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///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// Copyright (C) 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, //
// 2007, 2008, 2009, 2010, 2014, 2015, 2022 by Peter Spirtes, Richard //
// Scheines, Joseph Ramsey, and Clark Glymour. //
// //
// This program is free software; you can redistribute it and/or modify //
// it under the terms of the GNU General Public License as published by //
// the Free Software Foundation; either version 2 of the License, or //
// (at your option) any later version. //
// //
// This program is distributed in the hope that it will be useful, //
// but WITHOUT ANY WARRANTY; without even the implied warranty of //
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the //
// GNU General Public License for more details. //
// //
// You should have received a copy of the GNU General Public License //
// along with this program; if not, write to the Free Software //
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA //
///////////////////////////////////////////////////////////////////////////////
package edu.cmu.tetrad.study.gene.tetradapp.model;
import edu.cmu.tetrad.study.gene.tetrad.gene.history.BasalInitializer;
import edu.cmu.tetrad.study.gene.tetrad.gene.history.BooleanGlassFunction;
import edu.cmu.tetrad.study.gene.tetrad.gene.history.GeneHistory;
import edu.cmu.tetrad.study.gene.tetrad.gene.simulation.MeasurementSimulator;
import edu.cmu.tetrad.util.Parameters;
import edu.cmu.tetrad.util.TetradSerializable;
import java.io.IOException;
import java.io.ObjectInputStream;
/**
* Wraps MeasurementSimulator so that it may be used as a parameter object.
*
* @author josephramsey
*/
public class MeasurementSimulatorParams implements TetradSerializable {
private static final long serialVersionUID = 23L;
/**
* @serial Cannot be null.
*/
private final MeasurementSimulator simulator;
private boolean includeDishAndChipVariables;
//==============================CONSTRUCTORS=========================//
/**
* Constructs a measurement simulator using the given history. The history will be used to do the simulation of each
* cell.
*
* @throws NullPointerException if the history argument is null.
*/
public MeasurementSimulatorParams(Parameters parameters) {
this.simulator = new MeasurementSimulator(parameters);
}
/**
* Generates a simple exemplar of this class to test serialization.
*/
public static MeasurementSimulatorParams serializableInstance() {
MeasurementSimulatorParams params = new MeasurementSimulatorParams(new Parameters());
params.setHistory(new GeneHistory(
BasalInitializer.serializableInstance(),
BooleanGlassFunction.serializableInstance()));
return params;
}
//==============================PUBLIC METHODS======================//
public void setHistory(GeneHistory history) {
getSimulator().setHistory(history);
}
public double getDishDishVariability() {
return getSimulator().getDishDishVariability();
}
public void setDishDishVariability(double value) {
getSimulator().setDishDishVariability(value);
}
public double getSampleSampleVariability() {
return getSimulator().getSampleSampleVariability();
}
public void setSampleSampleVariability(double value) {
getSimulator().setSampleSampleVariability(value);
}
public double getChipChipVariability() {
return getSimulator().getChipChipVariability();
}
public void setChipChipVariability(double value) {
getSimulator().setChipChipVariability(value);
}
public double getPixelDigitalization() {
return getSimulator().getPixelDigitalization();
}
public void setPixelDigitalization(double value) {
getSimulator().setPixelDigitalization(value);
}
public int getNumDishes() {
return getSimulator().getNumDishes();
}
public void setNumDishes(int value) {
getSimulator().setNumDishes(value);
}
public int getNumCellsPerDish() {
return getSimulator().getNumCellsPerDish();
}
public void setNumCellsPerDish(int value) {
getSimulator().setNumCellsPerDish(value);
}
public int getNumSamplesPerDish() {
return getSimulator().getNumSamplesPerDish();
}
public void setNumSamplesPerDish(int value) {
getSimulator().setNumSamplesPerDish(value);
}
public int getStepsGenerated() {
return getSimulator().getStepsGenerated();
}
public void setStepsGenerated(int value) {
getSimulator().setStepsGenerated(value);
}
public int getFirstStepStored() {
return getSimulator().getFirstStepStored();
}
public void setFirstStepStored(int value) {
getSimulator().setFirstStepStored(value);
}
public int getInterval() {
return getSimulator().getInterval();
}
public void setInterval(int value) {
getSimulator().setInterval(value);
}
public boolean isInitSync() {
return getSimulator().isInitSync();
}
public void setInitSync(boolean selected) {
getSimulator().setInitSync(selected);
}
public boolean isRawDataSaved() {
return getSimulator().isRawDataSaved();
}
public void setRawDataSaved(boolean selected) {
getSimulator().setRawDataSaved(selected);
}
public boolean isAntilogCalculated() {
return getSimulator().isAntilogCalculated();
}
public void setAntilogCalculated(boolean selected) {
getSimulator().setAntilogCalculated(selected);
}
public MeasurementSimulator getSimulator() {
return this.simulator;
}
public void simulate(GeneHistory history) {
getSimulator().simulate(history);
}
public double[][][] getMeasuredData() {
return getSimulator().getMeasuredData();
}
public int[] getTimeSteps() {
return getSimulator().getTimeSteps();
}
public double[][][] getRawData() {
return getSimulator().getRawData();
}
/**
* Adds semantic checks to the default deserialization method. This method must have the standard signature for a
* readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any
* semantic checks can be specified and do not need to stay the same from version to version. A readObject method of
* this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the
* class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for
* help.
*/
private void readObject(ObjectInputStream s)
throws IOException, ClassNotFoundException {
s.defaultReadObject();
if (this.simulator == null) {
throw new NullPointerException();
}
}
public boolean isIncludeDishAndChipVariables() {
return getSimulator().isIncludeDishAndChipColumns();
}
public void setIncludeDishAndChipVariables(boolean includeDishAndChipVariables) {
getSimulator().setIncludeDishAndChipColumns(includeDishAndChipVariables);
}
}
