/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
buffer.append("PID");
}
-
- jalview.io.NewickFile fout = new jalview.io.NewickFile(tree
- .getTopNode());
- try {
+ jalview.io.NewickFile fout = new jalview.io.NewickFile(
+ tree.getTopNode());
+ try
+ {
cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
- tree.isHasRootDistance()));
+ tree.isHasRootDistance()));
Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
} catch (OutOfMemoryError oom)
{
- new OOMWarning("generating newick tree file",oom);
+ new OOMWarning("generating newick tree file", oom);
cap.dispose();
}
*/
public void saveAsNewick_actionPerformed(ActionEvent e)
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
- .getProperty("LAST_DIRECTORY"));
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Save tree as newick file");
chooser.setToolTipText("Save");
try
{
- jalview.io.NewickFile fout = new jalview.io.NewickFile(tree
- .getTopNode());
- String output = fout.print(tree.isHasBootstrap(), tree
- .isHasDistances(), tree.isHasRootDistance());
+ jalview.io.NewickFile fout = new jalview.io.NewickFile(
+ tree.getTopNode());
+ String output = fout.print(tree.isHasBootstrap(),
+ tree.isHasDistances(), tree.isHasRootDistance());
java.io.PrintWriter out = new java.io.PrintWriter(
new java.io.FileWriter(choice));
out.println(output);
if (sq != null)
{
// search dbrefs, features and annotation
- DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(sq
- .getDBRef(), new String[]
- { labelClass.toUpperCase() });
+ DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
+ sq.getDBRef(), new String[]
+ { labelClass.toUpperCase() });
if (refs != null)
{
for (int i = 0; i < refs.length; i++)