Package de.julielab.genemapper.mappingcores

Class DypsisMappingCore

java.lang.Object

de.julielab.genemapper.mappingcores.DypsisMappingCore

All Implemented Interfaces:

MappingCore

public class DypsisMappingCore
extends Object
implements MappingCore

This mapping core is named after the Dypsis lutescens, "Goldfruchtpalme" is is supposed to augment the older YukkaMappingCore with a document oriented integrity approach.

Author:

faessler

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	DypsisMappingCore.NameLevelUnificationStrategy

Field Summary

Fields

Modifier and Type	Field	Description
static org.slf4j.Logger	filterLog
static org.slf4j.Logger	timerLog

Constructor Summary

Constructors

Constructor	Description
DypsisMappingCore(de.julielab.geneexpbase.TermNormalizer normalizer, CandidateRetrieval candidateRetrieval, DypsisCandidateSetter candidateSetter, WikipediaEntityClassDecisionBear decisionBear, GeneCompositeNameResolver geneCompositeNameResolver, de.julielab.speciesassignment.GeneSpeciesAssigner speciesAssigner, de.julielab.speciesassignment.spi.SpeciesAssignmentFilter assignmentFilter)

Method Summary

Modifier and Type	Method	Description
void	checkSpeciesAssigner()	Performs a null check for the speciesAssigner and throws an exception if it is not present.
void	clear()
CandidateRetrieval	getCandidateRetrieval()
DypsisCandidateSetter	getCandidateSetter()
ContextRanker	getContextualRanking()
de.julielab.geneexpbase.TermNormalizer	getTermNormalizer()
void	loadCandidateSetter(File source)
void	loadParameters(File soruce)
de.julielab.geneexpbase.genemodel.DocumentMappingResult	map(de.julielab.geneexpbase.genemodel.GeneDocument document)	Maps the gene mentions in the passed document to database IDs.
de.julielab.geneexpbase.genemodel.DocumentMappingResult	map(de.julielab.geneexpbase.genemodel.GeneDocument document, de.julielab.geneexpbase.configuration.Parameters parameterMap, Stats stats)
de.julielab.geneexpbase.genemodel.MentionMappingResult	map(de.julielab.geneexpbase.genemodel.GeneMention predictedMention)
void	saveCandidateSetter(File destination, de.julielab.geneexpbase.configuration.Parameters parameters)
void	saveParameter(File destination)
void	setOmitCandidateSetting(boolean omitCandidateSetting)
void	shutdown()	Indicates that the mapping process has finished and all held resources should be freed.

Methods inherited from class java.lang.Object

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

Field Detail

filterLog

public static final org.slf4j.Logger filterLog

timerLog

public static final org.slf4j.Logger timerLog

Constructor Detail

DypsisMappingCore

@Inject
public DypsisMappingCore(de.julielab.geneexpbase.TermNormalizer normalizer,
                         CandidateRetrieval candidateRetrieval,
                         DypsisCandidateSetter candidateSetter,
                         WikipediaEntityClassDecisionBear decisionBear,
                         GeneCompositeNameResolver geneCompositeNameResolver,
                         de.julielab.speciesassignment.GeneSpeciesAssigner speciesAssigner,
                         de.julielab.speciesassignment.spi.SpeciesAssignmentFilter assignmentFilter)
                  throws GeneMapperException

Throws:

GeneMapperException

Method Detail

getCandidateSetter

public DypsisCandidateSetter getCandidateSetter()

setOmitCandidateSetting

public void setOmitCandidateSetting(boolean omitCandidateSetting)

saveCandidateSetter

public void saveCandidateSetter(File destination,
                                de.julielab.geneexpbase.configuration.Parameters parameters)

loadCandidateSetter

public void loadCandidateSetter(File source)
                         throws IOException,
                                ClassNotFoundException

Throws:

IOException

ClassNotFoundException

map

public de.julielab.geneexpbase.genemodel.DocumentMappingResult map(de.julielab.geneexpbase.genemodel.GeneDocument document)
                                                            throws GeneMapperException

Maps the gene mentions in the passed document to database IDs. Algorithm parameters are taken from Configuration the mapping core was constructed with.

Specified by:

map in interface MappingCore

Parameters:

document - The document for which to map the gene mentions.

Returns:

The result of the mapping.

Throws:

GeneMapperException - If the mapping process fails.

saveParameter

public void saveParameter(File destination)

loadParameters

public void loadParameters(File soruce)

map

public de.julielab.geneexpbase.genemodel.DocumentMappingResult map(de.julielab.geneexpbase.genemodel.GeneDocument document,
                                                                   de.julielab.geneexpbase.configuration.Parameters parameterMap,
                                                                   Stats stats)
                                                            throws GeneMapperException

Specified by:

map in interface MappingCore

Throws:

GeneMapperException

checkSpeciesAssigner

public void checkSpeciesAssigner()

Performs a null check for the speciesAssigner and throws an exception if it is not present.

Throws:

IllegalStateException - If the species assigner is null.

shutdown

public void shutdown()
              throws GeneMapperException

Description copied from interface: MappingCore

Indicates that the mapping process has finished and all held resources should be freed.

Specified by:

shutdown in interface MappingCore

Throws:

GeneMapperException

clear

public void clear()

Specified by:

clear in interface MappingCore

map

public de.julielab.geneexpbase.genemodel.MentionMappingResult map(de.julielab.geneexpbase.genemodel.GeneMention predictedMention)
                                                           throws GeneMapperException

Specified by:

map in interface MappingCore

Throws:

GeneMapperException

getContextualRanking

public ContextRanker getContextualRanking()

Specified by:

getContextualRanking in interface MappingCore

getCandidateRetrieval

public CandidateRetrieval getCandidateRetrieval()

Specified by:

getCandidateRetrieval in interface MappingCore

getTermNormalizer

public de.julielab.geneexpbase.TermNormalizer getTermNormalizer()

Specified by:

getTermNormalizer in interface MappingCore