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 (executable)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -347,6 +347,31 @@ public class JalviewLite extends Applet
 \r
              }\r
 \r
+             param = getParameter("jnetfile");\r
+             if (param != null)\r
+             {\r
+               try\r
+               {\r
+                 if (inArchive(param))\r
+                   protocol = AppletFormatAdapter.CLASSLOADER;\r
+                 else\r
+                 {\r
+                   protocol = AppletFormatAdapter.URL;\r
+                   param = addProtocol(param);\r
+                 }\r
+\r
+                 jalview.io.JPredFile predictions = new jalview.io.JPredFile(\r
+                     param, protocol);\r
+                 new JnetAnnotationMaker().add_annotation(predictions,\r
+                     currentAlignFrame.viewport.getAlignment(),\r
+                     0,false); // do not add sequence profile from concise output\r
+                 currentAlignFrame.alignPanel.fontChanged();\r
+                 currentAlignFrame.alignPanel.setScrollValues(0, 0);\r
+               } catch (Exception ex) {\r
+                 ex.printStackTrace();\r
+               }\r
+             }\r
+\r
 \r
                 String pdbfile = applet.getParameter("PDBFILE");\r
                 if(pdbfile!=null)\r