| 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.HashSet; |
| 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.EStructuralFeature; |
| import org.eclipse.emf.ecore.impl.ENotificationImpl; |
| import org.eclipse.osgi.util.NLS; |
| 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.core.model.NodeDecorator; |
| import org.eclipse.stem.core.model.STEMTime; |
| import org.eclipse.stem.core.scenario.ScenarioInitializationException; |
| import org.eclipse.stem.diseasemodels.Activator; |
| import org.eclipse.stem.diseasemodels.standard.DiseaseModelLabel; |
| import org.eclipse.stem.diseasemodels.standard.InfectorInoculatorCollection; |
| import org.eclipse.stem.diseasemodels.standard.SIRInoculator; |
| import org.eclipse.stem.diseasemodels.standard.StandardDiseaseModel; |
| import org.eclipse.stem.diseasemodels.standard.StandardDiseaseModelLabelValue; |
| import org.eclipse.stem.diseasemodels.standard.StandardPackage; |
| import org.eclipse.stem.definitions.LocationUtility; |
| |
| /** |
| * <!-- 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> |
| * <li>{@link org.eclipse.stem.diseasemodels.standard.impl.SIRInoculatorImpl#isInoculatePercentage <em>Inoculate 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; |
| |
| /** |
| * 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; |
| |
| /** |
| * The default value of the '{@link #isInoculatePercentage() <em>Inoculate Percentage</em>}' attribute. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @see #isInoculatePercentage() |
| * @generated |
| * @ordered |
| */ |
| protected static final boolean INOCULATE_PERCENTAGE_EDEFAULT = true; |
| |
| /** |
| * The cached value of the '{@link #isInoculatePercentage() <em>Inoculate Percentage</em>}' attribute. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @see #isInoculatePercentage() |
| * @generated |
| * @ordered |
| */ |
| protected boolean inoculatePercentage = INOCULATE_PERCENTAGE_EDEFAULT; |
| |
| /** |
| * 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; |
| |
| /** |
| * <!-- 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(STEMTime time) throws ScenarioInitializationException { |
| if(this.isGraphDecorated()) return; |
| Graph graph = getGraph(); |
| if(graph == null && this.eContainer() instanceof InfectorInoculatorCollection) // Might be part of a collection |
| graph = ((NodeDecorator)eContainer()).getGraph(); |
| |
| // Do we need to look up the disease model from its name? |
| if (getDiseaseModel() == 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 |
| setDiseaseModel(diseaseModel); |
| break; |
| } |
| } |
| } // for each decorator |
| } // if look up disease model |
| |
| // Did we find the disease model we're suppose to work for? |
| if (getDiseaseModel() != null) { |
| // Yes |
| // Now try to find the node to be infected |
| final Node parent = graph.getNode(getTargetURI()); |
| Set<Node> allNodes = null; |
| |
| if(this.isInoculatePercentage()) { |
| allNodes = LocationUtility.getAllChildren(parent); |
| allNodes.add(parent); |
| } else { |
| allNodes = new HashSet<Node>(); |
| 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() == getDiseaseModel() && |
| diseaseModelLabel.getPopulationModelLabel().getPopulationIdentifier().equals(getPopulationIdentifier())) { |
| // Yes |
| doInitialization(diseaseModelLabel); |
| getLabelsToInfect().add(diseaseModelLabel); |
| break; |
| } // if |
| } |
| } // for |
| } // if node to infect was found� |
| else { |
| // No |
| // The target URI was probably bad |
| throw new ScenarioInitializationException(NLS.bind(Messages.INF_NODE_NOT_FOUND, new Object[] {getTargetURI(), this.getURI().toString()}), this, new Exception()); |
| } // else node not found |
| }// all NODES |
| |
| } // if disease model found |
| else { |
| // No |
| // The disease name was probably wrong |
| throw new ScenarioInitializationException(NLS.bind(Messages.DISEASE_NOT_FOUND, new Object[] {this.getDiseaseName(), this.getURI().toString()}), this, new Exception()); |
| } // else node not found |
| |
| this.setProgress(1.0); // we're done |
| return; |
| } // decorateGraph |
| |
| /** |
| * @param diseaseModelLabel |
| * the disease model label to have its infectious value |
| * initialized |
| */ |
| @Override |
| protected void doInitialization(final DiseaseModelLabel diseaseModelLabel) throws ScenarioInitializationException{ |
| // The disease model in question must have an R state |
| // if it is not some type of SIR model then we can not inoculate |
| String inoculateFeature = this.getTargetFeature(); |
| // Fix for backwards compatability |
| if(inoculateFeature.equals("i")) inoculateFeature = "r"; //$NON-NLS-1$ //$NON-NLS-2$ |
| |
| EStructuralFeature recoveredFeature = this.findFeature(inoculateFeature, diseaseModelLabel.getCurrentValue()); |
| |
| if(recoveredFeature != null) { |
| // double currentPopulation = diseaseModelLabel.getPopulationLabel().getCurrentPopulationValue().getCount(); |
| StandardDiseaseModelLabelValue value = null; |
| IntegrationLabel iLabel = null; |
| iLabel = (IntegrationLabel)diseaseModelLabel; |
| |
| value = (StandardDiseaseModelLabelValue)iLabel.getCurrentValue(); |
| |
| double currentSValue = value.getS(); |
| double currentPop = value.getPopulationCount(); |
| |
| double treated = getInoculatedPercentage(); |
| |
| if(isInoculatePercentage() && treated > 100.0) { |
| Activator.logError(Messages.WRONG_PERCENT,null); //$NON-NLS-2$ |
| treated = 100.0; |
| } |
| |
| double inoculatedNumber = 0; |
| if(isInoculatePercentage()) |
| inoculatedNumber = currentPop*(treated/100.0); |
| else inoculatedNumber = treated; |
| if(inoculatedNumber > currentSValue) inoculatedNumber = currentSValue; |
| |
| double newSValue = currentSValue - inoculatedNumber; |
| // check for round off errors |
| newSValue = newSValue < 0 ? 0 : newSValue; |
| inoculatedNumber = inoculatedNumber < 0 ? 0 : inoculatedNumber; |
| |
| final double newRValue = (Double)value.eGet(recoveredFeature) + inoculatedNumber; |
| |
| ((StandardDiseaseModelLabelValue)iLabel.getCurrentValue()).setS(newSValue); |
| ((StandardDiseaseModelLabelValue)iLabel.getNextValue()).setS(newSValue); |
| |
| ((StandardDiseaseModelLabelValue)iLabel.getCurrentValue()).eSet(recoveredFeature, newRValue); |
| ((StandardDiseaseModelLabelValue)iLabel.getNextValue()).eSet(recoveredFeature, newRValue); |
| |
| }else { |
| // log error |
| Activator.logError(Messages.CANNOT_INOCULATE,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 |
| */ |
| public boolean isInoculatePercentage() { |
| return inoculatePercentage; |
| } |
| |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public void setInoculatePercentage(boolean newInoculatePercentage) { |
| boolean oldInoculatePercentage = inoculatePercentage; |
| inoculatePercentage = newInoculatePercentage; |
| if (eNotificationRequired()) |
| eNotify(new ENotificationImpl(this, Notification.SET, StandardPackage.SIR_INOCULATOR__INOCULATE_PERCENTAGE, oldInoculatePercentage, inoculatePercentage)); |
| } |
| |
| |
| /** |
| * <!-- 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(); |
| case StandardPackage.SIR_INOCULATOR__INOCULATE_PERCENTAGE: |
| return isInoculatePercentage(); |
| } |
| 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; |
| case StandardPackage.SIR_INOCULATOR__INOCULATE_PERCENTAGE: |
| setInoculatePercentage((Boolean)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; |
| case StandardPackage.SIR_INOCULATOR__INOCULATE_PERCENTAGE: |
| setInoculatePercentage(INOCULATE_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; |
| case StandardPackage.SIR_INOCULATOR__INOCULATE_PERCENTAGE: |
| return inoculatePercentage != INOCULATE_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(", inoculatePercentage: "); //$NON-NLS-1$ |
| result.append(inoculatePercentage); |
| result.append(')'); |
| return result.toString(); |
| } |
| |
| } //SIRInoculatorImpl |
