models/epidemiology/org.eclipse.stem.diseasemodels/src/org/eclipse/stem/diseasemodels/standard/impl/StandardDiseaseInitializerImpl.java - stem/org.eclipse.stem - Git at Google

 /*******************************************************************************
  * Copyright (c) 2011 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
  *******************************************************************************/

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

 import java.util.Collection;

 import org.eclipse.emf.common.notify.Notification;

 import org.eclipse.emf.common.util.BasicEList;
 import org.eclipse.emf.common.util.EList;
 import org.eclipse.emf.common.util.URI;

 import org.eclipse.emf.ecore.EAttribute;
 import org.eclipse.emf.ecore.EClass;

 import org.eclipse.emf.ecore.impl.ENotificationImpl;

 import org.eclipse.emf.ecore.util.EDataTypeEList;
 import org.eclipse.emf.ecore.util.EDataTypeUniqueEList;

 import org.eclipse.osgi.util.NLS;
 import org.eclipse.stem.core.graph.Graph;
 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.core.model.STEMTime;
 import org.eclipse.stem.core.model.impl.NodeDecoratorImpl;
 import org.eclipse.stem.core.scenario.ScenarioInitializationException;

 import org.eclipse.stem.definitions.LocationUtility;
 import org.eclipse.stem.definitions.nodes.impl.RegionImpl;
 import org.eclipse.stem.diseasemodels.standard.DiseaseModel;
 import org.eclipse.stem.diseasemodels.standard.DiseaseModelLabel;
 import org.eclipse.stem.diseasemodels.standard.DiseaseModelLabelValue;
 import org.eclipse.stem.diseasemodels.standard.StandardDiseaseInitializer;
 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>Disease Initializer</b></em>'.
  * <!-- end-user-doc -->
  * <p>
  * The following features are implemented:
  * <ul>
  *   <li>{@link org.eclipse.stem.diseasemodels.standard.impl.StandardDiseaseInitializerImpl#getTargetISOKey <em>Target ISO Key</em>}</li>
  *   <li>{@link org.eclipse.stem.diseasemodels.standard.impl.StandardDiseaseInitializerImpl#getTargetURI <em>Target URI</em>}</li>
  *   <li>{@link org.eclipse.stem.diseasemodels.standard.impl.StandardDiseaseInitializerImpl#getCompartments <em>Compartments</em>}</li>
  *   <li>{@link org.eclipse.stem.diseasemodels.standard.impl.StandardDiseaseInitializerImpl#getCompartmentValues <em>Compartment Values</em>}</li>
  *   <li>{@link org.eclipse.stem.diseasemodels.standard.impl.StandardDiseaseInitializerImpl#isUseFractions <em>Use Fractions</em>}</li>
  * </ul>
  * </p>
  *
  * @generated
  */
 public class StandardDiseaseInitializerImpl extends DiseaseInitializerImpl implements StandardDiseaseInitializer {

 	/**
 	 * All {@link DiseaseModelLabel}s that are initialized by this
 	 * {@link Initializer}.
 	 */
 	private EList<DiseaseModelLabel> labelsToInitialize;

 	/**
 	 * The default value of the '{@link #getTargetISOKey() <em>Target ISO Key</em>}' attribute.
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @see #getTargetISOKey()
 	 * @generated
 	 * @ordered
 	 */
 	protected static final String TARGET_ISO_KEY_EDEFAULT = null;

 	/**
 	 * The cached value of the '{@link #getTargetISOKey() <em>Target ISO Key</em>}' attribute.
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @see #getTargetISOKey()
 	 * @generated
 	 * @ordered
 	 */
 	protected String targetISOKey = TARGET_ISO_KEY_EDEFAULT;

 	/**
 	 * The default value of the '{@link #getTargetURI() <em>Target URI</em>}' attribute.
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @see #getTargetURI()
 	 * @generated
 	 * @ordered
 	 */
 	protected static final URI TARGET_URI_EDEFAULT = null;

 	/**
 	 * The cached value of the '{@link #getTargetURI() <em>Target URI</em>}' attribute.
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @see #getTargetURI()
 	 * @generated
 	 * @ordered
 	 */
 	protected URI targetURI = TARGET_URI_EDEFAULT;

 	/**
 	 * The cached value of the '{@link #getCompartments() <em>Compartments</em>}' attribute list.
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @see #getCompartments()
 	 * @generated
 	 * @ordered
 	 */
 	protected EList<String> compartments;

 	/**
 	 * The cached value of the '{@link #getCompartmentValues() <em>Compartment Values</em>}' attribute list.
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @see #getCompartmentValues()
 	 * @generated
 	 * @ordered
 	 */
 	protected EList<Double> compartmentValues;

 	/**
 	 * The default value of the '{@link #isUseFractions() <em>Use Fractions</em>}' attribute.
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @see #isUseFractions()
 	 * @generated
 	 * @ordered
 	 */
 	protected static final boolean USE_FRACTIONS_EDEFAULT = false;

 	/**
 	 * The cached value of the '{@link #isUseFractions() <em>Use Fractions</em>}' attribute.
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @see #isUseFractions()
 	 * @generated
 	 * @ordered
 	 */
 	protected boolean useFractions = USE_FRACTIONS_EDEFAULT;

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

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

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	public String getTargetISOKey() {
 		return targetISOKey;
 	}

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	public void setTargetISOKey(String newTargetISOKey) {
 		String oldTargetISOKey = targetISOKey;
 		targetISOKey = newTargetISOKey;
 		if (eNotificationRequired())
 			eNotify(new ENotificationImpl(this, Notification.SET, StandardPackage.STANDARD_DISEASE_INITIALIZER__TARGET_ISO_KEY, oldTargetISOKey, targetISOKey));
 	}

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	public URI getTargetURI() {
 		return targetURI;
 	}

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	public void setTargetURI(URI newTargetURI) {
 		URI oldTargetURI = targetURI;
 		targetURI = newTargetURI;
 		if (eNotificationRequired())
 			eNotify(new ENotificationImpl(this, Notification.SET, StandardPackage.STANDARD_DISEASE_INITIALIZER__TARGET_URI, oldTargetURI, targetURI));
 	}

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	public EList<String> getCompartments() {
 		if (compartments == null) {
 			compartments = new EDataTypeUniqueEList<String>(String.class, this, StandardPackage.STANDARD_DISEASE_INITIALIZER__COMPARTMENTS);
 		}
 		return compartments;
 	}

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	public EList<Double> getCompartmentValues() {
 		if (compartmentValues == null) {
 			compartmentValues = new EDataTypeEList<Double>(Double.class, this, StandardPackage.STANDARD_DISEASE_INITIALIZER__COMPARTMENT_VALUES);
 		}
 		return compartmentValues;
 	}

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	public boolean isUseFractions() {
 		return useFractions;
 	}

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	public void setUseFractions(boolean newUseFractions) {
 		boolean oldUseFractions = useFractions;
 		useFractions = newUseFractions;
 		if (eNotificationRequired())
 			eNotify(new ENotificationImpl(this, Notification.SET, StandardPackage.STANDARD_DISEASE_INITIALIZER__USE_FRACTIONS, oldUseFractions, useFractions));
 	}

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	@Override
 	public Object eGet(int featureID, boolean resolve, boolean coreType) {
 		switch (featureID) {
 			case StandardPackage.STANDARD_DISEASE_INITIALIZER__TARGET_ISO_KEY:
 				return getTargetISOKey();
 			case StandardPackage.STANDARD_DISEASE_INITIALIZER__TARGET_URI:
 				return getTargetURI();
 			case StandardPackage.STANDARD_DISEASE_INITIALIZER__COMPARTMENTS:
 				return getCompartments();
 			case StandardPackage.STANDARD_DISEASE_INITIALIZER__COMPARTMENT_VALUES:
 				return getCompartmentValues();
 			case StandardPackage.STANDARD_DISEASE_INITIALIZER__USE_FRACTIONS:
 				return isUseFractions();
 		}
 		return super.eGet(featureID, resolve, coreType);
 	}

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	@SuppressWarnings("unchecked")
 	@Override
 	public void eSet(int featureID, Object newValue) {
 		switch (featureID) {
 			case StandardPackage.STANDARD_DISEASE_INITIALIZER__TARGET_ISO_KEY:
 				setTargetISOKey((String)newValue);
 				return;
 			case StandardPackage.STANDARD_DISEASE_INITIALIZER__TARGET_URI:
 				setTargetURI((URI)newValue);
 				return;
 			case StandardPackage.STANDARD_DISEASE_INITIALIZER__COMPARTMENTS:
 				getCompartments().clear();
 				getCompartments().addAll((Collection<? extends String>)newValue);
 				return;
 			case StandardPackage.STANDARD_DISEASE_INITIALIZER__COMPARTMENT_VALUES:
 				getCompartmentValues().clear();
 				getCompartmentValues().addAll((Collection<? extends Double>)newValue);
 				return;
 			case StandardPackage.STANDARD_DISEASE_INITIALIZER__USE_FRACTIONS:
 				setUseFractions((Boolean)newValue);
 				return;
 		}
 		super.eSet(featureID, newValue);
 	}

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	@Override
 	public void eUnset(int featureID) {
 		switch (featureID) {
 			case StandardPackage.STANDARD_DISEASE_INITIALIZER__TARGET_ISO_KEY:
 				setTargetISOKey(TARGET_ISO_KEY_EDEFAULT);
 				return;
 			case StandardPackage.STANDARD_DISEASE_INITIALIZER__TARGET_URI:
 				setTargetURI(TARGET_URI_EDEFAULT);
 				return;
 			case StandardPackage.STANDARD_DISEASE_INITIALIZER__COMPARTMENTS:
 				getCompartments().clear();
 				return;
 			case StandardPackage.STANDARD_DISEASE_INITIALIZER__COMPARTMENT_VALUES:
 				getCompartmentValues().clear();
 				return;
 			case StandardPackage.STANDARD_DISEASE_INITIALIZER__USE_FRACTIONS:
 				setUseFractions(USE_FRACTIONS_EDEFAULT);
 				return;
 		}
 		super.eUnset(featureID);
 	}

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	@Override
 	public boolean eIsSet(int featureID) {
 		switch (featureID) {
 			case StandardPackage.STANDARD_DISEASE_INITIALIZER__TARGET_ISO_KEY:
 				return TARGET_ISO_KEY_EDEFAULT == null ? targetISOKey != null : !TARGET_ISO_KEY_EDEFAULT.equals(targetISOKey);
 			case StandardPackage.STANDARD_DISEASE_INITIALIZER__TARGET_URI:
 				return TARGET_URI_EDEFAULT == null ? targetURI != null : !TARGET_URI_EDEFAULT.equals(targetURI);
 			case StandardPackage.STANDARD_DISEASE_INITIALIZER__COMPARTMENTS:
 				return compartments != null && !compartments.isEmpty();
 			case StandardPackage.STANDARD_DISEASE_INITIALIZER__COMPARTMENT_VALUES:
 				return compartmentValues != null && !compartmentValues.isEmpty();
 			case StandardPackage.STANDARD_DISEASE_INITIALIZER__USE_FRACTIONS:
 				return useFractions != USE_FRACTIONS_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(" (targetISOKey: "); //$NON-NLS-1$
 		result.append(targetISOKey);
 		result.append(", targetURI: "); //$NON-NLS-1$
 		result.append(targetURI);
 		result.append(", compartments: "); //$NON-NLS-1$
 		result.append(compartments);
 		result.append(", compartmentValues: "); //$NON-NLS-1$
 		result.append(compartmentValues);
 		result.append(", useFractions: "); //$NON-NLS-1$
 		result.append(useFractions);
 		result.append(')');
 		return result.toString();
 	}

 	@Override
 	public void decorateGraph(STEMTime time) throws ScenarioInitializationException  {
 		if (isGraphDecorated()) {
 			return;
 		}

 		Graph graph = getGraph();
 		DiseaseModel diseaseModel = null;
 		labelsToInitialize = new BasicEList<DiseaseModelLabel>();

 		// Try to find disease model
 		for (Decorator decorator : graph.getDecorators()) {
 			if (decorator instanceof StandardDiseaseModel) {
 				StandardDiseaseModel model = (StandardDiseaseModel) decorator;

 				if (model.getDiseaseName().equals(getDiseaseName())) {
 					diseaseModel = model;
 					break;
 				}
 			}
 		}

 		if (diseaseModel == null) {
 			throw new ScenarioInitializationException(NLS.bind(Messages.INITIALIZER_DISEASE_NOT_FOUND, new Object[] {getDiseaseName(), this.getURI().toString()}), this, new Exception());
 		}

 		URI target = null;

 		if (getTargetURI() != null) {
 			target = getTargetURI();
 		} else if (getTargetISOKey() != null && !getTargetISOKey().isEmpty()) {
 			target = RegionImpl.createRegionNodeURI(getTargetISOKey());
 		}

 		Collection<Node> allNodes;

 		if (target != null) {
 			Node parent = graph.getNode(target);

 			allNodes = LocationUtility.getAllChildren(parent);
 			allNodes.add(parent);
 		} else {
 			// Initialize all nodes since no target is specified
 			allNodes = graph.getNodes().values();
 		}

 		for (Node node : allNodes) {
 			if (node == null) {
 				throw new ScenarioInitializationException(NLS.bind(Messages.INITIALIZER_NODE_NOT_FOUND, new Object[] {target, this.getURI().toString()}), this, new Exception());
 			}

 			// Try to find disease label
 			for (NodeLabel nodeLabel : node.getLabels()) {
 				if (nodeLabel instanceof DiseaseModelLabel) {
 					DiseaseModelLabel diseaseModelLabel = (DiseaseModelLabel) nodeLabel;

 					if (diseaseModelLabel.getDecorator() == diseaseModel
 							&& diseaseModelLabel.getPopulationModelLabel()
 									.getPopulationIdentifier()
 									.equals(this.getPopulationIdentifier())) {
 						doInitialization(diseaseModelLabel);
 						labelsToInitialize.add(diseaseModelLabel);
 						break;
 					}
 				}
 			}
 		}

 		setProgress(1.0);
 		return;
 	}

 	@Override
 	public void resetLabels() throws ScenarioInitializationException {
 		for (DiseaseModelLabel label : labelsToInitialize) {
 			doInitialization(label);
 		}
 	}

 	@SuppressWarnings("boxing")
 	private void doInitialization(DiseaseModelLabel label) throws ScenarioInitializationException {
 		DiseaseModelLabelValue current = (DiseaseModelLabelValue) label
 				.getCurrentValue();
 		double populationCount = current.getPopulationCount();
 		EList<EAttribute> attributes = current.eClass().getEAllAttributes();
 		double populationToInitialize = 0.0;

 		if (!isUseFractions()) {
 			for (double v : getCompartmentValues()) {
 				populationToInitialize += v;
 			}
 		}

 		if (populationToInitialize > populationCount) {
 			throw new ScenarioInitializationException(NLS.bind(Messages.INITIALIZER_INVALID_POPULATION_COUNT, new Object[] {populationToInitialize, populationCount, this.getURI().toString()}), this, new Exception());
 		}

 		for (EAttribute attribute : attributes) {
 			for (int i = 0; i < getCompartments().size(); i++) {
 				if (attribute.getName().equals(getCompartments().get(i))) {
 					if (isUseFractions()) {
 						current.eSet(attribute, getCompartmentValues().get(i)
 								* populationCount);
 					} else {
 						if (getCompartments().get(i).equals("s")) { //$NON-NLS-1$
 							current.eSet(attribute, populationCount
 									- populationToInitialize);
 						} else {
 							current.eSet(attribute,
 									getCompartmentValues().get(i));
 						}
 					}
 				}
 			}
 		}
 	}

 } //StandardDiseaseInitializerImpl
	/*******************************************************************************
	* Copyright (c) 2011 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
	*******************************************************************************/

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

	import java.util.Collection;

	import org.eclipse.emf.common.notify.Notification;

	import org.eclipse.emf.common.util.BasicEList;
	import org.eclipse.emf.common.util.EList;
	import org.eclipse.emf.common.util.URI;

	import org.eclipse.emf.ecore.EAttribute;
	import org.eclipse.emf.ecore.EClass;

	import org.eclipse.emf.ecore.impl.ENotificationImpl;

	import org.eclipse.emf.ecore.util.EDataTypeEList;
	import org.eclipse.emf.ecore.util.EDataTypeUniqueEList;

	import org.eclipse.osgi.util.NLS;
	import org.eclipse.stem.core.graph.Graph;
	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.core.model.STEMTime;
	import org.eclipse.stem.core.model.impl.NodeDecoratorImpl;
	import org.eclipse.stem.core.scenario.ScenarioInitializationException;

	import org.eclipse.stem.definitions.LocationUtility;
	import org.eclipse.stem.definitions.nodes.impl.RegionImpl;
	import org.eclipse.stem.diseasemodels.standard.DiseaseModel;
	import org.eclipse.stem.diseasemodels.standard.DiseaseModelLabel;
	import org.eclipse.stem.diseasemodels.standard.DiseaseModelLabelValue;
	import org.eclipse.stem.diseasemodels.standard.StandardDiseaseInitializer;
	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>Disease Initializer</b></em>'.
	* <!-- end-user-doc -->
	* <p>
	* The following features are implemented:
	* <ul>
	* <li>{@link org.eclipse.stem.diseasemodels.standard.impl.StandardDiseaseInitializerImpl#getTargetISOKey <em>Target ISO Key</em>}</li>
	* <li>{@link org.eclipse.stem.diseasemodels.standard.impl.StandardDiseaseInitializerImpl#getTargetURI <em>Target URI</em>}</li>
	* <li>{@link org.eclipse.stem.diseasemodels.standard.impl.StandardDiseaseInitializerImpl#getCompartments <em>Compartments</em>}</li>
	* <li>{@link org.eclipse.stem.diseasemodels.standard.impl.StandardDiseaseInitializerImpl#getCompartmentValues <em>Compartment Values</em>}</li>
	* <li>{@link org.eclipse.stem.diseasemodels.standard.impl.StandardDiseaseInitializerImpl#isUseFractions <em>Use Fractions</em>}</li>
	* </ul>
	* </p>
	*
	* @generated
	*/
	public class StandardDiseaseInitializerImpl extends DiseaseInitializerImpl implements StandardDiseaseInitializer {

	/**
	* All {@link DiseaseModelLabel}s that are initialized by this
	* {@link Initializer}.
	*/
	private EList<DiseaseModelLabel> labelsToInitialize;

	/**
	* The default value of the '{@link #getTargetISOKey() <em>Target ISO Key</em>}' attribute.
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @see #getTargetISOKey()
	* @generated
	* @ordered
	*/
	protected static final String TARGET_ISO_KEY_EDEFAULT = null;

	/**
	* The cached value of the '{@link #getTargetISOKey() <em>Target ISO Key</em>}' attribute.
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @see #getTargetISOKey()
	* @generated
	* @ordered
	*/
	protected String targetISOKey = TARGET_ISO_KEY_EDEFAULT;

	/**
	* The default value of the '{@link #getTargetURI() <em>Target URI</em>}' attribute.
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @see #getTargetURI()
	* @generated
	* @ordered
	*/
	protected static final URI TARGET_URI_EDEFAULT = null;

	/**
	* The cached value of the '{@link #getTargetURI() <em>Target URI</em>}' attribute.
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @see #getTargetURI()
	* @generated
	* @ordered
	*/
	protected URI targetURI = TARGET_URI_EDEFAULT;

	/**
	* The cached value of the '{@link #getCompartments() <em>Compartments</em>}' attribute list.
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @see #getCompartments()
	* @generated
	* @ordered
	*/
	protected EList<String> compartments;

	/**
	* The cached value of the '{@link #getCompartmentValues() <em>Compartment Values</em>}' attribute list.
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @see #getCompartmentValues()
	* @generated
	* @ordered
	*/
	protected EList<Double> compartmentValues;

	/**
	* The default value of the '{@link #isUseFractions() <em>Use Fractions</em>}' attribute.
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @see #isUseFractions()
	* @generated
	* @ordered
	*/
	protected static final boolean USE_FRACTIONS_EDEFAULT = false;

	/**
	* The cached value of the '{@link #isUseFractions() <em>Use Fractions</em>}' attribute.
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @see #isUseFractions()
	* @generated
	* @ordered
	*/
	protected boolean useFractions = USE_FRACTIONS_EDEFAULT;

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

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

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	public String getTargetISOKey() {
	return targetISOKey;
	}

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	public void setTargetISOKey(String newTargetISOKey) {
	String oldTargetISOKey = targetISOKey;
	targetISOKey = newTargetISOKey;
	if (eNotificationRequired())
	eNotify(new ENotificationImpl(this, Notification.SET, StandardPackage.STANDARD_DISEASE_INITIALIZER__TARGET_ISO_KEY, oldTargetISOKey, targetISOKey));
	}

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	public URI getTargetURI() {
	return targetURI;
	}

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	public void setTargetURI(URI newTargetURI) {
	URI oldTargetURI = targetURI;
	targetURI = newTargetURI;
	if (eNotificationRequired())
	eNotify(new ENotificationImpl(this, Notification.SET, StandardPackage.STANDARD_DISEASE_INITIALIZER__TARGET_URI, oldTargetURI, targetURI));
	}

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	public EList<String> getCompartments() {
	if (compartments == null) {
	compartments = new EDataTypeUniqueEList<String>(String.class, this, StandardPackage.STANDARD_DISEASE_INITIALIZER__COMPARTMENTS);
	}
	return compartments;
	}

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	public EList<Double> getCompartmentValues() {
	if (compartmentValues == null) {
	compartmentValues = new EDataTypeEList<Double>(Double.class, this, StandardPackage.STANDARD_DISEASE_INITIALIZER__COMPARTMENT_VALUES);
	}
	return compartmentValues;
	}

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	public boolean isUseFractions() {
	return useFractions;
	}

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	public void setUseFractions(boolean newUseFractions) {
	boolean oldUseFractions = useFractions;
	useFractions = newUseFractions;
	if (eNotificationRequired())
	eNotify(new ENotificationImpl(this, Notification.SET, StandardPackage.STANDARD_DISEASE_INITIALIZER__USE_FRACTIONS, oldUseFractions, useFractions));
	}

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	@Override
	public Object eGet(int featureID, boolean resolve, boolean coreType) {
	switch (featureID) {
	case StandardPackage.STANDARD_DISEASE_INITIALIZER__TARGET_ISO_KEY:
	return getTargetISOKey();
	case StandardPackage.STANDARD_DISEASE_INITIALIZER__TARGET_URI:
	return getTargetURI();
	case StandardPackage.STANDARD_DISEASE_INITIALIZER__COMPARTMENTS:
	return getCompartments();
	case StandardPackage.STANDARD_DISEASE_INITIALIZER__COMPARTMENT_VALUES:
	return getCompartmentValues();
	case StandardPackage.STANDARD_DISEASE_INITIALIZER__USE_FRACTIONS:
	return isUseFractions();
	}
	return super.eGet(featureID, resolve, coreType);
	}

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	@SuppressWarnings("unchecked")
	@Override
	public void eSet(int featureID, Object newValue) {
	switch (featureID) {
	case StandardPackage.STANDARD_DISEASE_INITIALIZER__TARGET_ISO_KEY:
	setTargetISOKey((String)newValue);
	return;
	case StandardPackage.STANDARD_DISEASE_INITIALIZER__TARGET_URI:
	setTargetURI((URI)newValue);
	return;
	case StandardPackage.STANDARD_DISEASE_INITIALIZER__COMPARTMENTS:
	getCompartments().clear();
	getCompartments().addAll((Collection<? extends String>)newValue);
	return;
	case StandardPackage.STANDARD_DISEASE_INITIALIZER__COMPARTMENT_VALUES:
	getCompartmentValues().clear();
	getCompartmentValues().addAll((Collection<? extends Double>)newValue);
	return;
	case StandardPackage.STANDARD_DISEASE_INITIALIZER__USE_FRACTIONS:
	setUseFractions((Boolean)newValue);
	return;
	}
	super.eSet(featureID, newValue);
	}

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	@Override
	public void eUnset(int featureID) {
	switch (featureID) {
	case StandardPackage.STANDARD_DISEASE_INITIALIZER__TARGET_ISO_KEY:
	setTargetISOKey(TARGET_ISO_KEY_EDEFAULT);
	return;
	case StandardPackage.STANDARD_DISEASE_INITIALIZER__TARGET_URI:
	setTargetURI(TARGET_URI_EDEFAULT);
	return;
	case StandardPackage.STANDARD_DISEASE_INITIALIZER__COMPARTMENTS:
	getCompartments().clear();
	return;
	case StandardPackage.STANDARD_DISEASE_INITIALIZER__COMPARTMENT_VALUES:
	getCompartmentValues().clear();
	return;
	case StandardPackage.STANDARD_DISEASE_INITIALIZER__USE_FRACTIONS:
	setUseFractions(USE_FRACTIONS_EDEFAULT);
	return;
	}
	super.eUnset(featureID);
	}

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	@Override
	public boolean eIsSet(int featureID) {
	switch (featureID) {
	case StandardPackage.STANDARD_DISEASE_INITIALIZER__TARGET_ISO_KEY:
	return TARGET_ISO_KEY_EDEFAULT == null ? targetISOKey != null : !TARGET_ISO_KEY_EDEFAULT.equals(targetISOKey);
	case StandardPackage.STANDARD_DISEASE_INITIALIZER__TARGET_URI:
	return TARGET_URI_EDEFAULT == null ? targetURI != null : !TARGET_URI_EDEFAULT.equals(targetURI);
	case StandardPackage.STANDARD_DISEASE_INITIALIZER__COMPARTMENTS:
	return compartments != null && !compartments.isEmpty();
	case StandardPackage.STANDARD_DISEASE_INITIALIZER__COMPARTMENT_VALUES:
	return compartmentValues != null && !compartmentValues.isEmpty();
	case StandardPackage.STANDARD_DISEASE_INITIALIZER__USE_FRACTIONS:
	return useFractions != USE_FRACTIONS_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(" (targetISOKey: "); //$NON-NLS-1$
	result.append(targetISOKey);
	result.append(", targetURI: "); //$NON-NLS-1$
	result.append(targetURI);
	result.append(", compartments: "); //$NON-NLS-1$
	result.append(compartments);
	result.append(", compartmentValues: "); //$NON-NLS-1$
	result.append(compartmentValues);
	result.append(", useFractions: "); //$NON-NLS-1$
	result.append(useFractions);
	result.append(')');
	return result.toString();
	}

	@Override
	public void decorateGraph(STEMTime time) throws ScenarioInitializationException {
	if (isGraphDecorated()) {
	return;
	}

	Graph graph = getGraph();
	DiseaseModel diseaseModel = null;
	labelsToInitialize = new BasicEList<DiseaseModelLabel>();

	// Try to find disease model
	for (Decorator decorator : graph.getDecorators()) {
	if (decorator instanceof StandardDiseaseModel) {
	StandardDiseaseModel model = (StandardDiseaseModel) decorator;

	if (model.getDiseaseName().equals(getDiseaseName())) {
	diseaseModel = model;
	break;
	}
	}
	}

	if (diseaseModel == null) {
	throw new ScenarioInitializationException(NLS.bind(Messages.INITIALIZER_DISEASE_NOT_FOUND, new Object[] {getDiseaseName(), this.getURI().toString()}), this, new Exception());
	}

	URI target = null;

	if (getTargetURI() != null) {
	target = getTargetURI();
	} else if (getTargetISOKey() != null && !getTargetISOKey().isEmpty()) {
	target = RegionImpl.createRegionNodeURI(getTargetISOKey());
	}

	Collection<Node> allNodes;

	if (target != null) {
	Node parent = graph.getNode(target);

	allNodes = LocationUtility.getAllChildren(parent);
	allNodes.add(parent);
	} else {
	// Initialize all nodes since no target is specified
	allNodes = graph.getNodes().values();
	}

	for (Node node : allNodes) {
	if (node == null) {
	throw new ScenarioInitializationException(NLS.bind(Messages.INITIALIZER_NODE_NOT_FOUND, new Object[] {target, this.getURI().toString()}), this, new Exception());
	}

	// Try to find disease label
	for (NodeLabel nodeLabel : node.getLabels()) {
	if (nodeLabel instanceof DiseaseModelLabel) {
	DiseaseModelLabel diseaseModelLabel = (DiseaseModelLabel) nodeLabel;

	if (diseaseModelLabel.getDecorator() == diseaseModel
	&& diseaseModelLabel.getPopulationModelLabel()
	.getPopulationIdentifier()
	.equals(this.getPopulationIdentifier())) {
	doInitialization(diseaseModelLabel);
	labelsToInitialize.add(diseaseModelLabel);
	break;
	}
	}
	}
	}

	setProgress(1.0);
	return;
	}

	@Override
	public void resetLabels() throws ScenarioInitializationException {
	for (DiseaseModelLabel label : labelsToInitialize) {
	doInitialization(label);
	}
	}

	@SuppressWarnings("boxing")
	private void doInitialization(DiseaseModelLabel label) throws ScenarioInitializationException {
	DiseaseModelLabelValue current = (DiseaseModelLabelValue) label
	.getCurrentValue();
	double populationCount = current.getPopulationCount();
	EList<EAttribute> attributes = current.eClass().getEAllAttributes();
	double populationToInitialize = 0.0;

	if (!isUseFractions()) {
	for (double v : getCompartmentValues()) {
	populationToInitialize += v;
	}
	}

	if (populationToInitialize > populationCount) {
	throw new ScenarioInitializationException(NLS.bind(Messages.INITIALIZER_INVALID_POPULATION_COUNT, new Object[] {populationToInitialize, populationCount, this.getURI().toString()}), this, new Exception());
	}

	for (EAttribute attribute : attributes) {
	for (int i = 0; i < getCompartments().size(); i++) {
	if (attribute.getName().equals(getCompartments().get(i))) {
	if (isUseFractions()) {
	current.eSet(attribute, getCompartmentValues().get(i)
	* populationCount);
	} else {
	if (getCompartments().get(i).equals("s")) { //$NON-NLS-1$
	current.eSet(attribute, populationCount
	- populationToInitialize);
	} else {
	current.eSet(attribute,
	getCompartmentValues().get(i));
	}
	}
	}
	}
	}
	}

	} //StandardDiseaseInitializerImpl