X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FNewickFile.java;h=92456d5aaccb7a96c5d6c39b52a8f52c3e161a4e;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=d664dcf0bf7e34177d9dcb7196082893853e6c0b;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index d664dcf..92456d5 100755
--- 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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
@@ -292,6 +296,7 @@ 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 +354,21 @@ 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 +437,8 @@ 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 +597,7 @@ public class NewickFile extends FileParse
         distance = DefDistance;
         bootstrap = DefBootstrap;
         commentString2 = null;
+        parsednodename = false;
       }
       if (nextcp == 0)
       {
@@ -598,11 +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())