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 (file)
--- 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