X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fio%2Fparsers%2Fphyloxml%2FPhyloXmlMapping.java;h=1db3384f49108dbc14ba405b585fe20950814da4;hb=803a2b32992b5944b73c6dfcb80ceb58c09b81c1;hp=4659fc210a80c2944a366de4d7636b77b1238ec6;hpb=f6de7e66f71bf840d3d68ed70dda9946ad2e0faa;p=jalview.git diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlMapping.java b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlMapping.java index 4659fc2..1db3384 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlMapping.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlMapping.java @@ -23,113 +23,112 @@ // 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() { }