| 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.
|
| 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 |
| Class and Description |
|---|
| ReadWriteParameterMap
Parameter map that allows to specify (optional) parameters to implementations of
JPhyloIOEventReader or
JPhyloIOEventWriter. |
| Class and Description |
|---|
| ReadWriteParameterMap
Parameter map that allows to specify (optional) parameters to implementations of
JPhyloIOEventReader or
JPhyloIOEventWriter. |
| 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 |
| Class and Description |
|---|
| ReadWriteParameterMap
Parameter map that allows to specify (optional) parameters to implementations of
JPhyloIOEventReader or
JPhyloIOEventWriter. |
| 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. |
| 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. |
| 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. |
| 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. |
| 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. |
| 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 |
| Class and Description |
|---|
| ReadWriteConstants
Provides general constants for reading and writing phylogenetic file formats.
|
| Class and Description |
|---|
| ReadWriteParameterMap
Parameter map that allows to specify (optional) parameters to implementations of
JPhyloIOEventReader or
JPhyloIOEventWriter. |
| 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 |
| Class and Description |
|---|
| ReadWriteConstants
Provides general constants for reading and writing phylogenetic file formats.
|
| Class and Description |
|---|
| ReadWriteConstants
Provides general constants for reading and writing phylogenetic file formats.
|
| Class and Description |
|---|
| ReadWriteConstants
Provides general constants for reading and writing phylogenetic file formats.
|
| Class and Description |
|---|
| ReadWriteConstants
Provides general constants for reading and writing phylogenetic file formats.
|
| Class and Description |
|---|
| ReadWriteConstants
Provides general constants for reading and writing phylogenetic file formats.
|
| Class and Description |
|---|
| ReadWriteConstants
Provides general constants for reading and writing phylogenetic file formats.
|
| 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. |
| 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. |
| 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 |
| Class and Description |
|---|
| ReadWriteParameterMap
Parameter map that allows to specify (optional) parameters to implementations of
JPhyloIOEventReader or
JPhyloIOEventWriter. |
| 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 |
| 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 |
| Class and Description |
|---|
| ReadWriteParameterMap
Parameter map that allows to specify (optional) parameters to implementations of
JPhyloIOEventReader or
JPhyloIOEventWriter. |
| 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. |
| 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 |
| Class and Description |
|---|
| ReaderStreamDataProvider
Stream data providers are objects used by helper classes of JPhyloIO event readers (e.g.
|
| WriterStreamDataProvider |
| Class and Description |
|---|
| JPhyloIOEventReader
This is main JPhyloIO interface to be implemented by all format specific event readers.
|
| 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. |