TissueConfig Class Reference
#include <TissueConfig.hpp>
Detailed Description
A special singleton class which holds all of the parameters used in the cancer simulations.Because this is a singleton class it can be called from whichever part of the code needs to find out a parameter value, the structure is quite simple with default values given upon initialisation and Set() and Get() methods for each parameter.
For details of each parameter refer to the member variable documentation for this class rather than the Get() and Set() function descriptions.
Definition at line 45 of file TissueConfig.hpp.
Constructor & Destructor Documentation
| TissueConfig::TissueConfig | ( | ) | [protected] |
Default constructor.
Definition at line 41 of file TissueConfig.cpp.
References mpInstance, and Reset().
| TissueConfig::TissueConfig | ( | const TissueConfig & | ) | [protected] |
Copy constructor.
Member Function Documentation
| TissueConfig * TissueConfig::Instance | ( | ) | [static] |
Call this method to access the global parameters holder.
- Returns:
- a single instance of the class
Definition at line 32 of file TissueConfig.cpp.
References mpInstance.
Referenced by TissueSimulation< DIM >::CalculateDividingCellCentreLocations(), CryptSimulation2d::CalculateDividingCellCentreLocations(), MeshBasedTissueWithGhostNodes< DIM >::CalculateForceBetweenNodes(), GeneralisedLinearSpringForce< DIM >::CalculateForceBetweenNodes(), CryptStatistics::CellIsInSectionPeriodic(), MeshBasedTissue< DIM >::CloseOutputFiles(), AbstractTissue< DIM >::CloseOutputFiles(), MeshBasedTissue< DIM >::CreateOutputFiles(), AbstractTissue< DIM >::CreateOutputFiles(), AbstractTissue< DIM >::GenerateCellResults(), AbstractTissue< DIM >::GetCellCyclePhaseCount(), AbstractTissue< DIM >::GetCellMutationStateCount(), AbstractTissue< DIM >::GetCellTypeCount(), CryptStatistics::GetCryptSection(), AbstractTwoBodyInteractionForce< DIM >::GetCutoffPoint(), MeshBasedTissue< DIM >::GetDampingConstant(), AbstractCellCentreBasedTissue< DIM >::GetDampingConstant(), AbstractCellCycleModel::GetG2Duration(), AbstractCellCycleModel::GetMDuration(), AbstractCellCycleModel::GetSDuration(), StochasticDurationGenerationBasedCellCycleModelCellsGenerator< DIM >::GetTypicalStemCellCycleTime(), SimpleWntCellCycleModelCellsGenerator< DIM >::GetTypicalStemCellCycleTime(), FixedDurationGenerationBasedCellCycleModelCellsGenerator< DIM >::GetTypicalStemCellCycleTime(), StochasticDurationGenerationBasedCellCycleModelCellsGenerator< DIM >::GetTypicalTransitCellCycleTime(), SimpleWntCellCycleModelCellsGenerator< DIM >::GetTypicalTransitCellCycleTime(), FixedDurationGenerationBasedCellCycleModelCellsGenerator< DIM >::GetTypicalTransitCellCycleTime(), WntConcentration< DIM >::GetWntGradient(), WntConcentration< DIM >::GetWntLevel(), HoneycombMeshGenerator::HoneycombMeshGenerator(), AbstractSimpleGenerationBasedCellCycleModel::InitialiseDaughterCell(), AbstractSimpleGenerationBasedCellCycleModel::ResetForDivision(), AbstractForce< DIM >::serialize(), SloughingCellKiller< DIM >::serialize(), WntConcentration< DIM >::serialize(), AbstractCellCycleModel::serialize(), TissueSimulation< 2 >::serialize(), SimpleWntCellCycleModel::SetG1Duration(), AbstractSimpleCellCycleModel::SetG1Duration(), StochasticWntCellCycleModel::SetG2Duration(), AbstractCancerTestSuite::setUp(), TissueCell::StartApoptosis(), SloughingCellKiller< DIM >::TestAndLabelCellsForApoptosisOrDeath(), TissueSimulation< DIM >::TissueSimulation(), NodeBasedTissue< DIM >::Update(), MeshBasedTissue< DIM >::Update(), SimpleWntCellCycleModel::UpdateCellCyclePhase(), MeshBasedTissueWithGhostNodes< DIM >::UpdateGhostPositions(), AbstractTwoBodyInteractionForce< DIM >::UseCutoffPoint(), LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor(), AbstractTissue< DIM >::WriteCellResultsToFiles(), MeshBasedTissue< DIM >::WriteResultsToFiles(), AbstractTissue< DIM >::WriteResultsToFiles(), and AbstractTissue< DIM >::WriteTimeAndNodeResultsToFiles().
| double TissueConfig::GetStemCellG1Duration | ( | ) |
- Returns:
- mStemCellG1Duration
Definition at line 148 of file TissueConfig.cpp.
References mStemCellG1Duration.
Referenced by StochasticDurationGenerationBasedCellCycleModelCellsGenerator< DIM >::GetTypicalStemCellCycleTime(), SimpleWntCellCycleModelCellsGenerator< DIM >::GetTypicalStemCellCycleTime(), FixedDurationGenerationBasedCellCycleModelCellsGenerator< DIM >::GetTypicalStemCellCycleTime(), SimpleWntCellCycleModel::SetG1Duration(), and AbstractSimpleCellCycleModel::SetG1Duration().
| double TissueConfig::GetTransitCellG1Duration | ( | ) |
- Returns:
- mTransitCellG1Duration
Definition at line 152 of file TissueConfig.cpp.
References mTransitCellG1Duration.
Referenced by StochasticDurationGenerationBasedCellCycleModelCellsGenerator< DIM >::GetTypicalTransitCellCycleTime(), SimpleWntCellCycleModelCellsGenerator< DIM >::GetTypicalTransitCellCycleTime(), FixedDurationGenerationBasedCellCycleModelCellsGenerator< DIM >::GetTypicalTransitCellCycleTime(), SimpleWntCellCycleModel::SetG1Duration(), and AbstractSimpleCellCycleModel::SetG1Duration().
| double TissueConfig::GetHepaOneCellG1Duration | ( | ) |
- Returns:
- mHepaOneCellG1Duration
Definition at line 156 of file TissueConfig.cpp.
References mHepaOneCellG1Duration.
| double TissueConfig::GetMinimumGapDuration | ( | ) |
- Returns:
- mMinimumGapDuration
Definition at line 160 of file TissueConfig.cpp.
References mMinimumGapDuration.
Referenced by SimpleWntCellCycleModel::SetG1Duration(), and StochasticWntCellCycleModel::SetG2Duration().
| double TissueConfig::GetSG2MDuration | ( | ) |
- Returns:
- mSDuration + mG2Duration + mMDuration
Definition at line 164 of file TissueConfig.cpp.
References mG2Duration, mMDuration, and mSDuration.
Referenced by StochasticDurationGenerationBasedCellCycleModelCellsGenerator< DIM >::GetTypicalStemCellCycleTime(), SimpleWntCellCycleModelCellsGenerator< DIM >::GetTypicalStemCellCycleTime(), FixedDurationGenerationBasedCellCycleModelCellsGenerator< DIM >::GetTypicalStemCellCycleTime(), StochasticDurationGenerationBasedCellCycleModelCellsGenerator< DIM >::GetTypicalTransitCellCycleTime(), SimpleWntCellCycleModelCellsGenerator< DIM >::GetTypicalTransitCellCycleTime(), and FixedDurationGenerationBasedCellCycleModelCellsGenerator< DIM >::GetTypicalTransitCellCycleTime().
| double TissueConfig::GetSDuration | ( | ) |
- Returns:
- mSDuration
Definition at line 168 of file TissueConfig.cpp.
References mSDuration.
Referenced by AbstractCellCycleModel::GetSDuration().
| double TissueConfig::GetG2Duration | ( | ) |
- Returns:
- mG2Duration
Definition at line 172 of file TissueConfig.cpp.
References mG2Duration.
Referenced by AbstractCellCycleModel::GetG2Duration(), and StochasticWntCellCycleModel::SetG2Duration().
| double TissueConfig::GetMDuration | ( | ) |
- Returns:
- mMDuration
Definition at line 176 of file TissueConfig.cpp.
References mMDuration.
Referenced by GeneralisedLinearSpringForce< DIM >::CalculateForceBetweenNodes(), and AbstractCellCycleModel::GetMDuration().
| unsigned TissueConfig::GetMaxTransitGenerations | ( | ) |
- Returns:
- mMaxTransitGenerations
Definition at line 180 of file TissueConfig.cpp.
References mMaxTransitGenerations.
| double TissueConfig::GetCryptLength | ( | ) |
- Returns:
- mCryptLength
Definition at line 184 of file TissueConfig.cpp.
References mCryptLength.
Referenced by WntConcentration< DIM >::GetWntGradient(), WntConcentration< DIM >::GetWntLevel(), and SloughingCellKiller< DIM >::TestAndLabelCellsForApoptosisOrDeath().
| double TissueConfig::GetCryptWidth | ( | ) |
- Returns:
- mCryptWidth
Definition at line 188 of file TissueConfig.cpp.
References mCryptWidth.
Referenced by CryptStatistics::CellIsInSectionPeriodic(), CryptStatistics::GetCryptSection(), and SloughingCellKiller< DIM >::TestAndLabelCellsForApoptosisOrDeath().
| double TissueConfig::GetSpringStiffness | ( | ) |
- Returns:
- mSpringStiffness
Definition at line 192 of file TissueConfig.cpp.
References mSpringStiffness.
Referenced by MeshBasedTissueWithGhostNodes< DIM >::CalculateForceBetweenNodes(), GeneralisedLinearSpringForce< DIM >::CalculateForceBetweenNodes(), and LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor().
| double TissueConfig::GetMechanicsCutOffLength | ( | ) |
- Returns:
- mMechanicsCutOffLength
Definition at line 196 of file TissueConfig.cpp.
References mMechanicsCutOffLength.
Referenced by AbstractTwoBodyInteractionForce< DIM >::GetCutoffPoint(), and NodeBasedTissue< DIM >::Update().
| double TissueConfig::GetDampingConstantNormal | ( | ) |
- Returns:
- mDampingConstantNormal
Definition at line 200 of file TissueConfig.cpp.
References mDampingConstantNormal.
Referenced by AbstractCellCentreBasedTissue< DIM >::GetDampingConstant(), and MeshBasedTissueWithGhostNodes< DIM >::UpdateGhostPositions().
| double TissueConfig::GetDampingConstantMutant | ( | ) |
- Returns:
- mDampingConstantMutant
Definition at line 204 of file TissueConfig.cpp.
References mDampingConstantMutant.
Referenced by AbstractCellCentreBasedTissue< DIM >::GetDampingConstant().
| double TissueConfig::GetBetaCatSpringScaler | ( | ) |
- Returns:
- mBetaCatSpringScaler
Definition at line 208 of file TissueConfig.cpp.
References mBetaCatSpringScaler.
Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor().
| double TissueConfig::GetApoptosisTime | ( | ) |
- Returns:
- mApoptosisTime
Definition at line 212 of file TissueConfig.cpp.
References mApoptosisTime.
Referenced by GeneralisedLinearSpringForce< DIM >::CalculateForceBetweenNodes(), and TissueCell::StartApoptosis().
| double TissueConfig::GetDivisionRestingSpringLength | ( | ) |
- Returns:
- mDivisionRestingSpringLength
Definition at line 216 of file TissueConfig.cpp.
References mDivisionRestingSpringLength.
Referenced by GeneralisedLinearSpringForce< DIM >::CalculateForceBetweenNodes().
| double TissueConfig::GetDivisionSeparation | ( | ) |
- Returns:
- mDivisionSeparation
Definition at line 220 of file TissueConfig.cpp.
References mDivisionSeparation.
Referenced by TissueSimulation< DIM >::CalculateDividingCellCentreLocations(), and CryptSimulation2d::CalculateDividingCellCentreLocations().
| double TissueConfig::GetHepaOneCellHypoxicConcentration | ( | ) |
- Returns:
- mHepaOneCellHypoxicConcentration
Definition at line 224 of file TissueConfig.cpp.
References mHepaOneCellHypoxicConcentration.
| double TissueConfig::GetHepaOneCellQuiescentConcentration | ( | ) |
- Returns:
- mHepaOneCellQuiescentConcentration
Definition at line 228 of file TissueConfig.cpp.
References mHepaOneCellQuiescentConcentration.
| double TissueConfig::GetWntTransitThreshold | ( | ) |
- Returns:
- mWntTransitThreshold
Definition at line 232 of file TissueConfig.cpp.
References mWntTransitThreshold.
Referenced by SimpleWntCellCycleModel::UpdateCellCyclePhase().
| double TissueConfig::GetWntStemThreshold | ( | ) |
- Returns:
- mWntStemThreshold
Definition at line 236 of file TissueConfig.cpp.
References mWntStemThreshold.
Referenced by SimpleWntCellCycleModel::UpdateCellCyclePhase().
| double TissueConfig::GetTopOfLinearWntConcentration | ( | ) |
- Returns:
- mTopOfLinearWntConcentration
Definition at line 240 of file TissueConfig.cpp.
References mTopOfLinearWntConcentration.
Referenced by WntConcentration< DIM >::GetWntGradient(), and WntConcentration< DIM >::GetWntLevel().
| double TissueConfig::GetCriticalHypoxicDuration | ( | ) |
- Returns:
- mCriticalHypoxicDuration
Definition at line 244 of file TissueConfig.cpp.
References mCriticalHypoxicDuration.
| double TissueConfig::GetCryptProjectionParameterA | ( | ) |
- Returns:
- mCryptProjectionParameterA
Definition at line 248 of file TissueConfig.cpp.
References mCryptProjectionParameterA.
Referenced by WntConcentration< DIM >::GetWntGradient(), and WntConcentration< DIM >::GetWntLevel().
| double TissueConfig::GetCryptProjectionParameterB | ( | ) |
- Returns:
- mCryptProjectionParameterB
Definition at line 252 of file TissueConfig.cpp.
References mCryptProjectionParameterB.
Referenced by WntConcentration< DIM >::GetWntGradient(), and WntConcentration< DIM >::GetWntLevel().
| double TissueConfig::GetApoptoticSpringTensionStiffness | ( | ) |
- Returns:
- mApoptoticSpringTensionStiffness
Definition at line 256 of file TissueConfig.cpp.
References mApoptoticSpringTensionStiffness.
Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor().
| double TissueConfig::GetApoptoticSpringCompressionStiffness | ( | ) |
- Returns:
- mApoptoticSpringCompressionStiffness
Definition at line 260 of file TissueConfig.cpp.
References mApoptoticSpringCompressionStiffness.
Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor().
| double TissueConfig::GetWntChemotaxisStrength | ( | ) |
- Returns:
- mWntChemotaxisStrength
Definition at line 264 of file TissueConfig.cpp.
References mWntChemotaxisStrength.
| double TissueConfig::GetSymmetricDivisionProbability | ( | ) |
- Returns:
- mSymmetricDivisionProbability
Definition at line 268 of file TissueConfig.cpp.
References mSymmetricDivisionProbability.
| double TissueConfig::GetAreaBasedDampingConstantParameter | ( | ) |
- Returns:
- mAreaBasedDampingConstantParameter
Definition at line 272 of file TissueConfig.cpp.
References mAreaBasedDampingConstantParameter.
Referenced by MeshBasedTissue< DIM >::GetDampingConstant().
| double TissueConfig::GetMatureCellTargetArea | ( | ) |
- Returns:
- mMatureCellTargetArea
Definition at line 276 of file TissueConfig.cpp.
References mMatureCellTargetArea.
| double TissueConfig::GetDeformationEnergyParameter | ( | ) |
- Returns:
- mDeformationEnergyParameter
Definition at line 280 of file TissueConfig.cpp.
References mDeformationEnergyParameter.
| double TissueConfig::GetMembraneSurfaceEnergyParameter | ( | ) |
- Returns:
- mMembraneSurfaceEnergyParameter
Definition at line 284 of file TissueConfig.cpp.
References mMembraneSurfaceEnergyParameter.
| double TissueConfig::GetCellCellAdhesionEnergyParameter | ( | ) |
- Returns:
- mCellCellAdhesionEnergyParameter
Definition at line 288 of file TissueConfig.cpp.
References mCellCellAdhesionEnergyParameter.
| double TissueConfig::GetCellBoundaryAdhesionEnergyParameter | ( | ) |
- Returns:
- mCellBoundaryAdhesionEnergyParameter
Definition at line 292 of file TissueConfig.cpp.
References mCellBoundaryAdhesionEnergyParameter.
| bool TissueConfig::GetOutputCellIdData | ( | ) |
- Returns:
- mOutputCellIdData
Definition at line 296 of file TissueConfig.cpp.
References mOutputCellIdData.
| bool TissueConfig::GetOutputCellMutationStates | ( | ) |
- Returns:
- mOutputCellMutationStates
Definition at line 300 of file TissueConfig.cpp.
References mOutputCellMutationStates.
Referenced by AbstractTissue< DIM >::GenerateCellResults().
| bool TissueConfig::GetOutputCellAncestors | ( | ) |
- Returns:
- mOutputCellAncestors
Definition at line 304 of file TissueConfig.cpp.
References mOutputCellAncestors.
Referenced by AbstractTissue< DIM >::GenerateCellResults().
| bool TissueConfig::GetOutputCellTypes | ( | ) |
- Returns:
- mOutputCellTypes
Definition at line 308 of file TissueConfig.cpp.
References mOutputCellTypes.
Referenced by AbstractTissue< DIM >::GenerateCellResults().
| bool TissueConfig::GetOutputCellVariables | ( | ) |
- Returns:
- mOutputCellVariables
Definition at line 312 of file TissueConfig.cpp.
References mOutputCellVariables.
Referenced by AbstractTissue< DIM >::GenerateCellResults().
| bool TissueConfig::GetOutputCellCyclePhases | ( | ) |
- Returns:
- mOutputCellCyclePhases
Definition at line 316 of file TissueConfig.cpp.
References mOutputCellCyclePhases.
| bool TissueConfig::GetOutputCellAges | ( | ) |
- Returns:
- mOutputCellAges
Definition at line 320 of file TissueConfig.cpp.
References mOutputCellAges.
Referenced by AbstractTissue< DIM >::GenerateCellResults().
| bool TissueConfig::GetOutputCellAreas | ( | ) |
- Returns:
- mOutputCellAreas
Definition at line 324 of file TissueConfig.cpp.
References mOutputCellAreas.
| bool TissueConfig::GetOutputVoronoiData | ( | ) |
- Returns:
- mOutputVoronoiData
Definition at line 328 of file TissueConfig.cpp.
References mOutputVoronoiData.
| bool TissueConfig::GetOutputTissueAreas | ( | ) |
- Returns:
- mOutputTissueAreas
Definition at line 332 of file TissueConfig.cpp.
References mOutputTissueAreas.
| void TissueConfig::SetStemCellG1Duration | ( | double | stemCellG1Duration | ) |
Set mStemCellG1Duration.
Definition at line 340 of file TissueConfig.cpp.
References mStemCellG1Duration.
| void TissueConfig::SetTransitCellG1Duration | ( | double | transitCellG1Duration | ) |
Set mTransitCellG1Duration.
Definition at line 345 of file TissueConfig.cpp.
References mTransitCellG1Duration.
| void TissueConfig::SetHepaOneCellG1Duration | ( | double | hepaOneCellG1Duration | ) |
Set mHepaOneCellG1Duration.
Definition at line 350 of file TissueConfig.cpp.
References mHepaOneCellG1Duration.
| void TissueConfig::SetMinimumGapDuration | ( | double | minimumGapDuration | ) |
Set mMinimumGapDuration.
Definition at line 355 of file TissueConfig.cpp.
References mMinimumGapDuration.
| void TissueConfig::SetSDuration | ( | double | SDuration | ) |
| void TissueConfig::SetG2Duration | ( | double | G2Duration | ) |
| void TissueConfig::SetMDuration | ( | double | MDuration | ) |
| void TissueConfig::SetMaxTransitGenerations | ( | unsigned | maxTransitGens | ) |
Set mMaxTransitGenerations.
Definition at line 375 of file TissueConfig.cpp.
References mMaxTransitGenerations.
| void TissueConfig::SetCryptLength | ( | double | cryptLength | ) |
Set mCryptLength.
Definition at line 379 of file TissueConfig.cpp.
References mCryptLength.
Referenced by HoneycombMeshGenerator::HoneycombMeshGenerator().
| void TissueConfig::SetCryptWidth | ( | double | cryptWidth | ) |
Set mCryptWidth.
Definition at line 384 of file TissueConfig.cpp.
References mCryptWidth.
Referenced by HoneycombMeshGenerator::HoneycombMeshGenerator().
| void TissueConfig::SetSpringStiffness | ( | double | springStiffness | ) |
| void TissueConfig::SetMechanicsCutOffLength | ( | double | mechanicsCutOffLength | ) |
Set mMechanicsCutOffLength.
Definition at line 394 of file TissueConfig.cpp.
References mMechanicsCutOffLength.
Referenced by AbstractTwoBodyInteractionForce< DIM >::UseCutoffPoint().
| void TissueConfig::SetDampingConstantNormal | ( | double | dampingConstantNormal | ) |
Set mDampingConstantNormal.
Definition at line 400 of file TissueConfig.cpp.
References mDampingConstantNormal.
| void TissueConfig::SetDampingConstantMutant | ( | double | dampingConstantMutant | ) |
Set mDampingConstantMutant.
Definition at line 405 of file TissueConfig.cpp.
References mDampingConstantMutant.
| void TissueConfig::SetBetaCatSpringScaler | ( | double | betaCatSpringScaler | ) |
Set mBetaCatSpringScaler.
Definition at line 410 of file TissueConfig.cpp.
References mBetaCatSpringScaler.
| void TissueConfig::SetApoptosisTime | ( | double | apoptosisTime | ) |
| void TissueConfig::SetDivisionRestingSpringLength | ( | double | divisionRestingSpringLength | ) |
Set mDivisionRestingSpringLength.
Definition at line 420 of file TissueConfig.cpp.
References mDivisionRestingSpringLength.
| void TissueConfig::SetDivisionSeparation | ( | double | divisionSeparation | ) |
Set mDivisionSeparation.
Definition at line 427 of file TissueConfig.cpp.
References mDivisionSeparation.
| void TissueConfig::SetHepaOneCellHypoxicConcentration | ( | double | hepaOneCellHypoxicConcentration | ) |
Set mHepaOneCellHypoxicConcentration.
Definition at line 433 of file TissueConfig.cpp.
References mHepaOneCellHypoxicConcentration.
| void TissueConfig::SetHepaOneCellQuiescentConcentration | ( | double | hepaOneCellQuiescentConcentration | ) |
Set mHepaOneCellQuiescentConcentration.
Definition at line 439 of file TissueConfig.cpp.
References mHepaOneCellQuiescentConcentration.
| void TissueConfig::SetWntTransitThreshold | ( | double | wntThreshold | ) |
Set mWntTransitThreshold.
Definition at line 445 of file TissueConfig.cpp.
References mWntTransitThreshold.
| void TissueConfig::SetWntStemThreshold | ( | double | wntThreshold | ) |
Set mWntStemThreshold.
Definition at line 451 of file TissueConfig.cpp.
References mWntStemThreshold.
| void TissueConfig::SetTopOfLinearWntConcentration | ( | double | top | ) |
Set mTopOfLinearWntConcentration.
Definition at line 457 of file TissueConfig.cpp.
References mTopOfLinearWntConcentration.
| void TissueConfig::SetCriticalHypoxicDuration | ( | double | criticalHypoxicDuration | ) |
Set mCriticalHypoxicDuration.
Definition at line 463 of file TissueConfig.cpp.
References mCriticalHypoxicDuration.
| void TissueConfig::SetHepaOneParameters | ( | ) |
Set mHepaOneParameters.
Definition at line 468 of file TissueConfig.cpp.
References mHepaOneCellG1Duration, and mStemCellG1Duration.
| void TissueConfig::SetCryptProjectionParameterA | ( | double | cryptProjectionParameterA | ) |
Set mCryptProjectionParameterA.
Definition at line 472 of file TissueConfig.cpp.
References mCryptProjectionParameterA.
| void TissueConfig::SetCryptProjectionParameterB | ( | double | cryptProjectionParameterB | ) |
Set mCryptProjectionParameterB.
Definition at line 477 of file TissueConfig.cpp.
References mCryptProjectionParameterB.
| void TissueConfig::SetApoptoticSpringTensionStiffness | ( | double | apoptoticSpringTensionStiffness | ) |
Set mApoptoticSpringTensionStiffness.
Definition at line 482 of file TissueConfig.cpp.
References mApoptoticSpringTensionStiffness.
| void TissueConfig::SetApoptoticSpringCompressionStiffness | ( | double | apoptoticSpringCompressionStiffness | ) |
Set mApoptoticSpringCompressionStiffness.
Definition at line 487 of file TissueConfig.cpp.
References mApoptoticSpringCompressionStiffness.
| void TissueConfig::SetWntChemotaxisStrength | ( | double | wntChemotaxisStrength | ) |
Set mWntChemotaxisStrength.
Definition at line 492 of file TissueConfig.cpp.
References mWntChemotaxisStrength.
| void TissueConfig::SetSymmetricDivisionProbability | ( | double | symmetricDivisionProbability | ) |
Set mSymmetricDivisionProbability.
Definition at line 497 of file TissueConfig.cpp.
References mSymmetricDivisionProbability.
| void TissueConfig::SetAreaBasedDampingConstantParameter | ( | double | areaBasedDampingConstantParameter | ) |
Set mAreaBasedDampingConstantParameter.
Definition at line 503 of file TissueConfig.cpp.
References mAreaBasedDampingConstantParameter.
| void TissueConfig::SetMatureCellTargetArea | ( | double | matureCellTargetArea | ) |
Set mMatureCellTargetArea.
Definition at line 508 of file TissueConfig.cpp.
References mMatureCellTargetArea.
| void TissueConfig::SetDeformationEnergyParameter | ( | double | deformationEnergyParameter | ) |
Set mDeformationEnergyParameter.
Definition at line 513 of file TissueConfig.cpp.
References mDeformationEnergyParameter.
| void TissueConfig::SetMembraneSurfaceEnergyParameter | ( | double | membraneSurfaceEnergyParameter | ) |
Set mMembraneSurfaceEnergyParameter.
Definition at line 517 of file TissueConfig.cpp.
References mMembraneSurfaceEnergyParameter.
| void TissueConfig::SetCellCellAdhesionEnergyParameter | ( | double | cellCellAdhesionEnergyParameter | ) |
Set mCellCellAdhesionEnergyParameter.
Definition at line 521 of file TissueConfig.cpp.
References mCellCellAdhesionEnergyParameter.
| void TissueConfig::SetCellBoundaryAdhesionEnergyParameter | ( | double | cellBoundaryAdhesionEnergyParameter | ) |
Set mCellBoundaryAdhesionEnergyParameter.
Definition at line 525 of file TissueConfig.cpp.
References mCellBoundaryAdhesionEnergyParameter.
| void TissueConfig::SetOutputCellIdData | ( | bool | writeCellIdData | ) |
Set mOutputCellIdData.
Definition at line 529 of file TissueConfig.cpp.
References mOutputCellIdData.
| void TissueConfig::SetOutputCellMutationStates | ( | bool | outputCellMutationStates | ) |
Set mOutputCellMutationStates.
Definition at line 533 of file TissueConfig.cpp.
References mOutputCellMutationStates.
| void TissueConfig::SetOutputCellAncestors | ( | bool | outputCellAncestors | ) |
Set mOutputCellAncestors.
Definition at line 537 of file TissueConfig.cpp.
References mOutputCellAncestors.
| void TissueConfig::SetOutputCellTypes | ( | bool | outputCellTypes | ) |
| void TissueConfig::SetOutputCellVariables | ( | bool | outputCellVariables | ) |
Set mOutputCellVariables.
Definition at line 545 of file TissueConfig.cpp.
References mOutputCellVariables.
| void TissueConfig::SetOutputCellCyclePhases | ( | bool | outputCellCyclePhases | ) |
Set mOutputCellCyclePhases.
Definition at line 549 of file TissueConfig.cpp.
References mOutputCellCyclePhases.
| void TissueConfig::SetOutputCellAges | ( | bool | outputCellAges | ) |
| void TissueConfig::SetOutputCellAreas | ( | bool | outputCellAreas | ) |
| void TissueConfig::SetOutputVoronoiData | ( | bool | outputVoronoiData | ) |
Set mOutputVoronoiData.
Definition at line 561 of file TissueConfig.cpp.
References mOutputVoronoiData.
| void TissueConfig::SetOutputTissueAreas | ( | bool | outputTissueAreas | ) |
Set mOutputTissueAreas.
Definition at line 565 of file TissueConfig.cpp.
References mOutputTissueAreas.
| void TissueConfig::Reset | ( | ) |
Reset all parameters to their defaults
mStemCellG1Duration has units of hours mTransitCellG1Duration has units of hours mHepaOneCellG1Duration has units of hours mMinimumGapDuration has units of hours mSDuration has units of hours mG2Duration has units of hours mMDuration has units of hours mMaxTransitGenerations has no units mCryptWidth has units of cell size at equilibrium rest length mCryptLength has units of cell size at equilibrium rest length mSpringStiffness has units of N/m = kg s^-2 mMechanicsCutOffLength has units of cell size at equilibrium rest length mDampingConstantNormal has units of kg s^-1 mDampingConstantMutant has units of kg s^-1 mBetaCatSpringScaler has no units mApoptosisTime has units of hours mDivisionRestingSpringLength has units of cell size at equilibrium rest length mDivisionSeparation has units of cell size at equilibrium rest length mHepaOneCellHypoxicConcentration has no units mHepaOneCellQuiescentConcentration has no units mWntTransitThreshold has no units mWntStemThreshold has no units mTopOfLinearWntConcentration has no units (proportion of mCryptLength) mCriticalHypoxicDuration has units of hours mCryptProjectionParameterA has no units mCryptProjectionParameterB has no units mApoptoticSpringTensionStiffness has the same units as mSpringStiffness mApoptoticSpringCompressionStiffness has the same units as mSpringStiffness mWntChemotaxisStrength has no units mSymmetricDivisionProbability has no units mAreaBasedDampingConstantParameter has no units mMatureCellTargetArea has no units mDeformationEnergyParameter has ? units mMembraneSurfaceEnergyParameter has ? units mCellCellAdhesionEnergyParameter has ? units mCellBoundaryAdhesionEnergyParameter has ? units
Definition at line 87 of file TissueConfig.cpp.
References mApoptosisTime, mApoptoticSpringCompressionStiffness, mApoptoticSpringTensionStiffness, mAreaBasedDampingConstantParameter, mBetaCatSpringScaler, mCellBoundaryAdhesionEnergyParameter, mCellCellAdhesionEnergyParameter, mCriticalHypoxicDuration, mCryptLength, mCryptProjectionParameterA, mCryptProjectionParameterB, mCryptWidth, mDampingConstantMutant, mDampingConstantNormal, mDeformationEnergyParameter, mDivisionRestingSpringLength, mDivisionSeparation, mG2Duration, mHepaOneCellG1Duration, mHepaOneCellHypoxicConcentration, mHepaOneCellQuiescentConcentration, mMatureCellTargetArea, mMaxTransitGenerations, mMDuration, mMechanicsCutOffLength, mMembraneSurfaceEnergyParameter, mMinimumGapDuration, mOutputCellAges, mOutputCellAncestors, mOutputCellAreas, mOutputCellCyclePhases, mOutputCellIdData, mOutputCellMutationStates, mOutputCellTypes, mOutputCellVariables, mOutputTissueAreas, mOutputVoronoiData, mSDuration, mSpringStiffness, mStemCellG1Duration, mSymmetricDivisionProbability, mTopOfLinearWntConcentration, mTransitCellG1Duration, mWntChemotaxisStrength, mWntStemThreshold, and mWntTransitThreshold.
Referenced by AbstractCancerTestSuite::setUp(), and TissueConfig().
| TissueConfig& TissueConfig::operator= | ( | const TissueConfig & | ) | [protected] |
Overloaded assignement operator.
| void TissueConfig::serialize | ( | Archive & | archive, | |
| const unsigned int | version | |||
| ) | [inline, private] |
As with other singleton classes, ensure the instance of this class is serialized directly before being serialized via a pointer.
- Parameters:
-
archive the archive version the current version of this class
Definition at line 723 of file TissueConfig.hpp.
References mApoptosisTime, mApoptoticSpringCompressionStiffness, mApoptoticSpringTensionStiffness, mAreaBasedDampingConstantParameter, mBetaCatSpringScaler, mCellBoundaryAdhesionEnergyParameter, mCellCellAdhesionEnergyParameter, mCriticalHypoxicDuration, mCryptLength, mCryptProjectionParameterA, mCryptProjectionParameterB, mCryptWidth, mDampingConstantMutant, mDampingConstantNormal, mDeformationEnergyParameter, mG2Duration, mHepaOneCellG1Duration, mHepaOneCellHypoxicConcentration, mHepaOneCellQuiescentConcentration, mMatureCellTargetArea, mMaxTransitGenerations, mMDuration, mMechanicsCutOffLength, mMembraneSurfaceEnergyParameter, mMinimumGapDuration, mOutputCellAges, mOutputCellAncestors, mOutputCellAreas, mOutputCellCyclePhases, mOutputCellIdData, mOutputCellMutationStates, mOutputCellTypes, mOutputCellVariables, mOutputTissueAreas, mOutputVoronoiData, mSDuration, mSpringStiffness, mStemCellG1Duration, mSymmetricDivisionProbability, mTopOfLinearWntConcentration, mTransitCellG1Duration, mWntChemotaxisStrength, mWntStemThreshold, and mWntTransitThreshold.
Friends And Related Function Documentation
friend class boost::serialization::access [friend] |
Needed for serialization.
Definition at line 713 of file TissueConfig.hpp.
Member Data Documentation
TissueConfig * TissueConfig::mpInstance = NULL [static, private] |
The single instance of the class
Definition at line 459 of file TissueConfig.hpp.
Referenced by Instance(), and TissueConfig().
double TissueConfig::mStemCellG1Duration [private] |
Duration of G1 phase for stem cells. May be used as a mean duration for stochastic cell cycle models.
Definition at line 466 of file TissueConfig.hpp.
Referenced by GetStemCellG1Duration(), Reset(), serialize(), SetHepaOneParameters(), and SetStemCellG1Duration().
double TissueConfig::mTransitCellG1Duration [private] |
Duration of G1 phase for transit cells. May be used as a mean duration for stochastic cell cycle models.
Definition at line 472 of file TissueConfig.hpp.
Referenced by GetTransitCellG1Duration(), Reset(), serialize(), and SetTransitCellG1Duration().
double TissueConfig::mHepaOneCellG1Duration [private] |
Duration of G1 phase for HEPA-1 cells, for use in monolayer/spheroid simulations. May be used as a mean duration for stochastic cell cycle models.
Definition at line 478 of file TissueConfig.hpp.
Referenced by GetHepaOneCellG1Duration(), Reset(), serialize(), SetHepaOneCellG1Duration(), and SetHepaOneParameters().
double TissueConfig::mMinimumGapDuration [private] |
Minimum possbile duration of either of the gap phases (G1 or G2). Used to guarantee a strictly positive duration in cell cycle models that use normal random deviates for G1 or G2 phases.
Definition at line 485 of file TissueConfig.hpp.
Referenced by GetMinimumGapDuration(), Reset(), serialize(), and SetMinimumGapDuration().
double TissueConfig::mSDuration [private] |
Duration of S phase for all cell types.
Definition at line 490 of file TissueConfig.hpp.
Referenced by GetSDuration(), GetSG2MDuration(), Reset(), serialize(), and SetSDuration().
double TissueConfig::mG2Duration [private] |
Duration of G2 phase for all cell types.
Definition at line 495 of file TissueConfig.hpp.
Referenced by GetG2Duration(), GetSG2MDuration(), Reset(), serialize(), and SetG2Duration().
double TissueConfig::mMDuration [private] |
Duration of M phase for all cell types.
Definition at line 500 of file TissueConfig.hpp.
Referenced by GetMDuration(), GetSG2MDuration(), Reset(), serialize(), and SetMDuration().
unsigned TissueConfig::mMaxTransitGenerations [private] |
How many generations a transit cell lives for before becoming fully differentiated.
Definition at line 505 of file TissueConfig.hpp.
Referenced by GetMaxTransitGenerations(), Reset(), serialize(), and SetMaxTransitGenerations().
double TissueConfig::mCryptLength [private] |
The length of the crypt, non-dimensionalised with cell length. This parameter determines when cells are sloughed from the crypt.
Definition at line 511 of file TissueConfig.hpp.
Referenced by GetCryptLength(), Reset(), serialize(), and SetCryptLength().
double TissueConfig::mCryptWidth [private] |
The width of the crypt, non-dimensionalised with cell length. This determines when cells are sloughed from the crypt in 2D.
Definition at line 517 of file TissueConfig.hpp.
Referenced by GetCryptWidth(), Reset(), serialize(), and SetCryptWidth().
double TissueConfig::mSpringStiffness [private] |
Spring stiffness.
Represented by the parameter mu in the model by Meineke et al (2001) in their off-lattice model of the intestinal crypt (doi:10.1046/j.0960-7722.2001.00216.x).
Definition at line 526 of file TissueConfig.hpp.
Referenced by GetSpringStiffness(), Reset(), serialize(), and SetSpringStiffness().
double TissueConfig::mMechanicsCutOffLength [private] |
Mechanics cut off length. Used in NodeBasedTissue.
Definition at line 532 of file TissueConfig.hpp.
Referenced by GetMechanicsCutOffLength(), Reset(), serialize(), and SetMechanicsCutOffLength().
double TissueConfig::mDampingConstantNormal [private] |
Damping constant for normal cells. Represented by the parameter eta in the model by Meineke et al (2001) in their off-lattice model of the intestinal crypt (doi:10.1046/j.0960-7722.2001.00216.x).
Definition at line 540 of file TissueConfig.hpp.
Referenced by GetDampingConstantNormal(), Reset(), serialize(), and SetDampingConstantNormal().
double TissueConfig::mDampingConstantMutant [private] |
Damping constant for mutant cells.
Definition at line 545 of file TissueConfig.hpp.
Referenced by GetDampingConstantMutant(), Reset(), serialize(), and SetDampingConstantMutant().
double TissueConfig::mBetaCatSpringScaler [private] |
Scaling factor for beta catenin to spring strength
Definition at line 550 of file TissueConfig.hpp.
Referenced by GetBetaCatSpringScaler(), Reset(), serialize(), and SetBetaCatSpringScaler().
double TissueConfig::mApoptosisTime [private] |
The time it takes for a cell to fully undergo apoptosis
Definition at line 555 of file TissueConfig.hpp.
Referenced by GetApoptosisTime(), Reset(), serialize(), and SetApoptosisTime().
double TissueConfig::mDivisionSeparation [private] |
Initial separation placement of mother/daughter cells at birth
Definition at line 560 of file TissueConfig.hpp.
Referenced by GetDivisionSeparation(), Reset(), and SetDivisionSeparation().
double TissueConfig::mDivisionRestingSpringLength [private] |
Initial resting spring length after cell division. The value of thiis parameter should be larger than mDivisionSeparation, because of pressure from neighbouring springs.
Definition at line 567 of file TissueConfig.hpp.
Referenced by GetDivisionRestingSpringLength(), Reset(), and SetDivisionRestingSpringLength().
double TissueConfig::mHepaOneCellHypoxicConcentration [private] |
Non-dimensionalized oxygen concentration below which HEPA-1 cells are considered to be hypoxic. A prolonged period of hypoxia causes the cell to become apoptotic.
Definition at line 574 of file TissueConfig.hpp.
Referenced by GetHepaOneCellHypoxicConcentration(), Reset(), serialize(), and SetHepaOneCellHypoxicConcentration().
double TissueConfig::mHepaOneCellQuiescentConcentration [private] |
Non-dimensionalized oxygen concentration below which HEPA-1 cells are considered to be quiescent and slow their progress through the G1 phase of the cell cycle.
Definition at line 581 of file TissueConfig.hpp.
Referenced by GetHepaOneCellQuiescentConcentration(), Reset(), serialize(), and SetHepaOneCellQuiescentConcentration().
double TissueConfig::mWntTransitThreshold [private] |
Non-dimensionalized Wnt threshold, above which cells progress through the cell cycle.
Definition at line 586 of file TissueConfig.hpp.
Referenced by GetWntTransitThreshold(), Reset(), serialize(), and SetWntTransitThreshold().
double TissueConfig::mWntStemThreshold [private] |
Non-dimensionalized Wnt threshold, above which cells behave as stem cells.
Definition at line 591 of file TissueConfig.hpp.
Referenced by GetWntStemThreshold(), Reset(), serialize(), and SetWntStemThreshold().
double TissueConfig::mTopOfLinearWntConcentration [private] |
The proportion of the crypt that has a Wnt gradient. The Wnt concentration goes to zero at this height up the crypt.
Definition at line 597 of file TissueConfig.hpp.
Referenced by GetTopOfLinearWntConcentration(), Reset(), serialize(), and SetTopOfLinearWntConcentration().
double TissueConfig::mCriticalHypoxicDuration [private] |
Non-dimensionalized critical hypoxic duration.
Definition at line 602 of file TissueConfig.hpp.
Referenced by GetCriticalHypoxicDuration(), Reset(), serialize(), and SetCriticalHypoxicDuration().
double TissueConfig::mCryptProjectionParameterA [private] |
Parameter a, for use in crypt projection simulations, in which the crypt surface is given in cylindrical polar coordinates by z = a*r^b.
Definition at line 608 of file TissueConfig.hpp.
Referenced by GetCryptProjectionParameterA(), Reset(), serialize(), and SetCryptProjectionParameterA().
double TissueConfig::mCryptProjectionParameterB [private] |
Parameter b, for use in crypt projection simulations, in which the crypt surface is given in cylindrical polar coordinates by z = a*r^b.
Definition at line 614 of file TissueConfig.hpp.
Referenced by GetCryptProjectionParameterB(), Reset(), serialize(), and SetCryptProjectionParameterB().
double TissueConfig::mApoptoticSpringTensionStiffness [private] |
Non-dimensionalized 'stiffness' of a apoptotic cell under tension.
Definition at line 619 of file TissueConfig.hpp.
Referenced by GetApoptoticSpringTensionStiffness(), Reset(), serialize(), and SetApoptoticSpringTensionStiffness().
double TissueConfig::mApoptoticSpringCompressionStiffness [private] |
Non-dimensionalized 'stiffness' of a apoptotic cell under compression.
Definition at line 624 of file TissueConfig.hpp.
Referenced by GetApoptoticSpringCompressionStiffness(), Reset(), serialize(), and SetApoptoticSpringCompressionStiffness().
double TissueConfig::mWntChemotaxisStrength [private] |
Strength of Wnt-based chemotactic force.
Definition at line 629 of file TissueConfig.hpp.
Referenced by GetWntChemotaxisStrength(), Reset(), serialize(), and SetWntChemotaxisStrength().
double TissueConfig::mSymmetricDivisionProbability [private] |
Probability of symmetric division.
Definition at line 634 of file TissueConfig.hpp.
Referenced by GetSymmetricDivisionProbability(), Reset(), serialize(), and SetSymmetricDivisionProbability().
double TissueConfig::mAreaBasedDampingConstantParameter [private] |
Non-dimensional parameter d0 for use in area-based damping constant calculations.
Definition at line 639 of file TissueConfig.hpp.
Referenced by GetAreaBasedDampingConstantParameter(), Reset(), serialize(), and SetAreaBasedDampingConstantParameter().
double TissueConfig::mMatureCellTargetArea [private] |
Non-dimensional target area of a mature (fully-grown) TissueCell. For use in vertex-based models.
Definition at line 645 of file TissueConfig.hpp.
Referenced by GetMatureCellTargetArea(), Reset(), serialize(), and SetMatureCellTargetArea().
double TissueConfig::mDeformationEnergyParameter [private] |
Cell deformation energy parameter. For use in vertex-based models.
Definition at line 651 of file TissueConfig.hpp.
Referenced by GetDeformationEnergyParameter(), Reset(), serialize(), and SetDeformationEnergyParameter().
double TissueConfig::mMembraneSurfaceEnergyParameter [private] |
Cell membrane energy parameter. For use in vertex-based models.
Definition at line 657 of file TissueConfig.hpp.
Referenced by GetMembraneSurfaceEnergyParameter(), Reset(), serialize(), and SetMembraneSurfaceEnergyParameter().
double TissueConfig::mCellCellAdhesionEnergyParameter [private] |
Cell-cell adhesion energy parameter. For use in vertex-based models.
Definition at line 663 of file TissueConfig.hpp.
Referenced by GetCellCellAdhesionEnergyParameter(), Reset(), serialize(), and SetCellCellAdhesionEnergyParameter().
double TissueConfig::mCellBoundaryAdhesionEnergyParameter [private] |
Cell-boundary adhesion energy parameter. For use in vertex-based models.
Definition at line 669 of file TissueConfig.hpp.
Referenced by GetCellBoundaryAdhesionEnergyParameter(), Reset(), serialize(), and SetCellBoundaryAdhesionEnergyParameter().
bool TissueConfig::mOutputCellIdData [private] |
Whether to write cell ID data to file.
Definition at line 672 of file TissueConfig.hpp.
Referenced by GetOutputCellIdData(), Reset(), serialize(), and SetOutputCellIdData().
bool TissueConfig::mOutputCellMutationStates [private] |
Whether to count the number of each cell mutation state and output to file.
Definition at line 678 of file TissueConfig.hpp.
Referenced by GetOutputCellMutationStates(), Reset(), serialize(), and SetOutputCellMutationStates().
bool TissueConfig::mOutputCellAncestors [private] |
Whether to output the ancestor of each cell to a visualizer file.
Definition at line 684 of file TissueConfig.hpp.
Referenced by GetOutputCellAncestors(), Reset(), serialize(), and SetOutputCellAncestors().
bool TissueConfig::mOutputCellTypes [private] |
Whether to count the number of each cell type and output to file.
Definition at line 690 of file TissueConfig.hpp.
Referenced by GetOutputCellTypes(), Reset(), serialize(), and SetOutputCellTypes().
bool TissueConfig::mOutputCellVariables [private] |
Whether to write the cell variables to a file.
Definition at line 695 of file TissueConfig.hpp.
Referenced by GetOutputCellVariables(), Reset(), serialize(), and SetOutputCellVariables().
bool TissueConfig::mOutputCellCyclePhases [private] |
Whether to write the cell cycle phases to a file.
Definition at line 698 of file TissueConfig.hpp.
Referenced by GetOutputCellCyclePhases(), Reset(), serialize(), and SetOutputCellCyclePhases().
bool TissueConfig::mOutputCellAges [private] |
Whether to write the cell ages to a file.
Definition at line 701 of file TissueConfig.hpp.
Referenced by GetOutputCellAges(), Reset(), serialize(), and SetOutputCellAges().
bool TissueConfig::mOutputCellAreas [private] |
Whether to write the cell areas to a file.
Definition at line 704 of file TissueConfig.hpp.
Referenced by GetOutputCellAreas(), Reset(), serialize(), and SetOutputCellAreas().
bool TissueConfig::mOutputVoronoiData [private] |
Whether to write cell area and perimeter information to file.
Definition at line 707 of file TissueConfig.hpp.
Referenced by GetOutputVoronoiData(), Reset(), serialize(), and SetOutputVoronoiData().
bool TissueConfig::mOutputTissueAreas [private] |
Whether to write the tissue areas to file.
Definition at line 710 of file TissueConfig.hpp.
Referenced by GetOutputTissueAreas(), Reset(), serialize(), and SetOutputTissueAreas().
The documentation for this class was generated from the following files:
- /tmp/release_1.1/cancer/src/common/TissueConfig.hpp
- /tmp/release_1.1/cancer/src/common/TissueConfig.cpp
