JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index b4f3a33..ab3c37c 100755 (executable)
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -26,10 +26,14 @@
 // TODO: Extended SequenceNodeI to hold parsed NHX strings
 package jalview.io;
 
-import java.io.*;
-import java.util.StringTokenizer;
+import jalview.datamodel.SequenceNode;
+import jalview.util.MessageManager;
 
-import jalview.datamodel.*;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.StringTokenizer;
 
 /**
  * Parse a new hanpshire style tree Caveats: NHX files are NOT supported and the
@@ -295,7 +299,7 @@ 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 +365,13 @@ 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 +440,8 @@ 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 +600,7 @@ public class NewickFile extends FileParse
         distance = DefDistance;
         bootstrap = DefBootstrap;
         commentString2 = null;
-        parsednodename=false;
+        parsednodename = false;
       }
       if (nextcp == 0)
       {
@@ -609,11 +615,14 @@ 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())