X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fmath%2FMatrixTest.java;h=9baacd513ac2abc65490da9e337ea4e109c322a6;hb=2d44b9594da6c691eca72697060c166d0389affd;hp=fa446e42af97e2b6cf2ccd49f312d86b21f775e0;hpb=1f3cf1db69c97ace5c0606e2ee0ccbf569970761;p=jalview.git diff --git a/test/jalview/math/MatrixTest.java b/test/jalview/math/MatrixTest.java index fa446e4..9baacd5 100644 --- a/test/jalview/math/MatrixTest.java +++ b/test/jalview/math/MatrixTest.java @@ -1,8 +1,27 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview 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 General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.math; import static org.testng.Assert.assertEquals; import static org.testng.Assert.assertFalse; -import static org.testng.Assert.assertNotEquals; import static org.testng.Assert.assertNotSame; import static org.testng.Assert.assertNull; import static org.testng.Assert.assertTrue; @@ -62,7 +81,8 @@ public class MatrixTest @Test( groups = "Functional", - expectedExceptions = { IllegalArgumentException.class }) + expectedExceptions = + { IllegalArgumentException.class }) public void testPreMultiply_tooManyColumns() { Matrix m1 = new Matrix(new double[][] { { 2, 3, 4 }, { 3, 4, 5 } }); // 2x3 @@ -77,7 +97,8 @@ public class MatrixTest @Test( groups = "Functional", - expectedExceptions = { IllegalArgumentException.class }) + expectedExceptions = + { IllegalArgumentException.class }) public void testPreMultiply_tooFewColumns() { Matrix m1 = new Matrix(new double[][] { { 2, 3, 4 }, { 3, 4, 5 } }); // 2x3 @@ -89,9 +110,9 @@ public class MatrixTest m1.preMultiply(m1); fail("Expected exception"); } - - - private boolean matrixEquals(Matrix m1, Matrix m2) { + + private boolean matrixEquals(Matrix m1, Matrix m2) + { if (m1.width() != m2.width() || m1.height() != m2.height()) { return false; @@ -118,7 +139,9 @@ public class MatrixTest * (5040 50400) */ MatrixI m1 = new Matrix(new double[][] { { 2, 3 }, { 4, 5 } }); - MatrixI m2 = new Matrix(new double[][] { { 10, 100 }, { 1000, 10000 } }); + MatrixI m2 = new Matrix( + new double[][] + { { 10, 100 }, { 1000, 10000 } }); MatrixI m3 = m1.postMultiply(m2); assertEquals(Arrays.toString(m3.getRow(0)), "[3020.0, 30200.0]"); assertEquals(Arrays.toString(m3.getRow(1)), "[5040.0, 50400.0]"); @@ -218,7 +241,7 @@ public class MatrixTest { int n = Integer.parseInt(args[0]); double[][] in = new double[n][n]; - + for (int i = 0; i < n; i++) { for (int j = 0; j < n; j++) @@ -226,31 +249,31 @@ public class MatrixTest in[i][j] = Math.random(); } } - + Matrix origmat = new Matrix(in); - + // System.out.println(" --- Original matrix ---- "); // / origmat.print(System.out); // System.out.println(); // System.out.println(" --- transpose matrix ---- "); MatrixI trans = origmat.transpose(); - + // trans.print(System.out); // System.out.println(); // System.out.println(" --- OrigT * Orig ---- "); MatrixI symm = trans.postMultiply(origmat); - + // symm.print(System.out); // System.out.println(); // Copy the symmetric matrix for later // Matrix origsymm = symm.copy(); - + // This produces the tridiagonal transformation matrix // long tstart = System.currentTimeMillis(); symm.tred(); - + // long tend = System.currentTimeMillis(); - + // System.out.println("Time take for tred = " + (tend-tstart) + "ms"); // System.out.println(" ---Tridiag transform matrix ---"); // symm.print(System.out); @@ -265,7 +288,7 @@ public class MatrixTest // tstart = System.currentTimeMillis(); symm.tqli(); // tend = System.currentTimeMillis(); - + // System.out.println("Time take for tqli = " + (tend-tstart) + " ms"); // System.out.println(" --- New diagonalization matrix ---"); // symm.print(System.out); @@ -335,7 +358,7 @@ public class MatrixTest } } return d; - + } /** @@ -351,7 +374,7 @@ public class MatrixTest int rows = 10; int cols = rows; double[][] d = getSparseValues(rows, cols, 3); - + /* * make a copy of the values so m1, m2 are not * sharing arrays! @@ -413,8 +436,8 @@ public class MatrixTest * normal case */ double[][] vals = new double[2][]; - vals[0] = new double[] {7d, 1d, -2.3d}; - vals[1] = new double[] {-12d, 94.3d, -102.34d}; + vals[0] = new double[] { 7d, 1d, -2.3d }; + vals[1] = new double[] { -12d, 94.3d, -102.34d }; m = new Matrix(vals); double[] minMax = m.findMinMax(); assertEquals(minMax[0], -102.34d); @@ -463,7 +486,8 @@ public class MatrixTest public void testReverseRange_maxToZero() { Matrix m1 = new Matrix( - new double[][] { { 2, 3.5, 4 }, { -3.4, 4, 15 } }); + new double[][] + { { 2, 3.5, 4 }, { -3.4, 4, 15 } }); /* * subtract all from max: range -3.4 to 15 becomes 18.4 to 0 @@ -495,8 +519,9 @@ public class MatrixTest public void testReverseRange_swapMinMax() { Matrix m1 = new Matrix( - new double[][] { { 2, 3.5, 4 }, { -3.4, 4, 15 } }); - + new double[][] + { { 2, 3.5, 4 }, { -3.4, 4, 15 } }); + /* * swap all values in min-max range * = subtract from (min + max = 11.6) @@ -509,7 +534,7 @@ public class MatrixTest assertEquals(m1.getValue(1, 0), 15d, DELTA); assertEquals(m1.getValue(1, 1), 7.6d, DELTA); assertEquals(m1.getValue(1, 2), -3.4d, DELTA); - + /* * repeat operation - original values restored */ @@ -525,7 +550,9 @@ public class MatrixTest @Test(groups = "Functional") public void testMultiply() { - Matrix m = new Matrix(new double[][] { { 2, 3.5, 4 }, { -3.4, 4, 15 } }); + Matrix m = new Matrix( + new double[][] + { { 2, 3.5, 4 }, { -3.4, 4, 15 } }); m.multiply(2d); assertEquals(m.getValue(0, 0), 4d, DELTA); assertEquals(m.getValue(0, 1), 7d, DELTA); @@ -551,37 +578,28 @@ public class MatrixTest } @Test(groups = "Functional") - public void testEquals_hashCode() + public void testEquals() { double[][] values = new double[][] { { 1, 2, 3 }, { 4, 5, 6 } }; Matrix m1 = new Matrix(values); double[][] values2 = new double[][] { { 1, 2, 3 }, { 4, 5, 6 } }; Matrix m2 = new Matrix(values2); - assertTrue(m1.equals(m1)); - assertTrue(m1.equals(m2)); - assertTrue(m2.equals(m1)); - // equal objects should have same hashCode - assertEquals(m1.hashCode(), m2.hashCode()); + double delta = 0.0001d; + assertTrue(m1.equals(m1, delta)); + assertTrue(m1.equals(m2, delta)); + assertTrue(m2.equals(m1, delta)); double[][] values3 = new double[][] { { 1, 2, 3 }, { 4, 5, 7 } }; m2 = new Matrix(values3); - assertFalse(m1.equals(m2)); - assertFalse(m2.equals(m1)); - assertNotEquals(m1.hashCode(), m2.hashCode()); - - // same hashCode doesn't always mean equal - values2 = new double[][] { { 1, 2, 3 }, { 4, 6, 5 } }; - m2 = new Matrix(values2); - assertFalse(m2.equals(m1)); - assertEquals(m1.hashCode(), m2.hashCode()); + assertFalse(m1.equals(m2, delta)); + assertFalse(m2.equals(m1, delta)); // must be same shape values2 = new double[][] { { 1, 2, 3 } }; m2 = new Matrix(values2); - assertFalse(m2.equals(m1)); + assertFalse(m2.equals(m1, delta)); - assertFalse(m1.equals(null)); - assertFalse(m1.equals("foo")); + assertFalse(m1.equals(null, delta)); } }