From 174a67aba96e55fdfbd4f33dfe4e658d790fc5c2 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 29 Aug 2006 15:22:15 +0000
Subject: [PATCH] jnetfile can be loaded onto alignment

---
 src/jalview/gui/AlignFrame.java |   26 ++++++++++++++++++++++----
 1 file changed, 22 insertions(+), 4 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index cd26b17..807b6e3 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -2818,17 +2818,35 @@ public void drop(DropTargetDropEvent evt)
    public void loadJalviewDataFile(String file)
   {
     try{
+      String protocol = "File";
+
+      if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
+      {
+        protocol = "URL";
+      }
+
       boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
           alignment, file);
 
       if (!isAnnotation)
       {
-        boolean isGroupsFile = parseFeaturesFile(file,
-                                                AppletFormatAdapter.FILE);
+        boolean isGroupsFile = parseFeaturesFile(file,protocol);
         if (!isGroupsFile)
         {
-          String format = new IdentifyFile().Identify(file, FormatAdapter.FILE);
-          new FileLoader().LoadFile(viewport, file, FormatAdapter.FILE, format);
+          String format = new IdentifyFile().Identify(file, protocol);
+
+          if(format.equalsIgnoreCase("JnetFile"))
+          {
+            jalview.io.JPredFile predictions = new jalview.io.JPredFile(
+                file, protocol);
+            new JnetAnnotationMaker().add_annotation(predictions,
+                viewport.getAlignment(),
+                0, false);
+            alignPanel.adjustAnnotationHeight();
+            alignPanel.repaint();
+          }
+          else
+            new FileLoader().LoadFile(viewport, file, protocol, format);
         }
       }
       else
-- 
1.7.10.2