import jalview.io.FileParse;
import jalview.io.ScoreMatrixFile;
import jalview.math.MatrixI;
+import jalview.schemes.ResidueProperties;
import java.io.IOException;
import java.net.MalformedURLException;
assertEquals(sm.getMatrixIndex('D'), 3);
assertEquals(sm.getMatrixIndex('X'), 22);
assertEquals(sm.getMatrixIndex('x'), 22);
- assertEquals(sm.getMatrixIndex(' '), 23);
+ assertEquals(sm.getMatrixIndex('-'), 23);
assertEquals(sm.getMatrixIndex('*'), 24);
assertEquals(sm.getMatrixIndex('.'), -1);
- assertEquals(sm.getMatrixIndex('-'), -1);
+ assertEquals(sm.getMatrixIndex(' '), -1);
assertEquals(sm.getMatrixIndex('?'), -1);
assertEquals(sm.getMatrixIndex((char) 128), -1);
}
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);
@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();
/*
@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();
/*
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));
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff