/*
 * This code is generated by BioUML FrameWork 
 * for BIOMD0000000005.xml diagram  at 2008.03.20 15:03:16
 */
import biouml.plugins.simulation.ae.NewtonSolver;
import biouml.plugins.simulation.java.JavaBaseModel;
import ru.biosoft.math.MathRoutines;

public class BIOMD0000000005 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_Reaction1 = Reaction1_k6*x[0];
        rate_Reaction2 = x[2]*Reaction2_k8notP;
        rate_Reaction3 = x[3]*Reaction3_k9;
        rate_Reaction4 = x[3]*Reaction4_k3*x[1];
        rate_Reaction5 = Reaction5_k5notP*x[0];
        rate_Reaction6 = Reaction6_k1aa;
        rate_Reaction7 = Reaction7_k2*x[1];
        rate_Reaction8 = Reaction8_k7*x[4];
        rate_Reaction9 = x[5]*(Reaction9_k4prime + Reaction9_k4*Math.pow(x[0], 2));
    }

    public void Init()
    {
        initialValues = getInitialValues();
/*
 * Initialize variables
 */
        Reaction1_k6 = 1.0; // initial value of Reaction1_k6
        Reaction2_k8notP = 1000000.0; // initial value of Reaction2_k8notP
        Reaction3_k9 = 1000.0; // initial value of Reaction3_k9
        Reaction4_k3 = 200.0; // initial value of Reaction4_k3
        Reaction6_k1aa = 0.015; // initial value of Reaction6_k1aa
        Reaction8_k7 = 0.6; // initial value of Reaction8_k7
        Reaction9_k4 = 180.0; // initial value of Reaction9_k4
        Reaction9_k4prime = 0.018; // initial value of Reaction9_k4prime
    }

    /*
     * Model variables initial values
     */
    protected double _cell_EmptySet_;
    protected double rate_Reaction1;
    protected double rate_Reaction2;
    protected double rate_Reaction3;
    protected double rate_Reaction4;
    protected double rate_Reaction5;
    protected double rate_Reaction6;
    protected double rate_Reaction7;
    protected double rate_Reaction8;
    protected double rate_Reaction9;
    protected double Reaction1_k6;
    protected double Reaction2_k8notP;
    protected double Reaction3_k9;
    protected double Reaction4_k3;
    protected double Reaction5_k5notP;
    protected double Reaction6_k1aa;
    protected double Reaction7_k2;
    protected double Reaction8_k7;
    protected double Reaction9_k4;
    protected double Reaction9_k4prime;

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


        double[] y = new double[6];
        y[0] = x[0];
        y[1] = x[1];
        y[2] = x[2];
        y[3] = x[3];
        y[4] = x[4];
        y[5] = x[5];
        return y;
    }
    public double[] getInitialValues()
    {
        double [] x = new double[6];
        this.time = 0.0;
        x[0] = 0.0; // - $"cell.M"
        x[1] = 0.0; // - $"cell.Y"
        x[2] = 0.0; // - $cell.C2
        x[3] = 1.0; // - $cell.CP
        x[4] = 0.0; // - $cell.YP
        x[5] = 0.3; // - $cell.pM

        __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 'BIOMD0000000005.xml' model
         */
    public void __internalDyDt_0(double time, double [] x, double[] result)
    {
        result[0] = -rate_Reaction1-rate_Reaction5+rate_Reaction9;
        result[1] = -rate_Reaction4+rate_Reaction6-rate_Reaction7;
        result[2] = +rate_Reaction1-rate_Reaction2+rate_Reaction3;
        result[3] = +rate_Reaction2-rate_Reaction3-rate_Reaction4;
        result[4] = +rate_Reaction1-rate_Reaction8;
        result[5] = +rate_Reaction4+rate_Reaction5-rate_Reaction9;
    }
    protected double [] calculateResult(double time, double[] x)
    {
        double[] result = new double[6];
        __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 ...