X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;fp=src%2Fjalview%2Fgui%2FAlignFrame.java;h=1b09868fe23694a9ab375096d4173a000dc4dc5d;hb=4f77328104498504339216829abf5ea87e2791ec;hp=bac06e9268598862cddacd96b50026f61ec60494;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index bac06e9..1b09868 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -28,12 +28,10 @@ import jalview.analysis.GeneticCodeI;
 import jalview.analysis.ParseProperties;
 import jalview.analysis.SequenceIdMatcher;
 import jalview.api.AlignExportSettingsI;
-import jalview.api.AlignFrameI;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
-//from JalviewLite imports import jalview.api.FeatureRenderer;
 import jalview.api.FeatureSettingsControllerI;
 import jalview.api.SplitContainerI;
 import jalview.api.ViewStyleI;
@@ -107,7 +105,6 @@ 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;
@@ -165,8 +162,7 @@ import ext.vamsas.ServiceHandle;
  * @version $Revision$
  */
 @SuppressWarnings("serial")
-public class AlignFrame extends GAlignFrame
-        implements AlignFrameI, DropTargetListener,
+public class AlignFrame extends GAlignFrame implements DropTargetListener,
         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 {
 
@@ -300,6 +296,9 @@ public class AlignFrame extends GAlignFrame
 
     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 
+    alignPanel = new AlignmentPanel(this, viewport);
+
+    addAlignmentPanel(alignPanel, true);
     init();
   }
 
@@ -319,6 +318,8 @@ public class AlignFrame extends GAlignFrame
     {
       viewport.hideSequence(hiddenSeqs);
     }
+    alignPanel = new AlignmentPanel(this, viewport);
+    addAlignmentPanel(alignPanel, true);
     init();
   }
 
@@ -334,6 +335,7 @@ public class AlignFrame extends GAlignFrame
   {
     viewport = ap.av;
     alignPanel = ap;
+    addAlignmentPanel(ap, false);
     init();
   }
 
@@ -343,34 +345,11 @@ public class AlignFrame extends GAlignFrame
    */
   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
+//	  setBackground(Color.white); // BH 2019
 	  	  
     if (!Jalview.isHeadlessMode())
     {
       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
-      statusPanel.setVisible(Jalview.getInstance().getShowStatus());
-      alignFrameMenuBar.setVisible(Jalview.getInstance().getAllowMenuBar());
     }
 
     avc = new jalview.controller.AlignViewController(this, viewport,
@@ -385,7 +364,7 @@ public class AlignFrame extends GAlignFrame
       // modifyPID.setEnabled(false);
     }
 
-    String sortby = jalview.bin.Cache.getDefault(Preferences.SORT_ALIGNMENT,
+    String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
             "No sort");
 
     if (sortby.equals("Id"))
@@ -397,6 +376,9 @@ public class AlignFrame extends GAlignFrame
       sortPairwiseMenuItem_actionPerformed(null);
     }
 
+    this.alignPanel.av
+            .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
+
     setMenusFromViewport(viewport);
     buildSortByAnnotationScoresMenu();
     calculateTree.addActionListener(new ActionListener()
@@ -410,7 +392,7 @@ public class AlignFrame extends GAlignFrame
     });
     buildColourMenu();
 
-    if (Desktop.getDesktopPane() != null)
+    if (Desktop.desktop != null)
     {
       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
       if (!Platform.isJS())
@@ -425,7 +407,7 @@ public class AlignFrame extends GAlignFrame
       wrapMenuItem_actionPerformed(null);
     }
 
-    if (jalview.bin.Cache.getDefault(Preferences.SHOW_OVERVIEW, false))
+    if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
     {
       this.overviewMenuItem_actionPerformed(null);
     }
@@ -569,7 +551,7 @@ public class AlignFrame extends GAlignFrame
         switch (evt.getKeyCode())
         {
 
-        case KeyEvent.VK_ESCAPE: // escape key
+        case 27: // escape key
           deselectAllSequenceMenuItem_actionPerformed(null);
 
           break;
@@ -808,12 +790,9 @@ public class AlignFrame extends GAlignFrame
       {
         ap.av.getAlignment().padGaps();
       }
-      if (Jalview.getInstance().getStartCalculations())
-      {
-        ap.av.updateConservation(ap);
-        ap.av.updateConsensus(ap);
-        ap.av.updateStrucConsensus(ap);
-      }
+      ap.av.updateConservation(ap);
+      ap.av.updateConsensus(ap);
+      ap.av.updateStrucConsensus(ap);
     }
   }
 
@@ -836,12 +815,14 @@ public class AlignFrame extends GAlignFrame
   private void addServiceListeners()
   {
     final java.beans.PropertyChangeListener thisListener;
-    Desktop.getInstance().addJalviewPropertyChangeListener("services",
+    Desktop.instance.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()
                   {
@@ -865,7 +846,7 @@ public class AlignFrame extends GAlignFrame
               javax.swing.event.InternalFrameEvent evt)
       {
         // System.out.println("deregistering discoverer listener");
-        Desktop.getInstance().removeJalviewPropertyChangeListener("services",
+        Desktop.instance.removeJalviewPropertyChangeListener("services",
                 thisListener);
         closeMenuItem_actionPerformed(true);
       }
@@ -942,8 +923,10 @@ public class AlignFrame extends GAlignFrame
     /*
      * Show/hide annotations only enabled if annotation panel is shown
      */
-    syncAnnotationMenuItems();
-
+    showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
+    hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
+    showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
+    hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
     viewBoxesMenuItem.setSelected(av.getShowBoxes());
     viewTextMenuItem.setSelected(av.getShowText());
     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
@@ -961,7 +944,7 @@ public class AlignFrame extends GAlignFrame
     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
-    autoCalculate.setSelected(av.getAutoCalculateConsensusAndConservation());
+    autoCalculate.setSelected(av.autoCalculateConsensus);
     sortByTree.setSelected(av.sortByTree);
     listenToViewSelections.setSelected(av.followSelection);
 
@@ -1044,7 +1027,7 @@ public class AlignFrame extends GAlignFrame
   @Override
   public void addFromFile_actionPerformed(ActionEvent e)
   {
-    Desktop.getInstance().inputLocalFileMenuItem_actionPerformed(viewport);
+    Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
   }
 
   @Override
@@ -1058,7 +1041,7 @@ public class AlignFrame extends GAlignFrame
       // file is reloaded.
       if (FileFormat.Jalview.equals(currentFileFormat))
       {
-        JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
+        JInternalFrame[] frames = Desktop.desktop.getAllFrames();
         for (int i = 0; i < frames.length; i++)
         {
           if (frames[i] instanceof AlignFrame && frames[i] != this
@@ -1068,20 +1051,20 @@ public class AlignFrame extends GAlignFrame
             try
             {
               frames[i].setSelected(true);
-              Desktop.getInstance().closeAssociatedWindows();
+              Desktop.instance.closeAssociatedWindows();
             } catch (java.beans.PropertyVetoException ex)
             {
             }
           }
 
         }
-        Desktop.getInstance().closeAssociatedWindows();
+        Desktop.instance.closeAssociatedWindows();
 
         FileLoader loader = new FileLoader();
         DataSourceType protocol = fileName.startsWith("http:")
                 ? DataSourceType.URL
                 : DataSourceType.FILE;
-        loader.loadFile(viewport, fileName, protocol, currentFileFormat);
+        loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
       }
       else
       {
@@ -1097,12 +1080,12 @@ public class AlignFrame extends GAlignFrame
           DataSourceType protocol = (fileName.startsWith("http:")
                   ? DataSourceType.URL
                   : DataSourceType.FILE);
-          newframe = loader.loadFileWaitTillLoaded(fileName, protocol,
+          newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
                   currentFileFormat);
         }
         else
         {
-          newframe = loader.loadFileWaitTillLoaded(fileObject,
+          newframe = loader.LoadFileWaitTillLoaded(fileObject,
                   DataSourceType.FILE, currentFileFormat);
         }
 
@@ -1133,14 +1116,14 @@ public class AlignFrame extends GAlignFrame
   @Override
   public void addFromText_actionPerformed(ActionEvent e)
   {
-    Desktop.getInstance()
+    Desktop.instance
             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
   }
 
   @Override
   public void addFromURL_actionPerformed(ActionEvent e)
   {
-    Desktop.getInstance().inputURLMenuItem_actionPerformed(viewport);
+    Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
   }
 
   @Override
@@ -1184,7 +1167,7 @@ public class AlignFrame extends GAlignFrame
     // todo is this (2005) test now obsolete - value is never null?
     while (currentFileFormat == null)
     {
-      JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
+      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
               MessageManager
                       .getString("label.select_file_format_before_saving"),
               MessageManager.getString("label.file_format_not_specified"),
@@ -1306,7 +1289,6 @@ public class AlignFrame extends GAlignFrame
             String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file;
 			PrintWriter out = new PrintWriter(
                     new FileWriter(tempFilePath));
-
             out.print(output);
             out.close();
             AlignFrame.this.setTitle(file);
@@ -1947,17 +1929,16 @@ public class AlignFrame extends GAlignFrame
 
     StringSelection ss = new StringSelection(output);
 
-    Desktop d = Desktop.getInstance();
     try
     {
-      d.internalCopy = true;
+      jalview.gui.Desktop.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());
+              Desktop.instance);
     } catch (OutOfMemoryError er)
     {
       new OOMWarning("copying region", er);
@@ -1977,7 +1958,7 @@ public class AlignFrame extends GAlignFrame
               hiddenCutoff, hiddenOffset);
     }
 
-    d.jalviewClipboard = new Object[] { seqs,
+    Desktop.jalviewClipboard = new Object[] { seqs,
         viewport.getAlignment().getDataset(), hiddenColumns };
     setStatus(MessageManager.formatMessage(
             "label.copied_sequences_to_clipboard", new Object[]
@@ -2049,14 +2030,12 @@ public class AlignFrame extends GAlignFrame
       boolean annotationAdded = false;
       AlignmentI alignment = null;
 
-      Desktop d = Desktop.getInstance();
-
-      if (d.jalviewClipboard != null)
+      if (Desktop.jalviewClipboard != null)
       {
         // The clipboard was filled from within Jalview, we must use the
         // sequences
         // And dataset from the copied alignment
-        SequenceI[] newseq = (SequenceI[]) d.jalviewClipboard[0];
+        SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
         // be doubly sure that we create *new* sequence objects.
         sequences = new SequenceI[newseq.length];
         for (int i = 0; i < newseq.length; i++)
@@ -2081,10 +2060,10 @@ public class AlignFrame extends GAlignFrame
       if (newAlignment)
       {
 
-        if (d.jalviewClipboard != null)
+        if (Desktop.jalviewClipboard != null)
         {
           // dataset is inherited
-          alignment.setDataset((Alignment) d.jalviewClipboard[1]);
+          alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
         }
         else
         {
@@ -2100,8 +2079,8 @@ public class AlignFrame extends GAlignFrame
         alignment = viewport.getAlignment();
         alwidth = alignment.getWidth() + 1;
         // decide if we need to import sequences from an existing dataset
-        boolean importDs = d.jalviewClipboard != null
-                && d.jalviewClipboard[1] != alignment.getDataset();
+        boolean importDs = Desktop.jalviewClipboard != null
+                && Desktop.jalviewClipboard[1] != alignment.getDataset();
         // importDs==true instructs us to copy over new dataset sequences from
         // an existing alignment
         Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
@@ -2178,7 +2157,7 @@ public class AlignFrame extends GAlignFrame
                     newGraphGroups.add(q, null);
                   }
                   newGraphGroups.set(newann.graphGroup,
-                          new Integer(++fgroup));
+                          Integer.valueOf(++fgroup));
                 }
                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
                         .intValue();
@@ -2225,7 +2204,7 @@ public class AlignFrame extends GAlignFrame
                     newGraphGroups.add(q, null);
                   }
                   newGraphGroups.set(newann.graphGroup,
-                          new Integer(++fgroup));
+                          Integer.valueOf(++fgroup));
                 }
                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
                         .intValue();
@@ -2303,9 +2282,10 @@ public class AlignFrame extends GAlignFrame
                 DEFAULT_HEIGHT);
         String newtitle = new String("Copied sequences");
 
-        if (d.jalviewClipboard != null && d.jalviewClipboard[2] != null)
+        if (Desktop.jalviewClipboard != null
+                && Desktop.jalviewClipboard[2] != null)
         {
-          HiddenColumns hc = (HiddenColumns) d.jalviewClipboard[2];
+          HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
           af.viewport.setHiddenColumns(hc);
         }
 
@@ -2358,11 +2338,10 @@ public class AlignFrame extends GAlignFrame
               DEFAULT_HEIGHT);
       String newtitle = new String("Flanking alignment");
 
-      Desktop d = Desktop.getInstance();
-
-      if (d.jalviewClipboard != null && d.jalviewClipboard[2] != null)
+      if (Desktop.jalviewClipboard != null
+              && Desktop.jalviewClipboard[2] != null)
       {
-        HiddenColumns hc = (HiddenColumns) d.jalviewClipboard[2];
+        HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
         af.viewport.setHiddenColumns(hc);
       }
 
@@ -2459,7 +2438,7 @@ public class AlignFrame extends GAlignFrame
             + 1) == viewport.getAlignment().getWidth()) ? true : false;
 	if (wholeHeight && wholeWidth)
 	{
-	    JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.getDesktopPane());
+	    JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
 		dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
 	    Object[] options = new Object[] { MessageManager.getString("action.ok"),
 	            MessageManager.getString("action.cancel") };
@@ -2933,7 +2912,7 @@ public class AlignFrame extends GAlignFrame
   @Override
   public void gatherViews_actionPerformed(ActionEvent e)
   {
-    Desktop.getInstance().gatherViews(this);
+    Desktop.instance.gatherViews(this);
   }
 
   /**
@@ -3311,20 +3290,13 @@ public class AlignFrame extends GAlignFrame
   {
     final boolean setVisible = annotationPanelMenuItem.isSelected();
     viewport.setShowAnnotation(setVisible);
-    syncAnnotationMenuItems();
+    this.showAllSeqAnnotations.setEnabled(setVisible);
+    this.hideAllSeqAnnotations.setEnabled(setVisible);
+    this.showAllAlAnnotations.setEnabled(setVisible);
+    this.hideAllAlAnnotations.setEnabled(setVisible);
     alignPanel.updateLayout();
   }
 
-  private void syncAnnotationMenuItems()
-  {
-    final boolean setVisible = annotationPanelMenuItem.isSelected();
-    showAllSeqAnnotations.setEnabled(setVisible);
-    hideAllSeqAnnotations.setEnabled(setVisible);
-    showAllAlAnnotations.setEnabled(setVisible);
-    hideAllAlAnnotations.setEnabled(setVisible);
-  }
-
-
   @Override
   public void alignmentProperties()
   {
@@ -3385,38 +3357,12 @@ public class AlignFrame extends GAlignFrame
     }
 
     JInternalFrame frame = new JInternalFrame();
-
-    // BH 2019.07.26 we allow for an embedded
-    // undecorated overview with defined size
-    frame.setName(Jalview.getAppID("overview"));
-    //
-    Dimension dim = (Dimension) Platform.getEmbeddedAttribute(frame,
-            Platform.EMBEDDED_DIM);
-    if (dim != null && dim.width == 0)
-    {
-      dim = null; // hidden, not embedded
-    }
-
-    OverviewPanel overview = new OverviewPanel(alignPanel, dim);
-
+    final OverviewPanel overview = new OverviewPanel(alignPanel);
     frame.setContentPane(overview);
-    if (dim == null)
-    {
-      dim = new Dimension();
-      // was frame.getSize(), but that is 0,0 at this point;
-    }
-    else
-    {
-      // we are imbedding, and so we have an undecorated frame
-      // and we can set the the frame dimensions accordingly.
-    }
-    // allowing for unresizable option using, style="resize:none"
-    boolean resizable = (Platform.getEmbeddedAttribute(frame,
-            "resize") != "none");
     Desktop.addInternalFrame(frame, MessageManager
             .formatMessage("label.overview_params", new Object[]
-            { this.getTitle() }), true, dim.width, dim.height, resizable,
-            true);
+            { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
+            true, true);
     frame.pack();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
     frame.addInternalFrameListener(
@@ -3696,8 +3642,8 @@ public class AlignFrame extends GAlignFrame
   @Override
   public void autoCalculate_actionPerformed(ActionEvent e)
   {
-    viewport.setAutoCalculateConsensusAndConservation(autoCalculate.isSelected());
-    if (viewport.getAutoCalculateConsensusAndConservation())
+    viewport.autoCalculateConsensus = autoCalculate.isSelected();
+    if (viewport.autoCalculateConsensus)
     {
       viewport.firePropertyChange("alignment", null,
               viewport.getAlignment().getSequences());
@@ -3743,7 +3689,7 @@ public class AlignFrame extends GAlignFrame
       {
         if (_s.getLength() < sg.getEndRes())
         {
-          JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
+          JvOptionPane.showMessageDialog(Desktop.desktop,
                   MessageManager.getString(
                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
                   MessageManager.getString(
@@ -4065,7 +4011,7 @@ public class AlignFrame extends GAlignFrame
           viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
         } catch (Exception ex)
         {
-          JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), ex.getMessage(),
+          JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
                   MessageManager
                           .getString("label.problem_reading_tree_file"),
                   JvOptionPane.WARNING_MESSAGE);
@@ -4073,7 +4019,7 @@ public class AlignFrame extends GAlignFrame
         }
         if (fin != null && fin.hasWarningMessage())
         {
-          JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
+          JvOptionPane.showMessageDialog(Desktop.desktop,
                   fin.getWarningMessage(),
                   MessageManager.getString(
                           "label.possible_problem_with_tree_file"),
@@ -4201,11 +4147,9 @@ public class AlignFrame extends GAlignFrame
           final JMenu dismenu = new JMenu("Protein Disorder");
           // JAL-940 - only show secondary structure prediction services from
           // the legacy server
-          Hashtable<String, Vector<ServiceHandle>> services = Discoverer
-                  .getInstance().getServices();
           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
-          // &&
-          services != null && (services.size() > 0))
+              // &&
+          Discoverer.services != null && (Discoverer.services.size() > 0))
           {
             // TODO: refactor to allow list of AbstractName/Handler bindings to
             // be
@@ -4213,7 +4157,8 @@ public class AlignFrame extends GAlignFrame
             // No MSAWS used any more:
             // Vector msaws = null; // (Vector)
             // Discoverer.services.get("MsaWS");
-            Vector<ServiceHandle> secstrpr = services.get("SecStrPred");
+            Vector<ServiceHandle> secstrpr = Discoverer.services
+                    .get("SecStrPred");
             if (secstrpr != null)
             {
               // Add any secondary structure prediction services
@@ -4264,10 +4209,10 @@ public class AlignFrame extends GAlignFrame
                   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();
+                  Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
                   if (jws2servs != null)
                   {
                     if (jws2servs.hasServices())
@@ -4454,7 +4399,7 @@ public class AlignFrame extends GAlignFrame
       final String errorTitle = MessageManager
               .getString("label.implementation_error")
               + MessageManager.getString("label.translation_failed");
-      JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), msg, errorTitle,
+      JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
               JvOptionPane.ERROR_MESSAGE);
       return;
     }
@@ -4464,7 +4409,7 @@ public class AlignFrame extends GAlignFrame
               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
       final String errorTitle = MessageManager
               .getString("label.translation_failed");
-      JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), msg, errorTitle,
+      JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
               JvOptionPane.WARNING_MESSAGE);
     }
     else
@@ -4478,7 +4423,7 @@ public class AlignFrame extends GAlignFrame
       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
       {
         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
-        AlignViewport.openSplitFrame(this, af, new Alignment(seqs));
+        viewport.openSplitFrame(af, new Alignment(seqs));
       }
       else
       {
@@ -4511,7 +4456,7 @@ public class AlignFrame extends GAlignFrame
   {
     // BH 2018
     return avc.parseFeaturesFile(file, sourceType,
-            Cache.getDefault(Preferences.RELAXEDSEQIDMATCHING, false));
+            Cache.getDefault("RELAXEDSEQIDMATCHING", false));
 
   }
 
@@ -4525,7 +4470,6 @@ public class AlignFrame extends GAlignFrame
     {
       viewport.setShowSequenceFeatures(true);
       showSeqFeatures.setSelected(true);
-      alignPanel.getAlignment().resetColors();
     }
 
   }
@@ -4655,7 +4599,7 @@ public class AlignFrame extends GAlignFrame
             if (filesmatched.size() > 0)
             {
               boolean autoAssociate = Cache
-                      .getDefault(Preferences.AUTOASSOCIATE_PDBANDSEQS, false);
+                      .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
               if (!autoAssociate)
               {
                 String msg = MessageManager.formatMessage(
@@ -4678,9 +4622,10 @@ public class AlignFrame extends GAlignFrame
                   // associating PDB files which have no IDs.
                   for (SequenceI toassoc : (SequenceI[]) fm[2])
                   {
-                    PDBEntry pe = AssociatePdbFileWithSeq
+                    PDBEntry pe = new AssociatePdbFileWithSeq()
                             .associatePdbWithSeq(fm[0].toString(),
-                                    (DataSourceType) fm[1], toassoc, false);
+                                    (DataSourceType) fm[1], toassoc, false,
+                                    Desktop.instance);
                     if (pe != null)
                     {
                       System.err.println("Associated file : "
@@ -4791,7 +4736,7 @@ public class AlignFrame extends GAlignFrame
             {
               // some problem - if no warning its probable that the ID matching
               // process didn't work
-              JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
+              JvOptionPane.showMessageDialog(Desktop.desktop,
                       tcf.getWarningMessage() == null
                               ? MessageManager.getString(
                                       "label.check_file_matches_sequence_ids_alignment")
@@ -4850,13 +4795,17 @@ public class AlignFrame extends GAlignFrame
           }
           else
           {
-            new FileLoader().loadFile(viewport, file, sourceType, format);
+            new FileLoader().LoadFile(viewport, file, sourceType, format);
           }
         }
       }
       if (isAnnotation)
       {
-        updateForAnnotations();
+
+        alignPanel.adjustAnnotationHeight();
+        viewport.updateSequenceIdColours();
+        buildSortByAnnotationScoresMenu();
+        alignPanel.paintAlignment(true, true);
       }
     } catch (Exception ex)
     {
@@ -4880,23 +4829,11 @@ public class AlignFrame extends GAlignFrame
                       + (format != null
                               ? "(parsing as '" + format + "' file)"
                               : ""),
-              oom, Desktop.getDesktopPane());
+              oom, Desktop.desktop);
     }
   }
 
   /**
-   * Do all updates necessary after an annotation file such as jnet. Also called
-   * from Jalview.loadAppletParams for "annotations", "jnetFile"
-   */
-  public void updateForAnnotations()
-  {
-    alignPanel.adjustAnnotationHeight();
-    viewport.updateSequenceIdColours();
-    buildSortByAnnotationScoresMenu();
-    alignPanel.paintAlignment(true, true);
-  }
-
-  /**
    * Method invoked by the ChangeListener on the tabbed pane, in other words
    * when a different tabbed pane is selected by the user or programmatically.
    */
@@ -4979,32 +4916,6 @@ public class AlignFrame extends GAlignFrame
   }
 
   /**
-   * Change the display state for the given feature groups -- Added by BH from
-   * JalviewLite
-   * 
-   * @param groups
-   *          list of group strings
-   * @param state
-   *          visible or invisible
-   */
-  public void setFeatureGroupState(String[] groups, boolean state)
-  {
-    jalview.api.FeatureRenderer fr = null;
-    viewport.setShowSequenceFeatures(true);
-    if (alignPanel != null
-            && (fr = alignPanel.getFeatureRenderer()) != null)
-    {
-
-      fr.setGroupVisibility(Arrays.asList(groups), state);
-      alignPanel.getSeqPanel().seqCanvas.repaint();
-      if (alignPanel.overviewPanel != null)
-      {
-        alignPanel.overviewPanel.updateOverviewImage();
-      }
-    }
-  }
-
-  /**
    * Open the dialog for regex description parsing.
    */
   @Override
@@ -5148,13 +5059,14 @@ public class AlignFrame extends GAlignFrame
       @Override
       public void run()
       {
+        final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
+                .getSequenceFetcherSingleton();
         javax.swing.SwingUtilities.invokeLater(new Runnable()
         {
           @Override
           public void run()
           {
-            String[] dbclasses = jalview.ws.SequenceFetcher.getInstance()
-                    .getNonAlignmentSources();
+            String[] dbclasses = sf.getNonAlignmentSources();
             List<DbSourceProxy> otherdb;
             JMenu dfetch = new JMenu();
             JMenu ifetch = new JMenu();
@@ -5164,8 +5076,7 @@ public class AlignFrame extends GAlignFrame
             int dbi = 0;
             for (String dbclass : dbclasses)
             {
-              otherdb = jalview.ws.SequenceFetcher.getInstance()
-                      .getSourceProxy(dbclass);
+              otherdb = sf.getSourceProxy(dbclass);
               // add a single entry for this class, or submenu allowing 'fetch
               // all' or pick one
               if (otherdb == null || otherdb.size() < 1)
@@ -5178,9 +5089,9 @@ public class AlignFrame extends GAlignFrame
               }
               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()
                 {
@@ -5727,7 +5638,7 @@ public class AlignFrame extends GAlignFrame
       } catch (Exception ex)
       {
         System.err.println((ex.toString()));
-        JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
+        JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                 MessageManager.getString("label.couldnt_run_groovy_script"),
                 MessageManager.getString("label.groovy_support_failed"),
                 JvOptionPane.ERROR_MESSAGE);
@@ -5838,67 +5749,6 @@ public class AlignFrame extends GAlignFrame
 
   }
 
-  /**
-   * BH 2019 from JalviewLite
-   * 
-   * get sequence feature groups that are hidden or shown
-   * 
-   * @param visible
-   *          true is visible
-   * @return list
-   */
-  public String[] getFeatureGroupsOfState(boolean visible)
-  {
-    jalview.api.FeatureRenderer fr = null;
-    if (alignPanel != null
-            && (fr = alignPanel
-                    .getFeatureRenderer()) != null)
-    {
-      List<String> gps = fr.getGroups(visible);
-      String[] _gps = gps.toArray(new String[gps.size()]);
-      return _gps;
-    }
-    return null;
-  }
-
-  public void scrollTo(int row, int column)
-  {
-    alignPanel.getSeqPanel().scrollTo(row, column);
-  }
-
-  public void scrollToRow(int row)
-  {
-    alignPanel.getSeqPanel().scrollToRow(row);
-  }
-
-  public void scrollToColumn(int column)
-  {
-    alignPanel.getSeqPanel().scrollToColumn(column);
-  }
-
-  /**
-   * 
-   * @return list of feature groups on the view
-   */
-  public String[] getFeatureGroups()
-  {
-    jalview.api.FeatureRenderer fr = null;
-    if (alignPanel != null
-            && (fr = alignPanel.getFeatureRenderer()) != null)
-    {
-      List<String> gps = fr.getFeatureGroups();
-      String[] _gps = gps.toArray(new String[gps.size()]);
-      return _gps;
-    }
-    return null;
-  }
-
-  public void select(SequenceGroup sel, ColumnSelection csel,
-          HiddenColumns hidden)
-  {
-    alignPanel.getSeqPanel().selection(sel, csel, hidden, null);
-  }
-
 }
 
 class PrintThread extends Thread
@@ -5937,5 +5787,4 @@ class PrintThread extends Thread
       }
     }
   }
-
 }