From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Mon, 17 Jun 2013 09:35:28 +0000 (+0100)
Subject: JAL-1318 - route warnings to stderr (need to find a better solution for JAL-1069)
X-Git-Tag: Jalview_2_9~240^2~10
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f51988e32f73bc830fdb2800b97f12cad8d9594e;p=jalview.git

JAL-1318 - route warnings to stderr (need to find a better solution for JAL-1069)
---

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index 5228413..cbe871d 100644
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -565,8 +565,11 @@ public class Dna
               protein.toString());
       if (rf != 0)
       {
-        jalview.bin.Cache.log
-                .debug("trimming contigs for incomplete terminal codon.");
+        if (jalview.bin.Cache.log!=null) {
+          jalview.bin.Cache.log.debug("trimming contigs for incomplete terminal codon.");
+        } else {
+          System.err.println("trimming contigs for incomplete terminal codon.");
+        }
         // map and trim contigs to ORF region
         vc = scontigs.length - 1;
         lastnpos = vismapping.shift(lastnpos); // place npos in context of