forester/java/src/org/forester/util/ForesterConstants.java

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   5 // Copyright (C) 2000-2009 Christian M. Zmasek
   6 // Copyright (C) 2007-2009 Burnham Institute for Medical Research
   7 // All rights reserved
   8 //
   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.
  13 //
  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.
  18 //
  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
  22 //
  23 // Contact: phylosoft @ gmail . com
  24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  25
  26 package org.forester.util;
  27
  28 public final class ForesterConstants {
  29
  30     public final static String  FORESTER_VERSION                 = "1.046";
  31     public final static String  FORESTER_DATE                    = "170830";
  32     public final static String  PHYLO_XML_VERSION                = "1.20";
  33     public final static String  PHYLO_XML_LOCATION               = "http://www.phyloxml.org";
  34     public final static String  PHYLO_XML_XSD                    = "phyloxml.xsd";
  35     public final static String  XML_SCHEMA_INSTANCE              = "http://www.w3.org/2001/XMLSchema-instance";
  36     public final static String  LOCAL_PHYLOXML_XSD_RESOURCE      = "resources/phyloxml.xsd";
  37     public final static String  PHYLO_XML_SUFFIX                 = ".xml";
  38     public final static String  ID_NORMALIZED_FASTA_FILE_SUFFIX  = "_ni.fasta";
  39     public final static String  ID_NORMALIZED_NEXUS_FILE_SUFFIX  = "_ni.nexus";
  40     public final static String  ID_NORMALIZED_PHYLIP_FILE_SUFFIX = "_ni.phylip";
  41     public final static String  FASTA_FILE_SUFFIX                = ".fasta";
  42     public final static String  NEXUS_FILE_SUFFIX                = ".nexus";
  43     public final static String  PHYLIP_FILE_SUFFIX               = ".phylip";
  44     public final static String  ID_MAP_FILE_SUFFIX               = ".nim";
  45     public final static String  UTF_8                            = "UTF-8";
  46     public final static String  ISO_8859_1                       = "ISO-8859-1";
  47     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";
  48     public final static boolean RELEASE                          = false;
  49
  50     public enum PhylogeneticTreeFormats {
  51                                          NH,
  52                                          NHX,
  53                                          NEXUS,
  54                                          PHYLOXML
  55     }
  56 }