MarkovSolverBase Class Reference

#include <MarkovSolverBase.h>

Inheritance diagram for MarkovSolverBase:

Collaboration diagram for MarkovSolverBase:

Public Member Functions
Vector *	bilinearInterpolate () const
virtual Matrix *	computeMatrixExponential ()
void	computeState ()
void	fillupTable ()
Vector	getInitialState () const
double	getInvDx () const
double	getInvDy () const
Matrix	getQ () const
Vector	getState () const
unsigned int	getXdivs () const
double	getXmax () const
double	getXmin () const
unsigned int	getYdivs () const
double	getYmax () const
double	getYmin () const
void	handleLigandConc (double)
void	handleVm (double)
void	init (Id, double)
void	innerFillupTable (vector< unsigned int >, string, unsigned int, unsigned int)
Vector *	linearInterpolate () const
	MarkovSolverBase ()
void	process (const Eref &, ProcPtr)
void	reinit (const Eref &, ProcPtr)
void	setInitialState (Vector)
void	setXdivs (unsigned int)
void	setXmax (double)
void	setXmin (double)
void	setYdivs (unsigned int)
void	setYmax (double)
void	setYmin (double)
virtual	~MarkovSolverBase ()

Static Public Member Functions
static const Cinfo *	initCinfo ()

Protected Attributes
Matrix *	Q_

Private Member Functions
void	setLookupParams ()

Private Attributes
double	dt_
Matrix *	expMat_
vector< Matrix * >	expMats1d_
vector< vector< Matrix * > >	expMats2d_
Vector	initialState_
double	invDx_
double	invDy_
double	ligandConc_
MarkovRateTable *	rateTable_
unsigned int	size_
Vector	state_
double	Vm_
unsigned int	xDivs_
double	xMax_
double	xMin_
unsigned int	yDivs_
double	yMax_
double	yMin_

Detailed Description

Definition at line 51 of file MarkovSolverBase.h.

Constructor & Destructor Documentation

MarkovSolverBase::MarkovSolverBase

(

)

Definition at line 189 of file MarkovSolverBase.cpp.

                                   : Q_(0), expMats1d_(0), expMat_(0),
    expMats2d_(0), xMin_(DBL_MAX), xMax_(DBL_MIN), xDivs_(0u),
    yMin_(DBL_MAX), yMax_(DBL_MIN), yDivs_(0u), size_(0u), Vm_(0),
    ligandConc_(0), dt_(0)
{
    ;
}

MarkovSolverBase::~MarkovSolverBase ( )

virtual

Definition at line 197 of file MarkovSolverBase.cpp.

References expMat_, expMats1d_, expMats2d_, and Q_.

{
    if ( Q_ )
        delete Q_;

    if ( !expMats1d_.empty() )
    {
        while ( !expMats1d_.empty() )
        {
            delete expMats1d_.back();
            expMats1d_.pop_back();
        }
    }

    if ( !expMats2d_.empty() )
    {
        unsigned int n = expMats2d_.size();
        for( unsigned int i = 0; i < n; ++i )
        {
            for ( unsigned int j = 0; j < expMats2d_[i].size(); ++j )
                delete expMats2d_[i][j];
        }
    }

    if ( expMat_ != 0 )
        delete expMat_;
}

Member Function Documentation

Vector * MarkovSolverBase::bilinearInterpolate

(

)

const

Definition at line 317 of file MarkovSolverBase.cpp.

References expMats2d_, invDx_, invDy_, ligandConc_, state_, vecMatMul(), vecVecScalAdd(), Vm_, xDivs_, xMin_, yDivs_, and yMin_.

Referenced by computeState().

{
    bool isEndOfX = false;
    bool isEndOfY = false;

    unsigned int xIndex =
        static_cast< unsigned int >( ( Vm_ - xMin_ ) * invDx_ );
    unsigned int yIndex =
        static_cast< unsigned int >( ( ligandConc_ - yMin_ ) * invDy_ );
    double xv = (Vm_ - xMin_) * invDx_;
    double yv = (ligandConc_ - yMin_) * invDy_;

    double xF = xv - xIndex;
    double yF = yv - yIndex;
    double xFyF = xF * yF;

    ( xIndex == xDivs_ ) ? isEndOfX = true : isEndOfX = false;
    ( yIndex == yDivs_ ) ? isEndOfY = true : isEndOfY = false;

    vector< vector< Matrix* > >::const_iterator iExpQ0 =
        expMats2d_.begin() + xIndex;
    vector< Matrix* >::const_iterator iExpQ00 = iExpQ0->begin() + yIndex;
    vector< Matrix* >::const_iterator iExpQ10;

    Matrix* expQ00 = *iExpQ00;
    Matrix* expQ01;
    Matrix* expQ10;
    Matrix* expQ11;

#if ENABLE_CPP1
    // Intialization to supress compiler warning.
    Vector *state00 = nullptr;
    Vector *state01 = nullptr;
    Vector *state10 = nullptr;
    Vector *state11 = nullptr;
    Vector *result = nullptr;
#else
    Vector *state00 = NULL, *state01 = NULL
        , *state10 = NULL, *state11 = NULL
        , *result = NULL
        ;
#endif

    state00 = vecMatMul( &state_, expQ00 );
    if ( isEndOfX )
    {
        if ( isEndOfY )
            return state00;
        else
        {
            expQ01 = *(iExpQ00 + 1);
            state01 = vecMatMul( &state_, expQ01 );
            result =  vecVecScalAdd( state00, state01,
                    (1 - yF), yF );
        }
    }
    else
    {
        iExpQ10 = ( iExpQ0 + 1 )->begin() + yIndex;
        expQ10 = *iExpQ10;
        state10 = vecMatMul( &state_, expQ10 );

        if ( isEndOfY )
        {
            result =  vecVecScalAdd( state00, state10, ( 1 - xF ), xF );
        }
        else
        {
            expQ01 = *( iExpQ00 + 1 );
            expQ11 = *( iExpQ10 + 1 );

            state01 = vecMatMul( &state_, expQ01 );
            state11 = vecMatMul( &state_, expQ11 );

            Vector *temp1, *temp2;

            temp1 = vecVecScalAdd( state00, state10,
                    ( 1 - xF - yF + xFyF ),
                    ( xF - xFyF )
                    );

            temp2 = vecVecScalAdd( state01, state11, ( yF - xFyF ), xFyF );

            result = vecVecScalAdd( temp1, temp2, 1.0, 1.0 );

            delete temp1;
            delete temp2;
        }
    }

    if ( state00 )
        delete state00;
    if ( state01 )
        delete state01;
    if ( state10 )
        delete state10;
    if ( state11 )
        delete state11;

    return result;
}

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Matrix * MarkovSolverBase::computeMatrixExponential ( )

virtual

Reimplemented in MarkovSolver.

Definition at line 600 of file MarkovSolverBase.cpp.

Referenced by fillupTable().

{
    return 0;
}

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void MarkovSolverBase::computeState

(

)

Definition at line 463 of file MarkovSolverBase.cpp.

References MarkovRateTable::areAllRates1d(), MarkovRateTable::areAnyRates2d(), MarkovRateTable::areAnyRatesLigandDep(), MarkovRateTable::areAnyRatesVoltageDep(), bilinearInterpolate(), linearInterpolate(), rateTable_, and state_.

Referenced by process().

{
    Vector* newState;
    bool useBilinear = false;
    // useLinear = false;

    if ( rateTable_->areAnyRates2d() ||
            ( rateTable_->areAllRates1d() &&
              rateTable_->areAnyRatesVoltageDep() &&
              rateTable_->areAnyRatesLigandDep()
            )  )
    {
        useBilinear = true;
    }
    /*
    else if ( rateTable_->areAllRatesVoltageDep() ||
                        rateTable_->areAllRatesLigandDep() )
    {
        useLinear = true;
    }
    */

    //Heavily borrows from the Interpol2D::interpolate function.
    if ( useBilinear )
        newState = bilinearInterpolate();
    else
        newState = linearInterpolate();

    state_ = *newState;

    delete newState;
}

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void MarkovSolverBase::fillupTable

(

)

Definition at line 524 of file MarkovSolverBase.cpp.

References MarkovRateTable::areAllRates1d(), MarkovRateTable::areAllRatesConstant(), MarkovRateTable::areAllRatesLigandDep(), MarkovRateTable::areAllRatesVoltageDep(), MarkovRateTable::areAnyRates2d(), MarkovRateTable::areAnyRatesLigandDep(), MarkovRateTable::areAnyRatesVoltageDep(), computeMatrixExponential(), expMat_, expMats1d_, expMats2d_, MarkovRateTable::getListOf1dRates(), MarkovRateTable::getListOf2dRates(), MarkovRateTable::getListOfConstantRates(), MarkovRateTable::getListOfLigandRates(), MarkovRateTable::getListOfVoltageRates(), innerFillupTable(), rateTable_, xDivs_, xMax_, xMin_, yDivs_, yMax_, and yMin_.

Referenced by init().

{
    double dx = (xMax_ - xMin_) / xDivs_;
    double dy = (yMax_ - yMin_) / yDivs_;

    vector< unsigned int > listOf1dRates = rateTable_->getListOf1dRates();
    vector< unsigned int > listOf2dRates = rateTable_->getListOf2dRates();
    vector< unsigned int > listOfConstantRates =
                                                 rateTable_->getListOfConstantRates();

    //Set constant rates in the Q matrix, if any.
    innerFillupTable( listOfConstantRates, "constant",
                                        0.0, 0.0 );

    //xIndex loops through all voltages, yIndex loops through all
    //ligand concentrations.
    if ( rateTable_->areAnyRates2d() ||
            ( rateTable_->areAllRates1d() &&
              rateTable_->areAnyRatesVoltageDep() &&
              rateTable_->areAnyRatesLigandDep()
            )  )
    {
        double voltage = xMin_, ligandConc = yMin_;

        for ( unsigned int xIndex = 0; xIndex < xDivs_ + 1; ++xIndex )
        {
            ligandConc = yMin_;
            for( unsigned int yIndex = 0; yIndex < yDivs_ + 1; ++yIndex )
            {
                innerFillupTable( listOf2dRates, "2D", xIndex, yIndex );

                //This is a very klutzy way of updating 1D rates as the same
                //lookup is done multiple times. But this all occurs at setup,
                //and lookups arent that slow either. This way is also easier
                //to maintain.
                innerFillupTable( listOf1dRates, "1D", xIndex, yIndex );

                expMats2d_[xIndex][yIndex] = computeMatrixExponential();
                ligandConc += dy;
            }
            voltage += dx;
        }
    }
    else if ( rateTable_->areAllRatesLigandDep() )
    {
        double x = xMin_;
        vector< unsigned int > listOfLigandRates =
                                                    rateTable_->getListOfLigandRates();

        for ( unsigned int xIndex = 0; xIndex < xDivs_ + 1; ++xIndex )
        {
            innerFillupTable( listOfLigandRates, "1D", xIndex, 0 );
            expMats1d_[xIndex] = computeMatrixExponential();
            x += dx;
        }
    }
    else if ( rateTable_->areAllRatesVoltageDep() )
    {
        double x = xMin_;
        vector< unsigned int > listOfVoltageRates =
                                                 rateTable_->getListOfVoltageRates();

        for ( unsigned int xIndex = 0; xIndex < xDivs_ + 1; ++xIndex )
        {
            innerFillupTable( listOfVoltageRates, "1D", xIndex, 0 );
            expMats1d_[xIndex] = computeMatrixExponential();
            x += dx;
        }
    }
    else if ( rateTable_->areAllRatesConstant() )
    {
        expMat_ = computeMatrixExponential();
        return;
    }
}

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Vector MarkovSolverBase::getInitialState

(

)

const

Definition at line 238 of file MarkovSolverBase.cpp.

References initialState_.

Referenced by initCinfo().

{
    return initialState_;
}

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double MarkovSolverBase::getInvDx

(

)

const

Definition at line 278 of file MarkovSolverBase.cpp.

References invDx_.

Referenced by initCinfo().

                                        {
    return invDx_;
}

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double MarkovSolverBase::getInvDy

(

)

const

Definition at line 312 of file MarkovSolverBase.cpp.

References invDy_.

Referenced by initCinfo().

{
    return invDy_;
}

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Matrix MarkovSolverBase::getQ

(

)

const

Definition at line 228 of file MarkovSolverBase.cpp.

References Q_.

Referenced by initCinfo().

{
    return *Q_;
}

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Vector MarkovSolverBase::getState

(

)

const

Definition at line 233 of file MarkovSolverBase.cpp.

References state_.

Referenced by initCinfo().

{
    return state_;
}

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unsigned int MarkovSolverBase::getXdivs

(

)

const

Definition at line 274 of file MarkovSolverBase.cpp.

References xDivs_.

Referenced by initCinfo().

                                               {
    return xDivs_;
}

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double MarkovSolverBase::getXmax

(

)

const

Definition at line 264 of file MarkovSolverBase.cpp.

References xMax_.

Referenced by initCinfo().

{
    return xMax_;
}

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double MarkovSolverBase::getXmin

(

)

const

Definition at line 254 of file MarkovSolverBase.cpp.

References xMin_.

Referenced by initCinfo().

{
    return xMin_;
}

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unsigned int MarkovSolverBase::getYdivs

(

)

const

Definition at line 307 of file MarkovSolverBase.cpp.

References yDivs_.

Referenced by initCinfo().

{
    return yDivs_;
}

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double MarkovSolverBase::getYmax

(

)

const

Definition at line 297 of file MarkovSolverBase.cpp.

References yMax_.

Referenced by initCinfo().

{
    return yMax_;
}

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double MarkovSolverBase::getYmin

(

)

const

Definition at line 287 of file MarkovSolverBase.cpp.

References yMin_.

Referenced by initCinfo().

{
    return yMin_;
}

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void MarkovSolverBase::handleLigandConc

(

double

ligandConc

)

Definition at line 634 of file MarkovSolverBase.cpp.

References ligandConc_.

Referenced by initCinfo().

{
    ligandConc_ = ligandConc;
}

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void MarkovSolverBase::handleVm

(

double

Vm

)

Definition at line 629 of file MarkovSolverBase.cpp.

References Vm_.

Referenced by initCinfo().

{
    Vm_ = Vm;
}

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void MarkovSolverBase::init	(	Id	rateTableId,
		double	dt
	)

Definition at line 641 of file MarkovSolverBase.cpp.

References MarkovRateTable::areAllRates1d(), MarkovRateTable::areAllRatesLigandDep(), MarkovRateTable::areAllRatesVoltageDep(), MarkovRateTable::areAnyRates2d(), MarkovRateTable::areAnyRatesLigandDep(), MarkovRateTable::areAnyRatesVoltageDep(), Eref::data(), dt_, Id::eref(), expMat_, expMats1d_, expMats2d_, fillupTable(), MarkovRateTable::getSize(), matAlloc(), Q_, rateTable_, resize(), setLookupParams(), size_, xDivs_, and yDivs_.

Referenced by initCinfo().

{
    MarkovRateTable* rateTable = reinterpret_cast< MarkovRateTable* >(
            rateTableId.eref().data() );

    size_ = rateTable->getSize();
    rateTable_ = rateTable;
    setLookupParams( );

    if ( rateTable->areAnyRates2d() ||
            ( rateTable->areAllRates1d() &&
              rateTable->areAnyRatesVoltageDep() &&
              rateTable->areAnyRatesLigandDep()
            )  )
    {
        expMats2d_.resize( xDivs_ + 1 );
        for( unsigned int i = 0; i < xDivs_ + 1; ++i )
            expMats2d_[i].resize( yDivs_ + 1);
    }
    else if ( rateTable->areAllRatesLigandDep() ||
                        rateTable->areAllRatesVoltageDep() )
    {
        expMats1d_.resize( xDivs_ + 1);
    }
    else    //All rates must be constant.
    {
        expMat_ = matAlloc( size_ );
    }

    //Initializing Q.
    Q_ = matAlloc( size_ );

    //The state at t = t0 + dt is exp( dt * Q ) * [state at t = t0].
    //Hence, we need to scale the terms of Q by dt.
    dt_ = dt;

    //Fills up the newly setup tables with exponentials.
    fillupTable( );
}

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const Cinfo * MarkovSolverBase::initCinfo ( )

static

Definition at line 28 of file MarkovSolverBase.cpp.

References getInitialState(), getInvDx(), getInvDy(), getQ(), getState(), getXdivs(), getXmax(), getXmin(), getYdivs(), getYmax(), getYmin(), handleLigandConc(), handleVm(), init(), Neutral::initCinfo(), markovSolverBaseCinfo, process(), reinit(), setInitialState(), setXdivs(), setXmax(), setXmin(), setYdivs(), setYmax(), setYmin(), and stateOut().

Referenced by MarkovSolver::initCinfo().

{
    //SharedFinfos
    static DestFinfo handleVm("handleVm",
            "Handles incoming message containing voltage information.",
            new OpFunc1< MarkovSolverBase, double >(&MarkovSolverBase::handleVm)
            );

    static Finfo* channelShared[] =
    {
        &handleVm
    };

    static SharedFinfo channel("channel",
            "This message couples the MarkovSolverBase to the Compartment. The "
            "compartment needs Vm in order to look up the correct matrix "
            "exponential for computing the state.",
            channelShared, sizeof( channelShared ) / sizeof( Finfo* )
            );

    //DestFinfos

    static DestFinfo process(   "process",
            "Handles process call",
            new ProcOpFunc< MarkovSolverBase >( &MarkovSolverBase::process ) );

    static DestFinfo reinit( "reinit",
            "Handles reinit call",
            new ProcOpFunc< MarkovSolverBase >( &MarkovSolverBase::reinit ) );

    static Finfo* processShared[] =
    {
        &process, &reinit
    };

    static SharedFinfo proc( "proc",
            "This is a shared message to receive Process message from the"
            "scheduler. The first entry is a MsgDest for the Process "
            "operation. It has a single argument, ProcInfo, which "
            "holds lots of information about current time, thread, dt and"
            "so on. The second entry is a MsgDest for the Reinit "
            "operation. It also uses ProcInfo.",
        processShared, sizeof( processShared ) / sizeof( Finfo* )
    );

    static DestFinfo ligandConc("ligandConc",
            "Handles incoming message containing ligand concentration.",
            new OpFunc1< MarkovSolverBase, double >(&MarkovSolverBase::handleLigandConc)
            );

    static DestFinfo init("init",
            "Setups the table of matrix exponentials associated with the"
            " solver object.",
            new OpFunc2< MarkovSolverBase, Id, double >(&MarkovSolverBase::init)
            );

    //*ValueFinfos

    static ReadOnlyValueFinfo< MarkovSolverBase, Matrix > Q("Q",
            "Instantaneous rate matrix.",
            &MarkovSolverBase::getQ
            );

    static ReadOnlyValueFinfo< MarkovSolverBase, Vector > state("state",
            "Current state of the channel.",
            &MarkovSolverBase::getState
            );

    static ValueFinfo< MarkovSolverBase, Vector > initialstate("initialState",
            "Initial state of the channel.",
            &MarkovSolverBase::setInitialState,
            &MarkovSolverBase::getInitialState
            );

    static ValueFinfo< MarkovSolverBase, double > xmin( "xmin",
        "Minimum value for x axis of lookup table",
            &MarkovSolverBase::setXmin,
            &MarkovSolverBase::getXmin
        );
    static ValueFinfo< MarkovSolverBase, double > xmax( "xmax",
        "Maximum value for x axis of lookup table",
            &MarkovSolverBase::setXmax,
            &MarkovSolverBase::getXmax
        );
    static ValueFinfo< MarkovSolverBase, unsigned int > xdivs( "xdivs",
        "# of divisions on x axis of lookup table",
            &MarkovSolverBase::setXdivs,
            &MarkovSolverBase::getXdivs
        );
    static ReadOnlyValueFinfo< MarkovSolverBase, double > invdx( "invdx",
        "Reciprocal of increment on x axis of lookup table",
            &MarkovSolverBase::getInvDx
        );
    static ValueFinfo< MarkovSolverBase, double > ymin( "ymin",
        "Minimum value for y axis of lookup table",
            &MarkovSolverBase::setYmin,
            &MarkovSolverBase::getYmin
        );
    static ValueFinfo< MarkovSolverBase, double > ymax( "ymax",
        "Maximum value for y axis of lookup table",
            &MarkovSolverBase::setYmax,
            &MarkovSolverBase::getYmax
        );
    static ValueFinfo< MarkovSolverBase, unsigned int > ydivs( "ydivs",
        "# of divisions on y axis of lookup table",
            &MarkovSolverBase::setYdivs,
            &MarkovSolverBase::getYdivs
        );
    static ReadOnlyValueFinfo< MarkovSolverBase, double > invdy( "invdy",
        "Reciprocal of increment on y axis of lookup table",
            &MarkovSolverBase::getInvDy
        );

    static Finfo* markovSolverFinfos[] =
    {
        &channel,                       //SharedFinfo
        &proc,                          //SharedFinfo
        stateOut(),                 //SrcFinfo
        &ligandConc,                //DestFinfo
        &init,                          //DestFinfo
        &Q,                                 //ReadOnlyValueFinfo
        &state,                         //ReadOnlyValueFinfo
        &initialstate,          //ReadOnlyValueFinfo
        &xmin,                          //ValueFinfo
        &xmax,                          //ValueFinfo
        &xdivs,                         //ValueFinfo
        &invdx,                         //ReadOnlyValueFinfo
        &ymin,                          //ValueFinfo
        &ymax,                          //ValueFinfo
        &ydivs,                         //ValueFinfo
        &invdy                          //ReadOnlyValueFinfo
    };

    static string doc[] =
    {
        "Name", "MarkovSolverBase",
        "Author", "Vishaka Datta S, 2011, NCBS",
        "Description", "Solver for Markov Channel."
    };
    static Dinfo< MarkovSolverBase > dinfo;
    static Cinfo markovSolverBaseCinfo(
            "MarkovSolverBase",
            Neutral::initCinfo(),
            markovSolverFinfos,
            sizeof( markovSolverFinfos ) / sizeof( Finfo* ),
            &dinfo,
            doc,
            sizeof(doc) / sizeof(string)
        );

    return &markovSolverBaseCinfo;
}

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void MarkovSolverBase::innerFillupTable	(	vector< unsigned int >	,
		string	,
		unsigned	int,
		unsigned	int
	)

Definition at line 496 of file MarkovSolverBase.cpp.

References dt_, MarkovRateTable::lookup1dIndex(), MarkovRateTable::lookup1dValue(), MarkovRateTable::lookup2dIndex(), Q_, and rateTable_.

Referenced by fillupTable().

{
    unsigned int n = rateIndices.size(), i, j;

    for ( unsigned int k = 0; k < n; ++k )
    {
        i = ( ( rateIndices[k] / 10 ) % 10 ) - 1;
        j = ( rateIndices[k] % 10 ) - 1;

        (*Q_)[i][i] += (*Q_)[i][j];

        if ( rateType.compare("2D") == 0 )
            (*Q_)[i][j] = rateTable_->lookup2dIndex( i, j, xIndex, yIndex );
        else if ( rateType.compare("1D") == 0 )
            (*Q_)[i][j] = rateTable_->lookup1dIndex( i, j, xIndex );
        else if ( rateType.compare("constant") == 0 )
            (*Q_)[i][j] = rateTable_->lookup1dValue( i, j, 1.0 );

        (*Q_)[i][j] *= dt_;

        (*Q_)[i][i] -= (*Q_)[i][j];
    }
}

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Vector * MarkovSolverBase::linearInterpolate

(

)

const

Definition at line 419 of file MarkovSolverBase.cpp.

References MarkovRateTable::areAllRatesVoltageDep(), expMats1d_, invDx_, ligandConc_, rateTable_, state_, vecMatMul(), vecVecScalAdd(), Vm_, xMax_, and xMin_.

Referenced by computeState().

{
    double x;

    if ( rateTable_->areAllRatesVoltageDep() )
        x = Vm_;
    else
        x = ligandConc_;

    if ( x < xMin_ )
        return vecMatMul( &state_, expMats1d_[0] );
    else if ( x > xMax_ )
        return vecMatMul( &state_, expMats1d_.back() );

    unsigned int xIndex = static_cast< unsigned int >( ( x - xMin_) * invDx_ );

    double xv = ( x - xMin_ ) * invDx_;
    double xF = xv - xIndex;

    vector< Matrix* >::const_iterator iExpQ =
                                                                                    expMats1d_.begin() + xIndex;

    Vector *state0, *state1, *result;

    state0 = vecMatMul( &state_, *iExpQ );
    state1 = vecMatMul( &state_, *( iExpQ + 1 ) );

    result = vecVecScalAdd( state0, state1, 1 - xF, xF );

    delete state0;
    delete state1;

    return result;
}

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void MarkovSolverBase::process	(	const Eref &	e,
		ProcPtr	p
	)

Definition at line 622 of file MarkovSolverBase.cpp.

References computeState(), state_, and stateOut().

Referenced by initCinfo(), and MarkovSolver::process().

{
    computeState();

    stateOut()->send( e, state_ );
}

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void MarkovSolverBase::reinit	(	const Eref &	e,
		ProcPtr	p
	)

Definition at line 609 of file MarkovSolverBase.cpp.

References initialState_, state_, and stateOut().

Referenced by initCinfo(), and MarkovSolver::reinit().

{
    if ( initialState_.empty() )
    {
        cerr << "MarkovSolverBase::reinit : Initial state has not been "
                        "set.\n";
        return;
    }
    state_ = initialState_;

    stateOut()->send( e, state_ );
}

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void MarkovSolverBase::setInitialState

(

Vector

state

)

Definition at line 243 of file MarkovSolverBase.cpp.

References initialState_, and state_.

Referenced by initCinfo().

{
    initialState_ = state;
    state_ = initialState_;
}

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void MarkovSolverBase::setLookupParams ( )

private

Definition at line 697 of file MarkovSolverBase.cpp.

References MarkovRateTable::areAllRates1d(), MarkovRateTable::areAllRatesLigandDep(), MarkovRateTable::areAnyRates1d(), MarkovRateTable::areAnyRates2d(), VectorTable::getDiv(), MarkovRateTable::getInt2dChildTable(), MarkovRateTable::getListOf2dRates(), MarkovRateTable::getListOfLigandRates(), MarkovRateTable::getListOfVoltageRates(), VectorTable::getMax(), VectorTable::getMin(), MarkovRateTable::getVtChildTable(), Interpol2D::getXdivs(), Interpol2D::getXmax(), Interpol2D::getXmin(), Interpol2D::getYdivs(), Interpol2D::getYmax(), Interpol2D::getYmin(), invDx_, invDy_, rateTable_, xDivs_, xMax_, xMin_, yDivs_, yMax_, and yMin_.

Referenced by init().

{
    if ( rateTable_->areAnyRates1d() )
    {
        vector< unsigned int > listOfLigandRates
                                                        = rateTable_->getListOfLigandRates();
        vector< unsigned int > listOfVoltageRates
                                                        = rateTable_->getListOfVoltageRates();

        double temp;
        double yMax = DBL_MIN, yMin = DBL_MAX;
        unsigned int yDivs = 0u;
        unsigned int divs, i, j;

        for( unsigned int k = 0; k < listOfLigandRates.size(); ++k )
        {
            i = ( ( listOfLigandRates[k] / 10 ) % 10 ) - 1;
            j = ( listOfLigandRates[k] % 10 ) - 1;

            temp = rateTable_->getVtChildTable( i, j )->getMin();
            if ( yMin > temp )
                yMin = temp;

            temp = rateTable_->getVtChildTable( i, j )->getMax();
            if ( yMax < temp )
                yMax = temp;

            divs = rateTable_->getVtChildTable( i, j )->getDiv();
            if ( yDivs < divs )
                yDivs = divs;
        }

        if ( ( rateTable_->areAllRatesLigandDep() &&
                     rateTable_->areAllRates1d() ) )
        {
            xMin_ = yMin;
            xMax_ = yMax;
            xDivs_ = yDivs;
            invDx_ = yDivs / ( yMax - yMin );
        }
        else
        {
            yMin_= yMin;
            yMax_ = yMax;
            yDivs_ = yDivs;
            invDy_ = yDivs / ( yMax - yMin );
        }

        for( unsigned int k = 0; k < listOfVoltageRates.size(); ++k )
        {
            i = ( ( listOfVoltageRates[k] / 10 ) % 10 ) - 1;
            j = ( listOfVoltageRates[k] % 10 ) - 1;

            temp = rateTable_->getVtChildTable( i, j )->getMin();
            if ( xMin_ > temp )
                xMin_ = temp;

            temp = rateTable_->getVtChildTable( i, j )->getMax();
            if ( xMax_ < temp )
                xMax_ = temp;

            divs = rateTable_->getVtChildTable( i, j )->getDiv();
            if ( xDivs_ < divs )
                xDivs_ = divs;
        }
    }

    if ( rateTable_->areAnyRates2d() )
    {
        vector< unsigned int > listOf2dRates = rateTable_->getListOf2dRates();
        double temp;
        unsigned int divs, i, j;

        for( unsigned int k = 0; k < listOf2dRates.size(); ++k )
        {
            i = ( ( listOf2dRates[k] / 10 ) % 10 ) - 1;
            j = ( listOf2dRates[k] % 10 ) - 1;

            temp = rateTable_->getInt2dChildTable( i, j )->getXmin();
            if ( xMin_ > temp )
                xMin_ = temp;

            temp = rateTable_->getInt2dChildTable( i, j )->getXmax();
            if ( xMax_ < temp )
                xMax_ = temp;

            temp = rateTable_->getInt2dChildTable( i, j )->getYmin();
            if ( yMin_ > temp )
                yMin_ = temp;

            temp = rateTable_->getInt2dChildTable( i, j )->getYmax();
            if ( yMax_ < temp )
                yMax_ = temp;

            divs = rateTable_->getInt2dChildTable( i, j )->getXdivs();
            if ( xDivs_ < divs )
                xDivs_ = divs;

            divs = rateTable_->getInt2dChildTable( i, j )->getYdivs();
            if ( yDivs_ < divs )
                yDivs_ = divs;
        }

        invDx_ = xDivs_ / ( xMax_ - xMin_ );
        invDy_ = yDivs_ / ( yMax_ - yMin_ );
    }
}

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void MarkovSolverBase::setXdivs

(

unsigned int

xDivs

)

Definition at line 269 of file MarkovSolverBase.cpp.

References xDivs_.

Referenced by initCinfo().

{
    xDivs_ = xDivs;
}

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void MarkovSolverBase::setXmax

(

double

xMax

)

Definition at line 259 of file MarkovSolverBase.cpp.

References xMax_.

Referenced by initCinfo().

{
    xMax_ = xMax;
}

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void MarkovSolverBase::setXmin

(

double

xMin

)

Definition at line 249 of file MarkovSolverBase.cpp.

References xMin_.

Referenced by initCinfo().

{
    xMin_ = xMin;
}

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void MarkovSolverBase::setYdivs

(

unsigned int

yDivs

)

Definition at line 302 of file MarkovSolverBase.cpp.

References yDivs_.

Referenced by initCinfo().

{
    yDivs_ = yDivs;
}

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void MarkovSolverBase::setYmax

(

double

yMax

)

Definition at line 292 of file MarkovSolverBase.cpp.

References yMax_.

Referenced by initCinfo().

{
    yMax_ = yMax;
}

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void MarkovSolverBase::setYmin

(

double

yMin

)

Definition at line 282 of file MarkovSolverBase.cpp.

References yMin_.

Referenced by initCinfo().

{
    yMin_ = yMin;
}

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Member Data Documentation

double MarkovSolverBase::dt_

private

Definition at line 211 of file MarkovSolverBase.h.

Referenced by init(), and innerFillupTable().

Matrix* MarkovSolverBase::expMat_

private

Definition at line 172 of file MarkovSolverBase.h.

Referenced by fillupTable(), init(), and ~MarkovSolverBase().

vector< Matrix* > MarkovSolverBase::expMats1d_

private

Definition at line 170 of file MarkovSolverBase.h.

Referenced by fillupTable(), init(), linearInterpolate(), and ~MarkovSolverBase().

vector< vector< Matrix* > > MarkovSolverBase::expMats2d_

private

Definition at line 175 of file MarkovSolverBase.h.

Referenced by bilinearInterpolate(), fillupTable(), init(), and ~MarkovSolverBase().

Vector MarkovSolverBase::initialState_

private

Definition at line 198 of file MarkovSolverBase.h.

Referenced by getInitialState(), reinit(), and setInitialState().

double MarkovSolverBase::invDx_

private

Definition at line 179 of file MarkovSolverBase.h.

Referenced by bilinearInterpolate(), getInvDx(), linearInterpolate(), and setLookupParams().

double MarkovSolverBase::invDy_

private

Definition at line 183 of file MarkovSolverBase.h.

Referenced by bilinearInterpolate(), getInvDy(), and setLookupParams().

double MarkovSolverBase::ligandConc_

private

Definition at line 207 of file MarkovSolverBase.h.

Referenced by bilinearInterpolate(), handleLigandConc(), and linearInterpolate().

Matrix* MarkovSolverBase::Q_

protected

Definition at line 130 of file MarkovSolverBase.h.

Referenced by MarkovSolver::computeMatrixExponential(), getQ(), init(), innerFillupTable(), and ~MarkovSolverBase().

MarkovRateTable* MarkovSolverBase::rateTable_

private

Definition at line 192 of file MarkovSolverBase.h.

Referenced by computeState(), fillupTable(), init(), innerFillupTable(), linearInterpolate(), and setLookupParams().

unsigned int MarkovSolverBase::size_

private

Definition at line 202 of file MarkovSolverBase.h.

Referenced by init().

Vector MarkovSolverBase::state_

private

Definition at line 195 of file MarkovSolverBase.h.

Referenced by bilinearInterpolate(), computeState(), getState(), linearInterpolate(), process(), reinit(), and setInitialState().

double MarkovSolverBase::Vm_

private

Definition at line 205 of file MarkovSolverBase.h.

Referenced by bilinearInterpolate(), handleVm(), and linearInterpolate().

unsigned int MarkovSolverBase::xDivs_

private

Definition at line 180 of file MarkovSolverBase.h.

Referenced by bilinearInterpolate(), fillupTable(), getXdivs(), init(), setLookupParams(), and setXdivs().

double MarkovSolverBase::xMax_

private

Definition at line 178 of file MarkovSolverBase.h.

Referenced by fillupTable(), getXmax(), linearInterpolate(), setLookupParams(), and setXmax().

double MarkovSolverBase::xMin_

private

Definition at line 177 of file MarkovSolverBase.h.

Referenced by bilinearInterpolate(), fillupTable(), getXmin(), linearInterpolate(), setLookupParams(), and setXmin().

unsigned int MarkovSolverBase::yDivs_

private

Definition at line 184 of file MarkovSolverBase.h.

Referenced by bilinearInterpolate(), fillupTable(), getYdivs(), init(), setLookupParams(), and setYdivs().

double MarkovSolverBase::yMax_

private

Definition at line 182 of file MarkovSolverBase.h.

Referenced by fillupTable(), getYmax(), setLookupParams(), and setYmax().

double MarkovSolverBase::yMin_

private

Definition at line 181 of file MarkovSolverBase.h.

Referenced by bilinearInterpolate(), fillupTable(), getYmin(), setLookupParams(), and setYmin().

---

The documentation for this class was generated from the following files:

• moose-core/biophysics/MarkovSolverBase.h
• moose-core/biophysics/MarkovSolverBase.cpp