#include <MarkovRateTable.h>

Collaboration diagram for MarkovRateTable:

Public Member Functions
bool	areAllRates1d ()

bool	areAllRates2d ()

bool	areAllRatesConstant ()

bool	areAllRatesLigandDep ()

bool	areAllRatesVoltageDep ()

bool	areAnyRates1d ()

bool	areAnyRates2d ()

bool	areAnyRatesLigandDep ()

bool	areAnyRatesVoltageDep ()

bool	areIndicesOutOfBounds (unsigned int, unsigned int) const

Interpol2D *	getInt2dChildTable (unsigned int, unsigned int) const

double	getLigandConc () const

vector< unsigned int >	getListOf1dRates ()

vector< unsigned int >	getListOf2dRates ()

vector< unsigned int >	getListOfConstantRates ()

vector< unsigned int >	getListOfLigandRates ()

vector< unsigned int >	getListOfVoltageRates ()

vector< vector< double > >	getQ () const

unsigned int	getSize () const

double	getVm () const

VectorTable *	getVtChildTable (unsigned int, unsigned int) const

void	handleLigandConc (double)

void	handleVm (double)

void	init (unsigned int)

void	initConstantRates ()

void	innerSetInt2dChildTable (unsigned int, unsigned int, Interpol2D)

void	innerSetVtChildTable (unsigned int, unsigned int, VectorTable, unsigned int)

bool	isRate1d (unsigned int, unsigned int) const

bool	isRate2d (unsigned int, unsigned int) const

bool	isRateConstant (unsigned int, unsigned int) const

bool	isRateLigandDep (unsigned int, unsigned int) const

bool	isRateZero (unsigned int, unsigned int) const

double	lookup1dIndex (unsigned int, unsigned int, unsigned int)

double	lookup1dValue (unsigned int, unsigned int, double)

double	lookup2dIndex (unsigned int, unsigned int, unsigned int, unsigned int)

double	lookup2dValue (unsigned int, unsigned int, double, double)

	MarkovRateTable ()

void	process (const Eref &, ProcPtr)

void	reinit (const Eref &, ProcPtr)

void	setConstantRate (unsigned int, unsigned int, double)

void	setInt2dChildTable (unsigned int, unsigned int, Id)

void	setLigandConc (double)

void	setVm (double)

void	setVtChildTable (unsigned int, unsigned int, Id, unsigned int)

void	updateRates ()

	~MarkovRateTable ()

Static Public Member Functions
static const Cinfo *	initCinfo ()

Private Member Functions
bool	isInitialized () const

Private Attributes
vector< vector< Interpol2D * > >	int2dTables_

double	ligandConc_

vector< unsigned int >	listOf1dRates_

vector< unsigned int >	listOf2dRates_

vector< unsigned int >	listOfConstantRates_

vector< unsigned int >	listOfLigandRates_

vector< unsigned int >	listOfVoltageRates_

vector< vector< double > >	Q_

unsigned int	size_

vector< vector< unsigned int > >	useLigandConc_

double	Vm_

vector< vector< VectorTable * > >	vtTables_

Friends
istream &	operator>> (istream &, MarkovRateTable &)

Detailed Description

Definition at line 48 of file MarkovRateTable.h.

Constructor & Destructor Documentation

MarkovRateTable::MarkovRateTable ( )

Definition at line 170 of file MarkovRateTable.cpp.

                                  :
     Vm_(0),
     ligandConc_(0),
     size_(0)
 { ; }

MarkovRateTable::~MarkovRateTable ( )

Definition at line 176 of file MarkovRateTable.cpp.

References int2dTables_, isRate1d(), isRate2d(), isRateConstant(), size_, and vtTables_.

 {
     for ( unsigned int i = 0; i < size_; ++i )
     {
         for ( unsigned int j = 0; j < size_; ++j )
         {
             if ( isRate1d( i, j ) || isRateConstant( i, j ) )
                 delete vtTables_[i][j];
             if ( isRate2d( i, j ) )
                 delete int2dTables_[i][j];
         }
     }
 }

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Member Function Documentation

bool MarkovRateTable::areAllRates1d ( )

Definition at line 444 of file MarkovRateTable.cpp.

References areAnyRates1d(), and areAnyRates2d().

Referenced by areAllRatesLigandDep(), areAllRatesVoltageDep(), MarkovSolverBase::computeState(), MarkovSolverBase::fillupTable(), MarkovSolverBase::init(), and MarkovSolverBase::setLookupParams().

 {
     return areAnyRates1d() && !areAnyRates2d();
 }

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bool MarkovRateTable::areAllRates2d ( )

Definition at line 455 of file MarkovRateTable.cpp.

References areAnyRates1d(), and areAnyRates2d().

 {
     return areAnyRates2d() && !areAnyRates1d();
 }

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bool MarkovRateTable::areAllRatesConstant ( )

Definition at line 432 of file MarkovRateTable.cpp.

References listOf1dRates_, listOf2dRates_, and listOfConstantRates_.

Referenced by MarkovSolverBase::fillupTable(), and process().

 {
     return listOf1dRates_.empty() && listOf2dRates_.empty() &&
             !listOfConstantRates_.empty();
 }

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bool MarkovRateTable::areAllRatesLigandDep ( )

Definition at line 466 of file MarkovRateTable.cpp.

References areAllRates1d(), areAnyRatesLigandDep(), and areAnyRatesVoltageDep().

Referenced by MarkovSolverBase::fillupTable(), MarkovSolverBase::init(), and MarkovSolverBase::setLookupParams().

 {
     return areAllRates1d() && !areAnyRatesVoltageDep() &&
             areAnyRatesLigandDep();
 }

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bool MarkovRateTable::areAllRatesVoltageDep ( )

Definition at line 478 of file MarkovRateTable.cpp.

References areAllRates1d(), areAnyRatesLigandDep(), and areAnyRatesVoltageDep().

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

 {
     return areAllRates1d() && areAnyRatesVoltageDep() &&
             !areAnyRatesLigandDep();
 }

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bool MarkovRateTable::areAnyRates1d ( )

Definition at line 439 of file MarkovRateTable.cpp.

References listOf1dRates_.

Referenced by areAllRates1d(), areAllRates2d(), and MarkovSolverBase::setLookupParams().

 {
     return !listOf1dRates_.empty();
 }

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bool MarkovRateTable::areAnyRates2d ( )

Definition at line 450 of file MarkovRateTable.cpp.

References listOf2dRates_.

Referenced by areAllRates1d(), areAllRates2d(), MarkovSolverBase::computeState(), MarkovSolverBase::fillupTable(), MarkovSolverBase::init(), and MarkovSolverBase::setLookupParams().

 {
     return !listOf2dRates_.empty();
 }

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bool MarkovRateTable::areAnyRatesLigandDep ( )

Definition at line 461 of file MarkovRateTable.cpp.

References listOfLigandRates_.

Referenced by areAllRatesLigandDep(), areAllRatesVoltageDep(), MarkovSolverBase::computeState(), MarkovSolverBase::fillupTable(), and MarkovSolverBase::init().

 {
     return !listOfLigandRates_.empty();
 }

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bool MarkovRateTable::areAnyRatesVoltageDep ( )

Definition at line 473 of file MarkovRateTable.cpp.

References listOfVoltageRates_.

Referenced by areAllRatesLigandDep(), areAllRatesVoltageDep(), MarkovSolverBase::computeState(), MarkovSolverBase::fillupTable(), and MarkovSolverBase::init().

 {
     return !listOfVoltageRates_.empty();
 }

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bool MarkovRateTable::areIndicesOutOfBounds	(	unsigned int	i,
		unsigned int	j
	)		const

Definition at line 427 of file MarkovRateTable.cpp.

References size_.

Referenced by innerSetInt2dChildTable(), innerSetVtChildTable(), lookup1dIndex(), lookup1dValue(), lookup2dIndex(), and lookup2dValue().

 {
     return ( i > size_ || j > size_ );
 }

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Interpol2D * MarkovRateTable::getInt2dChildTable	(	unsigned int	i,
		unsigned int	j
	)		const

Definition at line 236 of file MarkovRateTable.cpp.

References int2dTables_, and isRate2d().

Referenced by MarkovSolverBase::setLookupParams().

 {
     if ( isRate2d( i, j ) )
         return int2dTables_[i][j];
     else
     {
         cerr << "MarkovRateTable::getInt2dChildTable : Error : No two parameter"
                 " rate table set for (" << i+1 << "," << j+1 << "). Returning NULL.\n";
         return 0;
     }
 }

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double MarkovRateTable::getLigandConc ( ) const

Definition at line 383 of file MarkovRateTable.cpp.

References ligandConc_.

Referenced by initCinfo().

 {
     return ligandConc_;
 }

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vector< unsigned int > MarkovRateTable::getListOf1dRates ( )

Definition at line 543 of file MarkovRateTable.cpp.

References listOf1dRates_.

Referenced by MarkovSolverBase::fillupTable().

 {
     return listOf1dRates_;
 }

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vector< unsigned int > MarkovRateTable::getListOf2dRates ( )

Definition at line 548 of file MarkovRateTable.cpp.

References listOf2dRates_.

Referenced by MarkovSolverBase::fillupTable(), and MarkovSolverBase::setLookupParams().

 {
     return listOf2dRates_;
 }

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vector< unsigned int > MarkovRateTable::getListOfConstantRates ( )

Definition at line 563 of file MarkovRateTable.cpp.

References listOfConstantRates_.

Referenced by MarkovSolverBase::fillupTable().

 {
     return listOfConstantRates_;
 }

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vector< unsigned int > MarkovRateTable::getListOfLigandRates ( )

Definition at line 558 of file MarkovRateTable.cpp.

References listOfLigandRates_.

Referenced by MarkovSolverBase::fillupTable(), and MarkovSolverBase::setLookupParams().

 {
     return listOfLigandRates_;
 }

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vector< unsigned int > MarkovRateTable::getListOfVoltageRates ( )

Definition at line 553 of file MarkovRateTable.cpp.

References listOfVoltageRates_.

Referenced by MarkovSolverBase::fillupTable(), and MarkovSolverBase::setLookupParams().

 {
     return listOfVoltageRates_;
 }

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vector< vector< double > > MarkovRateTable::getQ ( ) const

Definition at line 363 of file MarkovRateTable.cpp.

References Q_.

Referenced by initCinfo().

 {
     return Q_;
 }

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unsigned int MarkovRateTable::getSize ( ) const

Definition at line 368 of file MarkovRateTable.cpp.

References size_.

Referenced by MarkovSolverBase::init(), and initCinfo().

 {
     return size_;
 }

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double MarkovRateTable::getVm ( ) const

Definition at line 373 of file MarkovRateTable.cpp.

References Vm_.

Referenced by initCinfo().

 {
     return Vm_;
 }

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VectorTable * MarkovRateTable::getVtChildTable	(	unsigned int	i,
		unsigned int	j
	)		const

Definition at line 190 of file MarkovRateTable.cpp.

References isRate1d(), isRateConstant(), and vtTables_.

Referenced by MarkovSolverBase::setLookupParams().

 {
     if ( isRate1d( i, j ) || isRateConstant( i, j ) )
         return vtTables_[i][j];
     else
     {
         cerr << "MarkovRateTable::getVtChildTable : Error : No one parameter rate "
                 "table set for (" << i+1 << "," << j+1 << "). Returing NULL.\n";
         return 0;
     }
 }

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void MarkovRateTable::handleLigandConc ( double ligandConc )

Definition at line 649 of file MarkovRateTable.cpp.

References ligandConc_.

Referenced by initCinfo().

 {
     ligandConc_ = ligandConc;
 }

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void MarkovRateTable::handleVm ( double Vm )

Definition at line 644 of file MarkovRateTable.cpp.

References Vm_.

Referenced by initCinfo().

 {
     Vm_ = Vm;
 }

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void MarkovRateTable::init ( unsigned int size )

Definition at line 630 of file MarkovRateTable.cpp.

References int2dTables_, Q_, size_, useLigandConc_, and vtTables_.

Referenced by initCinfo().

 {
     size_ = size;
 
     if ( vtTables_.empty() )
         vtTables_ = resize< VectorTable* >( vtTables_, size, 0 );
     if ( int2dTables_.empty() )
         int2dTables_ = resize< Interpol2D* >( int2dTables_, size, 0 );
     if ( useLigandConc_.empty() )
         useLigandConc_ = resize< unsigned int >( useLigandConc_, size, 0 );
     if ( Q_.empty() )
         Q_ = resize< double >( Q_, size, 0 );
 }

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const Cinfo * MarkovRateTable::initCinfo ( )

static

Definition at line 27 of file MarkovRateTable.cpp.

References getLigandConc(), getQ(), getSize(), getVm(), handleLigandConc(), handleVm(), init(), Neutral::initCinfo(), instRatesOut(), MarkovRateTableCinfo, process(), reinit(), setConstantRate(), setInt2dChildTable(), setLigandConc(), setVm(), and setVtChildTable().

 {
     //SharedFinfos
     static DestFinfo handleVm("handleVm",
                               "Handles incoming message containing voltage information.",
                               new OpFunc1< MarkovRateTable, double >(&MarkovRateTable::handleVm)
                               );
 
     static Finfo* channelShared[] =
             {
         &handleVm
             };
 
     static SharedFinfo channel("channel",
                                "This message couples the rate table to the compartment. The rate table"
                                " needs updates on voltage in order to compute the rate table.",
                                channelShared, sizeof( channelShared ) / sizeof( Finfo* )
                                );
 
     //DestFinfos
     static DestFinfo process(   "process",
                                 "Handles process call",
                                 new ProcOpFunc< MarkovRateTable >( &MarkovRateTable::process ) );
 
     static DestFinfo reinit( "reinit",
                              "Handles reinit call",
                              new ProcOpFunc< MarkovRateTable >( &MarkovRateTable::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 init("init",
                           "Initialization of the class. Allocates memory for all the tables.",
                           new OpFunc1< MarkovRateTable, unsigned int >(&MarkovRateTable::init) );
 
     static DestFinfo handleLigandConc("handleLigandConc",
                                       "Handles incoming message containing ligand concentration.",
                                       new OpFunc1< MarkovRateTable, double >(&MarkovRateTable::handleLigandConc) );
 
     static DestFinfo set1d("set1d",
                            "Setting up of 1D lookup table for the (i,j)'th rate.",
                            new OpFunc4< MarkovRateTable, unsigned int, unsigned int, Id,
                            unsigned int >
                            ( &MarkovRateTable::setVtChildTable )
                            );
 
     static DestFinfo set2d("set2d",
                            "Setting up of 2D lookup table for the (i,j)'th rate.",
                            new OpFunc3< MarkovRateTable, unsigned int, unsigned int, Id >
                            ( &MarkovRateTable::setInt2dChildTable )
                            );
 
     static DestFinfo setconst("setconst",
                               "Setting a constant value for the (i,j)'th rate. Internally, this is"
                               " stored as a 1-D rate with a lookup table containing 1 entry.",
                               new OpFunc3< MarkovRateTable, unsigned int, unsigned int, double >
                               ( &MarkovRateTable::setConstantRate )
                               );
 
     //Field information.
     static ValueFinfo< MarkovRateTable, double > ligandconc( "ligandConc",
                                                              "Ligand concentration.",
                                                              &MarkovRateTable::setLigandConc,
                                                              &MarkovRateTable::getLigandConc
                                                              );
 
     static ValueFinfo< MarkovRateTable, double > vm( "Vm",
                                                      "Membrane voltage.",
                                                      &MarkovRateTable::setVm,
                                                      &MarkovRateTable::getVm
                                                      );
 
     static ReadOnlyValueFinfo< MarkovRateTable, vector< vector< double > > >
             Q( "Q",
                "Instantaneous rate matrix.",
                &MarkovRateTable::getQ
                );
 
     //Really no point in allowing access to Vm_ and ligandConc_ when it is
     //available from the MarkovChannel class.
 
     static ReadOnlyValueFinfo< MarkovRateTable, unsigned int >
             size( "size",
                   "Dimension of the families of lookup tables. Is always equal to the number of states in the model.",
                   &MarkovRateTable::getSize
                   );
 
     static Finfo* markovRateTableFinfos[] =
             {
         &channel,                       //SharedFinfo
         instRatesOut(),         //SrcFinfo
         &proc,                          //DestFinfo
         &init,                          //DestFinfo
         &handleLigandConc,  //DestFinfo
         &set1d,                         //DestFinfo
         &set2d,                         //DestFinfo
         &setconst,                  //DestFinfo
         &vm,                                //ValueFinfo
         &ligandconc,                //ValueFinfo
         &Q,                                 //ReadOnlyValueFinfo
         &size,                          //ReadOnlyValueFinfo
             };
 
     static string doc[] =
     {
         "Name", "MarkovRateTable",
         "Author", "Vishaka Datta S, 2011, NCBS",
         "Description", "Rate Table for Markov channel calculations. "
     };
     static Dinfo< MarkovRateTable > dinfo;
     static Cinfo MarkovRateTableCinfo(
         "MarkovRateTable",
         Neutral::initCinfo(),
         markovRateTableFinfos,
         sizeof(markovRateTableFinfos)/sizeof(Finfo *),
         &dinfo,
         doc,
         sizeof( doc ) / sizeof( string )
                                       );
 
     return &MarkovRateTableCinfo;
 }

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void MarkovRateTable::initConstantRates ( )

Definition at line 525 of file MarkovRateTable.cpp.

References listOfConstantRates_, lookup1dValue(), and Q_.

Referenced by reinit().

 {
     unsigned int n = listOfConstantRates_.size(), i, j;
     for ( unsigned int k = 0; k < n; ++k )
     {
         i = ( ( listOfConstantRates_[k] / 10 ) % 10 ) - 1;
         j = ( listOfConstantRates_[k] % 10 ) - 1;
 
         Q_[i][i] += Q_[i][j];
 
         //Doesn't really matter which value is looked up as there is only one
         //entry in the table.
         Q_[i][j] = lookup1dValue( i, j, 0.0 );
 
         Q_[i][i] -= Q_[i][j];
     }
 }

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void MarkovRateTable::innerSetInt2dChildTable	(	unsigned int	i,
		unsigned int	j,
		Interpol2D	int2dTable
	)

Definition at line 248 of file MarkovRateTable.cpp.

References areIndicesOutOfBounds(), int2dTables_, isRate1d(), isRate2d(), and isRateConstant().

Referenced by setInt2dChildTable().

 {
     if ( areIndicesOutOfBounds( i, j ) )
     {
         cerr << "MarkovRateTable::innerSetInt2dChildTable : Error : Table requested"
                 "   is out of bounds\n";
         return;
     }
 
     if ( isRate1d( i, j ) || isRate2d( i, j ) || isRateConstant( i, j ) )
     {
         cerr << "MarkovRateTable::innerSetInt2dChildTable : Error : Rate (" <<
                 i+1 << "," << j+1 << ") has already been set!\n";
         return;
     }
 
     if ( i == j )
     {
         cerr << "MarkovRateTable::innerSetInt2dChildTable : Error : Cannot "
                 "set diagonal rate (" << i+1 << "," << i+1 << endl;
         return;
     }
 
     //If table isn't already initialized, do so.
     if ( int2dTables_[i][j] == 0 )
         int2dTables_[i][j] = new Interpol2D();
 
     //Checking to see if this rate has already been set with a one parameter rate
     //table.
     *int2dTables_[i][j] = int2dTable;
 }

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void MarkovRateTable::innerSetVtChildTable	(	unsigned int	i,
		unsigned int	j,
		VectorTable	vecTable,
		unsigned int	ligandFlag
	)

Definition at line 202 of file MarkovRateTable.cpp.

References areIndicesOutOfBounds(), isRate1d(), isRate2d(), isRateConstant(), useLigandConc_, and vtTables_.

Referenced by setConstantRate(), and setVtChildTable().

 {
     if ( areIndicesOutOfBounds( i, j ) )
     {
         cerr << "MarkovRateTable::innerSetVtChildTable : Error : Table requested"
                 "is out of bounds!.\n";
         return;
     }
 
     //Checking to see if this rate has already been set with a 2-parameter rate.
     if ( isRate2d( i, j ) || isRateConstant( i, j ) || isRate1d( i, j ) )
     {
         cerr << "MarkovRateTable::innerSetVtChildTable : Error : "
                 "Rate (" << i+1 << "," << j+1 << ")has already been set.\n";
         return;
     }
 
     if ( i == j )
     {
         cerr << "MarkovRateTable::innerSetVtChildTable : Error : Cannot "
                 "set diagonal rate (" << i+1 << "," << i+1 << endl;
         return;
     }
 
     //If table hasnt been allocated any memory, do so.
     if ( vtTables_[i][j] == 0 )
         vtTables_[i][j] = new VectorTable();
 
     *vtTables_[i][j] = vecTable;
     useLigandConc_[i][j] = ligandFlag;
 }

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bool MarkovRateTable::isInitialized ( ) const

private

Definition at line 600 of file MarkovRateTable.cpp.

References size_.

Referenced by reinit().

 {
     return ( size_ > 0 );
 }

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bool MarkovRateTable::isRate1d	(	unsigned int	i,
		unsigned int	j
	)		const

Definition at line 406 of file MarkovRateTable.cpp.

References vtTables_.

Referenced by getVtChildTable(), innerSetInt2dChildTable(), innerSetVtChildTable(), isRateLigandDep(), lookup1dIndex(), lookup1dValue(), operator>>(), and ~MarkovRateTable().

 {
     //Second condition is necessary because for a constant rate, the 1D lookup
     //table class is set, but has only one entry. So a constant rate would pass
     //off as a one-parameter rate transition if not for this check.
     if ( vtTables_[i][j] == 0 )
         return false;
     else
         return ( vtTables_[i][j]->getDiv() > 0 );
 }

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bool MarkovRateTable::isRate2d	(	unsigned int	i,
		unsigned int	j
	)		const

Definition at line 422 of file MarkovRateTable.cpp.

References int2dTables_.

Referenced by getInt2dChildTable(), innerSetInt2dChildTable(), innerSetVtChildTable(), isRateConstant(), lookup2dIndex(), lookup2dValue(), operator>>(), and ~MarkovRateTable().

 {
     return ( int2dTables_[i][j] != 0 );
 }

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bool MarkovRateTable::isRateConstant	(	unsigned int	i,
		unsigned int	j
	)		const

Definition at line 398 of file MarkovRateTable.cpp.

References isRate2d(), isRateZero(), and vtTables_.

Referenced by getVtChildTable(), innerSetInt2dChildTable(), innerSetVtChildTable(), lookup1dIndex(), lookup1dValue(), and ~MarkovRateTable().

 {
     if ( isRate2d( i, j ) || isRateZero( i, j ) )
         return false;
 
     return ( vtTables_[i][j]->getDiv() == 0 );
 }

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bool MarkovRateTable::isRateLigandDep	(	unsigned int	i,
		unsigned int	j
	)		const

Definition at line 417 of file MarkovRateTable.cpp.

References isRate1d(), and useLigandConc_.

Referenced by updateRates().

 {
     return ( isRate1d( i, j ) && useLigandConc_[i][j] > 0 );
 }

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bool MarkovRateTable::isRateZero	(	unsigned int	i,
		unsigned int	j
	)		const

Definition at line 393 of file MarkovRateTable.cpp.

References int2dTables_, and vtTables_.

Referenced by isRateConstant().

 {
     return ( vtTables_[i][j] == 0 && int2dTables_[i][j] == 0 );
 }

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double MarkovRateTable::lookup1dIndex	(	unsigned int	i,
		unsigned int	j,
		unsigned int	xIndex
	)

Definition at line 299 of file MarkovRateTable.cpp.

References areIndicesOutOfBounds(), isRate1d(), isRateConstant(), and vtTables_.

Referenced by MarkovSolverBase::innerFillupTable().

 {
     if ( areIndicesOutOfBounds( i, j ) )
     {
         cerr << "MarkovRateTable::lookup1dIndex : Lookup requested on non-"
                 "existent table at (" << i << "," << j << "). Returning 0.\n";
         return 0;
     }
 
     if ( !isRate1d( i, j ) && !isRateConstant( i, j ) )
     {
         cerr << "MarkovRateTable::lookup1dIndex : No 1D or constant rate set at ("
              << i << "," << j << "). Returning 0.\n";
         return 0;
     }
 
     return vtTables_[i][j]->lookupByIndex( xIndex );
 }

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double MarkovRateTable::lookup1dValue	(	unsigned int	i,
		unsigned int	j,
		double	x
	)

Definition at line 280 of file MarkovRateTable.cpp.

References areIndicesOutOfBounds(), isRate1d(), isRateConstant(), and vtTables_.

Referenced by initConstantRates(), MarkovSolverBase::innerFillupTable(), and updateRates().

 {
     if ( areIndicesOutOfBounds( i, j ) )
     {
         cerr << "MarkovRateTable::lookup1dValue : Lookup requested on non-existent"
                 "table at (" << i + 1 << "," << j + 1 << "). Returning 0.\n";
         return 0;
     }
 
     if ( !isRate1d( i, j ) && !isRateConstant( i, j ) )
     {
         cerr << "MarkovRateTable::lookup1dValue : No 1D or constant rate set at "
                 "(" << i + 1 << "," << j + 1 << "). Returning 0.\n";
         return 0;
     }
 
     return vtTables_[i][j]->lookupByValue( x );
 }

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double MarkovRateTable::lookup2dIndex	(	unsigned int	i,
		unsigned int	j,
		unsigned int	xIndex,
		unsigned int	yIndex
	)

Definition at line 339 of file MarkovRateTable.cpp.

References areIndicesOutOfBounds(), int2dTables_, and isRate2d().

Referenced by MarkovSolverBase::innerFillupTable().

 {
     if ( areIndicesOutOfBounds( i, j ) )
     {
         cerr << "MarkovRateTable::lookup2dIndex : Lookup requested on non-existent"
                 " table at (" << i+1 << "," << j+1 << "). Returning 0.\n";
         return 0;
     }
 
     if ( !isRate2d( i, j ) )
     {
         cerr << "MarkovRateTable::lookup2dIndex : No 2D rate set at (" << i+1 << ","
              << j+1 << "). Returning 0.\n";
         return 0;
     }
 
     vector< unsigned int > indices;
     indices.push_back( xIndex );
     indices.push_back( yIndex );
 
     return int2dTables_[i][j]->getTableValue( indices );
 }

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double MarkovRateTable::lookup2dValue	(	unsigned int	i,
		unsigned int	j,
		double	x,
		double	y
	)

Definition at line 319 of file MarkovRateTable.cpp.

References areIndicesOutOfBounds(), int2dTables_, and isRate2d().

Referenced by updateRates().

 {
     if ( areIndicesOutOfBounds( i, j ) )
     {
         cerr << "MarkovRateTable::lookup2dValue : Lookup requested on non-existent"
                 " table at (" << i + 1<< "," << j+1 << "). Returning 0.\n";
         return 0;
     }
 
     if ( !isRate2d( i, j ) )
     {
         cerr << "MarkovRateTable::lookup2dValue : No 2D rate set at (" << i+1 << ","
              << j+1 << "). Returning 0.\n";
         return 0;
     }
 
     return int2dTables_[i][j]->innerLookup( x, y );
 }

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void MarkovRateTable::process	(	const Eref &	e,
		ProcPtr	info
	)

Definition at line 608 of file MarkovRateTable.cpp.

References areAllRatesConstant(), instRatesOut(), Q_, and updateRates().

Referenced by initCinfo().

 {
     if ( !areAllRatesConstant() )
         updateRates();
 
     instRatesOut()->send( e, Q_ );
 }

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void MarkovRateTable::reinit	(	const Eref &	e,
		ProcPtr	info
	)

Definition at line 616 of file MarkovRateTable.cpp.

References initConstantRates(), instRatesOut(), isInitialized(), and Q_.

Referenced by initCinfo().

 {
     if ( isInitialized() )
         initConstantRates();
     else
         cerr << "MarkovRateTable::reinit : MarkovRateTable class has not been"
                 " initialized!.";
 
     instRatesOut()->send( e, Q_ );
 }

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void MarkovRateTable::setConstantRate	(	unsigned int	i,
		unsigned int	j,
		double	rate
	)

Definition at line 685 of file MarkovRateTable.cpp.

References innerSetVtChildTable(), listOfConstantRates_, VectorTable::setDiv(), VectorTable::setMax(), VectorTable::setMin(), and VectorTable::setTable().

Referenced by initCinfo().

 {
     VectorTable vecTable;
 
     vecTable.setMin( rate );
     vecTable.setMax( rate );
     vecTable.setDiv( 1 );
 
     vector< double > rateWrap;
     rateWrap.push_back( rate );
 
     vecTable.setTable( rateWrap );
 
     innerSetVtChildTable( i - 1, j - 1, vecTable, 0 );
 
     listOfConstantRates_.push_back( i * 10 + j );
 }

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void MarkovRateTable::setInt2dChildTable	(	unsigned int	i,
		unsigned int	j,
		Id	int2dTabId
	)

Definition at line 670 of file MarkovRateTable.cpp.

References Eref::data(), Id::eref(), innerSetInt2dChildTable(), and listOf2dRates_.

Referenced by initCinfo().

 {
     Interpol2D* int2dTable = reinterpret_cast< Interpol2D* >
             ( int2dTabId.eref().data() );
 
     innerSetInt2dChildTable( i - 1, j - 1, *int2dTable );
 
     listOf2dRates_.push_back( i * 10 + j );
 }

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void MarkovRateTable::setLigandConc ( double ligandConc )

Definition at line 388 of file MarkovRateTable.cpp.

References ligandConc_.

Referenced by initCinfo().

 {
     ligandConc_ = ligandConc;
 }

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void MarkovRateTable::setVm ( double Vm )

Definition at line 378 of file MarkovRateTable.cpp.

References Vm_.

Referenced by initCinfo().

 {
     Vm_ = Vm;
 }

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void MarkovRateTable::setVtChildTable	(	unsigned int	i,
		unsigned int	j,
		Id	vecTabId,
		unsigned int	ligandFlag
	)

Definition at line 654 of file MarkovRateTable.cpp.

References Eref::data(), Id::eref(), innerSetVtChildTable(), listOf1dRates_, listOfLigandRates_, and listOfVoltageRates_.

Referenced by initCinfo().

 {
     VectorTable* vecTable = reinterpret_cast< VectorTable* >
             ( vecTabId.eref().data() );
 
     innerSetVtChildTable( i - 1, j - 1, *vecTable, ligandFlag );
 
     listOf1dRates_.push_back( i * 10 + j );
 
     if ( ligandFlag > 0 )
         listOfLigandRates_.push_back( i * 10 + j );
     else
         listOfVoltageRates_.push_back( i * 10 + j );
 }

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void MarkovRateTable::updateRates ( )

Definition at line 484 of file MarkovRateTable.cpp.

References doubleEq(), isRateLigandDep(), ligandConc_, listOf1dRates_, listOf2dRates_, lookup1dValue(), lookup2dValue(), Q_, and Vm_.

Referenced by process().

 {
     double temp;
     unsigned int i,j;
 
     //Update 1D rates, if any.
     for( unsigned int k = 0; k < listOf1dRates_.size(); ++k )
     {
         j = ( listOf1dRates_[k] % 10 ) - 1;
         i = ( ( listOf1dRates_[k] / 10 ) % 10 ) - 1;
 
         temp = Q_[i][j];
 
         if ( isRateLigandDep( i, j ) )
             Q_[i][j] = lookup1dValue( i, j, ligandConc_ );
         else
         {
             Q_[i][j] = lookup1dValue( i, j, Vm_ );
         }
 
         //Ensures that the row sums to zero.
         if ( !doubleEq( temp, Q_[i][j] ) )
             Q_[i][i] = Q_[i][i] - Q_[i][j] + temp;
     }
 
     //Update 2D rates, if any.
     for( unsigned int k = 0; k < listOf2dRates_.size(); ++k )
     {
         j = ( listOf2dRates_[k] % 10 ) - 1;
         i = ( ( listOf2dRates_[k] / 10 ) % 10 ) - 1;
 
         temp = Q_[i][j];
 
         Q_[i][j] = lookup2dValue( i, j, Vm_, ligandConc_ );
 
         //Ensures that the row sums to zero.
         if ( !doubleEq( temp, Q_[i][j] ) )
             Q_[i][i] = Q_[i][i] - Q_[i][j] + temp;
     }
 }