X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fmath%2FMatrix.java;h=8910c67a7ec07f7ce4d2c5c13880640972db3e95;hb=refs%2Fheads%2Fbug%2FJAL-2842;hp=de0bf77334a5e49847e2b058b812363033150a92;hpb=cf78dc7e8c37a03da8e7e396fec7e7ec54666847;p=jalview.git diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java index de0bf77..8910c67 100755 --- a/src/jalview/math/Matrix.java +++ b/src/jalview/math/Matrix.java @@ -63,9 +63,10 @@ public class Matrix implements MatrixI { } - + /** - * Creates a new Matrix object. For example + * Creates a new Matrix object containing a copy of the supplied array values. + * For example * *
* new Matrix(new double[][] {{2, 3, 4}, {5, 6, 7}) @@ -85,13 +86,27 @@ public class Matrix implements MatrixI { this.rows = values.length; this.cols = this.rows == 0 ? 0 : values[0].length; - this.value = values; + + /* + * make a copy of the values array, for immutability + */ + this.value = new double[rows][]; + int i = 0; + for (double[] row : values) + { + if (row != null) + { + value[i] = new double[row.length]; + System.arraycopy(row, 0, value[i], 0, row.length); + } + i++; + } } /** * Returns a new matrix which is the transpose of this one * - * @return DOCUMENT ME! + * @return */ @Override public MatrixI transpose() @@ -467,8 +482,8 @@ public class Matrix implements MatrixI if (iter == maxIter) { throw new Exception(MessageManager.formatMessage( - "exception.matrix_too_many_iteration", new String[] { - "tqli", Integer.valueOf(maxIter).toString() })); + "exception.matrix_too_many_iteration", new String[] + { "tqli", Integer.valueOf(maxIter).toString() })); } else { @@ -514,7 +529,8 @@ public class Matrix implements MatrixI { f = getValue(k - 1, i); setValue(k - 1, i, (s * getValue(k - 1, i - 1)) + (c * f)); - setValue(k - 1, i - 1, (c * getValue(k - 1, i - 1)) - (s * f)); + setValue(k - 1, i - 1, + (c * getValue(k - 1, i - 1)) - (s * f)); } } @@ -532,6 +548,7 @@ public class Matrix implements MatrixI return value[i][j]; } + @Override public void setValue(int i, int j, double val) { value[i][j] = val; @@ -729,8 +746,8 @@ public class Matrix implements MatrixI if (iter == maxIter) { throw new Exception(MessageManager.formatMessage( - "exception.matrix_too_many_iteration", new String[] { - "tqli2", Integer.valueOf(maxIter).toString() })); + "exception.matrix_too_many_iteration", new String[] + { "tqli2", Integer.valueOf(maxIter).toString() })); } else { @@ -848,7 +865,8 @@ public class Matrix implements MatrixI * * @param ps * DOCUMENT ME! - * @param format TODO + * @param format + * TODO */ @Override public void printE(PrintStream ps, String format) @@ -870,9 +888,10 @@ public class Matrix implements MatrixI { return e; } - + @Override - public int height() { + public int height() + { return rows; } @@ -889,4 +908,91 @@ public class Matrix implements MatrixI System.arraycopy(value[i], 0, row, 0, cols); return row; } + + /** + * Returns a length 2 array of {minValue, maxValue} of all values in the + * matrix. Returns null if the matrix is null or empty. + * + * @return + */ + double[] findMinMax() + { + if (value == null) + { + return null; + } + double min = Double.MAX_VALUE; + double max = -Double.MAX_VALUE; + boolean empty = true; + for (double[] row : value) + { + if (row != null) + { + for (double x : row) + { + empty = false; + if (x > max) + { + max = x; + } + if (x < min) + { + min = x; + } + } + } + } + return empty ? null : new double[] { min, max }; + } + + /** + * {@inheritDoc} + */ + @Override + public void reverseRange(boolean maxToZero) + { + if (value == null) + { + return; + } + double[] minMax = findMinMax(); + if (minMax == null) + { + return; // empty matrix + } + double subtractFrom = maxToZero ? minMax[1] : minMax[0] + minMax[1]; + + for (double[] row : value) + { + if (row != null) + { + int j = 0; + for (double x : row) + { + row[j] = subtractFrom - x; + j++; + } + } + } + } + + /** + * Multiplies every entry in the matrix by the given value. + * + * @param + */ + @Override + public void multiply(double by) + { + for (double[] row : value) + { + if (row != null) + { + for (int i = 0; i < row.length; i++) + { + row[i] *= by; + } + } + } + } }