Merge branch 'feature/JAL-3686_slivka_client_js_update' into alpha/merge_212_JalviewJ...

Conflicts:
	src/jalview/gui/Desktop.java
	src/jalview/gui/Preferences.java
	src/jalview/jbgui/GPreferences.java

diff --cc src/jalview/gui/AlignFrame.java
Simple merge

diff --cc src/jalview/gui/Desktop.java
index 61f342f,2402aef..a99bab9
--- 1/src/jalview/gui/Desktop.java
--- 2/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@@ -92,37 -121,6 +92,38 @@@ import javax.swing.event.InternalFrameE
  
  import org.stackoverflowusers.file.WindowsShortcut;
  
 +import jalview.api.AlignViewportI;
 +import jalview.api.AlignmentViewPanel;
 +import jalview.bin.Cache;
 +import jalview.bin.Jalview;
 +import jalview.gui.ImageExporter.ImageWriterI;
 +import jalview.io.BackupFiles;
 +import jalview.io.DataSourceType;
 +import jalview.io.FileFormat;
 +import jalview.io.FileFormatException;
 +import jalview.io.FileFormatI;
 +import jalview.io.FileFormats;
 +import jalview.io.FileLoader;
 +import jalview.io.FormatAdapter;
 +import jalview.io.IdentifyFile;
 +import jalview.io.JalviewFileChooser;
 +import jalview.io.JalviewFileView;
 +import jalview.jbgui.GSplitFrame;
 +import jalview.jbgui.GStructureViewer;
 +import jalview.project.Jalview2XML;
 +import jalview.structure.StructureSelectionManager;
 +import jalview.urls.IdOrgSettings;
 +import jalview.util.BrowserLauncher;
 +import jalview.util.ImageMaker.TYPE;
 +import jalview.util.MessageManager;
 +import jalview.util.Platform;
 +import jalview.util.ShortcutKeyMaskExWrapper;
 +import jalview.util.UrlConstants;
 +import jalview.viewmodel.AlignmentViewport;
++import jalview.ws.WSDiscovererI;
 +import jalview.ws.params.ParamManager;
 +import jalview.ws.utils.UrlDownloadClient;
 +
  /**
   * Jalview Desktop
   * 

diff --cc src/jalview/gui/Preferences.java
index f720e0a,c921331..50ee476
--- 1/src/jalview/gui/Preferences.java
--- 2/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@@ -210,18 -212,13 +212,20 @@@ public class Preferences extends GPrefe
      super();
      frame = new JInternalFrame();
      frame.setContentPane(this);
 -    wsPrefs = new WsPreferences();
 -    wsTab.add(wsPrefs, BorderLayout.CENTER);
 -    slivkaTab.add(slivkaPrefs = new SlivkaPreferences(),
 -        BorderLayout.CENTER);
 +    if (!Platform.isJS())
 +    /**
 +     * Java only
 +     * 
 +     * @j2sIgnore
 +     */
 +    {
 +      wsPrefs = new WsPreferences();
 +      wsTab.add(wsPrefs, BorderLayout.CENTER);
++      slivkaPrefs = new SlivkaPreferences();
++      slivkaTab.add(slivkaPrefs, BorderLayout.CENTER);
 +    }
      int width = 500, height = 450;
 -    new jalview.util.Platform();
 -    if (Platform.isAMac())
 +    if (Platform.isAMacAndNotJS())
      {
        width = 570;
        height = 480;

diff --cc src/jalview/jbgui/GPreferences.java
index 8a6e8ae,34a7c75..b354acb
--- 1/src/jalview/jbgui/GPreferences.java
--- 2/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@@ -426,11 -421,10 +428,13 @@@ public class GPreferences extends JPane
      /*
       * See WsPreferences for the real work of configuring this tab.
       */
 -    wsTab.setLayout(new BorderLayout());
 -    tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
 -    slivkaTab.setLayout(new BorderLayout());
 -    tabbedPane.add(slivkaTab, "Slivka Services");
 +    if (!Platform.isJS())
 +    {
 +      wsTab.setLayout(new BorderLayout());
 +      tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
++      slivkaTab.setLayout(new BorderLayout());
++      tabbedPane.add(slivkaTab, "Slivka Services");
 +    }
  
      /*
       * Handler to validate a tab before leaving it - currently only for

diff --cc src/jalview/ws/jws2/Jws2Discoverer.java
Simple merge