From 6d35ae6c809d36b2e2fa984436134dbff712a377 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 20 Aug 2018 10:32:14 +0100
Subject: [PATCH] JAL-3084 hide startup file, Chimera, HTML/SVG, Web Services
 options/tab in JalviewJS

---
 src/jalview/gui/Preferences.java    |   21 +++++++++++++-----
 src/jalview/jbgui/GPreferences.java |   42 +++++++++++++++++++++++++++++------
 2 files changed, 50 insertions(+), 13 deletions(-)

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 31842e4..6271ba9 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -22,6 +22,7 @@ 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;
@@ -188,10 +189,12 @@ public class Preferences extends GPreferences
     super();
     frame = new JInternalFrame();
     frame.setContentPane(this);
-    wsPrefs = new WsPreferences();
-    wsTab.add(wsPrefs, BorderLayout.CENTER);
+    if (!Jalview.isJS())
+    {
+      wsPrefs = new WsPreferences();
+      wsTab.add(wsPrefs, BorderLayout.CENTER);
+    }
     int width = 500, height = 450;
-    new jalview.util.Platform();
     if (Platform.isAMac())
     {
       width = 570;
@@ -813,7 +816,10 @@ public class Preferences extends GPreferences
     Cache.applicationProperties.setProperty("PAD_GAPS",
             Boolean.toString(padGaps.isSelected()));
 
-    wsPrefs.updateAndRefreshWsMenuConfig(false);
+    if (!Jalview.isJS())
+    {
+      wsPrefs.updateAndRefreshWsMenuConfig(false);
+    }
     Cache.saveProperties();
     Desktop.instance.doConfigureStructurePrefs();
     try
@@ -887,8 +893,11 @@ public class Preferences extends GPreferences
   {
     try
     {
-      wsPrefs.updateWsMenuConfig(true);
-      wsPrefs.refreshWs_actionPerformed(e);
+      if (!Jalview.isJS())
+      {
+        wsPrefs.updateWsMenuConfig(true);
+        wsPrefs.refreshWs_actionPerformed(e);
+      }
       frame.setClosed(true);
     } catch (Exception ex)
     {
diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 4d8272b..351a030 100755
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -20,6 +20,7 @@
  */
 package jalview.jbgui;
 
+import jalview.bin.Jalview;
 import jalview.fts.core.FTSDataColumnPreferences;
 import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
 import jalview.fts.service.pdb.PDBFTSRestClient;
@@ -328,8 +329,11 @@ public class GPreferences extends JPanel
     /*
      * See WsPreferences for the real work of configuring this tab.
      */
-    wsTab.setLayout(new BorderLayout());
-    tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
+    if (!Jalview.isJS())
+    {
+      wsTab.setLayout(new BorderLayout());
+      tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
+    }
 
     /*
      * Handler to validate a tab before leaving it - currently only for
@@ -510,13 +514,19 @@ public class GPreferences extends JPanel
     outputTab.add(userIdWidth);
     outputTab.add(userIdWidthlabel);
     outputTab.add(modellerOutput);
-    outputTab.add(embbedBioJSON);
+    if (!Jalview.isJS())
+    {
+      outputTab.add(embbedBioJSON);
+    }
     outputTab.add(epsLabel);
     outputTab.add(epsRendering);
-    outputTab.add(htmlLabel);
-    outputTab.add(htmlRendering);
-    outputTab.add(svgLabel);
-    outputTab.add(svgRendering);
+    if (!Jalview.isJS())
+    {
+      outputTab.add(htmlLabel);
+      outputTab.add(htmlRendering);
+      outputTab.add(svgLabel);
+      outputTab.add(svgRendering);
+    }
     outputTab.add(jPanel11);
     return outputTab;
   }
@@ -1276,6 +1286,17 @@ public class GPreferences extends JPanel
     docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
     structureTab.add(docFieldPref);
 
+    /*
+     * hide Chimera options in JalviewJS
+     */
+    if (Jalview.isJS()) 
+    {
+      pathLabel.setVisible(false);
+      chimeraPath.setVisible(false);
+      viewerLabel.setVisible(false);
+      structViewer.setVisible(false);
+    }
+    
     return structureTab;
   }
 
@@ -1652,6 +1673,13 @@ public class GPreferences extends JPanel
     visualTab.add(fontNameCB);
     visualTab.add(fontSizeCB);
     visualTab.add(fontStyleCB);
+    
+    if (Jalview.isJS())
+    {
+      startupCheckbox.setVisible(false);
+      startupFileTextfield.setVisible(false);
+    }
+    
     return visualTab;
   }
 
-- 
1.7.10.2