X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreMatrixTest.java;h=1a5d43c98f91459a5effca9382d25029f9d2716f;hb=bd7b3138379c2db8507fe7e8d25f5a921e2d9df7;hp=85be5b77d8f34058264c3fbad64f4e3a28279dbe;hpb=baad2f0ba2b171dd3d52c17afa46ef800334ea5e;p=jalview.git diff --git a/test/jalview/analysis/scoremodels/ScoreMatrixTest.java b/test/jalview/analysis/scoremodels/ScoreMatrixTest.java index 85be5b7..1a5d43c 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; @@ -11,6 +14,7 @@ import jalview.io.DataSourceType; import jalview.io.FileParse; import jalview.io.ScoreMatrixFile; import jalview.math.MatrixI; +import jalview.schemes.ResidueProperties; import java.io.IOException; import java.net.MalformedURLException; @@ -26,7 +30,7 @@ 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); assertEquals(sm.getSize(), 3); @@ -34,9 +38,14 @@ public class ScoreMatrixTest 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( @@ -75,7 +84,12 @@ 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 @@ -83,12 +97,10 @@ 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 /* @@ -109,8 +121,13 @@ 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); @@ -147,10 +164,10 @@ 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('-'), -1); + assertEquals(sm.getMatrixIndex('*'), 23); + assertEquals(sm.getMatrixIndex('.'), -1); + assertEquals(sm.getMatrixIndex(' '), -1); assertEquals(sm.getMatrixIndex('?'), -1); assertEquals(sm.getMatrixIndex((char) 128), -1); } @@ -166,10 +183,9 @@ public class ScoreMatrixTest public void testComputePairwiseScores() { /* - * NB score matrix assumes space for gap - Jalview converts - * space to gap before computing PCA or Tree + * NB score matrix expects '-' for gap */ - String[] seqs = new String[] { "FKL", "R D", "QIA", "GWC" }; + String[] seqs = new String[] { "FKL", "R-D", "QIA", "GWC" }; ScoreMatrix sm = ScoreModels.getInstance().getBlosum62(); MatrixI pairwise = sm.findSimilarities(seqs, SimilarityParams.Jalview); @@ -244,25 +260,25 @@ public class ScoreMatrixTest .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")); } /** - * Tests for percentage identity variants where the longer length of two - * sequences is used + * Tests for scoring options where the longer length of two sequences is used */ @Test(groups = "Functional") public void testcomputeSimilarity_matchLongestSequence() { - // TODO params.matchGaps() is not used for ScoreMatrix - // - includeGaps is sufficient (there is no denominator) - // ==> bespoke parameters only 3 booleans? /* - * for now, using space for gap to match callers of - * AlignmentView.getSequenceStrings() - * may change this to '-' (with corresponding change to matrices) + * ScoreMatrix expects '-' for gaps */ - String s1 = "FR K S"; - String s2 = "FS L"; + String s1 = "FR-K-S"; + String s2 = "FS--L"; ScoreMatrix blosum = ScoreModels.getInstance().getBlosum62(); /* @@ -312,27 +328,22 @@ public class ScoreMatrixTest } /** - * Tests for percentage identity variants where only the shorter length of two - * sequences is used + * Tests for scoring options where only the shorter length of two sequences is + * used */ @Test(groups = "Functional") public void testcomputeSimilarity_matchShortestSequence() { - // TODO params.matchGaps() is not used for ScoreMatrix - // - includeGaps is sufficient (there is no denominator) - // ==> bespoke parameters only 3 booleans? /* - * for now, using space for gap to match callers of - * AlignmentView.getSequenceStrings() - * may change this to '-' (with corresponding change to matrices) + * ScoreMatrix expects '-' for gaps */ - String s1 = "FR K S"; - String s2 = "FS L"; + 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 + * match shorter sequence only * score = F^F + R^S + -^- + K^- + -^L * = 6 + -1 + 1 + -4 + -4 = -2 */ @@ -375,4 +386,203 @@ public class ScoreMatrixTest params = new SimilarityParams(false, true, false, true); assertEquals(blosum.computeSimilarity(s1, s2, params), 5d); } + + @Test(groups = "Functional") + public void testSymmetric() + { + verifySymmetric(ScoreModels.getInstance().getBlosum62()); + verifySymmetric(ScoreModels.getInstance().getPam250()); + verifySymmetric(ScoreModels.getInstance().getDefaultModel(false)); // dna + } + + private void verifySymmetric(ScoreMatrix sm) + { + float[][] m = sm.getMatrix(); + int rows = m.length; + for (int row = 0; row < rows; row++) + { + 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])); + } + } + } + + /** + * A test that just asserts the expected values in the Blosum62 score matrix + */ + @Test(groups = "Functional") + public void testBlosum62_values() + { + 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 }); + } + + /** + * Helper method to check pairwise scores for one residue + * + * @param sm + * @param res + * @param expected + * score values against 'res', in ResidueProperties.aaIndex order + */ + private void verifyValues(ScoreMatrix sm, char res, float[] expected) + { + for (int j = 0; j < expected.length; j++) + { + char c2 = ResidueProperties.aa[j].charAt(0); + assertEquals(sm.getPairwiseScore(res, c2), expected[j], + 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 = "
A | B | |
---|---|---|
A | 1.0 | 2.0 |
B | 4.0 | -5.3E-10 |