package org.eclipse.stem.diseasemodels.forcing.impl;
/*******************************************************************************
 * Copyright (c) 2010 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 java.io.FileWriter;
import java.util.ArrayList;
import java.util.Calendar;

import org.eclipse.emf.common.notify.Notification;
import org.eclipse.emf.ecore.EClass;
import org.eclipse.emf.ecore.impl.ENotificationImpl;
import org.eclipse.stem.core.graph.LabelValue;
import org.eclipse.stem.core.model.STEMTime;
import org.eclipse.stem.diseasemodels.forcing.ForcingPackage;
import org.eclipse.stem.diseasemodels.forcing.Gaussian2ForcingDiseaseModel;
import org.eclipse.stem.diseasemodels.standard.DiseaseModelLabelValue;
import org.eclipse.stem.diseasemodels.standard.SILabelValue;
import org.eclipse.stem.diseasemodels.standard.SIRLabelValue;
import org.eclipse.stem.diseasemodels.standard.StandardDiseaseModelLabel;
import org.eclipse.stem.diseasemodels.standard.StandardDiseaseModelLabelValue;
import org.eclipse.stem.diseasemodels.standard.StandardPackage;
import org.eclipse.stem.diseasemodels.standard.impl.SIRLabelValueImpl;

/**
 * <!-- begin-user-doc -->
 * An implementation of the model object '<em><b>Gaussian2 Forcing Disease Model</b></em>'.
 * <!-- end-user-doc -->
 * <p>
 * The following features are implemented:
 * <ul>
 *   <li>{@link org.eclipse.stem.diseasemodels.forcing.impl.Gaussian2ForcingDiseaseModelImpl#getSigma2_2 <em>Sigma2 2</em>}</li>
 *   <li>{@link org.eclipse.stem.diseasemodels.forcing.impl.Gaussian2ForcingDiseaseModelImpl#getAtt1 <em>Att1</em>}</li>
 *   <li>{@link org.eclipse.stem.diseasemodels.forcing.impl.Gaussian2ForcingDiseaseModelImpl#getAtt2 <em>Att2</em>}</li>
 *   <li>{@link org.eclipse.stem.diseasemodels.forcing.impl.Gaussian2ForcingDiseaseModelImpl#getAtt3 <em>Att3</em>}</li>
 *   <li>{@link org.eclipse.stem.diseasemodels.forcing.impl.Gaussian2ForcingDiseaseModelImpl#getAtt4 <em>Att4</em>}</li>
 * </ul>
 * </p>
 *
 * @generated
 */
public class Gaussian2ForcingDiseaseModelImpl extends GaussianForcingDiseaseModelImpl implements Gaussian2ForcingDiseaseModel {
	/**
	 * The default value of the '{@link #getSigma2_2() <em>Sigma2 2</em>}' attribute.
	 * <!-- begin-user-doc -->
	 * <!-- end-user-doc -->
	 * @see #getSigma2_2()
	 * @generated
	 * @ordered
	 */
	protected static final double SIGMA2_2_EDEFAULT = 100.0;

	/**
	 * The cached value of the '{@link #getSigma2_2() <em>Sigma2 2</em>}' attribute.
	 * <!-- begin-user-doc -->
	 * <!-- end-user-doc -->
	 * @see #getSigma2_2()
	 * @generated
	 * @ordered
	 */
	protected double sigma2_2 = SIGMA2_2_EDEFAULT;

	/**
	 * The default value of the '{@link #getAtt1() <em>Att1</em>}' attribute.
	 * <!-- begin-user-doc -->
	 * <!-- end-user-doc -->
	 * @see #getAtt1()
	 * @generated
	 * @ordered
	 */
	protected static final double ATT1_EDEFAULT = 1.0;

	/**
	 * The cached value of the '{@link #getAtt1() <em>Att1</em>}' attribute.
	 * <!-- begin-user-doc -->
	 * <!-- end-user-doc -->
	 * @see #getAtt1()
	 * @generated
	 * @ordered
	 */
	protected double att1 = ATT1_EDEFAULT;

	/**
	 * The default value of the '{@link #getAtt2() <em>Att2</em>}' attribute.
	 * <!-- begin-user-doc -->
	 * <!-- end-user-doc -->
	 * @see #getAtt2()
	 * @generated
	 * @ordered
	 */
	protected static final double ATT2_EDEFAULT = 1.0;

	/**
	 * The cached value of the '{@link #getAtt2() <em>Att2</em>}' attribute.
	 * <!-- begin-user-doc -->
	 * <!-- end-user-doc -->
	 * @see #getAtt2()
	 * @generated
	 * @ordered
	 */
	protected double att2 = ATT2_EDEFAULT;

	/**
	 * The default value of the '{@link #getAtt3() <em>Att3</em>}' attribute.
	 * <!-- begin-user-doc -->
	 * <!-- end-user-doc -->
	 * @see #getAtt3()
	 * @generated
	 * @ordered
	 */
	protected static final double ATT3_EDEFAULT = 1.0;

	/**
	 * The cached value of the '{@link #getAtt3() <em>Att3</em>}' attribute.
	 * <!-- begin-user-doc -->
	 * <!-- end-user-doc -->
	 * @see #getAtt3()
	 * @generated
	 * @ordered
	 */
	protected double att3 = ATT3_EDEFAULT;

	/**
	 * The default value of the '{@link #getAtt4() <em>Att4</em>}' attribute.
	 * <!-- begin-user-doc -->
	 * <!-- end-user-doc -->
	 * @see #getAtt4()
	 * @generated
	 * @ordered
	 */
	protected static final double ATT4_EDEFAULT = 1.0;

	/**
	 * The cached value of the '{@link #getAtt4() <em>Att4</em>}' attribute.
	 * <!-- begin-user-doc -->
	 * <!-- end-user-doc -->
	 * @see #getAtt4()
	 * @generated
	 * @ordered
	 */
	protected double att4 = ATT4_EDEFAULT;

	/**
	 * <!-- begin-user-doc -->
	 * <!-- end-user-doc -->
	 * @generated NOT
	 */
	public Gaussian2ForcingDiseaseModelImpl() {
		super();
	}

	/**
	 * <!-- begin-user-doc -->
	 * <!-- end-user-doc -->
	 * @generated
	 */
	@Override
	protected EClass eStaticClass() {
		return ForcingPackage.Literals.GAUSSIAN2_FORCING_DISEASE_MODEL;
	}

	/**
	 * <!-- begin-user-doc -->
	 * <!-- end-user-doc -->
	 * @generated
	 */
	public double getSigma2_2() {
		return sigma2_2;
	}

	/**
	 * <!-- begin-user-doc -->
	 * <!-- end-user-doc -->
	 * @generated
	 */
	public void setSigma2_2(double newSigma2_2) {
		double oldSigma2_2 = sigma2_2;
		sigma2_2 = newSigma2_2;
		if (eNotificationRequired())
			eNotify(new ENotificationImpl(this, Notification.SET, ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__SIGMA2_2, oldSigma2_2, sigma2_2));
	}

	/**
	 * <!-- begin-user-doc -->
	 * <!-- end-user-doc -->
	 * @generated
	 */
	public double getAtt1() {
		return att1;
	}

	/**
	 * <!-- begin-user-doc -->
	 * <!-- end-user-doc -->
	 * @generated
	 */
	public void setAtt1(double newAtt1) {
		double oldAtt1 = att1;
		att1 = newAtt1;
		if (eNotificationRequired())
			eNotify(new ENotificationImpl(this, Notification.SET, ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT1, oldAtt1, att1));
	}

	/**
	 * <!-- begin-user-doc -->
	 * <!-- end-user-doc -->
	 * @generated
	 */
	public double getAtt2() {
		return att2;
	}

	/**
	 * <!-- begin-user-doc -->
	 * <!-- end-user-doc -->
	 * @generated
	 */
	public void setAtt2(double newAtt2) {
		double oldAtt2 = att2;
		att2 = newAtt2;
		if (eNotificationRequired())
			eNotify(new ENotificationImpl(this, Notification.SET, ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT2, oldAtt2, att2));
	}

	/**
	 * <!-- begin-user-doc -->
	 * <!-- end-user-doc -->
	 * @generated
	 */
	public double getAtt3() {
		return att3;
	}

	/**
	 * <!-- begin-user-doc -->
	 * <!-- end-user-doc -->
	 * @generated
	 */
	public void setAtt3(double newAtt3) {
		double oldAtt3 = att3;
		att3 = newAtt3;
		if (eNotificationRequired())
			eNotify(new ENotificationImpl(this, Notification.SET, ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT3, oldAtt3, att3));
	}

	/**
	 * <!-- begin-user-doc -->
	 * <!-- end-user-doc -->
	 * @generated
	 */
	public double getAtt4() {
		return att4;
	}

	/**
	 * <!-- begin-user-doc -->
	 * <!-- end-user-doc -->
	 * @generated
	 */
	public void setAtt4(double newAtt4) {
		double oldAtt4 = att4;
		att4 = newAtt4;
		if (eNotificationRequired())
			eNotify(new ENotificationImpl(this, Notification.SET, ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT4, oldAtt4, att4));
	}

	private Long firstTime = new Long(Long.MAX_VALUE);
	private Calendar calendar = Calendar.getInstance();
	private Calendar calendar2 = Calendar.getInstance();
	private static final double MILLIS_PER_DAY = 1000.0*60.0*60.0*24.0;

	private ArrayList<Long> writtedTimes = new ArrayList<Long>();
	private FileWriter fw;
	@Override
	public StandardDiseaseModelLabelValue computeDiseaseDeltas(
			final STEMTime time,double t,
			final StandardDiseaseModelLabelValue currentState,
			final StandardDiseaseModelLabel diseaseLabel, final long timeDelta, DiseaseModelLabelValue returnValue) {
final SIRLabelValue currentSIR = (SIRLabelValue) currentState;
		
		long currentMillis = time.getTime().getTime();
		double seasonalModulationFloor = getModulationFloor();
		double modulationPeriod = getModulationPeriod();
		double phase = getModulationPhaseShift();	
		double sigma2 = getSigma2();
		double sigma2_2 = getSigma2_2();
		
		synchronized(this) {
			if(firstTime.longValue() == Long.MAX_VALUE)
				firstTime = Long.valueOf(time.getTime().getTime());
		}
		
		// Get the day from time and adjust for the phase	
		double day=0;
		// Shared calendar object not thread safe
		synchronized(calendar) {
			calendar.setTimeInMillis(currentMillis);
			calendar2.setTimeInMillis(firstTime.longValue());
			day = (calendar.getTimeInMillis() - calendar2.getTimeInMillis())/MILLIS_PER_DAY;
		}
		
		
		double mu1 = phase;
		double mu2 = phase + modulationPeriod;
		
		double modulation1 = (1/Math.sqrt(2*Math.PI*sigma2))*Math.exp(-(Math.pow(day-mu1,2))/(2*sigma2));						
		double modulation2 = (1/Math.sqrt(2*Math.PI*sigma2_2))*Math.exp(-(Math.pow(day-mu2,2))/(2*sigma2_2));
		
		// This is beta*
		double transmissionRate = seasonalModulationFloor + (getAdjustedTransmissionRate(timeDelta)) * (modulation1+modulation2);

		if(day >= 116 && day <= 119) // April 24 - 27
			transmissionRate = transmissionRate * this.getAtt1();
		else 	if(day >= 120 && day <= 127) // April 28 - May 5
			transmissionRate = transmissionRate * this.getAtt2();
		else if(day >= 128 && day <= 132) // May 6 - May 10
			transmissionRate = transmissionRate * this.getAtt3();
		
		synchronized(writtedTimes) {
			if(!writtedTimes.contains(time.getTime().getTime())) {
				try {
				if(fw == null) fw = new FileWriter("beta.csv");
				fw.write(time.getTime().getTime()+","+transmissionRate+"\n");
				} catch(Exception e) {
					e.printStackTrace();
				}
				writtedTimes.add(time.getTime().getTime());
			}
		}
		
		if(!this.isFrequencyDependent())  transmissionRate *= getTransmissionRateScaleFactor(diseaseLabel);
		
		// The effective Infectious population  is a dimensionles number normalize by total
		// population used in teh computation of bets*S*i where i = Ieffective/Pop.
		// This includes a correction to the current
		// infectious population (Ieffective) based on the conserved exchange of people (circulation)
		// between regions. Note that this is no the "arrivals" and "departures" which are
		// a different process.
		final double effectiveInfectious = getNormalizedEffectiveInfectious(diseaseLabel.getNode(), diseaseLabel, currentSIR.getI(), StandardPackage.Literals.SI_LABEL_VALUE__I);

		/*
		 * Compute state transitions
		 * 
		 * Regarding computing the number of transitions from Susceptible to Exposed:
		 * In a linear model the "effective" number of infectious people is just
		 * the number of infectious people In a nonlinear model we have a
		 * nonLinearity exponent that is > 1 this models the effect of immune
		 * system saturation when Susceptible people are exposed to large
		 * numbers of infectious people. then the "effective" number of
		 * infectious people is I^nonLinearity exponent to allow for either
		 * linear or nonlinear models we always calculate I^nonLinearity
		 * exponent and allow nonLinearity exponent >= 1.0
		 */
		double numberOfInfectedToRecovered = getAdjustedRecoveryRate(timeDelta)
		* currentSIR.getI();
		double numberOfRecoveredToSusceptible = getAdjustedImmunityLossRate(timeDelta)
		* currentSIR.getR();
		// Need to checked what do do here. If non linear coefficient is not 1 and
		// the effective infectious is negative (which is possible), what do do? 
		// Let's fall back on the linear method for now.
		double numberOfSusceptibleToInfected = 0.0;
		if(getNonLinearityCoefficient() != 1.0 && effectiveInfectious >= 0.0)
			numberOfSusceptibleToInfected = transmissionRate
			* currentSIR.getS()* Math.pow(effectiveInfectious, getNonLinearityCoefficient());
		else
			numberOfSusceptibleToInfected = transmissionRate
			* currentSIR.getS()* effectiveInfectious;
		
		
		// Determine delta S
		final double deltaS = numberOfRecoveredToSusceptible - numberOfSusceptibleToInfected;
			// Determine delta I
		final double deltaI = numberOfSusceptibleToInfected- numberOfInfectedToRecovered;
		// Determine delta R
		final double deltaR = numberOfInfectedToRecovered - numberOfRecoveredToSusceptible;
		
		SIRLabelValueImpl ret = (SIRLabelValueImpl)returnValue;
		ret.setS(deltaS);
		ret.setI(deltaI);
		ret.setIncidence(numberOfInfectedToRecovered);
		ret.setR(deltaR);
		ret.setDiseaseDeaths(0);
		return ret;
	} // computeTransitions
	
	/**
	 * ModelSpecificAdjustments for a Stochastic model adds noise to or adjusts 
	 * the disease state transition values by multiplying
	 * the additions by a random variable r ~ (1+/-x) with x small.
	 * The requirements that no more individuals can be moved from a state than are
	 * already in that state is still enforced.
	 * 
	 */
	@Override
	public void doModelSpecificAdjustments(final LabelValue state) {
			final SILabelValue currentSI = (SILabelValue) state;
			double oldI = currentSI.getI();
			double Inoisy = currentSI.getI()* computeNoise();
			double change = oldI-Inoisy;
			currentSI.setI(Inoisy);
			double newS = currentSI.getS() + change;
			if(newS < 0.0) {
				// Need to rescale
				double scale = (currentSI.getS() + newS) / currentSI.getS();
				currentSI.setI(Inoisy*scale);
			} else  currentSI.setS(newS);
			return;
	} // doModelSpecificAdjustments
	
	/**
	 * <!-- begin-user-doc -->
	 * <!-- end-user-doc -->
	 * @generated
	 */
	@Override
	public Object eGet(int featureID, boolean resolve, boolean coreType) {
		switch (featureID) {
			case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__SIGMA2_2:
				return getSigma2_2();
			case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT1:
				return getAtt1();
			case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT2:
				return getAtt2();
			case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT3:
				return getAtt3();
			case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT4:
				return getAtt4();
		}
		return super.eGet(featureID, resolve, coreType);
	}

	/**
	 * <!-- begin-user-doc -->
	 * <!-- end-user-doc -->
	 * @generated
	 */
	@Override
	public void eSet(int featureID, Object newValue) {
		switch (featureID) {
			case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__SIGMA2_2:
				setSigma2_2((Double)newValue);
				return;
			case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT1:
				setAtt1((Double)newValue);
				return;
			case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT2:
				setAtt2((Double)newValue);
				return;
			case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT3:
				setAtt3((Double)newValue);
				return;
			case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT4:
				setAtt4((Double)newValue);
				return;
		}
		super.eSet(featureID, newValue);
	}

	/**
	 * <!-- begin-user-doc -->
	 * <!-- end-user-doc -->
	 * @generated
	 */
	@Override
	public void eUnset(int featureID) {
		switch (featureID) {
			case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__SIGMA2_2:
				setSigma2_2(SIGMA2_2_EDEFAULT);
				return;
			case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT1:
				setAtt1(ATT1_EDEFAULT);
				return;
			case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT2:
				setAtt2(ATT2_EDEFAULT);
				return;
			case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT3:
				setAtt3(ATT3_EDEFAULT);
				return;
			case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT4:
				setAtt4(ATT4_EDEFAULT);
				return;
		}
		super.eUnset(featureID);
	}

	/**
	 * <!-- begin-user-doc -->
	 * <!-- end-user-doc -->
	 * @generated
	 */
	@Override
	public boolean eIsSet(int featureID) {
		switch (featureID) {
			case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__SIGMA2_2:
				return sigma2_2 != SIGMA2_2_EDEFAULT;
			case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT1:
				return att1 != ATT1_EDEFAULT;
			case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT2:
				return att2 != ATT2_EDEFAULT;
			case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT3:
				return att3 != ATT3_EDEFAULT;
			case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT4:
				return att4 != ATT4_EDEFAULT;
		}
		return super.eIsSet(featureID);
	}

	/**
	 * <!-- begin-user-doc -->
	 * <!-- end-user-doc -->
	 * @generated
	 */
	@Override
	public String toString() {
		if (eIsProxy()) return super.toString();

		StringBuffer result = new StringBuffer(super.toString());
		result.append(" (sigma2_2: "); //$NON-NLS-1$
		result.append(sigma2_2);
		result.append(", att1: "); //$NON-NLS-1$
		result.append(att1);
		result.append(", att2: "); //$NON-NLS-1$
		result.append(att2);
		result.append(", att3: "); //$NON-NLS-1$
		result.append(att3);
		result.append(", att4: "); //$NON-NLS-1$
		result.append(att4);
		result.append(')');
		return result.toString();
	}

} //Gaussian2ForcingDiseaseModelImpl