Merge branch 'documentation/JAL-3111_release_211' into bug/JAL-2830_editManglesDatase...

[jalview.git] / test / jalview / gui / CalculationChooserTest.java

diff --git a/test/jalview/gui/CalculationChooserTest.java b/test/jalview/gui/CalculationChooserTest.java
new file mode 100644 (file)
index 0000000..6c2e777
--- /dev/null
+++ b/test/jalview/gui/CalculationChooserTest.java
@@ -0,0 +1,98 @@
+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<ScoreModelI> 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);
+  }
+}