org.eclipse.ohf.stem.diseasemodels.standard.impl
Class StochasticSIRDiseaseModelImpl

java.lang.Object
  extended by org.eclipse.emf.common.notify.impl.BasicNotifierImpl
      extended by org.eclipse.emf.ecore.impl.BasicEObjectImpl
          extended by org.eclipse.emf.ecore.impl.EObjectImpl
              extended by org.eclipse.ohf.stem.core.common.impl.IdentifiableImpl
                  extended by org.eclipse.ohf.stem.core.model.impl.DecoratorImpl
                      extended by org.eclipse.ohf.stem.core.model.impl.NodeDecoratorImpl
                          extended by org.eclipse.ohf.stem.diseasemodels.standard.impl.DiseaseModelImpl
                              extended by org.eclipse.ohf.stem.diseasemodels.standard.impl.StandardDiseaseModelImpl
                                  extended by org.eclipse.ohf.stem.diseasemodels.standard.impl.SIImpl
                                      extended by org.eclipse.ohf.stem.diseasemodels.standard.impl.SIRImpl
                                          extended by org.eclipse.ohf.stem.diseasemodels.standard.impl.StochasticSIRDiseaseModelImpl
All Implemented Interfaces:
org.eclipse.emf.common.notify.Notifier, org.eclipse.emf.ecore.EObject, org.eclipse.emf.ecore.InternalEObject, Identifiable, SanityChecker, Decorator, NodeDecorator, DiseaseModel, SI, SIR, StandardDiseaseModel, StandardStochasticDiseaseModel, StochasticDiseaseModel, StochasticSIRDiseaseModel

public class StochasticSIRDiseaseModelImpl
extends SIRImpl
implements StochasticSIRDiseaseModel

An implementation of the model object 'Stochastic SIR Disease Model'.

The following features are implemented:


Nested Class Summary
 
Nested classes/interfaces inherited from class org.eclipse.emf.common.notify.impl.BasicNotifierImpl
org.eclipse.emf.common.notify.impl.BasicNotifierImpl.EAdapterList<E extends java.lang.Object & org.eclipse.emf.common.notify.Adapter>
 
Nested classes/interfaces inherited from interface org.eclipse.emf.ecore.InternalEObject
org.eclipse.emf.ecore.InternalEObject.EStore
 
Field Summary
 
Fields inherited from class org.eclipse.emf.ecore.impl.EObjectImpl
ELAST_EOBJECT_FLAG
 
Fields inherited from interface org.eclipse.ohf.stem.diseasemodels.standard.StochasticSIRDiseaseModel
URI_TYPE_STOCHASTIC_SIR_DISEASE_MODEL_SEGMENT
 
Fields inherited from interface org.eclipse.ohf.stem.diseasemodels.standard.SIR
URI_TYPE_STANDARD_SIR_DISEASE_MODEL, URI_TYPE_STANDARD_SIR_DISEASE_MODEL_SEGMENT
 
Fields inherited from interface org.eclipse.ohf.stem.diseasemodels.standard.SI
URI_TYPE_STANDARD_SI_DISEASE_MODEL_SEGMENT
 
Fields inherited from interface org.eclipse.ohf.stem.diseasemodels.standard.StandardDiseaseModel
URI_TYPE_STANDARD_DISEASEMODEL_SEGMENT
 
Fields inherited from interface org.eclipse.ohf.stem.diseasemodels.standard.DiseaseModel
URI_TYPE_DISEASEMODEL_SEGMENT
 
Fields inherited from interface org.eclipse.emf.ecore.InternalEObject
EOPPOSITE_FEATURE_BASE
 
Constructor Summary
StochasticSIRDiseaseModelImpl()
          The constructor needs to be public so that the new disease wizard can create an instance of the class without using the factory.
 
Method Summary
 double computeNoise()
          By default this calls the static method StandardStochasticDiseaseModelImpl.computeNoise(gain, rand)
static StochasticSIRDiseaseModel createStochasticSIRDiseaseModel(java.lang.String diseaseModelName, double backgroundMortalityRate, double infectiousMortality, double infectiousMortalityRate, double transmissionRate, double recoveryRate, double immunityLossRate, double nonLinearityCoefficient, long timePeriod, java.lang.String populationIdentifier)
           
 int eBaseStructuralFeatureID(int derivedFeatureID, java.lang.Class<?> baseClass)
           
 int eDerivedStructuralFeatureID(int baseFeatureID, java.lang.Class<?> baseClass)
           
 java.lang.Object eGet(int featureID, boolean resolve, boolean coreType)
           
 boolean eIsSet(int featureID)
           
 void eSet(int featureID, java.lang.Object newValue)
           
 void eUnset(int featureID)
           
 double getGain()
           
 java.util.Random getRandomGenerator()
           
 long getSeed()
           
 void setGain(double newGain)
           
 void setSeed(long newSeed)
           
 java.lang.String toString()
           
 
Methods inherited from class org.eclipse.ohf.stem.diseasemodels.standard.impl.SIRImpl
computeDeaths, computeTransitions, createDiseaseModelLabel, createDiseaseModelLabelValue, getAdjustedImmunityLossRate, getImmunityLossRate, sane, setImmunityLossRate
 
Methods inherited from class org.eclipse.ohf.stem.diseasemodels.standard.impl.SIImpl
computeAdditionalInfectious, createDiseaseModelState, createInfector, getAdjustedInfectiousMortalityRate, getAdjustedRecoveryRate, getAdjustedTransmissionRate, getInfectiousMortality, getInfectiousMortalityRate, getNonLinearityCoefficient, getPhysicallyAdjacentInfectious, getPhysicallyAdjacentInfectiousProportion, getRecoveryRate, getTransmissionRate, getTransmissionRateScaleFactor, setInfectiousMortality, setInfectiousMortalityRate, setNonLinearityCoefficient, setPhysicallyAdjacentInfectiousProportion, setRecoveryRate, setTransmissionRate
 
Methods inherited from class org.eclipse.ohf.stem.diseasemodels.standard.impl.StandardDiseaseModelImpl
addToTotalArea, addToTotalPopulationCount, computeBirths, computeTotalPopulationCountReciprocal, getTotalArea, getTotalPopulationCount, getTotalPopulationCountReciprocal, initializeDiseaseState, initializeDiseaseState, resetLabels, setTotalArea, setTotalPopulationCount, updateLabels
 
Methods inherited from class org.eclipse.ohf.stem.diseasemodels.standard.impl.DiseaseModelImpl
decorateGraph, getAdjustedBackgroundMortalityRate, getBackgroundMortalityRate, getDiseaseName, getPopulationIdentifier, getTimePeriod, setBackgroundMortalityRate, setDiseaseName, setPopulationIdentifier, setTimePeriod
 
Methods inherited from class org.eclipse.ohf.stem.core.model.impl.DecoratorImpl
basicSetGraph, eBasicRemoveFromContainerFeature, eInverseAdd, eInverseRemove, getGraph, getLabelsToUpdate, setGraph
 
Methods inherited from class org.eclipse.ohf.stem.core.common.impl.IdentifiableImpl
basicSetDublinCore, getDublinCore, getTypeURI, getURI, setDublinCore, setTypeURI, setURI
 
Methods inherited from class org.eclipse.emf.ecore.impl.EObjectImpl
eAdapters, eClass, eContainerFeatureID, eDeliver, eInternalContainer, eIsProxy, eSetClass, eSetDeliver, eSetProxyURI
 
Methods inherited from class org.eclipse.emf.ecore.impl.BasicEObjectImpl
eAllContents, eBasicRemoveFromContainer, eBasicSetContainer, eContainer, eContainingFeature, eContainmentFeature, eContains, eContents, eCrossReferences, eDerivedStructuralFeatureID, eDirectResource, eDynamicBasicRemoveFromContainer, eDynamicGet, eDynamicGet, eDynamicInverseAdd, eDynamicInverseRemove, eDynamicIsSet, eDynamicIsSet, eDynamicSet, eDynamicSet, eDynamicUnset, eDynamicUnset, eGet, eGet, eGet, eInternalResource, eInverseAdd, eInverseRemove, eIsSet, eObjectForURIFragmentSegment, eOpenGet, eOpenIsSet, eOpenSet, eOpenUnset, eProxyURI, eResolveProxy, eResource, eSet, eSetResource, eSetStore, eSetting, eStore, eUnset, eURIFragmentSegment, eVirtualGet, eVirtualGet, eVirtualIsSet, eVirtualSet, eVirtualUnset
 
Methods inherited from class org.eclipse.emf.common.notify.impl.BasicNotifierImpl
eNotificationRequired, eNotify
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface org.eclipse.ohf.stem.diseasemodels.standard.SIR
getAdjustedImmunityLossRate, getImmunityLossRate, setImmunityLossRate
 
Methods inherited from interface org.eclipse.ohf.stem.diseasemodels.standard.SI
getAdjustedInfectiousMortalityRate, getAdjustedRecoveryRate, getAdjustedTransmissionRate, getInfectiousMortality, getInfectiousMortalityRate, getNonLinearityCoefficient, getPhysicallyAdjacentInfectious, getPhysicallyAdjacentInfectiousProportion, getRecoveryRate, getTransmissionRate, setInfectiousMortality, setInfectiousMortalityRate, setNonLinearityCoefficient, setPhysicallyAdjacentInfectiousProportion, setRecoveryRate, setTransmissionRate
 
Methods inherited from interface org.eclipse.ohf.stem.diseasemodels.standard.StandardDiseaseModel
addToTotalArea, addToTotalPopulationCount, computeTotalPopulationCountReciprocal, getTotalArea, getTotalPopulationCount, getTotalPopulationCountReciprocal, setTotalArea, setTotalPopulationCount
 
Methods inherited from interface org.eclipse.ohf.stem.diseasemodels.standard.DiseaseModel
createDiseaseModelLabel, createDiseaseModelLabelValue, createDiseaseModelState, createInfector, getAdjustedBackgroundMortalityRate, getBackgroundMortalityRate, getDiseaseName, getPopulationIdentifier, getTimePeriod, initializeDiseaseState, initializeDiseaseState, setBackgroundMortalityRate, setDiseaseName, setPopulationIdentifier, setTimePeriod
 
Methods inherited from interface org.eclipse.ohf.stem.core.model.Decorator
decorateGraph, getGraph, getLabelsToUpdate, resetLabels, setGraph, updateLabels
 
Methods inherited from interface org.eclipse.ohf.stem.core.common.Identifiable
getDublinCore, getTypeURI, getURI, sane, setDublinCore, setTypeURI, setURI
 
Methods inherited from interface org.eclipse.emf.ecore.EObject
eAllContents, eClass, eContainer, eContainingFeature, eContainmentFeature, eContents, eCrossReferences, eGet, eGet, eIsProxy, eIsSet, eResource, eSet, eUnset
 
Methods inherited from interface org.eclipse.emf.common.notify.Notifier
eAdapters, eDeliver, eNotify, eSetDeliver
 
Methods inherited from interface org.eclipse.emf.ecore.InternalEObject
eNotificationRequired
 

Constructor Detail

StochasticSIRDiseaseModelImpl

public StochasticSIRDiseaseModelImpl()
The constructor needs to be public so that the new disease wizard can create an instance of the class without using the factory.

Method Detail

createStochasticSIRDiseaseModel

public static final StochasticSIRDiseaseModel createStochasticSIRDiseaseModel(java.lang.String diseaseModelName,
                                                                              double backgroundMortalityRate,
                                                                              double infectiousMortality,
                                                                              double infectiousMortalityRate,
                                                                              double transmissionRate,
                                                                              double recoveryRate,
                                                                              double immunityLossRate,
                                                                              double nonLinearityCoefficient,
                                                                              long timePeriod,
                                                                              java.lang.String populationIdentifier)
Parameters:
diseaseModelName - the name of the disease model
backgroundMortalityRate -
infectiousMortality -
infectiousMortalityRate - the rate at which fatally infectious population members die
transmissionRate -
recoveryRate -
immunityLossRate -
nonLinearityCoefficient -
timePeriod - the time period for the rates (milliseconds)
populationIdentifier - the identifier of the population affected by the disease
Returns:
an initialized instance of DeterministicSIRDiseaseModel

getSeed

public long getSeed()

Specified by:
getSeed in interface StochasticDiseaseModel
Returns:
the seed used to initialize the random number generator.

setSeed

public void setSeed(long newSeed)

Specified by:
setSeed in interface StochasticDiseaseModel
Parameters:
newSeed - the new value of the 'Seed' attribute.
See Also:
StochasticDiseaseModel.getSeed()

getRandomGenerator

public java.util.Random getRandomGenerator()

Specified by:
getRandomGenerator in interface StochasticDiseaseModel

getGain

public double getGain()

Specified by:
getGain in interface StandardStochasticDiseaseModel

setGain

public void setGain(double newGain)

Specified by:
setGain in interface StandardStochasticDiseaseModel
Parameters:
newGain - the new value of the 'Gain' attribute.
See Also:
StandardStochasticDiseaseModel.getGain()

computeNoise

public double computeNoise()
By default this calls the static method StandardStochasticDiseaseModelImpl.computeNoise(gain, rand)

Specified by:
computeNoise in interface StandardStochasticDiseaseModel

eGet

public java.lang.Object eGet(int featureID,
                             boolean resolve,
                             boolean coreType)

Specified by:
eGet in interface org.eclipse.emf.ecore.InternalEObject
Overrides:
eGet in class SIRImpl
Returns:

eSet

public void eSet(int featureID,
                 java.lang.Object newValue)

Specified by:
eSet in interface org.eclipse.emf.ecore.InternalEObject
Overrides:
eSet in class SIRImpl
newValue -

eUnset

public void eUnset(int featureID)

Specified by:
eUnset in interface org.eclipse.emf.ecore.InternalEObject
Overrides:
eUnset in class SIRImpl
Parameters:
featureID -

eIsSet

public boolean eIsSet(int featureID)

Specified by:
eIsSet in interface org.eclipse.emf.ecore.InternalEObject
Overrides:
eIsSet in class SIRImpl
Returns:

eBaseStructuralFeatureID

public int eBaseStructuralFeatureID(int derivedFeatureID,
                                    java.lang.Class<?> baseClass)

Specified by:
eBaseStructuralFeatureID in interface org.eclipse.emf.ecore.InternalEObject
Overrides:
eBaseStructuralFeatureID in class org.eclipse.emf.ecore.impl.BasicEObjectImpl

eDerivedStructuralFeatureID

public int eDerivedStructuralFeatureID(int baseFeatureID,
                                       java.lang.Class<?> baseClass)

Specified by:
eDerivedStructuralFeatureID in interface org.eclipse.emf.ecore.InternalEObject
Overrides:
eDerivedStructuralFeatureID in class org.eclipse.emf.ecore.impl.BasicEObjectImpl

toString

public java.lang.String toString()

Overrides:
toString in class SIRImpl
Returns: