JAL-3676 Documentation in Help for Java Console, Logging and Reporting Bugs

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

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 4dbf950..db29848 100755 (executable)
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -29,6 +29,7 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Locale;
 import java.util.StringTokenizer;
 
 /**
@@ -184,7 +185,7 @@ 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++)
     {
@@ -294,7 +295,7 @@ public class MSFfile extends AlignFile
     }
 
     long maxNB = 0;
-    out.append("   MSF: " + s[0].getSequence().length + "   Type: "
+    out.append("   MSF: " + s[0].getLength() + "   Type: "
             + (is_NA ? "N" : "P") + "    Check:  " + (bigChecksum % 10000)
             + "   ..");
     out.append(newline);
@@ -310,9 +311,9 @@ public class MSFfile extends AlignFile
 
       nameBlock[i] = new String("  Name: " + printId(s[i], jvSuffix) + " ");
 
-      idBlock[i] = new String("Len: "
-              + maxLenpad.form(s[i].getSequence().length) + "  Check: "
-              + maxChkpad.form(checksums[i]) + "  Weight: 1.00" + newline);
+      idBlock[i] = new String("Len: " + maxLenpad.form(s[i].getLength())
+              + "  Check: " + maxChkpad.form(checksums[i])
+              + "  Weight: 1.00" + newline);
 
       if (s[i].getName().length() > maxid)
       {
@@ -369,8 +370,9 @@ public class MSFfile extends AlignFile
           int start = (i * 50) + (k * 10);
           int end = start + 10;
 
-          if ((end < s[j].getSequence().length)
-                  && (start < s[j].getSequence().length))
+          int length = s[j].getLength();
+          if ((end < length)
+                  && (start < length))
           {
             out.append(s[j].getSequence(start, end));
 
@@ -385,7 +387,7 @@ public class MSFfile extends AlignFile
           }
           else
           {
-            if (start < s[j].getSequence().length)
+            if (start < length)
             {
               out.append(s[j].getSequenceAsString().substring(start));
               out.append(newline);