A B C D E F G I J L M N O P S T U V X
All Classes All Packages

A

addPair(String, String) - Method in class de.julielab.gene.candidateretrieval.scoring.MaxEntScorerPairExtractor

simple pair add rule: terms must not be the same and must have at least one token in common.

addPair(String, String, double, int) - Method in class de.julielab.gene.candidateretrieval.scoring.MaxEntScorerPairExtractor

overlap must be at least overlapRatio in both terms and both terms must not be longer than a maximal synonym length

addPairSpecialRules(String, String, double, int) - Method in class de.julielab.gene.candidateretrieval.scoring.MaxEntScorerPairExtractor

as addPair but pair is only allowed if - difference is not only a number or a single character - overlap is not only a number or a single character

ALL_FIELD_FUNCTIONS - Static variable in class de.julielab.gene.candidateretrieval.GeneRecordSynonymsQueryGenerator

ALL_FIELDS - Static variable in class de.julielab.gene.candidateretrieval.GeneRecordQueryGenerator

ALL_FIELDS - Static variable in class de.julielab.gene.candidateretrieval.GeneRecordSynonymsQueryGenerator

ALL_FIELDS_LIST - Static variable in class de.julielab.gene.candidateretrieval.GeneRecordQueryGenerator

APPROX_SCORER_TYPE - Static variable in class de.julielab.gene.candidateretrieval.Configuration

B

BIO_THESAURUS - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

Priority 7

BooleanQueryGenerator - Class in de.julielab.gene.candidateretrieval

BooleanQueryGenerator(BooleanClause.Occur, int) - Constructor for class de.julielab.gene.candidateretrieval.BooleanQueryGenerator

C

candidateLog - Static variable in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

candidateLog - Static variable in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

CandidateRetrieval - Interface in de.julielab.gene.candidateretrieval

CHROMOSOME - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

close() - Method in interface de.julielab.gene.candidateretrieval.CandidateRetrieval

close() - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

close() - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

compareStrings(String, String) - Method in class de.julielab.gene.candidateretrieval.scoring.MaxEntScorerPairExtractor

TODO: comment!

Configuration - Class in de.julielab.gene.candidateretrieval

Configuration() - Constructor for class de.julielab.gene.candidateretrieval.Configuration

Configuration(Configuration) - Constructor for class de.julielab.gene.candidateretrieval.Configuration

Configuration(File) - Constructor for class de.julielab.gene.candidateretrieval.Configuration

Configuration(String...) - Constructor for class de.julielab.gene.candidateretrieval.Configuration

configure() - Method in class de.julielab.gene.candidateretrieval.ioc.IndexModule

CONJUNCTION - Static variable in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

CONJUNCTION - Static variable in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

D

de.julielab.gene.candidateretrieval - package de.julielab.gene.candidateretrieval

de.julielab.gene.candidateretrieval.ioc - package de.julielab.gene.candidateretrieval.ioc

de.julielab.gene.candidateretrieval.scoring - package de.julielab.gene.candidateretrieval.scoring

DESCRIPTION - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

DISJUNCTION - Static variable in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

DISJUNCTION - Static variable in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

DISJUNCTION_MINUS_1 - Static variable in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

DISJUNCTION_MINUS_1 - Static variable in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

DISJUNCTION_MINUS_2 - Static variable in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

DISJUNCTION_MINUS_2 - Static variable in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

E

ECNUMBER - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

ENTITY_TYPE - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

The type of the entity denoted by this synonym, gene, protein or family.

eval(Classifier, InstanceList) - Method in class de.julielab.gene.candidateretrieval.scoring.MaxEntScorerML

EXACT_SCORER_TYPE - Static variable in class de.julielab.gene.candidateretrieval.Configuration

F

featureCreationTime - Static variable in class de.julielab.gene.candidateretrieval.scoring.MaxEntScorerFeaturePipe

FILTERED - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

A boolean-numerical (0 or 1) value to indicate whether the value was recognized as being unspecific or otherwise non-helpful.

FULL_NAMES - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

Priority 1

G

GENE_RECORD_INDEX - Static variable in class de.julielab.gene.candidateretrieval.Configuration

GENE_RECORD_ORIGINAL_NAMES_INDEX - Static variable in class de.julielab.gene.candidateretrieval.Configuration

GENE_RECORDS_CNF - Static variable in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

Conjunctive normal form query where all tokens must be found in any field.

GENE_RECORDS_CNF_WITH_SYNONYMS - Static variable in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

Just like LuceneCandidateRetrieval.GENE_RECORDS_CNF but with an additional BooleanClause.Occur.SHOULD clause only for synonym matches created via GeneRecordSynonymsQueryGenerator.

GENE_RECORDS_DISMAX - Static variable in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

GENE_RECORDS_FLAT_DISJUNCTION - Static variable in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

Puts all tokens on all fields in one large disjunction.

GENE_RECORDS_SYNONYMS_APPROX - Static variable in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

GENE_RECORDS_SYNONYMS_EXACT - Static variable in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

GeneNameQueries - Class in de.julielab.gene.candidateretrieval

This class creates different forms of Lucene queries for the retrieval of gene record matching an input gene name.

GeneNameQueries() - Constructor for class de.julielab.gene.candidateretrieval.GeneNameQueries

generateQuery(CandidateCacheKey) - Method in class de.julielab.gene.candidateretrieval.BooleanQueryGenerator

generateQuery(CandidateCacheKey) - Method in class de.julielab.gene.candidateretrieval.GeneRecordQueryGenerator

generateQuery(CandidateCacheKey) - Method in class de.julielab.gene.candidateretrieval.GeneRecordsEcNumberQueryGenerator

generateQuery(CandidateCacheKey) - Method in class de.julielab.gene.candidateretrieval.GeneRecordSynonymsQueryGenerator

generateQuery(CandidateCacheKey) - Method in class de.julielab.gene.candidateretrieval.NGramQueryGenerator

GeneRecordHit - Class in de.julielab.gene.candidateretrieval

GeneRecordHit(String, double, String, String) - Constructor for class de.julielab.gene.candidateretrieval.GeneRecordHit

GeneRecordQueryGenerator - Class in de.julielab.gene.candidateretrieval

GeneRecordQueryGenerator() - Constructor for class de.julielab.gene.candidateretrieval.GeneRecordQueryGenerator

GeneRecordQueryGenerator(boolean) - Constructor for class de.julielab.gene.candidateretrieval.GeneRecordQueryGenerator

GeneRecordQueryGenerator(boolean, boolean) - Constructor for class de.julielab.gene.candidateretrieval.GeneRecordQueryGenerator

GeneRecordQueryGenerator(boolean, boolean, boolean, boolean) - Constructor for class de.julielab.gene.candidateretrieval.GeneRecordQueryGenerator

GeneRecordQueryGenerator(boolean, boolean, boolean, boolean, boolean) - Constructor for class de.julielab.gene.candidateretrieval.GeneRecordQueryGenerator

GeneRecordQueryGenerator(boolean, boolean, boolean, boolean, boolean, boolean, boolean) - Constructor for class de.julielab.gene.candidateretrieval.GeneRecordQueryGenerator

GeneRecordQueryGenerator(boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean) - Constructor for class de.julielab.gene.candidateretrieval.GeneRecordQueryGenerator

GeneRecordQueryGenerator(boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, int) - Constructor for class de.julielab.gene.candidateretrieval.GeneRecordQueryGenerator

GeneRecordQueryGenerator(boolean, boolean, boolean, boolean, boolean, boolean, boolean, int) - Constructor for class de.julielab.gene.candidateretrieval.GeneRecordQueryGenerator

GeneRecordsEcNumberQueryGenerator - Class in de.julielab.gene.candidateretrieval

GeneRecordsEcNumberQueryGenerator() - Constructor for class de.julielab.gene.candidateretrieval.GeneRecordsEcNumberQueryGenerator

GeneRecordSynonymsQueryGenerator - Class in de.julielab.gene.candidateretrieval

GeneRecordSynonymsQueryGenerator(boolean) - Constructor for class de.julielab.gene.candidateretrieval.GeneRecordSynonymsQueryGenerator

GeneRecordSynonymsQueryGenerator(boolean, String[]) - Constructor for class de.julielab.gene.candidateretrieval.GeneRecordSynonymsQueryGenerator

GeneRecordSynonymsQueryGenerator(boolean, String[], BooleanClause.Occur) - Constructor for class de.julielab.gene.candidateretrieval.GeneRecordSynonymsQueryGenerator

GENERIF - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

getBioThesaurusNames() - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

getCacheHits() - Static method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getCacheMisses() - Static method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getCandidates(GeneMention, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getCandidates(GeneMention, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getCandidates(GeneMention, String, QueryGenerator) - Method in interface de.julielab.gene.candidateretrieval.CandidateRetrieval

getCandidates(GeneMention, String, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getCandidates(GeneMention, String, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getCandidates(GeneMention, Collection<String>, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getCandidates(GeneMention, Collection<String>, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getCandidates(GeneMention, Collection<String>, Parameters, QueryGenerator) - Method in interface de.julielab.gene.candidateretrieval.CandidateRetrieval

getCandidates(GeneMention, Collection<String>, Parameters, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getCandidates(GeneMention, Collection<String>, Parameters, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getCandidates(GeneMention, Collection<String>, Collection<String>, boolean, Parameters, int, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getCandidates(GeneMention, Collection<String>, Collection<String>, boolean, Parameters, QueryGenerator) - Method in interface de.julielab.gene.candidateretrieval.CandidateRetrieval

getCandidates(GeneMention, Collection<String>, Collection<String>, boolean, Parameters, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getCandidates(GeneMention, Collection<String>, Collection<String>, boolean, Parameters, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getCandidates(GeneMention, Collection<String>, Collection<String>, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getCandidates(GeneMention, Collection<String>, Collection<String>, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getCandidates(String, QueryGenerator) - Method in interface de.julielab.gene.candidateretrieval.CandidateRetrieval

getCandidates(String, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getCandidates(String, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getCandidates(String, String, QueryGenerator) - Method in interface de.julielab.gene.candidateretrieval.CandidateRetrieval

getCandidates(String, String, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getCandidates(String, String, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getCandidates(String, Collection<String>, QueryGenerator) - Method in interface de.julielab.gene.candidateretrieval.CandidateRetrieval

getCandidates(String, Collection<String>, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getCandidates(String, Collection<String>, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getCandidates(String, Collection<String>, Collection<String>, boolean, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getCandidates(String, Collection<String>, Collection<String>, boolean, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getCandidates(String, Collection<String>, Collection<String>, QueryGenerator) - Method in interface de.julielab.gene.candidateretrieval.CandidateRetrieval

getCandidates(String, Collection<String>, Collection<String>, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getCandidates(String, Collection<String>, Collection<String>, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getChromosome() - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

getCommonTokens(GeneMention) - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

getConfiguration() - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getDescriptions() - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

getEcNumber() - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

getFamilyNames(GeneMention, QueryGenerator) - Method in interface de.julielab.gene.candidateretrieval.CandidateRetrieval

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

getFamilyNames(GeneMention, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getFamilyNames(GeneMention, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getFullNames() - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

getGeneNames() - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

getGeneRecords(Collection<String>) - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getGeneRecords(Collection<String>) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getGeneRifs() - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

getGoDescriptors() - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

getIndexEntries(List<String>) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getIndexRecords(Collection<String>) - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

Returns GeneRecordHit instances with all fields loaded.

getIndexRecords(Collection<String>) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

The record-index equivalent to NameCentricRetrieval.getIndexEntries(List).

getIndexRecords(Collection<String>, GeneName, Function<GeneName, String>, IndexSearcher) - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getIndexRecords(Collection<String>, IndexSearcher) - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getInteractions() - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

getMajoritySpecifiers() - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

getMapLocation() - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

getName() - Method in class de.julielab.gene.candidateretrieval.BooleanQueryGenerator

getName() - Method in class de.julielab.gene.candidateretrieval.GeneRecordQueryGenerator

getName() - Method in class de.julielab.gene.candidateretrieval.GeneRecordsEcNumberQueryGenerator

getName() - Method in class de.julielab.gene.candidateretrieval.GeneRecordSynonymsQueryGenerator

getName() - Method in class de.julielab.gene.candidateretrieval.NGramQueryGenerator

getNormalizedExactMatchThenLuceneScoreComparator(String, boolean) - Static method in class de.julielab.gene.candidateretrieval.GeneRecordHit

Returns a comparator that sorts SynHits first according to their equality to the gene name and then by score.This helps to overcome the issue that Lucene's float scores sometimes fail to put an exact equal match to the top of the results.

getNormalizedGeneNameTokenSet() - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

getNormalizer() - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getNormalizer() - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getOriginalNamesIndexRecords(Collection<String>) - Method in interface de.julielab.gene.candidateretrieval.CandidateRetrieval

getOriginalNamesIndexRecords(Collection<String>) - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getOriginalNamesIndexRecords(Collection<String>) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getOriginalNamesIndexRecords(Collection<String>, GeneName) - Method in interface de.julielab.gene.candidateretrieval.CandidateRetrieval

getOriginalNamesIndexRecords(Collection<String>, GeneName) - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getOriginalNamesIndexRecords(Collection<String>, GeneName) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getOtherDesignations() - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

getPairs(File, File, int, float) - Method in class de.julielab.gene.candidateretrieval.scoring.MaxEntScorerPairExtractor

TODO: comment!

getPriorityNames(String, int) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getPriorityNames(Collection<String>, int) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getPriorityNamesMap(Collection<String>, int) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getScore(String, String) - Method in class de.julielab.gene.candidateretrieval.scoring.LuceneScorer

getScore(String, String) - Method in class de.julielab.gene.candidateretrieval.scoring.MaxEntScorer

get the score for an unlabeled pair

getScorer() - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getScorer() - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getScorerInfo() - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getScorerInfo() - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getScorerType() - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getScorerType() - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getScorerType() - Method in class de.julielab.gene.candidateretrieval.scoring.LuceneScorer

getScorerType() - Method in class de.julielab.gene.candidateretrieval.scoring.MaxEntScorer

getSpellingChecker() - Method in interface de.julielab.gene.candidateretrieval.CandidateRetrieval

getSpellingChecker() - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getSpellingChecker() - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getSummaries() - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

getSymbol() - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

getSymbolFromNomenclature() - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

getSynonymField() - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

getSynonyms() - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

getSynonyms(String) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getSynonymSimilarityScore() - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

getTFIDFOnGeneRecordNames() - Method in interface de.julielab.gene.candidateretrieval.CandidateRetrieval

getTFIDFOnGeneRecordNames() - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getTFIDFOnGeneRecordNames() - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getTFIDFOnGeneSynonyms() - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getTotalCacheGettime() - Static method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getTotalCacheGettime() - Static method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getTotalCachePuttime() - Static method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getTotalCachePuttime() - Static method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getTotalGeneRecordFieldLoadingTime() - Static method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getTotalLuceneQueryTime() - Static method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

getTotalLuceneQueryTime() - Static method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

getUniprotNames() - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

getXrefs() - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

GODESC - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

I

ID_FIELD - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

ID_FIELD_LEGACY - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

IndexModule - Class in de.julielab.gene.candidateretrieval.ioc

IndexModule(Configuration) - Constructor for class de.julielab.gene.candidateretrieval.ioc.IndexModule

info() - Method in class de.julielab.gene.candidateretrieval.scoring.LuceneScorer

info() - Method in class de.julielab.gene.candidateretrieval.scoring.MaxEntScorer

init() - Method in class de.julielab.gene.candidateretrieval.NGramQueryGenerator

INTERACTION - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

isUseContextGenesAsRelevanceSignal() - Method in class de.julielab.gene.candidateretrieval.GeneRecordQueryGenerator

J

JAROWINKLER_SCORER - Static variable in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

JAROWINKLER_SCORER - Static variable in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

L

LEVENSHTEIN_SCORER - Static variable in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

LEVENSHTEIN_SCORER - Static variable in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

LOGGER_NAME_CANDIDATES - Static variable in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

LOGGER_NAME_CANDIDATES - Static variable in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

LOOKUP_SYN_FIELD - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

The index field name for the normalized gene / protein name.

LOOKUP_SYN_FIELD_EXACT - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

LOOKUP_SYN_FIELD_NGRAMS - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

LOOKUP_SYN_FIELD_STEMMED - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

LUCENE_MAX_HITS - Static variable in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

the maximal number of hits lucene returns for a query

LUCENE_MAX_HITS - Static variable in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

the maximal number of hits lucene returns for a query

LUCENE_SCORER - Static variable in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

LUCENE_SCORER - Static variable in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

LuceneCandidateRetrieval - Class in de.julielab.gene.candidateretrieval

LuceneCandidateRetrieval(Configuration, ExecutorService, CacheService) - Constructor for class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

LuceneCandidateRetrieval(IndexSearcher, Scorer) - Constructor for class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

Deprecated.

LuceneScorer - Class in de.julielab.gene.candidateretrieval.scoring

LuceneScorer() - Constructor for class de.julielab.gene.candidateretrieval.scoring.LuceneScorer

M

main(String[]) - Static method in class de.julielab.gene.candidateretrieval.scoring.MaxEntScorer

makeBooleanQuery(String, String, BooleanClause.Occur, int) - Static method in class de.julielab.gene.candidateretrieval.GeneNameQueries

makeInstances(ArrayList<String[]>) - Method in class de.julielab.gene.candidateretrieval.scoring.MaxEntScorerML

makeInstances(ArrayList<String[]>, Pipe) - Method in class de.julielab.gene.candidateretrieval.scoring.MaxEntScorerML

mapGeneIdToTaxId(String) - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

mapGeneIdToTaxId(String) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

MAPLOCATION - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

MAXENT_SCORER - Static variable in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

MAXENT_SCORER - Static variable in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

MAXENT_SCORER_MODEL - Static variable in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

default model for MaxEntScorer

MAXENT_SCORER_MODEL - Static variable in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

default model for MaxEntScorer

MaxEntScorer - Class in de.julielab.gene.candidateretrieval.scoring

MaxEntScorer(File) - Constructor for class de.julielab.gene.candidateretrieval.scoring.MaxEntScorer

MaxEntScorer(InputStream) - Constructor for class de.julielab.gene.candidateretrieval.scoring.MaxEntScorer

MaxEntScorerFeaturePipe - Class in de.julielab.gene.candidateretrieval.scoring

MaxEntScorerFeaturePipe() - Constructor for class de.julielab.gene.candidateretrieval.scoring.MaxEntScorerFeaturePipe

MaxEntScorerFeaturePipe(Alphabet) - Constructor for class de.julielab.gene.candidateretrieval.scoring.MaxEntScorerFeaturePipe

MaxEntScorerML - Class in de.julielab.gene.candidateretrieval.scoring

MaxEntScorerML() - Constructor for class de.julielab.gene.candidateretrieval.scoring.MaxEntScorerML

MaxEntScorerPairExtractor - Class in de.julielab.gene.candidateretrieval.scoring

MaxEntScorerPairExtractor() - Constructor for class de.julielab.gene.candidateretrieval.scoring.MaxEntScorerPairExtractor

N

NAME_CENTRIC_INDEX - Static variable in class de.julielab.gene.candidateretrieval.Configuration

NAME_PRIO_DELIMITER - Static variable in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

NAME_PRIO_DELIMITER - Static variable in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

NameCentricRetrieval - Class in de.julielab.gene.candidateretrieval

NameCentricRetrieval(Configuration, CacheService) - Constructor for class de.julielab.gene.candidateretrieval.NameCentricRetrieval

NGRAM_2_3 - Static variable in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

NGRAM_2_3 - Static variable in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

NGramQueryGenerator - Class in de.julielab.gene.candidateretrieval

NGramQueryGenerator(int, int) - Constructor for class de.julielab.gene.candidateretrieval.NGramQueryGenerator

O

ORIGINAL_NAME - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

The index field name for the original, unnormalized (however, lower-cased) gene / protein name.

OTHER_DESIGNATIONS - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

Priority 3

P

PARAM_DISMAX_TIE_BREAKER - Static variable in class de.julielab.gene.candidateretrieval.Configuration

PARAM_SORT_CANDIDATES_BY_MATCHED_FIELD - Static variable in class de.julielab.gene.candidateretrieval.Configuration

PARAM_USE_QUERY_FIELD_WEIGHTS - Static variable in class de.julielab.gene.candidateretrieval.Configuration

Whether to use field weights in the Lucene query to the candidate index.

pipe(Instance) - Method in class de.julielab.gene.candidateretrieval.scoring.MaxEntScorerFeaturePipe

the main function of a pipe used to acutally build the features

predict(Instance, Classifier) - Method in class de.julielab.gene.candidateretrieval.scoring.MaxEntScorerML

return the probability of the true class

PREFIX_CANDIDATE_RETRIEVAL - Static variable in class de.julielab.gene.candidateretrieval.Configuration

PRIORITY - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

A numerical priority where 1 is the highest priority.

PROTEIN_NAMES - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

Priority 4

S

scoreIdsByBoWSynonyms(Collection<String>, Set<String>, QueryGenerator) - Method in interface de.julielab.gene.candidateretrieval.CandidateRetrieval

scoreIdsByBoWSynonyms(Collection<String>, Set<String>, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

scoreIdsByBoWSynonyms(Collection<String>, Set<String>, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

scoreIdsByExactSynonyms(Collection<String>, Set<String>) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

scoreIdsByNGramSynonyms(String, Set<String>) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

scoreSynonymsRecordIndex(String, Map<String, Collection<GeneName>>, Function<GeneRecordHit, String[]>, QueryGenerator) - Method in interface de.julielab.gene.candidateretrieval.CandidateRetrieval

scoreSynonymsRecordIndex(String, Map<String, Collection<GeneName>>, Function<GeneRecordHit, String[]>, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

Scores each synonym in allSynonym against the IDs in ids.

scoreSynonymsRecordIndex(String, Map<String, Collection<GeneName>>, Function<GeneRecordHit, String[]>, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

scoreSynonymsRecordIndex(Collection<GeneName>, Set<String>, Function<GeneRecordHit, String[]>, QueryGenerator) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

Scores each synonym in allSynonym against the IDs in ids.

setBioThesaurusNames(String[]) - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

setChromosome(String) - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

setDescriptions(String[]) - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

setEcNumber(String) - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

setFeatures(String, String, String, Map<String, Double>, int) - Method in class de.julielab.gene.candidateretrieval.scoring.MaxEntScorerFeaturePipe

setFullNames(String[]) - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

setFulltextFieldsToRecordHits(Collection<? extends SynHit>, Collection<String>) - Method in interface de.julielab.gene.candidateretrieval.CandidateRetrieval

setFulltextFieldsToRecordHits(Collection<? extends SynHit>, Collection<String>) - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

Sets the full text / gene context fields (generif, summary, interactions) to instances of GeneRecordHit.

setFulltextFieldsToRecordHits(Collection<? extends SynHit>, Collection<String>) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

setGeneRifs(String[]) - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

setGoDescriptors(String[]) - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

setInteractions(String[]) - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

setMapLocation(String) - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

setNomenclature(String) - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

setNormalizer(TermNormalizer) - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

setNormalizer(TermNormalizer) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

setOtherDesignations(String[]) - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

setScorerType(int) - Method in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

setScorerType(int) - Method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

setSummaries(String[]) - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

setSymbol(String) - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

setSynonymField(String) - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

setSynonyms(String[]) - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

setSynonymSimilarityScore(double) - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

setUniprotNames(String[]) - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

setXrefs(String[]) - Method in class de.julielab.gene.candidateretrieval.GeneRecordHit

showPairs(ArrayList<String[]>) - Method in class de.julielab.gene.candidateretrieval.scoring.MaxEntScorerPairExtractor

shutdownExecutor() - Static method in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

SIMPLE_SCORER - Static variable in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

SIMPLE_SCORER - Static variable in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

SOURCE - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

The source of the ID, e.g.

SPELLING_INDEX - Static variable in class de.julielab.gene.candidateretrieval.Configuration

STEMMED_NORMALIZED_NAME - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

The index field name for the normalized and then token-wise stemmed gene / protein name.

storePairs(ArrayList<String[]>, File) - Method in class de.julielab.gene.candidateretrieval.scoring.MaxEntScorerPairExtractor

SUMMARY - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

SYMBOL - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

Priority -1

SYMBOL_FROM_NOMCENCLATURE - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

Priority 0

SYNONYM_FIELDS - Static variable in class de.julielab.gene.candidateretrieval.GeneRecordQueryGenerator

SYNONYM_FIELDS_NOT_CHROMOSOMAL - Static variable in class de.julielab.gene.candidateretrieval.GeneRecordQueryGenerator

SynonymIndexFieldNames - Class in de.julielab.gene.candidateretrieval

SynonymIndexFieldNames() - Constructor for class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

SYNONYMS - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

Priority 2

T

TAX_ID_FIELD - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

TEST_MODE - Static variable in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

TFIDF - Static variable in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

TFIDF - Static variable in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

TOKEN_JAROWINKLER_SCORER - Static variable in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

TOKEN_JAROWINKLER_SCORER - Static variable in class de.julielab.gene.candidateretrieval.NameCentricRetrieval

train(InstanceList) - Method in class de.julielab.gene.candidateretrieval.scoring.MaxEntScorerML

train the classifier

U

UNIPROT_NAMES - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

Priority 5

UNIT_TEST_GENE_ID_ACCUMULATION_SET - Static variable in class de.julielab.gene.candidateretrieval.LuceneCandidateRetrieval

USE_LUCENE_CANDIDATES_CACHE - Static variable in class de.julielab.gene.candidateretrieval.Configuration

V

VALUE_FAMILY_ID_PREFIX - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

VARIANT_NAME - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

The index field name for the normalized variant of the original gene / protein name.

X

XREFS - Static variable in class de.julielab.gene.candidateretrieval.SynonymIndexFieldNames

Priority 6

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