JAL-1503 update version in GPL header

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

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index b7df38f..b86c170 100755 (executable)
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -1,19 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * 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.
- * 
+ *  
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 // NewickFile.java
 // Tree I/O
@@ -292,6 +293,7 @@ public class NewickFile extends FileParse
 
     int nextcp = 0;
     int ncp = cp;
+    boolean parsednodename=false;
     while (majorsyms.searchFrom(nf, cp) && (Error == null))
     {
       int fcp = majorsyms.matchedFrom();
@@ -349,14 +351,20 @@ public class NewickFile extends FileParse
       case '\'':
 
         com.stevesoft.pat.Regex qnodename = new com.stevesoft.pat.Regex(
-                "([^']|'')+'");
+                "'([^']|'')+'");
 
         if (qnodename.searchFrom(nf, fcp))
         {
           int nl = qnodename.stringMatched().length();
-          nodename = new String(qnodename.stringMatched().substring(0,
+          nodename = new String(qnodename.stringMatched().substring(1,
                   nl - 1));
-          cp = fcp + nl + 1;
+          // unpack any escaped colons
+          com.stevesoft.pat.Regex xpandquotes = com.stevesoft.pat.Regex.perlCode("s/''/'/");
+          String widernodename = xpandquotes.replaceAll(nodename);
+          nodename=widernodename;
+          // jump to after end of quoted nodename
+          nextcp = fcp + nl + 1;
+          parsednodename=true;
         }
         else
         {
@@ -425,7 +433,7 @@ public class NewickFile extends FileParse
         com.stevesoft.pat.Regex ndist = new com.stevesoft.pat.Regex(
                 ":([-0-9Ee.+]+)");
 
-        if (uqnodename.search(fstring)
+        if (!parsednodename && uqnodename.search(fstring)
                 && ((uqnodename.matchedFrom(1) == 0) || (fstring
                         .charAt(uqnodename.matchedFrom(1) - 1) != ':'))) // JBPNote
         // HACK!
@@ -584,6 +592,7 @@ public class NewickFile extends FileParse
         distance = DefDistance;
         bootstrap = DefBootstrap;
         commentString2 = null;
+        parsednodename=false;
       }
       if (nextcp == 0)
       {