JAL-2428 use 'correct' name for selected score model

[jalview.git] / src / jalview / appletgui / AlignFrame.java

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index b6a2430..11df2c7 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -22,7 +22,9 @@ package jalview.appletgui;
 
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.analysis.NJTree;
+import jalview.analysis.TreeBuilder;
+import jalview.analysis.scoremodels.PIDModel;
+import jalview.analysis.scoremodels.ScoreModels;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
@@ -2722,7 +2724,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
-            .getAlignment().getSequenceAt(0), null);
+            .getAlignment().getSequenceAt(0));
 
     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
             viewport.getAlignment()));
@@ -2814,29 +2816,31 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   public void averageDistanceTreeMenuItem_actionPerformed()
   {
-    NewTreePanel(NJTree.AVERAGE_DISTANCE, "PID",
+    newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
             "Average distance tree using PID");
   }
 
   public void neighbourTreeMenuItem_actionPerformed()
   {
-    NewTreePanel(NJTree.NEIGHBOUR_JOINING, "PID",
+    newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
             "Neighbour joining tree using PID");
   }
 
   protected void njTreeBlosumMenuItem_actionPerformed()
   {
-    NewTreePanel(NJTree.NEIGHBOUR_JOINING, "BL",
+    newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, ScoreModels.getInstance()
+            .getBlosum62().getName(),
             "Neighbour joining tree using BLOSUM62");
   }
 
   protected void avTreeBlosumMenuItem_actionPerformed()
   {
-    NewTreePanel(NJTree.AVERAGE_DISTANCE, "BL",
+    newTreePanel(TreeBuilder.AVERAGE_DISTANCE, ScoreModels.getInstance()
+            .getBlosum62().getName(),
             "Average distance tree using BLOSUM62");
   }
 
-  void NewTreePanel(String type, String pwType, String title)
+  void newTreePanel(String type, String pwType, String title)
   {
     // are the sequences aligned?
     if (!viewport.getAlignment().isAligned(false))