// 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.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 NODE_COLLAPSE = "collapse";
- 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_COMMENT_ATTR = "comment";
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 SEQUENCE_MOL_SEQ_ALIGNED_ATTR = "is_aligned";
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_REF_ATTR = "ref";
+ public static final String ANNOTATION_SOURCE_ATTR = "source";
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_CHARACTER = "bc";
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 = "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 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 static final String DISTRIBUTION = "distribution";
+ public static final String DISTRIBUTION_DESC = "desc";
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 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 static final String ANNOTATION_SOURCE_ATTR = "source";
- public static final String DISTRIBUTION_DESC = "desc";
+ 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_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";
+ 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_TYPE = "type";
+ 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_DISTANCE = "distance";
+ public final static String SEQUENCE_RELATION_TYPE = "type";
public final static String SEQUENCE_SOURCE_ID = "id_source";
- public final static String POLYGON = "polygon";
+ 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() {
}
git://source.jalview.org / jalview.git / blobdiff