X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FMSFfile.java;h=ed7049ecd804914e1ac71ee5e4718cc814e4e99f;hb=HEAD;hp=df2bed2a185239ae054549dca4dd7d3ad3b9c7d0;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index df2bed2..ed7049e 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -20,6 +20,8 @@
  */
 package jalview.io;
 
+import java.util.Locale;
+
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
@@ -134,7 +136,7 @@ public class MSFfile extends AlignFile
       }
     } catch (IOException e)
     {
-      System.err.println("Exception parsing MSFFile " + e);
+      jalview.bin.Console.errPrintln("Exception parsing MSFFile " + e);
       e.printStackTrace();
     }
 
@@ -167,8 +169,9 @@ public class MSFfile extends AlignFile
       }
       else
       {
-        System.err.println("MSFFile Parser: Can't find sequence for "
-                + headers.get(i));
+        jalview.bin.Console
+                .errPrintln("MSFFile Parser: Can't find sequence for "
+                        + headers.get(i));
       }
     }
   }
@@ -184,7 +187,7 @@ public class MSFfile extends AlignFile
   public int checkSum(String seq)
   {
     int check = 0;
-    String sequence = seq.toUpperCase();
+    String sequence = seq.toUpperCase(Locale.ROOT);
 
     for (int i = 0; i < sequence.length(); i++)
     {
@@ -198,7 +201,8 @@ public class MSFfile extends AlignFile
         }
       } catch (Exception e)
       {
-        System.err.println("Exception during MSF Checksum calculation");
+        jalview.bin.Console
+                .errPrintln("Exception during MSF Checksum calculation");
         e.printStackTrace();
       }
     }
@@ -370,8 +374,7 @@ public class MSFfile extends AlignFile
           int end = start + 10;
 
           int length = s[j].getLength();
-          if ((end < length)
-                  && (start < length))
+          if ((end < length) && (start < length))
           {
             out.append(s[j].getSequence(start, end));