A B C D E F G H I J K L M N O P Q R S T U V W X

P

ParentEventInformation - Class in info.bioinfweb.jphyloio

ParentEventInformation() - Constructor for class info.bioinfweb.jphyloio.ParentEventInformation

parseColumnType(String) - Static method in enum info.bioinfweb.jphyloio.formats.pde.PDEMetaColumnType

parseList(String) - Static method in class info.bioinfweb.jphyloio.objecttranslation.implementations.ListTranslator

Reads a string representation of a simple value list into an implementation of List.

parseNumericValue(String) - Static method in class info.bioinfweb.jphyloio.formats.newick.NewickUtils

parseQName(String, StartElement) - Method in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader

parseStateMeaning(String) - Static method in class info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractNeXMLElementReader

parseValue(String, ReaderStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.Base64BinaryTranslator

parseValue(String, ReaderStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.BigDecimalTranslator

parseValue(String, ReaderStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.BigIntegerTranslator

parseValue(String, ReaderStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.BooleanTranslator

parseValue(String, ReaderStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.ByteTranslator

parseValue(String, ReaderStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.ColorTranslator

parseValue(String, ReaderStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.DateTimeTranslator

parseValue(String, ReaderStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.DateTranslator

parseValue(String, ReaderStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.DoubleTranslator

parseValue(String, ReaderStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.EnumTranslator

parseValue(String, ReaderStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.FloatTranslator

parseValue(String, ReaderStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.HexadecimalColorTranslator

parseValue(String, ReaderStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.HexBinaryTranslator

parseValue(String, ReaderStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.IllegalArgumentExceptionSimpleValueTranslator

parseValue(String, ReaderStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.IntegerTranslator

parseValue(String, ReaderStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.LongTranslator

parseValue(String, ReaderStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.NumericValueTranslator

parseValue(String, ReaderStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.QNameTranslator

parseValue(String, ReaderStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.ShortTranslator

parseValue(String, ReaderStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.TimeTranslator

PartEndEvent - Class in info.bioinfweb.jphyloio.events

Indicates the end of a part of a sequence or character set definition.

PartEndEvent(EventContentType, boolean) - Constructor for class info.bioinfweb.jphyloio.events.PartEndEvent

Creates a new instance of this class.

PDE_FORMAT_ID - Static variable in interface info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs

PDE_FORMAT_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants

PDE_NAMESPACE_PREFIX - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants

PDE_PREDICATE_NAMESPACE - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants

PDEConstants - Interface in info.bioinfweb.jphyloio.formats.pde

Defines constants necessary to read PDE files.

PDEEventReader - Class in info.bioinfweb.jphyloio.formats.pde

Event reader for the PDE format used by the alignment editor PhyDE.

PDEEventReader(File, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.pde.PDEEventReader

PDEEventReader(InputStream, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.pde.PDEEventReader

PDEEventReader(Reader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.pde.PDEEventReader

PDEEventReader(XMLEventReader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.pde.PDEEventReader

PDEFactory - Class in info.bioinfweb.jphyloio.formats.pde

Reader and writer factory for the PDE format.

PDEFactory() - Constructor for class info.bioinfweb.jphyloio.formats.pde.PDEFactory

PDEMetaColumnDefintion - Class in info.bioinfweb.jphyloio.formats.pde

Models the definition of a metadata column in the PDE format.

PDEMetaColumnDefintion(long, String, PDEMetaColumnType) - Constructor for class info.bioinfweb.jphyloio.formats.pde.PDEMetaColumnDefintion

PDEMetaColumnType - Enum in info.bioinfweb.jphyloio.formats.pde

The type of a meta column in the PDE format.

PDEReaderStreamDataProvider - Class in info.bioinfweb.jphyloio.formats.pde

The XML stream data provider used by PDEEventReader.

PDEReaderStreamDataProvider(PDEEventReader) - Constructor for class info.bioinfweb.jphyloio.formats.pde.PDEReaderStreamDataProvider

peek() - Method in class info.bioinfweb.jphyloio.AbstractEventReader

peek() - Method in class info.bioinfweb.jphyloio.formats.newick.NewickScanner

peek() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLEventReader

peek() - Method in interface info.bioinfweb.jphyloio.JPhyloIOEventReader

Returns the event from the underlying document that will be returned in the next call of JPhyloIOEventReader.next() without moving forward.

PHYLIP_FORMAT_ID - Static variable in interface info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs

PHYLIP_FORMAT_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.phylip.PhylipConstants

PhylipConstants - Interface in info.bioinfweb.jphyloio.formats.phylip

Constants to be used by Phylip readers and writers.

PhylipEventReader - Class in info.bioinfweb.jphyloio.formats.phylip

Event based reader for Phylip alignment files.

PhylipEventReader(BufferedReader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.phylip.PhylipEventReader

Creates a new instance of this class.

PhylipEventReader(File, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.phylip.PhylipEventReader

Creates a new instance of this class.

PhylipEventReader(InputStream, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.phylip.PhylipEventReader

Creates a new instance of this class.

PhylipEventReader(Reader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.phylip.PhylipEventReader

Creates a new instance of this class.

PhylipEventWriter - Class in info.bioinfweb.jphyloio.formats.phylip

Event based writer for the Phylip format.

PhylipEventWriter() - Constructor for class info.bioinfweb.jphyloio.formats.phylip.PhylipEventWriter

Creates a new instance of this class.

PhylipFactory - Class in info.bioinfweb.jphyloio.formats.phylip

Reader and writer factory for the (non-sequential) Phylip format.

PhylipFactory() - Constructor for class info.bioinfweb.jphyloio.formats.phylip.PhylipFactory

PHYLOXML_DATA_TYPE_NAMESPACE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PHYLOXML_DEFAULT_PRE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PHYLOXML_FORMAT_ID - Static variable in interface info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs

PHYLOXML_FORMAT_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PHYLOXML_NAMESPACE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PHYLOXML_PREDICATE_NAMESPACE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PHYLOXML_SCHEMA_LOCATION_URI - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PhyloXMLCharactersElementReader - Class in info.bioinfweb.jphyloio.formats.phyloxml.elementreader

Element reader that is used to process the character content of PhyloXML tags.

PhyloXMLCharactersElementReader(QName) - Constructor for class info.bioinfweb.jphyloio.formats.phyloxml.elementreader.PhyloXMLCharactersElementReader

PhyloXMLCollectMetadataDataReceiver - Class in info.bioinfweb.jphyloio.formats.phyloxml.receivers

Receiver that is used to collect information from meta events (e.g.

PhyloXMLCollectMetadataDataReceiver(PhyloXMLWriterStreamDataProvider, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.phyloxml.receivers.PhyloXMLCollectMetadataDataReceiver

PhyloXMLColorTranslator - Class in info.bioinfweb.jphyloio.formats.phyloxml

Object translator between Color and the PhyloXML complex type BranchColor.

PhyloXMLColorTranslator() - Constructor for class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLColorTranslator

PhyloXMLConstants - Interface in info.bioinfweb.jphyloio.formats.phyloxml

Defines constants necessary to read and write PhyloXML files.

PhyloXMLEventReader - Class in info.bioinfweb.jphyloio.formats.phyloxml

Event reader for the PhyloXML format.

PhyloXMLEventReader(File, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLEventReader

PhyloXMLEventReader(InputStream, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLEventReader

PhyloXMLEventReader(Reader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLEventReader

PhyloXMLEventReader(XMLEventReader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLEventReader

PhyloXMLEventWriter - Class in info.bioinfweb.jphyloio.formats.phyloxml

Event writer for the PhyloXML format.

PhyloXMLEventWriter() - Constructor for class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLEventWriter

PhyloXMLFactory - Class in info.bioinfweb.jphyloio.formats.phyloxml

Reader and writer factory for the PhyloXML format.

PhyloXMLFactory() - Constructor for class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLFactory

PhyloXMLMetaDataReceiver - Class in info.bioinfweb.jphyloio.formats.phyloxml.receivers

Receiver that implements a general strategy of writing metadata to a PhyloXML document.

PhyloXMLMetaDataReceiver(PhyloXMLWriterStreamDataProvider, ReadWriteParameterMap, PropertyOwner) - Constructor for class info.bioinfweb.jphyloio.formats.phyloxml.receivers.PhyloXMLMetaDataReceiver

PhyloXMLMetadataTreatment - Enum in info.bioinfweb.jphyloio.formats.phyloxml

Instances of this enum can be used as parameter values for ReadWriteParameterNames.KEY_PHYLOXML_METADATA_TREATMENT.

PhyloXMLMetaEventInfo - Class in info.bioinfweb.jphyloio.formats.phyloxml

Class that is used by PhyloXMLEventWriter to model a meta event in a hierarchical structure of metadata.

PhyloXMLMetaEventInfo(String, List<String>, boolean) - Constructor for class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLMetaEventInfo

PhyloXMLOnlyCustomXMLDataReceiver - Class in info.bioinfweb.jphyloio.formats.phyloxml.receivers

Receiver, that writes only custom XML, e.g nested under document.

PhyloXMLOnlyCustomXMLDataReceiver(PhyloXMLWriterStreamDataProvider, ReadWriteParameterMap, PropertyOwner) - Constructor for class info.bioinfweb.jphyloio.formats.phyloxml.receivers.PhyloXMLOnlyCustomXMLDataReceiver

PhyloXMLPredicateInfo - Class in info.bioinfweb.jphyloio.formats.phyloxml

Class that is used as a value in PhyloXMLWriterStreamDataProvider.getPredicateInfoMap().

PhyloXMLPredicateInfo(PhyloXMLPredicateTreatment, QName, QName...) - Constructor for class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLPredicateInfo

PhyloXMLPredicateTreatment - Enum in info.bioinfweb.jphyloio.formats.phyloxml

This class enumerated ways to translate specific predicates to XML structures in a PhyloXML document.

PhyloXMLPrivateConstants - Interface in info.bioinfweb.jphyloio.formats.phyloxml

This interface contains constants used internally in JPhyloIO by PhyloXMLEventWriter and PhyloXML data receivers.

PhyloXMLPropertyMetadataReceiver - Class in info.bioinfweb.jphyloio.formats.phyloxml.receivers

This receiver is used to write the contents of meta events to a document, if their predicates indicate that they contain information about a PhyloXML property tag.

PhyloXMLPropertyMetadataReceiver(PhyloXMLWriterStreamDataProvider, ReadWriteParameterMap, PropertyOwner) - Constructor for class info.bioinfweb.jphyloio.formats.phyloxml.receivers.PhyloXMLPropertyMetadataReceiver

PhyloXMLReaderStreamDataProvider - Class in info.bioinfweb.jphyloio.formats.phyloxml

The XMLReaderStreamDataProvider used by PhyloXMLEventReader.

PhyloXMLReaderStreamDataProvider(PhyloXMLEventReader) - Constructor for class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLReaderStreamDataProvider

PhyloXMLSpecificPredicatesDataReceiver - Class in info.bioinfweb.jphyloio.formats.phyloxml.receivers

Receiver that is used to translate between meta events with certain predicates indicating they contain information about a PhyloXML tag and the actual tag.

PhyloXMLSpecificPredicatesDataReceiver(PhyloXMLWriterStreamDataProvider, ReadWriteParameterMap, PropertyOwner, QName) - Constructor for class info.bioinfweb.jphyloio.formats.phyloxml.receivers.PhyloXMLSpecificPredicatesDataReceiver

PhyloXMLStartDocumentElementReader - Class in info.bioinfweb.jphyloio.formats.phyloxml.elementreader

This element reader implements reading the start of a PhyloXML document.

PhyloXMLStartDocumentElementReader() - Constructor for class info.bioinfweb.jphyloio.formats.phyloxml.elementreader.PhyloXMLStartDocumentElementReader

PhyloXMLWriterStreamDataProvider - Class in info.bioinfweb.jphyloio.formats.phyloxml

The XMLWriterStreamDataProvider used by PhyloXMLEventWriter.

PhyloXMLWriterStreamDataProvider(PhyloXMLEventWriter) - Constructor for class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLWriterStreamDataProvider

pop() - Method in class info.bioinfweb.jphyloio.ParentEventInformation

PRE_LEGEND_ANCHOR - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_ACCESS_NUMBER - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants

PREDICATE_ANNOTATION - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_ANNOTATION_ATTR_EVIDENCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_ANNOTATION_ATTR_REF - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_ANNOTATION_ATTR_SOURCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_ANNOTATION_ATTR_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_ANNOTATION_CONFIDENCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_ANNOTATION_CONFIDENCE_ATTR_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_ANNOTATION_CONFIDENCE_VALUE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_ANNOTATION_DESC - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_ANNOTATION_PROPERTY - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_ANNOTATION_PROPERTY_ATTR_APPLIES_TO - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_ANNOTATION_PROPERTY_ATTR_DATATYPE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_ANNOTATION_PROPERTY_ATTR_ID_REF - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_ANNOTATION_PROPERTY_ATTR_UNIT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_ANNOTATION_URI - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_ANNOTATION_URI_ATTR_DESC - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_ANNOTATION_URI_ATTR_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_ANNOTATION_URI_VALUE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_ATTR_COLLAPSE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_ATTR_ID_SOURCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_BINARY_CHARACTERS - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_BINARY_CHARACTERS_ABSENT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_BINARY_CHARACTERS_ABSENT_BC - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_BINARY_CHARACTERS_ATTR_ABSENT_COUNT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_BINARY_CHARACTERS_ATTR_GAINED_COUNT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_BINARY_CHARACTERS_ATTR_LOST_COUNT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_BINARY_CHARACTERS_ATTR_PRESENT_COUNT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_BINARY_CHARACTERS_ATTR_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_BINARY_CHARACTERS_GAINED - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_BINARY_CHARACTERS_GAINED_BC - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_BINARY_CHARACTERS_LOST - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_BINARY_CHARACTERS_LOST_BC - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_BINARY_CHARACTERS_PRESENT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_BINARY_CHARACTERS_PRESENT_BC - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_BRANCH_CONSTANT_WIDTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_BRANCH_MIN_LENGTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_BRANCH_MIN_SPACE_ABOVE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_BRANCH_MIN_SPACE_BELOW - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_CHAR_ATTR_CODON_POSITION - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants

PREDICATE_CHAR_ATTR_TOKENS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants

PREDICATE_CHARACTER_COUNT - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants

PREDICATE_CHARSET_COLOR - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants

PREDICATE_CHARSET_VISIBILITY - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants

PREDICATE_CLADE_REL - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_CLADE_REL_ATTR_DISTANCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_CLADE_REL_ATTR_IDREF0 - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_CLADE_REL_ATTR_IDREF1 - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_CLADE_REL_ATTR_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_COLOR - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_COLOR_ALPHA - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_COLOR_BLUE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_COLOR_GREEN - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_COLOR_RED - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_COLUMN_ID - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_COMMENT - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants

PREDICATE_CONFIDENCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_CONFIDENCE_ATTR_STDDEV - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_CONFIDENCE_ATTR_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_CONFIDENCE_VALUE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_DATA_ID - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_DATA_ID_VALUE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_DATA_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_DATE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_DATE_ATTR_UNIT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_DATE_DESC - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_DATE_MAXIMUM - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_DATE_MINIMUM - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_DATE_VALUE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_DECIMAL_FORMAT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_DESCRIPTION - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants

PREDICATE_DISTRIBUTION - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_DISTRIBUTION_DESC - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_DISTRIBUTION_POINT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_DISTRIBUTION_POINT_ALT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_DISTRIBUTION_POINT_ATTR_ALT_UNIT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_DISTRIBUTION_POINT_ATTR_GEODETIC_DATUM - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_DISTRIBUTION_POINT_LAT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_DISTRIBUTION_POINT_LONG - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_DISTRIBUTION_POLYGON - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_DISTRIBUTION_POLYGON_POINT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_DISTRIBUTION_POLYGON_POINT_ALT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_DISTRIBUTION_POLYGON_POINT_ATTR_ALT_UNIT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_DISTRIBUTION_POLYGON_POINT_ATTR_GEODETIC_DATUM - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_DISTRIBUTION_POLYGON_POINT_LAT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_DISTRIBUTION_POLYGON_POINT_LONG - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_DOCUMENT_MARGIN - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_DOMAIN_ARCHITECTURE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_DOMAIN_ARCHITECTURE_ATTR_LENGTH - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_DOMAIN_ARCHITECTURE_DOMAIN - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_DOMAIN_ARCHITECTURE_DOMAIN_ATTR_CONFIDENCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_DOMAIN_ARCHITECTURE_DOMAIN_ATTR_FROM - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_DOMAIN_ARCHITECTURE_DOMAIN_ATTR_ID - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_DOMAIN_ARCHITECTURE_DOMAIN_ATTR_TO - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_DOMAIN_ARCHITECTURE_DOMAIN_VALUE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_E_NEWICK_EDGE_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants

PREDICATE_EDGE_LENGTH - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants

PREDICATE_EDGE_RADIUS - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_EDGE_SOURCE_NODE - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants

The following constants are currently only used in PhyloXML, but may be used by other formats in the future.

PREDICATE_EDGE_TARGET_NODE - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants

PREDICATE_EVENTS - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_EVENTS_CONFIDENCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_EVENTS_CONFIDENCE_ATTR_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_EVENTS_CONFIDENCE_VALUE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_EVENTS_DUPLICATIONS - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_EVENTS_LOSSES - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_EVENTS_SPECIATIONS - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_EVENTS_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_FONT_FAMILY - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_FORMAT - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants

PREDICATE_GLOBAL_FORMATS - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_GLOBAL_FORMATS_ALIGN_TO_SUBTREE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_GLOBAL_FORMATS_BG_COLOR - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_GLOBAL_FORMATS_BRANCH_LENGTH_SCALE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_GLOBAL_FORMATS_POSITION_LABELS_TO_LEFT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_GLOBAL_FORMATS_SHOW_ROOTED - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_GLOBAL_FORMATS_SHOW_SCALE_BAR - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_HAS_CUSTOM_XML - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants

PREDICATE_HAS_LITERAL_METADATA - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants

PREDICATE_HAS_RESOURCE_METADATA - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants

PREDICATE_HEIGHT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_ICON_LABEL - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_ICON_LABEL_ICON - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_ICON_LABEL_ICON_FILLED - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_INVISIBLE_DATA - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_IS_CROSSLINK - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants

PREDICATE_IS_DECIMAL - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_LABEL_ABOVE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_LABEL_LINE_NO - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_LABEL_LINE_POS - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_LABEL_MARGIN - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_LEAF_MARGIN - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_LEGEND - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_LEGEND_ANCHOR_0 - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_LEGEND_ANCHOR_1 - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_LEGEND_MARGIN - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_LEGEND_MIN_TREE_DISTANCE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_LEGEND_ORIENTATION - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_LEGEND_POSITION - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_LEGEND_SPACING - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_LEGEND_STYLE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_LINE_COLOR - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_LINE_WIDTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_LINKED_FILE - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants

PREDICATE_LOCALE_COUNTRY - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_LOCALE_LANG - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_LOCALE_VARIANT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_MARGIN_BOTTOM - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_MARGIN_LEFT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_MARGIN_RIGHT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_MARGIN_TOP - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_MATRIX - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants

PREDICATE_NAMESPACE_FOLDER - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants

PREDICATE_NODE_BRANCH_DATA_ADAPTERS - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_NODE_BRANCH_DATA_ADAPTERS_ADAPTER - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_NODE_BRANCH_DATA_ADAPTERS_ADAPTER_ID - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_NODE_BRANCH_DATA_ADAPTERS_ADAPTER_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_NODE_BRANCH_DATA_ADAPTERS_ADAPTER_PURPOSE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_NODE_ID - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_NODE_ID_ATTR_PROVIDER - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_NODE_ID_VALUE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_NODE_UNIQUE_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_ORIGINAL_LABEL - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants

PREDICATE_ORIGINAL_TOKEN_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants

PREDICATE_PART_SEPERATOR - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants

PREDICATE_PHYLOGENY_ATTR_BRANCH_LENGTH_UNIT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_PHYLOGENY_ATTR_REROOTABLE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_PHYLOGENY_ATTR_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_PHYLOGENY_DATE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_PHYLOGENY_DESCRIPTION - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_PHYLOGENY_ID - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_PHYLOGENY_ID_ATTR_PROVIDER - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_PHYLOGENY_ID_VALUE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_PIE_CAPTION - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_PIE_CHART_LABEL - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_PIE_CHART_LABEL_CAPTION_LINK_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_PIE_CHART_LABEL_CAPTION_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_PIE_CHART_LABEL_INTERNAL_LINES - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_PIE_CHART_LABEL_NULL_LINES - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_PIE_CHART_LABEL_SHOW_TITLE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_PIE_COLOR - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_PROPERTY - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_PROPERTY_ATTR_APPLIES_TO - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_PROPERTY_ATTR_ID_REF - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_PROPERTY_ATTR_UNIT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_REFERENCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_REFERENCE_ATTR_DOI - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_REFERENCE_DESC - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_REFERENCE_VALUE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SCALE_BAR - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_SCALE_BAR_ALIGN - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_SCALE_BAR_INCREASING - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_SCALE_BAR_LONG_INTERVAL - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_SCALE_BAR_SMALL_INTERVAL - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_SCALE_BAR_START_LEFT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_SCALE_BAR_TREE_DISTANCE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_SEQ_REL - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQ_REL_ATTR_DISTANCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQ_REL_ATTR_IDREF0 - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQ_REL_ATTR_IDREF1 - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQ_REL_ATTR_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQ_REL_CONFIDENCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQ_REL_CONFIDENCE_ATTR_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQ_REL_CONFIDENCE_VALUE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQUENCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQUENCE_ACCESSION - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQUENCE_ACCESSION_ATTR_COMMENT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQUENCE_ACCESSION_ATTR_SOURCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQUENCE_ACCESSION_VALUE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQUENCE_ATTR_ID_REF - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQUENCE_ATTR_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQUENCE_COUNT - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants

PREDICATE_SEQUENCE_CROSS_REFERENCES - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQUENCE_CROSS_REFERENCES_ACCESSION - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQUENCE_CROSS_REFERENCES_ACCESSION_ATTR_COMMENT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQUENCE_CROSS_REFERENCES_ACCESSION_ATTR_SOURCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQUENCE_CROSS_REFERENCES_ACCESSION_VALUE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQUENCE_GENE_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQUENCE_LOCATION - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQUENCE_MOL_SEQ - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQUENCE_MOL_SEQ_ATTR_IS_ALIGNED - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQUENCE_MOL_SEQ_VALUE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQUENCE_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQUENCE_SYMBOL - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQUENCE_URI - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQUENCE_URI_ATTR_DESC - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQUENCE_URI_ATTR_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_SEQUENCE_URI_VALUE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_TAXONOMY - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_TAXONOMY_AUTHORITY - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_TAXONOMY_CODE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_TAXONOMY_COMMON_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_TAXONOMY_ID - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_TAXONOMY_ID_ATTR_PROVIDER - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_TAXONOMY_ID_VALUE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_TAXONOMY_RANK - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_TAXONOMY_SCIENTIFIC_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_TAXONOMY_SYNONYM - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_TAXONOMY_URI - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_TAXONOMY_URI_ATTR_DESC - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_TAXONOMY_URI_ATTR_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_TAXONOMY_URI_VALUE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_TEXT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_TEXT_COLOR - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_TEXT_HEIGHT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_TEXT_LABEL - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_TEXT_STYLE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

PREDICATE_WIDTH - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

PREDICATE_WIDTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants

predicateByKey(String) - Method in class info.bioinfweb.jphyloio.formats.newick.NHXUtils

Returns the PhyloXML predicate associated with the specified NHX key.

PREMATURE_NAME_END_CHARACTER - Static variable in interface info.bioinfweb.jphyloio.formats.phylip.PhylipConstants

processEvent(JPhyloIOEventReader, JPhyloIOEvent) - Method in interface info.bioinfweb.jphyloio.push.JPhyloIOEventListener

Called after an event was received from a reader instance.

processIDs(NeXMLReaderStreamDataProvider, String[], QName) - Method in class info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractIDLinkSetElementReader

processIDs(NeXMLReaderStreamDataProvider, String[], QName) - Method in class info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractSetElementReader

Method that is called to process a list of IDs that has been found in an according attribute of the tag processed by this instance.

processLabel(String, boolean) - Method in class info.bioinfweb.jphyloio.formats.newick.DefaultNewickReaderNodeLabelProcessor

processLabel(String, boolean) - Method in interface info.bioinfweb.jphyloio.formats.newick.NewickReaderNodeLabelProcessor

Processes a label according to the format modeled by this implementation.

processLabel(String, boolean) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees.NexusNewickReaderNodeLabelProcessor

processLiteralContent(LiteralMetadataContentEvent, ObjectTranslator<?>, QName) - Method in class info.bioinfweb.jphyloio.formats.phyloxml.receivers.PhyloXMLMetaDataReceiver

processSubcommand(KeyValueInformation) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.AbstractKeyValueCommandReader

Inherited classes should implement this method by adding one or more events to the queue, which have been generated from the specified key value pair.

processSubcommand(KeyValueInformation) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.all.LinkReader

processSubcommand(KeyValueInformation) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.DimensionsReader

processSubcommand(KeyValueInformation) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.FormatReader

PropertyOwner - Enum in info.bioinfweb.jphyloio.formats.phyloxml

This enum is used by PhyloXMLEventWriter to give data receivers information about the data element the contents of a meta event belong to.

putDefaultBlockID(String, String) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.all.BlockTitleToIDMap

putElementReader(XMLElementReaderKey, XMLElementReader<P>) - Method in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader

putID(String, String, String) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.all.BlockTitleToIDMap

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