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package jalview.analysis.scoremodels; |
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import static org.testng.Assert.assertEquals; |
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import static org.testng.Assert.assertFalse; |
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import static org.testng.Assert.assertNotEquals; |
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import static org.testng.Assert.assertNotNull; |
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import static org.testng.Assert.assertNotSame; |
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import static org.testng.Assert.assertNull; |
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import static org.testng.Assert.assertTrue; |
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import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals; |
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import jalview.api.analysis.SimilarityParamsI; |
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import jalview.io.DataSourceType; |
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import jalview.io.FileParse; |
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import jalview.io.ScoreMatrixFile; |
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import jalview.math.MatrixI; |
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import jalview.schemes.ResidueProperties; |
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import java.io.IOException; |
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import java.net.MalformedURLException; |
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import java.util.Arrays; |
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import org.testng.annotations.Test; |
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| 100% |
Uncovered Elements: 0 (274) |
Complexity: 33 |
Complexity Density: 0.14 |
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public class ScoreMatrixTest |
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{ |
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| 100% |
Uncovered Elements: 0 (15) |
Complexity: 1 |
Complexity Density: 0.07 |
1PASS
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@Test(groups = "Functional")... |
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public void testConstructor() |
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{ |
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float[][] scores = new float[3][]; |
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scores[0] = new float[] { 1f, 2f, 3f }; |
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scores[1] = new float[] { -4f, 5f, 6f }; |
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scores[2] = new float[] { 7f, 8f, 9f }; |
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ScoreMatrix sm = new ScoreMatrix("Test", "ABC".toCharArray(), scores); |
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assertEquals(sm.getSize(), 3); |
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assertArrayEquals(scores, sm.getMatrix()); |
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assertEquals(sm.getPairwiseScore('A', 'a'), 1f); |
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assertEquals(sm.getPairwiseScore('b', 'c'), 6f); |
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assertEquals(sm.getPairwiseScore('c', 'b'), 8f); |
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assertEquals(sm.getMatrixIndex('c'), 2); |
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assertEquals(sm.getMatrixIndex(' '), -1); |
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assertEquals(sm.getPairwiseScore('A', 'D'), -4f); |
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assertEquals(sm.getPairwiseScore('D', 'A'), -4f); |
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assertEquals(sm.getPairwiseScore('D', 'D'), 1f); |
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} |
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| 100% |
Uncovered Elements: 0 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
1PASS
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@Test(... |
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groups = "Functional", |
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expectedExceptions = { IllegalArgumentException.class }) |
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public void testConstructor_matrixTooSmall() |
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{ |
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float[][] scores = new float[2][]; |
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scores[0] = new float[] { 1f, 2f }; |
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scores[1] = new float[] { 3f, 4f }; |
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new ScoreMatrix("Test", "ABC".toCharArray(), scores); |
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} |
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| 100% |
Uncovered Elements: 0 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
1PASS
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@Test(... |
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groups = "Functional", |
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expectedExceptions = { IllegalArgumentException.class }) |
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public void testConstructor_matrixTooBig() |
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{ |
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float[][] scores = new float[2][]; |
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scores[0] = new float[] { 1f, 2f }; |
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scores[1] = new float[] { 3f, 4f }; |
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new ScoreMatrix("Test", "A".toCharArray(), scores); |
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} |
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| 100% |
Uncovered Elements: 0 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
1PASS
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@Test(... |
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groups = "Functional", |
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expectedExceptions = { IllegalArgumentException.class }) |
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public void testConstructor_matrixNotSquare() |
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{ |
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float[][] scores = new float[2][]; |
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scores[0] = new float[] { 1f, 2f }; |
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scores[1] = new float[] { 3f }; |
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new ScoreMatrix("Test", "AB".toCharArray(), scores); |
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} |
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| 100% |
Uncovered Elements: 0 (22) |
Complexity: 3 |
Complexity Density: 0.17 |
1PASS
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@Test(groups = "Functional")... |
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public void testBuildSymbolIndex() |
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{ |
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float[][] scores = new float[2][]; |
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scores[0] = new float[] { 1f, 2f }; |
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scores[1] = new float[] { 3f, 4f }; |
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ScoreMatrix sm = new ScoreMatrix("Test", new char[] { 'A', '.' }, |
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scores); |
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short[] index = sm.buildSymbolIndex("AX-yxYp".toCharArray()); |
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assertEquals(index.length, 128); |
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assertEquals(index['A'], 0); |
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assertEquals(index['a'], 0); |
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assertEquals(index['X'], 1); |
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assertEquals(index['-'], 2); |
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assertEquals(index['y'], 3); |
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assertEquals(index['x'], 4); |
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assertEquals(index['Y'], 5); |
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assertEquals(index['p'], 6); |
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assertEquals(index['P'], -1); |
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for (int c = 0; c < index.length; c++) |
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{ |
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if (!"AaXx-. Yyp".contains(String.valueOf((char) c))) |
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{ |
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assertEquals(index[c], -1); |
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} |
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} |
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} |
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| 100% |
Uncovered Elements: 0 (16) |
Complexity: 4 |
Complexity Density: 0.33 |
1PASS
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1 |
@Test(groups = "Functional")... |
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public void testBuildSymbolIndex_nonAscii() |
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{ |
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float[][] scores = new float[2][]; |
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scores[0] = new float[] { 1f, 2f }; |
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scores[1] = new float[] { 3f, 4f }; |
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ScoreMatrix sm = new ScoreMatrix("Test", new char[] { 'A', '.' }, |
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scores); |
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char[] weird = new char[] { 128, 245, 'P' }; |
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short[] index = sm.buildSymbolIndex(weird); |
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assertEquals(index.length, 128); |
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assertEquals(index['P'], 2); |
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assertEquals(index['p'], 2); |
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for (int c = 0; c < index.length; c++) |
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{ |
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if (c != 'P' && c != 'p') |
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{ |
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assertEquals(index[c], -1); |
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} |
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} |
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} |
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| 100% |
Uncovered Elements: 0 (7) |
Complexity: 1 |
Complexity Density: 0.14 |
1PASS
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@Test(groups = "Functional")... |
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public void testGetMatrix() |
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{ |
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ScoreMatrix sm = ScoreModels.getInstance().getBlosum62(); |
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float[][] m = sm.getMatrix(); |
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assertEquals(m.length, sm.getSize()); |
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assertEquals(m[2][4], -3f); |
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float[][] m2 = sm.getMatrix(); |
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assertNotSame(m, m2); |
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assertTrue(Arrays.deepEquals(m, m2)); |
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} |
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| 100% |
Uncovered Elements: 0 (14) |
Complexity: 1 |
Complexity Density: 0.07 |
1PASS
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156 |
1 |
@Test(groups = "Functional")... |
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public void testGetMatrixIndex() |
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{ |
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ScoreMatrix sm = ScoreModels.getInstance().getBlosum62(); |
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assertEquals(sm.getMatrixIndex('A'), 0); |
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assertEquals(sm.getMatrixIndex('R'), 1); |
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assertEquals(sm.getMatrixIndex('r'), 1); |
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assertEquals(sm.getMatrixIndex('N'), 2); |
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assertEquals(sm.getMatrixIndex('D'), 3); |
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assertEquals(sm.getMatrixIndex('X'), 22); |
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assertEquals(sm.getMatrixIndex('x'), 22); |
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assertEquals(sm.getMatrixIndex('-'), -1); |
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assertEquals(sm.getMatrixIndex('*'), 23); |
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assertEquals(sm.getMatrixIndex('.'), -1); |
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assertEquals(sm.getMatrixIndex(' '), -1); |
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assertEquals(sm.getMatrixIndex('?'), -1); |
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assertEquals(sm.getMatrixIndex((char) 128), -1); |
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} |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
1PASS
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175 |
1 |
@Test(groups = "Functional")... |
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public void testGetSize() |
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{ |
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ScoreMatrix sm = ScoreModels.getInstance().getBlosum62(); |
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assertEquals(sm.getMatrix().length, sm.getSize()); |
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} |
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| 100% |
Uncovered Elements: 0 (22) |
Complexity: 3 |
Complexity Density: 0.17 |
1PASS
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182 |
1 |
@Test(groups = "Functional")... |
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public void testComputePairwiseScores() |
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{ |
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String[] seqs = new String[] { "FKL", "R-D", "QIA", "GWC" }; |
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ScoreMatrix sm = ScoreModels.getInstance().getBlosum62(); |
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MatrixI pairwise = sm.findSimilarities(seqs, SimilarityParams.Jalview); |
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assertEquals(pairwise.height(), 4); |
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assertEquals(pairwise.width(), 4); |
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for (int i = 0; i < pairwise.height(); i++) |
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{ |
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for (int j = i + 1; j < pairwise.width(); j++) |
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{ |
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assertEquals(pairwise.getValue(i, j), pairwise.getValue(j, i), |
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String.format("Not symmetric at [%d, %d]", i, j)); |
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} |
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} |
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assertEquals(pairwise.getValue(0, 0), 15d); |
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assertEquals(pairwise.getValue(1, 1), 12d); |
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assertEquals(pairwise.getValue(2, 2), 13d); |
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assertEquals(pairwise.getValue(3, 3), 26d); |
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assertEquals(pairwise.getValue(0, 1), -11d); |
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assertEquals(pairwise.getValue(0, 2), -7d); |
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assertEquals(pairwise.getValue(0, 3), -7d); |
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assertEquals(pairwise.getValue(1, 2), -5d); |
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assertEquals(pairwise.getValue(1, 3), -9d); |
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assertEquals(pairwise.getValue(2, 3), -5d); |
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} |
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@throws |
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@throws |
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| 100% |
Uncovered Elements: 0 (7) |
Complexity: 1 |
Complexity Density: 0.14 |
1PASS
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242 |
1 |
@Test(groups = "Functional")... |
243 |
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public void testOutputMatrix_roundTrip() throws MalformedURLException, |
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IOException |
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{ |
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ScoreMatrix sm = ScoreModels.getInstance().getBlosum62(); |
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String output = sm.outputMatrix(false); |
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FileParse fp = new FileParse(output, DataSourceType.PASTE); |
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ScoreMatrixFile parser = new ScoreMatrixFile(fp); |
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ScoreMatrix sm2 = parser.parseMatrix(); |
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assertNotNull(sm2); |
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assertTrue(sm2.equals(sm)); |
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} |
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| 100% |
Uncovered Elements: 0 (8) |
Complexity: 1 |
Complexity Density: 0.12 |
1PASS
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255 |
1 |
@Test(groups = "Functional")... |
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public void testEqualsAndHashCode() |
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{ |
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ScoreMatrix sm = ScoreModels.getInstance().getBlosum62(); |
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ScoreMatrix sm2 = new ScoreMatrix(sm.getName(), sm.getSymbols() |
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.toCharArray(), sm.getMatrix()); |
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assertTrue(sm.equals(sm2)); |
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assertEquals(sm.hashCode(), sm2.hashCode()); |
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sm2 = ScoreModels.getInstance().getPam250(); |
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assertFalse(sm.equals(sm2)); |
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assertNotEquals(sm.hashCode(), sm2.hashCode()); |
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assertFalse(sm.equals("hello")); |
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} |
270 |
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271 |
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272 |
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273 |
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| 100% |
Uncovered Elements: 0 (19) |
Complexity: 1 |
Complexity Density: 0.05 |
1PASS
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274 |
1 |
@Test(groups = "Functional")... |
275 |
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public void testcomputeSimilarity_matchLongestSequence() |
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{ |
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String s1 = "FR-K-S"; |
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String s2 = "FS--L"; |
282 |
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ScoreMatrix blosum = ScoreModels.getInstance().getBlosum62(); |
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SimilarityParamsI params = new SimilarityParams(true, true, true, false); |
291 |
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assertEquals(blosum.computeSimilarity(s1, s2, params), -6d); |
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params = new SimilarityParams(true, false, true, false); |
294 |
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assertEquals(blosum.computeSimilarity(s1, s2, params), -6d); |
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297 |
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298 |
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299 |
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300 |
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params = new SimilarityParams(false, true, true, false); |
302 |
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assertEquals(blosum.computeSimilarity(s1, s2, params), -7d); |
303 |
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304 |
1 |
params = new SimilarityParams(false, false, true, false); |
305 |
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assertEquals(blosum.computeSimilarity(s1, s2, params), -7d); |
306 |
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307 |
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308 |
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309 |
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310 |
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311 |
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312 |
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params = new SimilarityParams(true, false, false, false); |
313 |
1 |
assertEquals(blosum.computeSimilarity(s1, s2, params), 6d); |
314 |
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315 |
1 |
params = new SimilarityParams(true, true, false, false); |
316 |
1 |
assertEquals(blosum.computeSimilarity(s1, s2, params), 6d); |
317 |
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318 |
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319 |
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320 |
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321 |
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322 |
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323 |
1 |
params = new SimilarityParams(false, false, false, false); |
324 |
1 |
assertEquals(blosum.computeSimilarity(s1, s2, params), 5d); |
325 |
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326 |
1 |
params = new SimilarityParams(false, true, false, false); |
327 |
1 |
assertEquals(blosum.computeSimilarity(s1, s2, params), 5d); |
328 |
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} |
329 |
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330 |
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331 |
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332 |
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333 |
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| 100% |
Uncovered Elements: 0 (19) |
Complexity: 1 |
Complexity Density: 0.05 |
1PASS
|
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334 |
1 |
@Test(groups = "Functional")... |
335 |
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public void testcomputeSimilarity_matchShortestSequence() |
336 |
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{ |
337 |
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338 |
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339 |
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340 |
1 |
String s1 = "FR-K-S"; |
341 |
1 |
String s2 = "FS--L"; |
342 |
1 |
ScoreMatrix blosum = ScoreModels.getInstance().getBlosum62(); |
343 |
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344 |
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345 |
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346 |
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347 |
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348 |
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349 |
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350 |
1 |
SimilarityParamsI params = new SimilarityParams(true, true, true, true); |
351 |
1 |
assertEquals(blosum.computeSimilarity(s1, s2, params), -2d); |
352 |
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353 |
1 |
params = new SimilarityParams(true, false, true, true); |
354 |
1 |
assertEquals(blosum.computeSimilarity(s1, s2, params), -2d); |
355 |
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356 |
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357 |
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358 |
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359 |
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360 |
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361 |
1 |
params = new SimilarityParams(false, true, true, true); |
362 |
1 |
assertEquals(blosum.computeSimilarity(s1, s2, params), -3d); |
363 |
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|
364 |
1 |
params = new SimilarityParams(false, false, true, true); |
365 |
1 |
assertEquals(blosum.computeSimilarity(s1, s2, params), -3d); |
366 |
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367 |
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368 |
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369 |
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370 |
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371 |
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372 |
1 |
params = new SimilarityParams(true, false, false, true); |
373 |
1 |
assertEquals(blosum.computeSimilarity(s1, s2, params), 6d); |
374 |
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|
375 |
1 |
params = new SimilarityParams(true, true, false, true); |
376 |
1 |
assertEquals(blosum.computeSimilarity(s1, s2, params), 6d); |
377 |
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378 |
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379 |
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380 |
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381 |
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382 |
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383 |
1 |
params = new SimilarityParams(false, false, false, true); |
384 |
1 |
assertEquals(blosum.computeSimilarity(s1, s2, params), 5d); |
385 |
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386 |
1 |
params = new SimilarityParams(false, true, false, true); |
387 |
1 |
assertEquals(blosum.computeSimilarity(s1, s2, params), 5d); |
388 |
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} |
389 |
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|
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| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
1PASS
|
|
390 |
1 |
@Test(groups = "Functional")... |
391 |
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public void testSymmetric() |
392 |
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{ |
393 |
1 |
verifySymmetric(ScoreModels.getInstance().getBlosum62()); |
394 |
1 |
verifySymmetric(ScoreModels.getInstance().getPam250()); |
395 |
1 |
verifySymmetric(ScoreModels.getInstance().getDefaultModel(false)); |
396 |
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} |
397 |
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|
|
|
| 100% |
Uncovered Elements: 0 (10) |
Complexity: 3 |
Complexity Density: 0.5 |
|
398 |
3 |
private void verifySymmetric(ScoreMatrix sm)... |
399 |
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{ |
400 |
3 |
float[][] m = sm.getMatrix(); |
401 |
3 |
int rows = m.length; |
402 |
62 |
for (int row = 0; row < rows; row++) |
403 |
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{ |
404 |
59 |
assertEquals(m[row].length, rows); |
405 |
1332 |
for (int col = 0; col < rows; col++) |
406 |
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{ |
407 |
1273 |
assertEquals(m[row][col], m[col][row], String.format("%s [%s, %s]", |
408 |
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sm.getName(), ResidueProperties.aa[row], |
409 |
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ResidueProperties.aa[col])); |
410 |
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} |
411 |
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} |
412 |
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} |
413 |
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414 |
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|
415 |
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|
416 |
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|
|
|
| 100% |
Uncovered Elements: 0 (27) |
Complexity: 1 |
Complexity Density: 0.04 |
1PASS
|
|
417 |
1 |
@Test(groups = "Functional")... |
418 |
|
public void testBlosum62_values() |
419 |
|
{ |
420 |
1 |
ScoreMatrix sm = ScoreModels.getInstance().getBlosum62(); |
421 |
|
|
422 |
1 |
assertTrue(sm.isProtein()); |
423 |
1 |
assertFalse(sm.isDNA()); |
424 |
1 |
assertNull(sm.getDescription()); |
425 |
|
|
426 |
|
|
427 |
|
|
428 |
|
|
429 |
|
|
430 |
1 |
verifyValues(sm, 'A', new float[] { 4, -1, -2, -2, 0, -1, -1, 0, -2, |
431 |
|
-1, |
432 |
|
-1, -1, -1, -2, -1, 1, 0, -3, -2, 0, -2, -1, 0 }); |
433 |
1 |
verifyValues(sm, 'R', new float[] { -1, 5, 0, -2, -3, 1, 0, -2, 0, -3, |
434 |
|
-2, 2, -1, -3, -2, -1, -1, -3, -2, -3, -1, 0, -1 }); |
435 |
1 |
verifyValues(sm, 'N', new float[] { -2, 0, 6, 1, -3, 0, 0, 0, 1, -3, |
436 |
|
-3, |
437 |
|
0, -2, -3, -2, 1, 0, -4, -2, -3, 3, 0, -1 }); |
438 |
1 |
verifyValues(sm, 'D', new float[] { -2, -2, 1, 6, -3, 0, 2, -1, -1, -3, |
439 |
|
-4, -1, -3, -3, -1, 0, -1, -4, -3, -3, 4, 1, -1 }); |
440 |
1 |
verifyValues(sm, 'C', new float[] { 0, -3, -3, -3, 9, -3, -4, -3, -3, |
441 |
|
-1, |
442 |
|
-1, -3, -1, -2, -3, -1, -1, -2, -2, -1, -3, -3, -2 }); |
443 |
1 |
verifyValues(sm, 'Q', new float[] { -1, 1, 0, 0, -3, 5, 2, -2, 0, -3, |
444 |
|
-2, |
445 |
|
1, 0, -3, -1, 0, -1, -2, -1, -2, 0, 3, -1 }); |
446 |
1 |
verifyValues(sm, 'E', new float[] { -1, 0, 0, 2, -4, 2, 5, -2, 0, -3, |
447 |
|
-3, |
448 |
|
1, -2, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1 }); |
449 |
1 |
verifyValues(sm, 'G', new float[] { 0, -2, 0, -1, -3, -2, -2, 6, -2, |
450 |
|
-4, |
451 |
|
-4, -2, -3, -3, -2, 0, -2, -2, -3, -3, -1, -2, -1 }); |
452 |
1 |
verifyValues(sm, 'H', new float[] { -2, 0, 1, -1, -3, 0, 0, -2, 8, -3, |
453 |
|
-3, -1, -2, -1, -2, -1, -2, -2, 2, -3, 0, 0, -1 }); |
454 |
1 |
verifyValues(sm, 'I', new float[] { -1, -3, -3, -3, -1, -3, -3, -4, -3, |
455 |
|
4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3, -3, -3, -1 }); |
456 |
1 |
verifyValues(sm, 'L', new float[] { -1, -2, -3, -4, -1, -2, -3, -4, -3, |
457 |
|
2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1, -4, -3, -1 }); |
458 |
1 |
verifyValues(sm, 'K', new float[] { -1, 2, 0, -1, -3, 1, 1, -2, -1, -3, |
459 |
|
-2, 5, -1, -3, -1, 0, -1, -3, -2, -2, 0, 1, -1 }); |
460 |
1 |
verifyValues(sm, 'M', new float[] { -1, -1, -2, -3, -1, 0, -2, -3, -2, |
461 |
|
1, |
462 |
|
2, -1, 5, 0, -2, -1, -1, -1, -1, 1, -3, -1, -1 }); |
463 |
1 |
verifyValues(sm, 'F', new float[] { -2, -3, -3, -3, -2, -3, -3, -3, -1, |
464 |
|
0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1, -3, -3, -1 }); |
465 |
1 |
verifyValues(sm, 'P', new float[] { -1, -2, -2, -1, -3, -1, -1, -2, -2, |
466 |
|
-3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2, -2, -1, -2 }); |
467 |
1 |
verifyValues(sm, 'S', new float[] { 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, |
468 |
|
-2, |
469 |
|
0, -1, -2, -1, 4, 1, -3, -2, -2, 0, 0, 0 }); |
470 |
1 |
verifyValues(sm, 'T', new float[] { 0, -1, 0, -1, -1, -1, -1, -2, -2, |
471 |
|
-1, |
472 |
|
-1, -1, -1, -2, -1, 1, 5, -2, -2, 0, -1, -1, 0 }); |
473 |
1 |
verifyValues(sm, 'W', new float[] { -3, -3, -4, -4, -2, -2, -3, -2, -2, |
474 |
|
-3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3, -4, -3, -2 }); |
475 |
1 |
verifyValues(sm, 'Y', new float[] { -2, -2, -2, -3, -2, -1, -2, -3, 2, |
476 |
|
-1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1, -3, -2, -1 }); |
477 |
1 |
verifyValues(sm, 'V', new float[] { 0, -3, -3, -3, -1, -2, -2, -3, -3, |
478 |
|
3, |
479 |
|
1, -2, 1, -1, -2, -2, 0, -3, -1, 4, -3, -2, -1 }); |
480 |
1 |
verifyValues(sm, 'B', new float[] { -2, -1, 3, 4, -3, 0, 1, -1, 0, -3, |
481 |
|
-4, 0, -3, -3, -2, 0, -1, -4, -3, -3, 4, 1, -1 }); |
482 |
1 |
verifyValues(sm, 'Z', new float[] { -1, 0, 0, 1, -3, 3, 4, -2, 0, -3, |
483 |
|
-3, |
484 |
|
1, -1, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1 }); |
485 |
1 |
verifyValues(sm, 'X', new float[] { 0, -1, -1, -1, -2, -1, -1, -1, -1, |
486 |
|
-1, -1, -1, -1, -1, -2, 0, 0, -2, -1, -1, -1, -1, -1 }); |
487 |
|
} |
488 |
|
|
489 |
|
|
490 |
|
|
491 |
|
|
492 |
|
@param |
493 |
|
@param |
494 |
|
@param |
495 |
|
|
496 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
497 |
23 |
private void verifyValues(ScoreMatrix sm, char res, float[] expected)... |
498 |
|
{ |
499 |
552 |
for (int j = 0; j < expected.length; j++) |
500 |
|
{ |
501 |
529 |
char c2 = ResidueProperties.aa[j].charAt(0); |
502 |
529 |
assertEquals(sm.getPairwiseScore(res, c2), expected[j], |
503 |
|
String.format("%s->%s", res, c2)); |
504 |
|
} |
505 |
|
} |
506 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (15) |
Complexity: 1 |
Complexity Density: 0.07 |
1PASS
|
|
507 |
1 |
@Test(groups = "Functional")... |
508 |
|
public void testConstructor_gapDash() |
509 |
|
{ |
510 |
1 |
float[][] scores = new float[2][]; |
511 |
1 |
scores[0] = new float[] { 1f, 2f }; |
512 |
1 |
scores[1] = new float[] { 4f, 5f }; |
513 |
1 |
ScoreMatrix sm = new ScoreMatrix("Test", new char[] { 'A', '-' }, |
514 |
|
scores); |
515 |
1 |
assertEquals(sm.getSize(), 2); |
516 |
1 |
assertArrayEquals(scores, sm.getMatrix()); |
517 |
1 |
assertEquals(sm.getPairwiseScore('A', 'a'), 1f); |
518 |
1 |
assertEquals(sm.getPairwiseScore('A', 'A'), 1f); |
519 |
1 |
assertEquals(sm.getPairwiseScore('a', '-'), 2f); |
520 |
1 |
assertEquals(sm.getPairwiseScore('-', 'A'), 4f); |
521 |
1 |
assertEquals(sm.getMatrixIndex('a'), 0); |
522 |
1 |
assertEquals(sm.getMatrixIndex('A'), 0); |
523 |
1 |
assertEquals(sm.getMatrixIndex('-'), 1); |
524 |
1 |
assertEquals(sm.getMatrixIndex(' '), -1); |
525 |
1 |
assertEquals(sm.getMatrixIndex('.'), -1); |
526 |
|
} |
527 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (17) |
Complexity: 1 |
Complexity Density: 0.06 |
1PASS
|
|
528 |
1 |
@Test(groups = "Functional")... |
529 |
|
public void testGetPairwiseScore() |
530 |
|
{ |
531 |
1 |
float[][] scores = new float[2][]; |
532 |
1 |
scores[0] = new float[] { 1f, 2f }; |
533 |
1 |
scores[1] = new float[] { -4f, 5f }; |
534 |
1 |
ScoreMatrix sm = new ScoreMatrix("Test", new char[] { 'A', 'B' }, |
535 |
|
scores); |
536 |
1 |
assertEquals(sm.getPairwiseScore('A', 'A'), 1f); |
537 |
1 |
assertEquals(sm.getPairwiseScore('A', 'a'), 1f); |
538 |
1 |
assertEquals(sm.getPairwiseScore('A', 'B'), 2f); |
539 |
1 |
assertEquals(sm.getPairwiseScore('b', 'a'), -4f); |
540 |
1 |
assertEquals(sm.getPairwiseScore('B', 'b'), 5f); |
541 |
|
|
542 |
|
|
543 |
|
|
544 |
|
|
545 |
|
|
546 |
1 |
assertEquals(sm.getPairwiseScore('A', '-'), -4f); |
547 |
1 |
assertEquals(sm.getPairwiseScore('-', 'A'), -4f); |
548 |
1 |
assertEquals(sm.getPairwiseScore('-', '-'), 1f); |
549 |
1 |
assertEquals(sm.getPairwiseScore('Q', 'W'), -4f); |
550 |
1 |
assertEquals(sm.getPairwiseScore('Q', 'Q'), 1f); |
551 |
|
|
552 |
|
|
553 |
|
|
554 |
|
|
555 |
1 |
char c = (char) 200; |
556 |
1 |
assertEquals(sm.getPairwiseScore('Q', c), 0f); |
557 |
1 |
assertEquals(sm.getPairwiseScore(c, 'Q'), 0f); |
558 |
|
} |
559 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
1PASS
|
|
560 |
1 |
@Test(groups = "Functional")... |
561 |
|
public void testGetMinimumScore() |
562 |
|
{ |
563 |
1 |
ScoreMatrix sm = ScoreModels.getInstance().getBlosum62(); |
564 |
1 |
assertEquals(sm.getMinimumScore(), -4f); |
565 |
|
} |
566 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
1PASS
|
|
567 |
1 |
@Test(groups = "Functional")... |
568 |
|
public void testGetMaximumScore() |
569 |
|
{ |
570 |
1 |
ScoreMatrix sm = ScoreModels.getInstance().getBlosum62(); |
571 |
1 |
assertEquals(sm.getMaximumScore(), 11f); |
572 |
|
} |
573 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (7) |
Complexity: 1 |
Complexity Density: 0.14 |
1PASS
|
|
574 |
1 |
@Test(groups = "Functional")... |
575 |
|
public void testOutputMatrix_html() |
576 |
|
{ |
577 |
1 |
float[][] scores = new float[2][]; |
578 |
1 |
scores[0] = new float[] { 1f, 2f }; |
579 |
1 |
scores[1] = new float[] { 4f, -5.3E-10f }; |
580 |
1 |
ScoreMatrix sm = new ScoreMatrix("Test", "AB".toCharArray(), scores); |
581 |
1 |
String html = sm.outputMatrix(true); |
582 |
1 |
String expected = "<table border=\"1\"><tr><th></th><th> A </th><th> B </th></tr>\n" |
583 |
|
+ "<tr><td>A</td><td>1.0</td><td>2.0</td></tr>\n" |
584 |
|
+ "<tr><td>B</td><td>4.0</td><td>-5.3E-10</td></tr>\n" |
585 |
|
+ "</table>"; |
586 |
1 |
assertEquals(html, expected); |
587 |
|
} |
588 |
|
} |