#include <HHGate.h>

Collaboration diagram for HHGate:

Public Member Functions
bool	checkOriginal (Id id, const string &field) const

vector< double >	getAlpha (const Eref &e) const

vector< double >	getAlphaParms (const Eref &e) const

vector< double >	getBeta (const Eref &e) const

unsigned int	getDivs (const Eref &e) const

double	getMax (const Eref &e) const

double	getMin (const Eref &e) const

vector< double >	getMinfinity (const Eref &e) const

vector< double >	getTableA (const Eref &e) const

vector< double >	getTableB (const Eref &e) const

vector< double >	getTau (const Eref &e) const

bool	getUseInterpolation (const Eref &e) const

	HHGate ()

	HHGate (Id originalChanId, Id originalGateId)

bool	isOriginalChannel (Id id) const

bool	isOriginalGate (Id id) const

double	lookupA (double v) const

double	lookupB (double v) const

void	lookupBoth (double v, double A, double B) const

double	lookupTable (const vector< double > &tab, double v) const

Id	originalChannelId () const

Id	originalGateId () const

void	setAlpha (const Eref &e, vector< double > val)

void	setBeta (const Eref &e, vector< double > val)

void	setDivs (const Eref &e, unsigned int val)

void	setMax (const Eref &e, double val)

void	setMin (const Eref &e, double val)

void	setMinfinity (const Eref &e, vector< double > val)

void	setTableA (const Eref &e, vector< double > v)

void	setTableB (const Eref &e, vector< double > v)

void	setTau (const Eref &e, vector< double > val)

void	setupAlpha (const Eref &e, vector< double > parms)

void	setupGate (const Eref &e, vector< double > parms)

void	setupTables (const vector< double > &parms, bool doTau)

void	setupTau (const Eref &e, vector< double > parms)

void	setUseInterpolation (const Eref &e, bool val)

void	tabFill (vector< double > &table, unsigned int newXdivs, double newXmin, double newXmax)

void	tweakAlpha ()

void	tweakTables (bool doTau)

void	tweakTau ()

void	updateAlphaBeta ()

void	updateTables ()

void	updateTauMinf ()

Static Public Member Functions
static const Cinfo *	initCinfo ()

Private Attributes
vector< double >	A_
	The actual lookup table for calculations. Holds alpha(V). More...

vector< double >	alpha_
	5 parameters for alpha More...

vector< double >	B_
	The lookup table for calculations. Holds alpha(V) + beta(V). More...

vector< double >	beta_
	5 parameters for beta More...

double	invDx_
	increment of the range. More...

bool	isDirectTable_

bool	lookupByInterpolation_

vector< double >	mInfinity_
	5 parameters for mInfinity More...

Id	originalChanId_

Id	originalGateId_

vector< double >	tau_
	5 parameters for tau More...

double	xmax_
	Max of the voltage (or conc) range. More...

double	xmin_
	Minimum of the voltage (or conc) range. More...

Friends
void	testHHGateLookup ()

void	testHHGateSetup ()

Detailed Description

This class handles a single gate on an HHChannel. It is equivalent to the m and h terms on the Hodgkin-Huxley Na channel, or the n term on the K channel. It stores the voltage-dependence (sometimes concentration-dependence) of the gating variables for opening the channel. It does so in a tabular form which can be directly filled using experimental data points. It also provides a set of utility functions for defining the gate in functional forms, and accessing those original functional forms. The HHGate is accessed as a FieldElement, which means that it is available as a pointer on the HHChannel. HHGates are typically shared. This means that when you make a copy or a vector of an HHChannel, there is only a single HHGate created, and its pointer is used by all the copies. The lookup functions are thread-safe. Field assignment to the HHGate should be possible only from the original HHChannel, but all the others do have read permission.

Definition at line 31 of file HHGate.h.

Constructor & Destructor Documentation

HHGate::HHGate ( )

Dummy constructor, to keep Dinfo happy. Should never be used

Definition at line 227 of file HHGate.cpp.

   : xmin_(0), xmax_(1), invDx_(1),
     originalChanId_(0),
     originalGateId_(0),
     lookupByInterpolation_(0),
     isDirectTable_(0)
 {;}

HHGate::HHGate	(	Id	originalChanId,
		Id	originalGateId
	)

This constructor is the one meant to be used. It takes the originalId of the parent HHChannel as a required argument, so that any subsequent 'write' functions can be checked to see if they are legal. Also tracks its own Id.

Definition at line 235 of file HHGate.cpp.

   :
   A_( 1, 0.0 ),
   B_( 1, 0.0 ),
   xmin_(0), xmax_(1), invDx_(1),
   originalChanId_( originalChanId ),
   originalGateId_( originalGateId ),
   lookupByInterpolation_(0),
   isDirectTable_(0)
 {;}

Member Function Documentation

bool HHGate::checkOriginal	(	Id	id,
		const string &	field
	)		const

Checks if the provided Id is the one that the HHGate was created on. If true, fine, otherwise complains about trying to set the field.

Definition at line 776 of file HHGate.cpp.

References originalGateId_.

Referenced by setAlpha(), setBeta(), setDivs(), setMax(), setMin(), setMinfinity(), setTableA(), setTableB(), setTau(), setupAlpha(), setupGate(), setupTau(), and setUseInterpolation().

 {
   if ( id == originalGateId_ )
     return 1;
 
   cout << "Warning: HHGate: attempt to set field '" << field << "' on " <<
     id.path() << "\nwhich is not the original Gate element. Ignored.\n";
   return 0;
 }

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vector< double > HHGate::getAlpha ( const Eref & e ) const

Definition at line 298 of file HHGate.cpp.

References alpha_.

Referenced by initCinfo().

 {
   return alpha_;
 }

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vector< double > HHGate::getAlphaParms ( const Eref & e ) const

Definition at line 509 of file HHGate.cpp.

References A_, alpha_, beta_, xmax_, and xmin_.

Referenced by initCinfo().

 {
   vector< double > ret = alpha_;
   ret.insert( ret.end(), beta_.begin(), beta_.end() );
   ret.push_back( A_.size() );
   ret.push_back( xmin_ );
   ret.push_back( xmax_ );
 
   return ret;
 }

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vector< double > HHGate::getBeta ( const Eref & e ) const

Definition at line 318 of file HHGate.cpp.

References beta_.

Referenced by initCinfo().

 {
   return beta_;
 }

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unsigned int HHGate::getDivs ( const Eref & e ) const

Definition at line 421 of file HHGate.cpp.

References A_.

Referenced by initCinfo().

 {
   return A_.size() - 1;
 }

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double HHGate::getMax ( const Eref & e ) const

Definition at line 399 of file HHGate.cpp.

References xmax_.

Referenced by initCinfo().

 {
   return xmax_;
 }

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double HHGate::getMin ( const Eref & e ) const

Definition at line 378 of file HHGate.cpp.

References xmin_.

Referenced by initCinfo().

 {
   return xmin_;
 }

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vector< double > HHGate::getMinfinity ( const Eref & e ) const

Definition at line 358 of file HHGate.cpp.

References mInfinity_.

Referenced by initCinfo().

 {
   return mInfinity_;
 }

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vector< double > HHGate::getTableA ( const Eref & e ) const

Definition at line 443 of file HHGate.cpp.

References A_.

Referenced by initCinfo().

 {
   return A_;
 }

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vector< double > HHGate::getTableB ( const Eref & e ) const

Definition at line 463 of file HHGate.cpp.

References B_.

Referenced by initCinfo().

 {
   return B_;
 }

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vector< double > HHGate::getTau ( const Eref & e ) const

Definition at line 338 of file HHGate.cpp.

References tau_.

Referenced by initCinfo().

 {
   return tau_;
 }

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bool HHGate::getUseInterpolation ( const Eref & e ) const

Definition at line 480 of file HHGate.cpp.

References lookupByInterpolation_.

Referenced by initCinfo().

 {
   return lookupByInterpolation_;
 }

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const Cinfo * HHGate::initCinfo ( )

static

Definition at line 16 of file HHGate.cpp.

References getAlpha(), getAlphaParms(), getBeta(), getDivs(), getMax(), getMin(), getMinfinity(), getTableA(), getTableB(), getTau(), getUseInterpolation(), Neutral::initCinfo(), lookupA(), lookupB(), setAlpha(), setBeta(), setDivs(), setMax(), setMin(), setMinfinity(), setTableA(), setTableB(), setTau(), setupAlpha(), setupGate(), setupTau(), setUseInterpolation(), tweakAlpha(), and tweakTau().

Referenced by HHChannelBase::initCinfo().

 {
   // Field definitions.
   static ReadOnlyLookupValueFinfo< HHGate, double, double > A( "A",
                                    "lookupA: Look up the A gate value from a double. Usually does"
                                    "so by direct scaling and offset to an integer lookup, using"
                                    "a fine enough table granularity that there is little error."
                                    "Alternatively uses linear interpolation."
                                    "The range of the double is predefined based on knowledge of"
                                    "voltage or conc ranges, and the granularity is specified by"
                                    "the xmin, xmax, and dV fields.",
                                    &HHGate::lookupA );
   static ReadOnlyLookupValueFinfo< HHGate, double, double > B( "B",
                                    "lookupB: Look up the B gate value from a double."
                                    "Note that this looks up the raw tables, which are transformed"
                                    "from the reference parameters.",
                                    &HHGate::lookupB );
 
   static ElementValueFinfo< HHGate, vector< double > > alpha( "alpha",
                                   "Parameters for voltage-dependent rates, alpha:"
                                   "Set up alpha term using 5 parameters, as follows:"
                                   "y(x) = (A + B * x) / (C + exp((x + D) / F))"
                                   "The original HH equations can readily be cast into this form",
                                   &HHGate::setAlpha,
                                   &HHGate::getAlpha
                                   );
 
   static ElementValueFinfo< HHGate, vector< double > > beta( "beta",
                                  "Parameters for voltage-dependent rates, beta:"
                                  "Set up beta term using 5 parameters, as follows:"
                                  "y(x) = (A + B * x) / (C + exp((x + D) / F))"
                                  "The original HH equations can readily be cast into this form",
                                  &HHGate::setBeta,
                                  &HHGate::getBeta
                                  );
 
   static ElementValueFinfo< HHGate, vector< double > > tau( "tau",
                                 "Parameters for voltage-dependent rates, tau:"
                                 "Set up tau curve using 5 parameters, as follows:"
                                 "y(x) = (A + B * x) / (C + exp((x + D) / F))",
                                 &HHGate::setTau,
                                 &HHGate::getTau
                                 );
 
   static ElementValueFinfo< HHGate, vector< double > > mInfinity(
                                  "mInfinity",
                                  "Parameters for voltage-dependent rates, mInfinity:"
                                  "Set up mInfinity curve using 5 parameters, as follows:"
                                  "y(x) = (A + B * x) / (C + exp((x + D) / F))"
                                  "The original HH equations can readily be cast into this form",
                                  &HHGate::setMinfinity,
                                  &HHGate::getMinfinity
                                   );
 
   static ElementValueFinfo< HHGate, double > min( "min",
                           "Minimum range for lookup",
                           &HHGate::setMin,
                           &HHGate::getMin
                           );
 
   static ElementValueFinfo< HHGate, double > max( "max",
                           "Minimum range for lookup",
                           &HHGate::setMax,
                           &HHGate::getMax
                           );
 
   static ElementValueFinfo< HHGate, unsigned int > divs( "divs",
                              "Divisions for lookup. Zero means to use linear interpolation",
                              &HHGate::setDivs,
                              &HHGate::getDivs
                              );
 
   static ElementValueFinfo< HHGate, vector< double > > tableA(
                                   "tableA",
                                   "Table of A entries",
                                   &HHGate::setTableA,
                                   &HHGate::getTableA
                                    );
 
   static ElementValueFinfo< HHGate, vector< double > > tableB(
                                   "tableB",
                                   "Table of alpha + beta entries",
                                   &HHGate::setTableB,
                                   &HHGate::getTableB
                                    );
 
   static ElementValueFinfo< HHGate, bool > useInterpolation(
                                 "useInterpolation",
                                 "Flag: use linear interpolation if true, else direct lookup",
                                 &HHGate::setUseInterpolation,
                                 &HHGate::getUseInterpolation
                                  );
 
   static ElementValueFinfo< HHGate, vector< double > > alphaParms(
                                   "alphaParms",
                                   "Set up both gates using 13 parameters, as follows:"
                                   "setupAlpha AA AB AC AD AF BA BB BC BD BF xdivs xmin xmax"
                                   "Here AA-AF are Coefficients A to F of the alpha (forward) term"
                                   "Here BA-BF are Coefficients A to F of the beta (reverse) term"
                                   "Here xdivs is the number of entries in the table,"
                                   "xmin and xmax define the range for lookup."
                                   "Outside this range the returned value will be the low [high]"
                                   "entry of the table."
                                   "The equation describing each table is:"
                                   "y(x) = (A + B * x) / (C + exp((x + D) / F))"
                                   "The original HH equations can readily be cast into this form",
                                   &HHGate::setupAlpha,
                                   &HHGate::getAlphaParms
                                    );
 
   // DestFinfos
   static DestFinfo setupAlpha( "setupAlpha",
                    "Set up both gates using 13 parameters, as follows:"
                    "setupAlpha AA AB AC AD AF BA BB BC BD BF xdivs xmin xmax"
                    "Here AA-AF are Coefficients A to F of the alpha (forward) term"
                    "Here BA-BF are Coefficients A to F of the beta (reverse) term"
                    "Here xdivs is the number of entries in the table,"
                    "xmin and xmax define the range for lookup."
                    "Outside this range the returned value will be the low [high]"
                    "entry of the table."
                    "The equation describing each table is:"
                    "y(x) = (A + B * x) / (C + exp((x + D) / F))"
                    "The original HH equations can readily be cast into this form",
                    new EpFunc1< HHGate, vector< double > >( &HHGate::setupAlpha )
                    );
   static DestFinfo setupTau( "setupTau",
                  "Identical to setupAlpha, except that the forms specified by"
                  "the 13 parameters are for the tau and m-infinity curves rather"
                  "than the alpha and beta terms. So the parameters are:"
                  "setupTau TA TB TC TD TF MA MB MC MD MF xdivs xmin xmax"
                  "As before, the equation describing each curve is:"
                  "y(x) = (A + B * x) / (C + exp((x + D) / F))",
                  new EpFunc1< HHGate, vector< double > >( &HHGate::setupTau )
                  );
   static DestFinfo tweakAlpha( "tweakAlpha",
                    "Dummy function for backward compatibility. It used to convert"
                    "the tables from alpha, beta values to alpha, alpha+beta"
                    "because the internal calculations used these forms. Not"
                    "needed now, deprecated.",
                    new OpFunc0< HHGate >( &HHGate::tweakAlpha )
                    );
   static DestFinfo tweakTau( "tweakTau",
                  "Dummy function for backward compatibility. It used to convert"
                  "the tables from tau, minf values to alpha, alpha+beta"
                  "because the internal calculations used these forms. Not"
                  "needed now, deprecated.",
                  new OpFunc0< HHGate >( &HHGate::tweakTau )
                  );
   static DestFinfo setupGate( "setupGate",
                   "Sets up one gate at a time using the alpha/beta form."
                   "Has 9 parameters, as follows:"
                   "setupGate A B C D F xdivs xmin xmax is_beta"
                   "This sets up the gate using the equation:"
                   "y(x) = (A + B * x) / (C + exp((x + D) / F))"
                   "Deprecated.",
                   new EpFunc1< HHGate, vector< double > >( &HHGate::setupGate )
                   );
   static Finfo* HHGateFinfos[] =
     {
       &A,           // ReadOnlyLookupValue
       &B,           // ReadOnlyLookupValue
       &alpha,       // ElementValue
       &beta,        // ElementValue
       &tau,     // ElementValue
       &mInfinity,   // ElementValue
       &min,     // ElementValue
       &max,     // ElementValue
       &divs,        // ElementValue
       &tableA,  // ElementValue
       &tableB,  // ElementValue
       &useInterpolation,    // ElementValue
       &alphaParms,  // ElementValue
       &setupAlpha,  // Dest
       &setupTau,    // Dest
       &tweakAlpha,  // Dest
       &tweakTau,    // Dest
       &setupGate,   // Dest
     };
 
   static string doc[] =
     {
       "Name", "HHGate",
       "Author", "Upinder S. Bhalla, 2011, NCBS",
       "Description", "HHGate: Gate for Hodkgin-Huxley type channels, equivalent to the "
       "m and h terms on the Na squid channel and the n term on K. "
       "This takes the voltage and state variable from the channel, "
       "computes the new value of the state variable and a scaling, "
       "depending on gate power, for the conductance.",
     };
 
   static Dinfo< HHGate > dinfo;
   static Cinfo HHGateCinfo(
                "HHGate",
                Neutral::initCinfo(),
                HHGateFinfos, sizeof(HHGateFinfos)/sizeof(Finfo *),
                &dinfo,
                doc,
                sizeof(doc)/sizeof(string)
                );
 
   return &HHGateCinfo;
 }

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bool HHGate::isOriginalChannel ( Id id ) const

isOriginalChannel returns true if the provided Id is the Id of the channel on which the HHGate was created.

Definition at line 786 of file HHGate.cpp.

References originalChanId_.

Referenced by HHChannel::checkOriginal().

 {
   return ( id == originalChanId_ );
 }

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bool HHGate::isOriginalGate ( Id id ) const

isOriginalChannel returns true if the provided Id is the Id of the Gate created at the same time as the original channel.

Definition at line 791 of file HHGate.cpp.

References originalGateId_.

 {
   return ( id == originalGateId_ );
 }

double HHGate::lookupA ( double v ) const

lookupA: Look up the A vector from a double. Typically does so by direct scaling and offset to an integer lookup, using a fine enough table granularity that there is little error. Alternatively uses linear interpolation. The range of the double is predefined based on knowledge of voltage or conc ranges, and the granularity is specified by the xmin, xmax, and invDx fields.

Definition at line 265 of file HHGate.cpp.

References A_, and lookupTable().

Referenced by initCinfo().

 {
   return lookupTable( A_, v );
 }

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double HHGate::lookupB ( double v ) const

lookupB: Look up the B vector from a double, similar to lookupA.

Definition at line 270 of file HHGate.cpp.

References B_, and lookupTable().

Referenced by initCinfo().

 {
   return lookupTable( B_, v );
 }

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void HHGate::lookupBoth	(	double	v,
		double *	A,
		double *	B
	)		const

Single call to get both A and B values by lookup

Definition at line 275 of file HHGate.cpp.

References A_, B_, invDx_, lookupByInterpolation_, xmax_, and xmin_.

Referenced by HSolveUtils::rates(), HHChannel::vProcess(), and HHChannel::vReinit().

 {
   if ( v <= xmin_ ) {
     *A = A_[0];
     *B = B_[0];
   } else if ( v >= xmax_ ) {
     *A = A_.back();
     *B = B_.back();
   } else {
     unsigned int index =
       static_cast< unsigned int >( ( v - xmin_ ) * invDx_ );
     assert( A_.size() > index && B_.size() > index );
     if ( lookupByInterpolation_ ) {
       double frac = ( v - xmin_ - index / invDx_ ) * invDx_;
       *A = A_[ index ] * ( 1 - frac ) + A_[ index + 1 ] * frac;
       *B = B_[ index ] * ( 1 - frac ) + B_[ index + 1 ] * frac;
     } else {
       *A = A_[ index ];
       *B = B_[ index ];
     }
   }
 }

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double HHGate::lookupTable	(	const vector< double > &	tab,
		double	v
	)		const

Returns looked up value of specified table

Definition at line 250 of file HHGate.cpp.

References invDx_, lookupByInterpolation_, xmax_, and xmin_.

Referenced by lookupA(), lookupB(), and tabFill().

 {
   if ( v <= xmin_ ) return tab[0];
   if ( v >= xmax_ ) return tab.back();
   if ( lookupByInterpolation_ ) {
     unsigned int index =
       static_cast< unsigned int >( ( v - xmin_ ) * invDx_ );
     assert( tab.size() > index );
     double frac = ( v - xmin_ - index / invDx_ ) * invDx_;
     return tab[ index ] * ( 1 - frac ) + tab[ index + 1 ] * frac;
   } else {
     return tab[ static_cast< unsigned int >( (v - xmin_) * invDx_ ) ];
   }
 }

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Id HHGate::originalChannelId ( ) const

Returns the Id of the original Channel.

Definition at line 796 of file HHGate.cpp.

References originalChanId_.

 {
   return originalChanId_;
 }

Id HHGate::originalGateId ( ) const

Returns the Id of the original Gate.

Definition at line 801 of file HHGate.cpp.

References originalGateId_.

Referenced by HSolveUtils::gates(), and HSolveUtils::rates().

 {
   return originalGateId_;
 }

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void HHGate::setAlpha	(	const Eref &	e,
		vector< double >	val
	)

Definition at line 303 of file HHGate.cpp.

References alpha_, checkOriginal(), Eref::id(), Id::path(), updateTables(), and updateTauMinf().

Referenced by initCinfo().

 {
   if ( val.size() != 5 ) {
     cout << "Error: HHGate::setAlpha on " << e.id().path() <<
       ": Number of entries on argument vector should be 5, was " <<
       val.size() << endl;
     return;
   }
   if ( checkOriginal( e.id(), "alpha" ) ) {
     alpha_ = val;
     updateTauMinf();
     updateTables();
   }
 }

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void HHGate::setBeta	(	const Eref &	e,
		vector< double >	val
	)

Definition at line 323 of file HHGate.cpp.

References beta_, checkOriginal(), Eref::id(), Id::path(), updateTables(), and updateTauMinf().

Referenced by initCinfo().

 {
   if ( val.size() != 5 ) {
     cout << "Error: HHGate::setBeta on " << e.id().path() <<
       ": Number of entries on argument vector should be 5, was " <<
       val.size() << endl;
     return;
   }
   if ( checkOriginal( e.id(), "beta" ) ) {
     beta_ = val;
     updateTauMinf();
     updateTables();
   }
 }

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void HHGate::setDivs	(	const Eref &	e,
		unsigned int	val
	)

Stuff here to redo sizes.

Definition at line 426 of file HHGate.cpp.

References A_, B_, checkOriginal(), Eref::id(), invDx_, isDirectTable_, tabFill(), updateTables(), xmax_, and xmin_.

Referenced by initCinfo().

 {
   if ( checkOriginal( e.id(), "divs" ) ) {
     if ( isDirectTable_ ) {
       invDx_ = static_cast< double >( val ) / ( xmax_ - xmin_ );
       tabFill( A_, val, xmin_, xmax_ );
       tabFill( B_, val, xmin_, xmax_ );
     } else {
       A_.resize( val + 1 );
       B_.resize( val + 1 );
       invDx_ = static_cast< double >( val ) / ( xmax_ - xmin_ );
       updateTables();
     }
   }
 }

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void HHGate::setMax	(	const Eref &	e,
		double	val
	)

Definition at line 404 of file HHGate.cpp.

References A_, B_, checkOriginal(), Eref::id(), invDx_, isDirectTable_, tabFill(), updateTables(), xmax_, and xmin_.

Referenced by initCinfo().

 {
   if ( checkOriginal( e.id(), "max" ) ) {
     xmax_ = val;
     unsigned int xdivs = A_.size() - 1;
     if ( isDirectTable_ && xdivs > 0 ) {
       // Set up using direct assignment of table values.
       invDx_ = static_cast< double >( xdivs ) / ( val - xmin_ );
       tabFill( A_, xdivs, xmin_, val );
       tabFill( B_, xdivs, xmin_, val );
     } else {
       // Set up using functional form. here we just recalculate.
       updateTables();
     }
   }
 }

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void HHGate::setMin	(	const Eref &	e,
		double	val
	)

Definition at line 383 of file HHGate.cpp.

References A_, B_, checkOriginal(), Eref::id(), invDx_, isDirectTable_, tabFill(), updateTables(), xmax_, and xmin_.

Referenced by initCinfo().

 {
   if ( checkOriginal( e.id(), "min" ) ) {
     xmin_ = val;
     unsigned int xdivs = A_.size() - 1;
     if ( isDirectTable_ && xdivs > 0 ) {
       // Stuff here to stretch out table using interpolation.
       invDx_ = static_cast< double >( xdivs ) / ( xmax_ - val );
       tabFill( A_, xdivs, val, xmax_ );
       tabFill( B_, xdivs, val, xmax_ );
     } else {
       updateTables();
     }
   }
 }

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void HHGate::setMinfinity	(	const Eref &	e,
		vector< double >	val
	)

Definition at line 363 of file HHGate.cpp.

References checkOriginal(), Eref::id(), mInfinity_, Id::path(), updateAlphaBeta(), and updateTables().

Referenced by initCinfo().

 {
   if ( val.size() != 5 ) {
     cout << "Error: HHGate::setMinfinity on " << e.id().path() <<
       ": Number of entries on argument vector should be 5, was " <<
       val.size() << endl;
     return;
   }
   if ( checkOriginal( e.id(), "mInfinity" ) ) {
     mInfinity_ = val;
     updateAlphaBeta();
     updateTables();
   }
 }

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void HHGate::setTableA	(	const Eref &	e,
		vector< double >	v
	)

Definition at line 448 of file HHGate.cpp.

References A_, checkOriginal(), Eref::id(), invDx_, isDirectTable_, Id::path(), xmax_, and xmin_.

Referenced by initCinfo().

 {
   if ( v.size() < 2 ) {
     cout << "Warning: HHGate::setTableA: size must be >= 2 entries on "
      << e.id().path() << endl;
     return;
   }
   if ( checkOriginal( e.id(), "tableA" ) ) {
     isDirectTable_ = 1;
     A_ = v;
     unsigned int xdivs = A_.size() - 1;
     invDx_ = static_cast< double >( xdivs ) / ( xmax_ - xmin_ );
   }
 }

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void HHGate::setTableB	(	const Eref &	e,
		vector< double >	v
	)

Definition at line 468 of file HHGate.cpp.

References A_, B_, checkOriginal(), Eref::id(), and isDirectTable_.

Referenced by initCinfo().

 {
   if ( checkOriginal( e.id(), "tableB" ) ) {
     isDirectTable_ = 1;
     if ( A_.size() != v.size() ) {
       cout << "Warning: HHGate::setTableB: size should be same as table A: " << v.size() << " != " << A_.size() << ". Ignoring.\n";
       return;
     }
     B_ = v;
   }
 }

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void HHGate::setTau	(	const Eref &	e,
		vector< double >	val
	)

Definition at line 343 of file HHGate.cpp.

References checkOriginal(), Eref::id(), Id::path(), tau_, updateAlphaBeta(), and updateTables().

Referenced by initCinfo().

 {
   if ( val.size() != 5 ) {
     cout << "Error: HHGate::setTau on " << e.id().path() <<
       ": Number of entries on argument vector should be 5, was " <<
       val.size() << endl;
     return;
   }
   if ( checkOriginal( e.id(), "tau" ) ) {
     tau_ = val;
     updateAlphaBeta();
     updateTables();
   }
 }

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void HHGate::setupAlpha	(	const Eref &	e,
		vector< double >	parms
	)

Definition at line 491 of file HHGate.cpp.

References alpha_, beta_, checkOriginal(), Eref::id(), and setupTables().

Referenced by initCinfo().

 {
   if ( checkOriginal( e.id(), "setupAlpha" ) ) {
     if ( parms.size() != 13 ) {
       cout << "HHGate::setupAlpha: Error: parms.size() != 13\n";
       return;
     }
     setupTables( parms, false );
     alpha_.resize( 5, 0 );
     beta_.resize( 5, 0 );
     for ( unsigned int i = 0; i < 5; ++i )
       alpha_[i] = parms[i];
     for ( unsigned int i = 5; i < 10; ++i )
       beta_[i - 5] = parms[i];
   }
 }

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void HHGate::setupGate	(	const Eref &	e,
		vector< double >	parms
	)

Definition at line 674 of file HHGate.cpp.

References A_, B_, checkOriginal(), Eref::id(), SINGULARITY, tabFill(), tweakTables(), xmax_, and xmin_.

Referenced by initCinfo().

 {
   // The nine arguments are :
   // A B C D F size min max isbeta
   // If size == 0 then we check that the gate has already been allocated.
   // If isbeta is true then we also have to do the conversion to
   // HHGate form of alpha, alpha+beta, assuming that the alpha gate
   // has already been setup. This uses tweakTables.
   // We may need to resize the tables if they don't match here.
   if ( !checkOriginal( e.id(), "setupGate" ) )
     return;
 
   if ( parms.size() != 9 ) {
     cout << "HHGate::setupGate: Error: parms.size() != 9\n";
     return;
   }
 
   double A = parms[0];
   double B = parms[1];
   double C = parms[2];
   double D = parms[3];
   double F = parms[4];
   int size = static_cast< int > (parms[5] );
   double min = parms[6];
   double max = parms[7];
   bool isBeta = static_cast< bool >( parms[8] );
 
   vector< double >& ip = ( isBeta ) ? B_ : A_;
 
   if ( size <= 0 ) { // Look up size, min, max from the interpol
     size = ip.size() - 1;
     if ( size <= 0 ) {
       cout << "Error: setupGate has zero size\n";
       return;
     }
   } else {
     ip.resize( size + 1 );
   }
 
   double dx = ( max - min ) / static_cast< double >( size );
   double x = min + dx / 2.0;
   for ( int i = 0; i <= size; i++ ) {
     if ( fabs ( F ) < SINGULARITY ) {
       ip[i] = 0.0;
     } else {
       double temp2 = C + exp( ( x + D ) / F );
       if ( fabs( temp2 ) < SINGULARITY )
     ip[i] = ip[i-1];
       else
     ip[i] = ( A + B * x ) / temp2;
     }
   }
 
   if ( isBeta ) {
     assert( A_.size() > 0 );
     // Here we ensure that the tables are the same size
     if ( A_.size() != B_.size() ) {
       if ( A_.size() > B_.size() ) {
     // Note that the tabFill expects to allocate the
     // terminating entry, so we put in size - 1.
     tabFill( B_, A_.size() - 1, xmin_, xmax_ );
       } else {
     tabFill( A_, B_.size() - 1, xmin_, xmax_ );
       }
     }
     // Then we do the tweaking to convert to HHChannel form.
     tweakTables( 0 );
   }
 }

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void HHGate::setupTables	(	const vector< double > &	parms,
		bool	doTau
	)

Sets up the tables one at a time. Based on GENESIS/src/olf/new_interp.c, function setup_tab_values, fine tuned by Erik De Schutter.

Definition at line 551 of file HHGate.cpp.

References A_, B_, invDx_, SINGULARITY, xmax_, and xmin_.

Referenced by setupAlpha(), setupTau(), and updateTables().

 {
   assert( parms.size() == 13 );
   static const int XDIVS = 10;
   static const int XMIN = 11;
   static const int XMAX = 12;
   if ( parms[XDIVS] < 1 ) return;
   unsigned int xdivs = static_cast< unsigned int >( parms[XDIVS] );
 
   A_.resize( xdivs + 1 );
   B_.resize( xdivs + 1 );
   xmin_ = parms[XMIN];
   xmax_ = parms[XMAX];
   assert( xmax_ > xmin_ );
   invDx_ = xdivs / (xmax_ - xmin_ );
   double dx = ( xmax_ - xmin_ ) / xdivs;
 
   double x = xmin_;
   double prevAentry = 0.0;
   double prevBentry = 0.0;
   double temp;
   double temp2 = 0.0;
   unsigned int i;
 
   for( i = 0; i <= xdivs; i++ ) {
     if ( fabs( parms[4] ) < SINGULARITY ) {
       temp = 0.0;
       A_[i] = temp;
     } else {
       temp2 = parms[2] + exp( ( x + parms[3] ) / parms[4] );
       if ( fabs( temp2 ) < SINGULARITY ) {
     temp2 = parms[2] + exp( ( x + dx/10.0 + parms[3] ) / parms[4] );
     temp = ( parms[0] + parms[1] * (x + dx/10 ) ) / temp2;
 
     temp2 = parms[2] + exp( ( x - dx/10.0 + parms[3] ) / parms[4] );
     temp += ( parms[0] + parms[1] * (x - dx/10 ) ) / temp2;
     temp /= 2.0;
     // cout << "interpolated temp = " << temp << ", prev = " << prevAentry << endl;
 
     // temp = prevAentry;
     A_[i] = temp;
       } else {
     temp = ( parms[0] + parms[1] * x) / temp2;
     A_[i] = temp;
       }
     }
     if ( fabs( parms[9] ) < SINGULARITY ) {
       B_[i] = 0.0;
     } else {
       temp2 = parms[7] + exp( ( x + parms[8] ) / parms[9] );
       if ( fabs( temp2 ) < SINGULARITY ) {
     temp2 = parms[7] + exp( ( x + dx/10.0 + parms[8] ) / parms[9] );
     temp = (parms[5] + parms[6] * (x + dx/10) ) / temp2;
     temp2 = parms[7] + exp( ( x - dx/10.0 + parms[8] ) / parms[9] );
     temp += (parms[5] + parms[6] * (x - dx/10) ) / temp2;
     temp /= 2.0;
     B_[i] = temp;
     // B_[i] = prevBentry;
       } else {
     B_[i] = (parms[5] + parms[6] * x ) / temp2;
     // B_.table_[i] = ( parms[5] + parms[6] * x ) / temp2;
       }
     }
     // There are cleaner ways to do this, but this keeps
     // the relation to the GENESIS version clearer.
     // Note the additional SINGULARITY check, to fix a bug
     // in the earlier code.
     if ( doTau == 0 && fabs( temp2 ) > SINGULARITY )
       B_[i] += temp;
 
     prevAentry = A_[i];
     prevBentry = B_[i];
     x += dx;
   }
 
   prevAentry = 0.0;
   prevBentry = 0.0;
   if ( doTau ) {
     for( i = 0; i <= xdivs; i++ ) {
       temp = A_[i];
       temp2 = B_[i];
       if ( fabs( temp ) < SINGULARITY ) {
     A_[i] = prevAentry;
     B_[i] = prevBentry;
       } else {
     A_[i] = temp2 / temp;
     B_[i] = 1.0 / temp;
       }
       prevAentry = A_[i];
       prevBentry = B_[i];
     }
   }
 }

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void HHGate::setupTau	(	const Eref &	e,
		vector< double >	parms
	)

Definition at line 524 of file HHGate.cpp.

References checkOriginal(), Eref::id(), and setupTables().

Referenced by initCinfo().

 {
   if ( checkOriginal( e.id(), "setupTau" ) ) {
     if ( parms.size() != 13 ) {
       cout << "HHGate::setupTau: Error: parms.size() != 13\n";
       return;
     }
     setupTables( parms, true );
   }
 }

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void HHGate::setUseInterpolation	(	const Eref &	e,
		bool	val
	)

Definition at line 485 of file HHGate.cpp.

References checkOriginal(), Eref::id(), and lookupByInterpolation_.

Referenced by initCinfo(), and HSolveUtils::rates().

 {
   if ( checkOriginal( e.id(), "useInterpolation" ) )
     lookupByInterpolation_ = val;
 }

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void HHGate::tabFill	(	vector< double > &	table,
		unsigned int	newXdivs,
		double	newXmin,
		double	newXmax
	)

tabFill does interpolation and range resizing for a table representing a lookup function. newXdivs is one less than the size of the table; it is the number of subdivisions that the table represents. Does NOT alter the existing xmin and xmax, but it does resize the table.

This utility function does interpolation and range resizing for a table representing a lookup function. newXdivs is one less than the size of the table; it is the number of subdivisions that the table represents.

Definition at line 755 of file HHGate.cpp.

References lookupByInterpolation_, and lookupTable().

Referenced by setDivs(), setMax(), setMin(), and setupGate().

 {
   if ( newXdivs < 3 ) {
     cout << "Error: tabFill: # divs must be >= 3. Not filling table.\n";
     return;
   }
 
   vector< double > old = table;
   double newDx = ( newXmax - newXmin ) / newXdivs;
   table.resize( newXdivs + 1 );
   bool origLookupMode = lookupByInterpolation_;
   lookupByInterpolation_ = 1;
 
   for( unsigned int i = 0; i <= newXdivs; ++i ) {
     table[i] = lookupTable( table, newXmin + i * newDx );
   }
 
   lookupByInterpolation_ = origLookupMode;
 }

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void HHGate::tweakAlpha ( )

Definition at line 536 of file HHGate.cpp.

Referenced by initCinfo().

 {
   ; // Dummy
 }

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void HHGate::tweakTables ( bool doTau )

Tweaks the A and B entries in the tables from the original alpha/beta or minf/tau values. See code in GENESIS/src/olf/new_interp.c, function tweak_tab_values

Definition at line 650 of file HHGate.cpp.

References A_, B_, and SINGULARITY.

Referenced by setupGate().

 {
   unsigned int i;
   unsigned int size = A_.size();
   assert( size == B_.size() );
   if ( doTau ) {
     for ( i = 0; i < size; i++ ) {
       double temp = A_[ i ];
       double temp2 = B_[ i ];
       if ( fabs( temp ) < SINGULARITY )  {
     if ( temp < 0.0 )
       temp = -SINGULARITY;
     else
       temp = SINGULARITY;
       }
       A_[ i ] =  temp2 / temp;
       B_[ i ] =  1.0 / temp;
     }
   } else {
     for ( i = 0; i < size; i++ )
       B_[i] = A_[i] + B_[i];
   }
 }

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void HHGate::tweakTau ( )

Definition at line 541 of file HHGate.cpp.

Referenced by initCinfo().

 {
   ; // Dummy
 }

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void HHGate::updateAlphaBeta ( )

Update the alpha and beta parameters because the tau or minfinity tables have changed.

Definition at line 806 of file HHGate.cpp.

Referenced by setMinfinity(), and setTau().

807 {

808 }

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void HHGate::updateTables ( )

Take the current alpha/beta parameters, and xdivs, xmin, xmax; and rebuild the tables.

Definition at line 814 of file HHGate.cpp.

References A_, alpha_, beta_, setupTables(), xmax_, and xmin_.

Referenced by setAlpha(), setBeta(), setDivs(), setMax(), setMin(), setMinfinity(), and setTau().

 {
   if ( alpha_.size() == 0 || beta_.size() == 0 )
     return;
   vector< double > parms = alpha_;
   parms.insert( parms.end(), beta_.begin(), beta_.end() );
   parms.push_back( A_.size() );
   parms.push_back( xmin_ );
   parms.push_back( xmax_ );
 
   setupTables( parms, 0 );
 }

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void HHGate::updateTauMinf ( )

Update the Tau and Minfinity parameters because the alpha or beta tables have changed.

Definition at line 810 of file HHGate.cpp.

Referenced by setAlpha(), and setBeta().

811 {

812 }

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Friends And Related Function Documentation

void testHHGateLookup ( )

friend

void testHHGateSetup ( )

friend

Member Data Documentation

vector< double > HHGate::A_

private

The actual lookup table for calculations. Holds alpha(V).

Definition at line 199 of file HHGate.h.

Referenced by getAlphaParms(), getDivs(), getTableA(), lookupA(), lookupBoth(), setDivs(), setMax(), setMin(), setTableA(), setTableB(), setupGate(), setupTables(), tweakTables(), and updateTables().

vector< double > HHGate::alpha_

private

5 parameters for alpha

Definition at line 187 of file HHGate.h.

Referenced by getAlpha(), getAlphaParms(), setAlpha(), setupAlpha(), and updateTables().

vector< double > HHGate::B_

private

The lookup table for calculations. Holds alpha(V) + beta(V).

Definition at line 202 of file HHGate.h.

Referenced by getTableB(), lookupB(), lookupBoth(), setDivs(), setMax(), setMin(), setTableB(), setupGate(), setupTables(), and tweakTables().

vector< double > HHGate::beta_

private

5 parameters for beta

Definition at line 190 of file HHGate.h.

Referenced by getAlphaParms(), getBeta(), setBeta(), setupAlpha(), and updateTables().

double HHGate::invDx_

private

increment of the range.

Definition at line 211 of file HHGate.h.

Referenced by lookupBoth(), lookupTable(), setDivs(), setMax(), setMin(), setTableA(), and setupTables().

bool HHGate::isDirectTable_

private

Flag to indicate if table entries have been assigned directly (as direct experimental data, or an externally defined V-dep function). When zero it means that the curve-fit forms from setupAlpha etc. have been used.

Definition at line 238 of file HHGate.h.

Referenced by setDivs(), setMax(), setMin(), setTableA(), and setTableB().

bool HHGate::lookupByInterpolation_

private

Flag: Use linear interpolation for lookup if true, use direct table lookup if false.

Definition at line 230 of file HHGate.h.

Referenced by getUseInterpolation(), lookupBoth(), lookupTable(), setUseInterpolation(), and tabFill().

vector< double > HHGate::mInfinity_

private

5 parameters for mInfinity

Definition at line 196 of file HHGate.h.

Referenced by getMinfinity(), and setMinfinity().

Id HHGate::originalChanId_

private

Id of original channel, the one which has actually allocated it, All other Elements have to treat the values as readonly.

Definition at line 217 of file HHGate.h.

Referenced by isOriginalChannel(), and originalChannelId().

Id HHGate::originalGateId_

private

Id of original Gate, the one which was created with the original channel. All other Elements have to treat the values as readonly.

Definition at line 224 of file HHGate.h.

Referenced by checkOriginal(), isOriginalGate(), and originalGateId().

vector< double > HHGate::tau_

private

5 parameters for tau

Definition at line 193 of file HHGate.h.

Referenced by getTau(), and setTau().

double HHGate::xmax_

private

Max of the voltage (or conc) range.

Definition at line 208 of file HHGate.h.

Referenced by getAlphaParms(), getMax(), lookupBoth(), lookupTable(), setDivs(), setMax(), setMin(), setTableA(), setupGate(), setupTables(), and updateTables().

double HHGate::xmin_

private

Minimum of the voltage (or conc) range.

Definition at line 205 of file HHGate.h.

Referenced by getAlphaParms(), getMin(), lookupBoth(), lookupTable(), setDivs(), setMax(), setMin(), setTableA(), setupGate(), setupTables(), and updateTables().

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

moose-core/biophysics/HHGate.h
moose-core/biophysics/HHGate.cpp

Public Member Functions

Static Public Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation