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.ALDNativeArray1DDataIOSwing.ArrayConfigWindow.DataTabFileFilter
 
accept(File) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigWindow.DataTabFileFilter
 
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.ALDCollectionDataIOSwing.CollectionConfigWindow
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing.CollectionShowButton
 
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.ALDNativeArray1DDataIOSwing.ArrayConfigWindow
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayShowButton
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigWindow
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayShowButton
 
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.ALDOperatorDataIOSwing.OperatorHierarchyConfigPanel.AbstrOpClassPanel
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDParametrizedClassDataIOSwing.ParametrizedClassPanel
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDParametrizedClassDataIOSwing.ParametrizedClassShowButton
 
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.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.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.
addAttrToEdge(EdgeType, String, String) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Add an attribute to a graphml edge
addAttrToGraph(GraphType, String, String) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Add an attribute to a graphml graph
addAttrToGraphml(GraphmlType, String, String) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Add an attribute to a graphml element
addAttrToNode(NodeType, String, String) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Add an attribute to a graphml node
addAttrToPort(PortType, String, String) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Add an attribute to a graphml port
addChild(ALDOpNode) - Method in class de.unihalle.informatik.Alida.operator.ALDOpNode
Add a child found during back tracing.
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.
addData(ALDDataPort) - Method in class de.unihalle.informatik.Alida.operator.ALDOpNode
Add a data port found during back tracing.
addDataPortToGraphml(GraphType, ALDDataPort) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Add a data port to the graphML graph
addDirectChild(ALDOpNode) - Method in class de.unihalle.informatik.Alida.operator.ALDOpNode
Add a directly registered child during invocation.
addEdge(GraphType, ALDPort, ALDPort, int) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Add an graphml edge to graph with index idx
addEdge(ALDWorkflowEdge) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
 
addGraphmlHistory(GraphType, ALDDataPort) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Add the complete history of an object represented by a data port, which was read from a graphml file, to a graph object.
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.
addKey(GraphmlType, String, KeyForType.Enum, String, KeyTypeType.Enum) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
add a key definition to graphml
addNewWorkflow() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
Adds a new workflow (tab) to the workbench.
addNode(ALDWorkflowNode) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Add this node to the workflow, create a NodeId and update mapping.
addNodeToWorkflow(ALDOperatorLocation) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
 
addOpNodePortToGraphml(GraphType, ALDOpNodePort) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Add a opNode port object to the graphML graph
addOpNodeToGraph(GraphType, ALDOpNode) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Add an opNode to the graph of the enclosing opNode.
addParameter(String, Object, Field, String, StringBuffer) - Method in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDParametrizedClassDataIOCmdline
Format the parameter name of the object obj into the buffer bufstr using formatString to determine formating.
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.
addParameterHash(NodeType, ALDOpNode) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Add the parameter hash to to a graphml node.
addValueChangeEventListener(ALDSwingValueChangeListener) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.events.ALDSwingValueChangeReporter
Adds a listener to this reporter.
addXmlHistory(NodeType, XmlObject) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Add the complete history of a ALDData from a generic XML file to a graphml node.
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.ExecutionMode() - Constructor for enum de.unihalle.informatik.Alida.annotations.ALDAOperator.ExecutionMode
 
ALDAOperator.Level - Enum in de.unihalle.informatik.Alida.annotations
Enumerates the different levels of this operator.
ALDAOperator.Level() - Constructor for enum de.unihalle.informatik.Alida.annotations.ALDAOperator.Level
 
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() - Constructor for class de.unihalle.informatik.Alida.batch.ALDBatchInputManagerSwing
Private constructor which inits the provider map.
ALDBatchInputManagerSwing.ProviderInteractionLevel - Enum in de.unihalle.informatik.Alida.batch
Levels to enable/disable interactive provider behaviour.
ALDBatchInputManagerSwing.ProviderInteractionLevel() - Constructor for enum de.unihalle.informatik.Alida.batch.ALDBatchInputManagerSwing.ProviderInteractionLevel
 
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
 
ALDBatchInputNativeArray1DSwing.ALDBatchIteratorNativeArray1D - Class in de.unihalle.informatik.Alida.batch.provider.input.swing
Iterates row-wise over a 2D array.
ALDBatchInputNativeArray1DSwing.ALDBatchIteratorNativeArray1D(Object, Class<?>) - Constructor for class de.unihalle.informatik.Alida.batch.provider.input.swing.ALDBatchInputNativeArray1DSwing.ALDBatchIteratorNativeArray1D
Default constructor.
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.
ALDBatchIOManagerException.ALDBatchIOManagerExceptionType() - Constructor for enum de.unihalle.informatik.Alida.exceptions.ALDBatchIOManagerException.ALDBatchIOManagerExceptionType
 
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.
ALDBatchIOProviderException.ALDBatchIOProviderExceptionType() - Constructor for enum de.unihalle.informatik.Alida.exceptions.ALDBatchIOProviderException.ALDBatchIOProviderExceptionType
 
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() - Constructor for class de.unihalle.informatik.Alida.batch.ALDBatchOutputManagerSwing
Private constructor.
ALDBatchOutputManagerSwing.ProviderInteractionLevel - Enum in de.unihalle.informatik.Alida.batch
Levels to enable/disable interactive provider behaviour.
ALDBatchOutputManagerSwing.ProviderInteractionLevel() - Constructor for enum de.unihalle.informatik.Alida.batch.ALDBatchOutputManagerSwing.ProviderInteractionLevel
 
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.
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
Supplies helper methods to, e.g., lookup classes with annotations.
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
 
ALDCollectionDataIOSwing.CollectionConfigButton - Class in de.unihalle.informatik.Alida.dataio.provider.swing
GUI element for configuring collections.
ALDCollectionDataIOSwing.CollectionConfigButton(Field, Class<?>, Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing.CollectionConfigButton
Constructor.
ALDCollectionDataIOSwing.CollectionConfigWindow - Class in de.unihalle.informatik.Alida.dataio.provider.swing
Collection configuration window.
ALDCollectionDataIOSwing.CollectionConfigWindow(Field, Class<?>, Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing.CollectionConfigWindow
Default constructor.
ALDCollectionDataIOSwing.CollectionShowButton - Class in de.unihalle.informatik.Alida.dataio.provider.swing
GUI element for displaying collections.
ALDCollectionDataIOSwing.CollectionShowButton(Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing.CollectionShowButton
Constructor.
ALDConcReadWeakHashMap - Class in de.unihalle.informatik.Alida.helpers
A version of Hashtable that supports concurrent reading/exclusive writing.
ALDConcReadWeakHashMap(int, float) - Constructor for class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
Constructs a new, empty map with the specified initial capacity and the specified load factor.
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.
ALDControlEvent.ALDControlEventType() - Constructor for enum de.unihalle.informatik.Alida.operator.events.ALDControlEvent.ALDControlEventType
 
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.
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 Mangager for reading/writing from command line.
ALDDataIOManagerCmdline() - Constructor for class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerCmdline
private constructor
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.
ALDDataIOManagerException.ALDDataIOManagerExceptionType() - Constructor for enum de.unihalle.informatik.Alida.exceptions.ALDDataIOManagerException.ALDDataIOManagerExceptionType
 
ALDDataIOManagerSwing - Class in de.unihalle.informatik.Alida.dataio
This class implements a DataIO mangager for reading/writing from a graphical user interface.
ALDDataIOManagerSwing() - Constructor for class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerSwing
private constructor
ALDDataIOManagerSwing.ProviderInteractionLevel - Enum in de.unihalle.informatik.Alida.dataio
Levels to enable/disable interactive provider behaviour.
ALDDataIOManagerSwing.ProviderInteractionLevel() - Constructor for enum de.unihalle.informatik.Alida.dataio.ALDDataIOManagerSwing.ProviderInteractionLevel
 
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.
ALDDataIOProviderException.ALDDataIOProviderExceptionType() - Constructor for enum de.unihalle.informatik.Alida.exceptions.ALDDataIOProviderException.ALDDataIOProviderExceptionType
 
ALDDataIOSwing - Interface in de.unihalle.informatik.Alida.dataio.provider
Interface for Alida's automatic data I/O via GUIs based on Swing.
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.
ALDEdge(ALDPort, ALDPort) - Constructor for class de.unihalle.informatik.Alida.operator.ALDEdge
Construct an edge for given source and target ports.
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
 
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.
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.
ALDGrappaCellInfo - Class in de.unihalle.informatik.Alida.grappa
 
ALDGrappaCellInfo() - Constructor for class de.unihalle.informatik.Alida.grappa.ALDGrappaCellInfo
 
ALDGrappaCellInfo(String) - Constructor for class de.unihalle.informatik.Alida.grappa.ALDGrappaCellInfo
 
ALDGrappaCellInfo(String, Integer) - Constructor for class de.unihalle.informatik.Alida.grappa.ALDGrappaCellInfo
 
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
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
ALDGrappaWorkbenchTab - Class in de.unihalle.informatik.Alida.grappa
Grappa workflow graph component.
ALDGrappaWorkbenchTab(ALDGrappaWorkbench, mxGraph) - 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.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.
ALDInputParameterTester.EnumSelection - Enum in de.unihalle.informatik.Alida.demo
 
ALDInputParameterTester.EnumSelection() - Constructor for enum de.unihalle.informatik.Alida.demo.ALDInputParameterTester.EnumSelection
 
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.
ALDNativeArray1DDataIOSwing.ArrayConfigButton - Class in de.unihalle.informatik.Alida.dataio.provider.swing
GUI element for configuring 1D arrays of native data types and wrapper.
ALDNativeArray1DDataIOSwing.ArrayConfigButton(Field, Class<?>, Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayConfigButton
Constructor.
ALDNativeArray1DDataIOSwing.ArrayConfigWindow - Class in de.unihalle.informatik.Alida.dataio.provider.swing
Graphical user interface window for displaying objects of class ALDTableModel.
ALDNativeArray1DDataIOSwing.ArrayConfigWindow(Field, Class<?>, Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayConfigWindow
Default constructor.
ALDNativeArray1DDataIOSwing.ArrayConfigWindow.DataTabFileFilter - Class in de.unihalle.informatik.Alida.dataio.provider.swing
Internal class that realizes a java.swing.filechooser.FileFilter for text files where MiToBo table data is stored.
ALDNativeArray1DDataIOSwing.ArrayConfigWindow.DataTabFileFilter() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayConfigWindow.DataTabFileFilter
 
ALDNativeArray1DDataIOSwing.ArrayConfigWindow.TableFocusListener - Class in de.unihalle.informatik.Alida.dataio.provider.swing
Focus listener to commit edits if table looses the focus.
ALDNativeArray1DDataIOSwing.ArrayConfigWindow.TableFocusListener() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayConfigWindow.TableFocusListener
 
ALDNativeArray1DDataIOSwing.ArrayShowButton - Class in de.unihalle.informatik.Alida.dataio.provider.swing
GUI element for displaying 2D arrays.
ALDNativeArray1DDataIOSwing.ArrayShowButton(Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayShowButton
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.
ALDNativeArray2DDataIOSwing.ArrayConfigButton - Class in de.unihalle.informatik.Alida.dataio.provider.swing
GUI element for configuring collections.
ALDNativeArray2DDataIOSwing.ArrayConfigButton(Field, Class<?>, Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigButton
Constructor.
ALDNativeArray2DDataIOSwing.ArrayConfigWindow - Class in de.unihalle.informatik.Alida.dataio.provider.swing
Graphical user interface window for displaying objects of class DefaultTableModel.
ALDNativeArray2DDataIOSwing.ArrayConfigWindow(Field, Class<?>, Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigWindow
Default constructor.
ALDNativeArray2DDataIOSwing.ArrayConfigWindow.DataTabFileFilter - Class in de.unihalle.informatik.Alida.dataio.provider.swing
Internal class that realizes a FileFilter for text files where MiToBo table data is stored.
ALDNativeArray2DDataIOSwing.ArrayConfigWindow.DataTabFileFilter() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigWindow.DataTabFileFilter
 
ALDNativeArray2DDataIOSwing.ArrayConfigWindow.TableFocusListener - Class in de.unihalle.informatik.Alida.dataio.provider.swing
Focus listener to commit edits if table looses the focus.
ALDNativeArray2DDataIOSwing.ArrayConfigWindow.TableFocusListener() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigWindow.TableFocusListener
 
ALDNativeArray2DDataIOSwing.ArrayShowButton - Class in de.unihalle.informatik.Alida.dataio.provider.swing
GUI element for displaying 2D arrays.
ALDNativeArray2DDataIOSwing.ArrayShowButton(Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayShowButton
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
 
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.
ALDOperator.HidingMode() - Constructor for enum de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode
 
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.
ALDOperatorChooserTree.AuxNode - Class in de.unihalle.informatik.Alida.gui
Node to build up a tree of the package structure of ALDOperators.
ALDOperatorChooserTree.AuxNode(ALDOperatorLocation) - Constructor for class de.unihalle.informatik.Alida.gui.ALDOperatorChooserTree.AuxNode
Constructor.
ALDOperatorChooserTree.AuxNode() - Constructor for class de.unihalle.informatik.Alida.gui.ALDOperatorChooserTree.AuxNode
Default constructor.
ALDOperatorChooserTreeNode - Class in de.unihalle.informatik.Alida.gui
Class for managing nodes of the tree view.
ALDOperatorChooserTreeNode(String, ALDOperatorLocation) - Constructor for class de.unihalle.informatik.Alida.gui.ALDOperatorChooserTreeNode
constructor
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.
ALDOperatorControllable.OperatorControlStatus() - Constructor for enum de.unihalle.informatik.Alida.operator.ALDOperatorControllable.OperatorControlStatus
 
ALDOperatorDataIOCmdline - Class in de.unihalle.informatik.Alida.dataio.provider.cmdline
DataIO provider for ALDOperators from command line.
ALDOperatorDataIOCmdline() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDOperatorDataIOCmdline
 
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.OperatorConfigButton - Class in de.unihalle.informatik.Alida.dataio.provider.swing
GUI element for configuring a single operator.
ALDOperatorDataIOSwing.OperatorConfigButton(Class<?>, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorConfigButton
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.
ALDOperatorDataIOSwing.OperatorHierarchyConfigPanel - Class in de.unihalle.informatik.Alida.dataio.provider.swing
Element for handling operator inheritance hierarchies in configuration.
ALDOperatorDataIOSwing.OperatorHierarchyConfigPanel() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorHierarchyConfigPanel
Default constructor.
ALDOperatorDataIOSwing.OperatorHierarchyConfigPanel.AbstrOpClassPanel - Class in de.unihalle.informatik.Alida.dataio.provider.swing
GUI element class for parametrized class parameters.
ALDOperatorDataIOSwing.OperatorHierarchyConfigPanel.AbstrOpClassPanel(Field, Class<?>, Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorHierarchyConfigPanel.AbstrOpClassPanel
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.
ALDOperatorException.OperatorExceptionType() - Constructor for enum de.unihalle.informatik.Alida.exceptions.ALDOperatorException.OperatorExceptionType
 
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.
ALDOperatorGUIExecutionProxy.WorkflowThreadStatus() - Constructor for enum de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy.WorkflowThreadStatus
 
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
 
ALDOperatorLocation.LocationType() - Constructor for enum de.unihalle.informatik.Alida.operator.ALDOperatorLocation.LocationType
 
ALDOperatorLocationType - Interface in de.unihalle.informatik.Alida.operator
Describes different types of location from which an ALDOperator may be instantiated.
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.
ALDParameterWrapper - Class in de.unihalle.informatik.Alida.operator
This class is a wrapper for all parameters of a ALDOperator.
ALDParameterWrapper(ALDOperator) - Constructor for class de.unihalle.informatik.Alida.operator.ALDParameterWrapper
Create an instance for the parameters of op
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 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.
ALDParametrizedClassDataIOSwing.ParametrizedClassPanel - Class in de.unihalle.informatik.Alida.dataio.provider.swing
GUI element class for parametrized class parameters.
ALDParametrizedClassDataIOSwing.ParametrizedClassPanel(Field, Class<?>, Object) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.ALDParametrizedClassDataIOSwing.ParametrizedClassPanel
Default constructor.
ALDParametrizedClassDataIOSwing.ParametrizedClassShowButton - Class in de.unihalle.informatik.Alida.dataio.provider.swing
Button to visualize parametrized class objects.
ALDParametrizedClassDataIOSwing.ParametrizedClassShowButton(Object) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.ALDParametrizedClassDataIOSwing.ParametrizedClassShowButton
Default constructor.
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
ALDPortHash - Class in de.unihalle.informatik.Alida.operator
Hashmap keeping links between objects and data ports in processing history.
ALDPortHash() - Constructor for class de.unihalle.informatik.Alida.operator.ALDPortHash
Constructor without function.
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.
ALDProcessingDAG.HistoryType() - Constructor for enum de.unihalle.informatik.Alida.operator.ALDProcessingDAG.HistoryType
 
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.
ALDProcessingDAGException.DAGExceptionType() - Constructor for enum de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException.DAGExceptionType
 
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
 
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() - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentComboBox
Default constructor.
ALDSwingComponentComboBox(Vector<?>) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentComboBox
Default constructor.
ALDSwingComponentComboBox(String[]) - Constructor for class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentComboBox
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.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.
ALDTableWindow.TableModelDelimiter() - Constructor for enum de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow.TableModelDelimiter
 
ALDToplevelOperator - Class in de.unihalle.informatik.Alida.operator
This class is just a dummy opNode acting as the first opNode with the stack of active opNodes of each thread.
ALDToplevelOperator() - Constructor for class de.unihalle.informatik.Alida.operator.ALDToplevelOperator
Construct a (dummy) top level opNode
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.
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
 
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
 
ALDWeakHashMapEntry - Class in de.unihalle.informatik.Alida.helpers
Weak reference hashmap entry.
ALDWeakHashMapEntry(int, Object, Object, ALDWeakHashMapEntry, ReferenceQueue<Object>) - Constructor for class de.unihalle.informatik.Alida.helpers.ALDWeakHashMapEntry
Constructor.
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.
ALDWorkflow.ALDWorkflowContextType() - Constructor for enum de.unihalle.informatik.Alida.workflows.ALDWorkflow.ALDWorkflowContextType
 
ALDWorkflow.ExecuteThread - Class in de.unihalle.informatik.Alida.workflows
This thread executes all non-ready nodes in the given order.
ALDWorkflow.ExecuteThread(ALDWorkflow, List<ALDWorkflowNode>) - Constructor for class de.unihalle.informatik.Alida.workflows.ALDWorkflow.ExecuteThread
 
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.
ALDWorkflowClassEvent.ALDWorkflowClassEventType() - Constructor for enum de.unihalle.informatik.Alida.workflows.events.ALDWorkflowClassEvent.ALDWorkflowClassEventType
 
ALDWorkflowClassEventListener - Interface in de.unihalle.informatik.Alida.workflows.events
Listener interface for `Alida` workflow events.
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
ALDWorkflowEdgeID() - Constructor for class de.unihalle.informatik.Alida.workflows.ALDWorkflowEdgeID
Create a new edge is
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.
ALDWorkflowEvent.ALDWorkflowEventType() - Constructor for enum de.unihalle.informatik.Alida.workflows.events.ALDWorkflowEvent.ALDWorkflowEventType
 
ALDWorkflowEventListener - Interface in de.unihalle.informatik.Alida.workflows.events
Listener interface for `Alida` workflow events.
ALDWorkflowEventManager - Class in de.unihalle.informatik.Alida.workflows
 
ALDWorkflowEventManager(ALDWorkflowEventListener) - Constructor for class de.unihalle.informatik.Alida.workflows.ALDWorkflowEventManager
 
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
 
ALDWorkflowException.WorkflowExceptionType() - Constructor for enum de.unihalle.informatik.Alida.exceptions.ALDWorkflowException.WorkflowExceptionType
 
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
 
ALDWorkflowNode.ALDWorkflowNodeState() - Constructor for enum de.unihalle.informatik.Alida.workflows.ALDWorkflowNode.ALDWorkflowNodeState
 
ALDWorkflowNodeID - Class in de.unihalle.informatik.Alida.workflows
Class to index a work flow node.
ALDWorkflowNodeID() - Constructor for class de.unihalle.informatik.Alida.workflows.ALDWorkflowNodeID
Create a new node id.
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
 
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.
allDataports - Variable in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
 
allEdges - Variable in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
 
allInstances - Static variable in class de.unihalle.informatik.Alida.operator.ALDOpNode
 
allOpNodes - Variable in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
 
allowedClassForIO(Class) - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Is this class allowed as Input and/or Output?
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
ApplyToMatrix.SummarizeMode() - Constructor for enum de.unihalle.informatik.Alida.demo.ApplyToMatrix.SummarizeMode
 
args - Variable in class de.unihalle.informatik.Alida.tools.ALDOpRunner
command line arguments.
args - Variable in class de.unihalle.informatik.Alida.tools.PrintDataIOProvider
command line arguments.
array_Intege_2D - Variable in class de.unihalle.informatik.Alida.demo.ALDInputParameterTester
 
array_Integer - Variable in class de.unihalle.informatik.Alida.demo.ALDInputParameterTester
 
array_String - Variable in class de.unihalle.informatik.Alida.demo.ALDInputParameterTester
 
array_String_2D - Variable in class de.unihalle.informatik.Alida.demo.ALDInputParameterTester
 
arrayRows - Variable in class de.unihalle.informatik.Alida.batch.provider.input.swing.ALDBatchInputNativeArray1DSwing.ALDBatchIteratorNativeArray1D
Number of rows in array.
arrayToString(Object) - Static method in class de.unihalle.informatik.Alida.helpers.ALDParser
Formats an array according to Alida data I/O conventions.
availableClasses - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorHierarchyConfigPanel.AbstrOpClassPanel
List of available classes.
availableClasses - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDParametrizedClassDataIOSwing.ParametrizedClassPanel
List of available classes.

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.
buildInputPanel() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
Builds up the input panel.
buildWindow() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorConfigWindow
Generates the window.
buildWindow() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParametrizedClassConfigWindow
Generates the window.
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.
cell - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab.ContextMenuNodeEdge
 
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.
checkDataflowStateChange(ALDWorkflowNode) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Updates the state of this node according to the states of its parents.
checkLocalStateChange(ALDWorkflowNode) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Updates the state of this node according to its local configuration.
checkParentStates(ALDWorkflowNode, ALDWorkflowNode.ALDWorkflowNodeState) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Check if all parents of the given node have a state at least requiredState.
checkValue() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentTextField
Method that handles events triggered by the text field.
children - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorChooserTree.AuxNode
Children of this node.
children - Variable in class de.unihalle.informatik.Alida.operator.ALDOpNode
children of this opNode, will be set during back tracing
classes - Static variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing
List of supported classes.
classes - Static variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing
List of supported classes.
classesAllowed(ALDOpParameterDescriptor, ALDOpParameterDescriptor) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Check is class of source parameter is assignable to target parameter
classloader - Static variable in class de.unihalle.informatik.Alida.annotations.indexing.SezPozAdapter
Class loader to be used for searching SezPoz annotation indices.
className - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParametrizedClassConfigWindow
Name of parametrized class to configure.
classname - Variable in class de.unihalle.informatik.Alida.operator.ALDOpNodePort
The canaonical class name of the ALDData bound to the port.
className - Variable in class de.unihalle.informatik.Alida.operator.ALDParameterWrapper
 
classSelection - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorHierarchyConfigPanel.AbstrOpClassPanel
Combobox containing available classes to select.
classSelection - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDParametrizedClassDataIOSwing.ParametrizedClassPanel
Combobox containing available classes to select.
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.
clusters - Variable in class de.unihalle.informatik.Alida.demo.ALDClusterExperiment
Clusters represented as a list of clusters, where each cluster is a set of experiment Ids, i.e. indices into to input experimental data.
clusters - Variable in class de.unihalle.informatik.Alida.demo.ALDKmeansOp
Clusters represented as a list of clusters, where each cluster is a set of experiment Ids, i.e. indices into to input experimental data.
clusters - Variable in class de.unihalle.informatik.Alida.demo.AnalyzeExperiment
Clusters represented as a list of clusters, where each cluster is a set of experiment Ids, i.e. indices into to input experimental data.
clusters - Variable in class de.unihalle.informatik.Alida.demo.SummarizeClusters
Clusters represented as a list of clusters, where each cluster is a set of experiment Ids, i.e. indices into to input experimental data.
collectInstances - Static variable in class de.unihalle.informatik.Alida.operator.ALDOpNode
if true all instances of ALDOpNode will be collected in a static Vector.
comment - Variable in exception de.unihalle.informatik.Alida.exceptions.ALDException
Exception comment.
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.
completeDAG - Variable in class de.unihalle.informatik.Alida.operator.ALDOpNode
This opnode prefers a complete DAG to constructed for its invocation.
compMap - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
Maps a parameter descriptor to its component in the GUI.
compMapLinkBak - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
 
componentMap - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorResultFrame
Map of compenents displayed in frame.
compTextField - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDSwingComponentTextField
Associated Swing component.
confButton - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing.CollectionConfigButton
Button to open configuration window.
confButton - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayConfigButton
GUI component associated with this Swing component.
confButton - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigButton
Button to open configuration window.
confButton - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing
Configure button for operator as parameter.
configPanel - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorConfigWindow
Sub-panel containing operator parameters.
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.
configWins - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorHierarchyConfigPanel.AbstrOpClassPanel
Hashmap to store configuration windows for classes.
configWins - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDParametrizedClassDataIOSwing.ParametrizedClassPanel
Hashmap to store configuration windows for classes.
confWin - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing.CollectionConfigButton
Collection configuration window.
confWin - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayConfigButton
Array configuration window.
confWin - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigButton
Collection configuration window.
confWin - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorConfigButton
Operator configuration window.
constructionMode - Static variable in class de.unihalle.informatik.Alida.operator.ALDOperator
Mode of implicit construction of the processing graph.
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.
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.
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
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.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.ALDOperatorDataIOSwing.OperatorHierarchyConfigPanel
Generates the GUI element.
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDParametrizedClassDataIOSwing
 
createInParameterPanel(Boolean, Boolean) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
Create a panel with an entry for each input parameter as requested.
createNewWorkflowEdge(mxCell, ALDWorkflowNodeID, String, ALDWorkflowNodeID, String) - 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.
createOpTreeModel(Collection<ALDOperatorLocation>, String) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorChooserTree
 
createTree(String) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorChooserTree.AuxNode
Generates the ModelTree using the tree represented with AuxNodes.
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.
currentIndex - Variable in class de.unihalle.informatik.Alida.batch.provider.input.swing.ALDBatchInputNativeArray1DSwing.ALDBatchIteratorNativeArray1D
Index of iterator in set.

D

data - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing.CollectionShowButton
Data to be displayed.
data - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayShowButton
Data to be displayed.
data - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayShowButton
Data to be displayed.
data - Variable in class de.unihalle.informatik.Alida.demo.ALDCalcMean
Input data array.
data - Variable in class de.unihalle.informatik.Alida.demo.ALDSummarizeArrayOp
Input 1D array
data - Variable in class de.unihalle.informatik.Alida.demo.ALDTransposeMatrix
Input data array.
data - Variable in class de.unihalle.informatik.Alida.demo.ExperimentalData
The data
dataArray - Variable in class de.unihalle.informatik.Alida.batch.provider.input.swing.ALDBatchInputNativeArray1DSwing.ALDBatchIteratorNativeArray1D
Data.
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.ALDNativeArray1DDataIOSwing.ArrayConfigWindow
Data table (swing tables are nicer than imageJ tables).
dataTab - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigWindow
Data table (swing tables are nicer than imageJ tables).
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.ALDNativeArray1DDataIOSwing.ArrayConfigWindow
Reference object to the data.
dataTabModel - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigWindow
Reference object to the data.
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.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.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
debug - Variable in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDCollectionDataIOCmdline
output debugging info?
debug - Variable in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDOperatorDataIOCmdline
 
debug - Variable in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDStandardizedDataIOCmdline
debugging output
debug - Static variable in class de.unihalle.informatik.Alida.dataio.provider.helpers.ALDCollectionDataIOHelper
Flag to output debug infos.
debug - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing
Local debug flag, not accessible from outside of the class.
debug - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
Local debug flag, not accessible from outside of the class.
debug - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
Local debug flag, not accessible from outside of the class.
debug - Variable in class de.unihalle.informatik.Alida.gui.ALDBatchOperatorResultFrame
Local debug flag.
debug - Variable in class de.unihalle.informatik.Alida.gui.ALDChooseOpNameFrame
Debug flag (not accessible from outside).
debug - Static variable in class de.unihalle.informatik.Alida.gui.ALDOperatorChooserTree
Debug flag (not accessible from outside).
debug - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Local flag for debug output.
debug - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
Local flag for debug output.
debug - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorResultFrame
Local debug flag.
debug - Static variable in class de.unihalle.informatik.Alida.helpers.ALDClassInfo
Debug flag for internal usage only.
debug - Static variable in class de.unihalle.informatik.Alida.helpers.ALDParser
 
debug - Variable in class de.unihalle.informatik.Alida.operator.ALDOperator
 
debug - Static variable in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
debug flag for debugging output.
debug - Static variable in class de.unihalle.informatik.Alida.operator.GraphmlHelper
turns debugging on
debug - Variable in class de.unihalle.informatik.Alida.tools.ALDOpRunner
debug flag for additional debuging information.
debug - Variable in class de.unihalle.informatik.Alida.tools.PrintDataIOProvider
debug flag for additional debuging information.
debug - Static variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
For debugging information
debug - Static variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflowHelper
 
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
 
defaultVersionProvider - Static variable in class de.unihalle.informatik.Alida.version.ALDVersionProviderFactory
Fallback provider if nothing else specified.
defObject - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing.CollectionConfigWindow
Default collection object.
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.
depth - Variable in class de.unihalle.informatik.Alida.operator.ALDOpNode
depth in calling stack of Operators, set when back tracing
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 ':'
description - Variable in class de.unihalle.informatik.Alida.demo.ExperimentalData
 
descriptor - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing.CollectionShowButton
Descriptor associated with parameter object belongs to.
descriptor - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayConfigWindow
Optional descriptor for additional information on parameter.
descriptor - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayShowButton
Optional descriptor for additional information on parameter.
descriptor - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigWindow
Optional descriptor for additional information on parameter.
descriptor - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayShowButton
Optional descriptor for additional information on parameter.
descriptor - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorConfigWindow
Optional descriptor granting access to additional parameter information.
descriptorName - Variable in class de.unihalle.informatik.Alida.operator.ALDOpNodePort
The descriptor name of this port within opNode
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
 
directionAllowd(ALDWorkflowNode, ALDOpParameterDescriptor, ALDWorkflowNode, ALDOpParameterDescriptor) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Checks if the direction are allowed Source parameter
If the source node represents the workflow, the source parameter needs to be of direction IN or INOUT.
directlyRegisteredChildren - Variable in class de.unihalle.informatik.Alida.operator.ALDOpNode
children of this opNode, set when the operate() represented by this opNode calls nested operators.
dirPath - Variable in class de.unihalle.informatik.Alida.datatypes.ALDDirectoryString
Name of directory including full path.
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.
disableValueChecks - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayConfigWindow
Flag to disable entry validation checks.
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.dataio.provider.swing.components.ALDOperatorParameterPanel
Mode for displaying parameters.
displayMode - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParametrizedClassConfigWindow
Mode for displaying parameters.
displayMode - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Mode for displaying parameters.
displayOnly - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParametrizedClassConfigWindow
Flag to indicate if editing is allowed or only display is requested.
doHistory - Variable in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerCmdline
If true writeData should try to write the history to file if the object itself is written to a file
doMeanFree - Variable in class de.unihalle.informatik.Alida.demo.ALDCalcMean
Compute mean free data
doNextBatchModeStep() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
 
doNextStepInWorkflow() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
 
doNormalize - Variable in class de.unihalle.informatik.Alida.demo.ALDClusterExperiment
 
doNormalize - Variable in class de.unihalle.informatik.Alida.demo.AnalyzeExperiment
 
donotrun - Variable in class de.unihalle.informatik.Alida.tools.ALDOpRunner
If true, the operator will not be invoked but only its interface printed to stdout.
doPCA - Variable in class de.unihalle.informatik.Alida.demo.ALDClusterExperiment
 
doPCA - Variable in class de.unihalle.informatik.Alida.demo.AnalyzeExperiment
 
doStateChange(ALDWorkflowNode, ALDWorkflowNode.ALDWorkflowNodeState) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Set the new state in the node and fire corresponding event.
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

edgeAllowed(ALDWorkflowEdge) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Check if this edge is allowed.
edgeIdsToString(Collection<ALDWorkflowEdge>) - Static method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Formats the ids of the given edges into a string for debugging purposes.
edgeIdToEdge - Static variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Hash map of edges of this workflow.
edges - Variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
All edges of this workflow.
edgeToEdgeId - Static variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
 
elapsedTime - Variable in class de.unihalle.informatik.Alida.demo.ApplyToMatrix
Elpased time
elemClass - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing.CollectionConfigWindow
Collection element class.
elemComps - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing.CollectionConfigWindow
List of current GUI components in window.
elemCounter - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing.CollectionConfigWindow
Number of elements.
elementClass - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayConfigWindow
Class that table entries should represent.
elemField - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing.CollectionConfigWindow
Collection element field.
elemFieldType - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing.CollectionConfigWindow
Collection element type.
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.
entryClass - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigWindow
Class of objects to be filled in the table.
entryRefList - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayConfigWindow
List of currently specified values (to restore entry if check fails).
entryRefList - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigWindow
List of currently specified values (to restore entry if check fails).
eq(Object, Object) - Method in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
Check for equality of non-null references x and y.
errorListToMessage(LinkedList<Integer>) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayConfigWindow
Error function displaying an error message box.
errorListToMessage(LinkedList<int[]>) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigWindow
Error function displaying an error message box.
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.
eventQueue - Variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflowEventManager
The event queue associated with the listener
execProxy - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
Reference to the surrounding workflow manager.
executeNode(ALDWorkflow, ALDWorkflowNode, boolean) - Static method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
This actually runOps the operator in its own thread and takes care of firing events for state changes.
executeNonReadyNodes(List<ALDWorkflowNode>, boolean) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Run all not ready nodes of the list in the given order.
executeOperator(ALDOperatorLocation) - Method in class de.unihalle.informatik.Alida.gui.ALDChooseOpNameFrame
Executes the chosen operator, i.e. opens the config/control window.
executionInterrupted - Variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Deprecated. 
experiment - Variable in class de.unihalle.informatik.Alida.demo.ALDClusterExperiment
Input data
experiment - Variable in class de.unihalle.informatik.Alida.demo.ALDKmeansOp
Input data
experiment - Variable in class de.unihalle.informatik.Alida.demo.ALDPCAOp
Input data
experiment - Variable in class de.unihalle.informatik.Alida.demo.AnalyzeExperiment
Input data
experiment - Variable in class de.unihalle.informatik.Alida.demo.FilterExperimentalDataOp
Input data
experiment - Variable in class de.unihalle.informatik.Alida.demo.NormalizeExperimentalDataOp
Input data
experiment - Variable in class de.unihalle.informatik.Alida.demo.SummarizeClusters
Input data
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.ALDOpNodePort
The explanation of this port.
explanation - Variable in class de.unihalle.informatik.Alida.operator.ALDParameterDescriptor
 

F

fatal(String) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Output fatal error to stderr and throw an exception
favoriteOperators - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorChooserTree
List of favorite operators to be unfolded at startup.
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.
filename - Variable in class de.unihalle.informatik.Alida.workflows.events.ALDWorkflowStorageInfo
 
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.
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.
findCurrentThreadsOpNodeStack() - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Find the opNode stack for the current thread.
findDataIds(DataType, HashMap<String, String>, int) - Static method in class de.unihalle.informatik.Alida.operator.GraphmlHelper
 
findEdgeIds(EdgeType, HashMap<String, String>, int) - Static method in class de.unihalle.informatik.Alida.operator.GraphmlHelper
Insert edgeId and associated nodes into the translationTable.
findIds(GraphType, HashMap<String, String>, int) - Static method in class de.unihalle.informatik.Alida.operator.GraphmlHelper
Traverse the graph, find all graphIDs and insert into the translationTable.
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.
findSibblingsAndParent(ALDOpNode, Vector<ALDInputPort>, int) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Find all sibblings and the parent of opNode.
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.ALDNativeArray1DDataIOSwing.ArrayConfigWindow.TableFocusListener
 
focusGained(FocusEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigWindow.TableFocusListener
 
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.ALDNativeArray1DDataIOSwing.ArrayConfigWindow.TableFocusListener
 
focusLost(FocusEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigWindow.TableFocusListener
 
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.ALDOperatorDataIOCmdline
Format parameters of this operator into a string using the formatString.
formatAsString(Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDOperatorDataIOCmdline
Format all OUT and INOUT parameters of this operator into a string.
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 formater 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.
frameWidth - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing.CollectionConfigWindow
Fixed width of window.
frameWidth - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorConfigWindow
Fixed width of window.
frameWidth - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParametrizedClassConfigWindow
Fixed width of window.

G

generateAccessFunction(ALDOpParameterDescriptor, String) - Static method in class de.unihalle.informatik.Alida.tools.GenerateGetterSetter
Generate access function code.
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.
genuineInstance - Variable in class de.unihalle.informatik.Alida.operator.ALDOperator
Genuine object representing the operation.
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.
getAllInstances() - Static method in class de.unihalle.informatik.Alida.operator.ALDOpNode
 
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() - Method in class de.unihalle.informatik.Alida.operator.ALDParameterWrapper
 
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.
getData() - Method in class de.unihalle.informatik.Alida.demo.ALDSummarizeArrayOp
Returns the 1D array
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.
getDataPortId(ALDDataPort) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Return an ID used in graphml for a data port
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.ALDNativeArray1DDataIOSwing.ArrayConfigWindow.DataTabFileFilter
 
getDescription() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigWindow.DataTabFileFilter
 
getDescription() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDTableWindow.DataTabFileFilter
 
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
 
getDummyInitializer(Class<?>) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeDataIOSwing
Method to instantiate dummy object of requested class for default init.
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.
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.
getEntryNum() - Static method in class de.unihalle.informatik.Alida.operator.ALDPortHash
Returns the number of objects currently stored in the port hash.
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.
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.
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
 
getGraphId(String) - Static method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Get the graphIP at the beginning of an id up (exculing) idSeparator
getGraphmlHistory() - Method in class de.unihalle.informatik.Alida.operator.ALDDataPort
Get the grahphml history of this data port
getGraphName(int) - Static method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Return an ID used in graphml for graph
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) - Static method in class de.unihalle.informatik.Alida.operator.ALDPortHash
Get port to which object is currently linked in the history.
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.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.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.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
getJComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing.CollectionConfigButton
 
getJComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDFileDirectoryDataIOSwing.FileDirectoryDataIOPanel
 
getJComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayConfigButton
 
getJComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigButton
 
getJComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorConfigButton
 
getJComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorHierarchyConfigPanel.AbstrOpClassPanel
 
getJComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorHierarchyConfigPanel
 
getJComponent() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDParametrizedClassDataIOSwing.ParametrizedClassPanel
 
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.
getKey() - Method in class de.unihalle.informatik.Alida.helpers.ALDWeakHashMapEntry
Returns the key of this hashmap element.
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.
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.
getNext() - Method in class de.unihalle.informatik.Alida.helpers.ALDWeakHashMapEntry
Returns reference to subsequent hash element.
getNode(ALDWorkflowNodeID) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Get the workflow node associated with nodeId.
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.ALDGrappaCellInfo
 
getNodeStyleString(String) - Static method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Method to properly format node style string.
getNodeWithoutSources(HashMap<ALDWorkflowNode, Set<ALDWorkflowNode>>) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Returns one node from the sourceNodeMap with zero source nodes, if any.
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
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.
getOpNode() - Method in class de.unihalle.informatik.Alida.operator.ALDOpNodePort
Return the opNode of this port
getOpNodeId(ALDOpNode) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Return an ID used in graphml an opNode
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.
getPackageName() - Method in class de.unihalle.informatik.Alida.operator.ALDParameterWrapper
 
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.
getParameteres() - Method in class de.unihalle.informatik.Alida.operator.ALDParameterWrapper
 
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.
getPortId(ALDPort) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Return an ID used in graphml for a port
getPortIndex() - Method in class de.unihalle.informatik.Alida.operator.ALDOpNodePort
Return the index of the port within its opNode
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, 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.ALDGrappaCellInfo
 
getReleaseVersion(String) - Static method in class de.unihalle.informatik.Alida.version.ALDVersionProviderReleaseJar
Returns the release version/tag of the current jar archive.
getReleaseVersion() - Static method in class de.unihalle.informatik.Alida.version.ALDVersionProviderReleaseJar
Returns the tag/release version.
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.
getReturnElapsedTime() - Method in class de.unihalle.informatik.Alida.demo.ApplyToMatrix
Get value of returnElapsedTime.
getShadowNodeId() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
 
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
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.
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.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.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.helpers.ALDWeakHashMapEntry
Returns the value of this hashmap element.
getValue() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowParameterDescriptor
 
getValueStringFromFile(String) - Static method in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDStandardizedDataIOCmdline
The complete content of the file is return as one string.
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.operator.ALDParameterWrapper
 
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.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.
graphIndex - Variable in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
This index is the index used to build the prefix for all Ids for elements for the next history to add to the current graphml.
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
 
graphmlHistory - Variable in class de.unihalle.informatik.Alida.operator.ALDDataPort
The processing history as graphml if any.
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.
handleInputPorts(ALDOpNode, Vector<ALDInputPort>, Vector<ALDInputPort>, LinkedList<ALDOutputPort>) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Trace back each port of inputPorts which are input ports of a child of parentOpNode.
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.
handlePort(ALDOpNode, ALDPort) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Handle a port to register the incoming edge and to potentially register dataport to opNode.
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.ALDCollectionDataIOSwing.CollectionConfigButton
 
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing.CollectionConfigWindow
 
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.ALDNativeArray1DDataIOSwing.ArrayConfigButton
 
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigButton
 
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorConfigButton
 
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.ALDOperatorDataIOSwing.OperatorHierarchyConfigPanel.AbstrOpClassPanel
 
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorHierarchyConfigPanel
 
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDParametrizedClassDataIOSwing.ParametrizedClassPanel
 
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
 
hash(Object) - Static method in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
Return hash code for Object x.
hash - Variable in class de.unihalle.informatik.Alida.helpers.ALDWeakHashMapEntry
Hash value of referenced object.
hasNext() - Method in class de.unihalle.informatik.Alida.batch.provider.input.swing.ALDBatchInputNativeArray1DSwing.ALDBatchIteratorNativeArray1D
 
hb - Static variable in class de.unihalle.informatik.Alida.gui.OnlineHelpDisplayer
Local help broker.
helpHS - Static variable in class de.unihalle.informatik.Alida.gui.OnlineHelpDisplayer
Name of helpset to be used.
hideLeaves(TreePath) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorChooserTree
Hide all leaves of this tree below the given path.
hidingMode - Variable in class de.unihalle.informatik.Alida.operator.ALDOpNode
Hiding mode of this opnode in the processing history.
historyAnchors - Static variable in class de.unihalle.informatik.Alida.operator.ALDPortHash
Hashmap of port links into the processing history.
historyType - Variable in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Type of the history to be generated.

I

id - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab.ParameterChangeListener
 
id - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy.ParameterChangeListener
Corresponding node ID.
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
ignoreHiding - Variable in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Ignore hidden flag of opnodes when creating a processing history.
includedData - Variable in class de.unihalle.informatik.Alida.operator.ALDOpNode
ALDDataPorts created within this opNode, set during back tracing
includeInHistory(ALDOperator.HidingMode, ALDOperator.HidingMode) - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Is this invocation to be included into the history?
inconsistent(String) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Output error to stderr
inEdges - Variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflowNode
all incoming edges.
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.
initFavoriteOperators() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorChooserTree
Initialize list of favorite operators to be unfolded at startup.
initialInit - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
Flag to indicate if a node is initially added.
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(Class) - Static method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManager
Method to initialize the hashmap which registers DataIO providers.
initNewTab(mxGraph) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
 
initNewWorkflow() - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
 
initNewWorkflow(mxGraph) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
 
initOperatorWorkflow(ALDOperatorLocation) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
Adds the operator as node to the workflow.
initPanel() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
Inits the panel according to formerly specified descriptors.
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.
inputPorts - Variable in class de.unihalle.informatik.Alida.operator.ALDOpNode
the input ports of this opNode.
inputProviderComps - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
Components in GUI linked to the different input batch parameters.
insertGraphId(String, HashMap<String, String>, int) - Static method in class de.unihalle.informatik.Alida.operator.GraphmlHelper
Insert id into if not already included.
instance - Static variable in class de.unihalle.informatik.Alida.batch.ALDBatchInputManagerSwing
The singleton instance of this class.
instance - Static variable in class de.unihalle.informatik.Alida.batch.ALDBatchOutputManagerSwing
The singleton instance of this class
instance - Static variable in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerCmdline
The singleton instance of this class
instance - Static variable in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerSwing
The singleton instance of this class
instantiateObject(String) - Static method in class de.unihalle.informatik.Alida.version.ALDVersionProviderFactory
Instantiates an object of the specified version provider class.
interiorShadowNode - Variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
This node is used as an interior shadow (or substitute) for the node holding this workflow.
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
 
ioPanel - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDFileDirectoryDataIOSwing.FileDirectoryDataIOPanel
Swing component to be integrated in GUI.
isClassNameSpecified() - Static method in class de.unihalle.informatik.Alida.version.ALDVersionProviderFactory
Returns true if the factory can be properly configured.
isCompleteOpnode(ALDOpNode) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Is a complete history to be created for this opNode?
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.
isDirectory - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDFileDirectoryDataIOSwing.FileDirectoryDataIOPanel
Flag indicating if panel refers to a directory parameter or not.
isDoHistory() - Method in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerCmdline
 
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
isHiddenOpnode(ALDOpNode) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Should we hide this opnode.
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.
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?
isParamLinked - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
 
isRegistered(Object) - Static method in class de.unihalle.informatik.Alida.operator.ALDPortHash
Returns true if the given object is already registered in the hash.
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.
isTermiate() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowEventManager
 
isToplevelOpnode(ALDOpNode) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Is this an opNode of the toplevel operator.
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.
itemStateChanged(ItemEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorHierarchyConfigPanel.AbstrOpClassPanel
 
itemStateChanged(ItemEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDParametrizedClassDataIOSwing.ParametrizedClassPanel
 
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

killWorkflowThread() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
 

L

label - Variable in class de.unihalle.informatik.Alida.operator.ALDParameterDescriptor
 
labelMap - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
Maps a descriptor to its JLabel component in the panel.
lastAdded - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing.CollectionConfigWindow
Stores the index of last element added (may vary due to element swaps).
lastDir - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayConfigWindow
For convenience: always open last directory for saving.
lastDir - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigWindow
For convenience: always open last directory for saving.
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.dataio.provider.swing.ALDFileDirectoryDataIOSwing.FileDirectoryDataIOPanel
Last directory selected by user.
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.dataio.provider.swing.ALDFileDirectoryDataIOSwing.FileDirectoryDataIOPanel
Last file selected by user.
lastFile - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Last selected file.
lastID - Static variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflowEdgeID
variable to count IDs
lastID - Static variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflowNodeID
variable to count IDs
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.
listener - Variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflowEventManager
The listener for which to handle events
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).
location - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorChooserTree.AuxNode
location object for this node.
location - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorChooserTreeNode
The location object for this node.
locationType - Variable in class de.unihalle.informatik.Alida.operator.ALDOperatorLocation
Type of this location
longNameCheckBox - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorHierarchyConfigPanel.AbstrOpClassPanel
Checkbox to toggle between long and short class names.
longNameCheckBox - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDParametrizedClassDataIOSwing.ParametrizedClassPanel
Checkbox to toggle between long and short class names.
lookupExtendingClasses(Class) - Static method in class de.unihalle.informatik.Alida.helpers.ALDClassInfo
Collects all derived class of given class.
lookupOperators(ALDAOperator.Level, ALDAOperator.ExecutionMode) - Static method in class de.unihalle.informatik.Alida.helpers.ALDClassInfo
Collects all operators annotated with teh requested level and execution mode.
lookupParameternames(ALDOperator, String) - Static method in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDOperatorDataIOCmdline
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.
mainButton - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorConfigButton
Button to open configuration window.
mainFrame - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbench
 
mainPanel - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing.CollectionConfigWindow
Main panel of main frame.
mainPanel - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorConfigWindow
Main panel of main frame.
mainPanel - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorHierarchyConfigPanel.AbstrOpClassPanel
Main panel.
mainPanel - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDParametrizedClassDataIOSwing.ParametrizedClassPanel
Main panel containing elements for class selection.
mainPanel - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
Main panel containing all operator parameters.
mainPanel - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
The main panel containing everything.
mainPanel - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParametrizedClassConfigWindow
Main panel of main frame.
mainPanel - Variable in class de.unihalle.informatik.Alida.gui.ALDChooseOpNameFrame
Main panel of chooser window.
manager - Variable in class de.unihalle.informatik.Alida.tools.PrintDataIOProvider
 
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.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
matrix - Variable in class de.unihalle.informatik.Alida.demo.ApplyToMatrix
Input matrix
matrix - Variable in class de.unihalle.informatik.Alida.demo.MatrixSum
Input matrix
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
MatrixSum.SummarizeMode() - Constructor for enum de.unihalle.informatik.Alida.demo.MatrixSum.SummarizeMode
 
MAXIMUM_CAPACITY - Static variable in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
The maximum capacity, used if a higher value is implicitly specified by either of the constructors with arguments.
mean - Variable in class de.unihalle.informatik.Alida.demo.ALDCalcMean
Calculated average value.
meanFreeData - Variable in class de.unihalle.informatik.Alida.demo.ALDCalcMean
Mean free data
MINIMUM_CAPACITY - Static variable in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
The minimum capacity, used if a lower value is implicitly specified by either of the constructors with arguments.
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.dataio.provider.swing.components.ALDParametrizedClassConfigWindow
Parametrized class to configure.
myclass - Variable in class de.unihalle.informatik.Alida.operator.ALDParameterDescriptor
 
myObj - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParametrizedClassConfigWindow
Object to configure associated with window.

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.ALDOpNode
name of the operator for which an invocations is represented by this opNode
name - Variable in class de.unihalle.informatik.Alida.operator.ALDParameterDescriptor
 
nameParameterMap - Variable in class de.unihalle.informatik.Alida.tools.ALDOpRunner
Hashmap to collect parameter name as given on command line and matching parameter name.
nameValueMap - Variable in class de.unihalle.informatik.Alida.tools.ALDOpRunner
Hashmap to collect parameter name as given on command line and correspnding value string
next() - Method in class de.unihalle.informatik.Alida.batch.provider.input.swing.ALDBatchInputNativeArray1DSwing.ALDBatchIteratorNativeArray1D
 
next - Variable in class de.unihalle.informatik.Alida.helpers.ALDWeakHashMapEntry
Pointer to the next reference in hashmap list.
nextTimeStamp - Static variable in class de.unihalle.informatik.Alida.workflows.events.ALDWorkflowEvent
Count for (almost) unique time stamps (we allow wrap around).
noDefaultHistory - Variable in class de.unihalle.informatik.Alida.tools.ALDOpRunner
If true, history files are not read and written by default.
nodeIdsToString(Collection<ALDWorkflowNode>) - Static method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Formats the ids of the given nodes into a string for debugging purposes.
nodeIdToNode - Static variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Hash map of operator nodes of this workflow.
nodeName - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaCellInfo
 
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.
nodes - Variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflow.ExecuteThread
The nodes of the workflow to execute
nodes - Variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
All nodes contained in this workflow
nodeToNodeId - Static variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
 
normalized - Variable in class de.unihalle.informatik.Alida.demo.ExperimentalData
Are the data normalized to zero mean within each feature?
normalizedExperiment - Variable in class de.unihalle.informatik.Alida.demo.ALDClusterExperiment
Normalization experiment in case normalization was requested.
normalizedExperiment - Variable in class de.unihalle.informatik.Alida.demo.AnalyzeExperiment
Normalization experiment in case normalization was requested.
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.
numCluster - Variable in class de.unihalle.informatik.Alida.demo.ALDKmeansOp
Number of components to be used for the sub space to project into.
numComponents - Variable in class de.unihalle.informatik.Alida.demo.ALDPCAOp
Number of components to be used for the sub space to project into.

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
 
onlyDisplay - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
Flag to disable editability of GUI elements.
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.
op - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorResultFrame
Associated operator.
op - Variable in class de.unihalle.informatik.Alida.tools.ALDOpRunner
The operator to be invoked.
op - Variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflowNode
The operator object associated with this node.
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.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.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.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.operator.ALDToplevelOperator
The abstract method operate needs to be implemented, but this top levels operator is never to be invoked.
operate() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
 
operator - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorConfigWindow
Corresponding operator to be configured.
operator - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
The operator associated with this panel.
operatorClass - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorConfigWindow
Class of the operator to be configured.
operatorClass - Variable in class de.unihalle.informatik.Alida.operator.ALDOpNode
class of the operator for which an invocations is represented by this opNode
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.
opNode - Variable in class de.unihalle.informatik.Alida.operator.ALDOpNodePort
The opNode this port belongs to
opNodePortsTraced - Variable in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
 
opNodesClone - Variable in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
 
opNodesInGraph - Variable in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
 
opNodeStackHash - Static variable in class de.unihalle.informatik.Alida.operator.ALDOperator
A weak hashmap which contains for each thread a stack of opNodes reflecting the current state of the method stack.
opParamDescrips - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing
List of all parameter descriptors associated with operator.
opParamDescrips - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
List of all parameter descriptors associated with the 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.
origin - Variable in class de.unihalle.informatik.Alida.operator.ALDPort
The origin/producer of this port.
outEdges - Variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflowNode
outgoing edges.
outputCheckBoxes - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorControlFrame
Set of checkboxed to select parameters to summarize in batch mode.
outputOpNode(ALDOpNode, GraphType) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Output opNode and it ports, and recursively its children to the graph.
outputPorts - Variable in class de.unihalle.informatik.Alida.operator.ALDOpNode
the output ports of this opNode.

P

p2capacity(int) - Method in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
Returns appropriate capacity for argument.
packageName - Variable in class de.unihalle.informatik.Alida.operator.ALDParameterWrapper
 
panelMap - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
Maps a parameter descriptor to its panel in the GUI.
panelOptionalParams - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
Sub-panel managing the configuration of optional parameters.
panelRequiredParams - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
Sub-panel managing the configuration of required parameters.
panelSupplementalParams - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
Sub-panel managing the configuration of supplemental parameters.
param_boolean - Variable in class de.unihalle.informatik.Alida.demo.ALDInputParameterTester
 
param_Boolean - Variable in class de.unihalle.informatik.Alida.demo.ALDInputParameterTester
 
param_byte - Variable in class de.unihalle.informatik.Alida.demo.ALDInputParameterTester
 
param_Byte - Variable in class de.unihalle.informatik.Alida.demo.ALDInputParameterTester
 
param_dir - Variable in class de.unihalle.informatik.Alida.demo.ALDInputParameterTester
 
param_double - Variable in class de.unihalle.informatik.Alida.demo.ALDInputParameterTester
 
param_Double - Variable in class de.unihalle.informatik.Alida.demo.ALDInputParameterTester
 
param_enum - Variable in class de.unihalle.informatik.Alida.demo.ALDInputParameterTester
 
param_file - Variable in class de.unihalle.informatik.Alida.demo.ALDInputParameterTester
 
param_float - Variable in class de.unihalle.informatik.Alida.demo.ALDInputParameterTester
 
param_Float - Variable in class de.unihalle.informatik.Alida.demo.ALDInputParameterTester
 
param_int - Variable in class de.unihalle.informatik.Alida.demo.ALDInputParameterTester
 
param_Integer - Variable in class de.unihalle.informatik.Alida.demo.ALDInputParameterTester
 
param_long - Variable in class de.unihalle.informatik.Alida.demo.ALDInputParameterTester
 
param_Long - Variable in class de.unihalle.informatik.Alida.demo.ALDInputParameterTester
 
param_short - Variable in class de.unihalle.informatik.Alida.demo.ALDInputParameterTester
 
param_Short - Variable in class de.unihalle.informatik.Alida.demo.ALDInputParameterTester
 
param_String - Variable in class de.unihalle.informatik.Alida.demo.ALDInputParameterTester
 
param_vectorDouble - Variable in class de.unihalle.informatik.Alida.demo.ALDInputParameterTester
 
paramChangeListener - Variable in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
Listener object attached to the control window.
paramDescrips - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParametrizedClassConfigWindow
Listed of associated parametrized class parameters.
paramDescriptors - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
List of parameter descriptors managed by this panel.
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.Direction() - Constructor for enum de.unihalle.informatik.Alida.annotations.Parameter.Direction
 
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.ExpertMode() - Constructor for enum de.unihalle.informatik.Alida.annotations.Parameter.ExpertMode
 
Parameter.Type - Enum in de.unihalle.informatik.Alida.annotations
Deprecated. 
Parameter.Type() - Constructor for enum de.unihalle.informatik.Alida.annotations.Parameter.Type
Deprecated.  
parameterDescriptorsAll - Variable in class de.unihalle.informatik.Alida.operator.ALDOperator
Hash representing the interface of this operator.
parameterHash - Variable in class de.unihalle.informatik.Alida.operator.ALDOpNode
This hash contains the values of all parameters as return by the toString() method of the parameters at the time of invocation of the operator using runOp().
parameterHash - Variable in class de.unihalle.informatik.Alida.operator.ALDParameterWrapper
 
parameterHashAsXml - Variable in class de.unihalle.informatik.Alida.operator.ALDOpNode
parameteHash as an XmlObject
parameterName - Variable in class de.unihalle.informatik.Alida.batch.ALDBatchRunResultInfo
Name of parameter over which was iterated.
parameterPanel - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParametrizedClassConfigWindow
Parameter panel.
parametersToXmlObject() - Method in class de.unihalle.informatik.Alida.operator.ALDOperator
Parse the parameter values to an XmlObject.
paramPanel - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorHierarchyConfigPanel
GUI configuration element.
paramPanel - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDParametrizedClassDataIOSwing
GUI configuration element.
parent - Variable in class de.unihalle.informatik.Alida.operator.ALDOpNode
parent of this opNode, will be set during back tracing
parentWorkflow - Variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflowNode
This is the enclosing work flow.
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.ALDOperatorDataIOCmdline
Parser for ALDOperators.
parse(Field, Class<?>, String, ALDOperator) - Method in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDOperatorDataIOCmdline
Parser for ALDOperators.
parse(Field, Class<?>, String) - Method in class de.unihalle.informatik.Alida.dataio.provider.cmdline.ALDParametrizedClassDataIOCmdline
Generic parser for parametrized classes.
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.
portIndex - Variable in class de.unihalle.informatik.Alida.operator.ALDOpNodePort
The index of this port within opNode
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.
printData(DataType, String) - Static method in class de.unihalle.informatik.Alida.operator.GraphmlHelper
Print a Data item to standard out using an indentation string
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.
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
 
printPort(PortType, String) - Static method in class de.unihalle.informatik.Alida.operator.GraphmlHelper
Print a Port to standard out using an indentation string
printUsage() - Static method in class de.unihalle.informatik.Alida.tools.ALDOpRunner
Print short usage to stderr.
printUsage() - Static method in class de.unihalle.informatik.Alida.tools.PrintDataIOProvider
Print usage to stderr.
printUsageVerbose() - Method in class de.unihalle.informatik.Alida.tools.ALDOpRunner
Print verbose usage to stderr.
printUsageVerbose() - Method in class de.unihalle.informatik.Alida.tools.PrintDataIOProvider
Print verbose usage to stderr.
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.
properties - Variable in class de.unihalle.informatik.Alida.operator.ALDData
Properties of the data object
properties - Variable in class de.unihalle.informatik.Alida.operator.ALDDataPort
The properties of the underlying MTBData at the time of creation of this Dataport
properties - Variable in class de.unihalle.informatik.Alida.operator.ALDOpNodePort
The properties retrieved from the data as it passed the port into or out of the operator.
properties - Variable in class de.unihalle.informatik.Alida.operator.ALDOutputPort
Hash to hold properties copied upon return from runOp()
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 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.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.ALDOperatorDataIOCmdline
 
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.
providedClassesMethodName - Static variable in class de.unihalle.informatik.Alida.dataio.ALDDataIOManager
Name of the method which returns all classes supported by a DataIO provider class.
providedInputClassesMethodName - Static variable in class de.unihalle.informatik.Alida.batch.ALDBatchInputManager
Name of the method which returns all classes supported.
providedOutputClassesMethodName - Static variable in class de.unihalle.informatik.Alida.batch.ALDBatchOutputManager
Name of the method which returns all classes supported.
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.
providerInstances - Static variable in class de.unihalle.informatik.Alida.version.ALDVersionProviderFactory
Hashmap with global version provider objects.
provInterLevel - Variable in class de.unihalle.informatik.Alida.batch.ALDBatchInputManagerSwing
Interaction level the providers should obey.
provInterLevel - Variable in class de.unihalle.informatik.Alida.batch.ALDBatchOutputManagerSwing
Interaction level the providers should obey.
provInterLevel - Variable in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerSwing
Interaction level the providers should obey.
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<?>, 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<?>, 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<?>, 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<?>) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing.CollectionConfigButton
Gets the data from the configuration window.
readData(Field, Class<?>) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing.CollectionConfigWindow
Extracts current collection data.
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<?>) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayConfigButton
Gets the data from the configuration window.
readData(Field, Class<?>) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayConfigWindow
 
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing
 
readData(Field, Class<?>) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigButton
Gets the data from the configuration window.
readData(Field, Class<?>) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigWindow
 
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<?>) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorConfigButton
Read operator parameter values.
readData(Field, Class<?>) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorHierarchyConfigPanel.AbstrOpClassPanel
Function to read parameter values from GUI.
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorHierarchyConfigPanel
 
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing
 
readData(Field, Class<?>) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDParametrizedClassDataIOSwing.ParametrizedClassPanel
Function to read parameter values from GUI.
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.
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.
readParameterValues(int) - Method in class de.unihalle.informatik.Alida.tools.ALDOpRunner
Read all IN and INOUT parameters specified on the command line.
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.
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
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
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, String, String) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaWorkbenchTab
Redirects the workflow edge.
refID - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaCellInfo
 
refQueue - Static variable in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
Queue for managing references to deleted objects.
register(Object) - Static method in class de.unihalle.informatik.Alida.operator.ALDPortHash
Adds the object's port to the hash.
register(Object) - Method in class de.unihalle.informatik.Alida.operator.ALDPortHashAccess
Register the object in the hash.
register(ALDOpNode, ALDOpNode) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Register an opNode as child to its parents if not already found directly or indirectly before.
register(ALDOpNode, ALDDataPort) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Register the dataport as directly included in opNode.
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.
releaseVersion - Static variable in class de.unihalle.informatik.Alida.version.ALDVersionProviderReleaseJar
Release version or tag information.
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() - Method in class de.unihalle.informatik.Alida.batch.provider.input.swing.ALDBatchInputNativeArray1DSwing.ALDBatchIteratorNativeArray1D
 
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.
removeGraphId(String) - Static method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Remove the graphIP including idSeparator at the beginning of an id
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.
removeWeakKeys() - Method in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
Cleans-up the hashmap when called.
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.
renameDataIds(DataType, HashMap<String, String>) - Static method in class de.unihalle.informatik.Alida.operator.GraphmlHelper
 
renameEdgeIds(EdgeType, HashMap<String, String>) - Static method in class de.unihalle.informatik.Alida.operator.GraphmlHelper
 
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.
renameIds(GraphType, HashMap<String, String>) - Static method in class de.unihalle.informatik.Alida.operator.GraphmlHelper
Traverse the graph, find all graphIDs and do the renaming
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
 
requestedClass - Variable in class de.unihalle.informatik.Alida.batch.provider.input.swing.ALDBatchInputNativeArray1DSwing.ALDBatchIteratorNativeArray1D
Class of elements in array.
required - Variable in class de.unihalle.informatik.Alida.operator.ALDParameterDescriptor
 
resetDisconnectedInput - Variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
If true, an input parameter is reset (currently set to null) if is is disconnected (by removing or redirecting an edge) from its source.
resetParameter(String) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowNode
Reset the parameter parameterName in the operator associated to this node.
resizeTableEntries(int) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayConfigWindow
Method to resize the reference entry list.
resizeTableEntries(int, int) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigWindow
Method to resize the reference entry list.
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.
result - Variable in class de.unihalle.informatik.Alida.demo.ALDPCAOp
Experiment with sub experiments are projections into the subspace computed by the PCA
result - Variable in class de.unihalle.informatik.Alida.demo.FilterExperimentalDataOp
Filtered experiment to be returned
result - Variable in class de.unihalle.informatik.Alida.demo.NormalizeExperimentalDataOp
Normalized experiment to be returned
resultDataVec - Variable in class de.unihalle.informatik.Alida.batch.ALDBatchRunResultInfo
List of corresponding result data objects.
resumeWorkflow() - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorGUIExecutionProxy
 
returnElapsedTime - Variable in class de.unihalle.informatik.Alida.demo.ApplyToMatrix
Supplemental to request elapsed time to be returned
run() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow.ExecuteThread
 
run() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowEventManager
 
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.ALDNativeArray1DDataIOSwing.ArrayConfigWindow
Saves the contents of the table to a user-specified file.
saveTable() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigWindow
Saves the contents of the table to a user-specified 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
 
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.
setData(Double[]) - Method in class de.unihalle.informatik.Alida.demo.ALDSummarizeArrayOp
Sets the 1D array
setData(Double[][], boolean) - Method in class de.unihalle.informatik.Alida.demo.ExperimentalData
Set the data
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.
setDepth(int) - Method in class de.unihalle.informatik.Alida.operator.ALDOpNode
Set depth.
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
 
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) - Static method in class de.unihalle.informatik.Alida.operator.ALDPortHash
Set port to which data is currently linked in the history.
setHistoryLink(Object, ALDPort) - Method in class de.unihalle.informatik.Alida.operator.ALDPortHashAccess
Set the port to which the object is currently linked in history.
setInOrigin(int, Object, String) - Method in class de.unihalle.informatik.Alida.operator.ALDOpNode
Set the origin of the input port with index i.
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.
setNodeName(String) - Method in class de.unihalle.informatik.Alida.grappa.ALDGrappaCellInfo
 
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
 
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.
setOrigin(ALDPort) - Method in class de.unihalle.informatik.Alida.operator.ALDPort
Set the origin of this port, which is the parent in the processing graph.
setOutOrigin(int, Object, String) - Method in class de.unihalle.informatik.Alida.operator.ALDOpNode
Set the origin of the output port with index i.
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
 
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
 
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
 
setProperties(Object) - Method in class de.unihalle.informatik.Alida.operator.ALDOpNodePort
Set the properties to be associated with this port.
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.ALDGrappaCellInfo
 
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.
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.
setTabEntryToDefault(int, Class<?>) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayConfigWindow
Sets the specified table entry to the class default.
setTabEntryToDefault(int, int, Class<?>) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigWindow
Sets the specified table entry to the class default.
setTermiate(boolean) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflowEventManager
 
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.
setupTable() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayConfigWindow
Initializes the data table window.
setupTable() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigWindow
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.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<?>, Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing.CollectionConfigButton
Sets new values in configuration window.
setValue(Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing.CollectionConfigWindow
Updates current collection data.
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<?>, Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayConfigButton
Gets the data from the configuration window.
setValue(Field, Class<?>, Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayConfigWindow
Fills the table with specified values.
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing
 
setValue(Field, Class<?>, Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigButton
Gets the data from the configuration window.
setValue(Field, Class<?>, Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigWindow
 
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.OperatorHierarchyConfigPanel.AbstrOpClassPanel
 
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing
 
setValue(Field, Class<?>, Object) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDParametrizedClassDataIOSwing.ParametrizedClassPanel
Function to update values of parametrized class object.
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.helpers.ALDWeakHashMapEntry
Sets the value of the hashmap entry.
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.
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
 
SezPozAdapter() - Constructor for class de.unihalle.informatik.Alida.annotations.indexing.SezPozAdapter
Default constructor, should not be called from outside.
shortNames - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorHierarchyConfigPanel.AbstrOpClassPanel
Hashmap to remember short class names.
shortNames - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDParametrizedClassDataIOSwing.ParametrizedClassPanel
Hashmap to remember short class names.
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.
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.
sourceNode - Variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflowEdge
source node of this edge in the work flow
sourceParameterName - Variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflowEdge
parameter name in source node
sourcePort - Variable in class de.unihalle.informatik.Alida.operator.ALDEdge
Source port of the data flow
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.
state - Variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflowNode
The state of the node
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
 
subClassHandler - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing
Panel to configure sub-classed or abstract operators as parameters.
summaries - Variable in class de.unihalle.informatik.Alida.demo.ApplyToMatrix
1D Array of summaries.
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.
summarizeMode - Variable in class de.unihalle.informatik.Alida.demo.ApplyToMatrix
Mode of summarizing
summarizeMode - Variable in class de.unihalle.informatik.Alida.demo.MatrixSum
Mode of summarizing
summarizeOp - Variable in class de.unihalle.informatik.Alida.demo.ApplyToMatrix
Summarizing opererator
summary - Variable in class de.unihalle.informatik.Alida.demo.ALDSummarizeArrayOp
Summarizing scalar
summaryOfExperiment - Variable in class de.unihalle.informatik.Alida.demo.AnalyzeExperiment
Summary of experiment .
summaryOfExperiment - Variable in class de.unihalle.informatik.Alida.demo.SummarizeClusters
Summary of experiment .
sums - Variable in class de.unihalle.informatik.Alida.demo.MatrixSum
1D Array of sums.
supplemental - Variable in class de.unihalle.informatik.Alida.operator.ALDOpParameterDescriptor
 
supported1DArray(Class<?>) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeDataIOSwing
Checks if a given class is supported or not.

T

table - Variable in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
The hash table data.
tableChanged(TableModelEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayConfigWindow
 
tableChanged(TableModelEvent) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigWindow
 
tableScroller - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayConfigWindow
Scrollpane for table panel;
tableScroller - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigWindow
Scrollpane for table panel;
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
 
tabPanel - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayConfigWindow
Table component in window.
tabPanel - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigWindow
Table component in window.
targetNode - Variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflowEdge
target node of this edge in the work flow
targetParameterName - Variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflowEdge
parameter name in target node
targetPort - Variable in class de.unihalle.informatik.Alida.operator.ALDEdge
Target port of the data flow
tdata - Variable in class de.unihalle.informatik.Alida.demo.ALDTransposeMatrix
Output data array.
termiate - Variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflowEventManager
if true the thread is asked to terminate its run method
textField - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDFileDirectoryDataIOSwing.FileDirectoryDataIOPanel
Text field in the panel.
textField - Variable in class de.unihalle.informatik.Alida.grappa.ALDGrappaLinkDataIOSwing
 
threshold - Variable in class de.unihalle.informatik.Alida.helpers.ALDConcReadWeakHashMap
The table is rehashed when its size exceeds this threshold.
timeStamp - Variable in class de.unihalle.informatik.Alida.workflows.events.ALDWorkflowEvent
This is not a real time stamp rather an integer incremented each time a new event is instantiate with the only exception of using new ALDWorkflowEvent( event)
titleString - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
Optional title string for panel.
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.
topLevelCall - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
Flag indicating if panel is used on top level or not.
topLevelCall - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParameterPanel
Flag indicating if panel is used on top level or not.
topSort(Collection<ALDWorkflowNode>) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Topologically sorts the nodes given in nodes.
topSort() - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Topologically sorts all nodes of the workflow.
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.ALDGrappaCellInfo
 
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.
tracebackDAG(Object) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Trace back the implicit DAG created during processing for sourceObjOfHistory.
translate(HashMap<String, String>, String) - Static method in class de.unihalle.informatik.Alida.operator.GraphmlHelper
Translate the id using translationTable.
triggerValueChangeEvents - Variable in class de.unihalle.informatik.Alida.batch.ALDBatchInputManagerSwing
Flag to indicate if change value events should be triggered or not.
triggerValueChangeEvents - Variable in class de.unihalle.informatik.Alida.batch.ALDBatchOutputManagerSwing
Flag to indicate if change value events should be triggered or not.
triggerValueChangeEvents - Variable in class de.unihalle.informatik.Alida.dataio.ALDDataIOManagerSwing
Flag to indicate if change value events should be triggered or not.
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.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.ALDWorkflowException
Type of exception object.
typeID - Static variable in exception de.unihalle.informatik.Alida.exceptions.ALDBatchIOException
Identifier string.
typeID - Static variable in exception de.unihalle.informatik.Alida.exceptions.ALDBatchIOManagerException
Identifier string.
typeID - Static variable in exception de.unihalle.informatik.Alida.exceptions.ALDBatchIOProviderException
Identifier string.
typeID - Static variable in exception de.unihalle.informatik.Alida.exceptions.ALDDataIOException
Identifier string.
typeID - Static variable in exception de.unihalle.informatik.Alida.exceptions.ALDDataIOManagerException
Identifier string.
typeID - Static variable in exception de.unihalle.informatik.Alida.exceptions.ALDDataIOProviderException
Identifier string.
typeID - Static variable in exception de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Identifier string.
typeID - Static variable in exception de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
Exception identifier.
typeID - Static variable in exception de.unihalle.informatik.Alida.exceptions.ALDWorkflowException
Identifier string.
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.OperatorConfigButton
Update window with new operator parameter values.
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
 
updatePanel() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDOperatorParameterPanel
Updates panel according to values in currently given operator.
updateParamConfigurationStatus(Collection<String>) - Method in class de.unihalle.informatik.Alida.gui.ALDOperatorConfigurationFrame
Updates the window according to the status of the operator parameters.
updateState(ALDWorkflowNode) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Convenience method which just invokes ALDWorkflow.updateStates(Collection, boolean) with the single node.
updateStates(Collection<ALDWorkflowNode>, boolean) - Method in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Updates the states of nodesToCheck and their descendants.
updateWindow() - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing.CollectionConfigWindow
Updates the collection in the window.
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.
validateEntry(Class<?>, String) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayConfigWindow
Checks if a string can be cast to the desired class.
validateEntry(Class<?>, String) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigWindow
Checks if a string can be cast to the desired class.
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.
validateParameternames(int) - Method in class de.unihalle.informatik.Alida.tools.ALDOpRunner
Validate the parametername=valuestring pairs with respect to syntax and validate the existance of the parameter in the operator interface.
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.
value - Variable in class de.unihalle.informatik.Alida.helpers.ALDWeakHashMapEntry
Referenced object itself.
value - Variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflowParameterDescriptor
Holds the value of the parameter
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.ALDInputParameterTester.EnumSelection
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.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.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.ALDInputParameterTester.EnumSelection
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.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.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.
verbose - Variable in class de.unihalle.informatik.Alida.operator.ALDPortHashAccess
If true, verbose outputs are written to standard output on calling methods.
verbose - Variable in class de.unihalle.informatik.Alida.tools.ALDOpRunner
verbose flag to outout additional information to stdout.
verbose - Variable in class de.unihalle.informatik.Alida.tools.PrintDataIOProvider
verbose flag to outout additional information to stdout.
version - Variable in class de.unihalle.informatik.Alida.operator.ALDOpNode
version of the operator for which an invocations is represented by this opNode
version - Variable in class de.unihalle.informatik.Alida.operator.ALDParameterWrapper
 
versionProvider - Variable in class de.unihalle.informatik.Alida.operator.ALDOperator
Instance of a class providing version information.
visitOpNode(ALDOpNode, ALDOutputPort, int) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Visit the opNode either completely or according to data dependency as define by the opNode and the globale state of the processing DAG.
visitOpNodeComplete(ALDOpNode, int) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Completely visits this opNode.
visitOpNodeDatadependency(ALDOpNode, ALDOutputPort, int) - Method in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
Visit the opNode detecting all inner children and data ports on which the output port of interest portOfInterest depends on.

W

win - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDParametrizedClassDataIOSwing.ParametrizedClassShowButton
Associated parameter window.
window - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDCollectionDataIOSwing.CollectionConfigWindow
Main frame.
window - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayConfigWindow
Main frame.
window - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigWindow
Main window.
window - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorConfigWindow
Main configuration window.
window - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.components.ALDParametrizedClassConfigWindow
Main configuration window.
windowHasFocus - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray1DDataIOSwing.ArrayConfigWindow
Flag to indicate the table window has the focus.
windowHasFocus - Variable in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDNativeArray2DDataIOSwing.ArrayConfigWindow
Flag to indicate the table window has the focus.
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.
workflow - Variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflow.ExecuteThread
workflow to execute nodes for.
workflow - Variable in class de.unihalle.informatik.Alida.workflows.events.ALDWorkflowStorageInfo
 
workflowContext - Variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
Determines the context of this workflow
workflowEventMangerList - Variable in class de.unihalle.informatik.Alida.workflows.ALDWorkflow
List of control event listeners attached to this workflow.
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, 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, 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) - Method in class de.unihalle.informatik.Alida.dataio.provider.swing.ALDOperatorDataIOSwing.OperatorHierarchyConfigPanel
 
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
 
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, 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.
writeParameterValues(int) - Method in class de.unihalle.informatik.Alida.tools.ALDOpRunner
Write all OUT and INOUT parameters specified on the command line.
writtenDataports - Variable in class de.unihalle.informatik.Alida.operator.ALDProcessingDAG
 

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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