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

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

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index b9cad0a..9495f82 100755 (executable)
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -71,7 +71,8 @@ public class MSFfile extends AlignFile {
       }\r
     }\r
     } catch (IOException e) {\r
-      System.out.println("Exception parsing MSFFile " + e);\r
+      System.err.println("Exception parsing MSFFile " + e);\r
+      e.printStackTrace();\r
     }\r
 \r
     this.noSeqs = headers.size();\r
@@ -111,7 +112,7 @@ public class MSFfile extends AlignFile {
         seqs.addElement(newSeq);\r
 \r
       } else {\r
-        System.out.println("Can't find sequence for " + headers.elementAt(i));\r
+        System.err.println("MSFFile Parser: Can't find sequence for " + headers.elementAt(i));\r
       }\r
     }\r
 \r
@@ -133,7 +134,8 @@ public class MSFfile extends AlignFile {
           }\r
         }\r
       } catch (Exception e) {\r
-        System.err.println("Exception " + e);\r
+        System.err.println("Exception during MSF Checksum calculation");\r
+        e.printStackTrace();\r
       }\r
     }\r
     return check % 10000;\r