From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 10 May 2016 16:29:33 +0000 (+0100)
Subject: JAL-2103 don’t get full-width alignment if MSA based prediction
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d4c6c59a2f8f61c4a8f73b76630387bf0b0edd12;p=jalview.git

JAL-2103 don’t get full-width alignment if MSA based prediction
---

diff --git a/src/jalview/ws/jws1/JPredWSUtils.java b/src/jalview/ws/jws1/JPredWSUtils.java
index 7b74e2a..35447fd 100644
--- a/src/jalview/ws/jws1/JPredWSUtils.java
+++ b/src/jalview/ws/jws1/JPredWSUtils.java
@@ -10,6 +10,7 @@ import jalview.io.FileParse;
 import jalview.io.FormatAdapter;
 import jalview.util.MessageManager;
 
+import java.io.IOException;
 import java.util.Hashtable;
 import java.util.List;
 
@@ -134,12 +135,12 @@ public class JPredWSUtils
       try
       {
         // read full alignment if present.
-        if (full_alignment != null)
+        if (!msaPred && full_alignment != null)
         {
-        fullAlignment = new FormatAdapter().readFromFile(full_alignment,
-                "FASTA");
+          fullAlignment = new FormatAdapter().readFromFile(full_alignment,
+                  "FASTA");
         }
-      } catch (Exception q)
+      } catch (IOException q)
       {
 
       } finally