X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FNewickFile.java;h=4a30d738923ff65be70374fce1439892946c2dee;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=f3eaa45e2882fd08445dbbc85fbb8848bc46de6d;hpb=17e4ea278bc9a5fb280db1252ce78b7a295215f5;p=jalview.git

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index f3eaa45..4a30d73 100755
--- 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;
 
@@ -294,8 +296,7 @@ public class NewickFile extends FileParse
     boolean ascending = false; // flag indicating that we are leaving the
     // current node
 
-    Regex majorsyms = new Regex(
-            "[(\\['),;]");
+    Regex majorsyms = new Regex("[(\\['),;]");
 
     int nextcp = 0;
     int ncp = cp;
@@ -354,8 +355,7 @@ public class NewickFile extends FileParse
       // Deal with quoted fields
       case '\'':
 
-        Regex qnodename = new Regex(
-                "'([^']|'')+'");
+        Regex qnodename = new Regex("'([^']|'')+'");
 
         if (qnodename.searchFrom(nf, fcp))
         {
@@ -363,8 +363,7 @@ public class NewickFile extends FileParse
           nodename = new String(
                   qnodename.stringMatched().substring(1, nl - 1));
           // unpack any escaped colons
-          Regex xpandquotes = Regex
-                  .perlCode("s/''/'/");
+          Regex xpandquotes = Regex.perlCode("s/''/'/");
           String widernodename = xpandquotes.replaceAll(nodename);
           nodename = widernodename;
           // jump to after end of quoted nodename
@@ -398,8 +397,7 @@ public class NewickFile extends FileParse
            * '"+nf.substring(cp,fcp)+"'"); }
            */
           // verify termination.
-          Regex comment = new Regex(
-                  "]");
+          Regex comment = new Regex("]");
           if (comment.searchFrom(nf, fcp))
           {
             // Skip the comment field
@@ -430,12 +428,9 @@ public class NewickFile extends FileParse
                   + fstring.substring(cend + 1);
 
         }
-        Regex uqnodename = new Regex(
-                "\\b([^' :;\\](),]+)");
-        Regex nbootstrap = new Regex(
-                "\\s*([0-9+]+)\\s*:");
-        Regex ndist = new Regex(
-                ":([-0-9Ee.+]+)");
+        Regex uqnodename = new Regex("\\b([^' :;\\](),]+)");
+        Regex nbootstrap = new Regex("\\s*([0-9+]+)\\s*:");
+        Regex ndist = new Regex(":([-0-9Ee.+]+)");
 
         if (!parsednodename && uqnodename.search(fstring)
                 && ((uqnodename.matchedFrom(1) == 0) || (fstring
@@ -656,7 +651,7 @@ 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 = Float.valueOf(value);