## 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 `CharacterDefinitionEvent`s.
    `class` | `CharStateLabelsReader` Nexus reader for the `CHARSTATELABELS` command that produces `CharacterDefinitionEvent`s.
    `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 `SetElementEvent`s.
    `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.