X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fmath%2FMatrix.java;h=ad914646549386777670575772c86b2b85f5604b;hb=ce6d1e09276f8481e6975d0c28c60620dfb83883;hp=b39d3c91070fe4905561d1c1d36227e65534cc6f;hpb=94ed46d6216e3b3fd195144660815396e6c42683;p=jalview.git diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java index b39d3c9..ad91464 100755 --- a/src/jalview/math/Matrix.java +++ b/src/jalview/math/Matrix.java @@ -24,6 +24,7 @@ import jalview.util.Format; import jalview.util.MessageManager; import java.io.PrintStream; +import java.util.Arrays; /** * A class to model rectangular matrices of double values and operations on them @@ -31,39 +32,42 @@ import java.io.PrintStream; public class Matrix implements MatrixI { /* - * the cell values in row-major order + * maximum number of iterations for tqli */ - private double[][] value; + private static final int MAX_ITER = 45; + // fudge - add 15 iterations, just in case /* * the number of rows */ - protected int rows; + final protected int rows; /* * the number of columns */ - protected int cols; + final protected int cols; + + /* + * the cell values in row-major order + */ + private double[][] value; protected double[] d; // Diagonal protected double[] e; // off diagonal /** - * maximum number of iterations for tqli + * Constructor given number of rows and columns * + * @param colCount + * @param rowCount */ - private static final int maxIter = 45; // fudge - add 15 iterations, just in - // case - - /** - * Default constructor - */ - public Matrix() + protected Matrix(int rowCount, int colCount) { - + rows = rowCount; + cols = colCount; } - + /** * Creates a new Matrix object containing a copy of the supplied array values. * For example @@ -103,11 +107,6 @@ public class Matrix implements MatrixI } } - /** - * Returns a new matrix which is the transpose of this one - * - * @return - */ @Override public MatrixI transpose() { @@ -145,18 +144,6 @@ public class Matrix implements MatrixI } } - /** - * Returns a new matrix which is the result of premultiplying this matrix by - * the supplied argument. If this of size AxB (A rows and B columns), and the - * argument is CxA (C rows and A columns), the result is of size CxB. - * - * @param in - * - * @return - * @throws IllegalArgumentException - * if the number of columns in the pre-multiplier is not equal to - * the number of rows in the multiplicand (this) - */ @Override public MatrixI preMultiply(MatrixI in) { @@ -208,21 +195,6 @@ public class Matrix implements MatrixI return out; } - /** - * Returns a new matrix which is the result of postmultiplying this matrix by - * the supplied argument. If this of size AxB (A rows and B columns), and the - * argument is BxC (B rows and C columns), the result is of size AxC. - *

- * This method simply returns the result of in.preMultiply(this) - * - * @param in - * - * @return - * @throws IllegalArgumentException - * if the number of rows in the post-multiplier is not equal to the - * number of columns in the multiplicand (this) - * @see #preMultiply(Matrix) - */ @Override public MatrixI postMultiply(MatrixI in) { @@ -234,11 +206,6 @@ public class Matrix implements MatrixI return in.preMultiply(this); } - /** - * Answers a new matrix with a copy of the values in this one - * - * @return - */ @Override public MatrixI copy() { @@ -249,7 +216,17 @@ public class Matrix implements MatrixI System.arraycopy(value[i], 0, newmat[i], 0, value[i].length); } - return new Matrix(newmat); + Matrix m = new Matrix(newmat); + if (this.d != null) + { + m.d = Arrays.copyOf(this.d, this.d.length); + } + if (this.e != null) + { + m.e = Arrays.copyOf(this.e, this.e.length); + } + + return m; } /** @@ -479,15 +456,15 @@ public class Matrix implements MatrixI { iter++; - if (iter == maxIter) + if (iter == MAX_ITER) { 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(MAX_ITER).toString() })); } else { - // System.out.println("Iteration " + iter); + // jalview.bin.Console.outPrintln("Iteration " + iter); } g = (d[l] - d[l - 1]) / (2.0 * e[l - 1]); @@ -529,7 +506,8 @@ 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)); } } @@ -742,15 +720,15 @@ public class Matrix implements MatrixI { iter++; - if (iter == maxIter) + if (iter == MAX_ITER) { 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(MAX_ITER).toString() })); } else { - // System.out.println("Iteration " + iter); + // jalview.bin.Console.outPrintln("Iteration " + iter); } g = (d[l] - d[l - 1]) / (2.0 * e[l - 1]); @@ -864,7 +842,8 @@ public class Matrix implements MatrixI * * @param ps * DOCUMENT ME! - * @param format TODO + * @param format + * TODO */ @Override public void printE(PrintStream ps, String format) @@ -886,9 +865,10 @@ public class Matrix implements MatrixI { return e; } - + @Override - public int height() { + public int height() + { return rows; } @@ -992,4 +972,54 @@ public class Matrix implements MatrixI } } } + + @Override + public void setD(double[] v) + { + d = v; + } + + @Override + public void setE(double[] v) + { + e = v; + } + + public double getTotal() + { + double d = 0d; + for (int i = 0; i < this.height(); i++) + { + for (int j = 0; j < this.width(); j++) + { + d += value[i][j]; + } + } + return d; + } + + /** + * {@inheritDoc} + */ + @Override + public boolean equals(MatrixI m2, double delta) + { + if (m2 == null || this.height() != m2.height() + || this.width() != m2.width()) + { + return false; + } + for (int i = 0; i < this.height(); i++) + { + for (int j = 0; j < this.width(); j++) + { + double diff = this.getValue(i, j) - m2.getValue(i, j); + if (Math.abs(diff) > delta) + { + return false; + } + } + } + return true; + } }