// $Id: PhyloXmlMapping.java,v 1.12 2010/06/09 17:58:31 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
// Copyright (C) 2000-2001 Washington University School of Medicine
// and Howard Hughes Medical Institute
// 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.io.parsers.phyloxml;
/*
* @author Christian Zmasek TODO To change the template for this generated type
* comment go to Window - Preferences - Java - Code Style - Code Templates
*/
public final class PhyloXmlMapping {
public static final String PHYLOGENY = "phylogeny";
public static final String PHYLOGENY_NAME = "name";
public static final String PHYLOGENY_DESCRIPTION = "description";
public static final String PHYLOGENY_IS_REROOTABLE_ATTR = "rerootable";
public static final String PHYLOGENY_BRANCHLENGTH_UNIT_ATTR = "branch_length_unit";
public static final String PHYLOGENY_IS_ROOTED_ATTR = "rooted";
public static final String PHYLOGENY_TYPE_ATTR = "type";
public static final String CLADE = "clade";
public static final String NODE_NAME = "name";
public static final String SEQUENCE = "sequence";
public static final String SEQUENCE_NAME = "name";
public static final String SEQUENCE_SYMBOL = "symbol";
public static final String ACCESSION = "accession";
public static final String ACCESSION_SOURCE_ATTR = "source";
public static final String SEQUENCE_LOCATION = "location";
public static final String SEQUENCE_MOL_SEQ = "mol_seq";
public static final String ANNOTATION = "annotation";
public static final String ANNOTATION_DESC = "desc";
public static final String ANNOTATION_REF_ATTR = "ref";
public static final String ANNOTATION_EVIDENCE_ATTR = "evidence";
public static final String ANNOTATION_TYPE_ATTR = "type";
public static final String TAXONOMY = "taxonomy";
public static final String TAXONOMY_SCIENTIFIC_NAME = "scientific_name";
public static final String TAXONOMY_COMMON_NAME = "common_name";
public static final String TAXONOMY_CODE = "code";
public static final String TAXONOMY_RANK = "rank";
public static final String TAXONOMY_SYNONYM = "synonym";
public static final String TAXONOMY_AUTHORITY = "authority";
public static final String DISTRIBUTION = "distribution";
public static final String BINARY_CHARACTERS = "binary_characters";
public static final String BINARY_CHARACTERS_PRESENT = "present";
public static final String BINARY_CHARACTERS_GAINED = "gained";
public static final String BINARY_CHARACTERS_LOST = "lost";
public static final String BINARY_CHARACTERS_TYPE_ATTR = "type";
public static final String BINARY_CHARACTERS_PRESENT_COUNT_ATTR = "present_count";
public static final String BINARY_CHARACTERS_GAINED_COUNT_ATTR = "gained_count";
public static final String BINARY_CHARACTERS_LOST_COUNT_ATTR = "lost_count";
public static final String BRANCH_LENGTH = "branch_length";
public static final String CONFIDENCE = "confidence";
public static final String CONFIDENCE_TYPE_ATTR = "type";
public static final String COLOR = "color";
public static final String COLOR_RED = "red";
public static final String COLOR_GREEN = "green";
public static final String COLOR_BLUE = "blue";
public final static String SEQUENCE_DOMAIN_ARCHITECTURE_DOMAIN = "domain";
public final static String SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_FROM = "from";
public final static String SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_TO = "to";
public final static String SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_CONFIDENCE = "confidence";
// public final static String NODE_IDENTIFIER = "node_id";
public final static String IDENTIFIER = "id";
public final static String IDENTIFIER_PROVIDER_ATTR = "provider";
public static final String URI = "uri";
public static final String WIDTH = "width";
public final static String EVENTS = "events";
public final static String EVENT_TYPE = "type";
public final static String EVENT_DUPLICATIONS = "duplications";
public final static String EVENT_SPECIATIONS = "speciations";
public final static String EVENT_LOSSES = "losses";
public final static String SEQUENCE_DOMAIN_ARCHITECURE = "domain_architecture";
public final static String SEQUENCE_DOMAIN_ARCHITECTURE_LENGTH = "length";
public final static String SEQUENCE_TYPE = "type";
public static final String BINARY_CHARACTER = "bc";
public static final String URI_DESC_ATTR = "desc";
public static final String TYPE_ATTR = "type";
public static final String REFERENCE = "reference";
public static final String REFERENCE_DOI_ATTR = "doi";
public static final String REFERENCE_DESC = "desc";
public static final String PROPERTY = "property";
public static final String PROPERTY_REF = "ref";
public static final String PROPERTY_UNIT = "unit";
public static final String PROPERTY_DATATYPE = "datatype";
public static final String PROPERTY_APPLIES_TO = "applies_to";
public static final String ID_REF = "id_ref";
public static final String ANNOTATION_SOURCE_ATTR = "source";
public static final String DISTRIBUTION_DESC = "desc";
public static final String POINT = "point";
public static final String POINT_LONGITUDE = "long";
public static final String POINT_LATITUDE = "lat";
public static final String POINT_ALTITUDE = "alt";
public static final String POINT_ALTITUDE_UNIT_ATTR = "alt_unit";
public static final String POINT_GEODETIC_DATUM = "geodetic_datum";
public static final String CLADE_DATE = "date";
public static final String CLADE_DATE_UNIT = "unit";
public static final String CLADE_DATE_DESC = "desc";
public static final String CLADE_DATE_MIN = "minimum";
public static final String CLADE_DATE_MAX = "maximum";
public static final String CLADE_DATE_VALUE = "value";
/* GUILHEM_BEG */
public final static String SEQUENCE_RELATION = "sequence_relation";
public final static String SEQUENCE_RELATION_TYPE = "type";
public final static String SEQUENCE_RELATION_ID_REF0 = "id_ref_0";
public final static String SEQUENCE_RELATION_ID_REF1 = "id_ref_1";
public final static String SEQUENCE_RELATION_DISTANCE = "distance";
public final static String SEQUENCE_SOURCE_ID = "id_source";
public final static String POLYGON = "polygon";
/* GUILHEM_END */
/**
*
*/
private PhyloXmlMapping() {
}
}