X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FNewickFile.java;h=9ed14916c0e51b9fb1dbac0740175f2d4c2d4808;hb=8f2bef6f91e7a6e47e41e78a82f45f7e406ef90a;hp=8e374ac0d722eab205ae4112b8f53545ac4059f2;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 8e374ac..9ed1491 100755
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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
  * 
  * 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 
@@ -215,8 +215,8 @@ public class NewickFile extends FileParse
             + " at position "
             + p
             + " ( "
-            + s.substring(((p - r) < 0) ? 0 : (p - r), ((p + r) > s
-                    .length()) ? s.length() : (p + r)) + " )\n";
+            + s.substring(((p - r) < 0) ? 0 : (p - r),
+                    ((p + r) > s.length()) ? s.length() : (p + r)) + " )\n";
   }
 
   // @tree annotations
@@ -292,6 +292,7 @@ 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 +350,20 @@ 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 +432,7 @@ 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!
@@ -470,8 +477,8 @@ public class NewickFile extends FileParse
             } catch (Exception e)
             {
               Error = ErrorStringrange(Error,
-                      "Can't parse bootstrap value", 4, ncp
-                              + nbootstrap.matchedFrom(), nf);
+                      "Can't parse bootstrap value", 4,
+                      ncp + nbootstrap.matchedFrom(), nf);
             }
           }
         }
@@ -488,8 +495,8 @@ public class NewickFile extends FileParse
           } catch (Exception e)
           {
             Error = ErrorStringrange(Error,
-                    "Can't parse node distance value", 7, ncp
-                            + ndist.matchedFrom(), nf);
+                    "Can't parse node distance value", 7,
+                    ncp + ndist.matchedFrom(), nf);
           }
         }
 
@@ -584,6 +591,7 @@ public class NewickFile extends FileParse
         distance = DefDistance;
         bootstrap = DefBootstrap;
         commentString2 = null;
+        parsednodename=false;
       }
       if (nextcp == 0)
       {