| 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.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 |
AbstractEventReader<P extends ReaderStreamDataProvider<? extends AbstractEventReader<P>>>
Basic implementation for event readers in PhyloIO.
|
class |
ReaderStreamDataProvider<R extends AbstractEventReader<? extends ReaderStreamDataProvider<R>>>
Stream data providers are objects used by helper classes of JPhyloIO event readers (e.g.
|
| Modifier and Type | Class and Description |
|---|---|
class |
FASTAEventReader
Event based reader for FASTA alignment files.
|
| 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.
|
| Modifier and Type | Class and Description |
|---|---|
class |
NeXMLEventReader
An event reader for the NeXML format.
|
| Modifier and Type | Class and Description |
|---|---|
class |
NexusEventReader
Event based reader for Nexus files.
|
| 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 |
SequentialPhylipEventReader
Event based reader for sequential Phylip alignment files.
|
| Modifier and Type | Class and Description |
|---|---|
class |
PhyloXMLEventReader
Event reader 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. |
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractXMLEventReader<P extends XMLReaderStreamDataProvider<? extends AbstractXMLEventReader<P>>>
Implements shared functionality for reading 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.
|