/*
 * This code is generated by BioUML FrameWork 
 * for BIOMD0000000093.xml diagram  at 2008.03.20 15:08:29
 */
import biouml.plugins.simulation.ae.NewtonSolver;
import biouml.plugins.simulation.java.JavaBaseModel;
import ru.biosoft.math.MathRoutines;

public class BIOMD0000000093 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 = cytoplasm*(v1_kf*x[14]*x[12] - v1_kb*x[32]);
        rate_v10 = cytoplasm*v10_kf*x[4];
        rate_v11 = cytoplasm*(v11_kf*x[13]*x[19] - v11_kb*x[20]);
        rate_v12 = cytoplasm*v12_kf*x[20];
        rate_v13 = cytoplasm*(v13_kf*x[13]*x[21] - v13_kb*x[22]);
        rate_v14 = cytoplasm*v14_kf*x[22];
        rate_v15 = cytoplasm*(v15_kf*x[17]*x[19] - v15_kb*x[18]);
        rate_v16 = cytoplasm*v16_kf*x[21];
        rate_v17 = _cytoplasm_nucleus_*(v17_kf*x[27]*x[27] - v17_kb*x[29]);
        rate_v18 = _cytoplasm_nucleus_*(v18_kf*x[24]*x[27] - v18_kb*x[28]);
        rate_v19 = _cytoplasm_nucleus_*v19_kf*x[28];
        rate_v2 = cytoplasm*(v2_kf*_cytoplasm_IFN_*x[32] - v2_kb*x[1]);
        rate_v20 = _cytoplasm_nucleus_*(v20_kf*x[24]*x[29] - v20_kb*x[30]);
        rate_v21 = _cytoplasm_nucleus_*v21_kf*x[30];
        rate_v22 = _cytoplasm_nucleus_*(v22_kf*x[25]*x[27] - v22_kb*x[26]);
        rate_v23 = _cytoplasm_nucleus_*v23_kf*x[25];
        rate_v24 = _cytoplasm_nucleus_*v24_ka*x[29]/(v24_kb + x[29]);
        rate_v25 = _cytoplasm_nucleus_*v25_kf*x[31];
        rate_v26 = cytoplasm*v26_kf*x[23];
        rate_v27 = cytoplasm*v27_kf*x[23];
        rate_v28 = cytoplasm*v28_kf*x[16];
        rate_v29 = cytoplasm*(v29_kf*x[16]*x[3] - v29_kb*x[8]);
        rate_v3 = cytoplasm*(v3_kf*x[1]*x[1] - v3_kb*x[2]);
        rate_v30 = cytoplasm*(v30_kf*x[17]*x[8] - v30_kb*x[9]);
        rate_v31 = cytoplasm*(v31_kf*x[15]*x[9] - v31_kb*x[6]);
        rate_v32 = cytoplasm*v32_kf*x[6];
        rate_v33 = cytoplasm*v33_kf*x[6];
        rate_v34 = cytoplasm*(v34_kf*x[15]*x[8] - v34_kb*x[5]);
        rate_v35 = cytoplasm*(v35_kf*x[17]*x[5] - v35_kb*x[6]);
        rate_v36 = cytoplasm*(v36_kf*x[15]*x[10] - v36_kb*x[7]);
        rate_v37 = cytoplasm*v37_kf*x[7];
        rate_v38 = cytoplasm*v38_kf*x[9];
        rate_v39 = cytoplasm*v39_kf*x[5];
        rate_v4 = cytoplasm*v4_kf*x[2];
        rate_v40 = cytoplasm*v40_kf*x[5];
        rate_v41 = cytoplasm*v41_kf*x[8];
        rate_v42 = cytoplasm*(v42_kf*x[16]*x[10] - v42_kb*x[9]);
        rate_v43 = cytoplasm*(v43_kf*x[16]*x[4] - v43_kb*x[5]);
        rate_v44 = cytoplasm*(v44_kf*x[16]*x[7] - v44_kb*x[6]);
        rate_v45 = cytoplasm*(v45_kf*_cytoplasm_IFN_*x[14] - v45_kb*x[0]);
    }
    public void __internalRateVarInitFunc_1(double time, double[] x)
    {
        rate_v46 = cytoplasm*(v46_kf*x[0]*x[12] - v46_kb*x[1]);
        rate_v5 = cytoplasm*(v5_kf*x[17]*x[3] - v5_kb*x[10]);
        rate_v6 = cytoplasm*v6_kf*x[10];
        rate_v7 = cytoplasm*(v7_kf*x[3]*x[19] - v7_kb*x[11]);
        rate_v8 = cytoplasm*(v8_kf*x[19]*x[19] - v8_kb*x[21]);
        rate_v9 = cytoplasm*(v9_kf*x[3]*x[15] - v9_kb*x[4]);
    }

    public void Init()
    {
        initialValues = getInitialValues();
/*
 * Initialize variables
 */
        _cytoplasm_IFN_ = 10.0; // initial value of $"cytoplasm.IFN"
        _cytoplasm_nucleus_ = 1.0; // initial value of $"cytoplasm.nucleus"
        cytoplasm = 1.0; // initial value of $cytoplasm
        v10_kf = 0.0030; // initial value of v10_kf
        v11_kb = 0.2; // initial value of v11_kb
        v11_kf = 0.0010; // initial value of v11_kf
        v12_kf = 0.0030; // initial value of v12_kf
        v13_kb = 0.2; // initial value of v13_kb
        v13_kf = 0.0010; // initial value of v13_kf
        v14_kf = 0.0030; // initial value of v14_kf
        v15_kb = 0.2; // initial value of v15_kb
        v15_kf = 2.0E-7; // initial value of v15_kf
        v16_kf = 0.0050; // initial value of v16_kf
        v17_kb = 0.1; // initial value of v17_kb
        v17_kf = 0.02; // initial value of v17_kf
        v18_kb = 0.2; // initial value of v18_kb
        v18_kf = 0.0010; // initial value of v18_kf
        v19_kf = 0.0050; // initial value of v19_kf
        v1_kb = 0.05; // initial value of v1_kb
        v1_kf = 0.1; // initial value of v1_kf
        v20_kb = 0.2; // initial value of v20_kb
        v20_kf = 0.0010; // initial value of v20_kf
        v21_kf = 0.0050; // initial value of v21_kf
        v22_kb = 0.2; // initial value of v22_kb
        v22_kf = 2.0E-7; // initial value of v22_kf
        v23_kf = 0.05; // initial value of v23_kf
        v24_ka = 0.01; // initial value of v24_ka
        v24_kb = 400.0; // initial value of v24_kb
        v25_kf = 0.0010; // initial value of v25_kf
        v26_kf = 0.01; // initial value of v26_kf
        v27_kf = 5.0E-4; // initial value of v27_kf
        v28_kf = 5.0E-4; // initial value of v28_kf
        v29_kb = 0.1; // initial value of v29_kb
        v29_kf = 0.02; // initial value of v29_kf
        v2_kb = 0.02; // initial value of v2_kb
        v2_kf = 0.02; // initial value of v2_kf
        v30_kb = 0.8; // initial value of v30_kb
        v30_kf = 0.0080; // initial value of v30_kf
        v31_kb = 0.2; // initial value of v31_kb
        v31_kf = 0.0010; // initial value of v31_kf
        v32_kf = 0.0030; // initial value of v32_kf
        v33_kf = 5.0E-4; // initial value of v33_kf
        v34_kb = 0.2; // initial value of v34_kb
        v34_kf = 0.0010; // initial value of v34_kf
        v35_kb = 0.8; // initial value of v35_kb
        v35_kf = 0.0080; // initial value of v35_kf
        v36_kb = 0.2; // initial value of v36_kb
        v36_kf = 0.0010; // initial value of v36_kf
        v37_kf = 0.0030; // initial value of v37_kf
        v38_kf = 5.0E-4; // initial value of v38_kf
        v39_kf = 5.0E-4; // initial value of v39_kf
        v3_kb = 0.2; // initial value of v3_kb
        v3_kf = 0.04; // initial value of v3_kf
        v40_kf = 0.0030; // initial value of v40_kf
        v41_kf = 5.0E-4; // initial value of v41_kf
        v42_kb = 0.1; // initial value of v42_kb
        v42_kf = 0.02; // initial value of v42_kf
        v43_kb = 0.1; // initial value of v43_kb
        v43_kf = 0.02; // initial value of v43_kf
        v44_kb = 0.1; // initial value of v44_kb
        v44_kf = 0.02; // initial value of v44_kf
        v45_kb = 0.02; // initial value of v45_kb
        v45_kf = 0.02; // initial value of v45_kf
        v46_kb = 0.05; // initial value of v46_kb
        v46_kf = 0.1; // initial value of v46_kf
        v4_kf = 0.0050; // initial value of v4_kf
        v5_kb = 0.8; // initial value of v5_kb
        v5_kf = 0.0080; // initial value of v5_kf
        v6_kf = 0.4; // initial value of v6_kf
        v7_kb = 0.5; // initial value of v7_kb
        v7_kf = 0.0050; // initial value of v7_kf
        v8_kb = 0.1; // initial value of v8_kb
        v8_kf = 0.02; // initial value of v8_kf
        v9_kb = 0.2; // initial value of v9_kb
        v9_kf = 0.0010; // initial value of v9_kf
    }

    /*
     * Model variables initial values
     */
    protected double _cytoplasm_IFN_;
    protected double _cytoplasm_nucleus_;
    protected double rate_v1;
    protected double rate_v10;
    protected double rate_v11;
    protected double rate_v12;
    protected double rate_v13;
    protected double rate_v14;
    protected double rate_v15;
    protected double rate_v16;
    protected double rate_v17;
    protected double rate_v18;
    protected double rate_v19;
    protected double rate_v2;
    protected double rate_v20;
    protected double rate_v21;
    protected double rate_v22;
    protected double rate_v23;
    protected double rate_v24;
    protected double rate_v25;
    protected double rate_v26;
    protected double rate_v27;
    protected double rate_v28;
    protected double rate_v29;
    protected double rate_v3;
    protected double rate_v30;
    protected double rate_v31;
    protected double rate_v32;
    protected double rate_v33;
    protected double rate_v34;
    protected double rate_v35;
    protected double rate_v36;
    protected double rate_v37;
    protected double rate_v38;
    protected double rate_v39;
    protected double rate_v4;
    protected double rate_v40;
    protected double rate_v41;
    protected double rate_v42;
    protected double rate_v43;
    protected double rate_v44;
    protected double rate_v45;
    protected double rate_v46;
    protected double rate_v5;
    protected double rate_v6;
    protected double rate_v7;
    protected double rate_v8;
    protected double rate_v9;
    protected double cytoplasm;
    protected double v10_kf;
    protected double v11_kb;
    protected double v11_kf;
    protected double v12_kf;
    protected double v13_kb;
    protected double v13_kf;
    protected double v14_kf;
    protected double v15_kb;
    protected double v15_kf;
    protected double v16_kf;
    protected double v17_kb;
    protected double v17_kf;
    protected double v18_kb;
    protected double v18_kf;
    protected double v19_kf;
    protected double v1_kb;
    protected double v1_kf;
    protected double v20_kb;
    protected double v20_kf;
    protected double v21_kf;
    protected double v22_kb;
    protected double v22_kf;
    protected double v23_kf;
    protected double v24_ka;
    protected double v24_kb;
    protected double v25_kf;
    protected double v26_kf;
    protected double v27_kf;
    protected double v28_kf;
    protected double v29_kb;
    protected double v29_kf;
    protected double v2_kb;
    protected double v2_kf;
    protected double v30_kb;
    protected double v30_kf;
    protected double v31_kb;
    protected double v31_kf;
    protected double v32_kf;
    protected double v33_kf;
    protected double v34_kb;
    protected double v34_kf;
    protected double v35_kb;
    protected double v35_kf;
    protected double v36_kb;
    protected double v36_kf;
    protected double v37_kf;
    protected double v38_kf;
    protected double v39_kf;
    protected double v3_kb;
    protected double v3_kf;
    protected double v40_kf;
    protected double v41_kf;
    protected double v42_kb;
    protected double v42_kf;
    protected double v43_kb;
    protected double v43_kf;
    protected double v44_kb;
    protected double v44_kf;
    protected double v45_kb;
    protected double v45_kf;
    protected double v46_kb;
    protected double v46_kf;
    protected double v4_kf;
    protected double v5_kb;
    protected double v5_kf;
    protected double v6_kf;
    protected double v7_kb;
    protected double v7_kf;
    protected double v8_kb;
    protected double v8_kf;
    protected double v9_kb;
    protected double v9_kf;

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


        double[] y = new double[33];
        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];
        y[11] = x[11];
        y[12] = x[12];
        y[13] = x[13];
        y[14] = x[14];
        y[15] = x[15];
        y[16] = x[16];
        y[17] = x[17];
        y[18] = x[18];
        y[19] = x[19];
        y[20] = x[20];
        y[21] = x[21];
        y[22] = x[22];
        y[23] = x[23];
        y[24] = x[24];
        y[25] = x[25];
        y[26] = x[26];
        y[27] = x[27];
        y[28] = x[28];
        y[29] = x[29];
        y[30] = x[30];
        y[31] = x[31];
        y[32] = x[32];
        return y;
    }
    public double[] getInitialValues()
    {
        double [] x = new double[33];
        this.time = 0.0;
        x[0] = 0.0; // - $"cytoplasm.IFNR"
        x[1] = 0.0; // - $"cytoplasm.IFNRJ"
        x[2] = 0.0; // - $"cytoplasm.IFNRJ2"
        x[3] = 0.0; // - $"cytoplasm.IFNRJ2_star"
        x[4] = 0.0; // - $"cytoplasm.IFNRJ2_star_SHP2"
        x[5] = 0.0; // - $"cytoplasm.IFNRJ2_star_SHP2_SOCS1"
        x[6] = 0.0; // - $"cytoplasm.IFNRJ2_star_SHP2_SOCS1_STAT1c"
        x[7] = 0.0; // - $"cytoplasm.IFNRJ2_star_SHP2_STAT1c"
        x[8] = 0.0; // - $"cytoplasm.IFNRJ2_star_SOCS1"
        x[9] = 0.0; // - $"cytoplasm.IFNRJ2_star_SOCS1_STAT1c"
        x[10] = 0.0; // - $"cytoplasm.IFNRJ2_star_STAT1c"
        x[11] = 0.0; // - $"cytoplasm.IFNRJ2_star_STAT1c_star"
        x[12] = 10.0; // - $"cytoplasm.JAK"
        x[13] = 50.0; // - $"cytoplasm.PPX"
        x[14] = 10.0; // - $"cytoplasm.R"
        x[15] = 100.0; // - $"cytoplasm.SHP2"
        x[16] = 0.0; // - $"cytoplasm.SOCS1"
        x[17] = 1000.0; // - $"cytoplasm.STAT1c"
        x[18] = 0.0; // - $"cytoplasm.STAT1c_STAT1c_star"
        x[19] = 0.0; // - $"cytoplasm.STAT1c_star"
        x[20] = 0.0; // - $"cytoplasm.STAT1c_star_PPX"
        x[21] = 0.0; // - $"cytoplasm.STAT1c_star_STAT1c_star"
        x[22] = 0.0; // - $"cytoplasm.STAT1c_star_STAT1c_star_PPX"
        x[23] = 0.0; // - $"cytoplasm.mRNAc"
        x[24] = 60.0; // - $"cytoplasm.nucleus.PPN"
        x[25] = 0.0; // - $"cytoplasm.nucleus.STAT1n"
        x[26] = 0.0; // - $"cytoplasm.nucleus.STAT1n_STAT1n_star"
        x[27] = 0.0; // - $"cytoplasm.nucleus.STAT1n_star"
        x[28] = 0.0; // - $"cytoplasm.nucleus.STAT1n_star_PPN"
        x[29] = 0.0; // - $"cytoplasm.nucleus.STAT1n_star_STAT1n_star"
        x[30] = 0.0; // - $"cytoplasm.nucleus.STAT1n_star_STAT1n_star_PPN"
        x[31] = 0.0; // - $"cytoplasm.nucleus.mRNAn"
        x[32] = 0.0; // - $cytoplasm.RJ

        __internalRateVarInitFunc_0(time, x);
        __internalRateVarInitFunc_1(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);
        __internalRateVarInitFunc_1(time, x);

    }

        /*
         * calculate dy/dt for 'BIOMD0000000093.xml' model
         */
    public void __internalDyDt_0(double time, double [] x, double[] result)
    {
        result[0] = +rate_v45-rate_v46;
        result[1] = +rate_v2-rate_v3*2+rate_v46;
        result[2] = +rate_v10+rate_v32+rate_v37+rate_v3+rate_v40-rate_v4;
        result[3] = -rate_v29+rate_v41+rate_v4-rate_v5+rate_v6-rate_v7-rate_v9;
        result[4] = -rate_v10+rate_v39-rate_v43+rate_v9;
        result[5] = +rate_v34-rate_v35-rate_v39-rate_v40+rate_v43;
        result[6] = +rate_v31-rate_v32-rate_v33+rate_v35+rate_v44;
        result[7] = +rate_v33+rate_v36-rate_v37-rate_v44;
        result[8] = +rate_v29-rate_v30-rate_v34-rate_v41;
        result[9] = +rate_v30-rate_v31-rate_v38+rate_v42;
        result[10] = -rate_v36+rate_v38-rate_v42+rate_v5-rate_v6;
        result[11] = +rate_v7;
        result[12] = -rate_v1-rate_v46;
        result[13] = -rate_v11+rate_v12-rate_v13+rate_v14;
        result[14] = -rate_v1-rate_v45;
        result[15] = +rate_v10-rate_v31+rate_v32-rate_v34-rate_v36+rate_v37+rate_v40-rate_v9;
        result[16] = +rate_v26-rate_v28-rate_v29+rate_v32+rate_v40-rate_v42-rate_v43-rate_v44;
        result[17] = +rate_v12-rate_v15+rate_v23-rate_v30+rate_v32-rate_v35+rate_v37-rate_v5;
        result[18] = +rate_v14+rate_v15;
        result[19] = -rate_v11-rate_v15+rate_v6-rate_v7-rate_v8*2;
        result[20] = +rate_v11-rate_v12;
        result[21] = -rate_v13-rate_v16+rate_v8;
        result[22] = +rate_v13-rate_v14;
        result[23] = +rate_v25-rate_v27;
        result[24] = -rate_v18+rate_v19-rate_v20+rate_v21;
        result[25] = +rate_v19-rate_v22-rate_v23;
        result[26] = +rate_v21+rate_v22;
        result[27] = -rate_v17*2-rate_v18-rate_v22;
        result[28] = +rate_v18-rate_v19;
        result[29] = +rate_v16+rate_v17-rate_v20;
        result[30] = +rate_v20-rate_v21;
        result[31] = +rate_v24-rate_v25;
        result[32] = +rate_v1-rate_v2;
    }
    protected double [] calculateResult(double time, double[] x)
    {
        double[] result = new double[33];
        __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 ...