// $Id:
//
// forester -- software libraries and applications
// for evolutionary biology research and applications.
//
// Copyright (C) 2008-2011 Christian M. Zmasek
// Copyright (C) 2008-2011 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: phylosoft @ gmail . com
// WWW: https://sites.google.com/site/cmzmasek/home/software/forester

package org.forester.test.examples;

import org.forester.archaeopteryx.Archaeopteryx;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.data.Event;
import org.forester.phylogeny.data.Sequence;
import org.forester.phylogeny.data.Taxonomy;

public class Example5 {

    public static void main( final String[] args ) {
        // Creating a new rooted tree with two external nodes.
        final Phylogeny phy = new Phylogeny();
        final PhylogenyNode root = new PhylogenyNode();
        final PhylogenyNode d1 = new PhylogenyNode();
        final PhylogenyNode d2 = new PhylogenyNode();
        // Setting of distances.
        d1.setDistanceToParent( 1.2 );
        d2.setDistanceToParent( 2.4 );
        // Adding species information.
        final Taxonomy t1 = new Taxonomy();
        t1.setScientificName( "Nematostella vectensis" );
        d1.getNodeData().addTaxonomy( t1 );
        final Taxonomy t2 = new Taxonomy();
        t2.setScientificName( "Monosiga brevicollis" );
        d2.getNodeData().addTaxonomy( t2 );
        // Adding gene names.
        final Sequence s1 = new Sequence();
        s1.setName( "Bcl-2" );
        d1.getNodeData().addSequence( s1 );
        final Sequence s2 = new Sequence();
        s2.setName( "Bcl-2" );
        d2.getNodeData().addSequence( s2 );
        // Root is a speciation.
        final Event ev = new Event();
        ev.setSpeciations( 1 );
        ev.setDuplications( 0 );
        root.getNodeData().setEvent( ev );
        // Putting the tree together.
        root.addAsChild( d1 );
        root.addAsChild( d2 );
        phy.setRoot( root );
        phy.setRooted( true );
        // Displaying the newly created tree with Archaeopteryx.
        Archaeopteryx.createApplication( phy );
    }
}