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package jalview.analysis.scoremodels; |
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import static org.testng.Assert.assertEquals; |
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import jalview.api.analysis.SimilarityParamsI; |
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import jalview.util.Comparison; |
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import org.testng.annotations.Test; |
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| 100% |
Uncovered Elements: 0 (77) |
Complexity: 4 |
Complexity Density: 0.05 |
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public class PIDModelTest |
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{ |
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private static final double DELTA = 0.00001D; |
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| 100% |
Uncovered Elements: 0 (9) |
Complexity: 1 |
Complexity Density: 0.11 |
1PASS
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@Test(groups = "Functional")... |
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public void testGetPairwiseScore() |
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{ |
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PIDModel sm = new PIDModel(); |
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assertEquals(sm.getPairwiseScore('A', 'A'), 1f); |
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assertEquals(sm.getPairwiseScore('A', 'a'), 1f); |
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assertEquals(sm.getPairwiseScore('a', 'A'), 1f); |
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assertEquals(sm.getPairwiseScore('A', 'B'), 0f); |
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assertEquals(sm.getPairwiseScore('A', ' '), 0f); |
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assertEquals(sm.getPairwiseScore(' ', ' '), 0f); |
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assertEquals(sm.getPairwiseScore('.', '.'), 0f); |
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assertEquals(sm.getPairwiseScore('-', '-'), 0f); |
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} |
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| 100% |
Uncovered Elements: 0 (36) |
Complexity: 1 |
Complexity Density: 0.03 |
1PASS
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@Test(groups = "Functional")... |
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public void testComputePID_matchesComparisonPID() |
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{ |
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SimilarityParamsI params = new SimilarityParams(true, true, true, true); |
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String s1 = "ARFNQDWSGI"; |
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String s2 = "ARKNQDQSGI"; |
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new PIDModel(); |
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double newScore = PIDModel.computePID(s1, s2, params); |
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double oldScore = Comparison.PID(s1, s2); |
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assertEquals(newScore, oldScore, DELTA); |
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assertEquals(newScore, PIDModel.computePID(s2, s1, params)); |
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s1 = "-RFNQDWSGI"; |
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s2 = "ARKNQ-QSGI"; |
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new PIDModel(); |
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newScore = PIDModel.computePID(s1, s2, params); |
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oldScore = Comparison.PID(s1, s2); |
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assertEquals(newScore, oldScore, DELTA); |
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assertEquals(newScore, PIDModel.computePID(s2, s1, params)); |
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s1 = "ARK-"; |
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s2 = "-RFNQ"; |
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new PIDModel(); |
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newScore = PIDModel.computePID(s1, s2, params); |
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oldScore = Comparison.PID(s1, s2); |
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assertEquals(newScore, oldScore, DELTA); |
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assertEquals(newScore, PIDModel.computePID(s2, s1, params)); |
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s1 = "-RFNQ"; |
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s2 = "ARK-"; |
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new PIDModel(); |
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newScore = PIDModel.computePID(s1, s2, params); |
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oldScore = Comparison.PID(s1, s2); |
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assertEquals(newScore, oldScore, DELTA); |
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assertEquals(newScore, PIDModel.computePID(s2, s1, params)); |
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s1 = "-R-F-NQ"; |
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s2 = "AR-K--"; |
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new PIDModel(); |
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newScore = PIDModel.computePID(s1, s2, params); |
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oldScore = Comparison.PID(s1, s2); |
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assertEquals(newScore, oldScore, DELTA); |
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assertEquals(newScore, PIDModel.computePID(s2, s1, params)); |
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} |
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| 100% |
Uncovered Elements: 0 (14) |
Complexity: 1 |
Complexity Density: 0.07 |
1PASS
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@Test(groups = "Functional")... |
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public void testComputePID_matchShortestSequence() |
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String s1 = "FR-K-S"; |
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String s2 = "FS--L"; |
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SimilarityParamsI params = new SimilarityParams(true, true, true, true); |
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assertEquals(PIDModel.computePID(s1, s2, params), 80d); |
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assertEquals(PIDModel.computePID(s2, s1, params), 80d); |
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params = new SimilarityParams(false, true, true, true); |
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assertEquals(PIDModel.computePID(s1, s2, params), 75d); |
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assertEquals(PIDModel.computePID(s2, s1, params), 75d); |
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params = new SimilarityParams(true, false, true, true); |
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assertEquals(PIDModel.computePID(s1, s2, params), 40d); |
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assertEquals(PIDModel.computePID(s2, s1, params), 40d); |
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params = new SimilarityParams(false, false, true, true); |
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assertEquals(PIDModel.computePID(s1, s2, params), 25d); |
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assertEquals(PIDModel.computePID(s2, s1, params), 25d); |
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} |
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| 100% |
Uncovered Elements: 0 (14) |
Complexity: 1 |
Complexity Density: 0.07 |
1PASS
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@Test(groups = "Functional")... |
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public void testComputePID_matchLongestSequence() |
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{ |
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String s1 = "FR-K-S"; |
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String s2 = "FS--L"; |
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SimilarityParamsI params = new SimilarityParams(true, true, true, false); |
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assertEquals(PIDModel.computePID(s1, s2, params), 500d / 6); |
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assertEquals(PIDModel.computePID(s2, s1, params), 500d / 6); |
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params = new SimilarityParams(false, true, true, false); |
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assertEquals(PIDModel.computePID(s1, s2, params), 80d); |
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assertEquals(PIDModel.computePID(s2, s1, params), 80d); |
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params = new SimilarityParams(true, false, true, false); |
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assertEquals(PIDModel.computePID(s1, s2, params), 100d / 3); |
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assertEquals(PIDModel.computePID(s2, s1, params), 100d / 3); |
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params = new SimilarityParams(false, false, true, false); |
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assertEquals(PIDModel.computePID(s1, s2, params), 20d); |
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assertEquals(PIDModel.computePID(s2, s1, params), 20d); |
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} |
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} |