JAL-1620 version bump and release notes

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

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 9ed1491..ab76ab9 100755 (executable)
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 // NewickFile.java
 // Tree I/O
@@ -27,6 +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
@@ -292,7 +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();
@@ -358,12 +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
         {
@@ -432,7 +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!
@@ -591,7 +597,7 @@ public class NewickFile extends FileParse
         distance = DefDistance;
         bootstrap = DefBootstrap;
         commentString2 = null;
-        parsednodename=false;
+        parsednodename = false;
       }
       if (nextcp == 0)
       {
@@ -606,11 +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())