Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges
[jalview.git] / src / jalview / gui / AlignFrame.java
index 1850984..c38f336 100644 (file)
  */
 package jalview.gui;
 
+import java.util.Locale;
+
+import java.io.IOException;
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.swing.JFileChooser;
+import javax.swing.JOptionPane;
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Component;
@@ -47,12 +55,14 @@ import java.awt.event.MouseEvent;
 import java.awt.print.PageFormat;
 import java.awt.print.PrinterJob;
 import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
 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.Collection;
 import java.util.Deque;
 import java.util.Enumeration;
 import java.util.Hashtable;
@@ -71,6 +81,8 @@ import javax.swing.JMenuItem;
 import javax.swing.JPanel;
 import javax.swing.JScrollPane;
 import javax.swing.SwingUtilities;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
 
 import ext.vamsas.ServiceHandle;
 import jalview.analysis.AlignmentSorter;
@@ -91,6 +103,7 @@ import jalview.api.SplitContainerI;
 import jalview.api.ViewStyleI;
 import jalview.api.analysis.SimilarityParamsI;
 import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.bin.Jalview;
 import jalview.commands.CommandI;
 import jalview.commands.EditCommand;
@@ -117,6 +130,13 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.ColourMenuHelper.ColourChangeListener;
 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
+import jalview.hmmer.HMMAlign;
+import jalview.hmmer.HMMBuild;
+import jalview.hmmer.HMMERParamStore;
+import jalview.hmmer.HMMERPreset;
+import jalview.hmmer.HMMSearch;
+import jalview.hmmer.HmmerCommand;
+import jalview.hmmer.JackHMMER;
 import jalview.io.AlignmentProperties;
 import jalview.io.AnnotationFile;
 import jalview.io.BackupFiles;
@@ -144,6 +164,7 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemes;
 import jalview.schemes.ResidueColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
+import jalview.util.HttpUtils;
 import jalview.util.ImageMaker.TYPE;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -151,10 +172,81 @@ import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.ViewportRanges;
 import jalview.ws.DBRefFetcher;
 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
+import jalview.ws.ServiceChangeListener;
+import jalview.ws.WSDiscovererI;
+import jalview.ws.api.ServiceWithParameters;
 import jalview.ws.jws1.Discoverer;
 import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.jws2.PreferredServiceRegistry;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.WsParamSetI;
 import jalview.ws.seqfetcher.DbSourceProxy;
+import jalview.ws.slivkaws.SlivkaWSDiscoverer;
+import java.io.IOException;
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.swing.JFileChooser;
+import javax.swing.JOptionPane;
+
+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.beans.PropertyChangeListener;
+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.Collection;
+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 javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+
+import ext.vamsas.ServiceHandle;
 
 /**
  * DOCUMENT ME!
@@ -163,10 +255,12 @@ import jalview.ws.seqfetcher.DbSourceProxy;
  * @version $Revision$
  */
 @SuppressWarnings("serial")
-public class AlignFrame extends GAlignFrame implements DropTargetListener,
-        IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
+public class AlignFrame extends GAlignFrame
+        implements DropTargetListener, IProgressIndicator,
+        AlignViewControllerGuiI, ColourChangeListener, ServiceChangeListener
 {
 
+  public static int frameCount;
   public static final int DEFAULT_WIDTH = 700;
 
   public static final int DEFAULT_HEIGHT = 500;
@@ -192,8 +286,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   String fileName = null;
 
+  /**
+   * TODO: remove reference to 'FileObject' in AlignFrame - not correct mapping
+   */
   File fileObject;
 
+  private int id;
+
+  private DataSourceType protocol ;
   /**
    * Creates a new AlignFrame object with specific width and height.
    * 
@@ -288,6 +388,7 @@ 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)
@@ -297,9 +398,9 @@ 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();
   }
 
@@ -319,8 +420,8 @@ 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();
   }
 
@@ -336,7 +437,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport = ap.av;
     alignPanel = ap;
-    addAlignmentPanel(ap, false);
+    // addAlignmentPanel(ap, false);
     init();
   }
 
@@ -346,11 +447,34 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   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,
@@ -365,7 +489,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // modifyPID.setEnabled(false);
     }
 
-    String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
+    String sortby = Cache.getDefault(Preferences.SORT_ALIGNMENT,
             "No sort");
 
     if (sortby.equals("Id"))
@@ -377,8 +501,10 @@ 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();
@@ -396,9 +522,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (Desktop.getDesktopPane() != null)
     {
       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
+      addServiceListeners();
       if (!Platform.isJS())
       {
-        addServiceListeners();
       }
       setGUINucleotide();
     }
@@ -408,14 +534,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       wrapMenuItem_actionPerformed(null);
     }
 
-    if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
+    if (Cache.getDefault(Preferences.SHOW_OVERVIEW, false))
     {
       this.overviewMenuItem_actionPerformed(null);
     }
 
     addKeyListener();
 
-    final List<AlignmentPanel> selviews = new ArrayList<>();
+    final List<AlignmentViewPanel> selviews = new ArrayList<>();
     final List<AlignmentPanel> origview = new ArrayList<>();
     final String menuLabel = MessageManager
             .getString("label.copy_format_from");
@@ -483,10 +609,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 }
               }
             });
-    if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
+    if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT)
             .indexOf("devel") > -1
-            || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
-                    .indexOf("test") > -1)
+            || Cache.getDefault("VERSION", "DEVELOPMENT")
+                    .toLowerCase(Locale.ROOT).indexOf("test") > -1)
     {
       formatMenu.add(vsel);
     }
@@ -510,6 +636,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param format
    *          format of file
    */
+  @Deprecated
   public void setFileName(String file, FileFormatI format)
   {
     fileName = file;
@@ -518,6 +645,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
+   * 
+   * @param fileName
+   * @param file  from SwingJS; may contain bytes -- for reload
+   * @param protocol from SwingJS; may be RELATIVE_URL
+   * @param format
+   */
+  public void setFile(String fileName, File file, DataSourceType protocol, FileFormatI format)
+  {
+    this.fileName = fileName;
+    this.fileObject = file;
+    this.protocol = protocol;
+    setFileFormat(format);
+    reload.setEnabled(true);
+  }
+
+  /**
    * JavaScript will have this, maybe others. More dependable than a file name
    * and maintains a reference to the actual bytes loaded.
    * 
@@ -552,7 +695,8 @@ 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;
@@ -564,7 +708,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           if (viewport.cursorMode)
           {
-            alignPanel.getSeqPanel().moveCursor(0, 1);
+            alignPanel.getSeqPanel().moveCursor(0, 1, evt.isShiftDown());
           }
           break;
 
@@ -575,7 +719,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           if (viewport.cursorMode)
           {
-            alignPanel.getSeqPanel().moveCursor(0, -1);
+            alignPanel.getSeqPanel().moveCursor(0, -1, evt.isShiftDown());
           }
 
           break;
@@ -588,7 +732,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else
           {
-            alignPanel.getSeqPanel().moveCursor(-1, 0);
+            alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
           }
 
           break;
@@ -600,7 +744,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else
           {
-            alignPanel.getSeqPanel().moveCursor(1, 0);
+            alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
           }
           break;
 
@@ -736,16 +880,14 @@ 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;
         }
@@ -791,9 +933,13 @@ 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);
+        ap.av.initInformationWorker(ap);
+      }
     }
   }
 
@@ -812,55 +958,42 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return viewport;
   }
 
+  @Override
+  public void servicesChanged(WSDiscovererI discoverer,
+          Collection<? extends ServiceWithParameters> services)
+  {
+    buildWebServicesMenu();
+  }
   /* Set up intrinsic listeners for dynamically generated GUI bits. */
   private void addServiceListeners()
   {
-    final java.beans.PropertyChangeListener thisListener;
-    Desktop.getInstance().addJalviewPropertyChangeListener("services",
-            thisListener = new java.beans.PropertyChangeListener()
-            {
-              @Override
-              public void propertyChange(PropertyChangeEvent evt)
-              {
-                // // System.out.println("Discoverer property change.");
-                // if (evt.getPropertyName().equals("services"))
-                {
-                  SwingUtilities.invokeLater(new Runnable()
-                  {
-
-                    @Override
-                    public void run()
-                    {
-                      System.err.println(
-                              "Rebuild WS Menu for service change");
-                      BuildWebServiceMenu();
-                    }
-
-                  });
-                }
-              }
-            });
-    addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+    if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true))
+    {
+      WSDiscovererI discoverer = SlivkaWSDiscoverer.getInstance();
+      discoverer.addServiceChangeListener(this);
+    }
+    if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
     {
+      WSDiscovererI discoverer = Jws2Discoverer.getInstance();
+      discoverer.addServiceChangeListener(this);
+    }
+    // legacy event listener for compatibility with jws1
+    PropertyChangeListener legacyListener = (changeEvent) -> {
+      buildWebServicesMenu();
+    };
+    Desktop.getInstance().addJalviewPropertyChangeListener("services",legacyListener);
+    
+    addInternalFrameListener(new InternalFrameAdapter() {
       @Override
-      public void internalFrameClosed(
-              javax.swing.event.InternalFrameEvent evt)
-      {
-        // System.out.println("deregistering discoverer listener");
-        Desktop.getInstance().removeJalviewPropertyChangeListener(
-                "services", thisListener);
+      public void internalFrameClosed(InternalFrameEvent e) {
+        System.out.println("deregistering discoverer listener");
+        SlivkaWSDiscoverer.getInstance().removeServiceChangeListener(AlignFrame.this);
+        Jws2Discoverer.getInstance().removeServiceChangeListener(AlignFrame.this);
+        Desktop.getInstance().removeJalviewPropertyChangeListener("services", legacyListener);
         closeMenuItem_actionPerformed(true);
       }
     });
-    // Finally, build the menu once to get current service state
-    new Thread(new Runnable()
-    {
-      @Override
-      public void run()
-      {
-        BuildWebServiceMenu();
-      }
-    }).start();
+    buildWebServicesMenu();
   }
 
   /**
@@ -921,13 +1054,8 @@ 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());
@@ -936,6 +1064,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
     showSequenceLogo.setSelected(av.isShowSequenceLogo());
     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
+    showInformationHistogram.setSelected(av.isShowInformationHistogram());
+    showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
+    normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
 
     ColourMenuHelper.setColourSelected(colourMenu,
             av.getGlobalColourScheme());
@@ -945,7 +1076,8 @@ 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);
 
@@ -977,6 +1109,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     progressBar.setProgressBar(message, id);
   }
+  
+  @Override
+  public void removeProgressBar(long id)
+  {
+    progressBar.removeProgressBar(id);
+  }
 
   @Override
   public void registerHandler(final long id,
@@ -1011,7 +1149,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   public String getVersion()
   {
-    return jalview.bin.Cache.getProperty("VERSION");
+    return Cache.getProperty("VERSION");
   }
 
   public FeatureRenderer getFeatureRenderer()
@@ -1032,85 +1170,339 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   @Override
+  public void hmmBuild_actionPerformed(boolean withDefaults)
+  {
+    if (!alignmentIsSufficient(1))
+    {
+      return;
+    }
+
+    /*
+     * get default parameters, and optionally show a dialog
+     * to allow them to be modified
+     */
+    ParamDatastoreI store = HMMERParamStore.forBuild(viewport);
+    List<ArgumentI> args = store.getServiceParameters();
+
+    if (!withDefaults)
+    {
+      WsParamSetI set = new HMMERPreset();
+      WsJobParameters params = new WsJobParameters(store, set, args);
+      params.showRunDialog().thenAccept((startJob) -> {
+        if (startJob)
+        {
+          var args2 = params.getJobParams();
+          new Thread(new HMMBuild(this, args2)).start();
+        }
+      });
+    }
+    else
+    {
+      new Thread(new HMMBuild(this, args)).start();
+    }
+  }
+
+  @Override
+  public void hmmAlign_actionPerformed(boolean withDefaults)
+  {
+    if (!(checkForHMM() && alignmentIsSufficient(2)))
+    {
+      return;
+    }
+
+    /*
+     * get default parameters, and optionally show a dialog
+     * to allow them to be modified
+     */
+    ParamDatastoreI store = HMMERParamStore.forAlign(viewport);
+    List<ArgumentI> args = store.getServiceParameters();
+
+    if (!withDefaults)
+    {
+      WsParamSetI set = new HMMERPreset();
+      WsJobParameters params = new WsJobParameters(store, set, args);
+      params.showRunDialog().thenAccept((startJob) -> {
+        if (startJob)
+        {
+          var args2 = params.getJobParams();
+          new Thread(new HMMAlign(this, args2)).start();
+        }
+      });
+    }
+    else
+    {
+      new Thread(new HMMAlign(this, args)).start();
+    }
+  }
+
+  @Override
+  public void hmmSearch_actionPerformed(boolean withDefaults)
+  {
+    if (!checkForHMM())
+    {
+      return;
+    }
+
+    /*
+     * get default parameters, and (if requested) show 
+     * dialog to allow modification
+     */
+    ParamDatastoreI store = HMMERParamStore.forSearch(viewport);
+    List<ArgumentI> args = store.getServiceParameters();
+
+    if (!withDefaults)
+    {
+      WsParamSetI set = new HMMERPreset();
+      WsJobParameters params = new WsJobParameters(store, set, args);
+      params.showRunDialog().thenAccept((startJob) -> {
+        if (startJob)
+        {
+          var args2 = params.getJobParams();
+          new Thread(new HMMSearch(this, args2)).start();
+          alignPanel.repaint();
+        }
+      });
+    }
+    else
+    {
+      new Thread(new HMMSearch(this, args)).start();
+      alignPanel.repaint();
+    }
+  }
+
+  @Override
+  public void jackhmmer_actionPerformed(boolean withDefaults)
+  {
+
+    /*
+     * get default parameters, and (if requested) show 
+     * dialog to allow modification
+     */
+
+    ParamDatastoreI store = HMMERParamStore.forJackhmmer(viewport);
+    List<ArgumentI> args = store.getServiceParameters();
+
+    if (!withDefaults)
+    {
+      WsParamSetI set = new HMMERPreset();
+      WsJobParameters params = new WsJobParameters(store, set, args);
+      params.showRunDialog().thenAccept((startJob) -> {
+        if (startJob)
+        {
+          var args2 = params.getJobParams();
+          new Thread(new JackHMMER(this, args2)).start();
+          alignPanel.repaint();
+        }
+      });
+    }
+    else
+    {
+      new Thread(new JackHMMER(this, args)).start();
+      alignPanel.repaint();
+    }
+  }
+
+  /**
+   * Checks if the alignment has at least one hidden Markov model, if not shows
+   * a dialog advising to run hmmbuild or load an HMM profile
+   * 
+   * @return
+   */
+  private boolean checkForHMM()
+  {
+    if (viewport.getAlignment().getHmmSequences().isEmpty())
+    {
+      JOptionPane.showMessageDialog(this,
+              MessageManager.getString("warn.no_hmm"));
+      return false;
+    }
+    return true;
+  }
+
+  @Override
+  protected void filterByEValue_actionPerformed()
+  {
+    viewport.filterByEvalue(inputDouble("Enter E-Value Cutoff"));
+  }
+
+  @Override
+  protected void filterByScore_actionPerformed()
+  {
+    viewport.filterByScore(inputDouble("Enter Bit Score Threshold"));
+  }
+
+  private double inputDouble(String message)
+  {
+    String str = null;
+    Double d = null;
+    while (d == null || d <= 0)
+    {
+      str = JOptionPane.showInputDialog(this.alignPanel, message);
+      try
+      {
+        d = Double.valueOf(str);
+      } catch (NumberFormatException e)
+      {
+      }
+    }
+    return d;
+  }
+
+  /**
+   * Checks if the alignment contains the required number of sequences.
+   * 
+   * @param required
+   * @return
+   */
+  public boolean alignmentIsSufficient(int required)
+  {
+    if (getViewport().getSequenceSelection().length < required)
+    {
+      JOptionPane.showMessageDialog(this,
+              MessageManager.getString("label.not_enough_sequences"));
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * Opens a file browser and adds the selected file, if in Fasta, Stockholm or
+   * Pfam format, to the list held under preference key "HMMSEARCH_DBS" (as a
+   * comma-separated list)
+   */
+  @Override
+  public void addDatabase_actionPerformed() throws IOException
+  {
+    if (Cache.getProperty(Preferences.HMMSEARCH_DBS) == null)
+    {
+      Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
+    }
+
+    String path = openFileChooser(false);
+    if (path != null && new File(path).exists())
+    {
+      IdentifyFile identifier = new IdentifyFile();
+      FileFormatI format = identifier.identify(path, DataSourceType.FILE);
+      if (format == FileFormat.Fasta || format == FileFormat.Stockholm
+              || format == FileFormat.Pfam)
+      {
+        String currentDbPaths = Cache
+                .getProperty(Preferences.HMMSEARCH_DBS);
+        currentDbPaths += Preferences.COMMA + path;
+        Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths);
+      }
+      else
+      {
+        JOptionPane.showMessageDialog(this,
+                MessageManager.getString("warn.invalid_format"));
+      }
+    }
+  }
+
+  /**
+   * Opens a file chooser, optionally restricted to selecting folders
+   * (directories) only. Answers the path to the selected file or folder, or
+   * null if none is chosen.
+   * 
+   * @param
+   * @return
+   */
+  protected String openFileChooser(boolean forFolder)
+  {
+    // TODO duplicates GPreferences method - relocate to JalviewFileChooser?
+    String choice = null;
+    JFileChooser chooser = new JFileChooser();
+    if (forFolder)
+    {
+      chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+    }
+    chooser.setDialogTitle(
+            MessageManager.getString("label.open_local_file"));
+    chooser.setToolTipText(MessageManager.getString("action.open"));
+
+    int value = chooser.showOpenDialog(this);
+
+    if (value == JFileChooser.APPROVE_OPTION)
+    {
+      choice = chooser.getSelectedFile().getPath();
+    }
+    return choice;
+  }
+
+  @Override
   public void reload_actionPerformed(ActionEvent e)
   {
-    if (fileName != null)
+    if (fileName == null && fileObject == null)
+    {
+      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))
     {
-      // 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();
+      loader.LoadFile(viewport, (fileObject == null ? fileName : fileObject), 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)
+      {
+        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);
     }
   }
 
@@ -1131,7 +1523,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void save_actionPerformed(ActionEvent e)
   {
     if (fileName == null || (currentFileFormat == null)
-            || fileName.startsWith("http"))
+            || HttpUtils.startsWithHttpOrHttps(fileName))
     {
       saveAs_actionPerformed();
     }
@@ -1204,11 +1596,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (!lastSaveSuccessful)
     {
-      JvOptionPane.showInternalMessageDialog(this, MessageManager
-              .formatMessage("label.couldnt_save_file", new Object[]
-              { lastFilenameSaved }),
-              MessageManager.getString("label.error_saving_file"),
-              JvOptionPane.WARNING_MESSAGE);
+      if (!Platform.isHeadless())
+      {
+        JvOptionPane.showInternalMessageDialog(this, MessageManager
+                .formatMessage("label.couldnt_save_file", new Object[]
+                { lastFilenameSaved }),
+                MessageManager.getString("label.error_saving_file"),
+                JvOptionPane.WARNING_MESSAGE);
+      }
+      else
+      {
+        Console.error(MessageManager
+                .formatMessage("label.couldnt_save_file", new Object[]
+                { lastFilenameSaved }));
+      }
     }
     else
     {
@@ -1285,32 +1686,65 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         {
           // create backupfiles object and get new temp filename destination
           boolean doBackup = BackupFiles.getEnabled();
-          BackupFiles backupfiles = doBackup ? new BackupFiles(file) : null;
+          BackupFiles backupfiles = null;
+          if (doBackup)
+          {
+            Console.trace(
+                    "ALIGNFRAME making backupfiles object for " + file);
+            backupfiles = new BackupFiles(file);
+          }
           try
           {
             String tempFilePath = doBackup ? backupfiles.getTempFilePath()
                     : file;
+            Console.trace("ALIGNFRAME setting PrintWriter");
             PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
 
+            if (backupfiles != null)
+            {
+              Console.trace("ALIGNFRAME about to write to temp file "
+                      + backupfiles.getTempFilePath());
+            }
+
             out.print(output);
+            Console.trace("ALIGNFRAME about to close file");
             out.close();
+            Console.trace("ALIGNFRAME closed file");
             AlignFrame.this.setTitle(file);
             statusBar.setText(MessageManager.formatMessage(
                     "label.successfully_saved_to_file_in_format",
                     new Object[]
                     { fileName, format.getName() }));
             lastSaveSuccessful = true;
+          } catch (IOException e)
+          {
+            lastSaveSuccessful = false;
+            Console.error(
+                    "ALIGNFRAME Something happened writing the temp file");
+            Console.error(e.getMessage());
+            Console.debug(Cache.getStackTraceString(e));
           } catch (Exception ex)
           {
             lastSaveSuccessful = false;
-            ex.printStackTrace();
+            Console.error(
+                    "ALIGNFRAME Something unexpected happened writing the temp file");
+            Console.error(ex.getMessage());
+            Console.debug(Cache.getStackTraceString(ex));
           }
 
           if (doBackup)
           {
             backupfiles.setWriteSuccess(lastSaveSuccessful);
+            Console.debug("ALIGNFRAME writing temp file was "
+                    + (lastSaveSuccessful ? "" : "NOT ") + "successful");
             // do the backup file roll and rename the temp file to actual file
+            Console.trace(
+                    "ALIGNFRAME about to rollBackupsAndRenameTempFile");
             lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
+            Console.debug(
+                    "ALIGNFRAME performed rollBackupsAndRenameTempFile "
+                            + (lastSaveSuccessful ? "" : "un")
+                            + "successfully");
           }
         }
       }
@@ -1412,6 +1846,12 @@ 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.
@@ -1483,9 +1923,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   @Override
   public void associatedData_actionPerformed(ActionEvent e)
+          throws IOException, InterruptedException
   {
     final JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+            Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
     String tooltip = MessageManager
             .getString("label.load_jalview_annotations");
@@ -1497,7 +1938,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       public void run()
       {
         String choice = chooser.getSelectedFile().getPath();
-        jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+        Cache.setProperty("LAST_DIRECTORY", choice);
         loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
       }
     });
@@ -1684,7 +2125,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       if (originalSource != viewport)
       {
-        Cache.log.warn(
+        Console.warn(
                 "Implementation worry: mismatch of viewport origin for undo");
       }
       originalSource.updateHiddenColumns();
@@ -1693,8 +2134,7 @@ 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();
     }
   }
 
@@ -1724,7 +2164,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       if (originalSource != viewport)
       {
-        Cache.log.warn(
+        Console.warn(
                 "Implementation worry: mismatch of viewport origin for redo");
       }
       originalSource.updateHiddenColumns();
@@ -1733,8 +2173,7 @@ 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();
     }
   }
 
@@ -1781,10 +2220,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection
+   * or the sequence under cursor in keyboard mode
    * 
    * @param up
-   *          DOCUMENT ME!
+   *          or down (if !up)
    */
   public void moveSelectedSequences(boolean up)
   {
@@ -1792,8 +2232,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (sg == null)
     {
+      if (viewport.cursorMode)
+      {
+        sg = new SequenceGroup();
+        sg.addSequence(viewport.getAlignment().getSequenceAt(
+                alignPanel.getSeqPanel().seqCanvas.cursorY), false);
+      }
+      else
+      {
+        return;
+      }
+    }
+
+    if (sg.getSize() < 1)
+    {
       return;
     }
+
+    // TODO: JAL-3733 - add an event to the undo buffer for this !
+
     viewport.getAlignment().moveSelectedSequencesByOne(sg,
             viewport.getHiddenRepSequences(), up);
     alignPanel.paintAlignment(true, false);
@@ -1932,16 +2389,17 @@ 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()
               .setContents(new StringSelection(""), null);
 
       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
-              Desktop.getInstance());
+              d);
     } catch (OutOfMemoryError er)
     {
       new OOMWarning("copying region", er);
@@ -1961,7 +2419,7 @@ 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[]
@@ -1973,9 +2431,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param e
    *          DOCUMENT ME!
+   * @throws InterruptedException
+   * @throws IOException
    */
   @Override
   protected void pasteNew_actionPerformed(ActionEvent e)
+          throws IOException, InterruptedException
   {
     paste(true);
   }
@@ -1985,9 +2446,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param e
    *          DOCUMENT ME!
+   * @throws InterruptedException
+   * @throws IOException
    */
   @Override
   protected void pasteThis_actionPerformed(ActionEvent e)
+          throws IOException, InterruptedException
   {
     paste(false);
   }
@@ -1997,11 +2461,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param newAlignment
    *          true to paste to a new alignment, otherwise add to this.
+   * @throws InterruptedException
+   * @throws IOException
    */
-  void paste(boolean newAlignment)
+  void paste(boolean newAlignment) throws IOException, InterruptedException
   {
     boolean externalPaste = true;
-    Desktop d = Desktop.getInstance();
     try
     {
       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
@@ -2034,6 +2499,8 @@ 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
@@ -2265,8 +2732,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           buildSortByAnnotationScoresMenu();
         }
-        viewport.firePropertyChange("alignment", null,
-                alignment.getSequences());
+        viewport.notifyAlignment();
         if (alignPanels != null)
         {
           for (AlignmentPanel ap : alignPanels)
@@ -2340,6 +2806,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
               DEFAULT_HEIGHT);
       String newtitle = new String("Flanking alignment");
+
       Desktop d = Desktop.getInstance();
       if (d.jalviewClipboard != null && d.jalviewClipboard[2] != null)
       {
@@ -2420,8 +2887,7 @@ 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
@@ -2430,6 +2896,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           } catch (Exception ex)
           {
           }
+        } else {
+          updateAll(null);
         }
       }
     };
@@ -2471,10 +2939,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     if (avc.deleteGroups())
     {
-      PaintRefresher.Refresh(this, viewport.getSequenceSetId());
-      alignPanel.updateAnnotation();
+      updateAll(viewport.getSequenceSetId());
+    }
+  }
+
+  private void updateAll(String id)
+  {
+    if (id == null)
+    {
+      // this will force a non-fast repaint of both the IdPanel and SeqPanel
+      alignPanel.getIdPanel().getIdCanvas().setNoFastPaint();
+      alignPanel.getSeqPanel().seqCanvas.setNoFastPaint();
+      alignPanel.repaint();
+    }
+    else
+    {
+      // original version
+      PaintRefresher.Refresh(this, id);
       alignPanel.paintAlignment(true, true);
     }
+    alignPanel.updateAnnotation();
   }
 
   /**
@@ -2619,8 +3103,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         }
       }
 
-      viewport.firePropertyChange("alignment", null,
-              viewport.getAlignment().getSequences());
+      viewport.notifyAlignment();
     }
   }
 
@@ -2669,8 +3152,7 @@ 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();
 
   }
 
@@ -2708,8 +3190,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
 
-    viewport.firePropertyChange("alignment", null,
-            viewport.getAlignment().getSequences());
+    viewport.notifyAlignment();
 
   }
 
@@ -2723,20 +3204,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void padGapsMenuitem_actionPerformed(ActionEvent e)
   {
     viewport.setPadGaps(padGapsMenuitem.isSelected());
-    viewport.firePropertyChange("alignment", null,
-            viewport.getAlignment().getSequences());
+    viewport.notifyAlignment();
   }
 
   /**
-   * DOCUMENT ME!
+   * Opens a Finder dialog
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
-    new Finder();
+    new Finder(alignPanel, false, null);
   }
 
   /**
@@ -3280,11 +3759,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     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
@@ -3347,7 +3841,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     JInternalFrame frame = new JInternalFrame();
-
     // BH 2019.07.26 we allow for an embedded
     // undecorated overview with defined size
     frame.setName(Platform.getAppID("overview"));
@@ -3358,7 +3851,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       dim = null; // hidden, not embedded
     }
     OverviewPanel overview = new OverviewPanel(alignPanel, dim);
-
     frame.setContentPane(overview);
     if (dim == null)
     {
@@ -3375,8 +3867,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             "resize") != "none");
     Desktop.addInternalFrame(frame, MessageManager
             .formatMessage("label.overview_params", new Object[]
-            { this.getTitle() }), true, dim.width, dim.height, resizable,
-            true);
+            { 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(
@@ -3613,6 +4105,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     alignPanel.paintAlignment(true, false);
   }
 
+  @Override
+  public void sortEValueMenuItem_actionPerformed(ActionEvent e)
+  {
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+    AlignmentSorter.sortByEValue(viewport.getAlignment());
+    addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+            viewport.getAlignment()));
+    alignPanel.paintAlignment(true, false);
+
+  }
+
+  @Override
+  public void sortBitScoreMenuItem_actionPerformed(ActionEvent e)
+  {
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+    AlignmentSorter.sortByBitScore(viewport.getAlignment());
+    addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+            viewport.getAlignment()));
+    alignPanel.paintAlignment(true, false);
+
+  }
   /**
    * DOCUMENT ME!
    * 
@@ -3656,11 +4169,11 @@ 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.firePropertyChange("alignment", null,
-              viewport.getAlignment().getSequences());
+      viewport.notifyAlignment();
     }
   }
 
@@ -3823,37 +4336,48 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     if (viewport.getAlignment().getAlignmentAnnotation()
-            .hashCode() != _annotationScoreVectorHash)
+            .hashCode() == _annotationScoreVectorHash)
     {
-      sortByAnnotScore.removeAll();
-      // almost certainly a quicker way to do this - but we keep it simple
-      Hashtable<String, String> scoreSorts = new Hashtable<>();
-      AlignmentAnnotation aann[];
-      for (SequenceI sqa : viewport.getAlignment().getSequences())
+      return;
+    }
+
+    sortByAnnotScore.removeAll();
+    Set<String> scoreSorts = new HashSet<>();
+    for (SequenceI sqa : viewport.getAlignment().getSequences())
+    {
+      AlignmentAnnotation[] anns = sqa.getAnnotation();
+      for (int i = 0; anns != null && i < anns.length; i++)
       {
-        aann = sqa.getAnnotation();
-        for (int i = 0; aann != null && i < aann.length; i++)
+        AlignmentAnnotation aa = anns[i];
+        if (aa != null && aa.hasScore() && aa.sequenceRef != null)
         {
-          if (aann[i].hasScore() && aann[i].sequenceRef != null)
-          {
-            scoreSorts.put(aann[i].label, aann[i].label);
-          }
+          scoreSorts.add(aa.label);
         }
       }
-      Enumeration<String> labels = scoreSorts.keys();
-      while (labels.hasMoreElements())
-      {
-        addSortByAnnotScoreMenuItem(sortByAnnotScore, labels.nextElement());
-      }
-      sortByAnnotScore.setVisible(scoreSorts.size() > 0);
-      scoreSorts.clear();
-
-      _annotationScoreVectorHash = viewport.getAlignment()
-              .getAlignmentAnnotation().hashCode();
     }
+    for (String label : scoreSorts)
+    {
+      addSortByAnnotScoreMenuItem(sortByAnnotScore, label);
+    }
+    sortByAnnotScore.setVisible(!scoreSorts.isEmpty());
+
+    _annotationScoreVectorHash = viewport.getAlignment()
+            .getAlignmentAnnotation().hashCode();
   }
 
   /**
+   * 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
@@ -3865,24 +4389,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     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)
     {
@@ -3902,6 +4409,20 @@ 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();
@@ -4003,7 +4524,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     // Pick the tree file
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+            Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(
             MessageManager.getString("label.select_newick_like_tree_file"));
@@ -4088,6 +4609,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       if (nf.getTree() != null)
       {
         tp = new TreePanel(alignPanel, nf, treeTitle, input);
+
         Dimension dim = Platform.getDimIfEmbedded(tp, -1, -1);
         if (dim == null)
         {
@@ -4115,183 +4637,82 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return tp;
   }
 
-  private boolean buildingMenu = false;
 
   /**
-   * Generates menu items and listener event actions for web service clients
-   * 
+   * Schedule the web services menu rebuild to the event dispatch thread.
    */
-  public void BuildWebServiceMenu()
+  public void buildWebServicesMenu()
   {
-    while (buildingMenu)
-    {
-      try
+    SwingUtilities.invokeLater(() -> {
+      Console.info("Rebuiling WS menu");
+      webService.removeAll();
+      if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true))
       {
-        System.err.println("Waiting for building menu to finish.");
-        Thread.sleep(10);
-      } catch (Exception e)
+        Console.info("Building web service menu for slivka");
+        SlivkaWSDiscoverer discoverer = SlivkaWSDiscoverer.getInstance();
+        JMenu submenu = new JMenu("Slivka");
+        buildWebServicesMenu(discoverer, submenu);
+        webService.add(submenu);
+      }
+      if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
       {
+        WSDiscovererI jws2servs = Jws2Discoverer.getInstance();
+        JMenu submenu = new JMenu("JABAWS");
+        buildLegacyWebServicesMenu(submenu);
+        buildWebServicesMenu(jws2servs, submenu);
+        webService.add(submenu);
       }
-    }
-    final AlignFrame me = this;
-    buildingMenu = true;
-    new Thread(new Runnable()
+      build_fetchdbmenu(webService);
+    });
+  }
+
+  private void buildLegacyWebServicesMenu(JMenu menu)
+  {
+    JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
+    if (Discoverer.getServices() != null && Discoverer.getServices().size() > 0) 
     {
-      @Override
-      public void run()
+      var secstrpred = Discoverer.getServices().get("SecStrPred");
+      if (secstrpred != null) 
       {
-        final List<JMenuItem> legacyItems = new ArrayList<>();
-        try
-        {
-          // System.err.println("Building ws menu again "
-          // + Thread.currentThread());
-          // TODO: add support for context dependent disabling of services based
-          // on
-          // alignment and current selection
-          // TODO: add additional serviceHandle parameter to specify abstract
-          // handler
-          // class independently of AbstractName
-          // TODO: add in rediscovery GUI function to restart discoverer
-          // TODO: group services by location as well as function and/or
-          // introduce
-          // object broker mechanism.
-          final Vector<JMenu> wsmenu = new Vector<>();
-          final IProgressIndicator af = me;
-
-          /*
-           * do not i18n these strings - they are hard-coded in class
-           * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
-           * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
-           */
-          final JMenu msawsmenu = new JMenu("Alignment");
-          final JMenu secstrmenu = new JMenu(
-                  "Secondary Structure Prediction");
-          final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
-          final JMenu analymenu = new JMenu("Analysis");
-          final JMenu dismenu = new JMenu("Protein Disorder");
-          // JAL-940 - only show secondary structure prediction services from
-          // the legacy server
-          Hashtable<String, Vector<ServiceHandle>> ds = Discoverer
-                  .getServices();
-
-          if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
-              // &&
-          ds != null && (ds.size() > 0))
-          {
-            // TODO: refactor to allow list of AbstractName/Handler bindings to
-            // be
-            // stored or retrieved from elsewhere
-            // No MSAWS used any more:
-            // Vector msaws = null; // (Vector)
-            // Discoverer.services.get("MsaWS");
-            Vector<ServiceHandle> secstrpr = ds.get("SecStrPred");
-            if (secstrpr != null)
-            {
-              // Add any secondary structure prediction services
-              for (int i = 0, j = secstrpr.size(); i < j; i++)
-              {
-                final ext.vamsas.ServiceHandle sh = secstrpr.get(i);
-                jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
-                        .getServiceClient(sh);
-                int p = secstrmenu.getItemCount();
-                impl.attachWSMenuEntry(secstrmenu, me);
-                int q = secstrmenu.getItemCount();
-                for (int litm = p; litm < q; litm++)
-                {
-                  legacyItems.add(secstrmenu.getItem(litm));
-                }
-              }
-            }
-          }
-
-          // Add all submenus in the order they should appear on the web
-          // services menu
-          wsmenu.add(msawsmenu);
-          wsmenu.add(secstrmenu);
-          wsmenu.add(dismenu);
-          wsmenu.add(analymenu);
-          // No search services yet
-          // wsmenu.add(seqsrchmenu);
-
-          javax.swing.SwingUtilities.invokeLater(new Runnable()
-          {
-            @Override
-            public void run()
-            {
-              try
-              {
-                webService.removeAll();
-                // first, add discovered services onto the webservices menu
-                if (wsmenu.size() > 0)
-                {
-                  for (int i = 0, j = wsmenu.size(); i < j; i++)
-                  {
-                    webService.add(wsmenu.get(i));
-                  }
-                }
-                else
-                {
-                  webService.add(me.webServiceNoServices);
-                }
-                // TODO: move into separate menu builder class.
-                boolean new_sspred = false;
-                if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
-                {
-                  Jws2Discoverer jws2servs = Jws2Discoverer.getInstance();
-                  if (jws2servs != null)
-                  {
-                    if (jws2servs.hasServices())
-                    {
-                      jws2servs.attachWSMenuEntry(webService, me);
-                      for (Jws2Instance sv : jws2servs.getServices())
-                      {
-                        if (sv.description.toLowerCase().contains("jpred"))
-                        {
-                          for (JMenuItem jmi : legacyItems)
-                          {
-                            jmi.setVisible(false);
-                          }
-                        }
-                      }
-
-                    }
-                    if (jws2servs.isRunning())
-                    {
-                      JMenuItem tm = new JMenuItem(
-                              "Still discovering JABA Services");
-                      tm.setEnabled(false);
-                      webService.add(tm);
-                    }
-                  }
-                }
-                build_urlServiceMenu(me.webService);
-                build_fetchdbmenu(webService);
-                for (JMenu item : wsmenu)
-                {
-                  if (item.getItemCount() == 0)
-                  {
-                    item.setEnabled(false);
-                  }
-                  else
-                  {
-                    item.setEnabled(true);
-                  }
-                }
-              } catch (Exception e)
-              {
-                Cache.log.debug(
-                        "Exception during web service menu building process.",
-                        e);
-              }
-            }
-          });
-        } catch (Exception e)
+        for (ext.vamsas.ServiceHandle sh : secstrpred) 
         {
+          var menuProvider = Discoverer.getServiceClient(sh);
+          menuProvider.attachWSMenuEntry(secstrmenu, this);
         }
-        buildingMenu = false;
       }
-    }).start();
+    }
+    menu.add(secstrmenu);
+  }
 
+  /**
+   * Constructs the web services menu for the given discoverer under the
+   * specified menu. This method must be called on the EDT
+   * 
+   * @param discoverer
+   *          the discoverer used to build the menu
+   * @param menu
+   *          parent component which the elements will be attached to
+   */
+  private void buildWebServicesMenu(WSDiscovererI discoverer, JMenu menu)
+  {
+    if (discoverer.hasServices())
+    {
+      PreferredServiceRegistry.getRegistry().populateWSMenuEntry(
+              discoverer.getServices(), sv -> buildWebServicesMenu(), menu,
+              this, null);
+    }
+    if (discoverer.isRunning())
+    {
+      JMenuItem item = new JMenuItem("Service discovery in progress.");
+      item.setEnabled(false);
+      menu.add(item);
+    }
+    else if (!discoverer.hasServices())
+    {
+      JMenuItem item = new JMenuItem("No services available.");
+      item.setEnabled(false);
+      menu.add(item);
+    }
   }
 
   /**
@@ -4307,7 +4728,7 @@ 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); }
@@ -4376,7 +4797,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       showProducts.setEnabled(showp);
     } catch (Exception e)
     {
-      Cache.log.warn(
+      Console.warn(
               "canShowProducts threw an exception - please report to help@jalview.org",
               e);
       return false;
@@ -4417,8 +4838,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       al = dna.translateCdna(codeTable);
     } catch (Exception ex)
     {
-      jalview.bin.Cache.log.error(
-              "Exception during translation. Please report this !", ex);
+      Console.error("Exception during translation. Please report this !",
+              ex);
       final String msg = MessageManager.getString(
               "label.error_when_translating_sequences_submit_bug_report");
       final String errorTitle = MessageManager
@@ -4481,7 +4902,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     // BH 2018
     return avc.parseFeaturesFile(file, sourceType,
-            Cache.getDefault("RELAXEDSEQIDMATCHING", false));
+            Cache.getDefault(Preferences.RELAXEDSEQIDMATCHING, false));
 
   }
 
@@ -4537,6 +4958,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         new Thread(new Runnable()
         {
+
           @Override
           public void run()
           {
@@ -4569,25 +4991,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       for (int i = 0; i < files.size(); i++)
       {
         // BH 2018
-        Object file = files.get(i);
-        String fileName = file.toString();
+        Object fileObj = files.get(i);
+        String fileName = fileObj.toString();
         String pdbfn = "";
-        DataSourceType protocol = (file instanceof File
+        DataSourceType protocol = (fileObj instanceof File
                 ? DataSourceType.FILE
                 : FormatAdapter.checkProtocol(fileName));
         if (protocol == DataSourceType.FILE)
         {
-          File fl;
-          if (file instanceof File)
+          File file;
+          if (fileObj instanceof File)
           {
-            fl = (File) file;
-            Platform.cacheFileData(fl);
+            file = (File) fileObj;
+            Platform.cacheFileData(file);
           }
           else
           {
-            fl = new File(fileName);
+            file = new File(fileName);
           }
-          pdbfn = fl.getName();
+          pdbfn = file.getName();
         }
         else if (protocol == DataSourceType.URL)
         {
@@ -4616,27 +5038,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             FileFormatI type;
             try
             {
-              type = new IdentifyFile().identify(file, protocol);
+              type = new IdentifyFile().identify(fileObj, protocol);
             } catch (Exception ex)
             {
               type = null;
             }
             if (type != null && type.isStructureFile())
             {
-              filesmatched.add(new Object[] { file, protocol, mtch });
+              filesmatched.add(new Object[] { fileObj, protocol, mtch });
               continue;
             }
           }
           // File wasn't named like one of the sequences or wasn't a PDB
           // file.
-          filesnotmatched.add(file);
+          filesnotmatched.add(fileObj);
         }
       }
       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(
@@ -4658,16 +5080,16 @@ 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())
                         + " with " + toassoc.getDisplayId(true));
                 assocfiles++;
               }
+
             }
             // TODO: do we need to update overview ? only if features are
             // shown I guess
@@ -4725,6 +5147,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param file
    *          either a filename or a URL string.
+   * @throws InterruptedException
+   * @throws IOException
    */
   public void loadJalviewDataFile(Object file, DataSourceType sourceType,
           FileFormatI format, SequenceI assocSeq)
@@ -4783,7 +5207,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
         } catch (Exception x)
         {
-          Cache.log.debug(
+          Console.debug(
                   "Exception when processing data source as T-COFFEE score file",
                   x);
           tcf = null;
@@ -4840,6 +5264,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
       if (isAnnotation)
       {
+
         updateForAnnotations();
       }
     } catch (Exception ex)
@@ -4890,6 +5315,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param state
    *          visible or invisible
    */
+
   public void setFeatureGroupState(String[] groups, boolean state)
   {
     jalview.api.FeatureRenderer fr = null;
@@ -5155,13 +5581,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       @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();
@@ -5185,9 +5614,8 @@ 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()
                 {
@@ -5388,9 +5816,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @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();
   }
 
   /**
@@ -5399,9 +5826,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @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
@@ -5825,6 +6251,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
+  /**
+   * Sets the status of the HMMER menu
+   */
+  public void updateHMMERStatus()
+  {
+    hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
+  }
   @Override
   protected void loadVcf_actionPerformed()
   {
@@ -5887,6 +6320,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    *          true is visible
    * @return list
    */
+
   public String[] getFeatureGroupsOfState(boolean visible)
   {
     jalview.api.FeatureRenderer fr = null;
@@ -5904,6 +6338,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @return list of feature groups on the view
    */
+
   public String[] getFeatureGroups()
   {
     jalview.api.FeatureRenderer fr = null;
@@ -5923,41 +6358,45 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     alignPanel.getSeqPanel().selection(sel, csel, hidden, null);
   }
 
-}
-
-class PrintThread extends Thread
-{
-  AlignmentPanel ap;
-
-  public PrintThread(AlignmentPanel ap)
+  public int getID()
   {
-    this.ap = ap;
+    return id;
   }
 
-  static PageFormat pf;
-
-  @Override
-  public void run()
+  static class PrintThread extends Thread
   {
-    PrinterJob printJob = PrinterJob.getPrinterJob();
+    AlignmentPanel ap;
 
-    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.setPrintable(ap, pf);
+      }
+      else
       {
-        printJob.print();
-      } catch (Exception PrintException)
+        printJob.setPrintable(ap);
+      }
+
+      if (printJob.printDialog())
       {
-        PrintException.printStackTrace();
+        try
+        {
+          printJob.print();
+        } catch (Exception PrintException)
+        {
+          PrintException.printStackTrace();
+        }
       }
     }
   }