2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: www.phylosoft.org
26 package org.forester.application;
30 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
31 import org.forester.io.writers.PhylogenyWriter;
32 import org.forester.phylogeny.Phylogeny;
33 import org.forester.phylogeny.PhylogenyNode;
34 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
35 import org.forester.phylogeny.factories.PhylogenyFactory;
36 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
37 import org.forester.util.CommandLineArguments;
39 public class simple_node_processor {
41 private final static String BASE = "b_";
43 public static void main( final String args[] ) {
44 if ( ( args.length != 2 ) ) {
48 CommandLineArguments cla = null;
49 cla = new CommandLineArguments( args );
50 final File in = cla.getFile( 0 );
51 final File out = cla.getFile( 1 );
53 System.out.println( out + " already exists" );
56 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
57 final PhyloXmlParser xml_parser = new PhyloXmlParser();
58 final Phylogeny[] phylogenies_0 = factory.create( in, xml_parser );
59 final Phylogeny phylogeny_0 = phylogenies_0[ 0 ];
60 final PhylogenyNodeIterator it = phylogeny_0.iteratorPostorder();
62 while ( it.hasNext() ) {
63 final PhylogenyNode node = it.next();
64 processNode( node, i );
67 final PhylogenyWriter writer = new PhylogenyWriter();
68 writer.toPhyloXML( out, phylogeny_0, 0 );
70 catch ( final Exception e ) {
71 System.out.println( e.getLocalizedMessage() );
77 private static void processNode( final PhylogenyNode node, final int i ) {
78 node.setDistanceToParent( PhylogenyNode.DISTANCE_DEFAULT );
79 if ( !node.isExternal() ) {
80 if ( ( node.getName() == null ) || node.getName().isEmpty() ) {
81 node.setName( BASE + i );