X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FNewickFile.java;h=92456d5aaccb7a96c5d6c39b52a8f52c3e161a4e;hb=fddf3084802b37e5cee17829e32692a4aac3e60d;hp=15e901ae001369b9ea8e6d0aec5493104d09aae0;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 15e901a..92456d5 100755
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -1,19 +1,21 @@
/*
- * 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.
*
* 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
// NewickFile.java
@@ -28,6 +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
@@ -293,7 +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();
@@ -359,12 +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
{
@@ -433,7 +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!
@@ -592,7 +597,7 @@ public class NewickFile extends FileParse
distance = DefDistance;
bootstrap = DefBootstrap;
commentString2 = null;
- parsednodename=false;
+ parsednodename = false;
}
if (nextcp == 0)
{
@@ -607,11 +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())