X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=a06c6d8846ff658d5a2427325551d711a24282a9;hb=909eba506e9353290500a5d2e70eb53068cbdc5f;hp=f74eb3226a171a69f167506aec88621c4a2b2a3d;hpb=11fbdf6f34deffb5b179e23ffc3ca50dcae296dc;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index f74eb32..a06c6d8 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -20,59 +20,6 @@
  */
 package jalview.gui;
 
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Component;
-import java.awt.Dimension;
-import java.awt.Rectangle;
-import java.awt.Toolkit;
-import java.awt.datatransfer.Clipboard;
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.StringSelection;
-import java.awt.datatransfer.Transferable;
-import java.awt.dnd.DnDConstants;
-import java.awt.dnd.DropTargetDragEvent;
-import java.awt.dnd.DropTargetDropEvent;
-import java.awt.dnd.DropTargetEvent;
-import java.awt.dnd.DropTargetListener;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.FocusAdapter;
-import java.awt.event.FocusEvent;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.awt.event.KeyAdapter;
-import java.awt.event.KeyEvent;
-import java.awt.event.MouseEvent;
-import java.awt.print.PageFormat;
-import java.awt.print.PrinterJob;
-import java.beans.PropertyChangeEvent;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.PrintWriter;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Deque;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
-import javax.swing.ButtonGroup;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JComponent;
-import javax.swing.JEditorPane;
-import javax.swing.JInternalFrame;
-import javax.swing.JLabel;
-import javax.swing.JLayeredPane;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JPanel;
-import javax.swing.JScrollPane;
-import javax.swing.SwingUtilities;
-
-import ext.vamsas.ServiceHandle;
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.CrossRef;
@@ -156,6 +103,60 @@ import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
+import java.awt.dnd.DropTargetDragEvent;
+import java.awt.dnd.DropTargetDropEvent;
+import java.awt.dnd.DropTargetEvent;
+import java.awt.dnd.DropTargetListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseEvent;
+import java.awt.print.PageFormat;
+import java.awt.print.PrinterJob;
+import java.beans.PropertyChangeEvent;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.PrintWriter;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Deque;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JComponent;
+import javax.swing.JEditorPane;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JLayeredPane;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+
+import ext.vamsas.ServiceHandle;
+
 /**
  * DOCUMENT ME!
  * 
@@ -168,7 +169,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 {
 
   public static int frameCount;
-  
+
   public static final int DEFAULT_WIDTH = 700;
 
   public static final int DEFAULT_HEIGHT = 500;
@@ -292,9 +293,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
           int height, String sequenceSetId, String viewId)
   {
-    
+
     id = (++frameCount);
-    
+
     setSize(width, height);
 
     if (al.getDataset() == null)
@@ -304,9 +305,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 
-    alignPanel = new AlignmentPanel(this, viewport);
-
-    addAlignmentPanel(alignPanel, true);
+    // JalviewJS needs to distinguish a new panel from an old one in init()
+    // alignPanel = new AlignmentPanel(this, viewport);
+    // addAlignmentPanel(alignPanel, true);
     init();
   }
 
@@ -326,8 +327,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       viewport.hideSequence(hiddenSeqs);
     }
-    alignPanel = new AlignmentPanel(this, viewport);
-    addAlignmentPanel(alignPanel, true);
+    // alignPanel = new AlignmentPanel(this, viewport);
+    // addAlignmentPanel(alignPanel, true);
     init();
   }
 
@@ -343,7 +344,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport = ap.av;
     alignPanel = ap;
-    addAlignmentPanel(ap, false);
+    // addAlignmentPanel(ap, false);
     init();
   }
 
@@ -351,13 +352,39 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * initalise the alignframe from the underlying viewport data and the
    * configurations
    */
+
   void init()
   {
+
+    boolean newPanel = (alignPanel == null);
+    viewport.setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
+    if (newPanel)
+    {
+      if (Platform.isJS())
+      {
+        // need to set this up front if NOANNOTATION is
+        // used in conjunction with SHOWOVERVIEW.
+
+        // I have not determined if this is appropriate for
+        // Jalview/Java, as it means we are setting this flag
+        // for all subsequent AlignFrames. For now, at least,
+        // I am setting it to be JalviewJS-only.
+
+        boolean showAnnotation = Jalview.getInstance().getShowAnnotation();
+        viewport.setShowAnnotation(showAnnotation);
+      }
+      alignPanel = new AlignmentPanel(this, viewport);
+    }
+    addAlignmentPanel(alignPanel, newPanel);
+
     // setBackground(Color.white); // BH 2019
 
     if (!Jalview.isHeadlessMode())
     {
       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
+      // JalviewJS options
+      statusPanel.setVisible(Jalview.getInstance().getShowStatus());
+      alignFrameMenuBar.setVisible(Jalview.getInstance().getAllowMenuBar());
     }
 
     avc = new jalview.controller.AlignViewController(this, viewport,
@@ -372,7 +399,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // modifyPID.setEnabled(false);
     }
 
-    String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
+    String sortby = jalview.bin.Cache.getDefault(Preferences.SORT_ALIGNMENT,
             "No sort");
 
     if (sortby.equals("Id"))
@@ -384,8 +411,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       sortPairwiseMenuItem_actionPerformed(null);
     }
 
-    this.alignPanel.av
-            .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
+    // BH see above
+    //
+    // this.alignPanel.av
+    // .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 
     setMenusFromViewport(viewport);
     buildSortByAnnotationScoresMenu();
@@ -415,7 +444,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       wrapMenuItem_actionPerformed(null);
     }
 
-    if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
+    if (jalview.bin.Cache.getDefault(Preferences.SHOW_OVERVIEW, false))
     {
       this.overviewMenuItem_actionPerformed(null);
     }
@@ -499,6 +528,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     addFocusListener(new FocusAdapter()
     {
+
       @Override
       public void focusGained(FocusEvent e)
       {
@@ -517,6 +547,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param format
    *          format of file
    */
+
   public void setFileName(String file, FileFormatI format)
   {
     fileName = file;
@@ -530,6 +561,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param file
    */
+
   public void setFileObject(File file)
   {
     this.fileObject = file;
@@ -539,10 +571,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
    * events
    */
+
   void addKeyListener()
   {
     addKeyListener(new KeyAdapter()
     {
+
       @Override
       public void keyPressed(KeyEvent evt)
       {
@@ -559,7 +593,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         switch (evt.getKeyCode())
         {
 
-        case 27: // escape key
+        case KeyEvent.VK_ESCAPE: // escape key
+                                 // alignPanel.deselectAllSequences();
           alignPanel.deselectAllSequences();
 
           break;
@@ -743,16 +778,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         case KeyEvent.VK_LEFT:
           if (evt.isAltDown() || !viewport.cursorMode)
           {
-            viewport.firePropertyChange("alignment", null,
-                    viewport.getAlignment().getSequences());
+            viewport.notifyAlignment();
           }
           break;
 
         case KeyEvent.VK_RIGHT:
           if (evt.isAltDown() || !viewport.cursorMode)
           {
-            viewport.firePropertyChange("alignment", null,
-                    viewport.getAlignment().getSequences());
+            viewport.notifyAlignment();
           }
           break;
         }
@@ -798,9 +831,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         ap.av.getAlignment().padGaps();
       }
-      ap.av.updateConservation(ap);
-      ap.av.updateConsensus(ap);
-      ap.av.updateStrucConsensus(ap);
+      if (Jalview.getInstance().getStartCalculations())
+      {
+        ap.av.updateConservation(ap);
+        ap.av.updateConsensus(ap);
+        ap.av.updateStrucConsensus(ap);
+      }
     }
   }
 
@@ -826,6 +862,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     Desktop.getInstance().addJalviewPropertyChangeListener("services",
             thisListener = new java.beans.PropertyChangeListener()
             {
+
               @Override
               public void propertyChange(PropertyChangeEvent evt)
               {
@@ -849,6 +886,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             });
     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
     {
+
       @Override
       public void internalFrameClosed(
               javax.swing.event.InternalFrameEvent evt)
@@ -862,6 +900,7 @@ 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()
       {
@@ -874,6 +913,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * Configure menu items that vary according to whether the alignment is
    * nucleotide or protein
    */
+
   public void setGUINucleotide()
   {
     AlignmentI al = getViewport().getAlignment();
@@ -898,6 +938,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * operation that affects the data in the current view (selection changed,
    * etc) to update the menus to reflect the new state.
    */
+
   @Override
   public void setMenusForViewport()
   {
@@ -911,6 +952,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param av
    *          AlignViewport
    */
+
   public void setMenusFromViewport(AlignViewport av)
   {
     padGapsMenuitem.setSelected(av.isPadGaps());
@@ -928,13 +970,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     scaleLeft.setVisible(av.getWrapAlignment());
     scaleRight.setVisible(av.getWrapAlignment());
     annotationPanelMenuItem.setState(av.isShowAnnotation());
-    /*
-     * Show/hide annotations only enabled if annotation panel is shown
-     */
-    showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
-    hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
-    showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
-    hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
+    // Show/hide annotations only enabled if annotation panel is shown
+    syncAnnotationMenuItems(av.isShowAnnotation());
     viewBoxesMenuItem.setSelected(av.getShowBoxes());
     viewTextMenuItem.setSelected(av.getShowText());
     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
@@ -952,7 +989,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
-    autoCalculate.setSelected(av.autoCalculateConsensus);
+    autoCalculate
+            .setSelected(av.getAutoCalculateConsensusAndConservation());
     sortByTree.setSelected(av.sortByTree);
     listenToViewSelections.setSelected(av.followSelection);
 
@@ -967,6 +1005,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param b
    */
+
   public void setGroovyEnabled(boolean b)
   {
     runGroovy.setEnabled(b);
@@ -979,6 +1018,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
    */
+
   @Override
   public void setProgressBar(String message, long id)
   {
@@ -996,6 +1036,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @return true if any progress bars are still active
    */
+
   @Override
   public boolean operationInProgress()
   {
@@ -1007,6 +1048,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * will cause the status bar to be hidden, with possibly undesirable flicker
    * of the screen layout.
    */
+
   @Override
   public void setStatus(String text)
   {
@@ -1016,6 +1058,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /*
    * Added so Castor Mapping file can obtain Jalview Version
    */
+
   public String getVersion()
   {
     return jalview.bin.Cache.getProperty("VERSION");
@@ -1041,84 +1084,87 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void reload_actionPerformed(ActionEvent e)
   {
-    if (fileName != null)
+    if (fileName == null)
     {
-      // TODO: JAL-1108 - ensure all associated frames are closed regardless of
-      // originating file's format
-      // TODO: work out how to recover feature settings for correct view(s) when
-      // file is reloaded.
-      if (FileFormat.Jalview.equals(currentFileFormat))
+      return;
+    }
+    // TODO: JAL-1108 - ensure all associated frames are closed regardless of
+    // originating file's format
+    // TODO: work out how to recover feature settings for correct view(s) when
+    // file is reloaded.
+    if (FileFormat.Jalview.equals(currentFileFormat))
+    {
+      JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
+      for (int i = 0; i < frames.length; i++)
       {
-        JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
-        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))
         {
-          if (frames[i] instanceof AlignFrame && frames[i] != this
-                  && ((AlignFrame) frames[i]).fileName != null
-                  && ((AlignFrame) frames[i]).fileName.equals(fileName))
+          try
+          {
+            frames[i].setSelected(true);
+            Desktop.getInstance().closeAssociatedWindows();
+          } catch (java.beans.PropertyVetoException ex)
           {
-            try
-            {
-              frames[i].setSelected(true);
-              Desktop.getInstance().closeAssociatedWindows();
-            } catch (java.beans.PropertyVetoException ex)
-            {
-            }
           }
-
         }
-        Desktop.getInstance().closeAssociatedWindows();
 
-        FileLoader loader = new FileLoader();
-        DataSourceType protocol = fileName.startsWith("http:")
-                ? DataSourceType.URL
-                : DataSourceType.FILE;
-        loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
       }
-      else
-      {
-        Rectangle bounds = this.getBounds();
+      Desktop.getInstance().closeAssociatedWindows();
 
-        FileLoader loader = new FileLoader();
+      FileLoader loader = new FileLoader();
+      DataSourceType protocol = fileName.startsWith("http:")
+              ? DataSourceType.URL
+              : DataSourceType.FILE;
+      loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
+    }
+    else
+    {
+      Rectangle bounds = this.getBounds();
 
-        AlignFrame newframe = null;
+      FileLoader loader = new FileLoader();
 
-        if (fileObject == null)
-        {
+      AlignFrame newframe = null;
 
-          DataSourceType protocol = (fileName.startsWith("http:")
-                  ? DataSourceType.URL
-                  : DataSourceType.FILE);
-          newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
-                  currentFileFormat);
-        }
-        else
-        {
-          newframe = loader.LoadFileWaitTillLoaded(fileObject,
-                  DataSourceType.FILE, currentFileFormat);
-        }
+      if (fileObject == null)
+      {
+
+        DataSourceType protocol = (fileName.startsWith("http:")
+                ? DataSourceType.URL
+                : DataSourceType.FILE);
+        newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
+                currentFileFormat);
+      }
+      else
+      {
+        newframe = loader.LoadFileWaitTillLoaded(fileObject,
+                DataSourceType.FILE, currentFileFormat);
+      }
 
-        newframe.setBounds(bounds);
-        if (featureSettings != null && featureSettings.isShowing())
+      newframe.setBounds(bounds);
+      if (featureSettings != null && featureSettings.isShowing())
+      {
+        final Rectangle fspos = featureSettings.frame.getBounds();
+        // TODO: need a 'show feature settings' function that takes bounds -
+        // need to refactor Desktop.addFrame
+        newframe.featureSettings_actionPerformed(null);
+        final FeatureSettings nfs = newframe.featureSettings;
+        SwingUtilities.invokeLater(new Runnable()
         {
-          final Rectangle fspos = featureSettings.frame.getBounds();
-          // TODO: need a 'show feature settings' function that takes bounds -
-          // need to refactor Desktop.addFrame
-          newframe.featureSettings_actionPerformed(null);
-          final FeatureSettings nfs = newframe.featureSettings;
-          SwingUtilities.invokeLater(new Runnable()
+
+          @Override
+          public void run()
           {
-            @Override
-            public void run()
-            {
-              nfs.frame.setBounds(fspos);
-            }
-          });
-          this.featureSettings.close();
-          this.featureSettings = null;
-        }
-        this.closeMenuItem_actionPerformed(true);
+            nfs.frame.setBounds(fspos);
+          }
+        });
+        this.featureSettings.close();
+        this.featureSettings = null;
       }
+      this.closeMenuItem_actionPerformed(true);
     }
+
   }
 
   @Override
@@ -1152,6 +1198,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * Saves the alignment to a file with a name chosen by the user, if necessary
    * warning if a file would be overwritten
    */
+
   @Override
   public void saveAs_actionPerformed()
   {
@@ -1206,6 +1253,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    *
    * @return true if last call to saveAlignment(file, format) was successful.
    */
+
   public boolean isSaveAlignmentSuccessful()
   {
 
@@ -1238,6 +1286,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param file
    * @param format
    */
+
   public void saveAlignment(String file, FileFormatI format)
   {
     lastSaveSuccessful = true;
@@ -1265,6 +1314,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
     Runnable cancelAction = new Runnable()
     {
+
       @Override
       public void run()
       {
@@ -1273,6 +1323,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     };
     Runnable outputAction = new Runnable()
     {
+
       @Override
       public void run()
       {
@@ -1347,6 +1398,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param fileFormatName
    */
+
   @Override
   protected void outputText_actionPerformed(String fileFormatName)
   {
@@ -1355,6 +1407,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
     Runnable outputAction = new Runnable()
     {
+
       @Override
       public void run()
       {
@@ -1405,6 +1458,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
@@ -1419,12 +1473,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     bjs.exportHTML(null);
   }
 
+  // ??
+
+  public void createImageMap(File file, String image)
+  {
+    alignPanel.makePNGImageMap(file, image);
+  }
+
   /**
    * Creates a PNG image of the alignment and writes it to the given file. If
    * the file is null, the user is prompted to choose a file.
    * 
    * @param f
    */
+
   @Override
   public void createPNG(File f)
   {
@@ -1437,6 +1499,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param f
    */
+
   @Override
   public void createEPS(File f)
   {
@@ -1449,6 +1512,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param f
    */
+
   @Override
   public void createSVG(File f)
   {
@@ -1468,6 +1532,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void printMenuItem_actionPerformed(ActionEvent e)
   {
@@ -1500,6 +1565,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     chooser.setToolTipText(tooltip);
     chooser.setResponseHandler(0, new Runnable()
     {
+
       @Override
       public void run()
       {
@@ -1518,6 +1584,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param closeAllTabs
    */
+
   @Override
   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
   {
@@ -1572,6 +1639,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param panelToClose
    */
+
   public void closeView(AlignmentPanel panelToClose)
   {
     int index = tabbedPane.getSelectedIndex();
@@ -1595,6 +1663,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * DOCUMENT ME!
    */
+
   void updateEditMenuBar()
   {
 
@@ -1648,6 +1717,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @return alignment objects for all views
    */
+
   AlignmentI[] getViewAlignments()
   {
     if (alignPanels != null)
@@ -1673,6 +1743,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   protected void undoMenuItem_actionPerformed(ActionEvent e)
   {
@@ -1700,8 +1771,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // && viewport.getColumnSelection().getHiddenColumns() != null &&
       // viewport.getColumnSelection()
       // .getHiddenColumns().size() > 0);
-      originalSource.firePropertyChange("alignment", null,
-              originalSource.getAlignment().getSequences());
+      originalSource.notifyAlignment();
+
     }
   }
 
@@ -1711,6 +1782,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   protected void redoMenuItem_actionPerformed(ActionEvent e)
   {
@@ -1740,8 +1812,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // && viewport.getColumnSelection().getHiddenColumns() != null &&
       // viewport.getColumnSelection()
       // .getHiddenColumns().size() > 0);
-      originalSource.firePropertyChange("alignment", null,
-              originalSource.getAlignment().getSequences());
+      originalSource.notifyAlignment();
+
     }
   }
 
@@ -1793,6 +1865,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param up
    *          DOCUMENT ME!
    */
+
   public void moveSelectedSequences(boolean up)
   {
     SequenceGroup sg = viewport.getSelectionGroup();
@@ -1917,6 +1990,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   protected void copy_actionPerformed()
   {
@@ -1939,9 +2013,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     StringSelection ss = new StringSelection(output);
 
+    Desktop d = Desktop.getInstance();
     try
     {
-      Desktop.getInstance().internalCopy = true;
+      d.internalCopy = true;
       // Its really worth setting the clipboard contents
       // to empty before setting the large StringSelection!!
       Toolkit.getDefaultToolkit().getSystemClipboard()
@@ -1968,7 +2043,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               hiddenCutoff, hiddenOffset);
     }
 
-    Desktop.getInstance().jalviewClipboard = new Object[] { seqs,
+    d.jalviewClipboard = new Object[] { seqs,
         viewport.getAlignment().getDataset(), hiddenColumns };
     setStatus(MessageManager.formatMessage(
             "label.copied_sequences_to_clipboard", new Object[]
@@ -1981,6 +2056,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   protected void pasteNew_actionPerformed(ActionEvent e)
   {
@@ -1993,6 +2069,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   protected void pasteThis_actionPerformed(ActionEvent e)
   {
@@ -2005,10 +2082,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param newAlignment
    *          true to paste to a new alignment, otherwise add to this.
    */
+
   void paste(boolean newAlignment)
   {
     boolean externalPaste = true;
-    Desktop d = Desktop.getInstance();
     try
     {
       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
@@ -2041,6 +2118,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       boolean annotationAdded = false;
       AlignmentI alignment = null;
 
+      Desktop d = Desktop.getInstance();
+
       if (d.jalviewClipboard != null)
       {
         // The clipboard was filled from within Jalview, we must use the
@@ -2272,8 +2351,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           buildSortByAnnotationScoresMenu();
         }
-        viewport.firePropertyChange("alignment", null,
-                alignment.getSequences());
+        viewport.notifyAlignment();
         if (alignPanels != null)
         {
           for (AlignmentPanel ap : alignPanels)
@@ -2389,6 +2467,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Action Cut (delete and copy) the selected region
    */
+
   @Override
   protected void cut_actionPerformed()
   {
@@ -2399,6 +2478,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Performs menu option to Delete the currently selected region
    */
+
   @Override
   protected void delete_actionPerformed()
   {
@@ -2411,6 +2491,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     Runnable okAction = new Runnable()
     {
+
       @Override
       public void run()
       {
@@ -2427,8 +2508,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         viewport.sendSelection();
         viewport.getAlignment().deleteGroup(sg);
 
-        viewport.firePropertyChange("alignment", null,
-                viewport.getAlignment().getSequences());
+        viewport.notifyAlignment();
+
         if (viewport.getAlignment().getHeight() < 1)
         {
           try
@@ -2473,6 +2554,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
@@ -2490,6 +2572,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
@@ -2502,6 +2585,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
@@ -2514,6 +2598,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
   {
@@ -2553,6 +2638,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
   {
@@ -2565,6 +2651,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
   {
@@ -2626,8 +2713,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         }
       }
 
-      viewport.firePropertyChange("alignment", null,
-              viewport.getAlignment().getSequences());
+      viewport.notifyAlignment();
+
     }
   }
 
@@ -2637,6 +2724,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
   {
@@ -2676,8 +2764,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // if (viewport.hasHiddenColumns)
     // viewport.getColumnSelection().compensateForEdits(shifts);
     ranges.setStartRes(seq.findIndex(startRes) - 1);
-    viewport.firePropertyChange("alignment", null,
-            viewport.getAlignment().getSequences());
+    viewport.notifyAlignment();
+
 
   }
 
@@ -2687,6 +2775,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
   {
@@ -2714,9 +2803,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             viewport.getAlignment()));
 
     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
-
-    viewport.firePropertyChange("alignment", null,
-            viewport.getAlignment().getSequences());
+    viewport.notifyAlignment();
 
   }
 
@@ -2726,12 +2813,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void padGapsMenuitem_actionPerformed(ActionEvent e)
   {
     viewport.setPadGaps(padGapsMenuitem.isSelected());
-    viewport.firePropertyChange("alignment", null,
-            viewport.getAlignment().getSequences());
+    viewport.notifyAlignment();
+
   }
 
   /**
@@ -2740,6 +2828,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
@@ -2749,6 +2838,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Create a new view of the current alignment.
    */
+
   @Override
   public void newView_actionPerformed(ActionEvent e)
   {
@@ -2764,6 +2854,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    *          if true then duplicate all annnotation, groups and settings
    * @return new alignment panel, already displayed.
    */
+
   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
   {
     /*
@@ -2836,6 +2927,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param viewTitle
    * @return
    */
+
   protected String getNewViewName(String viewTitle)
   {
     int index = Desktop.getViewCount(viewport.getSequenceSetId());
@@ -2870,6 +2962,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param comps
    * @return
    */
+
   protected List<String> getExistingViewNames(List<Component> comps)
   {
     List<String> existingNames = new ArrayList<>();
@@ -2890,6 +2983,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Explode tabbed views into separate windows.
    */
+
   @Override
   public void expandViews_actionPerformed(ActionEvent e)
   {
@@ -2899,6 +2993,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Gather views in separate windows back into a tabbed presentation.
    */
+
   @Override
   public void gatherViews_actionPerformed(ActionEvent e)
   {
@@ -2911,6 +3006,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void font_actionPerformed(ActionEvent e)
   {
@@ -2923,6 +3019,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   protected void seqLimit_actionPerformed(ActionEvent e)
   {
@@ -2952,6 +3049,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
    */
+
   @Override
   protected void followHighlight_actionPerformed()
   {
@@ -2973,6 +3071,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
@@ -2986,6 +3085,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void wrapMenuItem_actionPerformed(ActionEvent e)
   {
@@ -3022,6 +3122,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param toggleSeqs
    * @param toggleCols
    */
+
   protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
   {
 
@@ -3089,6 +3190,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
    * event.ActionEvent)
    */
+
   @Override
   public void hideAllButSelection_actionPerformed(ActionEvent e)
   {
@@ -3103,6 +3205,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
    * .ActionEvent)
    */
+
   @Override
   public void hideAllSelection_actionPerformed(ActionEvent e)
   {
@@ -3122,6 +3225,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
    * ActionEvent)
    */
+
   @Override
   public void showAllhidden_actionPerformed(ActionEvent e)
   {
@@ -3153,6 +3257,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   protected void scaleAbove_actionPerformed(ActionEvent e)
   {
@@ -3167,6 +3272,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   protected void scaleLeft_actionPerformed(ActionEvent e)
   {
@@ -3181,6 +3287,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   protected void scaleRight_actionPerformed(ActionEvent e)
   {
@@ -3195,6 +3302,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
   {
@@ -3208,6 +3316,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void viewTextMenuItem_actionPerformed(ActionEvent e)
   {
@@ -3221,6 +3330,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
   {
@@ -3266,6 +3376,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param evt
    *          DOCUMENT ME!
    */
+
   @Override
   public void showSeqFeatures_actionPerformed(ActionEvent evt)
   {
@@ -3282,16 +3393,32 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param e
    */
+
   @Override
   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
   {
     final boolean setVisible = annotationPanelMenuItem.isSelected();
     viewport.setShowAnnotation(setVisible);
-    this.showAllSeqAnnotations.setEnabled(setVisible);
-    this.hideAllSeqAnnotations.setEnabled(setVisible);
-    this.showAllAlAnnotations.setEnabled(setVisible);
-    this.hideAllAlAnnotations.setEnabled(setVisible);
+    syncAnnotationMenuItems(setVisible);
     alignPanel.updateLayout();
+    repaint();
+    SwingUtilities.invokeLater(new Runnable() {
+
+      @Override
+      public void run()
+      {
+        alignPanel.updateScrollBarsFromRanges();
+      }
+      
+    });
+  }
+
+  private void syncAnnotationMenuItems(boolean setVisible)
+  {
+    showAllSeqAnnotations.setEnabled(setVisible);
+    hideAllSeqAnnotations.setEnabled(setVisible);
+    showAllAlAnnotations.setEnabled(setVisible);
+    hideAllAlAnnotations.setEnabled(setVisible);
   }
 
   @Override
@@ -3345,6 +3472,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void overviewMenuItem_actionPerformed(ActionEvent e)
   {
@@ -3382,13 +3510,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             "resize") != "none");
     Desktop.addInternalFrame(frame, MessageManager
             .formatMessage("label.overview_params", new Object[]
-            { this.getTitle() }), Desktop.FRAME_MAKE_VISIBLE, dim.width, dim.height, resizable,
-            Desktop.FRAME_ALLOW_ANY_SIZE);
+            { this.getTitle() }), Desktop.FRAME_MAKE_VISIBLE, dim.width,
+            dim.height, resizable, Desktop.FRAME_ALLOW_ANY_SIZE);
     frame.pack();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
     frame.addInternalFrameListener(
             new javax.swing.event.InternalFrameAdapter()
             {
+
               @Override
               public void internalFrameClosed(
                       javax.swing.event.InternalFrameEvent evt)
@@ -3417,6 +3546,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
    * ()[0])); }
    */
+
   @Override
   public void annotationColour_actionPerformed()
   {
@@ -3436,6 +3566,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param selected
    */
+
   @Override
   public void applyToAllGroups_actionPerformed(boolean selected)
   {
@@ -3448,6 +3579,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param name
    *          the name (not the menu item label!) of the colour scheme
    */
+
   @Override
   public void changeColour_actionPerformed(String name)
   {
@@ -3475,6 +3607,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param cs
    */
+
   @Override
   public void changeColour(ColourSchemeI cs)
   {
@@ -3489,6 +3622,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Show the PID threshold slider panel
    */
+
   @Override
   protected void modifyPID_actionPerformed()
   {
@@ -3500,6 +3634,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Show the Conservation slider panel
    */
+
   @Override
   protected void modifyConservation_actionPerformed()
   {
@@ -3511,6 +3646,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Action on selecting or deselecting (Colour) By Conservation
    */
+
   @Override
   public void conservationMenuItem_actionPerformed(boolean selected)
   {
@@ -3532,6 +3668,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Action on selecting or deselecting (Colour) Above PID Threshold
    */
+
   @Override
   public void abovePIDThreshold_actionPerformed(boolean selected)
   {
@@ -3560,6 +3697,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
   {
@@ -3577,6 +3715,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void sortIDMenuItem_actionPerformed(ActionEvent e)
   {
@@ -3593,6 +3732,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
   {
@@ -3609,6 +3749,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
   {
@@ -3626,6 +3767,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
   {
@@ -3638,6 +3780,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
   {
@@ -3663,11 +3806,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void autoCalculate_actionPerformed(ActionEvent e)
   {
-    viewport.autoCalculateConsensus = autoCalculate.isSelected();
-    if (viewport.autoCalculateConsensus)
+    viewport.setAutoCalculateConsensusAndConservation(
+            autoCalculate.isSelected());
+    if (viewport.getAutoCalculateConsensusAndConservation())
+    // ??
+    // viewport.autoCalculateConsensus = autoCalculate.isSelected();
+    // if (viewport.autoCalculateConsensus)
     {
-      viewport.firePropertyChange("alignment", null,
-              viewport.getAlignment().getSequences());
+      viewport.notifyAlignment();
     }
   }
 
@@ -3693,6 +3839,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param options
    *          parameters for the distance or similarity calculation
    */
+
   void newTreePanel(String type, String modelName,
           SimilarityParamsI options)
   {
@@ -3754,6 +3901,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param order
    *          DOCUMENT ME!
    */
+
   public void addSortByOrderMenuItem(String title,
           final AlignmentOrder order)
   {
@@ -3763,6 +3911,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     sort.add(item);
     item.addActionListener(new java.awt.event.ActionListener()
     {
+
       @Override
       public void actionPerformed(ActionEvent e)
       {
@@ -3789,6 +3938,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    *          the label used to retrieve scores for each sequence on the
    *          alignment
    */
+
   public void addSortByAnnotScoreMenuItem(JMenu sort,
           final String scoreLabel)
   {
@@ -3796,6 +3946,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     sort.add(item);
     item.addActionListener(new java.awt.event.ActionListener()
     {
+
       @Override
       public void actionPerformed(ActionEvent e)
       {
@@ -3815,12 +3966,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   protected int _annotationScoreVectorHash;
 
-  /**
+  /**g
    * 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()
   {
@@ -3861,41 +4013,38 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
+   * Enable (or, if desired, make visible) the By Tree 
+   * submenu only if it has at least one element (or will have).
+   * 
+   */
+  @Override
+  protected void enableSortMenuOptions()
+  {
+    List<TreePanel> treePanels = getTreePanels();
+    sortByTreeMenu.setEnabled(!treePanels.isEmpty());
+  }
+  
+  /**
    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
    * 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.
    */
+
   @Override
   public void buildTreeSortMenu()
   {
     sortByTreeMenu.removeAll();
 
-    List<Component> comps = PaintRefresher.components
-            .get(viewport.getSequenceSetId());
-    List<TreePanel> treePanels = new ArrayList<>();
-    for (Component comp : comps)
-    {
-      if (comp instanceof TreePanel)
-      {
-        treePanels.add((TreePanel) comp);
-      }
-    }
-
-    if (treePanels.size() < 1)
-    {
-      sortByTreeMenu.setVisible(false);
-      return;
-    }
-
-    sortByTreeMenu.setVisible(true);
+    List<TreePanel> treePanels = getTreePanels();
 
     for (final TreePanel tp : treePanels)
     {
       final JMenuItem item = new JMenuItem(tp.getTitle());
       item.addActionListener(new java.awt.event.ActionListener()
       {
+
         @Override
         public void actionPerformed(ActionEvent e)
         {
@@ -3909,6 +4058,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
+  private List<TreePanel> getTreePanels()
+  {
+    List<Component> comps = PaintRefresher.components
+            .get(viewport.getSequenceSetId());
+    List<TreePanel> treePanels = new ArrayList<>();
+    for (Component comp : comps)
+    {
+      if (comp instanceof TreePanel)
+      {
+        treePanels.add((TreePanel) comp);
+      }
+    }
+    return treePanels;
+  }
+
   public boolean sortBy(AlignmentOrder alorder, String undoname)
   {
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
@@ -3927,6 +4091,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * be submitted for multiple alignment.
    * 
    */
+
   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
   {
     // Now, check we have enough sequences
@@ -3972,6 +4137,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * region or the whole alignment. (where the first sequence in the set is the
    * one that the prediction will be for).
    */
+
   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
   {
     AlignmentView seqs = null;
@@ -4005,6 +4171,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
   {
@@ -4019,6 +4186,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     chooser.setResponseHandler(0, new Runnable()
     {
+
       @Override
       public void run()
       {
@@ -4083,6 +4251,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    *          position
    * @return TreePanel handle
    */
+
   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
           AlignmentView input, int w, int h, int x, int y)
   {
@@ -4128,6 +4297,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * Generates menu items and listener event actions for web service clients
    * 
    */
+
   public void BuildWebServiceMenu()
   {
     while (buildingMenu)
@@ -4144,6 +4314,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     buildingMenu = true;
     new Thread(new Runnable()
     {
+
       @Override
       public void run()
       {
@@ -4179,8 +4350,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           // JAL-940 - only show secondary structure prediction services from
           // the legacy server
           Hashtable<String, Vector<ServiceHandle>> ds = Discoverer
-                  .getServices();
-
+                  .getInstance().getServices();
           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
               // &&
           ds != null && (ds.size() > 0))
@@ -4222,6 +4392,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
           javax.swing.SwingUtilities.invokeLater(new Runnable()
           {
+
             @Override
             public void run()
             {
@@ -4241,7 +4412,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   webService.add(me.webServiceNoServices);
                 }
                 // TODO: move into separate menu builder class.
-                boolean new_sspred = false;
+                // boolean new_sspred = false;
                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
                 {
                   Jws2Discoverer jws2servs = Jws2Discoverer.getInstance();
@@ -4306,6 +4477,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param webService
    */
+
   protected void build_urlServiceMenu(JMenu webService)
   {
     // TODO: remove this code when 2.7 is released
@@ -4314,7 +4486,7 @@ 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) {
+     *  public void actionPerformed(ActionEvent e) {
      * jalview.datamodel.AlignmentView
      * .testSelectionViews(af.viewport.getAlignment(),
      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
@@ -4343,6 +4515,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @return true if Show Cross-references menu should be enabled
    */
+
   public boolean canShowProducts()
   {
     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
@@ -4370,6 +4543,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         JMenuItem xtype = new JMenuItem(source);
         xtype.addActionListener(new ActionListener()
         {
+
           @Override
           public void actionPerformed(ActionEvent e)
           {
@@ -4402,6 +4576,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param source
    *          the database to show cross-references for
    */
+
   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
           final String source)
   {
@@ -4413,6 +4588,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * Construct and display a new frame containing the translation of this
    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
    */
+
   @Override
   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
   {
@@ -4470,6 +4646,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param format
    */
+
   public void setFileFormat(FileFormatI format)
   {
     this.currentFileFormat = format;
@@ -4484,11 +4661,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    *          access mode of file (see jalview.io.AlignFile)
    * @return true if features file was parsed correctly.
    */
+
   public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
   {
     // BH 2018
     return avc.parseFeaturesFile(file, sourceType,
-            Cache.getDefault("RELAXEDSEQIDMATCHING", false));
+            Cache.getDefault(Preferences.RELAXEDSEQIDMATCHING, false));
 
   }
 
@@ -4544,6 +4722,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         new Thread(new Runnable()
         {
+
           @Override
           public void run()
           {
@@ -4642,8 +4821,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       int assocfiles = 0;
       if (filesmatched.size() > 0)
       {
-        boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS",
-                false);
+        boolean autoAssociate = Cache
+                .getDefault(Preferences.AUTOASSOCIATE_PDBANDSEQS, false);
         if (!autoAssociate)
         {
           String msg = MessageManager.formatMessage(
@@ -4665,10 +4844,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             // associating PDB files which have no IDs.
             for (SequenceI toassoc : (SequenceI[]) fm[2])
             {
-              PDBEntry pe = new AssociatePdbFileWithSeq()
-                      .associatePdbWithSeq(fm[0].toString(),
-                              (DataSourceType) fm[1], toassoc, false,
-                              Desktop.getInstance());
+              PDBEntry pe = AssociatePdbFileWithSeq.associatePdbWithSeq(
+                      fm[0].toString(), (DataSourceType) fm[1], toassoc,
+                      false);
               if (pe != null)
               {
                 System.err.println("Associated file : " + (fm[0].toString())
@@ -4733,6 +4911,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param file
    *          either a filename or a URL string.
    */
+
   public void loadJalviewDataFile(Object file, DataSourceType sourceType,
           FileFormatI format, SequenceI assocSeq)
   {
@@ -4897,6 +5076,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param state
    *          visible or invisible
    */
+
   public void setFeatureGroupState(String[] groups, boolean state)
   {
     jalview.api.FeatureRenderer fr = null;
@@ -4918,6 +5098,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * Method invoked by the ChangeListener on the tabbed pane, in other words
    * when a different tabbed pane is selected by the user or programmatically.
    */
+
   @Override
   public void tabSelectionChanged(int index)
   {
@@ -4988,6 +5169,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * On right mouse click on view tab, prompt for and set new view name.
    */
+
   @Override
   public void tabbedPane_mousePressed(MouseEvent e)
   {
@@ -5014,6 +5196,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Open the dialog for regex description parsing.
    */
+
   @Override
   protected void extractScores_actionPerformed(ActionEvent e)
   {
@@ -5037,6 +5220,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
    * )
    */
+
   @Override
   protected void showDbRefs_actionPerformed(ActionEvent e)
   {
@@ -5049,6 +5233,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
    * ActionEvent)
    */
+
   @Override
   protected void showNpFeats_actionPerformed(ActionEvent e)
   {
@@ -5061,6 +5246,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param av
    */
+
   public boolean closeView(AlignViewportI av)
   {
     if (viewport == av)
@@ -5104,6 +5290,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
     trimrs.addActionListener(new ActionListener()
     {
+
       @Override
       public void actionPerformed(ActionEvent e)
       {
@@ -5125,6 +5312,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         new Thread(new Runnable()
         {
+
           @Override
           public void run()
           {
@@ -5136,6 +5324,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     alignPanel.alignFrame.featureSettings, isNucleotide);
             dbRefFetcher.addListener(new FetchFinishedListenerI()
             {
+
               @Override
               public void finished()
               {
@@ -5159,16 +5348,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     rfetch.add(fetchr);
     new Thread(new Runnable()
     {
+
       @Override
       public void run()
       {
-        final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
-                .getSequenceFetcherSingleton();
+        // ??
+        // final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
+        // .getSequenceFetcherSingleton();
         javax.swing.SwingUtilities.invokeLater(new Runnable()
         {
+
           @Override
           public void run()
           {
+            jalview.ws.SequenceFetcher sf = jalview.ws.SequenceFetcher
+                    .getInstance();
             String[] dbclasses = sf.getNonAlignmentSources();
             List<DbSourceProxy> otherdb;
             JMenu dfetch = new JMenu();
@@ -5192,9 +5386,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               }
               if (otherdb.size() == 1)
               {
-                final DbSourceProxy[] dassource = otherdb
-                        .toArray(new DbSourceProxy[0]);
                 DbSourceProxy src = otherdb.get(0);
+                DbSourceProxy[] dassource = new DbSourceProxy[] { src };
                 fetchr = new JMenuItem(src.getDbSource());
                 fetchr.addActionListener(new ActionListener()
                 {
@@ -5219,6 +5412,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                         dbRefFetcher
                                 .addListener(new FetchFinishedListenerI()
                                 {
+
                                   @Override
                                   public void finished()
                                   {
@@ -5253,6 +5447,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                         { src.getDbSource() }));
                 fetchr.addActionListener(new ActionListener()
                 {
+
                   @Override
                   public void actionPerformed(ActionEvent e)
                   {
@@ -5273,6 +5468,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                         dbRefFetcher
                                 .addListener(new FetchFinishedListenerI()
                                 {
+
                                   @Override
                                   public void finished()
                                   {
@@ -5341,6 +5537,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                           dbRefFetcher
                                   .addListener(new FetchFinishedListenerI()
                                   {
+
                                     @Override
                                     public void finished()
                                     {
@@ -5392,23 +5589,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Left justify the whole alignment.
    */
+
   @Override
   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
   {
-    AlignmentI al = viewport.getAlignment();
-    al.justify(false);
-    viewport.firePropertyChange("alignment", null, al);
+    viewport.getAlignment().justify(false);
+    viewport.notifyAlignment();
   }
 
   /**
    * Right justify the whole alignment.
    */
+
   @Override
   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
   {
-    AlignmentI al = viewport.getAlignment();
-    al.justify(true);
-    viewport.firePropertyChange("alignment", null, al);
+    viewport.getAlignment().justify(true);
+    viewport.notifyAlignment();
   }
 
   @Override
@@ -5425,6 +5622,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
    * awt.event.ActionEvent)
    */
+
   @Override
   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
   {
@@ -5439,6 +5637,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
    * .ActionEvent)
    */
+
   @Override
   protected void showGroupConsensus_actionPerformed(ActionEvent e)
   {
@@ -5454,6 +5653,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
    * .event.ActionEvent)
    */
+
   @Override
   protected void showGroupConservation_actionPerformed(ActionEvent e)
   {
@@ -5468,6 +5668,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
    * .event.ActionEvent)
    */
+
   @Override
   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
   {
@@ -5482,6 +5683,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
    * .event.ActionEvent)
    */
+
   @Override
   protected void showSequenceLogo_actionPerformed(ActionEvent e)
   {
@@ -5511,6 +5713,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
    * .event.ActionEvent)
    */
+
   @Override
   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
   {
@@ -5562,6 +5765,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param alignmentPanel
    */
+
   public void setDisplayedView(AlignmentPanel alignmentPanel)
   {
     if (!viewport.getSequenceSetId()
@@ -5586,6 +5790,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param forAlignment
    *          update non-sequence-related annotations
    */
+
   @Override
   protected void setAnnotationsVisibility(boolean visible,
           boolean forSequences, boolean forAlignment)
@@ -5619,6 +5824,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Store selected annotation sort order for the view and repaint.
    */
+
   @Override
   protected void sortAnnotations_actionPerformed()
   {
@@ -5632,6 +5838,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @return alignment panels in this alignment frame
    */
+
   public List<? extends AlignmentViewPanel> getAlignPanels()
   {
     // alignPanels is never null
@@ -5643,6 +5850,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * Open a new alignment window, with the cDNA associated with this (protein)
    * alignment, aligned as is the protein.
    */
+
   protected void viewAsCdna_actionPerformed()
   {
     // TODO no longer a menu action - refactor as required
@@ -5693,6 +5901,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param show
    */
+
   @Override
   protected void showComplement_actionPerformed(boolean show)
   {
@@ -5707,6 +5916,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * Generate the reverse (optionally complemented) of the selected sequences,
    * and add them to the alignment
    */
+
   @Override
   protected void showReverse_actionPerformed(boolean complement)
   {
@@ -5732,6 +5942,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
    * be targeted at this alignment.
    */
+
   @Override
   protected void runGroovy_actionPerformed()
   {
@@ -5765,6 +5976,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param columnsContaining
    * @return
    */
+
   public boolean hideFeatureColumns(String featureType,
           boolean columnsContaining)
   {
@@ -5797,6 +6009,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * Rebuilds the Colour menu, including any user-defined colours which have
    * been loaded either on startup or during the session
    */
+
   public void buildColourMenu()
   {
     colourMenu.removeAll();
@@ -5824,6 +6037,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * Open a dialog (if not already open) that allows the user to select and
    * calculate PCA or Tree analysis
    */
+
   protected void openTreePcaDialog()
   {
     if (alignPanel.getCalculationDialog() == null)
@@ -5843,6 +6057,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     final AlignFrame us = this;
     chooser.setResponseHandler(0, new Runnable()
     {
+
       @Override
       public void run()
       {
@@ -5894,6 +6109,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    *          true is visible
    * @return list
    */
+
   public String[] getFeatureGroupsOfState(boolean visible)
   {
     jalview.api.FeatureRenderer fr = null;
@@ -5911,6 +6127,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @return list of feature groups on the view
    */
+
   public String[] getFeatureGroups()
   {
     jalview.api.FeatureRenderer fr = null;
@@ -5930,48 +6147,47 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     alignPanel.getSeqPanel().selection(sel, csel, hidden, null);
   }
 
-  
   public int getID()
   {
     return id;
   }
 
-}
-
-class PrintThread extends Thread
-{
-  AlignmentPanel ap;
-
-  public PrintThread(AlignmentPanel ap)
+  static class PrintThread extends Thread
   {
-    this.ap = ap;
-  }
-
-  static PageFormat pf;
+    AlignmentPanel ap;
 
-  @Override
-  public void run()
-  {
-    PrinterJob printJob = PrinterJob.getPrinterJob();
-
-    if (pf != null)
-    {
-      printJob.setPrintable(ap, pf);
-    }
-    else
+    public PrintThread(AlignmentPanel ap)
     {
-      printJob.setPrintable(ap);
+      this.ap = ap;
     }
 
-    if (printJob.printDialog())
+    static PageFormat pf;
+
+    @Override
+    public void run()
     {
-      try
+      PrinterJob printJob = PrinterJob.getPrinterJob();
+
+      if (pf != null)
       {
-        printJob.print();
-      } catch (Exception PrintException)
+        printJob.setPrintable(ap, pf);
+      }
+      else
       {
-        PrintException.printStackTrace();
+        printJob.setPrintable(ap);
+      }
+
+      if (printJob.printDialog())
+      {
+        try
+        {
+          printJob.print();
+        } catch (Exception PrintException)
+        {
+          PrintException.printStackTrace();
+        }
       }
     }
   }
 }
+