JAL-4386 Corrected failed test case.

diff --git a/test/jalview/gui/CalculationChooserTest.java b/test/jalview/gui/CalculationChooserTest.java
index 5e6d57c..dd22599 100644 (file)
--- a/test/jalview/gui/CalculationChooserTest.java
+++ b/test/jalview/gui/CalculationChooserTest.java
@@ -56,26 +56,28 @@ public class CalculationChooserTest
      */
     List<ScoreModelI> filtered = CalculationChooser
             .getApplicableScoreModels(false, true, true);
-    assertEquals(filtered.size(), 4);
+    assertEquals(filtered.size(), 5);
     assertSame(filtered.get(0), blosum62);
     assertSame(filtered.get(1), pam250);
     assertEquals(filtered.get(2).getName(), "PID");
     assertEquals(filtered.get(3).getName(), "Sequence Feature Similarity");
+    assertEquals(filtered.get(4).getName(), "Secondary Structure Similarity");
 
     /*
      * peptide models for Tree are the same
      */
     filtered = CalculationChooser.getApplicableScoreModels(false, false, true);
-    assertEquals(filtered.size(), 4);
+    assertEquals(filtered.size(), 5);
     assertSame(filtered.get(0), blosum62);
     assertSame(filtered.get(1), pam250);
     assertEquals(filtered.get(2).getName(), "PID");
     assertEquals(filtered.get(3).getName(), "Sequence Feature Similarity");
+    assertEquals(filtered.get(4).getName(), "Secondary Structure Similarity");
 
     /*
      * nucleotide models for PCA
      */
-    filtered = CalculationChooser.getApplicableScoreModels(true, true, true);
+    filtered = CalculationChooser.getApplicableScoreModels(true, true, false);
     assertEquals(filtered.size(), 3);
     assertSame(filtered.get(0), dna);
     assertEquals(filtered.get(1).getName(), "PID");
@@ -84,7 +86,7 @@ public class CalculationChooserTest
     /*
      * nucleotide models for Tree are the same
      */
-    filtered = CalculationChooser.getApplicableScoreModels(true, false, true);
+    filtered = CalculationChooser.getApplicableScoreModels(true, false, false);
     assertEquals(filtered.size(), 3);
     assertSame(filtered.get(0), dna);
     assertEquals(filtered.get(1).getName(), "PID");
@@ -100,7 +102,7 @@ public class CalculationChooserTest
      * nucleotide models for Tree are unchanged
      */
     filtered = CalculationChooser.getApplicableScoreModels(true, false, true);
-    assertEquals(filtered.size(), 3);
+    assertEquals(filtered.size(), 4);
     assertSame(filtered.get(0), dna);
     assertEquals(filtered.get(1).getName(), "PID");
     assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity");
@@ -108,7 +110,7 @@ public class CalculationChooserTest
     /*
      * nucleotide models for PCA add BLOSUM62 as last option
      */
-    filtered = CalculationChooser.getApplicableScoreModels(true, true, true);
+    filtered = CalculationChooser.getApplicableScoreModels(true, true, false);
     assertEquals(filtered.size(), 4);
     assertSame(filtered.get(0), dna);
     assertEquals(filtered.get(1).getName(), "PID");