Example usage for org.apache.commons.math.linear RealMatrix getEntry

Introduction

In this page you can find the example usage for org.apache.commons.math.linear RealMatrix getEntry.

Prototype

double getEntry(int row, int column) throws MatrixIndexException;

Source Link

Document

Returns the entry in the specified row and column.

Usage

From source file:juicebox.tools.utils.juicer.apa.APAUtils.java

public static RealMatrix centerNormalization(RealMatrix matrix) {

    int center = matrix.getRowDimension() / 2;
    double centerVal = matrix.getEntry(center, center);

    if (centerVal == 0) {
        centerVal = MatrixTools.minimumPositive(matrix);
        if (centerVal == 0)
            centerVal = 1;/* w ww.  ja v  a2 s  . c om*/
    }

    return matrix.copy().scalarMultiply(1. / centerVal);
}

From source file:juicebox.tools.utils.juicer.apa.APAUtils.java

public static double peakEnhancement(RealMatrix matrix) {
    int rows = matrix.getRowDimension();
    int center = rows / 2;
    double centerVal = matrix.getEntry(center, center);
    double remainingSum = APARegionStatistics.sum(matrix.getData()) - centerVal;
    double remainingAverage = remainingSum / (rows * rows - 1);
    return centerVal / remainingAverage;
}

From source file:juicebox.tools.utils.juicer.arrowhead.DynamicProgrammingUtils.java

/**
 * Dynamic programming to calculate "right" matrix
 * Initialize by setting the diagonal to the diagonal of original
 * Iterate to the right and up./*from   w w  w  .j av a 2 s . c  o m*/
 *
 * @param matrix
 * @param maxSize
 * @return rightMatrix
 */
public static RealMatrix right(RealMatrix matrix, int maxSize) {

    RealMatrix rightMatrix = MatrixTools.extractDiagonal(matrix);
    int n = rightMatrix.getRowDimension();

    // j is column, i is row
    for (int j = 1; j < n; j++) {
        int endPoint = Math.max(j - 1 - maxSize, 0);
        for (int i = j - 1; i >= endPoint; i--) {
            rightMatrix.setEntry(i, j, matrix.getEntry(i, j) + rightMatrix.getEntry(i + 1, j));
        }
    }
    return rightMatrix;
}

From source file:juicebox.tools.utils.juicer.arrowhead.DynamicProgrammingUtils.java

/**
 * Dynamic programming to calculate "upper" matrix
 * Initialize by setting the diagonal to the diagonal of original
 * Iterate down (for each row) and to the left.
 *
 * @param matrix//from   w  w  w . ja  v a  2s  .c om
 * @param maxSize
 * @return upperMatrix
 */
public static RealMatrix upper(RealMatrix matrix, int maxSize) {

    RealMatrix upperMatrix = MatrixTools.extractDiagonal(matrix);
    int n = upperMatrix.getRowDimension();

    // j is column, i is row
    for (int i = 0; i < n; i++) {
        int endPoint = Math.min(i + 1 + maxSize, n - 1);
        for (int j = i + 1; j <= endPoint; j++) {
            upperMatrix.setEntry(i, j, matrix.getEntry(i, j) + upperMatrix.getEntry(i, j - 1));
        }
    }
    return upperMatrix;
}

From source file:juicebox.tools.utils.juicer.apa.APAUtils.java

/**
 * @param data/* www .  j  a  va2s . c o  m*/
 * @return
 */
public static RealMatrix rankPercentile(RealMatrix data) {
    int n = data.getColumnDimension();
    StatPercentile percentile = new StatPercentile(MatrixTools.flattenedRowMajorOrderMatrix(data));

    RealMatrix matrix = new Array2DRowRealMatrix(n, n);
    for (int r = 0; r < n; r++) {
        for (int c = 0; c < n; c++) {
            double currValue = data.getEntry(r, c);
            if (currValue == 0) {
                matrix.setEntry(r, c, 0);
            } else {
                matrix.setEntry(r, c, percentile.evaluate(currValue));
            }
            //matrix.setEntry(r, c, percentile.evaluate());
        }
    }
    return matrix;
}

From source file:juicebox.tools.utils.common.MatrixTools.java

/**
 * @return max element in matrix/* w ww .j a  va  2  s .  c o m*/
 */
public static double calculateMax(RealMatrix matrix) {
    double max = matrix.getEntry(0, 0);
    for (int i = 0; i < matrix.getRowDimension(); i++) {
        for (int j = 0; j < matrix.getColumnDimension(); j++) {
            double val = matrix.getEntry(i, j);
            if (max < val) {
                max = val;
            }
        }
    }
    return max;
}

From source file:juicebox.tools.utils.juicer.arrowhead.DynamicProgrammingUtils.java

/**
 * Calculate cumulative sums across upper right matrix
 * iterative result is entry to left + entry below + orig value - diagonal down (else we double count)
 *
 * @param matrix/*from w  w  w  .  j  ava  2  s. com*/
 * @param superDiagonal
 * @return
 */
public static RealMatrix sum(RealMatrix matrix, int superDiagonal) {

    int n = Math.min(matrix.getRowDimension(), matrix.getColumnDimension());

    RealMatrix diagMatrix = MatrixTools.cleanArray2DMatrix(matrix.getRowDimension(),
            matrix.getColumnDimension());
    if (superDiagonal <= 0) {
        diagMatrix = MatrixTools.extractDiagonal(matrix);
        superDiagonal = 1;
    }

    // d = distance from diagonal
    for (int d = superDiagonal; d < n; d++) {
        // i = row, column is i +d;

        for (int i = 0; i < n - d; i++) {
            diagMatrix.setEntry(i, i + d, diagMatrix.getEntry(i, i + d - 1) + diagMatrix.getEntry(i + 1, i + d)
                    + matrix.getEntry(i, i + d) - diagMatrix.getEntry(i + 1, i + d - 1));
        }
    }
    return diagMatrix;
}

From source file:juicebox.tools.utils.common.MatrixTools.java

public static void thresholdValues(RealMatrix matrix, int val) {
    for (int i = 0; i < matrix.getRowDimension(); i++) {
        for (int j = 0; j < matrix.getColumnDimension(); j++) {
            if (matrix.getEntry(i, j) > val) {
                matrix.setEntry(i, j, val);
            }// ww  w . jav a  2s  . c  om
        }
    }
}

From source file:juicebox.tools.utils.common.MatrixTools.java

/**
 * Fill lower left triangle with values from upper right triangle
 *
 * @param matrix//  www  .  jav  a  2s . c  o m
 * @return
 */
public static RealMatrix fillLowerLeftTriangle(RealMatrix matrix) {
    for (int r = 0; r < matrix.getRowDimension(); r++)
        for (int c = 0; c < matrix.getColumnDimension(); c++)
            matrix.setEntry(c, r, matrix.getEntry(r, c));
    return matrix;
}

From source file:juicebox.tools.utils.common.MatrixTools.java

/**
 * Replace NaNs in given matrix with given value
 *//* www  .ja  va2  s . co  m*/
public static void setNaNs(RealMatrix matrix, int val) {
    for (int i = 0; i < matrix.getRowDimension(); i++) {
        for (int j = 0; j < matrix.getColumnDimension(); j++) {
            if (Double.isNaN(matrix.getEntry(i, j))) {
                matrix.setEntry(i, j, val);
            }
        }
    }
}