// $Id:
// FORESTER -- software libraries and applications
// for evolutionary biology research and applications.
//
// Copyright (C) 2000-2009 Christian M. Zmasek
// Copyright (C) 2007-2009 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: phylosoft @ gmail . com
// WWW: https://sites.google.com/site/cmzmasek/home/software/forester

package org.forester.util;

public final class ForesterConstants {

    public final static String  FORESTER_VERSION                = "1.045";
    public final static String  FORESTER_DATE                   = "161214";
    public final static String  PHYLO_XML_VERSION               = "1.20";
    public final static String  PHYLO_XML_LOCATION              = "http://www.phyloxml.org";
    public final static String  PHYLO_XML_XSD                   = "phyloxml.xsd";
    public final static String  XML_SCHEMA_INSTANCE             = "http://www.w3.org/2001/XMLSchema-instance";
    public final static String  LOCAL_PHYLOXML_XSD_RESOURCE     = "resources/phyloxml.xsd";
    public final static String  PHYLO_XML_SUFFIX                = ".xml";
    public final static String  ID_NORMALIZED_FASTA_FILE_SUFFIX = "_ni.fasta";
    public final static String  ID_MAP_FILE_SUFFIX              = ".nim";
    public final static String  UTF_8                           = "UTF-8";
    public final static String  ISO_8859_1                      = "ISO-8859-1";
    public final static String  PHYLO_XML_REFERENCE             = "Han MV and Zmasek CM (2009): \"phyloXML: XML for evolutionary biology and comparative genomics\", BMC Bioinformatics 10:356";
    public final static boolean RELEASE                         = false;

    public enum PhylogeneticTreeFormats {
                                         NH,
                                         NHX,
                                         NEXUS,
                                         PHYLOXML
    }
}