Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
|
#include <Mirams2010WntOdeSystem.hpp>
Public Member Functions | |
Mirams2010WntOdeSystem (double wntLevel=0.0, boost::shared_ptr< AbstractCellMutationState > pMutationState=boost::shared_ptr< AbstractCellMutationState >(), std::vector< double > stateVariables=std::vector< double >()) | |
~Mirams2010WntOdeSystem () | |
void | Init () |
void | SetMutationState (boost::shared_ptr< AbstractCellMutationState > pMutationState) |
const boost::shared_ptr< AbstractCellMutationState > | GetMutationState () const |
void | EvaluateYDerivatives (double time, const std::vector< double > &rY, std::vector< double > &rDY) |
double | GetWntLevel () const |
Public Member Functions inherited from AbstractOdeSystem | |
AbstractOdeSystem (unsigned numberOfStateVariables) | |
virtual | ~AbstractOdeSystem () |
virtual bool | CalculateStoppingEvent (double time, const std::vector< double > &rY) |
virtual double | CalculateRootFunction (double time, const std::vector< double > &rY) |
bool | GetUseAnalyticJacobian () |
const std::vector< double > & | rGetConstStateVariables () const |
Public Member Functions inherited from AbstractParameterisedSystem< std::vector< double > > | |
AbstractParameterisedSystem (unsigned numberOfStateVariables) | |
std::vector< double > & | rGetStateVariables () |
std::vector< double > | GetStateVariables () |
void | SetStateVariables (const std::vector< double > &rStateVariables) |
double | GetStateVariable (unsigned index) const |
double | GetStateVariable (const std::string &rName) const |
void | SetStateVariable (unsigned index, double newValue) |
void | SetStateVariable (const std::string &rName, double newValue) |
virtual void | VerifyStateVariables () |
void | SetDefaultInitialConditions (const std::vector< double > &rInitialConditions) |
void | SetDefaultInitialCondition (unsigned index, double initialCondition) |
std::vector< double > | GetInitialConditions () const |
void | ResetToInitialConditions () |
double | GetParameter (unsigned index) const |
double | GetParameter (const std::string &rName) const |
void | SetParameter (const std::string &rName, double value) |
void | SetParameter (unsigned index, double value) |
double | GetAnyVariable (unsigned index, double time=0.0, std::vector< double > *pDerivedQuantities=NULL) |
double | GetAnyVariable (const std::string &rName, double time=0.0, std::vector< double > *pDerivedQuantities=NULL) |
void | SetAnyVariable (unsigned index, double value) |
void | SetAnyVariable (const std::string &rName, double value) |
virtual std::vector< double > | ComputeDerivedQuantities (double time, const std::vector< double > &rState) |
std::vector< double > | ComputeDerivedQuantitiesFromCurrentState (double time) |
Public Member Functions inherited from AbstractUntemplatedParameterisedSystem | |
AbstractUntemplatedParameterisedSystem (unsigned numberOfStateVariables) | |
virtual | ~AbstractUntemplatedParameterisedSystem () |
boost::shared_ptr< const AbstractOdeSystemInformation > | GetSystemInformation () const |
std::string | GetSystemName () const |
unsigned | GetNumberOfAttributes () const |
bool | HasAttribute (const std::string &rName) const |
double | GetAttribute (const std::string &rName) const |
unsigned | GetNumberOfStateVariables () const |
const std::vector< std::string > & | rGetStateVariableNames () const |
const std::vector< std::string > & | rGetStateVariableUnits () const |
unsigned | GetStateVariableIndex (const std::string &rName) const |
bool | HasStateVariable (const std::string &rName) const |
std::string | GetStateVariableUnits (unsigned index) const |
unsigned | GetNumberOfParameters () const |
const std::vector< std::string > & | rGetParameterNames () const |
const std::vector< std::string > & | rGetParameterUnits () const |
unsigned | GetParameterIndex (const std::string &rName) const |
bool | HasParameter (const std::string &rName) const |
std::string | GetParameterUnits (unsigned index) const |
unsigned | GetNumberOfDerivedQuantities () const |
const std::vector< std::string > & | rGetDerivedQuantityNames () const |
const std::vector< std::string > & | rGetDerivedQuantityUnits () const |
unsigned | GetDerivedQuantityIndex (const std::string &rName) const |
bool | HasDerivedQuantity (const std::string &rName) const |
std::string | GetDerivedQuantityUnits (unsigned index) const |
unsigned | GetAnyVariableIndex (const std::string &rName) const |
bool | HasAnyVariable (const std::string &rName) const |
std::string | GetAnyVariableUnits (unsigned index) const |
std::string | GetAnyVariableUnits (const std::string &rName) const |
Private Member Functions | |
template<class Archive > | |
void | serialize (Archive &archive, const unsigned int version) |
Private Attributes | |
double | mA |
double | mB |
double | mC |
double | mD |
double | mE |
double | mF |
boost::shared_ptr< AbstractCellMutationState > | mpMutationState |
double | mWntLevel |
Friends | |
class | boost::serialization::access |
Additional Inherited Members | |
Protected Member Functions inherited from AbstractParameterisedSystem< std::vector< double > > | |
std::string | DumpState (const std::string &rMessage) |
std::string | DumpState (const std::string &rMessage, std::vector< double > Y) |
std::string | DumpState (const std::string &rMessage, std::vector< double > Y, double time) |
void | CheckParametersOnLoad (const std::vector< double > &rParameters, const std::vector< std::string > &rParameterNames) |
Protected Attributes inherited from AbstractOdeSystem | |
bool | mUseAnalyticJacobian |
Protected Attributes inherited from AbstractParameterisedSystem< std::vector< double > > | |
std::vector< double > | mStateVariables |
std::vector< double > | mParameters |
Protected Attributes inherited from AbstractUntemplatedParameterisedSystem | |
unsigned | mNumberOfStateVariables |
boost::shared_ptr< AbstractOdeSystemInformation > | mpSystemInfo |
Represents the Mirams et al. system of ODEs, based on Swat et al. (2004) [doi:10.1093/bioinformatics/bth110] and a simple Wnt model (unpublished)
The variables are
6. b1 = Beta-Catenin (from 1st allele) 7. b2 = Beta-Catenin (from 1st allele) 8. WntLevel
Definition at line 60 of file Mirams2010WntOdeSystem.hpp.
Mirams2010WntOdeSystem::Mirams2010WntOdeSystem | ( | double | wntLevel = 0.0 , |
boost::shared_ptr< AbstractCellMutationState > | pMutationState = boost::shared_ptr<AbstractCellMutationState>() , |
||
std::vector< double > | stateVariables = std::vector<double>() |
||
) |
Constructor.
wntLevel | is a non-dimensional Wnt value between 0 and 1. This sets up the Wnt pathway in its steady state. |
pMutationState | optional mutation state (affects the ODE system) |
stateVariables | optional initial conditions for state variables (only used in archiving) |
State variables.
0. b1 = Beta-Catenin (1st allele's copy) 1. b2 = Beta-Catenin (2nd allele's copy) 2. wntLevel
Definition at line 45 of file Mirams2010WntOdeSystem.cpp.
References Init(), mA, mB, mC, mD, mF, mpMutationState, AbstractUntemplatedParameterisedSystem::mpSystemInfo, AbstractParameterisedSystem< std::vector< double > >::SetDefaultInitialCondition(), and AbstractParameterisedSystem< std::vector< double > >::SetStateVariables().
Mirams2010WntOdeSystem::~Mirams2010WntOdeSystem | ( | ) |
Destructor.
Definition at line 96 of file Mirams2010WntOdeSystem.cpp.
|
virtual |
Compute the RHS of the WntCellCycle system of ODEs.
Returns a vector representing the RHS of the ODEs at each time step, y' = [y1' ... yn']. An ODE solver will call this function repeatedly to solve for y = [y1 ... yn].
time | used to evaluate the RHS. |
rY | value of the solution vector used to evaluate the RHS. |
rDY | filled in with the resulting derivatives (using Alarcons et al. (2004) system of equations). |
Implements AbstractOdeSystem.
Definition at line 112 of file Mirams2010WntOdeSystem.cpp.
const boost::shared_ptr< AbstractCellMutationState > Mirams2010WntOdeSystem::GetMutationState | ( | ) | const |
Called by the archive function on the Wnt cell-cycle model.
Definition at line 157 of file Mirams2010WntOdeSystem.cpp.
References mpMutationState.
double Mirams2010WntOdeSystem::GetWntLevel | ( | ) | const |
void Mirams2010WntOdeSystem::Init | ( | ) |
Initialise parameter values.
Definition at line 101 of file Mirams2010WntOdeSystem.cpp.
References mA, mB, mC, mD, mE, and mF.
Referenced by Mirams2010WntOdeSystem().
|
inlineprivate |
Serialize the object and its member variables.
archive | the archive |
version | the current version of this class |
Definition at line 95 of file Mirams2010WntOdeSystem.hpp.
void Mirams2010WntOdeSystem::SetMutationState | ( | boost::shared_ptr< AbstractCellMutationState > | pMutationState | ) |
Set the mutation state of the cell.
This should be called by the relevant cell-cycle model before any solving of the ODE system (as it is used to evaluate the Y derivatives).
pMutationState | the mutation state. |
Definition at line 91 of file Mirams2010WntOdeSystem.cpp.
References mpMutationState.
|
friend |
Definition at line 87 of file Mirams2010WntOdeSystem.hpp.
|
private |
Parameters for the Mirams et al. (2010) model Dimensional parameter a.
Definition at line 69 of file Mirams2010WntOdeSystem.hpp.
Referenced by Mirams2010WntOdeSystem(), EvaluateYDerivatives(), and Init().
|
private |
Dimensional parameter b.
Definition at line 71 of file Mirams2010WntOdeSystem.hpp.
Referenced by Mirams2010WntOdeSystem(), EvaluateYDerivatives(), and Init().
|
private |
Dimensional parameter c.
Definition at line 73 of file Mirams2010WntOdeSystem.hpp.
Referenced by Mirams2010WntOdeSystem(), EvaluateYDerivatives(), and Init().
|
private |
Dimensional parameter d.
Definition at line 75 of file Mirams2010WntOdeSystem.hpp.
Referenced by Mirams2010WntOdeSystem(), EvaluateYDerivatives(), and Init().
|
private |
Dimensional parameter e.
Definition at line 77 of file Mirams2010WntOdeSystem.hpp.
Referenced by EvaluateYDerivatives(), and Init().
|
private |
Dimensional parameter f.
Definition at line 79 of file Mirams2010WntOdeSystem.hpp.
Referenced by Mirams2010WntOdeSystem(), EvaluateYDerivatives(), and Init().
|
private |
The mutation state of the cell (this affects the ODE system).
Definition at line 82 of file Mirams2010WntOdeSystem.hpp.
Referenced by Mirams2010WntOdeSystem(), EvaluateYDerivatives(), GetMutationState(), and SetMutationState().
|
private |
The Wnt level (this affects the ODE system).
Definition at line 85 of file Mirams2010WntOdeSystem.hpp.
Referenced by GetWntLevel().