X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FNewickFile.java;h=f2a29ea4e54457dbbc9f2c2d8b33684cf6a3c481;hb=4935082f08648ab92743e14e5e2dfefa3e0dcd4d;hp=5a5c9ac8b1b0aabf42f23d20650bb1b385d24fa2;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git
diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 5a5c9ac..f2a29ea 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 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * 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.
- *
+ * 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
// 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
@@ -215,8 +219,8 @@ 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 +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!
@@ -470,8 +483,8 @@ 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 +501,8 @@ 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 +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())