| package name.milesparker.epi; |
| |
| import java.util.ArrayList; |
| import java.util.List; |
| import java.util.Collections; |
| |
| import org.eclipse.core.runtime.IAdapterFactory; |
| import org.eclipse.amp.agf.IGraphicsAdapted; |
| import org.eclipse.amp.agf.IGraphicsAdapter; |
| |
| import org.eclipse.swt.graphics.Color; |
| import org.eclipse.jface.viewers.IColorProvider; |
| |
| import org.ascape.model.Agent; |
| import org.ascape.model.Cell; |
| import org.ascape.model.CellOccupant; |
| import org.ascape.model.HostCell; |
| import org.ascape.model.LocatedAgent; |
| import org.ascape.model.Scape; |
| import org.ascape.model.event.ScapeEvent; |
| import org.ascape.model.rule.Rule; |
| import org.ascape.model.rule.ExecuteThenUpdate; |
| import org.ascape.model.space.CollectionSpace; |
| import org.ascape.model.space.Coordinate; |
| import org.ascape.model.space.Coordinate2DDiscrete; |
| import org.ascape.model.space.Graph; |
| import org.ascape.model.space.Location; |
| import org.ascape.model.space.Singleton; |
| import org.ascape.runtime.NonGraphicRunner; |
| import org.ascape.util.Conditional; |
| import org.ascape.util.data.DataPoint; |
| import org.ascape.util.data.DataPointConcrete; |
| import org.ascape.util.vis.ColorFeature; |
| import org.ascape.util.vis.ColorFeatureConcrete; |
| import org.ascape.view.vis.ChartView; |
| import org.ascape.view.vis.GEFView; |
| import org.ascape.view.vis.GraphView; |
| |
| import org.eclipse.amp.escape.runtime.extension.IAgentChild; |
| |
| /** |
| * <!-- begin-user-doc --> |
| * Individual Java Implementation. |
| * |
| * Generated by AMF for model: Epidemic.metaabm in project: org.eclipse.amp.amf.examples.escape |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public class Individual extends CellOccupant { |
| |
| /** |
| * <!-- begin-user-doc --> |
| * |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| private StatusEnum status = StatusEnum.susceptible; |
| /** |
| * <!-- begin-user-doc --> |
| * |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| private int exposureEndPeriod = 0; |
| /** |
| * <!-- begin-user-doc --> |
| * |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| private int asymptomaticEndPeriod = 0; |
| /** |
| * <!-- begin-user-doc --> |
| * |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| private int outcomePeriod = 0; |
| /** |
| * <!-- begin-user-doc --> |
| * |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| private double contactTransmissionProbability = 0.0; |
| |
| /** |
| * <!-- begin-user-doc --> |
| * |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| private List<IAgentChild> children; |
| |
| /** |
| * <!-- begin-user-doc --> |
| * |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public List<IAgentChild> getChildren() { |
| return children; |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * Constructs a new Individual. |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public Individual() { |
| |
| children = new ArrayList<IAgentChild>(); |
| |
| } |
| //todo, make this a useful value for evaluating compatibility of different versions of generated classes |
| |
| /** |
| * <!-- begin-user-doc --> |
| * |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| private static final long serialVersionUID = 89989998L; |
| |
| /** |
| * <!-- begin-user-doc --> |
| * |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| private static long nextUniqueID; |
| |
| /** |
| * <!-- begin-user-doc --> |
| * |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| private long uniqueID; |
| |
| /** |
| * <!-- begin-user-doc --> |
| * |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public long getUID() { |
| if (uniqueID == 0) { |
| uniqueID = nextUniqueID++; |
| } |
| return uniqueID; |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * Clones the agent, ensuring that a unique id is assigned. |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public Object clone() { |
| try { |
| Individual clone = (Individual) super.clone(); |
| clone.uniqueID = 0; |
| return clone; |
| } catch (Exception e) { |
| throw new RuntimeException("Unexpected cloning exception: " + e); |
| } |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public Epidemic getEpidemic() { |
| return (Epidemic) getScape().getScape(); |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| |
| public void startSimulationAgentChild(int timeStep) { |
| if (timeStep == getRoot().getRunner().getEarliestPeriod()) { |
| for (IAgentChild tmp : children) { |
| tmp.startSimulation(timeStep); |
| } |
| } |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| |
| public void calculateTimeStep(int timeStep) { |
| for (IAgentChild tmp : children) { |
| tmp.calculate(timeStep); |
| } |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * Initialize Location Initialization. Executed once at the beginning of each model run. |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public void initializeLocation() { |
| Object cityLocation = (Object) ((org.ascape.model.space.Discrete) getEpidemic() |
| .getCity().getSpace()).findRandomAvailable(); |
| if (cityLocation != null) { |
| if (getHostScape() != ((Agent) cityLocation).getScape()) { |
| die(); |
| getEpidemic().getIndividualScape().add(this); |
| } |
| moveTo(((HostCell) cityLocation)); |
| } |
| } |
| /** |
| * <!-- begin-user-doc --> |
| * Movement Rule. Executed every period. |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public void movement() { |
| double movementDraw = getRandom().nextDouble(); |
| if ((getStatus() != StatusEnum.dead |
| && movementDraw < getEpidemic().getMovementProbability() |
| && getStatus() != StatusEnum.symptomInfectious && movementDraw < getEpidemic() |
| .getMovementProbability())) { |
| Object neighboringLocation = (Object) ((org.ascape.model.space.Discrete) getEpidemic() |
| .getCity().getSpace()) |
| .findRandomAvailableNeighbor(((org.ascape.model.CellOccupant) this) |
| .getHostCell()); |
| if (neighboringLocation != null) { |
| if (getHostScape() != ((Agent) neighboringLocation).getScape()) { |
| die(); |
| getEpidemic().getIndividualScape().add(this); |
| } |
| moveTo(((HostCell) neighboringLocation)); |
| } |
| } |
| } |
| /** |
| * <!-- begin-user-doc --> |
| * Initialize State Initialization. Executed once at the beginning of each model run. |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public void initializeState() { |
| double infectionDraw = getRandom().nextDouble(); |
| double individualTransmissionRate = randomInRange(getEpidemic() |
| .getMinContactTransmissionProbability(), getEpidemic() |
| .getMaxContactTransmissionProbability()); |
| if (infectionDraw < getEpidemic().getInitialInfectionProbability()) { |
| setStatus(StatusEnum.exposed); |
| } |
| setContactTransmissionProbability(individualTransmissionRate); |
| } |
| /** |
| * <!-- begin-user-doc --> |
| * Transmission Rule. Executed every period. |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public void transmission() { |
| if ((getStatus() == StatusEnum.symptomInfectious || getStatus() == StatusEnum.asymptomInfectious)) { |
| Conditional potentialExposureCondition = new Conditional() { |
| |
| /** |
| * <!-- begin-user-doc --> |
| * |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| private static final long serialVersionUID = 6846144446402098985L; |
| |
| /** |
| * <!-- begin-user-doc --> |
| * |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public boolean meetsCondition(Object potentialExposureCell) { |
| if (potentialExposureCell instanceof Individual) { |
| return true; |
| } else { |
| return false; |
| } |
| } |
| }; |
| Individual potentialExposure = (Individual) ((org.ascape.model.space.Discrete) getEpidemic() |
| .getCity().getSpace()).findRandomNeighbor(this, |
| potentialExposureCondition); |
| if (potentialExposure != null) { |
| if (potentialExposure.getStatus() == StatusEnum.susceptible) { |
| double transmissionDraw = getRandom().nextDouble(); |
| if (transmissionDraw < potentialExposure |
| .getContactTransmissionProbability()) { |
| potentialExposure.setStatus(StatusEnum.exposed); |
| } |
| } |
| } |
| } |
| } |
| /** |
| * <!-- begin-user-doc --> |
| * Progression Rule. Executed every period. |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public void progression() { |
| int currentPeriod = getScape().getPeriod(); |
| if ((getExposureEndPeriod() != getAsymptomaticEndPeriod() && currentPeriod == getExposureEndPeriod())) { |
| setStatus(StatusEnum.asymptomInfectious); |
| } |
| if (currentPeriod == getOutcomePeriod()) { |
| double mortalityDraw = getRandom().nextDouble(); |
| if (mortalityDraw < getEpidemic().getCaseMortalityRate()) { |
| setStatus(StatusEnum.dead); |
| } |
| if (!(mortalityDraw < getEpidemic().getCaseMortalityRate())) { |
| setStatus(StatusEnum.recovered); |
| } |
| } |
| if ((currentPeriod == getExposureEndPeriod() && getExposureEndPeriod() == getAsymptomaticEndPeriod())) { |
| setStatus(StatusEnum.symptomInfectious); |
| } |
| if ((currentPeriod == getAsymptomaticEndPeriod() && getExposureEndPeriod() != getAsymptomaticEndPeriod())) { |
| setStatus(StatusEnum.symptomInfectious); |
| } |
| } |
| /** |
| * <!-- begin-user-doc --> |
| * Watch for changes in Status. |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public void exposure() { |
| if (getStatus() == StatusEnum.exposed) { |
| int exposureNow = getScape().getPeriod(); |
| int exposureLength = randomInRange(getEpidemic() |
| .getMinPeriodExposure(), getEpidemic() |
| .getMaxPeriodExposure()); |
| int endExposure = exposureNow + exposureLength; |
| setExposureEndPeriod(endExposure); |
| int asymptomaticLength = randomInRange(getEpidemic() |
| .getMinPeriodAsymptomInfection(), getEpidemic() |
| .getMaxPeriodAsymptomInfection()); |
| int endAsymptomatic = endExposure + asymptomaticLength; |
| setAsymptomaticEndPeriod(endAsymptomatic); |
| int symptomLength = randomInRange(getEpidemic() |
| .getMinPeriodSymptomInfection(), getEpidemic() |
| .getMaxPeriodSymptomInfection()); |
| int endInfection = endAsymptomatic + symptomLength; |
| setOutcomePeriod(endInfection); |
| } |
| } |
| /** |
| * <!-- begin-user-doc --> |
| * Gets the Status property for Individual. |
| * @return |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public StatusEnum getStatus() { |
| return status; |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * Sets the Status property for Individual. |
| * |
| * @param _status the new Status value |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public void setStatus(StatusEnum _status) { |
| status = _status; |
| exposure(); |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * Gets the Exposure End Period property for Individual. |
| * @return |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public int getExposureEndPeriod() { |
| return exposureEndPeriod; |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * Sets the Exposure End Period property for Individual. |
| * |
| * @param _exposureEndPeriod the new Exposure End Period value |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public void setExposureEndPeriod(int _exposureEndPeriod) { |
| exposureEndPeriod = _exposureEndPeriod; |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * Gets the Asymptomatic End Period property for Individual. |
| * @return |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public int getAsymptomaticEndPeriod() { |
| return asymptomaticEndPeriod; |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * Sets the Asymptomatic End Period property for Individual. |
| * |
| * @param _asymptomaticEndPeriod the new Asymptomatic End Period value |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public void setAsymptomaticEndPeriod(int _asymptomaticEndPeriod) { |
| asymptomaticEndPeriod = _asymptomaticEndPeriod; |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * Gets the Outcome Period property for Individual. |
| * @return |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public int getOutcomePeriod() { |
| return outcomePeriod; |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * Sets the Outcome Period property for Individual. |
| * |
| * @param _outcomePeriod the new Outcome Period value |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public void setOutcomePeriod(int _outcomePeriod) { |
| outcomePeriod = _outcomePeriod; |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * Gets the Contact Transmission Probability property for Individual. |
| * @return |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public double getContactTransmissionProbability() { |
| return contactTransmissionProbability; |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * Sets the Contact Transmission Probability property for Individual. |
| * |
| * @param _contactTransmissionProbability the new Contact Transmission Probability value |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public void setContactTransmissionProbability( |
| double _contactTransmissionProbability) { |
| contactTransmissionProbability = _contactTransmissionProbability; |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public String getName() { |
| if (name == null) { |
| return "Individual " + getUID(); |
| } else { |
| return name; |
| } |
| } |
| } |
