From 332b50975c0463993efaf16723b3bdb4080d16c5 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Mon, 27 Feb 2017 18:00:15 +0000 Subject: [PATCH] JAL-838 tests for PID calculation with parameter options --- src/jalview/analysis/scoremodels/PIDModel.java | 2 +- .../jalview/analysis/scoremodels/PIDModelTest.java | 106 ++++++++++++++++++-- 2 files changed, 98 insertions(+), 10 deletions(-) diff --git a/src/jalview/analysis/scoremodels/PIDModel.java b/src/jalview/analysis/scoremodels/PIDModel.java index aff1210..24e9a1c 100644 --- a/src/jalview/analysis/scoremodels/PIDModel.java +++ b/src/jalview/analysis/scoremodels/PIDModel.java @@ -103,7 +103,7 @@ public class PIDModel implements SimilarityScoreModelI, * @param options * @return */ - protected double computePID(String seq1, String seq2, + protected static double computePID(String seq1, String seq2, SimilarityParamsI options) { int len1 = seq1.length(); diff --git a/test/jalview/analysis/scoremodels/PIDModelTest.java b/test/jalview/analysis/scoremodels/PIDModelTest.java index 24b44a3..d968e0e 100644 --- a/test/jalview/analysis/scoremodels/PIDModelTest.java +++ b/test/jalview/analysis/scoremodels/PIDModelTest.java @@ -2,6 +2,7 @@ package jalview.analysis.scoremodels; import static org.testng.Assert.assertEquals; +import jalview.api.analysis.SimilarityParamsI; import jalview.util.Comparison; import org.testng.annotations.Test; @@ -31,13 +32,16 @@ public class PIDModelTest @Test(groups = "Functional") public void testComputePID_matchesComparisonPID() { + SimilarityParamsI params = new SimilarityParams(true, true, true, true); + /* * same length, no gaps */ String s1 = "ARFNQDWSGI"; String s2 = "ARKNQDQSGI"; - double newScore = new PIDModel().computePID(s1, s2, - SimilarityParams.Jalview); + + new PIDModel(); + double newScore = PIDModel.computePID(s1, s2, params); double oldScore = Comparison.PID(s1, s2); assertEquals(newScore, oldScore, DELTA); @@ -46,8 +50,8 @@ public class PIDModelTest */ s1 = "-RFNQDWSGI"; s2 = "ARKNQ-QSGI"; - newScore = new PIDModel().computePID(s1, s2, - SimilarityParams.Jalview); + new PIDModel(); + newScore = PIDModel.computePID(s1, s2, params); oldScore = Comparison.PID(s1, s2); assertEquals(newScore, oldScore, DELTA); @@ -56,8 +60,8 @@ public class PIDModelTest */ s1 = "ARK-"; s2 = "-RFNQ"; - newScore = new PIDModel().computePID(s1, s2, - SimilarityParams.Jalview); + new PIDModel(); + newScore = PIDModel.computePID(s1, s2, params); oldScore = Comparison.PID(s1, s2); assertEquals(newScore, oldScore, DELTA); @@ -66,8 +70,8 @@ public class PIDModelTest */ s1 = "-RFNQ"; s2 = "ARK-"; - newScore = new PIDModel().computePID(s1, s2, - SimilarityParams.Jalview); + new PIDModel(); + newScore = PIDModel.computePID(s1, s2, params); oldScore = Comparison.PID(s1, s2); assertEquals(newScore, oldScore, DELTA); @@ -76,8 +80,92 @@ public class PIDModelTest */ s1 = "-R-F-NQ"; s2 = "AR-K--"; - newScore = new PIDModel().computePID(s1, s2, SimilarityParams.Jalview); + new PIDModel(); + newScore = PIDModel.computePID(s1, s2, params); oldScore = Comparison.PID(s1, s2); assertEquals(newScore, oldScore, DELTA); } + + /** + * Tests for percentage identity variants where only the shorter length of two + * sequences is used + */ + @Test(groups = "Functional") + public void testComputePID_matchShortestSequence() + { + String s1 = "FR-K-S"; + String s2 = "FS--L"; + + /* + * match gap-gap and gap-char + * PID = 4/5 = 80% + */ + SimilarityParamsI params = new SimilarityParams(true, true, true, true); + assertEquals(PIDModel.computePID(s1, s2, params), 80d); + + /* + * match gap-char but not gap-gap + * PID = 3/4 = 75% + */ + params = new SimilarityParams(false, true, true, true); + assertEquals(PIDModel.computePID(s1, s2, params), 75d); + + /* + * include gaps but don't match them + * include gap-gap, counted as identity + * PID = 2/5 = 40% + */ + params = new SimilarityParams(true, false, true, true); + assertEquals(PIDModel.computePID(s1, s2, params), 40d); + + /* + * include gaps but don't match them + * exclude gap-gap + * PID = 1/4 = 25% + */ + params = new SimilarityParams(false, false, true, true); + assertEquals(PIDModel.computePID(s1, s2, params), 25d); + } + + /** + * Tests for percentage identity variants where the longer length of two + * sequences is used + */ + @Test(groups = "Functional") + public void testComputePID_matchLongestSequence() + { + String s1 = "FR-K-S"; + String s2 = "FS--L"; + + /* + * match gap-gap and gap-char + * shorter sequence treated as if with trailing gaps + * PID = 5/6 = 83.333...% + */ + SimilarityParamsI params = new SimilarityParams(true, true, true, false); + assertEquals(PIDModel.computePID(s1, s2, params), 500d / 6); + + /* + * match gap-char but not gap-gap + * PID = 4/5 = 80% + */ + params = new SimilarityParams(false, true, true, false); + assertEquals(PIDModel.computePID(s1, s2, params), 80d); + + /* + * include gaps but don't match them + * include gap-gap, counted as identity + * PID = 2/6 = 33.333...% + */ + params = new SimilarityParams(true, false, true, false); + assertEquals(PIDModel.computePID(s1, s2, params), 100d / 3); + + /* + * include gaps but don't match them + * exclude gap-gap + * PID = 1/5 = 25% + */ + params = new SimilarityParams(false, false, true, false); + assertEquals(PIDModel.computePID(s1, s2, params), 20d); + } } -- 1.7.10.2