Package de.julielab.genemapper.mappingcores

Class DypsisCandidateSetter

java.lang.Object

de.julielab.genemapper.mappingcores.DypsisCandidateSetter

public class DypsisCandidateSetter
extends Object

Field Summary

Fields

Modifier and Type	Field	Description
static boolean	recordStats

Constructor Summary

Constructors

Constructor	Description
DypsisCandidateSetter(Configuration config, CandidateRetrieval candidateRetrieval, NameCentricRetrieval nameCentricRetrieval, DypsisCandidateRanker candidateRanker, de.julielab.geneexpbase.genemodel.GeneOrthologs geneOrthologs)

Method Summary

Modifier and Type	Method	Description
void	clear()
CandidateRetrieval	getCandidateRetrieval()
de.julielab.geneexpbase.configuration.Parameters	getModelParameters()
void	load(File source)
void	loadLexicalCandidateRankingModel(Configuration config)
void	save(File destination, de.julielab.geneexpbase.configuration.Parameters parameters)
void	setCandidates(de.julielab.geneexpbase.genemodel.GeneDocument document, de.julielab.geneexpbase.configuration.Parameters parameterMap, Stats stats)
void	setCandidates(de.julielab.geneexpbase.genemodel.GeneMention gm, AtomicInteger gmidCounter, de.julielab.geneexpbase.configuration.Parameters parameterMap, Stats stats)
void	shutdown()

Methods inherited from class java.lang.Object

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

Field Detail

recordStats

public static final boolean recordStats

See Also:

Constant Field Values

Constructor Detail

DypsisCandidateSetter

@Inject
public DypsisCandidateSetter(Configuration config,
                             CandidateRetrieval candidateRetrieval,
                             NameCentricRetrieval nameCentricRetrieval,
                             DypsisCandidateRanker candidateRanker,
                             de.julielab.geneexpbase.genemodel.GeneOrthologs geneOrthologs)
                      throws GeneMapperInitializationException

Throws:

GeneMapperInitializationException

Method Detail

loadLexicalCandidateRankingModel

public void loadLexicalCandidateRankingModel(Configuration config)
                                      throws GeneMapperInitializationException

Throws:

GeneMapperInitializationException

save

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

load

public void load(File source)
          throws IOException,
                 ClassNotFoundException

Throws:

IOException

ClassNotFoundException

shutdown

public void shutdown()
              throws GeneMapperException

Throws:

GeneMapperException

getCandidateRetrieval

public CandidateRetrieval getCandidateRetrieval()

setCandidates

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

Throws:

GeneMapperException

setCandidates

public void setCandidates(de.julielab.geneexpbase.genemodel.GeneMention gm,
                          AtomicInteger gmidCounter,
                          de.julielab.geneexpbase.configuration.Parameters parameterMap,
                          Stats stats)
                   throws GeneMapperException

Throws:

GeneMapperException

clear

public void clear()

getModelParameters

public de.julielab.geneexpbase.configuration.Parameters getModelParameters()