ExperimentalData
Return number of features
getNumParameters() - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Get the number of parameters
getObject() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentComboBoxItem
Get the object associated with this item.
getOperator(String) - Method in class de.unihalle.informatik.Alida.tools.ALDOpRunner
This method is called to instantiate the ALDOperator.
getOperator(ALDWorkflowNodeID) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Get the operator associated with nodeId.
getOperator() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowNode
Returns the operator associated with this node.
getOperatorClass() - Method in class de.unihalle.informatik.Alida.operator.ALDOpNode
Get the class object of the operator represented by this opNode.
getOpNameFilter() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorChooserTree
 
getOpNode() - Method in class de.unihalle.informatik.Alida.operator.ALDOpNodePort
Return the opNode of this port
getOrigin() - Method in class de.unihalle.informatik.Alida.operator.ALDPort
Get the origin of this port, which is the parent in the processing graph.
getOutEdges() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowNode
Returns all outgoing edges.
getOutEdgesForParameter(String) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowNode
Return outgoing edges for this node which have their source at parameterName.
getOutInoutNames() - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Get the names of out or inout parameters
getOutNames() - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Get the names of out parameters
getOutputPort(int) - Method in class de.unihalle.informatik.Alida.operator.ALDOpNode
Get output port with index i of this opNode.
getOutputPorts() - Method in class de.unihalle.informatik.Alida.operator.ALDOpNode
Get all output ports of this opNode.
getParameter(String) - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Get the value of a parameter specified by name.
getParameter(String) - Method in class de.unihalle.informatik.Alida.operator.ALDOpNode
Get value of parameter for given key.
getParameter(String) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
 
getParameterDescriptor(String) - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Get the parameter descriptor for given name.
getParameterHashAsXml() - Method in class de.unihalle.informatik.Alida.operator.ALDOpNode
Get the parameter hash where values of parameters.
getParameterKeys() - Method in class de.unihalle.informatik.Alida.operator.ALDOpNode
Get all keys of the parameter hash.
getParameterNames() - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Get the names of all parameters
getParameterValueVec() - Method in class de.unihalle.informatik.Alida.batch.ALDBatchRunResultInfo
Get a reference to the input parameter value vector.
getParent() - Method in class de.unihalle.informatik.Alida.operator.ALDOpNode
Get the parent opNode.
getParents() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowNode
Return all parents of this node.
getParentWorkflow() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowNode
 
getPartsOfName() - Method in class de.unihalle.informatik.Alida.operator.ALDOperatorLocation
Return the parts of the name within a hierarchy, e.g. package structure or package structure
getPath(String) - Static method in class de.unihalle.informatik.Alida.helpers.ALDFilePathManipulator
Get path.
getPortClassName() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaNodePortInfo
Returns the class name of the port/parameter datatype.
getPortDirection() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaNodePortInfo
Returns the direction of the port/parameter.
getPortExplanation() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaNodePortInfo
Returns the explanation of the port/parameter.
getPortIndex() - Method in class de.unihalle.informatik.Alida.operator.ALDOpNodePort
Return the index of the port within its opNode
getPortLabel() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaNodePortInfo
Returns the label of the port/parameter.
getPortName() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaNodePortInfo
Returns the name of the port/parameter.
getProperties() - Method in class de.unihalle.informatik.Alida.operator.ALDOpNodePort
Return the properties associated with this port which have been retrieved from the data as it passed the port.
getProperty(String) - Method in class de.unihalle.informatik.Alida.operator.ALDData
Get a property value for the given key.
getProperty(String) - Method in class de.unihalle.informatik.Alida.operator.ALDDataPort
Get a property value for the given key.
getProperty(String) - Method in class de.unihalle.informatik.Alida.operator.ALDOutputPort
Return property with key
getPropertyKeys() - Method in class de.unihalle.informatik.Alida.operator.ALDData
Get the keys of all properties set in this data object
getPropertyKeys() - Method in class de.unihalle.informatik.Alida.operator.ALDDataPort
Get the keys of all properties set in this data object
getPropertyKeys() - Method in class de.unihalle.informatik.Alida.operator.ALDOutputPort
Return all keys of the property hash of this output port
getProvider(Class<?>, Class<?>) - Method in class de.unihalle.informatik.Alida.batch.ALDBatchInputManager
Method to return an instance of the batch input provider for given class.
getProvider(Class<?>, Class<?>) - Method in class de.unihalle.informatik.Alida.batch.ALDBatchOutputManager
Method to return an instance of the batch output provider of the requested class.
getProvider(Class<?>, Type[], Class<?>, Type[]) - Method in class de.unihalle.informatik.Alida.dataconverter.ALDDataConverterManager
Method to return an instance of the data converter provider for given classes.
getProvider(Class<?>, Field, Class<?>, Field) - Method in class de.unihalle.informatik.Alida.dataconverter.ALDDataConverterManager
 
getProvider(Class, Class) - Method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManager
Method to return an instance of the DataIO provider class for the class cl which implements the requested interface interfaceRequired (which has itself to implement ALDDataIO).
getProviderInstance() - Static method in class de.unihalle.informatik.Alida.version.ALDVersionProviderFactory
Returns a reference to the currently selected provider object.
getProviderInstance(String) - Static method in class de.unihalle.informatik.Alida.version.ALDVersionProviderFactory
Returns a reference to the provider object of the specified class.
getProviderInteractionLevel() - Method in class de.unihalle.informatik.Alida.batch.ALDBatchInputManagerSwing
Returns the current level of provider interaction.
getProviderInteractionLevel() - Method in class de.unihalle.informatik.Alida.batch.ALDBatchOutputManagerSwing
Returns the current level of provider interaction.
getProviderInteractionLevel() - Method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerSwing
Returns the current level of provider interaction.
getProviderMap() - Method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManager
Method to return a clone of the mapping of classes to dataIO providers.
getRefID() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaNodeInfo
Returns the reference ID of the node.
getResult() - Method in class de.unihalle.informatik.Alida.demo.ALDPCAOp
Get value of result.
getResult() - Method in class de.unihalle.informatik.Alida.demo.FilterExperimentalDataOp
Get value of result.
getResult() - Method in class de.unihalle.informatik.Alida.demo.NormalizeExperimentalDataOp
Get value of result.
getResultDataVec() - Method in class de.unihalle.informatik.Alida.batch.ALDBatchRunResultInfo
Get a reference to the result data vector.
getResultMean() - Method in class de.unihalle.informatik.Alida.demo.ALDCalcMean
Returns the calculated mean value.
getResultMean() - Method in class de.unihalle.informatik.Alida.demo.ALDCalcMeanArray
Returns the calculated mean value.
getReturnElapsedTime() - Method in class de.unihalle.informatik.Alida.demo.ApplyToMatrix
Get value of returnElapsedTime.
getShadowNodeId() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
 
getSourceClass() - Method in class de.unihalle.informatik.Alida.dataconverter.ALDDataConverterManager.ALDSourceTargetClassPair
 
getSourceNode() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowEdge
Returns the source node.
getSourceNodeId(ALDWorkflowEdgeID) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Return the NodeId of the source node of this edge
getSourceParameterName(ALDWorkflowEdgeID) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Return the source parameter name of this edge
getSourceParameterName() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowEdge
Returns the parameter name of the source.
getSourcePort() - Method in class de.unihalle.informatik.Alida.operator.ALDEdge
Return the source port of the edge.
getState(ALDWorkflowNodeID) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Get the state of node with nodeId.
getState() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowNode
Returns the current state of this node
getStepSize() - Method in class de.unihalle.informatik.Alida.operator.events.ALDConfigurationEvent
Return desired step size.
getStepSize() - Method in class de.unihalle.informatik.Alida.operator.events.ALDOpParameterChangeEvent
Return desired step size.
getSubExperiment(int) - Method in class de.unihalle.informatik.Alida.demo.ExperimentalData
 
getSummaries() - Method in class de.unihalle.informatik.Alida.demo.ApplyToMatrix
Get value of summaries.
getSummarizeMode() - Method in class de.unihalle.informatik.Alida.demo.ApplyToMatrix
Get value of summarizeMode.
getSummarizeOp() - Method in class de.unihalle.informatik.Alida.demo.ApplyToMatrix
Get value of summarizeOp.
getSummary() - Method in class de.unihalle.informatik.Alida.demo.ALDSummarizeArrayOp
Returns the Summarizing scalar
getSummaryOfExperiment() - Method in class de.unihalle.informatik.Alida.demo.SummarizeClusters
 
getSums() - Method in class de.unihalle.informatik.Alida.demo.MatrixSum
Returns the calculated sums.
getSupplemental() - Method in class de.unihalle.informatik.Alida.operator.ALDOpParameterDescriptor
Returns if parameter is supplemental.
getSupplementalNames() - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Get the names of supplemental parameters
getTableForReading() - Method in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
Get ref to table; the reference and the cells it accesses will be at least as fresh as from last use of barrierLock
getTargetClass() - Method in class de.unihalle.informatik.Alida.dataconverter.ALDDataConverterManager.ALDSourceTargetClassPair
 
getTargetNode() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowEdge
Returns the target node.
getTargetNodeId(ALDWorkflowEdgeID) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Return the NodeId of the target node of this edge
getTargetParameterName(ALDWorkflowEdgeID) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Return the target parameter name of this edge
getTargetParameterName() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowEdge
Returns the parameter name of the target.
getTargetPort() - Method in class de.unihalle.informatik.Alida.operator.ALDEdge
Return the target port of the edge.
getText() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentTextField
Returns text of text field.
getTimeStamp() - Method in class de.unihalle.informatik.Alida.workflows.events.ALDWorkflowEvent
Returns the timestamp of this event.
getTooltip() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentComboBoxItem
Get tooltip text.
getToolTipForCell(Object) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchGraph
 
getTooltipText(Object) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Function to return tooltip text for a cell.
getToplevelGraph(GraphmlType) - Static method in class de.unihalle.informatik.Alida.operator.GraphmlHelper
Return the first element of type Graph found at the top level of the graphml object
getType() - Method in exception de.unihalle.informatik.Alida.exceptions.ALDBatchIOManagerException
Returns the type of this exception.
getType() - Method in exception de.unihalle.informatik.Alida.exceptions.ALDBatchIOProviderException
Returns the type of this exception.
getType() - Method in exception de.unihalle.informatik.Alida.exceptions.ALDDataConverterException
Returns the type of this exception.
getType() - Method in exception de.unihalle.informatik.Alida.exceptions.ALDDataIOManagerException
Returns the type of this exception.
getType() - Method in exception de.unihalle.informatik.Alida.exceptions.ALDDataIOProviderException
Returns the type of this exception.
getType() - Method in exception de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Returns the type of this exception.
getType() - Method in exception de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
Returns the type of this exception.
getType() - Method in exception de.unihalle.informatik.Alida.exceptions.ALDProviderManagerException
Returns the type of this exception.
getType() - Method in exception de.unihalle.informatik.Alida.exceptions.ALDWorkflowException
Returns the type of this exception.
getValue(Field, Object) - Static method in class de.unihalle.informatik.Alida.dataio.provider.helpers.ALDParametrizedClassDataIOHelper
Return the value of the member variable associated with field in the object obj.
getValue() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowParameterDescriptor
 
getVerbose() - Method in class de.unihalle.informatik.Alida.demo.ApplyToMatrix
Get value of verbose.
getVerbose() - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Return the verbose state of this opertor.
getVersion() - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Get the version of this operator
getVersion() - Method in class de.unihalle.informatik.Alida.operator.ALDOpNode
Get the software version.
getVersion() - Method in class de.unihalle.informatik.Alida.version.ALDVersionProvider
Returns the software version of currently running instance.
getVersion() - Method in class de.unihalle.informatik.Alida.version.ALDVersionProviderCmdLine
 
getVersion() - Method in class de.unihalle.informatik.Alida.version.ALDVersionProviderDummy
 
getVersion() - Method in class de.unihalle.informatik.Alida.version.ALDVersionProviderGit
 
getVersion() - Method in class de.unihalle.informatik.Alida.version.ALDVersionProviderReleaseJar
 
getWorkflow() - Method in class de.unihalle.informatik.Alida.workflows.events.ALDWorkflowStorageInfo
 
getWorkflowContext() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
 
getWorkflowName() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
Returns name of currently active workflow.
getWorkflowThreadStatus() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
Returns current status of workflow thread.
getWorkflowTitle() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Returns the workflow title.
graphEdgeIDs - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Map of edge cells and their corresponding Alida workflow IDs.
graphEdges - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Map of Alida workflow IDs and their corresponding edge cells.
GraphmlHelper - Class in de.unihalle.informatik.Alida.operator
This class supplies some static auxiliary methods used when explicitly constructing a history graph.
GraphmlHelper() - Constructor for class de.unihalle.informatik.Alida.operator.GraphmlHelper
 
graphNodeIDs - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Map of node cells and their corresponding Alida workflow IDs.
graphNodes - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Map of Alida workflow IDs and their corresponding node cells.
grappaMainWin - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaMenuBar
Reference to main window of grappa.
grappaMenu - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaFrame
Menubar.
guiProxys - Variable in class de.unihalle.informatik.Alida.gui.ALDChooseOpNameFrame
List of active GUI managers.

H

handleAddNodeEvent(ALDOperator, ALDWorkflowNodeID, int, int) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Adds a node to the workflow graph.
handleAddNodeEvent(ALDOperator, ALDWorkflowNodeID) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
Adds a node to the workflow graph.
handleALDConfigurationEvent(ALDConfigurationEvent) - Method in class de.unihalle.informatik.Alida.operator.ALDOperatorControllable
 
handleALDConfigurationEvent(ALDConfigurationEvent) - Method in interface de.unihalle.informatik.Alida.operator.events.ALDConfigurationEventListener
Method which is called on event occurence.
handleALDControlEvent(ALDControlEvent) - Method in class de.unihalle.informatik.Alida.operator.ALDOperatorControllable
 
handleALDControlEvent(ALDControlEvent) - Method in interface de.unihalle.informatik.Alida.operator.events.ALDControlEventListener
Method which is called on event occurence.
handleALDParameterChangeEvent(ALDOpParameterChangeEvent) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab.ParameterChangeListener
 
handleALDParameterChangeEvent(ALDOpParameterChangeEvent) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy.ParameterChangeListener
 
handleALDParameterChangeEvent(ALDOpParameterChangeEvent) - Method in interface de.unihalle.informatik.Alida.operator.events.ALDOpParameterChangeEventListener
Method which is called on event occurence.
handleALDWorkflowClassEvent(ALDWorkflowClassEvent) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
 
handleALDWorkflowClassEvent(ALDWorkflowClassEvent) - Method in interface de.unihalle.informatik.Alida.workflows.events.ALDWorkflowClassEventListener
Method which is called on event occurrence.
handleALDWorkflowEvent(ALDWorkflowEvent) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
 
handleALDWorkflowEvent(ALDWorkflowEvent) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
 
handleALDWorkflowEvent(ALDWorkflowEvent) - Method in interface de.unihalle.informatik.Alida.workflows.events.ALDWorkflowEventListener
Method which is called on event occurrence.
handleLoadWorkflowEvent(ALDWorkflowClassEvent) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
 
handleNodeParameterChangeEvent(Collection<ALDWorkflowNodeID>) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Update node color according to node's state.
handleNodeParameterChangeEvent(Collection<ALDWorkflowNodeID>) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
Update parameter labels according to configuration states.
handleNodeStateChangeEvent(Collection<ALDWorkflowNodeID>) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Update node color according to node's state.
handleNodeStateChangeEvent(Collection<ALDWorkflowNodeID>) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
Update control window color according to node's state.
handleSaveWorkflowEvent(String) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Stores the workflow to the given file.
handleShowResultsEvent(ALDWorkflowNodeID) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Displays result frame for given node.
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDFileDirectoryDataIOSwing.FileDirectoryDataIOPanel
 
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorConfigWindow
 
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
 
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
 
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParametrizedClassConfigWindow
 
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in interface de.unihalle.informatik.Alida.dataio.provider.swing.events.ALDSwingValueChangeListener
Method which is called on event occurence.
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
 
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
 
handleWorkflowRenameEvent(String) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
 
handlingMode - Variable in class de.unihalle.informatik.Alida.operator.ALDParameterDescriptor
 

I

id - Variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflowID
This id is only to print debug information, but NOT to identify an object
idSeparator - Static variable in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Character separating graphId prefix from rest
info - Variable in class de.unihalle.informatik.Alida.workflows.events.ALDWorkflowClassEvent
ID of work flow object
info - Variable in class de.unihalle.informatik.Alida.workflows.events.ALDWorkflowEvent
ID of work flow object
init() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Does the main work to instantiate the frame.
init() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
 
initAdapter() - Static method in class de.unihalle.informatik.Alida.annotations.indexing.SezPozAdapter
Initialization routine for this class.
initAdapter(ClassLoader) - Static method in class de.unihalle.informatik.Alida.annotations.indexing.SezPozAdapter
Initialization routine for this class.
initDone - Static variable in class de.unihalle.informatik.Alida.annotations.indexing.SezPozAdapter
Variable to check if init routine was called.
initInterruptWin() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Setup of the window for renaming workflows.
initInterruptWin() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
Setup of the window for renaming workflows.
initMapTable(Class<?>) - Static method in class de.unihalle.informatik.Alida.batch.ALDBatchInputManager
Method to initialize the hashmap which registers batch input providers.
initMapTable(Class<?>) - Static method in class de.unihalle.informatik.Alida.batch.ALDBatchOutputManager
Method to initialize the hashmap which registers batch output providers.
initMapTable() - Static method in class de.unihalle.informatik.Alida.dataconverter.ALDDataConverterManager
Method to initialize the hashmap which registers data conversion providers.
initMapTable(Class) - Static method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManager
Method to initialize the hashmap which registers DataIO providers.
initNewTab(ALDGrappaWorkbenchGraph) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
 
initNewWorkflow() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
 
initNewWorkflow(ALDGrappaWorkbenchGraph) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
 
initOperator() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorConfigWindow
Initializes a new operator object with default configuration.
initOperatorWorkflow(ALDOperatorLocation) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
Adds the operator as node to the workflow.
initReloadedTab(mxGraph, ALDWorkflow) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
 
initReloadedWorkflow(mxGraph, ALDWorkflow) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
 
initRenameWin() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
Setup of the window for renaming workflows.
initWorkbench() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaFrame
 
inputCheckBoxes - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
Set of checkboxes to select input parameters in batch mode.
inputPanel - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
The top level panel of this frame.
inputParameterValues - Variable in class de.unihalle.informatik.Alida.batch.ALDBatchRunResultInfo
List of input values for parameter.
inputProviderComps - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
Components in GUI linked to the different input batch parameters.
interruptExecution() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Aborts running execution of the workflow.
interruptExecution() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
Aborts running execution of the workflow.
interruptExecution() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Deprecated. 
interruptWin - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Message window shown while workflow execution is aborted.
interruptWorkflowExecution() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
 
invoke(Object, mxEventObject) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab.GraphEventListener
 
isAllowAdditionalFields() - Method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerXmlbeans
 
isClassNameSpecified() - Static method in class de.unihalle.informatik.Alida.version.ALDVersionProviderFactory
Returns true if the factory can be properly configured.
isConfigured() - Method in interface de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator
Returns true if the object is properly configured.
isConfigured() - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
 
isConfigured() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowNode
Checks if this node is configured.
isDoHistory() - Method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerCmdline
 
isDoHistory() - Method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerXmlbeans
 
isEmpty() - Method in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
Returns true if this map contains no key-value mappings.
isExactSubstring(String, String) - Method in class de.unihalle.informatik.Alida.tools.ALDOpRunner
return true, if substr is a exact substring of str
isInteriorShadowNode - Variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflowNode
Is true it his node is used as an interior shadow (or substitute) for the node holding this work flow {see ALDWorkflow.
isNeedConverter() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowEdge
 
isNormalized() - Method in class de.unihalle.informatik.Alida.demo.CopyOfExperimentalData
Query if data are normalized to zero mean within each feature.
isNormalized() - Method in class de.unihalle.informatik.Alida.demo.ExperimentalData
Query if data are normalized to zero mean within each feature.
isOperator() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorChooserTreeNode
Is this node a operator?
isOperatorNull() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorConfigWindow
Allows to check if window is linked to operator object or not.
isRegistered(Object) - Method in class de.unihalle.informatik.Alida.operator.ALDPortHashAccess
Check if an object is registered in the hash.
isRequired() - Method in class de.unihalle.informatik.Alida.operator.ALDParameterDescriptor
Returns is parameter is required.
isResetDisconnectedInput() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
 
isTriggerValueChangeEvents() - Method in class de.unihalle.informatik.Alida.batch.ALDBatchInputManagerSwing
Returns value of event trigger flag.
isTriggerValueChangeEvents() - Method in class de.unihalle.informatik.Alida.batch.ALDBatchOutputManagerSwing
Returns value of event trigger flag.
isTriggerValueChangeEvents() - Method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerSwing
Returns value of event trigger flag.
isVisible() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParametrizedClassConfigWindow
Method to query if configuration window is visible.
itemStateChanged(ItemEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentCheckBox
 
itemStateChanged(ItemEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentComboBox
 
itemStateChanged(ItemEvent) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
 

K

keyPressed(KeyEvent) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab.GraphKeyListener
 
keyReleased(KeyEvent) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab.GraphKeyListener
 
keyTyped(KeyEvent) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab.GraphKeyListener
 
killWorkflowThread() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
 

L

label - Variable in class de.unihalle.informatik.Alida.operator.ALDParameterDescriptor
 
lastDir - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow
For convenience: always open last directory for saving.
lastDirectory - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Last directory visited, initially it's user's home.
lastFile - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Last selected file.
lastLoadFilePath - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
 
lastSaveFilePath - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
 
lastSelectedLocation - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaFrame
Stores the recently selected path in the chooser tree.
lastWrite - Variable in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
field written to only to guarantee lock ordering.
level - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorChooserTree
Mode of usage.
linkedDataObject - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow
Optional data object linked to the table model.
listenerList - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.events.ALDSwingValueChangeReporter
List of registered event listeners.
listenerList - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
List of registered event listeners.
load(Class<A>, Class<I>) - Static method in class de.unihalle.informatik.Alida.annotations.indexing.SezPozAdapter
 
load(String) - Static method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Load a workflow from file with filename and create a new workflow object.
load(String, boolean) - Static method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Load a workflow from file with filename and create a new workflow object.
load(File) - Static method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Load a workflow from File and create a new workflow object.
load(File, boolean) - Static method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Load a workflow from File and create a new workflow object.
loadFactor - Variable in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
The load factor for the hash table.
loadFactor() - Method in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
Returns the load factor.
loadWorkflow() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
Loads a new workflow from file(s).
locationType - Variable in class de.unihalle.informatik.Alida.operator.ALDOperatorLocation
Type of this location
lookupExtendingClasses(Class) - Static method in class de.unihalle.informatik.Alida.helpers.ALDClassInfo
Collects all derived class of given class.
lookupOperatorClassnames(ALDAOperator.Level, ALDAOperator.ExecutionMode) - Static method in class de.unihalle.informatik.Alida.helpers.ALDClassInfo
Collects all ALDOperators annotated with the requested level and execution mode and all ALDOperators found in a package specified by a JVM property alida_oprunner_favoriteops or the environment variable ALIDA_OPRUNNER_OPERATORPATH as a colon separated list of package names.
lookupOperators(ALDAOperator.Level, ALDAOperator.ExecutionMode) - Static method in class de.unihalle.informatik.Alida.helpers.ALDClassInfo
Collects all ALDOperators annotated with the requested level and execution mode and all ALDOperators found in a package specified by a JVM property alida_oprunner_favoriteops or the environment variable ALIDA_OPRUNNER_OPERATORPATH as a colon separated list of package names.
lookupParameternames(ALDOperator, String) - Static method in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDParametrizedClassDataIOCmdline
Lookup all parameter names of the operator with prefix pre.
lookupParameternames(ALDOperator, String) - Static method in class de.unihalle.informatik.Alida.dataio.provider.xmlbeans.ALDParametrizedClassDataIOXmlbeans
Lookup all parameter names of the operator with prefix pre.
lookupType(Field) - Static method in class de.unihalle.informatik.Alida.dataio.provider.helpers.ALDCollectionDataIOHelper
 
lookupWorkflows() - Static method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowHelper
Collects work flows from files and return location objects.
lookupWorkflows(String) - Static method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowHelper
Collects work flows from files and return location objects.

M

main(String[]) - Static method in class de.unihalle.informatik.Alida.tools.ALDGrappaRunner
Main function called from outside.
main(String[]) - Static method in class de.unihalle.informatik.Alida.tools.ALDOpRunner
Main routine of ALDOpRunner , see usage.
main(String[]) - Static method in class de.unihalle.informatik.Alida.tools.ALDOpRunnerGUI
 
main(String[]) - Static method in class de.unihalle.informatik.Alida.tools.GenerateGetterSetter
Main function.
main(String[]) - Static method in class de.unihalle.informatik.Alida.tools.PrintDataIOProvider
Main routine of ALDOpRunner , see usage.
main(String[]) - Static method in class de.unihalle.informatik.Alida.tools.PrintOperatorInterface
Extracts operator interface from given class.
mainFrame - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
 
mainPanel - Variable in class de.unihalle.informatik.Alida.gui.ALDChooseOpNameFrame
Main panel of chooser window.
mapeEdgeIdToEdge(ALDWorkflowEdgeID) - Static method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Map an edgeId to its edge.
mapEgdeToEdgeId(ALDWorkflowEdge) - Static method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
 
mapNodeIdToNode(ALDWorkflowNodeID) - Static method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Map a nodeId to its node.
mapNodeToNodeId(ALDWorkflowNode) - Static method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Map a node to its NodeId
mapTable - Variable in class de.unihalle.informatik.Alida.batch.ALDBatchInputManager
Hashtable containing mappings of datatypes to provider classes.
mapTable - Variable in class de.unihalle.informatik.Alida.batch.ALDBatchOutputManager
Hashtable containing mappings of datatypes to provider classes.
mapTable - Variable in class de.unihalle.informatik.Alida.dataconverter.ALDDataConverterManager
Hashtable containing mappings of class pairs to a collection of provider class names.
mapTable - Variable in class de.unihalle.informatik.Alida.dataio.ALDDataIOManager
Hashtable containing mappings of datatypes to DataIO provider classes.
markParameter(ALDParameterDescriptor) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
Sets label color of parameter to red (e.g. if validation failed).
markParameterProbablyConf(ALDParameterDescriptor) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
 
matchingClassNames - Variable in class de.unihalle.informatik.Alida.tools.ALDOpRunner
List of fully qualified class names of operators available
MatrixSum - Class in de.unihalle.informatik.Alida.demo
Demo operator to calculate colum or row sums of a 2D array.
MatrixSum() - Constructor for class de.unihalle.informatik.Alida.demo.MatrixSum
Default constructor.
MatrixSum(Double[][]) - Constructor for class de.unihalle.informatik.Alida.demo.MatrixSum
Constructor.
MatrixSum.SummarizeMode - Enum in de.unihalle.informatik.Alida.demo
Choose row or colum wise sum
mouseClicked(MouseEvent) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaFrame.ChooserTreeMouseAdapter
 
mousePressed(MouseEvent) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab.GraphMouseAdapter
 
mousePressed(MouseEvent) - Method in class de.unihalle.informatik.Alida.gui.ALDChooseOpNameFrame.MyMouseAdapter
 
myclass - Variable in class de.unihalle.informatik.Alida.operator.ALDParameterDescriptor
 

N

name - Variable in class de.unihalle.informatik.Alida.operator.ALDOperator
Name of the operator
name - Variable in class de.unihalle.informatik.Alida.operator.ALDOperatorLocation
The name of this location in the original form, e.g. a filename or a fully qualified class name
name - Variable in class de.unihalle.informatik.Alida.operator.ALDParameterDescriptor
 
nodeParameterChanged(ALDWorkflowNodeID) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Notify the workflow that parameters of the operator object associated with node nodeId have changed.
NormalizeExperimentalDataOp - Class in de.unihalle.informatik.Alida.demo
Demo operator to normalize experimental data.
NormalizeExperimentalDataOp() - Constructor for class de.unihalle.informatik.Alida.demo.NormalizeExperimentalDataOp
Default constructor.
NormalizeExperimentalDataOp(ExperimentalData) - Constructor for class de.unihalle.informatik.Alida.demo.NormalizeExperimentalDataOp
Constructor.
notifyListenersRecursively - Variable in class de.unihalle.informatik.Alida.operator.ALDOperatorControllable
Flag for recursive propagation of events to nested listeners.

O

objCl - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentTextField
Class of objects to be read through this text field.
okOption - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Ok label to be used on button of Ok message boxes.
oldEdgeTarget - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab.WorkflowModifyAction
 
oldEdgeTargetParamName - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab.WorkflowModifyAction
 
OnlineHelpDisplayer - Class in de.unihalle.informatik.Alida.gui
Convenience class for context-sensitive online help.
OnlineHelpDisplayer() - Constructor for class de.unihalle.informatik.Alida.gui.OnlineHelpDisplayer
 
op - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing
The operator of this frame, may be abstract!
op - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
The operator associated with this frame.
openWindow() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow
Shows the table window in graphical environment.
operate() - Method in class de.unihalle.informatik.Alida.dataconverter.ALDNumberConverter
 
operate() - Method in class de.unihalle.informatik.Alida.dataconverter.ALDVectorNativeArrayConverter
 
operate() - Method in class de.unihalle.informatik.Alida.demo.ALDArrayMean
 
operate() - Method in class de.unihalle.informatik.Alida.demo.ALDArrayMin
 
operate() - Method in class de.unihalle.informatik.Alida.demo.ALDArraySum
 
operate() - Method in class de.unihalle.informatik.Alida.demo.ALDCalcMean
 
operate() - Method in class de.unihalle.informatik.Alida.demo.ALDCalcMeanArray
 
operate() - Method in class de.unihalle.informatik.Alida.demo.ALDClusterExperiment
 
operate() - Method in class de.unihalle.informatik.Alida.demo.ALDDemoOpControllable
 
operate() - Method in class de.unihalle.informatik.Alida.demo.ALDInputParameterTester
 
operate() - Method in class de.unihalle.informatik.Alida.demo.ALDKmeansOp
 
operate() - Method in class de.unihalle.informatik.Alida.demo.ALDParameterTester
 
operate() - Method in class de.unihalle.informatik.Alida.demo.ALDPCAOp
 
operate() - Method in class de.unihalle.informatik.Alida.demo.ALDTransposeMatrix
 
operate() - Method in class de.unihalle.informatik.Alida.demo.AnalyzeExperiment
 
operate() - Method in class de.unihalle.informatik.Alida.demo.ApplyToMatrix
 
operate() - Method in class de.unihalle.informatik.Alida.demo.FilterExperimentalDataOp
 
operate() - Method in class de.unihalle.informatik.Alida.demo.MatrixSum
 
operate() - Method in class de.unihalle.informatik.Alida.demo.NormalizeExperimentalDataOp
 
operate() - Method in class de.unihalle.informatik.Alida.demo.SummarizeClusters
 
operate() - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
This method does the actual work and needs to be implemented by every subclass.
operate() - Method in class de.unihalle.informatik.Alida.operator.ALDOperatorControllable
 
operate() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
 
operator - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
The operator associated with this panel.
operatorNodeID - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
Reference ID of the operator node in Alida workflow;
operatorParameterPanel - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Panel where operator parameters are embedded.
operatorStatus - Variable in class de.unihalle.informatik.Alida.operator.ALDOperatorControllable
Status of operator, used to stop/pause/resume calculations.
opLocation - Variable in class de.unihalle.informatik.Alida.gui.ALDChooseOpNameFrame
Location of recently selected operator.
opNameJText - Variable in class de.unihalle.informatik.Alida.gui.ALDChooseOpNameFrame
Label to display selected operator.
opParamDescrips - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing
List of all parameter descriptors associated with operator.
optionsWindow - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow
Window for configuration of table options.
opTree - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaFrame
Tree of available operators.
opTree - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaMenuBar
Reference to the operator chooser tree of window this menubar belongs to.
opTree - Variable in class de.unihalle.informatik.Alida.gui.ALDChooseOpNameFrame
JComponent containing both trees of available operators.
opTreePane - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaFrame
Scroll pane displaying the operator tree.
opTreePane - Variable in class de.unihalle.informatik.Alida.gui.ALDChooseOpNameFrame
Scroll pane displaying the operator tree.
outputCheckBoxes - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
Set of checkboxed to select parameters to summarize in batch mode.

P

paramChangeListener - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
Listener object attached to the control window.
Parameter - Annotation Type in de.unihalle.informatik.Alida.annotations
Annotation definition for operator parameters.
Parameter.Direction - Enum in de.unihalle.informatik.Alida.annotations
Enumerates the different directions a parameter may, e.g. into or out of an operator.
Parameter.ExpertMode - Enum in de.unihalle.informatik.Alida.annotations
Enumerates the different modes which are defined for a parameter to be shown in automatically generated user interfaces.
Parameter.Type - Enum in de.unihalle.informatik.Alida.annotations
Deprecated. 
parameterName - Variable in class de.unihalle.informatik.Alida.batch.ALDBatchRunResultInfo
Name of parameter over which was iterated.
parametersToXmlObject() - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Parse the parameter values to an XmlObject.
parse(Field, Class<?>, String) - Method in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDCollectionDataIOCmdline
Returns a collection instantiated from valueString.
parse(Field, Class<?>, String) - Method in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDEnumDataIOCmdline
 
parse(Field, Class<?>, String) - Method in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDNativeDataIOCmdline
Method to parse native data from a string.
parse(Field, Class<?>, String) - Method in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDParametrizedClassDataIOCmdline
Parser for parametrized classes and ALDOperators.
parse(Field, Class<?>, String, ALDOperator) - Method in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDParametrizedClassDataIOCmdline
Generic Parser for parametrized classes and ALDOperators.
parse(Field, Class<?>, String) - Method in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDStandardizedDataIOCmdline
Returns an object instantiated from valueString.
parseBracket(String) - Static method in class de.unihalle.informatik.Alida.helpers.ALDParser
Parses a string for a matching bracket.
parseBracket(String, char) - Static method in class de.unihalle.informatik.Alida.helpers.ALDParser
Parses a string for a matching bracket.
parseNameValuePairs(String) - Static method in class de.unihalle.informatik.Alida.helpers.ALDParser
Parses a comma separated list of 'name=value' pairs into a hash map.
pauseButton - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
Pause button, changes its label.
pauseWorkflow() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
 
pLevel - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Level of interaction providers are allowed to perform.
popRecentlySelectedOperatorLocation() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaFrame
 
popRecentlySelectedOperatorPath() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
 
portHashAccess - Static variable in class de.unihalle.informatik.Alida.operator.ALDOperator
Access to the central port hash.
print() - Method in class de.unihalle.informatik.Alida.demo.CopyOfExperimentalData
 
print() - Method in class de.unihalle.informatik.Alida.demo.ExperimentalData
 
print() - Method in class de.unihalle.informatik.Alida.operator.ALDData
Print this data object to standard out
print() - Method in class de.unihalle.informatik.Alida.operator.ALDDataPort
Print some information to System.out.
print() - Method in class de.unihalle.informatik.Alida.operator.ALDEdge
Print this edge to stdout.
print(String) - Method in class de.unihalle.informatik.Alida.operator.ALDEdge
Print this edge to stdout with a given ident string.
print() - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Print some information of the current state this operator to System.out.
print(PrintStream) - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Print some information the current state of this operator to outfile.
print(PrintStream, boolean) - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Print information of the interface and values of this operator to outfile.
print() - Method in class de.unihalle.informatik.Alida.operator.ALDOpNode
Print information if this opNode to standard output.
print(String) - Method in class de.unihalle.informatik.Alida.operator.ALDOpNodePort
Print information of this port onto System.out
print(PrintStream) - Method in class de.unihalle.informatik.Alida.operator.ALDOpParameterDescriptor
Print this descriptor to outfile
print(PrintStream, ALDOperator) - Method in class de.unihalle.informatik.Alida.operator.ALDOpParameterDescriptor
Print this descriptor to outfile.
print() - Method in class de.unihalle.informatik.Alida.operator.ALDOutputPort
Print information to standard out
print() - Method in class de.unihalle.informatik.Alida.operator.ALDParameterDescriptor
Print this descriptor to standard out.
print(PrintStream) - Method in class de.unihalle.informatik.Alida.operator.ALDParameterDescriptor
Print this descriptor to outfile.
print() - Method in class de.unihalle.informatik.Alida.operator.ALDPort
Print some information on System.out
print(String) - Method in class de.unihalle.informatik.Alida.operator.ALDPort
Print some information on System.out
print() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
 
print() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowEdge
Print information of this edge to standard out.
print() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowNode
Print information of this node to standard out.
PrintDataIOProvider - Class in de.unihalle.informatik.Alida.tools
A helper class to adminstrate the ALDIA dataIO system.
PrintDataIOProvider(String[]) - Constructor for class de.unihalle.informatik.Alida.tools.PrintDataIOProvider
Construct a PrintDataIOProvider using args
printEdge(EdgeType, String) - Static method in class de.unihalle.informatik.Alida.operator.GraphmlHelper
Print an Edge to standard out using an indentation string
printGraph(GraphType, String) - Static method in class de.unihalle.informatik.Alida.operator.GraphmlHelper
Print a graph to standard out using an indentation string
printGraphml(GraphmlType) - Static method in class de.unihalle.informatik.Alida.operator.GraphmlHelper
Print a graphml element to standard out
printInstanceStatistics() - Static method in class de.unihalle.informatik.Alida.operator.ALDOpNode
 
printInstanceStatistics(PrintStream) - Static method in class de.unihalle.informatik.Alida.operator.ALDOpNode
 
printInterface() - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Print information of the interface of this operator to System.out.
printInterface(PrintStream) - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Print information of the interface of this operator to outfile.
printMap(HashMap<String, Collection<String>>) - Static method in class de.unihalle.informatik.Alida.dataconverter.ALDDataConverterManager
 
printNode(NodeType, String) - Static method in class de.unihalle.informatik.Alida.operator.GraphmlHelper
Print a Node to standard out using an indentation string
PrintOperatorInterface - Class in de.unihalle.informatik.Alida.tools
Prints the interface of an operator (inputs/outputs/parameters) to console.
PrintOperatorInterface() - Constructor for class de.unihalle.informatik.Alida.tools.PrintOperatorInterface
 
processEvents - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
Flag to indicate if the is an abortion currently going on.
processWorkflowEventQueue() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Processes all events that were recently added to the queue.
processWorkflowEventQueue() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
Processes all events that were recently added to the queue.
providedClasses() - Method in interface de.unihalle.informatik.Alida.batch.provider.input.ALDBatchInputIterator
Interface method to announce all classes handled by this provider.
providedClasses() - Method in class de.unihalle.informatik.Alida.batch.provider.input.swing.ALDBatchInputNativeArray1DSwing
Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in class de.unihalle.informatik.Alida.batch.provider.input.swing.ALDBatchInputNumberSwing
Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in interface de.unihalle.informatik.Alida.batch.provider.output.ALDBatchOutputSummarizer
Interface method to announce all classes handled by this provider.
providedClasses() - Method in class de.unihalle.informatik.Alida.batch.provider.output.swing.ALDSummarizerNativeDataSwing
Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in interface de.unihalle.informatik.Alida.dataconverter.ALDDataConverter
Announce all classes pairs which the converter can handle.
providedClasses() - Method in class de.unihalle.informatik.Alida.dataconverter.ALDNumberConverter
 
providedClasses() - Method in class de.unihalle.informatik.Alida.dataconverter.ALDVectorNativeArrayConverter
 
providedClasses() - Method in interface de.unihalle.informatik.Alida.dataio.provider.ALDDataIO
Interface method to announce all classes handled by this provider.
providedClasses() - Method in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDCollectionDataIOCmdline
 
providedClasses() - Method in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDEnumDataIOCmdline
 
providedClasses() - Method in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDFileDirectoryDataIOCmdline
 
providedClasses() - Method in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDNativeDataIOCmdline
 
providedClasses() - Method in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDParametrizedClassDataIOCmdline
Interface method to announce class for which IO is provided for
providedClasses() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing
Interface method to announce class for which IO is provided for.
providedClasses() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDEnumDataIOSwing
Interface method to announce class for which IO is provided for.
providedClasses() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDFileDirectoryDataIOSwing
Interface method to announce class for which IO is provided for.
providedClasses() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing
Interface method to announce class for which IO is provided for.
providedClasses() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing
Interface method to announce class for which IO is provided for.
providedClasses() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeDataIOSwing
Interface method to announce class for which IO is provided for.
providedClasses() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing
 
providedClasses() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDParametrizedClassDataIOSwing
Interface method to announce class for which IO is provided for.
providedClasses() - Method in class de.unihalle.informatik.Alida.dataio.provider.xmlbeans.ALDCollectionDataIOXmlbeans
 
providedClasses() - Method in class de.unihalle.informatik.Alida.dataio.provider.xmlbeans.ALDEnumDataIOXmlbeans
 
providedClasses() - Method in class de.unihalle.informatik.Alida.dataio.provider.xmlbeans.ALDFileDirectoryDataIOXmlbeans
 
providedClasses() - Method in class de.unihalle.informatik.Alida.dataio.provider.xmlbeans.ALDNativeDataIOXmlbeans
 
providedClasses() - Method in class de.unihalle.informatik.Alida.dataio.provider.xmlbeans.ALDParametrizedClassDataIOXmlbeans
Interface method to announce class for which IO is provided for
providedClasses() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowDataIOXmlbeans
Interface method to announce class for which IO is provided for
providerAvailable(Class<?>) - Method in class de.unihalle.informatik.Alida.batch.ALDBatchInputManager
Check if a provider has registered for the given class.
providerAvailable(Class<?>) - Method in class de.unihalle.informatik.Alida.batch.ALDBatchOutputManager
Check if a provider has registered for the given class.
providesMethodName - Static variable in interface de.unihalle.informatik.Alida.dataconverter.ALDDataConverter
Name of the method which returns all source classes supported.
put(Object, Object) - Method in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
Maps the specified key to the specified value in this table.

Q

quit() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaFrame
Terminates Grappa after some clean-ups.
quit() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
Closes the main window after cleaning up.
quit() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Does clean-up on termination, i.e. closes all open windows.
quit() - Method in class de.unihalle.informatik.Alida.gui.ALDChooseOpNameFrame
Cleans-up on termination, e.g. closes all windows.
quit() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Clean-up on termination.
quit() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
 
quit() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
Does clean-up on termination, i.e. closes all open windows.

R

radioItemAdvanced - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Radio button for selecting advanced configuration mode.
radioItemStandard - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Radio button for selecting standard configuration mode.
readArray1D(Class<?>, String) - Static method in class de.unihalle.informatik.Alida.helpers.ALDParser
Parses a string into a 1D-array.
readArray2D(Class<?>, String) - Static method in class de.unihalle.informatik.Alida.helpers.ALDParser
Parses a string into a 2D-array.
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.Alida.batch.ALDBatchInputManagerSwing
Reads data of given class from a specified source.
readData(Field, Class<?>, ALDSwingComponent) - Method in interface de.unihalle.informatik.Alida.batch.provider.input.swing.ALDBatchInputIteratorSwing
Interface method for getting parameter values via a GUI element.
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.Alida.batch.provider.input.swing.ALDBatchInputNativeArray1DSwing
 
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.Alida.batch.provider.input.swing.ALDBatchInputNumberSwing
 
readData(Field, Class<?>, String) - Method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerCmdline
Reads data of given class from a specified source.
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerSwing
Reads data of given class from a specified source.
readData(Field, Class<?>, ALDXMLObjectType) - Method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerXmlbeans
Reads data of given class from a specified source.
readData(Field, Class<?>, String) - Method in interface de.unihalle.informatik.Alida.dataio.provider.ALDDataIOCmdline
Interface for reading data from the given source.
readData(Field, Class<?>, ALDSwingComponent) - Method in interface de.unihalle.informatik.Alida.dataio.provider.ALDDataIOSwing
Interface method for getting parameter values via a GUI element.
readData(Field, Class<?>, ALDXMLObjectType) - Method in interface de.unihalle.informatik.Alida.dataio.provider.ALDDataIOXmlbeans
Interface for reading data from the given source.
readData(Field, Class<?>, String) - Method in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDFileDirectoryDataIOCmdline
 
readData(Field, Class<?>, String) - Method in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDStandardizedDataIOCmdline
Read an object using valueString.
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing
 
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDEnumDataIOSwing
 
readData(Field, Class<?>) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDFileDirectoryDataIOSwing.FileDirectoryDataIOPanel
Returns the contents of the text field.
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDFileDirectoryDataIOSwing
 
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing
 
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing
 
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeDataIOSwing
 
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing
 
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDParametrizedClassDataIOSwing
 
readData(Field, Class<?>) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParametrizedClassConfigWindow
Extracts current parametrized class configuration.
readData(Field, Class<?>, ALDXMLObjectType, Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.xmlbeans.ALDCollectionDataIOXmlbeans
Returns a collection instantiated from valueString.
readData(Field, Class<?>, ALDXMLObjectType, Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.xmlbeans.ALDEnumDataIOXmlbeans
 
readData(Field, Class<?>, ALDXMLObjectType) - Method in class de.unihalle.informatik.Alida.dataio.provider.xmlbeans.ALDFileDirectoryDataIOXmlbeans
 
readData(Field, Class<?>, ALDXMLObjectType, Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.xmlbeans.ALDNativeDataIOXmlbeans
Method to parse native data from a string.
readData(Field, Class<?>, ALDXMLObjectType, Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.xmlbeans.ALDParametrizedClassDataIOXmlbeans
Xmlbeans provider for parametrized classes and ALDOperators.
readData(Field, Class<?>, ALDXMLObjectType, Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.xmlbeans.ALDStandardizedDataIOXmlbeans
Returns an object instantiated from xmlObject.
readData(Field, Class<?>, ALDXMLObjectType) - Method in class de.unihalle.informatik.Alida.dataio.provider.xmlbeans.ALDStandardizedDataIOXmlbeans
Read an object using valueString.
readData(Field, Class<?>, ALDXMLObjectType, Object) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowDataIOXmlbeans
 
readHistory(Object, String) - Static method in class de.unihalle.informatik.Alida.operator.ALDOperator
Reads and set the history graph of the given object from file.
readHistory(Object, String) - Method in class de.unihalle.informatik.Alida.operator.ALDPortHashAccess
Read and set the processing history from file.
readParameter(ALDParameterDescriptor) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
Get value of given parameter from the GUI element.
readResolve() - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Init function for deserialized objects.
readResolve() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Init function for deserialized objects.
readXml(String, Class<?>) - Static method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerXmlbeans
Read Object from a file using xmlbeans providers
readXml(File, Class<?>) - Static method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerXmlbeans
Read Object from a file using xmlbeans providers
recordModification(Object) - Method in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
Force a memory synchronization that will cause all readers to see table.
redirectSource(ALDWorkflowEdgeID, ALDWorkflowNodeID, String) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Call redirectSource with with the argument allowDataConversion = false.
redirectSource(ALDWorkflowEdgeID, ALDWorkflowNodeID, String, Boolean) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Redirect the source of an edge.
redirectSource(ALDWorkflowNode, String) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowEdge
Redirect the source of this edge
redirectTarget(ALDWorkflowEdgeID, ALDWorkflowNodeID, String) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Calls redirectTarget with the argument allowDataConversion = false The same restrictions as for createEdge apply.
redirectTarget(ALDWorkflowEdgeID, ALDWorkflowNodeID, String, Boolean) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Redirect the target of an edge.
redirectTarget(ALDWorkflowNode, String) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowEdge
Redirect the target of this node.
redirectWorkflowEdge(mxCell, ALDWorkflowEdgeID, ALDWorkflowNodeID, ALDWorkflowNodeID, ALDGrappaNodePortInfo, ALDGrappaNodePortInfo) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Redirects the workflow edge.
refQueue - Static variable in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
Queue for managing references to deleted objects.
register(Object) - Method in class de.unihalle.informatik.Alida.operator.ALDPortHashAccess
Register the object in the hash.
registerDescriptor(LinkedList<ALDOpParameterDescriptor>, ALDOpParameterDescriptor) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
Register a descriptor.
rehash() - Method in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
Rehashes the contents of this map into a new table with a larger capacity.
reinitializeParameterDescriptors() - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Reinitialize the field member of all parameter descriptors.
relocateNode(ALDWorkflowNodeID, boolean) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Relocate the node to this workflow.
relocateNodes(Collection<ALDWorkflowNodeID>, boolean) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Relocate the nodes nodeIds and all edges of the sub graph induced by these nodes to this workflow.
remove(Object) - Method in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
Removes the key (and its corresponding value) from the table.
removeALDConfigurationEventListener(ALDConfigurationEventListener) - Method in class de.unihalle.informatik.Alida.operator.ALDOperatorControllable
 
removeALDConfigurationEventListener(ALDConfigurationEventListener) - Method in interface de.unihalle.informatik.Alida.operator.events.ALDConfigurationEventReporter
Removes a listener from this reporter.
removeALDControlEventListener(ALDControlEventListener) - Method in class de.unihalle.informatik.Alida.operator.ALDOperatorControllable
 
removeALDControlEventListener(ALDControlEventListener) - Method in interface de.unihalle.informatik.Alida.operator.events.ALDControlEventReporter
Removes a listener from this reporter.
removeALDWorkflowClassEventListener(ALDWorkflowEventListener) - Static method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Remove a listener for events thrown by the class ALDWorkflow (not an instance).
removeALDWorkflowEventListener(ALDWorkflowEventListener) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
 
removeALDWorkflowEventListener(ALDWorkflowEventListener) - Method in interface de.unihalle.informatik.Alida.workflows.events.ALDWorkflowEventReporter
Removes a listener from this reporter.
removeEdge(ALDWorkflowEdgeID) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Remove an edge from the workflow.
removeExtension(String) - Static method in class de.unihalle.informatik.Alida.helpers.ALDFilePathManipulator
Removes preceding path elements and extension from filename, if any.
removeLeadingDirectories(String) - Static method in class de.unihalle.informatik.Alida.helpers.ALDFilePathManipulator
Remove all leading pathname components from a filename.
removeNode(ALDWorkflowNodeID) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Remove a node with all incoming and outgoing edges from the workflow.
removeParameter(String) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Remove a parameter from this workflow.
removeParameterChangeEventListener(ALDOpParameterChangeEventListener) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Removes a listener from this reporter.
removeValueChangeEventListener(ALDSwingValueChangeListener) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.events.ALDSwingValueChangeReporter
Removes a listener from this reporter.
removeWorkflow() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
Removes the currently active workflow.
removeWorkflowEdge(mxCell) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Removes the specified edge from the workflow.
removeWorkflowNode(mxCell) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Removes the specified cell from the graph.
renameGraphIds(GraphType, int) - Static method in class de.unihalle.informatik.Alida.operator.GraphmlHelper
Rename all GraphIds of nodes, edges, data, etc with a new graphID.
renameNodeIds(NodeType, HashMap<String, String>) - Static method in class de.unihalle.informatik.Alida.operator.GraphmlHelper
Traverse the graph, find all graphIDs and actually rename.
renameTextField - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
 
renameWin - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
 
renameWorkflow() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
Rename the currently active workflow.
renameWorkflow(String) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
 
required - Variable in class de.unihalle.informatik.Alida.operator.ALDParameterDescriptor
 
restoreConfigWins() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Instantiates for each node in the current workflow a configuration window.
restoreIDs() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Restore maps of Alida workflow IDs and corresponding graph cells.
resultDataVec - Variable in class de.unihalle.informatik.Alida.batch.ALDBatchRunResultInfo
List of corresponding result data objects.
resultDisplayButton - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
Result display button.
resultFrame - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
Frame showing operator execution results.
resumeWorkflow() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
 
runButton - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
Run button.
runFromNode(ALDWorkflowNodeID) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Run the given node and all descendants of the given node.
runFromNode(ALDWorkflowNodeID, boolean) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Run the given node and all descendants of the given node.
runFromNode(ALDWorkflowNodeID, boolean, boolean) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Run the given node and all descendants of the given node.
runIt() - Method in class de.unihalle.informatik.Alida.tools.ALDOpRunner
This method does the complete work to scan arguments, read and write parameters and runOp the operator.
runIt() - Method in class de.unihalle.informatik.Alida.tools.PrintDataIOProvider
This method does the complete work to scan arguments, read and write parameters and runOp the operator.
runNode(ALDWorkflowNodeID) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Run the given node and all its ancestors.
runNode(ALDWorkflowNodeID, boolean) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Run the given node and all its ancestors.
runNode(ALDWorkflowNodeID, boolean, boolean) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Run the given node and all its ancestors.
runOp() - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
A legal method to invoke the operator and handles everything necessary to protocol the processing history.
runOp(boolean) - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
A legal method to invoke the operator and handles everything necessary to protocol the processing history.
runOp(ALDOperator.HidingMode) - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
A legal method to invoke the operator and handles everything necessary to protocol the processing history.
runWorkflow() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
Run the currently active workflow.
runWorkflow() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Executes the complete workflow, i.e. all nodes currently present.
runWorkflow() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
Executes the workflow.
runWorkflow() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Run the complete workflow.
runWorkflow(boolean) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Run the complete workflow.
runWorkflow(boolean, boolean) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Run the complete workflow.
runWorkflowFromNode(ALDWorkflowNodeID) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Executes the workflow from the specified node to the end.
runWorkflowInBatchMode() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
 
runWorkflowNode(ALDWorkflowNodeID) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Executes the workflow up to the specified node.

S

save(String) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Save this workflow to file.
save(String, boolean) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Save this workflow to file.
save(File) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Save this workflow to file.
save(File, boolean) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Save this workflow to file.
saveHeaders - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow
Flag to indicate if headers should be saved to file.
saveTable() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow
Saves the contents of the table to a user-specified file.
saveWorkflow() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
Saves the currently active workflow to file(s).
saveWorkflow(File) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Saves the workflow to the given file.
serializeToXmlFile(String) - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Serializes the operator to an XML file.
setActionPositionX(int) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab.WorkflowModifyAction
 
setActionPositionY(int) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab.WorkflowModifyAction
 
setAllowAdditionalFields(boolean) - Method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerXmlbeans
 
setClassname(String) - Method in class de.unihalle.informatik.Alida.operator.ALDOpNodePort
Set the canonical classname of the ALDData associated with this port
setClusters(List<Set<Integer>>) - Method in class de.unihalle.informatik.Alida.demo.SummarizeClusters
 
setConstructionMode(int) - Static method in class de.unihalle.informatik.Alida.operator.ALDOperator
Set the mode of implicit construction of the processing graph.
setConverter(ALDDataConverter) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowEdge
 
setData(Double[]) - Method in class de.unihalle.informatik.Alida.demo.ALDSummarizeArrayOp
Sets the 1D array
setDebug(boolean) - Static method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Set the debug state
setDefaultValue(Object) - Method in class de.unihalle.informatik.Alida.operator.ALDParameterDescriptor
Specify default value of parameter.
setDelimiter(ALDTableWindow.TableModelDelimiter) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow.TableConfigWindow
Set delimiter.
setDirection(String) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaNodePortInfo
 
setDisplayOnly(boolean) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParametrizedClassConfigWindow
Enable or display parameter editing.
setDoHistory(boolean) - Method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerCmdline
 
setDoHistory(boolean) - Method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerXmlbeans
 
setDoNormalize(Boolean) - Method in class de.unihalle.informatik.Alida.demo.ALDClusterExperiment
 
setDoPCA(Boolean) - Method in class de.unihalle.informatik.Alida.demo.ALDClusterExperiment
 
setEditable(boolean) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParametrizedClassConfigWindow
Disable or enable the elements in the window for editing.
setElapsedTime(long) - Method in class de.unihalle.informatik.Alida.demo.ApplyToMatrix
Set value of elapsedTime.
setEnabled(boolean) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
Function to enable or disable the panel.
setExperiment(ExperimentalData) - Method in class de.unihalle.informatik.Alida.demo.ALDClusterExperiment
Set value of data.
setExperiment(ExperimentalData) - Method in class de.unihalle.informatik.Alida.demo.ALDKmeansOp
Set value of data.
setExperiment(ExperimentalData) - Method in class de.unihalle.informatik.Alida.demo.ALDPCAOp
Set value of data.
setExperiment(ExperimentalData) - Method in class de.unihalle.informatik.Alida.demo.AnalyzeExperiment
Set value of data.
setExperiment(ExperimentalData) - Method in class de.unihalle.informatik.Alida.demo.FilterExperimentalDataOp
Set value of data.
setExperiment(ExperimentalData) - Method in class de.unihalle.informatik.Alida.demo.NormalizeExperimentalDataOp
Set value of data.
setExperiment(ExperimentalData) - Method in class de.unihalle.informatik.Alida.demo.SummarizeClusters
Set value of data.
setExplanation(String) - Method in class de.unihalle.informatik.Alida.operator.ALDOpNodePort
Set the explanation of the port copied from the argument descriptor
setGraphmlHistory(GraphmlType) - Method in class de.unihalle.informatik.Alida.operator.ALDDataPort
Set the grahphml history of this data port
setHidden(ALDOperator.HidingMode) - Method in class de.unihalle.informatik.Alida.operator.ALDOpNode
Set hidden flag of this opNode.
setHistoryLink(Object, ALDPort) - Method in class de.unihalle.informatik.Alida.operator.ALDPortHashAccess
Set the port to which the object is currently linked in history.
setLevel(ALDAOperator.Level) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorChooserTree
Set the level of the operators in this tree.
setLocation(String) - Method in class de.unihalle.informatik.Alida.operator.ALDData
Set the location property, i.e. property with key location
setMatrix(Double[][]) - Method in class de.unihalle.informatik.Alida.demo.ApplyToMatrix
Set value of matrix.
setName(String) - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Set the name of this operator
setName(String) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
 
setNewOperator(ALDOperator) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
Sets a new operator for the panel.
setNode(mxCell) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaNodePortInfo
 
setNodeName(String) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaNodeInfo
Set (new) name for operator.
setNotifyRecursiveFlag(boolean) - Method in class de.unihalle.informatik.Alida.operator.ALDOperatorControllable
Specify if events are to be passed forward to nested listeners or not.
setNumCluster(Integer) - Method in class de.unihalle.informatik.Alida.demo.ALDKmeansOp
 
setNumComponents(Integer) - Method in class de.unihalle.informatik.Alida.demo.ALDPCAOp
 
setOperator(ALDWorkflowNodeID, ALDOperator) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Set the operator associated with nodeId.
setOperator(ALDOperator) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowNode
Sets the operator associated with this node.
setOperatorParameters(Field, Class<?>) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorConfigWindow
 
setOperatorParameters() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
Retrieve parameter values from GUI and configure operator accordingly.
setOpNameFilter(String) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorChooserTree
 
setParameter(ALDParameterDescriptor, Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
Set value of given parameter, i.e. pass the value to GUI component.
setParameter(String, Object) - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Set the value of a parameter specified by name.
setParameter(String, Object) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
 
setParameterBatchModeInput(String) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
 
setParameterLinked(String, String, String) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
Changes panel for a parameter to indicate that it is linked.
setParameterLinked(String, String, String) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
 
setParameterNotLinked(String) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
Changes panel for a parameter to indicate that it is not linked anymore.
setParameterNotLinked(String) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
 
setParametersFromXml(String) - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Set the parameter values as read from an Xml file.
setParametersFromXml(String, String, String) - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Set the parameter values as read from an Xml file.
setParamExternallyConfigured(ALDParameterDescriptor, String) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
 
setParamNotExternallyConfigured(ALDParameterDescriptor) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
 
setParent(ALDOpNode) - Method in class de.unihalle.informatik.Alida.operator.ALDOpNode
Set the parent opNode.
setParentWorkflow(ALDWorkflow) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowNode
 
setPortClassName(String) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaNodePortInfo
 
setPortExplanation(String) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaNodePortInfo
 
setPortLabel(String) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaNodePortInfo
 
setPortName(String) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaNodePortInfo
 
setProperty(String, Object) - Method in class de.unihalle.informatik.Alida.operator.ALDData
Set the property with key to new value o.
setProperty(String, Object) - Method in class de.unihalle.informatik.Alida.operator.ALDDataPort
Set the property with key to new value o.
setProperty(String, Object) - Method in class de.unihalle.informatik.Alida.operator.ALDOutputPort
Set property with key to object o
setProviderInteractionLevel(ALDBatchInputManagerSwing.ProviderInteractionLevel) - Method in class de.unihalle.informatik.Alida.batch.ALDBatchInputManagerSwing
Set the level of provider interaction which is allowed.
setProviderInteractionLevel(ALDBatchOutputManagerSwing.ProviderInteractionLevel) - Method in class de.unihalle.informatik.Alida.batch.ALDBatchOutputManagerSwing
Set the level of provider interaction which is allowed.
setProviderInteractionLevel(ALDDataIOManagerSwing.ProviderInteractionLevel) - Method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerSwing
Set the level of provider interaction which is allowed.
setProviderInteractionLevel(ALDDataIOManagerSwing.ProviderInteractionLevel) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Specify the provider interaction level.
setRefID(Integer) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaNodeInfo
Set (new) reference ID.
setReturnElapsedTime(boolean) - Method in class de.unihalle.informatik.Alida.demo.ApplyToMatrix
Set value of returnElapsedTime.
setSaveHeaders(boolean) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow
Function to enable/disable saving of headers to file.
setSelectedItem(Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentComboBox
Selects the item associated with the given object.
setSourceClass(Class<?>) - Method in class de.unihalle.informatik.Alida.dataconverter.ALDDataConverterManager.ALDSourceTargetClassPair
 
setState(ALDWorkflowNode.ALDWorkflowNodeState) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowNode
Sets the state of this node
setStatus(String) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Changes the status message to the given string.
setStepsize(int) - Method in class de.unihalle.informatik.Alida.operator.events.ALDConfigurationEvent
Set size of steps in step-wise operator execution.
setStepsize(int) - Method in class de.unihalle.informatik.Alida.operator.events.ALDOpParameterChangeEvent
Set size of steps in step-wise operator execution.
setSummaries(Double[]) - Method in class de.unihalle.informatik.Alida.demo.ApplyToMatrix
Set value of summaries.
setSummarizeMode(ApplyToMatrix.SummarizeMode) - Method in class de.unihalle.informatik.Alida.demo.ApplyToMatrix
Set value of summarizeMode.
setSummarizeOp(ALDSummarizeArrayOp) - Method in class de.unihalle.informatik.Alida.demo.ApplyToMatrix
Set value of summarizeOp.
setTargetClass(Class<?>) - Method in class de.unihalle.informatik.Alida.dataconverter.ALDDataConverterManager.ALDSourceTargetClassPair
 
setText(String) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentTextField
Set text of associated text field.
setTriggerValueChangeEvents(boolean) - Method in class de.unihalle.informatik.Alida.batch.ALDBatchInputManagerSwing
Set the value change event trigger flag.
setTriggerValueChangeEvents(boolean) - Method in class de.unihalle.informatik.Alida.batch.ALDBatchOutputManagerSwing
Set the value change event trigger flag.
setTriggerValueChangeEvents(boolean) - Method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerSwing
Set the value change event trigger flag.
setupAboutIcon() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaMenuBar
Method to initialize the Grappa icon in the about box.
setupAdditionalMenus() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Adds additional menu items.
setupAdditionalMenus() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
 
setupAdditionalTabContents() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
 
setupAdditionalTabContents() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
 
setupBatchConfigPanel() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
 
setupMenu() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaMenuBar
Generates the menubar.
setupParamConfigPanel() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Adds operator parameter configuration panel to input panel.
setupResultTable() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow
Initializes the data table window.
setupWindow() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Construct the frame to configure an operator.
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in interface de.unihalle.informatik.Alida.batch.provider.input.swing.ALDBatchInputIteratorSwing
Interface method for setting new parameter values in GUI.
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.Alida.batch.provider.input.swing.ALDBatchInputNativeArray1DSwing
 
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.Alida.batch.provider.input.swing.ALDBatchInputNumberSwing
 
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerSwing
Update the value of a parameter in the GUI component.
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in interface de.unihalle.informatik.Alida.dataio.provider.ALDDataIOSwing
Interface method for setting new parameter values in GUI.
setValue(Field, Object, Object) - Static method in class de.unihalle.informatik.Alida.dataio.provider.helpers.ALDParametrizedClassDataIOHelper
Sets the value of the member variable associated with field in the object obj.
setValue(String, Object, Object) - Static method in class de.unihalle.informatik.Alida.dataio.provider.helpers.ALDParametrizedClassDataIOHelper
Sets the field with given name of object objto value.
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing
 
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDEnumDataIOSwing
 
setValue(Field, Class<?>, Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDFileDirectoryDataIOSwing.FileDirectoryDataIOPanel
Returns the contents of the text field.
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDFileDirectoryDataIOSwing
 
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing
 
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing
 
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeDataIOSwing
 
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing
 
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDParametrizedClassDataIOSwing
 
setValue(Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParametrizedClassConfigWindow
Update parameter values in GUI.
setValue(String) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaLinkDataIOSwing
 
setValue(Object) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowParameterDescriptor
 
setVerbose(Boolean) - Method in class de.unihalle.informatik.Alida.demo.ApplyToMatrix
Set value of verbose.
setVerbose(Boolean) - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Set the verbose state of this opertor.
setVisible(boolean) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorConfigWindow
Displays the window and inits an operator object (if not done before).
setVisible(boolean) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParametrizedClassConfigWindow
Show or hide the window.
setWorkbenchTab(ALDGrappaWorkbenchTab) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchGraph
Specify workbench tab associated with this graph.
setWorkflowNodeViewMode(mxCell, Parameter.ExpertMode) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Switches the mode for displaying parameters of a node.
setWorkflowTitle(String) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Changes the workflow title.
SezPozAdapter - Class in de.unihalle.informatik.Alida.annotations.indexing
 
showAboutBox() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaMenuBar
Show an about box window.
showAboutBox() - Method in class de.unihalle.informatik.Alida.gui.ALDChooseOpNameFrame
Show an about box window.
showGUI() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
Displays the configuration and control window.
showLoadFileSelectDialog() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
Show file dialog to load a workflow.
showResultFrame() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
(Re-)display the result frame again, if results available.
showSaveFileSelectDialog() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
Show file dialog to save a workflow.
size() - Method in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
Returns the number of key-value mappings in this map.
split(String, char) - Static method in class de.unihalle.informatik.Alida.helpers.ALDParser
Split a string at each occurance of sepChar.
sput(Object, Object, int) - Method in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
Continuation of put(), called only when synch lock is held and interference has been detected.
sremove(Object, int) - Method in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
Continuation of remove(), called only when synch lock is held and interference has been detected.
standardTreeModel - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorChooserTree
Tree of available operators for standard level.
stateGreaterEqual(ALDWorkflowNode.ALDWorkflowNodeState) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowNode
Return true if the state of this node is greater equal the compareState
status - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Label of status bar, changes dynamically.
stepButton - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
Button for stepping through optimization process.
stepSize - Variable in class de.unihalle.informatik.Alida.operator.ALDOperatorControllable
Step size in step-wise execution mode.
stepsize - Variable in class de.unihalle.informatik.Alida.operator.events.ALDConfigurationEvent
Size of one step in step-wise execution mode.
stepsize - Variable in class de.unihalle.informatik.Alida.operator.events.ALDOpParameterChangeEvent
Size of one step in step-wise execution mode.
stepThroughBox - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
Box for activating step-through mode.
stepThroughStepSize - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
Field for specifying number of iterations per step-through step.
stepWiseExecution - Variable in class de.unihalle.informatik.Alida.operator.ALDOperatorControllable
Flag for step-wise execution.
stepwiseExecution - Variable in class de.unihalle.informatik.Alida.operator.events.ALDConfigurationEvent
Flag for stepwise execution.
stepwiseExecution - Variable in class de.unihalle.informatik.Alida.operator.events.ALDOpParameterChangeEvent
Flag for stepwise execution.
stopButton - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
Stop button to stop snake optimization (after end of iteration).
stopWorkflow() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
 
SubclassFinder - Class in de.unihalle.informatik.Alida.helpers
Utility-class with static methods to find all sub-classes of a certain class (or interface) within the scope of the current class-loader find all sub-classes of a certain class (or interface) within the scope of the current class-loader that can be instantiated, i.e. that are neither interfaces nor abstract filter a set of classes by inheritance from a super-class obtain the class of an InstanceParameterSet that can be used to instantiate a sub-class of InstantiableFromParameterSet.
SubclassFinder() - Constructor for class de.unihalle.informatik.Alida.helpers.SubclassFinder
 
SummarizeClusters - Class in de.unihalle.informatik.Alida.demo
Demo operator to summarize the cluster detecteded within experimental data.
SummarizeClusters() - Constructor for class de.unihalle.informatik.Alida.demo.SummarizeClusters
Default constructor.
SummarizeClusters(ExperimentalData) - Constructor for class de.unihalle.informatik.Alida.demo.SummarizeClusters
Constructor.
summary - Variable in class de.unihalle.informatik.Alida.demo.ALDSummarizeArrayOp
Summarizing scalar
supplemental - Variable in class de.unihalle.informatik.Alida.operator.ALDOpParameterDescriptor
 
supportConversion(Class<?>, Type[], Class<?>, Type[]) - Method in interface de.unihalle.informatik.Alida.dataconverter.ALDDataConverter
Does the converter support this kind of conversion.
supportConversion(Class<?>, Type[], Class<?>, Type[]) - Method in class de.unihalle.informatik.Alida.dataconverter.ALDNumberConverter
 
supportConversion(Class<?>, Type[], Class<?>, Type[]) - Method in class de.unihalle.informatik.Alida.dataconverter.ALDVectorNativeArrayConverter
 

T

table - Variable in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
The hash table data.
tableToString(DefaultTableModel, String) - Static method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow
Converts the contents of the table to a string array in CSV format (suitable for import in Excel).
tableToString(DefaultTableModel) - Static method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow
Converts the contents of the table to a string array in CSV format (suitable for import in Excel).
tabPane - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
 
threshold - Variable in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
The table is rehashed when its size exceeds this threshold.
titleString - Variable in class de.unihalle.informatik.Alida.gui.ALDChooseOpNameFrame
Title of frame.
titleString - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Title string of window.
topLevelCall - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing
Local flag to indicate if object is created on OpRunner top level or not; flag modules if deep validation is done or not.
toString() - Method in class de.unihalle.informatik.Alida.dataconverter.ALDDataConverterManager.ALDSourceTargetClassPair
 
toString() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentComboBoxItem
 
toString() - Method in class de.unihalle.informatik.Alida.datatypes.ALDDirectoryString
 
toString() - Method in class de.unihalle.informatik.Alida.datatypes.ALDFileString
 
toString() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaNodeInfo
 
toString() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaNodePortInfo
Returns an identifier string.
toString() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowNodeID
 
toStringVerbose() - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Returns a string containing printable information about this operator including parameters.
type - Variable in exception de.unihalle.informatik.Alida.exceptions.ALDBatchIOManagerException
Type of exception.
type - Variable in exception de.unihalle.informatik.Alida.exceptions.ALDBatchIOProviderException
Type of exception.
type - Variable in exception de.unihalle.informatik.Alida.exceptions.ALDDataConverterException
Type of exception.
type - Variable in exception de.unihalle.informatik.Alida.exceptions.ALDDataIOManagerException
Type of exception.
type - Variable in exception de.unihalle.informatik.Alida.exceptions.ALDDataIOProviderException
Type of exception.
type - Variable in exception de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Type of exception object.
type - Variable in exception de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
Type of exception object.
type - Variable in exception de.unihalle.informatik.Alida.exceptions.ALDProviderManagerException
Type of exception.
type - Variable in exception de.unihalle.informatik.Alida.exceptions.ALDWorkflowException
Type of exception object.
typeName - Variable in class de.unihalle.informatik.Alida.operator.ALDPort
Typename of this port.

U

unconfiguredItems() - Method in interface de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator
Return a list of not or not properly configured items of this object.
unconfiguredItems() - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Returns all required IN an INOUT parameters which have a null value
unmarkAllParameters() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
Sets label colors of all parameter to black and of all links to blue.
unmarkParameter(ALDParameterDescriptor) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
Sets label color of parameter to black or of link to blue (e.g. if validation successful).
untitledWorkflowName - Static variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Name of a workflow with out a proper name
updateConfigurationStatus(Collection<String>) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
Marks configurations status of required parameters by color.
updateNodeID(ALDWorkflowNodeID) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy.ParameterChangeListener
Updates the ID of the workflow node associated with this listener.
updateNodeStatus(ALDWorkflowNode.ALDWorkflowNodeState) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
Updates the window according to the configuration status of the operator.
updateOperator(ALDOperator) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorConfigWindow
Update operator linked to window.
updateOperator(ALDOperator) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Updates the configuration window with settings of new operator.
updateOperator(ALDOperator) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
Tells the surrounding proxy that a new operator has been loaded.
updateOperator(ALDOperator) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
Method called by GUI if a new operator was loaded.
updateOperatorAfterConfigReload(ALDOperator) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
This method takes care of updating the GUI after reloading the operator.
updateOperatorDescriptors() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
Initializes all internal members dealing with operator descriptors.
updateOperatorDescriptors(LinkedList<ALDOpParameterDescriptor>) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
 
updateParamConfigurationStatus(Collection<String>) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Updates the window according to the status of the operator parameters.
updateWorkflowNodeStates() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Checks the states of all nodes and updates their color.
useRegEx - Variable in class de.unihalle.informatik.Alida.tools.ALDOpRunner
If true, matching of operator name from commandline to the annoteated ALDOperators uses regular expression matching, otherwise exact substring matching

V

validate() - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Validates the parameters and inputs of this operator.
validateCustom() - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Operator specific validation of parameters and inputs.
validateGeneric() - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Generic validation of the in and inout parameters of this operator.
validateOperatorParameters(boolean) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
Check if operator is ready to run.
validateParameters() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
Check if all GUI elements can deliver a proper (non-null) value.
value - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentTextField
Current value of the text field.
valueChanged(TreeSelectionEvent) - Method in class de.unihalle.informatik.Alida.gui.ALDChooseOpNameFrame
 
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.annotations.ALDAOperator.ExecutionMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.annotations.ALDAOperator.Level
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.annotations.Parameter.Direction
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.annotations.Parameter.ExpertMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.annotations.Parameter.Type
Deprecated. Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.batch.ALDBatchInputManagerSwing.ProviderInteractionLevel
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.batch.ALDBatchOutputManagerSwing.ProviderInteractionLevel
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.dataio.ALDDataIOManagerSwing.ProviderInteractionLevel
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow.TableModelDelimiter
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.demo.ApplyToMatrix.SummarizeMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.demo.MatrixSum.SummarizeMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.exceptions.ALDBatchIOManagerException.ALDBatchIOManagerExceptionType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.exceptions.ALDBatchIOProviderException.ALDBatchIOProviderExceptionType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.exceptions.ALDDataConverterException.ALDDataIOProviderExceptionType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.exceptions.ALDDataIOManagerException.ALDDataIOManagerExceptionType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.exceptions.ALDDataIOProviderException.ALDDataIOProviderExceptionType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.exceptions.ALDOperatorException.OperatorExceptionType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException.DAGExceptionType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.exceptions.ALDProviderManagerException.ALDProviderManagerExceptionType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.exceptions.ALDWorkflowException.WorkflowExceptionType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy.WorkflowThreadStatus
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.operator.ALDOperatorControllable.OperatorControlStatus
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.operator.ALDOperatorLocation.LocationType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.operator.ALDProcessingDAG.HistoryType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.operator.events.ALDControlEvent.ALDControlEventType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.workflows.ALDWorkflow.ALDWorkflowContextType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.workflows.ALDWorkflowNode.ALDWorkflowNodeState
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.workflows.events.ALDWorkflowClassEvent.ALDWorkflowClassEventType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.workflows.events.ALDWorkflowEvent.ALDWorkflowEventType
Returns the enum constant of this type with the specified name.
values() - Static method in enum de.unihalle.informatik.Alida.annotations.ALDAOperator.ExecutionMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.Alida.annotations.ALDAOperator.Level
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.Alida.annotations.Parameter.Direction
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.Alida.annotations.Parameter.ExpertMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.Alida.annotations.Parameter.Type
Deprecated. Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.Alida.batch.ALDBatchInputManagerSwing.ProviderInteractionLevel
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.Alida.batch.ALDBatchOutputManagerSwing.ProviderInteractionLevel
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.Alida.dataio.ALDDataIOManagerSwing.ProviderInteractionLevel
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow.TableModelDelimiter
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.Alida.demo.ApplyToMatrix.SummarizeMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.Alida.demo.MatrixSum.SummarizeMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.Alida.exceptions.ALDBatchIOManagerException.ALDBatchIOManagerExceptionType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.Alida.exceptions.ALDBatchIOProviderException.ALDBatchIOProviderExceptionType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.Alida.exceptions.ALDDataConverterException.ALDDataIOProviderExceptionType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.Alida.exceptions.ALDDataIOManagerException.ALDDataIOManagerExceptionType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.Alida.exceptions.ALDDataIOProviderException.ALDDataIOProviderExceptionType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.Alida.exceptions.ALDOperatorException.OperatorExceptionType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException.DAGExceptionType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.Alida.exceptions.ALDProviderManagerException.ALDProviderManagerExceptionType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.Alida.exceptions.ALDWorkflowException.WorkflowExceptionType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy.WorkflowThreadStatus
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.Alida.operator.ALDOperatorControllable.OperatorControlStatus
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.Alida.operator.ALDOperatorLocation.LocationType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.Alida.operator.ALDProcessingDAG.HistoryType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.Alida.operator.events.ALDControlEvent.ALDControlEventType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.Alida.workflows.ALDWorkflow.ALDWorkflowContextType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.Alida.workflows.ALDWorkflowNode.ALDWorkflowNodeState
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.Alida.workflows.events.ALDWorkflowClassEvent.ALDWorkflowClassEventType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.Alida.workflows.events.ALDWorkflowEvent.ALDWorkflowEventType
Returns an array containing the constants of this enum type, in the order they are declared.
verbose - Variable in class de.unihalle.informatik.Alida.operator.ALDOperator
Verbose flag to be inherited by all operators.
versionProvider - Variable in class de.unihalle.informatik.Alida.operator.ALDOperator
Instance of a class providing version information.

W

workBench - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaFrame
Component which holds the graph.
workBench - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaMenuBar
Reference to the workbench of window this menubar belongs to.
workBench - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Reference to the surrounding work bench object.
workflowLoadEventlistenerList - Static variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
List of control event listeners attached to this class used for loading workflows.
workflows - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
List of workflows currently managed.
workflowStatus - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
Current status of the operator execution thread.
workflowTitle - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Title of this workflow as shown on the tab.
workflowXMLFileExtension - Static variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Standard extension for a xml file holding the external representation of a workflow.
writeData(ALDBatchRunResultInfo, ALDParameterDescriptor) - Method in class de.unihalle.informatik.Alida.batch.ALDBatchOutputManagerSwing
Interface method for displaying a batch summary in the GUI.
writeData(ALDBatchRunResultInfo, ALDParameterDescriptor) - Method in interface de.unihalle.informatik.Alida.batch.provider.output.swing.ALDBatchOutputSummarizerSwing
Generates a graphical component to visualize set of result data.
writeData(ALDBatchRunResultInfo, ALDParameterDescriptor) - Method in class de.unihalle.informatik.Alida.batch.provider.output.swing.ALDSummarizerNativeDataSwing
 
writeData(Object, String) - Method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerCmdline
Writes data to the specified location.
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerSwing
Return a gui element displaying the obj or null.
writeData(Object) - Method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerXmlbeans
Writes data to the specified location.
writeData(Object, String) - Method in interface de.unihalle.informatik.Alida.dataio.provider.ALDDataIOCmdline
Interface for writing the object data to the target location.
writeData(Object, ALDParameterDescriptor) - Method in interface de.unihalle.informatik.Alida.dataio.provider.ALDDataIOSwing
Interface method for displaying an object in the GUI.
writeData(Object) - Method in interface de.unihalle.informatik.Alida.dataio.provider.ALDDataIOXmlbeans
Interface for writing the object data to the target location.
writeData(Object, String) - Method in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDFileDirectoryDataIOCmdline
 
writeData(Object, String) - Method in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDStandardizedDataIOCmdline
Return a string representation of given object value or print it to a file.
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing
 
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDEnumDataIOSwing
 
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDFileDirectoryDataIOSwing
 
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing
 
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing
 
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeDataIOSwing
 
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing
 
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDParametrizedClassDataIOSwing
 
writeData(Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.xmlbeans.ALDCollectionDataIOXmlbeans
Returns the string representations of collection.
writeData(Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.xmlbeans.ALDEnumDataIOXmlbeans
 
writeData(Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.xmlbeans.ALDFileDirectoryDataIOXmlbeans
 
writeData(Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.xmlbeans.ALDNativeDataIOXmlbeans
 
writeData(Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.xmlbeans.ALDParametrizedClassDataIOXmlbeans
Transient members are not written.
writeData(Object) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowDataIOXmlbeans
 
writeHistory(Object, String) - Static method in class de.unihalle.informatik.Alida.operator.ALDOperator
Write the processing history if any to a graphml file.
writeHistory(Object, String, ALDProcessingDAG.HistoryType) - Static method in class de.unihalle.informatik.Alida.operator.ALDOperator
Write the processing history if any to a graphml file.
writeHistory(Object, String, ALDProcessingDAG.HistoryType, boolean) - Static method in class de.unihalle.informatik.Alida.operator.ALDOperator
Write the processing history if any to a graphml file.
writeHistory(Object, String) - Method in class de.unihalle.informatik.Alida.operator.ALDPortHashAccess
Deprecated.  
writeHistory(Object, String, ALDProcessingDAG.HistoryType) - Method in class de.unihalle.informatik.Alida.operator.ALDPortHashAccess
Deprecated.  
writeHistory(Object, String, ALDProcessingDAG.HistoryType, boolean) - Method in class de.unihalle.informatik.Alida.operator.ALDPortHashAccess
Write the processing history (if available) to a graphml file.
writeParametersToXml(String) - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Write the parameter values to an xml file.
writeXml(String, Object) - Static method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerXmlbeans
Write to object to a file using xmlbeans providers
writeXml(File, Object) - Static method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerXmlbeans
Write to object to a file using xmlbeans providers

Y

yesnoOption - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Labels to be used on buttons of Yes/No message boxes.
yesnoOption - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
Labels to be used on buttons of Yes/No message boxes.

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