From: jprocter <Jim Procter>
Date: Wed, 17 May 2006 16:54:44 +0000 (+0000)
Subject: added the jnetfile parameter to specify a JNet concise file to be
X-Git-Tag: Release_2_1~398
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=47aec94b56baa5b666c3189280f4d1d5c7567a95;p=jalview.git

added the jnetfile parameter to specify a JNet concise file to be
parsed to add jnet predictions to the first sequence in the alignment
---

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 002b66b..cd0b835 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -347,6 +347,31 @@ 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)