Index

B

Bacterium (C++ class) Bacterium::Bacterium (C++ function), [1], [2], [3] Bacterium::GetIncVal (C++ function)

Bacterium::GetName (C++ function) Bacterium::MakeNew (C++ function) Bacterium::Mutate (C++ function) Bacterium::SetIncVal (C++ function)

E

EfficientHost (C++ class) EfficientHost::EfficientHost (C++ function), [1], [2], [3] EfficientHost::GetEfficiency (C++ function) EfficientHost::GetName (C++ function) EfficientHost::MakeNew (C++ function) EfficientHost::SetEfficiency (C++ function) EfficientSymbiont (C++ class) EfficientSymbiont::AddPoints (C++ function) EfficientSymbiont::EfficientSymbiont (C++ function), [1], [2], [3] EfficientSymbiont::GetEfficiency (C++ function) EfficientSymbiont::GetName (C++ function) EfficientSymbiont::HorizontalTransmission (C++ function) EfficientSymbiont::MakeNew (C++ function)

EfficientSymbiont::Mutate (C++ function) EfficientSymbiont::Reproduce (C++ function) EfficientSymbiont::SetEfficiency (C++ function) EfficientSymbiont::VerticalTransmission (C++ function) EfficientWorld (C++ class) EfficientWorld::CreateDataFiles (C++ function) EfficientWorld::EfficientWorld (C++ function) EfficientWorld::GetEfficiencyDataNode (C++ function) EfficientWorld::Setup (C++ function) EfficientWorld::SetupEfficiencyFile (C++ function) EfficientWorld::SetupHosts (C++ function) EfficientWorld::SetupSymbionts (C++ function) EfficientWorld::~EfficientWorld (C++ function)

H

Host (C++ class) Host::AddPoints (C++ function) Host::AddReproSym (C++ function) Host::AddSymbiont (C++ function) Host::ClearReproSyms (C++ function) Host::ClearSyms (C++ function) Host::DistribResources (C++ function) Host::DistribResToSym (C++ function) Host::GetAge (C++ function) Host::GetDead (C++ function) Host::GetDoEctosymbiosis (C++ function) Host::GetFromPartnerCount (C++ function) Host::GetIntVal (C++ function) Host::GetLocation (C++ function) Host::GetName (C++ function) Host::GetPoints (C++ function) Host::GetReproCount (C++ function) Host::GetReproSymbionts (C++ function) Host::GetResInProcess (C++ function) Host::GetSymbionts (C++ function) Host::GetTag (C++ function) Host::GetTowardsPartnerCount (C++ function) Host::GrowOlder (C++ function) Host::HandleEctosymbiosis (C++ function)

Host::HasSym (C++ function) Host::Host (C++ function), [1], [2], [3] Host::IsHost (C++ function) Host::MakeNew (C++ function) Host::Mutate (C++ function) Host::operator!= (C++ function) Host::operator= (C++ function), [1] Host::operator== (C++ function) Host::Process (C++ function) Host::RemoveSymbiont (C++ function) Host::Reproduce (C++ function) Host::SetAge (C++ function) Host::SetDead (C++ function) Host::SetFromPartnerCount (C++ function) Host::SetIntVal (C++ function) Host::SetLocation (C++ function) Host::SetPoints (C++ function) Host::SetReproCount (C++ function) Host::SetResInProcess (C++ function) Host::SetSymbionts (C++ function) Host::SetTag (C++ function) Host::SetTowardsPartnerCount (C++ function) Host::StealResources (C++ function) Host::SymAllowedIn (C++ function) Host::~Host (C++ function)

L

LysisWorld (C++ class) LysisWorld::CreateDataFiles (C++ function) LysisWorld::GetBurstCountDataNode (C++ function) LysisWorld::GetBurstSizeDataNode (C++ function) LysisWorld::GetCFUDataNode (C++ function) LysisWorld::GetIncorporationDifferenceDataNode (C++ function) LysisWorld::GetInductionChanceDataNode (C++ function) LysisWorld::GetLysisChanceDataNode (C++ function)

LysisWorld::LysisWorld (C++ function) LysisWorld::SetupHostFileColumns (C++ function) LysisWorld::SetupHosts (C++ function) LysisWorld::SetupIncorporationDifferenceFile (C++ function) LysisWorld::SetupInductionChanceFile (C++ function) LysisWorld::SetupLysisChanceFile (C++ function) LysisWorld::SetupSymbionts (C++ function) LysisWorld::~LysisWorld (C++ function)

P

PGGHost (C++ class) PGGHost::AddPool (C++ function) PGGHost::DistribPool (C++ function) PGGHost::DistribResources (C++ function) PGGHost::GetName (C++ function) PGGHost::GetPool (C++ function) PGGHost::MakeNew (C++ function) PGGHost::PGGHost (C++ function), [1], [2] PGGHost::SetPool (C++ function) PGGSymbiont (C++ class) PGGSymbiont::GetDonation (C++ function) PGGSymbiont::GetName (C++ function) PGGSymbiont::MakeNew (C++ function) PGGSymbiont::Mutate (C++ function) PGGSymbiont::operator= (C++ function), [1] PGGSymbiont::PGGSymbiont (C++ function), [1], [2] PGGSymbiont::PrintSym (C++ function) PGGSymbiont::ProcessPool (C++ function) PGGSymbiont::SetDonation (C++ function) PGGWorld (C++ class) PGGWorld::CreateDataFiles (C++ function) PGGWorld::GetPGGDataNode (C++ function) PGGWorld::PGGWorld (C++ function) PGGWorld::SetupHosts (C++ function)

PGGWorld::SetupPGGSymIntValFile (C++ function) PGGWorld::SetupSymbionts (C++ function) PGGWorld::~PGGWorld (C++ function) Phage (C++ class) Phage::GetBurstTimer (C++ function) Phage::GetIncVal (C++ function) Phage::GetInductionChance (C++ function) Phage::GetLysisChance (C++ function) Phage::GetLysogeny (C++ function) Phage::GetName (C++ function) Phage::IncBurstTimer (C++ function) Phage::IsPhage (C++ function) Phage::LysisBurst (C++ function) Phage::LysisStep (C++ function) Phage::MakeNew (C++ function) Phage::Mutate (C++ function) Phage::Phage (C++ function), [1], [2], [3] Phage::Process (C++ function) Phage::ProcessResources (C++ function) Phage::SetBurstTimer (C++ function) Phage::SetIncVal (C++ function) Phage::SetInductionChance (C++ function) Phage::SetLysisChance (C++ function) Phage::UponInjection (C++ function) Phage::VerticalTransmission (C++ function)

S

SymAnimate (C++ class) SymAnimate::DoFrame (C++ function) SymAnimate::drawPetriDish (C++ function) SymAnimate::initializeWorld (C++ function) SymAnimate::matchColor (C++ function) SymAnimate::setButtonStyle (C++ function) SymAnimate::SymAnimate (C++ function) Symbiont (C++ class) Symbiont::AddPoints (C++ function) Symbiont::GetAge (C++ function) Symbiont::GetDead (C++ function) Symbiont::GetFromPartnerCount (C++ function) Symbiont::GetHost (C++ function) Symbiont::GetInfectionChance (C++ function) Symbiont::GetIntVal (C++ function) Symbiont::GetLocation (C++ function) Symbiont::GetName (C++ function) Symbiont::GetPoints (C++ function) Symbiont::GetReproCount (C++ function) Symbiont::GetTag (C++ function) Symbiont::GetTaxon (C++ function) Symbiont::GetTowardsPartnerCount (C++ function) Symbiont::GrowOlder (C++ function) Symbiont::HorizontalTransmission (C++ function) Symbiont::InfectionFails (C++ function) Symbiont::IsHost (C++ function) Symbiont::IsPhage (C++ function) Symbiont::LoseResources (C++ function) Symbiont::MakeNew (C++ function) Symbiont::MeetsVTRequirements (C++ function) Symbiont::Mutate (C++ function) Symbiont::operator= (C++ function), [1] Symbiont::Process (C++ function) Symbiont::ProcessResources (C++ function) Symbiont::Reproduce (C++ function) Symbiont::SetAge (C++ function) Symbiont::SetDead (C++ function) Symbiont::SetFromPartnerCount (C++ function) Symbiont::SetHost (C++ function) Symbiont::SetInfectionChance (C++ function) Symbiont::SetIntVal (C++ function) Symbiont::SetLocation (C++ function) Symbiont::SetPoints (C++ function) Symbiont::SetReproCount (C++ function) Symbiont::SetTag (C++ function) Symbiont::SetTaxon (C++ function) Symbiont::SetTowardsPartnerCount (C++ function) Symbiont::Symbiont (C++ function), [1], [2], [3] Symbiont::UponInjection (C++ function) Symbiont::VerticalTransmission (C++ function) Symbiont::WantsToInfect (C++ function) Symbiont::~Symbiont (C++ function) SymWorld (C++ class) SymWorld::AddOrgAt (C++ function) SymWorld::AddSymToSystematic (C++ function) SymWorld::CleanupGraveyard (C++ function) SymWorld::CreateDataFiles (C++ function) SymWorld::CureHosts (C++ function) SymWorld::DoBirth (C++ function) SymWorld::DoSymDeath (C++ function) SymWorld::ExtractSym (C++ function) SymWorld::GetCalcHostInfoFun (C++ function) SymWorld::GetCalcSymInfoFun (C++ function) SymWorld::GetConfig (C++ function) SymWorld::GetCountFreeSymsDataNode (C++ function) SymWorld::GetCountHostedSymsDataNode (C++ function)

SymWorld::GetDominantInfo (C++ function) SymWorld::GetFreeSymInfectChanceDataNode (C++ function) SymWorld::GetFreeSymIntValDataNode (C++ function) SymWorld::GetGraveyard (C++ function) SymWorld::GetHorizontalTransmissionAttemptCount (C++ function) SymWorld::GetHorizontalTransmissionSizeFailCount (C++ function) SymWorld::GetHorizontalTransmissionSuccessCount (C++ function) SymWorld::GetHorizontalTransmissionTagFailCount (C++ function) SymWorld::GetHostCountDataNode (C++ function) SymWorld::GetHostedSymInfectChanceDataNode (C++ function) SymWorld::GetHostedSymIntValDataNode (C++ function) SymWorld::GetHostFromPartnerRateDataNode (C++ function) SymWorld::GetHostIntValDataNode (C++ function) SymWorld::GetHostReproCountDataNode (C++ function) SymWorld::GetHostSys (C++ function) SymWorld::GetHostTagRichness (C++ function) SymWorld::GetHostTagShannonDiversity (C++ function) SymWorld::GetHostTowardsPartnerRateDataNode (C++ function) SymWorld::GetNeighborHost (C++ function) SymWorld::GetPop (C++ function) SymWorld::GetSymbiontTagRichness (C++ function) SymWorld::GetSymbiontTagShannonDiversity (C++ function) SymWorld::GetSymCountDataNode (C++ function) SymWorld::GetSymFromPartnerRateDataNode (C++ function) SymWorld::GetSymInfectChanceDataNode (C++ function) SymWorld::GetSymIntValDataNode (C++ function) SymWorld::GetSymPop (C++ function) SymWorld::GetSymReproCountDataNode (C++ function) SymWorld::GetSymSys (C++ function) SymWorld::GetSymTowardsPartnerRateDataNode (C++ function) SymWorld::GetTagDistanceDataNode (C++ function) SymWorld::GetTagMetric (C++ function) SymWorld::GetUninfectedHostsDataNode (C++ function) SymWorld::GetVerticalTransmissionAttemptCount (C++ function) SymWorld::GetVerticalTransmissionSuccessCount (C++ function) SymWorld::InjectHost (C++ function) SymWorld::InjectSymbiont (C++ function) SymWorld::IsInboundsPos (C++ function) SymWorld::IsSymPopOccupied (C++ function) SymWorld::MapPhylogenyInteractions (C++ function) SymWorld::MoveFreeSym (C++ function) SymWorld::MoveIntoNewFreeWorldPos (C++ function) SymWorld::OnAnalyzePopulation (C++ function) SymWorld::PullResources (C++ function) SymWorld::Resize (C++ function), [1] SymWorld::RunExperiment (C++ function) SymWorld::SendToGraveyard (C++ function) SymWorld::SetMutationZero (C++ function) SymWorld::SetTagMetric (C++ function) SymWorld::Setup (C++ function) SymWorld::SetupFreeLivingSymFile (C++ function) SymWorld::SetupHostFileColumns (C++ function) SymWorld::SetupHostIntValFile (C++ function) SymWorld::SetupHosts (C++ function) SymWorld::SetupReproHistFile (C++ function) SymWorld::SetupSymbionts (C++ function) SymWorld::SetupSymIntValFile (C++ function) SymWorld::SetupTagDistFile (C++ function) SymWorld::SetupTransmissionFile (C++ function) SymWorld::SetupTransmissionFileColumns (C++ function) SymWorld::SymDoBirth (C++ function) SymWorld::SymWorld (C++ function) SymWorld::Update (C++ function) SymWorld::WillTransmit (C++ function) SymWorld::WriteOrgDumpFile (C++ function) SymWorld::WritePhylogenyFile (C++ function) SymWorld::~SymWorld (C++ function)