All Classes
AbstractCharLabelsReader
AbstractEventReader
AbstractEventWriter
AbstractEventWriter.NoEditUniqueLabelHandler
AbstractEventWriter.UniqueLabelHandler
AbstractIDLinkSetElementReader
AbstractKeyValueCommandReader
AbstractMetaXMLReader
AbstractMetaXMLWriter
AbstractNeXMLDataReceiver
AbstractNeXMLDataReceiverMixin
AbstractNeXMLElementReader
AbstractNeXMLElementReader.LabeledIDEventInformation
AbstractNeXMLElementReader.OTUorOTUsEventInformation
AbstractNexusBlockHandler
AbstractNexusCommandEventReader
AbstractNexusEventReceiver
AbstractNexusSetReader
AbstractNexusSetsEventReceiver
AbstractNexusSetWriter
AbstractObjectTranslator
AbstractPhylipEventReader
AbstractPhylipFactory
AbstractSequenceContentReceiver
AbstractSetElementReader
AbstractSingleMatrixEventWriter
AbstractSingleReaderWriterFactory
AbstractStartStringSingleFactory
AbstractTextEventReader
AbstractTextEventWriter
AbstractXMLDataReceiver
AbstractXMLElementReader
AbstractXMLEventReader
AbstractXMLEventWriter
AbstractXMLFactory
AbstractXMLObjectTranslator
AnnotatedDataAdapter
AttributeInfo
Base64BinaryTranslator
BasicEventReceiver
BasicTextCommentEventReceiver
BigDecimalTranslator
BigIntegerTranslator
BlockTitleToIDMap
BooleanTranslator
BufferedEventInfo
ByteTranslator
CharacterDefinitionEvent
CharactersDataUnalignedBlockHandler
CharacterSetEventReceiver
CharacterSetIntervalEvent
CharLabelsReader
CharSetReader
CharStateLabelsReader
ColorTranslator
CommentElementReader
CommentEvent
ConcreteJPhyloIOEvent
ContinuedEvent
DateTimeTranslator
DateTranslator
DefaultCommandReader
DefaultFormatInfo
DefaultNewickReaderNodeLabelProcessor
DefaultNewickWriterNodeLabelProcessor
DimensionsReader
DocumentDataAdapter
DoubleTranslator
EdgeEvent
ElementDataAdapter
EmptyAnnotatedDataAdapter
EmptyDocumentDataAdapter
EmptyObjectListDataAdapter
ENewickNetworkReader
ENewickNetworksBlockHandler
EnumTranslator
EventContentType
EventForwarder
EventTopologyType
EventType
FASTAConstants
FASTAEventReader
FASTAEventWriter
FASTAFactory
FloatTranslator
FormatReader
HexadecimalColorTranslator
HexBinaryTranslator
HotCommentDataReader
IDBasedSetsReader
IDToNameManager
IllegalArgumentExceptionSimpleValueTranslator
IllegalEventException
InconsistentAdapterDataException
IntegerTranslator
InvalidObjectSourceDataException
JPhyloIO
JPhyloIOContentExtensionFileFilter
JPhyloIOEvent
JPhyloIOEventListener
JPhyloIOEventReader
JPhyloIOEventReceiver
JPhyloIOEventWriter
JPhyloIOFormatIDs
JPhyloIOFormatInfo
JPhyloIOFormatSpecificObject
JPhyloIOReaderException
JPhyloIOReaderWriterFactory
JPhyloIOReadingUtils
JPhyloIOWriterException
JPhyloIOWritingUtils
JPhyloIOXMLEventReader
JPhyloIOXMLEventWriter
KeyValueInformation
LabeledEvent
LabeledIDEvent
LabelEditingReporter
LabelEditingReporter.LabelStatus
LinkedIDEvent
LinkedLabeledIDEvent
LinkReader
ListBasedDocumentDataAdapter
ListTranslator
LiteralContentSequenceType
LiteralMetadataContentEvent
LiteralMetadataEvent
LongTranslator
MatrixDataAdapter
MatrixReader
MEGAConstants
MEGAEventReader
MEGAFactory
MetadataModeling
MetadataTopologyType
MetaXMLEventReader
MetaXMLEventWriter
MetaXMLStreamReader
MetaXMLStreamWriter
NewickConstants
NewickEventReader
NewickEventWriter
NewickFactory
NewickNodeEdgeEventReceiver
NewickReaderNodeLabelProcessor
NewickScanner
NewickStringReader
NewickStringWriter
NewickToken
NewickTokenType
NewickUtils
NewickUtils.ReadElement
NewickWriterNodeLabelProcessor
NeXMLAttributeMetadataReceiver
NeXMLCharacterSetEventReceiver
NeXMLCollectCharSetDataReceiver
NeXMLCollectNamespaceReceiver
NeXMLCollectSequenceDataReceiver
NeXMLCollectSetMetadataReceiver
NeXMLCollectTokenSetDefinitionDataReceiver
NeXMLConstants
NeXMLEventReader
NeXMLEventWriter
NeXMLFactory
NeXMLHandleSequenceDataReceiver
NeXMLIgnoreCertainMetadataReceiver
NeXMLMetaDataReceiver
NeXMLMetaEndElementReader
NeXMLMetaStartElementReader
NeXMLMolecularDataTokenDefinitionReceiver
NeXMLOnlyWriteMetaDataReceiver
NeXMLPredicateMetaReceiver
NeXMLReaderStreamDataProvider
NeXMLReaderTokenSetInformation
NeXMLSequenceTokensReceiver
NeXMLSetEndElementReader
NeXMLSingleTokenDefinitionInformation
NeXMLStartDocumentElementReader
NeXMLTokenSetEventReceiver
NeXMLWriterAlignmentInformation
NeXMLWriterStreamDataProvider
NeXMLWriterTokenSetInformation
NexusBlockHandler
NexusBlockHandlerMap
NexusCommandEventReader
NexusCommandReaderFactory
NexusConstants
NexusEventReader
NexusEventWriter
NexusFactory
NexusMatrixWriteResult
NexusNewickReaderNodeLabelProcessor
NexusNewickWriterNodeLabelProcessor
NexusReaderStreamDataProvider
NexusTranslationTable
NexusWriterStreamDataProvider
NHXUtils
NoCharDefsNoSetsMatrixDataAdapter
NodeEdgeInfo
NodeEvent
NoSetsTreeNetworkDataAdapter
NoSetsTreeNetworkGroupDataAdapter
NumericValueTranslator
ObjectListDataAdapter
ObjectTranslator
ObjectTranslatorFactory
OTUListDataAdapter
ParentEventInformation
PartEndEvent
PDEConstants
PDEEventReader
PDEFactory
PDEMetaColumnDefintion
PDEMetaColumnType
PDEReaderStreamDataProvider
PhylipConstants
PhylipEventReader
PhylipEventWriter
PhylipFactory
PhyloXMLCharactersElementReader
PhyloXMLCollectMetadataDataReceiver
PhyloXMLColorTranslator
PhyloXMLConstants
PhyloXMLEventReader
PhyloXMLEventWriter
PhyloXMLFactory
PhyloXMLMetaDataReceiver
PhyloXMLMetadataTreatment
PhyloXMLMetaEventInfo
PhyloXMLOnlyCustomXMLDataReceiver
PhyloXMLPredicateInfo
PhyloXMLPredicateTreatment
PhyloXMLPrivateConstants
PhyloXMLPropertyMetadataReceiver
PhyloXMLReaderStreamDataProvider
PhyloXMLSpecificPredicatesDataReceiver
PhyloXMLStartDocumentElementReader
PhyloXMLWriterStreamDataProvider
PropertyOwner
QNameTranslator
ReaderStreamDataProvider
ReadWriteConstants
ReadWriteParameterMap
ReadWriteParameterNames
ReferenceOnlySetReceiver
ResourceMetadataEvent
SequenceTokensEvent
SequenceTokensEventManager
SequentialPhylipEventReader
SequentialPhylipFactory
SetElementEvent
ShortTranslator
SimpleValueTranslator
SingleReaderWriterFactory
SingleSequenceTokenEvent
SingleTokenDefinitionEvent
StartDocumentElementReader
StoreAnnotatedDataAdapter
StoreDocumentDataAdapter
StoreMatrixDataAdapter
StoreObjectData
StoreObjectListDataAdapter
StoreOTUListDataAdapter
StoreTreeNetworkDataAdapter
StoreTreeNetworkGroupDataAdapter
StringTranslator
TaxaBlockHandler
TaxLabelsReader
TaxSetReader
TextReaderStreamDataProvider
TextSequenceContentReceiver
TextWriterStreamDataProvider
TimeTranslator
TitleReader
TokenDefinitionLabelHandling
TokenSetDefinitionEvent
TokenSetEventReceiver
TokenTranslationStrategy
TopoplogicalNodeInfo
TranslateReader
TreeNetworkDataAdapter
TreeNetworkGroupDataAdapter
TreeReader
TreesBlockHandler
TreeSetReader
TreeTopologyExtractor
UndefinedOTUListDataAdapter
UnknownCommandEvent
UnsupportedFormatFeatureException
URIOrStringIdentifier
URITranslator
WriterStreamDataProvider
XMLElementReader
XMLElementReaderKey
XMLEndElementReader
XMLNoCharactersAllowedElementReader
XMLReaderStreamDataProvider
XMLReadWriteUtils
XMLStartElementReader
XMLWriterStreamDataProvider
XTGConstants
XTGEventReader
XTGFactory
XTGFormattedTextElementReader