| 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.nexus |
Contains classes for reading from and writing to streams/files in Nexus format.
|
| info.bioinfweb.jphyloio.formats.nexus.commandreaders |
Contains general classes for reading Nexus commands.
|
| info.bioinfweb.jphyloio.formats.nexus.commandreaders.all |
Contains implementations of
NexusCommandEventReader
for commands that are valid in all Nexus blocks. |
| info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters |
Contains classes for reading Nexus commands in a
CHARACTERS, UNALIGNED or DATA
block. |
| info.bioinfweb.jphyloio.formats.nexus.receivers |
Contains implementations of
JPhyloIOEventReceiver used internally by
NexusEventReader. |
| 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.
|
| Class and Description |
|---|
| AbstractTextEventWriter |
| TextWriterStreamDataProvider |
| Class and Description |
|---|
| AbstractTextEventReader
Abstract base class for all readers that read their data from a file using a
PeekReader. |
| AbstractTextEventWriter |
| TextWriterStreamDataProvider |
| Class and Description |
|---|
| AbstractTextEventReader
Abstract base class for all readers that read their data from a file using a
PeekReader. |
| Class and Description |
|---|
| AbstractTextEventReader
Abstract base class for all readers that read their data from a file using a
PeekReader. |
| AbstractTextEventWriter |
| TextReaderStreamDataProvider |
| TextWriterStreamDataProvider |
| Class and Description |
|---|
| AbstractTextEventReader
Abstract base class for all readers that read their data from a file using a
PeekReader. |
| AbstractTextEventWriter |
| KeyValueInformation
Used internally by
AbstractTextEventReader and inherited classes to store contents of commands
containing key value information. |
| TextReaderStreamDataProvider |
| TextWriterStreamDataProvider |
| Class and Description |
|---|
| KeyValueInformation
Used internally by
AbstractTextEventReader and inherited classes to store contents of commands
containing key value information. |
| Class and Description |
|---|
| KeyValueInformation
Used internally by
AbstractTextEventReader and inherited classes to store contents of commands
containing key value information. |
| Class and Description |
|---|
| KeyValueInformation
Used internally by
AbstractTextEventReader and inherited classes to store contents of commands
containing key value information. |
| Class and Description |
|---|
| BasicTextCommentEventReceiver
Basic event receiver implementation that writes comments to text formats that are delimited by a start and an end string.
|
| Class and Description |
|---|
| AbstractTextEventReader
Abstract base class for all readers that read their data from a file using a
PeekReader. |
| AbstractTextEventWriter |
| TextReaderStreamDataProvider |
| TextWriterStreamDataProvider |
| Class and Description |
|---|
| AbstractTextEventReader
Abstract base class for all readers that read their data from a file using a
PeekReader. |
| AbstractTextEventWriter |
| KeyValueInformation
Used internally by
AbstractTextEventReader and inherited classes to store contents of commands
containing key value information. |
| TextReaderStreamDataProvider |
| TextWriterStreamDataProvider |