VoxelPoolsBase.h

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/**********************************************************************
** This program is part of 'MOOSE', the
** Messaging Object Oriented Simulation Environment.
**           Copyright (C) 2003-2014 Upinder S. Bhalla. and NCBS
** It is made available under the terms of the
** GNU Lesser General Public License version 2.1
** See the file COPYING.LIB for the full notice.
**********************************************************************/

#ifndef _VOXEL_POOLS_BASE_H
#define _VOXEL_POOLS_BASE_H

#include <map>
#include <vector>

using namespace std;

class RateTerm;
class Stoich;
class Id;

class VoxelPoolsBase
{
public:
    VoxelPoolsBase();
    virtual ~VoxelPoolsBase();

    // Compute access operations.
    void resizeArrays( unsigned int totNumPools );

    unsigned int size() const;

    const double* S() const;

    vector< double >& Svec();

    double* varS();

    const double* Sinit() const;

    double* varSinit();

    void reinit();

    void setVolume( double vol );
    double getVolume() const;

    virtual void setVolumeAndDependencies( double vol );

    // Field assignment functions

    void setN( unsigned int i, double v );
    double getN( unsigned int ) const;
    void setNinit( unsigned int, double v );
    double getNinit( unsigned int ) const;
    void setDiffConst( unsigned int, double v );
    double getDiffConst( unsigned int ) const;
    // Functions to set up rates vector

    virtual void updateAllRateTerms( const vector< RateTerm* >& rates,
                                     unsigned int numCoreRates ) = 0;

    virtual void updateRateTerms( const vector< RateTerm* >& rates,
                                  unsigned int numCoreRates, unsigned int index ) = 0;

    void filterCrossRateTerms( const vector< Id >& offSolverReacs, const vector< pair< Id, Id > >& offSolverReacCompts );

    // Functions to handle cross-compartment reactions.

    void xferIn( const vector< unsigned int >& poolIndex,
                 const vector< double >& values,
                 const vector< double >& lastValues,
                 unsigned int voxelIndex );

    void xferInOnlyProxies(
        const vector< unsigned int >& poolIndex,
        const vector< double >& values,
        unsigned int numProxyPools,
        unsigned int voxelIndex );

    void xferOut( unsigned int voxelIndex,
                  vector< double >& values,
                  const vector< unsigned int >& poolIndex );
    void addProxyVoxy( unsigned int comptIndex,
                       Id comptId, unsigned int voxel );
    void addProxyTransferIndex( unsigned int comptIndex,
                                unsigned int transferIndex );

    bool hasXfer( unsigned int comptIndex ) const;

    bool isVoxelJunctionPresent( Id i1, Id i2 ) const;
    // Functions for cross-compartment rate scaling.

    void resetXreacScale( unsigned int size );

    void forwardReacVolumeFactor( unsigned int i, double volume );

    void backwardReacVolumeFactor( unsigned int i, double volume );

    double getXreacScaleSubstrates( unsigned int i ) const;

    double getXreacScaleProducts( unsigned int i ) const;

    void scaleVolsBufsRates( double ratio, const Stoich* stoichPtr );

    void print() const;

protected:
    const Stoich* stoichPtr_;
    vector< RateTerm* > rates_;

private:
    vector< double > S_;

    vector< double > Sinit_;

    vector< vector< unsigned int > > proxyPoolVoxels_;
    vector< vector< unsigned int > > proxyTransferIndex_;

    map< Id, unsigned int > proxyComptMap_;

    double volume_;

    vector< double > xReacScaleSubstrates_;

    vector< double > xReacScaleProducts_;
};

#endif  // _VOXEL_POOLS_BASE_H