org.eclipse.stem.diseasemodels/src/org/eclipse/stem/diseasemodels/standard/impl/SIRInoculatorImpl.java - stem/org.eclipse.stem - Git at Google

 package org.eclipse.stem.diseasemodels.standard.impl;

 /*******************************************************************************
  * Copyright (c) 2009 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.util.Iterator;
 import java.util.Set;

 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.Graph;
 import org.eclipse.stem.core.graph.IntegrationLabel;
 import org.eclipse.stem.core.graph.Node;
 import org.eclipse.stem.core.graph.NodeLabel;
 import org.eclipse.stem.core.model.Decorator;
 import org.eclipse.stem.diseasemodels.Activator;
 import org.eclipse.stem.diseasemodels.standard.DiseaseModelLabel;
 import org.eclipse.stem.diseasemodels.standard.SEIRLabel;
 import org.eclipse.stem.diseasemodels.standard.SILabel;
 import org.eclipse.stem.diseasemodels.standard.SILabelValue;
 import org.eclipse.stem.diseasemodels.standard.SIRInoculator;
 import org.eclipse.stem.diseasemodels.standard.SIRLabel;
 import org.eclipse.stem.diseasemodels.standard.SIRLabelValue;
 import org.eclipse.stem.diseasemodels.standard.StandardDiseaseModel;
 import org.eclipse.stem.diseasemodels.standard.StandardPackage;

 /**
  * <!-- begin-user-doc -->
  * An implementation of the model object '<em><b>SIR Inoculator</b></em>'.
  * <!-- end-user-doc -->
  * <p>
  * The following features are implemented:
  * <ul>
  *   <li>{@link org.eclipse.stem.diseasemodels.standard.impl.SIRInoculatorImpl#getInoculatedPercentage <em>Inoculated Percentage</em>}</li>
  * </ul>
  * </p>
  *
  * @generated
  */
 public class SIRInoculatorImpl extends SIInfectorImpl implements SIRInoculator {
 	/**
 	 * The default value of the '{@link #getInoculatedPercentage() <em>Inoculated Percentage</em>}' attribute.
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @see #getInoculatedPercentage()
 	 * @generated
 	 * @ordered
 	 */
 	protected static final double INOCULATED_PERCENTAGE_EDEFAULT = 1.0;

 	/**
 	 * OverrideThe default value of the '{@link #getInfectiousCount() <em>Infectious Count</em>}' attribute.
 	 * <!-- begin-user-doc --> <!-- end-user-doc -->
 	 * @see #getInfectiousCount()
 	 * @generated NOT
 	 * @ordered
 	 */
 	protected static final double INFECTIOUS_COUNT_EDEFAULT = 0.0;

 	/**
 	 * The cached value of the '{@link #getInoculatedPercentage() <em>Inoculated Percentage</em>}' attribute.
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @see #getInoculatedPercentage()
 	 * @generated
 	 * @ordered
 	 */
 	protected double inoculatedPercentage = INOCULATED_PERCENTAGE_EDEFAULT;

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	protected SIRInoculatorImpl() {
 		super();
 	}


 	/**
 	 * For the innoculator, we not only innoculate the present node but every child underneath it
 	 * @see org.eclipse.stem.core.model.impl.DecoratorImpl#decorateGraph(org.eclipse.stem.core.graph.Graph)
 	 */
 	@Override
 	public void decorateGraph() {

 		final Graph graph = getGraph();

 		// Do we need to look up the disease model from its name?
 		if (diseaseModel == null) {
 			// Yes
 			// There's a disease model out there with our name on it
 			// (maybe)...let's find it
 			for (Iterator<Decorator> decoratorIter = graph.getDecorators().iterator(); decoratorIter
 					.hasNext();) {
 				final Decorator decorator = decoratorIter.next();
 				// Disease Model?
 				if (decorator instanceof StandardDiseaseModel) {
 					final StandardDiseaseModel diseaseModel = (StandardDiseaseModel) decorator;
 					// Is this the one we're looking for?
 					if (diseaseModel.getDiseaseName().equalsIgnoreCase(
 							getDiseaseName())) {
 						// Yes
 						this.diseaseModel = diseaseModel;
 						break;
 					}
 				}
 			} // for each decorator
 		} // if look up disease model

 		// Did we find the disease model we're suppose to work for?
 		if (diseaseModel != null) {
 			// Yes
 			// Now try to find the node to be infected
 			final Node parent = getGraph().getNode(getTargetURI());
 			Set<Node> allNodes = getAllChildren(parent);

 			allNodes.add(parent);
 			Iterator<Node> iter = allNodes.iterator();
 			while(iter!=null && iter.hasNext()) {
 				Node node = iter.next();
 				// Did we find the Node?
 				if (node != null) {
 					// Yes
 					for (final Iterator<NodeLabel> labelIter = node.getLabels().iterator(); labelIter
 							.hasNext();) {
 						final NodeLabel nodeLabel = labelIter.next();
 						// Is this a disease label?
 						if (nodeLabel instanceof DiseaseModelLabel) {
 							final DiseaseModelLabel diseaseModelLabel = (DiseaseModelLabel) nodeLabel;
 							// Yes
 							// Is it updated by this disease model?
 							if (diseaseModelLabel.getDecorator() == diseaseModel) {
 								// Yes
 								doInitialization(diseaseModelLabel);
 								getLabelsToInfect().add(diseaseModelLabel);
 								break;
 							} // if
 						}
 					} // for
 				} // if node to infect was found
 				else {
 					// No
 					// The target URI was probably bad
 					Activator.logError("The node to infect specified by the URI \""
 							+ getTargetURI()
 							+ "\" was not found.  The URI is likely incorrect.",
 							null);
 				} // else node not found
 			}// all NODES

 		} // if disease model found
 		else {
 			// No
 			// The disease name was probably wrong
 			Activator.logError("The disease named \"" + diseaseName
 					+ "\" was not found.", null);
 		} // else node not found

 		this.setProgress(1.0); // we're done
 	} // decorateGraph

 	/**
 	 * @param diseaseModelLabel
 	 *            the disease model label to have its infectious value
 	 *            initialized
 	 */
 	@Override
 	protected void doInitialization(final DiseaseModelLabel diseaseModelLabel) {
 		// The disease model in question must have an R state
 		// if it is not some type of SIR model then we can not inoculate
 		if(diseaseModelLabel instanceof SIRLabel ||
 				diseaseModelLabel instanceof SEIRLabel) {
 			double currentPopulation = diseaseModelLabel.getPopulationLabel().getCurrentPopulationValue().getCount();
 			SIRLabelValue sirValue = null;
 			IntegrationLabel iLabel = null;
 			if(diseaseModelLabel instanceof SIRLabel) {
 				iLabel = (SIRLabel) diseaseModelLabel;
 				sirValue = (SIRLabelValue)iLabel.getCurrentValue();
 			} else if(diseaseModelLabel instanceof SEIRLabel) {
 				iLabel = (SEIRLabel) diseaseModelLabel;
 				sirValue = (SIRLabelValue)iLabel.getCurrentValue();
 			} else {
 				Activator.logError("SIRInoculatorImpl: Unknown or invalid disease model class for innoculation. ClassName= "+diseaseModelLabel.getClass().getName(),null);
 			}

 			double currentSValue = sirValue.getS();
 			double percentTreated = getInoculatedPercentage();
 			if(percentTreated > 100.0) {
 				Activator.logError("InoculatedPercentage must be <= 100%. Was "+percentTreated+" Now resetting to 100%",null);
 				percentTreated = 100.0;
 			}

 			double inoculatedNumber = currentSValue*(percentTreated/100.0);

 			double newSValue = currentSValue - inoculatedNumber;
 			// check for round off errors
 			newSValue = newSValue < 0 ? 0 : newSValue;
 			inoculatedNumber = inoculatedNumber < 0 ? 0 : inoculatedNumber;

 			final double newRValue = sirValue.getR() + inoculatedNumber;

 		    ((SIRLabelValue)iLabel.getCurrentValue()).setS(newSValue);
 			((SIRLabelValue)iLabel.getNextValue()).setS(newSValue);

 			((SIRLabelValue)iLabel.getCurrentValue()).setR(newRValue);
 			((SIRLabelValue)iLabel.getNextValue()).setR(newRValue);

 		}else {
 			// log error
 			Activator.logError("Can not Inoculated an SI diesase model. Disease Model must be SIR. Check compatibility of Innoculaor for Disease Model In scenario ",null);
 		}

 	} // doInitialization


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

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

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	public void setInoculatedPercentage(double newInoculatedPercentage) {
 		double oldInoculatedPercentage = inoculatedPercentage;
 		inoculatedPercentage = newInoculatedPercentage;
 		if (eNotificationRequired())
 			eNotify(new ENotificationImpl(this, Notification.SET, StandardPackage.SIR_INOCULATOR__INOCULATED_PERCENTAGE, oldInoculatedPercentage, inoculatedPercentage));
 	}

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	@Override
 	public Object eGet(int featureID, boolean resolve, boolean coreType) {
 		switch (featureID) {
 			case StandardPackage.SIR_INOCULATOR__INOCULATED_PERCENTAGE:
 				return getInoculatedPercentage();
 		}
 		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.SIR_INOCULATOR__INOCULATED_PERCENTAGE:
 				setInoculatedPercentage((Double)newValue);
 				return;
 		}
 		super.eSet(featureID, newValue);
 	}

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	@Override
 	public void eUnset(int featureID) {
 		switch (featureID) {
 			case StandardPackage.SIR_INOCULATOR__INOCULATED_PERCENTAGE:
 				setInoculatedPercentage(INOCULATED_PERCENTAGE_EDEFAULT);
 				return;
 		}
 		super.eUnset(featureID);
 	}

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	@Override
 	public boolean eIsSet(int featureID) {
 		switch (featureID) {
 			case StandardPackage.SIR_INOCULATOR__INOCULATED_PERCENTAGE:
 				return inoculatedPercentage != INOCULATED_PERCENTAGE_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(" (inoculatedPercentage: "); //$NON-NLS-1$
 		result.append(inoculatedPercentage);
 		result.append(')');
 		return result.toString();
 	}

 } //SIRInoculatorImpl
	package org.eclipse.stem.diseasemodels.standard.impl;

	/*******************************************************************************
	* Copyright (c) 2009 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.util.Iterator;
	import java.util.Set;

	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.Graph;
	import org.eclipse.stem.core.graph.IntegrationLabel;
	import org.eclipse.stem.core.graph.Node;
	import org.eclipse.stem.core.graph.NodeLabel;
	import org.eclipse.stem.core.model.Decorator;
	import org.eclipse.stem.diseasemodels.Activator;
	import org.eclipse.stem.diseasemodels.standard.DiseaseModelLabel;
	import org.eclipse.stem.diseasemodels.standard.SEIRLabel;
	import org.eclipse.stem.diseasemodels.standard.SILabel;
	import org.eclipse.stem.diseasemodels.standard.SILabelValue;
	import org.eclipse.stem.diseasemodels.standard.SIRInoculator;
	import org.eclipse.stem.diseasemodels.standard.SIRLabel;
	import org.eclipse.stem.diseasemodels.standard.SIRLabelValue;
	import org.eclipse.stem.diseasemodels.standard.StandardDiseaseModel;
	import org.eclipse.stem.diseasemodels.standard.StandardPackage;

	/**
	* <!-- begin-user-doc -->
	* An implementation of the model object '<em><b>SIR Inoculator</b></em>'.
	* <!-- end-user-doc -->
	* <p>
	* The following features are implemented:
	* <ul>
	* <li>{@link org.eclipse.stem.diseasemodels.standard.impl.SIRInoculatorImpl#getInoculatedPercentage <em>Inoculated Percentage</em>}</li>
	* </ul>
	* </p>
	*
	* @generated
	*/
	public class SIRInoculatorImpl extends SIInfectorImpl implements SIRInoculator {
	/**
	* The default value of the '{@link #getInoculatedPercentage() <em>Inoculated Percentage</em>}' attribute.
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @see #getInoculatedPercentage()
	* @generated
	* @ordered
	*/
	protected static final double INOCULATED_PERCENTAGE_EDEFAULT = 1.0;

	/**
	* OverrideThe default value of the '{@link #getInfectiousCount() <em>Infectious Count</em>}' attribute.
	* <!-- begin-user-doc --> <!-- end-user-doc -->
	* @see #getInfectiousCount()
	* @generated NOT
	* @ordered
	*/
	protected static final double INFECTIOUS_COUNT_EDEFAULT = 0.0;

	/**
	* The cached value of the '{@link #getInoculatedPercentage() <em>Inoculated Percentage</em>}' attribute.
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @see #getInoculatedPercentage()
	* @generated
	* @ordered
	*/
	protected double inoculatedPercentage = INOCULATED_PERCENTAGE_EDEFAULT;

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	protected SIRInoculatorImpl() {
	super();
	}


	/**
	* For the innoculator, we not only innoculate the present node but every child underneath it
	* @see org.eclipse.stem.core.model.impl.DecoratorImpl#decorateGraph(org.eclipse.stem.core.graph.Graph)
	*/
	@Override
	public void decorateGraph() {

	final Graph graph = getGraph();

	// Do we need to look up the disease model from its name?
	if (diseaseModel == null) {
	// Yes
	// There's a disease model out there with our name on it
	// (maybe)...let's find it
	for (Iterator<Decorator> decoratorIter = graph.getDecorators().iterator(); decoratorIter
	.hasNext();) {
	final Decorator decorator = decoratorIter.next();
	// Disease Model?
	if (decorator instanceof StandardDiseaseModel) {
	final StandardDiseaseModel diseaseModel = (StandardDiseaseModel) decorator;
	// Is this the one we're looking for?
	if (diseaseModel.getDiseaseName().equalsIgnoreCase(
	getDiseaseName())) {
	// Yes
	this.diseaseModel = diseaseModel;
	break;
	}
	}
	} // for each decorator
	} // if look up disease model

	// Did we find the disease model we're suppose to work for?
	if (diseaseModel != null) {
	// Yes
	// Now try to find the node to be infected
	final Node parent = getGraph().getNode(getTargetURI());
	Set<Node> allNodes = getAllChildren(parent);

	allNodes.add(parent);
	Iterator<Node> iter = allNodes.iterator();
	while(iter!=null && iter.hasNext()) {
	Node node = iter.next();
	// Did we find the Node?
	if (node != null) {
	// Yes
	for (final Iterator<NodeLabel> labelIter = node.getLabels().iterator(); labelIter
	.hasNext();) {
	final NodeLabel nodeLabel = labelIter.next();
	// Is this a disease label?
	if (nodeLabel instanceof DiseaseModelLabel) {
	final DiseaseModelLabel diseaseModelLabel = (DiseaseModelLabel) nodeLabel;
	// Yes
	// Is it updated by this disease model?
	if (diseaseModelLabel.getDecorator() == diseaseModel) {
	// Yes
	doInitialization(diseaseModelLabel);
	getLabelsToInfect().add(diseaseModelLabel);
	break;
	} // if
	}
	} // for
	} // if node to infect was found
	else {
	// No
	// The target URI was probably bad
	Activator.logError("The node to infect specified by the URI \""
	+ getTargetURI()
	+ "\" was not found. The URI is likely incorrect.",
	null);
	} // else node not found
	}// all NODES

	} // if disease model found
	else {
	// No
	// The disease name was probably wrong
	Activator.logError("The disease named \"" + diseaseName
	+ "\" was not found.", null);
	} // else node not found

	this.setProgress(1.0); // we're done
	} // decorateGraph

	/**
	* @param diseaseModelLabel
	* the disease model label to have its infectious value
	* initialized
	*/
	@Override
	protected void doInitialization(final DiseaseModelLabel diseaseModelLabel) {
	// The disease model in question must have an R state
	// if it is not some type of SIR model then we can not inoculate
	if(diseaseModelLabel instanceof SIRLabel \|\|
	diseaseModelLabel instanceof SEIRLabel) {
	double currentPopulation = diseaseModelLabel.getPopulationLabel().getCurrentPopulationValue().getCount();
	SIRLabelValue sirValue = null;
	IntegrationLabel iLabel = null;
	if(diseaseModelLabel instanceof SIRLabel) {
	iLabel = (SIRLabel) diseaseModelLabel;
	sirValue = (SIRLabelValue)iLabel.getCurrentValue();
	} else if(diseaseModelLabel instanceof SEIRLabel) {
	iLabel = (SEIRLabel) diseaseModelLabel;
	sirValue = (SIRLabelValue)iLabel.getCurrentValue();
	} else {
	Activator.logError("SIRInoculatorImpl: Unknown or invalid disease model class for innoculation. ClassName= "+diseaseModelLabel.getClass().getName(),null);
	}

	double currentSValue = sirValue.getS();
	double percentTreated = getInoculatedPercentage();
	if(percentTreated > 100.0) {
	Activator.logError("InoculatedPercentage must be <= 100%. Was "+percentTreated+" Now resetting to 100%",null);
	percentTreated = 100.0;
	}

	double inoculatedNumber = currentSValue*(percentTreated/100.0);

	double newSValue = currentSValue - inoculatedNumber;
	// check for round off errors
	newSValue = newSValue < 0 ? 0 : newSValue;
	inoculatedNumber = inoculatedNumber < 0 ? 0 : inoculatedNumber;

	final double newRValue = sirValue.getR() + inoculatedNumber;

	((SIRLabelValue)iLabel.getCurrentValue()).setS(newSValue);
	((SIRLabelValue)iLabel.getNextValue()).setS(newSValue);

	((SIRLabelValue)iLabel.getCurrentValue()).setR(newRValue);
	((SIRLabelValue)iLabel.getNextValue()).setR(newRValue);

	}else {
	// log error
	Activator.logError("Can not Inoculated an SI diesase model. Disease Model must be SIR. Check compatibility of Innoculaor for Disease Model In scenario ",null);
	}

	} // doInitialization


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

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

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	public void setInoculatedPercentage(double newInoculatedPercentage) {
	double oldInoculatedPercentage = inoculatedPercentage;
	inoculatedPercentage = newInoculatedPercentage;
	if (eNotificationRequired())
	eNotify(new ENotificationImpl(this, Notification.SET, StandardPackage.SIR_INOCULATOR__INOCULATED_PERCENTAGE, oldInoculatedPercentage, inoculatedPercentage));
	}

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	@Override
	public Object eGet(int featureID, boolean resolve, boolean coreType) {
	switch (featureID) {
	case StandardPackage.SIR_INOCULATOR__INOCULATED_PERCENTAGE:
	return getInoculatedPercentage();
	}
	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.SIR_INOCULATOR__INOCULATED_PERCENTAGE:
	setInoculatedPercentage((Double)newValue);
	return;
	}
	super.eSet(featureID, newValue);
	}

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	@Override
	public void eUnset(int featureID) {
	switch (featureID) {
	case StandardPackage.SIR_INOCULATOR__INOCULATED_PERCENTAGE:
	setInoculatedPercentage(INOCULATED_PERCENTAGE_EDEFAULT);
	return;
	}
	super.eUnset(featureID);
	}

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	@Override
	public boolean eIsSet(int featureID) {
	switch (featureID) {
	case StandardPackage.SIR_INOCULATOR__INOCULATED_PERCENTAGE:
	return inoculatedPercentage != INOCULATED_PERCENTAGE_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(" (inoculatedPercentage: "); //$NON-NLS-1$
	result.append(inoculatedPercentage);
	result.append(')');
	return result.toString();
	}

	} //SIRInoculatorImpl