X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreMatrixTest.java;h=ec3fab3c9dace22612a4a04936195005c8166ed9;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=5c699d1d32def3f538becc6f61975ff7c6b66e2f;hpb=613a7a5d1fe2758f0bb620e49eeb87fa45b5458f;p=jalview.git diff --git a/test/jalview/analysis/scoremodels/ScoreMatrixTest.java b/test/jalview/analysis/scoremodels/ScoreMatrixTest.java index 5c699d1..ec3fab3 100644 --- a/test/jalview/analysis/scoremodels/ScoreMatrixTest.java +++ b/test/jalview/analysis/scoremodels/ScoreMatrixTest.java @@ -1,8 +1,11 @@ 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; @@ -10,6 +13,7 @@ import jalview.api.analysis.SimilarityParamsI; import jalview.io.DataSourceType; import jalview.io.FileParse; import jalview.io.ScoreMatrixFile; +import jalview.math.Matrix; import jalview.math.MatrixI; import jalview.schemes.ResidueProperties; @@ -19,6 +23,8 @@ import java.util.Arrays; import org.testng.annotations.Test; +import junit.extensions.PA; + public class ScoreMatrixTest { @Test(groups = "Functional") @@ -27,22 +33,29 @@ public class ScoreMatrixTest // 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[1] = new float[] { -4f, 5f, 6f }; scores[2] = new float[] { 7f, 8f, 9f }; ScoreMatrix sm = new ScoreMatrix("Test", "ABC".toCharArray(), scores); + assertFalse(sm.isSymmetric()); 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); + + // substitution to or from unknown symbol gets minimum score + assertEquals(sm.getPairwiseScore('A', 'D'), -4f); + assertEquals(sm.getPairwiseScore('D', 'A'), -4f); + // unknown-to-self gets a score of 1 + assertEquals(sm.getPairwiseScore('D', 'D'), 1f); } @Test( groups = "Functional", - expectedExceptions = { IllegalArgumentException.class }) + expectedExceptions = + { IllegalArgumentException.class }) public void testConstructor_matrixTooSmall() { float[][] scores = new float[2][]; @@ -53,7 +66,8 @@ public class ScoreMatrixTest @Test( groups = "Functional", - expectedExceptions = { IllegalArgumentException.class }) + expectedExceptions = + { IllegalArgumentException.class }) public void testConstructor_matrixTooBig() { float[][] scores = new float[2][]; @@ -64,7 +78,8 @@ public class ScoreMatrixTest @Test( groups = "Functional", - expectedExceptions = { IllegalArgumentException.class }) + expectedExceptions = + { IllegalArgumentException.class }) public void testConstructor_matrixNotSquare() { float[][] scores = new float[2][]; @@ -76,7 +91,12 @@ public class ScoreMatrixTest @Test(groups = "Functional") public void testBuildSymbolIndex() { - short[] index = ScoreMatrix.buildSymbolIndex("AX-. yxYp".toCharArray()); + float[][] scores = new float[2][]; + scores[0] = new float[] { 1f, 2f }; + scores[1] = new float[] { 3f, 4f }; + ScoreMatrix sm = new ScoreMatrix("Test", new char[] { 'A', '.' }, + scores); + short[] index = sm.buildSymbolIndex("AX-yxYp".toCharArray()); assertEquals(index.length, 128); // ASCII character set size @@ -84,12 +104,10 @@ public class ScoreMatrixTest assertEquals(index['a'], 0); // lower-case mapping added assertEquals(index['X'], 1); assertEquals(index['-'], 2); - assertEquals(index['.'], 3); - assertEquals(index[' '], 4); - assertEquals(index['y'], 5); // lower-case override - assertEquals(index['x'], 6); // lower-case override - assertEquals(index['Y'], 7); - assertEquals(index['p'], 8); + assertEquals(index['y'], 3); // lower-case override + assertEquals(index['x'], 4); // lower-case override + assertEquals(index['Y'], 5); + assertEquals(index['p'], 6); assertEquals(index['P'], -1); // lower-case doesn't map upper-case /* @@ -110,8 +128,13 @@ public class ScoreMatrixTest @Test(groups = "Functional") public void testBuildSymbolIndex_nonAscii() { + float[][] scores = new float[2][]; + scores[0] = new float[] { 1f, 2f }; + scores[1] = new float[] { 3f, 4f }; + ScoreMatrix sm = new ScoreMatrix("Test", new char[] { 'A', '.' }, + scores); char[] weird = new char[] { 128, 245, 'P' }; - short[] index = ScoreMatrix.buildSymbolIndex(weird); + short[] index = sm.buildSymbolIndex(weird); assertEquals(index.length, 128); assertEquals(index['P'], 2); assertEquals(index['p'], 2); @@ -148,8 +171,8 @@ public class ScoreMatrixTest 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('*'), 23); assertEquals(sm.getMatrixIndex('.'), -1); assertEquals(sm.getMatrixIndex(' '), -1); assertEquals(sm.getMatrixIndex('?'), -1); @@ -224,8 +247,8 @@ public class ScoreMatrixTest * @throws MalformedURLException */ @Test(groups = "Functional") - public void testOutputMatrix_roundTrip() throws MalformedURLException, - IOException + public void testOutputMatrix_roundTrip() + throws MalformedURLException, IOException { ScoreMatrix sm = ScoreModels.getInstance().getBlosum62(); String output = sm.outputMatrix(false); @@ -240,10 +263,16 @@ public class ScoreMatrixTest public void testEqualsAndHashCode() { ScoreMatrix sm = ScoreModels.getInstance().getBlosum62(); - ScoreMatrix sm2 = new ScoreMatrix(sm.getName(), sm.getSymbols() - .toCharArray(), sm.getMatrix()); + ScoreMatrix sm2 = new ScoreMatrix(sm.getName(), + sm.getSymbols().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")); } /** @@ -258,19 +287,20 @@ public class ScoreMatrixTest String s1 = "FR-K-S"; String s2 = "FS--L"; ScoreMatrix blosum = ScoreModels.getInstance().getBlosum62(); - + /* * score gap-gap and gap-char * shorter sequence treated as if with trailing gaps * score = F^F + R^S + -^- + K^- + -^L + S^- * = 6 + -1 + 1 + -4 + -4 + -4 = -6 */ - SimilarityParamsI params = new SimilarityParams(true, true, true, false); + SimilarityParamsI params = new SimilarityParams(true, true, true, + false); assertEquals(blosum.computeSimilarity(s1, s2, params), -6d); // matchGap (arg2) is ignored: params = new SimilarityParams(true, false, true, false); assertEquals(blosum.computeSimilarity(s1, s2, params), -6d); - + /* * score gap-char but not gap-gap * score = F^F + R^S + 0 + K^- + -^L + S^- @@ -281,7 +311,7 @@ public class ScoreMatrixTest // matchGap (arg2) is ignored: params = new SimilarityParams(false, false, true, false); assertEquals(blosum.computeSimilarity(s1, s2, params), -7d); - + /* * score gap-gap but not gap-char * score = F^F + R^S + -^- + 0 + 0 + 0 @@ -292,7 +322,7 @@ public class ScoreMatrixTest // matchGap (arg2) is ignored: params = new SimilarityParams(true, true, false, false); assertEquals(blosum.computeSimilarity(s1, s2, params), 6d); - + /* * score neither gap-gap nor gap-char * score = F^F + R^S + 0 + 0 + 0 + 0 @@ -330,7 +360,7 @@ public class ScoreMatrixTest // matchGap (arg2) is ignored: params = new SimilarityParams(true, false, true, true); assertEquals(blosum.computeSimilarity(s1, s2, params), -2d); - + /* * score gap-char but not gap-gap * score = F^F + R^S + 0 + K^- + -^L @@ -341,7 +371,7 @@ public class ScoreMatrixTest // matchGap (arg2) is ignored: params = new SimilarityParams(false, false, true, true); assertEquals(blosum.computeSimilarity(s1, s2, params), -3d); - + /* * score gap-gap but not gap-char * score = F^F + R^S + -^- + 0 + 0 @@ -352,7 +382,7 @@ public class ScoreMatrixTest // matchGap (arg2) is ignored: params = new SimilarityParams(true, true, false, true); assertEquals(blosum.computeSimilarity(s1, s2, params), 6d); - + /* * score neither gap-gap nor gap-char * score = F^F + R^S + 0 + 0 + 0 @@ -373,6 +403,12 @@ public class ScoreMatrixTest verifySymmetric(ScoreModels.getInstance().getDefaultModel(false)); // dna } + /** + * A helper method that inspects a loaded matrix and reports any asymmetry as + * a test failure + * + * @param sm + */ private void verifySymmetric(ScoreMatrix sm) { float[][] m = sm.getMatrix(); @@ -382,9 +418,10 @@ public class ScoreMatrixTest assertEquals(m[row].length, rows); for (int col = 0; col < rows; col++) { - assertEquals(m[row][col], m[col][row], String.format("%s [%s, %s]", - sm.getName(), ResidueProperties.aa[row], - ResidueProperties.aa[col])); + assertEquals(m[row][col], m[col][row], + String.format("%s [%s, %s]", sm.getName(), + ResidueProperties.aa[row], + ResidueProperties.aa[col])); } } } @@ -397,67 +434,106 @@ public class ScoreMatrixTest { ScoreMatrix sm = ScoreModels.getInstance().getBlosum62(); + assertTrue(sm.isProtein()); + assertFalse(sm.isDNA()); + assertNull(sm.getDescription()); + /* * verify expected scores against ARNDCQEGHILKMFPSTWYVBZX * scraped from https://www.ncbi.nlm.nih.gov/Class/FieldGuide/BLOSUM62.txt */ - verifyValues(sm, 'A', new float[] { 4, -1, -2, -2, 0, -1, -1, 0, -2, - -1, - -1, -1, -1, -2, -1, 1, 0, -3, -2, 0, -2, -1, 0 }); - verifyValues(sm, 'R', new float[] { -1, 5, 0, -2, -3, 1, 0, -2, 0, -3, - -2, 2, -1, -3, -2, -1, -1, -3, -2, -3, -1, 0, -1 }); - verifyValues(sm, 'N', new float[] { -2, 0, 6, 1, -3, 0, 0, 0, 1, -3, - -3, - 0, -2, -3, -2, 1, 0, -4, -2, -3, 3, 0, -1 }); - verifyValues(sm, 'D', new float[] { -2, -2, 1, 6, -3, 0, 2, -1, -1, -3, - -4, -1, -3, -3, -1, 0, -1, -4, -3, -3, 4, 1, -1 }); - verifyValues(sm, 'C', new float[] { 0, -3, -3, -3, 9, -3, -4, -3, -3, - -1, - -1, -3, -1, -2, -3, -1, -1, -2, -2, -1, -3, -3, -2 }); - verifyValues(sm, 'Q', new float[] { -1, 1, 0, 0, -3, 5, 2, -2, 0, -3, - -2, - 1, 0, -3, -1, 0, -1, -2, -1, -2, 0, 3, -1 }); - verifyValues(sm, 'E', new float[] { -1, 0, 0, 2, -4, 2, 5, -2, 0, -3, - -3, - 1, -2, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1 }); - verifyValues(sm, 'G', new float[] { 0, -2, 0, -1, -3, -2, -2, 6, -2, - -4, - -4, -2, -3, -3, -2, 0, -2, -2, -3, -3, -1, -2, -1 }); - verifyValues(sm, 'H', new float[] { -2, 0, 1, -1, -3, 0, 0, -2, 8, -3, - -3, -1, -2, -1, -2, -1, -2, -2, 2, -3, 0, 0, -1 }); - verifyValues(sm, 'I', new float[] { -1, -3, -3, -3, -1, -3, -3, -4, -3, - 4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3, -3, -3, -1 }); - verifyValues(sm, 'L', new float[] { -1, -2, -3, -4, -1, -2, -3, -4, -3, - 2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1, -4, -3, -1 }); - verifyValues(sm, 'K', new float[] { -1, 2, 0, -1, -3, 1, 1, -2, -1, -3, - -2, 5, -1, -3, -1, 0, -1, -3, -2, -2, 0, 1, -1 }); - verifyValues(sm, 'M', new float[] { -1, -1, -2, -3, -1, 0, -2, -3, -2, - 1, - 2, -1, 5, 0, -2, -1, -1, -1, -1, 1, -3, -1, -1 }); - verifyValues(sm, 'F', new float[] { -2, -3, -3, -3, -2, -3, -3, -3, -1, - 0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1, -3, -3, -1 }); - verifyValues(sm, 'P', new float[] { -1, -2, -2, -1, -3, -1, -1, -2, -2, - -3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2, -2, -1, -2 }); - verifyValues(sm, 'S', new float[] { 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, - -2, - 0, -1, -2, -1, 4, 1, -3, -2, -2, 0, 0, 0 }); - verifyValues(sm, 'T', new float[] { 0, -1, 0, -1, -1, -1, -1, -2, -2, - -1, - -1, -1, -1, -2, -1, 1, 5, -2, -2, 0, -1, -1, 0 }); - verifyValues(sm, 'W', new float[] { -3, -3, -4, -4, -2, -2, -3, -2, -2, - -3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3, -4, -3, -2 }); - verifyValues(sm, 'Y', new float[] { -2, -2, -2, -3, -2, -1, -2, -3, 2, - -1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1, -3, -2, -1 }); - verifyValues(sm, 'V', new float[] { 0, -3, -3, -3, -1, -2, -2, -3, -3, - 3, - 1, -2, 1, -1, -2, -2, 0, -3, -1, 4, -3, -2, -1 }); - verifyValues(sm, 'B', new float[] { -2, -1, 3, 4, -3, 0, 1, -1, 0, -3, - -4, 0, -3, -3, -2, 0, -1, -4, -3, -3, 4, 1, -1 }); - verifyValues(sm, 'Z', new float[] { -1, 0, 0, 1, -3, 3, 4, -2, 0, -3, - -3, - 1, -1, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1 }); - verifyValues(sm, 'X', new float[] { 0, -1, -1, -1, -2, -1, -1, -1, -1, - -1, -1, -1, -1, -1, -2, 0, 0, -2, -1, -1, -1, -1, -1 }); + verifyValues(sm, 'A', + new float[] + { 4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, + -3, -2, 0, -2, -1, 0 }); + verifyValues(sm, 'R', + new float[] + { -1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, + -3, -2, -3, -1, 0, -1 }); + verifyValues(sm, 'N', + new float[] + { -2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, + -2, -3, 3, 0, -1 }); + verifyValues(sm, 'D', + new float[] + { -2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, + -4, -3, -3, 4, 1, -1 }); + verifyValues(sm, 'C', + new float[] + { 0, -3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, + -1, -2, -2, -1, -3, -3, -2 }); + verifyValues(sm, 'Q', + new float[] + { -1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, + -1, -2, 0, 3, -1 }); + verifyValues(sm, 'E', + new float[] + { -1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, + -3, -2, -2, 1, 4, -1 }); + verifyValues(sm, 'G', + new float[] + { 0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, + -2, -2, -3, -3, -1, -2, -1 }); + verifyValues(sm, 'H', + new float[] + { -2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, + -2, 2, -3, 0, 0, -1 }); + verifyValues(sm, 'I', + new float[] + { -1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, + -1, -3, -1, 3, -3, -3, -1 }); + verifyValues(sm, 'L', + new float[] + { -1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, + -1, -2, -1, 1, -4, -3, -1 }); + verifyValues(sm, 'K', + new float[] + { -1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, + -3, -2, -2, 0, 1, -1 }); + verifyValues(sm, 'M', + new float[] + { -1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, + -1, -1, 1, -3, -1, -1 }); + verifyValues(sm, 'F', + new float[] + { -2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, + -2, 1, 3, -1, -3, -3, -1 }); + verifyValues(sm, 'P', + new float[] + { -1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, + -1, -4, -3, -2, -2, -1, -2 }); + verifyValues(sm, 'S', + new float[] + { 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, + -2, -2, 0, 0, 0 }); + verifyValues(sm, 'T', + new float[] + { 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, + 5, -2, -2, 0, -1, -1, 0 }); + verifyValues(sm, 'W', + new float[] + { -3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, + -2, 11, 2, -3, -4, -3, -2 }); + verifyValues(sm, 'Y', + new float[] + { -2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, + -2, 2, 7, -1, -3, -2, -1 }); + verifyValues(sm, 'V', + new float[] + { 0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, + -3, -1, 4, -3, -2, -1 }); + verifyValues(sm, 'B', + new float[] + { -2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, + -4, -3, -3, 4, 1, -1 }); + verifyValues(sm, 'Z', + new float[] + { -1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, + -3, -2, -2, 1, 4, -1 }); + verifyValues(sm, 'X', + new float[] + { 0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, + 0, -2, -1, -1, -1, -1, -1 }); } /** @@ -477,4 +553,160 @@ public class ScoreMatrixTest String.format("%s->%s", res, c2)); } } + + @Test(groups = "Functional") + public void testConstructor_gapDash() + { + 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', '-' }, + scores); + assertEquals(sm.getSize(), 2); + assertArrayEquals(scores, sm.getMatrix()); + assertEquals(sm.getPairwiseScore('A', 'a'), 1f); + assertEquals(sm.getPairwiseScore('A', 'A'), 1f); + assertEquals(sm.getPairwiseScore('a', '-'), 2f); + assertEquals(sm.getPairwiseScore('-', 'A'), 4f); + assertEquals(sm.getMatrixIndex('a'), 0); + assertEquals(sm.getMatrixIndex('A'), 0); + assertEquals(sm.getMatrixIndex('-'), 1); + assertEquals(sm.getMatrixIndex(' '), -1); + assertEquals(sm.getMatrixIndex('.'), -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 minimum score + * or 1 for identity with self + */ + assertEquals(sm.getPairwiseScore('A', '-'), -4f); + assertEquals(sm.getPairwiseScore('-', 'A'), -4f); + assertEquals(sm.getPairwiseScore('-', '-'), 1f); + assertEquals(sm.getPairwiseScore('Q', 'W'), -4f); + assertEquals(sm.getPairwiseScore('Q', 'Q'), 1f); + + /* + * 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 = "\n" + + "\n" + + "\n" + + "
 A  B 
A1.02.0
B4.0-5.3E-10
"; + assertEquals(html, expected); + } + + @Test(groups = "Functional") + public void testIsSymmetric() + { + double delta = 0.0001d; + float[][] scores = new float[][] { { 1f, -2f }, { -2f, 3f } }; + ScoreMatrix sm = new ScoreMatrix("Test", "AB".toCharArray(), scores); + assertTrue(sm.isSymmetric()); + + /* + * verify that with a symmetric score matrix, + * pairwise similarity matrix is also symmetric + * seq1.seq1 = 5*A.A + 3*B.B = 5+9 = 14 + * seq1.seq2 = 3*A.A + 2*A.B + B.A + 2*B.B = 3 + -4 + -2 + 6 = 3 + * seq2.seq1 = 3*A.A + A.B + 2*B.A + 2*B.B = 3 + -2 + -4 + 6 = 3 + * seq2.seq2 = 4*A.A + 4*B.B = 4 + 12 = 16 + */ + SimilarityParamsI params = new SimilarityParams(true, true, true, + false); + String seq1 = "AAABBBAA"; + String seq2 = "AABBABBA"; + String[] seqs1 = new String[] { seq1, seq2 }; + MatrixI res1 = sm.findSimilarities(seqs1, params); + assertTrue( + res1.equals(new Matrix(new double[][] + { { 14d, 3d }, { 3d, 16d } }), delta)); + + /* + * order of sequences affects diagonal, but not off-diagonal values + * [0, 0] is now seq2.seq2, [1, 1] is seq1.seq1 + * [0, 1] is now seq2.seq1 = seq1.seq2 by symmetry + */ + String[] seqs2 = new String[] { seq2, seq1 }; + MatrixI res2 = sm.findSimilarities(seqs2, params); + assertFalse(res1.equals(res2)); + assertTrue( + res2.equals(new Matrix(new double[][] + { { 16d, 3d }, { 3d, 14d } }), delta)); + + /* + * now make the score matrix asymmetric + * seq1.seq1 = 5*A.A + 3*B.B = 5+9 = 14 + * seq1.seq2 = 3*A.A + 2*A.B + B.A + 2*B.B = 3 + -4 + 2 + 6 = 7 + * seq2.seq1 = 3*A.A + A.B + 2*B.A + 2*B.B = 3 + -2 + 4 + 6 = 11 + * seq2.seq2 = 4*A.A + 4*B.B = 4 + 12 = 16 + */ + scores = new float[][] { { 1f, -2f }, { 2f, 3f } }; + sm = new ScoreMatrix("Test", "AB".toCharArray(), scores); + assertFalse(sm.isSymmetric()); // [0, 1] != [1, 0] + res1 = sm.findSimilarities(seqs1, params); + assertTrue( + res1.equals(new Matrix(new double[][] + { { 14d, 7d }, { 11d, 16d } }), delta)); + + /* + * reverse order of sequences + * - reverses order of main diagonal + * - reflects off-diagonal values + */ + res2 = sm.findSimilarities(seqs2, params); + assertFalse(res1.equals(res2)); + assertTrue( + res2.equals(new Matrix(new double[][] + { { 16d, 11d }, { 7d, 14d } }), delta)); + + /* + * verify that forcing an asymmetric matrix to use + * symmetric calculation gives a different (wrong) result + */ + PA.setValue(sm, "symmetric", true); + assertTrue(sm.isSymmetric()); // it's not true! + res2 = sm.findSimilarities(seqs1, params); + assertFalse(res1.equals(res2, delta)); + } }