JAL-3725 restrict mapped virtual feature location to mapped region

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

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index 026c879..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.util.Locale;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
@@ -207,7 +208,7 @@ public class JPredFile extends AlignFile
           {
             ascore = symbols.nextToken();
 
-            Float score = new Float(ascore);
+            Float score = Float.valueOf(ascore);
             scores.addElement(score);
           }
 
@@ -283,7 +284,7 @@ public class JPredFile extends AlignFile
 
           seq_entries.addElement(newseq.toString());
           ids.addElement(id);
-          Symscores.put(id, new Integer(ids.size() - 1));
+          Symscores.put(id, Integer.valueOf(ids.size() - 1));
         }
       }
     }
@@ -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);
-      if (sq.getName().toUpperCase().startsWith("JPRED"))
+      if (sq.getName().toUpperCase(Locale.ROOT).startsWith("JPRED"))
       {
         annotSeqs.addElement(sq);
         seqs.removeElementAt(--j);