Class PhyloXMLBridge

java.lang.Object

org.episteme.natural.biology.loaders.phyloxml.PhyloXMLBridge

public class PhyloXMLBridge
extends Object

Bridge for converting PhyloXML DTOs to core Episteme evolutionary biology objects.

Constructor Summary

Constructors

Constructor	Description
PhyloXMLBridge()

Method Summary

Modifier and Type	Method	Description
Clade	convertClade(PhyloXMLClade dto)	Recursively converts PhyloXML clade DTO to core Episteme Clade.
Species	convertTaxonomy(PhyloXMLTaxonomy dto)	Converts PhyloXML taxonomy DTO to Episteme Species.
List<Species>	extractSpecies(PhylogeneticTree tree)	Extracts all species from a PhyloXML tree.
PhylogeneticTree	toPhylogeneticTree(PhyloXMLDocument doc)	Converts PhyloXML document to Episteme PhylogeneticTree.

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

PhyloXMLBridge

public PhyloXMLBridge()

Method Details

toPhylogeneticTree

public PhylogeneticTree toPhylogeneticTree(PhyloXMLDocument doc)

Converts PhyloXML document to Episteme PhylogeneticTree.

convertClade

public Clade convertClade(PhyloXMLClade dto)

Recursively converts PhyloXML clade DTO to core Episteme Clade.

convertTaxonomy

public Species convertTaxonomy(PhyloXMLTaxonomy dto)

Converts PhyloXML taxonomy DTO to Episteme Species.

extractSpecies

public List<Species> extractSpecies(PhylogeneticTree tree)

Extracts all species from a PhyloXML tree.