import jalview.io.DataSourceType;
import jalview.io.FileParse;
import jalview.io.ScoreMatrixFile;
+import jalview.math.Matrix;
import jalview.math.MatrixI;
import jalview.schemes.ResidueProperties;
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
public class ScoreMatrixTest
{
@Test(groups = "Functional")
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);
@Test(
groups = "Functional",
- expectedExceptions = { IllegalArgumentException.class })
+ expectedExceptions =
+ { IllegalArgumentException.class })
public void testConstructor_matrixTooSmall()
{
float[][] scores = new float[2][];
@Test(
groups = "Functional",
- expectedExceptions = { IllegalArgumentException.class })
+ expectedExceptions =
+ { IllegalArgumentException.class })
public void testConstructor_matrixTooBig()
{
float[][] scores = new float[2][];
@Test(
groups = "Functional",
- expectedExceptions = { IllegalArgumentException.class })
+ expectedExceptions =
+ { IllegalArgumentException.class })
public void testConstructor_matrixNotSquare()
{
float[][] scores = new float[2][];
* @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);
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());
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^-
// 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
// 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
// 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
// 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
// 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
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();
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]));
}
}
}
* 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 });
}
/**
+ "</table>";
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));
+ }
}
git://source.jalview.org / jalview.git / blobdiff