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Matrix data structures, linear solvers, least squares methods, eigenvalue, and singular value decompositions. For larger random dense matrices (above ~ 350 x 350) matrix-matrix multiplication C = A.B is about 50% faster than MTJ.
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/*
 * Copyright (C) 2003-2006 Bjørn-Ove Heimsund
 * 
 * This file is part of MTJ.
 * 
 * This library is free software; you can redistribute it and/or modify it
 * under the terms of the GNU Lesser General Public License as published by the
 * Free Software Foundation; either version 2.1 of the License, or (at your
 * option) any later version.
 * 
 * This library is distributed in the hope that it will be useful, but WITHOUT
 * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
 * FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
 * for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this library; if not, write to the Free Software Foundation,
 * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 */

package no.uib.cipr.matrix;

/**
 * Upper triangular dense matrix. It has the same storage layout as the
 * {@link no.uib.cipr.matrix.DenseMatrix DenseMatrix}, but only refers to
 * elements above or on the main diagonal. The remaining elements are assumed to
 * be zero, but since they are never accessed, they need not be.
 */
public class UpperTriangDenseMatrix extends AbstractTriangDenseMatrix {

    /**
     * Constructor for UpperTriangDenseMatrix
     * 
     * @param n
     *            Size of the matrix. Since the matrix must be square, this
     *            equals both the number of rows and columns
     */
    public UpperTriangDenseMatrix(int n) {
        super(n, UpLo.Upper, Diag.NonUnit);
    }

    /**
     * Constructor for UpperTriangDenseMatrix
     * 
     * @param n
     *            Size of the matrix. Since the matrix must be square, this
     *            equals both the number of rows and columns
     */
    UpperTriangDenseMatrix(int n, Diag diag) {
        super(n, UpLo.Upper, diag);
    }

    /**
     * Constructor for UpperTriangDenseMatrix
     * 
     * @param A
     *            Matrix to copy from. Only the upper triangular part is copied
     */
    public UpperTriangDenseMatrix(Matrix A) {
        this(A, Math.min(A.numRows(), A.numColumns()));
    }

    /**
     * Constructor for UpperTriangDenseMatrix
     * 
     * @param A
     *            Matrix to copy from. Only the upper triangular part is copied
     * @param deep
     *            True for deep copy, false for reference (in which case
     *            A must be a dense matrix)
     */
    public UpperTriangDenseMatrix(Matrix A, boolean deep) {
        this(A, Math.min(A.numRows(), A.numColumns()), deep);
    }

    /**
     * Constructor for UpperTriangDenseMatrix
     * 
     * @param A
     *            Matrix to copy from. Only the upper triangular part is copied
     * @param deep
     *            True for deep copy, false for reference (in which case
     *            A must be a dense matrix)
     */
    UpperTriangDenseMatrix(Matrix A, boolean deep, Diag diag) {
        this(A, Math.min(A.numRows(), A.numColumns()), deep, diag);
    }

    /**
     * Constructor for UpperTriangDenseMatrix
     * 
     * @param A
     *            Matrix to copy from. Only the upper triangular part is copied
     * @param k
     *            Size of matrix to refer.
     *            k<min(numRows,numColumns)
     */
    public UpperTriangDenseMatrix(Matrix A, int k) {
        this(A, k, true);
    }

    /**
     * Constructor for UpperTriangDenseMatrix
     * 
     * @param A
     *            Matrix to copy from. Only the upper triangular part is copied
     * @param k
     *            Size of matrix to refer.
     *            k<min(numRows,numColumns)
     * @param deep
     *            True for deep copy, false for reference (in which case
     *            A must be a dense matrix)
     */
    public UpperTriangDenseMatrix(Matrix A, int k, boolean deep) {
        super(A, k, deep, UpLo.Upper, Diag.NonUnit);
    }

    /**
     * Constructor for UpperTriangDenseMatrix
     * 
     * @param A
     *            Matrix to copy from. Only the upper triangular part is copied
     * @param k
     *            Size of matrix to refer.
     *            k<min(numRows,numColumns)
     * @param deep
     *            True for deep copy, false for reference (in which case
     *            A must be a dense matrix)
     */
    UpperTriangDenseMatrix(Matrix A, int k, boolean deep, Diag diag) {
        super(A, k, deep, UpLo.Upper, diag);
    }

    @Override
    public void add(int row, int column, double value) {
        if (row > column)
            throw new IllegalArgumentException("row > column");
        super.add(row, column, value);
    }

    @Override
    public double get(int row, int column) {
        if (row > column)
            return 0;
        return super.get(row, column);
    }

    @Override
    public void set(int row, int column, double value) {
        if (row > column)
            throw new IllegalArgumentException("row > column");
        super.set(row, column, value);
    }

    @Override
    void copy(Matrix A) {
        for (MatrixEntry e : A)
            if (e.row() <= e.column())
                set(e.row(), e.column(), e.get());
    }

    @Override
    public Matrix set(Matrix A) {
        zero();
        copy(A);
        return this;
    }

    @Override
    public UpperTriangDenseMatrix copy() {
        return new UpperTriangDenseMatrix(this);
    }

}