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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
f2a29ea
..
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.
*
*
* This file is part of Jalview.
*
@@
-26,12
+26,15
@@
// TODO: Extended SequenceNodeI to hold parsed NHX strings
package jalview.io;
// TODO: Extended SequenceNodeI to hold parsed NHX strings
package jalview.io;
-import java.io.*;
-import java.util.StringTokenizer;
-
-import jalview.datamodel.*;
+import jalview.datamodel.SequenceNode;
import jalview.util.MessageManager;
import jalview.util.MessageManager;
+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
* tree distances and topology are unreliable when they are parsed. TODO: on
/**
* Parse a new hanpshire style tree Caveats: NHX files are NOT supported and the
* tree distances and topology are unreliable when they are parsed. TODO: on
@@
-612,11
+615,14
@@
public class NewickFile extends FileParse
if (Error != null)
{
if (Error != null)
{
- throw (new IOException(MessageManager.formatMessage("exception.newfile", new String[]{Error.toString()})));
+ throw (new IOException(MessageManager.formatMessage(
+ "exception.newfile", new String[] { Error.toString() })));
}
if (root == null)
{
}
if (root == null)
{
- throw (new IOException(MessageManager.formatMessage("exception.newfile", new String[]{MessageManager.getString("label.no_tree_read_in")})));
+ 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())
}
// THe next line is failing for topali trees - not sure why yet. if
// (root.right()!=null && root.isDummy())