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JAL-3806 more lax allowance (3 positions) for stop codon
[jalview.git]
/
src
/
jalview
/
io
/
JPredFile.java
diff --git
a/src/jalview/io/JPredFile.java
b/src/jalview/io/JPredFile.java
index
6732e82
..
8f93b48
100755
(executable)
--- a/
src/jalview/io/JPredFile.java
+++ b/
src/jalview/io/JPredFile.java
@@
-33,6
+33,7
@@
import jalview.util.MessageManager;
import java.io.IOException;
import java.util.Hashtable;
import java.io.IOException;
import java.util.Hashtable;
+import java.util.Locale;
import java.util.StringTokenizer;
import java.util.Vector;
import java.util.StringTokenizer;
import java.util.Vector;
@@
-408,7
+409,7
@@
public class JPredFile extends AlignFile
// check that no stray annotations have been added at the end.
{
SequenceI sq = seqs.elementAt(j - 1);
// check that no stray annotations have been added at the end.
{
SequenceI sq = seqs.elementAt(j - 1);
- if (sq.getName().toUpperCase().startsWith("JPRED"))
+ if (sq.getName().toUpperCase(Locale.ROOT).startsWith("JPRED"))
{
annotSeqs.addElement(sq);
seqs.removeElementAt(--j);
{
annotSeqs.addElement(sq);
seqs.removeElementAt(--j);