models/epidemiology/org.eclipse.stem.diseasemodels.vector/src/org/eclipse/stem/diseasemodels/vector/impl/VectorDiseaseModelImpl.java - gerrit/stem/org.eclipse.stem - Git at Google

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

 /*******************************************************************************
  * 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
  *******************************************************************************/

 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.ecore.EClass;
 import org.eclipse.emf.ecore.impl.ENotificationImpl;
 import org.eclipse.osgi.util.NLS;
 import org.eclipse.stem.core.STEMURI;
 import org.eclipse.stem.core.graph.Graph;
 import org.eclipse.stem.core.graph.NodeLabel;
 import org.eclipse.stem.core.model.Model;
 import org.eclipse.stem.core.model.STEMTime;
 import org.eclipse.stem.core.scenario.ScenarioInitializationException;
 import org.eclipse.stem.diseasemodels.standard.impl.StandardDiseaseModelImpl;
 import org.eclipse.stem.diseasemodels.vector.VectorDiseaseModel;
 import org.eclipse.stem.diseasemodels.vector.VectorPackage;
 import org.eclipse.stem.populationmodels.standard.PopulationModelLabel;
 import org.eclipse.stem.populationmodels.standard.StandardPopulationModel;
 import org.eclipse.stem.populationmodels.standard.impl.StandardFactoryImpl;

 /**
  * <!-- begin-user-doc -->
  * An implementation of the model object '<em><b>Disease Model</b></em>'.
  * <!-- end-user-doc -->
  * <p>
  * The following features are implemented:
  * <ul>
  *   <li>{@link org.eclipse.stem.diseasemodels.vector.impl.VectorDiseaseModelImpl#getVectorPopulationIdentifier <em>Vector Population Identifier</em>}</li>
  * </ul>
  * </p>
  *
  * @generated
  */
 public abstract class VectorDiseaseModelImpl extends StandardDiseaseModelImpl implements VectorDiseaseModel {
 	/**
 	 * The default value of the '{@link #getVectorPopulationIdentifier() <em>Vector Population Identifier</em>}' attribute.
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @see #getVectorPopulationIdentifier()
 	 * @generated
 	 * @ordered
 	 */
 	protected static final String VECTOR_POPULATION_IDENTIFIER_EDEFAULT = "anopheles"; //$NON-NLS-1$

 	/**
 	 * The cached value of the '{@link #getVectorPopulationIdentifier() <em>Vector Population Identifier</em>}' attribute.
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @see #getVectorPopulationIdentifier()
 	 * @generated
 	 * @ordered
 	 */
 	protected String vectorPopulationIdentifier = VECTOR_POPULATION_IDENTIFIER_EDEFAULT;

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

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

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

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	public void setVectorPopulationIdentifier(String newVectorPopulationIdentifier) {
 		String oldVectorPopulationIdentifier = vectorPopulationIdentifier;
 		vectorPopulationIdentifier = newVectorPopulationIdentifier;
 		if (eNotificationRequired())
 			eNotify(new ENotificationImpl(this, Notification.SET, VectorPackage.VECTOR_DISEASE_MODEL__VECTOR_POPULATION_IDENTIFIER, oldVectorPopulationIdentifier, vectorPopulationIdentifier));
 	}

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	@Override
 	public Object eGet(int featureID, boolean resolve, boolean coreType) {
 		switch (featureID) {
 			case VectorPackage.VECTOR_DISEASE_MODEL__VECTOR_POPULATION_IDENTIFIER:
 				return getVectorPopulationIdentifier();
 		}
 		return super.eGet(featureID, resolve, coreType);
 	}

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	@Override
 	public void eSet(int featureID, Object newValue) {
 		switch (featureID) {
 			case VectorPackage.VECTOR_DISEASE_MODEL__VECTOR_POPULATION_IDENTIFIER:
 				setVectorPopulationIdentifier((String)newValue);
 				return;
 		}
 		super.eSet(featureID, newValue);
 	}

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	@Override
 	public void eUnset(int featureID) {
 		switch (featureID) {
 			case VectorPackage.VECTOR_DISEASE_MODEL__VECTOR_POPULATION_IDENTIFIER:
 				setVectorPopulationIdentifier(VECTOR_POPULATION_IDENTIFIER_EDEFAULT);
 				return;
 		}
 		super.eUnset(featureID);
 	}

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	@Override
 	public boolean eIsSet(int featureID) {
 		switch (featureID) {
 			case VectorPackage.VECTOR_DISEASE_MODEL__VECTOR_POPULATION_IDENTIFIER:
 				return VECTOR_POPULATION_IDENTIFIER_EDEFAULT == null ? vectorPopulationIdentifier != null : !VECTOR_POPULATION_IDENTIFIER_EDEFAULT.equals(vectorPopulationIdentifier);
 		}
 		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(" (vectorPopulationIdentifier: "); //$NON-NLS-1$
 		result.append(vectorPopulationIdentifier);
 		result.append(')');
 		return result.toString();
 	}

 	/**
 	 * We need to override to check all population groups
 	 */
 	@Override
 	public void prepare(Model model, STEMTime time) {
 		super.prepare(model, time);

 		boolean found = findPopulationModel(model, this.getVectorPopulationIdentifier());

 		if(!found) {
 			// Create a new standard population model
 			StandardPopulationModel spm = StandardFactoryImpl.eINSTANCE.createStandardPopulationModel();
 			spm.setPopulationIdentifier(this.getVectorPopulationIdentifier());
 			String title = "Auto Generated "+this.getVectorPopulationIdentifier()+" population model"; //$NON-NLS-1$ //$NON-NLS-2$
 			String name = "auto_gen_"+this.getVectorPopulationIdentifier()+"_population_model"; //$NON-NLS-1$ //$NON-NLS-2$
 			spm.setURI(STEMURI.createURI(name+"/"+STEMURI.generateUniquePart())); //$NON-NLS-1$
 			spm.setName(name);
 			spm.getDublinCore().setTitle(title);
 			model.getNodeDecorators().add(0, spm);
 		}
 	}

 	/**
 	 * We need to override this method to return all population model labels for both humans and the vector
 	 *
 	 * @param populationIdentifier
 	 *            the population being labeled
 	 * @param graph
 	 *            the graph to search
 	 * @return the PopulationLabel instances of the graph that match the
 	 *         identifier.
 	 */
 	@Override
 	public EList<PopulationModelLabel> getPopulationModelLabels(
 			String populationIdentifier, Graph graph) throws ScenarioInitializationException {
 		final EList<PopulationModelLabel> retValue = new BasicEList<PopulationModelLabel>();

 		// Iterate through all of the population labels in the graph
 		EList<NodeLabel> labels = graph.getNodeLabelsByTypeURI(
 				PopulationModelLabel.URI_TYPE_DYNAMIC_POPULATION_LABEL);

 		boolean foundHuman = false, foundVector = false;
 		for (NodeLabel pl:labels) {
 			final PopulationModelLabel populationLabel = (PopulationModelLabel) pl;
 			// Is this label for the population we're looking for?
 			boolean keep = false;
 			if(populationLabel.getPopulationIdentifier().equals(populationIdentifier))
 				{keep=true;foundHuman = true;}
 			else if(populationLabel.getPopulationIdentifier().equals(getVectorPopulationIdentifier()))
 				{keep=true;foundVector = true;}

 			if (keep) {
 				// Yes
 				// If there is a problem with the "node uri" of the population
 				// label then it would not have been associated with a node
 				// instance in the graph at this point. This is a problem for
 				// disease models that are trying to label the node (there isn't
 				// one!). So filter out those mistakes here.

 				// Does the population label have an associated node?
 				if (populationLabel.getNode() != null) {
 					// Yes
 					retValue.add(populationLabel);
 				} // if the population label has a node
 			} // if the population we're looking for
 		} // for each population label

 		// If we didn't find both humans and the vector, return an empty list.
 		// This will force a retry creating disease labels after all population model labels have
 		// had time to decorate the graph
 		if(!foundHuman)
 			throw new ScenarioInitializationException(NLS.bind(Messages.HOST_POP_MOD_LABEL_NOT_FOUND, new Object[] {this.getURI().toString(), this.getPopulationIdentifier()}), this, new Exception());
 		if(!foundVector)
 			throw new ScenarioInitializationException(NLS.bind(Messages.VECTOR_POP_MOD_LABEL_NOT_FOUND, new Object[] {this.getURI().toString(), this.getVectorPopulationIdentifier()}),this, new Exception());

 		return retValue;
 	}

 	@Override
 	public EList<String> getAllLabelIdentifiers() {
 		EList<String> identifiers = new BasicEList<String>();

 		identifiers.add(getPopulationIdentifier());
 		identifiers.add(getVectorPopulationIdentifier());

 		return identifiers;
 	}

 } //VectorDiseaseModelImpl
	package org.eclipse.stem.diseasemodels.vector.impl;

	/*******************************************************************************
	* 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
	*******************************************************************************/

	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.ecore.EClass;
	import org.eclipse.emf.ecore.impl.ENotificationImpl;
	import org.eclipse.osgi.util.NLS;
	import org.eclipse.stem.core.STEMURI;
	import org.eclipse.stem.core.graph.Graph;
	import org.eclipse.stem.core.graph.NodeLabel;
	import org.eclipse.stem.core.model.Model;
	import org.eclipse.stem.core.model.STEMTime;
	import org.eclipse.stem.core.scenario.ScenarioInitializationException;
	import org.eclipse.stem.diseasemodels.standard.impl.StandardDiseaseModelImpl;
	import org.eclipse.stem.diseasemodels.vector.VectorDiseaseModel;
	import org.eclipse.stem.diseasemodels.vector.VectorPackage;
	import org.eclipse.stem.populationmodels.standard.PopulationModelLabel;
	import org.eclipse.stem.populationmodels.standard.StandardPopulationModel;
	import org.eclipse.stem.populationmodels.standard.impl.StandardFactoryImpl;

	/**
	* <!-- begin-user-doc -->
	* An implementation of the model object '<em><b>Disease Model</b></em>'.
	* <!-- end-user-doc -->
	* <p>
	* The following features are implemented:
	* <ul>
	* <li>{@link org.eclipse.stem.diseasemodels.vector.impl.VectorDiseaseModelImpl#getVectorPopulationIdentifier <em>Vector Population Identifier</em>}</li>
	* </ul>
	* </p>
	*
	* @generated
	*/
	public abstract class VectorDiseaseModelImpl extends StandardDiseaseModelImpl implements VectorDiseaseModel {
	/**
	* The default value of the '{@link #getVectorPopulationIdentifier() <em>Vector Population Identifier</em>}' attribute.
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @see #getVectorPopulationIdentifier()
	* @generated
	* @ordered
	*/
	protected static final String VECTOR_POPULATION_IDENTIFIER_EDEFAULT = "anopheles"; //$NON-NLS-1$

	/**
	* The cached value of the '{@link #getVectorPopulationIdentifier() <em>Vector Population Identifier</em>}' attribute.
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @see #getVectorPopulationIdentifier()
	* @generated
	* @ordered
	*/
	protected String vectorPopulationIdentifier = VECTOR_POPULATION_IDENTIFIER_EDEFAULT;

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

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

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

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	public void setVectorPopulationIdentifier(String newVectorPopulationIdentifier) {
	String oldVectorPopulationIdentifier = vectorPopulationIdentifier;
	vectorPopulationIdentifier = newVectorPopulationIdentifier;
	if (eNotificationRequired())
	eNotify(new ENotificationImpl(this, Notification.SET, VectorPackage.VECTOR_DISEASE_MODEL__VECTOR_POPULATION_IDENTIFIER, oldVectorPopulationIdentifier, vectorPopulationIdentifier));
	}

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	@Override
	public Object eGet(int featureID, boolean resolve, boolean coreType) {
	switch (featureID) {
	case VectorPackage.VECTOR_DISEASE_MODEL__VECTOR_POPULATION_IDENTIFIER:
	return getVectorPopulationIdentifier();
	}
	return super.eGet(featureID, resolve, coreType);
	}

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	@Override
	public void eSet(int featureID, Object newValue) {
	switch (featureID) {
	case VectorPackage.VECTOR_DISEASE_MODEL__VECTOR_POPULATION_IDENTIFIER:
	setVectorPopulationIdentifier((String)newValue);
	return;
	}
	super.eSet(featureID, newValue);
	}

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	@Override
	public void eUnset(int featureID) {
	switch (featureID) {
	case VectorPackage.VECTOR_DISEASE_MODEL__VECTOR_POPULATION_IDENTIFIER:
	setVectorPopulationIdentifier(VECTOR_POPULATION_IDENTIFIER_EDEFAULT);
	return;
	}
	super.eUnset(featureID);
	}

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	@Override
	public boolean eIsSet(int featureID) {
	switch (featureID) {
	case VectorPackage.VECTOR_DISEASE_MODEL__VECTOR_POPULATION_IDENTIFIER:
	return VECTOR_POPULATION_IDENTIFIER_EDEFAULT == null ? vectorPopulationIdentifier != null : !VECTOR_POPULATION_IDENTIFIER_EDEFAULT.equals(vectorPopulationIdentifier);
	}
	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(" (vectorPopulationIdentifier: "); //$NON-NLS-1$
	result.append(vectorPopulationIdentifier);
	result.append(')');
	return result.toString();
	}

	/**
	* We need to override to check all population groups
	*/
	@Override
	public void prepare(Model model, STEMTime time) {
	super.prepare(model, time);

	boolean found = findPopulationModel(model, this.getVectorPopulationIdentifier());

	if(!found) {
	// Create a new standard population model
	StandardPopulationModel spm = StandardFactoryImpl.eINSTANCE.createStandardPopulationModel();
	spm.setPopulationIdentifier(this.getVectorPopulationIdentifier());
	String title = "Auto Generated "+this.getVectorPopulationIdentifier()+" population model"; //$NON-NLS-1$ //$NON-NLS-2$
	String name = "auto_gen_"+this.getVectorPopulationIdentifier()+"_population_model"; //$NON-NLS-1$ //$NON-NLS-2$
	spm.setURI(STEMURI.createURI(name+"/"+STEMURI.generateUniquePart())); //$NON-NLS-1$
	spm.setName(name);
	spm.getDublinCore().setTitle(title);
	model.getNodeDecorators().add(0, spm);
	}
	}

	/**
	* We need to override this method to return all population model labels for both humans and the vector
	*
	* @param populationIdentifier
	* the population being labeled
	* @param graph
	* the graph to search
	* @return the PopulationLabel instances of the graph that match the
	* identifier.
	*/
	@Override
	public EList<PopulationModelLabel> getPopulationModelLabels(
	String populationIdentifier, Graph graph) throws ScenarioInitializationException {
	final EList<PopulationModelLabel> retValue = new BasicEList<PopulationModelLabel>();

	// Iterate through all of the population labels in the graph
	EList<NodeLabel> labels = graph.getNodeLabelsByTypeURI(
	PopulationModelLabel.URI_TYPE_DYNAMIC_POPULATION_LABEL);

	boolean foundHuman = false, foundVector = false;
	for (NodeLabel pl:labels) {
	final PopulationModelLabel populationLabel = (PopulationModelLabel) pl;
	// Is this label for the population we're looking for?
	boolean keep = false;
	if(populationLabel.getPopulationIdentifier().equals(populationIdentifier))
	{keep=true;foundHuman = true;}
	else if(populationLabel.getPopulationIdentifier().equals(getVectorPopulationIdentifier()))
	{keep=true;foundVector = true;}

	if (keep) {
	// Yes
	// If there is a problem with the "node uri" of the population
	// label then it would not have been associated with a node
	// instance in the graph at this point. This is a problem for
	// disease models that are trying to label the node (there isn't
	// one!). So filter out those mistakes here.

	// Does the population label have an associated node?
	if (populationLabel.getNode() != null) {
	// Yes
	retValue.add(populationLabel);
	} // if the population label has a node
	} // if the population we're looking for
	} // for each population label

	// If we didn't find both humans and the vector, return an empty list.
	// This will force a retry creating disease labels after all population model labels have
	// had time to decorate the graph
	if(!foundHuman)
	throw new ScenarioInitializationException(NLS.bind(Messages.HOST_POP_MOD_LABEL_NOT_FOUND, new Object[] {this.getURI().toString(), this.getPopulationIdentifier()}), this, new Exception());
	if(!foundVector)
	throw new ScenarioInitializationException(NLS.bind(Messages.VECTOR_POP_MOD_LABEL_NOT_FOUND, new Object[] {this.getURI().toString(), this.getVectorPopulationIdentifier()}),this, new Exception());

	return retValue;
	}

	@Override
	public EList<String> getAllLabelIdentifiers() {
	EList<String> identifiers = new BasicEList<String>();

	identifiers.add(getPopulationIdentifier());
	identifiers.add(getVectorPopulationIdentifier());

	return identifiers;
	}

	} //VectorDiseaseModelImpl