package jalview.analysis.scoremodels;
import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNotEquals;
import static org.testng.Assert.assertNotNull;
import static org.testng.Assert.assertNotSame;
+import static org.testng.Assert.assertNull;
import static org.testng.Assert.assertTrue;
import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
assertEquals(sm.getMatrixIndex('X'), 22);
assertEquals(sm.getMatrixIndex('x'), 22);
assertEquals(sm.getMatrixIndex('-'), 23);
- assertEquals(sm.getMatrixIndex('*'), 24);
+ assertEquals(sm.getMatrixIndex('*'), -1);
assertEquals(sm.getMatrixIndex('.'), -1);
assertEquals(sm.getMatrixIndex(' '), -1);
assertEquals(sm.getMatrixIndex('?'), -1);
.toCharArray(), sm.getMatrix());
assertTrue(sm.equals(sm2));
assertEquals(sm.hashCode(), sm2.hashCode());
+
+ sm2 = ScoreModels.getInstance().getPam250();
+ assertFalse(sm.equals(sm2));
+ assertNotEquals(sm.hashCode(), sm2.hashCode());
+
+ assertFalse(sm.equals("hello"));
}
/**
{
ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
+ assertTrue(sm.isProtein());
+ assertFalse(sm.isDNA());
+ assertNull(sm.getDescription());
+ sm.setDescription("BLOSUM62");
+ assertEquals(sm.getDescription(), "BLOSUM62");
+
/*
* verify expected scores against ARNDCQEGHILKMFPSTWYVBZX
* scraped from https://www.ncbi.nlm.nih.gov/Class/FieldGuide/BLOSUM62.txt
assertEquals(sm.getGapIndex(), 1);
}
+
+ @Test(groups = "Functional")
+ public void testGetPairwiseScore()
+ {
+ float[][] scores = new float[2][];
+ scores[0] = new float[] { 1f, 2f };
+ scores[1] = new float[] { 4f, 5f };
+ ScoreMatrix sm = new ScoreMatrix("Test", new char[] { 'A', 'B' },
+ scores);
+ assertEquals(sm.getPairwiseScore('A', 'A'), 1f);
+ assertEquals(sm.getPairwiseScore('A', 'a'), 1f);
+ assertEquals(sm.getPairwiseScore('A', 'B'), 2f);
+ assertEquals(sm.getPairwiseScore('b', 'a'), 4f);
+ assertEquals(sm.getPairwiseScore('B', 'b'), 5f);
+
+ /*
+ * unknown symbols currently score zero
+ */
+ assertEquals(sm.getPairwiseScore('A', '-'), 0f);
+ assertEquals(sm.getPairwiseScore('-', '-'), 0f);
+ assertEquals(sm.getPairwiseScore('Q', 'W'), 0f);
+
+ /*
+ * symbols not in basic ASCII set score zero
+ */
+ char c = (char) 200;
+ assertEquals(sm.getPairwiseScore('Q', c), 0f);
+ assertEquals(sm.getPairwiseScore(c, 'Q'), 0f);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetMinimumScore()
+ {
+ ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
+ assertEquals(sm.getMinimumScore(), -4f);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetMaximumScore()
+ {
+ ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
+ assertEquals(sm.getMaximumScore(), 11f);
+ }
+
+ @Test(groups = "Functional")
+ public void testOutputMatrix_html()
+ {
+ float[][] scores = new float[2][];
+ scores[0] = new float[] { 1f, 2f };
+ scores[1] = new float[] { 4f, -5.3E-10f };
+ ScoreMatrix sm = new ScoreMatrix("Test", "AB".toCharArray(), scores);
+ String html = sm.outputMatrix(true);
+ String expected = "<table border=\"1\"><tr><th></th><th> A </th><th> B </th></tr>\n"
+ + "<tr><td>A</td><td>1.0</td><td>2.0</td></tr>\n"
+ + "<tr><td>B</td><td>4.0</td><td>-5.3E-10</td></tr>\n"
+ + "</table>";
+ assertEquals(html, expected);
+ }
}