| /******************************************************************************* |
| * Copyright (c) 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018 |
| * IBM Corporation, BfR, and others. |
| * All rights reserved. This program and the accompanying materials |
| * are made available under the terms of the Eclipse Public License v2.0 |
| * which accompanies this distribution, and is available at |
| * https://www.eclipse.org/legal/epl-2.0/ |
| * |
| * Contributors: |
| * IBM Corporation - initial API and implementation and new features |
| * Bundesinstitut für Risikobewertung - Pajek Graph interface, new Veterinary Models |
| *******************************************************************************/ |
| |
| package org.eclipse.stem.analysis.impl; |
| |
| import java.util.ArrayList; |
| import java.util.List; |
| |
| import org.eclipse.emf.common.notify.Notification; |
| import org.eclipse.emf.ecore.EClass; |
| import org.eclipse.emf.ecore.impl.ENotificationImpl; |
| import org.eclipse.emf.ecore.impl.EObjectImpl; |
| import org.eclipse.stem.analysis.AnalysisPackage; |
| import org.eclipse.stem.analysis.ErrorFunction; |
| import org.eclipse.stem.analysis.ErrorResult; |
| import org.eclipse.stem.analysis.ReferenceScenarioDataMap; |
| import org.eclipse.stem.analysis.States; |
| import org.eclipse.stem.analysis.impl.ReferenceScenarioDataMapImpl.ReferenceScenarioDataInstance; |
| |
| /** |
| * <!-- begin-user-doc --> |
| * An implementation of the model object '<em><b>Error Function</b></em>'. |
| * <!-- end-user-doc --> |
| * <p> |
| * The following features are implemented: |
| * </p> |
| * <ul> |
| * <li>{@link org.eclipse.stem.analysis.impl.ErrorFunctionImpl#getReferenceDataCompartment <em>Reference Data Compartment</em>}</li> |
| * <li>{@link org.eclipse.stem.analysis.impl.ErrorFunctionImpl#getComparisonCompartment <em>Comparison Compartment</em>}</li> |
| * </ul> |
| * |
| * @generated |
| */ |
| public class ErrorFunctionImpl extends EObjectImpl implements ErrorFunction { |
| /** |
| * The default value of the '{@link #getReferenceDataCompartment() <em>Reference Data Compartment</em>}' attribute. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @see #getReferenceDataCompartment() |
| * @generated |
| * @ordered |
| */ |
| protected static final String REFERENCE_DATA_COMPARTMENT_EDEFAULT = "Incidence"; |
| /** |
| * The cached value of the '{@link #getReferenceDataCompartment() <em>Reference Data Compartment</em>}' attribute. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @see #getReferenceDataCompartment() |
| * @generated |
| * @ordered |
| */ |
| protected String referenceDataCompartment = REFERENCE_DATA_COMPARTMENT_EDEFAULT; |
| /** |
| * The default value of the '{@link #getComparisonCompartment() <em>Comparison Compartment</em>}' attribute. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @see #getComparisonCompartment() |
| * @generated |
| * @ordered |
| */ |
| protected static final String COMPARISON_COMPARTMENT_EDEFAULT = "Incidence"; |
| /** |
| * The cached value of the '{@link #getComparisonCompartment() <em>Comparison Compartment</em>}' attribute. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @see #getComparisonCompartment() |
| * @generated |
| * @ordered |
| */ |
| protected String comparisonCompartment = COMPARISON_COMPARTMENT_EDEFAULT; |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| protected ErrorFunctionImpl() { |
| super(); |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| @Override |
| protected EClass eStaticClass() { |
| return AnalysisPackage.Literals.ERROR_FUNCTION; |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public String getReferenceDataCompartment() { |
| return referenceDataCompartment; |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public void setReferenceDataCompartment(String newReferenceDataCompartment) { |
| String oldReferenceDataCompartment = referenceDataCompartment; |
| referenceDataCompartment = newReferenceDataCompartment; |
| if (eNotificationRequired()) |
| eNotify(new ENotificationImpl(this, Notification.SET, AnalysisPackage.ERROR_FUNCTION__REFERENCE_DATA_COMPARTMENT, oldReferenceDataCompartment, referenceDataCompartment)); |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public String getComparisonCompartment() { |
| return comparisonCompartment; |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public void setComparisonCompartment(String newComparisonCompartment) { |
| String oldComparisonCompartment = comparisonCompartment; |
| comparisonCompartment = newComparisonCompartment; |
| if (eNotificationRequired()) |
| eNotify(new ENotificationImpl(this, Notification.SET, AnalysisPackage.ERROR_FUNCTION__COMPARISON_COMPARTMENT, oldComparisonCompartment, comparisonCompartment)); |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public ErrorResult calculateError(ReferenceScenarioDataMap reference, ReferenceScenarioDataMap data) { |
| // TODO: implement this method |
| // Ensure that you remove @generated or mark it @generated NOT |
| throw new UnsupportedOperationException(); |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| @Override |
| public Object eGet(int featureID, boolean resolve, boolean coreType) { |
| switch (featureID) { |
| case AnalysisPackage.ERROR_FUNCTION__REFERENCE_DATA_COMPARTMENT: |
| return getReferenceDataCompartment(); |
| case AnalysisPackage.ERROR_FUNCTION__COMPARISON_COMPARTMENT: |
| return getComparisonCompartment(); |
| } |
| return super.eGet(featureID, resolve, coreType); |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| @Override |
| public void eSet(int featureID, Object newValue) { |
| switch (featureID) { |
| case AnalysisPackage.ERROR_FUNCTION__REFERENCE_DATA_COMPARTMENT: |
| setReferenceDataCompartment((String)newValue); |
| return; |
| case AnalysisPackage.ERROR_FUNCTION__COMPARISON_COMPARTMENT: |
| setComparisonCompartment((String)newValue); |
| return; |
| } |
| super.eSet(featureID, newValue); |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| @Override |
| public void eUnset(int featureID) { |
| switch (featureID) { |
| case AnalysisPackage.ERROR_FUNCTION__REFERENCE_DATA_COMPARTMENT: |
| setReferenceDataCompartment(REFERENCE_DATA_COMPARTMENT_EDEFAULT); |
| return; |
| case AnalysisPackage.ERROR_FUNCTION__COMPARISON_COMPARTMENT: |
| setComparisonCompartment(COMPARISON_COMPARTMENT_EDEFAULT); |
| return; |
| } |
| super.eUnset(featureID); |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| @Override |
| public boolean eIsSet(int featureID) { |
| switch (featureID) { |
| case AnalysisPackage.ERROR_FUNCTION__REFERENCE_DATA_COMPARTMENT: |
| return REFERENCE_DATA_COMPARTMENT_EDEFAULT == null ? referenceDataCompartment != null : !REFERENCE_DATA_COMPARTMENT_EDEFAULT.equals(referenceDataCompartment); |
| case AnalysisPackage.ERROR_FUNCTION__COMPARISON_COMPARTMENT: |
| return COMPARISON_COMPARTMENT_EDEFAULT == null ? comparisonCompartment != null : !COMPARISON_COMPARTMENT_EDEFAULT.equals(comparisonCompartment); |
| } |
| return super.eIsSet(featureID); |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| @Override |
| public String toString() { |
| if (eIsProxy()) return super.toString(); |
| |
| StringBuilder result = new StringBuilder(super.toString()); |
| result.append(" (referenceDataCompartment: "); |
| result.append(referenceDataCompartment); |
| result.append(", comparisonCompartment: "); |
| result.append(comparisonCompartment); |
| result.append(')'); |
| return result.toString(); |
| } |
| |
| /** |
| * From the dataMap extract a list of infectious |
| * @param dataMap |
| * @return list of infectious people |
| */ |
| public List<Double> getInfectious(ReferenceScenarioDataInstance dataMap) { |
| |
| List<Double> infectious = dataMap.getItotals(); |
| |
| return infectious; |
| } |
| |
| |
| /** |
| * From the dataMap extract a list of infectious |
| * @param dataMap |
| * @return list of infectious people |
| */ |
| public List<Double> getIncidence(ReferenceScenarioDataInstance dataMap) { |
| final String INCIDENCE = States.statesToFit[States.INCIDENCE]; |
| |
| |
| // MUST exist |
| List<String> incidenceList = dataMap.getData(INCIDENCE); |
| assert(incidenceList!=null); |
| |
| List<Double> infectious = new ArrayList<Double>(); |
| for (int i = 0; i < incidenceList.size(); i ++) { |
| |
| double inf = (new Double(incidenceList.get(i))).doubleValue(); |
| infectious.add(new Double(inf)); |
| } |
| return infectious; |
| } |
| |
| /** |
| * From the dataMap extract a list of infectious |
| * @param dataMap |
| * @return list of infectious people |
| */ |
| public List<Double> getData(String state, ReferenceScenarioDataInstance dataMap) { |
| // MUST exist |
| |
| List<String> incidenceList = dataMap.getData(state); |
| assert(incidenceList!=null); |
| |
| List<Double> infectious = new ArrayList<Double>(); |
| for (int i = 0; i < incidenceList.size(); i ++) { |
| |
| double inf = (new Double(incidenceList.get(i))).doubleValue(); |
| infectious.add(new Double(inf)); |
| } |
| return infectious; |
| } |
| |
| /** |
| * From the dataMap extract a list of infectious |
| * @param dataMap |
| * @return list of infectious people |
| */ |
| public List<Double> getCumData(String state, ReferenceScenarioDataInstance dataMap) { |
| // MUST exist |
| |
| List<String> incidenceList = dataMap.getData(state); |
| assert(incidenceList!=null); |
| |
| List<Double> infectious = new ArrayList<Double>(); |
| for (int i = 0; i < incidenceList.size(); i ++) { |
| |
| double inf = (new Double(incidenceList.get(i))).doubleValue(); |
| infectious.add(new Double(inf)); |
| } |
| |
| List<Double>cumulative = dailyToCum(infectious); |
| return cumulative; |
| } |
| |
| /*** |
| * Getting cumulative values from the daily incidence data |
| * @param dailyValues |
| * @return list of daily cumulative sum |
| */ |
| private List<Double> dailyToCum(List<Double> dailyValues) { |
| List<Double>cumValues = new ArrayList<>(); |
| for(int i=0;i<dailyValues.size();i++){ |
| if(i==0){ |
| cumValues.add(dailyValues.get(i)); |
| }else{ |
| cumValues.add(dailyValues.get(i)+cumValues.get(i-1)); |
| } |
| } |
| return cumValues; |
| } |
| |
| /** |
| * From the dataMap extract a list of death values |
| * @param dataMap |
| * @return list of cumulative death by day |
| */ |
| public List<Double> getDeaths(ReferenceScenarioDataInstance dataMap) { |
| final String DISEASE_DEATHS = States.statesToFit[States.DISEASE_DEATHS]; |
| // MUST exist |
| List<String> deathList = dataMap.getData(DISEASE_DEATHS); |
| //we standardize on disease deaths to be "Disease Deaths" as header of |
| assert(deathList!=null); |
| |
| List<Double> deaths = new ArrayList<Double>(); |
| for (int i = 0; i < deathList.size(); i ++) { |
| |
| double d = (new Double(deathList.get(i))).doubleValue(); |
| deaths.add(new Double(d)); |
| } |
| return deaths; |
| } |
| |
| /** |
| * From the dataMap extract a list of population values |
| * @param dataMap |
| * @return list of infectious people |
| */ |
| public List<Double> getPopulation(ReferenceScenarioDataInstance dataMap) { |
| final String POPULATION = States.statesToFit[States.POPULATION]; |
| |
| |
| // MUST exist |
| List<String> popList = dataMap.getData(POPULATION); |
| // We should standardize on P for population count |
| if(popList == null) popList = dataMap.getData("Population Count"); |
| assert(popList!=null); |
| |
| List<Double> populations = new ArrayList<Double>(); |
| for (int i = 0; i < popList.size(); i ++) { |
| |
| double p = (new Double(popList.get(i))).doubleValue(); |
| populations.add(new Double(p)); |
| } |
| return populations; |
| } |
| |
| } //ErrorFunctionImpl |
