void VectorCohortIndividual::AcquireNewInfection( const IStrainIdentity *infstrain, int incubation_period_override )
{
if ( state != VectorStateEnum::STATE_ADULT )
{
// removing this as a mosquito can be exposed to multiple contagion populations (one for each antigen each time step) throw IllegalOperationException( __FILE__, __LINE__, __FUNCTION__, "Error trying to infect an already infected mosquito." );
}
else
{
progress = 0;
state = VectorStateEnum::STATE_INFECTED;
m_strain = StrainIdentity( infstrain );
}
}
Kernel::StrainIdentity* Outbreak::GetNewStrainIdentity(INodeEventContext *context)
{
StrainIdentity *outbreak_strainID = nullptr;
// Important: Use the instance method to obtain the intervention factory obj instead of static method to cross the DLL boundary
// NO usage of GET_CONFIGURABLE(SimulationConfig)->number_substrains in DLL
IGlobalContext *pGC = nullptr;
const SimulationConfig* simConfigObj = nullptr;
if (s_OK == context->QueryInterface(GET_IID(IGlobalContext), (void**)&pGC))
{
simConfigObj = pGC->GetSimulationConfigObj();
}
if (!simConfigObj)
{
throw GeneralConfigurationException( __FILE__, __LINE__, __FUNCTION__, "The pointer to IInterventionFactory object is not valid (could be DLL specific)" );
}
if (( antigen < 0 ) || ( antigen >= simConfigObj->number_basestrains ))
{
throw IncoherentConfigurationException( __FILE__, __LINE__, __FUNCTION__, "antigen", antigen, "number_basestrains", simConfigObj->number_basestrains );
}
if ( genome < 0 )
{
int ss = simConfigObj->number_substrains;
if (ss & (ss-1))
{
throw GeneralConfigurationException( __FILE__, __LINE__, __FUNCTION__, "Only supporting random genome generation for Number_Substrains as factor of two." );
}
unsigned int BARCODE_BITS = 0;
while(ss >>= 1) ++BARCODE_BITS;
uint32_t genome = context->GetRng()->ul() & ((1 << BARCODE_BITS)-1);
//genome = context->GetRng()->i(simConfigObj->number_substrains);
outbreak_strainID = _new_ StrainIdentity(antigen, genome);
LOG_DEBUG_F("random genome generation... antigen: %d\t genome: %d\n", antigen, genome);
}
void IndividualHumanMalaria::DepositFractionalContagionByStrain(float weight, IVectorInterventionsEffects* ivie, float antigenID, float geneticID)
{
StrainIdentity id = StrainIdentity(antigenID, geneticID);
parent->DepositFromIndividual( &id, weight*ivie->GetblockIndoorVectorTransmit(), &NodeVector::human_to_vector_indoor );
parent->DepositFromIndividual( &id, weight*ivie->GetblockOutdoorVectorTransmit(), &NodeVector::human_to_vector_outdoor );
}
