/*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertSame;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.api.analysis.ScoreModelI;
import jalview.bin.Cache;
import java.util.List;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class CalculationChooserTest
{
@BeforeClass(alwaysRun = true)
public void setUp()
{
// read-only Jalview properties
Cache.loadProperties("test/jalview/io/testProps.jvprops");
Cache.applicationProperties.setProperty("BLOSUM62_PCA_FOR_NUCLEOTIDE",
Boolean.FALSE.toString());
}
@Test(groups = "Functional")
public void testGetApplicableScoreModels()
{
ScoreModels models = ScoreModels.getInstance();
ScoreModelI blosum62 = models.getBlosum62();
ScoreModelI pam250 = models.getPam250();
ScoreModelI dna = models.getDefaultModel(false);
/*
* peptide models for PCA
*/
List filtered = CalculationChooser
.getApplicableScoreModels(false, true);
assertEquals(filtered.size(), 4);
assertSame(filtered.get(0), blosum62);
assertSame(filtered.get(1), pam250);
assertEquals(filtered.get(2).getName(), "PID");
assertEquals(filtered.get(3).getName(), "Sequence Feature Similarity");
/*
* peptide models for Tree are the same
*/
filtered = CalculationChooser.getApplicableScoreModels(false, false);
assertEquals(filtered.size(), 4);
assertSame(filtered.get(0), blosum62);
assertSame(filtered.get(1), pam250);
assertEquals(filtered.get(2).getName(), "PID");
assertEquals(filtered.get(3).getName(), "Sequence Feature Similarity");
/*
* nucleotide models for PCA
*/
filtered = CalculationChooser.getApplicableScoreModels(true, true);
assertEquals(filtered.size(), 3);
assertSame(filtered.get(0), dna);
assertEquals(filtered.get(1).getName(), "PID");
assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity");
/*
* nucleotide models for Tree are the same
*/
filtered = CalculationChooser.getApplicableScoreModels(true, false);
assertEquals(filtered.size(), 3);
assertSame(filtered.get(0), dna);
assertEquals(filtered.get(1).getName(), "PID");
assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity");
/*
* enable inclusion of BLOSUM62 for nucleotide PCA (JAL-2962)
*/
Cache.applicationProperties.setProperty("BLOSUM62_PCA_FOR_NUCLEOTIDE",
Boolean.TRUE.toString());
/*
* nucleotide models for Tree are unchanged
*/
filtered = CalculationChooser.getApplicableScoreModels(true, false);
assertEquals(filtered.size(), 3);
assertSame(filtered.get(0), dna);
assertEquals(filtered.get(1).getName(), "PID");
assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity");
/*
* nucleotide models for PCA add BLOSUM62 as last option
*/
filtered = CalculationChooser.getApplicableScoreModels(true, true);
assertEquals(filtered.size(), 4);
assertSame(filtered.get(0), dna);
assertEquals(filtered.get(1).getName(), "PID");
assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity");
assertSame(filtered.get(3), blosum62);
}
}