JAL-3253 preliminary static fixes for JavaScript part 3 of 3

[jalview.git] / src / jalview / gui / Preferences.java

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 8765b37..facc826 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -37,6 +37,7 @@ import jalview.urls.UrlLinkTableModel;
 import jalview.urls.api.UrlProviderFactoryI;
 import jalview.urls.api.UrlProviderI;
 import jalview.urls.desktop.DesktopUrlProviderFactory;
+import jalview.util.BrowserLauncher;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.util.UrlConstants;
@@ -139,7 +140,8 @@ public class Preferences extends GPreferences
    * (TODO: proper escape for using | to separate ids or sequences
    */
 
-  public static final List<String> groupURLLinks;
+  public static final List<String> groupURLLinks; // not implemented
+
   static
   {
     // get links selected to be in the menu (SEQUENCE_LINKS)
@@ -165,7 +167,7 @@ public class Preferences extends GPreferences
      * .properties file as '|' separated strings
      */
 
-    groupURLLinks = new ArrayList<>();
+    groupURLLinks = new ArrayList<>(); // not implemented
   }
 
   JInternalFrame frame;
@@ -724,12 +726,16 @@ public class Preferences extends GPreferences
     Cache.setPropertyNoSave("SVG_RENDERING",
             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 
-    /*
-     * Save Connections settings
+    if (!Platform.isJS())
+    /**
+     * @j2sNative
      */
-    Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
-
-    jalview.util.BrowserLauncher.resetBrowser();
+    {
+      // Java only
+      // Save Connections settings
+      Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
+      BrowserLauncher.resetBrowser();
+    }
 
     // save user-defined and selected links
     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
@@ -814,8 +820,6 @@ public class Preferences extends GPreferences
             Boolean.toString(modellerOutput.isSelected()));
     Cache.setPropertyNoSave("EXPORT_EMBBED_BIOJSON",
             Boolean.toString(embbedBioJSON.isSelected()));
-    jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
-
     Cache.setPropertyNoSave("FIGURE_AUTOIDWIDTH",
             Boolean.toString(autoIdWidth.isSelected()));
     userIdWidth_actionPerformed();
@@ -1108,6 +1112,11 @@ public class Preferences extends GPreferences
     super.showunconserved_actionPerformed(e);
   }
 
+  /**
+   * not implemented -- returns empty list
+   * 
+   * @return
+   */
   public static List<String> getGroupURLLinks()
   {
     return groupURLLinks;