| 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.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 | Class and Description |
|---|---|
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 | Method and Description |
|---|---|
JPhyloIOEventWriter |
ReadWriteParameterMap.getWriterInstance()
Returns the writer instance registered under
ReadWriteParameterNames.KEY_WRITER_INSTANCE. |
| Modifier and Type | Method and Description |
|---|---|
JPhyloIOEventWriter |
SingleReaderWriterFactory.getWriter()
Creates a new writer instance for the target format of this factory.
|
JPhyloIOEventWriter |
JPhyloIOReaderWriterFactory.getWriter(java.lang.String formatID) |
| Modifier and Type | Class and Description |
|---|---|
class |
FASTAEventWriter
Event based writer for the FASTA format.
|
| Modifier and Type | Method and Description |
|---|---|
JPhyloIOEventWriter |
FASTAFactory.getWriter() |
| Modifier and Type | Method and Description |
|---|---|
JPhyloIOEventWriter |
MEGAFactory.getWriter() |
| Modifier and Type | Class and Description |
|---|---|
class |
NewickEventWriter
Event writer for the Newick format.
|
| Modifier and Type | Method and Description |
|---|---|
JPhyloIOEventWriter |
NewickFactory.getWriter() |
| Modifier and Type | Class and Description |
|---|---|
class |
NeXMLEventWriter
Event based writer for the NeXML format.
|
| Modifier and Type | Method and Description |
|---|---|
JPhyloIOEventWriter |
NeXMLFactory.getWriter() |
| Modifier and Type | Class and Description |
|---|---|
class |
NexusEventWriter
Event based writer for the Nexus format.
|
| Modifier and Type | Method and Description |
|---|---|
JPhyloIOEventWriter |
NexusFactory.getWriter() |
| Modifier and Type | Method and Description |
|---|---|
JPhyloIOEventWriter |
PDEFactory.getWriter() |
| Modifier and Type | Class and Description |
|---|---|
class |
PhylipEventWriter
Event based writer for the Phylip format.
|
| Modifier and Type | Method and Description |
|---|---|
JPhyloIOEventWriter |
AbstractPhylipFactory.getWriter() |
| Modifier and Type | Class and Description |
|---|---|
class |
PhyloXMLEventWriter
Event writer for the PhyloXML format.
|
| Modifier and Type | Method and Description |
|---|---|
JPhyloIOEventWriter |
PhyloXMLFactory.getWriter() |
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractTextEventWriter<P extends TextWriterStreamDataProvider<? extends AbstractTextEventWriter<P>>> |
| Modifier and Type | Interface and Description |
|---|---|
interface |
JPhyloIOXMLEventWriter
Interface providing basic functionality for all JPhyloIO writers of XML formats.
|
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractXMLEventWriter<P extends XMLWriterStreamDataProvider<? extends AbstractXMLEventWriter<P>>>
Implements shared functionality for writing XML formats.
|
| Modifier and Type | Method and Description |
|---|---|
JPhyloIOEventWriter |
XTGFactory.getWriter() |