Simulation.h

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#ifndef SIMULATION_H
#define SIMULATION_H

#include <iostream>
#include <fstream>
#include <errno.h>
#include "NodeList.h"
#include "Node.h"
#include "PluginManager.h"
#include "lib/Matrix.h"

class Simulation {
public:
        Simulation(void);
        ~Simulation(void);
        void setup(int, char**);
        void run(void);
        void analysis(void);//runs post simulation analysis

private:
        void calcModeSetup(void);
        void visModeSetup(void);
        void inputFileCheck(void);      
        void simulate(void);//runs the simulation
        void load(void);//loads a previous simulation for analysis
        void inputGenerator(void);//runs the input conversion utility
        void ipause();//pauses (verbose mode)
        void print_help();//prints flags
        void patterns(void);
        string ROOTDIR;
        string SIMDIR;
        string NODESAVGDIR;
        string BITSDIR;
        string LOGICDIR;
        string EXTSDIR;
        string DUMP;
        bool noOutFiles;

        int n; //number of times to run simulation
        ofstream visout, outBits, outInputBits, outAvg, outDosage;
        string visualFile;
        string ext;
        string bitsFileName;
        string inputBitsFileName;
        string runName;
        string in_specsFile;                       
        string in_logicFile;
        string in_patternSpecsFile;
        string in_patternNodesFile;
        string outputFile;
        int seedVal;
        bool seed;
        bool ND2TT;
        bool TT2ND;
        bool postPatterns;
        bool patternAnal;
        bool rand_init;
        bool rand_logicMut;
        bool rand_nodeInputs;
        string iTables;
        bool analysisMode;
        int mutRate_nodes;
        int mutRate_logic;
        int cycleSize;
        string cmd;
        string runDir;
        string avgFileName;
        string iNodeList;
        vector< Matrix > cycles;
        bool ptime;
        int runStart;
        int progStart;
        bool visMode;
        bool noBits;
        bool usePlugins;
        bool outputAll;
        PluginManager pManager;
};

#endif

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