tidied up system.out messages and moved many to stderr.

[jalview.git] / src / jalview / io / ClustalFile.java

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