+/*
+ * 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 jalview.api.analysis.SimilarityParamsI;
import jalview.util.Comparison;
import org.testng.annotations.Test;
@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);
+ // and verify PIDModel calculation is symmetric
+ assertEquals(newScore, PIDModel.computePID(s2, s1, params));
/*
* same length, with gaps
*/
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);
+ assertEquals(newScore, PIDModel.computePID(s2, s1, params));
/*
* s2 longer than s1, with gaps
*/
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);
+ assertEquals(newScore, PIDModel.computePID(s2, s1, params));
/*
* s1 longer than s2, with gaps
*/
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);
+ assertEquals(newScore, PIDModel.computePID(s2, s1, params));
/*
* same but now also with gapped columns
*/
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);
+ assertEquals(newScore, PIDModel.computePID(s2, s1, params));
+ }
+
+ /**
+ * 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);
+ assertEquals(PIDModel.computePID(s2, s1, 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);
+ assertEquals(PIDModel.computePID(s2, s1, 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);
+ assertEquals(PIDModel.computePID(s2, s1, 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);
+ assertEquals(PIDModel.computePID(s2, s1, 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);
+ assertEquals(PIDModel.computePID(s2, s1, 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);
+ assertEquals(PIDModel.computePID(s2, s1, 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);
+ assertEquals(PIDModel.computePID(s2, s1, 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);
+ assertEquals(PIDModel.computePID(s2, s1, params), 20d);
+
+ /*
+ * no tests for matchGaps=true, includeGaps=false
+ * as it don't make sense
+ */
}
}
git://source.jalview.org / jalview.git / blobdiff