JAL-1645 source formatting and organise imports

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index b8eba8f..d2c86c8 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -43,6 +43,7 @@ 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;
@@ -138,7 +139,7 @@ public class TreePanel extends GTreePanel
     return treeCanvas.av.getAlignment();
   }
 
-  public AlignViewport getViewPort()
+  public AlignmentViewport getViewPort()
   {
     return treeCanvas.av;
   }
@@ -242,7 +243,8 @@ public class TreePanel extends GTreePanel
       associateLeavesMenu.add(item);
     }
 
-    final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
+    final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
+            MessageManager.getString("label.all_views"));
     buttonGroup.add(itemf);
     itemf.setSelected(treeCanvas.applyToAllViews);
     itemf.addActionListener(new ActionListener()
@@ -343,7 +345,7 @@ public class TreePanel extends GTreePanel
       av.setCurrentTree(tree);
       if (av.getSortByTree())
       {
-        sortByTree_actionPerformed(null);
+        sortByTree_actionPerformed();
       }
     }
   }
@@ -437,7 +439,8 @@ public class TreePanel extends GTreePanel
     JalviewFileChooser chooser = new JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(MessageManager.getString("label.save_tree_as_newick"));
+    chooser.setDialogTitle(MessageManager
+            .getString("label.save_tree_as_newick"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
 
     int value = chooser.showSaveDialog(null);
@@ -531,8 +534,8 @@ public class TreePanel extends GTreePanel
         // msaorder);
 
         Desktop.addInternalFrame(af, MessageManager.formatMessage(
-                "label.original_data_for_params", new String[]
-                { this.title }), AlignFrame.DEFAULT_WIDTH,
+                "label.original_data_for_params",
+                new Object[] { this.title }), AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
       }
     }
@@ -555,7 +558,8 @@ public class TreePanel extends GTreePanel
    * 
    * @param e
    */
-  public void sortByTree_actionPerformed(ActionEvent e)
+  @Override
+  public void sortByTree_actionPerformed()
   {
 
     if (treeCanvas.applyToAllViews)
@@ -617,7 +621,7 @@ 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;
@@ -730,10 +734,11 @@ public class TreePanel extends GTreePanel
     {
       jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
               jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-              { "eps" }, new String[]
-              { "Encapsulated Postscript" }, "Encapsulated Postscript");
+              { "eps" }, new String[] { "Encapsulated Postscript" },
+              "Encapsulated Postscript");
       chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle(MessageManager.getString("label.create_eps_from_tree"));
+      chooser.setDialogTitle(MessageManager
+              .getString("label.create_eps_from_tree"));
       chooser.setToolTipText(MessageManager.getString("action.save"));
 
       int value = chooser.showSaveDialog(this);
@@ -776,11 +781,12 @@ public class TreePanel extends GTreePanel
     {
       jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
               jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-              { "png" }, new String[]
-              { "Portable network graphics" }, "Portable network graphics");
+              { "png" }, new String[] { "Portable network graphics" },
+              "Portable network graphics");
 
       chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle(MessageManager.getString("label.create_png_from_tree"));
+      chooser.setDialogTitle(MessageManager
+              .getString("label.create_png_from_tree"));
       chooser.setToolTipText(MessageManager.getString("action.save"));
 
       int value = chooser.showSaveDialog(this);
@@ -834,8 +840,8 @@ public class TreePanel extends GTreePanel
           {
             // search dbrefs, features and annotation
             DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
-                    sq.getDBRef(), new String[]
-                    { labelClass.toUpperCase() });
+                    sq.getDBRef(),
+                    new String[] { labelClass.toUpperCase() });
             if (refs != null)
             {
               for (int i = 0; i < refs.length; i++)