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

## N

NAME_DELIMITER - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants
NAME_START_CHAR - Static variable in interface info.bioinfweb.jphyloio.formats.fasta.FASTAConstants
NAMESPACE_RDF - Static variable in class info.bioinfweb.jphyloio.formats.xml.XMLReadWriteUtils
NAMESPACE_URI - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
NEWICK_DATA_TYPE_NAMESPACE - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants
NEWICK_FORMAT_ID - Static variable in interface info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs
NEWICK_FORMAT_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants
NEWICK_NAMESPACE_PREFIX - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants
NewickConstants - Interface in info.bioinfweb.jphyloio.formats.newick
NewickEventReader - Class in info.bioinfweb.jphyloio.formats.newick
  Reads tree files in Newick format.
NewickEventReader(BufferedReader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.newick.NewickEventReader
  Creates a new instance of this class.
NewickEventReader(File, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.newick.NewickEventReader
  Creates a new instance of this class.
NewickEventReader(InputStream, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.newick.NewickEventReader
  Creates a new instance of this class.
NewickEventReader(Reader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.newick.NewickEventReader
  Creates a new instance of this class.
NewickEventWriter - Class in info.bioinfweb.jphyloio.formats.newick
  Event writer for the Newick format.
NewickEventWriter() - Constructor for class info.bioinfweb.jphyloio.formats.newick.NewickEventWriter
NewickFactory - Class in info.bioinfweb.jphyloio.formats.newick
  Reader and writer factory for the Newick format.
NewickFactory() - Constructor for class info.bioinfweb.jphyloio.formats.newick.NewickFactory
NewickNodeEdgeEventReceiver<E extends JPhyloIOEvent> - Class in info.bioinfweb.jphyloio.formats.newick
NewickNodeEdgeEventReceiver(TextWriterStreamDataProvider<?>, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.newick.NewickNodeEdgeEventReceiver
NewickReaderNodeLabelProcessor - Interface in info.bioinfweb.jphyloio.formats.newick
  Classes implementing this interface are used to modify a node label read from a Newick string (e.g., by using information from a taxon list or translation table.)
NewickScanner - Class in info.bioinfweb.jphyloio.formats.newick
  Reads Newick tokens from a stream.
NewickScanner(PeekReader, boolean) - Constructor for class info.bioinfweb.jphyloio.formats.newick.NewickScanner
  Creates a new instance of this class.
NewickStringReader - Class in info.bioinfweb.jphyloio.formats.newick
  Implementation to read Newick tree definitions to be used by `NewickEventReader` and `TreeReader`.
NewickStringReader(TextReaderStreamDataProvider<?>, String, String, NewickReaderNodeLabelProcessor, boolean) - Constructor for class info.bioinfweb.jphyloio.formats.newick.NewickStringReader
  Creates a new instance of this class.
NewickStringWriter - Class in info.bioinfweb.jphyloio.formats.newick
  Implementation to write Newick tree definitions to be used by `NewickEventWriter` and `NexusEventWriter`.
NewickStringWriter(TextWriterStreamDataProvider<?>, TreeNetworkDataAdapter, NewickWriterNodeLabelProcessor, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.newick.NewickStringWriter
  Creates a new instance of this class.
NewickToken - Class in info.bioinfweb.jphyloio.formats.newick
NewickToken(NewickTokenType, StreamLocationProvider) - Constructor for class info.bioinfweb.jphyloio.formats.newick.NewickToken
NewickToken(StreamLocationProvider, String, boolean) - Constructor for class info.bioinfweb.jphyloio.formats.newick.NewickToken
NewickToken(StreamLocationProvider, double) - Constructor for class info.bioinfweb.jphyloio.formats.newick.NewickToken
NewickTokenType - Enum in info.bioinfweb.jphyloio.formats.newick
NewickUtils - Class in info.bioinfweb.jphyloio.formats.newick
NewickUtils() - Constructor for class info.bioinfweb.jphyloio.formats.newick.NewickUtils
NewickUtils.ReadElement - Class in info.bioinfweb.jphyloio.formats.newick
NewickWriterNodeLabelProcessor - Interface in info.bioinfweb.jphyloio.formats.newick
  Classes implementing this interface are used to create a node label to be written to a Newick string from its event.
newInstance(JPhyloIOEventReceiver, JPhyloIOEvent, JPhyloIOEvent) - Static method in exception info.bioinfweb.jphyloio.exception.IllegalEventException
  Tool method that creates a new instance of this class.
newJPhyloIOInstance() - Static method in class info.bioinfweb.jphyloio.formats.nexus.blockhandlers.NexusBlockHandlerMap
  Returns a new instance of this class, already containing all block handlers available in the core module of JPhyloIO.
newJPhyloIOInstance() - Static method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.NexusCommandReaderFactory
  Returns a new instance of this class, already containing all command readers available in the core module of JPhyloIO.
NEXML_DEFAULT_NAMESPACE_PREFIX - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
NEXML_FORMAT_ID - Static variable in interface info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs
NEXML_FORMAT_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
NEXML_NAMESPACE - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
NEXML_NAMESPACE_PREFIX - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
NEXML_PREDICATE_NAMESPACE - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
NEXML_VERSION - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
NeXMLAttributeMetadataReceiver - Class in info.bioinfweb.jphyloio.formats.nexml.receivers
  Receiver that is used to store the contents of metadata events with certain predicates in a map to be written as attribute/value pairs later on.
NeXMLAttributeMetadataReceiver(NeXMLWriterStreamDataProvider, ReadWriteParameterMap, QName...) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLAttributeMetadataReceiver
NeXMLCharacterSetEventReceiver - Class in info.bioinfweb.jphyloio.formats.nexml.receivers
  Receiver that ensures no other events than character set intervals are contained in a character set.
NeXMLCharacterSetEventReceiver(NeXMLWriterStreamDataProvider, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLCharacterSetEventReceiver
NeXMLCollectCharSetDataReceiver - Class in info.bioinfweb.jphyloio.formats.nexml.receivers
  Receiver that collects the IDs of character set elements.
NeXMLCollectCharSetDataReceiver(NeXMLWriterStreamDataProvider, ReadWriteParameterMap, String) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLCollectCharSetDataReceiver
NeXMLCollectNamespaceReceiver - Class in info.bioinfweb.jphyloio.formats.nexml.receivers
  Receiver that collects namespace definitions occurring in document metadata by calling the according methods of the `AbstractNeXMLDataReceiverMixin`.
NeXMLCollectNamespaceReceiver(NeXMLWriterStreamDataProvider, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLCollectNamespaceReceiver
NeXMLCollectSequenceDataReceiver - Class in info.bioinfweb.jphyloio.formats.nexml.receivers
  Receiver that collects information about the sequence tokens contained in a document.
NeXMLCollectSequenceDataReceiver(NeXMLWriterStreamDataProvider, ReadWriteParameterMap, boolean) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLCollectSequenceDataReceiver
NeXMLCollectSetMetadataReceiver - Class in info.bioinfweb.jphyloio.formats.nexml.receivers
  Receiver that collects information about sets contained in a document.
NeXMLCollectSetMetadataReceiver(NeXMLWriterStreamDataProvider, ReadWriteParameterMap, String, boolean) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLCollectSetMetadataReceiver
NeXMLCollectTokenSetDefinitionDataReceiver - Class in info.bioinfweb.jphyloio.formats.nexml.receivers
  Receiver that is used to check the contents of a token set.
NeXMLCollectTokenSetDefinitionDataReceiver(NeXMLWriterStreamDataProvider, ReadWriteParameterMap, String) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLCollectTokenSetDefinitionDataReceiver
NeXMLConstants - Interface in info.bioinfweb.jphyloio.formats.nexml
  Defines constants necessary to read and write NeXML files.
NeXMLEventReader - Class in info.bioinfweb.jphyloio.formats.nexml
  An event reader for the NeXML format.
NeXMLEventReader(InputStream, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.NeXMLEventReader
NeXMLEventReader(Reader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.NeXMLEventReader
NeXMLEventReader(XMLEventReader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.NeXMLEventReader
NeXMLEventReader(File, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.NeXMLEventReader
NeXMLEventWriter - Class in info.bioinfweb.jphyloio.formats.nexml
  Event based writer for the NeXML format.
NeXMLEventWriter() - Constructor for class info.bioinfweb.jphyloio.formats.nexml.NeXMLEventWriter
NeXMLFactory - Class in info.bioinfweb.jphyloio.formats.nexml
  Reader and writer factory for the NeXML format.
NeXMLFactory() - Constructor for class info.bioinfweb.jphyloio.formats.nexml.NeXMLFactory
NeXMLHandleSequenceDataReceiver - Class in info.bioinfweb.jphyloio.formats.nexml.receivers
  General implementation of a receiver that processes sequence tokens.
NeXMLHandleSequenceDataReceiver(NeXMLWriterStreamDataProvider, ReadWriteParameterMap, boolean) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLHandleSequenceDataReceiver
NeXMLIgnoreCertainMetadataReceiver - Class in info.bioinfweb.jphyloio.formats.nexml.receivers
  Receiver that is able to ignore metadata events with certain predicates, e.g.
NeXMLIgnoreCertainMetadataReceiver(NeXMLWriterStreamDataProvider, ReadWriteParameterMap, boolean, QName...) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLIgnoreCertainMetadataReceiver
  Creates a new instance of this class.
NeXMLMetaDataReceiver - Class in info.bioinfweb.jphyloio.formats.nexml.receivers
  This receiver should be used if no other elements than meta are expected under an element.
NeXMLMetaDataReceiver(NeXMLWriterStreamDataProvider, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLMetaDataReceiver
NeXMLMetaEndElementReader - Class in info.bioinfweb.jphyloio.formats.nexml.elementreader
  Abstract element reader that processes end elements of NeXML meta tags.
NeXMLMetaEndElementReader() - Constructor for class info.bioinfweb.jphyloio.formats.nexml.elementreader.NeXMLMetaEndElementReader
NeXMLMetaStartElementReader - Class in info.bioinfweb.jphyloio.formats.nexml.elementreader
  Abstract element reader that processes start elements of NeXML meta tags.
NeXMLMetaStartElementReader() - Constructor for class info.bioinfweb.jphyloio.formats.nexml.elementreader.NeXMLMetaStartElementReader
NeXMLMolecularDataTokenDefinitionReceiver - Class in info.bioinfweb.jphyloio.formats.nexml.receivers
  Receiver that writes token definitions for molecular data, such as DNA, RNA or protein sequences.
NeXMLMolecularDataTokenDefinitionReceiver(NeXMLWriterStreamDataProvider, ReadWriteParameterMap, String) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLMolecularDataTokenDefinitionReceiver
NeXMLOnlyWriteMetaDataReceiver - Class in info.bioinfweb.jphyloio.formats.nexml.receivers
  Receiver that writes meta data but ignores other events that were processed previously.
NeXMLOnlyWriteMetaDataReceiver(NeXMLWriterStreamDataProvider, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLOnlyWriteMetaDataReceiver
NeXMLPredicateMetaReceiver - Class in info.bioinfweb.jphyloio.formats.nexml.receivers
  General implementation of a receiver that allows to process metadata events with certain predicates in a special way.
NeXMLPredicateMetaReceiver(NeXMLWriterStreamDataProvider, ReadWriteParameterMap, QName...) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLPredicateMetaReceiver
  Creates a new instance of this class.
NeXMLReaderStreamDataProvider - Class in info.bioinfweb.jphyloio.formats.nexml
  Stores data that shall be shared among different implementations of `AbstractNeXMLElementReader` reading from the same document.
NeXMLReaderStreamDataProvider(NeXMLEventReader) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider
NeXMLReaderTokenSetInformation - Class in info.bioinfweb.jphyloio.formats.nexml
  Class that is used by `NeXMLEventReader` to store information about a token set.
NeXMLReaderTokenSetInformation(String, String, CharacterStateSetType) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderTokenSetInformation
NeXMLSequenceTokensReceiver - Class in info.bioinfweb.jphyloio.formats.nexml.receivers
  Receiver that is used to write sequence tokens.
NeXMLSequenceTokensReceiver(NeXMLWriterStreamDataProvider, ReadWriteParameterMap, boolean) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLSequenceTokensReceiver
NeXMLSetEndElementReader - Class in info.bioinfweb.jphyloio.formats.nexml.elementreader
  Abstract element reader that processes end elements of NeXML set tags.
NeXMLSetEndElementReader(EventContentType) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.elementreader.NeXMLSetEndElementReader
NeXMLSingleTokenDefinitionInformation - Class in info.bioinfweb.jphyloio.formats.nexml
  Class that is used by `NeXMLEventReader` to store information about a single token definition.
NeXMLSingleTokenDefinitionInformation(String, String, String, Collection<String>) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.NeXMLSingleTokenDefinitionInformation
NeXMLStartDocumentElementReader - Class in info.bioinfweb.jphyloio.formats.nexml.elementreader
  This element reader implements reading the start of a NeXML document.
NeXMLStartDocumentElementReader() - Constructor for class info.bioinfweb.jphyloio.formats.nexml.elementreader.NeXMLStartDocumentElementReader
NeXMLTokenSetEventReceiver - Class in info.bioinfweb.jphyloio.formats.nexml.receivers
  Receiver that is used to write token sets.
NeXMLTokenSetEventReceiver(NeXMLWriterStreamDataProvider, ReadWriteParameterMap, String) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLTokenSetEventReceiver
NeXMLWriterAlignmentInformation - Class in info.bioinfweb.jphyloio.formats.nexml
  Class that is used by `NeXMLEventWriter` to store information about an alignment.
NeXMLWriterAlignmentInformation() - Constructor for class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterAlignmentInformation
NeXMLWriterStreamDataProvider - Class in info.bioinfweb.jphyloio.formats.nexml
  Stores data that shall be shared among different implementations of `AbstractNeXMLDataReceiver` and the writer instance that uses them.
NeXMLWriterStreamDataProvider(NeXMLEventWriter) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
NeXMLWriterTokenSetInformation - Class in info.bioinfweb.jphyloio.formats.nexml
  Class that is used by `NeXMLEventWriter` to store information about a token set.
NeXMLWriterTokenSetInformation() - Constructor for class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterTokenSetInformation
next() - Method in class info.bioinfweb.jphyloio.AbstractEventReader
next() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLEventReader
next() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
next() - Method in interface info.bioinfweb.jphyloio.JPhyloIOEventReader
  Returns the next event from the underlying document and moves one step forward.
nextCharID() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider
  Returns the next NeXML columns ID (ID of a `char` tag) at the current position of the underlying iterator and stores it in the property `NeXMLReaderStreamDataProvider.getCurrentExpectedCharID()`.
nextEvent() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLEventReader
nextOfType(Set<EventType>) - Method in class info.bioinfweb.jphyloio.AbstractEventReader
nextOfType(Set<EventType>) - Method in interface info.bioinfweb.jphyloio.JPhyloIOEventReader
  Reads elements from the underlying stream until one of the specified is found or the end of the document is reached.
nextTag() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLEventReader
nextTag() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
nextToken() - Method in class info.bioinfweb.jphyloio.formats.newick.NewickScanner
NEXUS_FORMAT_ID - Static variable in interface info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs
NEXUS_FORMAT_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
NEXUS_NAMESPACE_PREFIX - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
NEXUS_PREDICATE_NAMESPACE - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
NexusBlockHandler - Interface in info.bioinfweb.jphyloio.formats.nexus.blockhandlers
  A Nexus block handler implements methods that shall be executed by `NexusEventReader` each time an according block `BEGIN` or `END` command is read.
NexusBlockHandlerMap - Class in info.bioinfweb.jphyloio.formats.nexus.blockhandlers
  Manages Nexus block handlers for an instance of `NexusEventReader`.
NexusBlockHandlerMap() - Constructor for class info.bioinfweb.jphyloio.formats.nexus.blockhandlers.NexusBlockHandlerMap
  Creates a new empty instance of this class.
NexusCommandEventReader - Interface in info.bioinfweb.jphyloio.formats.nexus.commandreaders
  Interface to be implement by all classes and parse a single Nexus command and convert its contents into JPhyloIO events.
NexusCommandReaderFactory - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders
  A factory class that creates instance of `NexusCommandEventReader`.
NexusCommandReaderFactory() - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.NexusCommandReaderFactory
  Creates a new empty instance of this class.
NexusConstants - Interface in info.bioinfweb.jphyloio.formats.nexus
  Defines constants necessary to read and write Nexus files.
NexusEventReader - Class in info.bioinfweb.jphyloio.formats.nexus
  Event based reader for Nexus files.
NexusEventReader(File, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.NexusEventReader
  Creates a new instance of this class with a default block handler map and command reader factory.
NexusEventReader(InputStream, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.NexusEventReader
  Creates a new instance of this class.
NexusEventReader(PeekReader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.NexusEventReader
  Creates a new instance of this class with a default block handler map and command reader factory.
NexusEventReader(Reader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.NexusEventReader
  Creates a new instance of this class with a default block handler map and command reader factory.
NexusEventWriter - Class in info.bioinfweb.jphyloio.formats.nexus
  Event based writer for the Nexus format.
NexusEventWriter() - Constructor for class info.bioinfweb.jphyloio.formats.nexus.NexusEventWriter
NexusFactory - Class in info.bioinfweb.jphyloio.formats.nexus
  Reader and writer factory for the Nexus format.
NexusFactory() - Constructor for class info.bioinfweb.jphyloio.formats.nexus.NexusFactory
NexusMatrixWriteResult - Enum in info.bioinfweb.jphyloio.formats.nexus
NexusNewickReaderNodeLabelProcessor - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees
NexusNewickReaderNodeLabelProcessor(NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees.NexusNewickReaderNodeLabelProcessor
NexusNewickWriterNodeLabelProcessor - Class in info.bioinfweb.jphyloio.formats.nexus
  The node label processor used by `NexusEventWriter`.
NexusNewickWriterNodeLabelProcessor(OTUListDataAdapter, Map<String, Long>, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.NexusNewickWriterNodeLabelProcessor
NexusReaderStreamDataProvider - Class in info.bioinfweb.jphyloio.formats.nexus
  Stores data that shall be shared among different implementations of `NexusCommandEventReader` reading from the same document.
NexusReaderStreamDataProvider(NexusEventReader) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider
NexusTranslationTable - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees
  Stores the content of a translation table in a Nexus TREES block.
NexusTranslationTable() - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees.NexusTranslationTable
NexusWriterStreamDataProvider - Class in info.bioinfweb.jphyloio.formats.nexus
NexusWriterStreamDataProvider(NexusEventWriter) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.NexusWriterStreamDataProvider
NHX_KEY_CONFIDENCE - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants
NHX_KEY_EVENT - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants
NHX_KEY_GENE_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants
NHX_KEY_PREFIX - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants
NHX_KEY_SCIENTIFIC_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants
NHX_KEY_SEQUENCE_ACCESSION - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants
NHX_KEY_TAXONOMY_ID - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants
NHX_START - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants
NHX_VALUE_SEPARATOR_SYMBOL - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants
NHXUtils - Class in info.bioinfweb.jphyloio.formats.newick
  Tool method for working with NHX annotation on Newick strings.
NO_METADATA - Static variable in class info.bioinfweb.jphyloio.formatinfo.MetadataModeling
NoCharDefsNoSetsMatrixDataAdapter - Class in info.bioinfweb.jphyloio.dataadapters.implementations
  Abstract implementation of `MatrixDataAdapter`, which returns empty object list adapters for `NoCharDefsNoSetsMatrixDataAdapter.getCharacterDefinitions(ReadWriteParameterMap)`, `NoCharDefsNoSetsMatrixDataAdapter.getTokenSets(ReadWriteParameterMap)`, `NoCharDefsNoSetsMatrixDataAdapter.getSequenceSets(ReadWriteParameterMap)`, `NoCharDefsNoSetsMatrixDataAdapter.getCharacterSets(ReadWriteParameterMap)`.
NoCharDefsNoSetsMatrixDataAdapter() - Constructor for class info.bioinfweb.jphyloio.dataadapters.implementations.NoCharDefsNoSetsMatrixDataAdapter
NodeEdgeInfo - Class in info.bioinfweb.jphyloio.formats
  This class is used by `JPhyloIOEventReader`s processing phylogenetic trees or networks to model nodes and edges.
NodeEdgeInfo(String, double, Collection<JPhyloIOEvent>, Collection<JPhyloIOEvent>) - Constructor for class info.bioinfweb.jphyloio.formats.NodeEdgeInfo
NodeEvent - Class in info.bioinfweb.jphyloio.events
  Event indicating a node in a tree or network.
NodeEvent(String, String, String, boolean) - Constructor for class info.bioinfweb.jphyloio.events.NodeEvent
NoEditUniqueLabelHandler() - Constructor for class info.bioinfweb.jphyloio.AbstractEventWriter.NoEditUniqueLabelHandler
NoSetsTreeNetworkDataAdapter - Class in info.bioinfweb.jphyloio.dataadapters.implementations
  Abstract implementation of `TreeNetworkDataAdapter`, which returns an empty object list adapter for `NoSetsTreeNetworkDataAdapter.getNodeEdgeSets(ReadWriteParameterMap)`.
NoSetsTreeNetworkDataAdapter() - Constructor for class info.bioinfweb.jphyloio.dataadapters.implementations.NoSetsTreeNetworkDataAdapter
NoSetsTreeNetworkGroupDataAdapter - Class in info.bioinfweb.jphyloio.dataadapters.implementations
  Abstract implementation of `TreeNetworkGroupDataAdapter`, which returns an empty object list adapter for `NoSetsTreeNetworkGroupDataAdapter.getTreeSets(ReadWriteParameterMap)`.
NoSetsTreeNetworkGroupDataAdapter() - Constructor for class info.bioinfweb.jphyloio.dataadapters.implementations.NoSetsTreeNetworkGroupDataAdapter
NumericValueTranslator<O extends java.lang.Number> - Class in info.bioinfweb.jphyloio.objecttranslation.implementations
  Abstract base class for converting numeric types that wrappes `NumberFormatException`s as `InvalidObjectSourceDataException`s.
NumericValueTranslator() - Constructor for class info.bioinfweb.jphyloio.objecttranslation.implementations.NumericValueTranslator

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