| Package | Description |
|---|---|
| info.bioinfweb.jphyloio |
The main package of JPhyloIO.
|
| info.bioinfweb.jphyloio.formats.nexus |
Contains classes for reading from and writing to streams/files in Nexus format.
|
| info.bioinfweb.jphyloio.utils |
Contains general tool classes of JPhyloIO.
|
| Class and Description |
|---|
| LabelEditingReporter
Data storage class that allows instances of
JPhyloIOEventWriter to give feedback to the application
on how labels of different elements (e.g. |
| SequenceTokensEventManager
Class used by implementations of
JPhyloIOEventReader to keep track of the current alignment
position and replacing match tokens by the according tokens from the first sequence. |
| Class and Description |
|---|
| SequenceTokensEventManager
Class used by implementations of
JPhyloIOEventReader to keep track of the current alignment
position and replacing match tokens by the according tokens from the first sequence. |
| Class and Description |
|---|
| LabelEditingReporter.LabelStatus
Enumerates the possible cases of how the label associated with a data element was treated by an
instance of
JPhyloIOEventWriter. |
| TopoplogicalNodeInfo
This class is used by
TreeTopologyExtractor to model a node in a phylogenetic tree or network. |