X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fmath%2FMatrixTest.java;h=97ded5a345ff65da86ef602242995feb85a4169d;hb=56f696a86aea0c3fd8111870a6184d459a852ace;hp=bd5614fd8e83861b7c923c6cbb65079d8fd09630;hpb=8fea25daa8f1f1cc564497ddf4e3c9e15a64596c;p=jalview.git diff --git a/test/jalview/math/MatrixTest.java b/test/jalview/math/MatrixTest.java index bd5614f..97ded5a 100644 --- a/test/jalview/math/MatrixTest.java +++ b/test/jalview/math/MatrixTest.java @@ -1,6 +1,9 @@ package jalview.math; import static org.testng.Assert.assertEquals; +import static org.testng.Assert.assertNotSame; +import static org.testng.Assert.assertNull; +import static org.testng.Assert.assertTrue; import static org.testng.Assert.fail; import java.util.Arrays; @@ -11,13 +14,13 @@ import org.testng.internal.junit.ArrayAsserts; public class MatrixTest { - final static double DELTA = 0.0001d; + final static double DELTA = 0.000001d; @Test(groups = "Timing") public void testPreMultiply_timing() { - int rows = 500; - int cols = 1000; + int rows = 50; // increase to stress test timing + int cols = 100; double[][] d1 = new double[rows][cols]; double[][] d2 = new double[cols][rows]; Matrix m1 = new Matrix(d1); @@ -32,8 +35,8 @@ public class MatrixTest @Test(groups = "Functional") public void testPreMultiply() { - MatrixI m1 = new Matrix(new double[][] { { 2, 3, 4 } }); // 1x3 - MatrixI m2 = new Matrix(new double[][] { { 5 }, { 6 }, { 7 } }); // 3x1 + Matrix m1 = new Matrix(new double[][] { { 2, 3, 4 } }); // 1x3 + Matrix m2 = new Matrix(new double[][] { { 5 }, { 6 }, { 7 } }); // 3x1 /* * 1x3 times 3x1 is 1x1 @@ -169,6 +172,27 @@ public class MatrixTest assertEquals(m3.getRow(0)[1], 25d); } + @Test(groups = "Functional") + public void testCopy() + { + Random r = new Random(); + int rows = 5; + int cols = 11; + double[][] in = new double[rows][cols]; + + for (int i = 0; i < rows; i++) + { + for (int j = 0; j < cols; j++) + { + in[i][j] = r.nextDouble(); + } + } + Matrix m1 = new Matrix(in); + Matrix m2 = (Matrix) m1.copy(); + assertNotSame(m1, m2); + assertTrue(matrixEquals(m1, m2)); + } + /** * main method extracted from Matrix * @@ -357,4 +381,154 @@ public class MatrixTest ArrayAsserts.assertArrayEquals(m1.getD(), m2.getD(), 0.00001d); ArrayAsserts.assertArrayEquals(m1.getE(), m2.getE(), 0.00001d); } + + @Test(groups = "Functional") + public void testFindMinMax() + { + /* + * empty matrix case + */ + Matrix m = new Matrix(new double[][] { {} }); + assertNull(m.findMinMax()); + + /* + * normal case + */ + double[][] vals = new double[2][]; + 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); + assertEquals(minMax[1], 94.3d); + } + + @Test(groups = { "Functional", "Timing" }) + public void testFindMinMax_timing() + { + Random r = new Random(); + int size = 1000; // increase to stress test timing + double[][] vals = new double[size][size]; + double max = -Double.MAX_VALUE; + double min = Double.MAX_VALUE; + for (int i = 0; i < size; i++) + { + vals[i] = new double[size]; + for (int j = 0; j < size; j++) + { + // use nextLong rather than nextDouble to include negative values + double d = r.nextLong(); + if (d > max) + { + max = d; + } + if (d < min) + { + min = d; + } + vals[i][j] = d; + } + } + Matrix m = new Matrix(vals); + long now = System.currentTimeMillis(); + double[] minMax = m.findMinMax(); + System.out.println(String.format("findMinMax for %d x %d took %dms", + size, size, (System.currentTimeMillis() - now))); + assertEquals(minMax[0], min); + assertEquals(minMax[1], max); + } + + /** + * Test range reversal with maximum value becoming zero + */ + @Test(groups = "Functional") + public void testReverseRange_maxToZero() + { + Matrix m1 = new Matrix( + new double[][] { { 2, 3.5, 4 }, { -3.4, 4, 15 } }); + + /* + * subtract all from max: range -3.4 to 15 becomes 18.4 to 0 + */ + m1.reverseRange(true); + assertEquals(m1.getValue(0, 0), 13d, DELTA); + assertEquals(m1.getValue(0, 1), 11.5d, DELTA); + assertEquals(m1.getValue(0, 2), 11d, DELTA); + assertEquals(m1.getValue(1, 0), 18.4d, DELTA); + assertEquals(m1.getValue(1, 1), 11d, DELTA); + assertEquals(m1.getValue(1, 2), 0d, DELTA); + + /* + * repeat operation - range is now 0 to 18.4 + */ + m1.reverseRange(true); + assertEquals(m1.getValue(0, 0), 5.4d, DELTA); + assertEquals(m1.getValue(0, 1), 6.9d, DELTA); + assertEquals(m1.getValue(0, 2), 7.4d, DELTA); + assertEquals(m1.getValue(1, 0), 0d, DELTA); + assertEquals(m1.getValue(1, 1), 7.4d, DELTA); + assertEquals(m1.getValue(1, 2), 18.4d, DELTA); + } + + /** + * Test range reversal with minimum and maximum values swapped + */ + @Test(groups = "Functional") + public void testReverseRange_swapMinMax() + { + Matrix m1 = new Matrix( + new double[][] { { 2, 3.5, 4 }, { -3.4, 4, 15 } }); + + /* + * swap all values in min-max range + * = subtract from (min + max = 11.6) + * range -3.4 to 15 becomes 18.4 to -3.4 + */ + m1.reverseRange(false); + assertEquals(m1.getValue(0, 0), 9.6d, DELTA); + assertEquals(m1.getValue(0, 1), 8.1d, DELTA); + assertEquals(m1.getValue(0, 2), 7.6d, DELTA); + 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 + */ + m1.reverseRange(false); + assertEquals(m1.getValue(0, 0), 2d, DELTA); + assertEquals(m1.getValue(0, 1), 3.5d, DELTA); + assertEquals(m1.getValue(0, 2), 4d, DELTA); + assertEquals(m1.getValue(1, 0), -3.4d, DELTA); + assertEquals(m1.getValue(1, 1), 4d, DELTA); + assertEquals(m1.getValue(1, 2), 15d, DELTA); + } + + @Test(groups = "Functional") + public void testMultiply() + { + 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); + assertEquals(m.getValue(0, 2), 8d, DELTA); + assertEquals(m.getValue(1, 0), -6.8d, DELTA); + assertEquals(m.getValue(1, 1), 8d, DELTA); + assertEquals(m.getValue(1, 2), 30d, DELTA); + } + + @Test(groups = "Functional") + public void testConstructor() + { + double[][] values = new double[][] { { 1, 2, 3 }, { 4, 5, 6 } }; + Matrix m = new Matrix(values); + assertEquals(m.getValue(0, 0), 1d, DELTA); + + /* + * verify the matrix has a copy of the original array + */ + assertNotSame(values[0], m.getRow(0)); + values[0][0] = -1d; + assertEquals(m.getValue(0, 0), 1d, DELTA); // unchanged + } }