1 package jalview.analysis.scoremodels;
3 import static org.testng.Assert.assertEquals;
4 import static org.testng.Assert.assertFalse;
5 import static org.testng.Assert.assertNotNull;
6 import static org.testng.Assert.assertNull;
7 import static org.testng.Assert.assertTrue;
9 import java.io.ByteArrayInputStream;
11 import org.testng.annotations.Test;
13 public class ScoreMatrixTest
15 @Test(groups = "Functional")
16 public void testBuildSymbolIndex()
18 short[] index = ScoreMatrix.buildSymbolIndex("AX-. yxYp".toCharArray());
20 assertEquals(index.length, 128); // ASCII character set size
22 assertEquals(index['A'], 0);
23 assertEquals(index['a'], 0); // lower-case mapping added
24 assertEquals(index['X'], 1);
25 assertEquals(index['-'], 2);
26 assertEquals(index['.'], 3);
27 assertEquals(index[' '], 4);
28 assertEquals(index['y'], 5); // lower-case override
29 assertEquals(index['x'], 6); // lower-case override
30 assertEquals(index['Y'], 7);
31 assertEquals(index['p'], 8);
32 assertEquals(index['P'], -1); // lower-case doesn't map upper-case
35 * check all unmapped symbols have index for unmapped
37 for (int c = 0; c < index.length; c++)
39 if (!"AaXx-. Yyp".contains(String.valueOf((char) c)))
41 assertEquals(index[c], -1);
47 * check that characters not in the basic ASCII set are simply ignored
49 @Test(groups = "Functional")
50 public void testBuildSymbolIndex_nonAscii()
52 char[] weird = new char[] { 128, 245, 'P' };
53 short[] index = ScoreMatrix.buildSymbolIndex(weird);
54 assertEquals(index.length, 128);
55 assertEquals(index['P'], 2);
56 assertEquals(index['p'], 2);
57 for (int c = 0; c < index.length; c++)
59 if (c != 'P' && c != 'p')
61 assertEquals(index[c], -1);
67 * Test a successful parse of a (small) score matrix file
69 @Test(groups = "Functional")
70 public void testParse()
73 * some messy but valid input data, with comma, space
74 * or tab (or combinations) as score value delimiters
75 * this example includes 'guide' symbols on score rows
77 String data = "ScoreMatrix MyTest\n" + "ATU tx-\n"
78 + "A,1.1,1.2,1.3,1.4, 1.5, 1.6, 1.7\n"
79 + "T,2.1 2.2 2.3 2.4 2.5 2.6 2.7\n"
80 + "U\t3.1\t3.2\t3.3\t3.4\t3.5\t3.6\t3.7\n"
81 + " 4.1 ,4.2,\t,4.3 ,\t4.4\t, \4.5,4.6 4.7\n"
82 + "t, 5.1,5.3,5.3,5.4,5.5, 5.6, 5.7\n"
83 + "x\t6.1, 6.2 6.3 6.4 6.5 6.6 6.7\n"
84 + "-, \t7.1\t7.2 7.3, 7.4, 7.5\t,7.6,7.7\n";
85 ScoreMatrix sm = ScoreMatrix.parse(new ByteArrayInputStream(data
88 assertEquals(sm.getName(), "MyTest");
89 assertTrue(sm.isDNA());
90 assertFalse(sm.isProtein());
91 assertEquals(sm.getPairwiseScore('A', 'A'), 1.1f);
92 assertEquals(sm.getPairwiseScore('A', 'T'), 1.2f);
93 assertEquals(sm.getPairwiseScore('a', 'T'), 1.2f); // A/a equivalent
94 assertEquals(sm.getPairwiseScore('A', 't'), 1.5f); // T/t not equivalent
95 assertEquals(sm.getPairwiseScore('a', 't'), 1.5f);
96 assertEquals(sm.getPairwiseScore('T', ' '), 2.4f);
97 assertEquals(sm.getPairwiseScore('U', 'x'), 3.6f);
98 assertEquals(sm.getPairwiseScore('u', 'x'), 3.6f);
99 assertEquals(sm.getPairwiseScore('U', 'X'), 0f); // X (upper) unmapped
100 assertEquals(sm.getPairwiseScore('A', '.'), 0f); // . unmapped
101 assertEquals(sm.getPairwiseScore('-', '-'), 7.7f);
102 assertEquals(sm.getPairwiseScore('A', (char) 128), 0f); // out of range
105 * without guide symbols on score rows
107 data = "ScoreMatrix MyTest\nXY\n1 2\n3 4\n";
108 sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
110 assertEquals(sm.getPairwiseScore('X', 'X'), 1f);
111 assertEquals(sm.getPairwiseScore('X', 'y'), 2f);
112 assertEquals(sm.getPairwiseScore('y', 'x'), 3f);
113 assertEquals(sm.getPairwiseScore('y', 'Y'), 4f);
114 assertEquals(sm.getPairwiseScore('D', 'R'), 0f);
117 @Test(groups = "Functional")
118 public void testParse_invalidInput()
123 String data = "ScoreMatrix MyTest\nXY\n1 2\n3 4\n";
124 ScoreMatrix sm = ScoreMatrix.parse(new ByteArrayInputStream(data
131 data = "ScoreMatrix\nXY\n1 2\n3 4\n";
132 sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
136 * ScoreMatrix header missing
138 data = "XY\n1 2\n3 4\n";
139 sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
145 data = "ScoreMatrix MyTest\nXY\n1 2\n";
146 sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
152 data = "ScoreMatrix MyTest\nXY\n1 2\n3\n";
153 sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
159 data = "ScoreMatrix MyTest\nXY\n1 2\n3 4 5\n";
160 sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
166 data = "ScoreMatrix MyTest\nXY\n1 2\n3 4\n6 7";
167 sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
171 * unsupported delimiter |
173 data = "ScoreMatrix MyTest\nXY\n1|2\n3|4\n";
174 sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
180 data = "ScoreMatrix MyTest\nXY\n1 2\n3 four\n";
181 sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
185 * Bad guide character on scores row
187 data = "ScoreMatrix MyTest\nXY\nX 1 2\ny 3 4\n";
188 sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));