Examples with RationalMatrixFast cbit.vcell.matrix.RationalMatrixFast used on opensource projects

Example 1 with RationalMatrixFast

use of cbit.vcell.matrix.RationalMatrixFast in project vcell by virtualcell.

the class SVDTest method findNullSpaceVCell.

/**
 * Insert the method's description here.
 * Creation date: (5/13/2003 4:37:34 PM)
 * @param matrix Jama.Matrix
 */
public static RationalMatrix findNullSpaceVCell(RationalMatrix rA) {
    try {
        SimpleMatrix A = new SimpleMatrix(getJamaMatrix(rA).getArrayCopy());
        SimpleMatrix ns = SimpleMatrix.findNullSpace(A);
        // ns.show();
        RationalMatrixFast nsRationalMatrix = getRationalMatrixFast(ns);
        // nsRationalMatrix.show();
        return nsRationalMatrix;
    } catch (Throwable e) {
        e.printStackTrace(System.out);
        throw new RuntimeException(e.getMessage());
    }
}

Example 2 with RationalMatrixFast

use of cbit.vcell.matrix.RationalMatrixFast in project vcell by virtualcell.

the class SVDTest method getGEPASI_Brusselator.

/**
 * This method was created by a SmartGuide.
 * @return cbit.vcell.math.Matrix
 */
public static RationalMatrixFast getGEPASI_Brusselator() throws Exception {
    int numVars = 7;
    int numReactions = 8;
    RationalMatrixFast a = new RationalMatrixFast(numVars, numReactions);
    a.zero();
    String[] vars = new String[numVars];
    int A = 0;
    vars[A] = "A";
    int B = 1;
    vars[B] = "B";
    int D = 2;
    vars[D] = "D";
    int E = 3;
    vars[E] = "E";
    int F = 4;
    vars[F] = "F";
    int X = 5;
    vars[X] = "X";
    int Y = 6;
    vars[Y] = "Y";
    // 
    // A -> X
    // 2X + Y -> 3X
    // X + B -> Y + D
    // X -> E
    // A = E
    // A = F
    // 
    int r = 0;
    // A -> X
    a.set_elem(A, r, -1);
    a.set_elem(X, r, 1);
    r++;
    // 2X + Y -> 3X
    a.set_elem(Y, r, -1);
    a.set_elem(X, r, 1);
    r++;
    // X + B -> Y + D
    a.set_elem(X, r, -1);
    a.set_elem(B, r, -1);
    a.set_elem(Y, r, 1);
    a.set_elem(D, r, 1);
    r++;
    // X -> E
    a.set_elem(X, r, -1);
    a.set_elem(E, r, 1);
    r++;
    // A = E
    a.set_elem(A, r, -1);
    a.set_elem(E, r, 1);
    r++;
    a.set_elem(E, r, -1);
    a.set_elem(A, r, 1);
    r++;
    // A = F
    a.set_elem(A, r, -1);
    a.set_elem(F, r, 1);
    r++;
    a.set_elem(F, r, -1);
    a.set_elem(A, r, 1);
    r++;
    return a;
}

Example 3 with RationalMatrixFast

use of cbit.vcell.matrix.RationalMatrixFast in project vcell by virtualcell.

the class SVDTest method getRationalMatrixFast.

/**
 * Insert the method's description here.
 * Creation date: (5/13/2003 11:06:29 AM)
 * @return Jama.Matrix
 */
public static RationalMatrixFast getRationalMatrixFast(SimpleMatrix matrix) {
    RationalMatrixFast rMatrix = new RationalMatrixFast(matrix.getNumRows(), matrix.getNumCols());
    for (int i = 0; i < rMatrix.getNumRows(); i++) {
        for (int j = 0; j < rMatrix.getNumCols(); j++) {
            RationalNumber r = RationalNumber.getApproximateFraction(matrix.get_elem(i, j));
            rMatrix.set_elem(i, j, r.getNumBigInteger().longValue(), r.getDenBigInteger().longValue());
        }
    }
    return rMatrix;
}

Example 4 with RationalMatrixFast

use of cbit.vcell.matrix.RationalMatrixFast in project vcell by virtualcell.

the class SVDTest method main.

/**
 * Starts the application.
 * @param args an array of command-line arguments
 */
public static void main(java.lang.String[] args) {
    try {
        Jama.Matrix A = getJamaMatrix(getGEPASI_Brusselator());
        Jama.Matrix At = A.transpose();
        Jama.SingularValueDecomposition svdMatrix = new Jama.SingularValueDecomposition(At);
        Jama.Matrix U = svdMatrix.getU();
        Jama.Matrix V = svdMatrix.getV();
        double[] S = svdMatrix.getSingularValues();
        System.out.println("A' = U*S*V'");
        System.out.println("A' = ");
        At.print(8, 5);
        System.out.println("U = ");
        U.print(8, 5);
        System.out.println("V = ");
        V.print(8, 5);
        System.out.print("S = ");
        for (int i = 0; i < S.length; i++) {
            System.out.print(S[i] + " ");
        }
        System.out.println();
        int rank = svdMatrix.rank();
        System.out.println("rank = " + rank);
        Jama.Matrix Vt = V.transpose();
        Jama.Matrix nsMatrix = Vt.getMatrix(rank, Vt.getRowDimension() - 1, 0, Vt.getColumnDimension() - 1);
        System.out.println("NS = ");
        nsMatrix.print(8, 5);
        SimpleMatrix matrix = new SimpleMatrix(nsMatrix.getArrayCopy());
        matrix.show();
        SimpleMatrix.gaussianElimination(new SimpleMatrix(matrix.getNumRows(), matrix.getNumRows()), matrix);
        matrix.show();
        RationalMatrixFast nsRationalMatrix = getRationalMatrixFast(matrix);
        nsRationalMatrix.show();
    } catch (Throwable e) {
        e.printStackTrace(System.out);
    }
}

Example 5 with RationalMatrixFast

use of cbit.vcell.matrix.RationalMatrixFast in project vcell by virtualcell.

the class SVDTest method getRationalMatrixFast.

/**
 * Insert the method's description here.
 * Creation date: (5/13/2003 11:06:29 AM)
 * @return Jama.Matrix
 */
public static RationalMatrixFast getRationalMatrixFast(Jama.Matrix matrix) {
    RationalMatrixFast rMatrix = new RationalMatrixFast(matrix.getRowDimension(), matrix.getColumnDimension());
    for (int i = 0; i < rMatrix.getNumRows(); i++) {
        for (int j = 0; j < rMatrix.getNumCols(); j++) {
            RationalNumber r = RationalNumber.getApproximateFraction(matrix.get(i, j));
            rMatrix.set_elem(i, j, r.getNumBigInteger().longValue(), r.getDenBigInteger().longValue());
        }
    }
    return rMatrix;
}