X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=373e9163c8d827b32406645d42da7a073b15b122;hb=91c5d2144a780716e755e99882acffe46b40f18f;hp=68769761536f1f23e37a6545cdaa2f7b8a95db22;hpb=03c446f178b6a0b61ad33cb219398132d640fbef;p=jalview.git

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 6876976..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;
 
 
 /**
@@ -330,7 +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");
@@ -339,7 +344,7 @@ public class JalviewLite extends Applet
                if( !inArchive(param) )
                   param = addProtocol( param );
 
-               new AnnotationReader().readAnnotationFile(
+               new AnnotationFile().readAnnotationFile(
                    currentAlignFrame.viewport.getAlignment(),
                    param);
 
@@ -348,6 +353,31 @@ public class JalviewLite extends Applet
 
              }
 
+             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();
+               }
+             }
+
 
                 String pdbfile = applet.getParameter("PDBFILE");
                 if(pdbfile!=null)