package jalview.analysis.scoremodels;
import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertNotNull;
-import static org.testng.Assert.assertNull;
+import static org.testng.Assert.assertNotSame;
import static org.testng.Assert.assertTrue;
+import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
-import java.io.ByteArrayInputStream;
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.ScoreMatrixFile;
+import jalview.math.MatrixI;
+
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.util.Arrays;
import org.testng.annotations.Test;
public class ScoreMatrixTest
{
@Test(groups = "Functional")
+ public void testConstructor()
+ {
+ // note score matrix does not have to be symmetric (though it should be!)
+ float[][] scores = new float[3][];
+ scores[0] = new float[] { 1f, 2f, 3f };
+ scores[1] = new float[] { 4f, 5f, 6f };
+ scores[2] = new float[] { 7f, 8f, 9f };
+ ScoreMatrix sm = new ScoreMatrix("Test", "ABC".toCharArray(), scores);
+ assertEquals(sm.getSize(), 3);
+ assertArrayEquals(scores, sm.getMatrix());
+ assertEquals(sm.getPairwiseScore('A', 'a'), 1f);
+ assertEquals(sm.getPairwiseScore('b', 'c'), 6f);
+ assertEquals(sm.getPairwiseScore('c', 'b'), 8f);
+ assertEquals(sm.getPairwiseScore('A', 'D'), 0f);
+ assertEquals(sm.getMatrixIndex('c'), 2);
+ assertEquals(sm.getMatrixIndex(' '), -1);
+ }
+
+ @Test(
+ groups = "Functional",
+ expectedExceptions = { IllegalArgumentException.class })
+ public void testConstructor_matrixTooSmall()
+ {
+ float[][] scores = new float[2][];
+ scores[0] = new float[] { 1f, 2f };
+ scores[1] = new float[] { 3f, 4f };
+ new ScoreMatrix("Test", "ABC".toCharArray(), scores);
+ }
+
+ @Test(
+ groups = "Functional",
+ expectedExceptions = { IllegalArgumentException.class })
+ public void testConstructor_matrixTooBig()
+ {
+ float[][] scores = new float[2][];
+ scores[0] = new float[] { 1f, 2f };
+ scores[1] = new float[] { 3f, 4f };
+ new ScoreMatrix("Test", "A".toCharArray(), scores);
+ }
+
+ @Test(
+ groups = "Functional",
+ expectedExceptions = { IllegalArgumentException.class })
+ public void testConstructor_matrixNotSquare()
+ {
+ float[][] scores = new float[2][];
+ scores[0] = new float[] { 1f, 2f };
+ scores[1] = new float[] { 3f };
+ new ScoreMatrix("Test", "AB".toCharArray(), scores);
+ }
+
+ @Test(groups = "Functional")
public void testBuildSymbolIndex()
{
short[] index = ScoreMatrix.buildSymbolIndex("AX-. yxYp".toCharArray());
}
}
- /**
- * Test a successful parse of a (small) score matrix file
- */
@Test(groups = "Functional")
- public void testParse()
+ public void testGetMatrix()
{
- /*
- * some messy but valid input data, with comma, space
- * or tab (or combinations) as score value delimiters
- */
- String data = "ScoreMatrix MyTest\n" + "ATU tx-\n"
- + "1.1,1.2,1.3,1.4, 1.5, 1.6, 1.7\n"
- + "2.1 2.2 2.3 2.4 2.5 2.6 2.7\n"
- + "3.1\t3.2\t3.3\t3.4\t3.5\t3.6\t3.7\n"
- + " 4.1 ,4.2,\t,4.3 ,\t4.4\t, \4.5,4.6 4.7\n"
- + ", 5.1,5.3,5.3,5.4,5.5, 5.6, 5.7\n"
- + "\t6.1, 6.2 6.3 6.4 6.5 6.6 6.7\n"
- + ", \t7.1\t7.2 7.3, 7.4, 7.5\t,7.6,7.7\n";
- ScoreMatrix sm = ScoreMatrix.parse(new ByteArrayInputStream(data
- .getBytes()));
- assertNotNull(sm);
- assertEquals(sm.getName(), "MyTest");
- assertTrue(sm.isDNA());
- assertFalse(sm.isProtein());
- assertEquals(sm.getPairwiseScore('A', 'A'), 1.1f);
- assertEquals(sm.getPairwiseScore('A', 'T'), 1.2f);
- assertEquals(sm.getPairwiseScore('a', 'T'), 1.2f); // A/a equivalent
- assertEquals(sm.getPairwiseScore('A', 't'), 1.5f); // T/t not equivalent
- assertEquals(sm.getPairwiseScore('a', 't'), 1.5f);
- assertEquals(sm.getPairwiseScore('T', ' '), 2.4f);
- assertEquals(sm.getPairwiseScore('U', 'x'), 3.6f);
- assertEquals(sm.getPairwiseScore('u', 'x'), 3.6f);
- assertEquals(sm.getPairwiseScore('U', 'X'), 0f); // X (upper) unmapped
- assertEquals(sm.getPairwiseScore('A', '.'), 0f); // . unmapped
- assertEquals(sm.getPairwiseScore('-', '-'), 7.7f);
- assertEquals(sm.getPairwiseScore('A', (char) 128), 0f); // out of range
+ ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
+ float[][] m = sm.getMatrix();
+ assertEquals(m.length, sm.getSize());
+ assertEquals(m[2][4], -3f);
+ // verify a defensive copy is returned
+ float[][] m2 = sm.getMatrix();
+ assertNotSame(m, m2);
+ assertTrue(Arrays.deepEquals(m, m2));
}
@Test(groups = "Functional")
- public void testParse_invalidInput()
+ public void testGetMatrixIndex()
{
- /*
- * valid first
- */
- String data = "ScoreMatrix MyTest\nXY\n1 2\n3 4\n";
- ScoreMatrix sm = ScoreMatrix.parse(new ByteArrayInputStream(data
- .getBytes()));
- assertNotNull(sm);
-
- /*
- * Name missing
- */
- data = "ScoreMatrix\nXY\n1 2\n3 4\n";
- sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
- assertNull(sm);
+ ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
+ assertEquals(sm.getMatrixIndex('A'), 0);
+ assertEquals(sm.getMatrixIndex('R'), 1);
+ assertEquals(sm.getMatrixIndex('r'), 1);
+ assertEquals(sm.getMatrixIndex('N'), 2);
+ assertEquals(sm.getMatrixIndex('D'), 3);
+ 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((char) 128), -1);
+ }
- /*
- * ScoreMatrix header missing
- */
- data = "XY\n1 2\n3 4\n";
- sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
- assertNull(sm);
+ @Test(groups = "Functional")
+ public void testGetSize()
+ {
+ ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
+ assertEquals(sm.getMatrix().length, sm.getSize());
+ }
+ @Test(groups = "Functional")
+ public void testComputePairwiseScores()
+ {
/*
- * Not enough rows
+ * NB score matrix assumes space for gap - Jalview converts
+ * space to gap before computing PCA or Tree
*/
- data = "ScoreMatrix MyTest\nXY\n1 2\n";
- sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
- assertNull(sm);
+ String[] seqs = new String[] { "FKL", "R D", "QIA", "GWC" };
+ ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
- /*
- * Not enough columns
- */
- data = "ScoreMatrix MyTest\nXY\n1 2\n3\n";
- sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
- assertNull(sm);
+ MatrixI pairwise = sm.computePairwiseScores(seqs);
/*
- * Too many columns
+ * should be NxN where N = number of sequences
*/
- data = "ScoreMatrix MyTest\nXY\n1 2\n3 4 5\n";
- sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
- assertNull(sm);
+ assertEquals(pairwise.height(), 4);
+ assertEquals(pairwise.width(), 4);
/*
- * Too many rows
+ * should be symmetrical (because BLOSUM62 is)
*/
- data = "ScoreMatrix MyTest\nXY\n1 2\n3 4\n6 7";
- sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
- assertNull(sm);
-
+ for (int i = 0; i < pairwise.height(); i++)
+ {
+ for (int j = i + 1; j < pairwise.width(); j++)
+ {
+ assertEquals(pairwise.getValue(i, j), pairwise.getValue(j, i),
+ String.format("Not symmetric at [%d, %d]", i, j));
+ }
+ }
/*
- * unsupported delimiter |
+ * verify expected BLOSUM dot product scores
*/
- data = "ScoreMatrix MyTest\nXY\n1|2\n3|4\n";
- sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
- assertNull(sm);
+ // F.F + K.K + L.L = 6 + 5 + 4 = 15
+ assertEquals(pairwise.getValue(0, 0), 15d);
+ // R.R + -.- + D.D = 5 + 1 + 6 = 12
+ assertEquals(pairwise.getValue(1, 1), 12d);
+ // Q.Q + I.I + A.A = 5 + 4 + 4 = 13
+ assertEquals(pairwise.getValue(2, 2), 13d);
+ // G.G + W.W + C.C = 6 + 11 + 9 = 26
+ assertEquals(pairwise.getValue(3, 3), 26d);
+ // F.R + K.- + L.D = -3 + -4 + -4 = -11
+ assertEquals(pairwise.getValue(0, 1), -11d);
+ // F.Q + K.I + L.A = -3 + -3 + -1 = -7
+ assertEquals(pairwise.getValue(0, 2), -7d);
+ // F.G + K.W + L.C = -3 + -3 + -1 = -7
+ assertEquals(pairwise.getValue(0, 3), -7d);
+ // R.Q + -.I + D.A = 1 + -4 + -2 = -5
+ assertEquals(pairwise.getValue(1, 2), -5d);
+ // R.G + -.W + D.C = -2 + -4 + -3 = -9
+ assertEquals(pairwise.getValue(1, 3), -9d);
+ // Q.G + I.W + A.C = -2 + -3 + 0 = -5
+ assertEquals(pairwise.getValue(2, 3), -5d);
+ }
- /*
- * Bad float value
- */
- data = "ScoreMatrix MyTest\nXY\n1 2\n3 four\n";
- sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
- assertNull(sm);
+ /**
+ * Test that the result of outputMatrix can be reparsed to give an identical
+ * ScoreMatrix
+ *
+ * @throws IOException
+ * @throws MalformedURLException
+ */
+ @Test(groups = "Functional")
+ public void testOutputMatrix_roundTrip() throws MalformedURLException,
+ IOException
+ {
+ ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
+ String output = sm.outputMatrix(false);
+ FileParse fp = new FileParse(output, DataSourceType.PASTE);
+ ScoreMatrixFile parser = new ScoreMatrixFile(fp);
+ ScoreMatrix sm2 = parser.parseMatrix();
+ assertNotNull(sm2);
+ assertTrue(sm2.equals(sm));
+ }
+ @Test(groups = "Functional")
+ public void testEauals()
+ {
+ ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
+ ScoreMatrix sm2 = new ScoreMatrix(sm.getName(), sm.getSymbols()
+ .toCharArray(), sm.getMatrix());
+ assertTrue(sm.equals(sm2));
+ assertEquals(sm.hashCode(), sm2.hashCode());
}
}
git://source.jalview.org / jalview.git / blobdiff