Merge branch 'develop' into features/JAL-2393customMatrices

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 1e98535..d4c6009 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -170,11 +170,7 @@ public class TreePanel extends GTreePanel
       }
     });
 
-    TreeLoader tl = new TreeLoader(newTree);
-    if (inputData != null)
-    {
-      tl.odata = inputData;
-    }
+    TreeLoader tl = new TreeLoader(newTree, inputData);
     tl.start();
 
   }
@@ -246,13 +242,15 @@ public class TreePanel extends GTreePanel
 
   class TreeLoader extends Thread
   {
-    NewickFile newtree;
+    private NewickFile newtree;
 
-    AlignmentView odata = null;
+    private AlignmentView odata = null;
 
-    public TreeLoader(NewickFile newickFile)
+    public TreeLoader(NewickFile newickFile, AlignmentView inputData)
     {
       this.newtree = newickFile;
+      this.odata = inputData;
+
       if (newickFile != null)
       {
         // Must be outside run(), as Jalview2XML tries to
@@ -268,19 +266,11 @@ public class TreePanel extends GTreePanel
 
       if (newtree != null)
       {
-        if (odata == null)
+        tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
+                newtree);
+        if (tree.getOriginalData() == null)
         {
-          tree = new TreeModel(av.getAlignment().getSequencesArray(),
-                  newtree);
-        }
-        else
-        {
-          tree = new TreeModel(av.getAlignment().getSequencesArray(),
-                  odata, newtree);
-        }
-        if (!tree.hasOriginalSequenceData())
-        {
-          allowOriginalSeqData(false);
+          originalSeqData.setVisible(false);
         }
       }
       else
@@ -323,11 +313,6 @@ public class TreePanel extends GTreePanel
     treeCanvas.setMarkPlaceholders(b);
   }
 
-  private void allowOriginalSeqData(boolean b)
-  {
-    originalSeqData.setVisible(b);
-  }
-
   /**
    * DOCUMENT ME!
    * 
@@ -422,7 +407,8 @@ public class TreePanel extends GTreePanel
   @Override
   public void originalSeqData_actionPerformed(ActionEvent e)
   {
-    if (!tree.hasOriginalSequenceData())
+    AlignmentView originalData = tree.getOriginalData();
+    if (originalData == null)
     {
       jalview.bin.Cache.log
               .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
@@ -444,8 +430,9 @@ public class TreePanel extends GTreePanel
     } catch (Exception ex)
     {
     }
-    ;
-    Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
+
+    Object[] alAndColsel = originalData
+            .getAlignmentAndColumnSelection(gc);
 
     if (alAndColsel != null && alAndColsel[0] != null)
     {