PhylogenyData.java

// $Id: PhylogenyData.java,v 1.19 2009/01/13 19:49:29 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/forester

package org.forester.phylogeny.data;

import java.io.IOException;
import java.io.Writer;

/*
 * Interface for data for annotating a Phylogeny.
 */
public interface PhylogenyData {

    public StringBuffer asSimpleText();

    public StringBuffer asText();

    /**
     * Creates a new PhylogenyData object with identical values as this
     * PhylogenyData.
     * This ~should~ return a deep copy, but not there yet.
     * 
     * 
     * @return a ~deep~ copy of this PhylogenyData
     */
    public PhylogenyData copy();

    /**
     * Compares this PhylogenyData to PhylogenyData data. In general, this
     * should return true if and only if all fiels are exactly identical.
     * 
     * @param PhylogenyData
     *            the PhylogenyData to compare to
     * @return in general, true if and only if all fiels are exactly identical,
     *         false otherwise
     */
    public boolean isEqual( final PhylogenyData data );

    public StringBuffer toNHX();

    /**
     *  Writes a phyloXML representation of this phylogeny data.
     * 
     * @param writer
     * @param level
     * @param indentation
     * @throws IOException 
     */
    public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException;
}