+/*
+ * 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;
{
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);
+ 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
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