/* 
 * This program is free software; you can redistribute it and/or modify 
 * it under the terms of the GNU General Public License as published by 
 * the Free Software Foundation; either version 2 of the License, or 
 * (at your option) any later version.
 * 
 * This program is distributed in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY 
 * or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License 
 * for more details.
 * 
 * You should have received a copy of the GNU General Public License along 
 * with this program; if not, write to the Free Software Foundation, Inc., 
 * 59
 */

#include <iostream>
#include <math.h>
# include "CholeraRelaySystemHeader.h"

using namespace std;

        double kSynthConstLuxOmRNA      =0.5;
        double Y                                    =1;

        double kMaxRepressLuxO             =0;
        double kHalfRepressLuxO             =1;
        double b                                    =1;

        double kMaxRepressQrrsRNA         =0;
        double kHalfRepressQrrsRNA         =1;
        double c                                    =1;

         double kTranslation                    =0.1;

        double kPhosphorylationLuxO        =0.5;
        double kDePhosphorylationLuxOP   =0;

        double kMaxProdLuxOP                 =0.5;
        double kHalfProdLuxOP                 =0.01;
        double d                                     =1;

        double kMaxProdQrrHapR             =0.5;
        double kHalfProdHapR                  =0.01;
        double e                                    =1;

        double kDissQrrsRNAHapRmRNA     =0.001;
        double kAssQrrsRNAHapRmRNA      =1;
        double Hfq                                 =1;

        double kSynthConstHapRmRNA      =0.5;
        double X                                    =1;

        double kMaxRepressHapR             =0;
        double kHalfRepressHapR             =1;
        double g                                    =1;

        double kMaxProdHapA                 =0.5;
        double kHalfProdHapA                 =0.01;
        double h                                   =1;

        double kDegHapRmRNA                = 0.00288;
        double kDegLuxOP                      =0.01;
        double kDegLuxOmRNA                = 0.00288;
        double kDegQrrsRNA                   = 0.00288;
        double kDegHapR                        =0.01;
        double kDegLuxO                        =0.01;
        double kDegHapA                        =0.01;


double *ode(double y[], double dy[]) {

/// Section 0: LuxOmRNA,

dy[0] = kSynthConstLuxOmRNA * X - (kMaxRepressLuxO/(1 + (pow((y[1]/kHalfRepressLuxO),b)))) - (kMaxRepressQrrsRNA/(1 + (pow((y[3]/kHalfRepressQrrsRNA),c)))) - kDegLuxOmRNA * y[0] ;

/// Section 1: LuxO.

dy[1] = kTranslation * y[0] - kPhosphorylationLuxO * y[1] -kDegLuxO * y[1] - kDePhosphorylationLuxOP * y[2] ;

/// Section 2: LuxO-P.

dy[2] = kPhosphorylationLuxO * y[1] - kDePhosphorylationLuxOP * y[2] - kDegLuxOP * y[2] ;

/// Section 3: QrrsRNA.

dy[3] = kMaxProdLuxOP * (pow(y[2],d)/(pow(kHalfProdLuxOP,d) + pow(y[2],d))) + kMaxProdQrrHapR * (pow(y[6],e)/(pow(kHalfProdHapR,e) + pow(y[6],e)))  - kAssQrrsRNAHapRmRNA * y[3] * y[4] * Hfq - kDegQrrsRNA * y[3] ;

/// Section 4: HapRmRNA.

 dy[4] =  kSynthConstHapRmRNA * Y - (kMaxRepressHapR/(1 + (pow((y[6]/kHalfRepressHapR),g))))- kAssQrrsRNAHapRmRNA * y[3] * y[4] * Hfq - kDegHapRmRNA * y[4] ;

 /// Section 5: QrrsRNAHapRmRNA.

 dy[5] = kAssQrrsRNAHapRmRNA * y[3] * y[4] * Hfq - kDegHapRmRNA * y[5] - kDegQrrsRNA * y[5] ;

/// Section 6: HapR.

dy[6] = kTranslation * y[4] - kDegHapR * y[6] ;

/// Section 7: HapAmRNA.

dy[7] = kMaxProdHapA * (pow(y[6],h)/(pow(kHalfProdHapA,h) + pow(y[6],h))) ;

/// Section 8: HapA.

dy[8] = kTranslation * y[7] - kDegHapA * y[8] ;

return dy;

}