X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FNewickFile.java;h=f2a29ea4e54457dbbc9f2c2d8b33684cf6a3c481;hb=0155cd99a3b96570ad67dbc992c731ba2ce74bb9;hp=b4f3a33630c611bea85595ed44fd9d9f55fb913c;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index b4f3a33..f2a29ea 100755
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -30,6 +30,7 @@ import java.io.*;
 import java.util.StringTokenizer;
 
 import jalview.datamodel.*;
+import jalview.util.MessageManager;
 
 /**
  * Parse a new hanpshire style tree Caveats: NHX files are NOT supported and the
@@ -295,7 +296,7 @@ public class NewickFile extends FileParse
 
     int nextcp = 0;
     int ncp = cp;
-    boolean parsednodename=false;
+    boolean parsednodename = false;
     while (majorsyms.searchFrom(nf, cp) && (Error == null))
     {
       int fcp = majorsyms.matchedFrom();
@@ -361,12 +362,13 @@ public class NewickFile extends FileParse
           nodename = new String(qnodename.stringMatched().substring(1,
                   nl - 1));
           // unpack any escaped colons
-          com.stevesoft.pat.Regex xpandquotes = com.stevesoft.pat.Regex.perlCode("s/''/'/");
+          com.stevesoft.pat.Regex xpandquotes = com.stevesoft.pat.Regex
+                  .perlCode("s/''/'/");
           String widernodename = xpandquotes.replaceAll(nodename);
-          nodename=widernodename;
+          nodename = widernodename;
           // jump to after end of quoted nodename
           nextcp = fcp + nl + 1;
-          parsednodename=true;
+          parsednodename = true;
         }
         else
         {
@@ -435,7 +437,8 @@ public class NewickFile extends FileParse
         com.stevesoft.pat.Regex ndist = new com.stevesoft.pat.Regex(
                 ":([-0-9Ee.+]+)");
 
-        if (!parsednodename && uqnodename.search(fstring)
+        if (!parsednodename
+                && uqnodename.search(fstring)
                 && ((uqnodename.matchedFrom(1) == 0) || (fstring
                         .charAt(uqnodename.matchedFrom(1) - 1) != ':'))) // JBPNote
         // HACK!
@@ -594,7 +597,7 @@ public class NewickFile extends FileParse
         distance = DefDistance;
         bootstrap = DefBootstrap;
         commentString2 = null;
-        parsednodename=false;
+        parsednodename = false;
       }
       if (nextcp == 0)
       {
@@ -609,11 +612,11 @@ public class NewickFile extends FileParse
 
     if (Error != null)
     {
-      throw (new IOException("NewickFile: " + Error + "\n"));
+      throw (new IOException(MessageManager.formatMessage("exception.newfile", new String[]{Error.toString()})));
     }
     if (root == null)
     {
-      throw (new IOException("NewickFile: No Tree read in\n"));
+        throw (new IOException(MessageManager.formatMessage("exception.newfile", new String[]{MessageManager.getString("label.no_tree_read_in")})));
     }
     // THe next line is failing for topali trees - not sure why yet. if
     // (root.right()!=null && root.isDummy())