/*
 * This code is generated by BioUML FrameWork 
 * for BIOMD0000000006.xml diagram  at 2008.03.20 15:03:17
 */
import biouml.plugins.simulation.ae.NewtonSolver;
import biouml.plugins.simulation.java.JavaBaseModel;
import ru.biosoft.math.MathRoutines;

public class BIOMD0000000006 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_kappa;
        rate_Reaction2 = Reaction2_k6*x[0];
        rate_Reaction3 = Reaction3_k4*x[1]*(Reaction3_k4prime/Reaction3_k4 + Math.pow(x[0], 2));
    }

    public void Init()
    {
        initialValues = getInitialValues();
/*
 * Initialize variables
 */
        _cell_EmptySet_ = 1.0; // initial value of $"cell.EmptySet"
        Reaction1_kappa = 0.015; // initial value of Reaction1_kappa
        Reaction2_k6 = 1.0; // initial value of Reaction2_k6
        Reaction3_k4 = 180.0; // initial value of Reaction3_k4
        Reaction3_k4prime = 0.018; // initial value of Reaction3_k4prime
    }

    /*
     * Model variables initial values
     */
    protected double _cell_EmptySet_;
    protected double rate_Reaction1;
    protected double rate_Reaction2;
    protected double rate_Reaction3;
    protected double Reaction1_kappa;
    protected double Reaction2_k6;
    protected double Reaction3_k4;
    protected double Reaction3_k4prime;

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


        double[] y = new double[2];
        y[0] = x[0];
        y[1] = x[1];
        return y;
    }
    public double[] getInitialValues()
    {
        double [] x = new double[2];
        this.time = 0.0;
        x[0] = 0.0; // - $"cell.u"
        x[1] = 0.0; // - $"cell.z"

        __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 'BIOMD0000000006.xml' model
         */
    public void __internalDyDt_0(double time, double [] x, double[] result)
    {
        result[0] = -rate_Reaction2+rate_Reaction3;
        result[1] = +rate_Reaction1-rate_Reaction3;
    }
    protected double [] calculateResult(double time, double[] x)
    {
        double[] result = new double[2];
        __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 ...