# JPhyloIO 1.0.0 beta

Packages
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.events | Contains implementations of JPhyloIO events, triggered during event based parsing.
info.bioinfweb.jphyloio.events.meta | Contains event classes that model metadata, as well as related implementations.
info.bioinfweb.jphyloio.events.type | Contains classes used to indentify the type of an JPhyloIO event.
info.bioinfweb.jphyloio.exception | Contains exceptions that are of general use in 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 | The subpackages of this package contain implementations of JPhyloIO readers and writers for different formats.
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 | Contains general classes for reading Nexus commands.
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.nexus.receivers | Contains implementations of `JPhyloIOEventReceiver` used internally by `NexusEventReader`.
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.elementreader | Contains implementations of `XMLElementReader` used by `PhyloXMLEventReader`.
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.elementreaders | Contains general (abstract) implementations of `XMLElementReader` used by readers of XML formats.
info.bioinfweb.jphyloio.formats.xml.receivers | Contains general (abstract) implementations for `JPhyloIOEventReceiver` necessary for writing XML formats.
info.bioinfweb.jphyloio.formats.xml.stax | Contains implementations that allow StAX based reading and writing of XML metadata.
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.