/home/msneddon/eclipse/galileoSR1_cpp/workspace/NFsim/src/NFtest/agentcell/cell/cell.hh

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#ifndef NG_CELL_HH_
#define NG_CELL_HH_

#include <math.h>
#include <fstream>

#include "../../../NFcore/NFcore.hh"
#include "../../../NFutil/NFutil.hh"
#include "util.hh"

#include "environment.hh"



using namespace std;
using namespace NFcore;


class Environment;

class AgentCell
{
        public:

                AgentCell(
                                System *s,
                                Environment *e,
                                double speed,
                                double rotDiffusionConstant,
                                double cheYpThreshold,
                                double startTime,
                                string outputDirectoryPath
                                );

                ~AgentCell();

                double stepTo(double endTime, double dt);
                void equilibriate(double duration, double dt);

                //Functions to get current position and direction
                double getXposition() const { return pos[X]; };
                double getYposition() const { return pos[Y]; };
                double getZposition() const { return pos[Z]; };
                double getXdirection() const { return dir[X]; };
                double getYdirection() const { return dir[Y]; };
                double getZdirection() const { return dir[Z]; };

                //Constants that can be used
                static const int X = 0;
                static const int Y = 1;
                static const int Z = 2;

                static const int TUMBLE = 0;
                static const int SWIM = 1;

                static const int APART = 0;
                static const int BUNDLED = 1;

                void swimToNewPosition(double elapsedTime);


                void outputCellValues();

        protected:


                void changeDirRandom();
                void changeDirDistribution();
                void changeDirRotDiffusion(double elapsedTime);
                void moveToNewPosition(double elapsedTime);

                double speed;
                double rotDiffusionConstant;




                double * cheYhistory;
                int cheYhisPos;

                int cheYpThreshold;// = 1795;
                int motorState;// = this->CCW;
                int flagellaState;// = this->APART;
                int lastFlagellaState;
                double apartDuration;// = 0;
                bool droppingTumble;// = false;

                double boxcarTimeWidth;// = 0.3;
                int cheYhistorySize;// = (int)round(boxcarTimeWidth/dt);

                double meanCheYp;// = 0;
                double cheYhistorySum;// = 0;




                //Identify the cell with a number
                int cellId;

                //Keep track of current 3d position, direction, and local orientation
                // (could use a quanternion and save less numbers, but I like my intuitive vectors...)
                //  also, I ran a test using double values on a 64bit linux machine to test the error
                //  that develops between the orthogonality between the up and dir vectors.  Running
                //  10 million random rotations on dir and up, I get only a ~.005 error in the degree (meaning
                //  the degree between the two vectors was ~90.005 instead of 90 exactly).  I believe this to
                //  be a reasonable error, as if we apply a new rotation every .01 seconds in the simulation,
                //  we only get an error that is greater than about 0.005 degrees after 27.7 simulation hours,
                //  which is ok for me...  (note, in the same test, the magnitude of the vectors changes by
                //  less than 0.00001 (they were 0.999991 instead of exactly 1)
                double pos[3];
                double dir[3];
                double up[3];
                double rotMat[3][3];

                double lastPos[3];
                double lastDir[3];
                double lastUp[3];


                //Cell properties
                double currentTime;
                int currentMovement;
                int lastMovement;
                double currentLigConc;


                //Distribution of new swim direction angles, matched to experimental observations
                // With shape = 4, scale = 18.32045567939674, location = -4.606176605609249
                // These variables are now initialized in cell.cpp
                static const double DefaultGammaAlpha;// = 4.;
                static const double DefaultGammaBeta;// = 1./18.32045567939674;
                static const double DefaultGammaOffset;// = -4.606176605609249;

                static const double DefaultSpeed;// = 20; //uM per second
                static const double DefaultRotDifConst;// = 0.06205; // rad^2/s



                //Keep a copy of the chemotaxis system and environment
                System * system;
                Environment *env;

                //Also keep track of the output stream for the cell properties
                ofstream motorFileStream;
                ofstream outputFileStream;
                void outputCellHeader();

                double runTimeSpent;


                string fileName;
                unsigned int binaryFileOutputCounter;

                static const int CW = 1;
                static const int CCW = 0;



        private:
                static unsigned int cellIdCounter;
                ChemotaxisUtil::GammaSampler *gs;

};


#endif /*NG_CELL_HH_*/

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