All Classes

Class	Description
Acronym
AcronymLongform
AhoCorasickLongestMatchCallback	To be used with an instance of AhoCorasickOptimized.
AhoCorasickOptimized	TAKEN FROM: https://github.com/lagodiuk/aho-corasick-optimized/blob/master/src/main/java/com/lahodiuk/ahocorasick/AhoCorasickOptimized.java Implementation of the Aho-Corasick string matching algorithm, described in the paper "Efficient String Matching: An Aid to Bibliographic Search", written by Alfred V.
AhoCorasickOptimized.MatchCallback
AhoCorasickOptimized.Util
BioThesaurusIproClassMerger
CandidateCacheKey
CandidateFilter
CandidateRetrieval
Column
ContextGenerator
ContextIndexFieldNames
ContextItemsCacheKey
ContextItemsIndex
ContextUtils
DocumentDisambiguationData
DocumentMappingResult	This class is thought to be used as an overall result when all gene mentions of a document are mapped in a single process.
ExtensionFileFilter
GeneCandidateRetrievalException
GeneDocument
GeneDocumentFactory
GeneIdCandidate
GeneMapperRuntimeException
GeneMapping
GeneMappingAnnotator
GeneMappingConfiguration
GeneMappingException
GeneMention	A basic "gene mention" that most of all contains the text of the mention.
GeneMention.GeneTagger
GeneMention.SpecificType
GeneName
GeneSet
GeneSets
GeneSpeciesOccurrence	Descending order of reliability according to Hakenberg et al.
IOUtils
JaroWinklerScorer
LevenshteinScorer
LuceneCandidateRetrieval
LuceneScorer
MappingCore
MaxEntScorer
MaxEntScorerFeaturePipe
MaxEntScorerML
MaxEntScorerPairExtractor
MentionDisambiguationData
MentionMappingResult
MentionMappingResult.MatchType
MentionMappingResult.RejectionSynHit
MeshHeading
PosTag
QueryGenerator
ReaderInputStream	This class convert Reader to InputStream.
Scorer
SemanticContextIndex
SemanticDisambiguation	Implementing classes of this interface are used at the very end of the gene mapping process.
SemanticIndex	A common interface for all kinds of indices for gene mention disambiguation.
SimpleScorer
SpeciesCandidates
SpeciesMention
SynHit
SynHit.CompareType
SynHitUtils
SynonymIndexFieldNames
TermNormalizer
TokenJaroSimilarity	Jaro distance metric.
TokenJaroSimilarityScorer
UIMAUtils	copied from Ph.
Utils
WeepingTreeDisambiguation	Some simple disambiguation steps for ambiguous synonyms, nothing majorly fancy.
WeepingTreeDocumentDisambiguationData
WeepingTreeMappingCore	A rather relaxed mapping that doesn't try hard to disambiguate and does not filter out gene families or domains.
WeepingTreeMentionDisambiguationData