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A

Ab3P(String, String, String) - Method in class GNormPluslib.GNR

Abb2Longformtok_hash - Static variable in class GNormPluslib.GNormPlus

Annotations - Variable in class GNormPluslib.BioCDoc

B

BioC2PubTator(String, String) - Method in class GNormPluslib.BioCDoc

BioC2PubTator(String, String, String) - Method in class GNormPluslib.BioCDoc

BioCDoc - Class in GNormPluslib

BioCDoc() - Constructor for class GNormPluslib.BioCDoc

BioCFormatCheck(String) - Method in class GNormPluslib.BioCDoc

BioCOutput(String, String, ArrayList<ArrayList<ArrayList<String>>>, boolean, boolean) - Method in class GNormPluslib.BioCDoc

BioCReader(String) - Method in class GNormPluslib.BioCDoc

BioCReaderWithAnnotation(String) - Method in class GNormPluslib.BioCDoc

C

ChromosomeRecognition(String, String) - Method in class GNormPluslib.GN

CRF_learn(String, String) - Method in class GNormPluslib.GNR

CRF_learn(String, String) - Method in class GNormPluslib.SimConcept

CRF_test(String, String, String) - Method in class GNormPluslib.GNR

CRF_test(String, String, String) - Method in class GNormPluslib.SimConcept

CRF_test(String, String, String, String) - Method in class GNormPluslib.GNR

D

Dictionary2Tree_Combine(String, String, String) - Method in class GNormPluslib.PrefixTree

Dictionary2Tree_UniqueGene(String, String, String) - Method in class GNormPluslib.PrefixTree

Dictionary2Tree_UniqueSpecies(String, String, String) - Method in class GNormPluslib.PrefixTree

E

ent_hash - Static variable in class GNormPluslib.GNormPlus

F

FeatureExtraction(String, String, String) - Method in class GNormPluslib.GNR

FeatureExtraction_Test(String) - Method in class GNormPluslib.SimConcept

FeatureExtraction_Train(String) - Method in class GNormPluslib.SimConcept

Filtering_WithLongForm_hash - Static variable in class GNormPluslib.GNormPlus

G

GeneIDRecognition(String, String) - Method in class GNormPluslib.GN

GeneIDs_hash - Static variable in class GNormPluslib.GNormPlus

GeneNormalization(String, String, boolean) - Method in class GNormPluslib.GN

GeneScoring_hash - Static variable in class GNormPluslib.GNormPlus

GeneScoringDF_hash - Static variable in class GNormPluslib.GNormPlus

GeneWithoutSPPrefix_hash - Static variable in class GNormPluslib.GNormPlus

GenusID_hash - Static variable in class GNormPluslib.GNormPlus

getBioCDocobj() - Method in class GNormPluslib.GNPProcessingData

getDocId() - Method in exception GNormPluslib.InconsistentDataException

getFiltering_hash() - Method in class GNormPluslib.GNPProcessingData

getPmid2Abb_hash() - Method in class GNormPluslib.GNPProcessingData

getPmid2ChromosomeGene_hash() - Method in class GNormPluslib.GNPProcessingData

getPmidAbb2LF_hash() - Method in class GNormPluslib.GNPProcessingData

getPmidAbb2LF_lc_hash() - Method in class GNormPluslib.GNPProcessingData

getPmidLF2Abb_hash() - Method in class GNormPluslib.GNPProcessingData

getPmidLF2Abb_lc_hash() - Method in class GNormPluslib.GNPProcessingData

GN - Class in GNormPluslib

GN(GNPProcessingData) - Constructor for class GNormPluslib.GN

GNormPlus - Class in GNormPluslib

GNormPlus() - Constructor for class GNormPluslib.GNormPlus

GNormPluslib - package GNormPluslib

GNPProcessingData - Class in GNormPluslib

GNPProcessingData(Map<String, String>) - Constructor for class GNormPluslib.GNPProcessingData

GNR - Class in GNormPluslib

GNR(GNPProcessingData) - Constructor for class GNormPluslib.GNR

H

Hash2Tree(HashMap<String, String>) - Method in class GNormPluslib.PrefixTree

HomologeneID_hash - Static variable in class GNormPluslib.GNormPlus

I

InconsistentDataException - Exception in GNormPluslib

InconsistentDataException() - Constructor for exception GNormPluslib.InconsistentDataException

InconsistentDataException(String) - Constructor for exception GNormPluslib.InconsistentDataException

InconsistentDataException(String, Throwable) - Constructor for exception GNormPluslib.InconsistentDataException

InconsistentDataException(String, Throwable, boolean, boolean) - Constructor for exception GNormPluslib.InconsistentDataException

InconsistentDataException(Throwable) - Constructor for exception GNormPluslib.InconsistentDataException

initialized - Static variable in class GNormPluslib.GNormPlus

insertMention(String, String) - Method in class GNormPluslib.PrefixTree

L

loadConfiguration(InputStream, String) - Static method in class GNormPluslib.GNormPlus

LoadInputFile(String, String, String) - Method in class GNormPluslib.GNR

loadResources(String, double) - Static method in class GNormPluslib.GNormPlus

M

main(String[]) - Static method in class GNormPluslib.GNormPlus

MatchedTokens_hash - Static variable in class GNormPluslib.GN

MentionMatch(String) - Method in class GNormPluslib.PrefixTree

MentionMatch_species(String) - Method in class GNormPluslib.PrefixTree

N

Normalization2Protein_hash - Static variable in class GNormPluslib.GNormPlus

P

PassageContexts - Variable in class GNormPluslib.BioCDoc

PassageNames - Variable in class GNormPluslib.BioCDoc

PassageOffsets - Variable in class GNormPluslib.BioCDoc

PMIDs - Variable in class GNormPluslib.BioCDoc

PostProcessing(String, String) - Method in class GNormPluslib.GNR

PrefixID_hash - Static variable in class GNormPluslib.GNormPlus

PrefixTree - Class in GNormPluslib

PrefixTree() - Constructor for class GNormPluslib.PrefixTree

PreProcessing4GN(String, String) - Method in class GNormPluslib.GN

PrintTree() - Method in class GNormPluslib.PrefixTree

processFile(String, String, String, double, String) - Static method in class GNormPluslib.GNormPlus

PT_Cell - Static variable in class GNormPluslib.GNormPlus

PT_CTDGene - Static variable in class GNormPluslib.GNormPlus

PT_FamilyName - Static variable in class GNormPluslib.GNormPlus

PT_Gene - Static variable in class GNormPluslib.GNormPlus

PT_GeneChromosome - Static variable in class GNormPluslib.GNormPlus

PT_Species - Static variable in class GNormPluslib.GNormPlus

PubTator2BioC(String, String) - Method in class GNormPluslib.BioCDoc

R

ReadCRFresult(String, String, String) - Method in class GNormPluslib.SimConcept

ReadCRFresult(String, String, String, String) - Method in class GNormPluslib.GNR

ReadCRFresult(String, String, String, String, double, double) - Method in class GNormPluslib.GNR

resetBioCDocobj() - Method in class GNormPluslib.GNPProcessingData

S

SaveTree(String) - Method in class GNormPluslib.PrefixTree

SearchGeneIDLocation(String) - Method in class GNormPluslib.GN

SearchMentionLocation(String, String) - Method in class GNormPluslib.PrefixTree

setDocId(String) - Method in exception GNormPluslib.InconsistentDataException

setup_hash - Static variable in class GNormPluslib.GNormPlus

SetupFile - Static variable in class GNormPluslib.GNormPlus

SimConcept - Class in GNormPluslib

SimConcept(GNPProcessingData) - Constructor for class GNormPluslib.SimConcept

SimConceptMention2Type_hash - Static variable in class GNormPluslib.GNormPlus

SP_Virus2Human_hash - Static variable in class GNormPluslib.GNormPlus

SpeciesAssignment(String, String) - Method in class GNormPluslib.SR

SpeciesAssignment(String, String, String) - Method in class GNormPluslib.SR

SpeciesRecognition(String, String, String, String) - Method in class GNormPluslib.SR

SR - Class in GNormPluslib

SR(GNPProcessingData) - Constructor for class GNormPluslib.SR

StopWord_hash - Static variable in class GNormPluslib.PrefixTree

StrainID_ancestor2tax_hash - Static variable in class GNormPluslib.GNormPlus

StrainID_taxid2names_hash - Static variable in class GNormPluslib.GNormPlus

suffixprefix_orig2modified - Static variable in class GNormPluslib.GNormPlus

SuffixTranslationMap_hash - Static variable in class GNormPluslib.GNormPlus

SuffixTranslationMap2_hash - Static variable in class GNormPluslib.GNormPlus

T

TaxFreq_hash - Static variable in class GNormPluslib.GNormPlus

taxid4gene - Static variable in class GNormPluslib.GNormPlus

TreeFile2Tree(String) - Method in class GNormPluslib.PrefixTree

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