JAL-3446 from JAL-3253-applet Jalview2XML integration (retains
authorBobHanson <hansonr@stolaf.edu>
Tue, 2 Jun 2020 21:56:28 +0000 (16:56 -0500)
committerBobHanson <hansonr@stolaf.edu>
Tue, 2 Jun 2020 21:56:28 +0000 (16:56 -0500)
GeneLocus; switches to invokeLater)

src/jalview/project/Jalview2XML.java

index 751b297..84fda34 100644 (file)
@@ -28,6 +28,7 @@ import jalview.analysis.Conservation;
 import jalview.analysis.PCA;
 import jalview.analysis.scoremodels.ScoreModels;
 import jalview.analysis.scoremodels.SimilarityParams;
+import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureColourI;
 import jalview.api.ViewStyleI;
 import jalview.api.analysis.ScoreModelI;
@@ -60,6 +61,7 @@ import jalview.gui.AlignmentPanel;
 import jalview.gui.AppVarna;
 import jalview.gui.ChimeraViewFrame;
 import jalview.gui.Desktop;
+import jalview.gui.FeatureRenderer;
 import jalview.gui.JvOptionPane;
 import jalview.gui.OOMWarning;
 import jalview.gui.PCAPanel;
@@ -82,7 +84,6 @@ import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.FeatureColour;
 import jalview.schemes.ResidueProperties;
 import jalview.schemes.UserColourScheme;
-import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.Format;
 import jalview.util.MessageManager;
@@ -162,10 +163,10 @@ import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
 import java.io.IOException;
+import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
-import java.lang.reflect.InvocationTargetException;
 import java.math.BigInteger;
 import java.net.MalformedURLException;
 import java.net.URL;
@@ -268,6 +269,25 @@ public class Jalview2XML
   private Map<RnaModel, String> rnaSessions = new HashMap<>();
 
   /**
+   * contains last error message (if any) encountered by XML loader.
+   */
+  String errorMessage = null;
+
+  /**
+   * flag to control whether the Jalview2XML_V1 parser should be deferred to if
+   * exceptions are raised during project XML parsing
+   */
+  public boolean attemptversion1parse = false;
+
+  /*
+   * JalviewJS only -- to allow read file bytes to be saved in the
+   * created AlignFrame, allowing File | Reload of a project file to work
+   * 
+   * BH 2019 JAL-3436
+   */
+  private File jarFile;
+
+  /**
    * A helper method for safely using the value of an optional attribute that
    * may be null if not present in the XML. Answers the boolean value, or false
    * if null.
@@ -427,7 +447,7 @@ public class Jalview2XML
    * @param _jmap
    * @return
    */
-  public SeqFref newMappingRef(final String sref,
+  protected SeqFref newMappingRef(final String sref,
           final jalview.datamodel.Mapping _jmap)
   {
     SeqFref fref = new SeqFref(sref, "Mapping")
@@ -449,7 +469,7 @@ public class Jalview2XML
     return fref;
   }
 
-  public SeqFref newAlcodMapRef(final String sref,
+  protected SeqFref newAlcodMapRef(final String sref,
           final AlignedCodonFrame _cf,
           final jalview.datamodel.Mapping _jmap)
   {
@@ -481,7 +501,7 @@ public class Jalview2XML
     return fref;
   }
 
-  public void resolveFrefedSequences()
+  protected void resolveFrefedSequences()
   {
     Iterator<SeqFref> nextFref = frefedSequence.iterator();
     int toresolve = frefedSequence.size();
@@ -626,13 +646,14 @@ public class Jalview2XML
    * core method for storing state for a set of AlignFrames.
    * 
    * @param frames
-   *          - frames involving all data to be exported (including containing
-   *          splitframes)
+   *          - frames involving all data to be exported (including those
+   *          contained in splitframes, though not the split frames themselves)
    * @param jout
    *          - project output stream
    */
   private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
   {
+
     Hashtable<String, AlignFrame> dsses = new Hashtable<>();
 
     /*
@@ -655,21 +676,22 @@ public class Jalview2XML
       for (int i = frames.size() - 1; i > -1; i--)
       {
         AlignFrame af = frames.get(i);
+        AlignViewport vp = af.getViewport();
         // skip ?
         if (skipList != null && skipList
-                .containsKey(af.getViewport().getSequenceSetId()))
+                .containsKey(vp.getSequenceSetId()))
         {
           continue;
         }
 
         String shortName = makeFilename(af, shortNames);
 
-        int apSize = af.getAlignPanels().size();
-
+        AlignmentI alignment = vp.getAlignment();
+        List<? extends AlignmentViewPanel> panels = af.getAlignPanels();
+        int apSize = panels.size();
         for (int ap = 0; ap < apSize; ap++)
-        {
-          AlignmentPanel apanel = (AlignmentPanel) af.getAlignPanels()
-                  .get(ap);
+          {
+          AlignmentPanel apanel = (AlignmentPanel) panels.get(ap);
           String fileName = apSize == 1 ? shortName : ap + shortName;
           if (!fileName.endsWith(".xml"))
           {
@@ -677,11 +699,17 @@ public class Jalview2XML
           }
 
           saveState(apanel, fileName, jout, viewIds);
-
-          String dssid = getDatasetIdRef(
-                  af.getViewport().getAlignment().getDataset());
+        }
+        if (apSize > 0)
+        {
+          // BH moved next bit out of inner loop, not that it really matters.
+          // so we are testing to make sure we actually have an alignment,
+          // apparently.
+          String dssid = getDatasetIdRef(alignment.getDataset());
           if (!dsses.containsKey(dssid))
           {
+            // We have not already covered this data by reference from another
+            // frame.
             dsses.put(dssid, af);
           }
         }
@@ -799,10 +827,22 @@ public class Jalview2XML
     }
   }
 
+  /**
+   * Each AlignFrame has a single data set associated with it. Note that none of
+   * these frames are split frames, because Desktop.getAlignFrames() collects
+   * top and bottom separately here.
+   * 
+   * @param dsses
+   * @param fileName
+   * @param jout
+   */
   private void writeDatasetFor(Hashtable<String, AlignFrame> dsses,
           String fileName, JarOutputStream jout)
   {
 
+    // Note that in saveAllFrames we have associated each specific dataset to
+    // ONE of its associated frames.
+
     for (String dssids : dsses.keySet())
     {
       AlignFrame _af = dsses.get(dssids);
@@ -829,7 +869,7 @@ public class Jalview2XML
    * @param out
    *          jar entry name
    */
-  public JalviewModel saveState(AlignmentPanel ap, String fileName,
+  protected JalviewModel saveState(AlignmentPanel ap, String fileName,
           JarOutputStream jout, List<String> viewIds)
   {
     return saveState(ap, fileName, false, jout, viewIds);
@@ -851,7 +891,7 @@ public class Jalview2XML
    * @param out
    *          jar entry name
    */
-  public JalviewModel saveState(AlignmentPanel ap, String fileName,
+  protected JalviewModel saveState(AlignmentPanel ap, String fileName,
           boolean storeDS, JarOutputStream jout, List<String> viewIds)
   {
     if (viewIds == null)
@@ -1083,7 +1123,7 @@ public class Jalview2XML
            * only view *should* be coped with sensibly.
            */
           // This must have been loaded, is it still visible?
-          JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+          JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
           String matchedFile = null;
           for (int f = frames.length - 1; f > -1; f--)
           {
@@ -1235,9 +1275,9 @@ public class Jalview2XML
     {
       // FIND ANY ASSOCIATED TREES
       // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
-      if (Desktop.desktop != null)
+      if (Desktop.getDesktopPane() != null)
       {
-        JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+        JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
 
         for (int t = 0; t < frames.length; t++)
         {
@@ -1281,9 +1321,9 @@ public class Jalview2XML
     /*
      * save PCA viewers
      */
-    if (!storeDS && Desktop.desktop != null)
+    if (!storeDS && Desktop.getDesktopPane() != null)
     {
-      for (JInternalFrame frame : Desktop.desktop.getAllFrames())
+      for (JInternalFrame frame : Desktop.getDesktopPane().getAllFrames())
       {
         if (frame instanceof PCAPanel)
         {
@@ -1924,11 +1964,11 @@ public class Jalview2XML
           final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
           boolean storeDataset)
   {
-    if (Desktop.desktop == null)
+    if (Desktop.getDesktopPane() == null)
     {
       return;
     }
-    JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+    JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
     for (int f = frames.length - 1; f > -1; f--)
     {
       if (frames[f] instanceof AppVarna)
@@ -2384,7 +2424,7 @@ public class Jalview2XML
     if (calcIdParam.getVersion().equals("1.0"))
     {
       final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
-      Jws2Instance service = Jws2Discoverer.getDiscoverer()
+      Jws2Instance service = Jws2Discoverer.getInstance()
               .getPreferredServiceFor(calcIds);
       if (service != null)
       {
@@ -2723,17 +2763,6 @@ public class Jalview2XML
   }
 
   /**
-   * contains last error message (if any) encountered by XML loader.
-   */
-  String errorMessage = null;
-
-  /**
-   * flag to control whether the Jalview2XML_V1 parser should be deferred to if
-   * exceptions are raised during project XML parsing
-   */
-  public boolean attemptversion1parse = false;
-
-  /**
    * Load a jalview project archive from a jar file
    * 
    * @param file
@@ -2767,7 +2796,10 @@ public class Jalview2XML
     {
       try
       {
-        SwingUtilities.invokeAndWait(new Runnable()
+// was invokeAndWait
+         
+         // BH 2019 -- can't wait
+        SwingUtilities.invokeLater(new Runnable()
         {
           @Override
           public void run()
@@ -2780,55 +2812,55 @@ public class Jalview2XML
         System.err.println("Error loading alignment: " + x.getMessage());
       }
     }
+    this.jarFile = null;
     return af;
   }
 
        @SuppressWarnings("unused")
-       private jarInputStreamProvider createjarInputStreamProvider(final Object ofile) throws MalformedURLException {
-
-               // BH 2018 allow for bytes already attached to File object
-               try {
-                       String file = (ofile instanceof File ? ((File) ofile).getCanonicalPath() : ofile.toString());
+  private jarInputStreamProvider createjarInputStreamProvider(
+          final Object ofile) throws MalformedURLException
+  {
+    try
+    {
+      String file = (ofile instanceof File
+              ? ((File) ofile).getCanonicalPath()
+              : ofile.toString());
       byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile)
               : null;
-                       URL url = null;
-                       errorMessage = null;
-                       uniqueSetSuffix = null;
-                       seqRefIds = null;
-                       viewportsAdded.clear();
-                       frefedSequence = null;
-
-                       if (file.startsWith("http://")) {
-                               url = new URL(file);
-                       }
-                       final URL _url = url;
-                       return new jarInputStreamProvider() {
-
-                               @Override
-                               public JarInputStream getJarInputStream() throws IOException {
-                                       if (bytes != null) {
-//                                             System.out.println("Jalview2XML: opening byte jarInputStream for bytes.length=" + bytes.length);
-                                               return new JarInputStream(new ByteArrayInputStream(bytes));
-                                       }
-                                       if (_url != null) {
-//                                             System.out.println("Jalview2XML: opening url jarInputStream for " + _url);
-                                               return new JarInputStream(_url.openStream());
-                                       } else {
-//                                             System.out.println("Jalview2XML: opening file jarInputStream for " + file);
-                                               return new JarInputStream(new FileInputStream(file));
-                                       }
-                               }
-
-                               @Override
-                               public String getFilename() {
-                                       return file;
-                               }
-                       };
-               } catch (IOException e) {
-                       e.printStackTrace();
-                       return null;
-               }
-       }
+      if (bytes != null)
+      {
+        this.jarFile = (File) ofile;
+      }
+      errorMessage = null;
+      uniqueSetSuffix = null;
+      seqRefIds = null;
+      viewportsAdded.clear();
+      frefedSequence = null;
+
+      URL url = file.startsWith("http://") ? new URL(file) : null;
+      return new jarInputStreamProvider()
+      {
+        @Override
+        public JarInputStream getJarInputStream() throws IOException
+        {
+          InputStream is = bytes != null ? new ByteArrayInputStream(bytes)
+                  : (url != null ? url.openStream()
+                          : new FileInputStream(file));
+          return new JarInputStream(is);
+        }
+
+        @Override
+        public String getFilename()
+        {
+          return file;
+        }
+      };
+    } catch (IOException e)
+    {
+      e.printStackTrace();
+      return null;
+    }
+  }
 
   /**
    * Recover jalview session from a jalview project archive. Caller may
@@ -2854,12 +2886,19 @@ public class Jalview2XML
     IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
     Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
     final String file = jprovider.getFilename();
+
+    List<AlignFrame> alignFrames = new ArrayList<>();
+
     try
     {
       JarInputStream jin = null;
       JarEntry jarentry = null;
       int entryCount = 1;
 
+
+      // Look for all the entry names ending with ".xml"
+      // This includes all panels and at least one frame.
+//      Platform.timeCheck(null, Platform.TIME_MARK);
       do
       {
         jin = jprovider.getJarInputStream();
@@ -2867,9 +2906,27 @@ public class Jalview2XML
         {
           jarentry = jin.getNextJarEntry();
         }
+        String name = (jarentry == null ? null : jarentry.getName());
 
-        if (jarentry != null && jarentry.getName().endsWith(".xml"))
+//        System.out.println("Jalview2XML opening " + name);
+        if (name != null && name.endsWith(".xml"))
         {
+
+          // DataSet for.... is read last.
+          
+          
+          // The question here is what to do with the two
+          // .xml files in the jvp file.
+          // Some number of them, "...Dataset for...", will be the
+          // Only AlignPanels and will have Viewport.
+          // One or more will be the source data, with the DBRefs.
+          //
+          // JVP file writing (above) ensures tha the AlignPanels are written
+          // first, then all relevant datasets (which are
+          // Jalview.datamodel.Alignment).
+          //
+
+//          Platform.timeCheck("Jalview2XML JAXB " + name, Platform.TIME_MARK);
           JAXBContext jc = JAXBContext
                   .newInstance("jalview.xml.binding.jalview");
           XMLStreamReader streamReader = XMLInputFactory.newInstance()
@@ -2877,14 +2934,25 @@ public class Jalview2XML
           javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
           JAXBElement<JalviewModel> jbe = um
                   .unmarshal(streamReader, JalviewModel.class);
-          JalviewModel object = jbe.getValue();
+          JalviewModel model = jbe.getValue();
 
           if (true) // !skipViewport(object))
           {
-            _af = loadFromObject(object, file, true, jprovider);
-            if (_af != null && object.getViewport().size() > 0)
-            // getJalviewModelSequence().getViewportCount() > 0)
+            // Q: Do we have to load from the model, even if it
+            // does not have a viewport, could we discover that early on?
+            // Q: Do we need to load this object?
+            _af = loadFromObject(model, file, true, jprovider);
+//            Platform.timeCheck("Jalview2XML.loadFromObject",
+            // Platform.TIME_MARK);
+
+            if (_af != null)
             {
+              alignFrames.add(_af);
+            }
+            if (_af != null && model.getViewport().size() > 0)
+            {
+
+              // That is, this is one of the AlignmentPanel models
               if (af == null)
               {
                 // store a reference to the first view
@@ -2927,9 +2995,9 @@ public class Jalview2XML
       {
         // used to attempt to parse as V1 castor-generated xml
       }
-      if (Desktop.instance != null)
+      if (Desktop.getInstance() != null)
       {
-        Desktop.instance.stopLoading();
+        Desktop.getInstance().stopLoading();
       }
       if (af != null)
       {
@@ -2946,6 +3014,13 @@ public class Jalview2XML
       errorMessage = "Out of memory loading jalview XML file";
       System.err.println("Out of memory whilst loading jalview XML file");
       e.printStackTrace();
+    } finally
+    {
+      for (AlignFrame alf : alignFrames)
+      {
+        alf.alignPanel.setHoldRepaint(false);
+      }
+
     }
 
     /*
@@ -2957,7 +3032,7 @@ public class Jalview2XML
      */
     for (AlignFrame fr : gatherToThisFrame.values())
     {
-      Desktop.instance.gatherViews(fr);
+      Desktop.getInstance().gatherViews(fr);
     }
 
     restoreSplitFrames();
@@ -2965,8 +3040,7 @@ public class Jalview2XML
     {
       if (ds.getCodonFrames() != null)
       {
-        StructureSelectionManager
-                .getStructureSelectionManager(Desktop.instance)
+        Desktop.getStructureSelectionManager()
                 .registerMappings(ds.getCodonFrames());
       }
     }
@@ -2975,9 +3049,9 @@ public class Jalview2XML
       reportErrors();
     }
 
-    if (Desktop.instance != null)
+    if (Desktop.getInstance() != null)
     {
-      Desktop.instance.stopLoading();
+      Desktop.getInstance().stopLoading();
     }
 
     return af;
@@ -3058,7 +3132,7 @@ public class Jalview2XML
      */
     for (SplitFrame sf : gatherTo)
     {
-      Desktop.instance.gatherViews(sf);
+      Desktop.getInstance().gatherViews(sf);
     }
 
     splitFrameCandidates.clear();
@@ -3117,7 +3191,7 @@ public class Jalview2XML
           @Override
           public void run()
           {
-            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+            JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
                     finalErrorMessage,
                     "Error " + (saving ? "saving" : "loading")
                             + " Jalview file",
@@ -3178,25 +3252,25 @@ public class Jalview2XML
    * @param prefix
    *          a prefix for the temporary file name, must be at least three
    *          characters long
-   * @param suffixModel
+   * @param origFile
    *          null or original file - so new file can be given the same suffix
    *          as the old one
    * @return
    */
   protected String copyJarEntry(jarInputStreamProvider jprovider,
-          String jarEntryName, String prefix, String suffixModel)
+          String jarEntryName, String prefix, String origFile)
   {
     BufferedReader in = null;
     PrintWriter out = null;
     String suffix = ".tmp";
-    if (suffixModel == null)
+    if (origFile == null)
     {
-      suffixModel = jarEntryName;
+      origFile = jarEntryName;
     }
-    int sfpos = suffixModel.lastIndexOf(".");
-    if (sfpos > -1 && sfpos < (suffixModel.length() - 1))
+    int sfpos = origFile.lastIndexOf(".");
+    if (sfpos > -1 && sfpos < (origFile.length() - 3))
     {
-      suffix = "." + suffixModel.substring(sfpos + 1);
+      suffix = "." + origFile.substring(sfpos + 1);
     }
     try
     {
@@ -3276,7 +3350,9 @@ public class Jalview2XML
   }
 
   /**
-   * Load alignment frame from jalview XML DOM object
+   * Load alignment frame from jalview XML DOM object. For a DOM object that
+   * includes one or more Viewport elements (one with a title that does NOT
+   * contain "Dataset for"), create the frame.
    * 
    * @param jalviewModel
    *          DOM
@@ -3294,6 +3370,7 @@ public class Jalview2XML
     SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0);
     List<Sequence> vamsasSeqs = vamsasSet.getSequence();
 
+
     // JalviewModelSequence jms = object.getJalviewModelSequence();
 
     // Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
@@ -3589,8 +3666,7 @@ public class Jalview2XML
             {
               entry.setProperty(prop.getName(), prop.getValue());
             }
-            StructureSelectionManager
-                    .getStructureSelectionManager(Desktop.instance)
+            Desktop.getStructureSelectionManager()
                     .registerPDBEntry(entry);
             // adds PDBEntry to datasequence's set (since Jalview 2.10)
             if (al.getSequenceAt(i).getDatasetSequence() != null)
@@ -3603,6 +3679,7 @@ public class Jalview2XML
             }
           }
         }
+
       }
     } // end !multipleview
 
@@ -3740,6 +3817,7 @@ public class Jalview2XML
             }
           }
         }
+        // create the new AlignmentAnnotation
         jalview.datamodel.AlignmentAnnotation jaa = null;
 
         if (annotation.isGraph())
@@ -3776,6 +3854,7 @@ public class Jalview2XML
           jaa._linecolour = firstColour;
         }
         // register new annotation
+        // Annotation graphs such as Conservation will not have id.
         if (annotation.getId() != null)
         {
           annotationIds.put(annotation.getId(), jaa);
@@ -3987,8 +4066,6 @@ public class Jalview2XML
     // ///////////////////////////////
     // LOAD VIEWPORT
 
-    AlignFrame af = null;
-    AlignViewport av = null;
     // now check to see if we really need to create a new viewport.
     if (multipleView && viewportsAdded.size() == 0)
     {
@@ -4027,8 +4104,9 @@ public class Jalview2XML
     boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1",
             jalviewModel.getVersion());
 
+    AlignFrame af = null;
     AlignmentPanel ap = null;
-    boolean isnewview = true;
+    AlignViewport av = null;
     if (viewId != null)
     {
       // Check to see if this alignment already has a view id == viewId
@@ -4038,25 +4116,27 @@ public class Jalview2XML
       {
         for (int v = 0; v < views.length; v++)
         {
-          if (views[v].av.getViewId().equalsIgnoreCase(viewId))
+          ap = views[v];
+          av = ap.av;
+          if (av.getViewId().equalsIgnoreCase(viewId))
           {
             // recover the existing alignpanel, alignframe, viewport
-            af = views[v].alignFrame;
-            av = views[v].av;
-            ap = views[v];
+            af = ap.alignFrame;
+            break;
             // TODO: could even skip resetting view settings if we don't want to
             // change the local settings from other jalview processes
-            isnewview = false;
           }
         }
       }
     }
 
-    if (isnewview)
+    if (af == null)
     {
       af = loadViewport(file, jseqs, hiddenSeqs, al, jalviewModel, view,
               uniqueSeqSetId, viewId, autoAlan);
       av = af.getViewport();
+      // note that this only retrieves the most recently accessed
+      // tab of an AlignFrame.
       ap = af.alignPanel;
     }
 
@@ -4065,14 +4145,61 @@ public class Jalview2XML
      * 
      * Not done if flag is false (when this method is used for New View)
      */
+    final AlignFrame af0 = af;
+    final AlignViewport av0 = av;
+    final AlignmentPanel ap0 = ap;
+//    Platform.timeCheck("Jalview2XML.loadFromObject-beforetree",
+//            Platform.TIME_MARK);
     if (loadTreesAndStructures)
     {
-      loadTrees(jalviewModel, view, af, av, ap);
-      loadPCAViewers(jalviewModel, ap);
-      loadPDBStructures(jprovider, jseqs, af, ap);
-      loadRnaViewers(jprovider, jseqs, ap);
+      if (!jalviewModel.getTree().isEmpty())
+      {
+        SwingUtilities.invokeLater(new Runnable()
+        {
+          @Override
+          public void run()
+          {
+//            Platform.timeCheck(null, Platform.TIME_MARK);
+            loadTrees(jalviewModel, view, af0, av0, ap0);
+//            Platform.timeCheck("Jalview2XML.loadTrees", Platform.TIME_MARK);
+          }
+        });
+      }
+      if (!jalviewModel.getPcaViewer().isEmpty())
+      {
+        SwingUtilities.invokeLater(new Runnable()
+        {
+          @Override
+          public void run()
+          {
+//            Platform.timeCheck(null, Platform.TIME_MARK);
+            loadPCAViewers(jalviewModel, ap0);
+//            Platform.timeCheck("Jalview2XML.loadPCA", Platform.TIME_MARK);
+          }
+        });
+      }
+      SwingUtilities.invokeLater(new Runnable()
+      {
+        @Override
+        public void run()
+        {
+//          Platform.timeCheck(null, Platform.TIME_MARK);
+          loadPDBStructures(jprovider, jseqs, af0, ap0);
+//          Platform.timeCheck("Jalview2XML.loadPDB", Platform.TIME_MARK);
+        }
+      });
+      SwingUtilities.invokeLater(new Runnable()
+      {
+        @Override
+        public void run()
+        {
+          loadRnaViewers(jprovider, jseqs, ap0);
+        }
+      });
     }
     // and finally return.
+    // but do not set holdRepaint true just yet, because this could be the
+    // initial frame with just its dataset.
     return af;
   }
 
@@ -4089,7 +4216,7 @@ public class Jalview2XML
    * @param jseqs
    * @param ap
    */
-  private void loadRnaViewers(jarInputStreamProvider jprovider,
+  protected void loadRnaViewers(jarInputStreamProvider jprovider,
           List<JSeq> jseqs, AlignmentPanel ap)
   {
     /*
@@ -4308,7 +4435,7 @@ public class Jalview2XML
             int height = safeInt(structureState.getHeight());
 
             // Probably don't need to do this anymore...
-            // Desktop.desktop.getComponentAt(x, y);
+            // Desktop.getDesktop().getComponentAt(x, y);
             // TODO: NOW: check that this recovers the PDB file correctly.
             String pdbFile = loadPDBFile(jprovider, pdbid.getId(),
                     pdbid.getFile());
@@ -4550,7 +4677,8 @@ public class Jalview2XML
           String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
           filedat = oldFiles.get(new File(reformatedOldFilename));
         }
-        newFileLoc.append(Platform.escapeBackslashes(filedat.getFilePath()));
+        newFileLoc
+                .append(Platform.escapeBackslashes(filedat.getFilePath()));
         pdbfilenames.add(filedat.getFilePath());
         pdbids.add(filedat.getPdbId());
         seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
@@ -4627,9 +4755,11 @@ public class Jalview2XML
     final AlignFrame alf = af;
     final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
             svattrib.getWidth(), svattrib.getHeight());
-    try
-    {
-      javax.swing.SwingUtilities.invokeAndWait(new Runnable()
+    
+    // BH again was invokeAndWait
+    // try
+    // {
+      javax.swing.SwingUtilities.invokeLater(new Runnable()
       {
         @Override
         public void run()
@@ -4656,14 +4786,14 @@ public class Jalview2XML
           }
         }
       });
-    } catch (InvocationTargetException ex)
-    {
-      warn("Unexpected error when opening Jmol view.", ex);
-
-    } catch (InterruptedException e)
-    {
-      // e.printStackTrace();
-    }
+    // } catch (InvocationTargetException ex)
+    // {
+    // warn("Unexpected error when opening Jmol view.", ex);
+    //
+    // } catch (InterruptedException e)
+    // {
+    // // e.printStackTrace();
+    // }
 
   }
 
@@ -4792,7 +4922,7 @@ public class Jalview2XML
     {
       try
       {
-        frames = Desktop.desktop.getAllFrames();
+        frames = Desktop.getDesktopPane().getAllFrames();
       } catch (ArrayIndexOutOfBoundsException e)
       {
         // occasional No such child exceptions are thrown here...
@@ -4862,27 +4992,28 @@ public class Jalview2XML
     }
   }
 
-  AlignFrame loadViewport(String file, List<JSeq> JSEQ,
-          List<SequenceI> hiddenSeqs, AlignmentI al,
-          JalviewModel jm, Viewport view, String uniqueSeqSetId,
-          String viewId, List<JvAnnotRow> autoAlan)
+  AlignFrame loadViewport(String fileName, List<JSeq> JSEQ,
+          List<SequenceI> hiddenSeqs, AlignmentI al, JalviewModel jm,
+          Viewport view, String uniqueSeqSetId, String viewId,
+          List<JvAnnotRow> autoAlan)
   {
     AlignFrame af = null;
     af = new AlignFrame(al, safeInt(view.getWidth()),
-            safeInt(view.getHeight()), uniqueSeqSetId, viewId) 
-//    {
-//     
-//     @Override
-//     protected void processKeyEvent(java.awt.event.KeyEvent e) {
-//             System.out.println("Jalview2XML   AF " + e);
-//             super.processKeyEvent(e);
-//             
-//     }
-//     
-//    }
+            safeInt(view.getHeight()), uniqueSeqSetId, viewId)
+    // {
+    //
+    // @Override
+    // protected void processKeyEvent(java.awt.event.KeyEvent e) {
+    // System.out.println("Jalview2XML AF " + e);
+    // super.processKeyEvent(e);
+    //
+    // }
+    //
+    // }
     ;
-
-    af.setFileName(file, FileFormat.Jalview);
+    af.alignPanel.setHoldRepaint(true);
+    af.setFileName(fileName, FileFormat.Jalview);
+    af.setFileObject(jarFile); // BH 2019 JAL-3436
 
     final AlignViewport viewport = af.getViewport();
     for (int i = 0; i < JSEQ.size(); i++)
@@ -4957,9 +5088,8 @@ public class Jalview2XML
 
     viewport.setColourText(safeBoolean(view.isShowColourText()));
 
-    viewport
-            .setConservationSelected(
-                    safeBoolean(view.isConservationSelected()));
+    viewport.setConservationSelected(
+            safeBoolean(view.isConservationSelected()));
     viewport.setIncrement(safeInt(view.getConsThreshold()));
     viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
     viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
@@ -4990,8 +5120,18 @@ public class Jalview2XML
       viewport.setViewName(view.getViewName());
       af.setInitialTabVisible();
     }
-    af.setBounds(safeInt(view.getXpos()), safeInt(view.getYpos()),
-            safeInt(view.getWidth()), safeInt(view.getHeight()));
+    int x = safeInt(view.getXpos());
+    int y = safeInt(view.getYpos());
+    int w = safeInt(view.getWidth());
+    int h = safeInt(view.getHeight());
+    // // BH we cannot let the title bar go off the top
+    // if (Platform.isJS())
+    // {
+    // x = Math.max(50 - w, x);
+    // y = Math.max(0, y);
+    // }
+
+    af.setBounds(x, y, w, h);
     // startSeq set in af.alignPanel.updateLayout below
     af.alignPanel.updateLayout();
     ColourSchemeI cs = null;
@@ -5035,9 +5175,8 @@ public class Jalview2XML
     af.changeColour(cs);
     viewport.setColourAppliesToAllGroups(true);
 
-    viewport
-            .setShowSequenceFeatures(
-                    safeBoolean(view.isShowSequenceFeatures()));
+    viewport.setShowSequenceFeatures(
+            safeBoolean(view.isShowSequenceFeatures()));
 
     viewport.setCentreColumnLabels(view.isCentreColumnLabels());
     viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
@@ -5057,17 +5196,17 @@ public class Jalview2XML
     // recover feature settings
     if (jm.getFeatureSettings() != null)
     {
-      FeatureRendererModel fr = af.alignPanel.getSeqPanel().seqCanvas
+      FeatureRenderer fr = af.alignPanel.getSeqPanel().seqCanvas
               .getFeatureRenderer();
       FeaturesDisplayed fdi;
       viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
-      String[] renderOrder = new String[jm.getFeatureSettings()
-              .getSetting().size()];
+      String[] renderOrder = new String[jm.getFeatureSettings().getSetting()
+              .size()];
       Map<String, FeatureColourI> featureColours = new Hashtable<>();
       Map<String, Float> featureOrder = new Hashtable<>();
 
-      for (int fs = 0; fs < jm.getFeatureSettings()
-              .getSetting().size(); fs++)
+      for (int fs = 0; fs < jm.getFeatureSettings().getSetting()
+              .size(); fs++)
       {
         Setting setting = jm.getFeatureSettings().getSetting().get(fs);
         String featureType = setting.getType();
@@ -5079,8 +5218,8 @@ public class Jalview2XML
                 .getMatcherSet();
         if (filters != null)
         {
-          FeatureMatcherSetI filter = Jalview2XML
-                  .parseFilter(featureType, filters);
+          FeatureMatcherSetI filter = Jalview2XML.parseFilter(featureType,
+                  filters);
           if (!filter.isEmpty())
           {
             fr.setFeatureFilter(featureType, filter);
@@ -5112,8 +5251,7 @@ public class Jalview2XML
           float max = setting.getMax() == null ? 1f
                   : setting.getMax().floatValue();
           FeatureColourI gc = new FeatureColour(maxColour, minColour,
-                  maxColour,
-                  noValueColour, min, max);
+                  maxColour, noValueColour, min, max);
           if (setting.getAttributeName().size() > 0)
           {
             gc.setAttributeName(setting.getAttributeName().toArray(
@@ -5147,8 +5285,7 @@ public class Jalview2XML
         }
         else
         {
-          featureColours.put(featureType,
-                  new FeatureColour(maxColour));
+          featureColours.put(featureType, new FeatureColour(maxColour));
         }
         renderOrder[fs] = featureType;
         if (setting.getOrder() != null)
@@ -5485,7 +5622,7 @@ public class Jalview2XML
     return false;
   }
 
-  public void addToSkipList(AlignFrame af)
+  protected void addToSkipList(AlignFrame af)
   {
     if (skipList == null)
     {
@@ -5494,7 +5631,7 @@ public class Jalview2XML
     skipList.put(af.getViewport().getSequenceSetId(), af);
   }
 
-  public void clearSkipList()
+  protected void clearSkipList()
   {
     if (skipList != null)
     {
@@ -5563,8 +5700,8 @@ public class Jalview2XML
       SequenceI[] dsseqs = new SequenceI[dseqs.size()];
       dseqs.copyInto(dsseqs);
       ds = new jalview.datamodel.Alignment(dsseqs);
-      debug("Created new dataset " + vamsasSet.getDatasetId()
-              + " for alignment " + System.identityHashCode(al));
+//      debug("Jalview2XML Created new dataset " + vamsasSet.getDatasetId()
+//              + " for alignment " + System.identityHashCode(al));
       addDatasetRef(vamsasSet.getDatasetId(), ds);
     }
     // set the dataset for the newly imported alignment.
@@ -5994,6 +6131,8 @@ public class Jalview2XML
     AlignFrame af = loadFromObject(jm, null, false, null);
     af.getAlignPanels().clear();
     af.closeMenuItem_actionPerformed(true);
+    af.alignPanel.setHoldRepaint(false);
+    this.jarFile = null;
 
     /*
      * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
@@ -6351,7 +6490,11 @@ public class Jalview2XML
           panel.getRotatableCanvas().getAxisEndPoints()[i] = new Point(
                   axis.getXPos(), axis.getYPos(), axis.getZPos());
         }
-        PCAPanel.addToDesktop(panel, modelName);
+
+        Dimension dim = Platform.getDimIfEmbedded(panel, 475, 450);
+        Desktop.addInternalFrame(panel, MessageManager.formatMessage(
+                "label.calc_title", "PCA", modelName), dim.width,
+                dim.height);
       }
     } catch (Exception ex)
     {