+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
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;
-import java.io.ByteArrayInputStream;
+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;
+
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.util.Arrays;
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
public class ScoreMatrixTest
{
@Test(groups = "Functional")
+ public void testConstructor()
+ {
+ // 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[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.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 })
+ public void testConstructor_matrixTooSmall()
+ {
+ float[][] scores = new float[2][];
+ scores[0] = new float[] { 1f, 2f };
+ scores[1] = new float[] { 3f, 4f };
+ new ScoreMatrix("Test", "ABC".toCharArray(), scores);
+ }
+
+ @Test(
+ groups = "Functional",
+ expectedExceptions =
+ { IllegalArgumentException.class })
+ public void testConstructor_matrixTooBig()
+ {
+ float[][] scores = new float[2][];
+ scores[0] = new float[] { 1f, 2f };
+ scores[1] = new float[] { 3f, 4f };
+ new ScoreMatrix("Test", "A".toCharArray(), scores);
+ }
+
+ @Test(
+ groups = "Functional",
+ expectedExceptions =
+ { IllegalArgumentException.class })
+ public void testConstructor_matrixNotSquare()
+ {
+ float[][] scores = new float[2][];
+ scores[0] = new float[] { 1f, 2f };
+ scores[1] = new float[] { 3f };
+ new ScoreMatrix("Test", "AB".toCharArray(), scores);
+ }
+
+ @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
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
/*
@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);
}
}
+ @Test(groups = "Functional")
+ public void testGetMatrix()
+ {
+ ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
+ float[][] m = sm.getMatrix();
+ assertEquals(m.length, sm.getSize());
+ assertEquals(m[2][4], -3f);
+ // verify a defensive copy is returned
+ float[][] m2 = sm.getMatrix();
+ assertNotSame(m, m2);
+ assertTrue(Arrays.deepEquals(m, m2));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetMatrixIndex()
+ {
+ ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
+ assertEquals(sm.getMatrixIndex('A'), 0);
+ assertEquals(sm.getMatrixIndex('R'), 1);
+ assertEquals(sm.getMatrixIndex('r'), 1);
+ assertEquals(sm.getMatrixIndex('N'), 2);
+ assertEquals(sm.getMatrixIndex('D'), 3);
+ assertEquals(sm.getMatrixIndex('X'), 22);
+ assertEquals(sm.getMatrixIndex('x'), 22);
+ 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);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetSize()
+ {
+ ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
+ assertEquals(sm.getMatrix().length, sm.getSize());
+ }
+
+ @Test(groups = "Functional")
+ public void testComputePairwiseScores()
+ {
+ /*
+ * NB score matrix expects '-' for gap
+ */
+ String[] seqs = new String[] { "FKL", "R-D", "QIA", "GWC" };
+ ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
+
+ MatrixI pairwise = sm.findSimilarities(seqs, SimilarityParams.Jalview);
+
+ /*
+ * should be NxN where N = number of sequences
+ */
+ assertEquals(pairwise.height(), 4);
+ assertEquals(pairwise.width(), 4);
+
+ /*
+ * should be symmetrical (because BLOSUM62 is)
+ */
+ for (int i = 0; i < pairwise.height(); i++)
+ {
+ for (int j = i + 1; j < pairwise.width(); j++)
+ {
+ assertEquals(pairwise.getValue(i, j), pairwise.getValue(j, i),
+ String.format("Not symmetric at [%d, %d]", i, j));
+ }
+ }
+ /*
+ * verify expected BLOSUM dot product scores
+ */
+ // F.F + K.K + L.L = 6 + 5 + 4 = 15
+ assertEquals(pairwise.getValue(0, 0), 15d);
+ // R.R + -.- + D.D = 5 + 1 + 6 = 12
+ assertEquals(pairwise.getValue(1, 1), 12d);
+ // Q.Q + I.I + A.A = 5 + 4 + 4 = 13
+ assertEquals(pairwise.getValue(2, 2), 13d);
+ // G.G + W.W + C.C = 6 + 11 + 9 = 26
+ assertEquals(pairwise.getValue(3, 3), 26d);
+ // F.R + K.- + L.D = -3 + -4 + -4 = -11
+ assertEquals(pairwise.getValue(0, 1), -11d);
+ // F.Q + K.I + L.A = -3 + -3 + -1 = -7
+ assertEquals(pairwise.getValue(0, 2), -7d);
+ // F.G + K.W + L.C = -3 + -3 + -1 = -7
+ assertEquals(pairwise.getValue(0, 3), -7d);
+ // R.Q + -.I + D.A = 1 + -4 + -2 = -5
+ assertEquals(pairwise.getValue(1, 2), -5d);
+ // R.G + -.W + D.C = -2 + -4 + -3 = -9
+ assertEquals(pairwise.getValue(1, 3), -9d);
+ // Q.G + I.W + A.C = -2 + -3 + 0 = -5
+ assertEquals(pairwise.getValue(2, 3), -5d);
+ }
+
+ /**
+ * Test that the result of outputMatrix can be reparsed to give an identical
+ * ScoreMatrix
+ *
+ * @throws IOException
+ * @throws MalformedURLException
+ */
+ @Test(groups = "Functional")
+ public void testOutputMatrix_roundTrip()
+ throws MalformedURLException, IOException
+ {
+ ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
+ String output = sm.outputMatrix(false);
+ FileParse fp = new FileParse(output, DataSourceType.PASTE);
+ ScoreMatrixFile parser = new ScoreMatrixFile(fp);
+ ScoreMatrix sm2 = parser.parseMatrix();
+ assertNotNull(sm2);
+ assertTrue(sm2.equals(sm));
+ }
+
+ @Test(groups = "Functional")
+ public void testEqualsAndHashCode()
+ {
+ ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
+ 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"));
+ }
+
/**
- * Test a successful parse of a (small) score matrix file
+ * Tests for scoring options where the longer length of two sequences is used
*/
@Test(groups = "Functional")
- public void testParse()
+ public void testcomputeSimilarity_matchLongestSequence()
{
/*
- * some messy but valid input data, with comma, space
- * or tab (or combinations) as score value delimiters
- * this example includes 'guide' symbols on score rows
+ * ScoreMatrix expects '-' for gaps
+ */
+ 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);
+ 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^-
+ * = 6 + -1 + 0 + -4 + -4 + -4 = -7
*/
- String data = "ScoreMatrix MyTest\n" + "ATU tx-\n"
- + "A,1.1,1.2,1.3,1.4, 1.5, 1.6, 1.7\n"
- + "T,2.1 2.2 2.3 2.4 2.5 2.6 2.7\n"
- + "U\t3.1\t3.2\t3.3\t3.4\t3.5\t3.6\t3.7\n"
- + " 4.1 ,4.2,\t,4.3 ,\t4.4\t, \4.5,4.6 4.7\n"
- + "t, 5.1,5.3,5.3,5.4,5.5, 5.6, 5.7\n"
- + "x\t6.1, 6.2 6.3 6.4 6.5 6.6 6.7\n"
- + "-, \t7.1\t7.2 7.3, 7.4, 7.5\t,7.6,7.7\n";
- ScoreMatrix sm = ScoreMatrix.parse(new ByteArrayInputStream(data
- .getBytes()));
- assertNotNull(sm);
- assertEquals(sm.getName(), "MyTest");
- assertTrue(sm.isDNA());
- assertFalse(sm.isProtein());
- assertEquals(sm.getPairwiseScore('A', 'A'), 1.1f);
- assertEquals(sm.getPairwiseScore('A', 'T'), 1.2f);
- assertEquals(sm.getPairwiseScore('a', 'T'), 1.2f); // A/a equivalent
- assertEquals(sm.getPairwiseScore('A', 't'), 1.5f); // T/t not equivalent
- assertEquals(sm.getPairwiseScore('a', 't'), 1.5f);
- assertEquals(sm.getPairwiseScore('T', ' '), 2.4f);
- assertEquals(sm.getPairwiseScore('U', 'x'), 3.6f);
- assertEquals(sm.getPairwiseScore('u', 'x'), 3.6f);
- assertEquals(sm.getPairwiseScore('U', 'X'), 0f); // X (upper) unmapped
- assertEquals(sm.getPairwiseScore('A', '.'), 0f); // . unmapped
- assertEquals(sm.getPairwiseScore('-', '-'), 7.7f);
- assertEquals(sm.getPairwiseScore('A', (char) 128), 0f); // out of range
+ params = new SimilarityParams(false, true, true, false);
+ assertEquals(blosum.computeSimilarity(s1, s2, params), -7d);
+ // matchGap (arg2) is ignored:
+ params = new SimilarityParams(false, false, true, false);
+ assertEquals(blosum.computeSimilarity(s1, s2, params), -7d);
/*
- * without guide symbols on score rows
+ * score gap-gap but not gap-char
+ * score = F^F + R^S + -^- + 0 + 0 + 0
+ * = 6 + -1 + 1 = 6
*/
- data = "ScoreMatrix MyTest\nXY\n1 2\n3 4\n";
- sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
- assertNotNull(sm);
- assertEquals(sm.getPairwiseScore('X', 'X'), 1f);
- assertEquals(sm.getPairwiseScore('X', 'y'), 2f);
- assertEquals(sm.getPairwiseScore('y', 'x'), 3f);
- assertEquals(sm.getPairwiseScore('y', 'Y'), 4f);
- assertEquals(sm.getPairwiseScore('D', 'R'), 0f);
+ params = new SimilarityParams(true, false, false, false);
+ assertEquals(blosum.computeSimilarity(s1, s2, params), 6d);
+ // 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
+ * = 6 + -1 = 5
+ */
+ params = new SimilarityParams(false, false, false, false);
+ assertEquals(blosum.computeSimilarity(s1, s2, params), 5d);
+ // matchGap (arg2) is ignored:
+ params = new SimilarityParams(false, true, false, false);
+ assertEquals(blosum.computeSimilarity(s1, s2, params), 5d);
}
+ /**
+ * Tests for scoring options where only the shorter length of two sequences is
+ * used
+ */
@Test(groups = "Functional")
- public void testParse_invalidInput()
+ public void testcomputeSimilarity_matchShortestSequence()
{
/*
- * valid first
+ * ScoreMatrix expects '-' for gaps
*/
- String data = "ScoreMatrix MyTest\nXY\n1 2\n3 4\n";
- ScoreMatrix sm = ScoreMatrix.parse(new ByteArrayInputStream(data
- .getBytes()));
- assertNotNull(sm);
+ String s1 = "FR-K-S";
+ String s2 = "FS--L";
+ ScoreMatrix blosum = ScoreModels.getInstance().getBlosum62();
/*
- * Name missing
+ * score gap-gap and gap-char
+ * match shorter sequence only
+ * score = F^F + R^S + -^- + K^- + -^L
+ * = 6 + -1 + 1 + -4 + -4 = -2
*/
- data = "ScoreMatrix\nXY\n1 2\n3 4\n";
- sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
- assertNull(sm);
+ SimilarityParamsI params = new SimilarityParams(true, true, true, true);
+ assertEquals(blosum.computeSimilarity(s1, s2, params), -2d);
+ // matchGap (arg2) is ignored:
+ params = new SimilarityParams(true, false, true, true);
+ assertEquals(blosum.computeSimilarity(s1, s2, params), -2d);
/*
- * ScoreMatrix header missing
+ * score gap-char but not gap-gap
+ * score = F^F + R^S + 0 + K^- + -^L
+ * = 6 + -1 + 0 + -4 + -4 = -3
*/
- data = "XY\n1 2\n3 4\n";
- sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
- assertNull(sm);
+ params = new SimilarityParams(false, true, true, true);
+ assertEquals(blosum.computeSimilarity(s1, s2, params), -3d);
+ // matchGap (arg2) is ignored:
+ params = new SimilarityParams(false, false, true, true);
+ assertEquals(blosum.computeSimilarity(s1, s2, params), -3d);
/*
- * Not enough rows
+ * score gap-gap but not gap-char
+ * score = F^F + R^S + -^- + 0 + 0
+ * = 6 + -1 + 1 = 6
*/
- data = "ScoreMatrix MyTest\nXY\n1 2\n";
- sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
- assertNull(sm);
+ params = new SimilarityParams(true, false, false, true);
+ assertEquals(blosum.computeSimilarity(s1, s2, params), 6d);
+ // matchGap (arg2) is ignored:
+ params = new SimilarityParams(true, true, false, true);
+ assertEquals(blosum.computeSimilarity(s1, s2, params), 6d);
/*
- * Not enough columns
+ * score neither gap-gap nor gap-char
+ * score = F^F + R^S + 0 + 0 + 0
+ * = 6 + -1 = 5
*/
- data = "ScoreMatrix MyTest\nXY\n1 2\n3\n";
- sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
- assertNull(sm);
+ params = new SimilarityParams(false, false, false, true);
+ assertEquals(blosum.computeSimilarity(s1, s2, params), 5d);
+ // matchGap (arg2) is ignored:
+ 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
+ }
+
+ /**
+ * 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();
+ 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 = "<table border=\"1\"><tr><th></th><th> A </th><th> B </th></tr>\n"
+ + "<tr><td>A</td><td>1.0</td><td>2.0</td></tr>\n"
+ + "<tr><td>B</td><td>4.0</td><td>-5.3E-10</td></tr>\n"
+ + "</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());
/*
- * Too many columns
+ * 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
*/
- data = "ScoreMatrix MyTest\nXY\n1 2\n3 4 5\n";
- sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
- assertNull(sm);
+ 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));
/*
- * Too many rows
+ * 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
*/
- data = "ScoreMatrix MyTest\nXY\n1 2\n3 4\n6 7";
- sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
- assertNull(sm);
+ 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));
/*
- * unsupported delimiter |
+ * 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
*/
- data = "ScoreMatrix MyTest\nXY\n1|2\n3|4\n";
- sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
- assertNull(sm);
+ 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));
/*
- * Bad float value
+ * reverse order of sequences
+ * - reverses order of main diagonal
+ * - reflects off-diagonal values
*/
- data = "ScoreMatrix MyTest\nXY\n1 2\n3 four\n";
- sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
- assertNull(sm);
+ res2 = sm.findSimilarities(seqs2, params);
+ assertFalse(res1.equals(res2));
+ assertTrue(
+ res2.equals(new Matrix(new double[][]
+ { { 16d, 11d }, { 7d, 14d } }), delta));
/*
- * Bad guide character on scores row
+ * verify that forcing an asymmetric matrix to use
+ * symmetric calculation gives a different (wrong) result
*/
- data = "ScoreMatrix MyTest\nXY\nX 1 2\ny 3 4\n";
- sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
- assertNull(sm);
+ 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