X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJPredFile.java;h=8f93b48682acd732da9de6ed1e638b7b42d3600a;hb=d43c7d9caca02859542914401ec945744c026bf1;hp=fd971fd23df5dff4f90d8c2fec30efb514bcc6fe;hpb=4a5137b64f7ec23db2a09290bfcd392984a52150;p=jalview.git

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index fd971fd..8f93b48 100755
--- 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);
           }
 
@@ -219,8 +220,8 @@ public class JPredFile extends AlignFile
 
           for (int j = 0; j < i; j++)
           {
-            scores.setElementAt(
-                    ((Float) scores.elementAt(j)).toString(), j);
+            scores.setElementAt(((Float) scores.elementAt(j)).toString(),
+                    j);
           }
 
           scores.addElement(ascore);
@@ -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));
         }
       }
     }
@@ -299,20 +300,20 @@ public class JPredFile extends AlignFile
     {
       // Add all sequence like objects
       Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
-              seq_entries.elementAt(i).toString(), 1, seq_entries
-                      .elementAt(i).toString().length());
+              seq_entries.elementAt(i).toString(), 1,
+              seq_entries.elementAt(i).toString().length());
 
       if (maxLength != seq_entries.elementAt(i).toString().length())
       {
-        throw new IOException(
-                MessageManager
-                        .formatMessage(
-                                "exception.jpredconcide_entry_has_unexpected_number_of_columns",
-                                new String[] { ids.elementAt(i).toString() }));
+        throw new IOException(MessageManager.formatMessage(
+                "exception.jpredconcide_entry_has_unexpected_number_of_columns",
+                new String[]
+                { ids.elementAt(i).toString() }));
       }
 
-      if ((newSeq.getName().startsWith("QUERY") || newSeq.getName()
-              .startsWith("align;")) && (QuerySeqPosition == -1))
+      if ((newSeq.getName().startsWith("QUERY")
+              || newSeq.getName().startsWith("align;"))
+              && (QuerySeqPosition == -1))
       {
         QuerySeqPosition = seqs.size();
       }
@@ -332,11 +333,10 @@ public class JPredFile extends AlignFile
       } catch (Exception e)
       {
         tal = null;
-        IOException ex = new IOException(
-                MessageManager
-                        .formatMessage(
-                                "exception.couldnt_parse_concise_annotation_for_prediction",
-                                new String[] { e.getMessage() }));
+        IOException ex = new IOException(MessageManager.formatMessage(
+                "exception.couldnt_parse_concise_annotation_for_prediction",
+                new String[]
+                { e.getMessage() }));
         e.printStackTrace(); // java 1.1 does not have :
                              // ex.setStackTrace(e.getStackTrace());
         throw ex;
@@ -409,7 +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);