JAL-4366 fix up tests

diff --git a/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java b/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java
index 473abcf..0a602f5 100644 (file)
--- a/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java
+++ b/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java
@@ -394,7 +394,7 @@ public class SecondaryStructureDistanceModel extends DistanceScoreModel
   @Override
   public boolean isProtein()
   {
-    return false;
+    return true;
   }
 
   @Override

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index c9e999a..6d77f04 100644 (file)
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -661,8 +661,8 @@ public class CalculationChooser extends JPanel
     for (ScoreModelI sm : scoreModels.getModels())
     {
       if ((!forPasimap || sm instanceof ScoreMatrix)
-              && (!nucleotide && sm.isProtein() || nucleotide && sm.isDNA()
-                      || sm.isSecondaryStructure() && ssPresent))
+              && ((!nucleotide && sm.isProtein()) || (nucleotide && sm.isDNA()))
+              && (!sm.isSecondaryStructure() || ssPresent))
 
       {
         filtered.add(sm);

diff --git a/test/jalview/gui/CalculationChooserTest.java b/test/jalview/gui/CalculationChooserTest.java
index 3ee12cf..3d7e03e 100644 (file)
--- a/test/jalview/gui/CalculationChooserTest.java
+++ b/test/jalview/gui/CalculationChooserTest.java
@@ -76,7 +76,7 @@ public class CalculationChooserTest
     assertEquals(filtered.get(2).getName(), "Mat3di");
     assertEquals(filtered.get(3).getName(), "PID");
     assertEquals(filtered.get(4).getName(), "Sequence Feature Similarity");
-    assertEquals(filtered.get(4).getName(),
+    assertEquals(filtered.get(5).getName(),
             "Secondary Structure Similarity");
 
 
@@ -137,7 +137,7 @@ public class CalculationChooserTest
 
       assertEquals(CalculationChooser
               .getApplicableScoreModels(isDna, isPca, isSS, true).size(),
-              (isDna) ? 1 : 2);
+              (isDna) ? 1 : 3);
     }
   }
 }