X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=77c3b6acac1cf21985075a1967c47957e5c80bdb;hb=f52d7fc6ab9bf2c926f0208c225d3dc6e65c8ecf;hp=76001a5b561781b81c735bfb8fe46677f8af9fb1;hpb=b81d4d7d46ea8b1c89df086fb847baab6b69d427;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 76001a5..77c3b6a 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,13 +1,13 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 
  * 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 
@@ -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
    */
@@ -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();
@@ -718,7 +724,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     showSeqFeatures.setSelected(av.showSequenceFeatures);
     hiddenMarkers.setState(av.showHiddenMarkers);
-    applyToAllGroups.setState(av.colourAppliesToAllGroups);
+    applyToAllGroups.setState(av.getColourAppliesToAllGroups());
     showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
     showDbRefsMenuitem.setSelected(av.isShowDbRefs());
     autoCalculate.setSelected(av.autoCalculateConsensus);
@@ -732,6 +738,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     updateEditMenuBar();
   }
 
+  // methods for implementing IProgressIndicator
+  // need to refactor to a reusable stub class
   Hashtable progressBars, progressBarHandlers;
 
   /*
@@ -739,6 +747,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
    */
+  @Override
   public void setProgressBar(String message, long id)
   {
     if (progressBars == null)
@@ -786,6 +795,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     validate();
   }
 
+  @Override
   public void registerHandler(final long id,
           final IProgressIndicatorHandler handler)
   {
@@ -803,6 +813,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       cancel.addActionListener(new ActionListener()
       {
 
+        @Override
         public void actionPerformed(ActionEvent e)
         {
           handler.cancelActivity(id);
@@ -820,6 +831,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @return true if any progress bars are still active
    */
+  @Override
   public boolean operationInProgress()
   {
     if (progressBars != null && progressBars.size() > 0)
@@ -842,16 +854,19 @@ 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)
@@ -866,6 +881,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         for (int i = 0; i < frames.length; i++)
         {
           if (frames[i] instanceof AlignFrame && frames[i] != this
+                  && ((AlignFrame) frames[i]).fileName != null
                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
           {
             try
@@ -903,6 +919,7 @@ 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 +933,19 @@ 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
@@ -947,6 +967,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void saveAs_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
@@ -1038,9 +1059,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         }
       }
       FormatAdapter f = new FormatAdapter();
-      String output = f.formatSequences(
-              format,
-              (Alignment) viewport.getAlignment(), // class cast exceptions will
+      String output = f.formatSequences(format,
+              viewport.getAlignment(), // class cast exceptions will
               // occur in the distant future
               omitHidden, f.getCacheSuffixDefault(format),
               viewport.getColumnSelection());
@@ -1099,6 +1119,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void outputText_actionPerformed(ActionEvent e)
   {
     String[] omitHidden = null;
@@ -1144,6 +1165,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
     new HTMLOutput(alignPanel,
@@ -1162,6 +1184,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void createPNG(File f)
   {
     alignPanel.makePNG(f);
@@ -1173,11 +1196,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void createEPS(File f)
   {
     alignPanel.makeEPS(f);
   }
 
+  @Override
   public void pageSetup_actionPerformed(ActionEvent e)
   {
     PrinterJob printJob = PrinterJob.getPrinterJob();
@@ -1190,6 +1215,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void printMenuItem_actionPerformed(ActionEvent e)
   {
     // Putting in a thread avoids Swing painting problems
@@ -1197,11 +1223,13 @@ 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 +1239,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     .getAlignment()).alignmentProperties);
   }
 
+  @Override
   public void associatedData_actionPerformed(ActionEvent e)
   {
     // Pick the tree file
@@ -1237,6 +1266,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param closeAllTabs
    */
+  @Override
   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
   {
     if (alignPanels != null && alignPanels.size() < 2)
@@ -1384,6 +1414,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void undoMenuItem_actionPerformed(ActionEvent e)
   {
     if (viewport.historyList.empty())
@@ -1419,6 +1450,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void redoMenuItem_actionPerformed(ActionEvent e)
   {
     if (viewport.redoList.size() < 1)
@@ -1508,52 +1540,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       return;
     }
-
-    if (up)
-    {
-      for (int i = 1; i < viewport.getAlignment().getHeight(); i++)
-      {
-        SequenceI seq = viewport.getAlignment().getSequenceAt(i);
-
-        if (!sg.getSequences(null).contains(seq))
-        {
-          continue;
-        }
-
-        SequenceI temp = viewport.getAlignment().getSequenceAt(i - 1);
-
-        if (sg.getSequences(null).contains(temp))
-        {
-          continue;
-        }
-
-        viewport.getAlignment().getSequences().setElementAt(temp, i);
-        viewport.getAlignment().getSequences().setElementAt(seq, i - 1);
-      }
-    }
-    else
-    {
-      for (int i = viewport.getAlignment().getHeight() - 2; i > -1; i--)
-      {
-        SequenceI seq = viewport.getAlignment().getSequenceAt(i);
-
-        if (!sg.getSequences(null).contains(seq))
-        {
-          continue;
-        }
-
-        SequenceI temp = viewport.getAlignment().getSequenceAt(i + 1);
-
-        if (sg.getSequences(null).contains(temp))
-        {
-          continue;
-        }
-
-        viewport.getAlignment().getSequences().setElementAt(temp, i);
-        viewport.getAlignment().getSequences().setElementAt(seq, i + 1);
-      }
-    }
-
+    viewport.getAlignment().moveSelectedSequencesByOne(sg,
+            viewport.getHiddenRepSequences(), up);
     alignPanel.paintAlignment(true);
   }
 
@@ -1587,7 +1575,7 @@ 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);
@@ -1645,6 +1633,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void copy_actionPerformed(ActionEvent e)
   {
     System.gc();
@@ -1713,6 +1702,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void pasteNew_actionPerformed(ActionEvent e)
   {
     paste(true);
@@ -1724,6 +1714,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void pasteThis_actionPerformed(ActionEvent e)
   {
     paste(false);
@@ -1792,6 +1783,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
 
       int alwidth = 0;
+      ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
+      int fgroup = -1;
 
       if (newAlignment)
       {
@@ -1859,6 +1852,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         {
           newDs.clear(); // tidy up
         }
+        if (alignment.getAlignmentAnnotation() != null)
+        {
+          for (AlignmentAnnotation alan : alignment
+                  .getAlignmentAnnotation())
+          {
+            if (alan.graphGroup > fgroup)
+            {
+              fgroup = alan.graphGroup;
+            }
+          }
+        }
         if (pastedal.getAlignmentAnnotation() != null)
         {
           // Add any annotation attached to alignment.
@@ -1869,6 +1873,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
             {
               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
+              if (newann.graphGroup > -1)
+              {
+                if (newGraphGroups.size() <= newann.graphGroup
+                        || newGraphGroups.get(newann.graphGroup) == null)
+                {
+                  for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
+                  {
+                    newGraphGroups.add(q, null);
+                  }
+                  newGraphGroups.set(newann.graphGroup, new Integer(
+                          ++fgroup));
+                }
+                newann.graphGroup = newGraphGroups.get(newann.graphGroup)
+                        .intValue();
+              }
+
               newann.padAnnotation(alwidth);
               alignment.addAnnotation(newann);
             }
@@ -1888,11 +1908,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         if (sequences[i].getAnnotation() != null)
         {
+          AlignmentAnnotation newann;
           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
           {
             annotationAdded = true;
-            sequences[i].getAnnotation()[a].adjustForAlignment();
-            sequences[i].getAnnotation()[a].padAnnotation(alwidth);
+            newann = sequences[i].getAnnotation()[a];
+            newann.adjustForAlignment();
+            newann.padAnnotation(alwidth);
+            if (newann.graphGroup > -1)
+            {
+              if (newann.graphGroup > -1)
+              {
+                if (newGraphGroups.size() <= newann.graphGroup
+                        || newGraphGroups.get(newann.graphGroup) == null)
+                {
+                  for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
+                  {
+                    newGraphGroups.add(q, null);
+                  }
+                  newGraphGroups.set(newann.graphGroup, new Integer(
+                          ++fgroup));
+                }
+                newann.graphGroup = newGraphGroups.get(newann.graphGroup)
+                        .intValue();
+              }
+            }
             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
             // was
             // duplicated
@@ -1932,6 +1972,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   newann.padAnnotation(avwidth);
                   alview[avnum].addAnnotation(newann); // annotation was
                   // duplicated earlier
+                  // TODO JAL-1145 graphGroups are not updated for sequence
+                  // annotation added to several views. This may cause
+                  // strangeness
                   alview[avnum].setAnnotationIndex(newann, a);
                 }
               }
@@ -1941,6 +1984,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         }
         viewport.firePropertyChange("alignment", null,
                 alignment.getSequences());
+        if (alignPanels != null)
+        {
+          for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
+          {
+            ap.validateAnnotationDimensions(false);
+          }
+        }
+        else
+        {
+          alignPanel.validateAnnotationDimensions(false);
+        }
 
       }
       else
@@ -2004,6 +2058,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void cut_actionPerformed(ActionEvent e)
   {
     copy_actionPerformed(null);
@@ -2016,6 +2071,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void delete_actionPerformed(ActionEvent evt)
   {
 
@@ -2076,6 +2132,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
     viewport.getAlignment().deleteAllGroups();
@@ -2092,6 +2149,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
     SequenceGroup sg = new SequenceGroup();
@@ -2114,6 +2172,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
     if (viewport.cursorMode)
@@ -2137,6 +2196,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
   {
     SequenceGroup sg = viewport.getSelectionGroup();
@@ -2158,6 +2218,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.sendSelection();
   }
 
+  @Override
   public void invertColSel_actionPerformed(ActionEvent e)
   {
     viewport.invertColumnSelection();
@@ -2171,6 +2232,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
   {
     trimAlignment(true);
@@ -2182,6 +2244,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
   {
     trimAlignment(false);
@@ -2235,7 +2298,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       addHistoryItem(trimRegion);
 
-      for (SequenceGroup sg :viewport.getAlignment().getGroups())
+      for (SequenceGroup sg : viewport.getAlignment().getGroups())
       {
         if ((trimLeft && !sg.adjustForRemoveLeft(column))
                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
@@ -2255,6 +2318,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
   {
     int start = 0, end = viewport.getAlignment().getWidth() - 1;
@@ -2302,6 +2366,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
   {
     int start = 0, end = viewport.getAlignment().getWidth() - 1;
@@ -2340,6 +2405,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void padGapsMenuitem_actionPerformed(ActionEvent e)
   {
     viewport.setPadGaps(padGapsMenuitem.isSelected());
@@ -2363,11 +2429,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
     new Finder();
   }
 
+  @Override
   public void newView_actionPerformed(ActionEvent e)
   {
     newView(true);
@@ -2478,11 +2546,13 @@ 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);
@@ -2494,6 +2564,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void font_actionPerformed(ActionEvent e)
   {
     new FontChooser(alignPanel);
@@ -2505,6 +2576,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void seqLimit_actionPerformed(ActionEvent e)
   {
     viewport.setShowJVSuffix(seqLimits.isSelected());
@@ -2514,12 +2586,14 @@ 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();
@@ -2531,6 +2605,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
    */
+  @Override
   protected void followHighlight_actionPerformed()
   {
     if (viewport.followHighlight = this.followHighlightMenuItem.getState())
@@ -2546,6 +2621,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setColourText(colourTextMenuItem.isSelected());
@@ -2558,6 +2634,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void wrapMenuItem_actionPerformed(ActionEvent e)
   {
     scaleAbove.setVisible(wrapMenuItem.isSelected());
@@ -2567,17 +2644,20 @@ 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();
@@ -2661,6 +2741,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
    * event.ActionEvent)
    */
+  @Override
   public void hideAllButSelection_actionPerformed(ActionEvent e)
   {
     toggleHiddenRegions(false, false);
@@ -2673,6 +2754,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
    * .ActionEvent)
    */
+  @Override
   public void hideAllSelection_actionPerformed(ActionEvent e)
   {
     SequenceGroup sg = viewport.getSelectionGroup();
@@ -2689,6 +2771,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
    * ActionEvent)
    */
+  @Override
   public void showAllhidden_actionPerformed(ActionEvent e)
   {
     viewport.showAllHiddenColumns();
@@ -2696,12 +2779,14 @@ 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());
@@ -2714,6 +2799,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void scaleAbove_actionPerformed(ActionEvent e)
   {
     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
@@ -2726,6 +2812,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void scaleLeft_actionPerformed(ActionEvent e)
   {
     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
@@ -2738,6 +2825,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void scaleRight_actionPerformed(ActionEvent e)
   {
     viewport.setScaleRightWrapped(scaleRight.isSelected());
@@ -2750,6 +2838,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
@@ -2762,6 +2851,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void viewTextMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowText(viewTextMenuItem.isSelected());
@@ -2774,6 +2864,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
@@ -2782,6 +2873,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   public FeatureSettings featureSettings;
 
+  @Override
   public void featureSettings_actionPerformed(ActionEvent e)
   {
     if (featureSettings != null)
@@ -2804,6 +2896,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void showSeqFeatures_actionPerformed(ActionEvent evt)
   {
     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
@@ -2820,6 +2913,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
   {
     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
@@ -2843,12 +2937,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @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", "");
@@ -2869,6 +2965,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void overviewMenuItem_actionPerformed(ActionEvent e)
   {
     if (alignPanel.overviewPanel != null)
@@ -2885,6 +2982,7 @@ 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)
       {
@@ -2895,6 +2993,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     alignPanel.setOverviewPanel(overview);
   }
 
+  @Override
   public void textColour_actionPerformed(ActionEvent e)
   {
     new TextColourChooser().chooseColour(alignPanel, null);
@@ -2906,6 +3005,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void noColourmenuItem_actionPerformed(ActionEvent e)
   {
     changeColour(null);
@@ -2917,9 +3017,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void clustalColour_actionPerformed(ActionEvent e)
   {
-    changeColour(new ClustalxColourScheme(viewport.getAlignment(), viewport.getHiddenRepSequences()));
+    changeColour(new ClustalxColourScheme(viewport.getAlignment(),
+            viewport.getHiddenRepSequences()));
   }
 
   /**
@@ -2928,6 +3030,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void zappoColour_actionPerformed(ActionEvent e)
   {
     changeColour(new ZappoColourScheme());
@@ -2939,6 +3042,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void taylorColour_actionPerformed(ActionEvent e)
   {
     changeColour(new TaylorColourScheme());
@@ -2950,6 +3054,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void hydrophobicityColour_actionPerformed(ActionEvent e)
   {
     changeColour(new HydrophobicColourScheme());
@@ -2961,6 +3066,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void helixColour_actionPerformed(ActionEvent e)
   {
     changeColour(new HelixColourScheme());
@@ -2972,6 +3078,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void strandColour_actionPerformed(ActionEvent e)
   {
     changeColour(new StrandColourScheme());
@@ -2983,6 +3090,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void turnColour_actionPerformed(ActionEvent e)
   {
     changeColour(new TurnColourScheme());
@@ -2994,6 +3102,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void buriedColour_actionPerformed(ActionEvent e)
   {
     changeColour(new BuriedColourScheme());
@@ -3005,11 +3114,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void nucleotideColour_actionPerformed(ActionEvent e)
   {
     changeColour(new NucleotideColourScheme());
   }
 
+  @Override
   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
   {
     changeColour(new PurinePyrimidineColourScheme());
@@ -3021,11 +3132,13 @@ 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);
@@ -3037,6 +3150,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void applyToAllGroups_actionPerformed(ActionEvent e)
   {
     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
@@ -3098,8 +3212,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (viewport.getColourAppliesToAllGroups())
     {
 
-
-      for (SequenceGroup sg:viewport.getAlignment().getGroups())
+      for (SequenceGroup sg : viewport.getAlignment().getGroups())
       {
         if (cs == null)
         {
@@ -3109,8 +3222,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
         if (cs instanceof ClustalxColourScheme)
         {
-          sg.cs = new ClustalxColourScheme(sg, viewport
-                  .getHiddenRepSequences());
+          sg.cs = new ClustalxColourScheme(sg,
+                  viewport.getHiddenRepSequences());
         }
         else if (cs instanceof UserColourScheme)
         {
@@ -3172,6 +3285,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void modifyPID_actionPerformed(ActionEvent e)
   {
     if (viewport.getAbovePIDThreshold()
@@ -3189,6 +3303,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void modifyConservation_actionPerformed(ActionEvent e)
   {
     if (viewport.getConservationSelected()
@@ -3206,6 +3321,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void conservationMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setConservationSelected(conservationMenuItem.isSelected());
@@ -3224,6 +3340,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void abovePIDThreshold_actionPerformed(ActionEvent e)
   {
     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
@@ -3242,6 +3359,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void userDefinedColour_actionPerformed(ActionEvent e)
   {
     if (e.getActionCommand().equals("User Defined..."))
@@ -3283,6 +3401,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         radioItem.setName("USER_DEFINED");
         radioItem.addMouseListener(new MouseAdapter()
         {
+          @Override
           public void mousePressed(MouseEvent evt)
           {
             if (evt.isControlDown()
@@ -3305,6 +3424,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               {
                 radioItem.addActionListener(new ActionListener()
                 {
+                  @Override
                   public void actionPerformed(ActionEvent evt)
                   {
                     userDefinedColour_actionPerformed(evt);
@@ -3316,6 +3436,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         });
         radioItem.addActionListener(new ActionListener()
         {
+          @Override
           public void actionPerformed(ActionEvent evt)
           {
             userDefinedColour_actionPerformed(evt);
@@ -3334,6 +3455,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void PIDColour_actionPerformed(ActionEvent e)
   {
     changeColour(new PIDColourScheme());
@@ -3345,6 +3467,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
     changeColour(new Blosum62ColourScheme());
@@ -3356,6 +3479,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
   {
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
@@ -3372,6 +3496,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void sortIDMenuItem_actionPerformed(ActionEvent e)
   {
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
@@ -3387,6 +3512,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
   {
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
@@ -3402,6 +3528,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
   {
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
@@ -3418,6 +3545,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
   {
     new RedundancyPanel(alignPanel, this);
@@ -3429,6 +3557,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
   {
     if ((viewport.getSelectionGroup() == null)
@@ -3452,6 +3581,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void PCAMenuItem_actionPerformed(ActionEvent e)
   {
     if (((viewport.getSelectionGroup() != null)
@@ -3471,6 +3601,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     new PCAPanel(alignPanel);
   }
 
+  @Override
   public void autoCalculate_actionPerformed(ActionEvent e)
   {
     viewport.autoCalculateConsensus = autoCalculate.isSelected();
@@ -3481,6 +3612,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
+  @Override
   public void sortByTreeOption_actionPerformed(ActionEvent e)
   {
     viewport.sortByTree = sortByTree.isSelected();
@@ -3498,6 +3630,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
   {
     NewTreePanel("AV", "PID", "Average distance tree using PID");
@@ -3509,6 +3642,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
   {
     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
@@ -3520,6 +3654,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
   {
     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
@@ -3531,6 +3666,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
   {
     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
@@ -3550,7 +3686,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     TreePanel tp;
 
-    if (viewport.getSelectionGroup() != null)
+    if (viewport.getSelectionGroup() != null
+            && viewport.getSelectionGroup().getSize() > 0)
     {
       if (viewport.getSelectionGroup().getSize() < 3)
       {
@@ -3565,10 +3702,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       SequenceGroup sg = viewport.getSelectionGroup();
 
       /* Decide if the selection is a column region */
-      for (SequenceI _s:sg.getSequences())
+      for (SequenceI _s : sg.getSequences())
       {
-        if (_s.getLength() < sg
-                .getEndRes())
+        if (_s.getLength() < sg.getEndRes())
         {
           JOptionPane
                   .showMessageDialog(
@@ -3638,6 +3774,7 @@ 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();
@@ -3670,6 +3807,7 @@ 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();
@@ -3694,6 +3832,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * rebuilding in subsequence calls.
    * 
    */
+  @Override
   public void buildSortByAnnotationScoresMenu()
   {
     if (viewport.getAlignment().getAlignmentAnnotation() == null)
@@ -3707,10 +3846,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // almost certainly a quicker way to do this - but we keep it simple
       Hashtable scoreSorts = new Hashtable();
       AlignmentAnnotation aann[];
-      Enumeration sq = viewport.getAlignment().getSequences().elements();
-      while (sq.hasMoreElements())
+      for (SequenceI sqa : viewport.getAlignment().getSequences())
       {
-        aann = ((SequenceI) sq.nextElement()).getAnnotation();
+        aann = sqa.getAnnotation();
         for (int i = 0; aann != null && i < aann.length; i++)
         {
           if (aann[i].hasScore() && aann[i].sequenceRef != null)
@@ -3745,6 +3883,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param title
    *          SortBy menu item title.
    */
+  @Override
   public void buildTreeMenu()
   {
     sortByTreeMenu.removeAll();
@@ -3778,6 +3917,7 @@ 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);
@@ -3883,6 +4023,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
   {
     // Pick the tree file
@@ -4014,6 +4155,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     buildingMenu = true;
     new Thread(new Runnable()
     {
+      @Override
       public void run()
       {
         try
@@ -4037,7 +4179,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   "Secondary Structure Prediction");
           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
           final JMenu analymenu = new JMenu("Analysis");
-          final JMenu dismenu = new JMenu("Disorder");
+          final JMenu dismenu = new JMenu("Protein Disorder");
           // JAL-940 - only show secondary structure prediction services from
           // the legacy server
           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
@@ -4112,6 +4254,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
           javax.swing.SwingUtilities.invokeLater(new Runnable()
           {
+            @Override
             public void run()
             {
               try
@@ -4122,7 +4265,7 @@ 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
@@ -4164,6 +4307,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 }
               } catch (Exception e)
               {
+                Cache.log
+                        .debug("Exception during web service menu building process.",
+                                e);
               }
               ;
             }
@@ -4286,6 +4432,7 @@ 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
@@ -4319,6 +4466,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     Runnable foo = new Runnable()
     {
 
+      @Override
       public void run()
       {
         final long sttime = System.currentTimeMillis();
@@ -4402,6 +4550,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
+  @Override
   public void showProducts_actionPerformed(ActionEvent e)
   {
     // /////////////////////////////
@@ -4435,6 +4584,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
+  @Override
   public void showTranslation_actionPerformed(ActionEvent e)
   {
     // /////////////////////////////
@@ -4513,22 +4663,27 @@ 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();
@@ -4758,11 +4913,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             }
             else
             {
-              // some problem - if no warning its probable that the ID matching process didn't work
-              JOptionPane.showMessageDialog(Desktop.desktop,
-                      tcf.getWarningMessage()==null ? "Check that the file matches sequence IDs in the alignment." : tcf.getWarningMessage(),
-                      "Problem reading T-COFFEE score file",
-                      JOptionPane.WARNING_MESSAGE);
+              // some problem - if no warning its probable that the ID matching
+              // process didn't work
+              JOptionPane
+                      .showMessageDialog(
+                              Desktop.desktop,
+                              tcf.getWarningMessage() == null ? "Check that the file matches sequence IDs in the alignment."
+                                      : tcf.getWarningMessage(),
+                              "Problem reading T-COFFEE score file",
+                              JOptionPane.WARNING_MESSAGE);
             }
           }
           else
@@ -4771,7 +4930,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
         } catch (Exception x)
         {
-          Cache.log.debug("Exception when processing data source as T-COFFEE score file",x);
+          Cache.log
+                  .debug("Exception when processing data source as T-COFFEE score file",
+                          x);
           tcf = null;
         }
         if (tcf == null)
@@ -4840,9 +5001,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     } catch (Exception ex)
     {
       ex.printStackTrace();
+    } catch (OutOfMemoryError oom)
+    {
+      try
+      {
+        System.gc();
+      } catch (Exception x)
+      {
+      }
+      ;
+      new OOMWarning(
+              "loading data "
+                      + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
+                              : "using " + protocol + " from " + file)
+                              : ".")
+                      + (format != null ? "(parsing as '" + format
+                              + "' file)" : ""), oom, Desktop.desktop);
     }
   }
 
+  @Override
   public void tabSelectionChanged(int index)
   {
     if (index > -1)
@@ -4853,6 +5031,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
+  @Override
   public void tabbedPane_mousePressed(MouseEvent e)
   {
     if (SwingUtilities.isRightMouseButton(e))
@@ -4877,6 +5056,7 @@ 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(
@@ -4899,6 +5079,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
    * )
    */
+  @Override
   protected void showDbRefs_actionPerformed(ActionEvent e)
   {
     viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
@@ -4910,6 +5091,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
    * ActionEvent)
    */
+  @Override
   protected void showNpFeats_actionPerformed(ActionEvent e)
   {
     viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
@@ -4959,11 +5141,13 @@ 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
@@ -4979,12 +5163,14 @@ 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();
@@ -5025,11 +5211,13 @@ 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
@@ -5057,11 +5245,13 @@ 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
@@ -5102,11 +5292,13 @@ 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
@@ -5154,6 +5346,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Left justify the whole alignment.
    */
+  @Override
   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
   {
     AlignmentI al = viewport.getAlignment();
@@ -5164,6 +5357,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Right justify the whole alignment.
    */
+  @Override
   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
   {
     AlignmentI al = viewport.getAlignment();
@@ -5184,6 +5378,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
    * awt.event.ActionEvent)
    */
+  @Override
   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
@@ -5197,6 +5392,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
    * .ActionEvent)
    */
+  @Override
   protected void showGroupConsensus_actionPerformed(ActionEvent e)
   {
     viewport.setShowGroupConsensus(showGroupConsensus.getState());
@@ -5211,6 +5407,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
    * .event.ActionEvent)
    */
+  @Override
   protected void showGroupConservation_actionPerformed(ActionEvent e)
   {
     viewport.setShowGroupConservation(showGroupConservation.getState());
@@ -5224,6 +5421,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
    * .event.ActionEvent)
    */
+  @Override
   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
   {
     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
@@ -5237,18 +5435,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 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)
   {
+    showSequenceLogo.setState(true);
+    viewport.setShowSequenceLogo(true);
     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
   }
 
+  @Override
   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
   {
     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
@@ -5261,6 +5464,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
    * .event.ActionEvent)
    */
+  @Override
   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
   {
     if (viewport.getSelectionGroup() != null)
@@ -5282,10 +5486,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         Color col = new Color((int) (Math.random() * 255),
                 (int) (Math.random() * 255), (int) (Math.random() * 255));
         col = col.brighter();
-        for (SequenceI s:gps[g].getSequences())
-          viewport.setSequenceColour(
-                s, col)
-          ;
+        for (SequenceI s : gps[g].getSequences())
+          viewport.setSequenceColour(s, col);
       }
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
       alignPanel.updateAnnotation();
@@ -5326,6 +5528,7 @@ class PrintThread extends Thread
 
   static PageFormat pf;
 
+  @Override
   public void run()
   {
     PrinterJob printJob = PrinterJob.getPrinterJob();