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 JPhyloIOEventReaders 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 NumberFormatExceptions as InvalidObjectSourceDataExceptions.

NumericValueTranslator() - Constructor for class info.bioinfweb.jphyloio.objecttranslation.implementations.NumericValueTranslator

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