Library API

Class Hierarchy

• • Class Bacterium
  • Class EfficientHost
  • Class EfficientSymbiont
  • Class EfficientWorld
  • Class Host
  • Class LysisWorld
  • Class Organism
  • Class PGGHost
  • Class PGGSymbiont
  • Class PGGWorld
  • Class Phage
  • Class SymAnimate
  • Class Symbiont
  • Class SymWorld

File Hierarchy

• • Directory source
    • Directory catch
      • File catch.hpp
      • File main.cc
      • File README.md
      • File sanity_check.test.cc
    • Directory mode
      • File DataNodes.h
      • File Host.h
      • File Symbiont.h
      • File SymWorld.h
      • File WorldSetup.cc
    • Directory mode
      • File EfficientHost.h
      • File EfficientSymbiont.h
      • File EfficientWorld.h
      • File EfficientWorldSetup.cc
    • Directory mode
      • File Bacterium.h
      • File LysisWorld.h
      • File LysisWorldSetup.cc
      • File Phage.h
    • Directory native
      • File symbulation_default.cc
      • File symbulation_efficient.cc
      • File symbulation_lysis.cc
      • File symbulation_pgg.cc
    • Directory mode
      • File PGGHost.h
      • File PGGSymbiont.h
      • File PGGWorld.h
      • File PGGWorldSetup.cc
    • Directory test
      • Directory test
        • File DataNodes.test.cc
        • File Host.test.cc
        • File HostSymbiontInteraction.test.cc
        • File HostSymbiontUnitTest.test.cc
        • File Symbiont.test.cc
        • File SymWorld.test.cc
      • Directory test
        • File EfficientDataNodes.test.cc
        • File EfficientHost.test.cc
        • File EfficientSymbiont.test.cc
      • Directory test
        • Directory transmission
          • File hz_mut_rate.test.cc
        • Directory endosymbiosis
          • File res_distribute.test.cc
        • Directory lysogeny
          • File plr.test.cc
        • Directory structure
          • File vt.test.cc
        • File README.md
      • Directory test
        • File Bacterium.test.cc
        • File BacteriumPhageUnitTest.test.cc
        • File LysisDataNodes.test.cc
        • File LysisWorld.test.cc
        • File Phage.test.cc
      • Directory test
        • File PGGDataNodes.test.cc
        • File PGGHost.test.cc
        • File PGGHostPGGSymbiontUnitTest.test.cc
        • File PGGSymbiont.test.cc
        • File PGGWorld.test.cc
      • File end_to_end.test.cc
    • Directory web
      • File symbulation-web.cc
    • File ConfigSetup.h
    • File Organism.h
    • File SymAnimate.h
    • File SymJS.h

Full API

Namespaces

• Namespace std

Classes and Structs

• Class Bacterium
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class EfficientHost
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class EfficientSymbiont
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class EfficientWorld
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class Host
  • Inheritance Relationships
    • Base Type
    • Derived Types
  • Class Documentation

• Class LysisWorld
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class Organism
  • Inheritance Relationships
    • Derived Types
  • Class Documentation

• Class PGGHost
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class PGGSymbiont
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class PGGWorld
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class Phage
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class SymAnimate
  • Inheritance Relationships
    • Base Type
  • Class Documentation

• Class Symbiont
  • Inheritance Relationships
    • Base Type
    • Derived Types
  • Class Documentation

• Class SymWorld
  • Inheritance Relationships
    • Base Type
    • Derived Types
  • Class Documentation

Functions

• Function Cube
  • Function Documentation

• Function efficientWorldSetup
  • Function Documentation

• Function main(int, char *)
  • Function Documentation

• Function main(int, char *)
  • Function Documentation

• Function main(int, char *)
  • Function Documentation

• Function main(int, char *)
  • Function Documentation

• Function main(int, char *)
  • Function Documentation

• Function symbulation_main(int, char *)
  • Function Documentation

• Function symbulation_main(int, char *)
  • Function Documentation

• Function symbulation_main(int, char *)
  • Function Documentation

• Function symbulation_main(int, char *)
  • Function Documentation

• Function symbulation_main(int, char *)
  • Function Documentation

• Function Test
  • Function Documentation

• Function TEST_CASE()
  • Function Documentation

• Function TEST_CASE(“Cubes are computed”)
  • Function Documentation

• Function TEST_CASE(“GetHostCountDataNode”, “”)
  • Function Documentation

• Function TEST_CASE(“GetSymCountDataNode”, “”)
  • Function Documentation

• Function TEST_CASE(“GetCountHostedSymsDataNode”, “”)
  • Function Documentation

• Function TEST_CASE(“GetCountFreeSymsDataNode”, “”)
  • Function Documentation

• Function TEST_CASE(“GetUninfectedHostsDataNode”, “”)
  • Function Documentation

• Function TEST_CASE(“GetSymIntValDataNode”, “”)
  • Function Documentation

• Function TEST_CASE(“GetFreeSymIntValDataNode”, “”)
  • Function Documentation

• Function TEST_CASE(“GetHostedSymIntValDataNode”, “”)
  • Function Documentation

• Function TEST_CASE(“GetHostIntValDataNode”, “”)
  • Function Documentation

• Function TEST_CASE(“GetSymInfectChanceDataNode”, “”)
  • Function Documentation

• Function TEST_CASE(“GetFreeSymInfectChanceDataNode”, “”)
  • Function Documentation

• Function TEST_CASE(“GetHostedSymInfectChanceDataNode”, “”)
  • Function Documentation

• Function TEST_CASE(“Host Constructor”, “”)
  • Function Documentation

• Function TEST_CASE(“Host, GetIntVal”, “”)
  • Function Documentation

• Function TEST_CASE(“, AddPoints, GetPoints”, “”)
  • Function Documentation

• Function TEST_CASE(“, GetResTypes”, “”)
  • Function Documentation

• Function TEST_CASE(“HasSym”, “”)
  • Function Documentation

• Function TEST_CASE(“Host Mutate”, “”)
  • Function Documentation

• Function TEST_CASE(“DistributeResources”, “”)
  • Function Documentation

• Function TEST_CASE(“, GetResInProcess”, “”)
  • Function Documentation

• Function TEST_CASE(“Steal resources unit test”, “”)
  • Function Documentation

• Function TEST_CASE(“GetDoEctosymbiosis”, “”)
  • Function Documentation

• Function TEST_CASE(“Host GrowOlder”, “”)
  • Function Documentation

• Function TEST_CASE(“Host MakeNew”, “”)
  • Function Documentation

• Function TEST_CASE(“Host reproduce”, “”)
  • Function Documentation

• Function TEST_CASE(“Host-Symbiont interactions”, “”)
  • Function Documentation

• Function TEST_CASE(“Symbiont, GetHost”, “”)
  • Function Documentation

• Function TEST_CASE(“Host SetSymbionts”, “”)
  • Function Documentation

• Function TEST_CASE(“Host SymLimit”, “”)
  • Function Documentation

• Function TEST_CASE(“Host AddSymbiont”, “”)
  • Function Documentation

• Function TEST_CASE(“Host, ClearReproSym, GetReproSymbionts”, “”)
  • Function Documentation

• Function TEST_CASE(“Host DistribResources”, “”)
  • Function Documentation

• Function TEST_CASE(“Vertical Transmission of Symbiont”, “”)
  • Function Documentation

• Function TEST_CASE(“HandleEctosymbiosis”)
  • Function Documentation

• Function TEST_CASE(“Symbiont Constructor”, “”)
  • Function Documentation

• Function TEST_CASE(“, GetIntVal”, “”)
  • Function Documentation

• Function TEST_CASE(“, GetInfectionChance”, “”)
  • Function Documentation

• Function TEST_CASE(“, GetPoints”, “”)
  • Function Documentation

• Function TEST_CASE(“Symbiont, GetDead”, “”)
  • Function Documentation

• Function TEST_CASE(“WantsToInfect”, “”)
  • Function Documentation

• Function TEST_CASE(“InfectionFails”, “”)
  • Function Documentation

• Function TEST_CASE(“mutate”, “”)
  • Function Documentation

• Function TEST_CASE(“reproduce”, “”)
  • Function Documentation

• Function TEST_CASE(“Process”, “”)
  • Function Documentation

• Function TEST_CASE(“Symbiont ProcessResources”, “”)
  • Function Documentation

• Function TEST_CASE(“Symbiont GrowOlder”, “”)
  • Function Documentation

• Function TEST_CASE(“Symbiont MakeNew”, “”)
  • Function Documentation

• Function TEST_CASE(“PullResources”, “”)
  • Function Documentation

• Function TEST_CASE(“Vertical Transmission”, “”)
  • Function Documentation

• Function TEST_CASE(“World Capacity”, “”)
  • Function Documentation

• Function TEST_CASE(“Interaction Patterns”, “”)
  • Function Documentation

• Function TEST_CASE(“Hosts injected correctly”, “”)
  • Function Documentation

• Function TEST_CASE(“InjectSymbiont”, “”)
  • Function Documentation

• Function TEST_CASE(“DoBirth”, “”)
  • Function Documentation

• Function TEST_CASE(“SymDoBirth”, “”)
  • Function Documentation

• Function TEST_CASE(“Update without free living symbionts”, “”)
  • Function Documentation

• Function TEST_CASE(“Update with free living symbionts”, “”)
  • Function Documentation

• Function TEST_CASE(“MoveFreeSym”, “”)
  • Function Documentation

• Function TEST_CASE(“ExtractSym”, “”)
  • Function Documentation

• Function TEST_CASE(“MoveIntoNewFreeWorldPos”, “”)
  • Function Documentation

• Function TEST_CASE(“Resize”, “”)
  • Function Documentation

• Function TEST_CASE(“AddOrgAt”, “”)
  • Function Documentation

• Function TEST_CASE(“GetSymAt”, “”)
  • Function Documentation

• Function TEST_CASE(“DoSymDeath”, “”)
  • Function Documentation

• Function TEST_CASE(“Spatial structure”, “”)
  • Function Documentation

• Function TEST_CASE(“Host Phylogeny”, “”)
  • Function Documentation

• Function TEST_CASE(“Symbiont Phylogeny”, “”)
  • Function Documentation

• Function TEST_CASE(“SetMutationZero”, “”)
  • Function Documentation

• Function TEST_CASE(“No mutation updates”, ” “)
  • Function Documentation

• Function TEST_CASE(“GetEfficiencyDataNode”, “”)
  • Function Documentation

• Function TEST_CASE(“EfficientHost Constructor”, “”)
  • Function Documentation

• Function TEST_CASE(“EfficientHost MakeNew”, “”)
  • Function Documentation

• Function TEST_CASE(“EfficientHost SetEfficiency and GetEfficiency”, “”)
  • Function Documentation

• Function TEST_CASE(“EfficientSymbiont Constructor”, “”)
  • Function Documentation

• Function TEST_CASE(“EfficientSymbiont Mutate”, “”)
  • Function Documentation

• Function TEST_CASE(“EfficientSymbiont AddPoints”, “”)
  • Function Documentation

• Function TEST_CASE(“INT_VAL_MUT_RATE”, “”)
  • Function Documentation

• Function TEST_CASE(“EfficientSymbiont Reproduce”, “”)
  • Function Documentation

• Function TEST_CASE(“EfficientSymbiont HorizMutate”, “”)
  • Function Documentation

• Function TEST_CASE(“EfficientSymbiont Mutate with horizontal transmission”, “”)
  • Function Documentation

• Function TEST_CASE(“EfficientSymbiont Mutate with vertical transmission”, “”)
  • Function Documentation

• Function TEST_CASE(“EfficientSymbiont’s Process called from Host when mutation rate and size are zero”, “”)
  • Function Documentation

• Function TEST_CASE(“EfficientSymbiont MakeNew”, “”)
  • Function Documentation

• Function TEST_CASE(“EfficientSymbiont SetEfficiency and GetEfficiency”, “”)
  • Function Documentation

• Function TEST_CASE(“EfficientSymbiont VerticalTransmission”, “”)
  • Function Documentation

• Function TEST_CASE(“End To End”)
  • Function Documentation

• Function TEST_CASE(“Horizontal Mutation Rate Results”, “”)
  • Function Documentation

• Function TEST_CASE(“Resource Distribution Results”, “”)
  • Function Documentation

• Function TEST_CASE(“Prophage Loss Rate Results”, “”)
  • Function Documentation

• Function TEST_CASE(“Vertical Transmission Results”, “”)
  • Function Documentation

• Function TEST_CASE(“Bacterium, host_incorporation_val”, “”)
  • Function Documentation

• Function TEST_CASE(“Bacterium, GetIncVal”, “”)
  • Function Documentation

• Function TEST_CASE(“Bacterium mutate”, “”)
  • Function Documentation

• Function TEST_CASE(“ProcessLysogenResources”, “”)
  • Function Documentation

• Function TEST_CASE(“Bacterium Process”, “”)
  • Function Documentation

• Function TEST_CASE(“Phage Exclude”, “”)
  • Function Documentation

• Function TEST_CASE(“Bacterium MakeNew”, “”)
  • Function Documentation

• Function TEST_CASE(“Bacterium reproduce”, “”)
  • Function Documentation

• Function TEST_CASE(“Phage Process”, “”)
  • Function Documentation

• Function TEST_CASE(“Phage Vertical Transmission”, “”)
  • Function Documentation

• Function TEST_CASE(“Host phage death and removal from syms list”, “”)
  • Function Documentation

• Function TEST_CASE(“Phage LysisBurst”, “”)
  • Function Documentation

• Function TEST_CASE(“Phage LysisStep”, “”)
  • Function Documentation

• Function TEST_CASE(“Phage overwrites Symbiont ProcessResources”, “”)
  • Function Documentation

• Function TEST_CASE(“GetCFUDataNode”, “”)
  • Function Documentation

• Function TEST_CASE(“GetLysisChanceDataNode”, “”)
  • Function Documentation

• Function TEST_CASE(“GetInductionChanceDataNode”, “”)
  • Function Documentation

• Function TEST_CASE(“GetBurstSizeDataNode”, “”)
  • Function Documentation

• Function TEST_CASE(“GetBurstCountDataNode”, “”)
  • Function Documentation

• Function TEST_CASE(“GetIncorporationDifferenceDataNode”, “”)
  • Function Documentation

• Function TEST_CASE(“Lysis mode Update()”, “lysis”)
  • Function Documentation

• Function TEST_CASE(“Phage, GetIntVal”, “”)
  • Function Documentation

• Function TEST_CASE(“Phage Reproduce”, “”)
  • Function Documentation

• Function TEST_CASE(“, IncBurstTimer”, “”)
  • Function Documentation

• Function TEST_CASE(“Phage, GetLysisChance”, “”)
  • Function Documentation

• Function TEST_CASE(“Phage, GetInductionChance”, “”)
  • Function Documentation

• Function TEST_CASE(“Phage, GetIncVal”, “”)
  • Function Documentation

• Function TEST_CASE(“Phage UponInjection”, “”)
  • Function Documentation

• Function TEST_CASE(“Phage Mutate”, “”)
  • Function Documentation

• Function TEST_CASE(“Phage process”, “”)
  • Function Documentation

• Function TEST_CASE(“Phage ProcessResources”, “”)
  • Function Documentation

• Function TEST_CASE(“Phage MakeNew”, “”)
  • Function Documentation

• Function TEST_CASE(“GetPGGDataNode”, “”)
  • Function Documentation

• Function TEST_CASE(“PGGHost constructor”, “”)
  • Function Documentation

• Function TEST_CASE(“PGGHost get pool”, “”)
  • Function Documentation

• Function TEST_CASE(“PGGHost DistributeResources”, “”)
  • Function Documentation

• Function TEST_CASE(“PGGHost MakeNew”, “”)
  • Function Documentation

• Function TEST_CASE(“PGGSymbiont, GetHost”, “”)
  • Function Documentation

• Function TEST_CASE(“PGGHost DistribResources”, “”)
  • Function Documentation

• Function TEST_CASE(“PGGVertical Transmission of Symbiont”, “”)
  • Function Documentation

• Function TEST_CASE(“PGGSymbiont PGGHost Pool Interaction”, “”)
  • Function Documentation

• Function TEST_CASE(“PGGSym Dead and Removal”, “”)
  • Function Documentation

• Function TEST_CASE(“PGGSymbiont Constructor”, “”)
  • Function Documentation

• Function TEST_CASE(“PGGmutate”, “”)
  • Function Documentation

• Function TEST_CASE(“PGGSymbiont ProcessPool”, “”)
  • Function Documentation

• Function TEST_CASE(“PGGProcess”, “”)
  • Function Documentation

• Function TEST_CASE(“PGGSymbiont ProcessResources”, “”)
  • Function Documentation

• Function TEST_CASE(“PGGSymbiont MakeNew”, “”)
  • Function Documentation

• Function TEST_CASE(“PGG Interaction Patterns”, “”)
  • Function Documentation

• Function worldSetup(emp::Ptr<SymWorld>, emp::Ptr<SymConfigBase>)
  • Function Documentation

• Function worldSetup(emp::Ptr<LysisWorld>, emp::Ptr<SymConfigBase>)
  • Function Documentation

• Function worldSetup(emp::Ptr<PGGWorld>, emp::Ptr<SymConfigBase>)
  • Function Documentation

Variables

• Variable anim
  • Variable Documentation

• Variable config
  • Variable Documentation

Defines

• Define CATCH_CONFIG_MAIN
  • Define Documentation

• Define EFFWORLD_SETUP_C
  • Define Documentation

• Define LYSIS_WORLD_SETUP_C
  • Define Documentation

• Define PGG_WORLD_SETUP_C
  • Define Documentation

• Define WORLD_SETUP_C
  • Define Documentation