## Uses of Interface
info.bioinfweb.jphyloio.JPhyloIOFormatSpecificObject

- Packages that use JPhyloIOFormatSpecificObject
  Package | Description
  --- | ---
  info.bioinfweb.jphyloio | The main package of JPhyloIO.
  info.bioinfweb.jphyloio.factory | Contains interfaces and general implementations for creating JPhyloIO readers and writers related to `JPhyloIOReaderWriterFactory`.
  info.bioinfweb.jphyloio.formatinfo | Contains `JPhyloIOFormatInfo` and related classes that describe a format supported by 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.nexus | Contains classes for reading from and writing to streams/files in Nexus format.
  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.

- - ### Uses of JPhyloIOFormatSpecificObject in info.bioinfweb.jphyloio

    Subinterfaces of JPhyloIOFormatSpecificObject in info.bioinfweb.jphyloio
    Modifier and Type | Interface and Description
    --- | ---
    `interface` | `JPhyloIOEventReader` This is main JPhyloIO interface to be implemented by all format specific event readers.
    `interface` | `JPhyloIOEventWriter` The main JPhyloIO interface to be implemented by all format specific event writers.

    Classes in info.bioinfweb.jphyloio that implement JPhyloIOFormatSpecificObject
    Modifier and Type | Class and Description
    --- | ---
    `class` | `AbstractEventReader<P extends ReaderStreamDataProvider<? extends AbstractEventReader<P>>>` Basic implementation for event readers in PhyloIO.
    `class` | `AbstractEventWriter<P extends WriterStreamDataProvider<? extends AbstractEventWriter<P>>>` Implements shared functionality for JPhyloIO event writers.
    `class` | `AbstractSingleMatrixEventWriter<P extends TextWriterStreamDataProvider<? extends AbstractTextEventWriter<P>>>` Default implementation for writers that can only write a single matrix (multiple sequence alignment) to their target format, because that format does not support additional data.

  - ### Uses of JPhyloIOFormatSpecificObject in info.bioinfweb.jphyloio.factory

    Classes in info.bioinfweb.jphyloio.factory that implement JPhyloIOFormatSpecificObject
    Modifier and Type | Class and Description
    --- | ---
    `class` | `JPhyloIOContentExtensionFileFilter`

  - ### Uses of JPhyloIOFormatSpecificObject in info.bioinfweb.jphyloio.formatinfo

    Subinterfaces of JPhyloIOFormatSpecificObject in info.bioinfweb.jphyloio.formatinfo
    Modifier and Type | Interface and Description
    --- | ---
    `interface` | `JPhyloIOFormatInfo` Classes implementing this interface provide information about a phylogenetic file format that is supported by JPhyloIO.

    Classes in info.bioinfweb.jphyloio.formatinfo that implement JPhyloIOFormatSpecificObject
    Modifier and Type | Class and Description
    --- | ---
    `class` | `DefaultFormatInfo` Default implementation of `JPhyloIOFormatInfo`.

  - ### Uses of JPhyloIOFormatSpecificObject in info.bioinfweb.jphyloio.formats.fasta

    Classes in info.bioinfweb.jphyloio.formats.fasta that implement JPhyloIOFormatSpecificObject
    Modifier and Type | Class and Description
    --- | ---
    `class` | `FASTAEventReader` Event based reader for FASTA alignment files.
    `class` | `FASTAEventWriter` Event based writer for the FASTA format.

  - ### Uses of JPhyloIOFormatSpecificObject in info.bioinfweb.jphyloio.formats.mega

    Classes in info.bioinfweb.jphyloio.formats.mega that implement JPhyloIOFormatSpecificObject
    Modifier and Type | Class and Description
    --- | ---
    `class` | `MEGAEventReader` Event based reader for MEGA alignment files.

  - ### Uses of JPhyloIOFormatSpecificObject in info.bioinfweb.jphyloio.formats.newick

    Classes in info.bioinfweb.jphyloio.formats.newick that implement JPhyloIOFormatSpecificObject
    Modifier and Type | Class and Description
    --- | ---
    `class` | `NewickEventReader` Reads tree files in Newick format.
    `class` | `NewickEventWriter` Event writer for the Newick format.

  - ### Uses of JPhyloIOFormatSpecificObject in info.bioinfweb.jphyloio.formats.nexml

    Classes in info.bioinfweb.jphyloio.formats.nexml that implement JPhyloIOFormatSpecificObject
    Modifier and Type | Class and Description
    --- | ---
    `class` | `NeXMLEventReader` An event reader for the NeXML format.
    `class` | `NeXMLEventWriter` Event based writer for the NeXML format.

  - ### Uses of JPhyloIOFormatSpecificObject in info.bioinfweb.jphyloio.formats.nexus

    Classes in info.bioinfweb.jphyloio.formats.nexus that implement JPhyloIOFormatSpecificObject
    Modifier and Type | Class and Description
    --- | ---
    `class` | `NexusEventReader` Event based reader for Nexus files.
    `class` | `NexusEventWriter` Event based writer for the Nexus format.

  - ### Uses of JPhyloIOFormatSpecificObject in info.bioinfweb.jphyloio.formats.pde

    Classes in info.bioinfweb.jphyloio.formats.pde that implement JPhyloIOFormatSpecificObject
    Modifier and Type | Class and Description
    --- | ---
    `class` | `PDEEventReader` Event reader for the PDE format used by the alignment editor PhyDE.

  - ### Uses of JPhyloIOFormatSpecificObject in info.bioinfweb.jphyloio.formats.phylip

    Classes in info.bioinfweb.jphyloio.formats.phylip that implement JPhyloIOFormatSpecificObject
    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` | `PhylipEventWriter` Event based writer for the Phylip format.
    `class` | `SequentialPhylipEventReader` Event based reader for sequential Phylip alignment files.

  - ### Uses of JPhyloIOFormatSpecificObject in info.bioinfweb.jphyloio.formats.phyloxml

    Classes in info.bioinfweb.jphyloio.formats.phyloxml that implement JPhyloIOFormatSpecificObject
    Modifier and Type | Class and Description
    --- | ---
    `class` | `PhyloXMLEventReader` Event reader for the PhyloXML format.
    `class` | `PhyloXMLEventWriter` Event writer for the PhyloXML format.

  - ### Uses of JPhyloIOFormatSpecificObject in info.bioinfweb.jphyloio.formats.text

    Classes in info.bioinfweb.jphyloio.formats.text that implement JPhyloIOFormatSpecificObject
    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`.
    `class` | `AbstractTextEventWriter<P extends TextWriterStreamDataProvider<? extends AbstractTextEventWriter<P>>>`

  - ### Uses of JPhyloIOFormatSpecificObject in info.bioinfweb.jphyloio.formats.xml

    Subinterfaces of JPhyloIOFormatSpecificObject in info.bioinfweb.jphyloio.formats.xml
    Modifier and Type | Interface and Description
    --- | ---
    `interface` | `JPhyloIOXMLEventReader` Interface providing basic functionality for all JPhyloIO readers of XML formats.
    `interface` | `JPhyloIOXMLEventWriter` Interface providing basic functionality for all JPhyloIO writers of XML formats.

    Classes in info.bioinfweb.jphyloio.formats.xml that implement JPhyloIOFormatSpecificObject
    Modifier and Type | Class and Description
    --- | ---
    `class` | `AbstractXMLEventReader<P extends XMLReaderStreamDataProvider<? extends AbstractXMLEventReader<P>>>` Implements shared functionality for reading XML formats.
    `class` | `AbstractXMLEventWriter<P extends XMLWriterStreamDataProvider<? extends AbstractXMLEventWriter<P>>>` Implements shared functionality for writing XML formats.

  - ### Uses of JPhyloIOFormatSpecificObject in info.bioinfweb.jphyloio.formats.xtg

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