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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