2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
7 // Copyright (C) 2000-2001 Washington University School of Medicine
8 // and Howard Hughes Medical Institute
11 // This library is free software; you can redistribute it and/or
12 // modify it under the terms of the GNU Lesser General Public
13 // License as published by the Free Software Foundation; either
14 // version 2.1 of the License, or (at your option) any later version.
16 // This library is distributed in the hope that it will be useful,
17 // but WITHOUT ANY WARRANTY; without even the implied warranty of
18 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 // Lesser General Public License for more details.
21 // You should have received a copy of the GNU Lesser General Public
22 // License along with this library; if not, write to the Free Software
23 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
25 // Contact: phylosoft @ gmail . com
26 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
28 package org.forester.io.parsers.phyloxml;
30 public final class PhyloXmlMapping {
32 public static final String ACCESSION = "accession";
33 public static final String ACCESSION_COMMENT_ATTR = "comment";
34 public static final String ACCESSION_SOURCE_ATTR = "source";
35 public static final String ANNOTATION = "annotation";
36 public static final String ANNOTATION_DESC = "desc";
37 public static final String ANNOTATION_EVIDENCE_ATTR = "evidence";
38 public static final String ANNOTATION_REF_ATTR = "ref";
39 public static final String ANNOTATION_SOURCE_ATTR = "source";
40 public static final String ANNOTATION_TYPE_ATTR = "type";
41 public static final String BINARY_CHARACTER = "bc";
42 public static final String BINARY_CHARACTERS = "binary_characters";
43 public static final String BINARY_CHARACTERS_GAINED = "gained";
44 public static final String BINARY_CHARACTERS_GAINED_COUNT_ATTR = "gained_count";
45 public static final String BINARY_CHARACTERS_LOST = "lost";
46 public static final String BINARY_CHARACTERS_LOST_COUNT_ATTR = "lost_count";
47 public static final String BINARY_CHARACTERS_PRESENT = "present";
48 public static final String BINARY_CHARACTERS_PRESENT_COUNT_ATTR = "present_count";
49 public static final String BINARY_CHARACTERS_TYPE_ATTR = "type";
50 public static final String BRANCH_LENGTH = "branch_length";
51 public static final String CLADE = "clade";
52 public static final String CLADE_DATE = "date";
53 public static final String CLADE_DATE_DESC = "desc";
54 public static final String CLADE_DATE_MAX = "maximum";
55 public static final String CLADE_DATE_MIN = "minimum";
56 public static final String CLADE_DATE_UNIT = "unit";
57 public static final String CLADE_DATE_VALUE = "value";
58 public static final String COLOR = "color";
59 public static final String COLOR_BLUE = "blue";
60 public static final String COLOR_GREEN = "green";
61 public static final String COLOR_RED = "red";
62 public static final String CONFIDENCE = "confidence";
63 public static final String CONFIDENCE_SD_ATTR = "stddev";
64 public static final String CONFIDENCE_TYPE_ATTR = "type";
65 public static final String DISTRIBUTION = "distribution";
66 public static final String DISTRIBUTION_DESC = "desc";
67 public final static String EVENT_DUPLICATIONS = "duplications";
68 public final static String EVENT_LOSSES = "losses";
69 public final static String EVENT_SPECIATIONS = "speciations";
70 public final static String EVENT_TYPE = "type";
71 public final static String EVENTS = "events";
72 public static final String ID_REF = "id_ref";
73 public final static String IDENTIFIER = "id";
74 public final static String IDENTIFIER_PROVIDER_ATTR = "provider";
75 public static final String NODE_COLLAPSE = "collapse";
76 public static final String NODE_NAME = "name";
77 public static final String PHYLOGENY = "phylogeny";
78 public static final String PHYLOGENY_BRANCHLENGTH_UNIT_ATTR = "branch_length_unit";
79 public static final String PHYLOGENY_DESCRIPTION = "description";
80 public static final String PHYLOGENY_IS_REROOTABLE_ATTR = "rerootable";
81 public static final String PHYLOGENY_IS_ROOTED_ATTR = "rooted";
82 public static final String PHYLOGENY_NAME = "name";
83 public static final String PHYLOGENY_TYPE_ATTR = "type";
84 public static final String POINT = "point";
85 public static final String POINT_ALTITUDE = "alt";
86 public static final String POINT_ALTITUDE_UNIT_ATTR = "alt_unit";
87 public static final String POINT_GEODETIC_DATUM = "geodetic_datum";
88 public static final String POINT_LATITUDE = "lat";
89 public static final String POINT_LONGITUDE = "long";
90 public final static String POLYGON = "polygon";
91 public static final String PROPERTY = "property";
92 public static final String PROPERTY_APPLIES_TO = "applies_to";
93 public static final String PROPERTY_DATATYPE = "datatype";
94 public static final String PROPERTY_REF = "ref";
95 public static final String PROPERTY_UNIT = "unit";
96 public static final String REFERENCE = "reference";
97 public static final String REFERENCE_DESC = "desc";
98 public static final String REFERENCE_DOI_ATTR = "doi";
99 public static final String SEQUENCE = "sequence";
100 public final static String SEQUENCE_DOMAIN_ARCHITECTURE_DOMAIN = "domain";
101 public final static String SEQUENCE_DOMAIN_ARCHITECTURE_LENGTH = "length";
102 public final static String SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_CONFIDENCE = "confidence";
103 public final static String SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_FROM = "from";
104 public final static String SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_TO = "to";
105 public final static String SEQUENCE_DOMAIN_ARCHITECURE = "domain_architecture";
106 public static final String SEQUENCE_GENE_NAME = "gene_name";
107 public static final String SEQUENCE_LOCATION = "location";
108 public static final String SEQUENCE_MOL_SEQ = "mol_seq";
109 public static final String SEQUENCE_MOL_SEQ_ALIGNED_ATTR = "is_aligned";
110 public static final String SEQUENCE_NAME = "name";
111 public final static String SEQUENCE_RELATION = "sequence_relation";
112 public final static String SEQUENCE_RELATION_DISTANCE = "distance";
113 public final static String SEQUENCE_RELATION_ID_REF0 = "id_ref_0";
114 public final static String SEQUENCE_RELATION_ID_REF1 = "id_ref_1";
115 public final static String SEQUENCE_RELATION_TYPE = "type";
116 public final static String SEQUENCE_SOURCE_ID = "id_source";
117 public static final String SEQUENCE_SYMBOL = "symbol";
118 public final static String SEQUENCE_TYPE = "type";
119 public final static String SEQUENCE_X_REFS = "cross_references";
120 public static final String TAXONOMY = "taxonomy";
121 public static final String TAXONOMY_AUTHORITY = "authority";
122 public static final String TAXONOMY_CODE = "code";
123 public static final String TAXONOMY_COMMON_NAME = "common_name";
124 public static final String TAXONOMY_RANK = "rank";
125 public static final String TAXONOMY_SCIENTIFIC_NAME = "scientific_name";
126 public static final String TAXONOMY_SYNONYM = "synonym";
127 public static final String TYPE_ATTR = "type";
128 public static final String URI = "uri";
129 public static final String URI_DESC_ATTR = "desc";
130 public static final String WIDTH = "width";
132 private PhyloXmlMapping() {