JAL-3725 restrict mapped virtual feature location to mapped region

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

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 1e9c5ed..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;
 
@@ -475,7 +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)
@@ -492,7 +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)
@@ -656,10 +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);