Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
MatrixTest	36	227	42	0.8379310483.8%	Show methods

Class MatrixTest

Class MatrixTest	Line # 36	Total Statements 227	Complexity 42	TOTAL Coverage 0.8379310483.8%
testPreMultiply_timing() : void   testPreMultiply_timing() : void	4040	10.010	1.01	0.0 0.00%
testPreMultiply() : void   testPreMultiply() : void	5656	12.012	1.01	1.0 1.0100%
testPreMultiply_tooManyColumns() : void   testPreMultiply_tooManyColumns() : void	8282	3.03	1.01	0.6666667 0.666666766.7%
testPreMultiply_tooFewColumns() : void   testPreMultiply_tooFewColumns() : void	9898	3.03	1.01	0.6666667 0.666666766.7%
matrixEquals(Matrix,Matrix) : boolean   matrixEquals(Matrix,Matrix) : boolean	114114	6.06	5.05	0.6666667 0.666666766.7%
testPostMultiply() : void   testPostMultiply() : void	130130	32.032	1.01	1.0 1.0100%
testCopy() : void   testCopy() : void	200200	20.020	3.03	1.0 1.0100%
main(String[]) : void   main(String[]) : void	240240	10.010	3.03	0.0 0.00%
testSign() : void   testSign() : void	315315	6.06	1.01	0.0 0.00%
getSparseValues(int,int,int) : double[][]   getSparseValues(int,int,int) : double[][]	335335	11.011	5.05	0.8947368 0.894736889.5%
testTred_reproducible() : void   testTred_reproducible() : void	368368	13.013	3.03	1.0 1.0100%
assertMatricesMatch(MatrixI,MatrixI) : void   assertMatricesMatch(MatrixI,MatrixI) : void	398398	12.012	6.06	0.72727275 0.7272727572.7%
testFindMinMax() : void   testFindMinMax() : void	426426	9.09	1.01	1.0 1.0100%
testFindMinMax_timing() : void   testFindMinMax_timing() : void	447447	20.020	5.05	1.0 1.0100%
testReverseRange_maxToZero() : void   testReverseRange_maxToZero() : void	485485	15.015	1.01	1.0 1.0100%
testReverseRange_swapMinMax() : void   testReverseRange_swapMinMax() : void	518518	15.015	1.01	1.0 1.0100%
testMultiply() : void   testMultiply() : void	550550	8.08	1.01	1.0 1.0100%
testConstructor() : void   testConstructor() : void	565565	6.06	1.01	1.0 1.0100%
testEquals() : void   testEquals() : void	580580	16.016	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.18275861	jalview.math.MatrixTest.testTred_reproduciblejalview.math.MatrixTest.testTred_reproducible	1PASS
	0.11724138	jalview.math.MatrixTest.testCopyjalview.math.MatrixTest.testCopy	1PASS
	0.113793105	jalview.math.MatrixTest.testPostMultiplyjalview.math.MatrixTest.testPostMultiply	1PASS
	0.1	jalview.math.MatrixTest.testFindMinMax_timingjalview.math.MatrixTest.testFindMinMax_timing	1PASS
	0.05862069	jalview.math.MatrixTest.testEqualsjalview.math.MatrixTest.testEquals	1PASS
	0.055172414	jalview.math.MatrixTest.testReverseRange_swapMinMaxjalview.math.MatrixTest.testReverseRange_swapMinMax	1PASS
	0.055172414	jalview.math.MatrixTest.testReverseRange_maxToZerojalview.math.MatrixTest.testReverseRange_maxToZero	1PASS
	0.044827588	jalview.math.MatrixTest.testPreMultiplyjalview.math.MatrixTest.testPreMultiply	1PASS
	0.03448276	jalview.math.MatrixTest.testFindMinMaxjalview.math.MatrixTest.testFindMinMax	1PASS
	0.031034483	jalview.math.MatrixTest.testMultiplyjalview.math.MatrixTest.testMultiply	1PASS
	0.024137931	jalview.math.MatrixTest.testConstructorjalview.math.MatrixTest.testConstructor	1PASS
	0.010344828	jalview.math.MatrixTest.testPreMultiply_tooManyColumnsjalview.math.MatrixTest.testPreMultiply_tooManyColumns	1PASS
	0.010344828	jalview.math.MatrixTest.testPreMultiply_tooFewColumnsjalview.math.MatrixTest.testPreMultiply_tooFewColumns	1PASS

 

Source view

1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
7		* Jalview is free software: you can redistribute it and/or
8		* modify it under the terms of the GNU General Public License
9		* as published by the Free Software Foundation, either version 3
10		* of the License, or (at your option) any later version.
11		*
12		* Jalview is distributed in the hope that it will be useful, but
13		* WITHOUT ANY WARRANTY; without even the implied warranty
14		* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15		* PURPOSE. See the GNU General Public License for more details.
16		*
17		* You should have received a copy of the GNU General Public License
18		* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19		* The Jalview Authors are detailed in the 'AUTHORS' file.
20		*/
21		package jalview.math;
22
23		import static org.testng.Assert.assertEquals;
24		import static org.testng.Assert.assertFalse;
25		import static org.testng.Assert.assertNotSame;
26		import static org.testng.Assert.assertNull;
27		import static org.testng.Assert.assertTrue;
28		import static org.testng.Assert.fail;
29
30		import java.util.Arrays;
31		import java.util.Random;
32
33		import org.testng.annotations.Test;
34		import org.testng.internal.junit.ArrayAsserts;
35
		83.8% Uncovered Elements: 47 (290) Complexity: 42 Complexity Density: 0.19
36		public class MatrixTest
37		{
38		final static double DELTA = 0.000001d;
39
		0% Uncovered Elements: 10 (10) Complexity: 1 Complexity Density: 0.1 4-
40	0	@Test(groups = "Timing")...
41		public void testPreMultiply_timing()
42		{
43	0	int rows = 50; // increase to stress test timing
44	0	int cols = 100;
45	0	double[][] d1 = new double[rows][cols];
46	0	double[][] d2 = new double[cols][rows];
47	0	Matrix m1 = new Matrix(d1);
48	0	Matrix m2 = new Matrix(d2);
49	0	long start = System.currentTimeMillis();
50	0	m1.preMultiply(m2);
51	0	long elapsed = System.currentTimeMillis() - start;
52	0	System.out.println(rows + "x" + cols
53		+ " multiplications of double took " + elapsed + "ms");
54		}
55
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08 1PASS
56	1	@Test(groups = "Functional")...
57		public void testPreMultiply()
58		{
59	1	Matrix m1 = new Matrix(new double[][] { { 2, 3, 4 } }); // 1x3
60	1	Matrix m2 = new Matrix(new double[][] { { 5 }, { 6 }, { 7 } }); // 3x1
61
62		/*
63		* 1x3 times 3x1 is 1x1
64		* 2x5 + 3x6 + 4*7 = 56
65		*/
66	1	MatrixI m3 = m2.preMultiply(m1);
67	1	assertEquals(m3.height(), 1);
68	1	assertEquals(m3.width(), 1);
69	1	assertEquals(m3.getValue(0, 0), 56d);
70
71		/*
72		* 3x1 times 1x3 is 3x3
73		*/
74	1	m3 = m1.preMultiply(m2);
75	1	assertEquals(m3.height(), 3);
76	1	assertEquals(m3.width(), 3);
77	1	assertEquals(Arrays.toString(m3.getRow(0)), "[10.0, 15.0, 20.0]");
78	1	assertEquals(Arrays.toString(m3.getRow(1)), "[12.0, 18.0, 24.0]");
79	1	assertEquals(Arrays.toString(m3.getRow(2)), "[14.0, 21.0, 28.0]");
80		}
81
		66.7% Uncovered Elements: 1 (3) Complexity: 1 Complexity Density: 0.33 1PASS
82	1	@Test(...
83		groups = "Functional",
84		expectedExceptions =
85		{ IllegalArgumentException.class })
86		public void testPreMultiply_tooManyColumns()
87		{
88	1	Matrix m1 = new Matrix(new double[][] { { 2, 3, 4 }, { 3, 4, 5 } }); // 2x3
89
90		/*
91		* 2x3 times 2x3 invalid operation -
92		* multiplier has more columns than multiplicand has rows
93		*/
94	1	m1.preMultiply(m1);
95	0	fail("Expected exception");
96		}
97
		66.7% Uncovered Elements: 1 (3) Complexity: 1 Complexity Density: 0.33 1PASS
98	1	@Test(...
99		groups = "Functional",
100		expectedExceptions =
101		{ IllegalArgumentException.class })
102		public void testPreMultiply_tooFewColumns()
103		{
104	1	Matrix m1 = new Matrix(new double[][] { { 2, 3, 4 }, { 3, 4, 5 } }); // 2x3
105
106		/*
107		* 3x2 times 3x2 invalid operation -
108		* multiplier has more columns than multiplicand has row
109		*/
110	1	m1.preMultiply(m1);
111	0	fail("Expected exception");
112		}
113
		66.7% Uncovered Elements: 4 (12) Complexity: 5 Complexity Density: 0.83
114	1	private boolean matrixEquals(Matrix m1, Matrix m2)...
115		{
116	1	if (m1.width() != m2.width() || m1.height() != m2.height())
117		{
118	0	return false;
119		}
120	6	for (int i = 0; i < m1.height(); i++)
121		{
122	5	if (!Arrays.equals(m1.getRow(i), m2.getRow(i)))
123		{
124	0	return false;
125		}
126		}
127	1	return true;
128		}
129
		100% Uncovered Elements: 0 (32) Complexity: 1 Complexity Density: 0.03 1PASS
130	1	@Test(groups = "Functional")...
131		public void testPostMultiply()
132		{
133		/*
134		* Square matrices
135		* (2 3) . (10 100)
136		* (4 5) (1000 10000)
137		* =
138		* (3020 30200)
139		* (5040 50400)
140		*/
141	1	MatrixI m1 = new Matrix(new double[][] { { 2, 3 }, { 4, 5 } });
142	1	MatrixI m2 = new Matrix(
143		new double[][]
144		{ { 10, 100 }, { 1000, 10000 } });
145	1	MatrixI m3 = m1.postMultiply(m2);
146	1	assertEquals(Arrays.toString(m3.getRow(0)), "[3020.0, 30200.0]");
147	1	assertEquals(Arrays.toString(m3.getRow(1)), "[5040.0, 50400.0]");
148
149		/*
150		* also check m2.preMultiply(m1) - should be same as m1.postMultiply(m2)
151		*/
152	1	m3 = m2.preMultiply(m1);
153	1	assertEquals(Arrays.toString(m3.getRow(0)), "[3020.0, 30200.0]");
154	1	assertEquals(Arrays.toString(m3.getRow(1)), "[5040.0, 50400.0]");
155
156		/*
157		* m1 has more rows than columns
158		* (2).(10 100 1000) = (20 200 2000)
159		* (3) (30 300 3000)
160		*/
161	1	m1 = new Matrix(new double[][] { { 2 }, { 3 } });
162	1	m2 = new Matrix(new double[][] { { 10, 100, 1000 } });
163	1	m3 = m1.postMultiply(m2);
164	1	assertEquals(m3.height(), 2);
165	1	assertEquals(m3.width(), 3);
166	1	assertEquals(Arrays.toString(m3.getRow(0)), "[20.0, 200.0, 2000.0]");
167	1	assertEquals(Arrays.toString(m3.getRow(1)), "[30.0, 300.0, 3000.0]");
168	1	m3 = m2.preMultiply(m1);
169	1	assertEquals(m3.height(), 2);
170	1	assertEquals(m3.width(), 3);
171	1	assertEquals(Arrays.toString(m3.getRow(0)), "[20.0, 200.0, 2000.0]");
172	1	assertEquals(Arrays.toString(m3.getRow(1)), "[30.0, 300.0, 3000.0]");
173
174		/*
175		* m1 has more columns than rows
176		* (2 3 4) . (5 4) = (56 25)
177		* (6 3)
178		* (7 2)
179		* [0, 0] = 2*5 + 3*6 + 4*7 = 56
180		* [0, 1] = 2*4 + 3*3 + 4*2 = 25
181		*/
182	1	m1 = new Matrix(new double[][] { { 2, 3, 4 } });
183	1	m2 = new Matrix(new double[][] { { 5, 4 }, { 6, 3 }, { 7, 2 } });
184	1	m3 = m1.postMultiply(m2);
185	1	assertEquals(m3.height(), 1);
186	1	assertEquals(m3.width(), 2);
187	1	assertEquals(m3.getRow(0)[0], 56d);
188	1	assertEquals(m3.getRow(0)[1], 25d);
189
190		/*
191		* and check premultiply equivalent
192		*/
193	1	m3 = m2.preMultiply(m1);
194	1	assertEquals(m3.height(), 1);
195	1	assertEquals(m3.width(), 2);
196	1	assertEquals(m3.getRow(0)[0], 56d);
197	1	assertEquals(m3.getRow(0)[1], 25d);
198		}
199
		100% Uncovered Elements: 0 (24) Complexity: 3 Complexity Density: 0.15 1PASS
200	1	@Test(groups = "Functional")...
201		public void testCopy()
202		{
203	1	Random r = new Random();
204	1	int rows = 5;
205	1	int cols = 11;
206	1	double[][] in = new double[rows][cols];
207
208	6	for (int i = 0; i < rows; i++)
209		{
210	60	for (int j = 0; j < cols; j++)
211		{
212	55	in[i][j] = r.nextDouble();
213		}
214		}
215	1	Matrix m1 = new Matrix(in);
216
217	1	Matrix m2 = (Matrix) m1.copy();
218	1	assertNotSame(m1, m2);
219	1	assertTrue(matrixEquals(m1, m2));
220	1	assertNull(m2.d);
221	1	assertNull(m2.e);
222
223		/*
224		* now add d and e vectors and recopy
225		*/
226	1	m1.d = Arrays.copyOf(in[2], in[2].length);
227	1	m1.e = Arrays.copyOf(in[4], in[4].length);
228	1	m2 = (Matrix) m1.copy();
229	1	assertNotSame(m2.d, m1.d);
230	1	assertNotSame(m2.e, m1.e);
231	1	assertEquals(m2.d, m1.d);
232	1	assertEquals(m2.e, m1.e);
233		}
234
235		/**
236		* main method extracted from Matrix
237		*
238		* @param args
239		*/
		0% Uncovered Elements: 14 (14) Complexity: 3 Complexity Density: 0.3
240	0	public static void main(String[] args) throws Exception...
241		{
242	0	int n = Integer.parseInt(args[0]);
243	0	double[][] in = new double[n][n];
244
245	0	for (int i = 0; i < n; i++)
246		{
247	0	for (int j = 0; j < n; j++)
248		{
249	0	in[i][j] = Math.random();
250		}
251		}
252
253	0	Matrix origmat = new Matrix(in);
254
255		// System.out.println(" --- Original matrix ---- ");
256		// / origmat.print(System.out);
257		// System.out.println();
258		// System.out.println(" --- transpose matrix ---- ");
259	0	MatrixI trans = origmat.transpose();
260
261		// trans.print(System.out);
262		// System.out.println();
263		// System.out.println(" --- OrigT * Orig ---- ");
264	0	MatrixI symm = trans.postMultiply(origmat);
265
266		// symm.print(System.out);
267		// System.out.println();
268		// Copy the symmetric matrix for later
269		// Matrix origsymm = symm.copy();
270
271		// This produces the tridiagonal transformation matrix
272		// long tstart = System.currentTimeMillis();
273	0	symm.tred();
274
275		// long tend = System.currentTimeMillis();
276
277		// System.out.println("Time take for tred = " + (tend-tstart) + "ms");
278		// System.out.println(" ---Tridiag transform matrix ---");
279		// symm.print(System.out);
280		// System.out.println();
281		// System.out.println(" --- D vector ---");
282		// symm.printD(System.out);
283		// System.out.println();
284		// System.out.println(" --- E vector ---");
285		// symm.printE(System.out);
286		// System.out.println();
287		// Now produce the diagonalization matrix
288		// tstart = System.currentTimeMillis();
289	0	symm.tqli();
290		// tend = System.currentTimeMillis();
291
292		// System.out.println("Time take for tqli = " + (tend-tstart) + " ms");
293		// System.out.println(" --- New diagonalization matrix ---");
294		// symm.print(System.out);
295		// System.out.println();
296		// System.out.println(" --- D vector ---");
297		// symm.printD(System.out);
298		// System.out.println();
299		// System.out.println(" --- E vector ---");
300		// symm.printE(System.out);
301		// System.out.println();
302		// System.out.println(" --- First eigenvector --- ");
303		// double[] eigenv = symm.getColumn(0);
304		// for (int i=0; i < eigenv.length;i++) {
305		// Format.print(System.out,"%15.4f",eigenv[i]);
306		// }
307		// System.out.println();
308		// double[] neigenv = origsymm.vectorPostMultiply(eigenv);
309		// for (int i=0; i < neigenv.length;i++) {
310		// Format.print(System.out,"%15.4f",neigenv[i]/symm.d[0]);
311		// }
312		// System.out.println();
313		}
314
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17 1PASS
315	0	@Test(groups = "Timing")...
316		public void testSign()
317		{
318	0	assertEquals(Matrix.sign(-1, -2), -1d);
319	0	assertEquals(Matrix.sign(-1, 2), 1d);
320	0	assertEquals(Matrix.sign(-1, 0), 1d);
321	0	assertEquals(Matrix.sign(1, -2), -1d);
322	0	assertEquals(Matrix.sign(1, 2), 1d);
323	0	assertEquals(Matrix.sign(1, 0), 1d);
324		}
325
326		/**
327		* Helper method to make values for a sparse, pseudo-random symmetric matrix
328		*
329		* @param rows
330		* @param cols
331		* @param occupancy
332		* one in 'occupancy' entries will be non-zero
333		* @return
334		*/
		89.5% Uncovered Elements: 2 (19) Complexity: 5 Complexity Density: 0.45
335	1	public double[][] getSparseValues(int rows, int cols, int occupancy)...
336		{
337	1	Random r = new Random(1729);
338
339		/*
340		* generate whole number values between -12 and +12
341		* (to mimic score matrices used in Jalview)
342		*/
343	1	double[][] d = new double[rows][cols];
344	1	int m = 0;
345	11	for (int i = 0; i < rows; i++)
346		{
347	10	if (++m % occupancy == 0)
348		{
349	0	d[i][i] = r.nextInt() % 13; // diagonal
350		}
351	55	for (int j = 0; j < i; j++)
352		{
353	45	if (++m % occupancy == 0)
354		{
355	18	d[i][j] = r.nextInt() % 13;
356	18	d[j][i] = d[i][j];
357		}
358		}
359		}
360	1	return d;
361
362		}
363
364		/**
365		* Verify that the results of method tred() are the same if the calculation is
366		* redone
367		*/
		100% Uncovered Elements: 0 (17) Complexity: 3 Complexity Density: 0.23 1PASS
368	1	@Test(groups = "Functional")...
369		public void testTred_reproducible()
370		{
371		/*
372		* make a pseudo-random symmetric matrix as required for tred/tqli
373		*/
374	1	int rows = 10;
375	1	int cols = rows;
376	1	double[][] d = getSparseValues(rows, cols, 3);
377
378		/*
379		* make a copy of the values so m1, m2 are not
380		* sharing arrays!
381		*/
382	1	double[][] d1 = new double[rows][cols];
383	11	for (int row = 0; row < rows; row++)
384		{
385	110	for (int col = 0; col < cols; col++)
386		{
387	100	d1[row][col] = d[row][col];
388		}
389		}
390	1	Matrix m1 = new Matrix(d);
391	1	Matrix m2 = new Matrix(d1);
392	1	assertMatricesMatch(m1, m2); // sanity check
393	1	m1.tred();
394	1	m2.tred();
395	1	assertMatricesMatch(m1, m2);
396		}
397
		72.7% Uncovered Elements: 6 (22) Complexity: 6 Complexity Density: 0.5
398	2	public static void assertMatricesMatch(MatrixI m1, MatrixI m2)...
399		{
400	2	if (m1.height() != m2.height())
401		{
402	0	fail("height mismatch");
403		}
404	2	if (m1.width() != m2.width())
405		{
406	0	fail("width mismatch");
407		}
408	22	for (int row = 0; row < m1.height(); row++)
409		{
410	220	for (int col = 0; col < m1.width(); col++)
411		{
412	200	double v2 = m2.getValue(row, col);
413	200	double v1 = m1.getValue(row, col);
414	200	if (Math.abs(v1 - v2) > DELTA)
415		{
416	0	fail(String.format("At [%d, %d] %f != %f", row, col, v1, v2));
417		}
418		}
419		}
420	2	ArrayAsserts.assertArrayEquals("D vector", m1.getD(), m2.getD(),
421		0.00001d);
422	2	ArrayAsserts.assertArrayEquals("E vector", m1.getE(), m2.getE(),
423		0.00001d);
424		}
425
		100% Uncovered Elements: 0 (9) Complexity: 1 Complexity Density: 0.11 1PASS
426	1	@Test(groups = "Functional")...
427		public void testFindMinMax()
428		{
429		/*
430		* empty matrix case
431		*/
432	1	Matrix m = new Matrix(new double[][] { {} });
433	1	assertNull(m.findMinMax());
434
435		/*
436		* normal case
437		*/
438	1	double[][] vals = new double[2][];
439	1	vals[0] = new double[] { 7d, 1d, -2.3d };
440	1	vals[1] = new double[] { -12d, 94.3d, -102.34d };
441	1	m = new Matrix(vals);
442	1	double[] minMax = m.findMinMax();
443	1	assertEquals(minMax[0], -102.34d);
444	1	assertEquals(minMax[1], 94.3d);
445		}
446
		100% Uncovered Elements: 0 (28) Complexity: 5 Complexity Density: 0.25 1PASS
447	1	@Test(groups = { "Functional", "Timing" })...
448		public void testFindMinMax_timing()
449		{
450	1	Random r = new Random();
451	1	int size = 1000; // increase to stress test timing
452	1	double[][] vals = new double[size][size];
453	1	double max = -Double.MAX_VALUE;
454	1	double min = Double.MAX_VALUE;
455	1001	for (int i = 0; i < size; i++)
456		{
457	1000	vals[i] = new double[size];
458	1001000	for (int j = 0; j < size; j++)
459		{
460		// use nextLong rather than nextDouble to include negative values
461	1000000	double d = r.nextLong();
462	1000000	if (d > max)
463		{
464	18	max = d;
465		}
466	1000000	if (d < min)
467		{
468	15	min = d;
469		}
470	1000000	vals[i][j] = d;
471		}
472		}
473	1	Matrix m = new Matrix(vals);
474	1	long now = System.currentTimeMillis();
475	1	double[] minMax = m.findMinMax();
476	1	System.out.println(String.format("findMinMax for %d x %d took %dms",
477		size, size, (System.currentTimeMillis() - now)));
478	1	assertEquals(minMax[0], min);
479	1	assertEquals(minMax[1], max);
480		}
481
482		/**
483		* Test range reversal with maximum value becoming zero
484		*/
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
485	1	@Test(groups = "Functional")...
486		public void testReverseRange_maxToZero()
487		{
488	1	Matrix m1 = new Matrix(
489		new double[][]
490		{ { 2, 3.5, 4 }, { -3.4, 4, 15 } });
491
492		/*
493		* subtract all from max: range -3.4 to 15 becomes 18.4 to 0
494		*/
495	1	m1.reverseRange(true);
496	1	assertEquals(m1.getValue(0, 0), 13d, DELTA);
497	1	assertEquals(m1.getValue(0, 1), 11.5d, DELTA);
498	1	assertEquals(m1.getValue(0, 2), 11d, DELTA);
499	1	assertEquals(m1.getValue(1, 0), 18.4d, DELTA);
500	1	assertEquals(m1.getValue(1, 1), 11d, DELTA);
501	1	assertEquals(m1.getValue(1, 2), 0d, DELTA);
502
503		/*
504		* repeat operation - range is now 0 to 18.4
505		*/
506	1	m1.reverseRange(true);
507	1	assertEquals(m1.getValue(0, 0), 5.4d, DELTA);
508	1	assertEquals(m1.getValue(0, 1), 6.9d, DELTA);
509	1	assertEquals(m1.getValue(0, 2), 7.4d, DELTA);
510	1	assertEquals(m1.getValue(1, 0), 0d, DELTA);
511	1	assertEquals(m1.getValue(1, 1), 7.4d, DELTA);
512	1	assertEquals(m1.getValue(1, 2), 18.4d, DELTA);
513		}
514
515		/**
516		* Test range reversal with minimum and maximum values swapped
517		*/
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
518	1	@Test(groups = "Functional")...
519		public void testReverseRange_swapMinMax()
520		{
521	1	Matrix m1 = new Matrix(
522		new double[][]
523		{ { 2, 3.5, 4 }, { -3.4, 4, 15 } });
524
525		/*
526		* swap all values in min-max range
527		* = subtract from (min + max = 11.6)
528		* range -3.4 to 15 becomes 18.4 to -3.4
529		*/
530	1	m1.reverseRange(false);
531	1	assertEquals(m1.getValue(0, 0), 9.6d, DELTA);
532	1	assertEquals(m1.getValue(0, 1), 8.1d, DELTA);
533	1	assertEquals(m1.getValue(0, 2), 7.6d, DELTA);
534	1	assertEquals(m1.getValue(1, 0), 15d, DELTA);
535	1	assertEquals(m1.getValue(1, 1), 7.6d, DELTA);
536	1	assertEquals(m1.getValue(1, 2), -3.4d, DELTA);
537
538		/*
539		* repeat operation - original values restored
540		*/
541	1	m1.reverseRange(false);
542	1	assertEquals(m1.getValue(0, 0), 2d, DELTA);
543	1	assertEquals(m1.getValue(0, 1), 3.5d, DELTA);
544	1	assertEquals(m1.getValue(0, 2), 4d, DELTA);
545	1	assertEquals(m1.getValue(1, 0), -3.4d, DELTA);
546	1	assertEquals(m1.getValue(1, 1), 4d, DELTA);
547	1	assertEquals(m1.getValue(1, 2), 15d, DELTA);
548		}
549
		100% Uncovered Elements: 0 (8) Complexity: 1 Complexity Density: 0.12 1PASS
550	1	@Test(groups = "Functional")...
551		public void testMultiply()
552		{
553	1	Matrix m = new Matrix(
554		new double[][]
555		{ { 2, 3.5, 4 }, { -3.4, 4, 15 } });
556	1	m.multiply(2d);
557	1	assertEquals(m.getValue(0, 0), 4d, DELTA);
558	1	assertEquals(m.getValue(0, 1), 7d, DELTA);
559	1	assertEquals(m.getValue(0, 2), 8d, DELTA);
560	1	assertEquals(m.getValue(1, 0), -6.8d, DELTA);
561	1	assertEquals(m.getValue(1, 1), 8d, DELTA);
562	1	assertEquals(m.getValue(1, 2), 30d, DELTA);
563		}
564
		100% Uncovered Elements: 0 (6) Complexity: 1 Complexity Density: 0.17 1PASS
565	1	@Test(groups = "Functional")...
566		public void testConstructor()
567		{
568	1	double[][] values = new double[][] { { 1, 2, 3 }, { 4, 5, 6 } };
569	1	Matrix m = new Matrix(values);
570	1	assertEquals(m.getValue(0, 0), 1d, DELTA);
571
572		/*
573		* verify the matrix has a copy of the original array
574		*/
575	1	assertNotSame(values[0], m.getRow(0));
576	1	values[0][0] = -1d;
577	1	assertEquals(m.getValue(0, 0), 1d, DELTA); // unchanged
578		}
579
		100% Uncovered Elements: 0 (16) Complexity: 1 Complexity Density: 0.06 1PASS
580	1	@Test(groups = "Functional")...
581		public void testEquals()
582		{
583	1	double[][] values = new double[][] { { 1, 2, 3 }, { 4, 5, 6 } };
584	1	Matrix m1 = new Matrix(values);
585	1	double[][] values2 = new double[][] { { 1, 2, 3 }, { 4, 5, 6 } };
586	1	Matrix m2 = new Matrix(values2);
587
588	1	double delta = 0.0001d;
589	1	assertTrue(m1.equals(m1, delta));
590	1	assertTrue(m1.equals(m2, delta));
591	1	assertTrue(m2.equals(m1, delta));
592
593	1	double[][] values3 = new double[][] { { 1, 2, 3 }, { 4, 5, 7 } };
594	1	m2 = new Matrix(values3);
595	1	assertFalse(m1.equals(m2, delta));
596	1	assertFalse(m2.equals(m1, delta));
597
598		// must be same shape
599	1	values2 = new double[][] { { 1, 2, 3 } };
600	1	m2 = new Matrix(values2);
601	1	assertFalse(m2.equals(m1, delta));
602
603	1	assertFalse(m1.equals(null, delta));
604		}
605		}