Hierarchy For All Packages

Package Hierarchies:

• com.lahodiuk.ahocorasick,
• de.julielab.jules.ae.genemapping,
• de.julielab.jules.ae.genemapping.disambig,
• de.julielab.jules.ae.genemapping.genemodel,
• de.julielab.jules.ae.genemapping.index,
• de.julielab.jules.ae.genemapping.mappingcores,
• de.julielab.jules.ae.genemapping.scoring,
• de.julielab.jules.ae.genemapping.utils,
• de.julielab.jules.ae.genemapping.utils.dict,
• de.julielab.jules.ae.genemapping.utils.norm

Class Hierarchy

• java.lang.Object
  • java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    • java.util.AbstractSet<E> (implements java.util.Set<E>)
      • java.util.HashSet<E> (implements java.lang.Cloneable, java.io.Serializable, java.util.Set<E>)
        • de.julielab.jules.ae.genemapping.genemodel.GeneSet
        • de.julielab.jules.ae.genemapping.genemodel.GeneSets
  • com.wcohen.ss.AbstractStringDistance (implements com.wcohen.ss.api.StringDistance, com.wcohen.ss.api.StringDistanceLearner)
    • de.julielab.jules.ae.genemapping.scoring.TokenJaroSimilarity (implements java.io.Serializable)
  • de.julielab.jules.ae.genemapping.genemodel.Acronym (implements de.julielab.java.utilities.spanutils.Span)
  • de.julielab.jules.ae.genemapping.genemodel.AcronymLongform (implements de.julielab.java.utilities.spanutils.Span)
  • de.julielab.jules.ae.genemapping.AhoCorasickLongestMatchCallback (implements com.lahodiuk.ahocorasick.AhoCorasickOptimized.MatchCallback)
  • com.lahodiuk.ahocorasick.AhoCorasickOptimized
  • com.lahodiuk.ahocorasick.AhoCorasickOptimized.Util
  • org.apache.uima.analysis_component.AnalysisComponent_ImplBase (implements org.apache.uima.analysis_component.AnalysisComponent)
    • org.apache.uima.analysis_component.Annotator_ImplBase
      • org.apache.uima.analysis_component.JCasAnnotator_ImplBase
        • de.julielab.jules.ae.genemapping.GeneMappingAnnotator
  • de.julielab.jules.ae.genemapping.utils.dict.BioThesaurusIproClassMerger
  • de.julielab.jules.ae.genemapping.CandidateCacheKey
  • de.julielab.jules.ae.genemapping.CandidateFilter
  • de.julielab.jules.ae.genemapping.utils.dict.Column
  • de.julielab.jules.ae.genemapping.index.ContextGenerator
  • de.julielab.jules.ae.genemapping.index.ContextIndexFieldNames
  • de.julielab.jules.ae.genemapping.ContextItemsCacheKey
  • de.julielab.jules.ae.genemapping.disambig.ContextItemsIndex (implements de.julielab.jules.ae.genemapping.disambig.SemanticIndex)
  • de.julielab.jules.ae.genemapping.utils.ContextUtils
  • java.util.Dictionary<K,V>
    • java.util.Hashtable<K,V> (implements java.lang.Cloneable, java.util.Map<K,V>, java.io.Serializable)
      • java.util.Properties
        • de.julielab.jules.ae.genemapping.GeneMappingConfiguration
  • de.julielab.jules.ae.genemapping.DocumentMappingResult
  • de.julielab.jules.ae.genemapping.utils.ExtensionFileFilter (implements java.io.FilenameFilter)
  • de.julielab.jules.ae.genemapping.genemodel.GeneDocument
  • de.julielab.jules.ae.genemapping.genemodel.GeneDocumentFactory
  • de.julielab.jules.ae.genemapping.genemodel.GeneIdCandidate
  • de.julielab.jules.ae.genemapping.GeneMapping
  • de.julielab.jules.ae.genemapping.genemodel.GeneMention (implements de.julielab.java.utilities.spanutils.Span)
  • de.julielab.jules.ae.genemapping.genemodel.GeneName
  • java.io.InputStream (implements java.io.Closeable)
    • de.julielab.jules.ae.genemapping.utils.ReaderInputStream
  • de.julielab.jules.ae.genemapping.utils.IOUtils
  • de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval (implements de.julielab.jules.ae.genemapping.CandidateRetrieval)
  • de.julielab.jules.ae.genemapping.scoring.MaxEntScorerML
  • de.julielab.jules.ae.genemapping.scoring.MaxEntScorerPairExtractor
  • de.julielab.jules.ae.genemapping.MentionMappingResult (implements java.lang.Comparable<T>)
  • de.julielab.jules.ae.genemapping.genemodel.MeshHeading
  • cc.mallet.pipe.Pipe (implements cc.mallet.types.AlphabetCarrying, java.io.Serializable)
    • de.julielab.jules.ae.genemapping.scoring.MaxEntScorerFeaturePipe (implements java.io.Serializable)
  • de.julielab.jules.ae.genemapping.QueryGenerator
  • de.julielab.jules.ae.genemapping.scoring.Scorer
    • de.julielab.jules.ae.genemapping.scoring.JaroWinklerScorer
    • de.julielab.jules.ae.genemapping.scoring.LevenshteinScorer
    • de.julielab.jules.ae.genemapping.scoring.LuceneScorer
    • de.julielab.jules.ae.genemapping.scoring.MaxEntScorer
    • de.julielab.jules.ae.genemapping.scoring.SimpleScorer
    • de.julielab.jules.ae.genemapping.scoring.TokenJaroSimilarityScorer
  • de.julielab.jules.ae.genemapping.disambig.SemanticContextIndex (implements de.julielab.jules.ae.genemapping.disambig.SemanticIndex)
  • de.julielab.java.utilities.spanutils.SpanImplBase (implements de.julielab.java.utilities.spanutils.Span)
    • de.julielab.jules.ae.genemapping.genemodel.PosTag
  • de.julielab.jules.ae.genemapping.genemodel.SpeciesCandidates
  • de.julielab.jules.ae.genemapping.genemodel.SpeciesMention
  • de.julielab.jules.ae.genemapping.SynHit (implements java.lang.Cloneable, java.lang.Comparable<T>)
    • de.julielab.jules.ae.genemapping.MentionMappingResult.RejectionSynHit
  • de.julielab.jules.ae.genemapping.utils.SynHitUtils
  • de.julielab.jules.ae.genemapping.index.SynonymIndexFieldNames
  • de.julielab.jules.ae.genemapping.utils.norm.TermNormalizer
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • de.julielab.jules.ae.genemapping.utils.GeneMappingException
        • de.julielab.jules.ae.genemapping.utils.GeneCandidateRetrievalException
      • java.lang.RuntimeException
        • de.julielab.jules.ae.genemapping.utils.GeneMapperRuntimeException
  • de.julielab.jules.ae.genemapping.utils.UIMAUtils
  • de.julielab.jules.ae.genemapping.utils.Utils
  • de.julielab.jules.ae.genemapping.disambig.WeepingTreeDisambiguation (implements de.julielab.jules.ae.genemapping.disambig.SemanticDisambiguation)
  • de.julielab.jules.ae.genemapping.disambig.WeepingTreeDocumentDisambiguationData (implements de.julielab.jules.ae.genemapping.disambig.DocumentDisambiguationData)
  • de.julielab.jules.ae.genemapping.mappingcores.WeepingTreeMappingCore (implements de.julielab.jules.ae.genemapping.mappingcores.MappingCore)
  • de.julielab.jules.ae.genemapping.disambig.WeepingTreeMentionDisambiguationData (implements de.julielab.jules.ae.genemapping.disambig.MentionDisambiguationData)

Interface Hierarchy

• com.lahodiuk.ahocorasick.AhoCorasickOptimized.MatchCallback
• de.julielab.jules.ae.genemapping.CandidateRetrieval
• de.julielab.jules.ae.genemapping.disambig.DocumentDisambiguationData
• de.julielab.jules.ae.genemapping.mappingcores.MappingCore
• de.julielab.jules.ae.genemapping.disambig.MentionDisambiguationData
• de.julielab.jules.ae.genemapping.disambig.SemanticDisambiguation
• de.julielab.jules.ae.genemapping.disambig.SemanticIndex

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • de.julielab.jules.ae.genemapping.genemodel.GeneMention.GeneTagger
    • de.julielab.jules.ae.genemapping.genemodel.GeneMention.SpecificType
    • de.julielab.jules.ae.genemapping.genemodel.GeneSpeciesOccurrence
    • de.julielab.jules.ae.genemapping.MentionMappingResult.MatchType
    • de.julielab.jules.ae.genemapping.SynHit.CompareType