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/forester
26 package org.forester.phylogeny.data;
28 import java.io.IOException;
29 import java.io.Writer;
32 * Interface for data for annotating a Phylogeny.
34 public interface PhylogenyData {
36 public StringBuffer asSimpleText();
38 public StringBuffer asText();
41 * Creates a new PhylogenyData object with identical values as this
43 * This ~should~ return a deep copy, but not there yet.
46 * @return a ~deep~ copy of this PhylogenyData
48 public PhylogenyData copy();
51 * Compares this PhylogenyData to PhylogenyData data. In general, this
52 * should return true if and only if all fiels are exactly identical.
54 * @param PhylogenyData
55 * the PhylogenyData to compare to
56 * @return in general, true if and only if all fiels are exactly identical,
59 public boolean isEqual( final PhylogenyData data );
61 public StringBuffer toNHX();
64 * Writes a phyloXML representation of this phylogeny data.
71 public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException;