info.bioinfweb.jphyloio.formats.newick

Interface NewickReaderNodeLabelProcessor

All Known Implementing Classes:

DefaultNewickReaderNodeLabelProcessor, NexusNewickReaderNodeLabelProcessor

public interface NewickReaderNodeLabelProcessor

Classes implementing this interface are used to modify a node label read from a Newick string (e.g., by using information from a taxon list or translation table.)

Author:

Ben Stöver

Method Summary

Modifier and Type	Method and Description
java.lang.String	getLinkedOTUID(java.lang.String processedLabel) Returns the OTU ID that is associated with the specified label.
java.lang.String	processLabel(java.lang.String originalLabel, boolean isInternal) Processes a label according to the format modeled by this implementation.

Method Detail

processLabel

java.lang.String processLabel(java.lang.String originalLabel,
                              boolean isInternal)

Processes a label according to the format modeled by this implementation.

Parameters:

originalLabel - the label as it was read from the Newick string

isInternal - defines whether the node carrying this label is an internal node or not

Returns:

the processed label

getLinkedOTUID

java.lang.String getLinkedOTUID(java.lang.String processedLabel)

Returns the OTU ID that is associated with the specified label.

Parameters:

processedLabel - the processed label as it was returned by a call if #processLabel(String)

Returns:

the linked OTU ID or null if no associated OTU ID exists