JAL-1674 update both status bars when mousing over linked sequences

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index ce28d39..cde6d5f 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -22,6 +22,9 @@ package jalview.gui;
 
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.NJTree;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.ViewBasedAnalysisI;
+import jalview.bin.Cache;
 import jalview.commands.CommandI;
 import jalview.commands.OrderCommand;
 import jalview.datamodel.Alignment;
@@ -38,7 +41,9 @@ import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.io.NewickFile;
 import jalview.jbgui.GTreePanel;
+import jalview.schemes.ResidueProperties;
 import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.Font;
 import java.awt.Graphics;
@@ -134,7 +139,7 @@ public class TreePanel extends GTreePanel
     return treeCanvas.av.getAlignment();
   }
 
-  public AlignViewport getViewPort()
+  public AlignmentViewport getViewPort()
   {
     return treeCanvas.av;
   }
@@ -239,7 +244,7 @@ public class TreePanel extends GTreePanel
     }
 
     final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
-            MessageManager.getString("label.all_views"));
+            "label.all_views");
     buttonGroup.add(itemf);
     itemf.setSelected(treeCanvas.applyToAllViews);
     itemf.addActionListener(new ActionListener()
@@ -310,8 +315,26 @@ public class TreePanel extends GTreePanel
           seqs = av.getSelectionGroup().getSequencesInOrder(
                   av.getAlignment());
         }
-
-        tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
+        ScoreModelI sm = ResidueProperties.getScoreModel(pwtype);
+        if (sm instanceof ViewBasedAnalysisI)
+        {
+          try
+          {
+            sm = sm.getClass().newInstance();
+            ((ViewBasedAnalysisI) sm)
+                    .configureFromAlignmentView(treeCanvas.ap);
+          } catch (Exception q)
+          {
+            Cache.log.error("Couldn't create a scoremodel instance for "
+                    + sm.getName());
+          }
+          tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
+        }
+        else
+        {
+          tree = new NJTree(seqs, seqStrings, type, pwtype, null, start,
+                  end);
+        }
         showDistances(true);
       }
 
@@ -510,7 +533,7 @@ public class TreePanel extends GTreePanel
         // msaorder);
 
         Desktop.addInternalFrame(af, MessageManager.formatMessage(
-                "label.original_data_for_params", new String[]
+                "label.original_data_for_params", new Object[]
                 { this.title }), AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
       }
@@ -597,7 +620,7 @@ public class TreePanel extends GTreePanel
 
   public CommandI sortAlignmentIn(AlignmentPanel ap)
   {
-    AlignViewport av = ap.av;
+    AlignmentViewport av = ap.av;
     SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
     AlignmentSorter.sortByTree(av.getAlignment(), tree);
     CommandI undo;