From 8333f7266bd69f387a8c9c09cb844b615856a626 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Fri, 24 Mar 2017 09:57:31 +0000 Subject: [PATCH] JAL-2416 tests added for ScoreMatrix --- .../analysis/scoremodels/ScoreMatrixTest.java | 114 ++++++++++++++++++++ 1 file changed, 114 insertions(+) diff --git a/test/jalview/analysis/scoremodels/ScoreMatrixTest.java b/test/jalview/analysis/scoremodels/ScoreMatrixTest.java index 374d308..5051bf6 100644 --- a/test/jalview/analysis/scoremodels/ScoreMatrixTest.java +++ b/test/jalview/analysis/scoremodels/ScoreMatrixTest.java @@ -11,6 +11,7 @@ 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; @@ -374,4 +375,117 @@ 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(); + + /* + * 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)); + } + } } -- 1.7.10.2