| 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.
|