perfume.java

// $Id: perfume.java,v 1.5 2008/09/24 16:43:37 cmzmasek Exp $
// FORESTER -- software libraries and applications
// for evolutionary biology research and applications.
//
// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// All rights reserved
// 
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
//
// This library 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
// Lesser General Public License for more details.
// 
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: cmzmasek@yahoo.com
// WWW: www.phylosoft.org

package org.forester.application;

import java.io.File;

import org.forester.io.parsers.phyloxml.PhyloXmlParser;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.util.CommandLineArguments;

public class perfume {

    private final static String BASE = "b_";

    public static void main( final String args[] ) {
        if ( ( args.length != 2 ) ) {
            System.exit( -1 );
        }
        try {
            CommandLineArguments cla = null;
            cla = new CommandLineArguments( args );
            final File in = cla.getFile( 0 );
            final File out = cla.getFile( 1 );
            if ( out.exists() ) {
                System.out.println( out + " already exists" );
                System.exit( -1 );
            }
            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
            final PhyloXmlParser xml_parser = new PhyloXmlParser();
            final Phylogeny[] phylogenies_0 = factory.create( in, xml_parser );
            final Phylogeny phylogeny_0 = phylogenies_0[ 0 ];
            final PhylogenyNodeIterator it = phylogeny_0.iteratorPostorder();
            int i = 0;
            while ( it.hasNext() ) {
                final PhylogenyNode node = it.next();
                processNode( node, i );
                i++;
            }
            final PhylogenyWriter writer = new PhylogenyWriter();
            writer.toPhyloXML( out, phylogeny_0, 0 );
        }
        catch ( final Exception e ) {
            System.out.println( e.getLocalizedMessage() );
            e.printStackTrace();
            System.exit( -1 );
        }
    }

    private static void processNode( final PhylogenyNode node, final int i ) {
        node.setDistanceToParent( PhylogenyNode.DISTANCE_DEFAULT );
        if ( !node.isExternal() ) {
            if ( ( node.getNodeName() == null ) || node.getNodeName().isEmpty() ) {
                node.setName( BASE + i );
            }
        }
    }
}