| package org.eclipse.stem.diseasemodels.standard.impl; |
| |
| /******************************************************************************* |
| * Copyright (c) 2006 IBM Corporation and others. |
| * All rights reserved. This program and the accompanying materials |
| * are made available under the terms of the Eclipse Public License v1.0 |
| * which accompanies this distribution, and is available at |
| * http://www.eclipse.org/legal/epl-v10.html |
| * |
| * Contributors: |
| * IBM Corporation - initial API and implementation |
| *******************************************************************************/ |
| |
| import org.eclipse.emf.common.notify.Notification; |
| import java.util.Random; |
| |
| import org.eclipse.emf.ecore.EClass; |
| import org.eclipse.emf.ecore.impl.ENotificationImpl; |
| import org.eclipse.stem.core.graph.LabelValue; |
| import org.eclipse.stem.diseasemodels.standard.SIRLabelValue; |
| //import org.eclipse.stem.diseasemodels.standard.SIRLabelValue; |
| import org.eclipse.stem.diseasemodels.standard.SILabelValue; |
| import org.eclipse.stem.diseasemodels.standard.StandardDiseaseModelLabelValue; |
| import org.eclipse.stem.diseasemodels.standard.StandardFactory; |
| import org.eclipse.stem.diseasemodels.standard.StandardPackage; |
| import org.eclipse.stem.diseasemodels.standard.StandardStochasticDiseaseModel; |
| import org.eclipse.stem.diseasemodels.standard.StochasticDiseaseModel; |
| import org.eclipse.stem.diseasemodels.standard.StochasticSIRDiseaseModel; |
| |
| /** |
| * <!-- begin-user-doc --> An implementation of the model object '<em><b>Stochastic SIR Disease Model</b></em>'. |
| * <!-- end-user-doc --> |
| * <p> |
| * The following features are implemented: |
| * <ul> |
| * <li>{@link org.eclipse.stem.diseasemodels.standard.impl.StochasticSIRDiseaseModelImpl#getSeed <em>Seed</em>}</li> |
| * <li>{@link org.eclipse.stem.diseasemodels.standard.impl.StochasticSIRDiseaseModelImpl#getRandomGenerator <em>Random Generator</em>}</li> |
| * <li>{@link org.eclipse.stem.diseasemodels.standard.impl.StochasticSIRDiseaseModelImpl#getGain <em>Gain</em>}</li> |
| * </ul> |
| * </p> |
| * |
| * @generated |
| */ |
| public class StochasticSIRDiseaseModelImpl extends SIRImpl implements |
| StochasticSIRDiseaseModel { |
| |
| /** |
| * The default value of the '{@link #getSeed() <em>Seed</em>}' attribute. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @see #getSeed() |
| * @generated |
| * @ordered |
| */ |
| protected static final long SEED_EDEFAULT = 0L; |
| /** |
| * The cached value of the '{@link #getSeed() <em>Seed</em>}' attribute. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @see #getSeed() |
| * @generated |
| * @ordered |
| */ |
| protected long seed = SEED_EDEFAULT; |
| /** |
| * The default value of the '{@link #getRandomGenerator() <em>Random Generator</em>}' attribute. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @see #getRandomGenerator() |
| * @generated |
| * @ordered |
| */ |
| protected static final Random RANDOM_GENERATOR_EDEFAULT = (Random)StandardFactory.eINSTANCE.createFromString(StandardPackage.eINSTANCE.getRandom(), "0"); |
| /** |
| * The cached value of the '{@link #getRandomGenerator() <em>Random Generator</em>}' attribute. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @see #getRandomGenerator() |
| * @generated |
| * @ordered |
| */ |
| protected Random randomGenerator = RANDOM_GENERATOR_EDEFAULT; |
| /** |
| * The default value of the '{@link #getGain() <em>Gain</em>}' attribute. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @see #getGain() |
| * @generated |
| * @ordered |
| */ |
| protected static final double GAIN_EDEFAULT = 0.01; |
| /** |
| * The cached value of the '{@link #getGain() <em>Gain</em>}' attribute. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @see #getGain() |
| * @generated |
| * @ordered |
| */ |
| protected double gain = GAIN_EDEFAULT; |
| |
| /** |
| * <!-- begin-user-doc --> |
| * |
| * The constructor needs to be public so that the new disease wizard can |
| * create an instance of the class without using the factory. |
| * |
| * <!-- end-user-doc --> |
| * |
| * @generated NOT |
| */ |
| public StochasticSIRDiseaseModelImpl() { |
| super(); |
| } // StochasticSIRDiseaseModelImpl |
| |
| /** |
| * @param diseaseModelName |
| * the name of the disease model |
| * @param backgroundMortalityRate |
| * @param infectiousMortality |
| * @param infectiousMortalityRate |
| * the rate at which fatally infectious population members die |
| * @param transmissionRate |
| * @param recoveryRate |
| * @param immunityLossRate |
| * @param nonLinearityCoefficient |
| * @param timePeriod |
| * the time period for the rates (milliseconds) |
| * @param populationIdentifier |
| * the identifier of the population affected by the disease |
| * @param gain |
| * @return an initialized instance of DeterministicSIRDiseaseModel |
| */ |
| public static final StochasticSIRDiseaseModel createStochasticSIRDiseaseModel( |
| final String diseaseModelName, |
| final double backgroundMortalityRate, |
| final double infectiousMortalityRate, |
| final double transmissionRate, final double recoveryRate, |
| final double immunityLossRate, |
| final double nonLinearityCoefficient, final long timePeriod, |
| final String populationIdentifier, double gain) { |
| |
| final StochasticSIRDiseaseModel sirDiseaseModel = StandardFactory.eINSTANCE |
| .createStochasticSIRDiseaseModel(); |
| |
| initializeSIRDiseaseModel(sirDiseaseModel, diseaseModelName, |
| backgroundMortalityRate, |
| infectiousMortalityRate, transmissionRate, recoveryRate, |
| immunityLossRate, nonLinearityCoefficient, timePeriod, |
| populationIdentifier); |
| |
| sirDiseaseModel.setGain(gain); |
| |
| return sirDiseaseModel; |
| } // createStochasticSIRDiseaseModel |
| |
| /** |
| * ModelSpecificAdjustments for a Stochastic model adds noise to |
| * the I state. It will be propagated to other states automatically |
| * |
| */ |
| |
| public void doModelSpecificAdjustments( |
| final LabelValue state) { |
| final SILabelValue currentSI = (SILabelValue) state; |
| //double oldI = currentSI.getI(); |
| double incidence = currentSI.getIncidence(); |
| double newIncidence = incidence*computeNoise(); |
| double diff = newIncidence - incidence; |
| |
| double newI = currentSI.getI() + diff; |
| double newS = currentSI.getS() - diff; |
| if(newI < 0.0) { |
| double scale = (-newI) / currentSI.getI(); |
| if(Double.isInfinite(scale)) |
| scale = 0.0; // cancel noise if 0 |
| diff = diff * scale; |
| newI = currentSI.getI() + diff; // 0 |
| newS = currentSI.getS() - diff; |
| } |
| if(newS < 0.0) { |
| double scale = (-newS) / currentSI.getS(); |
| if(Double.isInfinite(scale)) |
| scale = 0.0; // cancel noise if 0 |
| diff = diff * scale; |
| newI = currentSI.getI() + diff; |
| newS = currentSI.getS() - diff; // 0 |
| } |
| newIncidence = incidence + diff; |
| currentSI.setS(newS); |
| currentSI.setI(newI); |
| currentSI.setIncidence(newIncidence); |
| return; |
| |
| } // doModelSpecificAdjustments |
| |
| @Override |
| public boolean isDeterministic() { |
| return true; |
| } |
| |
| /** |
| * <!-- begin-user-doc --> <!-- end-user-doc --> |
| * @generated |
| */ |
| @Override |
| protected EClass eStaticClass() { |
| return StandardPackage.Literals.STOCHASTIC_SIR_DISEASE_MODEL; |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public long getSeed() { |
| return seed; |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated NOT |
| */ |
| public void setSeed(long newSeed) { |
| long oldSeed = seed; |
| seed = newSeed; |
| if (eNotificationRequired()) |
| eNotify(new ENotificationImpl(this, Notification.SET, StandardPackage.STOCHASTIC_SIR_DISEASE_MODEL__SEED, oldSeed, seed)); |
| randomGenerator.setSeed(newSeed); |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public Random getRandomGenerator() { |
| return randomGenerator; |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public double getGain() { |
| return gain; |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public void setGain(double newGain) { |
| double oldGain = gain; |
| gain = newGain; |
| if (eNotificationRequired()) |
| eNotify(new ENotificationImpl(this, Notification.SET, StandardPackage.STOCHASTIC_SIR_DISEASE_MODEL__GAIN, oldGain, gain)); |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * By default this calls the static method StandardStochasticDiseaseModelImpl.computeNoise(gain, rand) |
| * <!-- end-user-doc --> |
| * @generated NOT |
| */ |
| public double computeNoise() { |
| return StandardStochasticDiseaseModelImpl.computeNoise(gain, randomGenerator); |
| } |
| |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| @Override |
| public Object eGet(int featureID, boolean resolve, boolean coreType) { |
| switch (featureID) { |
| case StandardPackage.STOCHASTIC_SIR_DISEASE_MODEL__SEED: |
| return getSeed(); |
| case StandardPackage.STOCHASTIC_SIR_DISEASE_MODEL__RANDOM_GENERATOR: |
| return getRandomGenerator(); |
| case StandardPackage.STOCHASTIC_SIR_DISEASE_MODEL__GAIN: |
| return getGain(); |
| } |
| return super.eGet(featureID, resolve, coreType); |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| @Override |
| public void eSet(int featureID, Object newValue) { |
| switch (featureID) { |
| case StandardPackage.STOCHASTIC_SIR_DISEASE_MODEL__SEED: |
| setSeed((Long)newValue); |
| return; |
| case StandardPackage.STOCHASTIC_SIR_DISEASE_MODEL__GAIN: |
| setGain((Double)newValue); |
| return; |
| } |
| super.eSet(featureID, newValue); |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| @Override |
| public void eUnset(int featureID) { |
| switch (featureID) { |
| case StandardPackage.STOCHASTIC_SIR_DISEASE_MODEL__SEED: |
| setSeed(SEED_EDEFAULT); |
| return; |
| case StandardPackage.STOCHASTIC_SIR_DISEASE_MODEL__GAIN: |
| setGain(GAIN_EDEFAULT); |
| return; |
| } |
| super.eUnset(featureID); |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| @Override |
| public boolean eIsSet(int featureID) { |
| switch (featureID) { |
| case StandardPackage.STOCHASTIC_SIR_DISEASE_MODEL__SEED: |
| return seed != SEED_EDEFAULT; |
| case StandardPackage.STOCHASTIC_SIR_DISEASE_MODEL__RANDOM_GENERATOR: |
| return RANDOM_GENERATOR_EDEFAULT == null ? randomGenerator != null : !RANDOM_GENERATOR_EDEFAULT.equals(randomGenerator); |
| case StandardPackage.STOCHASTIC_SIR_DISEASE_MODEL__GAIN: |
| return gain != GAIN_EDEFAULT; |
| } |
| return super.eIsSet(featureID); |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| @Override |
| public int eBaseStructuralFeatureID(int derivedFeatureID, Class<?> baseClass) { |
| if (baseClass == StochasticDiseaseModel.class) { |
| switch (derivedFeatureID) { |
| case StandardPackage.STOCHASTIC_SIR_DISEASE_MODEL__SEED: return StandardPackage.STOCHASTIC_DISEASE_MODEL__SEED; |
| case StandardPackage.STOCHASTIC_SIR_DISEASE_MODEL__RANDOM_GENERATOR: return StandardPackage.STOCHASTIC_DISEASE_MODEL__RANDOM_GENERATOR; |
| default: return -1; |
| } |
| } |
| if (baseClass == StandardStochasticDiseaseModel.class) { |
| switch (derivedFeatureID) { |
| case StandardPackage.STOCHASTIC_SIR_DISEASE_MODEL__GAIN: return StandardPackage.STANDARD_STOCHASTIC_DISEASE_MODEL__GAIN; |
| default: return -1; |
| } |
| } |
| return super.eBaseStructuralFeatureID(derivedFeatureID, baseClass); |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| @Override |
| public int eDerivedStructuralFeatureID(int baseFeatureID, Class<?> baseClass) { |
| if (baseClass == StochasticDiseaseModel.class) { |
| switch (baseFeatureID) { |
| case StandardPackage.STOCHASTIC_DISEASE_MODEL__SEED: return StandardPackage.STOCHASTIC_SIR_DISEASE_MODEL__SEED; |
| case StandardPackage.STOCHASTIC_DISEASE_MODEL__RANDOM_GENERATOR: return StandardPackage.STOCHASTIC_SIR_DISEASE_MODEL__RANDOM_GENERATOR; |
| default: return -1; |
| } |
| } |
| if (baseClass == StandardStochasticDiseaseModel.class) { |
| switch (baseFeatureID) { |
| case StandardPackage.STANDARD_STOCHASTIC_DISEASE_MODEL__GAIN: return StandardPackage.STOCHASTIC_SIR_DISEASE_MODEL__GAIN; |
| default: return -1; |
| } |
| } |
| return super.eDerivedStructuralFeatureID(baseFeatureID, baseClass); |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| @Override |
| public String toString() { |
| if (eIsProxy()) return super.toString(); |
| |
| StringBuffer result = new StringBuffer(super.toString()); |
| result.append(" (seed: "); //$NON-NLS-1$ |
| result.append(seed); |
| result.append(", randomGenerator: "); //$NON-NLS-1$ |
| result.append(randomGenerator); |
| result.append(", gain: "); //$NON-NLS-1$ |
| result.append(gain); |
| result.append(')'); |
| return result.toString(); |
| } |
| |
| } // StochasticSIRDiseaseModelImpl |
