Uses of Interface
jigcell.compare.IDataGenerator

Packages that use IDataGenerator

jigcell.compare
jigcell.compare.cellcycle
jigcell.compare.contrib
jigcell.compare.data
jigcell.compare.data.type
jigcell.compare.impl
jigcell.compare.objective
jigcell.compare.tests
jigcell.compare.transform
jigcell.compare.ui
jigcell.compare.views

Uses of IDataGenerator in jigcell.compare

Subinterfaces of IDataGenerator in jigcell.compare

interface	IEditableDataGenerator This interface is implemented by classes that wish to store data for the comparator.
interface	IProgrammableDataGenerator A data generator that can derive its value from some programmatic evaluation.

Methods in jigcell.compare that return IDataGenerator

IDataGenerator	IDataGenerator.copy(boolean shallow) An equivalent copy of this generator.
IDataGenerator	IDataGenerator.getCopiedFrom() The generator this was copied from or null if this is not a copy.
IDataGenerator	IEvaluationCallStack.getOrigin() The generator that will hold the final result or null if this is not available.

Methods in jigcell.compare with parameters of type IDataGenerator

boolean

IDataGenerator.isCopyRelated(IDataGenerator generator) Whether this generator was copied from or to another.

Uses of IDataGenerator in jigcell.compare.cellcycle

Classes in jigcell.compare.cellcycle that implement IDataGenerator

class	BuddingYeastPhenotypeObjective Measures the difference between two budding yeast phenotypes.
class	BuddingYeastScanTransform Computes the phenotype of a budding yeast mutant from a time course of concentrations.
class	GenericPhenotypeObjective Measures the difference between two generic phenotypes.
class	GenericScanTransform Computes the phenotype of a generic mutant from a time course of concentrations.
class	JigCellRunManagerTransform Uses the JigCell Run Manager to execute a simulation.
class	WildtypeScanTransform Quickly scans a time course to determine the mass at division and cycle time.

Methods in jigcell.compare.cellcycle that return IDataGenerator

private IDataGenerator	CellCycleDataDialog.DataModel.packageData(int row) Creates a data generator from an experiment and a transform.
IDataGenerator	CellCycleTransformView.processGenerator(IDataGenerator generator) Creates a replacement data generator for evaluation.
IDataGenerator	CellCycleObjectiveView.processGenerator(IDataGenerator generator) 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.

Methods in jigcell.compare.cellcycle with parameters of type IDataGenerator

protected void	CellCycleTransformView.evaluate(IDataGenerator[] generators) Evaluates a collection of data generators on a separate thread.
private ITransform	CellCycleReportGenerator.findLastTransform(IDataGenerator experiment, boolean useFirst) Picks a transform to use as input to the report plotter.
IDataGenerator	CellCycleTransformView.processGenerator(IDataGenerator generator) Creates a replacement data generator for evaluation.
IDataGenerator	CellCycleObjectiveView.processGenerator(IDataGenerator generator) 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.

Constructors in jigcell.compare.cellcycle with parameters of type IDataGenerator

CellCycleDataDialog(Compare compare, IDataGenerator generator, int row, int column, BasicTable.BasicTableModel model)
Creates a new dialog for side-by-side viewing of experimental and transform results.

Uses of IDataGenerator in jigcell.compare.contrib

Classes in jigcell.compare.contrib that implement IDataGenerator

class	DispatchedTransformHelper Methods for reducing the amount of work to make a transform.
class	DispatchedTransformTemplate A DESCRIPTION OF YOUR CLASS.
class	ObjectiveHelper Methods for reducing the amount of work to make an objective function.
class	ObjectiveTemplate A DESCRIPTION OF YOUR CLASS.
class	TransformHelper Methods for reducing the amount of work to make a transform.
class	TransformTemplate A DESCRIPTION OF YOUR CLASS.

Methods in jigcell.compare.contrib with parameters of type IDataGenerator

protected void	ObjectiveTemplate.copy(boolean shallow, IDataGenerator target) Copies state for this generator.
protected void	DispatchedTransformHelper.copy(boolean shallow, IDataGenerator target) Copies state for this generator.

Uses of IDataGenerator in jigcell.compare.data

Classes in jigcell.compare.data that implement IDataGenerator

class	DataGenerator A default implementation of DataGenerator.
class	EditableDataGenerator Implementation of DataGenerator that supports editing the generator fields.
class	ProgrammableDataGenerator A data generator type whose value is determined programmatically, usually with some kind of interface for controlling the program action.

Methods in jigcell.compare.data that return IDataGenerator

IDataGenerator	DataGenerator.copy(boolean shallow) An equivalent copy of this generator.
IDataGenerator	DataGeneratorMap.get(IDataGeneratorCollection.Key key) The generator associated with a particular key or null if there is no such mapping.
IDataGenerator	IDataGeneratorList.get(IDataGeneratorCollection.Key key) A generator in the list.
IDataGenerator	DataGeneratorList.get(IDataGeneratorCollection.Key key) A generator in the list.
IDataGenerator	IDataGeneratorMap.get(IDataGeneratorCollection.Key key) The generator associated with a particular key or null if there is no such mapping.
IDataGenerator	IDataGeneratorList.get(int index) A generator in the list.
IDataGenerator	DataGeneratorList.get(int index) A generator in the list.
IDataGenerator	IDataGeneratorList.get(java.lang.String name) A generator in the list by name.
IDataGenerator	DataGeneratorList.get(java.lang.String name) A generator in the list by name.
IDataGenerator	DataGenerator.getCopiedFrom() The generator this was copied from or null if this is not a copy.
IDataGenerator	DataGeneratorMap.put(IDataGeneratorCollection.Key key, IDataGenerator generator) Adds a mapping between a key and generator.
IDataGenerator	IDataGeneratorMap.put(IDataGeneratorCollection.Key key, IDataGenerator generator) Adds a mapping between a key and generator.
IDataGenerator	DataGeneratorMap.put(java.lang.String name, java.lang.String id, IDataGenerator generator) Adds a mapping between a name, id, and generator.
IDataGenerator	IDataGeneratorMap.put(java.lang.String name, java.lang.String id, IDataGenerator generator) Adds a mapping between a name, id, and generator.
IDataGenerator	IDataGeneratorList.remove(int index) Removes a generator from this list.
IDataGenerator	DataGeneratorList.remove(int index) Removes a generator from this list.
IDataGenerator	IDataGeneratorList.set(int index, IDataGenerator generator) Sets a generator in this list to a new value.
IDataGenerator	DataGeneratorList.set(int index, IDataGenerator generator) Sets a generator in this list to a new value.
IDataGenerator[]	IDataGeneratorList.toArray() This list of generators as an array.
IDataGenerator[]	DataGeneratorList.toArray() This list of generators as an array.

Methods in jigcell.compare.data with parameters of type IDataGenerator

void	IDataGeneratorList.add(IDataGenerator generator) Adds a generator.
void	DataGeneratorList.add(IDataGenerator generator) Adds a generator.
void	IDataGeneratorList.add(int index, IDataGenerator generator) Adds a generator at the specified index.
void	DataGeneratorList.add(int index, IDataGenerator generator) Adds a generator at the specified index.
protected void	DataGenerator.copy(boolean shallow, IDataGenerator target) Copies state for this generator.
protected void	ProgrammableDataGenerator.copy(boolean shallow, IDataGenerator target) Copies state for this generator.
private void	DataGeneratorList.index(IDataGenerator generator) Adds a generator to the index.
int	IDataGeneratorList.indexOf(IDataGenerator generator) The position of a generator in the list.
int	DataGeneratorList.indexOf(IDataGenerator generator) The position of a generator in the list.
boolean	DataGenerator.isCopyRelated(IDataGenerator generator) Whether this generator was copied from or to another.
IDataGenerator	DataGeneratorMap.put(IDataGeneratorCollection.Key key, IDataGenerator generator) Adds a mapping between a key and generator.
IDataGenerator	IDataGeneratorMap.put(IDataGeneratorCollection.Key key, IDataGenerator generator) Adds a mapping between a key and generator.
IDataGenerator	DataGeneratorMap.put(java.lang.String name, java.lang.String id, IDataGenerator generator) Adds a mapping between a name, id, and generator.
IDataGenerator	IDataGeneratorMap.put(java.lang.String name, java.lang.String id, IDataGenerator generator) Adds a mapping between a name, id, and generator.
IDataGenerator	IDataGeneratorList.set(int index, IDataGenerator generator) Sets a generator in this list to a new value.
IDataGenerator	DataGeneratorList.set(int index, IDataGenerator generator) Sets a generator in this list to a new value.
private void	DataGeneratorList.unindex(IDataGenerator generator) Removes a generator from the index.

Uses of IDataGenerator in jigcell.compare.data.type

Methods in jigcell.compare.data.type with parameters of type IDataGenerator

static ITypeChecker	TypeChecker.getTypeCheckerForGenerator(IDataGenerator generator) The type checker of a generator.
static boolean	TypeChecker.validate(ITypeChecker checker, IDataGenerator generator) Tests a type checker against the element of a generator.

Uses of IDataGenerator in jigcell.compare.impl

Fields in jigcell.compare.impl declared as IDataGenerator

protected IDataGenerator	DataGeneratorEvaluator.currentGenerator The data generator currently being evaluated
protected IDataGenerator[]	DataGeneratorEvaluator.generators The list of generators
private IDataGenerator	EvaluationCallStack.origin Generator that will hold the final result

Methods in jigcell.compare.impl that return IDataGenerator

IDataGenerator	EvaluationCallStack.getOrigin() The generator that will hold the final result or null if this is not available.
IDataGenerator	DataGeneratorEvaluator.IProcessor.processGenerator(IDataGenerator generator) Creates a replacement data generator for evaluation.

Methods in jigcell.compare.impl with parameters of type IDataGenerator

IDataGenerator

DataGeneratorEvaluator.IProcessor.processGenerator(IDataGenerator generator) Creates a replacement data generator for evaluation.

Constructors in jigcell.compare.impl with parameters of type IDataGenerator

DataGeneratorEvaluator(IDataGenerator[] generators)
Creates a new evaluator for data generators.

DataGeneratorEvaluator(IDataGenerator[] generators, DataGeneratorEvaluator.IProcessor processor)
Creates a new evaluator for data generators.

EvaluationCallStack(IDataGenerator origin)
Creates a new call stack.

Uses of IDataGenerator in jigcell.compare.objective

Subinterfaces of IDataGenerator in jigcell.compare.objective

interface	IDimensionWeightObjective A data generator supporting the concept of editable dimension weights.
interface	IElementWeightObjective A data generator supporting the concept of editable element weights.
interface	IInterpolationObjective A data generator supporting the concept of data interpolation.
interface	IObjective A DataGenerator that takes a functional expression and a collection of data to produce an element.
interface	IRelationalObjective A data generator supporting the concept of relational comparisons.

Classes in jigcell.compare.objective that implement IDataGenerator

class	BooleanRelationalObjective A generator whose function is the result of a boolean relation.
class	MetricObjective A FunctionalDataGenerator whose function is based upon a metric.
class	MinkowskiObjective A generator whose function is a Lebesgue p-norm.
class	Objective Implementation of DataGenerator whose associated element is a function result.
class	ScriptEvaluationObjective Executes a user provided script when evaluated.
class	WOSSObjective A generator whose function is a weighted orthogonal sum of squares.

Methods in jigcell.compare.objective that return IDataGenerator

IDataGenerator	ChainedDataGeneratorList.get(IDataGeneratorCollection.Key key) A generator in the list. The id is the primary search key. This operation will be significantly accelerated if an index exists.
IDataGenerator	ChainedDataGeneratorList.get(java.lang.String name) A generator in the list by name. This operation will be significantly accelerated if an index exists.

Methods in jigcell.compare.objective with parameters of type IDataGenerator

protected void	MinkowskiObjective.copy(boolean shallow, IDataGenerator target) Copies state for this generator.
protected void	MetricObjective.copy(boolean shallow, IDataGenerator target) Copies state for this generator.
static IObjective	Objective.getObjectiveForGenerator(IDataGenerator generator) The objective of a generator.

Uses of IDataGenerator in jigcell.compare.tests

Classes in jigcell.compare.tests that implement IDataGenerator

static class

MethodDispatcherTests.DispatchedTransform Test transform for dispatching.

Fields in jigcell.compare.tests declared as IDataGenerator

protected IDataGenerator	ObjectiveBenchmark.result Record of loading results
protected IDataGenerator	ExperimentBenchmark.result Record of loading results
protected IDataGenerator	TransformBenchmark.result Record of loading results
protected IDataGenerator	ModelBuilderBenchmark.result Record of benchmark results
protected IDataGenerator	RunManagerBenchmark.result Record of loading results

Methods in jigcell.compare.tests that return IDataGenerator

protected IDataGenerator	Benchmark.createBenchmarkReport(java.lang.String name, java.lang.String description, java.lang.String type, java.util.List results) Creates a data generator that represents a benchmark result.
static IDataGenerator	ExperimentBenchmark.generateGenerator(IEditableDataGenerator generator, int seed) Generates a new experimental setup.
IDataGenerator	ObjectiveBenchmark.runBenchmark() Runs a collection of benchmarks for loading objective files.
IDataGenerator	ExperimentBenchmark.runBenchmark() Runs a collection of benchmarks for loading experiment files.
IDataGenerator	TransformBenchmark.runBenchmark() Runs a collection of benchmarks for loading transform files.
IDataGenerator	ModelBuilderBenchmark.runBenchmark() Runs a collection of benchmarks for loading models.
IDataGenerator	RunManagerBenchmark.runBenchmark() Runs a collection of benchmarks for loading run files.
IDataGenerator	ModelBuilderBenchmark.runBenchmark2() Runs a collection of benchmarks for loading models.
IDataGenerator	RunManagerBenchmark.runBenchmark2() Runs a collection of benchmarks for loading run files.
IDataGenerator	ModelBuilderBenchmark.runBenchmark3() Runs a collection of benchmarks for loading models.
IDataGenerator	RunManagerBenchmark.runBenchmark3() Runs a collection of benchmarks for loading run files.
IDataGenerator	ObjectiveBenchmark.runBenchmarkAddRow() Runs a collection of benchmarks for configuring a new experiment.
IDataGenerator	ExperimentBenchmark.runBenchmarkAddRow() Runs a collection of benchmarks for adding to experiment files.
IDataGenerator	ModelBuilderBenchmark.runBenchmarkAddRow() Runs a collection of benchmarks for adding to model files.
IDataGenerator	RunManagerBenchmark.runBenchmarkAddRow() Runs a collection of benchmarks for adding to run files.
IDataGenerator	RunManagerBenchmark.runBenchmarkExecute() Runs a collection of benchmarks for executing runs.
IDataGenerator	RunManagerBenchmark.runBenchmarkModify() Runs a collection of benchmarks for modifying runs.

Uses of IDataGenerator in jigcell.compare.transform

Subinterfaces of IDataGenerator in jigcell.compare.transform

interface	IResultantTransform Indicates that this transform represents a result of potential interest.
interface	ITransform A DataGenerator that performs a part of a transform evaluation.
interface	ITransformContainer A transform that can manage a collection of other transforms.

Classes in jigcell.compare.transform that implement IDataGenerator

class	BoxTransformContainer A compositon of statements that acts as single transform.
class	ConstantTransform Transform for testing and use as a stub.
class	ExtremaTestTransform A transform that tests whether a sequence would be passed by a band-pass filter.
class	FileTransform A transform that tracks a file.
class	InputTransform Allows selection of a transform to create a transform chain.
class	ReadFromFileTransform A transform that reads data from a file.
class	ScriptEvaluationTransform Executes a user provided script when evaluated.
class	SelectColumnsTransform A transform that selects a set of columns out of an existing generator.
class	Transform An indvidual statement of a transform as a part of a sequence of steps.
class	TransformContainer A collection of transforms that combine to compute a result.
class	TransformEvaluationTransform A transform that evaluates another named transform.
class	WriteToFileTransform A transform that writes data to a file.

Methods in jigcell.compare.transform with parameters of type IDataGenerator

protected void	Transform.copy(boolean shallow, IDataGenerator target) Copies state for this generator.
protected void	TransformContainer.copy(boolean shallow, IDataGenerator target) Copies state for this generator.
protected void	ConstantTransform.copy(boolean shallow, IDataGenerator target) Copies state for this generator.
static ITransform	Transform.getTransformForGenerator(IDataGenerator generator) The transform of a generator.

Uses of IDataGenerator in jigcell.compare.ui

Fields in jigcell.compare.ui declared as IDataGenerator

protected IDataGenerator

SeriesDialog.generator Generator for the element being viewed

Constructors in jigcell.compare.ui with parameters of type IDataGenerator

SeriesDialog(Compare compare, IDataGenerator generator, IDataElement element, ITypeChecker checker, java.lang.String name, int row, int column, BasicTable.BasicTableModel model)
Creates a new dialog for viewing list based data.

SeriesDialog(Compare compare, IDataGenerator generator, int row, int column, BasicTable.BasicTableModel model)
Creates a new dialog for viewing list based data.

Uses of IDataGenerator in jigcell.compare.views

Methods in jigcell.compare.views that return IDataGenerator

protected static IDataGenerator	SeriesView.copyGenerator(IDataGenerator generator) Copies a generator.
IDataGenerator	ObjectiveSeriesView.processGenerator(IDataGenerator generator) Creates a replacement data generator for evaluation.

Methods in jigcell.compare.views with parameters of type IDataGenerator

protected TimeSeriesTypeChecker	EditableSeriesView.EditableSeriesModel.computeTypeForPlot(IDataGenerator generator) Builds a time series type for the generator.
protected static IDataGenerator	SeriesView.copyGenerator(IDataGenerator generator) Copies a generator.
protected void	ObjectiveSeriesView.evaluate(IDataGenerator[] generators) Evaluates a collection of data generators on a separate thread.
IDataGenerator	ObjectiveSeriesView.processGenerator(IDataGenerator generator) Creates a replacement data generator for evaluation.