public interface PhyloXMLConstants
Of interest for application developers are the predicates defined here that allow to read and write PhyloXML-specific tags for predefined annotations.
PhyloXMLEventReader
,
PhyloXMLEventWriter
,
Metadata demo applicationstatic final String PHYLOXML_FORMAT_NAME
static final String PHYLOXML_DEFAULT_PRE
static final String PHYLOXML_NAMESPACE
static final String JPHYLOIO_PHYLOXML_NAMESPACE
static final String PHYLOXML_SCHEMA_LOCATION_URI
static final QName TAG_PHYLOGENY
static final QName TAG_DESCRIPTION
static final QName TAG_CONFIDENCE
static final QName TAG_CLADE_RELATION
static final QName TAG_SEQUENCE_RELATION
static final QName TAG_PROPERTY
static final QName TAG_BRANCH_LENGTH
static final QName TAG_BRANCH_WIDTH
static final QName TAG_BRANCH_COLOR
static final QName TAG_NODE_ID
static final QName TAG_TAXONOMY
static final QName TAG_SCI_NAME
static final QName TAG_AUTHORITY
static final QName TAG_COMMON_NAME
static final QName TAG_SYNONYM
static final QName TAG_SEQUENCE
static final QName TAG_SYMBOL
static final QName TAG_ACCESSION
static final QName TAG_LOCATION
static final QName TAG_MOL_SEQ
static final QName TAG_ANNOTATION
static final QName TAG_DOMAIN_ARCHITECTURE
static final QName TAG_DOMAIN
static final QName TAG_GENE_NAME
static final QName TAG_CROSS_REFERENCES
static final QName TAG_EVENTS
static final QName TAG_DUPLICATIONS
static final QName TAG_SPECIATIONS
static final QName TAG_LOSSES
static final QName TAG_BINARY_CHARACTERS
static final QName TAG_GAINED
static final QName TAG_PRESENT
static final QName TAG_ABSENT
static final QName TAG_DISTRIBUTION
static final QName TAG_POLYGON
static final QName TAG_REFERENCE
static final QName TAG_MINIMUM
static final QName TAG_MAXIMUM
static final QName ATTR_ROOTED
static final QName ATTR_REROOTABLE
static final QName ATTR_BRANCH_LENGTH_UNIT
static final QName ATTR_BRANCH_LENGTH
static final QName ATTR_ID_SOURCE
static final QName ATTR_COLLAPSE
static final QName ATTR_ID_PROVIDER
static final QName ATTR_ID_REF_0
static final QName ATTR_ID_REF_1
static final QName ATTR_DISTANCE
static final QName ATTR_DATATYPE
static final QName ATTR_APPLIES_TO
static final QName ATTR_ID_REF
static final QName ATTR_SOURCE
static final QName ATTR_IS_ALIGNED
static final QName ATTR_EVIDENCE
static final QName ATTR_LENGTH
static final QName ATTR_GEO_DATUM
static final QName ATTR_ALT_UNIT
static final QName ATTR_GAINED_COUNT
static final QName ATTR_LOST_COUNT
static final QName ATTR_PRESENT_COUNT
static final QName ATTR_ABSENT_COUNT
static final QName ATTR_CONFIDENCE
static final QName ATTR_COMMENT
static final QName ATTR_STANDARD_DEVIATION
static final String APPLIES_TO_PHYLOGENY
static final String APPLIES_TO_CLADE
static final String APPLIES_TO_NODE
static final String APPLIES_TO_ANNOTATION
static final String APPLIES_TO_PARENT_BRANCH
static final String APPLIES_TO_OTHER
static final String TYPE_NETWORK_EDGE
static final String PHYLOXML_PREDICATE_NAMESPACE
static final QName PREDICATE_PHYLOGENY_ID
static final QName PREDICATE_PHYLOGENY_ID_VALUE
static final QName PREDICATE_PHYLOGENY_ID_ATTR_PROVIDER
static final QName PREDICATE_PHYLOGENY_DESCRIPTION
static final QName PREDICATE_PHYLOGENY_DATE
static final QName PREDICATE_PHYLOGENY_ATTR_REROOTABLE
static final QName PREDICATE_PHYLOGENY_ATTR_BRANCH_LENGTH_UNIT
static final QName PREDICATE_PHYLOGENY_ATTR_TYPE
static final QName PREDICATE_CLADE_REL
static final QName PREDICATE_CLADE_REL_ATTR_IDREF0
static final QName PREDICATE_CLADE_REL_ATTR_IDREF1
static final QName PREDICATE_CLADE_REL_ATTR_DISTANCE
static final QName PREDICATE_CLADE_REL_ATTR_TYPE
static final QName PREDICATE_SEQ_REL
static final QName PREDICATE_SEQ_REL_ATTR_IDREF0
static final QName PREDICATE_SEQ_REL_ATTR_IDREF1
static final QName PREDICATE_SEQ_REL_ATTR_DISTANCE
static final QName PREDICATE_SEQ_REL_ATTR_TYPE
static final QName PREDICATE_SEQ_REL_CONFIDENCE
static final QName PREDICATE_SEQ_REL_CONFIDENCE_VALUE
static final QName PREDICATE_SEQ_REL_CONFIDENCE_ATTR_TYPE
static final QName PREDICATE_ATTR_ID_SOURCE
static final QName PREDICATE_ATTR_COLLAPSE
static final QName PREDICATE_WIDTH
static final QName PREDICATE_COLOR
static final QName PREDICATE_COLOR_RED
static final QName PREDICATE_COLOR_GREEN
static final QName PREDICATE_COLOR_BLUE
static final QName PREDICATE_COLOR_ALPHA
static final QName PREDICATE_CONFIDENCE
static final QName PREDICATE_CONFIDENCE_VALUE
static final QName PREDICATE_CONFIDENCE_ATTR_TYPE
static final QName PREDICATE_CONFIDENCE_ATTR_STDDEV
static final QName PREDICATE_NODE_ID
static final QName PREDICATE_NODE_ID_VALUE
static final QName PREDICATE_NODE_ID_ATTR_PROVIDER
static final QName PREDICATE_TAXONOMY
static final QName PREDICATE_TAXONOMY_ID
static final QName PREDICATE_TAXONOMY_ID_VALUE
static final QName PREDICATE_TAXONOMY_ID_ATTR_PROVIDER
static final QName PREDICATE_TAXONOMY_CODE
static final QName PREDICATE_TAXONOMY_SCIENTIFIC_NAME
static final QName PREDICATE_TAXONOMY_AUTHORITY
static final QName PREDICATE_TAXONOMY_COMMON_NAME
static final QName PREDICATE_TAXONOMY_SYNONYM
static final QName PREDICATE_TAXONOMY_RANK
static final QName PREDICATE_TAXONOMY_URI
static final QName PREDICATE_TAXONOMY_URI_VALUE
static final QName PREDICATE_TAXONOMY_URI_ATTR_DESC
static final QName PREDICATE_TAXONOMY_URI_ATTR_TYPE
static final QName PREDICATE_SEQUENCE
static final QName PREDICATE_SEQUENCE_SYMBOL
static final QName PREDICATE_SEQUENCE_ACCESSION
static final QName PREDICATE_SEQUENCE_ACCESSION_VALUE
static final QName PREDICATE_SEQUENCE_ACCESSION_ATTR_COMMENT
static final QName PREDICATE_SEQUENCE_ACCESSION_ATTR_SOURCE
static final QName PREDICATE_SEQUENCE_NAME
static final QName PREDICATE_SEQUENCE_LOCATION
static final QName PREDICATE_SEQUENCE_MOL_SEQ
static final QName PREDICATE_SEQUENCE_MOL_SEQ_VALUE
static final QName PREDICATE_SEQUENCE_MOL_SEQ_ATTR_IS_ALIGNED
static final QName PREDICATE_SEQUENCE_URI
static final QName PREDICATE_SEQUENCE_URI_VALUE
static final QName PREDICATE_SEQUENCE_URI_ATTR_DESC
static final QName PREDICATE_SEQUENCE_URI_ATTR_TYPE
static final QName PREDICATE_SEQUENCE_GENE_NAME
static final QName PREDICATE_SEQUENCE_CROSS_REFERENCES
static final QName PREDICATE_SEQUENCE_CROSS_REFERENCES_ACCESSION
static final QName PREDICATE_SEQUENCE_CROSS_REFERENCES_ACCESSION_VALUE
static final QName PREDICATE_SEQUENCE_CROSS_REFERENCES_ACCESSION_ATTR_COMMENT
static final QName PREDICATE_SEQUENCE_CROSS_REFERENCES_ACCESSION_ATTR_SOURCE
static final QName PREDICATE_SEQUENCE_ATTR_TYPE
static final QName PREDICATE_SEQUENCE_ATTR_ID_REF
static final QName PREDICATE_DOMAIN_ARCHITECTURE
static final QName PREDICATE_DOMAIN_ARCHITECTURE_DOMAIN
static final QName PREDICATE_DOMAIN_ARCHITECTURE_DOMAIN_VALUE
static final QName PREDICATE_DOMAIN_ARCHITECTURE_DOMAIN_ATTR_FROM
static final QName PREDICATE_DOMAIN_ARCHITECTURE_DOMAIN_ATTR_TO
static final QName PREDICATE_DOMAIN_ARCHITECTURE_DOMAIN_ATTR_CONFIDENCE
static final QName PREDICATE_DOMAIN_ARCHITECTURE_DOMAIN_ATTR_ID
static final QName PREDICATE_DOMAIN_ARCHITECTURE_ATTR_LENGTH
static final QName PREDICATE_ANNOTATION
static final QName PREDICATE_ANNOTATION_DESC
static final QName PREDICATE_ANNOTATION_CONFIDENCE
static final QName PREDICATE_ANNOTATION_CONFIDENCE_VALUE
static final QName PREDICATE_ANNOTATION_CONFIDENCE_ATTR_TYPE
static final QName PREDICATE_ANNOTATION_PROPERTY
static final QName PREDICATE_ANNOTATION_PROPERTY_ATTR_UNIT
static final QName PREDICATE_ANNOTATION_PROPERTY_ATTR_DATATYPE
static final QName PREDICATE_ANNOTATION_PROPERTY_ATTR_APPLIES_TO
static final QName PREDICATE_ANNOTATION_PROPERTY_ATTR_ID_REF
static final QName PREDICATE_ANNOTATION_URI
static final QName PREDICATE_ANNOTATION_URI_VALUE
static final QName PREDICATE_ANNOTATION_URI_ATTR_DESC
static final QName PREDICATE_ANNOTATION_URI_ATTR_TYPE
static final QName PREDICATE_ANNOTATION_ATTR_REF
static final QName PREDICATE_ANNOTATION_ATTR_SOURCE
static final QName PREDICATE_ANNOTATION_ATTR_EVIDENCE
static final QName PREDICATE_ANNOTATION_ATTR_TYPE
static final QName PREDICATE_EVENTS
static final QName PREDICATE_EVENTS_TYPE
static final QName PREDICATE_EVENTS_DUPLICATIONS
static final QName PREDICATE_EVENTS_SPECIATIONS
static final QName PREDICATE_EVENTS_LOSSES
static final QName PREDICATE_EVENTS_CONFIDENCE
static final QName PREDICATE_EVENTS_CONFIDENCE_VALUE
static final QName PREDICATE_EVENTS_CONFIDENCE_ATTR_TYPE
static final QName PREDICATE_BINARY_CHARACTERS
static final QName PREDICATE_BINARY_CHARACTERS_GAINED
static final QName PREDICATE_BINARY_CHARACTERS_GAINED_BC
static final QName PREDICATE_BINARY_CHARACTERS_LOST
static final QName PREDICATE_BINARY_CHARACTERS_LOST_BC
static final QName PREDICATE_BINARY_CHARACTERS_PRESENT
static final QName PREDICATE_BINARY_CHARACTERS_PRESENT_BC
static final QName PREDICATE_BINARY_CHARACTERS_ABSENT
static final QName PREDICATE_BINARY_CHARACTERS_ABSENT_BC
static final QName PREDICATE_BINARY_CHARACTERS_ATTR_TYPE
static final QName PREDICATE_BINARY_CHARACTERS_ATTR_GAINED_COUNT
static final QName PREDICATE_BINARY_CHARACTERS_ATTR_LOST_COUNT
static final QName PREDICATE_BINARY_CHARACTERS_ATTR_PRESENT_COUNT
static final QName PREDICATE_BINARY_CHARACTERS_ATTR_ABSENT_COUNT
static final QName PREDICATE_DISTRIBUTION
static final QName PREDICATE_DISTRIBUTION_DESC
static final QName PREDICATE_DISTRIBUTION_POINT
static final QName PREDICATE_DISTRIBUTION_POINT_LAT
static final QName PREDICATE_DISTRIBUTION_POINT_LONG
static final QName PREDICATE_DISTRIBUTION_POINT_ALT
static final QName PREDICATE_DISTRIBUTION_POINT_ATTR_GEODETIC_DATUM
static final QName PREDICATE_DISTRIBUTION_POINT_ATTR_ALT_UNIT
static final QName PREDICATE_DISTRIBUTION_POLYGON
static final QName PREDICATE_DISTRIBUTION_POLYGON_POINT
static final QName PREDICATE_DISTRIBUTION_POLYGON_POINT_LAT
static final QName PREDICATE_DISTRIBUTION_POLYGON_POINT_LONG
static final QName PREDICATE_DISTRIBUTION_POLYGON_POINT_ALT
static final QName PREDICATE_DISTRIBUTION_POLYGON_POINT_ATTR_GEODETIC_DATUM
static final QName PREDICATE_DISTRIBUTION_POLYGON_POINT_ATTR_ALT_UNIT
static final QName PREDICATE_DATE
static final QName PREDICATE_DATE_DESC
static final QName PREDICATE_DATE_VALUE
static final QName PREDICATE_DATE_MINIMUM
static final QName PREDICATE_DATE_MAXIMUM
static final QName PREDICATE_DATE_ATTR_UNIT
static final QName PREDICATE_REFERENCE
static final QName PREDICATE_REFERENCE_DESC
static final QName PREDICATE_REFERENCE_VALUE
static final QName PREDICATE_REFERENCE_ATTR_DOI
static final QName PREDICATE_PROPERTY
static final QName PREDICATE_PROPERTY_ATTR_UNIT
static final QName PREDICATE_PROPERTY_ATTR_APPLIES_TO
static final QName PREDICATE_PROPERTY_ATTR_ID_REF
static final String PHYLOXML_DATA_TYPE_NAMESPACE
static final QName DATA_TYPE_BRANCH_COLOR
static final QName DATA_TYPE_EVENTTYPE
static final QName DATA_TYPE_RANK
static final QName DATA_TYPE_SEQUENCE_SYMBOL
static final QName DATA_TYPE_TAXONOMY_CODE