| Package | Description |
|---|---|
| info.bioinfweb.jphyloio |
The main package of 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.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.nexus |
Contains classes for reading from and writing to streams/files in Nexus format.
|
| 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.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.xtg |
Contains classes for reading from and writing to streams/files in XTG format.
|
| Modifier and Type | Interface and Description |
|---|---|
interface |
JPhyloIOEventReader
This is main JPhyloIO interface to be implemented by all format specific event readers.
|
interface |
JPhyloIOEventWriter
The main JPhyloIO interface to be implemented by all format specific event writers.
|
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractEventReader<P extends ReaderStreamDataProvider<? extends AbstractEventReader<P>>>
Basic implementation for event readers in PhyloIO.
|
class |
AbstractEventWriter<P extends WriterStreamDataProvider<? extends AbstractEventWriter<P>>>
Implements shared functionality for JPhyloIO event writers.
|
class |
AbstractSingleMatrixEventWriter<P extends TextWriterStreamDataProvider<? extends AbstractTextEventWriter<P>>>
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.
|
| Modifier and Type | Class and Description |
|---|---|
class |
JPhyloIOContentExtensionFileFilter |
| Modifier and Type | Interface and Description |
|---|---|
interface |
JPhyloIOFormatInfo
Classes implementing this interface provide information about a phylogenetic file format that is supported by JPhyloIO.
|
| Modifier and Type | Class and Description |
|---|---|
class |
DefaultFormatInfo
Default implementation of
JPhyloIOFormatInfo. |
| Modifier and Type | Class and Description |
|---|---|
class |
FASTAEventReader
Event based reader for FASTA alignment files.
|
class |
FASTAEventWriter
Event based writer for the FASTA format.
|
| Modifier and Type | Class and Description |
|---|---|
class |
MEGAEventReader
Event based reader for MEGA alignment files.
|
| Modifier and Type | Class and Description |
|---|---|
class |
NewickEventReader
Reads tree files in Newick format.
|
class |
NewickEventWriter
Event writer for the Newick format.
|
| Modifier and Type | Class and Description |
|---|---|
class |
NeXMLEventReader
An event reader for the NeXML format.
|
class |
NeXMLEventWriter
Event based writer for the NeXML format.
|
| Modifier and Type | Class and Description |
|---|---|
class |
NexusEventReader
Event based reader for Nexus files.
|
class |
NexusEventWriter
Event based writer for the Nexus format.
|
| Modifier and Type | Class and Description |
|---|---|
class |
PDEEventReader
Event reader for the PDE format used by the alignment editor PhyDE.
|
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractPhylipEventReader<P extends TextReaderStreamDataProvider<? extends AbstractPhylipEventReader<P>>>
Implements shared functionality of Phylip event readers.
|
class |
PhylipEventReader
Event based reader for Phylip alignment files.
|
class |
PhylipEventWriter
Event based writer for the Phylip format.
|
class |
SequentialPhylipEventReader
Event based reader for sequential Phylip alignment files.
|
| Modifier and Type | Class and Description |
|---|---|
class |
PhyloXMLEventReader
Event reader for the PhyloXML format.
|
class |
PhyloXMLEventWriter
Event writer for the PhyloXML format.
|
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractTextEventReader<P extends TextReaderStreamDataProvider<? extends AbstractTextEventReader<P>>>
Abstract base class for all readers that read their data from a file using a
PeekReader. |
class |
AbstractTextEventWriter<P extends TextWriterStreamDataProvider<? extends AbstractTextEventWriter<P>>> |
| Modifier and Type | Interface and Description |
|---|---|
interface |
JPhyloIOXMLEventReader
Interface providing basic functionality for all JPhyloIO readers of XML formats.
|
interface |
JPhyloIOXMLEventWriter
Interface providing basic functionality for all JPhyloIO writers of XML formats.
|
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractXMLEventReader<P extends XMLReaderStreamDataProvider<? extends AbstractXMLEventReader<P>>>
Implements shared functionality for reading XML formats.
|
class |
AbstractXMLEventWriter<P extends XMLWriterStreamDataProvider<? extends AbstractXMLEventWriter<P>>>
Implements shared functionality for writing XML formats.
|
| Modifier and Type | Class and Description |
|---|---|
class |
XTGEventReader
Event reader for the extensible TreeGraph 2 format (XTG) used by the
phylogenetic tree editor TreeGraph 2.
|