JAL-3116 parse EMBL XML with JAXB (todo: update unit tests)

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 2727db1..084f461 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -85,11 +85,11 @@ public class TreePanel extends GTreePanel
 
   SimilarityParamsI similarityParams;
 
-  TreeCanvas treeCanvas;
+  private TreeCanvas treeCanvas;
 
   TreeModel tree;
 
-  AlignViewport av;
+  private AlignViewport av;
 
   /**
    * Creates a new TreePanel object.
@@ -121,24 +121,24 @@ public class TreePanel extends GTreePanel
 
   public AlignmentI getAlignment()
   {
-    return treeCanvas.av.getAlignment();
+    return getTreeCanvas().getViewport().getAlignment();
   }
 
   public AlignmentViewport getViewPort()
   {
-    return treeCanvas.av;
+    return getTreeCanvas().getViewport();
   }
 
   void initTreePanel(AlignmentPanel ap, String type, String modelName,
           NewickFile newTree, AlignmentView inputData)
   {
 
-    av = ap.av;
+    setViewport(ap.av);
     this.treeType = type;
     this.scoreModelName = modelName;
 
     treeCanvas = new TreeCanvas(this, ap, scrollPane);
-    scrollPane.setViewportView(treeCanvas);
+    scrollPane.setViewportView(getTreeCanvas());
 
     PaintRefresher.Register(this, ap.av.getSequenceSetId());
 
@@ -155,9 +155,9 @@ public class TreePanel extends GTreePanel
       @Override
       public void internalFrameClosed(InternalFrameEvent evt)
       {
-        if (av != null)
+        if (getViewport() != null)
         {
-          av.removePropertyChangeListener(listener);
+          getViewport().removePropertyChangeListener(listener);
         }
       }
     });
@@ -194,13 +194,13 @@ public class TreePanel extends GTreePanel
           }
 
           tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
-          treeCanvas.nameHash.clear(); // reset the mapping between canvas
+          getTreeCanvas().nameHash.clear(); // reset the mapping between canvas
           // rectangles and leafnodes
           repaint();
         }
       }
     };
-    av.addPropertyChangeListener(listener);
+    getViewport().addPropertyChangeListener(listener);
     return listener;
   }
 
@@ -213,8 +213,8 @@ public class TreePanel extends GTreePanel
   void buildAssociatedViewMenu()
   {
     AlignmentPanel[] aps = PaintRefresher
-            .getAssociatedPanels(av.getSequenceSetId());
-    if (aps.length == 1 && treeCanvas.ap == aps[0])
+            .getAssociatedPanels(getViewport().getSequenceSetId());
+    if (aps.length == 1 && getTreeCanvas().getAssociatedPanel() == aps[0])
     {
       associateLeavesMenu.setVisible(false);
       return;
@@ -237,16 +237,16 @@ 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 == getTreeCanvas().getAssociatedPanel());
       buttonGroup.add(item);
       item.addActionListener(new ActionListener()
       {
         @Override
         public void actionPerformed(ActionEvent evt)
         {
-          treeCanvas.applyToAllViews = false;
-          treeCanvas.ap = ap;
-          treeCanvas.av = ap.av;
+          getTreeCanvas().applyToAllViews = false;
+          getTreeCanvas().setAssociatedPanel(ap);
+          getTreeCanvas().setViewport(ap.av);
           PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
         }
       });
@@ -257,13 +257,13 @@ public class TreePanel extends GTreePanel
     final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
             MessageManager.getString("label.all_views"));
     buttonGroup.add(itemf);
-    itemf.setSelected(treeCanvas.applyToAllViews);
+    itemf.setSelected(getTreeCanvas().applyToAllViews);
     itemf.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent evt)
       {
-        treeCanvas.applyToAllViews = itemf.isSelected();
+        getTreeCanvas().applyToAllViews = itemf.isSelected();
       }
     });
     associateLeavesMenu.add(itemf);
@@ -296,7 +296,7 @@ public class TreePanel extends GTreePanel
 
       if (newtree != null)
       {
-        tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
+        tree = new TreeModel(getViewport().getAlignment().getSequencesArray(), odata,
                 newtree);
         if (tree.getOriginalData() == null)
         {
@@ -306,20 +306,20 @@ public class TreePanel extends GTreePanel
       else
       {
         ScoreModelI sm = ScoreModels.getInstance()
-                .getScoreModel(scoreModelName, treeCanvas.ap);
+                .getScoreModel(scoreModelName, getTreeCanvas().getAssociatedPanel());
         TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
-                ? new NJTree(av, sm, similarityParams)
-                : new AverageDistanceTree(av, sm, similarityParams);
+                ? new NJTree(getViewport(), sm, similarityParams)
+                : new AverageDistanceTree(getViewport(), sm, similarityParams);
         tree = new TreeModel(njtree);
         showDistances(true);
       }
 
       tree.reCount(tree.getTopNode());
       tree.findHeight(tree.getTopNode());
-      treeCanvas.setTree(tree);
-      treeCanvas.repaint();
-      av.setCurrentTree(tree);
-      if (av.getSortByTree())
+      getTreeCanvas().setTree(tree);
+      getTreeCanvas().repaint();
+      getViewport().setCurrentTree(tree);
+      if (getViewport().getSortByTree())
       {
         sortByTree_actionPerformed();
       }
@@ -328,20 +328,20 @@ public class TreePanel extends GTreePanel
 
   public void showDistances(boolean b)
   {
-    treeCanvas.setShowDistances(b);
+    getTreeCanvas().setShowDistances(b);
     distanceMenu.setSelected(b);
   }
 
   public void showBootstrap(boolean b)
   {
-    treeCanvas.setShowBootstrap(b);
+    getTreeCanvas().setShowBootstrap(b);
     bootstrapMenu.setSelected(b);
   }
 
   public void showPlaceholders(boolean b)
   {
     placeholdersMenu.setState(b);
-    treeCanvas.setMarkPlaceholders(b);
+    getTreeCanvas().setMarkPlaceholders(b);
   }
 
   /**
@@ -432,7 +432,7 @@ public class TreePanel extends GTreePanel
   public void printMenu_actionPerformed(ActionEvent e)
   {
     // Putting in a thread avoids Swing painting problems
-    treeCanvas.startPrinting();
+    getTreeCanvas().startPrinting();
   }
 
   @Override
@@ -456,7 +456,7 @@ public class TreePanel extends GTreePanel
     {
       // we try to get the associated view's gap character
       // but this may fail if the view was closed...
-      gc = av.getGapCharacter();
+      gc = getViewport().getGapCharacter();
 
     } catch (Exception ex)
     {
@@ -469,8 +469,8 @@ public class TreePanel extends GTreePanel
       // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
 
       AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
-      AlignmentI dataset = (av != null && av.getAlignment() != null)
-              ? av.getAlignment().getDataset()
+      AlignmentI dataset = (getViewport() != null && getViewport().getAlignment() != null)
+              ? getViewport().getAlignment().getDataset()
               : null;
       if (dataset != null)
       {
@@ -507,7 +507,7 @@ public class TreePanel extends GTreePanel
   @Override
   public void fitToWindow_actionPerformed(ActionEvent e)
   {
-    treeCanvas.fitToWindow = fitToWindow.isSelected();
+    getTreeCanvas().fitToWindow = fitToWindow.isSelected();
     repaint();
   }
 
@@ -520,15 +520,15 @@ public class TreePanel extends GTreePanel
   public void sortByTree_actionPerformed()
   {
 
-    if (treeCanvas.applyToAllViews)
+    if (getTreeCanvas().applyToAllViews)
     {
       final ArrayList<CommandI> commands = new ArrayList<>();
       for (AlignmentPanel ap : PaintRefresher
-              .getAssociatedPanels(av.getSequenceSetId()))
+              .getAssociatedPanels(getViewport().getSequenceSetId()))
       {
         commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
       }
-      av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
+      getViewport().getAlignPanel().alignFrame.addHistoryItem(new CommandI()
       {
 
         @Override
@@ -563,7 +563,7 @@ public class TreePanel extends GTreePanel
         }
       });
       for (AlignmentPanel ap : PaintRefresher
-              .getAssociatedPanels(av.getSequenceSetId()))
+              .getAssociatedPanels(getViewport().getSequenceSetId()))
       {
         // ensure all the alignFrames refresh their GI after adding an undo item
         ap.alignFrame.updateEditMenuBar();
@@ -571,8 +571,8 @@ public class TreePanel extends GTreePanel
     }
     else
     {
-      treeCanvas.ap.alignFrame
-              .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
+      getTreeCanvas().getAssociatedPanel().alignFrame
+              .addHistoryItem(sortAlignmentIn(getTreeCanvas().getAssociatedPanel()));
     }
 
   }
@@ -599,7 +599,7 @@ public class TreePanel extends GTreePanel
   @Override
   public void font_actionPerformed(ActionEvent e)
   {
-    if (treeCanvas == null)
+    if (getTreeCanvas() == null)
     {
       return;
     }
@@ -609,14 +609,14 @@ public class TreePanel extends GTreePanel
 
   public Font getTreeFont()
   {
-    return treeCanvas.font;
+    return getTreeCanvas().font;
   }
 
   public void setTreeFont(Font f)
   {
-    if (treeCanvas != null)
+    if (getTreeCanvas() != null)
     {
-      treeCanvas.setFont(f);
+      getTreeCanvas().setFont(f);
     }
   }
 
@@ -629,7 +629,7 @@ public class TreePanel extends GTreePanel
   @Override
   public void distanceMenu_actionPerformed(ActionEvent e)
   {
-    treeCanvas.setShowDistances(distanceMenu.isSelected());
+    getTreeCanvas().setShowDistances(distanceMenu.isSelected());
   }
 
   /**
@@ -641,7 +641,7 @@ public class TreePanel extends GTreePanel
   @Override
   public void bootstrapMenu_actionPerformed(ActionEvent e)
   {
-    treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
+    getTreeCanvas().setShowBootstrap(bootstrapMenu.isSelected());
   }
 
   /**
@@ -653,7 +653,7 @@ public class TreePanel extends GTreePanel
   @Override
   public void placeholdersMenu_actionPerformed(ActionEvent e)
   {
-    treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
+    getTreeCanvas().setMarkPlaceholders(placeholdersMenu.isSelected());
   }
 
   /**
@@ -691,8 +691,8 @@ public class TreePanel extends GTreePanel
       accurateText = false;
     }
 
-    int width = treeCanvas.getWidth();
-    int height = treeCanvas.getHeight();
+    int width = getTreeCanvas().getWidth();
+    int height = getTreeCanvas().getHeight();
 
     try
     {
@@ -720,7 +720,7 @@ public class TreePanel extends GTreePanel
 
       pg.setAccurateTextMode(accurateText);
 
-      treeCanvas.draw(pg, width, height);
+      getTreeCanvas().draw(pg, width, height);
 
       pg.flush();
       pg.close();
@@ -739,8 +739,8 @@ public class TreePanel extends GTreePanel
   @Override
   public void pngTree_actionPerformed(ActionEvent e)
   {
-    int width = treeCanvas.getWidth();
-    int height = treeCanvas.getHeight();
+    int width = getTreeCanvas().getWidth();
+    int height = getTreeCanvas().getHeight();
 
     try
     {
@@ -769,7 +769,7 @@ public class TreePanel extends GTreePanel
               BufferedImage.TYPE_INT_RGB);
       Graphics png = bi.getGraphics();
 
-      treeCanvas.draw(png, width, height);
+      getTreeCanvas().draw(png, width, height);
 
       ImageIO.write(bi, "png", out);
       out.close();
@@ -883,4 +883,19 @@ public class TreePanel extends GTreePanel
             treecalcnm, smn);
     return ttl;
   }
+
+  public AlignViewport getViewport()
+  {
+    return av;
+  }
+
+  public void setViewport(AlignViewport av)
+  {
+    this.av = av;
+  }
+
+  public TreeCanvas getTreeCanvas()
+  {
+    return treeCanvas;
+  }
 }