JAL-3746 release notes.. in progress

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

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 517701b..ec5d267 100755 (executable)
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -26,6 +26,8 @@
 // TODO: Extended SequenceNodeI to hold parsed NHX strings
 package jalview.io;
 
+import java.util.Locale;
+
 import jalview.datamodel.SequenceNode;
 import jalview.util.MessageManager;
 
@@ -316,8 +318,6 @@ public class NewickFile extends FileParse
 
           continue;
         }
-
-        ;
         d++;
 
         if (c.right() == null)
@@ -417,8 +417,6 @@ public class NewickFile extends FileParse
             Error = ErrorStringrange(Error, "Unterminated comment", 3, fcp,
                     nf);
           }
-
-          ;
         }
         // Parse simpler field strings
         String fstring = nf.substring(ncp, fcp);
@@ -479,7 +477,7 @@ public class NewickFile extends FileParse
           {
             try
             {
-              bootstrap = (new Integer(nbootstrap.stringMatched(1)))
+              bootstrap = (Integer.valueOf(nbootstrap.stringMatched(1)))
                       .intValue();
               HasBootstrap = true;
             } catch (Exception e)
@@ -496,7 +494,7 @@ public class NewickFile extends FileParse
         {
           try
           {
-            distance = (new Float(ndist.stringMatched(1))).floatValue();
+            distance = (Float.valueOf(ndist.stringMatched(1))).floatValue();
             HasDistances = true;
             nodehasdistance = true;
           } catch (Exception e)
@@ -660,10 +658,10 @@ public class NewickFile extends FileParse
           try
           {
             // parse out code/value pairs
-            if (code.toLowerCase().equals("b"))
+            if (code.toLowerCase(Locale.ROOT).equals("b"))
             {
               int v = -1;
-              Float iv = new Float(value);
+              Float iv = Float.valueOf(value);
               v = iv.intValue(); // jalview only does integer bootstraps
               // currently
               c.setBootstrap(v);
@@ -942,7 +940,11 @@ public class NewickFile extends FileParse
     }
   }
 
-  // Test
+  /**
+   * 
+   * @param args
+   * @j2sIgnore
+   */
   public static void main(String[] args)
   {
     try