# Package info.bioinfweb.jphyloio.utils

Contains general tool classes of JPhyloIO.

See: Description

- Class Summary
  Class | Description
  --- | ---
  IDToNameManager | Allows to assign IDs to labels, without having multiple IDs for the same label.
  JPhyloIOReadingUtils | Provides tool methods to be used by application developers when implementing a reader class that processes events from an implementations of `JPhyloIOEventReader` and stores relevant content in the application business model.
  JPhyloIOWritingUtils |
  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.
  TopoplogicalNodeInfo | This class is used by `TreeTopologyExtractor` to model a node in a phylogenetic tree or network.
  TreeTopologyExtractor | Tool class that allows to determine a tree topology from a `TreeNetworkDataAdapter`.

- Enum Summary
  Enum | Description
  --- | ---
  LabelEditingReporter.LabelStatus | Enumerates the possible cases of how the label associated with a data element was treated by an instance of `JPhyloIOEventWriter`.

## Package info.bioinfweb.jphyloio.utils Description

Contains general tool classes of JPhyloIO. Some are of general use for application developers, while others are used internally as tool classes and can also be useful in developing third part event readers and writers.

Author:
  Ben Stöver