phenote.dataadapter.phenoxml
Class PhenoXmlAdapter

java.lang.Object
  phenote.dataadapter.AbstractFileAdapter
      phenote.dataadapter.phenoxml.PhenoXmlAdapter

All Implemented Interfaces:

DataAdapterI

public class PhenoXmlAdapter
extends AbstractFileAdapter

Field Summary

Fields inherited from class phenote.dataadapter.AbstractFileAdapter

file

Constructor Summary

PhenoXmlAdapter()

PhenoXmlAdapter(org.obo.datamodel.OBOSession session)
This constructor is used when the OBOSession needs to be specified, such as when the CharFieldManager is not in use.

Method Summary

void	commit(CharacterListI charList)
void	commit(CharacterListI charList, java.io.File f)
static org.bioontologies.obd.schema.pheno.PhenotypeDocument.Phenotype	createPhenotype(java.util.List<org.bioontologies.obd.schema.pheno.PhenotypeCharacterDocument.PhenotypeCharacter> phenotypeCharacters)
static org.bioontologies.obd.schema.pheno.PhenotypeCharacterDocument.PhenotypeCharacter	createPhenotypeCharacter(PhenotypeCharacterI phenoCharacter)
boolean	didCreateDanglers()
boolean	didMigrateSecondaryIDs()
java.util.Collection<java.lang.String>	getDanglersList()
java.util.Collection<java.lang.String>	getMigratedSecondaryIDsList()
void	load()
CharacterListI	load(java.io.File f)
java.util.List<PhenotypeCharacterI>	parsePhenotype(org.bioontologies.obd.schema.pheno.PhenotypeDocument.Phenotype phenotype, PhenotypeCharacterI.PhenotypeCharacterFactory factory)
PhenotypeCharacterI	parsePhenotypeCharacter(org.bioontologies.obd.schema.pheno.PhenotypeCharacterDocument.PhenotypeCharacter pc, PhenotypeCharacterI.PhenotypeCharacterFactory factory)

Methods inherited from class phenote.dataadapter.AbstractFileAdapter

getDescription, getExtensions, hasExtension, setAdapterValue, setDescription, setExtensions

Methods inherited from class java.lang.Object

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

Constructor Detail

PhenoXmlAdapter

public PhenoXmlAdapter(org.obo.datamodel.OBOSession session)

This constructor is used when the OBOSession needs to be specified, such as when the CharFieldManager is not in use.

PhenoXmlAdapter

public PhenoXmlAdapter()

Method Detail

load

public CharacterListI load(java.io.File f)

load

public void load()

didCreateDanglers

public boolean didCreateDanglers()

getDanglersList

public java.util.Collection<java.lang.String> getDanglersList()

didMigrateSecondaryIDs

public boolean didMigrateSecondaryIDs()

getMigratedSecondaryIDsList

public java.util.Collection<java.lang.String> getMigratedSecondaryIDsList()

commit

public void commit(CharacterListI charList)

commit

public void commit(CharacterListI charList,
                   java.io.File f)

createPhenotypeCharacter

public static org.bioontologies.obd.schema.pheno.PhenotypeCharacterDocument.PhenotypeCharacter createPhenotypeCharacter(PhenotypeCharacterI phenoCharacter)

createPhenotype

public static org.bioontologies.obd.schema.pheno.PhenotypeDocument.Phenotype createPhenotype(java.util.List<org.bioontologies.obd.schema.pheno.PhenotypeCharacterDocument.PhenotypeCharacter> phenotypeCharacters)

parsePhenotype

public java.util.List<PhenotypeCharacterI> parsePhenotype(org.bioontologies.obd.schema.pheno.PhenotypeDocument.Phenotype phenotype,
                                                          PhenotypeCharacterI.PhenotypeCharacterFactory factory)

parsePhenotypeCharacter

public PhenotypeCharacterI parsePhenotypeCharacter(org.bioontologies.obd.schema.pheno.PhenotypeCharacterDocument.PhenotypeCharacter pc,
                                                   PhenotypeCharacterI.PhenotypeCharacterFactory factory)