3 // forester -- software libraries and applications
4 // for evolutionary biology research and applications.
6 // Copyright (C) 2008-2011 Christian M. Zmasek
7 // Copyright (C) 2008-2011 Burnham Institute for Medical Research
10 // This library is free software; you can redistribute it and/or
11 // modify it under the terms of the GNU Lesser General Public
12 // License as published by the Free Software Foundation; either
13 // version 2.1 of the License, or (at your option) any later version.
15 // This library is distributed in the hope that it will be useful,
16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
18 // Lesser General Public License for more details.
20 // You should have received a copy of the GNU Lesser General Public
21 // License along with this library; if not, write to the Free Software
22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
24 // Contact: phylosoft @ gmail . com
25 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
27 package org.forester.test.examples;
30 import java.io.IOException;
32 import org.forester.io.parsers.PhylogenyParser;
33 import org.forester.io.parsers.util.ParserUtils;
34 import org.forester.io.writers.PhylogenyWriter;
35 import org.forester.phylogeny.Phylogeny;
36 import org.forester.phylogeny.PhylogenyMethods;
37 import org.forester.util.ForesterUtil;
39 public class Example4 {
41 public static void main( final String[] args ) {
42 // Reading-in of (a) tree(s) from a file.
43 final File treefile = new File( "/home/czmasek/tol_117_TEST.xml" );
44 PhylogenyParser parser = null;
46 parser = ParserUtils.createParserDependingOnFileType( treefile, true );
48 catch ( final IOException e ) {
51 Phylogeny[] phys = null;
53 phys = PhylogenyMethods.readPhylogenies( parser, treefile );
55 catch ( final IOException e ) {
58 // Writing trees to a file.
59 final File outfile = new File( "/home/czmasek/tol_117_TEST_out.xml" );
61 final PhylogenyWriter writer = new PhylogenyWriter();
62 writer.toPhyloXML( phys, 0, outfile, ForesterUtil.LINE_SEPARATOR );
64 catch ( final Exception e ) {