/*
 * This code is generated by BioUML FrameWork 
 * for BIOMD0000000026.xml diagram  at 2008.03.20 15:04:03
 */
import biouml.plugins.simulation.ae.NewtonSolver;
import biouml.plugins.simulation.java.JavaBaseModel;
import ru.biosoft.math.MathRoutines;

public class BIOMD0000000026 extends JavaBaseModel
{

/*
 * Write rules to calculate equation parameters
 */


/*
 * Write rules to calculate equation parameters excluding internal variables.
 */
    public void __internalRateVarInitFunc_0(double time, double[] x)
    {
        rate_v1a = uVol*(k1*x[0]*x[1] - k_1*x[3]);
        rate_v1b = uVol*k2*x[3];
        rate_v2a = uVol*(k3*x[10]*x[1] - k_3*x[5]);
        rate_v2b = uVol*k4*x[5];
        rate_v3a = uVol*(h1*x[8]*x[2] - h_1*x[9]);
        rate_v3b = uVol*h2*x[9];
        rate_v3c = h3*x[7] - h_3*x[10]*x[2];
        rate_v4a = uVol*(h4*x[10]*x[2] - h_4*x[6]);
        rate_v4b = uVol*h5*x[6];
        rate_v4c = uVol*(h6*x[4] - h_6*x[0]*x[2]);
    }

    public void Init()
    {
        initialValues = getInitialValues();
/*
 * Initialize variables
 */
        uVol = 1.0; // initial value of $uVol
        h1 = 0.045; // initial value of h1
        h2 = 0.092; // initial value of h2
        h3 = 1.0; // initial value of h3
        h4 = 0.01; // initial value of h4
        h5 = 0.5; // initial value of h5
        h6 = 0.086; // initial value of h6
        h_1 = 1.0; // initial value of h_1
        h_3 = 0.01; // initial value of h_3
        h_4 = 1.0; // initial value of h_4
        h_6 = 0.0011; // initial value of h_6
        k1 = 0.02; // initial value of k1
        k2 = 0.01; // initial value of k2
        k3 = 0.032; // initial value of k3
        k4 = 15.0; // initial value of k4
        k_1 = 1.0; // initial value of k_1
        k_3 = 1.0; // initial value of k_3
    }

    /*
     * Model variables initial values
     */
    protected double rate_v1a;
    protected double rate_v1b;
    protected double rate_v2a;
    protected double rate_v2b;
    protected double rate_v3a;
    protected double rate_v3b;
    protected double rate_v3c;
    protected double rate_v4a;
    protected double rate_v4b;
    protected double rate_v4c;
    protected double uVol;
    protected double h1;
    protected double h2;
    protected double h3;
    protected double h4;
    protected double h5;
    protected double h6;
    protected double h_1;
    protected double h_3;
    protected double h_4;
    protected double h_6;
    protected double k1;
    protected double k2;
    protected double k3;
    protected double k4;
    protected double k_1;
    protected double k_3;

    public double[] extendResult(double time,double [] x)
    {
        this.time = time;


        double[] y = new double[11];
        y[0] = x[0];
        y[1] = x[1];
        y[2] = x[2];
        y[3] = x[3];
        y[4] = x[4];
        y[5] = x[5];
        y[6] = x[6];
        y[7] = x[7];
        y[8] = x[8];
        y[9] = x[9];
        y[10] = x[10];
        return y;
    }
    public double[] getInitialValues()
    {
        double [] x = new double[11];
        this.time = 0.0;
        x[0] = 500.0; // - $"uVol.M"
        x[1] = 50.0; // - $"uVol.MAPKK"
        x[2] = 100.0; // - $"uVol.MKP3"
        x[3] = 0.0; // - $"uVol.M_MAPKK"
        x[4] = 0.0; // - $"uVol.M_MKP3"
        x[5] = 0.0; // - $"uVol.Mp_MAPKK"
        x[6] = 0.0; // - $"uVol.Mp_MKP3"
        x[7] = 0.0; // - $"uVol.Mp_MKP3_dep"
        x[8] = 0.0; // - $"uVol.Mpp"
        x[9] = 0.0; // - $"uVol.Mpp_MKP3"
        x[10] = 0.0; // - $uVol.Mp

        __internalRateVarInitFunc_0(time, x);

        return x;
    }

/*
 * code for algebraic rules calculations
 */

/*
 * end of code for algebraic rules calculations
 */

    protected void calculateRates(double time, double[] x)
    {

        __internalRateVarInitFunc_0(time, x);

    }

        /*
         * calculate dy/dt for 'BIOMD0000000026.xml' model
         */
    public void __internalDyDt_0(double time, double [] x, double[] result)
    {
        result[0] = -rate_v1a+rate_v4c;
        result[1] = -rate_v1a+rate_v1b-rate_v2a+rate_v2b;
        result[2] = -rate_v3a+rate_v3c-rate_v4a+rate_v4c;
        result[3] = +rate_v1a-rate_v1b;
        result[4] = +rate_v4b-rate_v4c;
        result[5] = +rate_v2a-rate_v2b;
        result[6] = +rate_v4a-rate_v4b;
        result[7] = +rate_v3b-rate_v3c;
        result[8] = +rate_v2b-rate_v3a;
        result[9] = +rate_v3a-rate_v3b;
        result[10] = +rate_v1b-rate_v2a+rate_v3c-rate_v4a;
    }
    protected double [] calculateResult(double time, double[] x)
    {
        double[] result = new double[11];
        __internalDyDt_0(time, x, result);
        return result;
    }
    public double[] dy_dt(double time, double[] x)
    {
        this.time = time;
        calculateRates( time,x );

        return calculateResult( time,x );
    }

} // class ...