// $Id: // 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: phylosoft @ gmail . com // WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.phyloxml; public final class PhyloXmlMapping { public static final String ACCESSION = "accession"; public static final String ACCESSION_COMMENT_ATTR = "comment"; public static final String ACCESSION_SOURCE_ATTR = "source"; public static final String ANNOTATION = "annotation"; public static final String ANNOTATION_DESC = "desc"; public static final String ANNOTATION_EVIDENCE_ATTR = "evidence"; public static final String ANNOTATION_REF_ATTR = "ref"; public static final String ANNOTATION_SOURCE_ATTR = "source"; public static final String ANNOTATION_TYPE_ATTR = "type"; public static final String BINARY_CHARACTER = "bc"; public static final String BINARY_CHARACTERS = "binary_characters"; public static final String BINARY_CHARACTERS_GAINED = "gained"; public static final String BINARY_CHARACTERS_GAINED_COUNT_ATTR = "gained_count"; public static final String BINARY_CHARACTERS_LOST = "lost"; public static final String BINARY_CHARACTERS_LOST_COUNT_ATTR = "lost_count"; public static final String BINARY_CHARACTERS_PRESENT = "present"; public static final String BINARY_CHARACTERS_PRESENT_COUNT_ATTR = "present_count"; public static final String BINARY_CHARACTERS_TYPE_ATTR = "type"; public static final String BRANCH_LENGTH = "branch_length"; public static final String CLADE = "clade"; public static final String CLADE_DATE = "date"; public static final String CLADE_DATE_DESC = "desc"; public static final String CLADE_DATE_MAX = "maximum"; public static final String CLADE_DATE_MIN = "minimum"; public static final String CLADE_DATE_UNIT = "unit"; public static final String CLADE_DATE_VALUE = "value"; public static final String COLOR = "color"; public static final String COLOR_BLUE = "blue"; public static final String COLOR_GREEN = "green"; public static final String COLOR_RED = "red"; public static final String COLOR_ALPHA = "alpha"; public static final String CONFIDENCE = "confidence"; public static final String CONFIDENCE_SD_ATTR = "stddev"; public static final String CONFIDENCE_TYPE_ATTR = "type"; public static final String DISTRIBUTION = "distribution"; public static final String DISTRIBUTION_DESC = "desc"; public final static String EVENT_DUPLICATIONS = "duplications"; public final static String EVENT_LOSSES = "losses"; public final static String EVENT_SPECIATIONS = "speciations"; public final static String EVENT_TYPE = "type"; public final static String EVENTS = "events"; public static final String ID_REF = "id_ref"; public final static String IDENTIFIER = "id"; public final static String IDENTIFIER_PROVIDER_ATTR = "provider"; public static final String NODE_COLLAPSE = "collapse"; public static final String NODE_NAME = "name"; public static final String PHYLOGENY = "phylogeny"; public static final String PHYLOGENY_BRANCHLENGTH_UNIT_ATTR = "branch_length_unit"; public static final String PHYLOGENY_DESCRIPTION = "description"; public static final String PHYLOGENY_IS_REROOTABLE_ATTR = "rerootable"; public static final String PHYLOGENY_IS_ROOTED_ATTR = "rooted"; public static final String PHYLOGENY_NAME = "name"; public static final String PHYLOGENY_TYPE_ATTR = "type"; public static final String POINT = "point"; 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 POINT_LATITUDE = "lat"; public static final String POINT_LONGITUDE = "long"; public final static String POLYGON = "polygon"; public static final String PROPERTY = "property"; public static final String PROPERTY_APPLIES_TO = "applies_to"; public static final String PROPERTY_DATATYPE = "datatype"; public static final String PROPERTY_REF = "ref"; public static final String PROPERTY_UNIT = "unit"; public static final String REFERENCE = "reference"; public static final String REFERENCE_DESC = "desc"; public static final String REFERENCE_DOI_ATTR = "doi"; public static final String SEQUENCE = "sequence"; public final static String SEQUENCE_DOMAIN_ARCHITECTURE_DOMAIN = "domain"; public final static String SEQUENCE_DOMAIN_ARCHITECTURE_LENGTH = "length"; public final static String SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_CONFIDENCE = "confidence"; 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_ARCHITECURE = "domain_architecture"; public static final String SEQUENCE_GENE_NAME = "gene_name"; public static final String SEQUENCE_LOCATION = "location"; public static final String SEQUENCE_MOL_SEQ = "mol_seq"; public static final String SEQUENCE_MOL_SEQ_ALIGNED_ATTR = "is_aligned"; public static final String SEQUENCE_NAME = "name"; public final static String SEQUENCE_RELATION = "sequence_relation"; public final static String SEQUENCE_RELATION_DISTANCE = "distance"; 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_TYPE = "type"; public final static String SEQUENCE_SOURCE_ID = "id_source"; public static final String SEQUENCE_SYMBOL = "symbol"; public final static String SEQUENCE_TYPE = "type"; public final static String SEQUENCE_X_REFS = "cross_references"; public static final String TAXONOMY = "taxonomy"; public static final String TAXONOMY_AUTHORITY = "authority"; public static final String TAXONOMY_CODE = "code"; public static final String TAXONOMY_COMMON_NAME = "common_name"; public static final String TAXONOMY_RANK = "rank"; public static final String TAXONOMY_SCIENTIFIC_NAME = "scientific_name"; public static final String TAXONOMY_SYNONYM = "synonym"; public static final String TYPE_ATTR = "type"; public static final String URI = "uri"; public static final String URI_DESC_ATTR = "desc"; public static final String WIDTH = "width"; private PhyloXmlMapping() { } }