# Uses of Package
info.bioinfweb.jphyloio

- Packages that use info.bioinfweb.jphyloio
  Package | Description
  --- | ---
  info.bioinfweb.jphyloio | The main package of JPhyloIO.
  info.bioinfweb.jphyloio.dataadapters | Contains adapter interfaces that should be implemented by adapters mediating between the business model of an application and implementations of `JPhyloIOEventWriter`.
  info.bioinfweb.jphyloio.dataadapters.implementations | Contains some basic (abstract) implementations of `JPhyloIOEventWriter`.
  info.bioinfweb.jphyloio.dataadapters.implementations.receivers | Contains some basic (abstract) implementations of `JPhyloIOEventReceiver` to be used by implementations of `JPhyloIOEventWriter`.
  info.bioinfweb.jphyloio.dataadapters.implementations.store | Contains implementations of data adapters that directly store their modeled data in mutable lists or maps instead of delegating to an application business model.
  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.nexml.elementreader | Contains implementations of `XMLElementReader` used by `NeXMLEventReader`.
  info.bioinfweb.jphyloio.formats.nexml.receivers | Contains implementations for `JPhyloIOEventReceiver` necessary for writing NeXML.
  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.phyloxml.receivers | Contains implementations for `JPhyloIOEventReceiver` necessary for writing PhyloXML.
  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.xml.receivers | Contains general (abstract) implementations for `JPhyloIOEventReceiver` necessary for writing 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.
  info.bioinfweb.jphyloio.objecttranslation.implementations | Contains implementations of `ObjectTranslator`.
  info.bioinfweb.jphyloio.push | Contains classes that allow push-parsing.
  info.bioinfweb.jphyloio.utils | Contains general tool classes of JPhyloIO.

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio
  Class and Description
  AbstractEventReader Basic implementation for event readers in PhyloIO.
  AbstractEventWriter Implements shared functionality for JPhyloIO event writers.
  AbstractEventWriter.UniqueLabelHandler
  JPhyloIO Singleton main class that provides information about this library at runtime.
  JPhyloIOEventReader This is main JPhyloIO interface to be implemented by all format specific event readers.
  JPhyloIOEventWriter The main JPhyloIO interface to be implemented by all format specific event writers.
  JPhyloIOFormatSpecificObject Interface to be implemented by all format-specific classes (e.g.
  ParentEventInformation
  ReaderStreamDataProvider Stream data providers are objects used by helper classes of JPhyloIO event readers (e.g.
  ReadWriteConstants Provides general constants for reading and writing phylogenetic file formats.
  ReadWriteParameterMap Parameter map that allows to specify (optional) parameters to implementations of `JPhyloIOEventReader` or `JPhyloIOEventWriter`.
  ReadWriteParameterNames Provides the names of parameters supported by one or more readers or writers included in JPhyloIO.
  WriterStreamDataProvider

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.dataadapters
  Class and Description
  ReadWriteParameterMap Parameter map that allows to specify (optional) parameters to implementations of `JPhyloIOEventReader` or `JPhyloIOEventWriter`.

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.dataadapters.implementations
  Class and Description
  ReadWriteParameterMap Parameter map that allows to specify (optional) parameters to implementations of `JPhyloIOEventReader` or `JPhyloIOEventWriter`.

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.dataadapters.implementations.receivers
  Class and Description
  AbstractEventWriter Implements shared functionality for JPhyloIO event writers.
  ReadWriteParameterMap Parameter map that allows to specify (optional) parameters to implementations of `JPhyloIOEventReader` or `JPhyloIOEventWriter`.
  WriterStreamDataProvider

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.dataadapters.implementations.store
  Class and Description
  ReadWriteParameterMap Parameter map that allows to specify (optional) parameters to implementations of `JPhyloIOEventReader` or `JPhyloIOEventWriter`.

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.factory
  Class and Description
  JPhyloIOEventReader This is main JPhyloIO interface to be implemented by all format specific event readers.
  JPhyloIOEventWriter The main JPhyloIO interface to be implemented by all format specific event writers.
  JPhyloIOFormatSpecificObject Interface to be implemented by all format-specific classes (e.g.
  ReadWriteParameterMap Parameter map that allows to specify (optional) parameters to implementations of `JPhyloIOEventReader` or `JPhyloIOEventWriter`.

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.formatinfo
  Class and Description
  JPhyloIOFormatSpecificObject Interface to be implemented by all format-specific classes (e.g.
  ReadWriteParameterMap Parameter map that allows to specify (optional) parameters to implementations of `JPhyloIOEventReader` or `JPhyloIOEventWriter`.

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.formats.fasta
  Class and Description
  AbstractEventReader Basic implementation for event readers in PhyloIO.
  AbstractEventWriter Implements shared functionality for JPhyloIO event writers.
  AbstractSingleMatrixEventWriter 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.
  JPhyloIOEventReader This is main JPhyloIO interface to be implemented by all format specific event readers.
  JPhyloIOEventWriter The main JPhyloIO interface to be implemented by all format specific event writers.
  JPhyloIOFormatSpecificObject Interface to be implemented by all format-specific classes (e.g.
  ReadWriteConstants Provides general constants for reading and writing phylogenetic file formats.
  ReadWriteParameterMap Parameter map that allows to specify (optional) parameters to implementations of `JPhyloIOEventReader` or `JPhyloIOEventWriter`.

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.formats.mega
  Class and Description
  AbstractEventReader Basic implementation for event readers in PhyloIO.
  JPhyloIOEventReader This is main JPhyloIO interface to be implemented by all format specific event readers.
  JPhyloIOEventWriter The main JPhyloIO interface to be implemented by all format specific event writers.
  JPhyloIOFormatSpecificObject Interface to be implemented by all format-specific classes (e.g.
  ReadWriteConstants Provides general constants for reading and writing phylogenetic file formats.
  ReadWriteParameterMap Parameter map that allows to specify (optional) parameters to implementations of `JPhyloIOEventReader` or `JPhyloIOEventWriter`.

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.formats.newick
  Class and Description
  AbstractEventReader Basic implementation for event readers in PhyloIO.
  AbstractEventWriter Implements shared functionality for JPhyloIO event writers.
  JPhyloIOEventReader This is main JPhyloIO interface to be implemented by all format specific event readers.
  JPhyloIOEventWriter The main JPhyloIO interface to be implemented by all format specific event writers.
  JPhyloIOFormatSpecificObject Interface to be implemented by all format-specific classes (e.g.
  ReadWriteConstants Provides general constants for reading and writing phylogenetic file formats.
  ReadWriteParameterMap Parameter map that allows to specify (optional) parameters to implementations of `JPhyloIOEventReader` or `JPhyloIOEventWriter`.

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.formats.nexml
  Class and Description
  AbstractEventReader Basic implementation for event readers in PhyloIO.
  AbstractEventWriter Implements shared functionality for JPhyloIO event writers.
  JPhyloIOEventReader This is main JPhyloIO interface to be implemented by all format specific event readers.
  JPhyloIOEventWriter The main JPhyloIO interface to be implemented by all format specific event writers.
  JPhyloIOFormatSpecificObject Interface to be implemented by all format-specific classes (e.g.
  ReaderStreamDataProvider Stream data providers are objects used by helper classes of JPhyloIO event readers (e.g.
  ReadWriteConstants Provides general constants for reading and writing phylogenetic file formats.
  ReadWriteParameterMap Parameter map that allows to specify (optional) parameters to implementations of `JPhyloIOEventReader` or `JPhyloIOEventWriter`.
  WriterStreamDataProvider

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.formats.nexml.elementreader
  Class and Description
  ReadWriteConstants Provides general constants for reading and writing phylogenetic file formats.

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.formats.nexml.receivers
  Class and Description
  ReadWriteParameterMap Parameter map that allows to specify (optional) parameters to implementations of `JPhyloIOEventReader` or `JPhyloIOEventWriter`.

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.formats.nexus
  Class and Description
  AbstractEventReader Basic implementation for event readers in PhyloIO.
  AbstractEventWriter Implements shared functionality for JPhyloIO event writers.
  JPhyloIOEventReader This is main JPhyloIO interface to be implemented by all format specific event readers.
  JPhyloIOEventWriter The main JPhyloIO interface to be implemented by all format specific event writers.
  JPhyloIOFormatSpecificObject Interface to be implemented by all format-specific classes (e.g.
  ReaderStreamDataProvider Stream data providers are objects used by helper classes of JPhyloIO event readers (e.g.
  ReadWriteConstants Provides general constants for reading and writing phylogenetic file formats.
  ReadWriteParameterMap Parameter map that allows to specify (optional) parameters to implementations of `JPhyloIOEventReader` or `JPhyloIOEventWriter`.
  WriterStreamDataProvider

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.formats.nexus.blockhandlers
  Class and Description
  ReadWriteConstants Provides general constants for reading and writing phylogenetic file formats.

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.formats.nexus.commandreaders.all
  Class and Description
  ReadWriteConstants Provides general constants for reading and writing phylogenetic file formats.

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters
  Class and Description
  ReadWriteConstants Provides general constants for reading and writing phylogenetic file formats.

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets
  Class and Description
  ReadWriteConstants Provides general constants for reading and writing phylogenetic file formats.

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.formats.nexus.commandreaders.taxa
  Class and Description
  ReadWriteConstants Provides general constants for reading and writing phylogenetic file formats.

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees
  Class and Description
  ReadWriteConstants Provides general constants for reading and writing phylogenetic file formats.

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.formats.pde
  Class and Description
  AbstractEventReader Basic implementation for event readers in PhyloIO.
  JPhyloIOEventReader This is main JPhyloIO interface to be implemented by all format specific event readers.
  JPhyloIOEventWriter The main JPhyloIO interface to be implemented by all format specific event writers.
  JPhyloIOFormatSpecificObject Interface to be implemented by all format-specific classes (e.g.
  ReaderStreamDataProvider Stream data providers are objects used by helper classes of JPhyloIO event readers (e.g.
  ReadWriteConstants Provides general constants for reading and writing phylogenetic file formats.
  ReadWriteParameterMap Parameter map that allows to specify (optional) parameters to implementations of `JPhyloIOEventReader` or `JPhyloIOEventWriter`.

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.formats.phylip
  Class and Description
  AbstractEventReader Basic implementation for event readers in PhyloIO.
  AbstractEventWriter Implements shared functionality for JPhyloIO event writers.
  AbstractSingleMatrixEventWriter 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.
  JPhyloIOEventReader This is main JPhyloIO interface to be implemented by all format specific event readers.
  JPhyloIOEventWriter The main JPhyloIO interface to be implemented by all format specific event writers.
  JPhyloIOFormatSpecificObject Interface to be implemented by all format-specific classes (e.g.
  ReadWriteConstants Provides general constants for reading and writing phylogenetic file formats.
  ReadWriteParameterMap Parameter map that allows to specify (optional) parameters to implementations of `JPhyloIOEventReader` or `JPhyloIOEventWriter`.

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.formats.phyloxml
  Class and Description
  AbstractEventReader Basic implementation for event readers in PhyloIO.
  AbstractEventWriter Implements shared functionality for JPhyloIO event writers.
  JPhyloIOEventReader This is main JPhyloIO interface to be implemented by all format specific event readers.
  JPhyloIOEventWriter The main JPhyloIO interface to be implemented by all format specific event writers.
  JPhyloIOFormatSpecificObject Interface to be implemented by all format-specific classes (e.g.
  ReaderStreamDataProvider Stream data providers are objects used by helper classes of JPhyloIO event readers (e.g.
  ReadWriteConstants Provides general constants for reading and writing phylogenetic file formats.
  ReadWriteParameterMap Parameter map that allows to specify (optional) parameters to implementations of `JPhyloIOEventReader` or `JPhyloIOEventWriter`.
  WriterStreamDataProvider

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.formats.phyloxml.receivers
  Class and Description
  ReadWriteParameterMap Parameter map that allows to specify (optional) parameters to implementations of `JPhyloIOEventReader` or `JPhyloIOEventWriter`.

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.formats.text
  Class and Description
  AbstractEventReader Basic implementation for event readers in PhyloIO.
  AbstractEventWriter Implements shared functionality for JPhyloIO event writers.
  JPhyloIOEventReader This is main JPhyloIO interface to be implemented by all format specific event readers.
  JPhyloIOEventWriter The main JPhyloIO interface to be implemented by all format specific event writers.
  JPhyloIOFormatSpecificObject Interface to be implemented by all format-specific classes (e.g.
  ReaderStreamDataProvider Stream data providers are objects used by helper classes of JPhyloIO event readers (e.g.
  ReadWriteConstants Provides general constants for reading and writing phylogenetic file formats.
  ReadWriteParameterMap Parameter map that allows to specify (optional) parameters to implementations of `JPhyloIOEventReader` or `JPhyloIOEventWriter`.
  WriterStreamDataProvider

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.formats.xml
  Class and Description
  AbstractEventReader Basic implementation for event readers in PhyloIO.
  AbstractEventWriter Implements shared functionality for JPhyloIO event writers.
  JPhyloIOEventReader This is main JPhyloIO interface to be implemented by all format specific event readers.
  JPhyloIOEventWriter The main JPhyloIO interface to be implemented by all format specific event writers.
  JPhyloIOFormatSpecificObject Interface to be implemented by all format-specific classes (e.g.
  ReaderStreamDataProvider Stream data providers are objects used by helper classes of JPhyloIO event readers (e.g.
  ReadWriteConstants Provides general constants for reading and writing phylogenetic file formats.
  ReadWriteParameterMap Parameter map that allows to specify (optional) parameters to implementations of `JPhyloIOEventReader` or `JPhyloIOEventWriter`.
  WriterStreamDataProvider

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.formats.xml.receivers
  Class and Description
  ReadWriteParameterMap Parameter map that allows to specify (optional) parameters to implementations of `JPhyloIOEventReader` or `JPhyloIOEventWriter`.

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.formats.xtg
  Class and Description
  AbstractEventReader Basic implementation for event readers in PhyloIO.
  JPhyloIOEventReader This is main JPhyloIO interface to be implemented by all format specific event readers.
  JPhyloIOEventWriter The main JPhyloIO interface to be implemented by all format specific event writers.
  JPhyloIOFormatSpecificObject Interface to be implemented by all format-specific classes (e.g.
  ReadWriteConstants Provides general constants for reading and writing phylogenetic file formats.
  ReadWriteParameterMap Parameter map that allows to specify (optional) parameters to implementations of `JPhyloIOEventReader` or `JPhyloIOEventWriter`.

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.objecttranslation
  Class and Description
  ReaderStreamDataProvider Stream data providers are objects used by helper classes of JPhyloIO event readers (e.g.
  ReadWriteConstants Provides general constants for reading and writing phylogenetic file formats.
  WriterStreamDataProvider

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.objecttranslation.implementations
  Class and Description
  ReaderStreamDataProvider Stream data providers are objects used by helper classes of JPhyloIO event readers (e.g.
  WriterStreamDataProvider

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.push
  Class and Description
  JPhyloIOEventReader This is main JPhyloIO interface to be implemented by all format specific event readers.

- Classes in info.bioinfweb.jphyloio used by info.bioinfweb.jphyloio.utils
  Class and Description
  JPhyloIOEventReader This is main JPhyloIO interface to be implemented by all format specific event readers.
  ReadWriteParameterMap Parameter map that allows to specify (optional) parameters to implementations of `JPhyloIOEventReader` or `JPhyloIOEventWriter`.