Jalview-JS/JAL-3253 applet params jpredfile, jnetfile

[jalview.git] / src / jalview / bin / Jalview.java

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 402f9bf..7bf0c72 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1177,13 +1177,18 @@ public class Jalview implements ApplicationSingletonI
     return id + (frameType == null ? "" : "-" + frameType);
   }
 
+  /**
+   * Handle all JalviewLite applet parameters
+   * 
+   * @param aparser
+   * @param af
+   */
   private void loadAppletParams(ArgsParser aparser, AlignFrame af)
   {
     Jalview me = this;
     JalviewApp app = new JalviewApp()
     {
 
-
       @Override
       public String getParameter(String name)
       {
@@ -1198,12 +1203,18 @@ public class Jalview implements ApplicationSingletonI
                 : "true".equalsIgnoreCase(stn));
       }
 
+      /**
+       * Get the applet-like document base even though this is an application.
+       */
       @Override
       public URL getDocumentBase()
       {
         return Platform.getDocumentBase();
       }
 
+      /**
+       * Get the applet-like code base even though this is an application.
+       */
       @Override
       public URL getCodeBase()
       {
@@ -1216,6 +1227,21 @@ public class Jalview implements ApplicationSingletonI
         return Jalview.getCurrentAlignFrame().getViewport();
       }
 
+      /**
+       * features
+       * 
+       */
+      @Override
+      public boolean parseFeaturesFile(String filename,
+              DataSourceType protocol)
+      {
+        return af.parseFeaturesFile(filename, protocol);
+      }
+
+      /**
+       * scorefile
+       * 
+       */
       @Override
       public boolean loadScoreFile(String sScoreFile) throws IOException
       {
@@ -1224,18 +1250,21 @@ public class Jalview implements ApplicationSingletonI
         return true;
       }
 
+      /**
+       * annotations, jpredfile, jnetfile
+       * 
+       */
       @Override
-      public boolean parseFeaturesFile(String filename,
-              DataSourceType protocol)
+      public void updateForAnnotations()
       {
-        return af.parseFeaturesFile(filename, protocol);
+        Jalview.getCurrentAlignFrame().updateForAnnotations();
       }
 
       @Override
       public void loadTree(NewickFile fin, String treeFile)
               throws IOException
       {
-        // n/a -- already done
+        // n/a -- already done by standard Jalview command line processing
       }
 
       @Override
@@ -1262,13 +1291,6 @@ public class Jalview implements ApplicationSingletonI
       }
 
       @Override
-      public void updateForLoader()
-      {
-        // TODO Auto-generated method stub
-
-      }
-
-      @Override
       public void setFeatureGroupState(String[] groups, boolean state)
       {
         // TODO Auto-generated method stub