| Package | Description |
|---|---|
| info.bioinfweb.jphyloio |
The main package of JPhyloIO.
|
| info.bioinfweb.jphyloio.dataadapters.implementations.receivers |
Contains some basic (abstract) implementations of
JPhyloIOEventReceiver
to be used by implementations of JPhyloIOEventWriter. |
| 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 |
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.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.
|
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractEventWriter<P extends WriterStreamDataProvider<? extends AbstractEventWriter<P>>>
Implements shared functionality for JPhyloIO event writers.
|
class |
WriterStreamDataProvider<R extends AbstractEventWriter<? extends WriterStreamDataProvider<R>>> |
| Modifier and Type | Class and Description |
|---|---|
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 |
AbstractSequenceContentReceiver<P extends WriterStreamDataProvider<? extends AbstractEventWriter<P>>> |
class |
BasicEventReceiver<P extends WriterStreamDataProvider<? extends AbstractEventWriter<P>>>
Most event receivers will be inherited from this class.
|
| Modifier and Type | Class and Description |
|---|---|
class |
FASTAEventWriter
Event based writer for the FASTA format.
|
| Modifier and Type | Class and Description |
|---|---|
class |
NewickEventWriter
Event writer for the Newick format.
|
| Modifier and Type | Class and Description |
|---|---|
class |
NeXMLEventWriter
Event based writer for the NeXML format.
|
| Modifier and Type | Class and Description |
|---|---|
class |
NexusEventWriter
Event based writer for the Nexus format.
|
| Modifier and Type | Class and Description |
|---|---|
class |
PhylipEventWriter
Event based writer for the Phylip format.
|
| Modifier and Type | Class and Description |
|---|---|
class |
PhyloXMLEventWriter
Event writer for the PhyloXML format.
|
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractTextEventWriter<P extends TextWriterStreamDataProvider<? extends AbstractTextEventWriter<P>>> |
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractXMLEventWriter<P extends XMLWriterStreamDataProvider<? extends AbstractXMLEventWriter<P>>>
Implements shared functionality for writing XML formats.
|