/*
 * This code is generated by BioUML FrameWork 
 * for BIOMD0000000012.xml diagram  at 2008.03.20 15:03:27
 */
import biouml.plugins.simulation.ae.NewtonSolver;
import biouml.plugins.simulation.java.JavaBaseModel;
import ru.biosoft.math.MathRoutines;

public class BIOMD0000000012 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 = x[0]/tau_mRNA;
        rate_Reaction10 = alpha0*eff/tau_mRNA + alpha*eff*Math.pow(KM, n)/(tau_mRNA*(Math.pow(KM, n) + Math.pow(x[5], n)));
        rate_Reaction11 = alpha0*eff/tau_mRNA + alpha*eff*Math.pow(KM, n)/(tau_mRNA*(Math.pow(KM, n) + Math.pow(x[3], n)));
        rate_Reaction12 = alpha0*eff/tau_mRNA + alpha*eff*Math.pow(KM, n)/(tau_mRNA*(Math.pow(KM, n) + Math.pow(x[4], n)));
        rate_Reaction2 = x[1]/tau_mRNA;
        rate_Reaction3 = x[2]/tau_mRNA;
        rate_Reaction4 = x[0]*KM*beta/(tau_mRNA*eff);
        rate_Reaction5 = x[1]*KM*beta/(tau_mRNA*eff);
        rate_Reaction6 = x[2]*KM*beta/(tau_mRNA*eff);
        rate_Reaction7 = x[3]*beta/tau_mRNA;
        rate_Reaction8 = x[4]*beta/tau_mRNA;
        rate_Reaction9 = x[5]*beta/tau_mRNA;
    }

    public void Init()
    {
        initialValues = getInitialValues();
/*
 * Initialize variables
 */
        KM = 40.0; // initial value of KM
        alpha = 250.0; // initial value of alpha
        alpha0 = 0.25; // initial value of alpha0
        beta = 0.2; // initial value of beta
        eff = 20.0; // initial value of eff
        n = 2.0; // initial value of n
        tau_mRNA = 2.0; // initial value of tau_mRNA
    }

    /*
     * Model variables initial values
     */
    protected double rate_Reaction1;
    protected double rate_Reaction10;
    protected double rate_Reaction11;
    protected double rate_Reaction12;
    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 KM;
    protected double alpha;
    protected double alpha0;
    protected double beta;
    protected double eff;
    protected double n;
    protected double tau_mRNA;

    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.X"
        x[1] = 0.0; // - $"cell.Y"
        x[2] = 0.0; // - $"cell.Z"
        x[3] = 5.0; // - $cell.PX
        x[4] = 0.0; // - $cell.PY
        x[5] = 15.0; // - $cell.PZ

        __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 'BIOMD0000000012.xml' model
         */
    public void __internalDyDt_0(double time, double [] x, double[] result)
    {
        result[0] = +rate_Reaction10-rate_Reaction1;
        result[1] = +rate_Reaction11-rate_Reaction2;
        result[2] = +rate_Reaction12-rate_Reaction3;
        result[3] = +rate_Reaction4-rate_Reaction7;
        result[4] = +rate_Reaction5-rate_Reaction8;
        result[5] = +rate_Reaction6-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 ...