Uses of Interface
info.bioinfweb.jphyloio.ReadWriteConstants

Packages that use ReadWriteConstants

Package	Description
info.bioinfweb.jphyloio	The main package of JPhyloIO.
info.bioinfweb.jphyloio.formats.fasta	Contains classes for reading from and writing to streams/files in FASTA format.
info.bioinfweb.jphyloio.formats.mega	Contains classes for reading from and writing to streams/files in MEGA format.
info.bioinfweb.jphyloio.formats.newick	Contains classes for reading from and writing to streams/files in Newick tree format.
info.bioinfweb.jphyloio.formats.nexml	Contains classes for reading from and writing to streams/files in NeXML format.
info.bioinfweb.jphyloio.formats.nexml.elementreader	Contains implementations of XMLElementReader used by NeXMLEventReader.
info.bioinfweb.jphyloio.formats.nexus	Contains classes for reading from and writing to streams/files in Nexus format.
info.bioinfweb.jphyloio.formats.nexus.blockhandlers	Contains implementations of NexusCommandEventReader for commands that are valid in all Nexus blocks.
info.bioinfweb.jphyloio.formats.nexus.commandreaders.all	Contains implementations of NexusCommandEventReader for commands that are valid in all Nexus blocks.
info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters	Contains classes for reading Nexus commands in a CHARACTERS, UNALIGNED or DATA block.
info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets	Contains classes for reading Nexus commands in a SETS block.
info.bioinfweb.jphyloio.formats.nexus.commandreaders.taxa	Contains classes for reading Nexus commands in a TAXA block.
info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees	Contains classes for reading Nexus commands in a TREES block.
info.bioinfweb.jphyloio.formats.pde	Contains classes for reading from streams/files in PDE format.
info.bioinfweb.jphyloio.formats.phylip	Contains classes for reading from and writing to streams/files in Phylip format.
info.bioinfweb.jphyloio.formats.phyloxml	Contains classes for reading from and writing to streams/files in PhyloXML format.
info.bioinfweb.jphyloio.formats.text	Contains classes implementing shared functionality for reading from and writing to streams/files in text formats.
info.bioinfweb.jphyloio.formats.xml	Contains classes implementing shared functionality for reading from and writing to streams/files in XML formats.
info.bioinfweb.jphyloio.formats.xtg	Contains classes for reading from and writing to streams/files in XTG format.
info.bioinfweb.jphyloio.objecttranslation	Contains classes used by readers and writers that convert between (complex) Java objects and their text or XML representation.

Uses of ReadWriteConstants in info.bioinfweb.jphyloio

Classes in info.bioinfweb.jphyloio that implement ReadWriteConstants

Modifier and Type	Class and Description
class	AbstractEventReader<P extends ReaderStreamDataProvider<? extends AbstractEventReader<P>>> Basic implementation for event readers in PhyloIO.

Uses of ReadWriteConstants in info.bioinfweb.jphyloio.formats.fasta

Classes in info.bioinfweb.jphyloio.formats.fasta that implement ReadWriteConstants

Modifier and Type	Class and Description
class	FASTAEventReader Event based reader for FASTA alignment files.

Uses of ReadWriteConstants in info.bioinfweb.jphyloio.formats.mega

Classes in info.bioinfweb.jphyloio.formats.mega that implement ReadWriteConstants

Modifier and Type	Class and Description
class	MEGAEventReader Event based reader for MEGA alignment files.

Uses of ReadWriteConstants in info.bioinfweb.jphyloio.formats.newick

Classes in info.bioinfweb.jphyloio.formats.newick that implement ReadWriteConstants

Modifier and Type	Class and Description
class	HotCommentDataReader Reads meta information from a hot comment in a Newick string like it is generated by MrBayes or BEAST.
class	NewickEventReader Reads tree files in Newick format.
class	NewickStringReader Implementation to read Newick tree definitions to be used by NewickEventReader and TreeReader.
class	NHXUtils Tool method for working with NHX annotation on Newick strings.

Uses of ReadWriteConstants in info.bioinfweb.jphyloio.formats.nexml

Classes in info.bioinfweb.jphyloio.formats.nexml that implement ReadWriteConstants

Modifier and Type	Class and Description
class	NeXMLEventReader An event reader for the NeXML format.

Uses of ReadWriteConstants in info.bioinfweb.jphyloio.formats.nexml.elementreader

Classes in info.bioinfweb.jphyloio.formats.nexml.elementreader that implement ReadWriteConstants

Modifier and Type	Class and Description
class	AbstractIDLinkSetElementReader Element reader for NeXML sets that are represented as a sequence of EventContentType.SET_ELEMENT events.
class	AbstractNeXMLElementReader Processes a NeXML tag without any of its subelements.
class	AbstractSetElementReader Abstract element reader that processes NeXML set tags that contain one or more attributes of the type xs:IDREFS.
class	NeXMLMetaEndElementReader Abstract element reader that processes end elements of NeXML meta tags.
class	NeXMLMetaStartElementReader Abstract element reader that processes start elements of NeXML meta tags.
class	NeXMLSetEndElementReader Abstract element reader that processes end elements of NeXML set tags.

Uses of ReadWriteConstants in info.bioinfweb.jphyloio.formats.nexus

Classes in info.bioinfweb.jphyloio.formats.nexus that implement ReadWriteConstants

Modifier and Type	Class and Description
class	NexusEventReader Event based reader for Nexus files.

Uses of ReadWriteConstants in info.bioinfweb.jphyloio.formats.nexus.blockhandlers

Classes in info.bioinfweb.jphyloio.formats.nexus.blockhandlers that implement ReadWriteConstants

Modifier and Type	Class and Description
class	CharactersDataUnalignedBlockHandler A Nexus block handler to read sequence data from the CHARACTERS, DATA or UNALIGNED blocks.
class	ENewickNetworksBlockHandler A Nexus block handler to read phylogenetic networks from a NETWORK block containing network definitions in the eNewick format.
class	TreesBlockHandler

Uses of ReadWriteConstants in info.bioinfweb.jphyloio.formats.nexus.commandreaders.all

Classes in info.bioinfweb.jphyloio.formats.nexus.commandreaders.all that implement ReadWriteConstants

Modifier and Type	Class and Description
class	TitleReader Reads the TITLE command of a Nexus block and stores the title in the shared information map of the stream data provider under the key NexusReaderStreamDataProvider.INFO_KEY_BLOCK_TITLE.

Uses of ReadWriteConstants in info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters

Classes in info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters that implement ReadWriteConstants

Modifier and Type	Class and Description
class	AbstractCharLabelsReader Implements shared functionality for Nexus command readers that process character (alignment column) definitions.
class	CharLabelsReader Nexus reader for the CHARLABELS command that produces CharacterDefinitionEvents.
class	CharStateLabelsReader Nexus reader for the CHARSTATELABELS command that produces CharacterDefinitionEvents.
class	DimensionsReader
class	FormatReader Parser for the Format command in a Characters, Unaligned or Data block.
class	MatrixReader Parser for the MATRIX command in a CHARACTERS, UNALIGNED or DATA block.

Uses of ReadWriteConstants in info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets

Classes in info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets that implement ReadWriteConstants

Modifier and Type	Class and Description
class	AbstractNexusSetReader General reader implementation to read the Nexus commands that define different kinds of sets.
class	CharSetReader Parser for the CHARSET command in the SETS block.
class	IDBasedSetsReader Base class for all Nexus readers that create set event streams that consist of SetElementEvents.
class	TaxSetReader
class	TreeSetReader

Uses of ReadWriteConstants in info.bioinfweb.jphyloio.formats.nexus.commandreaders.taxa

Classes in info.bioinfweb.jphyloio.formats.nexus.commandreaders.taxa that implement ReadWriteConstants

Modifier and Type	Class and Description
class	TaxLabelsReader

Uses of ReadWriteConstants in info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees

Classes in info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees that implement ReadWriteConstants

Modifier and Type	Class and Description
class	ENewickNetworkReader Nexus command reader for the custom NETWORK command.
class	TranslateReader
class	TreeReader

Uses of ReadWriteConstants in info.bioinfweb.jphyloio.formats.pde

Classes in info.bioinfweb.jphyloio.formats.pde that implement ReadWriteConstants

Modifier and Type	Class and Description
class	PDEEventReader Event reader for the PDE format used by the alignment editor PhyDE.

Uses of ReadWriteConstants in info.bioinfweb.jphyloio.formats.phylip

Classes in info.bioinfweb.jphyloio.formats.phylip that implement ReadWriteConstants

Modifier and Type	Class and Description
class	AbstractPhylipEventReader<P extends TextReaderStreamDataProvider<? extends AbstractPhylipEventReader<P>>> Implements shared functionality of Phylip event readers.
class	PhylipEventReader Event based reader for Phylip alignment files.
class	SequentialPhylipEventReader Event based reader for sequential Phylip alignment files.

Uses of ReadWriteConstants in info.bioinfweb.jphyloio.formats.phyloxml

Classes in info.bioinfweb.jphyloio.formats.phyloxml that implement ReadWriteConstants

Modifier and Type	Class and Description
class	PhyloXMLEventReader Event reader for the PhyloXML format.

Uses of ReadWriteConstants in info.bioinfweb.jphyloio.formats.text

Classes in info.bioinfweb.jphyloio.formats.text that implement ReadWriteConstants

Modifier and Type	Class and Description
class	AbstractTextEventReader<P extends TextReaderStreamDataProvider<? extends AbstractTextEventReader<P>>> Abstract base class for all readers that read their data from a file using a PeekReader.

Uses of ReadWriteConstants in info.bioinfweb.jphyloio.formats.xml

Classes in info.bioinfweb.jphyloio.formats.xml that implement ReadWriteConstants

Modifier and Type	Class and Description
class	AbstractXMLEventReader<P extends XMLReaderStreamDataProvider<? extends AbstractXMLEventReader<P>>> Implements shared functionality for reading XML formats.

Uses of ReadWriteConstants in info.bioinfweb.jphyloio.formats.xtg

Classes in info.bioinfweb.jphyloio.formats.xtg that implement ReadWriteConstants

Modifier and Type	Class and Description
class	XTGEventReader Event reader for the extensible TreeGraph 2 format (XTG) used by the phylogenetic tree editor TreeGraph 2.

Uses of ReadWriteConstants in info.bioinfweb.jphyloio.objecttranslation

Classes in info.bioinfweb.jphyloio.objecttranslation that implement ReadWriteConstants

Modifier and Type	Class and Description
class	ObjectTranslatorFactory Factory to create instances of ObjectTranslator to be used with readers and writers of JPhyloIO to read and write literal metadata objects.