forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlMapping.java

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   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
   9 // All rights reserved
  10 //
  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.
  15 //
  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.
  20 //
  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
  24 //
  25 // Contact: phylosoft @ gmail . com
  26 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  27
  28 package org.forester.io.parsers.phyloxml;
  29
  30 public final class PhyloXmlMapping {
  31
  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";
 131
 132     private PhyloXmlMapping() {
 133     }
 134 }