JAL-2403 JAL-1483 changes to ScoreModelI hierarchy and signatures to

[jalview.git] / src / jalview / gui / TreeChooser.java

diff --git a/src/jalview/gui/TreeChooser.java b/src/jalview/gui/TreeChooser.java
index 338fbb8..8e2bff0 100644 (file)
--- a/src/jalview/gui/TreeChooser.java
+++ b/src/jalview/gui/TreeChooser.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.analysis.NJTree;
 import jalview.analysis.scoremodels.ScoreModels;
 import jalview.api.analysis.ScoreModelI;
 import jalview.util.MessageManager;
@@ -85,12 +86,10 @@ public class TreeChooser extends JPanel
 
     matrixNames = new JComboBox<String>();
     ScoreModels scoreModels = ScoreModels.getInstance();
-    for (String scoreType : scoreModels.getModelNames())
+    for (ScoreModelI sm : scoreModels.getModels())
     {
-      ScoreModelI sm = scoreModels.forName(scoreType);
-      if (sm.isDNA() == af.getViewport().getAlignment().isNucleotide()
-              || sm.isProtein() == !af.getViewport().getAlignment()
-                      .isNucleotide())
+      boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
+      if (sm.isDNA() && nucleotide || sm.isProtein() && !nucleotide)
       {
         matrixNames.addItem(sm.getName());
       }
@@ -150,7 +149,8 @@ public class TreeChooser extends JPanel
     try
     {
       frame.setClosed(true);
-      String treeType = neighbourJoining.isSelected() ? "NJ" : "AV";
+      String treeType = neighbourJoining.isSelected() ? NJTree.NEIGHBOUR_JOINING
+              : NJTree.AVERAGE_DISTANCE;
       ScoreModelI sm = ScoreModels.getInstance().forName(
               matrixNames.getSelectedItem().toString());
       af.newTreePanel(treeType, sm);