Package de.julielab.genemapper.disambig

Class ContextItemsIndex

java.lang.Object

de.julielab.genemapper.disambig.ContextItemsIndex

All Implemented Interfaces:

SemanticIndex

public class ContextItemsIndex
extends Object
implements SemanticIndex

Field Summary

Fields

Modifier and Type	Field	Description
org.apache.lucene.search.IndexSearcher	searcher

Constructor Summary

Constructors

Constructor	Description
ContextItemsIndex(de.julielab.geneexpbase.services.CacheService cacheService, Configuration configuration)

Method Summary

Modifier and Type	Method	Description
Collection<String>	getContextItems(ContextItemsCacheKey key)
Collection<String>	getContextItems(String geneId, String field)
Map<String,org.apache.commons.lang3.tuple.Pair<Double,String>>	getContextItemScores(Collection<String> ids, org.apache.lucene.search.BooleanQuery contextQuery, String semanticItemFieldName, boolean returnContextItemValue)
org.apache.lucene.search.IndexSearcher	getContextItemsSearcher()
Map<String,org.apache.commons.lang3.tuple.Pair<Double,String>>	getIntraTaxAmbiguousContextItemScores(de.julielab.geneexpbase.candidateretrieval.SynHit synHit, org.apache.lucene.search.BooleanQuery contextQuery, String semanticItemFieldName, boolean returnContextItemValue)
Map<String,Float>	getSynonymGeneRifScoresForTaxIds(de.julielab.geneexpbase.candidateretrieval.SynHit synHit, Set<String> taxonomyIds)

Methods inherited from class java.lang.Object

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

Field Detail

searcher

public org.apache.lucene.search.IndexSearcher searcher

Constructor Detail

ContextItemsIndex

@Inject
public ContextItemsIndex(de.julielab.geneexpbase.services.CacheService cacheService,
                         Configuration configuration)
                  throws GeneMapperException

Throws:

GeneMapperException

Method Detail

getContextItems

public Collection<String> getContextItems(ContextItemsCacheKey key)
                                   throws ExecutionException

Throws:

ExecutionException

getContextItems

public Collection<String> getContextItems(String geneId,
                                          String field)
                                   throws ExecutionException

Throws:

ExecutionException

getSynonymGeneRifScoresForTaxIds

public Map<String,Float> getSynonymGeneRifScoresForTaxIds(de.julielab.geneexpbase.candidateretrieval.SynHit synHit,
                                                                Set<String> taxonomyIds)
                                                         throws IOException

Parameters:

synHit -

Returns:

Throws:

IOException

getIntraTaxAmbiguousContextItemScores

public Map<String,org.apache.commons.lang3.tuple.Pair<Double,String>> getIntraTaxAmbiguousContextItemScores(de.julielab.geneexpbase.candidateretrieval.SynHit synHit,
                                                                                                                        org.apache.lucene.search.BooleanQuery contextQuery,
                                                                                                                        String semanticItemFieldName,
                                                                                                                        boolean returnContextItemValue)
                                                                                                                 throws IOException

Throws:

IOException

getContextItemScores

public Map<String,org.apache.commons.lang3.tuple.Pair<Double,String>> getContextItemScores(Collection<String> ids,
                                                                                                       org.apache.lucene.search.BooleanQuery contextQuery,
                                                                                                       String semanticItemFieldName,
                                                                                                       boolean returnContextItemValue)
                                                                                                throws IOException

Throws:

IOException

getContextItemsSearcher

public org.apache.lucene.search.IndexSearcher getContextItemsSearcher()