From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 13 Dec 2019 15:57:42 +0000 (+0000)
Subject: JAL-1236 TODO: fix up parser to cope with the currently defined custom header...... 
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=refs%2Fheads%2Fpatch%2FJAL-1236_customClustalHeader;p=jalview.git

JAL-1236 TODO: fix up parser to cope with the currently defined custom header... (as well as sensible defaults: JAL-2440 - MUSCLE, CLUSTAL, CLUSTALW, CLUSTALO ...)
---

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index 537c154..c558186 100755
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -97,7 +97,7 @@ public class ClustalFile extends AlignFile
           if (str.hasMoreTokens())
           {
             id = str.nextToken();
-
+	    // TODO: JAL-1236 other tokens may be indicative of a header for Clustal format
             if (id.equalsIgnoreCase("CLUSTAL"))
             {
               flag = true;