X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=304cfb757ea8d90f802c12d56e3ca1c6b52fce88;hb=f52f7b378972cc884b5d3e5cc250f89667f558f7;hp=d8157c00cfa601c99c6644298150aef57ab98c00;hpb=6357db6c20614a666b7b446aeb3260c5379637eb;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d8157c0..304cfb7 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,18 +1,18 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- * 
+ *
  * This file is part of Jalview.
- * 
+ *
  * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License 
+ * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
- * Jalview is distributed in the hope that it will be useful, but 
- * WITHOUT ANY WARRANTY; without even the implied warranty 
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  * PURPOSE.  See the GNU General Public License for more details.
- * 
+ *
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.gui;
@@ -127,7 +127,7 @@ import javax.swing.SwingUtilities;
 
 /**
  * DOCUMENT ME!
- * 
+ *
  * @author $author$
  * @version $Revision$
  */
@@ -146,7 +146,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   AlignViewport viewport;
 
   Vector alignPanels = new Vector();
-  
+
   /**
    * Last format used to load or save alignments in this window
    */
@@ -159,7 +159,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * Creates a new AlignFrame object with specific width and height.
-   * 
+   *
    * @param al
    * @param width
    * @param height
@@ -172,7 +172,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Creates a new AlignFrame object with specific width, height and
    * sequenceSetId
-   * 
+   *
    * @param al
    * @param width
    * @param height
@@ -187,7 +187,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Creates a new AlignFrame object with specific width, height and
    * sequenceSetId
-   * 
+   *
    * @param al
    * @param width
    * @param height
@@ -202,7 +202,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * new alignment window with hidden columns
-   * 
+   *
    * @param al
    *          AlignmentI
    * @param hiddenColumns
@@ -221,7 +221,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Create alignment frame for al with hiddenColumns, a specific width and
    * height, and specific sequenceId
-   * 
+   *
    * @param al
    * @param hiddenColumns
    * @param width
@@ -238,7 +238,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Create alignment frame for al with hiddenColumns, a specific width and
    * height, and specific sequenceId
-   * 
+   *
    * @param al
    * @param hiddenColumns
    * @param width
@@ -267,7 +267,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * Make a new AlignFrame from exisiting alignmentPanels
-   * 
+   *
    * @param ap
    *          AlignmentPanel
    * @param av
@@ -335,7 +335,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Change the filename and format for the alignment, and enable the 'reload'
    * button functionality.
-   * 
+   *
    * @param file
    *          valid filename
    * @param format
@@ -352,6 +352,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     addKeyListener(new KeyAdapter()
     {
+      @Override
       public void keyPressed(KeyEvent evt)
       {
         if (viewport.cursorMode
@@ -532,6 +533,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         }
       }
 
+      @Override
       public void keyReleased(KeyEvent evt)
       {
         switch (evt.getKeyCode())
@@ -616,6 +618,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     Desktop.instance.addJalviewPropertyChangeListener("services",
             thisListener = new java.beans.PropertyChangeListener()
             {
+              @Override
               public void propertyChange(PropertyChangeEvent evt)
               {
                 // // System.out.println("Discoverer property change.");
@@ -624,6 +627,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   SwingUtilities.invokeLater(new Runnable()
                   {
 
+                    @Override
                     public void run()
                     {
                       System.err
@@ -637,6 +641,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             });
     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
     {
+      @Override
       public void internalFrameClosed(
               javax.swing.event.InternalFrameEvent evt)
       {
@@ -649,6 +654,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // Finally, build the menu once to get current service state
     new Thread(new Runnable()
     {
+      @Override
       public void run()
       {
         BuildWebServiceMenu();
@@ -685,7 +691,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Need to call this method when tabs are selected for multiple views, or when
    * loading from Jalview2XML.java
-   * 
+   *
    * @param av
    *          AlignViewport
    */
@@ -736,9 +742,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   * 
+   *
    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
    */
+  @Override
   public void setProgressBar(String message, long id)
   {
     if (progressBars == null)
@@ -786,6 +793,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     validate();
   }
 
+  @Override
   public void registerHandler(final long id,
           final IProgressIndicatorHandler handler)
   {
@@ -803,6 +811,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       cancel.addActionListener(new ActionListener()
       {
 
+        @Override
         public void actionPerformed(ActionEvent e)
         {
           handler.cancelActivity(id);
@@ -817,7 +826,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * 
+   *
    * @return true if any progress bars are still active
    */
   public boolean operationInProgress()
@@ -842,16 +851,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
   }
 
+  @Override
   public void fetchSequence_actionPerformed(ActionEvent e)
   {
     new SequenceFetcher(this);
   }
 
+  @Override
   public void addFromFile_actionPerformed(ActionEvent e)
   {
     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
   }
 
+  @Override
   public void reload_actionPerformed(ActionEvent e)
   {
     if (fileName != null)
@@ -903,6 +915,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           final FeatureSettings nfs = newframe.featureSettings;
           SwingUtilities.invokeLater(new Runnable()
           {
+            @Override
             public void run()
             {
               nfs.frame.setBounds(fspos);
@@ -916,16 +929,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
+  @Override
   public void addFromText_actionPerformed(ActionEvent e)
   {
     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
   }
 
+  @Override
   public void addFromURL_actionPerformed(ActionEvent e)
   {
     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
   }
 
+  @Override
   public void save_actionPerformed(ActionEvent e)
   {
     if (fileName == null
@@ -943,10 +959,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void saveAs_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
@@ -1040,7 +1057,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       FormatAdapter f = new FormatAdapter();
       String output = f.formatSequences(
               format,
-              (Alignment) viewport.getAlignment(), // class cast exceptions will
+              viewport.getAlignment(), // class cast exceptions will
               // occur in the distant future
               omitHidden, f.getCacheSuffixDefault(format),
               viewport.getColumnSelection());
@@ -1095,10 +1112,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void outputText_actionPerformed(ActionEvent e)
   {
     String[] omitHidden = null;
@@ -1140,10 +1158,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
     new HTMLOutput(alignPanel,
@@ -1158,10 +1177,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void createPNG(File f)
   {
     alignPanel.makePNG(f);
@@ -1169,15 +1189,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void createEPS(File f)
   {
     alignPanel.makeEPS(f);
   }
 
+  @Override
   public void pageSetup_actionPerformed(ActionEvent e)
   {
     PrinterJob printJob = PrinterJob.getPrinterJob();
@@ -1186,10 +1208,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void printMenuItem_actionPerformed(ActionEvent e)
   {
     // Putting in a thread avoids Swing painting problems
@@ -1197,11 +1220,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     thread.start();
   }
 
+  @Override
   public void exportFeatures_actionPerformed(ActionEvent e)
   {
     new AnnotationExporter().exportFeatures(alignPanel);
   }
 
+  @Override
   public void exportAnnotations_actionPerformed(ActionEvent e)
   {
     new AnnotationExporter().exportAnnotations(alignPanel,
@@ -1211,6 +1236,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     .getAlignment()).alignmentProperties);
   }
 
+  @Override
   public void associatedData_actionPerformed(ActionEvent e)
   {
     // Pick the tree file
@@ -1234,9 +1260,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Close the current view or all views in the alignment frame. If the frame
    * only contains one view then the alignment will be removed from memory.
-   * 
+   *
    * @param closeAllTabs
    */
+  @Override
   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
   {
     if (alignPanels != null && alignPanels.size() < 2)
@@ -1279,7 +1306,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * close alignPanel2 and shuffle tabs appropriately.
-   * 
+   *
    * @param alignPanel2
    */
   public void closeView(AlignmentPanel alignPanel2)
@@ -1355,7 +1382,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * 
+   *
    * @return alignment objects for all views
    */
   AlignmentI[] getViewAlignments()
@@ -1380,10 +1407,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void undoMenuItem_actionPerformed(ActionEvent e)
   {
     if (viewport.historyList.empty())
@@ -1415,10 +1443,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void redoMenuItem_actionPerformed(ActionEvent e)
   {
     if (viewport.redoList.size() < 1)
@@ -1496,7 +1525,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param up
    *          DOCUMENT ME!
    */
@@ -1542,7 +1571,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
-            
+
     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
     for (int i = 0; i < invertGroup.size(); i++)
       seqs2[i] = (SequenceI) invertGroup.elementAt(i);
@@ -1596,10 +1625,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void copy_actionPerformed(ActionEvent e)
   {
     System.gc();
@@ -1664,10 +1694,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void pasteNew_actionPerformed(ActionEvent e)
   {
     paste(true);
@@ -1675,10 +1706,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void pasteThis_actionPerformed(ActionEvent e)
   {
     paste(false);
@@ -1686,7 +1718,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * Paste contents of Jalview clipboard
-   * 
+   *
    * @param newAlignment
    *          true to paste to a new alignment, otherwise add to this.
    */
@@ -1955,10 +1987,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void cut_actionPerformed(ActionEvent e)
   {
     copy_actionPerformed(null);
@@ -1967,10 +2000,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void delete_actionPerformed(ActionEvent evt)
   {
 
@@ -2027,10 +2061,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
     viewport.getAlignment().deleteAllGroups();
@@ -2043,10 +2078,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
     SequenceGroup sg = new SequenceGroup();
@@ -2065,10 +2101,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
     if (viewport.cursorMode)
@@ -2088,10 +2125,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
   {
     SequenceGroup sg = viewport.getSelectionGroup();
@@ -2113,6 +2151,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.sendSelection();
   }
 
+  @Override
   public void invertColSel_actionPerformed(ActionEvent e)
   {
     viewport.invertColumnSelection();
@@ -2122,10 +2161,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
   {
     trimAlignment(true);
@@ -2133,10 +2173,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
   {
     trimAlignment(false);
@@ -2206,10 +2247,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
   {
     int start = 0, end = viewport.getAlignment().getWidth() - 1;
@@ -2253,10 +2295,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
   {
     int start = 0, end = viewport.getAlignment().getWidth() - 1;
@@ -2291,10 +2334,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void padGapsMenuitem_actionPerformed(ActionEvent e)
   {
     viewport.setPadGaps(padGapsMenuitem.isSelected());
@@ -2314,22 +2358,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
     new Finder();
   }
 
+  @Override
   public void newView_actionPerformed(ActionEvent e)
   {
     newView(true);
   }
 
   /**
-   * 
+   *
    * @param copyAnnotation
    *          if true then duplicate all annnotation, groups and settings
    * @return new alignment panel, already displayed.
@@ -2340,7 +2386,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * 
+   *
    * @param viewTitle
    *          title of newly created view
    * @return new alignment panel, already displayed.
@@ -2351,7 +2397,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * 
+   *
    * @param viewTitle
    *          title of newly created view
    * @param copyAnnotation
@@ -2433,11 +2479,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return newap;
   }
 
+  @Override
   public void expandViews_actionPerformed(ActionEvent e)
   {
     Desktop.instance.explodeViews(this);
   }
 
+  @Override
   public void gatherViews_actionPerformed(ActionEvent e)
   {
     Desktop.instance.gatherViews(this);
@@ -2445,10 +2493,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void font_actionPerformed(ActionEvent e)
   {
     new FontChooser(alignPanel);
@@ -2456,10 +2505,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void seqLimit_actionPerformed(ActionEvent e)
   {
     viewport.setShowJVSuffix(seqLimits.isSelected());
@@ -2469,12 +2519,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     alignPanel.paintAlignment(true);
   }
 
+  @Override
   public void idRightAlign_actionPerformed(ActionEvent e)
   {
     viewport.rightAlignIds = idRightAlign.isSelected();
     alignPanel.paintAlignment(true);
   }
 
+  @Override
   public void centreColumnLabels_actionPerformed(ActionEvent e)
   {
     viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
@@ -2483,9 +2535,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   * 
+   *
    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
    */
+  @Override
   protected void followHighlight_actionPerformed()
   {
     if (viewport.followHighlight = this.followHighlightMenuItem.getState())
@@ -2497,10 +2550,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setColourText(colourTextMenuItem.isSelected());
@@ -2509,10 +2563,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void wrapMenuItem_actionPerformed(ActionEvent e)
   {
     scaleAbove.setVisible(wrapMenuItem.isSelected());
@@ -2522,17 +2577,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
   }
 
+  @Override
   public void showAllSeqs_actionPerformed(ActionEvent e)
   {
     viewport.showAllHiddenSeqs();
   }
 
+  @Override
   public void showAllColumns_actionPerformed(ActionEvent e)
   {
     viewport.showAllHiddenColumns();
     repaint();
   }
 
+  @Override
   public void hideSelSequences_actionPerformed(ActionEvent e)
   {
     viewport.hideAllSelectedSeqs();
@@ -2541,7 +2599,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * called by key handler and the hide all/show all menu items
-   * 
+   *
    * @param toggleSeqs
    * @param toggleCols
    */
@@ -2611,11 +2669,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   * 
+   *
    * @see
    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
    * event.ActionEvent)
    */
+  @Override
   public void hideAllButSelection_actionPerformed(ActionEvent e)
   {
     toggleHiddenRegions(false, false);
@@ -2623,11 +2682,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   * 
+   *
    * @see
    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
    * .ActionEvent)
    */
+  @Override
   public void hideAllSelection_actionPerformed(ActionEvent e)
   {
     SequenceGroup sg = viewport.getSelectionGroup();
@@ -2639,11 +2699,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   * 
+   *
    * @see
    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
    * ActionEvent)
    */
+  @Override
   public void showAllhidden_actionPerformed(ActionEvent e)
   {
     viewport.showAllHiddenColumns();
@@ -2651,12 +2712,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     alignPanel.paintAlignment(true);
   }
 
+  @Override
   public void hideSelColumns_actionPerformed(ActionEvent e)
   {
     viewport.hideSelectedColumns();
     alignPanel.paintAlignment(true);
   }
 
+  @Override
   public void hiddenMarkers_actionPerformed(ActionEvent e)
   {
     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
@@ -2665,10 +2728,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void scaleAbove_actionPerformed(ActionEvent e)
   {
     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
@@ -2677,10 +2741,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void scaleLeft_actionPerformed(ActionEvent e)
   {
     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
@@ -2689,10 +2754,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void scaleRight_actionPerformed(ActionEvent e)
   {
     viewport.setScaleRightWrapped(scaleRight.isSelected());
@@ -2701,10 +2767,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
@@ -2713,10 +2780,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void viewTextMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowText(viewTextMenuItem.isSelected());
@@ -2725,10 +2793,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
@@ -2737,6 +2806,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   public FeatureSettings featureSettings;
 
+  @Override
   public void featureSettings_actionPerformed(ActionEvent e)
   {
     if (featureSettings != null)
@@ -2755,10 +2825,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * Set or clear 'Show Sequence Features'
-   * 
+   *
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void showSeqFeatures_actionPerformed(ActionEvent evt)
   {
     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
@@ -2771,10 +2842,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * Set or clear 'Show Sequence Features'
-   * 
+   *
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
   {
     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
@@ -2794,16 +2866,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
     alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
   }
 
+  @Override
   public void alignmentProperties()
   {
     JEditorPane editPane = new JEditorPane("text/html", "");
@@ -2820,10 +2894,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void overviewMenuItem_actionPerformed(ActionEvent e)
   {
     if (alignPanel.overviewPanel != null)
@@ -2840,6 +2915,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
     {
+      @Override
       public void internalFrameClosed(
               javax.swing.event.InternalFrameEvent evt)
       {
@@ -2850,6 +2926,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     alignPanel.setOverviewPanel(overview);
   }
 
+  @Override
   public void textColour_actionPerformed(ActionEvent e)
   {
     new TextColourChooser().chooseColour(alignPanel, null);
@@ -2857,10 +2934,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void noColourmenuItem_actionPerformed(ActionEvent e)
   {
     changeColour(null);
@@ -2868,10 +2946,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void clustalColour_actionPerformed(ActionEvent e)
   {
     changeColour(new ClustalxColourScheme(viewport.getAlignment(), viewport.getHiddenRepSequences()));
@@ -2879,10 +2958,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void zappoColour_actionPerformed(ActionEvent e)
   {
     changeColour(new ZappoColourScheme());
@@ -2890,10 +2970,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void taylorColour_actionPerformed(ActionEvent e)
   {
     changeColour(new TaylorColourScheme());
@@ -2901,10 +2982,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void hydrophobicityColour_actionPerformed(ActionEvent e)
   {
     changeColour(new HydrophobicColourScheme());
@@ -2912,10 +2994,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void helixColour_actionPerformed(ActionEvent e)
   {
     changeColour(new HelixColourScheme());
@@ -2923,10 +3006,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void strandColour_actionPerformed(ActionEvent e)
   {
     changeColour(new StrandColourScheme());
@@ -2934,10 +3018,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void turnColour_actionPerformed(ActionEvent e)
   {
     changeColour(new TurnColourScheme());
@@ -2945,10 +3030,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void buriedColour_actionPerformed(ActionEvent e)
   {
     changeColour(new BuriedColourScheme());
@@ -2956,15 +3042,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void nucleotideColour_actionPerformed(ActionEvent e)
   {
     changeColour(new NucleotideColourScheme());
   }
 
+  @Override
   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
   {
     changeColour(new PurinePyrimidineColourScheme());
@@ -2976,11 +3064,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
    * ()[0])); }
    */
+  @Override
   public void annotationColour_actionPerformed(ActionEvent e)
   {
     new AnnotationColourChooser(viewport, alignPanel);
   }
 
+  @Override
   public void rnahelicesColour_actionPerformed(ActionEvent e)
   {
     new RNAHelicesColourChooser(viewport, alignPanel);
@@ -2988,10 +3078,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void applyToAllGroups_actionPerformed(ActionEvent e)
   {
     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
@@ -2999,7 +3090,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param cs
    *          DOCUMENT ME!
    */
@@ -3123,10 +3214,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void modifyPID_actionPerformed(ActionEvent e)
   {
     if (viewport.getAbovePIDThreshold()
@@ -3140,10 +3232,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void modifyConservation_actionPerformed(ActionEvent e)
   {
     if (viewport.getConservationSelected()
@@ -3157,10 +3250,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void conservationMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setConservationSelected(conservationMenuItem.isSelected());
@@ -3175,10 +3269,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void abovePIDThreshold_actionPerformed(ActionEvent e)
   {
     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
@@ -3193,10 +3288,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void userDefinedColour_actionPerformed(ActionEvent e)
   {
     if (e.getActionCommand().equals("User Defined..."))
@@ -3238,6 +3334,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         radioItem.setName("USER_DEFINED");
         radioItem.addMouseListener(new MouseAdapter()
         {
+          @Override
           public void mousePressed(MouseEvent evt)
           {
             if (evt.isControlDown()
@@ -3260,6 +3357,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               {
                 radioItem.addActionListener(new ActionListener()
                 {
+                  @Override
                   public void actionPerformed(ActionEvent evt)
                   {
                     userDefinedColour_actionPerformed(evt);
@@ -3271,6 +3369,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         });
         radioItem.addActionListener(new ActionListener()
         {
+          @Override
           public void actionPerformed(ActionEvent evt)
           {
             userDefinedColour_actionPerformed(evt);
@@ -3285,10 +3384,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void PIDColour_actionPerformed(ActionEvent e)
   {
     changeColour(new PIDColourScheme());
@@ -3296,10 +3396,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
     changeColour(new Blosum62ColourScheme());
@@ -3307,10 +3408,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
   {
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
@@ -3323,10 +3425,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void sortIDMenuItem_actionPerformed(ActionEvent e)
   {
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
@@ -3338,10 +3441,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
   {
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
@@ -3353,10 +3457,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
   {
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
@@ -3369,10 +3474,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
   {
     new RedundancyPanel(alignPanel, this);
@@ -3380,10 +3486,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
   {
     if ((viewport.getSelectionGroup() == null)
@@ -3403,10 +3510,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void PCAMenuItem_actionPerformed(ActionEvent e)
   {
     if (((viewport.getSelectionGroup() != null)
@@ -3426,6 +3534,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     new PCAPanel(alignPanel);
   }
 
+  @Override
   public void autoCalculate_actionPerformed(ActionEvent e)
   {
     viewport.autoCalculateConsensus = autoCalculate.isSelected();
@@ -3436,6 +3545,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
+  @Override
   public void sortByTreeOption_actionPerformed(ActionEvent e)
   {
     viewport.sortByTree = sortByTree.isSelected();
@@ -3449,10 +3559,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
   {
     NewTreePanel("AV", "PID", "Average distance tree using PID");
@@ -3460,10 +3571,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
   {
     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
@@ -3471,10 +3583,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
   {
     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
@@ -3482,10 +3595,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
   {
     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
@@ -3493,7 +3607,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param type
    *          DOCUMENT ME!
    * @param pwType
@@ -3580,7 +3694,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param title
    *          DOCUMENT ME!
    * @param order
@@ -3593,6 +3707,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     sort.add(item);
     item.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
@@ -3611,7 +3726,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * Add a new sort by annotation score menu item
-   * 
+   *
    * @param sort
    *          the menu to add the option to
    * @param scoreLabel
@@ -3625,6 +3740,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     sort.add(item);
     item.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
@@ -3647,8 +3763,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * search the alignment and rebuild the sort by annotation score submenu the
    * last alignment annotation vector hash is stored to minimize cost of
    * rebuilding in subsequence calls.
-   * 
+   *
    */
+  @Override
   public void buildSortByAnnotationScoresMenu()
   {
     if (viewport.getAlignment().getAlignmentAnnotation() == null)
@@ -3693,12 +3810,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * call. Listeners are added to remove the menu item when the treePanel is
    * closed, and adjust the tree leaf to sequence mapping when the alignment is
    * modified.
-   * 
+   *
    * @param treePanel
    *          Displayed tree window.
    * @param title
    *          SortBy menu item title.
    */
+  @Override
   public void buildTreeMenu()
   {
     sortByTreeMenu.removeAll();
@@ -3732,6 +3850,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
       item.addActionListener(new java.awt.event.ActionListener()
       {
+        @Override
         public void actionPerformed(ActionEvent e)
         {
           tp.sortByTree_actionPerformed(null);
@@ -3760,7 +3879,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Work out whether the whole set of sequences or just the selected set will
    * be submitted for multiple alignment.
-   * 
+   *
    */
   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
   {
@@ -3775,7 +3894,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       /*
        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
        * SequenceI[sz = seqs.getSize(false)];
-       * 
+       *
        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
        * seqs.getSequenceAt(i); }
        */
@@ -3785,9 +3904,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       /*
        * Vector seqs = viewport.getAlignment().getSequences();
-       * 
+       *
        * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
-       * 
+       *
        * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
        * seqs.elementAt(i); } }
        */
@@ -3833,10 +3952,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
   {
     // Pick the tree file
@@ -3898,7 +4018,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Add a treeviewer for the tree extracted from a newick file object to the
    * current alignment view
-   * 
+   *
    * @param nf
    *          the tree
    * @param title
@@ -3949,7 +4069,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * Generates menu items and listener event actions for web service clients
-   * 
+   *
    */
   public void BuildWebServiceMenu()
   {
@@ -3968,6 +4088,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     buildingMenu = true;
     new Thread(new Runnable()
     {
+      @Override
       public void run()
       {
         try
@@ -4066,6 +4187,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
           javax.swing.SwingUtilities.invokeLater(new Runnable()
           {
+            @Override
             public void run()
             {
               try
@@ -4076,7 +4198,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 {
                   for (int i = 0, j = wsmenu.size(); i < j; i++)
                   {
-                    webService.add((JMenu) wsmenu.get(i));
+                    webService.add(wsmenu.get(i));
                   }
                 }
                 else
@@ -4135,7 +4257,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * construct any groupURL type service menu entries.
-   * 
+   *
    * @param webService
    */
   private void build_urlServiceMenu(JMenu webService)
@@ -4145,12 +4267,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     /*
      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
-     * 
+     *
      * @Override public void actionPerformed(ActionEvent e) {
      * jalview.datamodel.AlignmentView
      * .testSelectionViews(af.viewport.getAlignment(),
      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
-     * 
+     *
      * }); webService.add(testAlView);
      */
     // TODO: refactor to RestClient discoverer and merge menu entries for
@@ -4177,12 +4299,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
    * chooser = new JalviewFileChooser(jalview.bin.Cache.
    * getProperty("LAST_DIRECTORY"));
-   * 
+   *
    * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
    * to Vamsas file"); chooser.setToolTipText("Export");
-   * 
+   *
    * int value = chooser.showSaveDialog(this);
-   * 
+   *
    * if (value == JalviewFileChooser.APPROVE_OPTION) {
    * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
    * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
@@ -4190,7 +4312,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   /**
    * prototype of an automatically enabled/disabled analysis function
-   * 
+   *
    */
   protected void setShowProductsEnabled()
   {
@@ -4210,7 +4332,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * search selection for sequence xRef products and build the show products
    * menu.
-   * 
+   *
    * @param selection
    * @param dataset
    * @return true if showProducts menu should be enabled.
@@ -4240,6 +4362,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         xtype.addActionListener(new ActionListener()
         {
 
+          @Override
           public void actionPerformed(ActionEvent e)
           {
             // TODO: new thread for this call with vis-delay
@@ -4273,6 +4396,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     Runnable foo = new Runnable()
     {
 
+      @Override
       public void run()
       {
         final long sttime = System.currentTimeMillis();
@@ -4356,6 +4480,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
+  @Override
   public void showProducts_actionPerformed(ActionEvent e)
   {
     // /////////////////////////////
@@ -4389,6 +4514,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
+  @Override
   public void showTranslation_actionPerformed(ActionEvent e)
   {
     // /////////////////////////////
@@ -4427,7 +4553,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * Try to load a features file onto the alignment.
-   * 
+   *
    * @param file
    *          contents or path to retrieve file
    * @param type
@@ -4467,22 +4593,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return featuresFile;
   }
 
+  @Override
   public void dragEnter(DropTargetDragEvent evt)
   {
   }
 
+  @Override
   public void dragExit(DropTargetEvent evt)
   {
   }
 
+  @Override
   public void dragOver(DropTargetDragEvent evt)
   {
   }
 
+  @Override
   public void dropActionChanged(DropTargetDragEvent evt)
   {
   }
 
+  @Override
   public void drop(DropTargetDropEvent evt)
   {
     Transferable t = evt.getTransferable();
@@ -4671,7 +4802,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * it's and Annotation file, then a JNet file, and finally a features file. If
    * all are false then the user may have dropped an alignment file onto this
    * AlignFrame.
-   * 
+   *
    * @param file
    *          either a filename or a URL string.
    */
@@ -4749,7 +4880,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           {
             /*
              * if (format.equalsIgnoreCase("PDB")) {
-             * 
+             *
              * String pdbfn = ""; // try to match up filename with sequence id
              * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
              * new File(file); pdbfn = fl.getName(); } else if (protocol ==
@@ -4797,6 +4928,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
+  @Override
   public void tabSelectionChanged(int index)
   {
     if (index > -1)
@@ -4807,6 +4939,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
+  @Override
   public void tabbedPane_mousePressed(MouseEvent e)
   {
     if (SwingUtilities.isRightMouseButton(e))
@@ -4831,6 +4964,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Open the dialog for regex description parsing.
    */
+  @Override
   protected void extractScores_actionPerformed(ActionEvent e)
   {
     ParseProperties pp = new jalview.analysis.ParseProperties(
@@ -4848,11 +4982,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   * 
+   *
    * @see
    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
    * )
    */
+  @Override
   protected void showDbRefs_actionPerformed(ActionEvent e)
   {
     viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
@@ -4860,10 +4995,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   * 
+   *
    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
    * ActionEvent)
    */
+  @Override
   protected void showNpFeats_actionPerformed(ActionEvent e)
   {
     viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
@@ -4872,7 +5008,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * find the viewport amongst the tabs in this alignment frame and close that
    * tab
-   * 
+   *
    * @param av
    */
   public boolean closeView(AlignViewport av)
@@ -4913,11 +5049,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     fetchr.addActionListener(new ActionListener()
     {
 
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         new Thread(new Runnable()
         {
 
+          @Override
           public void run()
           {
             new jalview.ws.DBRefFetcher(alignPanel.av
@@ -4933,12 +5071,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     final AlignFrame me = this;
     new Thread(new Runnable()
     {
+      @Override
       public void run()
       {
         final jalview.ws.SequenceFetcher sf = SequenceFetcher
                 .getSequenceFetcherSingleton(me);
         javax.swing.SwingUtilities.invokeLater(new Runnable()
         {
+          @Override
           public void run()
           {
             String[] dbclasses = sf.getOrderedSupportedSources();
@@ -4979,11 +5119,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 fetchr.addActionListener(new ActionListener()
                 {
 
+                  @Override
                   public void actionPerformed(ActionEvent e)
                   {
                     new Thread(new Runnable()
                     {
 
+                      @Override
                       public void run()
                       {
                         new jalview.ws.DBRefFetcher(alignPanel.av
@@ -5011,11 +5153,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                         + "'");
                 fetchr.addActionListener(new ActionListener()
                 {
+                  @Override
                   public void actionPerformed(ActionEvent e)
                   {
                     new Thread(new Runnable()
                     {
 
+                      @Override
                       public void run()
                       {
                         new jalview.ws.DBRefFetcher(alignPanel.av
@@ -5056,11 +5200,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   fetchr.addActionListener(new ActionListener()
                   {
 
+                    @Override
                     public void actionPerformed(ActionEvent e)
                     {
                       new Thread(new Runnable()
                       {
 
+                        @Override
                         public void run()
                         {
                           new jalview.ws.DBRefFetcher(alignPanel.av
@@ -5108,6 +5254,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Left justify the whole alignment.
    */
+  @Override
   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
   {
     AlignmentI al = viewport.getAlignment();
@@ -5118,6 +5265,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Right justify the whole alignment.
    */
+  @Override
   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
   {
     AlignmentI al = viewport.getAlignment();
@@ -5133,11 +5281,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   * 
+   *
    * @see
    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
    * awt.event.ActionEvent)
    */
+  @Override
   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
@@ -5146,11 +5295,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   * 
+   *
    * @see
    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
    * .ActionEvent)
    */
+  @Override
   protected void showGroupConsensus_actionPerformed(ActionEvent e)
   {
     viewport.setShowGroupConsensus(showGroupConsensus.getState());
@@ -5160,11 +5310,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   * 
+   *
    * @see
    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
    * .event.ActionEvent)
    */
+  @Override
   protected void showGroupConservation_actionPerformed(ActionEvent e)
   {
     viewport.setShowGroupConservation(showGroupConservation.getState());
@@ -5173,11 +5324,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   * 
+   *
    * @see
    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
    * .event.ActionEvent)
    */
+  @Override
   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
   {
     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
@@ -5186,23 +5338,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   * 
+   *
    * @see
    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
    * .event.ActionEvent)
    */
+  @Override
   protected void showSequenceLogo_actionPerformed(ActionEvent e)
   {
     viewport.setShowSequenceLogo(showSequenceLogo.getState());
     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
   }
 
+  @Override
   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
   {
     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
   }
 
+  @Override
   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
   {
     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
@@ -5210,11 +5365,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   * 
+   *
    * @see
    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
    * .event.ActionEvent)
    */
+  @Override
   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
   {
     if (viewport.getSelectionGroup() != null)
@@ -5249,7 +5405,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * make the given alignmentPanel the currently selected tab
-   * 
+   *
    * @param alignmentPanel
    */
   public void setDisplayedView(AlignmentPanel alignmentPanel)
@@ -5280,6 +5436,7 @@ class PrintThread extends Thread
 
   static PageFormat pf;
 
+  @Override
   public void run()
   {
     PrinterJob printJob = PrinterJob.getPrinterJob();