Package edu.cmu.tetrad.study.gene.tetradapp.model

Class MeasurementSimulatorParams

java.lang.Object

edu.cmu.tetrad.study.gene.tetradapp.model.MeasurementSimulatorParams

All Implemented Interfaces:

TetradSerializable, Serializable

public class MeasurementSimulatorParams
extends Object
implements TetradSerializable

Wraps MeasurementSimulator so that it may be used as a parameter object.

Version:

$Id: $Id

Author:

josephramsey

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
MeasurementSimulatorParams(Parameters parameters)	Constructs a measurement simulator using the given history.

Method Summary

Modifier and Type	Method	Description
double	getChipChipVariability()	getChipChipVariability.
double	getDishDishVariability()	getDishDishVariability.
int	getFirstStepStored()	getFirstStepStored.
int	getInterval()	getInterval.
double[][][]	getMeasuredData()	getMeasuredData.
int	getNumCellsPerDish()	getNumCellsPerDish.
int	getNumDishes()	getNumDishes.
int	getNumSamplesPerDish()	getNumSamplesPerDish.
double	getPixelDigitalization()	getPixelDigitalization.
double[][][]	getRawData()	getRawData.
double	getSampleSampleVariability()	getSampleSampleVariability.
MeasurementSimulator	getSimulator()	Getter for the field simulator.
int	getStepsGenerated()	getStepsGenerated.
int[]	getTimeSteps()	getTimeSteps.
boolean	isAntilogCalculated()	isAntilogCalculated.
boolean	isIncludeDishAndChipVariables()	isIncludeDishAndChipVariables.
boolean	isInitSync()	isInitSync.
boolean	isRawDataSaved()	isRawDataSaved.
static MeasurementSimulatorParams	serializableInstance()	Generates a simple exemplar of this class to test serialization.
void	setAntilogCalculated(boolean selected)	setAntilogCalculated.
void	setChipChipVariability(double value)	setChipChipVariability.
void	setDishDishVariability(double value)	setDishDishVariability.
void	setFirstStepStored(int value)	setFirstStepStored.
void	setHistory(GeneHistory history)	setHistory.
void	setIncludeDishAndChipVariables(boolean includeDishAndChipVariables)	Setter for the field includeDishAndChipVariables.
void	setInitSync(boolean selected)	setInitSync.
void	setInterval(int value)	setInterval.
void	setNumCellsPerDish(int value)	setNumCellsPerDish.
void	setNumDishes(int value)	setNumDishes.
void	setNumSamplesPerDish(int value)	setNumSamplesPerDish.
void	setPixelDigitalization(double value)	setPixelDigitalization.
void	setRawDataSaved(boolean selected)	setRawDataSaved.
void	setSampleSampleVariability(double value)	setSampleSampleVariability.
void	setStepsGenerated(int value)	setStepsGenerated.
void	simulate(GeneHistory history)	simulate.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

MeasurementSimulatorParams

public MeasurementSimulatorParams(Parameters parameters)

Constructs a measurement simulator using the given history. The history will be used to do the simulation of each cell.

Parameters:

parameters - a Parameters object

Throws:

NullPointerException - if the history argument is null.

Method Details

serializableInstance

public static MeasurementSimulatorParams serializableInstance()

Generates a simple exemplar of this class to test serialization.

Returns:

a MeasurementSimulatorParams object

setHistory

public void setHistory(GeneHistory history)

setHistory.

Parameters:

history - a GeneHistory object

getDishDishVariability

public double getDishDishVariability()

getDishDishVariability.

Returns:

a double

setDishDishVariability

public void setDishDishVariability(double value)

setDishDishVariability.

Parameters:

value - a double

getSampleSampleVariability

public double getSampleSampleVariability()

getSampleSampleVariability.

Returns:

a double

setSampleSampleVariability

public void setSampleSampleVariability(double value)

setSampleSampleVariability.

Parameters:

value - a double

getChipChipVariability

public double getChipChipVariability()

getChipChipVariability.

Returns:

a double

setChipChipVariability

public void setChipChipVariability(double value)

setChipChipVariability.

Parameters:

value - a double

getPixelDigitalization

public double getPixelDigitalization()

getPixelDigitalization.

Returns:

a double

setPixelDigitalization

public void setPixelDigitalization(double value)

setPixelDigitalization.

Parameters:

value - a double

getNumDishes

public int getNumDishes()

getNumDishes.

Returns:

a int

setNumDishes

public void setNumDishes(int value)

setNumDishes.

Parameters:

value - a int

getNumCellsPerDish

public int getNumCellsPerDish()

getNumCellsPerDish.

Returns:

a int

setNumCellsPerDish

public void setNumCellsPerDish(int value)

setNumCellsPerDish.

Parameters:

value - a int

getNumSamplesPerDish

public int getNumSamplesPerDish()

getNumSamplesPerDish.

Returns:

a int

setNumSamplesPerDish

public void setNumSamplesPerDish(int value)

setNumSamplesPerDish.

Parameters:

value - a int

getStepsGenerated

public int getStepsGenerated()

getStepsGenerated.

Returns:

a int

setStepsGenerated

public void setStepsGenerated(int value)

setStepsGenerated.

Parameters:

value - a int

getFirstStepStored

public int getFirstStepStored()

getFirstStepStored.

Returns:

a int

setFirstStepStored

public void setFirstStepStored(int value)

setFirstStepStored.

Parameters:

value - a int

getInterval

public int getInterval()

getInterval.

Returns:

a int

setInterval

public void setInterval(int value)

setInterval.

Parameters:

value - a int

isInitSync

public boolean isInitSync()

isInitSync.

Returns:

a boolean

setInitSync

public void setInitSync(boolean selected)

setInitSync.

Parameters:

selected - a boolean

isRawDataSaved

public boolean isRawDataSaved()

isRawDataSaved.

Returns:

a boolean

setRawDataSaved

public void setRawDataSaved(boolean selected)

setRawDataSaved.

Parameters:

selected - a boolean

isAntilogCalculated

public boolean isAntilogCalculated()

isAntilogCalculated.

Returns:

a boolean

setAntilogCalculated

public void setAntilogCalculated(boolean selected)

setAntilogCalculated.

Parameters:

selected - a boolean

getSimulator

public MeasurementSimulator getSimulator()

Getter for the field simulator.

Returns:

a MeasurementSimulator object

simulate

public void simulate(GeneHistory history)

simulate.

Parameters:

history - a GeneHistory object

getMeasuredData

public double[][][] getMeasuredData()

getMeasuredData.

Returns:

an array of objects

getTimeSteps

public int[] getTimeSteps()

getTimeSteps.

Returns:

an array of objects

getRawData

public double[][][] getRawData()

getRawData.

Returns:

an array of objects

isIncludeDishAndChipVariables

public boolean isIncludeDishAndChipVariables()

isIncludeDishAndChipVariables.

Returns:

a boolean

setIncludeDishAndChipVariables

public void setIncludeDishAndChipVariables(boolean includeDishAndChipVariables)

Setter for the field includeDishAndChipVariables.

Parameters:

includeDishAndChipVariables - a boolean