Package org.apache.commons.math3.distribution

Examples of org.apache.commons.math3.distribution.BinomialDistribution

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                int m = idPWM.getColumnSum(j);
                int c_xj = idPWM.getMatrix()[i][j]; // count of residue at position j
                double p_xj = ((double) bGPWM.getMatrix()[i][j])/((double) bGPWM.getColumnSum(j));
                double bin_prob = 0.00;
                for(int trial = c_xj; trial <= m; trial++){
                    BinomialDistribution bnDistr = new BinomialDistribution(trial,p_xj);
                    bin_prob = bin_prob + bnDistr.probability(trial);
                    //int printbin = (m - c_xj)/20;
                    if(trial%10==0){
                        System.out.println("\t\t\tBinomial probability of "+ aminoA_symbols[i] + ", " +
                                relative_positions[j] + " at iteration " + trial + " of " + m + " is " +
                                   bin_prob);
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     * length.
     */
    protected double[] computeResiduals(double[] objectiveValue) {
        final double[] target = getTarget();
        if (objectiveValue.length != target.length) {
            throw new DimensionMismatchException(target.length,
                                                 objectiveValue.length);
        }

        final double[] residuals = new double[target.length];
        for (int i = 0; i < target.length; i++) {
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        /** {@inheritDoc} */
        public RealVector solve(final RealVector b) {
            final int m = lTData.length;
            if (b.getDimension() != m) {
                throw new DimensionMismatchException(b.getDimension(), m);
            }

            final double[] x = b.toArray();

            // Solve LY = b
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        /** {@inheritDoc} */
        public RealMatrix solve(RealMatrix b) {
            final int m = lTData.length;
            if (b.getRowDimension() != m) {
                throw new DimensionMismatchException(b.getRowDimension(), m);
            }

            final int nColB = b.getColumnDimension();
            final double[][] x = b.getData();

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     */
    public double correlation(final double[] xArray, final double[] yArray)
            throws DimensionMismatchException {

        if (xArray.length != yArray.length) {
            throw new DimensionMismatchException(xArray.length, yArray.length);
        }

        final int n = xArray.length;
        final long numPairs = sum(n - 1);

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     * @throws DimensionMismatchException if {@link #target} and
     * {@link #weightMatrix} have inconsistent dimensions.
     */
    private void checkParameters() {
        if (target.length != weightMatrix.getColumnDimension()) {
            throw new DimensionMismatchException(target.length,
                                                 weightMatrix.getColumnDimension());
        }
    }
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    public void increment(final double[] data)
        throws DimensionMismatchException {

        int length = data.length;
        if (length != dimension) {
            throw new DimensionMismatchException(length, dimension);
        }

        // only update the upper triangular part of the covariance matrix
        // as only these parts are actually stored
        for (int i = 0; i < length; i++){
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     * @throws DimensionMismatchException if the dimension of sc does not match this
     * @since 3.3
     */
    public void append(StorelessCovariance sc) throws DimensionMismatchException {
        if (sc.dimension != dimension) {
            throw new DimensionMismatchException(sc.dimension, dimension);
        }

        // only update the upper triangular part of the covariance matrix
        // as only these parts are actually stored
        for (int i = 0; i < dimension; i++) {
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            if (m.getColumnDimension() != m.getRowDimension()) {
                throw new NonSquareOperatorException(m.getColumnDimension(),
                                                     m.getRowDimension());
            }
            if (m.getRowDimension() != a.getRowDimension()) {
                throw new DimensionMismatchException(m.getRowDimension(),
                                                     a.getRowDimension());
            }
        }
    }
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   */
  public Rotation(Vector3D u, Vector3D v) throws MathArithmeticException {

    double normProduct = u.getNorm() * v.getNorm();
    if (normProduct == 0) {
        throw new MathArithmeticException(LocalizedFormats.ZERO_NORM_FOR_ROTATION_DEFINING_VECTOR);
    }

    double dot = u.dotProduct(v);

    if (dot < ((2.0e-15 - 1.0) * normProduct)) {
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