JAL-3638 shift+arrow keys in cursor mode jumps cursor in a gapped region to next...

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 5450102..37b4dac 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -84,11 +84,11 @@ public class TreePanel extends GTreePanel
 
   SimilarityParamsI similarityParams;
 
-  TreeCanvas treeCanvas;
+  private TreeCanvas treeCanvas;
 
   TreeModel tree;
 
-  AlignViewport av;
+  private AlignViewport av;
 
   /**
    * Creates a new TreePanel object.
@@ -120,12 +120,13 @@ public class TreePanel extends GTreePanel
 
   public AlignmentI getAlignment()
   {
-    return treeCanvas.av.getAlignment();
+    return getTreeCanvas().getViewport().getAlignment();
   }
 
   public AlignmentViewport getViewPort()
   {
-    return treeCanvas.av;
+    // @Mungo - Why don't we return our own viewport ???
+    return getTreeCanvas().getViewport();
   }
 
   void initTreePanel(AlignmentPanel ap, String type, String modelName,
@@ -213,7 +214,7 @@ public class TreePanel extends GTreePanel
   {
     AlignmentPanel[] aps = PaintRefresher
             .getAssociatedPanels(av.getSequenceSetId());
-    if (aps.length == 1 && treeCanvas.ap == aps[0])
+    if (aps.length == 1 && getTreeCanvas().getAssociatedPanel() == aps[0])
     {
       associateLeavesMenu.setVisible(false);
       return;
@@ -236,7 +237,8 @@ public class TreePanel extends GTreePanel
     for (i = 0; i < iSize; i++)
     {
       final AlignmentPanel ap = aps[i];
-      item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap);
+      item = new JRadioButtonMenuItem(ap.av.getViewName(),
+              ap == treeCanvas.getAssociatedPanel());
       buttonGroup.add(item);
       item.addActionListener(new ActionListener()
       {
@@ -244,8 +246,8 @@ public class TreePanel extends GTreePanel
         public void actionPerformed(ActionEvent evt)
         {
           treeCanvas.applyToAllViews = false;
-          treeCanvas.ap = ap;
-          treeCanvas.av = ap.av;
+          treeCanvas.setAssociatedPanel(ap);
+          treeCanvas.setViewport(ap.av);
           PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
         }
       });
@@ -305,7 +307,8 @@ public class TreePanel extends GTreePanel
       else
       {
         ScoreModelI sm = ScoreModels.getInstance()
-                .getScoreModel(scoreModelName, treeCanvas.ap);
+                .getScoreModel(scoreModelName,
+                        treeCanvas.getAssociatedPanel());
         TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
                 ? new NJTree(av, sm, similarityParams)
                 : new AverageDistanceTree(av, sm, similarityParams);
@@ -571,8 +574,9 @@ public class TreePanel extends GTreePanel
     }
     else
     {
-      treeCanvas.ap.alignFrame
-              .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
+      treeCanvas.getAssociatedPanel().alignFrame
+              .addHistoryItem(
+                      sortAlignmentIn(treeCanvas.getAssociatedPanel()));
     }
 
   }
@@ -705,20 +709,20 @@ public class TreePanel extends GTreePanel
           if (sq != null)
           {
             // search dbrefs, features and annotation
-            DBRefEntry[] refs = jalview.util.DBRefUtils
+            List<DBRefEntry> refs = jalview.util.DBRefUtils
                     .selectRefs(sq.getDBRefs(), new String[]
                     { labelClass.toUpperCase() });
             if (refs != null)
             {
-              for (int i = 0; i < refs.length; i++)
+              for (int i = 0, ni = refs.size(); i < ni; i++)
               {
                 if (newname == null)
                 {
-                  newname = new String(refs[i].getAccessionId());
+                  newname = new String(refs.get(i).getAccessionId());
                 }
                 else
                 {
-                  newname = newname + "; " + refs[i].getAccessionId();
+                  newname += "; " + refs.get(i).getAccessionId();
                 }
               }
             }
@@ -780,7 +784,7 @@ public class TreePanel extends GTreePanel
     /*
      * put them together as <method> Using <model>
      */
-    final String ttl = MessageManager.formatMessage("label.treecalc_title",
+    final String ttl = MessageManager.formatMessage("label.calc_title",
             treecalcnm, smn);
     return ttl;
   }
@@ -814,4 +818,19 @@ public class TreePanel extends GTreePanel
       ex.printStackTrace();
     }
   }
+  
+  public AlignViewport getViewport()
+  {
+    return av;
+  }
+
+  public void setViewport(AlignViewport av)
+  {
+    this.av = av;
+  }
+
+  public TreeCanvas getTreeCanvas()
+  {
+    return treeCanvas;
+  }
 }