From: hansonr <hansonr@STO24954W.ad.stolaf.edu>
Date: Sun, 24 Mar 2019 03:48:31 +0000 (-0500)
Subject: j2sNative references moved to Platform
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=2810f6cc6d3d820dde63b324efb1c8119ec2a818

j2sNative references moved to Platform
---

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 6d23bd0..b018f9c 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -28,6 +28,7 @@ import jalview.schemes.UserColourScheme;
 import jalview.structure.StructureImportSettings;
 import jalview.urls.IdOrgSettings;
 import jalview.util.ColorUtils;
+import jalview.util.Platform;
 import jalview.ws.sifts.SiftsSettings;
 
 import java.awt.Color;
@@ -286,8 +287,7 @@ public class Cache
   /** Default file is ~/.jalview_properties */
   static String propertiesFile;
 
-  private static boolean propsAreReadOnly = /** @j2sNative true || */
-          false;
+  private static boolean propsAreReadOnly = Platform.isJS();
 
   public static void initLogger()
   {
@@ -340,7 +340,7 @@ public class Cache
   public static void loadProperties(String propsFile)
   {
     propertiesFile = propsFile;
-    if (propsFile == null)
+    if (propsFile == null && !propsAreReadOnly)
     {
       propertiesFile = System.getProperty("user.home") + File.separatorChar
               + ".jalview_properties";
@@ -351,38 +351,39 @@ public class Cache
       propsAreReadOnly = true;
     }
 
-    try
-    {
-      InputStream fis;
-      try
-      {
-        fis = new java.net.URL(propertiesFile).openStream();
-        System.out.println(
-                "Loading jalview properties from : " + propertiesFile);
-        System.out.println(
-                "Disabling Jalview writing to user's local properties file.");
-        propsAreReadOnly = true;
-
-      } catch (Exception ex)
-      {
-        fis = null;
-      }
-      if (fis == null)
-      {
-        fis = new FileInputStream(propertiesFile);
-      }
-      applicationProperties.clear();
-      applicationProperties.load(fis);
-
-      // remove any old build properties
-
-      deleteBuildProperties();
-      fis.close();
-    } catch (Exception ex)
-    {
-      System.out.println("Error reading properties file: " + ex);
+    if (propertiesFile != null) {
+	    try
+	    {
+	      InputStream fis;
+	      try
+	      {
+	        fis = new java.net.URL(propertiesFile).openStream();
+	        System.out.println(
+	                "Loading jalview properties from : " + propertiesFile);
+	        System.out.println(
+	                "Disabling Jalview writing to user's local properties file.");
+	        propsAreReadOnly = true;
+	
+	      } catch (Exception ex)
+	      {
+	        fis = null;
+	      }
+	      if (fis == null)
+	      {
+	        fis = new FileInputStream(propertiesFile);
+	      }
+	      applicationProperties.clear();
+	      applicationProperties.load(fis);
+	
+	      // remove any old build properties
+	
+	      deleteBuildProperties();
+	      fis.close();
+	    } catch (Exception ex)
+	    {
+	      System.out.println("Error reading properties file: " + ex);
+	    }
     }
-
     if (getDefault("USE_PROXY", false))
     {
       String proxyServer = getDefault("PROXY_SERVER", ""),
@@ -396,47 +397,55 @@ public class Cache
     }
 
     // LOAD THE AUTHORS FROM THE authors.props file
+    String authorDetails = (Platform.isJS() ? null :
+            "jar:"
+            .concat(Cache.class.getProtectionDomain().getCodeSource()
+                    .getLocation().toString().concat("!/authors.props")));
+
     try
     {
-      String authorDetails = /** @j2sNative "xxx" || */
-              "jar:"
-              .concat(Cache.class.getProtectionDomain().getCodeSource()
-                      .getLocation().toString().concat("!/authors.props"));
-
-      java.net.URL localJarFileURL = new java.net.URL(authorDetails);
-
-      InputStream in = localJarFileURL.openStream();
-      applicationProperties.load(in);
-      in.close();
-    } catch (Exception ex)
+      if (authorDetails != null) {
+    	  java.net.URL localJarFileURL = new java.net.URL(authorDetails);
+    	  InputStream in = localJarFileURL.openStream();
+    	  applicationProperties.load(in);
+    	  in.close();
+      }
+    } catch (Exception ex) {
+    System.out.println("Error reading author details: " + ex);
+    	authorDetails = null;
+    }
+    if (authorDetails == null) 
     {
-      System.out.println("Error reading author details: " + ex);
-      applicationProperties.remove("AUTHORS");
-      applicationProperties.remove("AUTHORFNAMES");
-      applicationProperties.remove("YEAR");
+        applicationProperties.remove("AUTHORS");
+        applicationProperties.remove("AUTHORFNAMES");
+        applicationProperties.remove("YEAR");
     }
 
     // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
     // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
     // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
-    try
+    String buildDetails = (Platform.isJS() ? null :
+            "jar:".concat(Cache.class.getProtectionDomain()
+            .getCodeSource().getLocation().toString()
+            .concat("!/.build_properties")));
+    if (buildDetails != null) 
     {
-      String buildDetails = /** @j2sNative "xxx" || */
-              "jar:".concat(Cache.class.getProtectionDomain()
-              .getCodeSource().getLocation().toString()
-              .concat("!/.build_properties"));
-
-      java.net.URL localJarFileURL = new java.net.URL(buildDetails);
-
-      InputStream in = localJarFileURL.openStream();
-      applicationProperties.load(in);
-      in.close();
-    } catch (Exception ex)
+	    try
+	    {
+	      java.net.URL localJarFileURL = new java.net.URL(buildDetails);
+	      InputStream in = localJarFileURL.openStream();
+	      applicationProperties.load(in);
+	      in.close();
+	    } catch (Exception ex)
+	    {
+	      System.out.println("Error reading build details: " + ex);
+	      buildDetails = null;
+	    }
+    }
+    if (buildDetails == null) 
     {
-      System.out.println("Error reading build details: " + ex);
-      applicationProperties.remove("VERSION");
+	      applicationProperties.remove("VERSION");
     }
-
     String jnlpVersion = System.getProperty("jalview.version");
     String codeVersion = getProperty("VERSION");
     String codeInstallation = getProperty("INSTALLATION");
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 474c707..fbdb65f 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -41,8 +41,6 @@ import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.jws2.Jws2Discoverer;
 
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileOutputStream;
@@ -67,7 +65,6 @@ import java.util.logging.Level;
 import java.util.logging.Logger;
 
 import javax.swing.LookAndFeel;
-import javax.swing.Timer;
 import javax.swing.UIManager;
 
 import groovy.lang.Binding;
@@ -102,21 +99,9 @@ public class Jalview
 
   public static AlignFrame currentAlignFrame;
 
-  /**
-   * Answers true if Jalview is running as Javascript, else false. The value is
-   * set at compile time.
-   * 
-   * @return
-   */
-  public static boolean isJS()
-  {
-    return /** @j2sNative true || */
-    false;
-  }
-
   static
   {
-    if (!isJS())
+    if (!Platform.isJS())
     { // BH 2018
     // grab all the rights we can the JVM
     Policy.setPolicy(new Policy()
@@ -229,7 +214,7 @@ public class Jalview
   private static void setLogging() 
   {
 	  // BH - for event debugging in JavaScript (Java mode only)
-  	if (!(/** @j2sNative true ||*/false)) 
+  	if (!Platform.isJS()) 
   	{
   		Logger.getLogger("").setLevel(Level.ALL);
         logClass("java.awt.EventDispatchThread");
@@ -250,7 +235,7 @@ public class Jalview
   void doMain(String[] args)
   {
 
-    if (!isJS())
+    if (!Platform.isJS())
     {
       System.setSecurityManager(null);
     }
@@ -272,12 +257,7 @@ public class Jalview
               "CMD [-props " + usrPropsFile + "] executed successfully!");
     }
 
-    /**
-     * BH 2018 ignoring this section for JS
-     * 
-     * @j2sNative
-     */
-    {
+    if (!Platform.isJS()) {
       if (aparser.contains("help") || aparser.contains("h"))
       {
         showUsage();
@@ -413,13 +393,8 @@ public class Jalview
       desktop.setInBatchMode(true); // indicate we are starting up
       desktop.setVisible(true);
 
-      /**
-       * BH 2018 JS bypass this section
-       * 
-       * @j2sNative
-       * 
-       */
-      {
+
+      if (!Platform.isJS()) {
         desktop.startServiceDiscovery();
         if (!aparser.contains("nousagestats"))
         {
@@ -590,7 +565,7 @@ public class Jalview
       }
       System.out.println("CMD [-open " + file + "] executed successfully!");
 
-      if (!isJS() && !file.startsWith("http://"))
+      if (!Platform.isJS() && !file.startsWith("http://"))
       {
         if (!(new File(file)).exists())
         {
@@ -834,8 +809,7 @@ public class Jalview
     // And the user
     // ////////////////////
 
-    if (/** @j2sNative false && */ // BH 2018
-    !headless && file == null && vamsasImport == null
+    if (!Platform.isJS() && !headless && file == null && vamsasImport == null
             && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
     {
       file = jalview.bin.Cache.getDefault("STARTUP_FILE",
diff --git a/src/jalview/bin/JalviewJS.java b/src/jalview/bin/JalviewJS.java
index d7c4d19..70430ad 100644
--- a/src/jalview/bin/JalviewJS.java
+++ b/src/jalview/bin/JalviewJS.java
@@ -102,21 +102,9 @@ public class JalviewJS
 
   public static AlignFrame currentAlignFrame;
 
-  /**
-   * Answers true if Jalview is running as Javascript, else false. The value is
-   * set at compile time.
-   * 
-   * @return
-   */
-  public static boolean isJS()
-  {
-    return /** @j2sNative true || */
-    false;
-  }
-
   static
   {
-    if (!isJS())
+    if (!Platform.isJS())
     { // BH 2018
     // grab all the rights we can the JVM
     Policy.setPolicy(new Policy()
@@ -211,7 +199,9 @@ public class JalviewJS
   public static void main(String[] args)
   {
     instance = new JalviewJS();
-    instance.doMain(new String[] {"open","http://www.jalview.org/examples/uniref50.fa", "-features","http://www.jalview.org/examples/exampleFeatures.txt"});
+    instance.doMain(
+    		Platform.isJS() ? new String[0] 
+    				: new String[] {"open","http://www.jalview.org/examples/uniref50.fa", "-features","http://www.jalview.org/examples/exampleFeatures.txt"});
 }
 
   private static void logClass(String name) 
@@ -249,7 +239,7 @@ public class JalviewJS
   void doMain(String[] args)
   {
 
-    if (!isJS())
+    if (!Platform.isJS())
     {
       System.setSecurityManager(null);
     }
@@ -589,7 +579,7 @@ public class JalviewJS
       }
       System.out.println("CMD [-open " + file + "] executed successfully!");
 
-      if (!isJS() && !file.startsWith("http://"))
+      if (!Platform.isJS() && !file.startsWith("http://"))
       {
         if (!(new File(file)).exists())
         {
diff --git a/src/jalview/bin/JalviewJS2.java b/src/jalview/bin/JalviewJS2.java
index eff5334..ad01256 100644
--- a/src/jalview/bin/JalviewJS2.java
+++ b/src/jalview/bin/JalviewJS2.java
@@ -1,5 +1,7 @@
 package jalview.bin;
 
+import jalview.util.Platform;
+
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 
@@ -60,8 +62,7 @@ private static void showFocusTimer() {
 	});
 
 	t.setRepeats(true);
-	if (/** @j2sNative true || */
-	false)
+	if (Platform.isJS())
 		t.start();
   }
 
diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index 47d1082..008bb7c 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -20,6 +20,8 @@
  */
 package jalview.datamodel;
 
+import jalview.util.Platform;
+
 import java.lang.reflect.Field;
 import java.util.ArrayList;
 import java.util.List;
@@ -128,11 +130,12 @@ public class DBRefSource
   public static String[] allSources()
 
   {
+	  if (Platform.isJS()) {
+		  return allTypes;
+	  }
     /**
      * @j2sNative
      * 
-     *            return C$.allTypes;
-     * 
      */
 
     {
diff --git a/src/jalview/datamodel/StructureViewerModel.java b/src/jalview/datamodel/StructureViewerModel.java
index 1b78948..b271afb 100644
--- a/src/jalview/datamodel/StructureViewerModel.java
+++ b/src/jalview/datamodel/StructureViewerModel.java
@@ -27,7 +27,8 @@ import java.util.List;
 import java.util.Map;
 
 /**
- * A data bean to hold stored data about a structure viewer.
+ * A data bean to hold stored data about a structure viewer
+ * in the process of creating XML.
  */
 public class StructureViewerModel
 {
@@ -59,7 +60,7 @@ public class StructureViewerModel
     private String filePath;
 
     private String pdbId;
-
+    
     private List<SequenceI> seqList;
 
     // TODO and possibly a list of chains?
@@ -67,6 +68,8 @@ public class StructureViewerModel
     /**
      * Constructor given structure file path and id.
      * 
+     * Curiously, only called by Jalview2XML.
+     * 
      * @param pdbFile
      * @param id
      */
diff --git a/src/jalview/fts/service/pdb/PDBFTSRestClient.java b/src/jalview/fts/service/pdb/PDBFTSRestClient.java
index b4e5660..402efff 100644
--- a/src/jalview/fts/service/pdb/PDBFTSRestClient.java
+++ b/src/jalview/fts/service/pdb/PDBFTSRestClient.java
@@ -20,7 +20,6 @@
  */
 package jalview.fts.service.pdb;
 
-import jalview.bin.Jalview;
 import jalview.datamodel.SequenceI;
 import jalview.fts.api.FTSData;
 import jalview.fts.api.FTSDataColumnI;
@@ -30,6 +29,7 @@ import jalview.fts.core.FTSRestRequest;
 import jalview.fts.core.FTSRestResponse;
 import jalview.util.JSONUtils;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 
 import java.net.URI;
 import java.util.ArrayList;
@@ -125,7 +125,7 @@ public class PDBFTSRestClient extends FTSRestClient
       // different from the ones in Java yet still allow this to be correct for Java
       Client client;
       Class<ClientResponse> clientResponseClass;
-      if (Jalview.isJS())
+      if (Platform.isJS())
       {
         // JavaScript only -- coerce types to Java types for Java
         client = (Client) (Object) new jalview.javascript.web.Client();
diff --git a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
index c3ca893..e6620f8 100644
--- a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
+++ b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
@@ -22,7 +22,6 @@
 package jalview.fts.service.uniprot;
 
 import jalview.bin.Cache;
-import jalview.bin.Jalview;
 import jalview.fts.api.FTSData;
 import jalview.fts.api.FTSDataColumnI;
 import jalview.fts.api.FTSRestClientI;
@@ -30,6 +29,7 @@ import jalview.fts.core.FTSRestClient;
 import jalview.fts.core.FTSRestRequest;
 import jalview.fts.core.FTSRestResponse;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 
 import java.util.ArrayList;
 import java.util.Collection;
@@ -96,7 +96,7 @@ public class UniProtFTSRestClient extends FTSRestClient
       // Java
       Client client;
       Class<ClientResponse> clientResponseClass;
-      if (Jalview.isJS())
+      if (Platform.isJS())
       {
         // JavaScript only -- coerce types to Java types for Java
         client = (Client) (Object) new jalview.javascript.web.Client();
@@ -132,7 +132,7 @@ public class UniProtFTSRestClient extends FTSRestClient
         throw new Exception(errorMessage);
 
       }
-      int xTotalResults = Jalview.isJS() ? 1
+      int xTotalResults = Platform.isJS() ? 1
               : Integer.valueOf(clientResponse.getHeaders()
                       .get("X-Total-Results").get(0));
       clientResponse = null;
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 71ba94a..395fd98 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -89,6 +89,7 @@ import jalview.schemes.ResidueColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.util.ImageMaker.TYPE;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.ViewportRanges;
 import jalview.ws.DBRefFetcher;
@@ -387,12 +388,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (Desktop.desktop != null)
     {
       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
-      /**
-       * BH 2018 ignore service listeners
-       * 
-       * @j2sNative
-       * 
-       */
+      if (!Platform.isJS())
       {
         addServiceListeners();
       }
@@ -3289,7 +3285,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             { contents.toString() });
     contents = null;
 
-    if (Jalview.isJS())
+    if (Platform.isJS())
     {
       JLabel textLabel = new JLabel();
       textLabel.setText(content);
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index f1b8025..1554079 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -350,7 +350,7 @@ public class Desktop extends jalview.jbgui.GDesktop
      * are spawned off as threads rather than waited for during this constructor.
      */
     instance = this;
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       doVamsasClientCheck();
     }
@@ -374,7 +374,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     // getContentPane().add(sp, BorderLayout.CENTER);
     
     // BH 2018 - just an experiment to try unclipped JInternalFrames. 
-	if (Jalview.isJS()) 
+	if (Platform.isJS()) 
 	{
 	  getRootPane().putClientProperty("swingjs.overflow.hidden", "false");
 	}
@@ -404,7 +404,7 @@ public class Desktop extends jalview.jbgui.GDesktop
       setBounds(xPos, yPos, 900, 650);
     }
     
-    boolean doFullLoad = /** @j2sNative ! */true;
+    boolean doFullLoad = !Platform.isJS();
     
     if (doFullLoad) {
       
@@ -882,8 +882,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     frame.setResizable(resizable);
     frame.setMaximizable(resizable);
     frame.setIconifiable(resizable);
-    frame.setOpaque(/** @j2sNative true || */
-            false);
+    frame.setOpaque(Platform.isJS()); // BH this should not be necessary
 
     if (frame.getX() < 1 && frame.getY() < 1)
     {
@@ -1178,7 +1177,7 @@ public class Desktop extends jalview.jbgui.GDesktop
      */
     JComponent history;
     String urlBase = "http://www.";
-    if (Jalview.isJS())
+    if (Platform.isJS())
     {
       history = new JTextField(urlBase, 35);
     }
@@ -1206,7 +1205,7 @@ public class Desktop extends jalview.jbgui.GDesktop
       @Override
       public void run()
       {
-        String url = Jalview.isJS() ? ((JTextField) history).getText()
+        String url = Platform.isJS() ? ((JTextField) history).getText()
                 : ((JComboBox<String>) history).getSelectedItem()
                         .toString();
 
@@ -1431,7 +1430,7 @@ public class Desktop extends jalview.jbgui.GDesktop
   {
     try
     {
-      if (Jalview.isJS())
+      if (Platform.isJS())
       {
         BrowserLauncher.openURL("http://www.jalview.org/help.html");
       }
@@ -2087,7 +2086,7 @@ public class Desktop extends jalview.jbgui.GDesktop
   /**
    * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
    * 
-   * @param file
+   * @param fileName
    * @return true if import was a success and a session was started.
    */
   public boolean vamsasImport(URL url)
diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 26cb104..b657ed3 100644
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -22,7 +22,6 @@ package jalview.gui;
 
 import jalview.api.FeatureColourI;
 import jalview.api.FeatureSettingsControllerI;
-import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.features.FeatureMatcher;
@@ -1765,7 +1764,7 @@ class ColorEditor extends AbstractCellEditor
            * variable colour and filters dialog
            */
           chooser = new FeatureTypeSettings(fr, type);
-          if (!Jalview.isJS())
+          if (!Platform.isJS())
           {
             chooser.setRequestFocusEnabled(true);
             chooser.requestFocus();
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 9ee4750..d34c653 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -20,7 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.bin.Jalview;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
@@ -281,7 +280,7 @@ public class IdPanel extends JPanel
   void startScrolling(boolean up)
   {
     scrollThread = new ScrollThread(up);
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       /*
        * Java - run in a new thread
diff --git a/src/jalview/gui/ImageExporter.java b/src/jalview/gui/ImageExporter.java
index a43eef0..5fb6951 100644
--- a/src/jalview/gui/ImageExporter.java
+++ b/src/jalview/gui/ImageExporter.java
@@ -7,6 +7,7 @@ import jalview.io.JalviewFileView;
 import jalview.util.ImageMaker;
 import jalview.util.ImageMaker.TYPE;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 
 import java.awt.Component;
 import java.awt.Graphics;
@@ -124,7 +125,7 @@ public class ImageExporter
     String renderStyle = Cache.getDefault(
             imageType.getName() + "_RENDERING",
             LineartOptions.PROMPT_EACH_TIME);
-    if (Jalview.isJS())
+    if (Platform.isJS())
     {
       renderStyle = "Text";
     }
diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index 9548839..465b5f9 100755
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -104,7 +104,7 @@ public class Jalview2XML_V1
   /**
    * DOCUMENT ME!
    * 
-   * @param file
+   * @param fileName
    *          DOCUMENT ME!
    */
   public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
diff --git a/src/jalview/gui/JvOptionPane.java b/src/jalview/gui/JvOptionPane.java
index 2290b52..5bbe75f 100644
--- a/src/jalview/gui/JvOptionPane.java
+++ b/src/jalview/gui/JvOptionPane.java
@@ -21,7 +21,7 @@
 
 package jalview.gui;
 
-import jalview.bin.Jalview;
+import jalview.util.Platform;
 import jalview.util.dialogrunner.DialogRunnerI;
 
 import java.awt.Component;
@@ -58,7 +58,7 @@ public class JvOptionPane extends JOptionPane implements DialogRunnerI,
   
   public JvOptionPane(final Component parent)
   {
-    this.parentComponent = Jalview.isJS() ? this : parent;
+    this.parentComponent = Platform.isJS() ? this : parent;
   }
 
   public static int showConfirmDialog(Component parentComponent,
@@ -720,7 +720,7 @@ public class JvOptionPane extends JOptionPane implements DialogRunnerI,
     String prefix = ""; 
     
     // JavaScript only
-    if (Jalview.isJS())
+    if (Platform.isJS())
     {
       switch (messageType)
       {
@@ -789,7 +789,7 @@ public class JvOptionPane extends JOptionPane implements DialogRunnerI,
      * In Java, the response is returned to this thread and handled here;
      * (for Javascript, see propertyChange)
      */
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       handleResponse(response);
     }
@@ -818,7 +818,7 @@ public class JvOptionPane extends JOptionPane implements DialogRunnerI,
               yesNoCancelOption, questionMessage, icon, options,
               initresponse);
     }
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       handleResponse(response);
     }
diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 66634ee..34138aa 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -246,7 +246,7 @@ public class OverviewPanel extends JPanel
      * Javascript does not call componentResized on initial display,
      * so do the update here
      */
-    boolean doUpdate =  /** @j2sNative true || */ false;
+    boolean doUpdate =  Platform.isJS();
     if (doUpdate)
       updateOverviewImage();
   }
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 5f58d51..ec7ff22 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -25,7 +25,6 @@ import jalview.analysis.AlignmentAnnotationUtils;
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.Conservation;
 import jalview.bin.Cache;
-import jalview.bin.Jalview;
 import jalview.commands.ChangeCaseCommand;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
@@ -51,6 +50,7 @@ import jalview.schemes.PIDColourScheme;
 import jalview.util.GroupUrlLink;
 import jalview.util.GroupUrlLink.UrlStringTooLongException;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.util.StringUtils;
 import jalview.util.UrlLink;
 
@@ -597,7 +597,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
   protected void showFeatureDetails(SequenceFeature sf)
   {
     JInternalFrame details;
-    if (/** @j2sNative true || */ false)
+    if (Platform.isJS())
     {
       details = new JInternalFrame();
       JPanel panel = new JPanel(new BorderLayout());
@@ -1650,7 +1650,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     String report = contents.toString();
     
     JInternalFrame frame;
-    if (Jalview.isJS())
+    if (Platform.isJS())
     {
       JLabel textLabel = new JLabel();
       textLabel.setText(report);
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 6a558d5..6d1f79a 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -22,7 +22,6 @@ package jalview.gui;
 
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.bin.Cache;
-import jalview.bin.Jalview;
 import jalview.gui.Help.HelpId;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.FileFormatI;
@@ -189,7 +188,7 @@ public class Preferences extends GPreferences
     super();
     frame = new JInternalFrame();
     frame.setContentPane(this);
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       wsPrefs = new WsPreferences();
       wsTab.add(wsPrefs, BorderLayout.CENTER);
@@ -555,7 +554,7 @@ public class Preferences extends GPreferences
     /*
      * JalviewJS doesn't support Lineart so force it to Text
      */
-    String defaultOption = Jalview.isJS() ? "Text"
+    String defaultOption = Platform.isJS() ? "Text"
             : Cache.getDefault(propertyKey, "Prompt each time");
     if (defaultOption.equalsIgnoreCase("Text"))
     {
@@ -820,7 +819,7 @@ public class Preferences extends GPreferences
     Cache.applicationProperties.setProperty("PAD_GAPS",
             Boolean.toString(padGaps.isSelected()));
 
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       wsPrefs.updateAndRefreshWsMenuConfig(false);
     }
@@ -897,7 +896,7 @@ public class Preferences extends GPreferences
   {
     try
     {
-      if (!Jalview.isJS())
+      if (!Platform.isJS())
       {
         wsPrefs.updateWsMenuConfig(true);
         wsPrefs.refreshWs_actionPerformed(e);
@@ -1041,6 +1040,8 @@ public class Preferences extends GPreferences
   public void defaultBrowser_mouseClicked(MouseEvent e)
   {
     // TODO: JAL-3048 not needed for j2s
+	if (Platform.isJS())
+		return;
     /*
      * @j2sNative
      */
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 5e117ca..59f239f 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -22,7 +22,6 @@ package jalview.gui;
 
 import jalview.api.AlignViewportI;
 import jalview.bin.Cache;
-import jalview.bin.Jalview;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
 import jalview.commands.EditCommand.Edit;
@@ -2054,7 +2053,7 @@ public class SeqPanel extends JPanel
     {
       scrollThread = new ScrollThread();
       scrollThread.setMousePosition(mousePos);
-      if (!Jalview.isJS())
+      if (!Platform.isJS())
       {
         /*
          * Java - run in a new thread
diff --git a/src/jalview/gui/SplashScreen.java b/src/jalview/gui/SplashScreen.java
index a122eb6..9f66402 100755
--- a/src/jalview/gui/SplashScreen.java
+++ b/src/jalview/gui/SplashScreen.java
@@ -20,6 +20,8 @@
  */
 package jalview.gui;
 
+import jalview.util.Platform;
+
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Component;
@@ -86,7 +88,7 @@ public class SplashScreen extends JPanel
   {
     this.interactiveDialog = interactive;
     // show a splashscreen that will disapper
-    if (/** @j2sNative true || */ false)
+    if (Platform.isJS())
     {
       authlist = new JLabel("");
       run();
@@ -135,7 +137,7 @@ public class SplashScreen extends JPanel
       java.net.URL urllogo = getClass()
               .getResource("/images/Jalview_Logo_small.png");
 
-      if (/** @j2sNative false || */ url != null)
+      if (!Platform.isJS() || url != null)
       {
         image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
         Image logo = java.awt.Toolkit.getDefaultToolkit()
@@ -200,7 +202,7 @@ public class SplashScreen extends JPanel
     {
       iframe.setVisible(false);
       oldtext = newtext.length();
-      if (/** @j2sNative true  || */ false)
+      if (Platform.isJS())
       {
         authlist = new JLabel("<html><br/><br/><img src=\"swingjs/j2s/images/Jalview_Logo.png\"/><br/>"+newtext);
         ((JLabel) authlist).setOpaque(true);
diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 04266be..94f9a37 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -32,6 +32,7 @@ import jalview.schemes.UserColourScheme;
 import jalview.util.ColorUtils;
 import jalview.util.Format;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.xml.binding.jalview.JalviewUserColours;
 import jalview.xml.binding.jalview.JalviewUserColours.Colour;
 import jalview.xml.binding.jalview.ObjectFactory;
@@ -483,9 +484,7 @@ public class UserDefinedColours extends GUserDefinedColours
    */
   protected void warnIfUnsavedChanges()
   {
-    // BH 2018 no warning in JavaScript TODO
-    
-    if (/** @j2sNative true || */ !changedButNotSaved)
+    if (Platform.isJS() || !changedButNotSaved)
     {
       return;
     }
@@ -747,12 +746,12 @@ public class UserDefinedColours extends GUserDefinedColours
     if (ColourSchemes.getInstance().nameExists(name))
     {
       // BH 2018 SwingJS bypasses this question with YES_OPTION
-      int reply = /** @j2sNative  0 &&  */ JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
+      int reply = (Platform.isJS() ? 0 : JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
               MessageManager.formatMessage(
                       "label.colour_scheme_exists_overwrite", new Object[]
                       { name, name }),
               MessageManager.getString("label.duplicate_scheme_name"),
-              JvOptionPane.YES_NO_OPTION);
+              JvOptionPane.YES_NO_OPTION));
       if (reply != JvOptionPane.YES_OPTION)
       {
       }
diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 8c376fc..f4c1b89 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -444,7 +444,7 @@ public class AppletFormatAdapter
     {
       protocol = DataSourceType.URL;
     }
-    else if (jalview.bin.Jalview.isJS())
+    else if (jalview.util.Platform.isJS())
     {
       protocol = DataSourceType.RELATIVE_URL;
     }
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index f244d14..4be15d9 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -39,6 +39,7 @@ import jalview.project.Jalview2XML;
 import jalview.schemes.ColourSchemeI;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.ws.utils.UrlDownloadClient;
 
 import java.io.BufferedReader;
@@ -646,12 +647,11 @@ public class FileLoader implements Runnable
    * @return
    * @throws FileNotFoundException 
    */
-  @SuppressWarnings("unused")
   public static BufferedReader getBuffereReader(Object file) throws FileNotFoundException {
     if (file instanceof String)
       return new BufferedReader(new FileReader((String) file));
     
-    byte[] bytes = /** @j2sNative file._bytes || */ null;
+    byte[] bytes = Platform.getFileBytes((File) file);
     if (bytes != null)
       return new BufferedReader(new InputStreamReader(new ByteArrayInputStream(bytes)));
     return  new BufferedReader(new FileReader((File) file));
diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 809bc8f..80b6836 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -25,6 +25,7 @@ import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureSettingsModelI;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 
 import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;
@@ -333,12 +334,7 @@ public class FileParse
   private void parse(File file, String fileStr, DataSourceType sourceType,
           boolean isFileObject) throws MalformedURLException, IOException
   {
-    /**
-     * @j2sNative
-     * 
-     *            this.bytes = file && file._bytes;
-     * 
-     */
+	bytes = Platform.getFileBytes(file);
     this.dataSourceType = sourceType;
     error = false;
 
@@ -375,15 +371,7 @@ public class FileParse
     }
     else if (sourceType == DataSourceType.RELATIVE_URL)
     {
-      /**
-       * BH 2018 hack for no support for access-origin
-       * 
-       * @j2sNative
-       * 
-       * this.bytes = swingjs.JSUtil.getFileAsBytes$O(fileStr);
-       * 
-       */
-
+      bytes = Platform.getFileAsBytes(fileStr);
       dataIn = new BufferedReader(new java.io.InputStreamReader(new ByteArrayInputStream(bytes)));      
       dataName = fileStr;
 
diff --git a/src/jalview/io/JalviewFileChooser.java b/src/jalview/io/JalviewFileChooser.java
index f6455bf..67f1115 100755
--- a/src/jalview/io/JalviewFileChooser.java
+++ b/src/jalview/io/JalviewFileChooser.java
@@ -22,7 +22,6 @@
 package jalview.io;
 
 import jalview.bin.Cache;
-import jalview.bin.Jalview;
 import jalview.gui.JvOptionPane;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -194,7 +193,7 @@ public class JalviewFileChooser extends JFileChooser implements DialogRunnerI,
   {
     int value = super.showOpenDialog(this);
     
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       /*
        * code here is not run in JalviewJS, instead
diff --git a/src/jalview/io/cache/JvCacheableInputBox.java b/src/jalview/io/cache/JvCacheableInputBox.java
index b1b7ac5..cf21c62 100644
--- a/src/jalview/io/cache/JvCacheableInputBox.java
+++ b/src/jalview/io/cache/JvCacheableInputBox.java
@@ -21,8 +21,8 @@
 package jalview.io.cache;
 
 import jalview.bin.Cache;
-import jalview.bin.Jalview;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
@@ -92,7 +92,7 @@ public class JvCacheableInputBox<E>
   public JvCacheableInputBox(String newCacheKey)
   {
     super();
-    if (Jalview.isJS())
+    if (Platform.isJS())
     {
       textField = new JTextField();
       return;
@@ -202,7 +202,7 @@ public class JvCacheableInputBox<E>
    */
   public void updateCache()
   {
-    if (Jalview.isJS())
+    if (Platform.isJS())
     {
       return;
     }
@@ -278,7 +278,7 @@ public class JvCacheableInputBox<E>
    */
   public void persistCache()
   {
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       appCache.persistCache(cacheKey);
     }
@@ -291,7 +291,7 @@ public class JvCacheableInputBox<E>
    */
   public String getUserInput()
   {
-    if (Jalview.isJS())
+    if (Platform.isJS())
     {
       return textField.getText().trim();
     }
@@ -301,12 +301,12 @@ public class JvCacheableInputBox<E>
 
   public JComponent getComponent()
   {
-    return Jalview.isJS() ? textField : comboBox;
+    return Platform.isJS() ? textField : comboBox;
   }
 
   public void addActionListener(ActionListener actionListener)
   {
-    if (Jalview.isJS())
+    if (Platform.isJS())
     {
       textField.addActionListener(actionListener);
     }
@@ -318,7 +318,7 @@ public class JvCacheableInputBox<E>
 
   public void addDocumentListener(DocumentListener listener)
   {
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       ((JTextComponent) comboBox.getEditor().getEditorComponent())
               .getDocument().addDocumentListener(listener);
@@ -327,7 +327,7 @@ public class JvCacheableInputBox<E>
 
   public void addFocusListener(FocusListener focusListener)
   {
-    if (Jalview.isJS())
+    if (Platform.isJS())
     {
       textField.addFocusListener(focusListener);
     }
@@ -339,7 +339,7 @@ public class JvCacheableInputBox<E>
 
   public void addKeyListener(KeyListener kl)
   {
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       comboBox.getEditor().getEditorComponent().addKeyListener(kl);
     }
@@ -347,7 +347,7 @@ public class JvCacheableInputBox<E>
 
   public void setEditable(boolean b)
   {
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       comboBox.setEditable(b);
     }
@@ -355,7 +355,7 @@ public class JvCacheableInputBox<E>
 
   public void setPrototypeDisplayValue(String string)
   {
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       comboBox.setPrototypeDisplayValue(string);
     }
@@ -363,7 +363,7 @@ public class JvCacheableInputBox<E>
 
   public void setSelectedItem(String userInput)
   {
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       comboBox.setSelectedItem(userInput);
     }
@@ -371,7 +371,7 @@ public class JvCacheableInputBox<E>
 
   public boolean isPopupVisible()
   {
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       return comboBox.isPopupVisible();
     }
@@ -380,7 +380,7 @@ public class JvCacheableInputBox<E>
 
   public void addCaretListener(CaretListener caretListener)
   {
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       ((JTextComponent) comboBox.getEditor().getEditorComponent())
               .addCaretListener(caretListener);
@@ -389,7 +389,7 @@ public class JvCacheableInputBox<E>
 
   public void addItem(String item)
   {
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       comboBox.addItem(item);
     }
diff --git a/src/jalview/javascript/json/JSON.java b/src/jalview/javascript/json/JSON.java
index a1de56e..714f04f 100644
--- a/src/jalview/javascript/json/JSON.java
+++ b/src/jalview/javascript/json/JSON.java
@@ -162,7 +162,7 @@ public class JSON {
 
 		public JSONReader(String json) {
 			super((Reader) (Object) "");
-			data = toObject(/** @j2sNative  swingjs.JSUtil.parseJSON$S(json)|| */null); 
+			data = toObject(/** @j2sNative  swingjs.JSUtil.parseJSONRaw$S(json)|| */null); 
 		}
 
 		@Override
diff --git a/src/jalview/javascript/web/WebResource.java b/src/jalview/javascript/web/WebResource.java
index 6d12932..588dd49 100644
--- a/src/jalview/javascript/web/WebResource.java
+++ b/src/jalview/javascript/web/WebResource.java
@@ -1,5 +1,7 @@
 package jalview.javascript.web;
 
+import jalview.util.Platform;
+
 import java.net.URI;
 import java.net.URISyntaxException;
 
@@ -19,11 +21,7 @@ public class WebResource
   public WebResource queryParam(String key, String value)
   {
     params += (params == "" ? "?" : "&") + key + "=";
-    /**
-     * @j2sNative
-     * value = encodeURIComponent(value);
-     */
-    params += value;
+    params += Platform.encodeURI(value);
     return this;
   }
 
@@ -60,7 +58,7 @@ public class WebResource
       public ClientResponse get(Class<?> c) {
         String data = uri.toString();
         // c will be ClientResponse 
-        data = /** @j2sNative swingjs.JSUtil.getFileAsString$S(data) || */ null;
+        data = Platform.getFileAsString(data);
         return new ClientResponse(data, encoding);
       }
   }
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 15d5713..2e6aab8 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -23,7 +23,6 @@ package jalview.jbgui;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.api.SplitContainerI;
 import jalview.bin.Cache;
-import jalview.bin.Jalview;
 import jalview.gui.JvSwingUtils;
 import jalview.gui.Preferences;
 import jalview.io.FileFormats;
@@ -1711,7 +1710,7 @@ public class GAlignFrame extends JInternalFrame
     alignFrameMenuBar.add(formatMenu);
     alignFrameMenuBar.add(colourMenu);
     alignFrameMenuBar.add(calculateMenu);
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       alignFrameMenuBar.add(webService);
     }
@@ -1732,7 +1731,7 @@ public class GAlignFrame extends JInternalFrame
     fileMenu.add(exportAnnotations);
     fileMenu.add(loadTreeMenuItem);
     fileMenu.add(associatedData);
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       fileMenu.add(loadVcf);
     }
@@ -1830,7 +1829,7 @@ public class GAlignFrame extends JInternalFrame
     calculateMenu.addSeparator();
     calculateMenu.add(expandAlignment);
     calculateMenu.add(extractScores);
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       calculateMenu.addSeparator();
       calculateMenu.add(runGroovy);
@@ -1839,14 +1838,14 @@ public class GAlignFrame extends JInternalFrame
     webServiceNoServices = new JMenuItem(
             MessageManager.getString("label.no_services"));
     webService.add(webServiceNoServices);
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       exportImageMenu.add(htmlMenuItem);
     }
     exportImageMenu.add(epsFile);
     exportImageMenu.add(createPNG);
     exportImageMenu.add(createBioJS);
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       exportImageMenu.add(createSVG);
     }
diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java
index b301f6e..7dfc3d4 100755
--- a/src/jalview/jbgui/GDesktop.java
+++ b/src/jalview/jbgui/GDesktop.java
@@ -21,7 +21,6 @@
 package jalview.jbgui;
 
 import jalview.api.AlignmentViewPanel;
-import jalview.bin.Jalview;
 import jalview.io.FileFormatException;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -48,17 +47,7 @@ public class GDesktop extends JFrame
 
   public static javax.swing.JTabbedPane createTabbedPane()
   {
-    // now just always return JTabbedPane
    return new javax.swing.JTabbedPane();
-//    // BH 2018 coercing jalview.jbgui.swing.JTabbedPane() for now
-//    if (/** @j2sNative false && */
-//    true)
-//    {
-//      // Java
-//      return new javax.swing.JTabbedPane();
-//    }
-//    // JavaScript
-//    return (javax.swing.JTabbedPane) (Object) new jalview.jbgui.swing.JTabbedPane();
   }
 
   
@@ -464,7 +453,7 @@ public class GDesktop extends JFrame
     FileMenu.addSeparator();
     FileMenu.add(saveAsJaxb);
     FileMenu.add(loadAsJaxb);
-    if (!Jalview.isJS()) 
+    if (!Platform.isJS()) 
     {
       FileMenu.add(saveState);
       FileMenu.add(loadState);
@@ -480,12 +469,12 @@ public class GDesktop extends JFrame
     VamsasMenu.add(vamsasSave);
     VamsasMenu.add(vamsasStop);
     toolsMenu.add(preferences);
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       toolsMenu.add(showMemusage);
       toolsMenu.add(showConsole);
     }
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       toolsMenu.add(showNews);
       toolsMenu.add(garbageCollect);
diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 9fc0398..1e01cc3 100755
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -20,13 +20,13 @@
  */
 package jalview.jbgui;
 
-import jalview.bin.Jalview;
 import jalview.fts.core.FTSDataColumnPreferences;
 import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
 import jalview.fts.service.pdb.PDBFTSRestClient;
 import jalview.gui.JvSwingUtils;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -329,7 +329,7 @@ public class GPreferences extends JPanel
     /*
      * See WsPreferences for the real work of configuring this tab.
      */
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       wsTab.setLayout(new BorderLayout());
       tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
@@ -514,7 +514,7 @@ public class GPreferences extends JPanel
     outputTab.add(userIdWidth);
     outputTab.add(userIdWidthlabel);
     outputTab.add(modellerOutput);
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       /*
        * JalviewJS doesn't support Lineart option or SVG output
@@ -1289,7 +1289,7 @@ public class GPreferences extends JPanel
     /*
      * hide Chimera options in JalviewJS
      */
-    if (Jalview.isJS()) 
+    if (Platform.isJS()) 
     {
       pathLabel.setVisible(false);
       chimeraPath.setVisible(false);
@@ -1674,7 +1674,7 @@ public class GPreferences extends JPanel
     visualTab.add(fontSizeCB);
     visualTab.add(fontStyleCB);
     
-    if (Jalview.isJS())
+    if (Platform.isJS())
     {
       startupCheckbox.setVisible(false);
       startupFileTextfield.setVisible(false);
diff --git a/src/jalview/jbgui/GSplitFrame.java b/src/jalview/jbgui/GSplitFrame.java
index a40e260..db346b8 100644
--- a/src/jalview/jbgui/GSplitFrame.java
+++ b/src/jalview/jbgui/GSplitFrame.java
@@ -49,6 +49,8 @@ public class GSplitFrame extends JInternalFrame
    */
   private double dividerRatio;
 
+  private static boolean doSetDivider = !Platform.isJS(); // BH why? Old?
+
   /**
    * Constructor
    * 
@@ -79,11 +81,7 @@ public class GSplitFrame extends JInternalFrame
      * project
      */
     int topFrameHeight = topFrame.getHeight();
-    /**
-     * TODO SplitFrame.setDividerLocation
-     * 
-     * @j2sNative
-     */
+    if (doSetDivider)
     {
       splitPane.setDividerSize(DIVIDER_SIZE);
       if (topFrameHeight == 0)
@@ -118,9 +116,7 @@ public class GSplitFrame extends JInternalFrame
     }
     else
     {
-      /**
-       * @j2sNative
-       */
+    	if (doSetDivider)
       {
         ((BasicInternalFrameUI) topFrame.getUI()).setNorthPane(null);
         ((BasicInternalFrameUI) bottomFrame.getUI()).setNorthPane(null);
@@ -212,9 +208,8 @@ public class GSplitFrame extends JInternalFrame
   public void setRelativeDividerLocation(double r)
   {
     this.dividerRatio = r;
-    /**
-     * @j2sNative
-     */
+    // BH why?
+    if (!Platform.isJS())
     {
       splitPane.setDividerLocation(r);
     }
@@ -227,9 +222,7 @@ public class GSplitFrame extends JInternalFrame
    */
   protected void setDividerLocation(int p)
   {
-    /**
-     * @j2sNative
-     */
+	if (doSetDivider )
     {
       splitPane.setDividerLocation(p);
     }
diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 646cab5..efe643e 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -191,21 +191,9 @@ public class Jalview2XML
   // BH 2018 we add the .jvp binary extension to J2S so that
   // it will declare that binary when we do the file save from the browser
 
-  private static void addJ2SBinaryType(String ext)
-  {
-    ext = "." + ext + "?";
-
-    /**
-     * @j2sNative
-     * 
-     *            J2S._binaryTypes.push(ext);
-     * 
-     */
-  }
-
   static
   {
-    addJ2SBinaryType(".jvp?");
+    Platform.addJ2SBinaryType(".jvp?");
   }
 
   private static final String VIEWER_PREFIX = "viewer_";
@@ -2531,8 +2519,7 @@ public class Jalview2XML
 		// BH 2018 allow for bytes already attached to File object
 		try {
 			String file = (ofile instanceof File ? ((File) ofile).getCanonicalPath() : ofile.toString());
-			byte[] bytes = /** @j2sNative ofile._bytes || */
-					null;
+			byte[] bytes = Platform.getFileBytes((File) ofile);
 			URL url = null;
 			errorMessage = null;
 			uniqueSetSuffix = null;
diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 4d3445b..ed266ae 100644
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -25,7 +25,6 @@ import jalview.analysis.CodingUtils;
 import jalview.analysis.Rna;
 import jalview.analysis.StructureFrequency;
 import jalview.api.AlignViewportI;
-import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
@@ -1485,7 +1484,7 @@ public class AnnotationRenderer
             // int hght = (int) (ht + (newAsc - newDec);
             // - lm.getBaselineOffsets()[lm.getBaselineIndex()]));
 
-            if (Jalview.isJS())
+            if (Platform.isJS())
             {
               /*
                * SwingJS does not implement font.deriveFont()
diff --git a/src/jalview/util/BrowserLauncher.java b/src/jalview/util/BrowserLauncher.java
index a55a65c..5ce996d 100755
--- a/src/jalview/util/BrowserLauncher.java
+++ b/src/jalview/util/BrowserLauncher.java
@@ -236,87 +236,88 @@ public class BrowserLauncher
 
     loadedWithoutErrors = true;
 
-    /**
-     * 
-     * @j2sNative
-     * 
-     */
-    {
-    String osName = System.getProperty("os.name");
-
-    if (osName.startsWith("Mac OS"))
-    {
-      String mrjVersion = System.getProperty("mrj.version");
-      String majorMRJVersion;
-      if (mrjVersion == null)
-      {
-        // must be on some later build with mrj support
-        majorMRJVersion = "3.1";
-      }
-      else
-      {
-        majorMRJVersion = mrjVersion.substring(0, 3);
-      }
-
-      try
-      {
-        double version = Double.valueOf(majorMRJVersion).doubleValue();
-
-        if (version == 2)
-        {
-          jvm = MRJ_2_0;
-        }
-        else if ((version >= 2.1) && (version < 3))
-        {
-          // Assume that all 2.x versions of MRJ work the same. MRJ 2.1 actually
-          // works via Runtime.exec() and 2.2 supports that but has an openURL()
-          // method
-          // as well that we currently ignore.
-          jvm = MRJ_2_1;
-        }
-        else if (version == 3.0)
-        {
-          jvm = MRJ_3_0;
-        }
-        else if (version >= 3.1)
-        {
-          // Assume that all 3.1 and later versions of MRJ work the same.
-          jvm = MRJ_3_1;
-        }
-        else
-        {
-          loadedWithoutErrors = false;
-          errorMessage = "Unsupported MRJ version: " + version;
-        }
-      } catch (NumberFormatException nfe)
-      {
-        loadedWithoutErrors = false;
-        errorMessage = "Invalid MRJ version: " + mrjVersion;
-      }
-    }
-    else if (osName.startsWith("Windows"))
-    {
-      if (osName.indexOf("9") != -1)
-      {
-        jvm = WINDOWS_9x;
-      }
-      else
-      {
-        jvm = WINDOWS_NT;
-      }
-    }
-    else
-    {
-      jvm = OTHER;
-    }
-
-    if (loadedWithoutErrors)
-    { // if we haven't hit any errors yet
-      loadedWithoutErrors = loadClasses();
-    }
-    }
+    if (!Platform.isJS()) {
+	    /**
+	     * 
+	     * @j2sNative
+	     * 
+	     */
+	    {
+	    String osName = System.getProperty("os.name");
+	
+	    if (osName.startsWith("Mac OS"))
+	    {
+	      String mrjVersion = System.getProperty("mrj.version");
+	      String majorMRJVersion;
+	      if (mrjVersion == null)
+	      {
+	        // must be on some later build with mrj support
+	        majorMRJVersion = "3.1";
+	      }
+	      else
+	      {
+	        majorMRJVersion = mrjVersion.substring(0, 3);
+	      }
+	
+	      try
+	      {
+	        double version = Double.valueOf(majorMRJVersion).doubleValue();
+	
+	        if (version == 2)
+	        {
+	          jvm = MRJ_2_0;
+	        }
+	        else if ((version >= 2.1) && (version < 3))
+	        {
+	          // Assume that all 2.x versions of MRJ work the same. MRJ 2.1 actually
+	          // works via Runtime.exec() and 2.2 supports that but has an openURL()
+	          // method
+	          // as well that we currently ignore.
+	          jvm = MRJ_2_1;
+	        }
+	        else if (version == 3.0)
+	        {
+	          jvm = MRJ_3_0;
+	        }
+	        else if (version >= 3.1)
+	        {
+	          // Assume that all 3.1 and later versions of MRJ work the same.
+	          jvm = MRJ_3_1;
+	        }
+	        else
+	        {
+	          loadedWithoutErrors = false;
+	          errorMessage = "Unsupported MRJ version: " + version;
+	        }
+	      } catch (NumberFormatException nfe)
+	      {
+	        loadedWithoutErrors = false;
+	        errorMessage = "Invalid MRJ version: " + mrjVersion;
+	      }
+	    }
+	    else if (osName.startsWith("Windows"))
+	    {
+	      if (osName.indexOf("9") != -1)
+	      {
+	        jvm = WINDOWS_9x;
+	      }
+	      else
+	      {
+	        jvm = WINDOWS_NT;
+	      }
+	    }
+	    else
+	    {
+	      jvm = OTHER;
+	    }
+	
+	    if (loadedWithoutErrors)
+	    { // if we haven't hit any errors yet
+	      loadedWithoutErrors = loadClasses();
+	    }
+	    }
+	  }
   }
-
   /**
    * This class should be never be instantiated; this just ensures so.
    */
@@ -334,10 +335,7 @@ public class BrowserLauncher
   private static boolean loadClasses()
   {
 
-    /**
-     * @j2sNative
-     * 
-     */
+	if (!Platform.isJS())
     {
     switch (jvm)
     {
@@ -538,6 +536,8 @@ public class BrowserLauncher
    */
   private static Object locateBrowser()
   {
+	if (Platform.isJS())
+		return browser;
     /**
      * @j2sNative
      * 
@@ -735,11 +735,11 @@ public class BrowserLauncher
   public static void openURL(String url) throws IOException
   {
 
+	if (Platform.openURL(url))
+		return;
     /**
      * @j2sNative
      * 
-     *            window.open(url);
-     * 
      * 
      */
 
diff --git a/src/jalview/util/Platform.java b/src/jalview/util/Platform.java
index 1f03f88..0a788d9 100644
--- a/src/jalview/util/Platform.java
+++ b/src/jalview/util/Platform.java
@@ -22,6 +22,7 @@ package jalview.util;
 
 import java.awt.Toolkit;
 import java.awt.event.MouseEvent;
+import java.io.File;
 
 import javax.swing.SwingUtilities;
 
@@ -59,12 +60,14 @@ public class Platform
   }
 
   /**
+   * Answers true if Jalview is running as Javascript, else false. The value is
+   * set at compile time.
    * 
-   * @return true if HTML5 JavaScript
+   * @return
    */
   public static boolean isJS()
   {
-	return isJS;
+    return /** @j2sNative true || */ false;
   }
 
   /**
@@ -219,5 +222,74 @@ public class Platform
 		  break;
 	  }
   }
+
+public static void cacheFileData(String path, byte[] data) {
+	if (!isJS())
+		return;
+	  /**
+	   * @j2sNative 
+	   *   
+	   *   swingjs.JSUtil.cacheFileData$S$O(path, data);
+	   * 
+	   */
+}
+
+public static byte[] getFileBytes(File f) {
+	return /** @j2sNative   f && f._bytes || */null;
+}
+
+public static byte[] getFileAsBytes(String fileStr) {
+    // BH 2018 hack for no support for access-origin
+		return /** @j2sNative swingjs.JSUtil.getFileAsBytes$O(fileStr) || */ null;
+}
+
+public static String getFileAsString(String data) {
+	return /** @j2sNative swingjs.JSUtil.getFileAsString$S(data) || */ null;
+}
+
+public static boolean setFileBytes(File f, String urlstring) {
+	if (!isJS()) 
+		return false;
+	@SuppressWarnings("unused")
+	byte[] bytes = getFileAsBytes(urlstring);
+		    /** @j2sNative 
+		     * f._bytes = bytes; 
+		     */
+	return true;
+}
+
    
+public static void addJ2SBinaryType(String ext)
+{
+  ext = "." + ext + "?";
+
+  /**
+   * @j2sNative
+   * 
+   *            J2S._binaryTypes.push(ext);
+   * 
+   */
+}
+
+public static String encodeURI(String value) {
+    /**
+     * @j2sNative
+     * return encodeURIComponent(value);
+     */
+	return value;
+}
+
+public static boolean openURL(String url) {
+	if (!isJS()) 
+		return false;
+		/**
+		 * @j2sNative
+		 * 
+		 * 
+		 * 			window.open(url);
+		 */
+	return true;
+}
+
+
 }
diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index 668aab5..6d0c60b 100644
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -116,7 +116,7 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
    *          either EMBL or EMBLCDS strings are allowed - anything else will
    *          not retrieve emblxml
    * @param query
-   * @param file
+   * @param fileName
    *          the EMBL XML file containing the results of a query
    * @return
    * @throws Exception
diff --git a/src/jalview/ws/ebi/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java
index 5dc3c94..d8bd1dd 100644
--- a/src/jalview/ws/ebi/EBIFetchClient.java
+++ b/src/jalview/ws/ebi/EBIFetchClient.java
@@ -22,6 +22,7 @@ package jalview.ws.ebi;
 
 import jalview.datamodel.DBRefSource;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 
 import java.io.BufferedInputStream;
 import java.io.BufferedReader;
@@ -216,12 +217,14 @@ public class EBIFetchClient
       InputStream is = new BufferedInputStream(conn.getInputStream());
       if (outFile != null)
       {
+    	if (Platform.isJS()) {
         /**@j2sNative 
          * if (outFile._isTemp) {
          * outFile._bytes = is.$in.$in.buf;
          * return null;
          * }
          */
+    	}
         FileOutputStream fio = new FileOutputStream(outFile);
         byte[] bb = new byte[32 * 1024];
         int l;
diff --git a/src/jalview/ws/utils/UrlDownloadClient.java b/src/jalview/ws/utils/UrlDownloadClient.java
index cfe080c..77fbd5b 100644
--- a/src/jalview/ws/utils/UrlDownloadClient.java
+++ b/src/jalview/ws/utils/UrlDownloadClient.java
@@ -21,6 +21,8 @@
 
 package jalview.ws.utils;
 
+import jalview.util.Platform;
+
 import java.io.ByteArrayInputStream;
 import java.io.File;
 import java.io.FileOutputStream;
@@ -114,13 +116,8 @@ public class UrlDownloadClient
 
   public static void download(String urlstring, File tempFile) throws IOException
   {
-    if (/** @j2sNative 1?false: */true) {
-      download(urlstring, tempFile.toString());
+    if (!Platform.setFileBytes(tempFile, urlstring)) {
+        download(urlstring, tempFile.toString());    	
     }
-    // JavaScript only
-
-    /** @j2sNative 
-     * tempFile._bytes = swingjs.JSUtil.getFileAsBytes(urlstring); 
-     */
   }
 }