| Package | Description |
|---|---|
| info.bioinfweb.jphyloio |
The main package of 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.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.text |
Contains classes implementing shared functionality for reading from and writing to streams/files in text formats.
|
| 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 | Method and Description |
|---|---|
protected TextWriterStreamDataProvider<FASTAEventWriter> |
FASTAEventWriter.createStreamDataProvider() |
| Modifier and Type | Method and Description |
|---|---|
protected TextWriterStreamDataProvider<NewickEventWriter> |
NewickEventWriter.createStreamDataProvider() |
TextWriterStreamDataProvider |
NewickNodeEdgeEventReceiver.getStreamDataProvider() |
| Constructor and Description |
|---|
NewickNodeEdgeEventReceiver(TextWriterStreamDataProvider<?> streamDataProvider,
ReadWriteParameterMap parameterMap) |
NewickStringWriter(TextWriterStreamDataProvider<?> streamDataProvider,
TreeNetworkDataAdapter tree,
NewickWriterNodeLabelProcessor nodeLabelProcessor,
ReadWriteParameterMap parameters)
Creates a new instance of this class.
|
| Modifier and Type | Class and Description |
|---|---|
class |
NexusWriterStreamDataProvider |
| Modifier and Type | Method and Description |
|---|---|
protected TextWriterStreamDataProvider<PhylipEventWriter> |
PhylipEventWriter.createStreamDataProvider() |
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractTextEventWriter<P extends TextWriterStreamDataProvider<? extends AbstractTextEventWriter<P>>> |
class |
BasicTextCommentEventReceiver<P extends TextWriterStreamDataProvider<? extends AbstractTextEventWriter<P>>>
Basic event receiver implementation that writes comments to text formats that are delimited by a start and an end string.
|
class |
TextSequenceContentReceiver<P extends TextWriterStreamDataProvider<? extends AbstractTextEventWriter<P>>>
Receiver that writes all encountered sequence tokens and comments to the current line and ignores all metadata.
|
class |
TextWriterStreamDataProvider<W extends AbstractTextEventWriter<? extends TextWriterStreamDataProvider<W>>> |