Package de.julielab.gene.candidateretrieval

Interface CandidateRetrieval

All Superinterfaces:

AutoCloseable, de.julielab.geneexpbase.candidateretrieval.CandidateRetrieval, Closeable

All Known Implementing Classes:

LuceneCandidateRetrieval, NameCentricRetrieval

public interface CandidateRetrieval
extends de.julielab.geneexpbase.candidateretrieval.CandidateRetrieval, Closeable

Method Summary

Modifier and Type	Method	Description
void	close()
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	getCandidates(de.julielab.geneexpbase.genemodel.GeneMention geneMention, String organism, de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	getCandidates(de.julielab.geneexpbase.genemodel.GeneMention gm, Collection<String> taxId, de.julielab.geneexpbase.configuration.Parameters parameters, de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	getCandidates(de.julielab.geneexpbase.genemodel.GeneMention geneMention, Collection<String> geneIdsFilter, Collection<String> organisms, boolean loadFields, de.julielab.geneexpbase.configuration.Parameters parameters, de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	getCandidates(String originalSearchTerm, de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	getCandidates(String geneMentionText, String organism, de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	getCandidates(String geneMentionText, Collection<String> organism, de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	getCandidates(String geneMentionText, Collection<String> geneIdsFilter, Collection<String> organism, de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	getFamilyNames(de.julielab.geneexpbase.genemodel.GeneMention gm, de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)	Searches the index for the given gene mention filtered for family names.
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	getOriginalNamesIndexRecords(Collection<String> geneIds)
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	getOriginalNamesIndexRecords(Collection<String> geneIds, de.julielab.geneexpbase.genemodel.GeneName geneName)
org.apache.lucene.search.spell.SpellChecker	getSpellingChecker()
de.julielab.geneexpbase.scoring.TFIDFScorer	getTFIDFOnGeneRecordNames()
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	scoreIdsByBoWSynonyms(Collection<String> allSynonyms, Set<String> ids, de.julielab.geneexpbase.candidateretrieval.QueryGenerator disjunction)
org.apache.commons.lang3.tuple.Pair<Map<String,Double>,Map<String,Set<String>>>	scoreSynonymsRecordIndex(String queryType, Map<String,Collection<de.julielab.geneexpbase.genemodel.GeneName>> ids2entities, Function<GeneRecordHit,String[]> synhit2namesFunc, de.julielab.geneexpbase.candidateretrieval.QueryGenerator qg)
void	setFulltextFieldsToRecordHits(Collection<? extends de.julielab.geneexpbase.candidateretrieval.SynHit> recordHits, Collection<String> recordContextFieldNames)

Methods inherited from interface de.julielab.geneexpbase.candidateretrieval.CandidateRetrieval

getCandidates, getCandidates, getCandidates, mapGeneIdToTaxId

Method Detail

getCandidates

List<de.julielab.geneexpbase.candidateretrieval.SynHit> getCandidates(String originalSearchTerm,
                                                                      de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)

getCandidates

List<de.julielab.geneexpbase.candidateretrieval.SynHit> getCandidates(de.julielab.geneexpbase.genemodel.GeneMention geneMention,
                                                                      String organism,
                                                                      de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)

getCandidates

List<de.julielab.geneexpbase.candidateretrieval.SynHit> getCandidates(String geneMentionText,
                                                                      String organism,
                                                                      de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)

getCandidates

List<de.julielab.geneexpbase.candidateretrieval.SynHit> getCandidates(String geneMentionText,
                                                                      Collection<String> organism,
                                                                      de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)

getCandidates

List<de.julielab.geneexpbase.candidateretrieval.SynHit> getCandidates(de.julielab.geneexpbase.genemodel.GeneMention geneMention,
                                                                      Collection<String> geneIdsFilter,
                                                                      Collection<String> organisms,
                                                                      boolean loadFields,
                                                                      de.julielab.geneexpbase.configuration.Parameters parameters,
                                                                      de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)

getCandidates

List<de.julielab.geneexpbase.candidateretrieval.SynHit> getCandidates(String geneMentionText,
                                                                      Collection<String> geneIdsFilter,
                                                                      Collection<String> organism,
                                                                      de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)

scoreIdsByBoWSynonyms

List<de.julielab.geneexpbase.candidateretrieval.SynHit> scoreIdsByBoWSynonyms(Collection<String> allSynonyms,
                                                                              Set<String> ids,
                                                                              de.julielab.geneexpbase.candidateretrieval.QueryGenerator disjunction)

getCandidates

List<de.julielab.geneexpbase.candidateretrieval.SynHit> getCandidates(de.julielab.geneexpbase.genemodel.GeneMention gm,
                                                                      Collection<String> taxId,
                                                                      de.julielab.geneexpbase.configuration.Parameters parameters,
                                                                      de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)

close

void close()

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

getFamilyNames

List<de.julielab.geneexpbase.candidateretrieval.SynHit> getFamilyNames(de.julielab.geneexpbase.genemodel.GeneMention gm,
                                                                       de.julielab.geneexpbase.candidateretrieval.QueryGenerator queryGenerator)

Searches the index for the given gene mention filtered for family names.

Parameters:

gm - The gene mention to check for family names.

queryGenerator - The query generator to use.

Returns:

getOriginalNamesIndexRecords

List<de.julielab.geneexpbase.candidateretrieval.SynHit> getOriginalNamesIndexRecords(Collection<String> geneIds,
                                                                                     de.julielab.geneexpbase.genemodel.GeneName geneName)

getOriginalNamesIndexRecords

List<de.julielab.geneexpbase.candidateretrieval.SynHit> getOriginalNamesIndexRecords(Collection<String> geneIds)

getTFIDFOnGeneRecordNames

de.julielab.geneexpbase.scoring.TFIDFScorer getTFIDFOnGeneRecordNames()

setFulltextFieldsToRecordHits

void setFulltextFieldsToRecordHits(Collection<? extends de.julielab.geneexpbase.candidateretrieval.SynHit> recordHits,
                                   Collection<String> recordContextFieldNames)

scoreSynonymsRecordIndex

org.apache.commons.lang3.tuple.Pair<Map<String,Double>,Map<String,Set<String>>> scoreSynonymsRecordIndex(String queryType,
                                                                                                                           Map<String,Collection<de.julielab.geneexpbase.genemodel.GeneName>> ids2entities,
                                                                                                                           Function<GeneRecordHit,String[]> synhit2namesFunc,
                                                                                                                           de.julielab.geneexpbase.candidateretrieval.QueryGenerator qg)

getSpellingChecker

org.apache.lucene.search.spell.SpellChecker getSpellingChecker()