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

A

about(ITab) - Method in class jigcell.compare.ui.CompareFrontEnd
Displays information about a Comparator tab.
about - Variable in class jigcell.compare.ui.CompareFrontEnd.FrontEndTabInfo
About the tab
accelerator - Variable in class jigcell.compare.ui.MenuBuilder.Builder.Item
Accelerator for the item
accept(File) - Method in class jigcell.compare.impl.SuffixFileFilter
 
accessory - Variable in class jigcell.compare.ui.CompareFrontEnd.FrontEndTabInfo
Tab accessory
acquireSync(Sync) - Static method in class jigcell.compare.impl.Compare
Acquires the lock of a Sync object.
ACROSS - Static variable in class jigcell.compare.plotter.IPlotter.Combine
Combine across series option.
action - Variable in class jigcell.compare.cellcycle.BuddingYeastScanTransform.BuddingYeastScanEvent
Code for the action that occurred
action - Variable in class jigcell.compare.cellcycle.GenericScanTransform.GenericScanEvent
Code for the action that occurred
actionPerformed(ActionEvent) - Method in class jigcell.compare.cellcycle.CellCycleReportGenerator
 
actionPerformed(ActionEvent) - Method in class jigcell.compare.cellcycle.JigCellRunManagerInterface
 
actionPerformed(ActionEvent) - Method in class jigcell.compare.compare2.Compare2
 
actionPerformed(ActionEvent) - Method in class jigcell.compare.compare2.ThresholdEditor
 
actionPerformed(ActionEvent) - Method in class jigcell.compare.objectiveui.MinkowskiInterface
 
actionPerformed(ActionEvent) - Method in class jigcell.compare.objectiveui.WOSSInterface
 
actionPerformed(ActionEvent) - Method in class jigcell.compare.transformui.ExtremaTestInterface
 
actionPerformed(ActionEvent) - Method in class jigcell.compare.transformui.FileInterface
 
actionPerformed(ActionEvent) - Method in class jigcell.compare.transformui.InputInterface
 
actionPerformed(ActionEvent) - Method in class jigcell.compare.transformui.SelectColumnsInterface
 
actionPerformed(ActionEvent) - Method in class jigcell.compare.transformui.TransformEvaluationInterface
 
actionPerformed(ActionEvent) - Method in class jigcell.compare.transformui.TransformInterface
 
actionPerformed(ActionEvent) - Method in class jigcell.compare.ui.CompareFrontEnd.SplashScreen
 
actionPerformed(ActionEvent) - Method in class jigcell.compare.ui.ConfigEditor
 
actionPerformed(ActionEvent) - Method in class jigcell.compare.ui.EditorDialog
 
actionPerformed(ActionEvent) - Method in class jigcell.compare.ui.FindAccessory
 
actionPerformed(ActionEvent) - Method in class jigcell.compare.ui.MenuBuilder.ScriptActionTrampoline
 
actionPerformed(ActionEvent) - Method in class jigcell.compare.ui.ProgressMonitor
 
actionPerformed(ActionEvent) - Method in class jigcell.compare.ui.SeriesDialog
 
actionPerformed(ActionEvent) - Method in class jigcell.compare.views.EvaluationErrorViewer
 
actionPerformed(ActionEvent) - Method in class jigcell.compare.views.EvaluationErrorViewer.MoreButtonEditor
 
actionPerformed(ActionEvent) - Method in class jigcell.compare.views.ProgrammableDataGeneratorEditor
 
actionPerformed(ActionEvent) - Method in class jigcell.compare.views.TransformDebugger
 
actualPos - Variable in class jigcell.compare.data.MethodDispatcher.MethodScorer
Current parsing position in the actual argument values
actualValues - Variable in class jigcell.compare.data.MethodDispatcher.MethodScorer
Function arguments currently being worked on for the target
add(int, IDataGenerator) - Method in class jigcell.compare.data.DataGeneratorList
Adds a generator at the specified index.
add(IDataGenerator) - Method in class jigcell.compare.data.DataGeneratorList
Adds a generator.
add(int, IDataGenerator) - Method in interface jigcell.compare.data.IDataGeneratorList
Adds a generator at the specified index.
add(IDataGenerator) - Method in interface jigcell.compare.data.IDataGeneratorList
Adds a generator.
add(IProgrammableDataGenerator) - Method in class jigcell.compare.views.EvaluationErrorViewer
Adds a new data generator for this viewer to monitor.
add(ITransformContext) - Method in class jigcell.compare.views.EvaluationErrorViewer
Adds a transform evaluation context for this viewer to monitor.
add(String) - Method in class jigcell.compare.views.ObjectiveEditor
Adds a new object.
add() - Method in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Adds a new object.
add(String) - Method in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Adds a new object.
add(String, IProgrammableDataGenerator) - Method in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Adds a new object.
add(String) - Method in class jigcell.compare.views.TransformEditor
Adds a new object.
addAll(Collection) - Method in class jigcell.compare.data.DataGeneratorList
Adds all the generators in a collection.
addAll(IDataGeneratorList) - Method in class jigcell.compare.data.DataGeneratorList
Adds all the generators in a collection.
addAll(Collection) - Method in interface jigcell.compare.data.IDataGeneratorList
Adds all the generators in a collection.
addAll(IDataGeneratorList) - Method in interface jigcell.compare.data.IDataGeneratorList
Adds all the generators in a collection.
addButton(String) - Method in class jigcell.compare.ui.InterfaceBuilder
Adds a button to the interface.
addButton(String, String) - Method in class jigcell.compare.ui.InterfaceBuilder
Adds a button to the interface.
addCheckBox(String) - Method in class jigcell.compare.ui.InterfaceBuilder
Adds a check box to the interface.
addCheckBox(String, String) - Method in class jigcell.compare.ui.InterfaceBuilder
Adds a check box to the interface.
addChoiceEditor(String, String, Object[], boolean) - Method in class jigcell.compare.ui.ConfigEditor
Adds an editor to the interface for selecting from a list of choices.
addColorEditor(String, String) - Method in class jigcell.compare.ui.ConfigEditor
Adds an editor to the interface for Color data.
addColumn() - Method in class jigcell.compare.compare2.Compare2
Adds a new column to the view.
addColumn() - Method in interface jigcell.compare.ui.IColumnEditorTab
Adds a new column to the view.
addColumns(int) - Method in class jigcell.compare.compare2.Compare2
Adds several new columns to the view.
addColumns(int) - Method in interface jigcell.compare.ui.IColumnEditorTab
Adds several new columns to the view.
addComboBox(String, ComboBoxModel) - Method in class jigcell.compare.ui.InterfaceBuilder
Adds a combo box to the interface.
addComboBox(String, ComboBoxModel, String) - Method in class jigcell.compare.ui.InterfaceBuilder
Adds a combo box to the interface.
addComponent(String, JComponent) - Method in class jigcell.compare.ui.InterfaceBuilder
Adds a component to the interface.
addComponentRow(JComponent, GridBagLayout, GridBagConstraints, JComponent[], ActionListener, ChangeListener, ItemListener) - Static method in class jigcell.compare.ui.InterfaceBuilder
Adds a row of components to an interface and attaches listeners as appropriate.
addComponentRow(JComponent, GridBagLayout, GridBagConstraints, JComponent[], ActionListener, ChangeListener, ItemListener, boolean) - Static method in class jigcell.compare.ui.InterfaceBuilder
Adds a row of components to an interface and attaches listeners as appropriate.
addData(String, Object) - Method in class jigcell.compare.impl.Blackboard
Adds a data item to the blackboard.
addDelegate(Class, PersistenceDelegate) - Static method in class jigcell.compare.impl.Compare
 
addDelegate(Class, PersistenceDelegate) - Method in class jigcell.compare.impl.XMLFormatter
Sets the mapping between a class and a delegate.
addElement(Object) - Method in class jigcell.compare.ui.ListComboBoxModel
 
addErrorRecordToView() - Method in class jigcell.compare.views.EvaluationErrorViewer
Adds a new error record to the view.
addEvaluationListener(IEvaluationListener) - Method in class jigcell.compare.data.ProgrammableDataGenerator
Adds a listener to this generator.
addEvaluationListener(IEvaluationListener) - Method in interface jigcell.compare.IProgrammableDataGenerator
Adds a listener to this generator.
addEvaluationListener(IEvaluationListener) - Method in interface jigcell.compare.transform.ITransformContext
Adds a listener for all generators in this context.
addEvaluationListener(IEvaluationListener) - Method in class jigcell.compare.transform.TransformContext
Adds a listener for all generators in this context.
addExtension(ComparatorDataFlavor, String) - Static method in class jigcell.compare.impl.Transferer
Adds a mapping between a data flavor and a preferred serialization extension.
addFlavor(Class, ComparatorDataFlavor) - Static method in class jigcell.compare.impl.Transferer
Adds a mapping between a class and a data flavor.
addGeneratorControl(String, double) - Method in class jigcell.compare.cellcycle.GenericPhenotypeInterface
Adds a new control value to the interface.
addGeneratorControl(String, double) - Method in class jigcell.compare.cellcycle.GenericScanInterface
Adds a new control value to the interface.
addLabel(Icon) - Method in class jigcell.compare.ui.InterfaceBuilder
Adds a label to the interface.
addLabel(String) - Method in class jigcell.compare.ui.InterfaceBuilder
Adds a label to the interface.
addList(String, ListModel, boolean) - Method in class jigcell.compare.ui.InterfaceBuilder
Adds a list to the interface.
addList(String, ListModel, boolean, ListSelectionModel) - Method in class jigcell.compare.ui.InterfaceBuilder
Adds a list to the interface.
addList(String, ListModel, boolean, ListSelectionModel, String) - Method in class jigcell.compare.ui.InterfaceBuilder
Adds a list to the interface.
addListener(PropertyChangeListener) - Method in class jigcell.compare.impl.Blackboard
Adds a listener to the blackboard.
addListener(String, PropertyChangeListener) - Method in class jigcell.compare.impl.Blackboard
Adds a listener to the blackboard for a specific property.
addMethod(Class, String, Object, String) - Method in class jigcell.compare.impl.ProxyBuilder
Adds a new method to this invocation handler.
addNamespace(String) - Method in class jigcell.compare.impl.Blackboard
Adds a namespace to the blackboard.
addNumberEditor(String, String) - Method in class jigcell.compare.ui.ConfigEditor
Adds an editor to the interface for numeric data.
addOption(String, String, Class) - Method in interface jigcell.compare.IConfigEditor
Adds a new option to edit.
addOption(String, String, Object[], boolean, Class) - Method in interface jigcell.compare.IConfigEditor
Adds a new option to edit.
addOption(String, IDataSource.Option) - Method in interface jigcell.compare.IDataSource
Adds a new configuration option.
addOption(String, IDataSource.Option) - Method in class jigcell.compare.impl.DataSource
Adds a new configuration option.
addOption(String, String, Class) - Method in class jigcell.compare.ui.ConfigEditor
Adds a new option to edit.
addOption(String, String, Object[], boolean, Class) - Method in class jigcell.compare.ui.ConfigEditor
Adds a new option to edit.
addPlotNames(Plot) - Method in class jigcell.compare.plotter.PTPlotBridge
Adds the names of series to the plotter.
addPointToPlot(Plot, int, double, double) - Method in class jigcell.compare.plotter.PTPlotBridge
Adds a a point to the plotter.
addPropertyChangeListener(PropertyChangeListener) - Method in class jigcell.compare.impl.Compare
Adds a PropertyChangeListener to the listener list.
addPropertyChangeListener(String, PropertyChangeListener) - Method in class jigcell.compare.impl.Compare
Adds a PropertyChangeListener for a specific property.
addPropertyChangeListener(PropertyChangeListener) - Method in class jigcell.compare.impl.DataGeneratorEvaluator
Adds a PropertyChangeListener to the listener list.
addPropertyChangeListener(PropertyChangeListener) - Method in class jigcell.compare.impl.DataSource
Adds a PropertyChangeListener to the listener list.
addPropertyChangeListener(String, PropertyChangeListener) - Method in class jigcell.compare.impl.DataSource
Adds a PropertyChangeListener for a specific property.
addPrototypeSource(IDataSource) - Method in class jigcell.compare.impl.DataManager
Adds the prototype source of a data transfer agent.
addRadioButton(String, String, ButtonGroup) - Method in class jigcell.compare.ui.InterfaceBuilder
Adds a radio button to the interface.
addReaction(Reaction) - Method in class jigcell.compare.tests.ModelBuilderPlugin
Adds a new reaction to the model.
addRecentSource(IPersistableDataSource) - Method in class jigcell.compare.ui.DataEditorPanelTab
Adds a recently used data source.
addResource(String, Object) - Method in class jigcell.compare.impl.Compare
Adds a mapping between the give name and resource.
addResourceBundle(String) - Static method in class jigcell.compare.impl.Compare
Loads a table of resource strings for the current locale.
addRow() - Method in class jigcell.compare.cellcycle.CellCycleTransformView
Adds a new row to the view.
addRow() - Method in class jigcell.compare.compare2.Compare2
Adds a new row to the view.
addRow() - Method in interface jigcell.compare.ui.IRowEditorTab
Adds a new row to the view.
addRow() - Method in class jigcell.compare.ui.SeriesEditorDialog
Adds a new row to the view.
addRow() - Method in class jigcell.compare.views.EditableSeriesView
Adds a new row to the view.
addRow() - Method in class jigcell.compare.views.ObjectiveSeriesView
Adds a new row to the view.
addRows(int) - Method in class jigcell.compare.cellcycle.CellCycleTransformView
Adds several new rows to the view.
addRows(int) - Method in class jigcell.compare.compare2.Compare2
Adds several new rows to the view.
addRows(int) - Method in interface jigcell.compare.ui.IRowEditorTab
Adds several new rows to the view.
addRows(int) - Method in class jigcell.compare.ui.SeriesEditorDialog
Adds several new rows to the view.
addRows(int) - Method in class jigcell.compare.views.EditableSeriesView
Adds several new rows to the view.
addRows(int) - Method in class jigcell.compare.views.ObjectiveSeriesView
Adds several new rows to the view.
addRun(Run) - Method in class jigcell.compare.tests.RunManagerPlugin
Adds a new run to the run set.
addSeparator(int) - Method in class jigcell.compare.ui.InterfaceBuilder
Adds a separator to the interface.
addSlider(String, BoundedRangeModel) - Method in class jigcell.compare.ui.InterfaceBuilder
Adds a slider to the interface.
addSpinner(String, SpinnerModel) - Method in class jigcell.compare.ui.InterfaceBuilder
Adds a spinner to the interface.
addStringEditor(String, String) - Method in class jigcell.compare.ui.ConfigEditor
Adds an editor to the interface for String data.
addTab(ITab) - Method in class jigcell.compare.impl.Compare
Adds a tab to the main Comparator display.
addTab(ITab) - Method in class jigcell.compare.ui.CompareFrontEnd
Adds a tab to the main Comparator display.
addTab(ITab, boolean, JMenu[], JButton[]) - Method in class jigcell.compare.ui.CompareFrontEnd
Adds a tab to the main Comparator display.
addTable(String, BasicTable.BasicTableModel) - Method in class jigcell.compare.ui.InterfaceBuilder
Adds a table to the interface.
addTabToView() - Method in class jigcell.compare.ui.CompareFrontEnd
Inserts a new tab into the interface.
addTextArea(String, Document) - Method in class jigcell.compare.ui.InterfaceBuilder
Adds a text area to the interface.
addTextArea(String, Document, int, int, boolean) - Method in class jigcell.compare.ui.InterfaceBuilder
Adds a text area to the interface.
addTextField(String, Document) - Method in class jigcell.compare.ui.InterfaceBuilder
Adds a text field to the interface.
addTextField(String, Document, int) - Method in class jigcell.compare.ui.InterfaceBuilder
Adds a text field to the interface.
addToClipboardContents(Clipboard, Transferable) - Method in class jigcell.compare.impl.ClipboardDataSource
Adds a transferable to the clipboard contents option.
addTransformEvaluationContextListener(ITransformContextListener) - Method in interface jigcell.compare.transform.ITransformContext
Adds a listener for this context.
addTransformEvaluationContextListener(ITransformContextListener) - Method in class jigcell.compare.transform.TransformContext
Adds a listener for this context.
addTransient(Class, String) - Static method in class jigcell.compare.impl.Compare
 
addTransient(Class, String) - Method in class jigcell.compare.impl.XMLFormatter
Adds a field to be made transient.
agentName - Variable in class jigcell.compare.cellcycle.OAAConnector
Agent name to expose
ALIGNEDSTAGE - Static variable in class jigcell.compare.cellcycle.BuddingYeastScanTransform.BuddingYeastScanEvent
Entry to aligned
allowContextInsertion - Variable in class jigcell.compare.transform.Transform
Whether transforms can be inserted around this transform through a context menu
allowContextRemoval - Variable in class jigcell.compare.transform.Transform
Whether this transform can be removed through a context menu
allowDescriptionQuery - Variable in class jigcell.compare.data.ProgrammableDataGenerator
Whether this generator can have its input description queried
allowShutdown - Variable in class jigcell.compare.impl.Compare.CompareSecurityManager
Whether a shutdown should be allowed to proceed.
allowThresholdEdit - Variable in class jigcell.compare.compare2.Compare2Model
Whether threholds can be edited
allowWildcardMatches - Variable in class jigcell.compare.data.MethodDispatcher
Whether wildcard matches of the method name are allowed
ANNOTATION_DESCRIPTION - Static variable in class jigcell.compare.transform.annotation.ColumnCountAnnotationDescriptor
Description of this annotation
ANNOTATION_DESCRIPTION - Static variable in class jigcell.compare.transform.annotation.ColumnNameAnnotationDescriptor
Description of this annotation
ANNOTATION_DESCRIPTION - Static variable in class jigcell.compare.transform.annotation.CommentAnnotationDescriptor
Description of this annotation
ANNOTATION_DESCRIPTION - Static variable in class jigcell.compare.transform.annotation.ElementNameAnnotationDescriptor
Description of this annotation
ANNOTATION_DESCRIPTION - Static variable in class jigcell.compare.transform.annotation.ElementSizeAnnotationDescriptor
Description of this annotation
ANNOTATION_DESCRIPTION - Static variable in class jigcell.compare.transform.annotation.ElementTypeAnnotationDescriptor
Description of this annotation
ANNOTATION_DESCRIPTION - Static variable in class jigcell.compare.transform.annotation.TransformAnnotation.AnnotationDescriptor
Description of this annotation
ANNOTATION_NAME - Static variable in class jigcell.compare.transform.annotation.ColumnCountAnnotationDescriptor
Name of this annotation
ANNOTATION_NAME - Static variable in class jigcell.compare.transform.annotation.ColumnNameAnnotationDescriptor
Name of this annotation
ANNOTATION_NAME - Static variable in class jigcell.compare.transform.annotation.CommentAnnotationDescriptor
Name of this annotation
ANNOTATION_NAME - Static variable in class jigcell.compare.transform.annotation.ElementNameAnnotationDescriptor
Name of this annotation
ANNOTATION_NAME - Static variable in class jigcell.compare.transform.annotation.ElementSizeAnnotationDescriptor
Name of this annotation
ANNOTATION_NAME - Static variable in class jigcell.compare.transform.annotation.ElementTypeAnnotationDescriptor
Name of this annotation
ANNOTATION_NAME - Static variable in class jigcell.compare.transform.annotation.TransformAnnotation.AnnotationDescriptor
Name of this annotation
annotationModel - Variable in class jigcell.compare.views.TransformDebugger
Tabular display of transform annotations
anonymousCount - Static variable in class jigcell.compare.transform.TransformContext
Unique identifier counter
applyColumnSelection(ITransform, IDataElement) - Method in class jigcell.compare.cellcycle.CellCycleReportGenerator
Applies the column selection to a transform.
area - Variable in class jigcell.compare.ui.ViewerDialog
Editor control
asList() - Method in class jigcell.compare.data.DataGeneratorList
This list of generators as an untyped list.
asList() - Method in interface jigcell.compare.data.IDataGeneratorList
This list of generators as an untyped list.
asMap() - Method in interface jigcell.compare.data.IResultSetGroupMap
This map of result sets as an untyped map.
asMap() - Method in class jigcell.compare.data.ResultSetGroupMap
This map of result sets as an untyped map.
assertion(String) - Static method in class jigcell.compare.impl.Compare
Logs an exceptional condition and asserts if debugging is enabled.
assertion(String, Throwable) - Static method in class jigcell.compare.impl.Compare
Logs an exceptional condition and asserts if debugging is enabled.
attemptSync(Sync) - Static method in class jigcell.compare.impl.Compare
Acquires the lock of a Sync object or returns false if this operation would block.
ATTRIBUTE_ACCELERATOR - Static variable in class jigcell.compare.ui.MenuBuilder.Builder
Attribute for item accelerator
ATTRIBUTE_COLUMNS - Static variable in class jigcell.compare.transform.SelectColumnsTransform
Attribute for the selected columns
ATTRIBUTE_COMMAND - Static variable in class jigcell.compare.ui.MenuBuilder.Builder
Attribute for action command
ATTRIBUTE_COMMENT - Static variable in interface jigcell.compare.IDataGenerator
Attribute key for the displayable comment of this generator
ATTRIBUTE_COMPARISONTYPE - Static variable in class jigcell.compare.views.ObjectiveSeriesView
Attribute key for the comparison type
ATTRIBUTE_DEFAULTDIMENSIONWEIGHT - Static variable in interface jigcell.compare.objective.IDimensionWeightObjective
Attribute key for the current dimension weight default
ATTRIBUTE_DEFAULTELEMENTWEIGHT - Static variable in interface jigcell.compare.objective.IElementWeightObjective
Attribute key for the current element weight default
ATTRIBUTE_DIMENSIONWEIGHTS - Static variable in interface jigcell.compare.objective.IDimensionWeightObjective
Attribute key for the user specified dimension weights
ATTRIBUTE_ELEMENTWEIGHTS - Static variable in interface jigcell.compare.objective.IElementWeightObjective
Attribute key for the user specified element weights
ATTRIBUTE_ESP1CHECKED - Static variable in class jigcell.compare.cellcycle.BuddingYeastScanTransform
Attribute for whether esp1 is checked
ATTRIBUTE_FILENAME - Static variable in class jigcell.compare.transform.FileTransform
Attribute for name of file this transform uses
ATTRIBUTE_GUID - Static variable in interface jigcell.compare.IDataGenerator
Attribute key for a global identifier
ATTRIBUTE_HANDLER - Static variable in class jigcell.compare.ui.MenuBuilder.Builder
Attribute for item handler
ATTRIBUTE_ICON - Static variable in class jigcell.compare.ui.MenuBuilder.Builder
Attribute for item icon
ATTRIBUTE_INTERPOLATION - Static variable in interface jigcell.compare.objective.IInterpolationObjective
Attribute key for the current interpolation method
ATTRIBUTE_MAXIMUM - Static variable in class jigcell.compare.transform.ExtremaTestTransform
Attribute for the maximum value this transform lets through
ATTRIBUTE_MINIMUM - Static variable in class jigcell.compare.transform.ExtremaTestTransform
Attribute for the minimum value this transform lets through
ATTRIBUTE_MODIFIER - Static variable in class jigcell.compare.ui.MenuBuilder.Builder
Attribute for item modifier
ATTRIBUTE_NAME - Static variable in class jigcell.compare.ui.IconLoader
Attribute for icon name
ATTRIBUTE_NAME - Static variable in class jigcell.compare.ui.MenuBuilder.Builder
Attribute for item name
ATTRIBUTE_PARENT - Static variable in class jigcell.compare.ui.MenuBuilder.Builder
Attribute for item parent
ATTRIBUTE_PATH - Static variable in class jigcell.compare.ui.IconLoader
Attribute for icon path
ATTRIBUTE_RELATION - Static variable in interface jigcell.compare.objective.IRelationalObjective
Attribute key for the currently selected relation
ATTRIBUTE_RESULTNAME - Static variable in interface jigcell.compare.transform.IResultantTransform
Attribute for the result name this transform uses
ATTRIBUTE_RUNFILE - Static variable in class jigcell.compare.cellcycle.JigCellRunManagerTransform
Attribute for the name of the run file
ATTRIBUTE_RUNNUMBER - Static variable in class jigcell.compare.cellcycle.JigCellRunManagerTransform
Attribute for the number of the run within the run file
ATTRIBUTE_THRESHOLD - Static variable in class jigcell.compare.views.ObjectiveSeriesView
Attribute key for the objective threshold
ATTRIBUTE_TRANSFORMNAME - Static variable in class jigcell.compare.transform.TransformEvaluationTransform
Attribute for the name of the transform to evaluate
ATTRIBUTE_TYPE - Static variable in interface jigcell.compare.ITypeChecker
Attribute key for generators who wish to associate a type name
ATTRIBUTE_WILDTYPETRANSFORMNAME - Static variable in class jigcell.compare.cellcycle.GenericScanTransform
Attribute for the name of the transform that computes the wildtype properties

B

BasicTable - Class in jigcell.compare.ui
Extends JTable by enhancing the default table editor, renderer, and layout.
BasicTable(BasicTable.BasicTableModel) - Constructor for class jigcell.compare.ui.BasicTable
Creates a new table.
BasicTable.BasicEditor - Class in jigcell.compare.ui
Default editor for a BasicTable.
BasicTable.BasicEditor() - Constructor for class jigcell.compare.ui.BasicTable.BasicEditor
Creates a new editor.
BasicTable.BasicEditor(IBasicTableHost) - Constructor for class jigcell.compare.ui.BasicTable.BasicEditor
Creates a new editor.
BasicTable.BasicEditor(IBasicTableHost, JCheckBox) - Constructor for class jigcell.compare.ui.BasicTable.BasicEditor
Creates a new editor.
BasicTable.BasicEditor(IBasicTableHost, JComboBox) - Constructor for class jigcell.compare.ui.BasicTable.BasicEditor
Creates a new editor.
BasicTable.BasicEditor(IBasicTableHost, JTextField) - Constructor for class jigcell.compare.ui.BasicTable.BasicEditor
Creates a new editor.
BasicTable.BasicRenderer - Class in jigcell.compare.ui
Default renderer for a BasicTable.
BasicTable.BasicRenderer() - Constructor for class jigcell.compare.ui.BasicTable.BasicRenderer
Creates a new renderer.
BasicTable.BasicRenderer(IBasicTableHost) - Constructor for class jigcell.compare.ui.BasicTable.BasicRenderer
Creates a new renderer.
BasicTable.BasicTableModel - Class in jigcell.compare.ui
Base class of the data model used by views.
BasicTable.BasicTableModel() - Constructor for class jigcell.compare.ui.BasicTable.BasicTableModel
Creates a new table model.
BasicTable.BasicTableModel.Marker - Class in jigcell.compare.ui
Provides quick access to information about columns in this model.
BasicTable.BasicTableModel.Marker(String, String) - Constructor for class jigcell.compare.ui.BasicTable.BasicTableModel.Marker
Creates a new table marker.
BasicTable.ButtonEditor - Class in jigcell.compare.ui
Editor that displays a button in a table cell
BasicTable.ButtonEditor() - Constructor for class jigcell.compare.ui.BasicTable.ButtonEditor
Creates a new button editor.
BasicTable.ButtonRenderer - Class in jigcell.compare.ui
Renderer for displaying a button in a table cell
BasicTable.ButtonRenderer() - Constructor for class jigcell.compare.ui.BasicTable.ButtonRenderer
Creates a new button renderer.
BasicTableView - Class in jigcell.compare.views
A default implementation for displaying data in a table.
BasicTableView(Compare, String) - Constructor for class jigcell.compare.views.BasicTableView
Creates a new table view with no additional functionality.
beanshell - Variable in class jigcell.compare.cellcycle.OAAConnector
Interpreter for commands
Benchmark - Class in jigcell.compare.tests
Supports running performance tests in the Comparator.
Benchmark(Compare) - Constructor for class jigcell.compare.tests.Benchmark
Creates a new performance tester.
benchmark(Class, int, int) - Method in class jigcell.compare.tests.ElementBenchmark
Runs a creation benchmark on an element type.
benchmark(int) - Method in class jigcell.compare.tests.ExperimentBenchmark
Runs a benchmark that loads an experiment file.
benchmark(int) - Method in class jigcell.compare.tests.ModelBuilderBenchmark
Runs a model builder benchmark.
benchmark(int) - Method in class jigcell.compare.tests.ObjectiveBenchmark
Runs an objective loading benchmark.
benchmark(int) - Method in class jigcell.compare.tests.RunManagerBenchmark
Runs a run manager benchmark.
benchmark(int) - Method in class jigcell.compare.tests.TransformBenchmark
Runs a benchmark that loads an experiment file then loads a transform file.
benchmark2(int) - Method in class jigcell.compare.tests.ModelBuilderBenchmark
Runs a model builder benchmark.
benchmark2(int) - Method in class jigcell.compare.tests.RunManagerBenchmark
Runs a run manager benchmark.
benchmark3(int) - Method in class jigcell.compare.tests.ModelBuilderBenchmark
Runs a model builder benchmark.
benchmark3(int) - Method in class jigcell.compare.tests.RunManagerBenchmark
Runs a run manager benchmark.
benchmarkAddRow(int) - Method in class jigcell.compare.tests.ExperimentBenchmark
Runs a benchmark that loads an experiment file, adds a new row, and saves the experiment file.
benchmarkAddRow(int) - Method in class jigcell.compare.tests.ModelBuilderBenchmark
Runs a benchmark that loads a model file, adds a new row, and saves the model file.
benchmarkAddRow(int) - Method in class jigcell.compare.tests.ObjectiveBenchmark
Runs a benchmark that loads an experiment file, adds a new row, saves the experiment file, loads a transform file, adds a new transform, and saves the transform file.
benchmarkAddRow(int) - Method in class jigcell.compare.tests.RunManagerBenchmark
Runs a benchmark that loads a run file, adds a new row, and saves the run file.
benchmarkAddRow(int) - Method in class jigcell.compare.tests.TransformBenchmark
Runs a benchmark that loads an experiment file, adds a new row, saves the experiment file, loads a transform file, adds a new transform, and saves the transform file.
benchmarkExecute(int) - Method in class jigcell.compare.tests.RunManagerBenchmark
Runs a benchmark that loads a run file and executes a run.
benchmarkModify(int) - Method in class jigcell.compare.tests.RunManagerBenchmark
Runs a benchmark that loads a run file, modifies the settings for a run, and saves the run file.
benchmarkRunnable - Variable in class jigcell.compare.tests.Benchmark
Runnable instance to start benchmarking
benchmarkType(Class, int, int) - Static method in class jigcell.compare.tests.ElementBenchmark
Runs a creation benchmark for an element type.
Blackboard - Class in jigcell.compare.impl
A wrapper for the Comparator backend that supports a blackboard style interface.
Blackboard(Compare) - Constructor for class jigcell.compare.impl.Blackboard
Creates a new blackboard wrapper.
Blackboard(Compare, Map, String) - Constructor for class jigcell.compare.impl.Blackboard
Creates a new blackboard wrapper.
blocks - Variable in class jigcell.compare.ui.InterfaceBuilder
Blocks in the curernt interface
BOOLEAN - Static variable in class jigcell.compare.IDataElement.Type
A scalar value that is either true or false
BooleanRelationalInterface - Class in jigcell.compare.objectiveui
Interface for a BooleanRelationalObjective.
BooleanRelationalInterface(IProgrammableDataGenerator) - Constructor for class jigcell.compare.objectiveui.BooleanRelationalInterface
Creates a new interface for a BooleanRelationalObjective.
BooleanRelationalObjective - Class in jigcell.compare.objective
A generator whose function is the result of a boolean relation.
BooleanRelationalObjective() - Constructor for class jigcell.compare.objective.BooleanRelationalObjective
Creates a new generator based upon a boolean relation.
BooleanTypeChecker - Class in jigcell.compare.data.type
Type for boolean data.
BooleanTypeChecker() - Constructor for class jigcell.compare.data.type.BooleanTypeChecker
Creates a new type checker.
BORDER_ACCESSORY - Static variable in class jigcell.compare.ui.FindAccessory
Border around the accessory panel
BORDER_ACCESSORY - Static variable in class jigcell.compare.ui.MemoryMonitorAccessory
Border around the accessory panel
BORDER_NOTHING - Static variable in class jigcell.compare.ui.InterfaceBuilder
Clean border for nested components
BoxInterface - Class in jigcell.compare.transformui
Interface for a box transform container.
BoxInterface(IProgrammableDataGenerator) - Constructor for class jigcell.compare.transformui.BoxInterface
Creates a new interface for a transform.
BoxTransformContainer - Class in jigcell.compare.transform
A compositon of statements that acts as single transform.
BoxTransformContainer() - Constructor for class jigcell.compare.transform.BoxTransformContainer
Creates a new box container.
BUD - Static variable in class jigcell.compare.cellcycle.BuddingYeastScanTransform.BuddingYeastScanEvent
Bud emergence
bud - Variable in class jigcell.compare.cellcycle.BuddingYeastScanTransform.BuddingYeastScanPoint
Value of the species bud
BuddingYeastNocPhenotype - Class in jigcell.compare.cellcycle
Type for the budding yeast nocodazole arrest phenotype.
BuddingYeastNocPhenotype() - Constructor for class jigcell.compare.cellcycle.BuddingYeastNocPhenotype
Creates a new type checker.
BuddingYeastPhenotype - Class in jigcell.compare.cellcycle
Type for the budding yeast cell cycle phenotype.
BuddingYeastPhenotype() - Constructor for class jigcell.compare.cellcycle.BuddingYeastPhenotype
Creates a new type checker.
BuddingYeastPhenotypeInterface - Class in jigcell.compare.cellcycle
Interface for a BuddingYeastPhenotypeObjective.
BuddingYeastPhenotypeInterface(IProgrammableDataGenerator) - Constructor for class jigcell.compare.cellcycle.BuddingYeastPhenotypeInterface
Creates a new interface for a BuddingYeastPhenotypeObjective.
BuddingYeastPhenotypeObjective - Class in jigcell.compare.cellcycle
Measures the difference between two budding yeast phenotypes.
BuddingYeastPhenotypeObjective() - Constructor for class jigcell.compare.cellcycle.BuddingYeastPhenotypeObjective
Creates a new objective function that can evaluate a phenotype.
BuddingYeastScanInterface - Class in jigcell.compare.cellcycle
Interface for a BuddingYeastScanTransform.
BuddingYeastScanInterface(IProgrammableDataGenerator) - Constructor for class jigcell.compare.cellcycle.BuddingYeastScanInterface
Creates a new interface for a BuddingYeastScanTransform.
BuddingYeastScanTransform - Class in jigcell.compare.cellcycle
Computes the phenotype of a budding yeast mutant from a time course of concentrations.
BuddingYeastScanTransform() - Constructor for class jigcell.compare.cellcycle.BuddingYeastScanTransform
Creates a new transform that can perform a run evaluation.
BuddingYeastScanTransform(boolean) - Constructor for class jigcell.compare.cellcycle.BuddingYeastScanTransform
Creates a new transform that can perform a run evaluation.
BuddingYeastScanTransform.BuddingYeastScanEvent - Class in jigcell.compare.cellcycle
An event that occurs during the scan.
BuddingYeastScanTransform.BuddingYeastScanEvent(double, int) - Constructor for class jigcell.compare.cellcycle.BuddingYeastScanTransform.BuddingYeastScanEvent
Creates a new event.
BuddingYeastScanTransform.BuddingYeastScanPoint - Class in jigcell.compare.cellcycle
A single time course point used by the scan.
BuddingYeastScanTransform.BuddingYeastScanPoint(IDataElement, double) - Constructor for class jigcell.compare.cellcycle.BuddingYeastScanTransform.BuddingYeastScanPoint
Extracts the point values from a time course observation.
BuddingYeastWildtypeProperties - Class in jigcell.compare.cellcycle
Type for the budding yeast wildtype properties.
BuddingYeastWildtypeProperties() - Constructor for class jigcell.compare.cellcycle.BuddingYeastWildtypeProperties
Creates a new type checker.
BUFFER_LENGTH - Static variable in class jigcell.compare.objective.MinkowskiObjective
Length of slices to work with
BUFFER_LENGTH_ELEMENT - Static variable in class jigcell.compare.objective.WOSSObjective
Length of element slices to work with
BUFFER_LENGTH_VALUE - Static variable in class jigcell.compare.objective.WOSSObjective
Length of value slices to work with
buildDispatch(int, String, String) - Method in class jigcell.compare.cellcycle.OAAConnector
Constructs a new dispatch solvable.
builder - Variable in class jigcell.compare.cellcycle.CellCycleReportGenerator
Builder for current configuration interface
builder - Variable in class jigcell.compare.ui.MenuBuilder
Menu builder
BUILDERS - Static variable in class jigcell.compare.ui.MenuBuilder
Known menu builders
buildPlotter(Plot) - Method in class jigcell.compare.plotter.PTPlotBridge
Adds data to the PTPlot plotter.
buildRangeElement() - Method in class jigcell.compare.cellcycle.CellCycleReportGenerator
Constructs a data element with the user's plotter range.
BUNDLE_LOCK - Static variable in class jigcell.compare.impl.Compare
Lock for controlling resource bundle manipulation
button - Variable in class jigcell.compare.ui.BasicTable.ButtonEditor
Button
BUTTON_ADD - Static variable in class jigcell.compare.transformui.SelectColumnsInterface
Button to add a selected column
BUTTON_ADD - Static variable in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Label for add button
BUTTON_APPLY - Static variable in class jigcell.compare.ui.ConfigEditor
Text for apply button
BUTTON_BROWSE - Static variable in class jigcell.compare.transformui.FileInterface
Button label for browse
BUTTON_CLEAR - Static variable in class jigcell.compare.views.EvaluationErrorViewer
Button to clear the list of errors
BUTTON_CLOSE - Static variable in class jigcell.compare.ui.SeriesDialog
Close button label
BUTTON_HIDE - Static variable in class jigcell.compare.views.EvaluationErrorViewer
Button to hide the dialog
BUTTON_REMOVE - Static variable in class jigcell.compare.transformui.SelectColumnsInterface
Button to remove a selected column
BUTTON_RESET - Static variable in class jigcell.compare.ui.ConfigEditor
Text for reset button
BUTTON_SHOWINPUT - Static variable in class jigcell.compare.views.TransformDebugger
Button text to show the input description of the currently selected transform
BUTTON_SHOWOUTPUT - Static variable in class jigcell.compare.views.TransformDebugger
Button text to show the output description of the currently selected transform
BUTTON_UPDATE - Static variable in class jigcell.compare.ui.EditorDialog
Update button label

C

cache - Variable in class jigcell.compare.data.CachedDataElement
Element for use in memory locking
CachedDataElement - Class in jigcell.compare.data
A data element that provides a memory sensitive cache wrapped around another data element.
CachedDataElement(IDataElement) - Constructor for class jigcell.compare.data.CachedDataElement
Creates a new data element cache.
CachedDataElement() - Constructor for class jigcell.compare.data.CachedDataElement
Creates a new data element cache.
CachedDataElement.CachedDataElementDelegate - Class in jigcell.compare.data
Persists the element by creating a new wrapper around the cached element.
CachedDataElement.CachedDataElementDelegate() - Constructor for class jigcell.compare.data.CachedDataElement.CachedDataElementDelegate
 
callStack - Variable in class jigcell.compare.data.ProgrammableDataGenerator
The current evaluation call stack
cancel - Variable in class jigcell.compare.impl.DataGeneratorEvaluator
Whether the evaluation was cancelled
cancel() - Method in class jigcell.compare.impl.DataGeneratorEvaluator
Attempts to cancel the current evaluation.
cancel - Variable in class jigcell.compare.ui.ProgressMonitor
Text to use for cancel button
CellCycleDataDialog - Class in jigcell.compare.cellcycle
Supports side-by-side viewing of experimental and transform results.
CellCycleDataDialog(Compare, IDataGenerator, int, int, BasicTable.BasicTableModel) - Constructor for class jigcell.compare.cellcycle.CellCycleDataDialog
Creates a new dialog for side-by-side viewing of experimental and transform results.
CellCycleDataDialog.DataModel - Class in jigcell.compare.cellcycle
Table model for a ETListViewerDialog.
CellCycleDataDialog.DataModel() - Constructor for class jigcell.compare.cellcycle.CellCycleDataDialog.DataModel
Creates a new table model.
CellCycleExperimentView - Class in jigcell.compare.cellcycle
An editable display for working with experimental data.
CellCycleExperimentView(Compare, String) - Constructor for class jigcell.compare.cellcycle.CellCycleExperimentView
Creates a new table view with the ability to display experiment data.
CellCycleExperimentView.ExperimentModel - Class in jigcell.compare.cellcycle
Table model for the data in an ExperimentDataSeriesView.
CellCycleExperimentView.ExperimentModel() - Constructor for class jigcell.compare.cellcycle.CellCycleExperimentView.ExperimentModel
Creates a new table model.
CellCycleExperimentView.ExperimentViewRenderer - Class in jigcell.compare.cellcycle
Colors cells when a type error is detected.
CellCycleExperimentView.ExperimentViewRenderer() - Constructor for class jigcell.compare.cellcycle.CellCycleExperimentView.ExperimentViewRenderer
Creates a new view renderer.
CellCycleFrontEnd - Class in jigcell.compare.cellcycle
The Comparator frontend.
CellCycleFrontEnd(String) - Constructor for class jigcell.compare.cellcycle.CellCycleFrontEnd
Creates a new graphical Comparator.
CellCycleObjectiveView - Class in jigcell.compare.cellcycle
An editable display for working with objective data.
CellCycleObjectiveView(Compare, String) - Constructor for class jigcell.compare.cellcycle.CellCycleObjectiveView
Creates a new table view with the ability to display objective, model, and experiment data.
CellCycleObjectiveView.ObjectiveModel - Class in jigcell.compare.cellcycle
Table model for the data in an MEOSummaryView.
CellCycleObjectiveView.ObjectiveModel() - Constructor for class jigcell.compare.cellcycle.CellCycleObjectiveView.ObjectiveModel
Creates a new table model.
CellCycleObjectiveView.ObjectiveViewRenderer - Class in jigcell.compare.cellcycle
Colors cells when a type error is detected.
CellCycleObjectiveView.ObjectiveViewRenderer(boolean) - Constructor for class jigcell.compare.cellcycle.CellCycleObjectiveView.ObjectiveViewRenderer
Creates a new view renderer.
CellCycleReportGenerator - Class in jigcell.compare.cellcycle
Prints a summary report of a set of comparisons to a PDF file.
CellCycleReportGenerator(Compare, IDataGeneratorList) - Constructor for class jigcell.compare.cellcycle.CellCycleReportGenerator
Constructs a data source that produces a report for a set of generators.
CellCycleTransformView - Class in jigcell.compare.cellcycle
An editable display for working with model data.
CellCycleTransformView(Compare, String) - Constructor for class jigcell.compare.cellcycle.CellCycleTransformView
Creates a new table view with the ability to display model and experiment data.
CellCycleTransformView.TransformModel - Class in jigcell.compare.cellcycle
Table model for the data in an ModelDataSeriesView.
CellCycleTransformView.TransformModel() - Constructor for class jigcell.compare.cellcycle.CellCycleTransformView.TransformModel
Creates a new table model.
CellCycleTransformView.TransformViewRenderer - Class in jigcell.compare.cellcycle
Colors cells when a type error is detected.
CellCycleTransformView.TransformViewRenderer() - Constructor for class jigcell.compare.cellcycle.CellCycleTransformView.TransformViewRenderer
Creates a new view renderer.
centerTextLabels - Variable in class jigcell.compare.views.ObjectiveSeriesView.ObjectiveSeriesRenderer
Whether to center a text label
ChainedDataGeneratorList - Class in jigcell.compare.objective
Compactly stores additions to an existing data generator list.
ChainedDataGeneratorList(IDataGeneratorList) - Constructor for class jigcell.compare.objective.ChainedDataGeneratorList
Chains to an existing data generator list.
changedUpdate(DocumentEvent) - Method in class jigcell.compare.objectiveui.ScriptEvaluationInterface
 
changedUpdate(DocumentEvent) - Method in class jigcell.compare.transformui.ScriptEvaluationInterface
 
changedUpdate(DocumentEvent) - Method in class jigcell.compare.ui.ConfigEditor
 
CHECK - Static variable in class jigcell.compare.impl.ExceptionRecorder
Flag to cause a checked assertion
checker - Variable in class jigcell.compare.ui.SeriesDialog
Type checker for the element
checkExit(int) - Method in class jigcell.compare.impl.Compare.CompareSecurityManager
 
checkPermission(Permission) - Method in class jigcell.compare.impl.Compare.CompareSecurityManager
 
checkPermission(Permission, Object) - Method in class jigcell.compare.impl.Compare.CompareSecurityManager
 
checkPhenotype(IDataElement, long, IDataElement.Type, boolean, String) - Static method in class jigcell.compare.cellcycle.GenericPhenotypeObjective
Validates that the data in a given element matches the phenotype pattern.
checkScalarTypes(IDataElement.Type, IDataElement.Type) - Method in class jigcell.compare.objective.BooleanRelationalObjective
Ensures that both inputs are scalar types.
checkToken(StreamingStringTokenizer, String) - Method in class jigcell.compare.tests.StreamingStringTokenizerTests
Gets the next token from a tokenizer, trims it, and checks for a match.
childClear(ITransform) - Method in class jigcell.compare.transform.BoxTransformContainer
A clear request for this container initiated by one of its children.
childClear(ITransform) - Method in interface jigcell.compare.transform.ITransformContainer
A clear request for this container initiated by one of its children.
childFlush(ITransform) - Method in class jigcell.compare.transform.BoxTransformContainer
A flush request for this container initiated by one of its children.
childFlush(ITransform) - Method in interface jigcell.compare.transform.ITransformContainer
A flush request for this container initiated by one of its children.
CLASS_ACTIONLISTENER - Static variable in class jigcell.compare.impl.ProxyBuilder
Parameter type for an ActionListener
CLASS_ARRAY - Static variable in class jigcell.compare.data.MethodDispatcher
Character representing an array reference
CLASS_BOOLEAN - Static variable in class jigcell.compare.data.MethodDispatcher
Character representing a boolean reference
CLASS_CHARACTER - Static variable in class jigcell.compare.data.MethodDispatcher
Character representing a character reference
CLASS_COMPARATOR - Static variable in class jigcell.compare.impl.ProxyBuilder
Parameter type for a Comparator
CLASS_DOUBLE - Static variable in class jigcell.compare.data.MethodDispatcher
Character representing a double reference
CLASS_EVALUATIONLISTENER - Static variable in class jigcell.compare.impl.ProxyBuilder
Parameter type for a ProgarmmaticDataGeneratorListener
CLASS_FLOAT - Static variable in class jigcell.compare.data.MethodDispatcher
Character representing a float reference
CLASS_INTEGER - Static variable in class jigcell.compare.data.MethodDispatcher
Character representing an integer reference
CLASS_LONG - Static variable in class jigcell.compare.data.MethodDispatcher
Character representing a long reference
CLASS_OBJECT_END - Static variable in class jigcell.compare.data.MethodDispatcher
Character representing an object reference
CLASS_OBJECT_START - Static variable in class jigcell.compare.data.MethodDispatcher
Character representing an object reference
CLASS_PROPERTYCHANGELISTENER - Static variable in class jigcell.compare.impl.ProxyBuilder
Parameter type for a PropertyChangeListener
CLASS_RUNNABLE - Static variable in class jigcell.compare.impl.ProxyBuilder
Parameter type for a Runnable
CLASS_SHORT - Static variable in class jigcell.compare.data.MethodDispatcher
Character representing a short reference
classLabel - Variable in class jigcell.compare.views.TransformDebugger
Label displaying the type of the currently selected transform
clazz - Variable in class jigcell.compare.ui.IconLoader
Owning class for resources
cleanup(IProgrammableDataGenerator) - Method in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Performs any necessary cleanup operations on an object before it's removed from the view.
cleanup(IProgrammableDataGenerator) - Method in class jigcell.compare.views.TransformEditor
Performs any necessary cleanup operations on an object before it's removed from the view.
clear() - Method in class jigcell.compare.cellcycle.CellCycleTransformView
Clears all data for this view.
clear() - Method in class jigcell.compare.cellcycle.GenericScanTransform
Nulls out the stored element.
clear() - Method in class jigcell.compare.compare2.Compare2
Clears all data for this view.
clear() - Method in class jigcell.compare.data.DataGeneratorList
Removes all generators from this list.
clear() - Method in class jigcell.compare.data.EditableDataGenerator
Nulls out the stored element.
clear() - Method in interface jigcell.compare.data.IDataGeneratorList
Removes all generators from this list.
clear() - Method in class jigcell.compare.data.PackedDoubleDataElement
Deletes all values in this element.
clear() - Method in class jigcell.compare.data.ProgrammableDataGenerator
Nulls out the stored element.
clear() - Method in class jigcell.compare.data.TreeDataElement
Deletes all values in this element.
clear() - Method in interface jigcell.compare.IEditableDataElement
Deletes all values in this element.
clear() - Method in interface jigcell.compare.IEditableDataGenerator
Nulls out the stored element.
clear() - Method in class jigcell.compare.impl.ExceptionRecorder
Clears any exceptions caught by this handler.
clear() - Method in interface jigcell.compare.objective.IObjective
Destroys all work done by this generator.
clear() - Method in class jigcell.compare.transform.BoxTransformContainer
Nulls out the stored element.
clear() - Method in interface jigcell.compare.transform.ITransform
Destroys all work done by this generator.
clear() - Method in class jigcell.compare.transform.SelectColumnsTransform
Nulls out the stored element.
clear() - Method in class jigcell.compare.transform.Transform
Nulls out the stored element.
clear() - Method in interface jigcell.compare.ui.IDataEditorTab
Clears all data for this view.
clear() - Method in class jigcell.compare.ui.SeriesEditorDialog
 
clear() - Method in class jigcell.compare.views.EditableSeriesView
Clears all data for this view.
clear() - Method in class jigcell.compare.views.ObjectiveSeriesView
Clears all data for this view.
clear() - Method in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Deletes all objects owned by this editor.
clearAndNew() - Method in class jigcell.compare.compare2.Compare2
Create a new data set for editing.
clearAndNew() - Method in interface jigcell.compare.ui.IDataEditorTab
Create a new data set for editing.
clearAndNew() - Method in class jigcell.compare.views.EditableSeriesView
Create a new data set for editing.
clearAndNew() - Method in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Create a new data set for editing.
clearCommandIndex() - Method in class jigcell.compare.ui.MenuBuilder
Clears the command index for menu elements.
clearObjective(IObjective) - Static method in class jigcell.compare.views.ObjectiveSeriesView
Clears an objective.
clearSelected() - Method in class jigcell.compare.views.TransformDebugger
Clears the currently selected transform.
clearThresholds() - Method in class jigcell.compare.compare2.Compare2
Clears the threshold values.
CLIENT_COMPONENTNAME - Static variable in class jigcell.compare.ui.InterfaceBuilder
Component client property for customizer name
CLIENT_COMPONENTSHOWN - Static variable in class jigcell.compare.ui.BasicTable
Client property for delayed initialization
CLIENT_COMPONENTSHOWN - Static variable in class jigcell.compare.ui.ConfigEditor
Client property for delayed initialization
CLIENT_COMPONENTSHOWN - Static variable in class jigcell.compare.views.TransformDebugger
Client property for delayed initialization
CLIENT_FOCUSED - Static variable in class jigcell.compare.ui.ProgressMonitor
Client property indicating this monitor dialog has been focused
clipboard - Variable in class jigcell.compare.views.BasicTableView
Clipboard to use
clipboardCopy() - Method in interface jigcell.compare.ui.IClipboardTab
Copies all rows to the clipboard.
clipboardCopy(int[]) - Method in interface jigcell.compare.ui.IClipboardTab
Copies selected rows to the clipboard.
clipboardCopy() - Method in class jigcell.compare.views.SeriesView
Copies all rows to the clipboard.
clipboardCopy(int[]) - Method in class jigcell.compare.views.SeriesView
Copies selected rows to the clipboard.
clipboardCut() - Method in class jigcell.compare.cellcycle.CellCycleTransformView
Cuts all rows to the clipboard.
clipboardCut() - Method in interface jigcell.compare.ui.IClipboardTab
Cuts all rows to the clipboard.
clipboardCut(int[]) - Method in interface jigcell.compare.ui.IClipboardTab
Cuts selected rows to the clipboard.
clipboardCut() - Method in class jigcell.compare.views.EditableSeriesView
Cuts all rows to the clipboard.
clipboardCut(int[]) - Method in class jigcell.compare.views.EditableSeriesView
Cuts selected rows to the clipboard.
clipboardCut() - Method in class jigcell.compare.views.ObjectiveSeriesView
Cuts all rows to the clipboard.
clipboardCut() - Method in class jigcell.compare.views.SeriesView
Cuts all rows to the clipboard.
clipboardCut(int[]) - Method in class jigcell.compare.views.SeriesView
Cuts selected rows to the clipboard.
ClipboardDataSource - Class in jigcell.compare.impl
A generic transfer agent for a source of data that supports reading and writing to a clipboard.
ClipboardDataSource() - Constructor for class jigcell.compare.impl.ClipboardDataSource
Creates a new data source that represents a clipboard.
ClipboardDataSource(Clipboard) - Constructor for class jigcell.compare.impl.ClipboardDataSource
Creates a new data source that represents a file.
clipboardPaste() - Method in class jigcell.compare.cellcycle.CellCycleTransformView
Pastes from the clipboard.
clipboardPaste() - Method in interface jigcell.compare.ui.IClipboardTab
Pastes from the clipboard.
clipboardPaste() - Method in class jigcell.compare.views.EditableSeriesView
Pastes from the clipboard.
clipboardPaste() - Method in class jigcell.compare.views.ObjectiveSeriesView
Pastes from the clipboard.
clipboardPaste() - Method in class jigcell.compare.views.SeriesView
Pastes from the clipboard.
clipboardWrite(Object, String) - Method in class jigcell.compare.views.BasicTableView
Writes data to the clipboard.
clone() - Method in class jigcell.compare.data.DataGenerator
 
clone() - Method in class jigcell.compare.data.DataGeneratorList
 
clone() - Method in class jigcell.compare.data.DataGeneratorMap
 
clone() - Method in interface jigcell.compare.data.IDataGeneratorCollection
 
clone() - Method in interface jigcell.compare.data.IResultSetGroupMap
 
clone() - Method in class jigcell.compare.data.ResultSetGroupMap
 
clone() - Method in class jigcell.compare.data.ResultSetMap
 
clone() - Method in interface jigcell.compare.IDataSource
A copy of this data source.
clone() - Method in class jigcell.compare.impl.DataSource
A copy of this data source.
close() - Method in class jigcell.compare.ui.ProgressMonitor
Closes the progress dialog.
closeModel() - Method in class jigcell.compare.tests.ModelBuilderPlugin
Closes the current model in the Model Builder.
closeRunFile() - Method in class jigcell.compare.tests.RunManagerPlugin
Closes the current run set in the Run Manager.
colorer - Variable in class jigcell.compare.compare2.Compare2
Current view colorer being used
colorerMode - Variable in class jigcell.compare.compare2.Compare2
Colorer display mode
colorers - Variable in class jigcell.compare.compare2.Compare2
Map[MenuItem,IViewColorer] of the triggers for the loaded view colorers
column - Variable in class jigcell.compare.ui.BasicTable.ButtonEditor
Column being edited
column - Variable in class jigcell.compare.ui.ViewerDialog
Column in the parent table
COLUMN_ANNOTATION - Variable in class jigcell.compare.views.TransformDebugger.AnnotationModel
Annotation column
COLUMN_COMMENT - Variable in class jigcell.compare.views.SeriesView.SeriesModel
Comment column
COLUMN_COMPARISONTYPE - Variable in class jigcell.compare.compare2.Compare2Model
Comparison type column
COLUMN_COMPARISONTYPE - Variable in class jigcell.compare.views.ObjectiveSeriesView.ObjectiveSeriesModel
Comparison type column
COLUMN_MESSAGE - Variable in class jigcell.compare.views.EvaluationErrorViewer.ErrorModel
Error message column
COLUMN_MODELVALUE - Variable in class jigcell.compare.cellcycle.CellCycleDataDialog.DataModel
Model value column
COLUMN_MODELVALUE - Variable in class jigcell.compare.cellcycle.CellCycleObjectiveView.ObjectiveModel
Transform value column name
COLUMN_MODELVALUE - Variable in class jigcell.compare.cellcycle.CellCycleTransformView.TransformModel
Transform value column
COLUMN_MORE - Variable in class jigcell.compare.views.EvaluationErrorViewer.ErrorModel
More information column
COLUMN_NAME - Variable in class jigcell.compare.compare2.Compare2Model
Name column
COLUMN_NAME - Variable in class jigcell.compare.ui.SeriesDialog.SeriesModel
Name column
COLUMN_NAME - Variable in class jigcell.compare.views.EvaluationErrorViewer.ErrorModel
Generator name column
COLUMN_NAME - Variable in class jigcell.compare.views.SeriesView.SeriesModel
Name column
COLUMN_OBJECTIVE - Variable in class jigcell.compare.views.ObjectiveSeriesView.ObjectiveSeriesModel
Objective column
COLUMN_OBJECTIVEVALUE - Variable in class jigcell.compare.views.ObjectiveSeriesView.ObjectiveSeriesModel
Objective value column
COLUMN_POSITION - Variable in class jigcell.compare.views.TransformDebugger.AnnotationModel
Position column
COLUMN_POSITION - Variable in class jigcell.compare.views.TransformDebugger.ValueModel
Position column
COLUMN_REFERENCE - Variable in class jigcell.compare.objectiveui.ElementWeightEditorDialog.ElementWeightModel
Weight reference column
COLUMN_THRESHOLD - Variable in class jigcell.compare.compare2.Compare2Model
Threshold column
COLUMN_THRESHOLD - Variable in class jigcell.compare.views.ObjectiveSeriesView.ObjectiveSeriesModel
Threshold column
COLUMN_TRANSFORM - Variable in class jigcell.compare.cellcycle.CellCycleTransformView.TransformModel
Transform column
COLUMN_TYPE - Variable in class jigcell.compare.cellcycle.CellCycleExperimentView.ExperimentModel
Type column
COLUMN_TYPE - Variable in class jigcell.compare.cellcycle.CellCycleObjectiveView.ObjectiveModel
Type column name
COLUMN_TYPE - Variable in class jigcell.compare.cellcycle.CellCycleTransformView.TransformModel
Type column
COLUMN_TYPE - Variable in class jigcell.compare.views.TransformDebugger.AnnotationModel
Type column
COLUMN_VALUE - Variable in class jigcell.compare.ui.SeriesDialog.SeriesModel
Value column
COLUMN_VALUE - Variable in class jigcell.compare.views.SeriesView.SeriesModel
Value column
COLUMN_VALUE - Variable in class jigcell.compare.views.TransformDebugger.ValueModel
Value column
columnAdded(TableColumnModelEvent) - Method in class jigcell.compare.compare2.Compare2
 
ColumnCountAnnotationDescriptor - Class in jigcell.compare.transform.annotation
A data generator annotation description for the name of a column.
ColumnCountAnnotationDescriptor() - Constructor for class jigcell.compare.transform.annotation.ColumnCountAnnotationDescriptor
Creates an annotation object describing an element name.
columnMarginChanged(ChangeEvent) - Method in class jigcell.compare.compare2.Compare2
 
columnMoved(TableColumnModelEvent) - Method in class jigcell.compare.compare2.Compare2
 
ColumnNameAnnotationDescriptor - Class in jigcell.compare.transform.annotation
A data generator annotation description for the name of a column.
ColumnNameAnnotationDescriptor() - Constructor for class jigcell.compare.transform.annotation.ColumnNameAnnotationDescriptor
Creates an annotation object describing an element name.
columnNames - Variable in class jigcell.compare.transform.SelectColumnsTransform
Last updated values for the column names
columnRemoved(TableColumnModelEvent) - Method in class jigcell.compare.compare2.Compare2
 
columnsDocument - Variable in class jigcell.compare.transformui.SelectColumnsInterface
Columns assignment selection document
columnSelectionChanged(ListSelectionEvent) - Method in class jigcell.compare.compare2.Compare2
 
columnWeights - Variable in class jigcell.compare.ui.BasicTable.BasicTableModel
Weights for resizing columns
command - Variable in class jigcell.compare.ui.MenuBuilder.Builder.Item
Action command for the item
commandIndex - Variable in class jigcell.compare.ui.MenuBuilder
Map from commands to menu elements if indexing is enabled
CommentAnnotationDescriptor - Class in jigcell.compare.transform.annotation
A data generator annotation description for making a general comment.
CommentAnnotationDescriptor() - Constructor for class jigcell.compare.transform.annotation.CommentAnnotationDescriptor
Creates an annotation object describing an element name.
COMPARATOR_NAME - Static variable in class jigcell.compare.data.DataGenerator
Sorts data generators by name in alphabetical order.
COMPARATOR_NAME - Static variable in class jigcell.compare.data.type.TypeChecker
Sorts type checkers by name in alphabetical order.
COMPARATOR_NAME - Static variable in class jigcell.compare.transformui.TransformEvaluationInterface
Sorts transform names in alphabetical order.
ComparatorDataFlavor - Class in jigcell.compare.impl
A data flavor that represents a specialized format used by the Comparator.
ComparatorDataFlavor(String, Class) - Constructor for class jigcell.compare.impl.ComparatorDataFlavor
Creates a new data flavor.
ComparatorDataFlavor(String, Transferable) - Constructor for class jigcell.compare.impl.ComparatorDataFlavor
Creates a new data flavor.
ComparatorDataFlavor(String, Class, ComparatorDataFlavor) - Constructor for class jigcell.compare.impl.ComparatorDataFlavor
Creates a new data flavor.
ComparatorDataFlavor(String, Class, Map) - Constructor for class jigcell.compare.impl.ComparatorDataFlavor
Creates a new data flavor.
ComparatorDataFlavor(String, Class, String) - Constructor for class jigcell.compare.impl.ComparatorDataFlavor
Creates a new data flavor.
ComparatorDataFlavor(String, Transferable, ComparatorDataFlavor) - Constructor for class jigcell.compare.impl.ComparatorDataFlavor
Creates a new data flavor.
ComparatorDataFlavor(String, Transferable, Map) - Constructor for class jigcell.compare.impl.ComparatorDataFlavor
Creates a new data flavor.
ComparatorDataFlavor(String, Transferable, String) - Constructor for class jigcell.compare.impl.ComparatorDataFlavor
Creates a new data flavor.
ComparatorDataFlavor(String, Class, ComparatorDataFlavor, Map) - Constructor for class jigcell.compare.impl.ComparatorDataFlavor
Creates a new data flavor.
ComparatorDataFlavor(String, Class, String, Map) - Constructor for class jigcell.compare.impl.ComparatorDataFlavor
Creates a new data flavor.
ComparatorDataFlavor(String, Transferable, ComparatorDataFlavor, Map) - Constructor for class jigcell.compare.impl.ComparatorDataFlavor
Creates a new data flavor.
ComparatorDataFlavor(String, Transferable, String, Map) - Constructor for class jigcell.compare.impl.ComparatorDataFlavor
Creates a new data flavor.
ComparatorDataFlavor(String) - Constructor for class jigcell.compare.impl.ComparatorDataFlavor
Creates a new data flavor.
compare - Variable in class jigcell.compare.cellcycle.CellCycleReportGenerator
Comparator of parent window
compare - Variable in class jigcell.compare.compare2.Compare2Model
Comparator for model users
compare - Variable in class jigcell.compare.compare2.ThresholdEditor
Comparator of parent view
compare - Variable in class jigcell.compare.impl.Blackboard
Wrapped Comparator
Compare - Class in jigcell.compare.impl
The Comparator backend and some support for a shell servicing the Comparator frontend.
Compare(String) - Constructor for class jigcell.compare.impl.Compare
Creates a new headless Comparator.
compare - Variable in class jigcell.compare.impl.ExceptionRecorder
Comparator
compare - Variable in class jigcell.compare.tests.Benchmark
Comparator to abuse
compare - Variable in class jigcell.compare.ui.ConfigEditor
Parent of view
compare - Variable in class jigcell.compare.ui.FindAccessory
Comparator display this accessory is currently installed in
compare - Variable in class jigcell.compare.ui.PanelTab
Parent Comparator
compare - Variable in class jigcell.compare.ui.ViewerDialog
Associated comparator
Compare.CompareSecurityManager - Class in jigcell.compare.impl
Controls termination of the Comparator to prevent badly behaving tabs from causing problems.
Compare.CompareSecurityManager() - Constructor for class jigcell.compare.impl.Compare.CompareSecurityManager
Creates a new security manager.
Compare.TabInfo - Class in jigcell.compare.impl
Information about a Comparator tab.
Compare.TabInfo(ITab) - Constructor for class jigcell.compare.impl.Compare.TabInfo
Creates a new tab description.
Compare.TabInfo() - Constructor for class jigcell.compare.impl.Compare.TabInfo
Not allowed.
Compare2 - Class in jigcell.compare.compare2
A visualization tool for performing comparisons across multiple comparisons.
Compare2(Compare, String) - Constructor for class jigcell.compare.compare2.Compare2
Creates a new table view that compares multiple sets of comparisons.
Compare2.SetReadHelper - Class in jigcell.compare.compare2
Helper class for performing read operations on other threads.
Compare2.SetReadHelper(IReadableDataSource, String) - Constructor for class jigcell.compare.compare2.Compare2.SetReadHelper
Creates a new reading helper thread.
Compare2.ThresholdReadHelper - Class in jigcell.compare.compare2
Helper class for performing read operations on other threads.
Compare2.ThresholdReadHelper(IReadableDataSource) - Constructor for class jigcell.compare.compare2.Compare2.ThresholdReadHelper
Creates a new reading helper thread.
Compare2Model - Class in jigcell.compare.compare2
Table model for Compare^2.
Compare2Model(Compare, List, Map, Map, List, Map) - Constructor for class jigcell.compare.compare2.Compare2Model
Creates a new table model.
compareByName(Object, Object) - Static method in class jigcell.compare.data.DataGenerator
Compares two data generators by name.
compareByName(Object, Object) - Static method in class jigcell.compare.data.type.TypeChecker
Compares two type checkers by name.
CompareFrontEnd - Class in jigcell.compare.ui
The Comparator frontend.
CompareFrontEnd(String) - Constructor for class jigcell.compare.ui.CompareFrontEnd
Creates a new graphical Comparator.
CompareFrontEnd.FrontEndTabInfo - Class in jigcell.compare.ui
Information about a Comparator tab.
CompareFrontEnd.FrontEndTabInfo(ITab, JMenu[], JButton[], JDialog, IConfigEditor) - Constructor for class jigcell.compare.ui.CompareFrontEnd.FrontEndTabInfo
Creates a new tab description.
CompareFrontEnd.SplashScreen - Class in jigcell.compare.ui
A splash screen to display while things are loading.
CompareFrontEnd.SplashScreen(JFrame, String) - Constructor for class jigcell.compare.ui.CompareFrontEnd.SplashScreen
 
compareTo(Object) - Method in class jigcell.compare.cellcycle.BuddingYeastScanTransform.BuddingYeastScanEvent
 
compareTo(Object) - Method in class jigcell.compare.cellcycle.GenericScanTransform.GenericScanEvent
 
compareTransformName(Object, Object) - Static method in class jigcell.compare.transformui.TransformEvaluationInterface
Compares two transform names.
comparisonNames - Variable in class jigcell.compare.compare2.Compare2
Map[IResultSetMap,String] of comparisons to the set name
comparisonNames - Variable in class jigcell.compare.compare2.Compare2Model
Map[IResultSetMap,String] of comparisons to the set name
comparisons - Variable in class jigcell.compare.compare2.Compare2
List[IResultSetMap] of comparisons
comparisons - Variable in class jigcell.compare.compare2.Compare2Model
List[IResultSetMap] of comparisons
componentHidden(ComponentEvent) - Method in class jigcell.compare.compare2.ResultViewZoom
 
componentHidden(ComponentEvent) - Method in class jigcell.compare.ui.CompareFrontEnd
 
componentMoved(ComponentEvent) - Method in class jigcell.compare.compare2.ResultViewZoom
 
componentMoved(ComponentEvent) - Method in class jigcell.compare.ui.CompareFrontEnd
 
componentResized(ComponentEvent) - Method in class jigcell.compare.compare2.ResultViewZoom
 
componentResized(ComponentEvent) - Method in class jigcell.compare.ui.CompareFrontEnd
 
components - Variable in class jigcell.compare.ui.InterfaceBuilder
Components in the current interface row
componentShown(ComponentEvent) - Method in class jigcell.compare.compare2.ResultViewZoom
 
componentShown(ComponentEvent) - Method in class jigcell.compare.ui.CompareFrontEnd
 
computeDispatches(Set, String, Object) - Method in class jigcell.compare.cellcycle.OAAConnector
Constructs a list of dispatch solvables that can be accessed from an object.
computePrimitiveBox(Class) - Static method in class jigcell.compare.data.MethodDispatcher
Boxes a primitive formalType or returns the formalType unchanged if it is not a primitive formalType.
computeTrace(ITransform, boolean) - Method in class jigcell.compare.views.TransformDebugger
Finds a trace from the specified transform.
computeTypeForPlot(IDataGenerator) - Method in class jigcell.compare.views.EditableSeriesView.EditableSeriesModel
Builds a time series type for the generator.
computeWildtypeProperties() - Method in class jigcell.compare.cellcycle.GenericScanTransform
Computes the wildtype properties for the growth medium of this mutant.
Config - Class in jigcell.compare.impl
Controls the configuration of the Comparator and its various components.
Config() - Constructor for class jigcell.compare.impl.Config
Creates a new configuration for a Comparator component.
config - Variable in class jigcell.compare.ui.CompareFrontEnd.FrontEndTabInfo
Configures the tab
Config.ConfigDelegate - Class in jigcell.compare.impl
Filters the temporary instance markers before persisting the configuration.
Config.ConfigDelegate() - Constructor for class jigcell.compare.impl.Config.ConfigDelegate
 
CONFIG_AGENTNAME - Static variable in class jigcell.compare.cellcycle.OAAConnector
Property key for agent name
CONFIG_BACKGROUNDEDITABLE - Static variable in class jigcell.compare.ui.BasicTable.BasicRenderer
Configuration property key for the editable cell background color
CONFIG_BACKGROUNDOVERTHRESHOLD - Static variable in class jigcell.compare.views.ObjectiveSeriesView
Property key for the threshold exceeded background
CONFIG_BACKGROUNDTYPEERROR - Static variable in class jigcell.compare.cellcycle.CellCycleExperimentView
Property key for the type error background
CONFIG_BACKGROUNDUNDERTHRESHOLD - Static variable in class jigcell.compare.compare2.TriColorViewColorer
Property key for the threshold not exceeded background
CONFIG_BACKGROUNDUNEDITABLE - Static variable in class jigcell.compare.ui.BasicTable.BasicRenderer
Configuration property key for the uneditable cell background color
CONFIG_BACKGROUNDUNKNOWNTHRESHOLD - Static variable in class jigcell.compare.views.ObjectiveSeriesView
Property key for the threshold not comparable background
CONFIG_CLASSNAME - Static variable in class jigcell.compare.impl.Compare
Property key for class names
CONFIG_DATASOURCE - Static variable in class jigcell.compare.impl.Compare
Property key for data source prototypes
CONFIG_FOREGROUNDMODIFIED - Static variable in class jigcell.compare.ui.BasicTable.BasicEditor
Configuration property key for the modified cell foreground color
CONFIG_FOREGROUNDRUNNING - Static variable in class jigcell.compare.views.TransformDebugger
Property key for the running transform foreground
CONFIG_FOREGROUNDSELECTED - Static variable in class jigcell.compare.views.TransformDebugger
Property key for the selected transform foreground
CONFIG_FOREGROUNDTRACED - Static variable in class jigcell.compare.views.TransformDebugger
Property key for the traced transform foreground
CONFIG_FOREGROUNDUNSELECTED - Static variable in class jigcell.compare.views.TransformDebugger
Property key for the unselected transform foreground
CONFIG_LOCK - Variable in class jigcell.compare.impl.Config
Lock for manipulating configuration data
CONFIG_LOOKFEEL - Static variable in class jigcell.compare.ui.CompareFrontEnd
Property key for look and feel class
CONFIG_OBJECTIVES - Static variable in class jigcell.compare.views.ObjectiveEditor
Property key for available primitives
CONFIG_PLOTTER - Static variable in class jigcell.compare.views.EditableSeriesView
Property key for the plotter class
CONFIG_RECENTSOURCE - Static variable in class jigcell.compare.ui.DataEditorPanelTab
Beginning of property key for recent source options
CONFIG_RECENTSOURCECOUNT - Static variable in class jigcell.compare.ui.DataEditorPanelTab
Property key for number of recent sources supported
CONFIG_SIMULATORS - Static variable in class jigcell.compare.cellcycle.JigCellRunManagerTransform
Property key for the list of simulators to register
CONFIG_TABCONFIG - Static variable in class jigcell.compare.ui.CompareFrontEnd
Property key for tab config names
CONFIG_TABNAME - Static variable in interface jigcell.compare.ITab
Configuration key for tab name
CONFIG_TEXTCUTOFF - Static variable in class jigcell.compare.views.SeriesView
Property key for text cutoff value
CONFIG_TRANSFORMS - Static variable in class jigcell.compare.views.TransformEditor
Property key for available transform primitives
CONFIG_TYPES - Static variable in class jigcell.compare.cellcycle.CellCycleExperimentView
Property key for generator types
CONFIG_VIEWCOLORERS - Static variable in class jigcell.compare.compare2.Compare2
Property key for available view colorers
CONFIG_WINDOWCOORDINATES - Static variable in class jigcell.compare.ui.CompareFrontEnd
Property key for window coordinates
CONFIG_WINDOWMAXIMIZED - Static variable in class jigcell.compare.ui.CompareFrontEnd
Property key for window maximized state
ConfigEditor - Class in jigcell.compare.ui
A simple options editor in the style of the Java Beans property editor.
ConfigEditor(Compare, ITab, List, Config) - Constructor for class jigcell.compare.ui.ConfigEditor
Creates a new editor for the configuration.
configMarkers - Variable in class jigcell.compare.impl.Compare
Standard configuration markers for this component
configMarkers - Variable in class jigcell.compare.ui.PanelTab
Configuration markers
configs - Variable in class jigcell.compare.impl.Config
Map of marker-configurator pairs
configSource - Variable in class jigcell.compare.impl.Compare
Data source for the configuration file
configure() - Method in class jigcell.compare.cellcycle.CellCycleReportGenerator
Does whatever configuration this data source requires and returns whether the configuration was completed successfully.
configure() - Method in interface jigcell.compare.IDataSource
Does whatever configuration this data source requires and returns whether the configuration was completed successfully.
configure() - Method in class jigcell.compare.impl.DataSource
Does whatever configuration this data source requires and returns whether the configuration was completed successfully.
configure() - Method in class jigcell.compare.impl.FileDataSource
Does whatever configuration this data source requires and returns whether the configuration was completed successfully.
configure() - Method in class jigcell.compare.impl.PDFPrinterDataSource
Does whatever configuration this data source requires and returns whether the configuration was completed successfully.
configure() - Method in class jigcell.compare.impl.SystemPrinterDataSource
Does whatever configuration this data source requires and returns whether the configuration was completed successfully.
configure(ITab) - Method in class jigcell.compare.ui.CompareFrontEnd
Starts configuring a Comparator tab.
configurePlotRange(Plot) - Method in class jigcell.compare.plotter.PTPlotBridge
Configures the range of a plotter according to the currently selected plot range.
connect(String) - Static method in class jigcell.compare.cellcycle.OAAConnector
Creates an OAA connection suitable for sending commands through an OAAConnector.
Console - Class in jigcell.compare.views
A simple debugging interface giving scripted access to the internals of the Comparator.
Console(Compare, String) - Constructor for class jigcell.compare.views.Console
 
ConstantDataSource - Class in jigcell.compare.tests
A data source that returns a constant value.
ConstantDataSource(Object) - Constructor for class jigcell.compare.tests.ConstantDataSource
Creates a new data source with constant value.
ConstantDataSource() - Constructor for class jigcell.compare.tests.ConstantDataSource
Creates a new data source with constant value.
ConstantInterface - Class in jigcell.compare.transformui
Interface for an ConstantTransform.
ConstantInterface(IProgrammableDataGenerator) - Constructor for class jigcell.compare.transformui.ConstantInterface
Creates a new interface for an ConstantTransform.
ConstantTransform - Class in jigcell.compare.transform
Transform for testing and use as a stub.
ConstantTransform() - Constructor for class jigcell.compare.transform.ConstantTransform
Creates a new transform with constant value.
ConstantTransform(IDataElement) - Constructor for class jigcell.compare.transform.ConstantTransform
Creates a new transform with constant value.
constraints - Variable in class jigcell.compare.transformui.TransformInterface
Constraints for layout
constraints - Variable in class jigcell.compare.ui.InterfaceBuilder
Layout constraints
constructNew() - Method in class jigcell.compare.data.EditableDataElement
Constructs a new element of the same type as this element.
constructNew() - Method in class jigcell.compare.data.PackedDoubleDataElement
Constructs a new element of the same type as this element.
constructNew() - Method in class jigcell.compare.data.PackedTreeDataElement
Constructs a new element of the same type as this element.
constructNew() - Method in class jigcell.compare.data.PackedTreeDataElement2
Constructs a new element of the same type as this element.
constructNew() - Method in class jigcell.compare.data.SparseTreeDataElement
Constructs a new element of the same type as this element.
constructNew() - Method in class jigcell.compare.data.SparseTreeDataElement2
Constructs a new element of the same type as this element.
container - Variable in class jigcell.compare.transform.Transform
Transform container
context - Variable in class jigcell.compare.cellcycle.CellCycleObjectiveView
Context for performing transform evaluations
context - Variable in class jigcell.compare.cellcycle.CellCycleTransformView
Context for performing transform evaluations
context - Variable in class jigcell.compare.transform.Transform
Context for performing evaluations
convertArrayClass(Object, Class, Method) - Static method in class jigcell.compare.data.MethodDispatcher
Converts an array from one formalType to another.
convertColumnIndexToData(int) - Method in class jigcell.compare.compare2.Compare2
Converts the column to the corresponding data column.
convertColumnIndexToData(JTable, int) - Method in class jigcell.compare.compare2.ViewColorer
Converts the column to the corresponding data column.
CONVERTER_LONGDOUBLE - Static variable in class jigcell.compare.data.MethodDispatcher
Converter from Long to Double
convertFromElement(IDataElement) - Static method in class jigcell.compare.data.MethodDispatcher
Converts a DataElement to a collection of objects.
convertLongDouble(Long) - Static method in class jigcell.compare.data.MethodDispatcher
Converts a Long to a Double.
convertToBoolean(String) - Static method in class jigcell.compare.impl.Config
Converts a configuration value to a boolean.
convertToBoolean(String, boolean) - Static method in class jigcell.compare.impl.Config
Converts a configuration value to a boolean.
convertToClassMarker(Object) - Static method in class jigcell.compare.impl.Config
Converts a class or instance to a class canonical marker.
convertToColor(String) - Static method in class jigcell.compare.impl.Config
Converts a configuration value to a color.
convertToColor(String, Color) - Static method in class jigcell.compare.impl.Config
Converts a configuration value to a color.
convertToElement(Object) - Static method in class jigcell.compare.data.MethodDispatcher
Converts a collection of objects to a DataElement.
convertToInstanceMarker(Object) - Static method in class jigcell.compare.impl.Config
Converts an instance to an instance canonical marker.
convertToInteger(String) - Static method in class jigcell.compare.impl.Config
Converts a configuration value to an integer.
convertToInteger(String, long) - Static method in class jigcell.compare.impl.Config
Converts a configuration value to an integer.
convertToList(String) - Static method in class jigcell.compare.impl.Config
Converts a configuration value to a list.
convertToRectangle(String) - Static method in class jigcell.compare.impl.Config
Converts a configuration value to a rectangle.
copiedFrom - Variable in class jigcell.compare.data.DataGenerator
Generator this was copied from
copy(boolean, IDataGenerator) - Method in class jigcell.compare.contrib.DispatchedTransformHelper
Copies state for this generator.
copy(boolean, IDataGenerator) - Method in class jigcell.compare.contrib.ObjectiveTemplate
Copies state for this generator.
copy(boolean) - Method in class jigcell.compare.data.DataGenerator
An equivalent copy of this generator.
copy(boolean, IDataGenerator) - Method in class jigcell.compare.data.DataGenerator
Copies state for this generator.
copy(boolean, IDataGenerator) - Method in class jigcell.compare.data.ProgrammableDataGenerator
Copies state for this generator.
copy(boolean) - Method in interface jigcell.compare.IDataGenerator
An equivalent copy of this generator.
copy(boolean, IDataGenerator) - Method in class jigcell.compare.objective.MetricObjective
Copies state for this generator.
copy(boolean, IDataGenerator) - Method in class jigcell.compare.objective.MinkowskiObjective
Copies state for this generator.
copy(boolean, IDataGenerator) - Method in class jigcell.compare.transform.ConstantTransform
Copies state for this generator.
copy(boolean, IDataGenerator) - Method in class jigcell.compare.transform.Transform
Copies state for this generator.
copy(boolean, IDataGenerator) - Method in class jigcell.compare.transform.TransformContainer
Copies state for this generator.
copyGenerator(IDataGenerator) - Static method in class jigcell.compare.views.SeriesView
Copies a generator.
copyName - Variable in class jigcell.compare.data.DataGenerator
Whether to link the name of this generator with the one it was copied from
COPYONLY - Static variable in class jigcell.compare.IDataSource.Option
Indicates that an option should be copied but not persisted with the data source
copyPrototypes(Set) - Method in class jigcell.compare.impl.DataManager
Copies sources from one of the master lists.
copyValue(long, long) - Method in class jigcell.compare.data.EditableDataElement
Copies a value within the element.
copyValue(long, long) - Method in interface jigcell.compare.IEditableDataElement
Copies a value within the element.
COUNT_FRAMEBUFFER - Static variable in class jigcell.compare.ui.CompareFrontEnd
Number of screen buffers to request
createAboutDialog() - Method in interface jigcell.compare.ITab
Creates an about dialog for this tab or null if this tab does not describe itself.
createAboutDialog() - Method in class jigcell.compare.ui.CompareFrontEnd
Creates an about dialog for this tab or null if this tab does not describe itself.
createAboutDialog() - Method in class jigcell.compare.ui.PanelTab
Creates an about dialog for this tab or null if this tab does not describe itself.
createAboutDialog() - Method in class jigcell.compare.ui.SeriesDialog
Creates an about dialog for this tab or null if this tab does not describe itself.
createAboutDialogForTab(Class, InterfaceBuilder) - Static method in class jigcell.compare.ui.PanelTab
A standard builder for about dialogs from an external resource.
createArrayClass(Class, int) - Static method in class jigcell.compare.data.MethodDispatcher
Creates a multidimensional array formalType.
createBenchmarkReport(String, String, String, List) - Method in class jigcell.compare.tests.Benchmark
Creates a data generator that represents a benchmark result.
createButtonPanel(JButton[]) - Static method in class jigcell.compare.ui.InterfaceBuilder
Creates a panel holding a collection of buttons.
createButtons() - Method in class jigcell.compare.ui.EditorDialog
The buttons to be displayed in the dialog.
createButtons() - Method in class jigcell.compare.ui.SeriesDialog
The buttons to be displayed in the dialog.
createCachedElement(IDataElement) - Method in class jigcell.compare.data.CachedDataElement
Creates the backend representation of the cached element.
createCheckBoxMenuItem(String, String, KeyStroke, ActionListener) - Static method in class jigcell.compare.ui.MenuBuilder
A single checkbox menu item for a view.
createConfigDialog() - Method in interface jigcell.compare.IConfigEditor
Creates a dialog based configuration editor.
createConfigDialog() - Method in class jigcell.compare.ui.ConfigEditor
Creates a dialog based configuration editor.
createConfigEditor() - Method in class jigcell.compare.cellcycle.CellCycleExperimentView
Creates a configuration editor for this tab or null if this tab does not support graphical configuration.
createConfigEditor() - Method in class jigcell.compare.cellcycle.CellCycleObjectiveView
Creates a configuration editor for this tab or null if this tab does not support graphical configuration.
createConfigEditor() - Method in class jigcell.compare.cellcycle.CellCycleTransformView
Creates a configuration editor for this tab or null if this tab does not support graphical configuration.
createConfigEditor() - Method in class jigcell.compare.compare2.Compare2
Creates a configuration editor for this tab or null if this tab does not support graphical configuration.
createConfigEditor() - Method in interface jigcell.compare.ITab
Creates a configuration editor for this tab or null if this tab does not support graphical configuration.
createConfigEditor() - Method in class jigcell.compare.ui.CompareFrontEnd
Creates a configuration editor for this tab or null if this tab does not support graphical configuration.
createConfigEditor() - Method in class jigcell.compare.ui.PanelTab
Creates a configuration editor for this tab or null if this tab does not support graphical configuration.
createConfigEditor() - Method in class jigcell.compare.ui.SeriesDialog
Creates a configuration editor for this tab or null if this tab does not support graphical configuration.
createConfigEditor() - Method in class jigcell.compare.views.EditableSeriesView
Creates a configuration editor for this tab or null if this tab does not support graphical configuration.
createConfigEditor() - Method in class jigcell.compare.views.ObjectiveEditor
Creates a configuration editor for this tab or null if this tab does not support graphical configuration.
createConfigEditor() - Method in class jigcell.compare.views.ObjectiveSeriesView
Creates a configuration editor for this tab or null if this tab does not support graphical configuration.
createConfigEditor() - Method in class jigcell.compare.views.TransformDebugger
Creates a configuration editor for this tab or null if this tab does not support graphical configuration.
createConfigEditor() - Method in class jigcell.compare.views.TransformEditor
Creates a configuration editor for this tab or null if this tab does not support graphical configuration.
createControl() - Method in class jigcell.compare.cellcycle.CellCycleDataDialog
The contents to be displayed in the dialog.
createControl() - Method in class jigcell.compare.objectiveui.DimensionWeightEditorDialog
The contents to be displayed in the dialog.
createControl(DimensionWeightEditorDialog.DimensionWeightModel) - Method in class jigcell.compare.objectiveui.DimensionWeightEditorDialog
The contents to be displayed in the dialog.
createControl() - Method in class jigcell.compare.objectiveui.ElementWeightEditorDialog
The contents to be displayed in the dialog.
createControl(ElementWeightEditorDialog.ElementWeightModel) - Method in class jigcell.compare.objectiveui.ElementWeightEditorDialog
The contents to be displayed in the dialog.
createControl(WeightEditorDialog.WeightModel) - Method in class jigcell.compare.objectiveui.WeightEditorDialog
The contents to be displayed in the dialog.
createControl() - Method in class jigcell.compare.ui.EditorDialog
The contents to be displayed in the dialog.
createControl() - Method in class jigcell.compare.ui.SeriesDialog
The contents to be displayed in the dialog.
createControl(SeriesDialog.SeriesModel) - Method in class jigcell.compare.ui.SeriesDialog
The contents to be displayed in the dialog.
createControl() - Method in class jigcell.compare.ui.SeriesEditorDialog
The contents to be displayed in the dialog.
createControl(SeriesEditorDialog.SeriesEditorModel) - Method in class jigcell.compare.ui.SeriesEditorDialog
The contents to be displayed in the dialog.
createControl() - Method in class jigcell.compare.ui.ViewerDialog
The contents to be displayed in the dialog.
createCSVTable(TableModel) - Static method in class jigcell.compare.impl.Transferer
 
createCustomizer() - Method in class jigcell.compare.cellcycle.BuddingYeastPhenotypeInterface
Generates a new customizer for the generator.
createCustomizer() - Method in class jigcell.compare.cellcycle.BuddingYeastScanInterface
Generates a new customizer for the generator.
createCustomizer() - Method in class jigcell.compare.cellcycle.GenericPhenotypeInterface
Generates a new customizer for the generator.
createCustomizer() - Method in class jigcell.compare.cellcycle.GenericScanInterface
Generates a new customizer for the generator.
createCustomizer() - Method in class jigcell.compare.cellcycle.JigCellRunManagerInterface
Generates a new customizer for the generator.
createCustomizer() - Method in class jigcell.compare.cellcycle.WildtypeScanInterface
Generates a new customizer for the generator.
createCustomizer() - Method in class jigcell.compare.contrib.DispatchedTransformTemplate
createCustomizer() - Method in class jigcell.compare.contrib.ObjectiveHelper
 
createCustomizer(String) - Method in class jigcell.compare.contrib.ObjectiveHelper
A customization component for this generator.
createCustomizer() - Method in class jigcell.compare.contrib.ObjectiveTemplate
createCustomizer() - Method in class jigcell.compare.contrib.TransformHelper
 
createCustomizer(String) - Method in class jigcell.compare.contrib.TransformHelper
A customization component for this generator.
createCustomizer() - Method in class jigcell.compare.contrib.TransformTemplate
createCustomizer(String) - Method in class jigcell.compare.data.ProgrammableDataGenerator
A customization component for this generator.
createCustomizer(String) - Method in class jigcell.compare.data.ProgrammableDataGenerator.DummyCustomizableInterface
A customization component for a generator.
createCustomizer(String) - Method in interface jigcell.compare.ICustomizableInterface
A customization component for a generator.
createCustomizer() - Method in class jigcell.compare.objectiveui.BooleanRelationalInterface
Generates a new customizer for the generator.
createCustomizer() - Method in class jigcell.compare.objectiveui.MinkowskiInterface
Generates a new customizer for the generator.
createCustomizer(String) - Method in class jigcell.compare.objectiveui.ObjectiveInterface
A customization component for a generator.
createCustomizer() - Method in class jigcell.compare.objectiveui.ScriptEvaluationInterface
Generates a new customizer for the generator.
createCustomizer() - Method in class jigcell.compare.objectiveui.WOSSInterface
Generates a new customizer for the generator.
createCustomizer(String) - Method in class jigcell.compare.transformui.BoxInterface
A customization component for a generator.
createCustomizer() - Method in class jigcell.compare.transformui.BoxInterface
Generates a new customizer for the generator.
createCustomizer() - Method in class jigcell.compare.transformui.ConstantInterface
Generates a new customizer for the generator.
createCustomizer() - Method in class jigcell.compare.transformui.ExtremaTestInterface
Generates a new customizer for the generator.
createCustomizer() - Method in class jigcell.compare.transformui.FileInterface
Generates a new customizer for the generator.
createCustomizer() - Method in class jigcell.compare.transformui.InputInterface
Generates a new customizer for the generator.
createCustomizer() - Method in class jigcell.compare.transformui.ScriptEvaluationInterface
Generates a new customizer for the generator.
createCustomizer() - Method in class jigcell.compare.transformui.SelectColumnsInterface
Generates a new customizer for the generator.
createCustomizer() - Method in class jigcell.compare.transformui.TransformEvaluationInterface
Generates a new customizer for the generator.
createCustomizer(String) - Method in class jigcell.compare.transformui.TransformInterface
A customization component for a generator.
createCustomizer(String) - Method in class jigcell.compare.ui.CustomizableInterface
A customization component for a generator.
createCustomizer() - Method in class jigcell.compare.ui.CustomizableInterface
Generates a new customizer for the generator.
createDataManager() - Method in class jigcell.compare.impl.Compare
Builds the repository of external data sources.
createDefaultPlotter() - Static method in class jigcell.compare.plotter.PTPlotBridge
Constructs a plotter with no data and all options set to the default values.
createDialog(String) - Method in class jigcell.compare.ui.ProgressMonitor
Constructs a new progress dialog.
createDisplay() - Method in interface jigcell.compare.IComponentDescription
Creates a display for the component description.
createDisplay() - Method in class jigcell.compare.ui.HTMLComponentDescription
Creates a display for the component description.
createDisplay() - Method in class jigcell.compare.ui.TextComponentDescription
Creates a display for the component description.
createDocument(String) - Static method in class jigcell.compare.ui.InterfaceBuilder
Creates a new document from existing text.
createElement(IDataElement) - Static method in class jigcell.compare.data.EditableDataElement
Generates an element from an existing DataElement.
createElement(EditableDataElement, Reader) - Static method in class jigcell.compare.data.EditableDataElement
Generates the map for an element from a streaming input.
createElement(String) - Static method in class jigcell.compare.data.EditableDataElement
Generates an element from a text string.
createElement(Reader) - Static method in class jigcell.compare.data.EditableDataElement
Generates an element from streaming input.
createElement(EditableDataElement, StreamingStringTokenizer, long) - Static method in class jigcell.compare.data.EditableDataElement
Generates the map for an element from a text string.
createElement(Reader) - Static method in class jigcell.compare.data.PackedDoubleDataElement
Generates a PackedDoubleDataElement from streaming input.
createElement(Reader) - Static method in class jigcell.compare.data.PackedTreeDataElement
Generates a PackedTreeDataElement from streaming input.
createElement(Reader) - Static method in class jigcell.compare.data.PackedTreeDataElement2
Generates a PackedTreeDataElement2 from streaming input.
createElement(Reader) - Static method in class jigcell.compare.data.SparseTreeDataElement
Generates a SparseTreeDataElement from streaming input.
createElement(Reader) - Static method in class jigcell.compare.data.SparseTreeDataElement2
Generates a SparseTreeDataElement2 from streaming input.
createElementSafe(IDataElement) - Static method in class jigcell.compare.data.EditableDataElement
Generates an element from an existing DataElement.
createElementSafe(String) - Static method in class jigcell.compare.data.EditableDataElement
Generates an element from a text string.
createElementSafe(Reader) - Static method in class jigcell.compare.data.EditableDataElement
Generates an element from streaming input.
createElementSafe(Reader) - Static method in class jigcell.compare.data.PackedDoubleDataElement
Generates a PackedDoubleDataElement from streaming input.
createElementSafe(Reader) - Static method in class jigcell.compare.data.PackedTreeDataElement
Generates a PackedTreeDataElement from streaming input.
createElementSafe(Reader) - Static method in class jigcell.compare.data.PackedTreeDataElement2
Generates a PackedTreeDataElement2 from streaming input.
createElementSafe(Reader) - Static method in class jigcell.compare.data.SparseTreeDataElement
Generates a SparseTreeDataElement from streaming input.
createElementSafe(Reader) - Static method in class jigcell.compare.data.SparseTreeDataElement2
Generates a SparseTreeDataElement from streaming input.
createFileChooser() - Method in class jigcell.compare.cellcycle.CellCycleTransformView
A file chooser specialized for the view.
createFileChooser() - Method in class jigcell.compare.cellcycle.JigCellRunManagerInterface
A file chooser specialized for the view.
createFileChooser() - Method in class jigcell.compare.compare2.Compare2
A file chooser specialized for the view.
createFileChooser() - Method in class jigcell.compare.transformui.FileInterface
A file chooser specialized for the view.
createFileChooser() - Method in class jigcell.compare.ui.DataEditorPanelTab
A file chooser specialized for the view.
createFileChooser() - Static method in class jigcell.compare.ui.InterfaceBuilder
The standard file chooser used by views.
createFileChooser(FileFilter) - Static method in class jigcell.compare.ui.InterfaceBuilder
The standard file chooser used by views.
createFileChooser() - Method in class jigcell.compare.views.EditableSeriesView
A file chooser specialized for the view.
createFileChooser() - Method in class jigcell.compare.views.ObjectiveEditor
A file chooser specialized for the view.
createFileChooser() - Method in class jigcell.compare.views.ObjectiveSeriesView
A file chooser specialized for the view.
createFileChooser() - Method in class jigcell.compare.views.TransformEditor
A file chooser specialized for the view.
createFileChooserResults() - Method in class jigcell.compare.cellcycle.CellCycleTransformView
A file chooser specialized for the view results.
createFileChooserResults() - Method in class jigcell.compare.views.ObjectiveSeriesView
A file chooser specialized for the view results.
createFileChooserSet() - Method in class jigcell.compare.compare2.Compare2
A file chooser specialized for the view.
createFileChooserSet() - Method in class jigcell.compare.views.ObjectiveEditor
A file chooser specialized for the view.
createFileChooserSet() - Method in class jigcell.compare.views.ProgrammableDataGeneratorEditor
A file chooser specialized for the view.
createFileChooserSet() - Method in class jigcell.compare.views.TransformEditor
A file chooser specialized for the view.
createFileChooserThreshold() - Method in class jigcell.compare.compare2.Compare2
A file chooser specialized for the view.
createFileInput(String) - Method in class jigcell.compare.impl.FileDataSource
Creates an input stream for a file.
createFileInput(String) - Method in class jigcell.compare.impl.RawFileDataSource
Creates an input stream for a file.
createFileOutput(String) - Method in class jigcell.compare.impl.FileDataSource
Creates an output stream for a file.
createFileOutput(String) - Method in class jigcell.compare.impl.RawFileDataSource
Creates an output stream for a file.
createFormattedTable(TableModel, String, String, String, String, String, String, String) - Static method in class jigcell.compare.impl.Transferer
Creates a formatted version of the table model contents.
createGenerators() - Method in class jigcell.compare.cellcycle.CellCycleTransformView
A list of generators for the view.
createGenerators() - Method in class jigcell.compare.objectiveui.WeightEditorDialog
The generators to select from.
createGenerators() - Method in class jigcell.compare.views.EditableSeriesView
A list of generators for the view.
createGenerators() - Method in class jigcell.compare.views.ObjectiveSeriesView
A list of generators for the view.
createGenerators() - Method in class jigcell.compare.views.SeriesView
A list of generators for the view.
createHTMLTable(TableModel) - Static method in class jigcell.compare.impl.Transferer
 
createHTMLViewer(String, int) - Static method in class jigcell.compare.ui.InterfaceBuilder
Creates a viewer for HTML.
createHTMLViewer(URL, int) - Static method in class jigcell.compare.ui.InterfaceBuilder
Creates a viewer for HTML.
createIndex() - Method in class jigcell.compare.data.DataGeneratorList
Creates an index of generator ids and names to speed up searches.
createIndex() - Method in interface jigcell.compare.data.IDataGeneratorList
Creates an index of generator ids and names to speed up searches.
createInstanceMarker() - Static method in class jigcell.compare.impl.Config
Creates a session unique instance marker.
createInviablePhenotype(long, long) - Static method in class jigcell.compare.cellcycle.BuddingYeastPhenotype
A phenotype which describes an inviable mutant.
createInviablePhenotype(double, long, long) - Static method in class jigcell.compare.cellcycle.GenericPhenotype
A phenotype which describes an inviable mutant.
createKey(Object) - Static method in class jigcell.compare.data.IDataGeneratorCollection.Key
Converts an object to a key.
createList(Object) - Static method in class jigcell.compare.data.DataGeneratorList
Converts a collection to a list of data generators.
createMap(Object) - Static method in class jigcell.compare.data.DataGeneratorMap
Converts a map to a map of data generators.
createMap(Object) - Static method in class jigcell.compare.data.ResultSetGroupMap
Creates a map of result sets.
createMap(Object) - Static method in class jigcell.compare.data.ResultSetMap
Converts a collection to a map of results.
createMenu(String, String, Icon, ActionListener) - Static method in class jigcell.compare.ui.MenuBuilder
A single menu for a view.
createMenuItem(String, String, Icon, KeyStroke, ActionListener) - Static method in class jigcell.compare.ui.MenuBuilder
A single menu item for a view.
createMenus() - Method in class jigcell.compare.compare2.Compare2
A list of menus for the view.
createMenus() - Method in class jigcell.compare.ui.DataEditorPanelTab
A list of menus for the view.
createMenus(String, ActionListener, Map) - Method in class jigcell.compare.ui.MenuBuilder.Builder
Creates menus for a menu bar.
createMenus(String[], String[][], String[][], Icon[][], KeyStroke[][], ActionListener) - Static method in class jigcell.compare.ui.MenuBuilder
A list of menus for a view.
createMenus(String) - Method in class jigcell.compare.ui.MenuBuilder
Creates menus for a menu bar.
createMenus() - Method in class jigcell.compare.ui.PanelTab
A list of menus for the view.
createMenus() - Method in class jigcell.compare.views.TransformDebugger
A list of menus for the view.
createObjectives() - Method in class jigcell.compare.views.ObjectiveSeriesView
A list of objectives for the view.
createObjects() - Method in class jigcell.compare.views.ProgrammableDataGeneratorEditor
A list of objects for the view.
createPointFile() - Method in class jigcell.compare.plotter.JPlotBridge
Builds a point file with the plot data.
createPopup() - Method in class jigcell.compare.transformui.TransformInterface
/** Creates a context menu for the view.
createPopup() - Method in class jigcell.compare.ui.CustomizableInterface
Creates a context menu for the view.
createPopup(String, ActionListener, Map) - Method in class jigcell.compare.ui.MenuBuilder.Builder
Creates a popup menu
createPopup(String[], String[], Icon[], ActionListener) - Static method in class jigcell.compare.ui.MenuBuilder
Creates a context menu for a view.
createPopup(String) - Method in class jigcell.compare.ui.MenuBuilder
Creates a popup menu
createPopup() - Method in class jigcell.compare.views.BasicTableView
Creates a context menu for the view.
createPopup() - Method in class jigcell.compare.views.EditableSeriesView
Creates a context menu for the view.
createPrimitiveList(String) - Method in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Constructs a list of primitives for this editor.
createRadioButtonMenuItem(String, String, KeyStroke, ActionListener, ButtonGroup) - Static method in class jigcell.compare.ui.MenuBuilder
A single radio button menu item for a view.
createReadableRecentSourceMenuItems() - Method in class jigcell.compare.ui.DataEditorPanelTab
Menu items that correspond to the most recently used readable data sources.
createResultImage() - Method in class jigcell.compare.compare2.Compare2
Creates an image corresponding to the comparison results.
createScalarElement(boolean) - Static method in class jigcell.compare.data.EditableDataElement
Generates an element from a boolean.
createScalarElement(double) - Static method in class jigcell.compare.data.EditableDataElement
Generates an element from a double.
createScalarElement(long) - Static method in class jigcell.compare.data.EditableDataElement
Generates an element from a long.
createScalarElement(String) - Static method in class jigcell.compare.data.EditableDataElement
Generates an element from a string.
createScriptFile(String) - Method in class jigcell.compare.plotter.JPlotBridge
Builds a script file to control the plot.
createSharedMenus() - Method in class jigcell.compare.cellcycle.CellCycleFrontEnd
Creates the menus that will appear for all tabs.
createSharedMenus() - Method in class jigcell.compare.ui.CompareFrontEnd
Creates the menus that will appear for all tabs.
createSimpleMenu(List, ActionListener, Map, boolean) - Static method in class jigcell.compare.ui.MenuBuilder.Builder
Creates a simple menu (popup or tool bar).
createStandardMarkers(Object) - Static method in class jigcell.compare.impl.Config
Creates the standard set of markers for an instance to match against: an instance and class marker.
createToolbar(String[], String[], Icon[], ActionListener) - Static method in class jigcell.compare.ui.MenuBuilder
Creates a collection of toolbar buttons.
createTools() - Method in class jigcell.compare.ui.DataEditorPanelTab
Creates a tool list for the view.
createTools(String, ActionListener, Map) - Method in class jigcell.compare.ui.MenuBuilder.Builder
Creates buttons for a tool bar.
createTools(String) - Method in class jigcell.compare.ui.MenuBuilder
Creates buttons for a tool bar.
createTools() - Method in class jigcell.compare.ui.PanelTab
Creates a tool list for the view.
createTools() - Method in class jigcell.compare.views.TransformDebugger
Creates a tool list for the view.
createTransferable(JComponent) - Method in class jigcell.compare.views.SeriesView.SeriesViewTransferer
 
createTransforms() - Method in class jigcell.compare.cellcycle.CellCycleTransformView
A list of transforms for the view.
createTransformTree(DefaultMutableTreeNode, IDataGeneratorList) - Method in class jigcell.compare.views.TransformDebugger
Computes the tree of transformations from a given root transform.
createTypeCache() - Method in class jigcell.compare.data.MethodDispatcher
Fills in the entries of the parameter formalType cache.
createUI() - Method in class jigcell.compare.cellcycle.CellCycleExperimentView
Creates an interface for the view.
createUI(CellCycleExperimentView.ExperimentModel) - Method in class jigcell.compare.cellcycle.CellCycleExperimentView
 
createUI() - Method in class jigcell.compare.cellcycle.CellCycleObjectiveView
Creates an interface for the view.
createUI(CellCycleObjectiveView.ObjectiveModel) - Method in class jigcell.compare.cellcycle.CellCycleObjectiveView
 
createUI() - Method in class jigcell.compare.cellcycle.CellCycleTransformView
Creates an interface for the view.
createUI(CellCycleTransformView.TransformModel) - Method in class jigcell.compare.cellcycle.CellCycleTransformView
 
createUI() - Method in class jigcell.compare.compare2.Compare2
Creates an interface for the view.
createUI(Compare2Model) - Method in class jigcell.compare.compare2.Compare2
 
createUI() - Method in class jigcell.compare.compare2.ThresholdEditor
 
createUI() - Method in class jigcell.compare.ui.EditorDialog
Lays out the dialog.
createUI() - Method in class jigcell.compare.ui.PanelTab
Creates an interface for the view.
createUI() - Method in class jigcell.compare.ui.SeriesDialog
Lays out the dialog.
createUI() - Method in class jigcell.compare.ui.ViewerDialog
Lays out the dialog.
createUI() - Method in class jigcell.compare.views.BasicTableView
Creates an interface for the view.
createUI(BasicTable.BasicTableModel) - Method in class jigcell.compare.views.BasicTableView
Creates an interface for the view.
createUI() - Method in class jigcell.compare.views.Console
Creates an interface for the view.
createUI() - Method in class jigcell.compare.views.EditableSeriesView
Creates an interface for the view.
createUI(EditableSeriesView.EditableSeriesModel) - Method in class jigcell.compare.views.EditableSeriesView
 
createUI() - Method in class jigcell.compare.views.EvaluationErrorViewer
Creates an interface for the viewer.
createUI() - Method in class jigcell.compare.views.ObjectiveEditor
Creates an interface for the view.
createUI() - Method in class jigcell.compare.views.ObjectiveSeriesView
Creates an interface for the view.
createUI(ObjectiveSeriesView.ObjectiveSeriesModel) - Method in class jigcell.compare.views.ObjectiveSeriesView
 
createUI() - Method in class jigcell.compare.views.SeriesView
Creates an interface for the view.
createUI(SeriesView.SeriesModel) - Method in class jigcell.compare.views.SeriesView
 
createUI() - Method in class jigcell.compare.views.TransformDebugger
Creates an interface for the view.
createUI() - Method in class jigcell.compare.views.TransformEditor
Creates an interface for the view.
createViablePhenotype(double, double) - Static method in class jigcell.compare.cellcycle.BuddingYeastPhenotype
A phenotype which describes a viable mutant.
createViablePhenotype(double, double, long) - Static method in class jigcell.compare.cellcycle.BuddingYeastPhenotype
A phenotype which describes a viable mutant.
createViablePhenotype(double, double, double) - Static method in class jigcell.compare.cellcycle.GenericPhenotype
A phenotype which describes a viable mutant.
createViablePhenotype(double, double, double, long) - Static method in class jigcell.compare.cellcycle.GenericPhenotype
A phenotype which describes a viable mutant.
CSV_FOOTER - Static variable in class jigcell.compare.impl.Transferer
Footer for CSV data
CSV_LINEPOSTPEND - Static variable in class jigcell.compare.impl.Transferer
Line postpender for CSV data
CSV_LINEPREPEND - Static variable in class jigcell.compare.impl.Transferer
Line prepender for CSV data
CSV_LINESEPARATOR - Static variable in class jigcell.compare.impl.Transferer
Item separator for CSV data
currentExperiment - Variable in class jigcell.compare.compare2.ThresholdEditor
Experiment currently being edited
currentGenerator - Variable in class jigcell.compare.impl.DataGeneratorEvaluator
The data generator currently being evaluated
currentItems - Variable in class jigcell.compare.ui.MenuBuilder.Builder
Collection of current menu items
currentMenus - Variable in class jigcell.compare.ui.MenuBuilder.Builder
Currently building menu
currentProperty - Variable in class jigcell.compare.tests.SystemTests
Current property change to monitor for
currentRankings - Variable in class jigcell.compare.compare2.Compare2
Menu item to toggle rankings display
currentSource - Variable in class jigcell.compare.ui.DataEditorPanelTab
Data source the current content should be saved to
currentSourceThreshold - Variable in class jigcell.compare.compare2.Compare2
Data source the current content should be saved to
currentTabAccessory - Variable in class jigcell.compare.ui.CompareFrontEnd
Current tab accessory
currentTime() - Static method in class jigcell.compare.tests.Benchmark
Current run execution time in seconds.
customEvaluate() - Method in class jigcell.compare.contrib.DispatchedTransformTemplate
Evaluates the associated element.
customEvaluate(double[]) - Method in class jigcell.compare.tests.MethodDispatcherTests.DispatchedTransform
Evaluates the associated element.
customEvaluate(long[], long[]) - Method in class jigcell.compare.tests.MethodDispatcherTests.DispatchedTransform
Evaluates the associated element.
customEvaluate(double[], double[]) - Method in class jigcell.compare.tests.MethodDispatcherTests.DispatchedTransform
Evaluates the associated element.
customEvaluate(double[][]) - Method in class jigcell.compare.tests.MethodDispatcherTests.DispatchedTransform
Evaluates the associated element.
customEvaluate(String[][]) - Method in class jigcell.compare.tests.MethodDispatcherTests.DispatchedTransform
Evaluates the associated element.
customEvaluate2(IDataElement) - Method in class jigcell.compare.tests.MethodDispatcherTests.DispatchedTransform
Evaluates the associated element.
customEvaluate2(double) - Method in class jigcell.compare.tests.MethodDispatcherTests.DispatchedTransform
Evaluates the associated element.
customEvaluate2(long) - Method in class jigcell.compare.tests.MethodDispatcherTests.DispatchedTransform
Evaluates the associated element.
customEvaluate2(long[]) - Method in class jigcell.compare.tests.MethodDispatcherTests.DispatchedTransform
Evaluates the associated element.
customEvaluate2(long[][]) - Method in class jigcell.compare.tests.MethodDispatcherTests.DispatchedTransform
Evaluates the associated element.
CustomizableInterface - Class in jigcell.compare.ui
Interface for a ProgrammableDataGenerator.
CustomizableInterface(IProgrammableDataGenerator) - Constructor for class jigcell.compare.ui.CustomizableInterface
Creates a new interface for a ProgrammableDataGenerator.
customizer - Variable in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Customizer for object
customizer - Variable in class jigcell.compare.views.TransformDebugger
Panel for transform customizers
customizers - Variable in class jigcell.compare.ui.CustomizableInterface
Customizers managed by this view
cycB - Variable in class jigcell.compare.cellcycle.GenericScanTransform.GenericScanPoint
Value of the cyclin-B species

D

data - Variable in class jigcell.compare.cellcycle.CellCycleReportGenerator
Source of data from the currently selected experiment
data - Variable in class jigcell.compare.plotter.Plotter
Data aggregate
data - Variable in class jigcell.compare.tests.ConstantDataSource
Value of data source
DataEditorPanelTab - Class in jigcell.compare.ui
A default implementation of a tab providing some basic services.
DataEditorPanelTab(Compare, String) - Constructor for class jigcell.compare.ui.DataEditorPanelTab
A panel tab with services for reading and writing data.
DataEditorPanelTab.ReadHelper - Class in jigcell.compare.ui
Helper class for performing read operations on other threads.
DataEditorPanelTab.ReadHelper(IReadableDataSource) - Constructor for class jigcell.compare.ui.DataEditorPanelTab.ReadHelper
Creates a new reading helper thread.
DataElement - Class in jigcell.compare.data
A helper implementation for data element classes.
DataElement() - Constructor for class jigcell.compare.data.DataElement
Creates a new data element.
DataGenerator - Class in jigcell.compare.data
A default implementation of DataGenerator.
DataGenerator() - Constructor for class jigcell.compare.data.DataGenerator
Creates a new data generator.
DataGeneratorEvaluator - Class in jigcell.compare.impl
Evaluates a list of data generators on a background thread.
DataGeneratorEvaluator(IDataGenerator[]) - Constructor for class jigcell.compare.impl.DataGeneratorEvaluator
Creates a new evaluator for data generators.
DataGeneratorEvaluator(IDataGenerator[], DataGeneratorEvaluator.IProcessor) - Constructor for class jigcell.compare.impl.DataGeneratorEvaluator
Creates a new evaluator for data generators.
DataGeneratorEvaluator.IProcessor - Interface in jigcell.compare.impl
Performs any needed processing on the data generator before evaluation.
DataGeneratorList - Class in jigcell.compare.data
Manages a list of data generators.
DataGeneratorList() - Constructor for class jigcell.compare.data.DataGeneratorList
Creates a new list of data generators.
DataGeneratorList(int) - Constructor for class jigcell.compare.data.DataGeneratorList
Creates a new list of data generators.
DataGeneratorList(IDataGeneratorList) - Constructor for class jigcell.compare.data.DataGeneratorList
Copies an existing list of data generators.
DataGeneratorList.DataGeneratorListDelegate - Class in jigcell.compare.data
Persists the list by using a series of add statements.
DataGeneratorList.DataGeneratorListDelegate() - Constructor for class jigcell.compare.data.DataGeneratorList.DataGeneratorListDelegate
 
DataGeneratorMap - Class in jigcell.compare.data
Manages a map of data generators.
DataGeneratorMap() - Constructor for class jigcell.compare.data.DataGeneratorMap
Creates a new map between names and data generators.
DataGeneratorMap(int, float) - Constructor for class jigcell.compare.data.DataGeneratorMap
Creates a new map between names and data generators.
DataGeneratorMap.DataGeneratorMapDelegate - Class in jigcell.compare.data
Persists the mapping by using a series of put statements.
DataGeneratorMap.DataGeneratorMapDelegate() - Constructor for class jigcell.compare.data.DataGeneratorMap.DataGeneratorMapDelegate
 
DataManager - Class in jigcell.compare.impl
Maintains and distributes data sources on demand.
DataManager() - Constructor for class jigcell.compare.impl.DataManager
Creates a new repository for data sources.
DataSource - Class in jigcell.compare.impl
A helper implementation for data source classes.
DataSource() - Constructor for class jigcell.compare.impl.DataSource
Creates a new data source.
DEBUG_EXCEPTIONS - Static variable in class jigcell.compare.impl.Compare
Whether to provide debugging information for exceptions
debugDelay - Variable in class jigcell.compare.views.TransformDebugger.DebuggerThread
Delay between continuing a debug trace
debugThread - Variable in class jigcell.compare.views.TransformDebugger
Thread for executing play events
debugTransform - Variable in class jigcell.compare.views.TransformDebugger
Transform being debugged
debugUI() - Method in class jigcell.compare.cellcycle.CellCycleFrontEnd
Adds debugging information to all UI components.
debugUI(Container, Set) - Method in class jigcell.compare.cellcycle.CellCycleFrontEnd
Adds debugging information to all UI components.
debugValue - Variable in class jigcell.compare.views.TransformDebugger
Value being debugged
decoder - Variable in class jigcell.compare.impl.XMLFileEncoder
Decoder currently being read
decorateCustomizer(JComponent) - Method in class jigcell.compare.ui.CustomizableInterface
Applies standard decorations to a customizer.
DEFAULT_BACKGROUND - Static variable in class jigcell.compare.plotter.PTPlotBridge
Default background color
DEFAULT_BACKGROUNDEDITABLE - Static variable in class jigcell.compare.ui.BasicTable.BasicRenderer
Default background color for editable cells
DEFAULT_BACKGROUNDOVERTHRESHOLD - Static variable in class jigcell.compare.compare2.TriColorViewColorer
Default background color for cells over the threshold value
DEFAULT_BACKGROUNDOVERTHRESHOLD - Static variable in class jigcell.compare.views.ObjectiveSeriesView
Default background color for cells over the threshold value
DEFAULT_BACKGROUNDTYPEERROR - Static variable in class jigcell.compare.cellcycle.CellCycleExperimentView
Default background color for cells with type errors
DEFAULT_BACKGROUNDUNDERTHRESHOLD - Static variable in class jigcell.compare.compare2.TriColorViewColorer
Default background color for cells under the threshold value
DEFAULT_BACKGROUNDUNEDITABLE - Static variable in class jigcell.compare.ui.BasicTable.BasicRenderer
Default backgorund color for uneditable cells
DEFAULT_BACKGROUNDUNKNOWNTHRESHOLD - Static variable in class jigcell.compare.views.ObjectiveSeriesView
Default background color for cells that cannot be compared to the threshold value
DEFAULT_COMBOBOXPROTOTYPE - Static variable in class jigcell.compare.ui.InterfaceBuilder
Default label for a combo box
DEFAULT_CONFIG - Static variable in class jigcell.compare.impl.Compare
Parameters if none specified
DEFAULT_FILECHOOSER - Static variable in class jigcell.compare.impl.FileDataSource
Default option for file chooser
DEFAULT_FILECHOOSER - Static variable in class jigcell.compare.impl.PDFPrinterDataSource
Default option for file chooser
DEFAULT_FOREGROUNDMODIFIED - Static variable in class jigcell.compare.ui.BasicTable.BasicEditor
Default foreground color for modified cells
DEFAULT_FOREGROUNDRUNNING - Static variable in class jigcell.compare.views.TransformDebugger
Default foreground color for running transforms
DEFAULT_FOREGROUNDSELECTED - Static variable in class jigcell.compare.views.TransformDebugger
Default foreground color for selected transforms
DEFAULT_FOREGROUNDTRACED - Static variable in class jigcell.compare.views.TransformDebugger
Default foreground color for traced transforms
DEFAULT_FOREGROUNDUNSELECTED - Static variable in class jigcell.compare.views.TransformDebugger
Default foreground color for unselected transforms
DEFAULT_HEIGHT - Static variable in class jigcell.compare.ui.ViewerDialog
Default height in pixels
DEFAULT_INSETS - Static variable in class jigcell.compare.ui.InterfaceBuilder
Insets for spacing components
DEFAULT_LISTPROTOTYPE - Static variable in class jigcell.compare.ui.InterfaceBuilder
Default label for a list
DEFAULT_MARKSTYLE - Static variable in class jigcell.compare.plotter.PTPlotBridge
Default mark style
DEFAULT_PAGEHEIGHT - Static variable in class jigcell.compare.impl.PrinterDataSource
Default page height when the paper size is unknown
DEFAULT_PAGEWIDTH - Static variable in class jigcell.compare.impl.PrinterDataSource
Default page width when the paper size is unknown
DEFAULT_PENALTYLENGTH - Static variable in class jigcell.compare.data.MethodDispatcher
Default penalty value for length mismatches
DEFAULT_PENALTYLOOSEMATCH - Static variable in class jigcell.compare.data.MethodDispatcher
Default penalty value for loose matches.
DEFAULT_REWARDMATCH - Static variable in class jigcell.compare.data.MethodDispatcher
Default value for a match.
DEFAULT_REWARDSUBCLASS - Static variable in class jigcell.compare.data.MethodDispatcher
Default value for having a specialized match.
DEFAULT_SCREENDPI - Static variable in class jigcell.compare.impl.PrinterDataSource
Default resolution when the screen DPI is unknown
DEFAULT_SERIESNAME - Static variable in class jigcell.compare.data.type.TimeSeriesTypeChecker
Default prefix for series with no names
DEFAULT_SERVICEUIX - Static variable in class jigcell.compare.impl.SystemPrinterDataSource
Default popup location for the printer service control
DEFAULT_SERVICEUIY - Static variable in class jigcell.compare.impl.SystemPrinterDataSource
Default popup location for the printer service control
DEFAULT_SIZE - Static variable in class jigcell.compare.compare2.ResultViewZoom
Default size of a view zoom display area
DEFAULT_TEXTFIELDSIZE - Static variable in class jigcell.compare.ui.InterfaceBuilder
Default width for a text field
DEFAULT_TIMEPOPUP - Static variable in class jigcell.compare.ui.ProgressMonitor
Default milliseconds before popup
DEFAULT_TRANSPARENCY - Static variable in class jigcell.compare.compare2.TriColorViewColorer
Normal transparency for a cell
DEFAULT_TREESPLIT - Static variable in class jigcell.compare.views.TransformDebugger
Splitting proportion to give to the tree component
DEFAULT_WIDTH - Static variable in class jigcell.compare.ui.ViewerDialog
Default width in pixels
defaultModel - Variable in class jigcell.compare.objectiveui.WeightEditorDialog
Choice for available weight defaults
defaultTabAccessory - Variable in class jigcell.compare.ui.CompareFrontEnd
Default tab accessory
delay() - Method in class jigcell.compare.views.TransformDebugger.DebuggerThread
Sleeps for the length of the debug delay.
DELAY_PAUSE - Static variable in class jigcell.compare.views.TransformDebugger
Milliseconds to pause after receiving a transform event
delegates - Variable in class jigcell.compare.impl.XMLFormatter
Persistence delegates organized by class
delete(IProgrammableDataGenerator) - Method in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Deletes an object owned by this editor.
deleteColumn(int) - Method in class jigcell.compare.compare2.Compare2
Deletes a column from the table.
deleteColumn(int) - Method in interface jigcell.compare.ui.IColumnEditorTab
Deletes a column from the table.
deleteColumns(int[]) - Method in class jigcell.compare.compare2.Compare2
Deletes columns from the table.
deleteColumns(int[]) - Method in interface jigcell.compare.ui.IColumnEditorTab
Deletes columns from the table.
deleteRow(int) - Method in class jigcell.compare.cellcycle.CellCycleTransformView
Deletes a row from the table.
deleteRow(int) - Method in class jigcell.compare.compare2.Compare2
Deletes a row from the table.
deleteRow(int) - Method in interface jigcell.compare.ui.IRowEditorTab
Deletes a row from the table.
deleteRow(int) - Method in class jigcell.compare.ui.SeriesEditorDialog
Deletes a row from the table.
deleteRow(int) - Method in class jigcell.compare.views.EditableSeriesView
Deletes a row from the table.
deleteRow(int) - Method in class jigcell.compare.views.ObjectiveSeriesView
Deletes a row from the table.
deleteRows(int[]) - Method in class jigcell.compare.cellcycle.CellCycleTransformView
Deletes rows from the table.
deleteRows(int[]) - Method in class jigcell.compare.compare2.Compare2
Deletes rows from the table.
deleteRows(int[]) - Method in interface jigcell.compare.ui.IRowEditorTab
Deletes rows from the table.
deleteRows(int[]) - Method in class jigcell.compare.ui.SeriesEditorDialog
Deletes rows from the table.
deleteRows(int[]) - Method in class jigcell.compare.views.EditableSeriesView
Deletes rows from the table.
deleteRows(int[]) - Method in class jigcell.compare.views.ObjectiveSeriesView
Deletes rows from the table.
delimiters - Variable in class jigcell.compare.impl.StreamingStringTokenizer
Token delimiters
description - Variable in class jigcell.compare.impl.SuffixFileFilter
Description of this filter
DESCRIPTION_INPUT - Static variable in class jigcell.compare.contrib.DispatchedTransformTemplate
Description for the input of this transform
DESCRIPTION_INPUT - Static variable in class jigcell.compare.contrib.ObjectiveTemplate
Description for the input of this objective function
DESCRIPTION_INPUT - Static variable in class jigcell.compare.contrib.TransformTemplate
Description for the input of this transform
DESCRIPTION_INPUT - Static variable in class jigcell.compare.ui.CustomizableInterface
Description for the input of a generator
DESCRIPTION_OUTPUT - Static variable in class jigcell.compare.contrib.DispatchedTransformTemplate
Description for the output of this transform
DESCRIPTION_OUTPUT - Static variable in class jigcell.compare.contrib.TransformTemplate
Description for the output of this transform
DESCRIPTION_OUTPUT - Static variable in class jigcell.compare.ui.CustomizableInterface
Description for the output of a generator
DESCRIPTION_READ - Static variable in class jigcell.compare.data.DataGenerator
Read operation description
DESCRIPTION_READ - Static variable in class jigcell.compare.impl.ClipboardDataSource
Read operation description
DESCRIPTION_READ - Static variable in class jigcell.compare.impl.FileDataSource
Read operation description
DESCRIPTION_WRITE - Static variable in class jigcell.compare.cellcycle.CellCycleReportGenerator
Write operation description
DESCRIPTION_WRITE - Static variable in class jigcell.compare.impl.ClipboardDataSource
Write operation description
DESCRIPTION_WRITE - Static variable in class jigcell.compare.impl.FileDataSource
Write operation description
DESCRIPTION_WRITE - Static variable in class jigcell.compare.impl.PrinterDataSource
Write operation description
DESCRIPTOR_TRANSIENT - Static variable in class jigcell.compare.impl.XMLFormatter
Bean descriptor to mark elements transient
descriptorMap - Variable in class jigcell.compare.transform.annotation.TransformAnnotation
Storage for annotation descriptors
destroyCustomizer(String) - Method in class jigcell.compare.data.ProgrammableDataGenerator.DummyCustomizableInterface
Destroys a customization component created by this interface.
destroyCustomizer(String) - Method in interface jigcell.compare.ICustomizableInterface
Destroys a customization component created by this interface.
destroyCustomizer(String) - Method in class jigcell.compare.objectiveui.ObjectiveInterface
Destroys a customization component created by this interface.
destroyCustomizer(String) - Method in class jigcell.compare.transformui.TransformInterface
Destroys a customization component created by this interface.
destroyCustomizer(String) - Method in class jigcell.compare.ui.CustomizableInterface
Destroys a customization component created by this interface.
dialog - Variable in class jigcell.compare.ui.ProgressMonitor
Progress monitor dialog
DIMENSION_HELP - Static variable in interface jigcell.compare.ICustomizableInterface
Initial dimensions of a help window
DIMENSION_WINDOW - Static variable in class jigcell.compare.ui.CompareFrontEnd
Initial dimensions of the Comparator window
DIMENSIONWEIGHT_0 - Static variable in interface jigcell.compare.objective.IDimensionWeightObjective
Default dimension weight of 0.0
DIMENSIONWEIGHT_1 - Static variable in interface jigcell.compare.objective.IDimensionWeightObjective
Default dimension weight of 1.0
DIMENSIONWEIGHT_RECIPROCALSQUARE - Static variable in class jigcell.compare.objective.WOSSObjective
Default dimension weight of the square of the reciprocal of the element
DimensionWeightEditorDialog - Class in jigcell.compare.objectiveui
Supports editing and viewing dimension weights.
DimensionWeightEditorDialog(Compare, IDimensionWeightObjective) - Constructor for class jigcell.compare.objectiveui.DimensionWeightEditorDialog
Creates a new dialog for editing dimension weights.
DimensionWeightEditorDialog(Compare, IDimensionWeightObjective, String) - Constructor for class jigcell.compare.objectiveui.DimensionWeightEditorDialog
Creates a new dialog for editing dimension weights.
DimensionWeightEditorDialog.DimensionWeightModel - Class in jigcell.compare.objectiveui
Table model for a DimensionWeightEditorDialog.
DimensionWeightEditorDialog.DimensionWeightModel() - Constructor for class jigcell.compare.objectiveui.DimensionWeightEditorDialog.DimensionWeightModel
Creates a new table model.
DISABLE - Static variable in class jigcell.compare.views.TransformDebugger
Disable the indicated control
dispatch(LibOaa, String, String, String) - Static method in class jigcell.compare.cellcycle.OAAConnector
Dispatches a command through an OAAConnector.
dispatch(IDataElement) - Method in class jigcell.compare.data.MethodDispatcher
Performs method dispatching on the target with a DataElement.
dispatch(Object) - Method in class jigcell.compare.data.MethodDispatcher
Performs method dispatching on the target with a collection of objects.
dispatch(String, String, String) - Method in class jigcell.compare.tests.OAAConnectorTest
Dispatches a command through the OAAConnector.
DISPATCH_ARGUMENTS - Static variable in class jigcell.compare.cellcycle.OAAConnector
Argument lists for dispatch solvables
DispatchedTransformHelper - Class in jigcell.compare.contrib
Methods for reducing the amount of work to make a transform.
DispatchedTransformHelper() - Constructor for class jigcell.compare.contrib.DispatchedTransformHelper
Creates a new helper for writing dispatched transforms.
DispatchedTransformTemplate - Class in jigcell.compare.contrib
A DESCRIPTION OF YOUR CLASS.
DispatchedTransformTemplate() - Constructor for class jigcell.compare.contrib.DispatchedTransformTemplate
 
dispatcher - Variable in class jigcell.compare.contrib.DispatchedTransformHelper
Method dispatcher for this transform
dispatcher - Variable in class jigcell.compare.tests.MethodDispatcherTests.DispatchedTransform
Method dispatcher for this transform
dispatchExact(MethodDispatcher.MethodScorer, Method) - Method in class jigcell.compare.data.MethodDispatcher
Dispatches an exact match.
dispatchLoose(MethodDispatcher.MethodScorer, Method) - Method in class jigcell.compare.data.MethodDispatcher
Dispatches a loose match.
display() - Method in class jigcell.compare.compare2.ResultViewZoom
Displays the zoom view.
display - Variable in class jigcell.compare.ui.InterfaceBuilder
Display for this interface
displayComponent - Variable in class jigcell.compare.transform.ConstantTransform
Information to display for transform interface
displayFrame - Variable in class jigcell.compare.ui.CompareFrontEnd
Display frame for frontend shell
displayOutput() - Method in class jigcell.compare.views.Console
Displays a line of output on the console.
dispose() - Method in class jigcell.compare.ui.CompareFrontEnd.SplashScreen
Destroys the splash screen.
DIVIDE - Static variable in class jigcell.compare.cellcycle.BuddingYeastScanTransform.BuddingYeastScanEvent
Cellular division
DIVIDE - Static variable in class jigcell.compare.cellcycle.GenericScanTransform.GenericScanEvent
Cell division
doDispatch(String, IclTerm, IclTerm) - Method in class jigcell.compare.cellcycle.OAAConnector
Performs a function dispatch in this Comparator.
doEvaluate() - Method in class jigcell.compare.impl.DataGeneratorEvaluator
Perform a generator evaluation.
doExecute(IclTerm, IclTerm) - Method in class jigcell.compare.cellcycle.OAAConnector
Executes a command in this Comparator.
doLayout() - Method in class jigcell.compare.ui.BasicTable
 
doOAAEvent(IclTerm, IclList, IclList) - Method in class jigcell.compare.cellcycle.OAAConnector
 
doPostUpdate() - Method in class jigcell.compare.impl.DataGeneratorEvaluator
Perform a status update following generator evaluation.
doPreUpdate() - Method in class jigcell.compare.impl.DataGeneratorEvaluator
Perform a status update before generator evaluation.
doSendFile(IclTerm, IclTerm, boolean) - Method in class jigcell.compare.cellcycle.OAAConnector
Receives a file or part.
DOUBLE_NaN - Static variable in class jigcell.compare.data.EditableDataElement
NaN
DOUBLE_NINFINITY - Static variable in class jigcell.compare.data.EditableDataElement
-Infinity
DOUBLE_PINFINITY - Static variable in class jigcell.compare.data.EditableDataElement
+Infinity
duplicate(String) - Method in class jigcell.compare.views.ObjectiveEditor
Duplicates the currently selected object.
duplicate() - Method in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Duplicates the currently selected object.
duplicate(String) - Method in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Duplicates the currently selected object.
duplicate(String) - Method in class jigcell.compare.views.TransformEditor
Duplicates the currently selected object.

E

EditableDataElement - Class in jigcell.compare.data
A helper implementation for editable data element classes.
EditableDataElement() - Constructor for class jigcell.compare.data.EditableDataElement
 
EditableDataElement.EditableDataElementDelegate - Class in jigcell.compare.data
Persists the element using a flat string rather than trying to save the values table.
EditableDataElement.EditableDataElementDelegate() - Constructor for class jigcell.compare.data.EditableDataElement.EditableDataElementDelegate
 
EditableDataGenerator - Class in jigcell.compare.data
Implementation of DataGenerator that supports editing the generator fields.
EditableDataGenerator() - Constructor for class jigcell.compare.data.EditableDataGenerator
Creates a new data generator that supports editing.
EditableDataGenerator(IDataElement) - Constructor for class jigcell.compare.data.EditableDataGenerator
Creates a new data generator that supports editing.
EditableDataGenerator.EditableDataGeneratorDelegate - Class in jigcell.compare.data
Persist the generator using the setElement method with a flat string rather than trying to expand the element.
EditableDataGenerator.EditableDataGeneratorDelegate() - Constructor for class jigcell.compare.data.EditableDataGenerator.EditableDataGeneratorDelegate
 
EditableSeriesView - Class in jigcell.compare.views
An editable display for presenting a two-dimensional set of data organized by generators.
EditableSeriesView(Compare, String) - Constructor for class jigcell.compare.views.EditableSeriesView
Creates a new table view with the ability to edit data.
EditableSeriesView.EditableSeriesModel - Class in jigcell.compare.views
Table model for an EditableDataSeriesView.
EditableSeriesView.EditableSeriesModel() - Constructor for class jigcell.compare.views.EditableSeriesView.EditableSeriesModel
Creates a new table model.
editCell(int, int) - Method in class jigcell.compare.compare2.Compare2
Starts editing a cell.
editCell(int, int) - Method in interface jigcell.compare.ui.ICellEditorTab
Starts editing a cell.
editCell(int, int) - Method in class jigcell.compare.ui.SeriesDialog
Starts editing a cell.
editCell(int, int) - Method in class jigcell.compare.ui.SeriesEditorDialog
Starts editing a cell.
editCell(int, int) - Method in class jigcell.compare.views.EditableSeriesView
Starts editing a cell.
editCellAt(int, int) - Method in class jigcell.compare.cellcycle.CellCycleTransformView.TransformModel
Starts editing a cell in the table.
editCellAt(int, int) - Method in class jigcell.compare.compare2.Compare2Model
Starts editing a cell in the table.
editCellAt(int, int) - Method in class jigcell.compare.ui.SeriesEditorDialog.SeriesEditorModel
Starts editing a cell in the table.
editCellAt(int, int) - Method in class jigcell.compare.views.EditableSeriesView.EditableSeriesModel
Starts editing a cell in the table.
editCellAt(int, int) - Method in class jigcell.compare.views.ObjectiveSeriesView.ObjectiveSeriesModel
Starts editing a cell in the table.
EditorDialog - Class in jigcell.compare.ui
A simple dialog-based cell editor.
EditorDialog(Compare, String, int, int, BasicTable.BasicTableModel) - Constructor for class jigcell.compare.ui.EditorDialog
Creates a new dialog for editing.
editThresholds() - Method in class jigcell.compare.compare2.Compare2
Edits all of the threshold values at the same time.
element - Variable in class jigcell.compare.data.EditableDataGenerator
Cached version of the associated element
element - Variable in class jigcell.compare.data.FlippedDataElement
Untied element
element - Variable in class jigcell.compare.ui.SeriesDialog
DataElement being viewed
element - Variable in class jigcell.compare.ui.SeriesEditorDialog
DataElement being edited
ELEMENT_ICON - Static variable in class jigcell.compare.ui.IconLoader
Element for icon entry
ELEMENT_ICONS - Static variable in class jigcell.compare.ui.IconLoader
Root element
ELEMENT_MENU - Static variable in class jigcell.compare.ui.MenuBuilder.Builder
Element for menu
ELEMENT_MENUBAR - Static variable in class jigcell.compare.ui.MenuBuilder.Builder
Element for menu bar
ELEMENT_MENUITEM - Static variable in class jigcell.compare.ui.MenuBuilder.Builder
Element for menu item
ELEMENT_MENUS - Static variable in class jigcell.compare.ui.MenuBuilder.Builder
Element for menus
ELEMENT_POPUP - Static variable in class jigcell.compare.ui.MenuBuilder.Builder
Element for popup menu
ELEMENT_SEPARATOR - Static variable in class jigcell.compare.ui.MenuBuilder.Builder
Element for menu separator item
ELEMENT_TOOLBAR - Static variable in class jigcell.compare.ui.MenuBuilder.Builder
Element for tool bar
ElementBenchmark - Class in jigcell.compare.tests
A collection of tests for evaluating element performance.
ElementBenchmark(Compare) - Constructor for class jigcell.compare.tests.ElementBenchmark
Creates a new tester for element creation performance.
ElementNameAnnotationDescriptor - Class in jigcell.compare.transform.annotation
A data generator annotation description for element names.
ElementNameAnnotationDescriptor() - Constructor for class jigcell.compare.transform.annotation.ElementNameAnnotationDescriptor
Creates an annotation object describing an element name.
ElementSizeAnnotationDescriptor - Class in jigcell.compare.transform.annotation
A data generator annotation description for element sizes.
ElementSizeAnnotationDescriptor() - Constructor for class jigcell.compare.transform.annotation.ElementSizeAnnotationDescriptor
Creates an annotation object describing an element size.
ElementTests - Class in jigcell.compare.tests
A collection of tests to exercise the included data element types.
ElementTests(String) - Constructor for class jigcell.compare.tests.ElementTests
Creates a new element test.
ElementTypeAnnotationDescriptor - Class in jigcell.compare.transform.annotation
A data generator annotation description for element types.
ElementTypeAnnotationDescriptor() - Constructor for class jigcell.compare.transform.annotation.ElementTypeAnnotationDescriptor
Creates an annotation object describing an element type.
ELEMENTWEIGHT_0 - Static variable in interface jigcell.compare.objective.IElementWeightObjective
Default element weight of 0.0
ELEMENTWEIGHT_1 - Static variable in interface jigcell.compare.objective.IElementWeightObjective
Default element weight of 1.0
ELEMENTWEIGHT_PRECIPROCAL - Static variable in class jigcell.compare.objective.MinkowskiObjective
Default element weight of the pth power of the reciprocal of the element
ELEMENTWEIGHT_RECIPROCAL - Static variable in class jigcell.compare.objective.MinkowskiObjective
Default element weight of the reciprocal of the element
ELEMENTWEIGHT_RECIPROCALSQUARE - Static variable in class jigcell.compare.objective.MinkowskiObjective
Default element weight of the square of the reciprocal of the element
ElementWeightEditorDialog - Class in jigcell.compare.objectiveui
Supports editing and viewing element weights.
ElementWeightEditorDialog(Compare, IElementWeightObjective) - Constructor for class jigcell.compare.objectiveui.ElementWeightEditorDialog
Creates a new dialog for editing element weights.
ElementWeightEditorDialog(Compare, IElementWeightObjective, String) - Constructor for class jigcell.compare.objectiveui.ElementWeightEditorDialog
Creates a new dialog for editing element weights.
ElementWeightEditorDialog.ElementWeightModel - Class in jigcell.compare.objectiveui
Table model for an ElementWeightEditorDialog.
ElementWeightEditorDialog.ElementWeightModel() - Constructor for class jigcell.compare.objectiveui.ElementWeightEditorDialog.ElementWeightModel
Creates a new table model.
ENABLE - Static variable in class jigcell.compare.views.TransformDebugger
Enable the indicated control
encode(Object, Object, Class) - Static method in class jigcell.compare.impl.OwnedDataSource
Encodes the data object using the callback if necessary.
encoder - Variable in class jigcell.compare.impl.XMLFileEncoder
Encoder currently being written
endBlock() - Method in class jigcell.compare.ui.InterfaceBuilder
Signals that a block in the interface has been completed.
endElement(String, String, String) - Method in class jigcell.compare.ui.MenuBuilder.Builder
 
endInterface() - Method in class jigcell.compare.ui.InterfaceBuilder
Creates the described interface.
endRow() - Method in class jigcell.compare.ui.InterfaceBuilder
Signals that a row in the interface has been completed.
endRow(boolean) - Method in class jigcell.compare.ui.InterfaceBuilder
Signals that a row in the interface has been completed.
endRow(boolean, int) - Method in class jigcell.compare.ui.InterfaceBuilder
Signals that a row in the interface has been completed.
equals(Object) - Method in class jigcell.compare.data.IDataGeneratorCollection.Key
 
equals(Object) - Method in class jigcell.compare.ui.BasicTable.BasicTableModel.Marker
 
EQUIVALENT - Static variable in class jigcell.compare.views.ObjectiveSeriesView.Comparison
Accept equivalent values only
ERROR - Static variable in class jigcell.compare.data.MethodDispatcher
Maximally bad score
ERROR - Static variable in class jigcell.compare.objective.Objective
Error result
error(Object) - Method in class jigcell.compare.views.Console
 
errorRecord - Variable in class jigcell.compare.views.EvaluationErrorViewer
Next error to add to the viewer
errors - Variable in class jigcell.compare.views.EvaluationErrorViewer
Errors that this viewer has detected
errorViewer - Variable in class jigcell.compare.cellcycle.CellCycleObjectiveView
Displays errors encountered during evaluation
errorViewer - Variable in class jigcell.compare.cellcycle.CellCycleTransformView
Displays errors encountered during evaluation
esp1 - Variable in class jigcell.compare.cellcycle.BuddingYeastScanTransform.BuddingYeastScanPoint
Value of the species esp1
evaluate(IDataElement) - Method in class jigcell.compare.cellcycle.BuddingYeastScanTransform
Evaluates the transform.
evaluate() - Method in class jigcell.compare.cellcycle.CellCycleTransformView
Evaluates all of the specified functions.
evaluate(int[]) - Method in class jigcell.compare.cellcycle.CellCycleTransformView
Evaluates a subset of the specified functions.
evaluate(IDataGenerator[]) - Method in class jigcell.compare.cellcycle.CellCycleTransformView
Evaluates a collection of data generators on a separate thread.
evaluate(IDataElement) - Method in class jigcell.compare.cellcycle.GenericPhenotypeObjective
Computes the values of this generator.
evaluate(IDataElement) - Method in class jigcell.compare.cellcycle.GenericScanTransform
Evaluates the transform.
evaluate() - Method in class jigcell.compare.cellcycle.JigCellRunManagerTransform
Evaluates the associated element.
evaluate(IDataElement) - Method in class jigcell.compare.cellcycle.WildtypeScanTransform
Evaluates the transform.
evaluate(IDataElement) - Method in class jigcell.compare.contrib.DispatchedTransformHelper
Evaluates the transform.
evaluate(IDataElement) - Method in class jigcell.compare.contrib.ObjectiveHelper
Evaluates and returns the associated element.
evaluate(IDataElement, IDataElement) - Method in class jigcell.compare.contrib.ObjectiveHelper
Evaluates and returns the associated element.
evaluate(IDataElement, IDataElement) - Method in class jigcell.compare.contrib.ObjectiveTemplate
Evaluates and returns the associated element.
evaluate(IDataElement) - Method in class jigcell.compare.contrib.TransformTemplate
Evaluates the transform.
evaluate() - Method in class jigcell.compare.data.ProgrammableDataGenerator
Evaluates the associated element.
evaluate() - Method in class jigcell.compare.impl.DataGeneratorEvaluator
Evaluates the list of generators.
evaluate(IDataElement) - Method in class jigcell.compare.objective.BooleanRelationalObjective
Computes the values of this generator.
evaluate() - Method in class jigcell.compare.objective.MetricObjective
Evaluates the associated element.
evaluate(IDataElement) - Method in class jigcell.compare.objective.MinkowskiObjective
Computes the values of this generator.
evaluate() - Method in class jigcell.compare.objective.Objective
Evaluates the associated element.
evaluate(IDataElement) - Method in class jigcell.compare.objective.Objective
Computes the values of this generator.
evaluate(IDataElement) - Method in class jigcell.compare.objective.ScriptEvaluationObjective
Computes the values of this generator.
evaluate(IDataElement) - Method in class jigcell.compare.objective.WOSSObjective
Computes the values of this generator.
evaluate(IDataElement) - Method in class jigcell.compare.tests.MethodDispatcherTests.DispatchedTransform
Evaluates the associated element.
evaluate() - Method in class jigcell.compare.transform.BoxTransformContainer
Evaluates the associated element.
evaluate(IDataElement) - Method in class jigcell.compare.transform.ConstantTransform
Evaluates the transform.
evaluate(IDataElement) - Method in class jigcell.compare.transform.ExtremaTestTransform
Evaluates the transform.
evaluate() - Method in class jigcell.compare.transform.ReadFromFileTransform
Evaluates the associated element.
evaluate(IDataElement) - Method in class jigcell.compare.transform.ScriptEvaluationTransform
Evaluates the transform.
evaluate(IDataElement) - Method in class jigcell.compare.transform.SelectColumnsTransform
Evaluates the transform.
evaluate() - Method in class jigcell.compare.transform.Transform
Evaluates the associated element.
evaluate(IDataElement) - Method in class jigcell.compare.transform.Transform
Evaluates the transform.
evaluate() - Method in class jigcell.compare.transform.TransformEvaluationTransform
Evaluates the associated element.
evaluate(IDataElement) - Method in class jigcell.compare.transform.WriteToFileTransform
Evaluates the transform.
evaluate() - Method in interface jigcell.compare.ui.IResultTab
Evaluates all of the specified functions.
evaluate(int[]) - Method in interface jigcell.compare.ui.IResultTab
Evaluates a subset of the specified functions.
evaluate() - Method in class jigcell.compare.views.ObjectiveSeriesView
Evaluates all of the specified functions.
evaluate(int[]) - Method in class jigcell.compare.views.ObjectiveSeriesView
Evaluates a subset of the specified functions.
evaluate(IDataGenerator[]) - Method in class jigcell.compare.views.ObjectiveSeriesView
Evaluates a collection of data generators on a separate thread.
evaluate1(IDataElement, IDataElement, IDataElement, double, double[], double[], double[]) - Method in class jigcell.compare.objective.MinkowskiObjective
Evaluates and returns the associated element for p = 1.0.
evaluate2(IDataElement, IDataElement, IDataElement, double, double[], double[], double[]) - Method in class jigcell.compare.objective.MinkowskiObjective
Evaluates and returns the associated element for p = 2.0.
evaluateEquality(IDataElement, IDataElement) - Method in class jigcell.compare.objective.BooleanRelationalObjective
Evaluates and returns the associated element for equality.
evaluateGreaterThan(IDataElement, IDataElement) - Method in class jigcell.compare.objective.BooleanRelationalObjective
Evaluates and returns the associated element for greater than.
evaluateGreaterThanEqual(IDataElement, IDataElement) - Method in class jigcell.compare.objective.BooleanRelationalObjective
Evaluates and returns the associated element for greater than or equal.
evaluateInequality(IDataElement, IDataElement) - Method in class jigcell.compare.objective.BooleanRelationalObjective
Evaluates and returns the associated element for inequality.
evaluateInviable(IDataElement, IDataElement) - Method in class jigcell.compare.cellcycle.BuddingYeastPhenotypeObjective
Computes the objective for an experiment that is inviable.
evaluateInviable(IDataElement, IDataElement) - Method in class jigcell.compare.cellcycle.GenericPhenotypeObjective
Computes the objective for an experiment that is inviable.
evaluateLessThan(IDataElement, IDataElement) - Method in class jigcell.compare.objective.BooleanRelationalObjective
Evaluates and returns the associated element for greater than or equal.
evaluateLessThanEqual(IDataElement, IDataElement) - Method in class jigcell.compare.objective.BooleanRelationalObjective
Evaluates and returns the associated element for greater than or equal.
evaluateLinear(IDataElement, IDataElement, IDataElement, double, IDataElement, double) - Method in class jigcell.compare.objective.WOSSObjective
Computes weighted orthogonal sum of squares with linear interpolation.
evaluateLinear(IDataElement, long, double[], IDataElement, IDataElement[], long, double[], double[], IDataElement, double, long, double[]) - Method in class jigcell.compare.objective.WOSSObjective
Helper function for computing weighted orthogonal sum of squares with linear interpolation.
evaluateLinear(IDataElement, long, double[], IDataElement, IDataElement, double[], double[], IDataElement, double, long, double[]) - Method in class jigcell.compare.objective.WOSSObjective
Helper function for computing weighted orthogonal sum of squares with linear interpolation.
evaluateLinear(IDataElement, long, double[], IDataElement, IDataElement, double[], double[], IDataElement, long, double[]) - Method in class jigcell.compare.objective.WOSSObjective
Helper function for computing weighted orthogonal sum of squares with linear interpolation.
evaluateMax(IDataElement, IDataElement, IDataElement, double, double[], double[], double[]) - Method in class jigcell.compare.objective.MinkowskiObjective
Evaluates and returns the associated element for p = infinity.
evaluateNone(IDataElement, IDataElement, IDataElement, double, IDataElement, double) - Method in class jigcell.compare.objective.WOSSObjective
Computes weighted orthogonal sum of squares without interpolation.
evaluateNone(IDataElement, long, double[], IDataElement, IDataElement[], long, double[], IDataElement, double, long, double[]) - Method in class jigcell.compare.objective.WOSSObjective
Helper function for computing weighted orthogonal sum of squares without interpolation.
evaluateNone(IDataElement, long, double[], IDataElement, double[], IDataElement, double, long, double[]) - Method in class jigcell.compare.objective.WOSSObjective
Helper function for computing weighted orthogonal sum of squares without interpolation.
evaluateNone(IDataElement, long, double[], IDataElement, double[], IDataElement, long, double[]) - Method in class jigcell.compare.objective.WOSSObjective
Helper function for computing weighted orthogonal sum of squares without interpolation.
evaluatep(IDataElement, IDataElement, IDataElement, double, double[], double[], double[]) - Method in class jigcell.compare.objective.MinkowskiObjective
Evaluates and returns the associated element for finite p.
evaluateViable(IDataElement, IDataElement) - Method in class jigcell.compare.cellcycle.BuddingYeastPhenotypeObjective
Computes the objective for an experiment that is viable.
evaluateViable(IDataElement, IDataElement) - Method in class jigcell.compare.cellcycle.GenericPhenotypeObjective
Computes the objective for an experiment that is viable.
EvaluationCallStack - Class in jigcell.compare.impl
The call stack for an IProgrammableDataGenerator evaluation.
EvaluationCallStack() - Constructor for class jigcell.compare.impl.EvaluationCallStack
Creates a new call stack.
EvaluationCallStack(IDataGenerator) - Constructor for class jigcell.compare.impl.EvaluationCallStack
Creates a new call stack.
evaluationError(IProgrammableDataGenerator, Throwable) - Method in interface jigcell.compare.IEvaluationListener
Notification that an error occurred during evaluation.
evaluationError(IProgrammableDataGenerator, Throwable) - Method in class jigcell.compare.transform.TransformContext
 
evaluationError(IProgrammableDataGenerator, Throwable) - Method in class jigcell.compare.views.EvaluationErrorViewer
Notification that an error occurred during evaluation.
evaluationError(IProgrammableDataGenerator, Throwable) - Method in class jigcell.compare.views.TransformDebugger.DebuggerThread
Notification that an error occurred during evaluation.
EvaluationErrorViewer - Class in jigcell.compare.views
Displays errors encountered during data generator evaluation.
EvaluationErrorViewer(Compare, ITab) - Constructor for class jigcell.compare.views.EvaluationErrorViewer
Creates a new viewer for evaluation errors.
EvaluationErrorViewer.ErrorModel - Class in jigcell.compare.views
Model for an evaluation error viewer dialog.
EvaluationErrorViewer.ErrorModel() - Constructor for class jigcell.compare.views.EvaluationErrorViewer.ErrorModel
Creates a new table model.
EvaluationErrorViewer.ErrorRecord - Class in jigcell.compare.views
Error record.
EvaluationErrorViewer.ErrorRecord(String, Throwable) - Constructor for class jigcell.compare.views.EvaluationErrorViewer.ErrorRecord
Creates a new error record.
EvaluationErrorViewer.MoreButtonEditor - Class in jigcell.compare.views
Editor for the more information button.
EvaluationErrorViewer.MoreButtonEditor() - Constructor for class jigcell.compare.views.EvaluationErrorViewer.MoreButtonEditor
Creates a new button editor.
evaluationStart(IProgrammableDataGenerator) - Method in interface jigcell.compare.IEvaluationListener
Notification for the start of an evaluation.
evaluationStart(IProgrammableDataGenerator) - Method in class jigcell.compare.transform.TransformContext
 
evaluationStart(IProgrammableDataGenerator) - Method in class jigcell.compare.views.EvaluationErrorViewer
Notification for the start of an evaluation.
evaluationStart(IProgrammableDataGenerator) - Method in class jigcell.compare.views.TransformDebugger.DebuggerThread
Notification for the start of an evaluation.
evaluationStop(IProgrammableDataGenerator, IDataElement) - Method in interface jigcell.compare.IEvaluationListener
Notification for the end of an evaluation.
evaluationStop(IProgrammableDataGenerator, IDataElement) - Method in class jigcell.compare.transform.TransformContext
 
evaluationStop(IProgrammableDataGenerator, IDataElement) - Method in class jigcell.compare.views.EvaluationErrorViewer
Notification for the end of an evaluation.
evaluationStop(IProgrammableDataGenerator, IDataElement) - Method in class jigcell.compare.views.TransformDebugger.DebuggerThread
Notification for the end of an evaluation.
exception - Variable in class jigcell.compare.data.CachedDataElement
Cached exception recorder for this transferer
exception - Variable in class jigcell.compare.impl.ExceptionRecorder
The most recent exception we've caught
exception - Variable in class jigcell.compare.ui.DataEditorPanelTab
Exception handler
exception - Variable in class jigcell.compare.views.SeriesView.SeriesViewTransferer
Cached exception recorder for this transferer
ExceptionRecorder - Class in jigcell.compare.impl
Provides listening and reporting options for asynchronous exception handling.
ExceptionRecorder(Compare, String, boolean) - Constructor for class jigcell.compare.impl.ExceptionRecorder
Creates a new asynchronous exception handler that reports using the shell handler.
ExceptionRecorder(String, boolean, boolean, boolean) - Constructor for class jigcell.compare.impl.ExceptionRecorder
Creates a new asynchronous exception handler.
exceptionThrown(Exception) - Method in class jigcell.compare.impl.ExceptionRecorder
 
execute(LibOaa, String) - Static method in class jigcell.compare.cellcycle.OAAConnector
Executes a command through an OAAConnector.
execute() - Method in class jigcell.compare.impl.DataGeneratorEvaluator
Starts evaluating the given generators.
execute(String) - Method in class jigcell.compare.tests.OAAConnectorTest
Executes a command through the OAAConnector.
executeCommands() - Method in class jigcell.compare.views.Console
Performs command evaluations off of the event thread.
executeRun(int) - Method in class jigcell.compare.tests.RunManagerPlugin
Executes a run from the current run set.
executeScriptFile(String) - Method in class jigcell.compare.cellcycle.CellCycleFrontEnd
Loads an external script file and executes it in the Comparator.
executor - Variable in class jigcell.compare.impl.DataGeneratorEvaluator
Thread for evaluation
exit(int) - Method in class jigcell.compare.impl.Compare
Exits from the Comparator.
exit(int) - Method in class jigcell.compare.ui.CompareFrontEnd
Exits from the Comparator.
experimentBaseNames - Variable in class jigcell.compare.compare2.Compare2
List[IDataGeneratorCollection.Key] of the keys of experiments used in the objective set
ExperimentBenchmark - Class in jigcell.compare.tests
A collection of tests for evaluating experiment loading performance.
ExperimentBenchmark(Compare) - Constructor for class jigcell.compare.tests.ExperimentBenchmark
Creates a new tester for experiment loading performance.
experimentBoxModel - Variable in class jigcell.compare.compare2.ThresholdEditor
Model for the list of experiments
experimentComparisons - Variable in class jigcell.compare.compare2.Compare2
Map[IDataGeneratorCollection.Key,String] of the keys of experiments to the comparison type
experimentComparisons - Variable in class jigcell.compare.compare2.Compare2Model
Map[IDataGeneratorCollection.Key,String] of the keys of experiments to the comparison type
experimentModel - Variable in class jigcell.compare.cellcycle.CellCycleReportGenerator
Selection model for prototype experiment
experimentNames - Variable in class jigcell.compare.compare2.Compare2
List[IDataGeneratorCollection.Key] of the keys of results used in comparisons
experimentNames - Variable in class jigcell.compare.compare2.Compare2Model
List[IDataGeneratorCollection.Key] of the keys of results used in comparisons
experimentThresholds - Variable in class jigcell.compare.compare2.Compare2
Map[IDataGeneratorCollection.Key,String] of the keys of experiments to the threshold
experimentThresholds - Variable in class jigcell.compare.compare2.Compare2Model
Map[IDataGeneratorCollection.Key,String] of the keys of experiments to the threshold
experimentThresholds - Variable in class jigcell.compare.compare2.ThresholdEditor
Map[IDataGeneratorCollection.Key,String] of the keys of experiments to the threshold
experimentView - Variable in class jigcell.compare.tests.ExperimentBenchmark
View to load in
experimentView - Variable in class jigcell.compare.tests.ObjectiveBenchmark
View to load experimental data in
experimentView - Variable in class jigcell.compare.tests.TransformBenchmark
View to load experimental data in
extensions - Static variable in class jigcell.compare.impl.Transferer
System data extensions map
ExtremaTestInterface - Class in jigcell.compare.transformui
Interface for an ExtremaTestTransform.
ExtremaTestInterface(IProgrammableDataGenerator) - Constructor for class jigcell.compare.transformui.ExtremaTestInterface
Creates a new interface for an ExtremaTestTransform.
ExtremaTestTransform - Class in jigcell.compare.transform
A transform that tests whether a sequence would be passed by a band-pass filter.
ExtremaTestTransform() - Constructor for class jigcell.compare.transform.ExtremaTestTransform
Creates a new transform for range testing.

F

FALSE - Static variable in class jigcell.compare.objective.BooleanRelationalObjective
False result
FALSE - Static variable in class jigcell.compare.transform.ExtremaTestTransform
False value
FIELD_ACCELERATOR - Static variable in class jigcell.compare.ui.MenuBuilder.Builder.Item
Field fragment for key accelerators
FIELD_ICON - Static variable in class jigcell.compare.ui.MenuBuilder.Builder.Item
Field fragment for icons
FIELD_MODIFIER - Static variable in class jigcell.compare.ui.MenuBuilder.Builder.Item
Field fragment for key modifiers
file - Variable in class jigcell.compare.data.CachedDataElement
File where the data element can be found
FileDataSource - Class in jigcell.compare.impl
A generic transfer agent for a source of data that supports reading and writing to a file.
FileDataSource() - Constructor for class jigcell.compare.impl.FileDataSource
Creates a new data source that represents a file.
FileDataSource(String) - Constructor for class jigcell.compare.impl.FileDataSource
Creates a new data source that represents a file.
FileDataSource.IFileEncoder - Interface in jigcell.compare.impl
An encoder for a FileDataSource.
FileInterface - Class in jigcell.compare.transformui
Interface for a FileTransform.
FileInterface(IProgrammableDataGenerator) - Constructor for class jigcell.compare.transformui.FileInterface
Creates a new interface for a FileTransform.
fileName - Variable in class jigcell.compare.tests.ModelBuilderBenchmark
File name to load from
fileName - Variable in class jigcell.compare.tests.RunManagerBenchmark
File name to load from
filenameDocument - Variable in class jigcell.compare.transformui.FileInterface
Name selection document
FileTransform - Class in jigcell.compare.transform
A transform that tracks a file.
FileTransform() - Constructor for class jigcell.compare.transform.FileTransform
Creates a new transform that tracks a file.
fillDown(int, int) - Method in class jigcell.compare.compare2.Compare2
Fills a column down with a value.
fillDown(int, int) - Method in interface jigcell.compare.ui.ICellEditorTab
Fills a column down with a value.
fillDown(int, int) - Method in class jigcell.compare.ui.SeriesDialog
Fills a column down with a value.
fillDown(int, int) - Method in class jigcell.compare.ui.SeriesEditorDialog
Fills a column down with a value.
fillDown(int, int) - Method in class jigcell.compare.views.EditableSeriesView
Fills a column down with a value.
fillPrint(String, int) - Static method in class jigcell.compare.tests.ElementBenchmark
Prints a right aligned string.
fillRange(int, int, int, Object) - Method in class jigcell.compare.ui.BasicTable.BasicTableModel
Fills along a column with a particular value.
fillRangeAt(int, int, int, int) - Method in class jigcell.compare.cellcycle.CellCycleTransformView.TransformModel
Fills along a column.
fillRangeAt(int, int, int, int) - Method in class jigcell.compare.ui.BasicTable.BasicTableModel
Fills along a column.
fillRangeAt(int, int, int, int) - Method in class jigcell.compare.views.ObjectiveSeriesView.ObjectiveSeriesModel
Fills along a column.
fillSelected(int, int, int[]) - Method in class jigcell.compare.compare2.Compare2
Fills a column at selected spots with a value.
fillSelected(int, int, int[]) - Method in class jigcell.compare.ui.BasicTable.BasicTableModel
 
fillSelected(int, int, int[]) - Method in interface jigcell.compare.ui.ICellEditorTab
Fills a column at selected spots with a value.
fillSelected(int, int, int[]) - Method in class jigcell.compare.ui.SeriesDialog
Fills a column at selected spots with a value.
fillSelected(int, int, int[]) - Method in class jigcell.compare.ui.SeriesEditorDialog
Fills a column at selected spots with a value.
fillSelected(int, int, int[]) - Method in class jigcell.compare.views.EditableSeriesView
Fills a column at selected spots with a value.
fillUp(int, int) - Method in class jigcell.compare.compare2.Compare2
Fills a column up with a value.
fillUp(int, int) - Method in interface jigcell.compare.ui.ICellEditorTab
Fills a column up with a value.
fillUp(int, int) - Method in class jigcell.compare.ui.SeriesDialog
Fills a column up with a value.
fillUp(int, int) - Method in class jigcell.compare.ui.SeriesEditorDialog
Fills a column up with a value.
fillUp(int, int) - Method in class jigcell.compare.views.EditableSeriesView
Fills a column up with a value.
FILTER_EXPERIMENT - Static variable in class jigcell.compare.views.EditableSeriesView
File filter for experimental data files
FILTER_GENERATOR - Static variable in class jigcell.compare.transformui.FileInterface
File filter for data generator files
FILTER_OBJECTIVECATALOG - Static variable in class jigcell.compare.views.ObjectiveEditor
File filter for objective catalog files
FILTER_OBJECTIVERESULT - Static variable in class jigcell.compare.views.ObjectiveSeriesView
File filter for objective result set files
FILTER_OBJECTIVESET - Static variable in class jigcell.compare.views.ObjectiveSeriesView
File filter for objective files
FILTER_PDF - Static variable in class jigcell.compare.impl.PDFPrinterDataSource
File filter for PDF data files
FILTER_RESULTSETGROUP - Static variable in class jigcell.compare.compare2.Compare2
File filter for result set group files
FILTER_RUN - Static variable in class jigcell.compare.cellcycle.JigCellRunManagerInterface
File filter for run files
FILTER_TRANSFORM - Static variable in class jigcell.compare.cellcycle.CellCycleTransformView
File filter for transform files
FILTER_TRANSFORMCATALOG - Static variable in class jigcell.compare.views.TransformEditor
File filter for transform catalog files
FILTER_TRANSFORMRESULT - Static variable in class jigcell.compare.cellcycle.CellCycleTransformView
File filter for transform result set files
FILTER_TRANSFORMSET - Static variable in class jigcell.compare.views.TransformEditor
File filter for transform files
FindAccessory - Class in jigcell.compare.ui
 
FindAccessory() - Constructor for class jigcell.compare.ui.FindAccessory
Creates a new accessory for searching.
findButton(JButton[], String) - Static method in class jigcell.compare.ui.MenuBuilder
Returns a JButton with the given action command or returns null to indicate that no such button exists.
findByName(String, int, boolean) - Method in class jigcell.compare.compare2.Compare2
Searches for a name starting from an initial row in a specified direction.
findByName() - Method in interface jigcell.compare.ui.INameFinderTab
Starts a search operation using the user interface.
findByName(boolean) - Method in interface jigcell.compare.ui.INameFinderTab
Resumes a search for a name.
findByName(boolean, boolean) - Method in interface jigcell.compare.ui.INameFinderTab
Performs a search operation using the user interface.
findByName(String, boolean) - Method in interface jigcell.compare.ui.INameFinderTab
Searches for a name.
findByName() - Method in class jigcell.compare.views.BasicTableView
 
findByName(boolean) - Method in class jigcell.compare.views.BasicTableView
 
findByName(boolean, boolean) - Method in class jigcell.compare.views.BasicTableView
 
findByName(String, boolean) - Method in class jigcell.compare.views.BasicTableView
 
findByName(String, int, boolean) - Method in class jigcell.compare.views.BasicTableView
Searches for a name starting from an initial row in a specified direction.
findByName(String, int, boolean) - Method in class jigcell.compare.views.SeriesView
Searches for a name starting from an initial row in a specified direction.
findColumn(BasicTable.BasicTableModel.Marker) - Method in class jigcell.compare.ui.BasicTable.BasicTableModel
The index of a column.
findColumn(BasicTable.BasicTableModel.Marker) - Method in class jigcell.compare.ui.BasicTable
The index of a column in this table.
findCommonSuperclass(Object[]) - Static method in class jigcell.compare.data.MethodDispatcher
The common superclass for a collection of objects.
findInstance(String) - Static method in class jigcell.compare.views.ObjectiveSeriesView.Comparison
Finds an instance of this class based on a given name.
findInstanceForDispatch(String) - Method in class jigcell.compare.cellcycle.OAAConnector
Finds the object that should be dispatched against from the tab name or null if no object can be found.
findLastTransform(IDataGenerator, boolean) - Method in class jigcell.compare.cellcycle.CellCycleReportGenerator
Picks a transform to use as input to the report plotter.
findLookAndFeelClass(String) - Static method in class jigcell.compare.ui.CompareFrontEnd
Finds the class for a given look and feel name.
findMenuItem(MenuElement, String, boolean) - Static method in class jigcell.compare.ui.MenuBuilder
Returns an item with the given action command or returns null to indicate that no such menu item exists.
findMenuItem(MenuElement[], String, boolean) - Static method in class jigcell.compare.ui.MenuBuilder
Returns an item with the given action command or returns null to indicate that no such menu item exists.
findMethodForDispatch(Object, String) - Method in class jigcell.compare.cellcycle.OAAConnector
Finds the method that should be dispatched against from the dispatch instance and method name or null if no method can be found.
findNameForTransform(ITransform) - Method in interface jigcell.compare.transform.ITransformContext
The name this transform was registered with.
findNameForTransform(ITransform) - Method in class jigcell.compare.transform.TransformContext
The name this transform was registered with.
findParentMenu(MenuElement, String, boolean) - Static method in class jigcell.compare.ui.MenuBuilder
Returns a menu containing an item with the given action command or returns null to indicate that no such menu exists.
findParentMenu(MenuElement[], String, boolean) - Static method in class jigcell.compare.ui.MenuBuilder
Returns an item with the given action command or returns null to indicate that no such menu item exists.
findParentMenuElement(MenuElement, String, boolean) - Static method in class jigcell.compare.ui.MenuBuilder
Returns a menu containing an item with the given action command or returns null to indicate that no such menu exists.
findTabByClass(Class) - Method in class jigcell.compare.impl.Compare
A tab registered with the Comparator of the specified type or null if no such tab exists.
findTabByClassExact(Class) - Method in class jigcell.compare.impl.Compare
A tab registered with the Comparator of the specified type or null if no such tab exists.
findTabByName(String) - Method in class jigcell.compare.impl.Compare
A tab registered with the Comparator of the specified name or null if no such tab exists.
findTransformForName(String) - Method in interface jigcell.compare.transform.ITransformContext
Finds a transform based on an evaluation name.
findTransformForName(String) - Method in class jigcell.compare.transform.TransformContext
Finds a transform based on an evaluation name.
findValue(List, String) - Method in class jigcell.compare.impl.Config
A value in this configurator or a subconfigurator.
findValue(List, String, String) - Method in class jigcell.compare.impl.Config
A value in this configurator or a subconfigurator.
findValue(List, String, boolean, boolean, boolean) - Method in class jigcell.compare.impl.Config
A value in this configurator or one of its subconfigurators.
findValue(List, String, boolean, boolean, boolean, String) - Method in class jigcell.compare.impl.Config
A value in this configurator or a subconfigurator.
finish() - Method in class jigcell.compare.compare2.Compare2.SetReadHelper
Sends data read from some external source off for processing.
finish() - Method in class jigcell.compare.compare2.Compare2.ThresholdReadHelper
Sends data read from some external source off for processing.
finish() - Method in class jigcell.compare.impl.FileDataSource
Indicates that all of the objects have been acted upon and the next operation should start from the beginning.
finish() - Method in interface jigcell.compare.impl.FileDataSource.IFileEncoder
 
finish() - Method in class jigcell.compare.impl.XMLFileEncoder
finish() - Method in interface jigcell.compare.IMultipleDataSource
Indicates that all of the objects have been acted upon and the next operation should start from the beginning.
finish() - Method in class jigcell.compare.ui.DataEditorPanelTab.ReadHelper
Sends data read from some external source off for processing.
finish() - Method in class jigcell.compare.views.ProgrammableDataGeneratorEditor.SetReadHelper
Sends data read from some external source off for processing.
FIREDSTAGE - Static variable in class jigcell.compare.cellcycle.BuddingYeastScanTransform.BuddingYeastScanEvent
Entry to fired
fireEvaluationError(String) - Method in class jigcell.compare.data.ProgrammableDataGenerator
Notifies listeners of an evaluation error event.
fireEvaluationError(Throwable) - Method in class jigcell.compare.data.ProgrammableDataGenerator
Notifies listeners of an evaluation error event.
fireEvaluationStart() - Method in class jigcell.compare.data.ProgrammableDataGenerator
Notifies listeners of an evaluation start event.
fireEvaluationStop(IDataElement) - Method in class jigcell.compare.data.ProgrammableDataGenerator
Notifies listeners of an evaluation stop event.
firePropertyChange(String) - Method in class jigcell.compare.impl.Compare
Fires a property change message about a named resource.
firePropertyChange(String, Object, Object) - Method in class jigcell.compare.impl.Compare
Fires a property change message about a named resource.
fireTableDataChanged() - Method in class jigcell.compare.ui.SeriesEditorDialog.SeriesEditorModel
 
fireTableRowsUpdated(int, int) - Method in class jigcell.compare.ui.SeriesEditorDialog.SeriesEditorModel
 
fireTransformAdded(ITransform, String) - Method in class jigcell.compare.transform.TransformContext
Notifies listeners of a transform added event.
fireTransformRemoved(ITransform, String) - Method in class jigcell.compare.transform.TransformContext
Notifies listeners of a transform removed event.
fitComponentInDialog(JDialog, JComponent, int, int) - Static method in class jigcell.compare.ui.InterfaceBuilder
Checks that a component fits in the desired space or wraps it in a scroll pane.
flags - Variable in class jigcell.compare.impl.ExceptionRecorder
How to handle the received exception
FLAVOR_GENERICOBJECT - Static variable in class jigcell.compare.impl.ComparatorDataFlavor
The flavor for a generic object
FLAVOR_LOCALOBJECT - Static variable in class jigcell.compare.impl.ComparatorDataFlavor
The flavor corresponding to a local JVM object
FLAVOR_PDF - Static variable in class jigcell.compare.impl.ComparatorDataFlavor
The flavor corresponding to a PDF document
FLAVOR_POSTSCRIPT - Static variable in class jigcell.compare.impl.ComparatorDataFlavor
The flavor corresponding to a Postscript document
FLAVOR_REMOTEOBJECT - Static variable in class jigcell.compare.impl.ComparatorDataFlavor
The flavor corresponding to a remote JVM object
FLAVOR_SERIALIZEDOBJECT - Static variable in class jigcell.compare.impl.ComparatorDataFlavor
The flavor corresponding to a serialized Java object
FLAVOR_TEXTHTML - Static variable in class jigcell.compare.impl.ComparatorDataFlavor
The flavor corresponding to HTML text
FLAVOR_TEXTPLAIN - Static variable in class jigcell.compare.impl.ComparatorDataFlavor
The flavor corresponding to plain text
FLAVOR_TEXTXML - Static variable in class jigcell.compare.impl.ComparatorDataFlavor
The flavor corresponding to XML text
FLAVOR_XMLSERIALIZEDOBJECT - Static variable in class jigcell.compare.impl.ComparatorDataFlavor
The flavor corresponding to an XML serialized Java object
flavors - Static variable in class jigcell.compare.impl.Transferer
System data flavors map
flip(IDataElement) - Static method in class jigcell.compare.data.FlippedDataElement
Produces a DataElement that acts as the transpose of another DataElement.
flip(IDataElement, boolean) - Static method in class jigcell.compare.data.FlippedDataElement
Produces a DataElement that acts as the transpose of another DataElement.
FlippedDataElement - Class in jigcell.compare.data
An implementation of DataElement that acts as the transpose of another DataElement.
FlippedDataElement(IDataElement) - Constructor for class jigcell.compare.data.FlippedDataElement
Creates a new flipped data element from an existing data element.
FlippedDataElement(IDataElement, boolean) - Constructor for class jigcell.compare.data.FlippedDataElement
Creates a new flipped data element from an existing data element.
FlippedDataElement(IDataElement, boolean, long) - Constructor for class jigcell.compare.data.FlippedDataElement
Creates a new flipped data element from an existing data element.
flush() - Method in class jigcell.compare.transform.BoxTransformContainer
Destroys all work leading into this generator.
flush() - Method in interface jigcell.compare.transform.ITransform
Destroys all work leading into this generator.
flush() - Method in class jigcell.compare.transform.SelectColumnsTransform
Destroys all work leading into this generator.
flush() - Method in class jigcell.compare.transform.Transform
Destroys all work leading into this generator.
flushIndex() - Method in class jigcell.compare.data.DataGeneratorList
Erases the index of generator ids and names.
flushIndex() - Method in interface jigcell.compare.data.IDataGeneratorList
Erases the index of generator ids and names.
flushSelected() - Method in class jigcell.compare.views.TransformDebugger
Flushes the currently selected transform.
flushTransform(ITransform) - Static method in class jigcell.compare.cellcycle.CellCycleTransformView
Flushes a transform.
forceBooleanValue() - Method in class jigcell.compare.data.DataElement
This element represented as a boolean when evaluated in a scalar context.
forceBooleanValue(long) - Method in class jigcell.compare.data.DataElement
The element at position pos represented as a boolean.
forceBooleanValue() - Method in interface jigcell.compare.IDataElement
This element represented as a boolean when evaluated in a scalar context.
forceBooleanValue(long) - Method in interface jigcell.compare.IDataElement
The element at position pos represented as a boolean.
forceIntegralValue() - Method in class jigcell.compare.data.DataElement
This element represented as an integer when evaluated in a scalar context.
forceIntegralValue(long) - Method in class jigcell.compare.data.DataElement
The element at position pos represented as an integer.
forceIntegralValue() - Method in interface jigcell.compare.IDataElement
This element represented as an integer when evaluated in a scalar context.
forceIntegralValue(long) - Method in interface jigcell.compare.IDataElement
The element at position pos represented as an integer.
forceListValue(long) - Method in class jigcell.compare.data.DataElement
This element at position pos represented as a list.
forceListValue(long) - Method in interface jigcell.compare.IDataElement
This element at position pos represented as a list.
forceLiteralValue() - Method in class jigcell.compare.data.DataElement
This element represented as a string literal when evaluated in a scalar context.
forceLiteralValue(long) - Method in class jigcell.compare.data.DataElement
The element at position pos represented as a string literal.
forceLiteralValue() - Method in interface jigcell.compare.IDataElement
This element represented as a string literal when evaluated in a scalar context.
forceLiteralValue(long) - Method in interface jigcell.compare.IDataElement
The element at position pos represented as a string literal.
forceRealValue() - Method in class jigcell.compare.data.DataElement
This element represented as a real when evaluated in a scalar context.
forceRealValue(long) - Method in class jigcell.compare.data.DataElement
The element at position pos represented as a real.
forceRealValue() - Method in interface jigcell.compare.IDataElement
This element represented as a real when evaluated in a scalar context.
forceRealValue(long) - Method in interface jigcell.compare.IDataElement
The element at position pos represented as a real.
forceSlice(boolean[], long, int, long) - Method in class jigcell.compare.data.DataElement
A dense, homogeneous subset of this element represented as a boolean list.
forceSlice(IDataElement[], long, int, long) - Method in class jigcell.compare.data.DataElement
A dense, homogeneous subset of this element represented as a list of elements.
forceSlice(double[], long, int, long) - Method in class jigcell.compare.data.DataElement
A dense, homogeneous subset of this element represented as a real list.
forceSlice(long[], long, int, long) - Method in class jigcell.compare.data.DataElement
A dense, homogeneous subset of this element represented as an integral list.
forceSlice(String[], long, int, long) - Method in class jigcell.compare.data.DataElement
A dense, homogeneous subset of this element represented as a string literal list.
forceSlice(boolean[], long, int, long) - Method in class jigcell.compare.data.EditableDataElement
A dense, homogeneous subset of this element represented as a boolean list. If slice cannot hold the requested range, a new array is created and returned. Slice may be null. If the given length has no valid meaning, the value is null. Elements not of type boolean are suitably coerced. Past the defined range of the list, all values are considered false. Position 0 in the returned slice corresponds to position start in the original element.
forceSlice(IDataElement[], long, int, long) - Method in class jigcell.compare.data.EditableDataElement
A dense, homogeneous subset of this element represented as a list of elements. If slice cannot hold the requested range, a new array is created and returned. Slice may be null. If the given length has no valid meaning, the value is null. Elements not of type list are suitably coerced. Past the defined range of the list, all values are considered scalars of no type. Position 0 in the returned slice corresponds to position start in the original element.
forceSlice(double[], long, int, long) - Method in class jigcell.compare.data.EditableDataElement
A dense, homogeneous subset of this element represented as a real list. If slice cannot hold the requested range, a new array is created and returned. Slice may be null. If the given length has no valid meaning, the value is null. Elements not of type real are suitably coerced. Past the defined range of the list, all values are considered NaN. Position 0 in the returned slice corresponds to position start in the original element.
forceSlice(long[], long, int, long) - Method in class jigcell.compare.data.EditableDataElement
A dense, homogeneous subset of this element represented as an integral list. If slice cannot hold the requested range, a new array is created and returned. Slice may be null. If the given length has no valid meaning, the value is null. Elements not of type integral are suitably coerced. Past the defined range of the list, all values are considered 0. Position 0 in the returned slice corresponds to position start in the original element.
forceSlice(boolean[], long, int, long) - Method in interface jigcell.compare.IDataElement
A dense, homogeneous subset of this element represented as a boolean list.
forceSlice(IDataElement[], long, int, long) - Method in interface jigcell.compare.IDataElement
A dense, homogeneous subset of this element represented as a list of elements.
forceSlice(double[], long, int, long) - Method in interface jigcell.compare.IDataElement
A dense, homogeneous subset of this element represented as a real list.
forceSlice(long[], long, int, long) - Method in interface jigcell.compare.IDataElement
A dense, homogeneous subset of this element represented as an integral list.
forceSlice(String[], long, int, long) - Method in interface jigcell.compare.IDataElement
A dense, homogeneous subset of this element represented as a string literal list.
formalPos - Variable in class jigcell.compare.data.MethodDispatcher.MethodScorer
Current parsing position in the formal argument formalTypes
formalTypes - Variable in class jigcell.compare.data.MethodDispatcher.MethodScorer
Argument formalTypes currently being worked on for the target
FORMAT_PNG - Static variable in class jigcell.compare.impl.SystemPrinterDataSource
Format descriptor for png data
formatString(String, Object) - Static method in class jigcell.compare.impl.Compare
Looks up a string in the table of resources and applies a message format to it.
formatString(String, Object[]) - Static method in class jigcell.compare.impl.Compare
Looks up a string in the table of resources and applies a message format to it.
formatter - Static variable in class jigcell.compare.impl.Compare
Formatter for controlling how XML persistence behaves
foundIndicator - Variable in class jigcell.compare.ui.FindAccessory
Indicator for an unsuccessful find
frameList - Variable in class jigcell.compare.impl.EvaluationCallStack
Stack frames
FUNCTION_DISPATCH - Static variable in class jigcell.compare.cellcycle.OAAConnector
Start of function names for performing dispatches
FUNCTION_EXECUTE - Static variable in class jigcell.compare.cellcycle.OAAConnector
Function name for executing a command
FUNCTION_SENDFILE - Static variable in class jigcell.compare.cellcycle.OAAConnector
Function name for sending a file
FUNCTION_SENDFILEPART - Static variable in class jigcell.compare.cellcycle.OAAConnector
Function name for sending part of a file

G

G1LENGTH - Static variable in class jigcell.compare.cellcycle.BuddingYeastScanTransform.BuddingYeastScanEvent
Wildtype G1 length reached
G1LENGTH - Static variable in class jigcell.compare.cellcycle.GenericScanTransform.GenericScanEvent
Wildtype G1 length reached
G1STAGE - Static variable in class jigcell.compare.cellcycle.GenericScanTransform.GenericScanEvent
Entry to G1
generateData(int) - Static method in class jigcell.compare.tests.ExperimentBenchmark
Generates some experimental data.
generateData(int) - Static method in class jigcell.compare.tests.ObjectiveBenchmark
Generates some objective functions.
generateData(int) - Static method in class jigcell.compare.tests.TransformBenchmark
Generates some transforms.
generateGenerator(IEditableDataGenerator, int) - Static method in class jigcell.compare.tests.ExperimentBenchmark
Generates a new experimental setup.
generateGUID() - Method in class jigcell.compare.data.DataGenerator
Generates a guid based on this instance.
generateObjective(IObjective, int) - Static method in class jigcell.compare.tests.ObjectiveBenchmark
Generates a new objective function.
generatePlotImage(IDataElement, ITransform) - Static method in class jigcell.compare.cellcycle.CellCycleReportGenerator
Produces a plot image of the time series data in the transform.
generateReport() - Method in class jigcell.compare.cellcycle.CellCycleObjectiveView
Produces a report containing the results of the comparison.
generateTransform(int) - Static method in class jigcell.compare.tests.TransformBenchmark
Generates a new transform.
generator - Variable in class jigcell.compare.cellcycle.BuddingYeastPhenotypeInterface
Generator
generator - Variable in class jigcell.compare.cellcycle.BuddingYeastScanInterface
Generator
generator - Variable in class jigcell.compare.cellcycle.GenericPhenotypeInterface
Generator
generator - Variable in class jigcell.compare.cellcycle.GenericScanInterface
Generator
generator - Variable in class jigcell.compare.cellcycle.JigCellRunManagerInterface
Generator
generator - Variable in class jigcell.compare.cellcycle.WildtypeScanInterface
Generator
generator - Variable in class jigcell.compare.data.ProgrammableDataGenerator.DummyCustomizableInterface
Data generator being wrapped
generator - Variable in class jigcell.compare.objectiveui.BooleanRelationalInterface
Generator
generator - Variable in class jigcell.compare.objectiveui.DimensionWeightEditorDialog
Currently selected generator
generator - Variable in class jigcell.compare.objectiveui.ElementWeightEditorDialog
Currently selected generator
generator - Variable in class jigcell.compare.objectiveui.MinkowskiInterface
Generator
generator - Variable in class jigcell.compare.objectiveui.ObjectiveInterface
Generator
generator - Variable in class jigcell.compare.objectiveui.ScriptEvaluationInterface
Generator
generator - Variable in class jigcell.compare.objectiveui.WOSSInterface
Generator
generator - Variable in class jigcell.compare.transformui.BoxInterface
Generator
generator - Variable in class jigcell.compare.transformui.ConstantInterface
Generator
generator - Variable in class jigcell.compare.transformui.ExtremaTestInterface
Generator
generator - Variable in class jigcell.compare.transformui.FileInterface
Generator
generator - Variable in class jigcell.compare.transformui.InputInterface
Generator
generator - Variable in class jigcell.compare.transformui.ScriptEvaluationInterface
Generator
generator - Variable in class jigcell.compare.transformui.SelectColumnsInterface
Generator
generator - Variable in class jigcell.compare.transformui.TransformContainerInterface
Generator
generator - Variable in class jigcell.compare.transformui.TransformEvaluationInterface
Generator
generator - Variable in class jigcell.compare.transformui.TransformInterface
Generator
generator - Variable in class jigcell.compare.ui.CustomizableInterface
Generator
generator - Variable in class jigcell.compare.ui.SeriesDialog
Generator for the element being viewed
generator - Variable in class jigcell.compare.ui.SeriesEditorDialog
Generator for the element being edited
generators - Variable in class jigcell.compare.impl.DataGeneratorEvaluator
The list of generators
generators - Variable in class jigcell.compare.views.SeriesView
List of displayed generators
generators - Variable in class jigcell.compare.views.SeriesView.SeriesModel
List of displayed generators
generators - Variable in class jigcell.compare.views.SeriesView.SeriesViewTransferer
List of displayed generators
GenericPhenotype - Class in jigcell.compare.cellcycle
Type for the generic cell cycle phenotype.
GenericPhenotype() - Constructor for class jigcell.compare.cellcycle.GenericPhenotype
Creates a new type checker.
GenericPhenotypeInterface - Class in jigcell.compare.cellcycle
Interface for a GenericPhenotypeObjective.
GenericPhenotypeInterface(IProgrammableDataGenerator) - Constructor for class jigcell.compare.cellcycle.GenericPhenotypeInterface
Creates a new interface for a GenericPhenotypeObjective.
GenericPhenotypeObjective - Class in jigcell.compare.cellcycle
Measures the difference between two generic phenotypes.
GenericPhenotypeObjective() - Constructor for class jigcell.compare.cellcycle.GenericPhenotypeObjective
Creates a new objective function that can evaluate a phenotype.
GenericScanInterface - Class in jigcell.compare.cellcycle
Interface for a GenericScanTransform.
GenericScanInterface(IProgrammableDataGenerator) - Constructor for class jigcell.compare.cellcycle.GenericScanInterface
Creates a new interface for a GenericScanTransform.
GenericScanTransform - Class in jigcell.compare.cellcycle
Computes the phenotype of a generic mutant from a time course of concentrations.
GenericScanTransform() - Constructor for class jigcell.compare.cellcycle.GenericScanTransform
Creates a new transform that can perform a run evaluation.
GenericScanTransform.CellCycleReport - Class in jigcell.compare.cellcycle
The statistics collected from a cycle.
GenericScanTransform.CellCycleReport(long, double, double) - Constructor for class jigcell.compare.cellcycle.GenericScanTransform.CellCycleReport
Records the statistics for a scan number.
GenericScanTransform.GenericScanEvent - Class in jigcell.compare.cellcycle
An event that occurs during the scan.
GenericScanTransform.GenericScanEvent(double, int) - Constructor for class jigcell.compare.cellcycle.GenericScanTransform.GenericScanEvent
Creates a new event.
GenericScanTransform.GenericScanPoint - Class in jigcell.compare.cellcycle
A single time course point used by the scan.
GenericScanTransform.GenericScanPoint(IDataElement, double) - Constructor for class jigcell.compare.cellcycle.GenericScanTransform.GenericScanPoint
Extracts the point values from a time course observation.
get(int) - Method in class jigcell.compare.data.DataGeneratorList
A generator in the list.
get(IDataGeneratorCollection.Key) - Method in class jigcell.compare.data.DataGeneratorList
A generator in the list.
get(String) - Method in class jigcell.compare.data.DataGeneratorList
A generator in the list by name.
get(IDataGeneratorCollection.Key) - Method in class jigcell.compare.data.DataGeneratorMap
The generator associated with a particular key or null if there is no such mapping.
get(int) - Method in interface jigcell.compare.data.IDataGeneratorList
A generator in the list.
get(IDataGeneratorCollection.Key) - Method in interface jigcell.compare.data.IDataGeneratorList
A generator in the list.
get(String) - Method in interface jigcell.compare.data.IDataGeneratorList
A generator in the list by name.
get(IDataGeneratorCollection.Key) - Method in interface jigcell.compare.data.IDataGeneratorMap
The generator associated with a particular key or null if there is no such mapping.
get(IResultSetMap) - Method in interface jigcell.compare.data.IResultSetGroupMap
The name associated with a particular result set or null if there is no such mapping.
get(IDataGeneratorCollection.Key) - Method in interface jigcell.compare.data.IResultSetMap
The result associated with a particular key or null if there is no such mapping.
get(IResultSetMap) - Method in class jigcell.compare.data.ResultSetGroupMap
The name associated with a particular result set or null if there is no such mapping.
get(IDataGeneratorCollection.Key) - Method in class jigcell.compare.data.ResultSetMap
The result associated with a particular key or null if there is no such mapping.
get(IDataGeneratorCollection.Key) - Method in class jigcell.compare.objective.ChainedDataGeneratorList
A generator in the list. The id is the primary search key. This operation will be significantly accelerated if an index exists.
get(String) - Method in class jigcell.compare.objective.ChainedDataGeneratorList
A generator in the list by name. This operation will be significantly accelerated if an index exists.
getAbout() - Method in class jigcell.compare.ui.CompareFrontEnd.FrontEndTabInfo
About the tab.
getAccelerator() - Method in class jigcell.compare.ui.MenuBuilder.Builder.Item
The item accelerator.
getAccessory() - Method in class jigcell.compare.ui.CompareFrontEnd.FrontEndTabInfo
The tab accessory.
getAllowContextInsertion() - Method in class jigcell.compare.transform.Transform
Whether this transform allows insertions through the context menu.
getAllowContextRemoval() - Method in class jigcell.compare.transform.Transform
Whether this transform allows removals through the context menu.
getAllowDescriptionQuery() - Method in class jigcell.compare.data.ProgrammableDataGenerator
Whether this generator allows the input description to be queried.
getAllowResultNameEditing() - Method in class jigcell.compare.transform.InputTransform
Whether result name editing is allowed.
getAllowThresholdEdit() - Method in class jigcell.compare.compare2.Compare2Model
Whether thresholds can be edited.
getAllowWildcardMatches() - Method in class jigcell.compare.data.MethodDispatcher
Whether wildcard matches are allowed.
getAnnotation() - Method in class jigcell.compare.cellcycle.GenericScanTransform
An annotation object for this generator.
getAnnotation() - Method in class jigcell.compare.cellcycle.JigCellRunManagerTransform
An annotation object for this generator.
getAnnotation() - Method in class jigcell.compare.cellcycle.WildtypeScanTransform
An annotation object for this generator.
getAnnotation() - Method in class jigcell.compare.contrib.DispatchedTransformTemplate
An annotation object for this generator.
getAnnotation() - Method in class jigcell.compare.contrib.TransformTemplate
An annotation object for this generator.
getAnnotation() - Method in class jigcell.compare.transform.BoxTransformContainer
An annotation object for this generator.
getAnnotation() - Method in class jigcell.compare.transform.ExtremaTestTransform
An annotation object for this generator.
getAnnotation() - Method in interface jigcell.compare.transform.ITransform
An annotation object for this generator.
getAnnotation() - Method in class jigcell.compare.transform.ReadFromFileTransform
An annotation object for this generator.
getAnnotation() - Method in class jigcell.compare.transform.ScriptEvaluationTransform
An annotation object for this generator.
getAnnotation() - Method in class jigcell.compare.transform.SelectColumnsTransform
An annotation object for this generator.
getAnnotation() - Method in class jigcell.compare.transform.Transform
An annotation object for this generator.
getAnnotation() - Method in class jigcell.compare.transform.TransformEvaluationTransform
An annotation object for this generator.
getAnnotationDescriptor(String) - Method in interface jigcell.compare.transform.annotation.ITransformAnnotation
Description for a particular annotation type.
getAnnotationDescriptor(String) - Method in class jigcell.compare.transform.annotation.TransformAnnotation
Description for a particular annotation type.
getAnnotationDescriptors() - Method in interface jigcell.compare.transform.annotation.ITransformAnnotation
All known annotation types.
getAnnotationDescriptors() - Method in class jigcell.compare.transform.annotation.TransformAnnotation
All known annotation types.
getAnnotationRecord(long) - Method in interface jigcell.compare.transform.annotation.ITransformAnnotation
The annotation record at a particular position.
getAnnotationRecord(long) - Method in class jigcell.compare.transform.annotation.TransformAnnotation
The annotation record at a particular position.
getAnnotationValue(String) - Method in interface jigcell.compare.transform.annotation.ITransformAnnotation
The specified annotation value.
getAnnotationValue(String, long) - Method in interface jigcell.compare.transform.annotation.ITransformAnnotation
The specified annotation value at a particular position.
getAnnotationValue(String) - Method in class jigcell.compare.transform.annotation.TransformAnnotation
The specified annotation value.
getAnnotationValue(String, long) - Method in class jigcell.compare.transform.annotation.TransformAnnotation
The specified annotation value at a particular position.
getAnnotationValues() - Method in interface jigcell.compare.transform.annotation.ITransformAnnotation
All annotation values.
getAnnotationValues(long) - Method in interface jigcell.compare.transform.annotation.ITransformAnnotation
All annotation values at a particular position.
getAnnotationValues() - Method in class jigcell.compare.transform.annotation.TransformAnnotation
All annotation values.
getAnnotationValues(long) - Method in class jigcell.compare.transform.annotation.TransformAnnotation
All annotation values at a particular position.
getAttribute(String) - Method in class jigcell.compare.data.DataGenerator
A keyed attribute that must be persisted with this generator.
getAttribute(String) - Method in interface jigcell.compare.IDataGenerator
A keyed attribute that must be persisted with this generator.
getBooleanValue(long) - Method in class jigcell.compare.data.CachedDataElement
The element at position pos represented as a boolean. If the given position has no valid meaning for this element, the value is false.
getBooleanValue() - Method in class jigcell.compare.data.DataElement
This element represented as a boolean when evaluated in a scalar context.
getBooleanValue(long) - Method in class jigcell.compare.data.DataElement
The element at position pos represented as a boolean.
getBooleanValue(long) - Method in class jigcell.compare.data.EditableDataElement
The element at position pos represented as a boolean. If the given position has no valid meaning for this element, the value is false.
getBooleanValue() - Method in class jigcell.compare.data.FlippedDataElement
This element represented as a boolean when evaluated in a scalar context.
getBooleanValue(long) - Method in class jigcell.compare.data.FlippedDataElement
The element at position pos represented as a boolean.
getBooleanValue() - Method in interface jigcell.compare.IDataElement
This element represented as a boolean when evaluated in a scalar context.
getBooleanValue(long) - Method in interface jigcell.compare.IDataElement
The element at position pos represented as a boolean.
getBoxedTransform() - Method in class jigcell.compare.transform.BoxTransformContainer
The transform this box holds.
getCachedElement() - Method in class jigcell.compare.data.CachedDataElement
Retrieves the cached element for use.
getCallStack() - Method in class jigcell.compare.data.ProgrammableDataGenerator
The call stack for the current evaluation.
getCallStack() - Method in interface jigcell.compare.IProgrammableDataGenerator
The call stack for the current evaluation.
getCellEditorValue() - Method in class jigcell.compare.ui.BasicTable.ButtonEditor
 
getChecked(long) - Method in class jigcell.compare.data.EditableDataElement
Gets the value at a position.
getChildSource(ITransform) - Method in interface jigcell.compare.transform.ITransformContainer
The source for one of the transforms managed by this container.
getChildSource(ITransform) - Method in class jigcell.compare.transform.TransformContainer
The source for one of the transforms managed by this container.
getClipboardContentsOption() - Method in class jigcell.compare.impl.ClipboardDataSource
The clipboard contents option.
getClipboardOption() - Method in class jigcell.compare.impl.ClipboardDataSource
The clipboard option.
getColor(String) - Method in class jigcell.compare.ui.BasicTable.BasicEditor
A color for use with this table.
getColor(String) - Method in class jigcell.compare.ui.BasicTable.BasicRenderer
A color for use with this renderer.
getColor(String) - Method in class jigcell.compare.views.TransformDebugger.TransformTreeRenderer
A color for use with this renderer.
getColorerMode() - Method in class jigcell.compare.compare2.Compare2
The colorer display mode.
getColorForCell(JTable, int, int, int, double) - Method in class jigcell.compare.compare2.ImmediateHistoryRelativeViewColorer
The color of a cell as it will appear in the table.
getColorForCell(JTable, Object, boolean, boolean, int, int) - Method in interface jigcell.compare.compare2.IViewColorer
The color of a cell as it will appear in the table.
getColorForCell(JTable, int, int, int, double) - Method in class jigcell.compare.compare2.ThresholdAbsoluteViewColorer
The color of a cell as it will appear in the table.
getColorForCell(JTable, int, int, int, double) - Method in class jigcell.compare.compare2.ThresholdRelativeViewColorer
The color of a cell as it will appear in the table.
getColorForCell(JTable, int, int, int) - Method in class jigcell.compare.compare2.TriColorViewColorer
The color of a cell as it will appear in the table.
getColorForCell(JTable, int, int, int, double) - Method in class jigcell.compare.compare2.TriColorViewColorer
The color of a cell as it will appear in the table.
getColorForCell(JTable, Object, boolean, boolean, int, int) - Method in class jigcell.compare.compare2.ViewColorer
The color of a cell as it will appear in the table.
getColorForCell(JTable, int, int, int) - Method in class jigcell.compare.compare2.ViewColorer
The color of a cell as it will appear in the table.
getColorForHistoryComparison(ObjectiveSeriesView.Comparison, double, double) - Method in class jigcell.compare.compare2.TriColorViewColorer
The base color to use for a tricolor display.
getColorForThresholdComparison(ObjectiveSeriesView.Comparison, double, double) - Method in class jigcell.compare.compare2.TriColorViewColorer
The base color to use for a tricolor display.
getColorFromConfig(String, Color) - Method in class jigcell.compare.ui.BasicTable.BasicEditor
Color specified by the configuration of the host view.
getColorFromConfig(String, Color) - Method in class jigcell.compare.ui.BasicTable.BasicRenderer
Color specified by the configuration of the host view.
getColumn() - Method in class jigcell.compare.ui.BasicTable.ButtonEditor
Column being edited.
getColumnClass(int) - Method in class jigcell.compare.ui.BasicTable.BasicTableModel
The type of objects in a column.
getColumnCount() - Method in class jigcell.compare.compare2.Compare2Model
The number of columns in the table.
getColumnCount() - Method in class jigcell.compare.ui.BasicTable.BasicTableModel
The number of columns in the table.
getColumnCount() - Method in interface jigcell.compare.ui.IColumnEditorTab
The number of columns in the table.
getColumnCount() - Method in class jigcell.compare.views.BasicTableView
 
getColumnData(int) - Method in interface jigcell.compare.ui.IColumnEditorTab
The data for a column in the table or null if the column is not valid.
getColumnData(int) - Method in class jigcell.compare.views.BasicTableView
 
getColumnHeaders(int) - Method in class jigcell.compare.cellcycle.JigCellRunManagerTransform
Retrieves the names of the columns that will come back when a run is executed.
getColumnName(int) - Method in class jigcell.compare.compare2.Compare2Model
The name of a column.
getColumnName(long) - Method in class jigcell.compare.transform.SelectColumnsTransform
The name of a column to select from.
getColumnName(int) - Method in class jigcell.compare.ui.BasicTable.BasicTableModel
The name of a column.
getColumnNames() - Method in class jigcell.compare.transform.SelectColumnsTransform
The names of the columns to select from.
getColumns() - Method in class jigcell.compare.transform.SelectColumnsTransform
The selected columns.
getColumnSelection() - Method in class jigcell.compare.cellcycle.CellCycleReportGenerator
The column selection option.
getColumnWeights() - Method in class jigcell.compare.ui.BasicTable.BasicTableModel
 
getCommand() - Method in class jigcell.compare.ui.MenuBuilder.Builder.Item
The item action command.
getComment() - Method in class jigcell.compare.data.DataGenerator
A comment suitable for display to the user.
getComment() - Method in interface jigcell.compare.IDataGenerator
A comment suitable for display to the user.
getCompare() - Method in class jigcell.compare.ui.CustomizableInterface
Comparator for the generator.
getCompare() - Method in interface jigcell.compare.ui.IBasicTableHost
The Comparator that this host belongs to.
getCompare() - Method in class jigcell.compare.ui.PanelTab
 
getComparisonType(int) - Method in class jigcell.compare.compare2.Compare2Model
Comparison type for a particular row.
getCompatibleTransforms() - Method in interface jigcell.compare.transform.ITransform
The transforms compatible with this statement.
getCompatibleTransforms() - Method in class jigcell.compare.transform.Transform
The transforms compatible with this statement.
getComponentName(JComponent) - Method in class jigcell.compare.ui.InterfaceBuilder
The name given for this particular component.
getComponentName(Object) - Method in class jigcell.compare.ui.InterfaceBuilder
The name given for this particular component.
getConfig() - Method in class jigcell.compare.impl.Compare
The configuration resource.
getConfig(String) - Method in class jigcell.compare.impl.Config
The config for a particular marker from this configurator.
getConfigEditor() - Method in class jigcell.compare.ui.CompareFrontEnd.FrontEndTabInfo
Configures the tab.
getConfigForView() - Method in class jigcell.compare.ui.PanelTab
The configuration for this view.
getConfigMarkers() - Method in interface jigcell.compare.ui.IBasicTableHost
The configuration markers that this host uses.
getConfigMarkers() - Method in class jigcell.compare.ui.PanelTab
 
getConfigs() - Method in class jigcell.compare.impl.Config
The mapping between markers and configurators.
getContainedTransforms() - Method in interface jigcell.compare.transform.ITransformContainer
The transforms managed by this container.
getContainedTransforms() - Method in class jigcell.compare.transform.TransformContainer
The transforms managed by this container.
getContainer() - Method in interface jigcell.compare.transform.ITransform
The container of this transform.
getContainer() - Method in class jigcell.compare.transform.Transform
The container of this transform.
getCopiedFrom() - Method in class jigcell.compare.data.DataGenerator
The generator this was copied from or null if this is not a copy.
getCopiedFrom() - Method in interface jigcell.compare.IDataGenerator
The generator this was copied from or null if this is not a copy.
getCurrentSource() - Method in class jigcell.compare.ui.DataEditorPanelTab
The current data source to work from.
getCurrentSource() - Method in interface jigcell.compare.ui.IDataEditorTab
The current data source to work from.
getCustomizableInstances() - Static method in class jigcell.compare.cellcycle.BuddingYeastPhenotypeObjective
Generates an instance.
getCustomizableInstances() - Static method in class jigcell.compare.cellcycle.BuddingYeastScanTransform
Generates an instance.
getCustomizableInstances() - Static method in class jigcell.compare.cellcycle.GenericPhenotypeObjective
Generates an instance.
getCustomizableInstances() - Static method in class jigcell.compare.cellcycle.GenericScanTransform
Generates an instance.
getCustomizableInstances() - Static method in class jigcell.compare.cellcycle.JigCellRunManagerTransform
Generates an instance.
getCustomizableInstances() - Static method in class jigcell.compare.cellcycle.WildtypeScanTransform
Generates an instance.
getCustomizableInstances() - Static method in class jigcell.compare.contrib.DispatchedTransformTemplate
Generates an instance.
getCustomizableInstances() - Static method in class jigcell.compare.contrib.ObjectiveTemplate
Generates an instance.
getCustomizableInstances() - Static method in class jigcell.compare.contrib.TransformTemplate
Generates an instance.
getCustomizableInstances() - Static method in class jigcell.compare.objective.BooleanRelationalObjective
Generates an instance.
getCustomizableInstances() - Static method in class jigcell.compare.objective.MinkowskiObjective
Generates an instance of a 1-norm, 2-norm, and max-norm.
getCustomizableInstances() - Static method in class jigcell.compare.objective.ScriptEvaluationObjective
Generates an instance.
getCustomizableInstances() - Static method in class jigcell.compare.objective.WOSSObjective
Generates an instance.
getCustomizableInstances() - Static method in class jigcell.compare.tests.MethodDispatcherTests.DispatchedTransform
Generates an instance.
getCustomizableInstances() - Static method in class jigcell.compare.transform.BoxTransformContainer
Generates an instance.
getCustomizableInstances() - Static method in class jigcell.compare.transform.ConstantTransform
Generates an instance.
getCustomizableInstances() - Static method in class jigcell.compare.transform.ExtremaTestTransform
Generates an instance.
getCustomizableInstances() - Static method in class jigcell.compare.transform.ReadFromFileTransform
Generates an instance.
getCustomizableInstances() - Static method in class jigcell.compare.transform.ScriptEvaluationTransform
Generates an instance.
getCustomizableInstances() - Static method in class jigcell.compare.transform.SelectColumnsTransform
Generates an instance.
getCustomizableInstances() - Static method in class jigcell.compare.transform.TransformEvaluationTransform
Generates an instance.
getCustomizableInstances() - Static method in class jigcell.compare.transform.WriteToFileTransform
Generates an instance.
getCycleExtent() - Method in class jigcell.compare.cellcycle.WildtypeScanTransform
The number of cycles to take for the initial length.
getData(String) - Method in class jigcell.compare.impl.Blackboard
Retrieves a data item from the blackboard.
getData() - Method in interface jigcell.compare.ITransferProxy
A transformed version of the transfer data.
getData() - Method in interface jigcell.compare.objective.IObjective
The set of data used.
getData() - Method in class jigcell.compare.objective.Objective
The set of data used.
getData() - Method in class jigcell.compare.views.SeriesView.SeriesViewTransferer
A transformed version of the transfer data.
getDataManager() - Method in class jigcell.compare.impl.Compare
The data manager resource.
getDataValueAt(JTable, int, int) - Method in class jigcell.compare.compare2.ViewColorer
A value in the corresponding table.
getDataValues(JTable, int) - Method in class jigcell.compare.compare2.ViewColorer
All of the values in a row of the corresponding table.
getDebugDelay() - Method in class jigcell.compare.views.TransformDebugger.DebuggerThread
The delay before continuing a debug trace.
getDebugExceptions() - Static method in class jigcell.compare.impl.Compare
Whether to display exception debugging information
getDefaultDimensionWeight() - Method in interface jigcell.compare.objective.IDimensionWeightObjective
The dimension weight default.
getDefaultDimensionWeight() - Method in class jigcell.compare.objective.WOSSObjective
The dimension weight default.
getDefaultDimensionWeights() - Method in interface jigcell.compare.objective.IDimensionWeightObjective
Valid dimension weight defaults.
getDefaultDimensionWeights() - Method in class jigcell.compare.objective.WOSSObjective
Valid dimension weight defaults.
getDefaultElementWeight() - Method in interface jigcell.compare.objective.IElementWeightObjective
The element weight default.
getDefaultElementWeight() - Method in class jigcell.compare.objective.MinkowskiObjective
The element weight default.
getDefaultElementWeight() - Method in class jigcell.compare.objective.WOSSObjective
The element weight default.
getDefaultElementWeights() - Method in interface jigcell.compare.objective.IElementWeightObjective
Valid element weight defaults.
getDefaultElementWeights() - Method in class jigcell.compare.objective.MinkowskiObjective
Valid element weight defaults.
getDefaultElementWeights() - Method in class jigcell.compare.objective.WOSSObjective
Valid element weight defaults.
getDefaultRunNumber() - Method in class jigcell.compare.cellcycle.JigCellRunManagerTransform
The run number to use if the default run is selected.
getDefaultSeriesColor(long) - Static method in class jigcell.compare.plotter.JPlotBridge
The color of series pos.
getDependencies() - Method in interface jigcell.compare.transform.ITransform
The dependencies of this transform.
getDependencies() - Method in class jigcell.compare.transform.Transform
The dependencies of this transform.
getDependencies() - Method in class jigcell.compare.transform.TransformContainer
The dependencies of this transform. Additionally, a transform is considered dependent on the previous, next, children, and parent transforms. This function may return any subset of dependencies with the same transitive closure as the full set. A null result may be used to indicate that no dependencies exist.
getDependencies() - Method in class jigcell.compare.transform.TransformEvaluationTransform
The dependencies of this transform. Additionally, a transform is considered dependent on the previous, next, children, and parent transforms. This function may return any subset of dependencies with the same transitive closure as the full set. A null result may be used to indicate that no dependencies exist.
getDescription(long) - Method in class jigcell.compare.contrib.StructuredTypeCheckerTemplate
A description for the element at this position. Implementations that do not want to provide a description should return null.
getDescription(long) - Method in class jigcell.compare.data.type.StructuredTypeChecker
A description for the element at this position.
getDescription() - Method in class jigcell.compare.data.type.TypeChecker
A description for this type.
getDescription() - Method in class jigcell.compare.impl.SuffixFileFilter
 
getDescription(long) - Method in interface jigcell.compare.IStructuredTypeChecker
A description for the element at this position.
getDescription() - Method in interface jigcell.compare.ITypeChecker
A description for this type.
getDescription() - Method in interface jigcell.compare.transform.annotation.ITransformAnnotation.IAnnotationDescriptor
A description of what this annotation represents.
getDescription() - Method in class jigcell.compare.transform.annotation.TransformAnnotation.AnnotationDescriptor
A description of what this annotation represents.
getDimension(Class) - Static method in class jigcell.compare.data.MethodDispatcher
The dimension of a formalType.
getDimensionWeights() - Method in interface jigcell.compare.objective.IDimensionWeightObjective
The dimension weights.
getDimensionWeights() - Method in class jigcell.compare.objective.WOSSObjective
The dimension weights.
getDirect(long) - Method in class jigcell.compare.data.EditableDataElement
Gets the value at a position.
getDirect(long) - Method in class jigcell.compare.data.PackedDoubleDataElement
Gets the value at a position.
getDirect(long) - Method in class jigcell.compare.data.PackedTreeDataElement
Gets the value at a position.
getDirect(long) - Method in class jigcell.compare.data.PackedTreeDataElement2
Gets the value at a position. Boolean values are represented by Boolean. Empty values are represented by null. Integral values are represented by Integer. Literal values are represented by String. Multiple values are represented by DataElement. Real values are represented by Double. The position of the object may be anything.
getDirect(long) - Method in class jigcell.compare.data.SparseTreeDataElement
Gets the value at a position.
getDirect(long) - Method in class jigcell.compare.data.SparseTreeDataElement2
Gets the value at a position. Boolean values are represented by Boolean. Empty values are represented by null. Integral values are represented by Integer. Literal values are represented by String. Multiple values are represented by DataElement. Real values are represented by Double. The position of the object may be anything.
getDisplay() - Method in class jigcell.compare.ui.FindAccessory
The interface display for the accessory.
getDisplay() - Method in class jigcell.compare.ui.InterfaceBuilder
The display for this manager.
getDisplay() - Method in interface jigcell.compare.ui.ITabAccessory
The interface display for the accessory.
getDisplay() - Method in class jigcell.compare.ui.MemoryMonitorAccessory
The interface display for the accessory.
getDisplayComponent() - Method in class jigcell.compare.transform.ConstantTransform
The component that will be displayed in the transform interface.
getDisplayFrame() - Method in class jigcell.compare.impl.Compare
The frontend shell display frame.
getDisplayFrame() - Method in class jigcell.compare.ui.CompareFrontEnd
The frontend shell display frame.
getElement() - Method in class jigcell.compare.data.DataGenerator
A DataElement corresponding to this object.
getElement() - Method in class jigcell.compare.data.EditableDataGenerator
A DataElement corresponding to this object. This may be a potentially expensive operation if isCached is false.
getElement() - Method in class jigcell.compare.data.ProgrammableDataGenerator
A DataElement corresponding to this object. This may be a potentially expensive operation if isCached is false.
getElement(IEvaluationCallStack) - Method in class jigcell.compare.data.ProgrammableDataGenerator
A DataElement corresponding to this object.
getElement() - Method in interface jigcell.compare.IDataGenerator
A DataElement corresponding to this object.
getElement(IEvaluationCallStack) - Method in interface jigcell.compare.IProgrammableDataGenerator
A DataElement corresponding to this object.
getElementAt(int) - Method in class jigcell.compare.transformui.SelectColumnsInterface.SelectedModel
The element at position index.
getElementAt(int) - Method in class jigcell.compare.ui.ListComboBoxModel
 
getElementWeights() - Method in interface jigcell.compare.objective.IElementWeightObjective
The element weights.
getElementWeights() - Method in class jigcell.compare.objective.MinkowskiObjective
The element weights.
getElementWeights() - Method in class jigcell.compare.objective.WOSSObjective
The element weights.
getEncoderOption() - Method in class jigcell.compare.impl.FileDataSource
The file encoder to control reading and writing from this source.
getErr() - Method in class jigcell.compare.views.Console
 
getEvaluationContext() - Method in interface jigcell.compare.transform.ITransform
The runtime context for performing an evaluation.
getEvaluationContext() - Method in class jigcell.compare.transform.Transform
The runtime context for performing an evaluation.
getEvaluationLock() - Method in class jigcell.compare.data.ProgrammableDataGenerator
Lock for preventing concurrent access during evaluation.
getEvaluationLock() - Method in interface jigcell.compare.IProgrammableDataGenerator
Lock for preventing concurrent access during evaluation.
getException() - Method in class jigcell.compare.impl.FileDataSource
Returns and clears any exception associated with the last operation.
getExceptionListenerOption() - Method in class jigcell.compare.impl.FileDataSource
The exception listener option.
getExceptionRecorder() - Method in class jigcell.compare.data.CachedDataElement
The exception recorder this transferer should use.
getExceptionRecorder() - Method in class jigcell.compare.impl.FileDataSource
The exception recorder this transferer should use.
getExceptionRecorder() - Method in class jigcell.compare.impl.Transferer
The exception recorder this transferer should use.
getExceptionRecorder() - Method in class jigcell.compare.views.SeriesView.SeriesViewTransferer
The exception recorder this transferer should use.
getExpectedClasses(ComparatorDataFlavor) - Static method in class jigcell.compare.impl.Transferer
The expected classes given a data flavor as a List[Class].
getExpectedClasses(File) - Static method in class jigcell.compare.impl.Transferer
The expected classes given a file as a List[Class].
getExpectedClasses(String) - Static method in class jigcell.compare.impl.Transferer
The expected classes given a file name as a List[Class].
getFileChooserOption() - Method in class jigcell.compare.impl.FileDataSource
The file chooser option.
getFileChooserSelectOption() - Method in class jigcell.compare.impl.FileDataSource
The file chooser select option.
getFileInputOption() - Method in class jigcell.compare.impl.FileDataSource
The file input option.
getFilename() - Method in class jigcell.compare.transform.FileTransform
The file name.
getFileOutputOption() - Method in class jigcell.compare.impl.FileDataSource
The file output option.
getFilePathOption() - Method in class jigcell.compare.impl.FileDataSource
The file path option.
getFileSource() - Method in class jigcell.compare.transform.FileTransform
File source to use.
getFileSourceOption() - Method in class jigcell.compare.impl.PDFPrinterDataSource
The file that will hold the PDF document.
getFixedColumnCount() - Method in class jigcell.compare.compare2.Compare2Model
The number of fixed columns in the table.
getFlavors(Class) - Static method in class jigcell.compare.impl.Transferer
The associated flavors for any class in the supporting hierarchy as a List[ComparatorDataFlavor].
getFlavors(Transferable) - Static method in class jigcell.compare.impl.Transferer
The associated flavors for any class in the supporting hierarchy of an instance as a List[ComparatorDataFlavor].
getFlavorsOption() - Method in class jigcell.compare.impl.ClipboardDataSource
The clipboard flavors option.
getFrames() - Method in interface jigcell.compare.IEvaluationCallStack
A list of the stack frames.
getFrames() - Method in class jigcell.compare.impl.EvaluationCallStack
A list of the stack frames.
getFunction() - Method in interface jigcell.compare.objective.IObjective
The function used for the objective computation.
getFunction() - Method in class jigcell.compare.objective.Objective
The function used for the objective computation.
getGenerators() - Method in class jigcell.compare.views.SeriesView.SeriesModel
The generators for this model.
getGlobal() - Method in class jigcell.compare.ui.MenuBuilder.Builder
The global handler for this class.
getGroups() - Method in class jigcell.compare.compare2.ThresholdRelativeViewColorer
The number of groups to divide the cells into.
getHandler() - Method in class jigcell.compare.ui.MenuBuilder.Builder.Item
The item handler.
getHandlers() - Method in class jigcell.compare.ui.MenuBuilder.ScriptActionTrampoline
The script handlers.
getHostIdentifier() - Method in interface jigcell.compare.ui.IBasicTableHost
A unique identifier within the current Comparator for this host.
getHostIdentifier() - Method in class jigcell.compare.ui.PanelTab
 
getIcon() - Method in class jigcell.compare.ui.MenuBuilder.Builder.Item
The item icon.
getId() - Method in class jigcell.compare.data.IDataGeneratorCollection.Key
The key id.
getIn() - Method in class jigcell.compare.views.Console
 
getIndexOf(Object) - Method in class jigcell.compare.ui.ListComboBoxModel
Index of an item in this model or -1 if the item is not present.
getInitialHeight() - Method in class jigcell.compare.ui.ViewerDialog
The initial height of the dialog in pixels.
getInitialWidth() - Method in class jigcell.compare.ui.ViewerDialog
The initial width of the dialog in pixels.
getInputDescription() - Method in class jigcell.compare.data.ProgrammableDataGenerator.DummyCustomizableInterface
A description of the input of this data source.
getInputDescription() - Method in interface jigcell.compare.ICustomizableInterface
A description of the input of this data source.
getInputDescription() - Method in class jigcell.compare.ui.CustomizableInterface
A description of the input of this data source.
getInputTypeChecker() - Method in class jigcell.compare.data.ProgrammableDataGenerator
Type checker that can validate the input to this generator.
getInputTypeChecker() - Method in interface jigcell.compare.IProgrammableDataGenerator
Type checker that can validate the input to this generator.
getInputTypeChecker() - Method in class jigcell.compare.objective.MetricObjective
Type checker that can validate the input to this generator.
getInputTypeChecker() - Method in class jigcell.compare.transform.SelectColumnsTransform
Type checker that can validate the input to this generator.
getInstance() - Static method in class jigcell.compare.cellcycle.BuddingYeastNocPhenotype
A type checker.
getInstance() - Static method in class jigcell.compare.cellcycle.BuddingYeastPhenotype
A type checker.
getInstance() - Static method in class jigcell.compare.cellcycle.BuddingYeastWildtypeProperties
A type checker.
getInstance() - Static method in class jigcell.compare.cellcycle.GenericPhenotype
A type checker.
getInstance() - Static method in class jigcell.compare.contrib.StructuredTypeCheckerTemplate
A type checker.
getInstance() - Static method in class jigcell.compare.contrib.TypeCheckerTemplate
A type checker.
getInstance() - Static method in class jigcell.compare.data.type.BooleanTypeChecker
A type checker.
getInstance() - Static method in class jigcell.compare.data.type.IntegerTypeChecker
A type checker.
getInstance() - Static method in class jigcell.compare.data.type.ListTypeChecker
A type checker.
getInstance() - Static method in class jigcell.compare.data.type.RealTypeChecker
A type checker.
getInstance() - Static method in class jigcell.compare.data.type.StringTypeChecker
A type checker.
getInstance() - Static method in class jigcell.compare.data.type.StructuredTypeChecker
A type checker.
getInstance() - Static method in class jigcell.compare.data.type.TimeSeriesTypeChecker
A type checker.
getInstance() - Static method in class jigcell.compare.data.type.UntypedTypeChecker
A type checker.
getInstance() - Static method in class jigcell.compare.transform.annotation.CommentAnnotationDescriptor
An instance of this class.
getInstance() - Static method in class jigcell.compare.transform.annotation.ElementNameAnnotationDescriptor
An instance of this class.
getInstance() - Static method in class jigcell.compare.transform.annotation.ElementSizeAnnotationDescriptor
An instance of this class.
getInstance() - Static method in class jigcell.compare.transform.annotation.ElementTypeAnnotationDescriptor
An instance of this class.
getInstances(Compare2) - Static method in class jigcell.compare.compare2.ImmediateHistoryRelativeViewColorer
A single or collection of colorers that can color a view.
getInstances(Compare2) - Static method in class jigcell.compare.compare2.ThresholdAbsoluteViewColorer
A single or collection of colorers that can color a view.
getInstances(Compare2) - Static method in class jigcell.compare.compare2.ThresholdRelativeViewColorer
A single or collection of colorers that can color a view.
getInstances(Compare2) - Static method in class jigcell.compare.compare2.ViewColorer
A single or collection of colorers that can color a view.
getIntegralValue(long) - Method in class jigcell.compare.data.CachedDataElement
The element at position pos represented as an integer. If the given position has no valid meaning for this element, the value is 0.
getIntegralValue() - Method in class jigcell.compare.data.DataElement
This element represented as an integer when evaluated in a scalar context.
getIntegralValue(long) - Method in class jigcell.compare.data.DataElement
The element at position pos represented as an integer.
getIntegralValue(long) - Method in class jigcell.compare.data.EditableDataElement
The element at position pos represented as an integer. If the given position has no valid meaning for this element, the value is 0.
getIntegralValue() - Method in class jigcell.compare.data.FlippedDataElement
This element represented as an integer when evaluated in a scalar context.
getIntegralValue(long) - Method in class jigcell.compare.data.FlippedDataElement
The element at position pos represented as an integer.
getIntegralValue() - Method in interface jigcell.compare.IDataElement
This element represented as an integer when evaluated in a scalar context.
getIntegralValue(long) - Method in interface jigcell.compare.IDataElement
The element at position pos represented as an integer.
getInterface() - Method in class jigcell.compare.data.ProgrammableDataGenerator
The customizable interface for this generator.
getInterface() - Method in interface jigcell.compare.IProgrammableDataGenerator
The customizable interface for this generator.
getInterpolation() - Method in interface jigcell.compare.objective.IInterpolationObjective
The interpolation.
getInterpolation() - Method in class jigcell.compare.objective.WOSSObjective
The interpolation.
getInterpolations() - Method in interface jigcell.compare.objective.IInterpolationObjective
The valid interpolations
getInterpolations() - Method in class jigcell.compare.objective.WOSSObjective
The valid interpolations
getKnownTransforms() - Method in class jigcell.compare.transform.TransformEvaluationTransform
The transforms known to this transform.
getLastException() - Method in class jigcell.compare.impl.ExceptionRecorder
The last exception caught by this handler.
getLastInstance() - Static method in class jigcell.compare.cellcycle.CellCycleFrontEnd
The last instance created of this class or null if no instance of this class has been created or the last instance created of this class has been destroyed.
getLastSearchName() - Method in interface jigcell.compare.ui.INameFinderTab
Text of the last search performed.
getLastSearchName() - Method in class jigcell.compare.views.BasicTableView
 
getLength() - Method in class jigcell.compare.data.CachedDataElement
The number of elements in this element, or 0 if this element is scalar.
getLength() - Method in class jigcell.compare.data.DataElement
The number of elements in this element, or 0 if this element is scalar.
getLength() - Method in class jigcell.compare.data.FlippedDataElement
The number of elements in this element, or 0 if this element is scalar.
getLength() - Method in class jigcell.compare.data.PackedDoubleDataElement
The number of elements in this element, or 0 if this element is scalar.
getLength() - Method in class jigcell.compare.data.TreeDataElement
The number of elements in this element, or 0 if this element is scalar.
getLength() - Method in interface jigcell.compare.IDataElement
The number of elements in this element, or 0 if this element is scalar.
getLength() - Method in interface jigcell.compare.transform.annotation.ITransformAnnotation
The last position with a recorded annotation.
getLength() - Method in class jigcell.compare.transform.annotation.TransformAnnotation
The last position with a recorded annotation.
getListValue(long) - Method in class jigcell.compare.data.CachedDataElement
This element at position pos represented as a list. If the given position has no valid meaning for this element, the value is null.
getListValue(long) - Method in class jigcell.compare.data.DataElement
This element at position pos represented as a list.
getListValue(long) - Method in class jigcell.compare.data.EditableDataElement
This element at position pos represented as a list. If the given position has no valid meaning for this element, the value is null.
getListValue(long) - Method in class jigcell.compare.data.FlippedDataElement
This element at position pos represented as a list.
getListValue(long) - Method in interface jigcell.compare.IDataElement
This element at position pos represented as a list.
getLiteralValue(long) - Method in class jigcell.compare.data.CachedDataElement
The element at position pos represented as a string literal. If the given position has no valid meaning for this element, the value is null. The literal is not quoted.
getLiteralValue() - Method in class jigcell.compare.data.DataElement
This element represented as a string literal when evaluated in a scalar context.
getLiteralValue(long) - Method in class jigcell.compare.data.DataElement
The element at position pos represented as a string literal.
getLiteralValue(long) - Method in class jigcell.compare.data.EditableDataElement
The element at position pos represented as a string literal. If the given position has no valid meaning for this element, the value is null. The literal is not quoted.
getLiteralValue() - Method in class jigcell.compare.data.FlippedDataElement
This element represented as a string literal when evaluated in a scalar context.
getLiteralValue(long) - Method in class jigcell.compare.data.FlippedDataElement
The element at position pos represented as a string literal.
getLiteralValue() - Method in interface jigcell.compare.IDataElement
This element represented as a string literal when evaluated in a scalar context.
getLiteralValue(long) - Method in interface jigcell.compare.IDataElement
The element at position pos represented as a string literal.
getLocation() - Method in class jigcell.compare.impl.FileDataSource
A unique identifier for this data source.
getLocation() - Method in interface jigcell.compare.IPersistableDataSource
A unique identifier for this data source.
getLocation() - Method in class jigcell.compare.ui.HTMLComponentDescription
The location of the component description.
getLocation() - Method in class jigcell.compare.ui.TextComponentDescription
The location of the component description.
getLock() - Method in class jigcell.compare.impl.Config
The configuration lock.
getLongObject(long) - Static method in class jigcell.compare.data.DataElement
Returns a constant out of the long constant pool or a new constant.
getMaximum() - Method in class jigcell.compare.transform.ExtremaTestTransform
The maximum.
getMaximumMass() - Method in class jigcell.compare.cellcycle.GenericScanTransform
The maximum mass before the mutant is declared inviable.
getMenus() - Method in class jigcell.compare.ui.CompareFrontEnd.FrontEndTabInfo
The tab menus.
getMethodName() - Method in class jigcell.compare.data.MethodDispatcher
Name of the method to invoke.
getMetric() - Method in class jigcell.compare.objective.MetricObjective
The distance metric.
getMinimum() - Method in class jigcell.compare.transform.ExtremaTestTransform
The minimum.
getMinimumMass() - Method in class jigcell.compare.cellcycle.GenericScanTransform
The minimum mass before the mutant is declared inviable.
getName() - Method in class jigcell.compare.cellcycle.BuddingYeastNocPhenotype
A name for this type.
getName(long) - Method in class jigcell.compare.cellcycle.BuddingYeastNocPhenotype
A name for the element at this position. Implementations that do not want to provide a name should return null.
getName() - Method in class jigcell.compare.cellcycle.BuddingYeastPhenotype
A name for this type.
getName(long) - Method in class jigcell.compare.cellcycle.BuddingYeastPhenotype
A name for the element at this position. Implementations that do not want to provide a name should return null.
getName() - Method in class jigcell.compare.cellcycle.BuddingYeastWildtypeProperties
A name for this type.
getName(long) - Method in class jigcell.compare.cellcycle.BuddingYeastWildtypeProperties
A name for the element at this position. Implementations that do not want to provide a name should return null.
getName() - Method in class jigcell.compare.cellcycle.GenericPhenotype
A name for this type.
getName(long) - Method in class jigcell.compare.cellcycle.GenericPhenotype
A name for the element at this position. Implementations that do not want to provide a name should return null.
getName() - Method in class jigcell.compare.compare2.ImmediateHistoryRelativeViewColorer
The name of this renderer.
getName() - Method in interface jigcell.compare.compare2.IViewColorer
The name of this renderer.
getName() - Method in class jigcell.compare.compare2.ThresholdAbsoluteViewColorer
The name of this renderer.
getName() - Method in class jigcell.compare.compare2.ThresholdRelativeViewColorer
The name of this renderer.
getName() - Method in class jigcell.compare.compare2.ViewColorer
The name of this renderer.
getName() - Method in class jigcell.compare.contrib.StructuredTypeCheckerTemplate
A name for this type.
getName(long) - Method in class jigcell.compare.contrib.StructuredTypeCheckerTemplate
A name for the element at this position. Implementations that do not want to provide a name should return null.
getName() - Method in class jigcell.compare.contrib.TypeCheckerTemplate
A name for this type.
getName() - Method in class jigcell.compare.data.DataGenerator
The name of this data source.
getName() - Method in class jigcell.compare.data.IDataGeneratorCollection.Key
The key name.
getName() - Method in class jigcell.compare.data.type.BooleanTypeChecker
A name for this type.
getName() - Method in class jigcell.compare.data.type.IntegerTypeChecker
A name for this type.
getName() - Method in class jigcell.compare.data.type.ListTypeChecker
A name for this type.
getName() - Method in class jigcell.compare.data.type.RealTypeChecker
A name for this type.
getName() - Method in class jigcell.compare.data.type.StringTypeChecker
A name for this type.
getName(long) - Method in class jigcell.compare.data.type.StructuredTypeChecker
A name for the element at this position.
getName() - Method in class jigcell.compare.data.type.TimeSeriesTypeChecker
A name for this type.
getName(long) - Method in class jigcell.compare.data.type.TimeSeriesTypeChecker
A name for the element at this position. Implementations that do not want to provide a name should return null.
getName() - Method in class jigcell.compare.data.type.UntypedTypeChecker
A name for this type.
getName() - Method in interface jigcell.compare.IDataSource
The name of this data source.
getName() - Method in class jigcell.compare.impl.Compare.TabInfo
The tab display name.
getName() - Method in class jigcell.compare.impl.DataSource
The name of this data source.
getName(long) - Method in interface jigcell.compare.IStructuredTypeChecker
A name for the element at this position.
getName() - Method in interface jigcell.compare.ITab
The name of this tab.
getName() - Method in interface jigcell.compare.ITypeChecker
A name for this type.
getName() - Method in class jigcell.compare.plotter.JPlotBridge
The name of this data source.
getName() - Method in class jigcell.compare.plotter.Plotter
The name of this data source.
getName() - Method in class jigcell.compare.plotter.PTPlotBridge
The name of this data source.
getName() - Method in interface jigcell.compare.transform.annotation.ITransformAnnotation.IAnnotationDescriptor
The name of this descriptor.
getName() - Method in class jigcell.compare.transform.annotation.TransformAnnotation.AnnotationDescriptor
The name of this descriptor.
getName() - Method in class jigcell.compare.ui.BasicTable.BasicTableModel.Marker
The name of this column for the table header.
getName() - Method in class jigcell.compare.ui.CompareFrontEnd
The name of this tab.
getName() - Method in class jigcell.compare.ui.MenuBuilder.Builder.Item
The item name.
getName() - Method in class jigcell.compare.ui.PanelTab
The name of this tab.
getName() - Method in class jigcell.compare.ui.SeriesDialog
The name of this tab.
getNamespace(String) - Method in class jigcell.compare.impl.Blackboard
Retrieves a namespace from the blackboard.
getNextStatement() - Method in interface jigcell.compare.transform.ITransform
The next generator in the sequence of transforms.
getNextStatement() - Method in class jigcell.compare.transform.Transform
The next generator in the sequence of transforms.
getObjectiveForGenerator(IDataGenerator) - Static method in class jigcell.compare.objective.Objective
The objective of a generator.
getObjectiveForGenerator(int) - Method in class jigcell.compare.views.ObjectiveSeriesView
The objective of a generator.
getOption(String) - Method in interface jigcell.compare.IDataSource
A configuration option.
getOption(String) - Method in class jigcell.compare.impl.DataSource
A configuration option.
getOption(String) - Method in class jigcell.compare.impl.RawFileDataSource
A configuration option.
getOptions() - Method in class jigcell.compare.impl.DataSource
The configuration options map.
getOptionType(String) - Static method in class jigcell.compare.impl.DataSource
The persistence type for an option.
getOrigin() - Method in interface jigcell.compare.IEvaluationCallStack
The generator that will hold the final result or null if this is not available.
getOrigin() - Method in class jigcell.compare.impl.EvaluationCallStack
The generator that will hold the final result or null if this is not available.
getOut() - Method in class jigcell.compare.views.Console
 
getOutputDescription() - Method in class jigcell.compare.data.ProgrammableDataGenerator.DummyCustomizableInterface
A description of the output of this data source.
getOutputDescription() - Method in interface jigcell.compare.ICustomizableInterface
A description of the output of this data source.
getOutputDescription() - Method in class jigcell.compare.ui.CustomizableInterface
A description of the output of this data source.
getOutputTypeChecker() - Method in class jigcell.compare.data.ProgrammableDataGenerator
Type checker that can validate the output from this generator.
getOutputTypeChecker() - Method in interface jigcell.compare.IProgrammableDataGenerator
Type checker that can validate the output from this generator.
getOutputTypeChecker() - Method in class jigcell.compare.transform.BoxTransformContainer
Type checker that can validate the output from this generator.
getOutputTypeChecker() - Method in class jigcell.compare.transform.InputTransform
Type checker that can validate the output from this generator.
getOutputTypeChecker() - Method in class jigcell.compare.transform.SelectColumnsTransform
Type checker that can validate the output from this generator.
getOutputTypeChecker() - Method in class jigcell.compare.transform.WriteToFileTransform
Type checker that can validate the output from this generator.
getOwnerOption() - Method in class jigcell.compare.impl.OwnedDataSource
The owner object that will be supplied to the callback.
getP() - Method in class jigcell.compare.objective.MinkowskiObjective
The p.
getParameter(String) - Method in class jigcell.compare.impl.ComparatorDataFlavor
The value of a named parameter.
getParameterMap() - Method in class jigcell.compare.impl.ComparatorDataFlavor
The parameter map.
getParent() - Method in class jigcell.compare.ui.MenuBuilder.Builder
The parent for this class.
getPenaltyLength() - Method in class jigcell.compare.data.MethodDispatcher
The penalty for length mismatches.
getPenaltyLengthChecked() - Method in class jigcell.compare.data.MethodDispatcher
Whether length mismatches are allowed.
getPenaltyLooseMatch() - Method in class jigcell.compare.data.MethodDispatcher
The penalty for loose formalType matches.
getPenaltyLooseMatchChecked() - Method in class jigcell.compare.data.MethodDispatcher
Whether loose formalType matches are allowed.
getPredictedCompatibility(Class) - Method in class jigcell.compare.cellcycle.CellCycleReportGenerator
A prediction on whether this data source can hold a particular type.
getPredictedCompatibility(Object) - Method in class jigcell.compare.cellcycle.CellCycleReportGenerator
A prediction on whether this data source can hold a particular type.
getPredictedCompatibility(Class) - Method in class jigcell.compare.data.EditableDataGenerator
A prediction on whether this data source can hold a particular type.
getPredictedCompatibility(Object) - Method in class jigcell.compare.data.EditableDataGenerator
A prediction on whether this data source can hold a particular type.
getPredictedCompatibility(Class) - Method in class jigcell.compare.impl.FileDataSource
A prediction on whether this data source can hold a particular type.
getPredictedCompatibility(Object) - Method in class jigcell.compare.impl.FileDataSource
A prediction on whether this data source can hold a particular type.
getPredictedCompatibility(Class) - Method in interface jigcell.compare.impl.FileDataSource.IFileEncoder
 
getPredictedCompatibility(Class) - Method in class jigcell.compare.impl.OwnedDataSource
A prediction on whether this data source can hold a particular type.
getPredictedCompatibility(Object) - Method in class jigcell.compare.impl.OwnedDataSource
A prediction on whether this data source can hold a particular type.
getPredictedCompatibility(Class) - Method in class jigcell.compare.impl.XMLFileEncoder
getPredictedCompatibility(Class) - Method in interface jigcell.compare.IWriteableDataSource
A prediction on whether this data source can hold a particular type.
getPredictedCompatibility(Object) - Method in interface jigcell.compare.IWriteableDataSource
A prediction on whether this data source can hold a particular type.
getPredictedCompatibility(Class) - Method in class jigcell.compare.plotter.Plotter
A prediction on whether this data source can hold a particular type.
getPredictedCompatibility(Object) - Method in class jigcell.compare.plotter.Plotter
A prediction on whether this data source can hold a particular type.
getPredictedContents() - Method in class jigcell.compare.data.DataGenerator
A prediction on the type of data this source contains.
getPredictedContents() - Method in class jigcell.compare.impl.ClipboardDataSource
A prediction on the type of data this source contains.
getPredictedContents() - Method in class jigcell.compare.impl.FileDataSource
A prediction on the type of data this source contains.
getPredictedContents() - Method in interface jigcell.compare.impl.FileDataSource.IFileEncoder
 
getPredictedContents() - Method in class jigcell.compare.impl.XMLFileEncoder
getPredictedContents() - Method in interface jigcell.compare.IReadableDataSource
A prediction on the type of data this source contains.
getPredictedContents() - Method in class jigcell.compare.tests.ConstantDataSource
A prediction on the type of data this source contains.
getPreferredExtensions(Class) - Static method in class jigcell.compare.impl.Transferer
The preferred serialization extensions for a given class as a List[String].
getPreferredExtensions(Transferable) - Static method in class jigcell.compare.impl.Transferer
The preferred serialization extensions for a given instance as a List[String].
getPreferredSource(Class) - Method in class jigcell.compare.impl.DataManager
The preferred data source of a particular type.
getPreviousAnnotation() - Method in class jigcell.compare.contrib.TransformHelper
Data annotation that should be used in evaluation.
getPreviousElement() - Method in class jigcell.compare.contrib.TransformHelper
Data element that should be used in evaluation.
getPreviousElement() - Method in class jigcell.compare.transform.Transform
Data element that should be used in evaluation.
getPreviousStatement() - Method in interface jigcell.compare.transform.ITransform
The previous generator in the sequence of transforms.
getPreviousStatement() - Method in class jigcell.compare.transform.Transform
The previous generator in the sequence of transforms.
getPrintServiceOption() - Method in class jigcell.compare.impl.SystemPrinterDataSource
The print service option.
getPropertyChangeListeners() - Method in class jigcell.compare.impl.Compare
An array of all the PropertyChangeListeners added to this Compare with addPropertyChangeListener.
getPropertyChangeListeners(String) - Method in class jigcell.compare.impl.Compare
An array of all the listeners which have been associated with the named property.
getPropertyChangeListeners() - Method in class jigcell.compare.impl.DataSource
An array of all the PropertyChangeListeners added to this Compare with addPropertyChangeListener.
getPropertyChangeListeners(String) - Method in class jigcell.compare.impl.DataSource
An array of all the listeners which have been associated with the named property.
getPrototype() - Method in class jigcell.compare.cellcycle.BuddingYeastNocPhenotype
A prototype for data elements of this type. Implementations that do not want to provide a prototype element should return null.
getPrototype() - Method in class jigcell.compare.cellcycle.BuddingYeastPhenotype
A prototype for data elements of this type. Implementations that do not want to provide a prototype element should return null.
getPrototype() - Method in class jigcell.compare.cellcycle.BuddingYeastWildtypeProperties
A prototype for data elements of this type. Implementations that do not want to provide a prototype element should return null.
getPrototype() - Method in class jigcell.compare.cellcycle.GenericPhenotype
A prototype for data elements of this type. Implementations that do not want to provide a prototype element should return null.
getPrototype() - Method in class jigcell.compare.contrib.StructuredTypeCheckerTemplate
A prototype for data elements of this type. Implementations that do not want to provide a prototype element should return null.
getPrototype() - Method in class jigcell.compare.data.type.StructuredTypeChecker
A prototype for data elements of this type.
getPrototype() - Method in interface jigcell.compare.IStructuredTypeChecker
A prototype for data elements of this type.
getPrototypeChild() - Method in class jigcell.compare.data.EditableDataElement
The prototypical instance of a subelement.
getPrototypeExperiments() - Method in class jigcell.compare.cellcycle.CellCycleReportGenerator
The list of experimental prototypes to select from.
getPrototypeReadables() - Method in class jigcell.compare.impl.DataManager
The readable data sources known to this manager.
getPrototypeSources() - Method in class jigcell.compare.impl.DataManager
The data sources known to this manager.
getPrototypeWriteables() - Method in class jigcell.compare.impl.DataManager
The writeable data sources known to this manager.
getReadDescriptionOption() - Method in class jigcell.compare.impl.DataSource
The read description option.
getReadDescriptionOption() - Method in interface jigcell.compare.IReadableDataSource
The read description option.
getReadIconOption() - Method in class jigcell.compare.impl.DataSource
The read description icon.
getReadIconOption() - Method in interface jigcell.compare.IReadableDataSource
The read description icon.
getRealValue(long) - Method in class jigcell.compare.data.CachedDataElement
The element at position pos represented as a real. If the given position has no valid meaning for this element, the value is NaN.
getRealValue() - Method in class jigcell.compare.data.DataElement
This element represented as a real when evaluated in a scalar context.
getRealValue(long) - Method in class jigcell.compare.data.DataElement
The element at position pos represented as a real.
getRealValue(long) - Method in class jigcell.compare.data.EditableDataElement
The element at position pos represented as a real. If the given position has no valid meaning for this element, the value is NaN.
getRealValue() - Method in class jigcell.compare.data.FlippedDataElement
This element represented as a real when evaluated in a scalar context.
getRealValue(long) - Method in class jigcell.compare.data.FlippedDataElement
The element at position pos represented as a real.
getRealValue() - Method in interface jigcell.compare.IDataElement
This element represented as a real when evaluated in a scalar context.
getRealValue(long) - Method in interface jigcell.compare.IDataElement
The element at position pos represented as a real.
getRecentSource(long) - Method in class jigcell.compare.ui.DataEditorPanelTab
A recently used data source.
getRecentSourceCount() - Method in class jigcell.compare.ui.DataEditorPanelTab
The number of recent data sources that can be remembered.
getReferencedTransform() - Method in class jigcell.compare.transform.TransformEvaluationTransform
The transform to invoke.
getRegisteredNames() - Method in interface jigcell.compare.transform.ITransformContext
All registered transform names.
getRegisteredNames() - Method in class jigcell.compare.transform.TransformContext
All registered transform names.
getRegisteredTransforms() - Method in interface jigcell.compare.transform.ITransformContext
All registered transforms.
getRegisteredTransforms() - Method in class jigcell.compare.transform.TransformContext
All registered transforms.
getRelation() - Method in class jigcell.compare.objective.BooleanRelationalObjective
The relation.
getRelation() - Method in interface jigcell.compare.objective.IRelationalObjective
The relation.
getRelations() - Method in class jigcell.compare.objective.BooleanRelationalObjective
The valid relations
getRelations() - Method in interface jigcell.compare.objective.IRelationalObjective
The valid relations
getRepresentationClass() - Method in class jigcell.compare.impl.ComparatorDataFlavor
The underlying class of this data flavor.
getRepresentationClassName() - Method in class jigcell.compare.impl.ComparatorDataFlavor
The name of the underlying class of this data flavor.
getResource(String) - Method in class jigcell.compare.impl.Compare
A named resource.
getResourceMap(String) - Method in class jigcell.compare.impl.Compare
A named resource known to be a map.
getResourceNames() - Method in class jigcell.compare.impl.Compare
The currently used resource names.
getResultName() - Method in class jigcell.compare.transform.ConstantTransform
The name of the result to publish or null if this transform does not publish a result.
getResultName() - Method in class jigcell.compare.transform.InputTransform
The name of the result to publish or null if this transform does not publish a result.
getResultName() - Method in interface jigcell.compare.transform.IResultantTransform
The name of the result to publish or null if this transform does not publish a result.
getRewardMatch() - Method in class jigcell.compare.data.MethodDispatcher
The reward for matches.
getRewardSubclass() - Method in class jigcell.compare.data.MethodDispatcher
The reward for specialized matches.
getRewardSubclassChecked() - Method in class jigcell.compare.data.MethodDispatcher
Whether specialized matches are rewarded.
getRow() - Method in class jigcell.compare.ui.BasicTable.ButtonEditor
Row being edited.
getRowCount() - Method in class jigcell.compare.cellcycle.CellCycleDataDialog.DataModel
The number of rows in the current table
getRowCount() - Method in class jigcell.compare.compare2.Compare2Model
The number of generators.
getRowCount() - Method in class jigcell.compare.objectiveui.WeightEditorDialog.WeightModel
The number of rows in the current table
getRowCount() - Method in interface jigcell.compare.ui.IRowEditorTab
The number of rows in the table.
getRowCount() - Method in class jigcell.compare.ui.SeriesDialog.SeriesModel
getRowCount() - Method in class jigcell.compare.ui.SeriesEditorDialog
 
getRowCount() - Method in class jigcell.compare.views.BasicTableView
 
getRowCount() - Method in class jigcell.compare.views.EvaluationErrorViewer.ErrorModel
The number of rows in the current table
getRowCount() - Method in class jigcell.compare.views.SeriesView
getRowCount() - Method in class jigcell.compare.views.SeriesView.SeriesModel
The number of generators.
getRowCount() - Method in class jigcell.compare.views.TransformDebugger.AnnotationModel
The number of values.
getRowCount() - Method in class jigcell.compare.views.TransformDebugger.ValueModel
The number of values.
getRowData(int) - Method in interface jigcell.compare.ui.IRowEditorTab
The data for a row in the table or null if the row is not valid.
getRowData(int) - Method in class jigcell.compare.ui.SeriesEditorDialog
 
getRowData(int) - Method in class jigcell.compare.views.BasicTableView
 
getRowData(int) - Method in class jigcell.compare.views.SeriesView
getRunData() - Method in class jigcell.compare.cellcycle.JigCellRunManagerTransform
Loads the run file if one is specified and not already cached.
getRunFile() - Method in class jigcell.compare.cellcycle.JigCellRunManagerTransform
The run file to read from.
getRunNames() - Method in class jigcell.compare.cellcycle.JigCellRunManagerTransform
A List[String] containing the names of the runs in the current run file.
getRunNumber() - Method in class jigcell.compare.cellcycle.JigCellRunManagerTransform
The run number to use.
getScaleCycleCount() - Method in class jigcell.compare.cellcycle.GenericPhenotypeObjective
Scale factor for cycle counts.
getScaleDivisionMass() - Method in class jigcell.compare.cellcycle.GenericPhenotypeObjective
Scale factor for division mass.
getScaleG1Length() - Method in class jigcell.compare.cellcycle.GenericPhenotypeObjective
Scale factor for time in G1.
getScaleSubcycleCount() - Method in class jigcell.compare.cellcycle.GenericPhenotypeObjective
Scale factor for subcycle counts.
getScript() - Method in class jigcell.compare.objective.ScriptEvaluationObjective
Beanshell script to execute during evaluation.
getScript() - Method in class jigcell.compare.transform.ScriptEvaluationTransform
Beanshell script to execute during evaluation.
getSelectedColumns() - Method in interface jigcell.compare.ui.IColumnSelectionTab
The selected columns of the table.
getSelectedColumns() - Method in class jigcell.compare.views.BasicTableView
 
getSelectedIndex(long) - Method in class jigcell.compare.transform.SelectColumnsTransform
The index of a selected column in the columns to select from.
getSelectedIndex() - Method in class jigcell.compare.ui.ListComboBoxModel
The index of the selected item or -1 if no item is selected.
getSelectedIndices(ListSelectionModel) - Static method in class jigcell.compare.ui.InterfaceBuilder
The selected indices of a list selection model.
getSelectedItem() - Method in class jigcell.compare.ui.ListComboBoxModel
 
getSelectedName(long) - Method in class jigcell.compare.transform.SelectColumnsTransform
The name of a selected column.
getSelectedRows() - Method in interface jigcell.compare.ui.IRowSelectionTab
The selected rows of the table.
getSelectedRows() - Method in class jigcell.compare.ui.SeriesDialog
The selected rows of the table.
getSelectedRows() - Method in class jigcell.compare.views.BasicTableView
 
getSelectedTab() - Method in class jigcell.compare.ui.CompareFrontEnd
The currently selected tab in the display frame.
getSelectedTransform() - Method in class jigcell.compare.views.TransformDebugger
The current object selected in the tree.
getSelectionGroup() - Method in class jigcell.compare.views.BasicTableView
The selection group this view is part of.
getSeries(long) - Method in interface jigcell.compare.plotter.IPlotter
A data series from the data aggregate.
getSeries(long) - Method in class jigcell.compare.plotter.Plotter
A data series from the data aggregate.
getSeriesColor(long) - Method in interface jigcell.compare.plotter.IPlotter
The color of a series.
getSeriesColor(long) - Method in class jigcell.compare.plotter.Plotter
The color of a series.
getSeriesColorOption(long) - Static method in class jigcell.compare.plotter.Plotter
The option indicating the color of a series.
getSeriesCombine() - Method in interface jigcell.compare.plotter.IPlotter
The series combine option.
getSeriesCombine() - Method in class jigcell.compare.plotter.Plotter
The series combine option.
getSeriesCount() - Method in class jigcell.compare.plotter.Plotter
The number of series to plot.
getSeriesName(long) - Method in interface jigcell.compare.plotter.IPlotter
The name of a series.
getSeriesName(long) - Method in class jigcell.compare.plotter.Plotter
The name of a series.
getSeriesNameOption(long) - Static method in class jigcell.compare.plotter.Plotter
The option indicating the name of a series.
getSize() - Method in class jigcell.compare.transformui.SelectColumnsInterface.SelectedModel
The size of this model.
getSize() - Method in class jigcell.compare.ui.ListComboBoxModel
 
getSlice(boolean[], long, int, long) - Method in class jigcell.compare.data.DataElement
A dense, homogeneous subset of this element represented as a boolean list.
getSlice(IDataElement[], long, int, long) - Method in class jigcell.compare.data.DataElement
A dense, homogeneous subset of this element represented as a list of elements.
getSlice(double[], long, int, long) - Method in class jigcell.compare.data.DataElement
A dense, homogeneous subset of this element represented as a real list.
getSlice(long[], long, int, long) - Method in class jigcell.compare.data.DataElement
A dense, homogeneous subset of this element represented as an integral list.
getSlice(String[], long, int, long) - Method in class jigcell.compare.data.DataElement
A dense, homogeneous subset of this element represented as a string literal list.
getSlice(double[], long, int, long) - Method in class jigcell.compare.data.PackedDoubleDataElement
A dense, homogeneous subset of this element represented as a real list. If slice cannot hold the requested range, a new array is created and returned. Slice may be null. If the given start or length has no valid meaning for this element, the value is null. If the subset is not a dense list of reals or slices are not available, the value is null. Position 0 in the returned slice corresponds to position start in the original element.
getSlice(boolean[], long, int, long) - Method in interface jigcell.compare.IDataElement
A dense, homogeneous subset of this element represented as a boolean list.
getSlice(IDataElement[], long, int, long) - Method in interface jigcell.compare.IDataElement
A dense, homogeneous subset of this element represented as a list of elements.
getSlice(double[], long, int, long) - Method in interface jigcell.compare.IDataElement
A dense, homogeneous subset of this element represented as a real list.
getSlice(long[], long, int, long) - Method in interface jigcell.compare.IDataElement
A dense, homogeneous subset of this element represented as an integral list.
getSlice(String[], long, int, long) - Method in interface jigcell.compare.IDataElement
A dense, homogeneous subset of this element represented as a string literal list.
getSource() - Method in class jigcell.compare.transform.Transform
The data source that should be used as the previous computation value.
getSourceActions(JComponent) - Method in class jigcell.compare.views.SeriesView.SeriesViewTransferer
 
getState() - Method in interface jigcell.compare.IDataSource
A textual representation of the configuration of this data source or null if the configuration of this generator cannot be represented.
getState() - Method in class jigcell.compare.impl.DataSource
A textual representation of the configuration of this data source or null if the configuration of this generator cannot be represented.
getString(String) - Static method in class jigcell.compare.impl.Compare
Looks up a string in the table of resources.
getSuffix() - Method in class jigcell.compare.impl.SuffixFileFilter
The file suffix to match against.
getTab() - Method in class jigcell.compare.impl.Compare.TabInfo
The tab.
getTabAccessory(ITab) - Method in class jigcell.compare.ui.CompareFrontEnd
The accessory component for a tab.
getTabInfo(ITab) - Method in class jigcell.compare.ui.CompareFrontEnd
The tab info for a tab.
getTable() - Method in interface jigcell.compare.ui.IBasicTableHost
The table this host is displaying.
getTable() - Method in class jigcell.compare.views.BasicTableView
The table this host is displaying.
getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class jigcell.compare.ui.BasicTable.BasicEditor
 
getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class jigcell.compare.ui.BasicTable.ButtonEditor
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class jigcell.compare.cellcycle.CellCycleExperimentView.ExperimentViewRenderer
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class jigcell.compare.cellcycle.CellCycleObjectiveView.ObjectiveViewRenderer
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class jigcell.compare.cellcycle.CellCycleTransformView.TransformViewRenderer
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class jigcell.compare.compare2.ViewColorer
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class jigcell.compare.ui.BasicTable.BasicRenderer
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class jigcell.compare.ui.BasicTable.ButtonRenderer
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class jigcell.compare.views.ObjectiveSeriesView.ObjectiveSeriesRenderer
 
getTabMap() - Method in class jigcell.compare.impl.Compare
The tab resource map.
getTabs() - Method in class jigcell.compare.impl.Compare
All of the tabs currently registered with the Comparator.
getTarget() - Method in class jigcell.compare.data.MethodDispatcher
The target to invoke.
getThresholdBud() - Method in class jigcell.compare.cellcycle.BuddingYeastScanTransform
The threshold for budding.
getThresholdCycB() - Method in class jigcell.compare.cellcycle.GenericScanTransform
The threshold for cyclin-B.
getThresholdEsp1() - Method in class jigcell.compare.cellcycle.BuddingYeastScanTransform
The threshold for activation.
getThresholdOriHigh() - Method in class jigcell.compare.cellcycle.BuddingYeastScanTransform
The threshold for origin firing.
getThresholdOriLow() - Method in class jigcell.compare.cellcycle.BuddingYeastScanTransform
The threshold for origin licensing.
getThresholdSpn() - Method in class jigcell.compare.cellcycle.BuddingYeastScanTransform
The threshold for spindle alignment.
getThresholdValue(int) - Method in class jigcell.compare.compare2.Compare2Model
Threshold value for a particular row.
getTiedElement() - Method in class jigcell.compare.data.FlippedDataElement
The tied data element if this element is tied or null otherwise.
getTools() - Method in class jigcell.compare.ui.CompareFrontEnd.FrontEndTabInfo
The tab toolbar tools.
getTransferClass(List, Transferable) - Static method in class jigcell.compare.impl.Transferer
The type that will be returned from a transfer operation or null if the transfer will fail.
getTransferClassOption() - Method in class jigcell.compare.impl.OwnedDataSource
The callback class that will be invoked.
getTransferData(DataFlavor) - Method in class jigcell.compare.data.DataElement
A transferable object for the given data flavor.
getTransferData(DataFlavor) - Method in class jigcell.compare.data.DataGenerator
A transferable object for the given data flavor.
getTransferData(DataFlavor) - Method in class jigcell.compare.impl.Config
A transferable object for the given data flavor.
getTransferData(DataFlavor) - Method in class jigcell.compare.impl.Transferer
A transferable object for the given data flavor.
getTransferData(DataFlavor) - Method in class jigcell.compare.views.SeriesView.SeriesViewTransferer
 
getTransferDataFlavors() - Method in class jigcell.compare.impl.Transferer
The data flavors this transferable supports.
getTransferFlavor(List, Transferable) - Static method in class jigcell.compare.impl.Transferer
The type that will be returned from a transfer operation or null if the transfer will fail.
getTransformCursor() - Method in class jigcell.compare.views.TransformDebugger
The current transform cursor.
getTransformForGenerator(int) - Method in class jigcell.compare.cellcycle.CellCycleTransformView
The transform of a generator.
getTransformForGenerator(IDataGenerator) - Static method in class jigcell.compare.transform.Transform
The transform of a generator.
getTransformName() - Method in class jigcell.compare.transform.TransformEvaluationTransform
The name of the transform to execute.
getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class jigcell.compare.views.TransformDebugger.TransformTreeRenderer
 
getType() - Method in class jigcell.compare.data.CachedDataElement
The type of this element.
getType(long) - Method in class jigcell.compare.data.CachedDataElement
The type of the element at position pos. If the given position has no valid meaning for this object, the type is TYPE_NONE.
getType() - Method in class jigcell.compare.data.DataElement
The type of this element.
getType(long) - Method in class jigcell.compare.data.DataElement
The type of the element at position pos.
getType() - Method in class jigcell.compare.data.EditableDataElement
The type of this element.
getType(long) - Method in class jigcell.compare.data.EditableDataElement
The type of the element at position pos. If the given position has no valid meaning for this object, the type is TYPE_NONE.
getType() - Method in class jigcell.compare.data.FlippedDataElement
The type of this element.
getType(long) - Method in class jigcell.compare.data.FlippedDataElement
The type of the element at position pos.
getType() - Method in class jigcell.compare.data.type.BooleanTypeChecker
The structural type this checker matches.
getType() - Method in class jigcell.compare.data.type.IntegerTypeChecker
The structural type this checker matches.
getType() - Method in class jigcell.compare.data.type.ListTypeChecker
The structural type this checker matches.
getType() - Method in class jigcell.compare.data.type.RealTypeChecker
The structural type this checker matches.
getType() - Method in class jigcell.compare.data.type.StringTypeChecker
The structural type this checker matches.
getType() - Method in class jigcell.compare.data.type.TypeChecker
The structural type this checker matches.
getType() - Method in interface jigcell.compare.IDataElement
The type of this element.
getType(long) - Method in interface jigcell.compare.IDataElement
The type of the element at position pos.
getType() - Method in interface jigcell.compare.ITypeChecker
The structural type this checker matches.
getTypeChecker(long) - Method in class jigcell.compare.cellcycle.BuddingYeastNocPhenotype
A type checker for the element at this position. Implementations that do not want to provide a type checker should return null.
getTypeChecker(long) - Method in class jigcell.compare.cellcycle.BuddingYeastPhenotype
A type checker for the element at this position. Implementations that do not want to provide a type checker should return null.
getTypeChecker(long) - Method in class jigcell.compare.cellcycle.BuddingYeastWildtypeProperties
A type checker for the element at this position. Implementations that do not want to provide a type checker should return null.
getTypeChecker(long) - Method in class jigcell.compare.cellcycle.GenericPhenotype
A type checker for the element at this position. Implementations that do not want to provide a type checker should return null.
getTypeChecker(long) - Method in class jigcell.compare.contrib.StructuredTypeCheckerTemplate
A type checker for the element at this position. Implementations that do not want to provide a type checker should return null.
getTypeChecker(long) - Method in class jigcell.compare.data.type.StructuredTypeChecker
A type checker for the element at this position.
getTypeChecker(long) - Method in class jigcell.compare.data.type.TimeSeriesTypeChecker
A type checker for the element at this position. Implementations that do not want to provide a type checker should return null.
getTypeChecker(long) - Method in interface jigcell.compare.IStructuredTypeChecker
A type checker for the element at this position.
getTypeCheckerForGenerator(IDataGenerator) - Static method in class jigcell.compare.data.type.TypeChecker
The type checker of a generator.
getTypes() - Static method in class jigcell.compare.views.ObjectiveSeriesView.Comparison
List of possible types.
getUnderlyingClass(Class) - Static method in class jigcell.compare.data.MethodDispatcher
The non-array formalType of a formalType.
getValue(String) - Method in class jigcell.compare.impl.Config
The value for a particular key from this configurator.
getValue() - Method in class jigcell.compare.transform.ConstantTransform
The value this transform will generate.
getValue() - Method in class jigcell.compare.ui.EditorDialog
The value being edited.
getValue() - Method in class jigcell.compare.ui.SeriesEditorDialog
The value being edited.
getValueAt(int, int) - Method in class jigcell.compare.cellcycle.CellCycleDataDialog.DataModel
A value in the current table.
getValueAt(int, int) - Method in class jigcell.compare.cellcycle.CellCycleExperimentView.ExperimentModel
A value in the table.
getValueAt(int, int) - Method in class jigcell.compare.cellcycle.CellCycleObjectiveView.ObjectiveModel
A value in the table.
getValueAt(int, int) - Method in class jigcell.compare.cellcycle.CellCycleTransformView.TransformModel
A value in the table.
getValueAt(int, int) - Method in class jigcell.compare.compare2.Compare2Model
A value in the table.
getValueAt(int, int) - Method in class jigcell.compare.objectiveui.ElementWeightEditorDialog.ElementWeightModel
A value in the current table.
getValueAt(int, int) - Method in class jigcell.compare.ui.BasicTable.BasicTableModel
getValueAt(int, int) - Method in class jigcell.compare.ui.SeriesDialog.SeriesModel
getValueAt(int, int) - Method in class jigcell.compare.views.EvaluationErrorViewer.ErrorModel
A value in the current table.
getValueAt(int, int) - Method in class jigcell.compare.views.ObjectiveSeriesView.ObjectiveSeriesModel
A value in the table.
getValueAt(int, int) - Method in class jigcell.compare.views.SeriesView.SeriesModel
A value in the table.
getValueAt(int, int) - Method in class jigcell.compare.views.TransformDebugger.AnnotationModel
A value in the table.
getValueAt(int, int) - Method in class jigcell.compare.views.TransformDebugger.ValueModel
A value in the table.
getValues() - Method in class jigcell.compare.data.PackedDoubleDataElement
The underlying array of this element.
getValues() - Method in class jigcell.compare.data.TreeDataElement
A sorted map of the values in this element.
getValues() - Method in class jigcell.compare.impl.Config
The mapping between keys and values.
getViewRange() - Method in class jigcell.compare.cellcycle.CellCycleReportGenerator
The view range option.
getViewRange() - Method in interface jigcell.compare.plotter.IPlotter
The view range option.
getViewRange() - Method in class jigcell.compare.plotter.Plotter
The view range option.
getWeightArrestStage() - Method in class jigcell.compare.cellcycle.GenericPhenotypeObjective
Penalty weight for arrest stage.
getWeightArrestType() - Method in class jigcell.compare.cellcycle.GenericPhenotypeObjective
Penalty weight for arrest type.
getWeightCycleCount() - Method in class jigcell.compare.cellcycle.GenericPhenotypeObjective
Penalty weight for cycle count.
getWeightDivisionMass() - Method in class jigcell.compare.cellcycle.GenericPhenotypeObjective
Penalty weight for division mass.
getWeightG1Length() - Method in class jigcell.compare.cellcycle.GenericPhenotypeObjective
Penalty weight for time in G1.
getWeightSubcycleCount() - Method in class jigcell.compare.cellcycle.GenericPhenotypeObjective
Penalty weight for subcycle count.
getWeightViability() - Method in class jigcell.compare.cellcycle.GenericPhenotypeObjective
Penalty weight for viability.
getWildtypeMass() - Method in class jigcell.compare.cellcycle.GenericScanTransform
The mass at division for the wildtype cell.
getWildtypeTime() - Method in class jigcell.compare.cellcycle.GenericScanTransform
The cycle time for the wildtype cell.
getWildtypeTransformName() - Method in class jigcell.compare.cellcycle.GenericScanTransform
The name of the transform to evaluate for the wildtype properties.
getWriteDescriptionOption() - Method in class jigcell.compare.impl.DataSource
The write description option.
getWriteDescriptionOption() - Method in interface jigcell.compare.IWriteableDataSource
The write description option.
getWriteIconOption() - Method in class jigcell.compare.impl.DataSource
The write description icon.
getWriteIconOption() - Method in interface jigcell.compare.IWriteableDataSource
The write description icon.
global - Variable in class jigcell.compare.ui.MenuBuilder.Builder
Global handler
global - Variable in class jigcell.compare.ui.MenuBuilder
Global handler
GREATERTHAN - Static variable in class jigcell.compare.views.ObjectiveSeriesView.Comparison
Accept values greater than the threshold
GREATERTHANEQUAL - Static variable in class jigcell.compare.views.ObjectiveSeriesView.Comparison
Accept values greater than or equal to the threshold
groups - Variable in class jigcell.compare.compare2.ThresholdRelativeViewColorer
Number of groups to divide into

H

handler - Variable in class jigcell.compare.ui.MenuBuilder.Builder.Item
Handler for the item
handlers - Variable in class jigcell.compare.ui.MenuBuilder.ScriptActionTrampoline
Item handlers
hasException() - Method in class jigcell.compare.impl.ExceptionRecorder
Whether this handler has caught an exception.
hashCode() - Method in class jigcell.compare.data.IDataGeneratorCollection.Key
 
hashCode() - Method in class jigcell.compare.ui.BasicTable.BasicTableModel.Marker
 
hasMultipleViewSupport() - Method in class jigcell.compare.data.ProgrammableDataGenerator.DummyCustomizableInterface
Whether this interface supports multiple, simultaneous views.
hasMultipleViewSupport() - Method in interface jigcell.compare.ICustomizableInterface
Whether this interface supports multiple, simultaneous views.
hasMultipleViewSupport() - Method in class jigcell.compare.transformui.TransformContainerInterface
Whether this interface supports multiple, simultaneous views.
hasMultipleViewSupport() - Method in class jigcell.compare.transformui.TransformInterface
Whether this interface supports multiple, simultaneous views.
hasMultipleViewSupport() - Method in class jigcell.compare.ui.CustomizableInterface
Whether this interface supports multiple, simultaneous views.
hasNext() - Method in class jigcell.compare.impl.StreamingStringTokenizer
Whether there is another token to read.
hasNextStatement() - Method in interface jigcell.compare.transform.ITransform
Whether this transform has a next statement.
hasNextStatement() - Method in class jigcell.compare.transform.Transform
Whether this transform has a next statement.
hasPreviousStatement() - Method in interface jigcell.compare.transform.ITransform
Whether this transform has a previous statement.
hasPreviousStatement() - Method in class jigcell.compare.transform.Transform
Whether this transform has a previous statement.
haveDelimiter - Variable in class jigcell.compare.impl.StreamingStringTokenizer
Whether the next token is a delimiter
hierarchyChanged(HierarchyEvent) - Method in class jigcell.compare.views.TransformDebugger
 
host - Variable in class jigcell.compare.ui.BasicTable.BasicEditor
Host view of this table
host - Variable in class jigcell.compare.ui.BasicTable.BasicRenderer
Host view of this table
HTML_FOOTER - Static variable in class jigcell.compare.impl.Transferer
Footer for HTML data
HTML_HEADPOSTPEND - Static variable in class jigcell.compare.impl.Transferer
Header postpender for HTML data
HTML_HEADPREPEND - Static variable in class jigcell.compare.impl.Transferer
Header for HTML data
HTML_HEADSEPARATOR - Static variable in class jigcell.compare.impl.Transferer
Header separator for HTML data
HTML_LINEPOSTPEND - Static variable in class jigcell.compare.impl.Transferer
Line postpender for HTML data
HTML_LINEPREPEND - Static variable in class jigcell.compare.impl.Transferer
Line prepender for HTML data
HTML_LINESEPARATOR - Static variable in class jigcell.compare.impl.Transferer
Item separator for HTML data
HTMLComponentDescription - Class in jigcell.compare.ui
Description for one of the Comparator components.
HTMLComponentDescription(String, int) - Constructor for class jigcell.compare.ui.HTMLComponentDescription
Creates a new component description.
HTMLComponentDescription(URL, int) - Constructor for class jigcell.compare.ui.HTMLComponentDescription
Creates a new component description.

I

IBasicTableHost - Interface in jigcell.compare.ui
Provides information about the view that is hosting a BasicTable.
ICellEditorTab - Interface in jigcell.compare.ui
Represents a Comparator tab that has promised functionality for manipulating individual cells of tabular data.
IClipboardTab - Interface in jigcell.compare.ui
Represents a Comparator tab that has promised functionality for using a clipboard with tabular data.
IColumnEditorTab - Interface in jigcell.compare.ui
Represents a Comparator tab that has promised functionality for manipulating the columns of a table view.
IColumnSelectionTab - Interface in jigcell.compare.ui
Represents a Comparator tab that has promised functionality for manipulating the column selection of a table view.
IComponentDescription - Interface in jigcell.compare
Description for one of the Comparator components.
icon - Variable in class jigcell.compare.ui.MenuBuilder.Builder.Item
Icon for the item
ICON_BLANK - Static variable in class jigcell.compare.ui.MenuBuilder
Blank image for popup and menu entries without icons
IConfigEditor - Interface in jigcell.compare
A component that supports the editing of configuration options.
IconLoader - Class in jigcell.compare.ui
Loads a collection of icon resources.
IconLoader(Class) - Constructor for class jigcell.compare.ui.IconLoader
Creates a new icon loader.
ICustomizableInterface - Interface in jigcell.compare
Provides an interface for a ICustomizableDataGenerator.
id - Variable in class jigcell.compare.data.IDataGeneratorCollection.Key
Key id
IDataEditorTab - Interface in jigcell.compare.ui
Represents a Comparator tab that has promised functionality for manipulating a collection of data.
IDataElement - Interface in jigcell.compare
This interface is implemented by classes that wish to provide a data element to the comparator.
IDataElement.Type - Class in jigcell.compare
The types of a data element.
IDataElement.Type(String) - Constructor for class jigcell.compare.IDataElement.Type
Creates a new data element type.
IDataGenerator - Interface in jigcell.compare
This interface is implemented by classes that wish to provide data to the comparator.
IDataGeneratorCollection - Interface in jigcell.compare.data
Manages a collection of data generators.
IDataGeneratorCollection.Key - Class in jigcell.compare.data
Key elements for a generator collections.
IDataGeneratorCollection.Key() - Constructor for class jigcell.compare.data.IDataGeneratorCollection.Key
Creates a new key element.
IDataGeneratorCollection.Key(String, String) - Constructor for class jigcell.compare.data.IDataGeneratorCollection.Key
Creates a new key element.
IDataGeneratorList - Interface in jigcell.compare.data
Manages a list of data generators.
IDataGeneratorMap - Interface in jigcell.compare.data
Manages a map of data generators.
IDataSource - Interface in jigcell.compare
A generic transfer agent for a source of data.
IDataSource.Option - Class in jigcell.compare
An enumeration of possible persistence types for an option.
IDataSource.Option() - Constructor for class jigcell.compare.IDataSource.Option
Not allowed
IDataSource.Option(String) - Constructor for class jigcell.compare.IDataSource.Option
Create a new type of option.
identifier - Variable in class jigcell.compare.ui.BasicTable.BasicTableModel.Marker
Unique identifier for this column.
IDimensionWeightObjective - Interface in jigcell.compare.objective
A data generator supporting the concept of editable dimension weights.
idToGenerator - Variable in class jigcell.compare.data.DataGeneratorList
Map[String,IDataGenerator] from generator id keys to generators
IEditableDataElement - Interface in jigcell.compare
This interface is implemented by classes that wish to provide a data element to the Comparator with additional editing capabilities.
IEditableDataGenerator - Interface in jigcell.compare
This interface is implemented by classes that wish to store data for the comparator.
IElementWeightObjective - Interface in jigcell.compare.objective
A data generator supporting the concept of editable element weights.
IEvaluationCallStack - Interface in jigcell.compare
The call stack for an IProgrammableDataGenerator evaluation.
IEvaluationListener - Interface in jigcell.compare
A listener for data generator evaluation events.
IGNORE - Static variable in class jigcell.compare.views.ObjectiveSeriesView.Comparison
Ignore the value of this comparison
IGNORE - Static variable in class jigcell.compare.views.TransformDebugger
Ignore the setting of the indicated control
IInterpolationObjective - Interface in jigcell.compare.objective
A data generator supporting the concept of data interpolation.
ImmediateHistoryRelativeViewColorer - Class in jigcell.compare.compare2
A table renderer that can color the view of a Compare^2.
ImmediateHistoryRelativeViewColorer(Compare2) - Constructor for class jigcell.compare.compare2.ImmediateHistoryRelativeViewColorer
Creates a new view colorer that colors by performance relative to the immediate history.
importConfig(Config) - Method in class jigcell.compare.impl.Config
Copies the configuration information from another configurator.
importNamesFromRunFile() - Method in class jigcell.compare.cellcycle.CellCycleExperimentView
Prompts the user for a run file on their disk and then creates new experiments for each run in the run file.
importNamesFromRunFile(RunFile) - Method in class jigcell.compare.cellcycle.CellCycleExperimentView
Creates new experiments for each run in the run file.
IMultipleDataSource - Interface in jigcell.compare
A generic transfer agent that supports multiple objects.
INameFinderTab - Interface in jigcell.compare.ui
Represents a Comparator tab that has promised functionality for finding by name.
index(IDataGenerator) - Method in class jigcell.compare.data.DataGeneratorList
Adds a generator to the index.
index - Variable in class jigcell.compare.data.FlippedDataElement
Index within the flip to access
indexCommand(AbstractButton) - Method in class jigcell.compare.ui.MenuBuilder
Indexes the command from a button.
indexCommands(AbstractButton[]) - Method in class jigcell.compare.ui.MenuBuilder
Indexes the commands from a set of buttons.
indexCommands(MenuElement[]) - Method in class jigcell.compare.ui.MenuBuilder
Indexes the commands from a set of menu elements.
indexed - Variable in class jigcell.compare.data.DataGeneratorList
Whether indexing is currently being used
indexExperiments() - Method in class jigcell.compare.compare2.Compare2
Indexes the known comparisons to produce a list of experiment names used.
indexExperiments() - Method in class jigcell.compare.compare2.ThresholdEditor
Creates a list of the known experiments.
indexNames(IDataGeneratorList, List) - Method in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Creates a sorted index of names from a list of generators.
indexOf(IDataGenerator) - Method in class jigcell.compare.data.DataGeneratorList
The position of a generator in the list.
indexOf(IDataGenerator) - Method in interface jigcell.compare.data.IDataGeneratorList
The position of a generator in the list.
initialHeight - Variable in class jigcell.compare.ui.ViewerDialog
Initial height of dialog in pixels
initialize() - Method in class jigcell.compare.cellcycle.OAAConnector
Performs any initialization work for the view.
initialize() - Method in class jigcell.compare.compare2.Compare2
Performs any initialization work for the view.
initialize(Class, Object, Object, Encoder) - Method in class jigcell.compare.data.DataGeneratorList.DataGeneratorListDelegate
 
initialize(Class, Object, Object, Encoder) - Method in class jigcell.compare.data.DataGeneratorMap.DataGeneratorMapDelegate
 
initialize(Class, Object, Object, Encoder) - Method in class jigcell.compare.data.EditableDataElement.EditableDataElementDelegate
 
initialize(Class, Object, Object, Encoder) - Method in class jigcell.compare.data.EditableDataGenerator.EditableDataGeneratorDelegate
 
initialize(Class, Object, Object, Encoder) - Method in class jigcell.compare.data.ResultSetGroupMap.ResultSetGroupMapDelegate
 
initialize(Class, Object, Object, Encoder) - Method in class jigcell.compare.data.ResultSetMap.ResultSetMapDelegate
 
initialize(Class, Object, Object, Encoder) - Method in class jigcell.compare.impl.Config.ConfigDelegate
 
initialize() - Method in class jigcell.compare.ui.DataEditorPanelTab
Performs any initialization work for the view.
initialize() - Method in class jigcell.compare.ui.PanelTab
Performs any initialization work for the view.
initialize() - Method in class jigcell.compare.ui.SeriesDialog
Performs initialization work for the view.
initialize() - Method in class jigcell.compare.views.Console
Performs any initialization work for the view.
initialize() - Method in class jigcell.compare.views.EditableSeriesView
Performs any initialization work for the view.
initialize() - Method in class jigcell.compare.views.ObjectiveEditor
Performs any initialization work for the view.
initialize() - Method in class jigcell.compare.views.ObjectiveSeriesView
Performs any initialization work for the view.
initialize() - Method in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Performs any initialization work for the view.
initialize() - Method in class jigcell.compare.views.SeriesView
Performs any initialization work for the view.
initialize() - Method in class jigcell.compare.views.TransformDebugger
Performs any initialization work for the view.
initialize() - Method in class jigcell.compare.views.TransformEditor
Performs any initialization work for the view.
initializeData() - Method in class jigcell.compare.cellcycle.CellCycleTransformView
Initializes data for the view.
initializeData() - Method in class jigcell.compare.views.ObjectiveSeriesView
Initializes data for the view.
initializeData() - Method in class jigcell.compare.views.SeriesView
Initializes data for the view.
initializeSimulators(Config) - Static method in class jigcell.compare.cellcycle.JigCellRunManagerTransform
Registers any simulators identified by the configuration.
initializeSource() - Method in class jigcell.compare.data.DataGenerator
Performs any initialization work for the view that must be duplicated for each new instance.
initializeSource() - Method in class jigcell.compare.data.ProgrammableDataGenerator
Performs any initialization work for the view that must be duplicated for each new instance. This method is called exactly once and only during object construction.
initializeSource() - Method in class jigcell.compare.impl.ClipboardDataSource
Performs any initialization work for the view that must be duplicated for each new instance.
initializeSource() - Method in class jigcell.compare.impl.DataSource
Performs any initialization work for the view that must be duplicated for each new instance.
initializeSource() - Method in class jigcell.compare.impl.PDFPrinterDataSource
Performs any initialization work for the view that must be duplicated for each new instance.
initializeSource() - Method in class jigcell.compare.impl.RawFileDataSource
Performs any initialization work for the view that must be duplicated for each new instance.
initializeSource() - Method in class jigcell.compare.impl.XMLFileDataSource
Performs any initialization work for the view that must be duplicated for each new instance. This method is called exactly once and only during object construction.
initializeSource() - Method in class jigcell.compare.transform.Transform
Performs any initialization work for the view that must be duplicated for each new instance. This method is called exactly once and only during object construction.
initializeSource() - Method in class jigcell.compare.transform.TransformContainer
Performs any initialization work for the view that must be duplicated for each new instance. This method is called exactly once and only during object construction.
initialWidth - Variable in class jigcell.compare.ui.ViewerDialog
Initial width of dialog in pixels
input - Variable in class jigcell.compare.views.Console
Text box for command input
inputChannel - Variable in class jigcell.compare.views.Console
Channel for sending console input to the evaluator
InputInterface - Class in jigcell.compare.transformui
Interface for an InputTransform.
InputInterface(IProgrammableDataGenerator) - Constructor for class jigcell.compare.transformui.InputInterface
Creates a new interface for an InputTransform.
InputTransform - Class in jigcell.compare.transform
Allows selection of a transform to create a transform chain.
InputTransform() - Constructor for class jigcell.compare.transform.InputTransform
 
insertColumn(int) - Method in class jigcell.compare.compare2.Compare2
Inserts a column at a specified location.
insertColumn(int) - Method in interface jigcell.compare.ui.IColumnEditorTab
Inserts a column at a specified location.
insertColumns(int, int) - Method in class jigcell.compare.compare2.Compare2
Inserts a number of new columns at a specified location.
insertColumns(int, int) - Method in interface jigcell.compare.ui.IColumnEditorTab
Inserts a number of new columns at a specified location.
insertElementAt(Object, int) - Method in class jigcell.compare.ui.ListComboBoxModel
 
insertRow(int) - Method in class jigcell.compare.cellcycle.CellCycleTransformView
Inserts a row at a specified location.
insertRow(int) - Method in class jigcell.compare.compare2.Compare2
Inserts a row at a specified location.
insertRow(int) - Method in interface jigcell.compare.ui.IRowEditorTab
Inserts a row at a specified location.
insertRow(int) - Method in class jigcell.compare.ui.SeriesEditorDialog
Inserts a row at a specified location.
insertRow(int) - Method in class jigcell.compare.views.EditableSeriesView
Inserts a row at a specified location.
insertRow(int) - Method in class jigcell.compare.views.ObjectiveSeriesView
Inserts a row at a specified location.
insertRows(int, int) - Method in class jigcell.compare.cellcycle.CellCycleTransformView
Inserts a number of new rows at a specified location.
insertRows(int, int) - Method in class jigcell.compare.compare2.Compare2
Inserts a number of new rows at a specified location.
insertRows(int, int) - Method in interface jigcell.compare.ui.IRowEditorTab
Inserts a number of new rows at a specified location.
insertRows(int, int) - Method in class jigcell.compare.ui.SeriesEditorDialog
Inserts a number of new rows at a specified location.
insertRows(int, int) - Method in class jigcell.compare.views.EditableSeriesView
Inserts a number of new rows at a specified location.
insertRows(int, int) - Method in class jigcell.compare.views.ObjectiveSeriesView
Inserts a number of new rows at a specified location.
insertUpdate(DocumentEvent) - Method in class jigcell.compare.objectiveui.ScriptEvaluationInterface
 
insertUpdate(DocumentEvent) - Method in class jigcell.compare.transformui.ScriptEvaluationInterface
 
insertUpdate(DocumentEvent) - Method in class jigcell.compare.ui.ConfigEditor
 
install(CompareFrontEnd, ITab) - Method in class jigcell.compare.ui.FindAccessory
Notifies the accessory that it has been inserted into a Comparator interface for a particular tab.
install(CompareFrontEnd, ITab) - Method in interface jigcell.compare.ui.ITabAccessory
Notifies the accessory that it has been inserted into a Comparator interface for a particular tab.
install(CompareFrontEnd, ITab) - Method in class jigcell.compare.ui.MemoryMonitorAccessory
Notifies the accessory that it has been inserted into a Comparator interface for a particular tab.
installLookAndFeel(String, String) - Static method in class jigcell.compare.ui.CompareFrontEnd
Installs a new look and feel if it has not already been registered.
instance - Variable in class jigcell.compare.impl.ProxyBuilder
Instance that implements the interface methods
instance - Static variable in class jigcell.compare.transform.annotation.ColumnCountAnnotationDescriptor
Instance of this annotation
instance - Static variable in class jigcell.compare.transform.annotation.ColumnNameAnnotationDescriptor
Instance of this annotation
instance - Static variable in class jigcell.compare.transform.annotation.CommentAnnotationDescriptor
Instance of this annotation
instance - Static variable in class jigcell.compare.transform.annotation.ElementNameAnnotationDescriptor
Instance of this annotation
instance - Static variable in class jigcell.compare.transform.annotation.ElementSizeAnnotationDescriptor
Instance of this annotation
instance - Static variable in class jigcell.compare.transform.annotation.ElementTypeAnnotationDescriptor
Instance of this annotation
instance - Static variable in class jigcell.compare.transform.annotation.TransformAnnotation.AnnotationDescriptor
Instance of this annotation
instantiate(Object, Encoder) - Method in class jigcell.compare.data.CachedDataElement.CachedDataElementDelegate
 
instantiate(Object, Encoder) - Method in class jigcell.compare.data.DataGeneratorList.DataGeneratorListDelegate
 
instantiate(Object, Encoder) - Method in class jigcell.compare.data.DataGeneratorMap.DataGeneratorMapDelegate
 
instantiate(Object, Encoder) - Method in class jigcell.compare.data.ResultSetGroupMap.ResultSetGroupMapDelegate
 
instantiate(Object, Encoder) - Method in class jigcell.compare.data.ResultSetMap.ResultSetMapDelegate
 
instantiate(Object, Encoder) - Method in class jigcell.compare.objective.MetricObjective.MetricObjectiveDelegate
 
instantiate(Object, Encoder) - Method in class jigcell.compare.objective.MinkowskiObjective.MinkowskiObjectiveDelegate
 
instantiate(Object, Encoder) - Method in class jigcell.compare.views.ObjectiveSeriesView.Comparison.ComparisonDelegate
 
IntegerTypeChecker - Class in jigcell.compare.data.type
Type for integer data.
IntegerTypeChecker() - Constructor for class jigcell.compare.data.type.IntegerTypeChecker
Creates a new type checker.
INTEGRAL - Static variable in class jigcell.compare.IDataElement.Type
A scalar value contained in the integers
InterfaceBuilder - Class in jigcell.compare.ui
Generates and manages interfaces for another component.
InterfaceBuilder(Object) - Constructor for class jigcell.compare.ui.InterfaceBuilder
Creates a new managed interface.
InterfaceBuilder(Object, Component) - Constructor for class jigcell.compare.ui.InterfaceBuilder
Creates a new managed interface.
INTERPOLATION_LINEAR - Static variable in class jigcell.compare.objective.WOSSObjective
Linear interpolation
INTERPOLATION_NONE - Static variable in interface jigcell.compare.objective.IInterpolationObjective
Default interpolation of none
interpolationsModel - Variable in class jigcell.compare.objectiveui.WOSSInterface
Interpolations box model
interruptDebug() - Method in class jigcell.compare.views.TransformDebugger.DebuggerThread
Attempts to interrupt the debug delay only.
invoke(Object, Method, Object[]) - Method in class jigcell.compare.impl.ProxyBuilder
 
IObjective - Interface in jigcell.compare.objective
A DataGenerator that takes a functional expression and a collection of data to produce an element.
IPersistableDataSource - Interface in jigcell.compare
A source of data that has persistent storage and a uniquely identifiable address.
IPlotter - Interface in jigcell.compare.plotter
This interface is implemented by classes that wish to provide plotting services to some other program.
IPlotter.Combine - Class in jigcell.compare.plotter
The types of series combine options.
IPlotter.Combine(String) - Constructor for class jigcell.compare.plotter.IPlotter.Combine
Creates a new combine option.
IProgrammableDataGenerator - Interface in jigcell.compare
A data generator that can derive its value from some programmatic evaluation.
IReadableDataSource - Interface in jigcell.compare
A generic transfer agent for a source of data that supports reading.
IRelationalObjective - Interface in jigcell.compare.objective
A data generator supporting the concept of relational comparisons.
IResultantTransform - Interface in jigcell.compare.transform
Indicates that this transform represents a result of potential interest.
IResultSetGroupMap - Interface in jigcell.compare.data
Manages a map of result sets.
IResultSetMap - Interface in jigcell.compare.data
Manages a map of results.
IResultTab - Interface in jigcell.compare.ui
Represents a Comparator tab that has promised functionality for evaluating results.
IRowEditorTab - Interface in jigcell.compare.ui
Represents a Comparator tab that has promised functionality for manipulating the rows of a table view.
IRowSelectionTab - Interface in jigcell.compare.ui
Represents a Comparator tab that has promised functionality for manipulating the row selection of a table view.
isAvailable() - Method in class jigcell.compare.data.CachedDataElement
Whether the element data can currently be worked with. Editing the internal state of a data generator while locked may cause subsequent calls to isAvailable to incorrectly report that the element data is available.
isAvailable() - Method in class jigcell.compare.data.DataElement
Whether the element data can currently be worked with.
isAvailable() - Method in class jigcell.compare.data.FlippedDataElement
Whether the element data can currently be worked with.
isAvailable() - Method in class jigcell.compare.data.PackedDoubleDataElement
Whether the element data can currently be worked with. Editing the internal state of a data generator while locked may cause subsequent calls to isAvailable to incorrectly report that the element data is available. The array store of this element is always available.
isAvailable() - Method in class jigcell.compare.data.TreeDataElement
Whether the element data can currently be worked with. Editing the internal state of a data generator while locked may cause subsequent calls to isAvailable to incorrectly report that the element data is available.
isAvailable() - Method in interface jigcell.compare.IDataElement
Whether the element data can currently be worked with.
isCached() - Method in class jigcell.compare.data.EditableDataGenerator
Whether a cached value of the corresponding DataElement exists.
isCached() - Method in class jigcell.compare.data.ProgrammableDataGenerator
Whether a cached value of the corresponding DataElement exists.
isCached() - Method in interface jigcell.compare.IDataGenerator
Whether a cached value of the corresponding DataElement exists.
isCancelled() - Method in class jigcell.compare.ui.ProgressMonitor
Whether the progress dialog was cancelled.
isCellEditable(int, int) - Method in class jigcell.compare.cellcycle.CellCycleTransformView.TransformModel
Whether a value in the table is editable.
isCellEditable(int, int) - Method in class jigcell.compare.compare2.Compare2Model
Whether a value in the table is editable.
isCellEditable(int, int) - Method in class jigcell.compare.ui.SeriesEditorDialog.SeriesEditorModel
Whether a value in the current table is editable.
isCellEditable(int, int) - Method in class jigcell.compare.views.EditableSeriesView.EditableSeriesModel
Whether a value in the table is editable.
isCellEditable(int, int) - Method in class jigcell.compare.views.EvaluationErrorViewer.ErrorModel
 
isCellEditable(int, int) - Method in class jigcell.compare.views.ObjectiveSeriesView.ObjectiveSeriesModel
Whether a value in the table is editable.
isCompatible(ITypeChecker) - Method in class jigcell.compare.cellcycle.BuddingYeastNocPhenotype
Whether a data type can be converted to this type.
isCompatible(ITypeChecker) - Method in class jigcell.compare.cellcycle.BuddingYeastPhenotype
Whether a data type can be converted to this type.
isCompatible(ITypeChecker) - Method in class jigcell.compare.cellcycle.BuddingYeastWildtypeProperties
Whether a data type can be converted to this type.
isCompatible(ITypeChecker) - Method in class jigcell.compare.cellcycle.GenericPhenotype
Whether a data type can be converted to this type.
isCompatible(ITypeChecker) - Method in class jigcell.compare.contrib.StructuredTypeCheckerTemplate
Whether a data type can be converted to this type.
isCompatible(ITypeChecker) - Method in class jigcell.compare.contrib.TypeCheckerTemplate
Whether a data type can be converted to this type.
isCompatible(ITypeChecker) - Method in class jigcell.compare.data.type.TimeSeriesTypeChecker
Whether a data type can be converted to this type.
isCompatible(ITypeChecker, ITypeChecker) - Static method in class jigcell.compare.data.type.TypeChecker
Tests that two type checkers are compatible.
isCompatible(ITypeChecker) - Method in class jigcell.compare.data.type.TypeChecker
Whether a data type can be converted to this type.
isCompatible(ITypeChecker) - Method in interface jigcell.compare.ITypeChecker
Whether a data type can be converted to this type.
isConvertibleClass(Class) - Static method in class jigcell.compare.data.MethodDispatcher
Whether a class is of a convertible formalType.
isCopy() - Method in class jigcell.compare.data.DataGenerator
Whether this generator is a copy of another.
isCopy() - Method in interface jigcell.compare.IDataGenerator
Whether this generator is a copy of another.
isCopyRelated(IDataGenerator) - Method in class jigcell.compare.data.DataGenerator
Whether this generator was copied from or to another.
isCopyRelated(IDataGenerator) - Method in interface jigcell.compare.IDataGenerator
Whether this generator was copied from or to another.
isDataColumn(int) - Method in class jigcell.compare.compare2.Compare2Model
Whether a particular column contains a result set or a special value.
isDataFlavorSupported(DataFlavor) - Method in class jigcell.compare.impl.Transferer
Whether this transferable supports a particular data flavor.
isEmpty() - Method in class jigcell.compare.data.DataGeneratorList
Whether this list is empty.
isEmpty() - Method in interface jigcell.compare.data.IDataGeneratorList
Whether this list is empty.
isEsp1Checked() - Method in class jigcell.compare.cellcycle.BuddingYeastScanTransform
Whether Esp1 is checked during the cell cycle.
isFlavorHTMLTextType() - Method in class jigcell.compare.impl.ComparatorDataFlavor
Whether this flavor represents an HTML text representation.
isFlavorLocalObjectType() - Method in class jigcell.compare.impl.ComparatorDataFlavor
Whether this flavor represents a local object representation.
isFlavorPlainTextType() - Method in class jigcell.compare.impl.ComparatorDataFlavor
Whether this flavor represents a plain text representation.
isFlavorXMLSerializedObjectType() - Method in class jigcell.compare.impl.ComparatorDataFlavor
Whether this flavor represents an XML serialized object representation.
isImmutable() - Method in interface jigcell.compare.plotter.IPlotter
Whether the data aggregate is immutable.
isImmutable() - Method in class jigcell.compare.plotter.Plotter
Whether the data aggregate is immutable.
isReorderable() - Method in class jigcell.compare.cellcycle.JigCellRunManagerTransform
Whether the evaluation of this transform has no indirect dependencies.
isReorderable() - Method in class jigcell.compare.transform.FileTransform
Whether the evaluation of this transform has no indirect dependencies.
isReorderable() - Method in interface jigcell.compare.transform.ITransform
Whether the evaluation of this transform has no indirect dependencies.
isReorderable() - Method in class jigcell.compare.transform.Transform
Whether the evaluation of this transform has no indirect dependencies.
isReorderable() - Method in class jigcell.compare.transform.TransformContainer
Whether the evaluation of this transform has no indirect dependencies.
isRunnable() - Method in class jigcell.compare.cellcycle.JigCellRunManagerTransform
Whether this transform can be executed.
isRunnable() - Method in class jigcell.compare.transform.InputTransform
Whether this transform can be executed.
isRunnable() - Method in interface jigcell.compare.transform.ITransform
Whether this transform can be executed.
isRunnable() - Method in class jigcell.compare.transform.ReadFromFileTransform
Whether this transform can be executed.
isRunnable() - Method in class jigcell.compare.transform.Transform
Whether this transform can be executed.
isRunnable() - Method in class jigcell.compare.transform.TransformContainer
Whether this transform can be executed.
isRunnable() - Method in class jigcell.compare.transform.TransformEvaluationTransform
Whether this transform can be executed.
isRunnable() - Method in class jigcell.compare.transform.WriteToFileTransform
Whether this transform can be executed.
isRunnableSet() - Method in class jigcell.compare.transform.InputTransform
Whether the runnable flag is set for this transform.
isScalar() - Method in class jigcell.compare.data.DataElement
Whether this element is scalar.
isScalar() - Method in interface jigcell.compare.IDataElement
Whether this element is scalar.
isSet() - Method in class jigcell.compare.data.EditableDataGenerator
Whether this generator has a set value.
isSpecialNonNumeric(String) - Static method in class jigcell.compare.data.DataElement
Whether a text string represents a special non-numeric value.
isSteadyState(GenericScanTransform.CellCycleReport, GenericScanTransform.CellCycleReport) - Method in class jigcell.compare.cellcycle.GenericScanTransform
Whether the system is in steady state.
IStructuredTypeChecker - Interface in jigcell.compare
A type that further describes the structure of data.
ITab - Interface in jigcell.compare
A component that can sit in the Comparator interface.
ITabAccessory - Interface in jigcell.compare.ui
Represents a Comparator tab accessory.
itemStateChanged(ItemEvent) - Method in class jigcell.compare.cellcycle.CellCycleReportGenerator
 
itemStateChanged(ItemEvent) - Method in class jigcell.compare.cellcycle.JigCellRunManagerInterface
 
itemStateChanged(ItemEvent) - Method in class jigcell.compare.compare2.ThresholdEditor
 
itemStateChanged(ItemEvent) - Method in class jigcell.compare.objectiveui.BooleanRelationalInterface
 
itemStateChanged(ItemEvent) - Method in class jigcell.compare.objectiveui.DimensionWeightEditorDialog
 
itemStateChanged(ItemEvent) - Method in class jigcell.compare.objectiveui.ElementWeightEditorDialog
 
itemStateChanged(ItemEvent) - Method in class jigcell.compare.objectiveui.WOSSInterface
 
itemStateChanged(ItemEvent) - Method in class jigcell.compare.transformui.InputInterface
 
itemStateChanged(ItemEvent) - Method in class jigcell.compare.transformui.TransformEvaluationInterface
 
itemStateChanged(ItemEvent) - Method in class jigcell.compare.ui.ConfigEditor
 
itemStateChanged(ItemEvent) - Method in class jigcell.compare.views.ObjectiveEditor
 
itemStateChanged(ItemEvent) - Method in class jigcell.compare.views.TransformEditor
 
iterator() - Method in class jigcell.compare.data.DataGeneratorList
An iterator over the generators in the list.
iterator(int) - Method in class jigcell.compare.data.DataGeneratorList
An iterator over the generators in the list starting at a particular index.
iterator() - Method in class jigcell.compare.data.DataGeneratorMap
An iterator over the entries of this map.
iterator() - Method in interface jigcell.compare.data.IDataGeneratorList
An iterator over the generators in the list.
iterator(int) - Method in interface jigcell.compare.data.IDataGeneratorList
An iterator over the generators in the list starting at a particular index.
iterator() - Method in interface jigcell.compare.data.IDataGeneratorMap
An iterator over the entries of this map.
iterator() - Method in interface jigcell.compare.data.IResultSetGroupMap
An iterator over the entries of this map.
iterator() - Method in interface jigcell.compare.data.IResultSetMap
An iterator over the entries of this map.
iterator() - Method in class jigcell.compare.data.ResultSetGroupMap
An iterator over the entries of this map.
iterator() - Method in class jigcell.compare.data.ResultSetMap
An iterator over the entries of this map.
ITransferProxy - Interface in jigcell.compare
An interface for intercepting transferer operations.
ITransform - Interface in jigcell.compare.transform
A DataGenerator that performs a part of a transform evaluation.
ITransformAnnotation - Interface in jigcell.compare.transform.annotation
A data generator annotation.
ITransformAnnotation.IAnnotationDescriptor - Interface in jigcell.compare.transform.annotation
A data generator annotation description.
ITransformContainer - Interface in jigcell.compare.transform
A transform that can manage a collection of other transforms.
ITransformContext - Interface in jigcell.compare.transform
A runtime context for evaluating transforms.
ITransformContextListener - Interface in jigcell.compare.transform
A listener for transform evaluation context membership events.
ITypeChecker - Interface in jigcell.compare
A type that describes the structure of a data element.
IViewColorer - Interface in jigcell.compare.compare2
A table renderer that can color the view of a Compare^2.
IWriteableDataSource - Interface in jigcell.compare
A generic transfer agent for a source of data that supports writing.

J

jigcell.compare - package jigcell.compare
 
jigcell.compare.cellcycle - package jigcell.compare.cellcycle
 
jigcell.compare.compare2 - package jigcell.compare.compare2
 
jigcell.compare.contrib - package jigcell.compare.contrib
 
jigcell.compare.data - package jigcell.compare.data
 
jigcell.compare.data.type - package jigcell.compare.data.type
 
jigcell.compare.impl - package jigcell.compare.impl
 
jigcell.compare.objective - package jigcell.compare.objective
 
jigcell.compare.objectiveui - package jigcell.compare.objectiveui
 
jigcell.compare.plotter - package jigcell.compare.plotter
 
jigcell.compare.tests - package jigcell.compare.tests
 
jigcell.compare.transform - package jigcell.compare.transform
 
jigcell.compare.transform.annotation - package jigcell.compare.transform.annotation
 
jigcell.compare.transformui - package jigcell.compare.transformui
 
jigcell.compare.ui - package jigcell.compare.ui
 
jigcell.compare.views - package jigcell.compare.views
 
JigCellRunManagerInterface - Class in jigcell.compare.cellcycle
Interface for a JigCellRunManagerTransform.
JigCellRunManagerInterface(IProgrammableDataGenerator) - Constructor for class jigcell.compare.cellcycle.JigCellRunManagerInterface
Creates a new interface for a JigCellRunManagerTransform.
JigCellRunManagerTransform - Class in jigcell.compare.cellcycle
Uses the JigCell Run Manager to execute a simulation.
JigCellRunManagerTransform() - Constructor for class jigcell.compare.cellcycle.JigCellRunManagerTransform
Creates a new transform that can perform a run evaluation.
JPlotBridge - Class in jigcell.compare.plotter
Standard interface for JPlot.
JPlotBridge() - Constructor for class jigcell.compare.plotter.JPlotBridge
Creates a new JPlot bridge.

K

keySet() - Method in interface jigcell.compare.data.IResultSetGroupMap
All of the keys in this map.
keySet() - Method in interface jigcell.compare.data.IResultSetMap
All of the keys in this map.
keySet() - Method in class jigcell.compare.data.ResultSetGroupMap
All of the keys in this map.
keySet() - Method in class jigcell.compare.data.ResultSetMap
All of the keys in this map.
kill() - Method in class jigcell.compare.views.TransformDebugger.DebuggerThread
Kill this thread at the next opportunity.
killed - Variable in class jigcell.compare.views.TransformDebugger.DebuggerThread
Whether this thread has been killed

L

LABEL_AVAILABLE - Static variable in class jigcell.compare.transformui.SelectColumnsInterface
Label for available columns
LABEL_BUDTHRESHOLD - Static variable in class jigcell.compare.cellcycle.BuddingYeastScanInterface
Label for start of budding threshold
LABEL_CANCEL - Static variable in class jigcell.compare.ui.InterfaceBuilder
Button label for closing a dialog without accepting choice
LABEL_CLASS - Static variable in class jigcell.compare.views.TransformDebugger
Label for current transform class display
LABEL_COLUMNS - Static variable in class jigcell.compare.transformui.SelectColumnsInterface
Label for columns field
LABEL_CYCBTHRESHOLD - Static variable in class jigcell.compare.cellcycle.GenericScanInterface
Label for G1 transition threshold
LABEL_CYCLEEXTENT - Static variable in class jigcell.compare.cellcycle.WildtypeScanInterface
Label for cycle extent
LABEL_DEFAULTRUN - Static variable in class jigcell.compare.cellcycle.JigCellRunManagerInterface
Label for automatically selected run name
LABEL_EDITDIMENSIONWEIGHTS - Static variable in class jigcell.compare.objectiveui.WOSSInterface
Label used to indicate dimension weights will be edited
LABEL_EDITELEMENTWEIGHTS - Static variable in class jigcell.compare.objectiveui.MinkowskiInterface
Label used to indicate element weights will be edited
LABEL_EDITELEMENTWEIGHTS - Static variable in class jigcell.compare.objectiveui.WOSSInterface
Label used to indicate element weights will be edited
LABEL_EDITINTERPOLATION - Static variable in class jigcell.compare.objectiveui.WOSSInterface
Interpolation name label
LABEL_EDITRELATION - Static variable in class jigcell.compare.objectiveui.BooleanRelationalInterface
Relation name label
LABEL_ERRORCLOSE - Static variable in class jigcell.compare.ui.InterfaceBuilder
Button label for closing an error dialog normally
LABEL_ERRORSHOWMORE - Static variable in class jigcell.compare.ui.InterfaceBuilder
Button label for closing an error dialog and wanting to see a stack trace
LABEL_ESP1CHECKED - Static variable in class jigcell.compare.cellcycle.BuddingYeastScanInterface
Label for whether Esp1 concentration is checked for stage transitions
LABEL_ESP1THRESHOLD - Static variable in class jigcell.compare.cellcycle.BuddingYeastScanInterface
Label for start of active state threshold
LABEL_EXPERIMENT - Static variable in class jigcell.compare.cellcycle.CellCycleReportGenerator
Label for experimental prototype selection
LABEL_EXPERIMENT - Static variable in class jigcell.compare.compare2.ThresholdEditor
Label for the experiment name
LABEL_EXPLICITRANGE - Static variable in class jigcell.compare.cellcycle.CellCycleReportGenerator
Label for the explicit range selection option
LABEL_EXPLICITSELECTION - Static variable in class jigcell.compare.cellcycle.CellCycleReportGenerator
Label for the explicit column selection option
LABEL_FILENAME - Static variable in class jigcell.compare.transformui.FileInterface
Label for file name
LABEL_HIDE - Static variable in class jigcell.compare.ui.FindAccessory
Label for the hide button
LABEL_MASSLIMITHIGH - Static variable in class jigcell.compare.cellcycle.GenericScanInterface
Label for maximum mass
LABEL_MASSLIMITLOW - Static variable in class jigcell.compare.cellcycle.GenericScanInterface
Label for maximum mass
LABEL_MAXIMUM - Static variable in class jigcell.compare.transformui.ExtremaTestInterface
Label for maximum value
LABEL_METRIC - Static variable in class jigcell.compare.views.ObjectiveEditor
Metric label
LABEL_MINIMUM - Static variable in class jigcell.compare.transformui.ExtremaTestInterface
Label for minimum value
LABEL_NAME - Static variable in class jigcell.compare.views.TransformDebugger
Label for current transform name display
LABEL_NEXT - Static variable in class jigcell.compare.ui.FindAccessory
Label for the next button
LABEL_NEXTSTATEMENT - Static variable in class jigcell.compare.transformui.InputInterface
Label for next statement
LABEL_OBJECTIVE - Static variable in class jigcell.compare.views.ObjectiveEditor
Objective name label
LABEL_ORIHIGHTHRESHOLD - Static variable in class jigcell.compare.cellcycle.BuddingYeastScanInterface
Label for start of fired state threshold
LABEL_ORILOWTHRESHOLD - Static variable in class jigcell.compare.cellcycle.BuddingYeastScanInterface
Label for start of licensed state threshold
LABEL_PREVIOUS - Static variable in class jigcell.compare.ui.FindAccessory
Label for the previous button
LABEL_RESULTNAME - Static variable in class jigcell.compare.transformui.InputInterface
Label for the result name
LABEL_RUNFILE - Static variable in class jigcell.compare.cellcycle.JigCellRunManagerInterface
Label for run file
LABEL_RUNFILEBROWSE - Static variable in class jigcell.compare.cellcycle.JigCellRunManagerInterface
Label for run file browser
LABEL_RUNNABLE - Static variable in class jigcell.compare.transformui.InputInterface
Label for runnable state
LABEL_SCALECYCLE - Static variable in class jigcell.compare.cellcycle.GenericPhenotypeInterface
Label for scale of cycle count
LABEL_SCALEG1 - Static variable in class jigcell.compare.cellcycle.GenericPhenotypeInterface
Label for scale of G1 length
LABEL_SCALEMASS - Static variable in class jigcell.compare.cellcycle.GenericPhenotypeInterface
Label for scale of division mass
LABEL_SCALESUBCYCLE - Static variable in class jigcell.compare.cellcycle.GenericPhenotypeInterface
Label for scale of subcycle count
LABEL_SELECTED - Static variable in class jigcell.compare.transformui.SelectColumnsInterface
Label for selected columns
LABEL_SPNTHRESHOLD - Static variable in class jigcell.compare.cellcycle.BuddingYeastScanInterface
Label for start of aligned state threshold
LABEL_TRANSFORM - Static variable in class jigcell.compare.cellcycle.CellCycleReportGenerator
Label for column selection transform
LABEL_TRANSFORM - Static variable in class jigcell.compare.transformui.TransformEvaluationInterface
Label to select a transform
LABEL_TRANSFORM - Static variable in class jigcell.compare.views.TransformEditor
Transform name label
LABEL_USERRUN - Static variable in class jigcell.compare.cellcycle.JigCellRunManagerInterface
Label for user selected run name
LABEL_VIEWELEMENT - Static variable in class jigcell.compare.objectiveui.WeightEditorDialog
Label for viewing the element
LABEL_WEIGHT - Static variable in class jigcell.compare.objectiveui.WeightEditorDialog
Label for the default weight
LABEL_WEIGHTCYCLE - Static variable in class jigcell.compare.cellcycle.GenericPhenotypeInterface
Label for weight of cycle count
LABEL_WEIGHTG1 - Static variable in class jigcell.compare.cellcycle.GenericPhenotypeInterface
Label for weight of G1 length
LABEL_WEIGHTMASS - Static variable in class jigcell.compare.cellcycle.GenericPhenotypeInterface
Label for weight of mass of division
LABEL_WEIGHTSTAGE - Static variable in class jigcell.compare.cellcycle.GenericPhenotypeInterface
Label for weight of arrest stage
LABEL_WEIGHTSUBCYCLE - Static variable in class jigcell.compare.cellcycle.GenericPhenotypeInterface
Label for weight of subcycle count
LABEL_WEIGHTTYPE - Static variable in class jigcell.compare.cellcycle.GenericPhenotypeInterface
Label for weight of arrest type
LABEL_WEIGHTVIABILITY - Static variable in class jigcell.compare.cellcycle.GenericPhenotypeInterface
Label for weight of viability
LABEL_WTTRANSFORM - Static variable in class jigcell.compare.cellcycle.GenericScanInterface
Label for name of wildtype transform to evaluate
LABEL_XAXIS - Static variable in class jigcell.compare.cellcycle.CellCycleReportGenerator
Label for the plotter x-axis option
LABEL_YAXIS - Static variable in class jigcell.compare.cellcycle.CellCycleReportGenerator
Label for the plotter y-axis option
LABELS_ERROR - Static variable in class jigcell.compare.ui.InterfaceBuilder
Button labels for closing an error dialog with no stack trace available
LABELS_ERROR2 - Static variable in class jigcell.compare.ui.InterfaceBuilder
Button label for closing an error dialog with stack trace available
lastInstance - Static variable in class jigcell.compare.cellcycle.CellCycleFrontEnd
Last instance of this class
lastSearchName - Variable in class jigcell.compare.views.BasicTableView
Last name searched for
lastValue() - Method in class jigcell.compare.data.PackedTreeDataElement
Finds the last defined value.
lastValue() - Method in class jigcell.compare.data.PackedTreeDataElement2
Finds the last defined value.
lastValue() - Method in class jigcell.compare.data.SparseTreeDataElement
Finds the last defined value.
lastValue() - Method in class jigcell.compare.data.SparseTreeDataElement2
Finds the last defined value.
lastValue() - Method in class jigcell.compare.data.TreeDataElement
Finds the last defined value.
layout - Variable in class jigcell.compare.transformui.TransformInterface
Layout for this transform
layout - Variable in class jigcell.compare.ui.InterfaceBuilder
Interface layout
length - Variable in class jigcell.compare.data.PackedDoubleDataElement
Element length
length - Variable in class jigcell.compare.data.TreeDataElement
Element length
lengthG1 - Variable in class jigcell.compare.cellcycle.GenericScanTransform.CellCycleReport
G1 length
LESSTHAN - Static variable in class jigcell.compare.views.ObjectiveSeriesView.Comparison
Accept values less than the threshold
LESSTHANEQUAL - Static variable in class jigcell.compare.views.ObjectiveSeriesView.Comparison
Accept values less than or equal to the threshold
LICENSEDSTAGE - Static variable in class jigcell.compare.cellcycle.BuddingYeastScanTransform.BuddingYeastScanEvent
Entry to licensed
LinkedPropertyResourceBundle - Class in jigcell.compare.impl
A property resource bundle that links back to a parent resource bundle.
LinkedPropertyResourceBundle(InputStream, ResourceBundle) - Constructor for class jigcell.compare.impl.LinkedPropertyResourceBundle
Loads a resource bundle.
list - Variable in class jigcell.compare.data.DataGeneratorList
Internal List[IDataGenerator] implementation
list - Variable in class jigcell.compare.ui.ListComboBoxModel
Items contained in this model
ListComboBoxModel - Class in jigcell.compare.ui
Combo box model that uses a list for storage.
ListComboBoxModel() - Constructor for class jigcell.compare.ui.ListComboBoxModel
Creates a new combo box model with no initial values.
ListComboBoxModel(List) - Constructor for class jigcell.compare.ui.ListComboBoxModel
Creates a new combo box model with initial values from a list.
listener - Variable in class jigcell.compare.impl.XMLFileEncoder
Handler for reporting asynchronous exceptions
listener - Variable in class jigcell.compare.transform.TransformContext
Listener for IProgrammableDataGenerator events
listenerList - Variable in class jigcell.compare.data.ProgrammableDataGenerator
Manages listeners for this generator
listenerList - Variable in class jigcell.compare.transform.TransformContext
Manages listeners for this context
ListTypeChecker - Class in jigcell.compare.data.type
Type for list data.
ListTypeChecker() - Constructor for class jigcell.compare.data.type.ListTypeChecker
Creates a new type checker.
LITERAL - Static variable in class jigcell.compare.IDataElement.Type
A scalar value that is a string literal
load(IReadableDataSource) - Method in class jigcell.compare.ui.DataEditorPanelTab
Loads the data for the view from some external source.
load(IReadableDataSource) - Method in interface jigcell.compare.ui.IDataEditorTab
Loads the data for the view from some external source.
loadDirect(IReadableDataSource) - Method in class jigcell.compare.ui.DataEditorPanelTab
Loads the data for the view from some external source without user prompting.
loadDirect(IReadableDataSource) - Method in interface jigcell.compare.ui.IDataEditorTab
Loads the data for the view from some external source without user prompting.
loader - Static variable in class jigcell.compare.impl.ProxyBuilder
The class loader that proxy classes are defined in
loadInView(IDataEditorTab, IReadableDataSource) - Method in class jigcell.compare.tests.Benchmark
Loads data in a view.
loadModel(String) - Method in class jigcell.compare.tests.ModelBuilderPlugin
Loads a model in the Model Builder.
loadRecentSource(ActionEvent) - Method in class jigcell.compare.ui.DataEditorPanelTab
Loads a recent source.
loadSet(IReadableDataSource) - Method in class jigcell.compare.compare2.Compare2
Loads the data for the view from some external source.
loadSet(IReadableDataSource) - Method in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Loads the data for the view from some external source.
loadSetDirect(IReadableDataSource, String) - Method in class jigcell.compare.compare2.Compare2
Loads the data for the view from some external source without user prompting.
loadSetDirect(IReadableDataSource) - Method in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Loads the data for the view from some external source without user prompting.
loadThreshold(IReadableDataSource) - Method in class jigcell.compare.compare2.Compare2
Loads the data for the view from some external source.
loadThresholdDirect(IReadableDataSource) - Method in class jigcell.compare.compare2.Compare2
Loads the data for the view from some external source without user prompting.
localNames - Variable in class jigcell.compare.views.ProgrammableDataGeneratorEditor
List of object names created in this editor
localObjects - Variable in class jigcell.compare.views.ProgrammableDataGeneratorEditor
List of objects created in this editor
location - Variable in class jigcell.compare.ui.HTMLComponentDescription
Location of the component description
location - Variable in class jigcell.compare.ui.TextComponentDescription
Location of the component description
LOCK - Variable in class jigcell.compare.impl.XMLFormatter
Lock for manipulating XML persistence information
LOCK_CUSTOMIZERS - Variable in class jigcell.compare.ui.CustomizableInterface
Lock for manipulating customizers map
LOCK_ERRORRECORD - Variable in class jigcell.compare.views.EvaluationErrorViewer
Lock to prevent concurrent access on errorRecord
LOCK_EVALUATION - Variable in class jigcell.compare.data.ProgrammableDataGenerator
Lock for controlling element evaluation
LOCK_INTERFACE - Variable in class jigcell.compare.data.ProgrammableDataGenerator
Lock for controlling user interface
lockCount - Variable in class jigcell.compare.data.DataElement
Count of number of locking operations committed to
LOG - Static variable in class jigcell.compare.impl.ExceptionRecorder
Flag to log the exception
LOG_COUNT - Static variable in class jigcell.compare.impl.Compare
Maximum number of files to log
LOG_LIMIT - Static variable in class jigcell.compare.impl.Compare
Maximum number of bytes to log
LOG_PATTERN - Static variable in class jigcell.compare.impl.Compare
Logging filename pattern
logger - Static variable in class jigcell.compare.impl.Compare
Logger to output to
LONG_ZERO - Static variable in class jigcell.compare.transform.annotation.TransformAnnotation
Zero
LONG_ZERO - Static variable in class jigcell.compare.views.TransformDebugger
Zero
LONGPOOL - Static variable in class jigcell.compare.data.DataElement
Long constant pool
lostOwnership(Clipboard, Transferable) - Method in class jigcell.compare.impl.ClipboardDataSource
 

M

main(String[]) - Static method in class jigcell.compare.cellcycle.CellCycleFrontEnd
Starts a new graphical Comparator.
main(String[]) - Static method in class jigcell.compare.impl.Compare
Starts a new headless Comparator.
main(String[]) - Static method in class jigcell.compare.tests.ElementBenchmark
Compares the performance of two implemetations of IEditableDataElement.
main(String[]) - Static method in class jigcell.compare.tests.ElementTests
Starts a new test suite run.
main(String[]) - Static method in class jigcell.compare.tests.MethodDispatcherTests
Starts a new test suite run.
main(String[]) - Static method in class jigcell.compare.tests.OAAConnectorTest
Tests the OAAConnector class.
main(String[]) - Static method in class jigcell.compare.tests.StreamingStringTokenizerTests
Starts a new test suite run.
main(String[]) - Static method in class jigcell.compare.tests.SystemTests
Starts a new test suite run.
main(String[]) - Static method in class jigcell.compare.tests.TabTests
Starts a new test suite run.
main(String[]) - Static method in class jigcell.compare.tests.Tests
Starts a new test suite run.
main(String[]) - Static method in class jigcell.compare.tests.TransformTests
Starts a new test suite run.
main(String[]) - Static method in class jigcell.compare.ui.CompareFrontEnd
Starts a new graphical Comparator.
makeList() - Method in class jigcell.compare.data.EditableDataElement
Converts this element to a list.
makeList() - Method in interface jigcell.compare.IEditableDataElement
Converts this element to a list.
manager - Variable in class jigcell.compare.compare2.Compare2Model
Provides interface help for the view
manager - Variable in class jigcell.compare.compare2.ThresholdEditor
Manages the interface for this editor
manager - Variable in class jigcell.compare.objectiveui.WeightEditorDialog
Interface manager for this dialog
manager - Variable in class jigcell.compare.ui.CompareFrontEnd
Provides interface help for the view
manager - Variable in class jigcell.compare.ui.ConfigEditor
Manages the interface for the dialog
manager - Variable in class jigcell.compare.ui.CustomizableInterface
Interface manager
manager - Variable in class jigcell.compare.ui.DataEditorPanelTab
Provides interface help for the view
manager - Variable in class jigcell.compare.views.EvaluationErrorViewer
Interface manager for this viewer
map - Variable in class jigcell.compare.data.DataGeneratorMap
Internal Map[Key,IDataGenerator] implementation
map - Variable in class jigcell.compare.data.ResultSetGroupMap
Internal Map[IResultSetMap,String] implementation
map - Variable in class jigcell.compare.data.ResultSetMap
Internal Map[Key,IDataElement] implementation
MAP_CLASSNAMETYPE - Static variable in class jigcell.compare.data.MethodDispatcher
Map from primitive class names to formalTypes
MAP_CLASSTYPENAME - Static variable in class jigcell.compare.data.MethodDispatcher
Map from primitive class formalTypes to names
MARKER_UNIVERSAL - Static variable in class jigcell.compare.impl.Config
Universal marker
MARKER_UNIVERSALCLASS - Static variable in class jigcell.compare.impl.Config
Universal class marker
MARKER_UNIVERSALINSTANCE - Static variable in class jigcell.compare.impl.Config
Universal instance marker
markerCount - Static variable in class jigcell.compare.impl.Config
Counter for unique instance markers
markers - Variable in class jigcell.compare.ui.BasicTable.BasicTableModel
Column markers of the table
markers - Variable in class jigcell.compare.ui.ConfigEditor
Configuration markers for the owner of this dialog
mass - Variable in class jigcell.compare.cellcycle.BuddingYeastScanTransform.BuddingYeastScanPoint
Size of the cell
mass - Variable in class jigcell.compare.cellcycle.GenericScanTransform.CellCycleReport
Mass at division
mass - Variable in class jigcell.compare.cellcycle.GenericScanTransform.GenericScanPoint
Size of the cell
MASSHIGH - Static variable in class jigcell.compare.cellcycle.BuddingYeastScanTransform.BuddingYeastScanEvent
Mass is too high
MASSHIGH - Static variable in class jigcell.compare.cellcycle.GenericScanTransform.GenericScanEvent
Mass is too high
MASSLOW - Static variable in class jigcell.compare.cellcycle.BuddingYeastScanTransform.BuddingYeastScanEvent
Mass it too low
MASSLOW - Static variable in class jigcell.compare.cellcycle.GenericScanTransform.GenericScanEvent
Mass is too low
maximumDocument - Variable in class jigcell.compare.transformui.ExtremaTestInterface
Maximum selection document
medianBenchmark(Class, int, int) - Static method in class jigcell.compare.tests.ElementBenchmark
Runs benchmarks on an element type and reports the median speed and memory results.
memoryLock() - Method in class jigcell.compare.data.CachedDataElement
Forces the element to guarantee that the element data can currently be worked with. Implementations may or may not support reentrancy or other forms of multiple locking. Editing the internal state of a data generator while locked may cause subsequent calls to memoryLock to incorrectly terminate without guarantee that the element data can currently be worked with.
memoryLock() - Method in class jigcell.compare.data.DataElement
Forces the element to guarantee that the element data can currently be worked with.
memoryLock() - Method in class jigcell.compare.data.FlippedDataElement
Forces the element to guarantee that the element data can currently be worked with.
memoryLock() - Method in class jigcell.compare.data.PackedDoubleDataElement
Forces the element to guarantee that the element data can currently be worked with. Implementations may or may not support reentrancy or other forms of multiple locking. Editing the internal state of a data generator while locked may cause subsequent calls to memoryLock to incorrectly terminate without guarantee that the element data can currently be worked with. Locking is unnecessary for this element.
memoryLock() - Method in class jigcell.compare.data.TreeDataElement
Forces the element to guarantee that the element data can currently be worked with. Implementations may or may not support reentrancy or other forms of multiple locking. Editing the internal state of a data generator while locked may cause subsequent calls to memoryLock to incorrectly terminate without guarantee that the element data can currently be worked with.
memoryLock() - Method in interface jigcell.compare.IDataElement
Forces the element to guarantee that the element data can currently be worked with.
MemoryMonitorAccessory - Class in jigcell.compare.ui
A tab accessory that displays the program title and version, and tracks memory usage.
MemoryMonitorAccessory() - Constructor for class jigcell.compare.ui.MemoryMonitorAccessory
Creates a new memory monitoring accessory.
memoryUnlock() - Method in class jigcell.compare.data.CachedDataElement
Releases the element from the guarantee that the element data can currently be worked with. Implementations may or may not support reentrancy or other forms of multiple locking.
memoryUnlock() - Method in class jigcell.compare.data.DataElement
Releases the element from the guarantee that the element data can currently be worked with.
memoryUnlock() - Method in class jigcell.compare.data.FlippedDataElement
Releases the element from the guarantee that the element data can currently be worked with.
memoryUnlock() - Method in class jigcell.compare.data.PackedDoubleDataElement
Releases the element from the guarantee that the element data can currently be worked with. Implementations may or may not support reentrancy or other forms of multiple locking. Locking is unnecessary for this element.
memoryUnlock() - Method in class jigcell.compare.data.TreeDataElement
Releases the element from the guarantee that the element data can currently be worked with. Implementations may or may not support reentrancy or other forms of multiple locking.
memoryUnlock() - Method in interface jigcell.compare.IDataElement
Releases the element from the guarantee that the element data can currently be worked with.
MENU_OPENRECENT - Static variable in class jigcell.compare.ui.DataEditorPanelTab
Name of menu containing recent sources to open
MENU_VIEW - Static variable in class jigcell.compare.compare2.Compare2
View menu label
MENUBAR_DEFAULT - Static variable in class jigcell.compare.ui.CompareFrontEnd
Default menu bar name
MENUBAR_DEFAULT - Static variable in class jigcell.compare.ui.DataEditorPanelTab
Name of default menubar
MENUBAR_DEFAULT - Static variable in class jigcell.compare.views.TransformDebugger
Name of default menubar
MenuBuilder - Class in jigcell.compare.ui
Generates and manages menus and popups for another component.
MenuBuilder(Object) - Constructor for class jigcell.compare.ui.MenuBuilder
Creates a new manager for menus.
MenuBuilder(Object, boolean) - Constructor for class jigcell.compare.ui.MenuBuilder
Creates a new manager for menus.
MenuBuilder.Builder - Class in jigcell.compare.ui
Builder for creating the item scripts.
MenuBuilder.Builder(Class) - Constructor for class jigcell.compare.ui.MenuBuilder.Builder
Creates a new launcher for evaluating item scripts.
MenuBuilder.Builder.Item - Class in jigcell.compare.ui
Values need to build an item for the menu.
MenuBuilder.Builder.Item() - Constructor for class jigcell.compare.ui.MenuBuilder.Builder.Item
Creates a new separator item.
MenuBuilder.Builder.Item(String, String, String, String, String, String) - Constructor for class jigcell.compare.ui.MenuBuilder.Builder.Item
Creates a new item record.
MenuBuilder.ScriptActionTrampoline - Class in jigcell.compare.ui
Handles and dispatches menu events to handlers.
MenuBuilder.ScriptActionTrampoline() - Constructor for class jigcell.compare.ui.MenuBuilder.ScriptActionTrampoline
 
MENUITEM_DELETE - Static variable in class jigcell.compare.transformui.TransformInterface
Delete menu item label
MENUITEM_INSERTAFTER - Static variable in class jigcell.compare.transformui.TransformInterface
Insert after menu item label
MENUITEM_INSERTBEFORE - Static variable in class jigcell.compare.transformui.TransformInterface
Insert before menu item label
MENUITEM_SEPARATOR - Static variable in class jigcell.compare.ui.MenuBuilder
Special menu separator
MENUITEM_VIEWCOLORER - Static variable in class jigcell.compare.compare2.Compare2
A view colorer menu item
MENUITEM_VIEWRANKS - Static variable in class jigcell.compare.compare2.Compare2
View values menu item label
menuManager - Variable in class jigcell.compare.ui.CompareFrontEnd
Menu builder
menuManager - Variable in class jigcell.compare.ui.CustomizableInterface
Builds menus for the interface
menuManager - Variable in class jigcell.compare.ui.DataEditorPanelTab
Creates menus for the view
menuManager - Variable in class jigcell.compare.ui.SeriesDialog
Menu manager
menuManager - Variable in class jigcell.compare.views.TransformDebugger
Menu manager
menus - Variable in class jigcell.compare.ui.CompareFrontEnd.FrontEndTabInfo
Tab menus
menus - Variable in class jigcell.compare.ui.DataEditorPanelTab
The menus that this view is presenting
menus - Variable in class jigcell.compare.ui.MenuBuilder.Builder
Description for a menu bar
message(String) - Static method in class jigcell.compare.impl.Compare
Logs a message.
message - Variable in class jigcell.compare.ui.CompareFrontEnd.SplashScreen
Status text to update to
MESSAGE_BADDIRECTORYERROR - Static variable in class jigcell.compare.impl.FileDataSource
Error message when the directory to place the file in cannot be created
MESSAGE_BADPARAMETERERROR - Static variable in class jigcell.compare.impl.ComparatorDataFlavor
Error message when a bad parameter is encountered
MESSAGE_CHOOSERCOMPARISON - Static variable in class jigcell.compare.views.ObjectiveSeriesView.ObjectiveSeriesModel
Prompt to choose an objective
MESSAGE_CHOOSEROBJECTIVE - Static variable in class jigcell.compare.views.ObjectiveSeriesView.ObjectiveSeriesModel
Prompt to choose an objective
MESSAGE_CHUNKSIZEERROR - Static variable in class jigcell.compare.data.PackedDoubleDataElement
Error message when the chunk size is too small
MESSAGE_CHUNKSIZEERROR - Static variable in class jigcell.compare.data.PackedTreeDataElement
Error message when the chunk size is too small
MESSAGE_CREATEERROR - Static variable in class jigcell.compare.ui.ProgressMonitor
Error message when a second create is attempted
MESSAGE_ERROR - Static variable in class jigcell.compare.impl.Compare
Dialog title for error dialogs
MESSAGE_ERROR - Static variable in class jigcell.compare.transformui.FileInterface
General error message for unexpected exception
MESSAGE_EXCEPTIONCAUGHT - Static variable in class jigcell.compare.impl.ExceptionRecorder
Error message when an exception is caught
MESSAGE_LASTERROR - Static variable in class jigcell.compare.data.PackedTreeDataElement
Error message when the last value in a pack is incorrect
MESSAGE_LOADDATAERROR - Static variable in class jigcell.compare.cellcycle.CellCycleTransformView
Error message when load data is invalid
MESSAGE_LOADERROR - Static variable in class jigcell.compare.ui.DataEditorPanelTab
General error message for failed load
MESSAGE_LOADING - Static variable in class jigcell.compare.ui.DataEditorPanelTab
Status message when loading
MESSAGE_METHOD - Static variable in class jigcell.compare.data.MethodDispatcher
Beginning of a method error message
MESSAGE_NOCLIPBOARDERROR - Static variable in class jigcell.compare.impl.ClipboardDataSource
Error message when no clipboard is provided
MESSAGE_NOFLAVORERROR - Static variable in class jigcell.compare.impl.ClipboardDataSource
Error message when no transfer flavors are provided
MESSAGE_NOFLAVORERROR - Static variable in class jigcell.compare.impl.PrinterDataSource
Error message when no transfer flavor is supported
MESSAGE_NOMESSAGE - Static variable in class jigcell.compare.ui.InterfaceBuilder
Message text to use when no error message is available
MESSAGE_NOPNGPRINTERERROR - Static variable in class jigcell.compare.impl.SystemPrinterDataSource
Error message when no png printers are available
MESSAGE_NOPSPRINTERERROR - Static variable in class jigcell.compare.impl.SystemPrinterDataSource
Error message when no postscript printers are available
MESSAGE_NOTIMPLEMENTED - Static variable in class jigcell.compare.data.MethodDispatcher
Error message when an unimplemented function is invoked
MESSAGE_PACKERROR - Static variable in class jigcell.compare.impl.OwnedDataSource
Error message when data packing fails
MESSAGE_PARAMETERERROR - Static variable in class jigcell.compare.data.MethodDispatcher
Error message when the parameter formalType of a method is illegal
MESSAGE_PARSEBLOCKERROR - Static variable in class jigcell.compare.data.EditableDataElement
Message when unable to parse element text due to bad block nesting
MESSAGE_PARSEERROR - Static variable in class jigcell.compare.data.EditableDataElement
Message when unable to parse element text
MESSAGE_PARSEEXTRAERROR - Static variable in class jigcell.compare.data.EditableDataElement
Message when unable to parse element text due to too much input
MESSAGE_PARSELITERALERROR - Static variable in class jigcell.compare.data.EditableDataElement
Message when unable to parse element text due to unterminated literal
MESSAGE_PLOTNODATAERROR - Static variable in class jigcell.compare.cellcycle.CellCycleTransformView.TransformModel
Error message when plotting a cell with no data
MESSAGE_PLOTNODATAERROR - Static variable in class jigcell.compare.views.EditableSeriesView.EditableSeriesModel
Error message when plotting a cell with no data
MESSAGE_PROXYERROR - Static variable in class jigcell.compare.impl.OwnedDataSource
Error message when an unusable transfer proxy is provided
MESSAGE_REPORTERROR - Static variable in class jigcell.compare.cellcycle.CellCycleObjectiveView
Error message when generating a report
MESSAGE_RESULTNAMEEDITERROR - Static variable in class jigcell.compare.transform.InputTransform
Error message when an attempt is made to edit the result name when the result name is not editable
MESSAGE_RETURNERROR - Static variable in class jigcell.compare.data.MethodDispatcher
Error message when the return formalType of a method is illegal
MESSAGE_SAVEERROR - Static variable in class jigcell.compare.ui.DataEditorPanelTab
General error message for failed save
MESSAGE_SCRIPTERROR - Static variable in class jigcell.compare.cellcycle.CellCycleFrontEnd
Error message when executing a script fails
MESSAGE_SCRIPTSTARTERROR - Static variable in class jigcell.compare.cellcycle.CellCycleFrontEnd
Error message when unable to start script interpreter
MESSAGE_SMALLPERROR - Static variable in class jigcell.compare.objective.MinkowskiObjective
Error message when the p-value is too small
MESSAGE_TARGETNOTFOUNDERROR - Static variable in class jigcell.compare.cellcycle.CellCycleTransformView
Error message when load data contains an unbound transform
MESSAGE_TOOBIGERROR - Static variable in class jigcell.compare.data.MethodDispatcher
Error message when an element is larger than can be reflected
MESSAGE_TYPEERROR - Static variable in class jigcell.compare.cellcycle.CellCycleExperimentView
Error message when a type checker fails to load
MESSAGE_UNTIEERROR - Static variable in class jigcell.compare.data.FlippedDataElement
Error message when an element cannot be untied
MESSAGE_VALUEERROR - Static variable in class jigcell.compare.ui.SeriesEditorDialog
Error message for unapplyable value
MESSAGE_WARNING - Static variable in class jigcell.compare.impl.Compare
Dialog title for warning dialogs
messageLabel - Variable in class jigcell.compare.ui.CompareFrontEnd.SplashScreen
Status display
METHOD_GENERATE - Static variable in interface jigcell.compare.compare2.IViewColorer
Name of the static method to be invoked for view colorers
METHOD_GENERATE - Static variable in interface jigcell.compare.IProgrammableDataGenerator
Name of the static method to be invoked for customizable generators
METHOD_GENERATE - Static variable in interface jigcell.compare.ITypeChecker
Name of the static method to be invoked for type checkers
METHOD_LONGDOUBLE - Static variable in class jigcell.compare.data.MethodDispatcher
Name of the method to convert a Long to a Double
MethodDispatcher - Class in jigcell.compare.data
Performs automated method dispatching based on a tuneable heuristic.
MethodDispatcher(Object, String) - Constructor for class jigcell.compare.data.MethodDispatcher
Creates a new method dispatcher.
MethodDispatcher.MethodScorer - Class in jigcell.compare.data
Intermediate results for computing a method score.
MethodDispatcher.MethodScorer() - Constructor for class jigcell.compare.data.MethodDispatcher.MethodScorer
Creates a new score keeper for method dispatch.
MethodDispatcher.MethodScorer(Class[], Object[]) - Constructor for class jigcell.compare.data.MethodDispatcher.MethodScorer
Creates a new score keeper for method dispatch.
MethodDispatcher.NoDispatchableMethodException - Exception in jigcell.compare.data
Indicates that method dispatching failed because no suitable methods were found.
MethodDispatcher.NoDispatchableMethodException() - Constructor for exception jigcell.compare.data.MethodDispatcher.NoDispatchableMethodException
 
MethodDispatcher.NoDispatchableMethodException(String) - Constructor for exception jigcell.compare.data.MethodDispatcher.NoDispatchableMethodException
 
MethodDispatcherTests - Class in jigcell.compare.tests
A collection of tests to exercise jigcell.compare.impl.MethodDispatcher.
MethodDispatcherTests(String) - Constructor for class jigcell.compare.tests.MethodDispatcherTests
Creates a new method dispatcher test.
MethodDispatcherTests.DispatchedTransform - Class in jigcell.compare.tests
Test transform for dispatching.
MethodDispatcherTests.DispatchedTransform() - Constructor for class jigcell.compare.tests.MethodDispatcherTests.DispatchedTransform
Creates a new dispatching transform.
methodName - Variable in class jigcell.compare.data.MethodDispatcher
Name of the method to invoke
methods - Variable in class jigcell.compare.impl.ProxyBuilder
Map[Method,Method] from the method that an interface defines to the method that implements the interface
metricModel - Variable in class jigcell.compare.views.ObjectiveEditor
Model for metrics
MetricObjective - Class in jigcell.compare.objective
A FunctionalDataGenerator whose function is based upon a metric.
MetricObjective() - Constructor for class jigcell.compare.objective.MetricObjective
Creates a new data generator based upon a metric evaluation.
MetricObjective.MetricObjectiveDelegate - Class in jigcell.compare.objective
Uses the copy method to replicate the chain of creation.
MetricObjective.MetricObjectiveDelegate() - Constructor for class jigcell.compare.objective.MetricObjective.MetricObjectiveDelegate
 
MIME_LOCK - Static variable in class jigcell.compare.impl.Transferer
Lock for manipulating MIME type information
MIMETYPE_DEFAULT - Static variable in class jigcell.compare.impl.ComparatorDataFlavor
MIME type for Comparator transfers
MIMETYPE_GENERIC - Static variable in class jigcell.compare.impl.ComparatorDataFlavor
MIME type for generic data
MIMETYPE_LOCALOBJECT - Static variable in class jigcell.compare.impl.ComparatorDataFlavor
MIME type for local JVM objects
MIMETYPE_PDF - Static variable in class jigcell.compare.impl.ComparatorDataFlavor
MIME type for PDF
MIMETYPE_POSTSCRIPT - Static variable in class jigcell.compare.impl.ComparatorDataFlavor
MIME type for postscript
MIMETYPE_TEXTHTML - Static variable in class jigcell.compare.impl.ComparatorDataFlavor
MIME type for HTML text
MIMETYPE_TEXTPLAIN - Static variable in class jigcell.compare.impl.ComparatorDataFlavor
MIME type for plain text
MIMETYPE_TEXTXML - Static variable in class jigcell.compare.impl.ComparatorDataFlavor
MIME type for XML text
MIMETYPE_XMLSERIALIZEDOBJECT - Static variable in class jigcell.compare.impl.ComparatorDataFlavor
MIME type for XML serialized objects
minimumDocument - Variable in class jigcell.compare.transformui.ExtremaTestInterface
Minimum selection document
MinkowskiInterface - Class in jigcell.compare.objectiveui
Interface for a MinkowskiObjective.
MinkowskiInterface(IProgrammableDataGenerator) - Constructor for class jigcell.compare.objectiveui.MinkowskiInterface
Creates a new interface for a MinkowskiObjective.
MinkowskiObjective - Class in jigcell.compare.objective
A generator whose function is a Lebesgue p-norm.
MinkowskiObjective() - Constructor for class jigcell.compare.objective.MinkowskiObjective
Creatas a new data generator based upon a vector norm.
MinkowskiObjective(double) - Constructor for class jigcell.compare.objective.MinkowskiObjective
Creatas a new data generator based upon a vector norm.
MinkowskiObjective.MinkowskiObjectiveDelegate - Class in jigcell.compare.objective
Persists the generator using the p-value rather than storing any state information.
MinkowskiObjective.MinkowskiObjectiveDelegate() - Constructor for class jigcell.compare.objective.MinkowskiObjective.MinkowskiObjectiveDelegate
 
mode - Variable in class jigcell.compare.compare2.ViewColorer
Display mode
MODE_RANKINGS - Static variable in interface jigcell.compare.compare2.IViewColorer
Display comparison rankings
MODE_VALUES - Static variable in interface jigcell.compare.compare2.IViewColorer
Display raw comparison values
model - Variable in class jigcell.compare.cellcycle.CellCycleTransformView
Data model of the generators
model - Variable in class jigcell.compare.compare2.Compare2
Data model of the comparisons
model - Variable in class jigcell.compare.compare2.ThresholdEditor
View model
model - Variable in class jigcell.compare.compare2.ViewColorer
The view model
model - Variable in class jigcell.compare.ui.BasicTable
Table model
model - Variable in class jigcell.compare.ui.ViewerDialog
Data model of the parent table
model - Variable in class jigcell.compare.views.BasicTableView
Data model
model - Variable in class jigcell.compare.views.EditableSeriesView
Data model of the generators
model - Variable in class jigcell.compare.views.EvaluationErrorViewer
Table model
model - Variable in class jigcell.compare.views.ObjectiveSeriesView
Data model of the generators
model - Variable in class jigcell.compare.views.SeriesView
Data model of the generators
model - Variable in class jigcell.compare.views.SeriesView.SeriesViewTransferer
Model for the data
modelBuilder - Variable in class jigcell.compare.tests.ModelBuilderPlugin
Model builder application
ModelBuilderBenchmark - Class in jigcell.compare.tests
A collection of tests for evaluating model builder performance.
ModelBuilderBenchmark(Compare) - Constructor for class jigcell.compare.tests.ModelBuilderBenchmark
Creates a new tester for model builder performance.
ModelBuilderPlugin - Class in jigcell.compare.tests
A test class for using the Model Builder as a plugin.
ModelBuilderPlugin(Compare, String) - Constructor for class jigcell.compare.tests.ModelBuilderPlugin
Creates a new model builder instance.
modifyRunChanges(int, String) - Method in class jigcell.compare.tests.RunManagerPlugin
Modifies the changes of a run.
mouseClicked(MouseEvent) - Method in class jigcell.compare.transformui.SelectColumnsInterface
 
mouseClicked(MouseEvent) - Method in class jigcell.compare.ui.CompareFrontEnd.SplashScreen
 
mouseClicked(MouseEvent) - Method in class jigcell.compare.ui.CustomizableInterface
 
mouseClicked(MouseEvent) - Method in class jigcell.compare.ui.SeriesDialog
 
mouseClicked(MouseEvent) - Method in class jigcell.compare.views.BasicTableView
 
mouseEntered(MouseEvent) - Method in class jigcell.compare.ui.CompareFrontEnd.SplashScreen
 
mouseEntered(MouseEvent) - Method in class jigcell.compare.ui.CustomizableInterface
 
mouseEntered(MouseEvent) - Method in class jigcell.compare.ui.SeriesDialog
 
mouseEntered(MouseEvent) - Method in class jigcell.compare.views.BasicTableView
 
mouseExited(MouseEvent) - Method in class jigcell.compare.ui.CompareFrontEnd.SplashScreen
 
mouseExited(MouseEvent) - Method in class jigcell.compare.ui.CustomizableInterface
 
mouseExited(MouseEvent) - Method in class jigcell.compare.ui.SeriesDialog
 
mouseExited(MouseEvent) - Method in class jigcell.compare.views.BasicTableView
 
mousePressed(MouseEvent) - Method in class jigcell.compare.ui.CompareFrontEnd.SplashScreen
 
mousePressed(MouseEvent) - Method in class jigcell.compare.ui.CustomizableInterface
 
mousePressed(MouseEvent) - Method in class jigcell.compare.ui.SeriesDialog
 
mousePressed(MouseEvent) - Method in class jigcell.compare.views.BasicTableView
 
mouseReleased(MouseEvent) - Method in class jigcell.compare.ui.CompareFrontEnd.SplashScreen
 
mouseReleased(MouseEvent) - Method in class jigcell.compare.ui.CustomizableInterface
 
mouseReleased(MouseEvent) - Method in class jigcell.compare.ui.SeriesDialog
 
mouseReleased(MouseEvent) - Method in class jigcell.compare.views.BasicTableView
 
moveRowsDown(int[]) - Method in class jigcell.compare.cellcycle.CellCycleTransformView
Moves selected rows down.
moveRowsDown(int[]) - Method in class jigcell.compare.compare2.Compare2
Moves selected rows down.
moveRowsDown(int[]) - Method in interface jigcell.compare.ui.IRowEditorTab
Moves selected rows down.
moveRowsDown(int[]) - Method in class jigcell.compare.ui.SeriesEditorDialog
Moves selected rows down.
moveRowsDown(int[]) - Method in class jigcell.compare.views.EditableSeriesView
Moves selected rows down.
moveRowsDown(int[]) - Method in class jigcell.compare.views.ObjectiveSeriesView
Moves selected rows down.
moveRowsUp(int[]) - Method in class jigcell.compare.cellcycle.CellCycleTransformView
Moves selected rows up.
moveRowsUp(int[]) - Method in class jigcell.compare.compare2.Compare2
Moves selected rows up.
moveRowsUp(int[]) - Method in interface jigcell.compare.ui.IRowEditorTab
Moves selected rows up.
moveRowsUp(int[]) - Method in class jigcell.compare.ui.SeriesEditorDialog
Moves selected rows up.
moveRowsUp(int[]) - Method in class jigcell.compare.views.EditableSeriesView
Moves selected rows up.
moveRowsUp(int[]) - Method in class jigcell.compare.views.ObjectiveSeriesView
Moves selected rows up.
moveValue(long, long) - Method in class jigcell.compare.data.EditableDataElement
Moves a value within the element.
moveValue(long, long) - Method in interface jigcell.compare.IEditableDataElement
Moves a value within the element.
MULTIPLE - Static variable in class jigcell.compare.IDataElement.Type
A non-scalar value
multipleViewSupport - Variable in class jigcell.compare.ui.CustomizableInterface
Whether this interface support multiple, simultaneous views
mungeKey(String) - Method in class jigcell.compare.ui.BasicTable.BasicEditor
Creates the actual key value based on a generic key value.
mungeKey(String) - Method in class jigcell.compare.ui.BasicTable.BasicRenderer
Creates the actual key value based on a generic key value.
mungeTabName(String) - Method in class jigcell.compare.cellcycle.OAAConnector
Converts a tab name into a solvable friendly form.
myOaa - Variable in class jigcell.compare.cellcycle.OAAConnector
OAA connection
myOaa - Variable in class jigcell.compare.tests.OAAConnectorTest
OAA connection

N

name - Variable in class jigcell.compare.compare2.Compare2.SetReadHelper
Name of the new set
name - Variable in class jigcell.compare.data.IDataGeneratorCollection.Key
Key name
name - Variable in class jigcell.compare.IDataElement.Type
Name of this type
name - Variable in class jigcell.compare.impl.Blackboard
Name of the current namespace, or null if the current namespace is not a top-level namespace
name - Variable in class jigcell.compare.plotter.IPlotter.Combine
Name of this option
name - Variable in class jigcell.compare.transformui.BoxInterface
Temporary storage for the name of the customizer currently being created
name - Variable in class jigcell.compare.ui.BasicTable.BasicTableModel.Marker
Name of this column for the table header.
name - Variable in class jigcell.compare.ui.MenuBuilder.Builder.Item
Name of the item
name - Variable in class jigcell.compare.views.EvaluationErrorViewer.ErrorRecord
Generator name
name - Variable in class jigcell.compare.views.ObjectiveSeriesView.Comparison
Name of this type
NAME_CALLBACK - Static variable in class jigcell.compare.cellcycle.OAAConnector
Name of the OAA callback method
NAME_COMPARATOR - Static variable in class jigcell.compare.cellcycle.OAAConnector
Name of the dispatch target for the Comparator
NAME_CUSTOMIZERS - Variable in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Name for customizers requested by this component
NAME_CUSTOMIZERS - Static variable in class jigcell.compare.views.TransformDebugger
Name for customizers requested by this component
NAME_DISPATCHMETHOD - Static variable in class jigcell.compare.contrib.DispatchedTransformHelper
Method name to dispatch for
NAME_EXPORTEDFLAVOR - Static variable in class jigcell.compare.views.SeriesView.SeriesViewTransferer
Readable name of the exported data flavor
NAME_FACILITATOR - Static variable in class jigcell.compare.cellcycle.OAAConnector
Name of the facilitator connection ID
NAME_FUNCTION - Static variable in class jigcell.compare.cellcycle.OAAConnector
Prefix name of a dispatch function
NAME_GENERATOR - Static variable in class jigcell.compare.objective.BooleanRelationalObjective
Display name of this generator
NAME_GENERATOR - Static variable in class jigcell.compare.objective.WOSSObjective
Display name of this generator
NAME_GENERATOR_POSTPEND - Static variable in class jigcell.compare.objective.MinkowskiObjective
End of generator name for arbitrary p
NAME_GENERATOR_PREPEND - Static variable in class jigcell.compare.objective.MinkowskiObjective
Beginning of generator name for arbitrary p
NAME_GENERATORINF - Static variable in class jigcell.compare.objective.MinkowskiObjective
Generator name for p = +infinity
NAME_OBJECTIVE - Static variable in class jigcell.compare.cellcycle.BuddingYeastPhenotypeObjective
Display name of this objective function
NAME_OBJECTIVE - Static variable in class jigcell.compare.cellcycle.GenericPhenotypeObjective
Display name of this objective function
NAME_OBJECTIVE - Static variable in class jigcell.compare.contrib.ObjectiveTemplate
Display name of this objective function
NAME_OBJECTIVE - Static variable in class jigcell.compare.objective.ScriptEvaluationObjective
Display name for this objective
NAME_THRESHOLD - Static variable in class jigcell.compare.compare2.ThresholdEditor
Name for experiment threshold components
NAME_TRANSFORM - Static variable in class jigcell.compare.cellcycle.BuddingYeastScanTransform
Display name of this transform
NAME_TRANSFORM - Static variable in class jigcell.compare.cellcycle.GenericScanTransform
Display name of this transform
NAME_TRANSFORM - Static variable in class jigcell.compare.cellcycle.JigCellRunManagerTransform
Display name of this transform
NAME_TRANSFORM - Static variable in class jigcell.compare.cellcycle.WildtypeScanTransform
Display name of this transform
NAME_TRANSFORM - Static variable in class jigcell.compare.contrib.DispatchedTransformTemplate
Display name of this transform
NAME_TRANSFORM - Static variable in class jigcell.compare.contrib.TransformTemplate
Display name of this transform
NAME_TRANSFORM - Static variable in class jigcell.compare.transform.BoxTransformContainer
Display name for this transform
NAME_TRANSFORM - Static variable in class jigcell.compare.transform.ExtremaTestTransform
Display name for this transform
NAME_TRANSFORM - Static variable in class jigcell.compare.transform.ReadFromFileTransform
Display name for this transform
NAME_TRANSFORM - Static variable in class jigcell.compare.transform.ScriptEvaluationTransform
Display name for this transform
NAME_TRANSFORM - Static variable in class jigcell.compare.transform.SelectColumnsTransform
Display name for this transform
NAME_TRANSFORM - Static variable in class jigcell.compare.transform.TransformEvaluationTransform
Display name for this transform
NAME_TRANSFORM - Static variable in class jigcell.compare.transform.WriteToFileTransform
Display name for this transform
NAME_USERRUN - Static variable in class jigcell.compare.cellcycle.JigCellRunManagerInterface
Name of the user selected run box
NAME_VARIANT - Static variable in class jigcell.compare.cellcycle.OAAConnector
Prefix name of a dispatch function with multiple variants
nameLabel - Variable in class jigcell.compare.views.TransformDebugger
Label displaying the name of the currently selected transform
names - Variable in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Selectable object names
namespace - Variable in class jigcell.compare.impl.Blackboard
Current working namespace
nameToGenerator - Variable in class jigcell.compare.data.DataGeneratorList
Map[String,IDataGenerator] from generator names to generators
NAN - Static variable in class jigcell.compare.data.PackedDoubleDataElement
NaN
needToClear - Variable in class jigcell.compare.transform.SelectColumnsTransform
Whether there is an outstanding clear caused by a flush to process
newModel - Variable in class jigcell.compare.ui.SeriesDialog
Model of current table
newModel - Variable in class jigcell.compare.ui.SeriesEditorDialog
Model of current table
next - Variable in class jigcell.compare.impl.StreamingStringTokenizer
One character buffer
next() - Method in class jigcell.compare.impl.StreamingStringTokenizer
Next token from the input or an empty string if there are no more tokens.
nextAnonymousId() - Static method in class jigcell.compare.transform.TransformContext
Generates a unique identifier
NONE - Static variable in class jigcell.compare.IDataElement.Type
A non-value
NONE - Static variable in class jigcell.compare.plotter.IPlotter.Combine
No series combining option.
notify(String) - Method in class jigcell.compare.impl.Blackboard
Notifies other blackboard users about a resource change.
NULL_KEY - Static variable in class jigcell.compare.transform.annotation.TransformAnnotation
Hash key for non-positional elements
number - Variable in class jigcell.compare.cellcycle.GenericScanTransform.CellCycleReport
Cycle number

O

oaaConnect() - Method in class jigcell.compare.cellcycle.OAAConnector
Creates the OAA connection.
OAAConnector - Class in jigcell.compare.cellcycle
A connector allowing the Comparator to be controlled through OAA requests.
OAAConnector(Compare, String) - Constructor for class jigcell.compare.cellcycle.OAAConnector
Creates a new connector for receiving commands from OAA.
OAAConnectorTest - Class in jigcell.compare.tests
Tests the OAAConnector class.
OAAConnectorTest() - Constructor for class jigcell.compare.tests.OAAConnectorTest
Tests the OAAConnector class.
oaaDisconnect() - Method in class jigcell.compare.cellcycle.OAAConnector
Destroys the OAA connection.
oaaDisconnect(String, Exception) - Method in class jigcell.compare.cellcycle.OAAConnector
Destroys the OAA connection.
object1 - Static variable in class jigcell.compare.tests.MethodDispatcherTests
A test object
object2 - Static variable in class jigcell.compare.tests.MethodDispatcherTests
A test object
object3 - Static variable in class jigcell.compare.tests.MethodDispatcherTests
A test object
object4 - Static variable in class jigcell.compare.tests.MethodDispatcherTests
A test object
objectEquals - Static variable in class jigcell.compare.impl.ProxyBuilder
Object.equals
objectHashCode - Static variable in class jigcell.compare.impl.ProxyBuilder
Object.hashCode
Objective - Class in jigcell.compare.objective
Implementation of DataGenerator whose associated element is a function result.
Objective() - Constructor for class jigcell.compare.objective.Objective
Creates a new data generator based upon a function evaluation.
ObjectiveBenchmark - Class in jigcell.compare.tests
A collection of tests for evaluating objective function loading performance.
ObjectiveBenchmark(Compare) - Constructor for class jigcell.compare.tests.ObjectiveBenchmark
Creates a new tester for objective function loading performance.
ObjectiveEditor - Class in jigcell.compare.views
Supports creating and editing objective functions.
ObjectiveEditor(Compare, String) - Constructor for class jigcell.compare.views.ObjectiveEditor
Creates a new editor for working with objective functions.
ObjectiveHelper - Class in jigcell.compare.contrib
Methods for reducing the amount of work to make an objective function.
ObjectiveHelper() - Constructor for class jigcell.compare.contrib.ObjectiveHelper
Creates a new helper for writing objective functions.
ObjectiveInterface - Class in jigcell.compare.objectiveui
Generic customizable interface for an objective.
ObjectiveInterface(IProgrammableDataGenerator) - Constructor for class jigcell.compare.objectiveui.ObjectiveInterface
Creates a new interface for a objective.
objectiveModel - Variable in class jigcell.compare.views.ObjectiveSeriesView
Display for list of known objectives
objectiveResultFormat - Variable in class jigcell.compare.views.ObjectiveSeriesView.ObjectiveSeriesModel
Formatter for objective result
objectives - Variable in class jigcell.compare.compare2.Compare2
Objective set used for comparison thresholds
objectives - Variable in class jigcell.compare.views.ObjectiveSeriesView
List of known objectives
ObjectiveSeriesView - Class in jigcell.compare.views
An editable display for working with objective data.
ObjectiveSeriesView(Compare, String) - Constructor for class jigcell.compare.views.ObjectiveSeriesView
Creates a new table view with the ability to display experimental and objective data.
ObjectiveSeriesView.Comparison - Class in jigcell.compare.views
Comparison type for threshold flagging.
ObjectiveSeriesView.Comparison(String) - Constructor for class jigcell.compare.views.ObjectiveSeriesView.Comparison
Creates a new type of objective comparison.
ObjectiveSeriesView.Comparison.ComparisonDelegate - Class in jigcell.compare.views
Looks up the singleton value instead of creating a new instance.
ObjectiveSeriesView.Comparison.ComparisonDelegate() - Constructor for class jigcell.compare.views.ObjectiveSeriesView.Comparison.ComparisonDelegate
 
ObjectiveSeriesView.ObjectiveSeriesModel - Class in jigcell.compare.views
Table model for an ObjectiveSummaryView.
ObjectiveSeriesView.ObjectiveSeriesModel() - Constructor for class jigcell.compare.views.ObjectiveSeriesView.ObjectiveSeriesModel
Creates a new table model.
ObjectiveSeriesView.ObjectiveSeriesRenderer - Class in jigcell.compare.views
Cell renderer for a ObjectiveSummaryView.
ObjectiveSeriesView.ObjectiveSeriesRenderer(boolean) - Constructor for class jigcell.compare.views.ObjectiveSeriesView.ObjectiveSeriesRenderer
Creates a new view renderer.
ObjectiveTemplate - Class in jigcell.compare.contrib
A DESCRIPTION OF YOUR CLASS.
ObjectiveTemplate() - Constructor for class jigcell.compare.contrib.ObjectiveTemplate
 
objectiveView - Variable in class jigcell.compare.tests.ObjectiveBenchmark
View to load objective functions in
objectModel - Variable in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Model for object list
objects - Variable in class jigcell.compare.views.ProgrammableDataGeneratorEditor
List of known objects
objectToString - Static variable in class jigcell.compare.impl.ProxyBuilder
Object.toString
oldPrevious - Variable in class jigcell.compare.transformui.TransformInterface
Old previous statement for the generator
openRunFile(String) - Method in class jigcell.compare.tests.RunManagerPlugin
Loads a run set in the Run Manager.
OPTION_ANNOTATION - Static variable in interface jigcell.compare.transform.ITransform
Option for the annotation record
OPTION_CHOOSERADD - Static variable in class jigcell.compare.compare2.Compare2
File chooser option when adding a file
OPTION_CHOOSEROPEN - Static variable in class jigcell.compare.ui.DataEditorPanelTab
File chooser option when opening a file
OPTION_CHOOSERSAVE - Static variable in class jigcell.compare.ui.DataEditorPanelTab
File chooser option when saving a file
OPTION_CLIPBOARD - Static variable in class jigcell.compare.impl.ClipboardDataSource
Clipboard to use
OPTION_CLIPCONTENTS - Static variable in class jigcell.compare.impl.ClipboardDataSource
Owned clipboard contents
OPTION_COLUMNHEADERS - Static variable in class jigcell.compare.cellcycle.JigCellRunManagerTransform
Option for the column headers
OPTION_COMBINE - Static variable in interface jigcell.compare.plotter.IPlotter
Series combining key
OPTION_COMPARE - Static variable in interface jigcell.compare.IProgrammableDataGenerator
The Comparator this generator is acting as a part of
OPTION_COMPATIBLE - Static variable in interface jigcell.compare.transform.ITransform
Attribute for the list of transforms compatible with this generator
OPTION_CONTAINEDTRANSFORMS - Static variable in interface jigcell.compare.transform.ITransformContainer
The transforms held by this container
OPTION_DATA - Static variable in class jigcell.compare.objective.Objective
Option for the data this generator uses
OPTION_DEFAULTDIMENSIONWEIGHTS - Static variable in interface jigcell.compare.objective.IDimensionWeightObjective
Option for all supported dimension weight defaults
OPTION_DEFAULTELEMENTWEIGHTS - Static variable in interface jigcell.compare.objective.IElementWeightObjective
Option for all supported element weight defaults
OPTION_DEFAULTRUN - Static variable in class jigcell.compare.cellcycle.JigCellRunManagerTransform
Option for the run number to use if the default run has been selected
OPTION_DISPLAYCONSTRUCTOR - Static variable in class jigcell.compare.data.ProgrammableDataGenerator
Option for the main display of this generator
OPTION_DISPLAYINSTANCE - Static variable in class jigcell.compare.data.ProgrammableDataGenerator
Option for the main display of this generator
OPTION_ENCODER - Static variable in class jigcell.compare.impl.FileDataSource
Encoder for controlling the format this source uses for reading and writing
OPTION_EVALUATIONNAME - Static variable in class jigcell.compare.impl.DataGeneratorEvaluator
Option for name to display when evaluating a generator
OPTION_EVALUATIONTARGET - Static variable in class jigcell.compare.impl.DataGeneratorEvaluator
Option for indicating the target result when evaluating a generator
OPTION_EXCEPTIONLISTENER - Static variable in class jigcell.compare.impl.FileDataSource
Exception listener to use for detecting errors
OPTION_FILECHOOSER - Static variable in class jigcell.compare.impl.FileDataSource
File chooser to use when selecting the file
OPTION_FILECHOOSER_SELECT - Static variable in class jigcell.compare.impl.FileDataSource
File chooser selection description
OPTION_FILEINPUT - Static variable in class jigcell.compare.impl.FileDataSource
Option indicating the input handle to the file
OPTION_FILEOUTPUT - Static variable in class jigcell.compare.impl.FileDataSource
Option indicating the output handle to the file
OPTION_FILEPATH - Static variable in class jigcell.compare.impl.FileDataSource
Option indicating the path of the file
OPTION_FILESOURCE - Static variable in class jigcell.compare.impl.PDFPrinterDataSource
File that will hold the PDF document
OPTION_FLAVORS - Static variable in class jigcell.compare.impl.ClipboardDataSource
Flavors to request data in
OPTION_FUNCTION - Static variable in class jigcell.compare.objective.Objective
Option for the function this generator uses
OPTION_GENERATORS - Static variable in class jigcell.compare.cellcycle.CellCycleReportGenerator
Option name for generators that the report can be based on
OPTION_INPUTDESCRIPTION - Static variable in interface jigcell.compare.ICustomizableInterface
Option for the input description
OPTION_INPUTTYPECHECKER - Static variable in interface jigcell.compare.IProgrammableDataGenerator
Option for a type checker that can validate the input
OPTION_INTERPOLATIONS - Static variable in interface jigcell.compare.objective.IInterpolationObjective
Option for all supported interpolation methods
OPTION_KNOWNTRANSFORMS - Static variable in class jigcell.compare.transform.TransformEvaluationTransform
Option for transforms that this transform knows it can invoke
OPTION_METRIC - Static variable in class jigcell.compare.objective.MetricObjective
Option for the metric this generator uses
OPTION_NAME - Static variable in interface jigcell.compare.IDataSource
Option indicating the name of this generator
OPTION_NEXTSTATEMENT - Static variable in interface jigcell.compare.transform.ITransform
Option for the next statement of this transform
OPTION_OBJECTIVE - Static variable in interface jigcell.compare.objective.IObjective
Option for the objective function
OPTION_OUTPUTDESCRIPTION - Static variable in interface jigcell.compare.ICustomizableInterface
Option for the output description
OPTION_OUTPUTTYPECHECKER - Static variable in interface jigcell.compare.IProgrammableDataGenerator
Option for a type checker that can validate the output
OPTION_OWNER - Static variable in class jigcell.compare.impl.OwnedDataSource
Owner of the source
OPTION_PREVIOUSSTATEMENT - Static variable in interface jigcell.compare.transform.ITransform
Option for the previous statement of this transform
OPTION_PRINTSERVICE - Static variable in class jigcell.compare.impl.SystemPrinterDataSource
Option indicating the print service to use
OPTION_READDESCRIPTION - Static variable in interface jigcell.compare.IReadableDataSource
Option indicating the suggested description for acting on this data source
OPTION_READICON - Static variable in interface jigcell.compare.IReadableDataSource
Option indicating the suggested icon for this data source
OPTION_RELATIONS - Static variable in interface jigcell.compare.objective.IRelationalObjective
Option for all supported relations
OPTION_RESULTNAMEEDIT - Static variable in class jigcell.compare.transform.InputTransform
Attribute for whether the result name this transform uses can be edited
OPTION_RUNDATA - Static variable in class jigcell.compare.cellcycle.JigCellRunManagerTransform
Option for the run data
OPTION_RUNNABLE - Static variable in class jigcell.compare.transform.InputTransform
Attribute for whether this transform is permitted to run
OPTION_SCRIPT - Static variable in class jigcell.compare.objective.ScriptEvaluationObjective
Attribute for the script this objective executes during evaluation
OPTION_SCRIPT - Static variable in class jigcell.compare.transform.ScriptEvaluationTransform
Attribute for the script this transform executes during evaluation
OPTION_SELECTION - Static variable in class jigcell.compare.cellcycle.CellCycleReportGenerator
Option name for the plotter column selection
OPTION_TRANSFERCLASS - Static variable in class jigcell.compare.impl.OwnedDataSource
Callback class
OPTION_TRANSFORM - Static variable in interface jigcell.compare.transform.ITransform
Attribute key for the transform
OPTION_TYPECHECKER - Static variable in interface jigcell.compare.ITypeChecker
Attribute key for generators who wish to associate a type checker
OPTION_VIEWRANGE - Static variable in class jigcell.compare.cellcycle.CellCycleReportGenerator
Option name for the plotter view range
OPTION_VIEWRANGE - Static variable in interface jigcell.compare.plotter.IPlotter
View range key
OPTION_VIEWTITLE - Static variable in interface jigcell.compare.plotter.IPlotter
View title key
OPTION_WILDTYPETRANSFORM - Static variable in class jigcell.compare.cellcycle.GenericScanTransform
Option for the transform that computes the wildtype properties
OPTION_WRITEDESCRIPTION - Static variable in interface jigcell.compare.IWriteableDataSource
Option indicating the suggested description for acting on this data source
OPTION_WRITEICON - Static variable in interface jigcell.compare.IWriteableDataSource
Option indicating the suggested icon for this data source
options - Variable in class jigcell.compare.impl.DataSource
Options for this data source
options - Variable in class jigcell.compare.ui.ConfigEditor
Options in this dialog
OPTIONS_LOCK - Variable in class jigcell.compare.impl.DataSource
Lock for manipulating source options
optionsTable - Static variable in class jigcell.compare.impl.DataSource
Options persistence table organized by name
OPTIONTYPE_LOCK - Static variable in class jigcell.compare.impl.DataSource
Lock for manipulating the options persistence table
ori - Variable in class jigcell.compare.cellcycle.BuddingYeastScanTransform.BuddingYeastScanPoint
Value of the species ori
origin - Variable in class jigcell.compare.impl.EvaluationCallStack
Generator that will hold the final result
originalThreshold - Variable in class jigcell.compare.compare2.ThresholdEditor
Threshold value before any adjustments were made
output - Variable in class jigcell.compare.views.Console
Text display for evaluation output
outputChannel - Variable in class jigcell.compare.views.Console
Channel for sending output to the display
OwnedDataSource - Class in jigcell.compare.impl
A data source that provides a callback for wrapping native objects prior to data transfer.
OwnedDataSource() - Constructor for class jigcell.compare.impl.OwnedDataSource
 
owner - Variable in class jigcell.compare.ui.InterfaceBuilder
Owner of this interface
owner - Variable in class jigcell.compare.views.EvaluationErrorViewer
The tab that launched this error viewer

P

p - Variable in class jigcell.compare.objective.MinkowskiObjective
Power
packageData(int) - Method in class jigcell.compare.cellcycle.CellCycleDataDialog.DataModel
Creates a data generator from an experiment and a transform.
PackedDoubleDataElement - Class in jigcell.compare.data
An implementation of EditableDataElement that uses an array of doubles to store values.
PackedDoubleDataElement() - Constructor for class jigcell.compare.data.PackedDoubleDataElement
Creates a new data element backed by an array of doubles.
PackedDoubleDataElement(int) - Constructor for class jigcell.compare.data.PackedDoubleDataElement
Creates a new data element with packed storage.
PackedTreeDataElement - Class in jigcell.compare.data
An implementation of EditableDataElement that uses a red-black tree to store values.
PackedTreeDataElement() - Constructor for class jigcell.compare.data.PackedTreeDataElement
Creates a new data element backed by a tree with packed storage.
PackedTreeDataElement(int) - Constructor for class jigcell.compare.data.PackedTreeDataElement
Creates a new data element with packed storage.
PackedTreeDataElement2 - Class in jigcell.compare.data
An implementation of EditableDataElement that uses an AVL tree to store values.
PackedTreeDataElement2() - Constructor for class jigcell.compare.data.PackedTreeDataElement2
Creates a new data element backed by a tree with packed storage.
PackedTreeDataElement2(int) - Constructor for class jigcell.compare.data.PackedTreeDataElement2
Creates a new data element with packed storage.
pane - Variable in class jigcell.compare.ui.CompareFrontEnd
Main interface
panel - Variable in class jigcell.compare.ui.InterfaceBuilder
Interface block holder
PanelTab - Class in jigcell.compare.ui
A default implementation of a tab providing no services.
PanelTab(Compare, String) - Constructor for class jigcell.compare.ui.PanelTab
Creates a new view with no additional functionality.
PARAMETER_CLASS - Static variable in class jigcell.compare.impl.ComparatorDataFlavor
Parameter name for the class value
PARAMETER_CLASSINTERNAL - Static variable in class jigcell.compare.impl.ComparatorDataFlavor
Parameter name for the class value
PARAMETER_CLASSINTERNALRAW - Static variable in class jigcell.compare.impl.ComparatorDataFlavor
Raw parameter name for the class value
PARAMETER_DEBUG_EXCEPTIONS - Static variable in class jigcell.compare.impl.Compare
Command line parameter to enable exception debugging
parameters - Variable in class jigcell.compare.impl.ComparatorDataFlavor
Extra parameters for this flavor
parameterTypeCache - Variable in class jigcell.compare.data.MethodDispatcher
Map between the known methods and their formalType signature
parent - Variable in class jigcell.compare.objective.ChainedDataGeneratorList
Another data generator list
parent - Variable in class jigcell.compare.ui.MenuBuilder.Builder
Parent class for global handler
parent - Variable in class jigcell.compare.ui.ProgressMonitor
Owner of this monitor
partWriters - Variable in class jigcell.compare.cellcycle.OAAConnector
Currently open file parts
PATH_ABOUT - Static variable in class jigcell.compare.ui.PanelTab
Path where about files are stored
PATH_DESCRIPTION - Static variable in class jigcell.compare.ui.IconLoader
Path fragment where icon list description is stored
PATH_DESCRIPTION - Static variable in class jigcell.compare.ui.MenuBuilder.Builder
Path fragment where menu description is stored
PATH_DESCRIPTION_ABOUT - Static variable in class jigcell.compare.ui.PanelTab
Path fragment where about description is stored
PATH_DESCRIPTION_INPUT - Static variable in class jigcell.compare.ui.CustomizableInterface
Path fragment where input description is stored
PATH_DESCRIPTION_OUTPUT - Static variable in class jigcell.compare.ui.CustomizableInterface
Path fragment where output description is stored
PATH_HELP - Static variable in class jigcell.compare.ui.CustomizableInterface
Path where help files are stored
PATH_ICON - Static variable in class jigcell.compare.ui.IconLoader
Path where icon list files are stored
PATH_MENU - Static variable in class jigcell.compare.ui.MenuBuilder.Builder
Path where menu files are stored
PATTERN_DISPATCH - Static variable in class jigcell.compare.cellcycle.OAAConnector
Pattern for matching a dispatch
PATTERN_FALSE - Static variable in class jigcell.compare.data.DataElement
Pattern for boolean false
PATTERN_FP - Static variable in class jigcell.compare.data.EditableDataElement
Pattern indicating value is floating point
PATTERN_NAN - Static variable in class jigcell.compare.data.DataElement
Pattern for NaN
PATTERN_NINFINITY - Static variable in class jigcell.compare.data.DataElement
Pattern for -Infinity
PATTERN_NINFINITY2 - Static variable in class jigcell.compare.data.DataElement
Alternate pattern for -Infinity
PATTERN_NULL - Static variable in class jigcell.compare.data.DataElement
Pattern for null
PATTERN_PINFINITY - Static variable in class jigcell.compare.data.DataElement
Pattern for +Infinity
PATTERN_PINFINITY2 - Static variable in class jigcell.compare.data.DataElement
Alternate pattern for +Infinity
PATTERN_TRUE - Static variable in class jigcell.compare.data.DataElement
Pattern for boolean true
PATTERN_VARIANT - Static variable in class jigcell.compare.cellcycle.OAAConnector
Pattern for matching a dispatch
PATTERN_VOID - Static variable in class jigcell.compare.data.DataElement
Pattern for void
pause() - Method in class jigcell.compare.views.TransformDebugger
Pauses the debugging thread.
PDFPrinterDataSource - Class in jigcell.compare.impl
A data source that prints tables to a PDF file.
PDFPrinterDataSource() - Constructor for class jigcell.compare.impl.PDFPrinterDataSource
Creates a new printer that uses PDF files.
peekElement() - Method in class jigcell.compare.data.ProgrammableDataGenerator
The element for this generator if no one holds a lock and it is available according to isCached.
peekElement() - Method in interface jigcell.compare.IProgrammableDataGenerator
The element for this generator if no one holds a lock and it is available according to isCached.
peekInterface() - Method in class jigcell.compare.data.ProgrammableDataGenerator
Retrieves the current interface without creating a new one.
penaltyLength - Variable in class jigcell.compare.data.MethodDispatcher
Penalty value for length mismatches
penaltyLengthChecked - Variable in class jigcell.compare.data.MethodDispatcher
Whether length mismatches are allowed
penaltyLooseMatch - Variable in class jigcell.compare.data.MethodDispatcher
Penalty value for loose matches
penaltyLooseMatchChecked - Variable in class jigcell.compare.data.MethodDispatcher
Whether loose formalType matches are allowed
persistSource(IPersistableDataSource) - Static method in class jigcell.compare.impl.DataSource
Persists a data source.
play(long) - Method in class jigcell.compare.views.TransformDebugger
Starts executing transforms from the transform cursor.
plot() - Method in interface jigcell.compare.plotter.IPlotter
Produces a plot from the underlying data.
plot() - Method in class jigcell.compare.plotter.JPlotBridge
Produces a plot from the underlying data.
plot() - Method in class jigcell.compare.plotter.PTPlotBridge
Produces a plot from the underlying data.
plotCell(int, int) - Method in class jigcell.compare.views.EditableSeriesView
Plots the data contained in a table cell.
plotCellAt(int, int) - Method in class jigcell.compare.cellcycle.CellCycleObjectiveView.ObjectiveModel
Plots the data contained in a table cell.
plotCellAt(int, int) - Method in class jigcell.compare.cellcycle.CellCycleTransformView.TransformModel
Plots the data contained in a table cell.
plotCellAt(int, int) - Method in class jigcell.compare.views.EditableSeriesView.EditableSeriesModel
Plots the data contained in a table cell.
plotCombineAcross(Plot) - Method in class jigcell.compare.plotter.PTPlotBridge
Produces a plot using the combine across option.
plotCombineNone(Plot) - Method in class jigcell.compare.plotter.PTPlotBridge
Produces a plot using the combine none option.
PlotException - Exception in jigcell.compare.plotter
Exception type for errors encountered when attempting to plot.
PlotException() - Constructor for exception jigcell.compare.plotter.PlotException
 
PlotException(String) - Constructor for exception jigcell.compare.plotter.PlotException
 
PlotException(Throwable) - Constructor for exception jigcell.compare.plotter.PlotException
 
PlotException(String, Throwable) - Constructor for exception jigcell.compare.plotter.PlotException
 
plotImage() - Method in class jigcell.compare.plotter.PTPlotBridge
Produces a plot image.
plotImage(Rectangle) - Method in class jigcell.compare.plotter.PTPlotBridge
Produces a plot image of the specified size.
Plotter - Class in jigcell.compare.plotter
A default implementation of PlotterInteface.
Plotter() - Constructor for class jigcell.compare.plotter.Plotter
Creates a new plotter bridge.
plotter - Variable in class jigcell.compare.views.EditableSeriesView
Plotter
plugin - Variable in class jigcell.compare.tests.ModelBuilderBenchmark
Model builder plugin
plugin - Variable in class jigcell.compare.tests.RunManagerBenchmark
Run manager plugin
popFrame() - Method in interface jigcell.compare.IEvaluationCallStack
Removes the top frame from the stack.
popFrame() - Method in class jigcell.compare.impl.EvaluationCallStack
Removes the top frame from the stack.
popup - Variable in class jigcell.compare.ui.CustomizableInterface
Context menu
popup - Variable in class jigcell.compare.ui.SeriesDialog
Context menu
popup - Variable in class jigcell.compare.views.BasicTableView
Context menu
POPUP_DEFAULT - Static variable in class jigcell.compare.ui.CustomizableInterface
Default name for the popup menu
POPUP_DEFAULT - Static variable in class jigcell.compare.ui.SeriesDialog
Default name for a popup
POPUP_DEFAULT - Static variable in class jigcell.compare.views.BasicTableView
Name of default popup
POPUP_PLOTTER - Static variable in class jigcell.compare.views.EditableSeriesView
Name of popup with plotter options
popupPoint - Variable in class jigcell.compare.ui.SeriesDialog
Location of last popup invocation
popupPoint - Variable in class jigcell.compare.views.BasicTableView
Location of last popup invocation
popups - Variable in class jigcell.compare.ui.MenuBuilder.Builder
Description for a menu bar
position - Variable in class jigcell.compare.impl.DataGeneratorEvaluator
Current position in the list of generators
POSTSCRIPT_EOF - Static variable in class jigcell.compare.impl.SystemPrinterDataSource
End of file marker in postscript documents
POSTSCRIPT_NEWLINE - Static variable in class jigcell.compare.impl.SystemPrinterDataSource
Line separator in postscript documents
POSTSCRIPT_ONEPAGE - Static variable in class jigcell.compare.impl.SystemPrinterDataSource
One page marker in postscript documents
POSTSCRIPT_PAGE - Static variable in class jigcell.compare.impl.SystemPrinterDataSource
Page marker in postscript documents
POSTSCRIPT_PAGECOUNT - Static variable in class jigcell.compare.impl.SystemPrinterDataSource
Page count operator in postscript documents
POSTSCRIPT_PAGESEPARATOR - Static variable in class jigcell.compare.impl.SystemPrinterDataSource
Page separator in postscript documents
preferredSources - Variable in class jigcell.compare.impl.DataManager
Preferred data source for each class
PREFIX_EXPERIMENT - Static variable in class jigcell.compare.cellcycle.CellCycleObjectiveView.ObjectiveModel
Prefix for experimental data
PREFIX_EXPERIMENT - Static variable in class jigcell.compare.cellcycle.CellCycleTransformView.TransformModel
Prefix for experimental data
PREFIX_TEMPFILE - Static variable in class jigcell.compare.plotter.JPlotBridge
Prefix for temporary file names
PREFIX_TRANSFORM - Static variable in class jigcell.compare.cellcycle.CellCycleObjectiveView.ObjectiveModel
Prefix for transform data
PREFIX_TRANSFORM - Static variable in class jigcell.compare.cellcycle.CellCycleTransformView.TransformModel
Prefix for transform data
prepareEditor(TableCellEditor, int, int) - Method in class jigcell.compare.ui.BasicTable
 
prepareForRead() - Method in interface jigcell.compare.impl.FileDataSource.IFileEncoder
Loads any data the encoder needs from the source's options prior to reading.
prepareForRead() - Method in class jigcell.compare.impl.XMLFileEncoder
Loads any data the encoder needs from the source's options prior to reading.
prepareForWrite() - Method in interface jigcell.compare.impl.FileDataSource.IFileEncoder
Loads any data the encoder needs from the source's options prior to writing.
prepareForWrite() - Method in class jigcell.compare.impl.XMLFileEncoder
Loads any data the encoder needs from the source's options prior to writing.
preparePopup(int, int) - Method in class jigcell.compare.compare2.Compare2
Prepares the popup for display.
preparePopup(int, int) - Method in class jigcell.compare.views.BasicTableView
Prepares the popup for display.
preparePopup(int, int) - Method in class jigcell.compare.views.EditableSeriesView
Prepares the popup for display.
preventSelectionUpdate - Variable in class jigcell.compare.views.TransformDebugger
Prevent automatic selection updating
primitives - Variable in class jigcell.compare.views.ProgrammableDataGeneratorEditor
List of primitives to build objects out of
print(Object) - Method in class jigcell.compare.views.Console
 
print() - Method in class jigcell.compare.views.SeriesView
Prints the view.
printer - Variable in class jigcell.compare.views.BasicTableView
Printer to use
printer - Variable in class jigcell.compare.views.Console
Text printer
PrinterDataSource - Class in jigcell.compare.impl
A data source that supports writing to a printer.
PrinterDataSource() - Constructor for class jigcell.compare.impl.PrinterDataSource
Creates a new data source that writes to a printer.
println(Object) - Method in class jigcell.compare.views.Console
 
processGenerator(IDataGenerator) - Method in class jigcell.compare.cellcycle.CellCycleObjectiveView
Creates a replacement data generator for evaluation. This callback will be made on the event thread. No processing will be done on the generator prior to performing this callback.
processGenerator(IDataGenerator) - Method in class jigcell.compare.cellcycle.CellCycleTransformView
Creates a replacement data generator for evaluation.
processGenerator(IDataGenerator) - Method in interface jigcell.compare.impl.DataGeneratorEvaluator.IProcessor
Creates a replacement data generator for evaluation.
processGenerator(IDataGenerator) - Method in class jigcell.compare.views.ObjectiveSeriesView
Creates a replacement data generator for evaluation.
processKeyBinding(KeyStroke, KeyEvent, int, boolean) - Method in class jigcell.compare.ui.BasicTable
 
processor - Variable in class jigcell.compare.impl.DataGeneratorEvaluator
Callback for processing generators prior to execution
ProgrammableDataGenerator - Class in jigcell.compare.data
A data generator type whose value is determined programmatically, usually with some kind of interface for controlling the program action.
ProgrammableDataGenerator() - Constructor for class jigcell.compare.data.ProgrammableDataGenerator
Creates a new data generator.
ProgrammableDataGenerator.DummyCustomizableInterface - Class in jigcell.compare.data
Acts as a placeholder for data generators that do not define a user interface handler.
ProgrammableDataGenerator.DummyCustomizableInterface(IProgrammableDataGenerator) - Constructor for class jigcell.compare.data.ProgrammableDataGenerator.DummyCustomizableInterface
Wraps the data generator with a dummy interface.
ProgrammableDataGeneratorEditor - Class in jigcell.compare.views
Supports shared functionality between the transform and objective editors.
ProgrammableDataGeneratorEditor(Compare, String) - Constructor for class jigcell.compare.views.ProgrammableDataGeneratorEditor
Creates a new editor for working with transorm or objective functions.
ProgrammableDataGeneratorEditor.SetReadHelper - Class in jigcell.compare.views
Helper class for performing read operations on other threads.
ProgrammableDataGeneratorEditor.SetReadHelper(IReadableDataSource) - Constructor for class jigcell.compare.views.ProgrammableDataGeneratorEditor.SetReadHelper
Creates a new reading helper thread.
progress - Variable in class jigcell.compare.ui.ProgressMonitor
Progress bar
ProgressMonitor - Class in jigcell.compare.ui
A progress monitor dialog similar to javax.swing.ProgressMonitor.
ProgressMonitor(Component, Object) - Constructor for class jigcell.compare.ui.ProgressMonitor
Creates a new progress monitor.
ProgressMonitor(Component, Object, int) - Constructor for class jigcell.compare.ui.ProgressMonitor
Creates a new indeterminate progress monitor.
ProgressMonitor(Component, Object, int, int) - Constructor for class jigcell.compare.ui.ProgressMonitor
Creates a new progress monitor.
promptForName(String, String) - Method in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Prompts for an object name.
PROPERTY_CANCEL - Static variable in class jigcell.compare.impl.DataGeneratorEvaluator
Event name for cancelling the evaluation
PROPERTY_COMPARISONNAMES_EDIT - Static variable in class jigcell.compare.compare2.Compare2
Property key for changing an existing comparison name
PROPERTY_COMPARISONS_EDIT - Static variable in class jigcell.compare.compare2.Compare2
Property key for changing an existing comparison
PROPERTY_CONFIG_EDIT - Static variable in class jigcell.compare.impl.Compare
Property name used when the central configuration repository has changed
PROPERTY_CUSTOMIZERNAME - Static variable in class jigcell.compare.ui.CustomizableInterface
Component client property for customizer name
PROPERTY_DEBUG_EXCEPTIONS - Static variable in class jigcell.compare.impl.Compare
Configuration property to enable exception debugging
PROPERTY_EVALUATIONFINISHED - Static variable in class jigcell.compare.impl.DataGeneratorEvaluator
Event name for a complete evaluation
PROPERTY_EVALUATIONUPDATE - Static variable in class jigcell.compare.impl.DataGeneratorEvaluator
Event name for updates
PROPERTY_EXPERIMENTTHRESHOLDS_EDIT - Static variable in class jigcell.compare.compare2.Compare2Model
Property key for changing an existing experiment threshold
PROPERTY_GENERATOR_EDIT - Static variable in interface jigcell.compare.IDataGenerator
Property key for notifications that a generator has changed
PROPERTY_MESSAGE - Static variable in class jigcell.compare.impl.DataGeneratorEvaluator
Event name for a message update
PROPERTY_OBJECTIVE_EDIT - Static variable in interface jigcell.compare.objective.IObjective
Property key for notifications that a function has changed
PROPERTY_PROGRESS - Static variable in class jigcell.compare.impl.DataGeneratorEvaluator
Event name for a progress update
PROPERTY_PROGRESSMONITOR - Static variable in class jigcell.compare.ui.ProgressMonitor
Property for the creation and destruction of this monitor's view
PROPERTY_RECENTSOURCETARGET - Static variable in class jigcell.compare.ui.DataEditorPanelTab
Property for storing recent sources within a menu item
PROPERTY_TRANSFORM_EDIT - Static variable in interface jigcell.compare.transform.ITransform
Property key for notifications that a transform has changed
propertyChange(PropertyChangeEvent) - Method in class jigcell.compare.cellcycle.CellCycleObjectiveView
 
propertyChange(PropertyChangeEvent) - Method in class jigcell.compare.cellcycle.CellCycleReportGenerator
 
propertyChange(PropertyChangeEvent) - Method in class jigcell.compare.cellcycle.CellCycleTransformView
 
propertyChange(PropertyChangeEvent) - Method in class jigcell.compare.compare2.ThresholdEditor
 
propertyChange(PropertyChangeEvent) - Method in class jigcell.compare.compare2.ViewColorer
 
propertyChange(PropertyChangeEvent) - Method in class jigcell.compare.data.ProgrammableDataGenerator
 
propertyChange(PropertyChangeEvent) - Method in class jigcell.compare.impl.Compare
 
propertyChange(PropertyChangeEvent) - Method in class jigcell.compare.impl.DataGeneratorEvaluator
 
propertyChange(PropertyChangeEvent) - Method in class jigcell.compare.impl.DataSource
 
propertyChange(PropertyChangeEvent) - Method in class jigcell.compare.tests.ExperimentBenchmark
 
propertyChange(PropertyChangeEvent) - Method in class jigcell.compare.tests.ObjectiveBenchmark
 
propertyChange(PropertyChangeEvent) - Method in class jigcell.compare.tests.SystemTests
 
propertyChange(PropertyChangeEvent) - Method in class jigcell.compare.tests.TransformBenchmark
 
propertyChange(PropertyChangeEvent) - Method in class jigcell.compare.transform.InputTransform
 
propertyChange(PropertyChangeEvent) - Method in class jigcell.compare.transform.TransformContainer
 
propertyChange(PropertyChangeEvent) - Method in class jigcell.compare.ui.BasicTable.BasicEditor
 
propertyChange(PropertyChangeEvent) - Method in class jigcell.compare.ui.BasicTable.BasicRenderer
 
propertyChange(PropertyChangeEvent) - Method in class jigcell.compare.ui.CompareFrontEnd
 
propertyChange(PropertyChangeEvent) - Method in class jigcell.compare.ui.PanelTab
 
propertyChange(PropertyChangeEvent) - Method in class jigcell.compare.ui.ProgressMonitor
 
propertyChange(PropertyChangeEvent) - Method in class jigcell.compare.views.EditableSeriesView
 
propertyChange(PropertyChangeEvent) - Method in class jigcell.compare.views.ObjectiveSeriesView
 
propertyChange(PropertyChangeEvent) - Method in class jigcell.compare.views.ProgrammableDataGeneratorEditor
 
propertyChange(PropertyChangeEvent) - Method in class jigcell.compare.views.TransformDebugger.TransformTreeRenderer
 
propertyHit - Variable in class jigcell.compare.tests.SystemTests
Whether the currently monitored property change has been detected
propertyKey - Variable in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Edit property key to advertise in events
propertySupport - Variable in class jigcell.compare.impl.Compare
Support for handling property change events
propertySupport - Variable in class jigcell.compare.impl.DataGeneratorEvaluator
Support for handling property change events
propertySupport - Variable in class jigcell.compare.impl.DataSource
Support for handling property change events
prototypeChild - Variable in class jigcell.compare.data.EditableDataElement
Prototypical instance of a subelement
proxyActionListener(Object, String) - Static method in class jigcell.compare.impl.ProxyBuilder
Creates a new proxy object for an ActionListener.
ProxyBuilder - Class in jigcell.compare.impl
Constructs proxy instances for commonly used Comparator interfaces.
ProxyBuilder(Object) - Constructor for class jigcell.compare.impl.ProxyBuilder
Creates a new invocation handler.
proxyComparator(Object, String) - Static method in class jigcell.compare.impl.ProxyBuilder
Creates a new proxy object for a Comparator.
proxyEvaluationListener(Object, String, String, String) - Static method in class jigcell.compare.impl.ProxyBuilder
Creates a new proxy object for a Runnable.
proxyPropertyChangeListener(Object, String) - Static method in class jigcell.compare.impl.ProxyBuilder
Creates a new proxy object for a PropertyChangeListener.
proxyRunnable(Object, String) - Static method in class jigcell.compare.impl.ProxyBuilder
Creates a new proxy object for a Runnable.
PTPlotBridge - Class in jigcell.compare.plotter
Standard interface for PTPlot.
PTPlotBridge() - Constructor for class jigcell.compare.plotter.PTPlotBridge
Creates a new Ptplot bridge.
pumpInput(ActionEvent) - Method in class jigcell.compare.views.Console
Runs a single command.
pumpOutput() - Method in class jigcell.compare.views.Console
Posts events to write text back to the console.
pushFrame(IProgrammableDataGenerator) - Method in interface jigcell.compare.IEvaluationCallStack
Adds a new frame to the stack.
pushFrame(IProgrammableDataGenerator) - Method in class jigcell.compare.impl.EvaluationCallStack
Adds a new frame to the stack.
put(IDataGeneratorCollection.Key, IDataGenerator) - Method in class jigcell.compare.data.DataGeneratorMap
Adds a mapping between a key and generator.
put(String, String, IDataGenerator) - Method in class jigcell.compare.data.DataGeneratorMap
Adds a mapping between a name, id, and generator.
put(IDataGeneratorCollection.Key, IDataGenerator) - Method in interface jigcell.compare.data.IDataGeneratorMap
Adds a mapping between a key and generator.
put(String, String, IDataGenerator) - Method in interface jigcell.compare.data.IDataGeneratorMap
Adds a mapping between a name, id, and generator.
put(IResultSetMap, String) - Method in interface jigcell.compare.data.IResultSetGroupMap
Adds a mapping between a result set and a name.
put(IDataGeneratorCollection.Key, IDataElement) - Method in interface jigcell.compare.data.IResultSetMap
Adds a mapping between a key and result.
put(IDataGeneratorCollection.Key, String) - Method in interface jigcell.compare.data.IResultSetMap
Adds a mapping between a key and result.
put(String, String, IDataElement) - Method in interface jigcell.compare.data.IResultSetMap
Adds a mapping between a name, id, and result.
put(String, String, String) - Method in interface jigcell.compare.data.IResultSetMap
Adds a mapping between a name, id, and result.
put(IResultSetMap, String) - Method in class jigcell.compare.data.ResultSetGroupMap
Adds a mapping between a result set and a name.
put(IDataGeneratorCollection.Key, IDataElement) - Method in class jigcell.compare.data.ResultSetMap
Adds a mapping between a key and result.
put(IDataGeneratorCollection.Key, String) - Method in class jigcell.compare.data.ResultSetMap
Adds a mapping between a key and result.
put(String, String, IDataElement) - Method in class jigcell.compare.data.ResultSetMap
Adds a mapping between a name, id, and result.
put(String, String, String) - Method in class jigcell.compare.data.ResultSetMap
Adds a mapping between a name, id, and result.
putAll(Map) - Method in class jigcell.compare.data.DataGeneratorMap
Adds all the entries from the map to this map.
putAll(Map) - Method in interface jigcell.compare.data.IDataGeneratorMap
Adds all the entries from the map to this map.
putAll(Map) - Method in interface jigcell.compare.data.IResultSetGroupMap
Adds all the entries from the map to this map.
putAll(Map) - Method in interface jigcell.compare.data.IResultSetMap
Adds all the entries from the map to this map.
putAll(Map) - Method in class jigcell.compare.data.ResultSetGroupMap
Adds all the entries from the map to this map.
putAll(Map) - Method in class jigcell.compare.data.ResultSetMap
Adds all the entries from the map to this map.
putChecked(long, Object) - Method in class jigcell.compare.data.EditableDataElement
Sets the value at a position.
putColor(String, Color) - Method in class jigcell.compare.ui.BasicTable.BasicEditor
Sets a color for use with this editor.
putColor(String, Color) - Method in class jigcell.compare.ui.BasicTable.BasicRenderer
Sets a color for use with this renderer.
putColor(String, Color) - Method in class jigcell.compare.views.TransformDebugger.TransformTreeRenderer
Sets a color for use with this renderer.
putDirect(long, Object) - Method in class jigcell.compare.data.EditableDataElement
Sets the value at a position.
putDirect(long, Object) - Method in class jigcell.compare.data.PackedDoubleDataElement
Sets the value at a position.
putDirect(long, Object) - Method in class jigcell.compare.data.PackedTreeDataElement
Sets the value at a position.
putDirect(long, Object) - Method in class jigcell.compare.data.PackedTreeDataElement2
Sets the value at a position. Boolean values are represented by Boolean. Empty values are represented by null. Integral values are represented by Integer. Literal values are represented by String. Multiple values are represented by DataElement. Real values are represented by Double. The position of the object may be anything.
putDirect(long, Object) - Method in class jigcell.compare.data.SparseTreeDataElement
Sets the value at a position.
putDirect(long, Object) - Method in class jigcell.compare.data.SparseTreeDataElement2
Sets the value at a position. Boolean values are represented by Boolean. Empty values are represented by null. Integral values are represented by Integer. Literal values are represented by String. Multiple values are represented by DataElement. Real values are represented by Double. The position of the object may be anything.

R

RawFileDataSource - Class in jigcell.compare.impl
A transfer agent that supports reading and writing data to a regular file.
RawFileDataSource() - Constructor for class jigcell.compare.impl.RawFileDataSource
Creates a new data source that represents a file.
RawFileDataSource(String) - Constructor for class jigcell.compare.impl.RawFileDataSource
Creates a new data source that represents a file.
read() - Method in class jigcell.compare.data.DataGenerator
The contents of this data source or the first available content if multiple objects are supported.
read() - Method in class jigcell.compare.impl.ClipboardDataSource
The contents of this data source or the first available content if multiple objects are supported.
read() - Method in interface jigcell.compare.impl.FileDataSource.IFileEncoder
 
read() - Method in class jigcell.compare.impl.FileDataSource
The contents of this data source or the first available content if multiple objects are supported. If the file input option has not been initialized, this method may have to do some file work while holding the options lock to avoid race conditions.
read() - Method in class jigcell.compare.impl.XMLFileEncoder
read() - Method in interface jigcell.compare.IReadableDataSource
The contents of this data source or the first available content if multiple objects are supported.
read() - Method in class jigcell.compare.tests.ConstantDataSource
The contents of this data source or the first available content if multiple objects are supported.
read() - Method in class jigcell.compare.ui.DataEditorPanelTab.ReadHelper
Reads data from some external source.
READ_LOCK - Variable in class jigcell.compare.ui.DataEditorPanelTab
Lock for temporary read result
readables - Variable in class jigcell.compare.impl.DataManager
Readable data sources
readConfiguration(String) - Method in class jigcell.compare.cellcycle.CellCycleExperimentView.ExperimentViewRenderer
readConfiguration(String) - Method in class jigcell.compare.cellcycle.CellCycleExperimentView
Reads the view configuration from the Comparator.
readConfiguration(String) - Method in class jigcell.compare.cellcycle.CellCycleObjectiveView.ObjectiveViewRenderer
readConfiguration(String) - Method in class jigcell.compare.cellcycle.CellCycleTransformView
Reads the view configuration from the Comparator.
readConfiguration(String) - Method in class jigcell.compare.cellcycle.CellCycleTransformView.TransformViewRenderer
readConfiguration(String) - Method in class jigcell.compare.compare2.Compare2
Reads the view configuration from the Comparator.
readConfiguration(String) - Method in class jigcell.compare.compare2.TriColorViewColorer
readConfiguration(String) - Method in interface jigcell.compare.ITab
Reads the view configuration from the Comparator.
readConfiguration(String) - Method in class jigcell.compare.ui.BasicTable.BasicEditor
 
readConfiguration(String) - Method in class jigcell.compare.ui.BasicTable.BasicRenderer
 
readConfiguration(String) - Method in class jigcell.compare.ui.CompareFrontEnd
Reads the view configuration from the Comparator.
readConfiguration(String) - Method in class jigcell.compare.ui.DataEditorPanelTab
Reads the view configuration from the Comparator.
readConfiguration(String) - Method in class jigcell.compare.ui.PanelTab
Reads the view configuration from the Comparator.
readConfiguration(String) - Method in class jigcell.compare.ui.SeriesDialog
Reads the view configuration from the Comparator.
readConfiguration(String) - Method in class jigcell.compare.views.EditableSeriesView
Reads the view configuration from the Comparator.
readConfiguration(String) - Method in class jigcell.compare.views.ObjectiveEditor
Reads the view configuration from the Comparator.
readConfiguration(String) - Method in class jigcell.compare.views.ObjectiveSeriesView.ObjectiveSeriesRenderer
readConfiguration(String) - Method in class jigcell.compare.views.SeriesView
Reads the view configuration from the Comparator.
readConfiguration(String) - Method in class jigcell.compare.views.TransformDebugger.TransformTreeRenderer
Reads the renderer configuration from the Comparator.
readConfiguration(String) - Method in class jigcell.compare.views.TransformEditor
Reads the view configuration from the Comparator.
readDocument(Document) - Static method in class jigcell.compare.ui.InterfaceBuilder
Reads the text out of document.
reader - Variable in class jigcell.compare.impl.StreamingStringTokenizer
Input for tokenizer
reader - Variable in class jigcell.compare.views.Console
Data coming in through the printer
ReadFromFileTransform - Class in jigcell.compare.transform
A transform that reads data from a file.
ReadFromFileTransform() - Constructor for class jigcell.compare.transform.ReadFromFileTransform
Creates a new transform to read from a file.
readInternal(Object) - Method in class jigcell.compare.cellcycle.CellCycleExperimentView
Processes data that has been read from some external source.
readInternal(Object) - Method in class jigcell.compare.cellcycle.CellCycleTransformView
Processes data that has been read from some external source.
readInternal(Object) - Method in class jigcell.compare.compare2.Compare2
Processes data that has been read from some external source.
readInternal(Object) - Method in class jigcell.compare.ui.DataEditorPanelTab
Processes data that has been read from some external source.
readInternal(Object) - Method in class jigcell.compare.views.EditableSeriesView
Processes data that has been read from some external source.
readInternal(Object) - Method in class jigcell.compare.views.ObjectiveSeriesView
Processes data that has been read from some external source.
readInternal(Object) - Method in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Processes data that has been read from some external source.
readInternalSet(Object, String) - Method in class jigcell.compare.compare2.Compare2
Processes data that has been read from some external source.
readInternalSet(Object) - Method in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Imports all of the entries from the range of a data generator map.
readInternalThreshold(Object) - Method in class jigcell.compare.compare2.Compare2
Processes data that has been read from some external source.
readNotify() - Method in class jigcell.compare.cellcycle.CellCycleTransformView
Notifies listeners after a read operation has completed.
readNotify() - Method in class jigcell.compare.compare2.Compare2
Notifies listeners after a read operation has completed.
readNotify() - Method in class jigcell.compare.ui.DataEditorPanelTab
Notifies listeners after a read operation has completed.
readNotify() - Method in class jigcell.compare.views.EditableSeriesView
Notifies listeners after a read operation has completed.
readNotify() - Method in class jigcell.compare.views.ObjectiveSeriesView
Notifies listeners after a read operation has completed.
readNotify() - Method in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Notifies listeners after a read operation has completed.
readNotifySet() - Method in class jigcell.compare.compare2.Compare2
Notifies listeners after a read operation has completed.
readNotifyThreshold() - Method in class jigcell.compare.compare2.Compare2
Notifies listeners after a read operation has completed.
readObject(ObjectInputStream) - Method in class jigcell.compare.data.CachedDataElement
 
readResult - Variable in class jigcell.compare.ui.DataEditorPanelTab.ReadHelper
Temporary read result
readSource - Variable in class jigcell.compare.ui.DataEditorPanelTab.ReadHelper
Data source to read from
REAL - Static variable in class jigcell.compare.IDataElement.Type
A scalar value contained in the reals
RealTypeChecker - Class in jigcell.compare.data.type
Type for real data.
RealTypeChecker() - Constructor for class jigcell.compare.data.type.RealTypeChecker
Creates a new type checker.
reap() - Method in class jigcell.compare.transform.TransformContext.ReaperReference
Cleans up the context holding this reference.
reaperReferenceRun() - Static method in class jigcell.compare.transform.TransformContext
Removes unreachable transforms from contexts.
recentReadablesMenu - Variable in class jigcell.compare.ui.DataEditorPanelTab
Menu listing the recently used readable data sources
recordMap - Variable in class jigcell.compare.transform.annotation.TransformAnnotation
Storage for annotation records
ref - Variable in class jigcell.compare.data.CachedDataElement
Data element to cache
referenceElement - Variable in class jigcell.compare.objectiveui.WeightEditorDialog
Data element of the reference selection
referenceQueue - Static variable in class jigcell.compare.transform.TransformContext
Reference queue for finding out that a registered transform has been collected
references - Variable in class jigcell.compare.transform.TransformContext
Map[Reference,String] from references to registered transforms to registered names
refreshTree() - Method in class jigcell.compare.views.TransformDebugger
Reconstructs the transform tree.
registerDescriptor(ITransformAnnotation) - Static method in class jigcell.compare.transform.annotation.TransformAnnotation.AnnotationDescriptor
Registers this descriptor with an annotation.
registered - Variable in class jigcell.compare.transform.TransformContext
Map[ITransform,String] from registered transforms to registered names
registered - Variable in class jigcell.compare.ui.InterfaceBuilder
Components registered by this interface
registerHost(IBasicTableHost) - Method in class jigcell.compare.ui.BasicTable.BasicEditor
Hooks this editor up to the host so that configuration data can be obtained.
registerHost(IBasicTableHost) - Method in class jigcell.compare.ui.BasicTable.BasicRenderer
Hooks this renderer up to the host so that configuration data can be obtained.
registerTransform(ITransform) - Method in interface jigcell.compare.transform.ITransformContext
Gives a name to an anonymous transform.
registerTransform(ITransform, String) - Method in interface jigcell.compare.transform.ITransformContext
Registers a transform so that it can later be identified by this context.
registerTransform(ITransform) - Method in class jigcell.compare.transform.TransformContext
Gives a name to an anonymous transform.
registerTransform(ITransform, String) - Method in class jigcell.compare.transform.TransformContext
Registers a transform so that it can later be identified by this context.
registrationLock - Static variable in class jigcell.compare.transform.TransformContext
Lock for manipulating transform registration information
RELATION_EQUALITY - Static variable in interface jigcell.compare.objective.IRelationalObjective
Default relation of equality
RELATION_GREATERTHAN - Static variable in interface jigcell.compare.objective.IRelationalObjective
Default relation of greater than
RELATION_GREATERTHANEQUAL - Static variable in interface jigcell.compare.objective.IRelationalObjective
Default relation of greater than or equal
RELATION_INEQUALITY - Static variable in interface jigcell.compare.objective.IRelationalObjective
Default relation of inequality
RELATION_LESSTHAN - Static variable in interface jigcell.compare.objective.IRelationalObjective
Default relation of less than
RELATION_LESSTHANEQUAL - Static variable in interface jigcell.compare.objective.IRelationalObjective
Default relation of less then or equal
relationsModel - Variable in class jigcell.compare.objectiveui.BooleanRelationalInterface
Relations box model
remove(int) - Method in class jigcell.compare.data.DataGeneratorList
Removes a generator from this list.
remove(int) - Method in interface jigcell.compare.data.IDataGeneratorList
Removes a generator from this list.
remove(String) - Method in class jigcell.compare.impl.Blackboard
Removes a data item or namespace from the blackboard.
remove(IProgrammableDataGenerator) - Method in class jigcell.compare.views.EvaluationErrorViewer
Stops monitoring for a data generator.
remove(ITransformContext) - Method in class jigcell.compare.views.EvaluationErrorViewer
Stops monitoring for a transform evaluation context.
removeAll() - Method in class jigcell.compare.ui.ListComboBoxModel
Removes all entries in this model.
removeAll() - Method in class jigcell.compare.views.EvaluationErrorViewer
Stops all monitoring.
removeConfig(String) - Method in class jigcell.compare.impl.Config
Removes a marker from this configurator.
removeDirect(long) - Method in class jigcell.compare.data.EditableDataElement
Removes the value at a position.
removeDirect(long) - Method in class jigcell.compare.data.PackedDoubleDataElement
Removes the value at a position.
removeDirect(long) - Method in class jigcell.compare.data.PackedTreeDataElement
Removes the value at a position.
removeDirect(long) - Method in class jigcell.compare.data.PackedTreeDataElement2
Removes the value at a position. The position of the object may be anything.
removeDirect(long) - Method in class jigcell.compare.data.SparseTreeDataElement
Removes the value at a position.
removeDirect(long) - Method in class jigcell.compare.data.SparseTreeDataElement2
Removes the value at a position. The position of the object may be anything.
removeElement(Object) - Method in class jigcell.compare.ui.ListComboBoxModel
 
removeElementAt(int) - Method in class jigcell.compare.ui.ListComboBoxModel
 
removeEvaluationListener(IEvaluationListener) - Method in class jigcell.compare.data.ProgrammableDataGenerator
Removes a listener from this generator.
removeEvaluationListener(IEvaluationListener) - Method in interface jigcell.compare.IProgrammableDataGenerator
Removes a listener from this generator.
removeEvaluationListener(IEvaluationListener) - Method in interface jigcell.compare.transform.ITransformContext
Removes a listener for all generators in this context.
removeEvaluationListener(IEvaluationListener) - Method in class jigcell.compare.transform.TransformContext
Removes a listener for all generators in this context.
removeFromClipboardContents(Clipboard, Transferable) - Method in class jigcell.compare.impl.ClipboardDataSource
Removes a transferable from the clipboard contents option.
removeListener(PropertyChangeListener) - Method in class jigcell.compare.impl.Blackboard
Removes a listener to the blackboard.
removeListener(String, PropertyChangeListener) - Method in class jigcell.compare.impl.Blackboard
Removes a listener to the blackboard for a specific property.
removePropertyChangeListener(PropertyChangeListener) - Method in class jigcell.compare.impl.Compare
Removes a PropertyChangeListener from the listener list.
removePropertyChangeListener(String, PropertyChangeListener) - Method in class jigcell.compare.impl.Compare
Removes a PropertyChangeListener for a specific property.
removePropertyChangeListener(PropertyChangeListener) - Method in class jigcell.compare.impl.DataGeneratorEvaluator
Removes a PropertyChangeListener from the listener list.
removePropertyChangeListener(PropertyChangeListener) - Method in class jigcell.compare.impl.DataSource
Removes a PropertyChangeListener from the listener list.
removePropertyChangeListener(String, PropertyChangeListener) - Method in class jigcell.compare.impl.DataSource
Removes a PropertyChangeListener for a specific property.
removeResource(String) - Method in class jigcell.compare.impl.Compare
Deletes a named resource.
removeTransformEvaluationContextListener(ITransformContextListener) - Method in interface jigcell.compare.transform.ITransformContext
Removes a listener for this context.
removeTransformEvaluationContextListener(ITransformContextListener) - Method in class jigcell.compare.transform.TransformContext
Removes a listener for this context.
removeUpdate(DocumentEvent) - Method in class jigcell.compare.objectiveui.ScriptEvaluationInterface
 
removeUpdate(DocumentEvent) - Method in class jigcell.compare.transformui.ScriptEvaluationInterface
 
removeUpdate(DocumentEvent) - Method in class jigcell.compare.ui.ConfigEditor
 
removeValue(String) - Method in class jigcell.compare.impl.Config
Removes a key from this configurator.
rename(IProgrammableDataGenerator) - Method in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Renames an object.
replaceAll(List) - Method in class jigcell.compare.ui.ListComboBoxModel
Replaces all elements in this model with a new list.
replaceDocument(Document, String) - Static method in class jigcell.compare.ui.InterfaceBuilder
Replaces the text in a document.
replaceResource(String, Object) - Method in class jigcell.compare.impl.Compare
Adds a mapping between the give name and resource replacing any existing mapping.
REPORT - Static variable in class jigcell.compare.impl.ExceptionRecorder
Flag to report the exception to the user
reportMessage - Variable in class jigcell.compare.impl.ExceptionRecorder
Message to use when reporting an exception
requestUpdate() - Method in class jigcell.compare.compare2.ResultViewZoom
Requests that the zoom view update the display.
reset() - Method in class jigcell.compare.cellcycle.CellCycleTransformView
Resets results computed by this view.
reset(int[]) - Method in class jigcell.compare.cellcycle.CellCycleTransformView
Resets a subset of the results computed by this view.
reset() - Method in class jigcell.compare.data.MethodDispatcher.MethodScorer
Resets any progress recorded for this method score.
reset() - Static method in class jigcell.compare.tests.Benchmark
Attempts to bring the VM to a controlled state.
reset() - Method in interface jigcell.compare.ui.IResultTab
Resets results computed by this view.
reset(int[]) - Method in interface jigcell.compare.ui.IResultTab
Resets a subset of the results computed by this view.
reset() - Method in class jigcell.compare.views.ObjectiveSeriesView
Resets results computed by this view.
reset(int[]) - Method in class jigcell.compare.views.ObjectiveSeriesView
Resets a subset of the results computed by this view.
resetControls() - Method in class jigcell.compare.compare2.ThresholdEditor
Resets the editing controls.
resizeColumns() - Method in class jigcell.compare.ui.BasicTable
Sets the widths for table columns.
resizeColumnsEqually(int, int, int[]) - Static method in class jigcell.compare.ui.BasicTable
Computes the widths for table columns, trying to make every column the same size.
resizeColumnsUnequally(int, int, int[], int[], double[]) - Static method in class jigcell.compare.ui.BasicTable
Computes the widths for table columns, trying to make the ratios of column width to column weight the same.
resizeTableColumns() - Method in class jigcell.compare.compare2.Compare2
Resizes the table columns.
resizeTableColumnsRunnable - Variable in class jigcell.compare.compare2.Compare2
Runnable for resizing the table columns after all events have been processed.
resource - Variable in class jigcell.compare.ui.HTMLComponentDescription
Cached copy of the description
resource - Variable in class jigcell.compare.ui.TextComponentDescription
Cached copy of the description
RESOURCE_COMPARISONNAMES - Static variable in class jigcell.compare.compare2.Compare2
Resource key for the list of available comparison names
RESOURCE_COMPARISONS - Static variable in class jigcell.compare.compare2.Compare2
Resource key for the list of available comparisons
RESOURCE_CONFIG - Static variable in class jigcell.compare.impl.Compare
Resource key for the central configuration repository
RESOURCE_DATAMANAGER - Static variable in class jigcell.compare.impl.Compare
Resource key for the central data source maintainer
RESOURCE_EXPERIMENTCOMPARISONS - Static variable in class jigcell.compare.compare2.Compare2Model
Resource key for the list of available experiment comparison types
RESOURCE_EXPERIMENTTHRESHOLDS - Static variable in class jigcell.compare.compare2.Compare2Model
Resource key for the list of available experiment thresholds
RESOURCE_GENERATORS - Static variable in interface jigcell.compare.IDataGenerator
Resource key for the list of available generators
RESOURCE_LASTTABLESELECTION - Static variable in class jigcell.compare.views.BasicTableView
Resource key for last table selection
RESOURCE_LOCK - Variable in class jigcell.compare.impl.Compare
Lock for controlling resource manipulation
RESOURCE_OBJECTIVES - Static variable in interface jigcell.compare.objective.IObjective
Resource key for the list of available objective functions
RESOURCE_TABLESELECTION - Static variable in class jigcell.compare.views.BasicTableView
Resource key for table selection
RESOURCE_TABS - Static variable in class jigcell.compare.impl.Compare
Resource key for tabs added to the Comparator
RESOURCE_TRANSFORMS - Static variable in interface jigcell.compare.transform.ITransform
Resource key for the list of available transform functions
resourceBundle - Static variable in class jigcell.compare.impl.Compare
Resource bundle for string translation
resourceKey - Variable in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Resource key to advertise in events
resources - Variable in class jigcell.compare.impl.Compare
Collection of resources maintained for system
result - Variable in class jigcell.compare.tests.ExperimentBenchmark
Record of loading results
result - Variable in class jigcell.compare.tests.ModelBuilderBenchmark
Record of benchmark results
result - Variable in class jigcell.compare.tests.ObjectiveBenchmark
Record of loading results
result - Variable in class jigcell.compare.tests.RunManagerBenchmark
Record of loading results
result - Variable in class jigcell.compare.tests.TransformBenchmark
Record of loading results
resultNameDocument - Variable in class jigcell.compare.transformui.InputInterface
Inputting name of the result to publish
ResultSetGroupMap - Class in jigcell.compare.data
Manages a map of result sets.
ResultSetGroupMap() - Constructor for class jigcell.compare.data.ResultSetGroupMap
Creates a new map between result sets and names.
ResultSetGroupMap(int, float) - Constructor for class jigcell.compare.data.ResultSetGroupMap
Creates a new map between result sets and names.
ResultSetGroupMap.ResultSetGroupMapDelegate - Class in jigcell.compare.data
Persists the mapping by using a series of put statements.
ResultSetGroupMap.ResultSetGroupMapDelegate() - Constructor for class jigcell.compare.data.ResultSetGroupMap.ResultSetGroupMapDelegate
 
ResultSetMap - Class in jigcell.compare.data
Manages a map of results.
ResultSetMap() - Constructor for class jigcell.compare.data.ResultSetMap
Creates a new map between names and results.
ResultSetMap(int, float) - Constructor for class jigcell.compare.data.ResultSetMap
Creates a new map between names and results.
ResultSetMap.ResultSetMapDelegate - Class in jigcell.compare.data
Persists the mapping by using a series of put statements.
ResultSetMap.ResultSetMapDelegate() - Constructor for class jigcell.compare.data.ResultSetMap.ResultSetMapDelegate
 
ResultViewZoom - Class in jigcell.compare.compare2
A visualization tool that displays a zoomable image of models against results.
ResultViewZoom(Compare, Compare2) - Constructor for class jigcell.compare.compare2.ResultViewZoom
Creates a new display for viewing models against results.
reverseRegistered - Variable in class jigcell.compare.transform.TransformContext
Map[String,ITransform] from registered names to references to registered transforms
rewardMatch - Variable in class jigcell.compare.data.MethodDispatcher
Reward value for a match
rewardSubclass - Variable in class jigcell.compare.data.MethodDispatcher
Reward value for having a specialized match
rewardSubclassChecked - Variable in class jigcell.compare.data.MethodDispatcher
Whether specialized matches are rewarded
root - Variable in class jigcell.compare.views.TransformDebugger
Root of the transform tree
rootConfig - Variable in class jigcell.compare.ui.ConfigEditor
Source of config information
row - Variable in class jigcell.compare.ui.BasicTable.ButtonEditor
Row being edited
row - Variable in class jigcell.compare.ui.ViewerDialog
Row in the parent table
run(int) - Method in class jigcell.compare.cellcycle.JigCellRunManagerTransform
Executes one of the runs from the run file.
run() - Method in class jigcell.compare.ui.CompareFrontEnd.SplashScreen
 
run() - Method in class jigcell.compare.views.TransformDebugger.DebuggerThread
 
RUN_DEFAULT - Static variable in class jigcell.compare.cellcycle.JigCellRunManagerTransform
Run number when a run should be picked automatically
RUN_UNKNOWN - Static variable in class jigcell.compare.cellcycle.JigCellRunManagerTransform
Run number when no run has been selected
runBenchmark() - Method in class jigcell.compare.tests.ExperimentBenchmark
Runs a collection of benchmarks for loading experiment files.
runBenchmark() - Method in class jigcell.compare.tests.ModelBuilderBenchmark
Runs a collection of benchmarks for loading models.
runBenchmark() - Method in class jigcell.compare.tests.ObjectiveBenchmark
Runs a collection of benchmarks for loading objective files.
runBenchmark() - Method in class jigcell.compare.tests.RunManagerBenchmark
Runs a collection of benchmarks for loading run files.
runBenchmark() - Method in class jigcell.compare.tests.TransformBenchmark
Runs a collection of benchmarks for loading transform files.
runBenchmark2() - Method in class jigcell.compare.tests.ModelBuilderBenchmark
Runs a collection of benchmarks for loading models.
runBenchmark2() - Method in class jigcell.compare.tests.RunManagerBenchmark
Runs a collection of benchmarks for loading run files.
runBenchmark3() - Method in class jigcell.compare.tests.ModelBuilderBenchmark
Runs a collection of benchmarks for loading models.
runBenchmark3() - Method in class jigcell.compare.tests.RunManagerBenchmark
Runs a collection of benchmarks for loading run files.
runBenchmarkAddRow() - Method in class jigcell.compare.tests.ExperimentBenchmark
Runs a collection of benchmarks for adding to experiment files.
runBenchmarkAddRow() - Method in class jigcell.compare.tests.ModelBuilderBenchmark
Runs a collection of benchmarks for adding to model files.
runBenchmarkAddRow() - Method in class jigcell.compare.tests.ObjectiveBenchmark
Runs a collection of benchmarks for configuring a new experiment.
runBenchmarkAddRow() - Method in class jigcell.compare.tests.RunManagerBenchmark
Runs a collection of benchmarks for adding to run files.
runBenchmarkExecute() - Method in class jigcell.compare.tests.RunManagerBenchmark
Runs a collection of benchmarks for executing runs.
runBenchmarkModify() - Method in class jigcell.compare.tests.RunManagerBenchmark
Runs a collection of benchmarks for modifying runs.
runFileDocument - Variable in class jigcell.compare.cellcycle.JigCellRunManagerInterface
Run name selector document
runGroup - Variable in class jigcell.compare.cellcycle.JigCellRunManagerInterface
Button group for run selection
runManager - Variable in class jigcell.compare.tests.RunManagerPlugin
Run manager application
RunManagerBenchmark - Class in jigcell.compare.tests
A collection of tests for evaluating run manager performance.
RunManagerBenchmark(Compare) - Constructor for class jigcell.compare.tests.RunManagerBenchmark
Creates a new tester for run manager loading performance.
RunManagerPlugin - Class in jigcell.compare.tests
A test class for using the Run Manager as a plugin.
RunManagerPlugin(Compare, String) - Constructor for class jigcell.compare.tests.RunManagerPlugin
Creates a new run manager instance.
runNumberModel - Variable in class jigcell.compare.cellcycle.JigCellRunManagerInterface
Model for run number selector
runOffEventThread() - Method in class jigcell.compare.tests.Benchmark
Performs the tester computations that do not interact with the interface.
runOffEventThread() - Method in class jigcell.compare.tests.ElementBenchmark
Performs the tester computations that do not interact with the interface.
runOffEventThread() - Method in class jigcell.compare.tests.ExperimentBenchmark
Performs the tester computations that do not interact with the interface.
runOffEventThread() - Method in class jigcell.compare.tests.ModelBuilderBenchmark
Performs the tester computations that do not interact with the interface.
runOffEventThread() - Method in class jigcell.compare.tests.ObjectiveBenchmark
Performs the tester computations that do not interact with the interface.
runOffEventThread() - Method in class jigcell.compare.tests.RunManagerBenchmark
Performs the tester computations that do not interact with the interface.
runOffEventThread() - Method in class jigcell.compare.tests.TransformBenchmark
Performs the tester computations that do not interact with the interface.
runOnEventThread(int) - Method in class jigcell.compare.tests.Benchmark
Performs an operation that interacts with the interface.
runOnEventThread(int) - Method in class jigcell.compare.tests.ElementBenchmark
Performs an operation that interacts with the interface.
runOnEventThread(int) - Method in class jigcell.compare.tests.ExperimentBenchmark
Performs an operation that interacts with the interface.
runOnEventThread(int) - Method in class jigcell.compare.tests.ModelBuilderBenchmark
Performs an operation that interacts with the interface.
runOnEventThread(int) - Method in class jigcell.compare.tests.ObjectiveBenchmark
Performs an operation that interacts with the interface.
runOnEventThread(int) - Method in class jigcell.compare.tests.RunManagerBenchmark
Performs an operation that interacts with the interface.
runOnEventThread(int) - Method in class jigcell.compare.tests.TransformBenchmark
Performs an operation that interacts with the interface.
runState(int) - Method in class jigcell.compare.tests.Benchmark
Starts an operation that will interact with the interface.

S

SAFE - Static variable in class jigcell.compare.IDataSource.Option
Indicates that an option should be copied and persisted with the data source.
SAVE - Static variable in class jigcell.compare.impl.ExceptionRecorder
Flag to save the exception
save(IWriteableDataSource) - Method in class jigcell.compare.ui.DataEditorPanelTab
Saves the data for the view to some external source.
save(IWriteableDataSource) - Method in interface jigcell.compare.ui.IDataEditorTab
Saves the data for the view to some external source.
saveDirect(IWriteableDataSource) - Method in class jigcell.compare.ui.DataEditorPanelTab
Saves the data for the view to some external source without user prompting.
saveDirect(IWriteableDataSource) - Method in interface jigcell.compare.ui.IDataEditorTab
Saves the data for the view to some external source without user prompting.
saveModel(String) - Method in class jigcell.compare.tests.ModelBuilderPlugin
Saves the current model.
saveResults(IWriteableDataSource) - Method in class jigcell.compare.cellcycle.CellCycleTransformView
Saves the data for the results to some external source.
saveResults(IWriteableDataSource) - Method in interface jigcell.compare.ui.IResultTab
Saves the data for the results to some external source.
saveResults(IWriteableDataSource) - Method in class jigcell.compare.views.ObjectiveSeriesView
Saves the data for the results to some external source.
saveResultsDirect(IWriteableDataSource) - Method in class jigcell.compare.cellcycle.CellCycleTransformView
Saves the data for the results to some external source without user prompting.
saveResultsDirect(IWriteableDataSource) - Method in interface jigcell.compare.ui.IResultTab
Saves the data for the results to some external source without user prompting.
saveResultsDirect(IWriteableDataSource) - Method in class jigcell.compare.views.ObjectiveSeriesView
Saves the data for the results to some external source without user prompting.
saveRunFile(String) - Method in class jigcell.compare.tests.RunManagerPlugin
Saves the current run set in the Run Manager.
saveThreshold(IWriteableDataSource) - Method in class jigcell.compare.compare2.Compare2
Saves the data for the view to some external source.
saveThresholdDirect(IWriteableDataSource) - Method in class jigcell.compare.compare2.Compare2
Saves the data for the view to some external source without user prompting.
saveWindowSettings() - Method in class jigcell.compare.ui.CompareFrontEnd
 
scalar - Variable in class jigcell.compare.data.PackedDoubleDataElement
Placeholder for scalar value
scan() - Method in class jigcell.compare.impl.Blackboard
Returns all of the data items and namespaces in this namespace as a list.
scanResourceCatalog(String) - Method in class jigcell.compare.impl.Compare
Compiles the contents of a resource catalog.
scanResourceMap(String) - Method in class jigcell.compare.impl.Compare
Compiles the contents of a resource map.
scanResources() - Method in class jigcell.compare.impl.Compare
Compiles the contents of all resources.
scoreExact(MethodDispatcher.MethodScorer) - Method in class jigcell.compare.data.MethodDispatcher
Scores for exact matches.
scoreLoose(MethodDispatcher.MethodScorer) - Method in class jigcell.compare.data.MethodDispatcher
Scores for loose matches.
scriptDocument - Variable in class jigcell.compare.objectiveui.ScriptEvaluationInterface
Script document
scriptDocument - Variable in class jigcell.compare.transformui.ScriptEvaluationInterface
Script document
ScriptEvaluationInterface - Class in jigcell.compare.objectiveui
Interface for an ScriptEvaluationObjective.
ScriptEvaluationInterface(IProgrammableDataGenerator) - Constructor for class jigcell.compare.objectiveui.ScriptEvaluationInterface
Creates a new interface for an ScriptEvaluationObjective.
ScriptEvaluationInterface - Class in jigcell.compare.transformui
Interface for an ScriptEvaluationTransform.
ScriptEvaluationInterface(IProgrammableDataGenerator) - Constructor for class jigcell.compare.transformui.ScriptEvaluationInterface
Creates a new interface for an ScriptEvaluationTransform.
ScriptEvaluationObjective - Class in jigcell.compare.objective
Executes a user provided script when evaluated.
ScriptEvaluationObjective() - Constructor for class jigcell.compare.objective.ScriptEvaluationObjective
Creates a new objective that evaluates a script.
ScriptEvaluationTransform - Class in jigcell.compare.transform
Executes a user provided script when evaluated.
ScriptEvaluationTransform() - Constructor for class jigcell.compare.transform.ScriptEvaluationTransform
Creates a new transform that evaluates a script.
securityManager - Variable in class jigcell.compare.impl.Compare
Security manager for Comparator
selectAll() - Method in interface jigcell.compare.ui.IColumnSelectionTab
Selects all cells in the table.
selectAll() - Method in interface jigcell.compare.ui.IRowSelectionTab
Selects all cells in the table.
selectAll() - Method in class jigcell.compare.ui.SeriesDialog
Selects all cells in the table.
selectAll() - Method in class jigcell.compare.views.BasicTableView
 
SelectColumnsInterface - Class in jigcell.compare.transformui
Interface for a SelectColumnsTransform.
SelectColumnsInterface(IProgrammableDataGenerator) - Constructor for class jigcell.compare.transformui.SelectColumnsInterface
Creates a new interface for a SelectColumnsTransform.
SelectColumnsInterface.SelectedModel - Class in jigcell.compare.transformui
Controls the appearance of the selected column.
SelectColumnsInterface.SelectedModel() - Constructor for class jigcell.compare.transformui.SelectColumnsInterface.SelectedModel
Creates a new table model.
SelectColumnsTransform - Class in jigcell.compare.transform
A transform that selects a set of columns out of an existing generator.
SelectColumnsTransform() - Constructor for class jigcell.compare.transform.SelectColumnsTransform
Creates a new transform to select columns from a larger set of data.
selected - Variable in class jigcell.compare.ui.ListComboBoxModel
Currently selected item
selectedModel - Variable in class jigcell.compare.transformui.SelectColumnsInterface
Selected table model
selectedSelectionModel - Variable in class jigcell.compare.transformui.SelectColumnsInterface
Selection for selected list
selectedTab - Variable in class jigcell.compare.ui.CompareFrontEnd
Currently selected tab in the display frame
selectInvert() - Method in interface jigcell.compare.ui.IColumnSelectionTab
Inverts the table selection along the default direction.
selectInvert() - Method in interface jigcell.compare.ui.IRowSelectionTab
Inverts the table selection along the default direction.
selectInvert() - Method in class jigcell.compare.ui.SeriesDialog
Inverts the table selection along the default direction.
selectInvert() - Method in class jigcell.compare.views.BasicTableView
 
selectInvertColumns() - Method in interface jigcell.compare.ui.IColumnSelectionTab
Inverts the table selection along the columns.
selectInvertColumns() - Method in class jigcell.compare.views.BasicTableView
 
selectInvertRows() - Method in interface jigcell.compare.ui.IRowSelectionTab
Inverts the table selection along the rows.
selectInvertRows() - Method in class jigcell.compare.ui.SeriesDialog
Inverts the table selection along the rows.
selectInvertRows() - Method in class jigcell.compare.views.BasicTableView
 
selectionGroup - Variable in class jigcell.compare.views.BasicTableView
Selection group to be a part of
SELECTIONGROUP_CELLCYCLE - Static variable in class jigcell.compare.cellcycle.CellCycleExperimentView
Selection group for the cellcycle components
selectionModel - Variable in class jigcell.compare.transformui.SelectColumnsInterface
Selection table model
selectionSelectionModel - Variable in class jigcell.compare.transformui.SelectColumnsInterface
Selection for selection list
selectNone() - Method in interface jigcell.compare.ui.IColumnSelectionTab
Unselects all cells in the table.
selectNone() - Method in interface jigcell.compare.ui.IRowSelectionTab
Unselects all cells in the table.
selectNone() - Method in class jigcell.compare.ui.SeriesDialog
Unselects all cells in the table.
selectNone() - Method in class jigcell.compare.views.BasicTableView
 
selectTab(ITab) - Method in class jigcell.compare.ui.CompareFrontEnd
Selects one of the tabs for the display frame.
sendFile(LibOaa, String, String) - Static method in class jigcell.compare.cellcycle.OAAConnector
Sends a file through an OAAConnector.
sendFile(String, String) - Method in class jigcell.compare.tests.OAAConnectorTest
Sends a file through the OAAConnector.
SEPARATEDSTAGE - Static variable in class jigcell.compare.cellcycle.BuddingYeastScanTransform.BuddingYeastScanEvent
Entry to separated
SEPARATOR_ANNOTATION - Static variable in class jigcell.compare.cellcycle.JigCellRunManagerTransform
Separator between files and numbers
SEPARATOR_ESCAPE - Static variable in class jigcell.compare.data.DataGenerator
Separator for escaped values
SEPARATOR_PAIR - Static variable in class jigcell.compare.impl.DataSource
Separator between option name and value when providing state information
SEPARATOR_PART - Static variable in class jigcell.compare.impl.DataSource
Separator between two options when providing state information
SEPARATORS - Static variable in class jigcell.compare.impl.DataSource
All separators used when providing state information
SERIES_COLOR - Static variable in class jigcell.compare.plotter.Plotter
Series color key
SERIES_NAME - Static variable in class jigcell.compare.plotter.Plotter
Series name key
SeriesDialog - Class in jigcell.compare.ui
A dialog-based cell viewer for multi-dimensional data.
SeriesDialog(Compare, IDataElement, String, int, int, BasicTable.BasicTableModel) - Constructor for class jigcell.compare.ui.SeriesDialog
Creates a new dialog for viewing list based data.
SeriesDialog(Compare, IDataGenerator, int, int, BasicTable.BasicTableModel) - Constructor for class jigcell.compare.ui.SeriesDialog
Creates a new dialog for viewing list based data.
SeriesDialog(Compare, IDataGenerator, IDataElement, ITypeChecker, String, int, int, BasicTable.BasicTableModel) - Constructor for class jigcell.compare.ui.SeriesDialog
Creates a new dialog for viewing list based data.
SeriesDialog.SeriesModel - Class in jigcell.compare.ui
Model for a list viewer dialog.
SeriesDialog.SeriesModel() - Constructor for class jigcell.compare.ui.SeriesDialog.SeriesModel
Creates a new table model.
SeriesEditorDialog - Class in jigcell.compare.ui
A dialog-based cell editor for multi-dimensional data.
SeriesEditorDialog(Compare, IEditableDataElement, String, int, int, BasicTable.BasicTableModel) - Constructor for class jigcell.compare.ui.SeriesEditorDialog
Creates a new dialog for editing list based data.
SeriesEditorDialog(Compare, IEditableDataGenerator, int, int, BasicTable.BasicTableModel) - Constructor for class jigcell.compare.ui.SeriesEditorDialog
Creates a new dialog for editing list based data.
SeriesEditorDialog(Compare, IEditableDataGenerator, IEditableDataElement, ITypeChecker, String, int, int, BasicTable.BasicTableModel) - Constructor for class jigcell.compare.ui.SeriesEditorDialog
Creates a new dialog for editing list based data.
SeriesEditorDialog.SeriesEditorModel - Class in jigcell.compare.ui
Model for a list editor dialog.
SeriesEditorDialog.SeriesEditorModel() - Constructor for class jigcell.compare.ui.SeriesEditorDialog.SeriesEditorModel
Creates a new table model.
seriesNames - Variable in class jigcell.compare.data.type.TimeSeriesTypeChecker
Series names
SeriesView - Class in jigcell.compare.views
A static display for presenting a two-dimensional set of data organized by generators.
SeriesView(Compare, String) - Constructor for class jigcell.compare.views.SeriesView
Creates a new with an integrated model and data store.
SeriesView.SeriesModel - Class in jigcell.compare.views
Table model for a SimpleDataSeriesView.
SeriesView.SeriesModel() - Constructor for class jigcell.compare.views.SeriesView.SeriesModel
Creates a new table model.
SeriesView.SeriesViewTransferer - Class in jigcell.compare.views
Converts the internal format of the view to and from a Transferable.
SeriesView.SeriesViewTransferer() - Constructor for class jigcell.compare.views.SeriesView.SeriesViewTransferer
Creates a new transferer proxy.
SeriesView.SeriesViewTransferer(Object, Object) - Constructor for class jigcell.compare.views.SeriesView.SeriesViewTransferer
Creates a new transferer proxy.
set(int, IDataGenerator) - Method in class jigcell.compare.data.DataGeneratorList
Sets a generator in this list to a new value.
set(int, IDataGenerator) - Method in interface jigcell.compare.data.IDataGeneratorList
Sets a generator in this list to a new value.
setAccessory(ITabAccessory) - Method in class jigcell.compare.ui.CompareFrontEnd.FrontEndTabInfo
Sets the tab accessory.
setAllowContextInsertion(boolean) - Method in class jigcell.compare.transform.Transform
Sets whether this transform allows insertions through the context menu.
setAllowContextRemoval(boolean) - Method in class jigcell.compare.transform.Transform
Sets whether this transform allows removals through the context menu.
setAllowDescriptionQuery(boolean) - Method in class jigcell.compare.data.ProgrammableDataGenerator
Sets whether this generator allows the input description to be queried.
setAllowResultNameEditing(boolean) - Method in class jigcell.compare.transform.InputTransform
Sets whether result name editing is allowed.
setAllowThresholdEdit(boolean) - Method in class jigcell.compare.compare2.Compare2Model
Sets whether thresholds can be edited.
setAllowWildcardMatches(boolean) - Method in class jigcell.compare.data.MethodDispatcher
Sets whether wildcard matches are allowed.
setAnnotation(ITransformAnnotation) - Method in class jigcell.compare.transform.ConstantTransform
Sets the annotation data for this transform.
setAnnotation(ITransformAnnotation) - Method in class jigcell.compare.transform.Transform
Sets the annotation data for this transform.
setAnnotationDescriptor(String, ITransformAnnotation.IAnnotationDescriptor) - Method in interface jigcell.compare.transform.annotation.ITransformAnnotation
Sets description for a particular annotation type.
setAnnotationDescriptor(String, ITransformAnnotation.IAnnotationDescriptor) - Method in class jigcell.compare.transform.annotation.TransformAnnotation
Sets description for a particular annotation type.
setAnnotationRecord(long, ITransformAnnotation) - Method in interface jigcell.compare.transform.annotation.ITransformAnnotation
Sets the annotation record at a particular position.
setAnnotationRecord(long, ITransformAnnotation) - Method in class jigcell.compare.transform.annotation.TransformAnnotation
Sets the annotation record at a particular position.
setAnnotationValue(String, String) - Method in interface jigcell.compare.transform.annotation.ITransformAnnotation
Sets an annotation value.
setAnnotationValue(String, long, String) - Method in interface jigcell.compare.transform.annotation.ITransformAnnotation
Sets an annotation value at a particular position.
setAnnotationValue(String, String) - Method in class jigcell.compare.transform.annotation.TransformAnnotation
Sets an annotation value.
setAnnotationValue(String, long, String) - Method in class jigcell.compare.transform.annotation.TransformAnnotation
Sets an annotation value at a particular position.
setAttribute(String, String) - Method in class jigcell.compare.data.EditableDataGenerator
Sets a permanent attribute of this generator.
setAttribute(String, String) - Method in interface jigcell.compare.IDataGenerator
Sets a permanent attribute of this generator.
setButtonState(boolean) - Method in class jigcell.compare.ui.ConfigEditor
Controls whether the dialog buttons are enabled.
setCheckBoxSelection(String, boolean) - Method in class jigcell.compare.ui.InterfaceBuilder
Sets the selection state for a group of checkboxes.
setClipboardContentsOption(Map) - Method in class jigcell.compare.impl.ClipboardDataSource
Sets the clipboard contents option.
setClipboardOption(Clipboard) - Method in class jigcell.compare.impl.ClipboardDataSource
Sets the clipboard option.
setColorerMode(int) - Method in class jigcell.compare.compare2.Compare2
Sets the colorer display mode.
setColumnMarkers(BasicTable.BasicTableModel.Marker[]) - Method in class jigcell.compare.ui.BasicTable.BasicTableModel
Sets the table markers used by this mode.
setColumns(String) - Method in class jigcell.compare.transform.SelectColumnsTransform
Sets the selected columns.
setColumnSelection(IDataElement) - Method in class jigcell.compare.cellcycle.CellCycleReportGenerator
The column selection option.
setColumnWeights(double[]) - Method in class jigcell.compare.ui.BasicTable.BasicTableModel
 
setCommandEnabled(String, boolean) - Method in class jigcell.compare.ui.MenuBuilder
Enables or disables all of the menu elements with a given action command.
setComment(String) - Method in class jigcell.compare.data.EditableDataGenerator
Sets the displayable description.
setComment(String) - Method in interface jigcell.compare.IEditableDataGenerator
Sets the displayable description.
setCompatibleTransforms(IDataGeneratorList) - Method in interface jigcell.compare.transform.ITransform
Sets the transforms compatible with this statement.
setCompatibleTransforms(IDataGeneratorList) - Method in class jigcell.compare.transform.Transform
Sets the transforms compatible with this statement.
setCompatibleTransforms(IDataGeneratorList) - Method in class jigcell.compare.transform.TransformContainer
Sets the transforms compatible with this statement.
setComponentEnabled(String, boolean) - Method in class jigcell.compare.ui.InterfaceBuilder
Sets the enabled state for a group of components.
setComponentTreeEnabled(String, boolean) - Method in class jigcell.compare.ui.InterfaceBuilder
Sets the enabled state for a group of component trees.
setConfig(Config) - Method in class jigcell.compare.impl.Compare
Sets the configuration resource.
setConfig(String, Config) - Method in class jigcell.compare.impl.Config
Sets the config for a particular marker in this configurator.
setConfigs(HashMap) - Method in class jigcell.compare.impl.Config
Sets the mapping between markers and configurators.
setContainedTransforms(IDataGeneratorList) - Method in class jigcell.compare.transform.TransformContainer
Sets the transforms held by this contained.
setContainer(ITransformContainer) - Method in interface jigcell.compare.transform.ITransform
Sets the container of this transform.
setContainer(ITransformContainer) - Method in class jigcell.compare.transform.Transform
Sets the container of this transform.
setCopyName(boolean) - Method in class jigcell.compare.data.DataGenerator
 
setCopyName(boolean) - Method in interface jigcell.compare.IEditableDataGenerator
Sets whether this generator takes its name from the generator it was copied from.
setCurrentProperty(String) - Method in class jigcell.compare.tests.SystemTests
Sets the currently monitored property.
setCurrentSource(IWriteableDataSource) - Method in class jigcell.compare.compare2.Compare2
Sets the current data source to work from.
setCurrentSource(IWriteableDataSource) - Method in class jigcell.compare.ui.DataEditorPanelTab
Sets the current data source to work from.
setCurrentSource(IWriteableDataSource) - Method in interface jigcell.compare.ui.IDataEditorTab
Sets the current data source to work from.
setCurrentSource(IWriteableDataSource) - Method in class jigcell.compare.views.EditableSeriesView
Sets the current data source to work from.
setCurrentSource(IWriteableDataSource) - Method in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Sets the current data source to work from.
setCurrentSourceThreshold(IWriteableDataSource) - Method in class jigcell.compare.compare2.Compare2
Sets the value of the current data source to work from.
setCustomizerComponents(Container, JComponent, ITransform) - Method in class jigcell.compare.transformui.TransformInterface
Lays out the customizers for a transform.
setCustomizerView(IProgrammableDataGenerator) - Method in class jigcell.compare.views.ObjectiveEditor
Updates the customizer view for the edited object.
setCustomizerView(IProgrammableDataGenerator) - Method in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Updates the customizer view for the edited object.
setCustomizerView(ITransform) - Method in class jigcell.compare.views.TransformDebugger
Updates the customizer view for the currently selected transform.
setData(IDataGeneratorList) - Method in interface jigcell.compare.objective.IObjective
Sets the collection of data to draw from.
setData(IDataGeneratorList) - Method in class jigcell.compare.objective.Objective
Sets the collection of data to draw from.
setData(IDataElement) - Method in interface jigcell.compare.plotter.IPlotter
Sets the data aggregate.
setData(IDataElement) - Method in class jigcell.compare.plotter.Plotter
Sets the data aggregate.
setDataManager(DataManager) - Method in class jigcell.compare.impl.Compare
Sets the data manager resource.
setDebugDelay(long) - Method in class jigcell.compare.views.TransformDebugger.DebuggerThread
Sets the delay before continuing a debug trace.
setDebugExceptions(boolean) - Static method in class jigcell.compare.impl.Compare
Sets whether to display exception debugging information
setDefaultDimensionWeight(String) - Method in interface jigcell.compare.objective.IDimensionWeightObjective
Sets the dimension weights.
setDefaultDimensionWeight(String) - Method in class jigcell.compare.objective.WOSSObjective
Sets the dimension weights.
setDefaultElementWeight(String) - Method in interface jigcell.compare.objective.IElementWeightObjective
Sets the element weights.
setDefaultElementWeight(String) - Method in class jigcell.compare.objective.MinkowskiObjective
Sets the element weights.
setDefaultElementWeight(String) - Method in class jigcell.compare.objective.WOSSObjective
Sets the element weights.
setDefaultRunNumber(int) - Method in class jigcell.compare.cellcycle.JigCellRunManagerTransform
Sets the run number to use if the default run is selected.
setDescription(String) - Method in class jigcell.compare.impl.SuffixFileFilter
Sets the description of this filter.
setDimensionWeights(IDataElement) - Method in interface jigcell.compare.objective.IDimensionWeightObjective
Sets the suggested dimension weights.
setDimensionWeights(IDataElement) - Method in class jigcell.compare.objective.WOSSObjective
Sets the suggested dimension weights.
setDisplayComponent(JComponent) - Method in class jigcell.compare.transform.ConstantTransform
Sets the information to display in the transform interface.
setDisplayMode(int) - Method in interface jigcell.compare.compare2.IViewColorer
Sets the display mode of this view colorer.
setDisplayMode(int) - Method in class jigcell.compare.compare2.ViewColorer
Sets the display mode of this view colorer.
setElement(IDataElement) - Method in class jigcell.compare.data.EditableDataGenerator
Sets the associated data element.
setElement(String) - Method in class jigcell.compare.data.EditableDataGenerator
Creates a new associated data element and initializes it with the given text.
setElement(IDataElement) - Method in interface jigcell.compare.IEditableDataGenerator
Sets the associated data element.
setElementWeights(IDataElement) - Method in interface jigcell.compare.objective.IElementWeightObjective
Sets the suggested element weights.
setElementWeights(IDataElement) - Method in class jigcell.compare.objective.MinkowskiObjective
Sets the suggested element weights.
setElementWeights(IDataElement) - Method in class jigcell.compare.objective.WOSSObjective
Sets the suggested element weights.
setEncoderOption(FileDataSource.IFileEncoder) - Method in class jigcell.compare.impl.FileDataSource
Sets the file encoder to control reading and writing from this source.
setEsp1Checked(boolean) - Method in class jigcell.compare.cellcycle.BuddingYeastScanTransform
Controls whether the concentration of Esp1 is a requirement for proceeding through checkpoints.
setEvaluationContext(ITransformContext) - Method in class jigcell.compare.cellcycle.GenericScanTransform
Sets the runtime context for performing an evaluation.
setEvaluationContext(ITransformContext) - Method in interface jigcell.compare.transform.ITransform
Sets the runtime context for performing an evaluation.
setEvaluationContext(ITransformContext) - Method in class jigcell.compare.transform.Transform
Sets the runtime context for performing an evaluation.
setEvaluationContext(ITransformContext) - Method in class jigcell.compare.transform.TransformContainer
Sets the runtime context for performing an evaluation.
setEvaluationContext(ITransformContext) - Method in class jigcell.compare.transform.TransformEvaluationTransform
Sets the runtime context for performing an evaluation.
setExceptionListenerOption(ExceptionRecorder) - Method in class jigcell.compare.impl.FileDataSource
Sets the exception listener option.
setExperiment(IDataGeneratorCollection.Key) - Method in class jigcell.compare.compare2.ThresholdEditor
Sets the experiment which this editor is working with.
setExtremaTestTransformBadMaxMin(ExtremaTestTransform, String) - Static method in class jigcell.compare.tests.TransformTests
Sets the maximum and minimum values expecting failure.
setFileChooserOption(JFileChooser) - Method in class jigcell.compare.impl.FileDataSource
Sets the file chooser option.
setFileChooserSelectOption(String) - Method in class jigcell.compare.impl.FileDataSource
Sets the file chooser select option.
setFileInputOption(InputStream) - Method in class jigcell.compare.impl.FileDataSource
Sets the file input option.
setFilename(String) - Method in class jigcell.compare.transform.FileTransform
Sets the file name.
setFilename(String) - Method in class jigcell.compare.transform.ReadFromFileTransform
Sets the file name.
setFileOutputOption(OutputStream) - Method in class jigcell.compare.impl.FileDataSource
Sets the file output option.
setFilePathOption(String) - Method in class jigcell.compare.impl.FileDataSource
Sets the file path option.
setFileSourceOption(RawFileDataSource) - Method in class jigcell.compare.impl.PDFPrinterDataSource
Sets the file that will hold the PDF document.
setFlavorsOption(List) - Method in class jigcell.compare.impl.ClipboardDataSource
Sets the clipboard flavors option.
setFound(boolean) - Method in class jigcell.compare.ui.FindAccessory
Sets whether the last search was successful.
setFunction(String) - Method in interface jigcell.compare.objective.IObjective
Sets the function used to compute the objective.
setFunction(String) - Method in class jigcell.compare.objective.Objective
Sets the function used to compute the objective.
setGenerators(IDataGeneratorList) - Method in class jigcell.compare.views.SeriesView.SeriesModel
Sets the generators for this model.
setGroups(int) - Method in class jigcell.compare.compare2.ThresholdRelativeViewColorer
Sets the number of groups to divide cells into.
setId(String) - Method in class jigcell.compare.data.IDataGeneratorCollection.Key
Sets the key id.
setInitialHeight(int) - Method in class jigcell.compare.ui.ViewerDialog
Sets the initial height of the dialog in pixels.
setInitialWidth(int) - Method in class jigcell.compare.ui.ViewerDialog
Sets the initial width of the dialog in pixels.
setInputDescription(String) - Method in class jigcell.compare.contrib.ObjectiveHelper
Sets an HTML formatted description of the input of this transform.
setInputDescription(String) - Method in class jigcell.compare.contrib.TransformHelper
Sets an HTML formatted description of the input of this transform.
setInputDescription(IComponentDescription) - Method in class jigcell.compare.ui.CustomizableInterface
Sets an HTML formatted description of the input of this generator.
setInputTypeChecker(ITypeChecker) - Method in class jigcell.compare.data.ProgrammableDataGenerator
Sets a type checker that can validate the input to this generator.
setInterfaceClass(String) - Method in class jigcell.compare.data.ProgrammableDataGenerator
Sets an interface class for this generator.
setInterpolation(String) - Method in interface jigcell.compare.objective.IInterpolationObjective
Sets the suggested interpolation.
setInterpolation(String) - Method in class jigcell.compare.objective.WOSSObjective
Sets the suggested interpolation.
setKnownTransforms(Set) - Method in class jigcell.compare.transform.TransformEvaluationTransform
Sets the transforms known to this transform.
setLengthDirect(long) - Method in class jigcell.compare.data.EditableDataElement
Sets the known length of an element.
setLengthDirect(long) - Method in class jigcell.compare.data.PackedDoubleDataElement
Sets the known length of an element.
setLengthDirect(long) - Method in class jigcell.compare.data.TreeDataElement
Sets the known length of an element.
setLocation(String) - Method in class jigcell.compare.impl.FileDataSource
Sets the unique identifier for this data source.
setLocation(String) - Method in interface jigcell.compare.IPersistableDataSource
Sets the unique identifier for this data source.
setLocation(URL) - Method in class jigcell.compare.ui.HTMLComponentDescription
Sets the location of the component description.
setLocation(URL) - Method in class jigcell.compare.ui.TextComponentDescription
Sets the location of the component description.
setMaximum(String) - Method in class jigcell.compare.transform.ExtremaTestTransform
Sets the maximum.
setMaximum(int) - Method in class jigcell.compare.ui.ProgressMonitor
 
setMessage(Object) - Method in class jigcell.compare.ui.ProgressMonitor
 
setMethodName(String) - Method in class jigcell.compare.data.MethodDispatcher
Sets the name of the method to invoke.
setMethodName(String) - Method in class jigcell.compare.tests.MethodDispatcherTests.DispatchedTransform
Sets the name of the dispatch method to use.
setMetric(IObjective) - Method in class jigcell.compare.objective.MetricObjective
Sets the distance metric.
setMinimum(String) - Method in class jigcell.compare.transform.ExtremaTestTransform
Sets the minimum.
setModel(TableModel) - Method in class jigcell.compare.ui.BasicTable
 
setMultipleViewSupport(boolean) - Method in class jigcell.compare.ui.CustomizableInterface
Sets whether this interface supports multiple views.
setName(String) - Method in class jigcell.compare.data.DataGenerator
Sets the data source name.
setName(String) - Method in class jigcell.compare.data.IDataGeneratorCollection.Key
Sets the key name.
setName(String) - Method in interface jigcell.compare.IEditableDataGenerator
Sets the generator name.
setName(String) - Method in class jigcell.compare.impl.DataSource
Sets the data source name.
setName(String) - Method in class jigcell.compare.ui.BasicTable.BasicTableModel.Marker
Sets the name of this column for the table header.
setNextStatement(ITransform) - Method in interface jigcell.compare.transform.ITransform
The next generator in the sequence of transforms.
setNextStatement(ITransform) - Method in class jigcell.compare.transform.Transform
The next generator in the sequence of transforms.
setOption(String, Object) - Method in class jigcell.compare.data.EditableDataGenerator
Sets a configuration optoin. Returns whether the configuration was changed.
setOption(String, Object) - Method in interface jigcell.compare.IDataSource
Sets a configuration optoin.
setOption(String, Object) - Method in class jigcell.compare.impl.DataSource
Sets a configuration optoin.
setOptions(Map) - Method in class jigcell.compare.impl.DataSource
Sets the configuration options map.
setOptionType(String, IDataSource.Option) - Static method in class jigcell.compare.impl.DataSource
Sets the persistence type for an option.
setOutputDescription(String) - Method in class jigcell.compare.contrib.TransformHelper
Sets an HTML formatted description of the output of this transform.
setOutputDescription(IComponentDescription) - Method in class jigcell.compare.ui.CustomizableInterface
Sets an HTML formatted description of the output of this generator.
setOutputTypeChecker(ITypeChecker) - Method in class jigcell.compare.data.ProgrammableDataGenerator
Sets a type checker that can validate the output from this generator.
setOwnerOption(Object) - Method in class jigcell.compare.impl.OwnedDataSource
Sets the owner object that will be supplied to the callback.
setPenaltyLength(long) - Method in class jigcell.compare.data.MethodDispatcher
Sets the penalty for length mismatches.
setPenaltyLengthChecked(boolean) - Method in class jigcell.compare.data.MethodDispatcher
Sets whether length mismatches are allowed.
setPenaltyLooseMatch(long) - Method in class jigcell.compare.data.MethodDispatcher
Sets the penalty for loose formalType matches.
setPenaltyLooseMatchChecked(boolean) - Method in class jigcell.compare.data.MethodDispatcher
Sets whether loose formalType matches are allowed.
setPreviousStatement(ITransform) - Method in interface jigcell.compare.transform.ITransform
Sets the previous generator in the sequence of transforms.
setPreviousStatement(ITransform) - Method in class jigcell.compare.transform.Transform
Sets the previous generator in the sequence of transforms.
setPrintServiceOption(PrintService) - Method in class jigcell.compare.impl.SystemPrinterDataSource
Sets the print service option.
setProgress(int) - Method in class jigcell.compare.ui.ProgressMonitor
Updates the progress bar.
setPrototypeChild(EditableDataElement) - Method in class jigcell.compare.data.EditableDataElement
Sets the prototypical instance of a subelement
setPrototypeExperiments(IDataGeneratorList) - Method in class jigcell.compare.cellcycle.CellCycleReportGenerator
Sets the list of experimental prototypes to select from.
setReadDescriptionOption(String) - Method in class jigcell.compare.impl.DataSource
Sets the read description option.
setReadDescriptionOption(String) - Method in interface jigcell.compare.IReadableDataSource
Sets the read description option.
setReadIconOption(Icon) - Method in class jigcell.compare.impl.DataSource
Sets the read description icon.
setReadIconOption(Icon) - Method in interface jigcell.compare.IReadableDataSource
Sets the read description icon.
setRelation(String) - Method in class jigcell.compare.objective.BooleanRelationalObjective
Sets the suggested relation.
setRelation(String) - Method in interface jigcell.compare.objective.IRelationalObjective
Sets the suggested relation.
setResultName(String) - Method in class jigcell.compare.transform.InputTransform
Sets the result name to publish.
setResultName(String, boolean) - Method in class jigcell.compare.transform.InputTransform
Sets the result name to publish.
setRewardMatch(long) - Method in class jigcell.compare.data.MethodDispatcher
Sets the reward for matches.
setRewardSubclass(long) - Method in class jigcell.compare.data.MethodDispatcher
Sets the reward for specialized matches.
setRewardSubclassChecked(boolean) - Method in class jigcell.compare.data.MethodDispatcher
Sets whether specialized matches are rewarded.
setRunFile(String) - Method in class jigcell.compare.cellcycle.JigCellRunManagerTransform
Sets the currently used run file.
setRunnable(boolean) - Method in class jigcell.compare.transform.InputTransform
Sets whether the transform is runnable.
setRunNumber(int) - Method in class jigcell.compare.cellcycle.JigCellRunManagerTransform
Sets the currently used run number.
setScript(String) - Method in class jigcell.compare.objective.ScriptEvaluationObjective
Sets the Beanshell script to execute during evaluation.
setScript(String) - Method in class jigcell.compare.transform.ScriptEvaluationTransform
Sets the Beanshell script to execute during evaluation.
setSelectedColumns(int[]) - Method in interface jigcell.compare.ui.IColumnSelectionTab
Sets the table column selection.
setSelectedColumns(int[]) - Method in class jigcell.compare.views.BasicTableView
 
setSelectedIndex(int) - Method in class jigcell.compare.ui.ListComboBoxModel
Sets the selected item by index.
setSelectedItem(Object) - Method in class jigcell.compare.ui.ListComboBoxModel
 
setSelectedRows(int[]) - Method in interface jigcell.compare.ui.IRowSelectionTab
Sets the table row selection.
setSelectedRows(int[]) - Method in class jigcell.compare.ui.SeriesDialog
Sets the table row selection.
setSelectedRows(int[]) - Method in class jigcell.compare.views.BasicTableView
 
setSelectedTransform(ITransform) - Method in class jigcell.compare.views.TransformDebugger
Sets the current object selected in the tree.
setSelectionGroup(String) - Method in class jigcell.compare.views.BasicTableView
Sets the selection group to be a part of.
setSeries(long, IDataElement) - Method in interface jigcell.compare.plotter.IPlotter
Sets one of the data series in the aggregate.
setSeries(long, IDataElement) - Method in class jigcell.compare.plotter.Plotter
Sets one of the data series in the aggregate.
setSeriesColor(long, Color) - Method in interface jigcell.compare.plotter.IPlotter
Sets the color of a series.
setSeriesColor(long, Color) - Method in class jigcell.compare.plotter.Plotter
Sets the color of a series.
setSeriesCombine(IPlotter.Combine) - Method in interface jigcell.compare.plotter.IPlotter
Sets the series combine option.
setSeriesCombine(IPlotter.Combine) - Method in class jigcell.compare.plotter.Plotter
Sets the series combine option.
setSeriesName(long, String) - Method in interface jigcell.compare.plotter.IPlotter
Sets the name of a series.
setSeriesName(long, String) - Method in class jigcell.compare.plotter.Plotter
Sets the name of a series.
setSeriesNames(String[]) - Method in class jigcell.compare.plotter.Plotter
Sets the name of every series.
setState(String) - Method in class jigcell.compare.data.EditableDataGenerator
Completely replaces the previous configuration of this data source.
setState(String) - Method in interface jigcell.compare.IDataSource
Completely replaces the previous configuration of this data source.
setState(String) - Method in class jigcell.compare.impl.DataSource
Completely replaces the previous configuration of this data source.
setSuffix(String) - Method in class jigcell.compare.impl.SuffixFileFilter
Sets the file suffix to match against.
setTabAccessory(ITab, ITabAccessory) - Method in class jigcell.compare.ui.CompareFrontEnd
Sets the accessory component displayed for a tab.
setTarget(Object) - Method in class jigcell.compare.data.MethodDispatcher
Sets the target to invoke.
setThreshold(String, boolean) - Method in class jigcell.compare.compare2.ThresholdEditor
Sets the threshold for the experiment this editor is working with.
setThreshold(double, boolean) - Method in class jigcell.compare.compare2.ThresholdEditor
Sets the threshold for the experiment this editor is working with.
setTitle(String) - Method in interface jigcell.compare.plotter.IPlotter
Sets the title of the plot window.
setTitle(String) - Method in class jigcell.compare.plotter.Plotter
Sets the title of the plot window.
setTransferClassOption(Class) - Method in class jigcell.compare.impl.OwnedDataSource
Sets the callback class that will be invoked.
setTransformCursor(ITransform) - Method in class jigcell.compare.views.TransformDebugger
Sets the current transform cursor.
setTransformName(String) - Method in class jigcell.compare.transform.TransformEvaluationTransform
Sets the name of the transform to execute.
setUseRangeControls(boolean) - Method in class jigcell.compare.cellcycle.CellCycleReportGenerator
Sets whether the view range controls should be enabled.
setUseSelectionControls(boolean) - Method in class jigcell.compare.cellcycle.CellCycleReportGenerator
Sets whether the column selection controls should be enabled.
setValue(boolean) - Method in class jigcell.compare.data.EditableDataElement
Sets the element to a boolean.
setValue(IDataElement) - Method in class jigcell.compare.data.EditableDataElement
Sets the element to a list.
setValue(double) - Method in class jigcell.compare.data.EditableDataElement
Sets the element to a double.
setValue(long) - Method in class jigcell.compare.data.EditableDataElement
Sets the element to a long.
setValue(String) - Method in class jigcell.compare.data.EditableDataElement
Sets the element to a String.
setValue(long, boolean) - Method in class jigcell.compare.data.EditableDataElement
Sets an element value to a boolean.
setValue(long, IDataElement) - Method in class jigcell.compare.data.EditableDataElement
Sets an element value to a list.
setValue(long, double) - Method in class jigcell.compare.data.EditableDataElement
Sets an element value to a double.
setValue(long, long) - Method in class jigcell.compare.data.EditableDataElement
Sets an element value to a long.
setValue(long, String) - Method in class jigcell.compare.data.EditableDataElement
Sets an element value to a string.
setValue(IDataElement) - Method in class jigcell.compare.data.PackedDoubleDataElement
Sets the element to a list.
setValue(IDataElement) - Method in class jigcell.compare.data.TreeDataElement
Sets the element to a list.
setValue(boolean) - Method in interface jigcell.compare.IEditableDataElement
Sets the element to a boolean.
setValue(IDataElement) - Method in interface jigcell.compare.IEditableDataElement
Sets the element to a list.
setValue(double) - Method in interface jigcell.compare.IEditableDataElement
Sets the element to a double.
setValue(long) - Method in interface jigcell.compare.IEditableDataElement
Sets the element to a long.
setValue(String) - Method in interface jigcell.compare.IEditableDataElement
Sets the element to a String.
setValue(long, boolean) - Method in interface jigcell.compare.IEditableDataElement
Sets an element value to a boolean.
setValue(long, IDataElement) - Method in interface jigcell.compare.IEditableDataElement
Sets an element value to a list.
setValue(long, double) - Method in interface jigcell.compare.IEditableDataElement
Sets an element value to a double.
setValue(long, long) - Method in interface jigcell.compare.IEditableDataElement
Sets an element value to a long.
setValue(long, String) - Method in interface jigcell.compare.IEditableDataElement
Sets an element value to a string.
setValue(String, boolean) - Method in class jigcell.compare.impl.Config
Sets the value for a particular key in this configurator to a boolean.
setValue(String, Color) - Method in class jigcell.compare.impl.Config
Sets the value for a particular key in this configurator to a color.
setValue(String, long) - Method in class jigcell.compare.impl.Config
Sets the value for a particular key in this configurator to an integer.
setValue(String, List) - Method in class jigcell.compare.impl.Config
Sets the value for a particular key in this configurator to a list.
setValue(String, Rectangle) - Method in class jigcell.compare.impl.Config
Sets the value for a particular key in this configurator to a rectangle.
setValue(String, String) - Method in class jigcell.compare.impl.Config
Sets the value for a particular key in this configurator.
setValue(IDataElement) - Method in class jigcell.compare.transform.ConstantTransform
Sets the value this transform will generate.
setValueAt(Object, int, int) - Method in class jigcell.compare.cellcycle.CellCycleExperimentView.ExperimentModel
Sets a value in the table.
setValueAt(Object, int, int) - Method in class jigcell.compare.cellcycle.CellCycleTransformView.TransformModel
Sets a value in the table.
setValueAt(Object, int, int) - Method in class jigcell.compare.compare2.Compare2Model
Sets a value in the table.
setValueAt(Object, int, int) - Method in class jigcell.compare.objectiveui.DimensionWeightEditorDialog.DimensionWeightModel
Sets a value in the current table.
setValueAt(Object, int, int) - Method in class jigcell.compare.objectiveui.ElementWeightEditorDialog.ElementWeightModel
Sets a value in the current table.
setValueAt(Object, int, int) - Method in class jigcell.compare.ui.SeriesEditorDialog.SeriesEditorModel
Sets a value in the current table.
setValueAt(Object, int, int) - Method in class jigcell.compare.views.EditableSeriesView.EditableSeriesModel
Sets a value in the table.
setValueAt(Object, int, int) - Method in class jigcell.compare.views.ObjectiveSeriesView.ObjectiveSeriesModel
Sets a value in the table.
setValueInterpreted(String) - Method in class jigcell.compare.data.EditableDataElement
Sets the element by parsing the textual representation of an element.
setValueInterpreted(long, String) - Method in class jigcell.compare.data.EditableDataElement
Sets an element value by parsing the textual representation of an element.
setValueInterpreted(String) - Method in interface jigcell.compare.IEditableDataElement
Sets the element by parsing the textual representation of an element.
setValueInterpreted(long, String) - Method in interface jigcell.compare.IEditableDataElement
Sets an element value by parsing the textual representation of an element.
setValues(double[], int) - Method in class jigcell.compare.data.PackedDoubleDataElement
Sets the underlying array of this element.
setValues(SortedMap) - Method in class jigcell.compare.data.TreeDataElement
Sets the map of values in this element.
setValues(HashMap) - Method in class jigcell.compare.impl.Config
Sets the mapping between keys and values.
setViewColorer(IViewColorer) - Method in class jigcell.compare.compare2.Compare2
Changes the current view coloring.
setViewRange(IDataElement) - Method in class jigcell.compare.cellcycle.CellCycleReportGenerator
Sets the view range option.
setViewRange(IDataElement) - Method in interface jigcell.compare.plotter.IPlotter
Sets the view range option.
setViewRange(IDataElement) - Method in class jigcell.compare.plotter.Plotter
Sets the view range option.
setVisible(boolean) - Method in class jigcell.compare.objectiveui.DimensionWeightEditorDialog
 
setVisible(boolean) - Method in class jigcell.compare.objectiveui.ElementWeightEditorDialog
 
setVisible(boolean) - Method in class jigcell.compare.ui.ConfigEditor
 
setVisible(boolean) - Method in class jigcell.compare.ui.SeriesDialog
 
setVisible(boolean) - Method in class jigcell.compare.ui.ViewerDialog
 
setVisible(boolean) - Method in class jigcell.compare.views.EvaluationErrorViewer
 
setWeights(String, String) - Method in class jigcell.compare.objective.MinkowskiObjective
Sets a weight.
setWeights(String, String) - Method in class jigcell.compare.objective.WOSSObjective
Sets a weight.
setWildtypeTransformName(String) - Method in class jigcell.compare.cellcycle.GenericScanTransform
Sets the name of the transform to evaluate for the wildtype properties.
setWriteDescriptionOption(String) - Method in class jigcell.compare.impl.DataSource
Sets the write description option.
setWriteDescriptionOption(String) - Method in interface jigcell.compare.IWriteableDataSource
Sets the write description option.
setWriteIconOption(Icon) - Method in class jigcell.compare.impl.DataSource
Sets the write description icon.
setWriteIconOption(Icon) - Method in interface jigcell.compare.IWriteableDataSource
Sets the write description icon.
shellHandleException(String, Object) - Method in class jigcell.compare.impl.Compare
Handle an exception in a Comparator component.
shellHandleException(String, Object, Throwable) - Method in class jigcell.compare.impl.Compare
Handle an exception in a Comparator component.
shellHandleException(String, Object, Throwable) - Method in class jigcell.compare.ui.CompareFrontEnd
Handle an exception in a Comparator component.
shellHandleMessage(String, Object) - Method in class jigcell.compare.impl.Compare
Handle an informational message in a Comparator component.
shellHandleMessage(String, Object) - Method in class jigcell.compare.ui.CompareFrontEnd
Handle an informational message in a Comparator component.
shellStableHook() - Method in class jigcell.compare.impl.Compare
Stable hook for frontend shell.
shellStableHook() - Method in class jigcell.compare.ui.CompareFrontEnd
Stable hook for frontend shell.
shellStartHook() - Method in class jigcell.compare.cellcycle.CellCycleFrontEnd
Start hook for frontend shell. No initialization is guaranteed to have taken place at this point.
shellStartHook() - Method in class jigcell.compare.impl.Compare
Start hook for frontend shell.
shellStartHook() - Method in class jigcell.compare.ui.CompareFrontEnd
Start hook for frontend shell.
showBackwards() - Method in class jigcell.compare.views.TransformDebugger
Computes and displays the backwards trace set.
showChoiceDialog(String, Object, String[], int) - Method in class jigcell.compare.ui.InterfaceBuilder
Prompts the user to make a choice from among several options.
showErrorDialog(String, Object, Throwable) - Method in class jigcell.compare.ui.InterfaceBuilder
Informs the user of an error or warning in the Comparator.
showErrorTrace(String, Object, Throwable) - Method in class jigcell.compare.ui.InterfaceBuilder
Informs the user of an error or warning in the Comparator.
showForwards() - Method in class jigcell.compare.views.TransformDebugger
Computes and displays the forwards trace set.
showInputDialog(String, Object, String) - Method in class jigcell.compare.ui.InterfaceBuilder
Prompts the user for input.
showInputDialog(String, Object[], Object, String) - Method in class jigcell.compare.ui.InterfaceBuilder
Prompts the user for input.
showInputDialog(String, Object[], Object, String, boolean) - Method in class jigcell.compare.ui.InterfaceBuilder
Prompts the user for input.
showMessageDialog(String, Object) - Method in class jigcell.compare.ui.InterfaceBuilder
Shows the user a message.
SIGNATURE_DATASOURCE - Static variable in class jigcell.compare.impl.Compare
Method signature of data sources
SIGNATURE_TAB - Static variable in class jigcell.compare.ui.CompareFrontEnd
Method signature of tabs
SIGNATURE_TRANSFER - Static variable in class jigcell.compare.impl.OwnedDataSource
Constructor signature for callback class
size() - Method in class jigcell.compare.data.DataGeneratorList
The number of generators in this list.
size() - Method in interface jigcell.compare.data.IDataGeneratorList
The number of generators in this list.
size - Variable in class jigcell.compare.data.PackedDoubleDataElement
Element pack size
size - Variable in class jigcell.compare.data.PackedTreeDataElement
Element packing size
SIZE_DEFAULTPACK - Static variable in class jigcell.compare.data.PackedDoubleDataElement
Size of default element pack
SIZE_DEFAULTPACK - Static variable in class jigcell.compare.data.PackedTreeDataElement
Size of default element pack
SIZE_LONGPOOL - Static variable in class jigcell.compare.data.DataElement
Size of long constant pool
SIZE_MINIMUM - Variable in class jigcell.compare.ui.CompareFrontEnd.SplashScreen
Minimum size splash to display
SIZE_READBUFFER - Static variable in class jigcell.compare.views.Console
Size of the communication buffer
SIZES - Static variable in class jigcell.compare.tests.ElementBenchmark
Parameter sizes for benchmarks
sleeping - Variable in class jigcell.compare.views.TransformDebugger.DebuggerThread
Whether the thread is sleeping
SLIDER_BASE - Static variable in class jigcell.compare.compare2.ThresholdEditor
Base point for the threshold slider
SLIDER_MAX - Static variable in class jigcell.compare.compare2.ThresholdEditor
Maximum point for the threshold slider
SMALL_VALUE - Static variable in class jigcell.compare.objective.MinkowskiObjective
Size of the largest small double
SMALL_VALUE - Static variable in class jigcell.compare.objective.WOSSObjective
Size of the largest small double
smashTransformDisplayComponent(JComponent) - Method in class jigcell.compare.cellcycle.CellCycleReportGenerator
Heavily constrains the dimensions of most of the components in a transform display.
SOLVABLE_EXECUTE - Static variable in class jigcell.compare.cellcycle.OAAConnector
Solvable for executing a command
SOLVABLE_SENDFILE - Static variable in class jigcell.compare.cellcycle.OAAConnector
Solvable for sending a file
SOLVABLE_SENDFILEPART - Static variable in class jigcell.compare.cellcycle.OAAConnector
Solvable for sending part of a file
solve(LibOaa, IclTerm) - Static method in class jigcell.compare.cellcycle.OAAConnector
Requests an OAA solvable.
sort(Comparator) - Method in class jigcell.compare.data.DataGeneratorList
Sorts this list according to a specified criterion.
sort(Comparator) - Method in interface jigcell.compare.data.IDataGeneratorList
Sorts this list according to a specified criterion.
source - Variable in class jigcell.compare.impl.XMLFileEncoder
Source for reading and writing
source - Variable in class jigcell.compare.tests.ElementBenchmark
Source to load from
source - Variable in class jigcell.compare.tests.ExperimentBenchmark
Source to load from
source - Variable in class jigcell.compare.tests.ObjectiveBenchmark
Source to load from
source - Variable in class jigcell.compare.tests.TransformBenchmark
Source to load from
SOURCE_LOCK - Variable in class jigcell.compare.impl.DataManager
Lock for manipulating sources
SparseTreeDataElement - Class in jigcell.compare.data
An implementation of EditableDataElement that uses a red-black tree to store values.
SparseTreeDataElement() - Constructor for class jigcell.compare.data.SparseTreeDataElement
Creates a new data element backed by a tree.
SparseTreeDataElement2 - Class in jigcell.compare.data
An implementation of EditableDataElement that uses an AVL tree to store values.
SparseTreeDataElement2() - Constructor for class jigcell.compare.data.SparseTreeDataElement2
Creates a new data element backed by a tree.
SPECIAL_CHARS - Static variable in class jigcell.compare.data.DataGenerator
Characters that should not be used in a name
splash - Variable in class jigcell.compare.ui.CompareFrontEnd
Splash screen while loading
SPLASH_LOCK - Variable in class jigcell.compare.ui.CompareFrontEnd.SplashScreen
Lock for controlling the splash screen
splitMultipleSeries(IDataElement) - Static method in class jigcell.compare.plotter.Plotter
Splits time series data with multiple series to multiple time series with a single series.
splitter - Variable in class jigcell.compare.views.TransformDebugger
Splitter between tree and display
spn - Variable in class jigcell.compare.cellcycle.BuddingYeastScanTransform.BuddingYeastScanPoint
Value of the species spn
startBenchmark() - Method in class jigcell.compare.tests.Benchmark
Starts running the benchmark.
startBlock() - Method in class jigcell.compare.ui.InterfaceBuilder
Starts a new block.
startElement(String, String, String, Attributes) - Method in class jigcell.compare.ui.IconLoader
 
startElement(String, String, String, Attributes) - Method in class jigcell.compare.ui.MenuBuilder.Builder
 
startInterface() - Method in class jigcell.compare.ui.InterfaceBuilder
Starts a new interface.
startRow() - Method in class jigcell.compare.ui.InterfaceBuilder
Starts a new interface row.
state - Variable in class jigcell.compare.tests.Benchmark
Current state of the tester
STATE_ENDINITIALIZE - Static variable in interface jigcell.compare.ITab
Indicates that the current Comparator state is exiting normal initialization
STATE_ENDUI - Static variable in interface jigcell.compare.ITab
Indicates that the current Comparator state is exiting UI construction
STATE_INITIALIZE - Static variable in interface jigcell.compare.ITab
Indicates that the current Comparator state is initializing
STATE_RUNNING - Static variable in interface jigcell.compare.ITab
Indicates that the current Comparator state is the normal running mode
stateChanged(ChangeEvent) - Method in class jigcell.compare.compare2.ThresholdEditor
 
stateChanged(ChangeEvent) - Method in class jigcell.compare.ui.CompareFrontEnd
 
stateChanged(ChangeEvent) - Method in class jigcell.compare.ui.ConfigEditor
 
statementModel - Variable in class jigcell.compare.transformui.InputInterface
Model for transform list
STATES - Static variable in interface jigcell.compare.ITab
The defined Comparator states in temporal order
step() - Method in class jigcell.compare.views.TransformDebugger
Steps the debugging thread forwards.
stop() - Method in class jigcell.compare.views.TransformDebugger
Stops the debugging thread.
stopDebugging() - Method in class jigcell.compare.views.TransformDebugger.DebuggerThread
Terminates a debugging session.
stopDebugging() - Method in class jigcell.compare.views.TransformDebugger
Stops the debugger.
stopDebuggingRunnable - Variable in class jigcell.compare.views.TransformDebugger
Stops debugging
StreamingStringTokenizer - Class in jigcell.compare.impl
An implementation of StringTokenizer that can directly use streaming input.
StreamingStringTokenizer(Reader, String) - Constructor for class jigcell.compare.impl.StreamingStringTokenizer
Creates a new tokenizer with streaming input.
StreamingStringTokenizerTests - Class in jigcell.compare.tests
A collection of tests to exercise jigcell.compare.impl.StreamingStringTokenizer.
StreamingStringTokenizerTests(String) - Constructor for class jigcell.compare.tests.StreamingStringTokenizerTests
Creates a new system test.
string1 - Static variable in class jigcell.compare.tests.MethodDispatcherTests
A test string
string2 - Static variable in class jigcell.compare.tests.MethodDispatcherTests
A test string
string3 - Static variable in class jigcell.compare.tests.MethodDispatcherTests
A test string
string4 - Static variable in class jigcell.compare.tests.MethodDispatcherTests
A test string
StringTypeChecker - Class in jigcell.compare.data.type
Type for string data.
StringTypeChecker() - Constructor for class jigcell.compare.data.type.StringTypeChecker
Creates a new type checker.
StructuredTypeChecker - Class in jigcell.compare.data.type
Type for structured list data.
StructuredTypeChecker() - Constructor for class jigcell.compare.data.type.StructuredTypeChecker
Creates a new type checker.
StructuredTypeCheckerTemplate - Class in jigcell.compare.contrib
A DESCRIPTION OF YOUR CLASS.
StructuredTypeCheckerTemplate() - Constructor for class jigcell.compare.contrib.StructuredTypeCheckerTemplate
Creates a new type checker.
SUBCYCLEDROP - Static variable in class jigcell.compare.cellcycle.GenericScanTransform.GenericScanEvent
Subcycle species is dropping
SUBCYCLERISE - Static variable in class jigcell.compare.cellcycle.GenericScanTransform.GenericScanEvent
Subcycle species is rising
subcycleSpecies - Variable in class jigcell.compare.cellcycle.GenericScanTransform.GenericScanPoint
Value of the species being measured for subcycling
suffix - Variable in class jigcell.compare.impl.SuffixFileFilter
File suffix to match against
SuffixFileFilter - Class in jigcell.compare.impl
A file filter that matches against a given suffix string.
SuffixFileFilter() - Constructor for class jigcell.compare.impl.SuffixFileFilter
Creates a new file filter.
SuffixFileFilter(String, String) - Constructor for class jigcell.compare.impl.SuffixFileFilter
Creates a new file filter.
suite() - Static method in class jigcell.compare.tests.ElementTests
All of the tests in this test.
suite() - Static method in class jigcell.compare.tests.MethodDispatcherTests
All of the tests in this test.
suite() - Static method in class jigcell.compare.tests.StreamingStringTokenizerTests
All of the tests in this test.
suite() - Static method in class jigcell.compare.tests.SystemTests
All of the tests in this test.
suite() - Static method in class jigcell.compare.tests.TabTests
All of the tests in this test.
suite() - Static method in class jigcell.compare.tests.Tests
A suite containing all test suites for the Comparator.
suite() - Static method in class jigcell.compare.tests.TransformTests
All of the tests in this test.
swapValues(long, long) - Method in class jigcell.compare.data.EditableDataElement
Exchanges values within the element.
swapValues(long, long) - Method in interface jigcell.compare.IEditableDataElement
Exchanges values within the element.
SystemPrinterDataSource - Class in jigcell.compare.impl
A transfer agent for a source of data that supports writing to a printer.
SystemPrinterDataSource() - Constructor for class jigcell.compare.impl.SystemPrinterDataSource
Creates a new printer that uses the system printer service.
SystemTests - Class in jigcell.compare.tests
A collection of tests to exercise the standard cellcycle components.
SystemTests(String) - Constructor for class jigcell.compare.tests.SystemTests
Creates a new system test.

T

t - Variable in class jigcell.compare.views.EvaluationErrorViewer.ErrorRecord
Error
tab - Variable in class jigcell.compare.impl.Compare.TabInfo
Tab
tab - Variable in class jigcell.compare.ui.FindAccessory
Tab this accessory is currently installed in
TAB_LOCK - Variable in class jigcell.compare.impl.Compare
Lock for controlling tab manipulation
tabComponent - Variable in class jigcell.compare.ui.CompareFrontEnd
Component of the tab to add to pane
tabConfig - Variable in class jigcell.compare.ui.ConfigEditor
Destination for config information
tabImplementation - Variable in class jigcell.compare.ui.CompareFrontEnd
Tab to add to pane
table - Variable in class jigcell.compare.ui.SeriesDialog
Current table
table - Variable in class jigcell.compare.views.BasicTableView
Display
table - Variable in class jigcell.compare.views.EvaluationErrorViewer
Table
TABLE_COLORS - Static variable in class jigcell.compare.plotter.JPlotBridge
Table of plotter colors
tableChanged(TableModelEvent) - Method in class jigcell.compare.compare2.Compare2
 
tabName - Variable in class jigcell.compare.ui.PanelTab
Name of this tab
TABNAME_ANNOTATION - Static variable in class jigcell.compare.views.TransformDebugger
Tab name for the transform annotation
TABNAME_TRANSFORM - Static variable in class jigcell.compare.views.TransformDebugger
Tab name for the transform editor
TABNAME_VALUE - Static variable in class jigcell.compare.views.TransformDebugger
Tabe name for the transform value
TabTests - Class in jigcell.compare.tests
A collection of tests to exercise basic tab functions.
TabTests(String) - Constructor for class jigcell.compare.tests.TabTests
Creates a new system test.
target - Variable in class jigcell.compare.data.MethodDispatcher
Target of method invocations
target - Variable in class jigcell.compare.ui.MenuBuilder
Target of event actions
TEMPFILE_PREFIX - Static variable in class jigcell.compare.data.CachedDataElement
Prefix for temporary cache files
terminate(int) - Method in class jigcell.compare.impl.Compare.CompareSecurityManager
Shuts down the virtual machine.
test(Compare) - Static method in class jigcell.compare.tests.ElementBenchmark
Runs a creation benchmark on all known element types.
test(Class) - Static method in class jigcell.compare.tests.ElementBenchmark
Performs validation tests on an element type.
test(Compare) - Static method in class jigcell.compare.tests.ExperimentBenchmark
Runs a loading benchmark.
test(Compare) - Static method in class jigcell.compare.tests.ModelBuilderBenchmark
Runs a model builder benchmark.
test() - Method in class jigcell.compare.tests.OAAConnectorTest
Tests the OAAConnector class.
test(Compare) - Static method in class jigcell.compare.tests.ObjectiveBenchmark
Runs a loading benchmark.
test(Compare) - Static method in class jigcell.compare.tests.RunManagerBenchmark
Runs a loading benchmark.
test(Compare) - Static method in class jigcell.compare.tests.TransformBenchmark
Runs a loading benchmark.
testAcceptable(double, double) - Method in class jigcell.compare.views.ObjectiveSeriesView.Comparison
Tests whether the value is acceptable for this comparison.
testAddRow() - Method in class jigcell.compare.tests.TabTests
A test for adding rows.
testAddRows() - Method in class jigcell.compare.tests.TabTests
Test for adding rows.
testBoxTransformContainer() - Method in class jigcell.compare.tests.TransformTests
Test for data passing through.
testClear() - Method in class jigcell.compare.tests.TabTests
Test for clearing experimental data view.
testClearAndNew() - Method in class jigcell.compare.tests.TabTests
Test for creating a new experimental data view.
testConstantTransform() - Method in class jigcell.compare.tests.TransformTests
Test for data passing through.
testConvertArrayClassLongdouble() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for converting Long array to double array.
testConvertArrayClasslongDouble() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for converting long array to Double array.
testConvertArrayClasslongdouble() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for converting Long array to Double array.
testConvertArrayClasslonglongdoubledouble() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for converting multidimensional long array to multidimensional double array.
testConvertArrayClassNull() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for converting with null input.
testConvertFromElement1() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for converting a time series of integers.
testConvertFromElement2() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for converting a time series of reals.
testConvertFromElement3() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for converting a time series of mixed longs and reals.
testConvertFromElement4() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for converting a time series of mixed all types.
testConvertLongDouble0() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for converting integer zero to real.
testConvertLongDouble1() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for converting integer nonzero to real.
testConvertLongDoubleEmpty() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for converting null.
testConvertToElement1() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for converting a time series of integers.
testConvertToElement2() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for converting a time series of reals.
testConvertToElement3() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for converting a time series of mixed longs and reals.
testConvertToElement4() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for converting a time series of mixed all types.
testCreateArrayClassBoolean2() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for creating a multidimensional boolean array class.
testCreateArrayClassCharacter2() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for creating a multidimensional character array class.
testCreateArrayClassDataElement0() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for creating a data element array class.
testCreateArrayClassDataElement1() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for creating a multidimensional data element array class from an array class.
testCreateArrayClassDataElement2() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for creating a multidimensional data element array class from a base class.
testCreateArrayClassDouble2() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for creating a multidimensional real array class.
testCreateArrayClassFloat2() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for creating a multidimensional real array class.
testCreateArrayClassInteger2() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for creating a multidimensional integral array class.
testCreateArrayClassLong2() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for creating a multidimensional integral array class.
testCreateArrayClassLong5() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for creating a large multidimensional array class.
testCreateArrayClassShort2() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for creating a multidimensional integral array class.
testCurrentSource() - Method in class jigcell.compare.tests.TabTests
Test for recording the current tab data source.
testCurrentSource2() - Method in class jigcell.compare.tests.TabTests
Test for clearing the current tab data source.
testDispatch1() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for dispatching an integer list with conversion.
testDispatch2() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for dispatching an integer list list with conversion.
testDispatch3() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for dispatching string lists.
testDispatch4() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for dispatching integer lists.
testDispatch5() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for dispatching an integer with no match.
testDispatch6() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for dispatching real lists.
testDispatch7() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for dispatching an integer with a custom method.
testDispatch8() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for dispatching an integer list with a custom method.
testDispatch9() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for dispatching integer lists with a custom method.
testEmptyString() - Method in class jigcell.compare.tests.StreamingStringTokenizerTests
Test for tokenizing an empty string.
testExtremaTestTransform1() - Method in class jigcell.compare.tests.TransformTests
Test for extrema testing empty input.
testExtremaTestTransform2() - Method in class jigcell.compare.tests.TransformTests
Test for extrema testing numeric input.
testExtremaTestTransform3() - Method in class jigcell.compare.tests.TransformTests
Test for extrema testing invalid input.
testExtremaTestTransform4() - Method in class jigcell.compare.tests.TransformTests
Test for extrema testing numeric input with a minimum that will fail.
testExtremaTestTransform5() - Method in class jigcell.compare.tests.TransformTests
Test for extrema testing numeric input with a minimum that will pass.
testExtremaTestTransform6() - Method in class jigcell.compare.tests.TransformTests
Test for extrema testing numeric input with a maximum that will fail.
testExtremaTestTransform7() - Method in class jigcell.compare.tests.TransformTests
Test for extrema testing numeric input with a maximum that will pass.
testExtremaTestTransform8() - Method in class jigcell.compare.tests.TransformTests
Test for extrema testing with a minimum and maximum that will pass.
testExtremaTestTransform9() - Method in class jigcell.compare.tests.TransformTests
Test for setting invalid minimums and maximums.
testFileTransforms1() - Method in class jigcell.compare.tests.TransformTests
Test for marking as runnable.
testFileTransforms2() - Method in class jigcell.compare.tests.TransformTests
Test for persisting data.
testFindCommonSuperclassArrayList() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for finding superclass of one class.
testFindCommonSuperclassArrayListHashMap() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for finding superclass of unrelated classes.
testFindCommonSuperclassIntIntInt() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for finding superclass of one array class.
testFindCommonSuperclassIntIntIntIntInt() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for finding superclass of mismatched array classes.
testFindCommonSuperclassIntIntIntIntIntInt() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for finding superclass of array classes.
testFindCommonSuperclassTreeMapHashMap() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for finding superclass of related classes.
testFindCompare() - Method in class jigcell.compare.tests.SystemTests
Test for finding a Comparator instance.
testFindTab() - Method in class jigcell.compare.tests.SystemTests
Test for finding a tab instance by class.
testFindTab2() - Method in class jigcell.compare.tests.SystemTests
Test for finding a tab instance by name.
testGetDimensionDataElementDataElementDataElement() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for computing the dimensionality of a multidimensional data element array class.
testGetDimensionInt() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for computing the dimensionality of an array class.
testGetDimensionNull() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for computing the dimensionality of a null class.
testGetDimensionVoid() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for computing the dimensionality of a non-array class.
testGetUnderlyingClassBoolean() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for the underlying class of an array class.
testGetUnderlyingClassDataElement() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for the underlying class of a data element class.
testGetUnderlyingClassDataElementDataElementDataElement() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for the underlying class of a multidimensional data element array class.
testGetUnderlyingClassDouble() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for the underlying class of a primitive class.
testGetUnderlyingClassDoubleDouble() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for the underlying class of a multidimensional primitive array class.
testGetUnderlyingClassEmpty() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for the underlying class of a null class.
testGetUnderlyingClassFloatFloat() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for the underlying class of a multidimensional primitive array class.
testGetUnderlyingClassIntegerIntegerInteger() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for the underlying class of a multidimensional primitive array class.
testGetUnderlyingClassLong() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for the underlying class of a primitive class.
testGetUnderlyingClassShortShort() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for the underlying class of a multidimensional primitive array class.
testGetUnderlyingClassString() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for the underlying class of an object class.
testGetUnderlyingClassStringString() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for the underlying class of a multidimensional object array class.
testImproving(double, double) - Method in class jigcell.compare.views.ObjectiveSeriesView.Comparison
Whether the second value is better than the first value for this comparison.
testInputTransform1() - Method in class jigcell.compare.tests.TransformTests
Test for enabling result name control.
testInputTransform2() - Method in class jigcell.compare.tests.TransformTests
Test for setting the result name.
testInputTransform3() - Method in class jigcell.compare.tests.TransformTests
Test for setting the runnable state.
testInputTransform4() - Method in class jigcell.compare.tests.TransformTests
Test for passing data through.
testIsConvertibleClassBoolean() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for checking convertibility of boolean primitive class.
testIsConvertibleClassDataElement() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for checking convertibility of data element class.
testIsConvertibleClassDataElementDataElement() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for checking convertibility of multidimensional data element array class.
testIsConvertibleClassDouble() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for checking convertibility of double primitive class.
testIsConvertibleClassDoubleDouble() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for checking convertibility of multidimensional double primitive array class.
testIsConvertibleClassEmpty() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for checking convertibility of null class.
testIsConvertibleClassLong() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for checking convertibility of long primitive class.
testIsConvertibleClassLongLong() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for checking convertibility of multidimensional long primitive array class.
testIsConvertibleClassShortShort() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for checking convertibility of multidimensional short primitive array class.
testIsConvertibleClassString() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for checking convertibility of string object class.
testIsConvertibleClassVoid() - Method in class jigcell.compare.tests.MethodDispatcherTests
Test for checking convertibility of void primitive class.
testLoad() - Method in class jigcell.compare.tests.SystemTests
Test for loading experimental data.
testMultipleTokenString() - Method in class jigcell.compare.tests.StreamingStringTokenizerTests
Test for tokenizing the complicated time series example string.
testOneTokenString() - Method in class jigcell.compare.tests.StreamingStringTokenizerTests
Test for tokenizing a one token string.
testPackedTreeDataElement2Boolean() - Method in class jigcell.compare.tests.ElementTests
Test for true element.
testPackedTreeDataElement2Boolean2() - Method in class jigcell.compare.tests.ElementTests
Test for false element.
testPackedTreeDataElement2Empty() - Method in class jigcell.compare.tests.ElementTests
Test for empty element.
testPackedTreeDataElement2Integral() - Method in class jigcell.compare.tests.ElementTests
Test for positive integer element.
testPackedTreeDataElement2Integral2() - Method in class jigcell.compare.tests.ElementTests
Test for zero integer element.
testPackedTreeDataElement2Integral3() - Method in class jigcell.compare.tests.ElementTests
Test for negative integer element.
testPackedTreeDataElement2Integral4() - Method in class jigcell.compare.tests.ElementTests
Test for maximum integer element.
testPackedTreeDataElement2Integral5() - Method in class jigcell.compare.tests.ElementTests
Test for minimum integer element.
testPackedTreeDataElement2List() - Method in class jigcell.compare.tests.ElementTests
Test for empty list element.
testPackedTreeDataElement2List2() - Method in class jigcell.compare.tests.ElementTests
Test for mixed type list element.
testPackedTreeDataElement2Mixed() - Method in class jigcell.compare.tests.ElementTests
Assorted tests for PackedTreeDataElement2 used in benchmarks.
testPackedTreeDataElement2Real() - Method in class jigcell.compare.tests.ElementTests
Test for positive real element.
testPackedTreeDataElement2Real2() - Method in class jigcell.compare.tests.ElementTests
Test for negative infinite element.
testPackedTreeDataElement2Real3() - Method in class jigcell.compare.tests.ElementTests
Test for positive infinite element.
testPackedTreeDataElement2Real4() - Method in class jigcell.compare.tests.ElementTests
Test for maximum real element.
testPackedTreeDataElement2Real5() - Method in class jigcell.compare.tests.ElementTests
Test for minimum real element.
testPackedTreeDataElement2Real6() - Method in class jigcell.compare.tests.ElementTests
Test for undefined real element.
testPackedTreeDataElement2Real7() - Method in class jigcell.compare.tests.ElementTests
Test for negative real element.
testPackedTreeDataElement2Real8() - Method in class jigcell.compare.tests.ElementTests
Test for zero real element.
testPackedTreeDataElement2String() - Method in class jigcell.compare.tests.ElementTests
Test for string of an integer element.
testPackedTreeDataElement2String2() - Method in class jigcell.compare.tests.ElementTests
Test for string of a real element.
testPackedTreeDataElement2String3() - Method in class jigcell.compare.tests.ElementTests
Test for string of a boolean element.
testPackedTreeDataElement2String4() - Method in class jigcell.compare.tests.ElementTests
Test for string of a list element.
testPackedTreeDataElement2String5() - Method in class jigcell.compare.tests.ElementTests
Test for string of a string element.
testPackedTreeDataElementBoolean() - Method in class jigcell.compare.tests.ElementTests
Test for true element.
testPackedTreeDataElementBoolean2() - Method in class jigcell.compare.tests.ElementTests
Test for false element.
testPackedTreeDataElementEmpty() - Method in class jigcell.compare.tests.ElementTests
Test for empty element.
testPackedTreeDataElementIntegral() - Method in class jigcell.compare.tests.ElementTests
Test for positive integer element.
testPackedTreeDataElementIntegral2() - Method in class jigcell.compare.tests.ElementTests
Test for zero integer element.
testPackedTreeDataElementIntegral3() - Method in class jigcell.compare.tests.ElementTests
Test for negative integer element.
testPackedTreeDataElementIntegral4() - Method in class jigcell.compare.tests.ElementTests
Test for maximum integer element.
testPackedTreeDataElementIntegral5() - Method in class jigcell.compare.tests.ElementTests
Test for minimum integer element.
testPackedTreeDataElementList() - Method in class jigcell.compare.tests.ElementTests
Test for empty list element.
testPackedTreeDataElementList2() - Method in class jigcell.compare.tests.ElementTests
Test for mixed type list element.
testPackedTreeDataElementMixed() - Method in class jigcell.compare.tests.ElementTests
Assorted tests for PackedTreeDataElement used in benchmarks.
testPackedTreeDataElementReal() - Method in class jigcell.compare.tests.ElementTests
Test for positive real element.
testPackedTreeDataElementReal2() - Method in class jigcell.compare.tests.ElementTests
Test for negative infinite element.
testPackedTreeDataElementReal3() - Method in class jigcell.compare.tests.ElementTests
Test for positive infinite element.
testPackedTreeDataElementReal4() - Method in class jigcell.compare.tests.ElementTests
Test for maximum real element.
testPackedTreeDataElementReal5() - Method in class jigcell.compare.tests.ElementTests
Test for minimum real element.
testPackedTreeDataElementReal6() - Method in class jigcell.compare.tests.ElementTests
Test for undefined real element.
testPackedTreeDataElementReal7() - Method in class jigcell.compare.tests.ElementTests
Test for negative real element.
testPackedTreeDataElementReal8() - Method in class jigcell.compare.tests.ElementTests
Test for zero real element.
testPackedTreeDataElementString() - Method in class jigcell.compare.tests.ElementTests
Test for string of an integer element.
testPackedTreeDataElementString2() - Method in class jigcell.compare.tests.ElementTests
Test for string of a real element.
testPackedTreeDataElementString3() - Method in class jigcell.compare.tests.ElementTests
Test for string of a boolean element.
testPackedTreeDataElementString4() - Method in class jigcell.compare.tests.ElementTests
Test for string of a list element.
testPackedTreeDataElementString5() - Method in class jigcell.compare.tests.ElementTests
Test for string of a string element.
testRemoveRow() - Method in class jigcell.compare.tests.TabTests
Test for removing the last row.
testRemoveRow2() - Method in class jigcell.compare.tests.TabTests
Test for removing a row.
testRemoveRows() - Method in class jigcell.compare.tests.TabTests
Test for removing a list of rows.
testRemoveRows2() - Method in class jigcell.compare.tests.TabTests
Test for removing an empty list of rows.
testRunFrogEgg() - Method in class jigcell.compare.tests.SystemTests
Test for executing the frog egg model.
TESTS - Static variable in class jigcell.compare.tests.ElementBenchmark
Tests for the time series format
Tests - Class in jigcell.compare.tests
Test harness for all Comparator tests.
Tests() - Constructor for class jigcell.compare.tests.Tests
Tests should never be instantiated.
testScriptEvaluationTransform1() - Method in class jigcell.compare.tests.TransformTests
Test for evaluating an empty script.
testScriptEvaluationTransform2() - Method in class jigcell.compare.tests.TransformTests
Test for evaluating a simple script.
testScriptEvaluationTransform3() - Method in class jigcell.compare.tests.TransformTests
Test for setting the Comparator option.
testScriptEvaluationTransform4() - Method in class jigcell.compare.tests.TransformTests
Test for class import resolution.
testScriptEvaluationTransform5() - Method in class jigcell.compare.tests.TransformTests
Test for a script with no input.
testScriptEvaluationTransform6() - Method in class jigcell.compare.tests.TransformTests
Test for a script with simple input.
testScriptEvaluationTransform7() - Method in class jigcell.compare.tests.TransformTests
Test for using math in a script.
testScriptEvaluationTransform8() - Method in class jigcell.compare.tests.TransformTests
Test for defining functions in a script.
testScriptEvaluationTransform9() - Method in class jigcell.compare.tests.TransformTests
Test for passing object data through a script.
testSelectColumnsTransform1() - Method in class jigcell.compare.tests.TransformTests
Test for selecting no columns.
testSelectColumnsTransform2() - Method in class jigcell.compare.tests.TransformTests
Test for selecting one column.
testSelectColumnsTransform3() - Method in class jigcell.compare.tests.TransformTests
Test for selecting multiple columns.
testSelectColumnsTransform4() - Method in class jigcell.compare.tests.TransformTests
Test for selecting repeating and out of order columns.
testSparseTreeDataElement2Boolean() - Method in class jigcell.compare.tests.ElementTests
Test for true element.
testSparseTreeDataElement2Boolean2() - Method in class jigcell.compare.tests.ElementTests
Test for false element.
testSparseTreeDataElement2Empty() - Method in class jigcell.compare.tests.ElementTests
Test for empty element.
testSparseTreeDataElement2Integral() - Method in class jigcell.compare.tests.ElementTests
Test for positive integer element.
testSparseTreeDataElement2Integral2() - Method in class jigcell.compare.tests.ElementTests
Test for zero integer element.
testSparseTreeDataElement2Integral3() - Method in class jigcell.compare.tests.ElementTests
Test for negative integer element.
testSparseTreeDataElement2Integral4() - Method in class jigcell.compare.tests.ElementTests
Test for maximum integer element.
testSparseTreeDataElement2Integral5() - Method in class jigcell.compare.tests.ElementTests
Test for minimum integer element.
testSparseTreeDataElement2List() - Method in class jigcell.compare.tests.ElementTests
Test for empty list element.
testSparseTreeDataElement2List2() - Method in class jigcell.compare.tests.ElementTests
Test for mixed type list element.
testSparseTreeDataElement2Mixed() - Method in class jigcell.compare.tests.ElementTests
Assorted tests for SparseTreeDataElement2 used in benchmarks.
testSparseTreeDataElement2Real() - Method in class jigcell.compare.tests.ElementTests
Test for positive real element.
testSparseTreeDataElement2Real2() - Method in class jigcell.compare.tests.ElementTests
Test for negative infinite element.
testSparseTreeDataElement2Real3() - Method in class jigcell.compare.tests.ElementTests
Test for positive infinite element.
testSparseTreeDataElement2Real4() - Method in class jigcell.compare.tests.ElementTests
Test for maximum real element.
testSparseTreeDataElement2Real5() - Method in class jigcell.compare.tests.ElementTests
Test for minimum real element.
testSparseTreeDataElement2Real6() - Method in class jigcell.compare.tests.ElementTests
Test for undefined real element.
testSparseTreeDataElement2Real7() - Method in class jigcell.compare.tests.ElementTests
Test for negative real element.
testSparseTreeDataElement2Real8() - Method in class jigcell.compare.tests.ElementTests
Test for zero real element.
testSparseTreeDataElement2String() - Method in class jigcell.compare.tests.ElementTests
Test for string of an integer element.
testSparseTreeDataElement2String2() - Method in class jigcell.compare.tests.ElementTests
Test for string of a real element.
testSparseTreeDataElement2String3() - Method in class jigcell.compare.tests.ElementTests
Test for string of a boolean element.
testSparseTreeDataElement2String4() - Method in class jigcell.compare.tests.ElementTests
Test for string of a list element.
testSparseTreeDataElement2String5() - Method in class jigcell.compare.tests.ElementTests
Test for string of a string element.
testSparseTreeDataElementBoolean() - Method in class jigcell.compare.tests.ElementTests
Test for true element.
testSparseTreeDataElementBoolean2() - Method in class jigcell.compare.tests.ElementTests
Test for false element.
testSparseTreeDataElementEmpty() - Method in class jigcell.compare.tests.ElementTests
Test for empty element.
testSparseTreeDataElementIntegral() - Method in class jigcell.compare.tests.ElementTests
Test for positive integer element.
testSparseTreeDataElementIntegral2() - Method in class jigcell.compare.tests.ElementTests
Test for zero integer element.
testSparseTreeDataElementIntegral3() - Method in class jigcell.compare.tests.ElementTests
Test for negative integer element.
testSparseTreeDataElementIntegral4() - Method in class jigcell.compare.tests.ElementTests
Test for maximum integer element.
testSparseTreeDataElementIntegral5() - Method in class jigcell.compare.tests.ElementTests
Test for minimum integer element.
testSparseTreeDataElementList() - Method in class jigcell.compare.tests.ElementTests
Test for empty list element.
testSparseTreeDataElementList2() - Method in class jigcell.compare.tests.ElementTests
Test for mixed type list element.
testSparseTreeDataElementMixed() - Method in class jigcell.compare.tests.ElementTests
Assorted tests for SparseTreeDataElement used in benchmarks.
testSparseTreeDataElementReal() - Method in class jigcell.compare.tests.ElementTests
Test for positive real element.
testSparseTreeDataElementReal2() - Method in class jigcell.compare.tests.ElementTests
Test for negative infinite element.
testSparseTreeDataElementReal3() - Method in class jigcell.compare.tests.ElementTests
Test for positive infinite element.
testSparseTreeDataElementReal4() - Method in class jigcell.compare.tests.ElementTests
Test for maximum real element.
testSparseTreeDataElementReal5() - Method in class jigcell.compare.tests.ElementTests
Test for minimum real element.
testSparseTreeDataElementReal6() - Method in class jigcell.compare.tests.ElementTests
Test for undefined real element.
testSparseTreeDataElementReal7() - Method in class jigcell.compare.tests.ElementTests
Test for negative real element.
testSparseTreeDataElementReal8() - Method in class jigcell.compare.tests.ElementTests
Test for zero real element.
testSparseTreeDataElementString() - Method in class jigcell.compare.tests.ElementTests
Test for string of an integer element.
testSparseTreeDataElementString2() - Method in class jigcell.compare.tests.ElementTests
Test for string of a real element.
testSparseTreeDataElementString3() - Method in class jigcell.compare.tests.ElementTests
Test for string of a boolean element.
testSparseTreeDataElementString4() - Method in class jigcell.compare.tests.ElementTests
Test for string of a list element.
testSparseTreeDataElementString5() - Method in class jigcell.compare.tests.ElementTests
Test for string of a string element.
testTransformEvaluationTransform1() - Method in class jigcell.compare.tests.TransformTests
Test finding a target transform.
testTransformEvaluationTransform2() - Method in class jigcell.compare.tests.TransformTests
Test finding a target transform when multiple transforms to choose from.
testTransformEvaluationTransform3() - Method in class jigcell.compare.tests.TransformTests
Test finding a target transform when multiple transforms to choose from.
testTransformEvaluationTransform4() - Method in class jigcell.compare.tests.TransformTests
Test for runnable state.
testTransformEvaluationTransform5() - Method in class jigcell.compare.tests.TransformTests
Test for failing when no transforms exists.
testTransformEvaluationTransform6() - Method in class jigcell.compare.tests.TransformTests
Test for failing when no transform with target name exists.
TextComponentDescription - Class in jigcell.compare.ui
Description for one of the Comparator components.
TextComponentDescription(String) - Constructor for class jigcell.compare.ui.TextComponentDescription
Creates a new component description.
TextComponentDescription(URL) - Constructor for class jigcell.compare.ui.TextComponentDescription
Creates a new component description.
textCutoff - Variable in class jigcell.compare.views.SeriesView
Column to cutoff excessively long values at
textField - Variable in class jigcell.compare.ui.FindAccessory
Field for search text entry
THRESHOLD_EQUIVALENT - Static variable in class jigcell.compare.compare2.Compare2Model
Threshold display for equivalent values
THRESHOLD_EQUIVALENT - Static variable in class jigcell.compare.views.ObjectiveSeriesView.ObjectiveSeriesModel
Threshold display for equivalent values
ThresholdAbsoluteViewColorer - Class in jigcell.compare.compare2
A table renderer that can color the view of a Compare^2.
ThresholdAbsoluteViewColorer(Compare2) - Constructor for class jigcell.compare.compare2.ThresholdAbsoluteViewColorer
Creates a new view colorer that colors by absolute distances to threshold.
thresholdDialog - Variable in class jigcell.compare.compare2.Compare2
Dialog view for threshold editor
thresholdDocument - Variable in class jigcell.compare.compare2.ThresholdEditor
Document storing the threshold value
ThresholdEditor - Class in jigcell.compare.compare2
Editor for comparison thresholds.
ThresholdEditor(Compare, Compare2Model, Map) - Constructor for class jigcell.compare.compare2.ThresholdEditor
Creates a new display for editing thresholds.
thresholdFormat - Variable in class jigcell.compare.compare2.ThresholdEditor
Formatter for displaying threshold values
ThresholdRelativeViewColorer - Class in jigcell.compare.compare2
A table renderer that can color the view of a Compare^2.
ThresholdRelativeViewColorer(Compare2, int) - Constructor for class jigcell.compare.compare2.ThresholdRelativeViewColorer
Creates a new view colorer that colors by relative distances to threshold.
thresholdSlider - Variable in class jigcell.compare.compare2.ThresholdEditor
Slider for adjusting the threshold value
throwUncheckedException(Throwable) - Static method in class jigcell.compare.impl.Compare
Converts a throwable from a potentially checked exception type to an unchecked exception type and throws it.
tie - Variable in class jigcell.compare.data.FlippedDataElement
Original element
time - Variable in class jigcell.compare.cellcycle.BuddingYeastScanTransform.BuddingYeastScanEvent
Time when the event occurred
time - Variable in class jigcell.compare.cellcycle.BuddingYeastScanTransform.BuddingYeastScanPoint
Clock time
time - Variable in class jigcell.compare.cellcycle.GenericScanTransform.GenericScanEvent
Time when the event occurred
time - Variable in class jigcell.compare.cellcycle.GenericScanTransform.GenericScanPoint
Clock time
timer - Variable in class jigcell.compare.ui.CompareFrontEnd.SplashScreen
Delay timer
timer - Variable in class jigcell.compare.ui.MemoryMonitorAccessory
Update timer
timer - Variable in class jigcell.compare.ui.ProgressMonitor
Timer to display monitor dialog
TIMER_LENGTH - Static variable in class jigcell.compare.ui.CompareFrontEnd.SplashScreen
Length to display splash screen after loading is done
timeRunState(int) - Method in class jigcell.compare.tests.Benchmark
Executes an operation that interacts with the interface and returns how long it took to complete.
TimeSeriesTypeChecker - Class in jigcell.compare.data.type
Type for time series data.
TimeSeriesTypeChecker(String) - Constructor for class jigcell.compare.data.type.TimeSeriesTypeChecker
Creates a new type checker.
TimeSeriesTypeChecker() - Constructor for class jigcell.compare.data.type.TimeSeriesTypeChecker
Creates a new type checker.
TITLE_CONFIGURE - Static variable in class jigcell.compare.cellcycle.CellCycleReportGenerator
Configure window title
TITLE_NAMEPOPUP - Static variable in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Title of popup dialog for inputting name
TITLE_ROW - Static variable in class jigcell.compare.ui.SeriesDialog.SeriesModel
Title for generic row descriptions
toArray() - Method in class jigcell.compare.data.DataGeneratorList
This list of generators as an array.
toArray() - Method in interface jigcell.compare.data.IDataGeneratorList
This list of generators as an array.
TOKEN_ALL - Static variable in class jigcell.compare.data.EditableDataElement
All of the tokens used by the parser
TOKEN_BLOCKELEMENT - Static variable in class jigcell.compare.data.EditableDataElement
Token to separate block elements
TOKEN_BLOCKEND - Static variable in class jigcell.compare.data.EditableDataElement
Token to end a block
TOKEN_BLOCKSTART - Static variable in class jigcell.compare.data.EditableDataElement
Token to start a block
TOKEN_ENDTERM - Static variable in class jigcell.compare.cellcycle.OAAConnector
Token marking the end of a term
TOKEN_LISTSEPARATOR - Static variable in class jigcell.compare.impl.Config
Separator between two entries in a list
TOKEN_LITERAL - Static variable in class jigcell.compare.data.EditableDataElement
Token to delimit a literal
TOKEN_NEXTTERM - Static variable in class jigcell.compare.cellcycle.OAAConnector
Token marking the start of the next term
TOKEN_SESSION - Static variable in class jigcell.compare.impl.Config
Session token marker
TOKEN_STARTTERM - Static variable in class jigcell.compare.cellcycle.OAAConnector
Token marking the start of a term
toolbar - Variable in class jigcell.compare.ui.CompareFrontEnd
Toolbar
TOOLBAR_DEFAULT - Static variable in class jigcell.compare.ui.DataEditorPanelTab
Name of default toolbar
TOOLBAR_DEFAULT - Static variable in class jigcell.compare.views.TransformDebugger
Name of default toolbar
tools - Variable in class jigcell.compare.ui.CompareFrontEnd.FrontEndTabInfo
Tab toolbar tools
tools - Variable in class jigcell.compare.ui.MenuBuilder.Builder
Description for a tool bar
toString(IDataElement) - Static method in class jigcell.compare.data.DataElement
Renders the DataElement as an ordered tuple.
toString(IDataElement, long) - Static method in class jigcell.compare.data.DataElement
Renders the value of a specified position.
toString(IDataElement, NumberFormat) - Static method in class jigcell.compare.data.DataElement
Renders the DataElement as an ordered tuple.
toString(IDataElement, boolean, int) - Static method in class jigcell.compare.data.DataElement
Renders the DataElement as an ordered tuple.
toString(IDataElement, long, NumberFormat) - Static method in class jigcell.compare.data.DataElement
Renders the value of a specified position.
toString(IDataElement, boolean, int, NumberFormat) - Static method in class jigcell.compare.data.DataElement
Renders the DataElement as an ordered tuple.
toString(IDataElement, boolean, int, long) - Static method in class jigcell.compare.data.DataElement
Renders the value of a specified position.
toString(IDataElement, boolean, int, long, NumberFormat) - Static method in class jigcell.compare.data.DataElement
Renders the value of a specified position.
toString() - Method in class jigcell.compare.data.DataElement
Renders the DataElement as an ordered tuple.
toString(NumberFormat) - Method in class jigcell.compare.data.DataElement
Renders the value with a particular format.
toString(long) - Method in class jigcell.compare.data.DataElement
Renders the value of a specified position.
toString(boolean, int) - Method in class jigcell.compare.data.DataElement
Renders the DataElement as an ordered tuple.
toString(long, NumberFormat) - Method in class jigcell.compare.data.DataElement
Renders the value of a specified position with a particular format.
toString(boolean, int, NumberFormat) - Method in class jigcell.compare.data.DataElement
Renders the DataElement as an ordered tuple with a particular format.
toString(boolean, int, long) - Method in class jigcell.compare.data.DataElement
Renders the value of a specified position.
toString(boolean, int, long, NumberFormat) - Method in class jigcell.compare.data.DataElement
Renders the value of a specified position with a particular format.
toString() - Method in class jigcell.compare.data.DataGenerator
The name of this generator.
toString() - Method in class jigcell.compare.data.DataGeneratorList
 
toString() - Method in class jigcell.compare.data.DataGeneratorMap
 
toString() - Method in class jigcell.compare.data.IDataGeneratorCollection.Key
 
toString() - Method in class jigcell.compare.data.type.TypeChecker
 
toString(NumberFormat) - Method in interface jigcell.compare.IDataElement
Renders the value with a particular format.
toString(long) - Method in interface jigcell.compare.IDataElement
Renders the value of a specified position.
toString(boolean, int) - Method in interface jigcell.compare.IDataElement
Renders the DataElement as an ordered tuple.
toString(long, NumberFormat) - Method in interface jigcell.compare.IDataElement
Renders the value of a specified position with a particular format.
toString(boolean, int, NumberFormat) - Method in interface jigcell.compare.IDataElement
Renders the DataElement as an ordered tuple with a particular format.
toString(boolean, int, long) - Method in interface jigcell.compare.IDataElement
Renders the value of a specified position.
toString(boolean, int, long, NumberFormat) - Method in interface jigcell.compare.IDataElement
Renders the value of a specified position with a particular format.
toString() - Method in class jigcell.compare.IDataElement.Type
 
toString() - Method in class jigcell.compare.IDataSource.Option
 
toString() - Method in class jigcell.compare.impl.DataSource
 
toString() - Method in class jigcell.compare.impl.EvaluationCallStack
 
toString() - Method in class jigcell.compare.plotter.IPlotter.Combine
 
toString() - Method in class jigcell.compare.ui.BasicTable.BasicTableModel.Marker
 
toString() - Method in class jigcell.compare.views.ObjectiveSeriesView.Comparison
 
traceSet - Variable in class jigcell.compare.views.TransformDebugger
Set of elements identified as connected to the transform cursor
trackSetPosition - Variable in class jigcell.compare.compare2.Compare2
Whether to track the column position when adding a set
transfer(List, Transferable) - Static method in class jigcell.compare.impl.Transferer
The first successful transfer for a given list of flavors.
Transferer - Class in jigcell.compare.impl
A helper class for transfering data between the Comparator and other applications.
Transferer() - Constructor for class jigcell.compare.impl.Transferer
Creates a new data transferer.
Transform - Class in jigcell.compare.transform
An indvidual statement of a transform as a part of a sequence of steps.
Transform() - Constructor for class jigcell.compare.transform.Transform
Creates a new transform.
transformAdded(ITransformContext, ITransform, String) - Method in interface jigcell.compare.transform.ITransformContextListener
Notification that a transform was added to a context.
transformAdded(ITransformContext, ITransform, String) - Method in class jigcell.compare.transform.TransformEvaluationTransform
Notification that a transform was added to a context.
TransformAnnotation - Class in jigcell.compare.transform.annotation
A default implementation of DataGeneratorAnnotation.
TransformAnnotation() - Constructor for class jigcell.compare.transform.annotation.TransformAnnotation
Creates a new annotation.
transformAnnotation - Variable in class jigcell.compare.views.TransformDebugger
Annotation for the currently selected transform
TransformAnnotation.AnnotationDescriptor - Class in jigcell.compare.transform.annotation
A default implementation of AnnotationDescriptor.
TransformAnnotation.AnnotationDescriptor() - Constructor for class jigcell.compare.transform.annotation.TransformAnnotation.AnnotationDescriptor
Creates a new annotation descriptor.
TransformBenchmark - Class in jigcell.compare.tests
A collection of tests for evaluating transform loading performance.
TransformBenchmark(Compare) - Constructor for class jigcell.compare.tests.TransformBenchmark
Creates a new tester for transform loading performance.
TransformContainer - Class in jigcell.compare.transform
A collection of transforms that combine to compute a result.
TransformContainer() - Constructor for class jigcell.compare.transform.TransformContainer
Creates a new transform container.
TransformContainerInterface - Class in jigcell.compare.transformui
Generic customizable interface for a transform container.
TransformContainerInterface(IProgrammableDataGenerator) - Constructor for class jigcell.compare.transformui.TransformContainerInterface
Creates a new interface for a transform.
TransformContext - Class in jigcell.compare.transform
A default implementation of the runtime context for evaluating transforms.
TransformContext() - Constructor for class jigcell.compare.transform.TransformContext
Creates a new evaluation context.
TransformContext.ReaperReference - Class in jigcell.compare.transform
Reference class for transforms that deletes the transform information from the context when the transform is reclaimed.
TransformContext.ReaperReference(ITransform) - Constructor for class jigcell.compare.transform.TransformContext.ReaperReference
Creates a new transform reference.
TRANSFORMCONTEXT_CELLCYCLE - Static variable in class jigcell.compare.cellcycle.CellCycleTransformView
Transform evaluation context for the cellcycle components
transformCursor - Variable in class jigcell.compare.views.TransformDebugger
Currently selected transform
TransformDebugger - Class in jigcell.compare.views
Supports debugging transform functions.
TransformDebugger(Compare, String) - Constructor for class jigcell.compare.views.TransformDebugger
Creates a new debugger for working with transforms.
TransformDebugger.AnnotationModel - Class in jigcell.compare.views
Table model for a Transform Debugger annotation table.
TransformDebugger.AnnotationModel() - Constructor for class jigcell.compare.views.TransformDebugger.AnnotationModel
Creates a new table model.
TransformDebugger.DebuggerThread - Class in jigcell.compare.views
Thread for executing play events.
TransformDebugger.DebuggerThread(long) - Constructor for class jigcell.compare.views.TransformDebugger.DebuggerThread
Creates a new thread for performing debug evaluations.
TransformDebugger.TransformTreeRenderer - Class in jigcell.compare.views
Renderer for the cells of the transform tree.
TransformDebugger.TransformTreeRenderer() - Constructor for class jigcell.compare.views.TransformDebugger.TransformTreeRenderer
Creates a new tree cell renderer for a transform debugger.
TransformDebugger.ValueModel - Class in jigcell.compare.views
Table model for a Transform Debugger value table.
TransformDebugger.ValueModel() - Constructor for class jigcell.compare.views.TransformDebugger.ValueModel
Creates a new table model.
TransformEditor - Class in jigcell.compare.views
Supports creating and editing transform functions.
TransformEditor(Compare, String) - Constructor for class jigcell.compare.views.TransformEditor
Creates a new editor for working with transforms.
transformElement - Variable in class jigcell.compare.cellcycle.CellCycleDataDialog
Data element of the transform result
TransformEvaluationInterface - Class in jigcell.compare.transformui
Interface for a TransformEvaluationTransform.
TransformEvaluationInterface(IProgrammableDataGenerator) - Constructor for class jigcell.compare.transformui.TransformEvaluationInterface
Creates a new interface for a TransformEvaluationTransform.
TransformEvaluationTransform - Class in jigcell.compare.transform
A transform that evaluates another named transform.
TransformEvaluationTransform() - Constructor for class jigcell.compare.transform.TransformEvaluationTransform
Creates a new transform to evaluate another transform.
TransformEvaluationTransform(String) - Constructor for class jigcell.compare.transform.TransformEvaluationTransform
Creates a new transform to evaluate another transform.
TransformHelper - Class in jigcell.compare.contrib
Methods for reducing the amount of work to make a transform.
TransformHelper() - Constructor for class jigcell.compare.contrib.TransformHelper
Creates a new helper for writing transforms.
TransformInterface - Class in jigcell.compare.transformui
Generic customizable interface for a transform.
TransformInterface(IProgrammableDataGenerator) - Constructor for class jigcell.compare.transformui.TransformInterface
Creates a new interface for a transform.
transformMap - Variable in class jigcell.compare.views.TransformDebugger
Map from transforms to tree nodes
transformModel - Variable in class jigcell.compare.cellcycle.CellCycleTransformView
Display for list of known transforms
transformModel - Variable in class jigcell.compare.transformui.TransformEvaluationInterface
Model for transform list
transformRemoved(ITransformContext, ITransform, String) - Method in interface jigcell.compare.transform.ITransformContextListener
Notification that a transform was removed from a context.
transformRemoved(ITransformContext, ITransform, String) - Method in class jigcell.compare.transform.TransformEvaluationTransform
Notification that a transform was removed from a context.
transforms - Variable in class jigcell.compare.cellcycle.CellCycleTransformView
List of known transforms
TransformTemplate - Class in jigcell.compare.contrib
A DESCRIPTION OF YOUR CLASS.
TransformTemplate() - Constructor for class jigcell.compare.contrib.TransformTemplate
 
TransformTests - Class in jigcell.compare.tests
A collection of tests to exercise the included transforms.
TransformTests(String) - Constructor for class jigcell.compare.tests.TransformTests
Creates a new transform test.
transformValue - Variable in class jigcell.compare.views.TransformDebugger
Value for the currently selected transform
transformView - Variable in class jigcell.compare.tests.TransformBenchmark
View to load transforms in
transients - Variable in class jigcell.compare.impl.XMLFormatter
Property descriptors to make transient
TRANSPARENCY_ADJUST - Static variable in class jigcell.compare.compare2.ThresholdAbsoluteViewColorer
Transparency adjustment value
TRANSPARENCY_ADJUST - Static variable in class jigcell.compare.compare2.ThresholdRelativeViewColorer
Transparency adjustment value
tree - Variable in class jigcell.compare.views.TransformDebugger
Transform tree model
TreeDataElement - Class in jigcell.compare.data
Base class for implementations of EditableDataElement that want to use some form of tree to store values.
TreeDataElement() - Constructor for class jigcell.compare.data.TreeDataElement
 
treeModel - Variable in class jigcell.compare.views.TransformDebugger
Transform tree model
TriColorViewColorer - Class in jigcell.compare.compare2
A table renderer that can color the view of a Compare^2.
TriColorViewColorer(Compare2) - Constructor for class jigcell.compare.compare2.TriColorViewColorer
Creates a new view colorer that colors with three categories.
trimToSize(int) - Method in class jigcell.compare.data.PackedDoubleDataElement
Trims the underlying array to a particular size.
TRUE - Static variable in class jigcell.compare.objective.BooleanRelationalObjective
True result
TRUE - Static variable in class jigcell.compare.transform.ExtremaTestTransform
True value
type - Variable in class jigcell.compare.IDataSource.Option
Type of option
TYPE_ANNOTATION - Static variable in class jigcell.compare.cellcycle.JigCellRunManagerTransform
The type of objects this transform produces
TYPE_DESCRIPTION - Static variable in class jigcell.compare.contrib.StructuredTypeCheckerTemplate
Description of this type
TYPE_DESCRIPTION - Static variable in class jigcell.compare.contrib.TypeCheckerTemplate
Description of this type
TYPE_NAME - Static variable in class jigcell.compare.cellcycle.BuddingYeastNocPhenotype
Name of this type
TYPE_NAME - Static variable in class jigcell.compare.cellcycle.BuddingYeastPhenotype
Name of this type
TYPE_NAME - Static variable in class jigcell.compare.cellcycle.BuddingYeastWildtypeProperties
Name of this type
TYPE_NAME - Static variable in class jigcell.compare.cellcycle.GenericPhenotype
Name of this type
TYPE_NAME - Static variable in class jigcell.compare.contrib.StructuredTypeCheckerTemplate
Name of this type
TYPE_NAME - Static variable in class jigcell.compare.contrib.TypeCheckerTemplate
Name of this type
TYPE_NAME - Static variable in class jigcell.compare.data.type.BooleanTypeChecker
Name of this type
TYPE_NAME - Static variable in class jigcell.compare.data.type.IntegerTypeChecker
Name of this type
TYPE_NAME - Static variable in class jigcell.compare.data.type.ListTypeChecker
Name of this type
TYPE_NAME - Static variable in class jigcell.compare.data.type.RealTypeChecker
Name of this type
TYPE_NAME - Static variable in class jigcell.compare.data.type.StringTypeChecker
Name of this type
TYPE_NAME - Static variable in class jigcell.compare.data.type.TimeSeriesTypeChecker
Name of this type
TYPE_NAME - Static variable in class jigcell.compare.data.type.UntypedTypeChecker
Name of this type
TYPE_SINGLETON - Static variable in class jigcell.compare.cellcycle.BuddingYeastNocPhenotype
Instance of this type
TYPE_SINGLETON - Static variable in class jigcell.compare.cellcycle.BuddingYeastPhenotype
Instance of this type
TYPE_SINGLETON - Static variable in class jigcell.compare.cellcycle.BuddingYeastWildtypeProperties
Instance of this type
TYPE_SINGLETON - Static variable in class jigcell.compare.cellcycle.GenericPhenotype
Instance of this type
TYPE_SINGLETON - Static variable in class jigcell.compare.contrib.StructuredTypeCheckerTemplate
Instance of this type
TYPE_SINGLETON - Static variable in class jigcell.compare.contrib.TypeCheckerTemplate
Instance of this type
TYPE_SINGLETON - Static variable in class jigcell.compare.data.type.BooleanTypeChecker
Instance of this type
TYPE_SINGLETON - Static variable in class jigcell.compare.data.type.IntegerTypeChecker
Instance of this type
TYPE_SINGLETON - Static variable in class jigcell.compare.data.type.ListTypeChecker
Instance of this type
TYPE_SINGLETON - Static variable in class jigcell.compare.data.type.RealTypeChecker
Instance of this type
TYPE_SINGLETON - Static variable in class jigcell.compare.data.type.StringTypeChecker
Instance of this type
TYPE_SINGLETON - Static variable in class jigcell.compare.data.type.TimeSeriesTypeChecker
Instance of this type
TYPE_SINGLETON - Static variable in class jigcell.compare.data.type.UntypedTypeChecker
Instance of this type
TypeChecker - Class in jigcell.compare.data.type
Base class for type checkers.
TypeChecker() - Constructor for class jigcell.compare.data.type.TypeChecker
Creates a new type checker.
TypeCheckerTemplate - Class in jigcell.compare.contrib
A DESCRIPTION OF YOUR CLASS.
TypeCheckerTemplate() - Constructor for class jigcell.compare.contrib.TypeCheckerTemplate
Creates a new type checker.
typeModel - Variable in class jigcell.compare.cellcycle.CellCycleExperimentView
Display for list of known types
types - Variable in class jigcell.compare.cellcycle.CellCycleExperimentView
List of known types
types - Static variable in class jigcell.compare.views.ObjectiveSeriesView.Comparison
List of available types

U

UIDEBUG_BORDER - Static variable in class jigcell.compare.cellcycle.CellCycleFrontEnd
Border to wrap around debugged objects
UIDEBUG_COLOR - Static variable in class jigcell.compare.cellcycle.CellCycleFrontEnd
Color to highlight debug objects
UIDEBUG_PROPERTY - Static variable in class jigcell.compare.cellcycle.CellCycleFrontEnd
Property indicating a debugged component
unindex(IDataGenerator) - Method in class jigcell.compare.data.DataGeneratorList
Removes a generator from the index.
uninstall() - Method in class jigcell.compare.ui.FindAccessory
Notifies the accessory that it has been removed from the the Comparator interface.
uninstall() - Method in interface jigcell.compare.ui.ITabAccessory
Notifies the accessory that it has been removed from the the Comparator interface.
uninstall() - Method in class jigcell.compare.ui.MemoryMonitorAccessory
Notifies the accessory that it has been removed from the the Comparator interface.
unpersistSource(String) - Static method in class jigcell.compare.impl.DataSource
Unpersists a data source.
unregisterTransform(ITransform) - Method in interface jigcell.compare.transform.ITransformContext
Unregisters a transform so that it can no longer be identified by this context.
unregisterTransform(ITransform) - Method in class jigcell.compare.transform.TransformContext
Unregisters a transform so that it can no longer be identified by this context.
UNSAFE - Static variable in class jigcell.compare.IDataSource.Option
Indicates that an option should neither be copied nor persisted with the data source
unsetValue(long) - Method in class jigcell.compare.data.EditableDataElement
Deletes an element value.
unsetValue(long) - Method in class jigcell.compare.data.TreeDataElement
Deletes an element value.
unsetValue(long) - Method in interface jigcell.compare.IEditableDataElement
Deletes an element value.
untie() - Method in class jigcell.compare.data.FlippedDataElement
Converts a FlippedDataElement to an untied FlippedDataElement or throws an exception if not possible.
UntypedTypeChecker - Class in jigcell.compare.data.type
Type for unstructured data.
UntypedTypeChecker() - Constructor for class jigcell.compare.data.type.UntypedTypeChecker
Creates a new type checker.
update() - Method in class jigcell.compare.transformui.SelectColumnsInterface.SelectedModel
Updates the listeners of this model.
update(ActionEvent) - Method in class jigcell.compare.ui.MemoryMonitorAccessory
Updates the memory monitor display.
UPDATE_LOCK - Variable in class jigcell.compare.ui.CompareFrontEnd.SplashScreen
Lock for controlling update manipulation
updateColumnSelector() - Method in class jigcell.compare.cellcycle.CellCycleReportGenerator
Places the columns of the latest experiment selection into the column selector.
updateColumnWeights() - Method in class jigcell.compare.compare2.Compare2Model
Adjusts the column weights for the current number of columns.
updateCount - Variable in class jigcell.compare.compare2.ResultViewZoom
Whether the view zoom is currently being updated
updateDisplay() - Method in class jigcell.compare.compare2.ResultViewZoom
Updates the zoom view to display any changes made to the model or coloring.
updateDisplay(boolean) - Method in class jigcell.compare.compare2.ThresholdEditor
Updates the display with the latest threshold value.
updateDisplay(ITransform, IDataElement) - Method in class jigcell.compare.views.TransformDebugger.DebuggerThread
Updates the display after a debug event.
updateDisplay() - Method in class jigcell.compare.views.TransformDebugger
Updates the display based on the current debugging state.
updateDisplayRunnable - Variable in class jigcell.compare.views.TransformDebugger
Updates the display based on debug information
updateEncoder(Encoder) - Static method in class jigcell.compare.impl.Compare
 
updateEncoder(Encoder) - Method in class jigcell.compare.impl.XMLFormatter
Passes on all collected persistence information to an encoder.
updateInterface(String) - Method in class jigcell.compare.cellcycle.JigCellRunManagerInterface
Updates customizers based on the generator state.
updateInterface(String) - Method in class jigcell.compare.data.ProgrammableDataGenerator.DummyCustomizableInterface
Updates customizers based on the generator state.
updateInterface(String) - Method in class jigcell.compare.data.ProgrammableDataGenerator
Notifies the interface that a property has change.
updateInterface(String) - Method in interface jigcell.compare.ICustomizableInterface
Updates customizers based on the generator state.
updateInterface(String) - Method in class jigcell.compare.objectiveui.BooleanRelationalInterface
Updates customizers based on the generator state.
updateInterface(String) - Method in class jigcell.compare.objectiveui.ScriptEvaluationInterface
Updates customizers based on the generator state.
updateInterface(String) - Method in class jigcell.compare.objectiveui.WOSSInterface
Updates customizers based on the generator state.
updateInterface(String) - Method in class jigcell.compare.transformui.ExtremaTestInterface
Updates customizers based on the generator state.
updateInterface(String) - Method in class jigcell.compare.transformui.FileInterface
Updates customizers based on the generator state.
updateInterface(String) - Method in class jigcell.compare.transformui.InputInterface
Updates customizers based on the generator state.
updateInterface(String) - Method in class jigcell.compare.transformui.ScriptEvaluationInterface
Updates customizers based on the generator state.
updateInterface(String) - Method in class jigcell.compare.transformui.SelectColumnsInterface
Updates customizers based on the generator state.
updateInterface(String) - Method in class jigcell.compare.transformui.TransformEvaluationInterface
Updates customizers based on the generator state.
updateInterface(String) - Method in class jigcell.compare.transformui.TransformInterface
Updates customizers based on the generator state.
updateInterface(String) - Method in class jigcell.compare.ui.CustomizableInterface
Updates customizers based on the generator state.
updateInterfaceControls(int, int, int, int, int, int, int) - Method in class jigcell.compare.views.TransformDebugger
Updates interface controls.
updateList() - Method in class jigcell.compare.views.ObjectiveEditor
Updates the internal list of objects to match the master list.
updateList() - Method in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Updates the internal list of objects to match the master list.
updateList() - Method in class jigcell.compare.views.TransformEditor
Updates the internal list of objects to match the master list.
updateLookAndFeel(String) - Method in class jigcell.compare.ui.CompareFrontEnd
Modifies the application look and feel to match the current configuration.
updateMetricSelection() - Method in class jigcell.compare.views.ObjectiveEditor
Updates the internal metric selection to match the selection in the view.
updateNames() - Method in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Updates the names of all known objects.
updateObjectiveSelection() - Method in class jigcell.compare.views.ObjectiveEditor
Updates the internal objective selection to match the selection in the view.
updateResourceMap(String, Object, Object) - Method in class jigcell.compare.impl.Compare
Changes a mapping in a named resource known to be a map.
updateStatus(String) - Method in class jigcell.compare.ui.CompareFrontEnd.SplashScreen
Changes the status message displayed on the splash screen.
updateStatus(String, boolean) - Method in class jigcell.compare.ui.CompareFrontEnd.SplashScreen
Changes the status message displayed on the splash screen.
updateTransformInformation() - Method in class jigcell.compare.views.TransformDebugger
Updates the transform information display.
updateTransformSelection() - Method in class jigcell.compare.views.TransformEditor
Updates the internal transform selection to match the selection in the view.
updateViewAccessory(CompareFrontEnd.FrontEndTabInfo) - Method in class jigcell.compare.ui.CompareFrontEnd
Fills in the tab accessory using the provided tab info.
updateViewMenus(CompareFrontEnd.FrontEndTabInfo) - Method in class jigcell.compare.ui.CompareFrontEnd
Fills in the menu bar using the provided tab info.
updateViewTools(CompareFrontEnd.FrontEndTabInfo) - Method in class jigcell.compare.ui.CompareFrontEnd
Fills in the toolbar using the provided tab info.
updating - Variable in class jigcell.compare.objectiveui.ScriptEvaluationInterface
Whether the interface is currently being updated
updating - Variable in class jigcell.compare.transformui.ScriptEvaluationInterface
Whether the interface is currently being updated
usedMemory - Variable in class jigcell.compare.ui.MemoryMonitorAccessory
Memory monitor

V

validate(IDataElement) - Method in class jigcell.compare.cellcycle.BuddingYeastNocPhenotype
Whether a data element is an instance of this type.
validate(IDataElement) - Method in class jigcell.compare.cellcycle.BuddingYeastPhenotype
Whether a data element is an instance of this type.
validate(IDataElement) - Method in class jigcell.compare.cellcycle.BuddingYeastWildtypeProperties
Whether a data element is an instance of this type.
validate(IDataElement) - Method in class jigcell.compare.cellcycle.GenericPhenotype
Whether a data element is an instance of this type.
validate(IDataElement) - Method in class jigcell.compare.contrib.StructuredTypeCheckerTemplate
Whether a data element is an instance of this type.
validate(IDataElement) - Method in class jigcell.compare.data.type.TimeSeriesTypeChecker
Whether a data element is an instance of this type.
validate(ITypeChecker, IDataGenerator) - Static method in class jigcell.compare.data.type.TypeChecker
Tests a type checker against the element of a generator.
validate(IDataElement) - Method in class jigcell.compare.data.type.TypeChecker
Whether a data element is an instance of this type.
validate(IDataElement) - Method in interface jigcell.compare.ITypeChecker
Whether a data element is an instance of this type.
value - Variable in class jigcell.compare.transform.ConstantTransform
Value to generate
value - Variable in class jigcell.compare.ui.BasicTable.ButtonEditor
Editor value
VALUE_NOTAVAILABLE - Static variable in class jigcell.compare.views.SeriesView
Display value for data that is not available
VALUE_NOTEVALUATED - Static variable in class jigcell.compare.cellcycle.CellCycleTransformView
Display value for an unevaluated value
VALUE_NOTEVALUATED - Static variable in class jigcell.compare.views.ObjectiveSeriesView
Display value for an unevaluated value
VALUE_NOVALUE - Static variable in class jigcell.compare.cellcycle.CellCycleTransformView
Display value for a non-existent value
VALUE_NOVALUE - Static variable in class jigcell.compare.compare2.Compare2Model
Display value for a non-existent value
VALUE_NOVALUE - Static variable in class jigcell.compare.views.ObjectiveSeriesView
Display value for a non-existent value
valueChanged(ListSelectionEvent) - Method in class jigcell.compare.views.BasicTableView
 
valueChanged(TreeSelectionEvent) - Method in class jigcell.compare.views.TransformDebugger
 
valueMap - Variable in class jigcell.compare.transform.annotation.TransformAnnotation
Storage for annotation values
valueModel - Variable in class jigcell.compare.views.TransformDebugger
Tabular display of transform values
values - Variable in class jigcell.compare.data.PackedDoubleDataElement
Element values
values - Variable in class jigcell.compare.data.PackedTreeDataElement2
Element values
values - Variable in class jigcell.compare.data.SparseTreeDataElement2
Element values
values - Variable in class jigcell.compare.data.TreeDataElement
Element values
values - Variable in class jigcell.compare.impl.Config
Map of key-value pairs
VARIABLE_COMPARE - Static variable in class jigcell.compare.cellcycle.CellCycleFrontEnd
Variable to attach to Comparator when running scripts
VARIABLE_COMPARE - Static variable in class jigcell.compare.cellcycle.OAAConnector
Variable to attach to compare
VARIABLE_COMPARE - Static variable in class jigcell.compare.objective.ScriptEvaluationObjective
Variable to attach to compare
VARIABLE_COMPARE - Static variable in class jigcell.compare.transform.ScriptEvaluationTransform
Variable to attach to compare
VARIABLE_COMPARE - Static variable in class jigcell.compare.views.Console
Variable to attach to Comparator
VARIABLE_EVENT - Static variable in class jigcell.compare.ui.MenuBuilder.ScriptActionTrampoline
Variable at which the event can be reached
VARIABLE_INPUT - Static variable in class jigcell.compare.objective.ScriptEvaluationObjective
Variable to attach to objective input
VARIABLE_INPUT - Static variable in class jigcell.compare.transform.ScriptEvaluationTransform
Variable to attach to transform input
VARIABLE_INSTANCE - Static variable in class jigcell.compare.cellcycle.OAAConnector
Variable to attach to a dispatch instance
VARIABLE_METHOD - Static variable in class jigcell.compare.cellcycle.OAAConnector
Variable to attach to a dispatch method
VARIABLE_OBJECTIVE - Static variable in class jigcell.compare.objective.ScriptEvaluationObjective
Variable to attach to objective
VARIABLE_TARGET - Static variable in class jigcell.compare.ui.MenuBuilder.ScriptActionTrampoline
Variable at which the target can be reached
VARIABLE_TRANSFORM - Static variable in class jigcell.compare.transform.ScriptEvaluationTransform
Variable to attach to transform
view - Variable in class jigcell.compare.compare2.ResultViewZoom
View containing the data
view - Variable in class jigcell.compare.tests.ElementBenchmark
View to load in
view - Variable in class jigcell.compare.tests.ModelBuilderBenchmark
View to load in
view - Variable in class jigcell.compare.tests.RunManagerBenchmark
View to load in
viewables - Variable in class jigcell.compare.views.EvaluationErrorViewer
Objects that this viewer is monitoring
viewCell(int, int) - Method in class jigcell.compare.compare2.Compare2
Starts viewing a cell.
viewCell(int, int) - Method in interface jigcell.compare.ui.ICellEditorTab
Starts viewing a cell.
viewCell(int, int) - Method in class jigcell.compare.ui.SeriesDialog
Starts viewing a cell.
viewCell(int, int) - Method in class jigcell.compare.views.EditableSeriesView
Starts viewing a cell.
viewCellAt(int, int) - Method in class jigcell.compare.cellcycle.CellCycleDataDialog.DataModel
Starts viewing a cell in the table but does not allow editing.
viewCellAt(int, int) - Method in class jigcell.compare.cellcycle.CellCycleObjectiveView.ObjectiveModel
Starts viewing a cell in the table but does not allow editing.
viewCellAt(int, int) - Method in class jigcell.compare.cellcycle.CellCycleTransformView.TransformModel
Starts viewing a cell in the table but does not allow editing.
viewCellAt(int, int) - Method in class jigcell.compare.compare2.Compare2Model
Starts viewing a cell in the table but does not allow editing.
viewCellAt(int, int) - Method in class jigcell.compare.ui.SeriesDialog.SeriesModel
Starts viewing a cell in the table but does not allow editing.
viewCellAt(int, int) - Method in class jigcell.compare.ui.SeriesEditorDialog.SeriesEditorModel
Starts viewing a cell in the table but does not allow editing.
viewCellAt(int, int) - Method in class jigcell.compare.views.SeriesView.SeriesModel
Starts viewing a cell in the table but does not allow editing.
ViewColorer - Class in jigcell.compare.compare2
A table renderer that can color the view of a Compare^2.
ViewColorer(Compare2) - Constructor for class jigcell.compare.compare2.ViewColorer
Creates a new view colorer.
viewColorerGroup - Variable in class jigcell.compare.compare2.Compare2
Group of available view colorers
ViewerDialog - Class in jigcell.compare.ui
A simple dialog-based cell viewer.
ViewerDialog(Compare, String, int, int, BasicTable.BasicTableModel) - Constructor for class jigcell.compare.ui.ViewerDialog
Creates a new dialog for viewing.
ViewerDialog(Compare, String, int, int, BasicTable.BasicTableModel, int, int) - Constructor for class jigcell.compare.ui.ViewerDialog
Creates a new dialog for viewing.

W

waitForLoad(Compare, String, IDataEditorTab, IReadableDataSource) - Method in class jigcell.compare.tests.SystemTests
Waits for a data source to load in a tab.
waitForProperty() - Method in class jigcell.compare.tests.SystemTests
Waits until the current property detects a hit.
warning(String) - Static method in class jigcell.compare.impl.Compare
Logs an exceptional condition.
warning(String, Throwable) - Static method in class jigcell.compare.impl.Compare
Logs an exceptional condition.
WeightEditorDialog - Class in jigcell.compare.objectiveui
Supports editing and viewing weights.
WeightEditorDialog(Compare, IDataElement, String) - Constructor for class jigcell.compare.objectiveui.WeightEditorDialog
Creates a new dialog for editing weights.
WeightEditorDialog.WeightModel - Class in jigcell.compare.objectiveui
Table model for a WeightEditorDialog.
WeightEditorDialog.WeightModel() - Constructor for class jigcell.compare.objectiveui.WeightEditorDialog.WeightModel
Creates a new table model.
width - Variable in class jigcell.compare.ui.HTMLComponentDescription
Width of the HTML viewer
WildtypeScanInterface - Class in jigcell.compare.cellcycle
Interface for a WildtypeScanTransform.
WildtypeScanInterface(IProgrammableDataGenerator) - Constructor for class jigcell.compare.cellcycle.WildtypeScanInterface
Creates a new interface for a WildtypeScanTransform.
WildtypeScanTransform - Class in jigcell.compare.cellcycle
Quickly scans a time course to determine the mass at division and cycle time.
WildtypeScanTransform() - Constructor for class jigcell.compare.cellcycle.WildtypeScanTransform
Creates a new transform that can perform a run evaluation.
windowActivated(WindowEvent) - Method in class jigcell.compare.ui.CompareFrontEnd
 
windowActivated(WindowEvent) - Method in class jigcell.compare.ui.ProgressMonitor
 
windowClosed(WindowEvent) - Method in class jigcell.compare.ui.CompareFrontEnd
 
windowClosed(WindowEvent) - Method in class jigcell.compare.ui.ProgressMonitor
 
windowClosing(WindowEvent) - Method in class jigcell.compare.ui.CompareFrontEnd
 
windowClosing(WindowEvent) - Method in class jigcell.compare.ui.ProgressMonitor
 
windowDeactivated(WindowEvent) - Method in class jigcell.compare.ui.CompareFrontEnd
 
windowDeactivated(WindowEvent) - Method in class jigcell.compare.ui.ProgressMonitor
 
windowDeiconified(WindowEvent) - Method in class jigcell.compare.ui.CompareFrontEnd
 
windowDeiconified(WindowEvent) - Method in class jigcell.compare.ui.ProgressMonitor
 
windowIconified(WindowEvent) - Method in class jigcell.compare.ui.CompareFrontEnd
 
windowIconified(WindowEvent) - Method in class jigcell.compare.ui.ProgressMonitor
 
windowOpened(WindowEvent) - Method in class jigcell.compare.ui.CompareFrontEnd
 
windowOpened(WindowEvent) - Method in class jigcell.compare.ui.ProgressMonitor
 
windowStateChanged(WindowEvent) - Method in class jigcell.compare.ui.CompareFrontEnd
 
WOSSInterface - Class in jigcell.compare.objectiveui
Interface for a WOSSObjective.
WOSSInterface(IProgrammableDataGenerator) - Constructor for class jigcell.compare.objectiveui.WOSSInterface
Creates a new interface for a WOSSObjective.
WOSSObjective - Class in jigcell.compare.objective
A generator whose function is a weighted orthogonal sum of squares.
WOSSObjective() - Constructor for class jigcell.compare.objective.WOSSObjective
Creates a new data generator based upon a least squares computation.
wrapHTMLEditor(JEditorPane) - Static method in class jigcell.compare.ui.InterfaceBuilder
Fixes up an editor pane to be an HTML viewer and wraps it in a panel.
write(Object) - Method in class jigcell.compare.cellcycle.CellCycleReportGenerator
Writes data to the source destroying the previous contents if multiple objects are not supported.
write(IWriteableDataSource) - Method in class jigcell.compare.cellcycle.CellCycleTransformView
Writes data to some external source.
write(IWriteableDataSource) - Method in class jigcell.compare.compare2.Compare2
Writes data to some external source.
write(Object) - Method in class jigcell.compare.data.EditableDataGenerator
Writes data to the source destroying the previous contents if multiple objects are not supported.
write(Object) - Method in class jigcell.compare.impl.ClipboardDataSource
Writes data to the source destroying the previous contents if multiple objects are not supported.
write(Object) - Method in interface jigcell.compare.impl.FileDataSource.IFileEncoder
 
write(Object) - Method in class jigcell.compare.impl.FileDataSource
Writes data to the source destroying the previous contents if multiple objects are not supported. If the file output option has not been initialized, this method may have to do some file work while holding the options lock to avoid race conditions.
write(Object) - Method in class jigcell.compare.impl.PDFPrinterDataSource
Writes data to the source destroying the previous contents if multiple objects are not supported.
write(Object) - Method in class jigcell.compare.impl.SystemPrinterDataSource
Writes data to the source destroying the previous contents if multiple objects are not supported.
write(Object) - Method in class jigcell.compare.impl.XMLFileEncoder
write(Object) - Method in interface jigcell.compare.IWriteableDataSource
Writes data to the source destroying the previous contents if multiple objects are not supported.
write(Object) - Method in class jigcell.compare.plotter.Plotter
Writes data to the source destroying the previous contents if multiple objects are not supported.
write(IWriteableDataSource) - Method in class jigcell.compare.ui.DataEditorPanelTab
Writes data to some external source.
write(IWriteableDataSource) - Method in class jigcell.compare.views.EditableSeriesView
Writes data to some external source.
write(IWriteableDataSource) - Method in class jigcell.compare.views.ObjectiveSeriesView
Writes data to some external source.
write(IWriteableDataSource) - Method in class jigcell.compare.views.ProgrammableDataGeneratorEditor
Writes data to some external source.
writeables - Variable in class jigcell.compare.impl.DataManager
Writeable data sources
writeCombineAcrossData(PrintWriter) - Method in class jigcell.compare.plotter.JPlotBridge
Produces a plot using the combine across option.
writeCombineNoneData(PrintWriter) - Method in class jigcell.compare.plotter.JPlotBridge
Produces a plot using the combine none option.
writeData(PrintWriter) - Method in class jigcell.compare.plotter.JPlotBridge
Writes data information for the graph to the writer.
writeHeader(PrintWriter) - Method in class jigcell.compare.plotter.JPlotBridge
Writes header information for the graph to the writer.
writeObject(ObjectOutputStream) - Method in class jigcell.compare.data.CachedDataElement
 
writeResults(IWriteableDataSource) - Method in class jigcell.compare.cellcycle.CellCycleTransformView
Writes results data to some external source.
writeResults(IWriteableDataSource) - Method in class jigcell.compare.views.ObjectiveSeriesView
Writes results data to some external source.
writeScript(PrintWriter, String) - Method in class jigcell.compare.plotter.JPlotBridge
Writes script information for the graph to the writer.
writeThreshold(IWriteableDataSource) - Method in class jigcell.compare.compare2.Compare2
Writes data from some external source.
WriteToFileTransform - Class in jigcell.compare.transform
A transform that writes data to a file.
WriteToFileTransform() - Constructor for class jigcell.compare.transform.WriteToFileTransform
Creates a new transform to write to a file.

X

XMLFileDataSource - Class in jigcell.compare.impl
A transfer agent that supports reading and writing data to a file using XML persistence.
XMLFileDataSource() - Constructor for class jigcell.compare.impl.XMLFileDataSource
Creates a new data source that represents a file.
XMLFileDataSource(String) - Constructor for class jigcell.compare.impl.XMLFileDataSource
Creates a new data source that represents a file.
XMLFileEncoder - Class in jigcell.compare.impl
An encoder for FileDataSource that supports reading and writing data to a file using XML persistence.
XMLFileEncoder(FileDataSource) - Constructor for class jigcell.compare.impl.XMLFileEncoder
Creates a new encoder for XML data.
XMLFormatter - Class in jigcell.compare.impl
Controls XML serialization behavior by modifying how classes get persisted.
XMLFormatter() - Constructor for class jigcell.compare.impl.XMLFormatter
 
xRangeDocument - Variable in class jigcell.compare.cellcycle.CellCycleReportGenerator
Range of x-axis to use for plots

Y

yRangeDocument - Variable in class jigcell.compare.cellcycle.CellCycleReportGenerator
Range of y-axis to use for plots

Z

zoomColors() - Method in class jigcell.compare.compare2.Compare2
Displays a zoomed view of the current data set with color.
zoomDialog - Variable in class jigcell.compare.compare2.Compare2
Dialog view for zoom popup
zoomDialogUpdateRunnable - Variable in class jigcell.compare.compare2.ResultViewZoom
Runnable for updating the zoom display after all events have been processed.
zoomImage - Variable in class jigcell.compare.compare2.ResultViewZoom
Image for display in a zoom window

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