X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=53d55f31c94da5007297e6f3b595acd71ba8b66b;hb=37a5dfc3c72a42689e90ad8a0e118e8855d9868b;hp=002b66b282677201ad0d0ef1ed9f9a895ccadb3b;hpb=46bcdb06851cdf7800d74d720d49cf6960cd0c55;p=jalview.git

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 002b66b..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);
 
@@ -347,6 +355,31 @@ 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)