// 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
// 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: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.io.parsers.nhx;
public final class NHXtags {
- public static final String CUSTOM_DATA_ON_NODE = "XN=";
- public static final String COLOR = "C=";
- public static final String PARENT_BRANCH_WIDTH = "W=";
- public static final String SUBTREE_NEIGHBORS = "SNn=";
- public static final String SUPER_ORTHOLOGOUS = "SOn=";
- public static final String ORTHOLOGOUS = "On=";
- public static final String TAXONOMY_ID = "T=";
- public static final String SUPPORT = "B=";
- public static final String IS_DUPLICATION = "D=";
- public static final String ANNOTATION = "AN="; //TODO fix on website NHXv2
- public static final String SPECIES_NAME = "S=";
- public static final String DOMAIN_STRUCTURE = "DS=";
- public static final String GENE_NAME = "GN=";
- public static final String GENE_NAME_SYNONYM = "G=";
- public static final String SEQUENCE_ACCESSION = "AC=";
- public static final String NODE_IDENTIFIER = "ID="; //TODO fix on website NHXv2
- public static final Object BRANCH_WIDTH = "W=";
- @Deprecated
- public static final String BINARY_DOMAIN_COMBINATIONS = "GDC=";
- @Deprecated
- public static final String DOMAINS_SEPARATOR = "\\|";
- @Deprecated
- public static final String DOMAINS = "GD=";
- @Deprecated
- public static final String EC_NUMBER = "E=";
+ public static final String TAXONOMY_ID = "T=";
+ public static final String SUPPORT = "B=";
+ public static final String IS_DUPLICATION = "D=";
+ public static final String SPECIES_NAME = "S=";
+ public static final String DOMAIN_STRUCTURE = "DS=";
+ public static final String GENE_NAME = "GN=";
+ public static final String SEQUENCE_ACCESSION = "AC=";
}