= Archaeopteryx Tutorial and Examples =
<wiki:toc max_depth="3" />

= Introduction =

Under development!

Documentation, tutorial, and examples for [http://www.phylosoft.org/archaeopteryx/ Archaeopteryx] (visualization, analysis, and editing of phylogenetic trees).

*All examples require jar-file "forester.jar" to be in the class-path.*

Download: http://code.google.com/p/forester/downloads/list

Author: [http://www.cmzmasek.net/ Christian M Zmasek], Sanford-Burnham Medical Research Institute

 
Copyright (C) 2012 Christian M Zmasek. All rights reserved.



= Reading and writing of phylogenetic trees =



{{{

package examples;

import java.io.File;
import java.io.IOException;

import org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.util.ParserUtils;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.util.ForesterUtil;

public class Example {

    public static void main( final String[] args ) {
        // Reading-in of (a) tree(s) from a file.
        final File treefile = new File( "/path/to/tree.xml" );
        PhylogenyParser parser = null;
        try {
            parser = ParserUtils.createParserDependingOnFileType( treefile, true );
        }
        catch ( final IOException e ) {
            e.printStackTrace();
        }
        Phylogeny[] phys = null;
        try {
            phys = PhylogenyMethods.readPhylogenies( parser, treefile );
        }
        catch ( final IOException e ) {
            e.printStackTrace();
        }
        // Writing trees to a file.
        final File outfile = new File( "/path/to/out_tree.xml" );
        try {
            final PhylogenyWriter writer = new PhylogenyWriter();
            writer.toPhyloXML( phys, 0, outfile, ForesterUtil.LINE_SEPARATOR );
        }
        catch ( final Exception e ) {
            e.printStackTrace();
        }
    }
}

}}}



= Reading of phylogenetic trees and displaying them with Archaeopteryx =


{{{

package examples;

import java.io.File;
import java.io.IOException;

import org.forester.archaeopteryx.Archaeopteryx;
import org.forester.io.parsers.util.ParserUtils;
import org.forester.io.parsers.PhylogenyParser;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;

public class Example {

    public static void main( final String[] args ) {
        // Reading-in of (a) tree(s) from a file.
        final File treefile = new File( "/path/to/tree.xml" );
        PhylogenyParser parser = null;
        try {
            parser = ParserUtils.createParserDependingOnFileType( treefile, true );
        }
        catch ( final IOException e ) {
            e.printStackTrace();
        }
        Phylogeny[] phys = null;
        try {
            phys = PhylogenyMethods.readPhylogenies( parser, treefile );
        }
        catch ( final IOException e ) {
            e.printStackTrace();
        }
        // Display of the tree(s) with Archaeopteryx.
        Archaeopteryx.createApplication( phys );
    }
}

}}}