X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=373e9163c8d827b32406645d42da7a073b15b122;hb=91c5d2144a780716e755e99882acffe46b40f18f;hp=199a843cb66245466bb2e7eea32288a72ef16f23;hpb=6a60c733dc23235562e32583e68284efa5d29ac9;p=jalview.git

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 199a843..373e916 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -28,7 +28,6 @@ import java.applet.*;
 
 import java.awt.*;
 import java.awt.event.*;
-import jalview.appletgui.TreePanel;
 
 
 /**
@@ -290,6 +289,7 @@ public class JalviewLite extends Applet
                                                  file,
                                                  embedded);
 
+
               initialAlignFrame = currentAlignFrame;
 
               currentAlignFrame.statusBar.setText("Successfully loaded file " + file);
@@ -329,7 +329,13 @@ 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");
@@ -338,11 +344,38 @@ public class JalviewLite extends Applet
                if( !inArchive(param) )
                   param = addProtocol( param );
 
-               new AnnotationReader().readAnnotationFile(
+               new AnnotationFile().readAnnotationFile(
                    currentAlignFrame.viewport.getAlignment(),
                    param);
 
                currentAlignFrame.alignPanel.fontChanged();
+               currentAlignFrame.alignPanel.setScrollValues(0,0);
+
+             }
+
+             param = getParameter("jnetfile");
+             if (param != null)
+             {
+               try
+               {
+                 if (inArchive(param))
+                   protocol = AppletFormatAdapter.CLASSLOADER;
+                 else
+                 {
+                   protocol = AppletFormatAdapter.URL;
+                   param = addProtocol(param);
+                 }
+
+                 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
+                     param, protocol);
+                 new JnetAnnotationMaker().add_annotation(predictions,
+                     currentAlignFrame.viewport.getAlignment(),
+                     0,false); // do not add sequence profile from concise output
+                 currentAlignFrame.alignPanel.fontChanged();
+                 currentAlignFrame.alignPanel.setScrollValues(0, 0);
+               } catch (Exception ex) {
+                 ex.printStackTrace();
+               }
              }