X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=53d55f31c94da5007297e6f3b595acd71ba8b66b;hb=37a5dfc3c72a42689e90ad8a0e118e8855d9868b;hp=cd0b8359bb12b2ac03623a05e1c30d3f0c29262a;hpb=47aec94b56baa5b666c3189280f4d1d5c7567a95;p=jalview.git

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index cd0b835..53d55f3 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -295,7 +295,9 @@ public class JalviewLite extends Applet
               currentAlignFrame.statusBar.setText("Successfully loaded file " + file);
 
 
-                String treeFile = applet.getParameter("treeFile");
+                String treeFile = applet.getParameter("tree");
+                if(treeFile==null)
+                  applet.getParameter("treeFile");
                 if (treeFile != null)
                 {
                   try
@@ -329,7 +331,13 @@ public class JalviewLite extends Applet
                 if( !inArchive(param) )
                   param = addProtocol( param );
 
-                currentAlignFrame.parseFeaturesFile(param);
+                currentAlignFrame.parseFeaturesFile(param, protocol);
+              }
+
+              param = getParameter("showFeatureSettings");
+              if(param !=null && param.equalsIgnoreCase("true"))
+              {
+                currentAlignFrame.featureSettings_actionPerformed();
               }
 
              param = getParameter("annotations");
@@ -338,7 +346,7 @@ public class JalviewLite extends Applet
                if( !inArchive(param) )
                   param = addProtocol( param );
 
-               new AnnotationReader().readAnnotationFile(
+               new AnnotationFile().readAnnotationFile(
                    currentAlignFrame.viewport.getAlignment(),
                    param);