X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FClustalFile.java;h=1d2590b825868118ac04f284c6b616b0dc92052c;hb=e5127e5f27f02c8f328539eaac68eabfbee1d135;hp=98c500abae471d5c117feb49a2137605da977213;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index 98c500a..1d2590b 100755
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -67,7 +67,8 @@ public class ClustalFile extends AlignFile {
 	}
       }
     } catch (IOException e) {
-      System.out.println("Exception parsing clustal file " + e);
+      System.err.println("Exception parsing clustal file " + e);
+      e.stacktrace();
     }
 
     if (flag) {
@@ -111,7 +112,7 @@ public class ClustalFile extends AlignFile {
           seqs.addElement(newSeq);
 
         } else {
-          System.out.println("Can't find sequence for " + headers.elementAt(i));
+          System.err.println("Clustal File Reader: Can't find sequence for " + headers.elementAt(i));
         }
       }
     }