| 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.exception |
Contains exceptions that are of general use in JPhyloIO.
|
| info.bioinfweb.jphyloio.formats.fasta |
Contains classes for reading from and writing to streams/files in FASTA 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.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.receivers |
Contains implementations of
JPhyloIOEventReceiver used internally by
NexusEventReader. |
| info.bioinfweb.jphyloio.formats.phylip |
Contains classes for reading from and writing to streams/files in Phylip 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.xml.stax |
Contains implementations that allow StAX based reading and writing of XML metadata.
|
| info.bioinfweb.jphyloio.utils |
Contains general tool classes of JPhyloIO.
|
| Class and Description |
|---|
| DocumentDataAdapter
The root adapter interface to be used with
JPhyloIOEventWriters. |
| ElementDataAdapter
Data adapters that model a data element identified by a certain start event should implement this interface.
|
| JPhyloIOEventReceiver
Implementations of this interface are used by JPhyloIO writers to receive events
from the application (generated from its business model).
|
| MatrixDataAdapter
Adapter interface used to provide any type of character matrix data to instances of
JPhyloIOEventWriter, including token and character set definitions related to this
matrix. |
| OTUListDataAdapter
Allows to access data from the application business model that make up an OTU list.
|
| Class and Description |
|---|
| AnnotatedDataAdapter
Superinterface for all data adapters providing metadata to the object they model.
|
| ElementDataAdapter
Data adapters that model a data element identified by a certain start event should implement this interface.
|
| JPhyloIOEventReceiver
Implementations of this interface are used by JPhyloIO writers to receive events
from the application (generated from its business model).
|
| MatrixDataAdapter
Adapter interface used to provide any type of character matrix data to instances of
JPhyloIOEventWriter, including token and character set definitions related to this
matrix. |
| ObjectListDataAdapter
Allows to provide data for a list of phylogenetic objects.
|
| OTUListDataAdapter
Allows to access data from the application business model that make up an OTU list.
|
| TreeNetworkDataAdapter
Data adapter interface that provides data for a tree or a network.
|
| TreeNetworkGroupDataAdapter |
| Class and Description |
|---|
| AnnotatedDataAdapter
Superinterface for all data adapters providing metadata to the object they model.
|
| DocumentDataAdapter
The root adapter interface to be used with
JPhyloIOEventWriters. |
| ElementDataAdapter
Data adapters that model a data element identified by a certain start event should implement this interface.
|
| JPhyloIOEventReceiver
Implementations of this interface are used by JPhyloIO writers to receive events
from the application (generated from its business model).
|
| MatrixDataAdapter
Adapter interface used to provide any type of character matrix data to instances of
JPhyloIOEventWriter, including token and character set definitions related to this
matrix. |
| ObjectListDataAdapter
Allows to provide data for a list of phylogenetic objects.
|
| OTUListDataAdapter
Allows to access data from the application business model that make up an OTU list.
|
| TreeNetworkDataAdapter
Data adapter interface that provides data for a tree or a network.
|
| TreeNetworkGroupDataAdapter |
| Class and Description |
|---|
| JPhyloIOEventReceiver
Implementations of this interface are used by JPhyloIO writers to receive events
from the application (generated from its business model).
|
| Class and Description |
|---|
| AnnotatedDataAdapter
Superinterface for all data adapters providing metadata to the object they model.
|
| DocumentDataAdapter
The root adapter interface to be used with
JPhyloIOEventWriters. |
| ElementDataAdapter
Data adapters that model a data element identified by a certain start event should implement this interface.
|
| JPhyloIOEventReceiver
Implementations of this interface are used by JPhyloIO writers to receive events
from the application (generated from its business model).
|
| MatrixDataAdapter
Adapter interface used to provide any type of character matrix data to instances of
JPhyloIOEventWriter, including token and character set definitions related to this
matrix. |
| ObjectListDataAdapter
Allows to provide data for a list of phylogenetic objects.
|
| OTUListDataAdapter
Allows to access data from the application business model that make up an OTU list.
|
| TreeNetworkDataAdapter
Data adapter interface that provides data for a tree or a network.
|
| TreeNetworkGroupDataAdapter |
| Class and Description |
|---|
| JPhyloIOEventReceiver
Implementations of this interface are used by JPhyloIO writers to receive events
from the application (generated from its business model).
|
| Class and Description |
|---|
| DocumentDataAdapter
The root adapter interface to be used with
JPhyloIOEventWriters. |
| MatrixDataAdapter
Adapter interface used to provide any type of character matrix data to instances of
JPhyloIOEventWriter, including token and character set definitions related to this
matrix. |
| Class and Description |
|---|
| DocumentDataAdapter
The root adapter interface to be used with
JPhyloIOEventWriters. |
| JPhyloIOEventReceiver
Implementations of this interface are used by JPhyloIO writers to receive events
from the application (generated from its business model).
|
| OTUListDataAdapter
Allows to access data from the application business model that make up an OTU list.
|
| TreeNetworkDataAdapter
Data adapter interface that provides data for a tree or a network.
|
| Class and Description |
|---|
| JPhyloIOEventReceiver
Implementations of this interface are used by JPhyloIO writers to receive events
from the application (generated from its business model).
|
| Class and Description |
|---|
| DocumentDataAdapter
The root adapter interface to be used with
JPhyloIOEventWriters. |
| ElementDataAdapter
Data adapters that model a data element identified by a certain start event should implement this interface.
|
| ObjectListDataAdapter
Allows to provide data for a list of phylogenetic objects.
|
| OTUListDataAdapter
Allows to access data from the application business model that make up an OTU list.
|
| Class and Description |
|---|
| JPhyloIOEventReceiver
Implementations of this interface are used by JPhyloIO writers to receive events
from the application (generated from its business model).
|
| Class and Description |
|---|
| DocumentDataAdapter
The root adapter interface to be used with
JPhyloIOEventWriters. |
| MatrixDataAdapter
Adapter interface used to provide any type of character matrix data to instances of
JPhyloIOEventWriter, including token and character set definitions related to this
matrix. |
| Class and Description |
|---|
| JPhyloIOEventReceiver
Implementations of this interface are used by JPhyloIO writers to receive events
from the application (generated from its business model).
|
| Class and Description |
|---|
| DocumentDataAdapter
The root adapter interface to be used with
JPhyloIOEventWriters. |
| JPhyloIOEventReceiver
Implementations of this interface are used by JPhyloIO writers to receive events
from the application (generated from its business model).
|
| Class and Description |
|---|
| DocumentDataAdapter
The root adapter interface to be used with
JPhyloIOEventWriters. |
| JPhyloIOEventReceiver
Implementations of this interface are used by JPhyloIO writers to receive events
from the application (generated from its business model).
|
| Class and Description |
|---|
| JPhyloIOEventReceiver
Implementations of this interface are used by JPhyloIO writers to receive events
from the application (generated from its business model).
|
| Class and Description |
|---|
| JPhyloIOEventReceiver
Implementations of this interface are used by JPhyloIO writers to receive events
from the application (generated from its business model).
|
| Class and Description |
|---|
| JPhyloIOEventReceiver
Implementations of this interface are used by JPhyloIO writers to receive events
from the application (generated from its business model).
|
| TreeNetworkDataAdapter
Data adapter interface that provides data for a tree or a network.
|