/*
 * This code is generated by BioUML FrameWork 
 * for BIOMD0000000101.xml diagram  at 2008.03.20 15:08:37
 */
import biouml.plugins.simulation.ae.NewtonSolver;
import biouml.plugins.simulation.java.JavaBaseModel;
import ru.biosoft.math.MathRoutines;

public class BIOMD0000000101 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_v1 = ka*ligand*x[5]*x[3];
        rate_v10 = pRII;
        rate_v11 = kcd*x[3];
        rate_v12 = ki*x[3];
        rate_v13 = kr*x[0];
        rate_v2 = kcd*x[4];
        rate_v3 = klid*x[4];
        rate_v4 = ki*x[4];
        rate_v5 = pRI;
        rate_v6 = kcd*x[5];
        rate_v7 = ki*x[5];
        rate_v8 = kr*x[1];
        rate_v9 = kr*x[2];
    }

    public void Init()
    {
        initialValues = getInitialValues();
/*
 * Initialize variables
 */
        ka = 1.0; // initial value of ka
        kcd = 0.0277777778; // initial value of kcd
        ki = 0.3333333333333; // initial value of ki
        klid = 0.25; // initial value of klid
        kr = 0.0333333333333333; // initial value of kr
        ligand = 3.0E-5; // initial value of ligand
        pRI = 8.0; // initial value of pRI
        pRII = 4.0; // initial value of pRII
    }

    /*
     * Model variables initial values
     */
    protected double rate_v1;
    protected double rate_v10;
    protected double rate_v11;
    protected double rate_v12;
    protected double rate_v13;
    protected double rate_v2;
    protected double rate_v3;
    protected double rate_v4;
    protected double rate_v5;
    protected double rate_v6;
    protected double rate_v7;
    protected double rate_v8;
    protected double rate_v9;
    protected double ka;
    protected double kcd;
    protected double ki;
    protected double klid;
    protected double kr;
    protected double ligand;
    protected double pRI;
    protected double pRII;
    protected double time;

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


        double[] y = new double[7];
        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] = ligand;
        return y;
    }
    public double[] getInitialValues()
    {
        double [] x = new double[6];
        this.time = 0.0;
        x[0] = 0.0; // - $"PM.Endosome.RII_endo"
        x[1] = 0.0; // - $"PM.Endosome.RI_endo"
        x[2] = 40.0; // - $"PM.Endosome.lRIRII_endo"
        x[3] = 20.0; // - $"PM.RII"
        x[4] = 0.0; // - $"PM.lRIRII"
        x[5] = 20.0; // - $PM.RI

        __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 'BIOMD0000000101.xml' model
         */
    public void __internalDyDt_0(double time, double [] x, double[] result)
    {
        result[0] = +rate_v12-rate_v13;
        result[1] = +rate_v7-rate_v8;
        result[2] = +rate_v4-rate_v9;
        result[3] = +rate_v10-rate_v11-rate_v12+rate_v13-rate_v1+rate_v9;
        result[4] = +rate_v1-rate_v2-rate_v3-rate_v4;
        result[5] = -rate_v1+rate_v5-rate_v6-rate_v7+rate_v8+rate_v9;
    }
    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 );
    }

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

        __internalRateVarInitFunc_0(time, x);

        double [] flags = new double[1];
        flags[0] = (time >= 2500.0) ? +1 : -1; //event_0000001
        return flags;
    }

    public void processEvent(int __internalVar12060041175150, double time, double[] x)
    {
        this.time = time;
        if ( __internalVar12060041175150 == 0) //event_0000001
        {
            ligand = 0.01;
        }
    }

} // class ...