BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.

core-1.8.1.jar is the Core module of BioJava 1.8.

JAR File Size and Download Location:

File name: core.jar, core-1.8.1.jar
File size: 2466702 bytes
Date modified: 14-Feb-2011
Download: BioJava - Core

Manifest of the JAR:

Archiver-Version: Plexus Archiver
Built-By: andreas
Build-Jdk: 1.6.0_0

List of Classes in the JAR:

org/biojava/directory/RegistryConfiguration
org/biojava/directory/ProviderNotFoundException
org/biojava/directory/SystemRegistry
org/biojava/directory/RegistryException
org/biojava/directory/SequenceDBProvider
org/biojava/directory/OBDARegistryParser
org/biojava/directory/Registry
org/biojava/stats/svm/TrainingContext
org/biojava/stats/svm/TrainingEvent
org/biojava/stats/svm/SimpleItemValue
org/biojava/stats/svm/CachingKernel
org/biojava/stats/svm/SimpleSVMTarget
org/biojava/stats/svm/SVMRegressionModel
org/biojava/stats/svm/RadialBaseKernel
org/biojava/stats/svm/SigmoidKernel
org/biojava/stats/svm/AbstractSVMTarget
org/biojava/stats/svm/ItemValue
org/biojava/stats/svm/ListSumKernel
org/biojava/stats/svm/DiagonalCachingKernel
org/biojava/stats/svm/NormalizingKernel
org/biojava/stats/svm/PolynomialKernel
org/biojava/stats/svm/DiagonalAddKernel
org/biojava/stats/svm/AbstractSVMClassifierModel
org/biojava/stats/svm/TrainingListener
org/biojava/stats/svm/LinearKernel
org/biojava/stats/svm/tools/TrainRegression
org/biojava/stats/svm/tools/Classify
org/biojava/stats/svm/tools/ClassifierExample
org/biojava/stats/svm/tools/SVM_Light
org/biojava/stats/svm/tools/SuffixTreeKernel
org/biojava/stats/svm/tools/Train
org/biojava/stats/svm/SparseVector
org/biojava/stats/svm/SMORegressionTrainer
org/biojava/stats/svm/NestedKernel
org/biojava/stats/svm/SVMTarget
org/biojava/stats/svm/SVMClassifierModel
org/biojava/stats/svm/SimpleSVMClassifierModel
org/biojava/stats/svm/SMOTrainer
org/biojava/stats/svm/SVMKernel
org/biojava/naming/ObdaInitialContextFactory
org/biojava/naming/ObdaUriParser
org/biojava/naming/ObdaContext
org/biojava/bio/AbstractAnnotation
org/biojava/bio/NoneCollectionConstraint
org/biojava/bio/seq/Up
org/biojava/bio/seq/SequenceTools
org/biojava/bio/seq/ByHierarchy
org/biojava/bio/seq/SequenceIterator
org/biojava/bio/seq/FeatureHolderUtils
org/biojava/bio/seq/impl/NewAssembledSymbolList
org/biojava/bio/seq/impl/SimpleSequence
org/biojava/bio/seq/impl/SimpleRemoteFeature
org/biojava/bio/seq/impl/SimpleGappedSequence
org/biojava/bio/seq/impl/SimpleSequenceFactory
org/biojava/bio/seq/impl/SimpleHomologyFeature
org/biojava/bio/seq/impl/AssembledSymbolList
org/biojava/bio/seq/impl/SubSequence
org/biojava/bio/seq/impl/SimpleFramedFeature
org/biojava/bio/seq/impl/LazyFilterFeatureHolder
org/biojava/bio/seq/impl/DummySequence
org/biojava/bio/seq/impl/RevCompSequence
org/biojava/bio/seq/impl/SimpleFeature
org/biojava/bio/seq/impl/SimpleSimilarityPairFeature
org/biojava/bio/seq/impl/TemplateUtils
org/biojava/bio/seq/impl/FeatureImpl
org/biojava/bio/seq/impl/SimpleStrandedFeature
org/biojava/bio/seq/impl/SimpleRestrictionSite
org/biojava/bio/seq/impl/ViewSequence
org/biojava/bio/seq/RNATools
org/biojava/bio/seq/SimpleComponentFeature
org/biojava/bio/seq/Sequence
org/biojava/bio/seq/FramedFeature
org/biojava/bio/seq/FilterUtils
org/biojava/bio/seq/SequenceFactory
org/biojava/bio/seq/FeatureFilter
org/biojava/bio/seq/LazyFeatureHolder
org/biojava/bio/seq/AcceptNoneFilter
org/biojava/bio/seq/io/SequenceBuilderFactory
org/biojava/bio/seq/io/GenbankContext
org/biojava/bio/seq/io/EmblLikeFormat
org/biojava/bio/seq/io/EmblProcessor
org/biojava/bio/seq/io/SequenceFormat
org/biojava/bio/seq/io/NameTokenization
org/biojava/bio/seq/io/SimpleSequenceBuilder
org/biojava/bio/seq/io/SymbolReader
org/biojava/bio/seq/io/GenbankFormat
org/biojava/bio/seq/io/EmblLikeLocationParser
org/biojava/bio/seq/io/OrganismParser
org/biojava/bio/seq/io/SequenceBuilderBase
org/biojava/bio/seq/io/SequenceBuilder
org/biojava/bio/seq/io/StreamWriter
org/biojava/bio/seq/io/FeatureTableParser
org/biojava/bio/seq/io/SeqFileFormer
org/biojava/bio/seq/io/SequenceBuilderFilter
org/biojava/bio/seq/io/agave/AGAVESeqPropHandler
org/biojava/bio/seq/io/agave/StAXHandlerFactory
org/biojava/bio/seq/io/agave/AGAVESeqLocationPropHandler
org/biojava/bio/seq/io/agave/AGAVEMatchRegionPropHandler
org/biojava/bio/seq/io/agave/AGAVEMatchAlignPropHandler
org/biojava/bio/seq/io/agave/AGAVEDescPropHandler
org/biojava/bio/seq/io/agave/PCDATAFilterWriter
org/biojava/bio/seq/io/agave/AGAVEBioSeqHandler
org/biojava/bio/seq/io/agave/AGAVEQualifierPropHandler
org/biojava/bio/seq/io/agave/AGAVEAssemblyHandler
org/biojava/bio/seq/io/agave/DelegationManager
org/biojava/bio/seq/io/agave/AGAVECdsHandler
org/biojava/bio/seq/io/agave/AGAVEExonsPropHandler
org/biojava/bio/seq/io/agave/AGAVESeqMapHandler
org/biojava/bio/seq/io/agave/Embl2AgaveAnnotFilter
org/biojava/bio/seq/io/agave/Agave2AgaveAnnotFilter
org/biojava/bio/seq/io/agave/AGAVEChromosomeCallbackItf
org/biojava/bio/seq/io/agave/AGAVERelatedAnnotPropHandler
org/biojava/bio/seq/io/agave/AGAVEIdAliasPropHandler
org/biojava/bio/seq/io/agave/AGAVEAltIdsPropHandler
org/biojava/bio/seq/io/agave/AGAVECompResultHandler
org/biojava/bio/seq/io/agave/SAX2StAXAdaptor
org/biojava/bio/seq/io/agave/AGAVEQueryRegion
org/biojava/bio/seq/io/agave/AGAVECallbackItf
org/biojava/bio/seq/io/agave/AGAVEBioSeqCallbackItf
org/biojava/bio/seq/io/agave/AGAVEBioSequenceHandler
org/biojava/bio/seq/io/agave/AGAVEQueryRegionPropHandler
org/biojava/bio/seq/io/agave/AGAVEViewPropHandler
org/biojava/bio/seq/io/agave/AGAVEEvidenceHandler
org/biojava/bio/seq/io/agave/AGAVEHandler
org/biojava/bio/seq/io/agave/AGAVESciPropertyPropHandler
org/biojava/bio/seq/io/agave/AGAVEMapLocation
org/biojava/bio/seq/io/agave/AGAVEMatchRegion
org/biojava/bio/seq/io/agave/ElementRecognizer
org/biojava/bio/seq/io/agave/AGAVEXrefs
org/biojava/bio/seq/io/agave/AGAVEGeneHandler
org/biojava/bio/seq/io/agave/AGAVEUnorderedFragmentsHandler
org/biojava/bio/seq/io/agave/AGAVEChromosomeHandler
org/biojava/bio/seq/io/agave/AGAVEKeywordPropHandler
org/biojava/bio/seq/io/agave/AGAVEXref
org/biojava/bio/seq/io/agave/AGAVEMrnaHandler
org/biojava/bio/seq/io/agave/AGAVEXrefPropHandler
org/biojava/bio/seq/io/agave/AGAVEClassificationHandler
org/biojava/bio/seq/io/agave/AGAVEResultGroupHandler
org/biojava/bio/seq/io/agave/AGAVEPredictedProteinHandler
org/biojava/bio/seq/io/agave/AGAVEEvidenceCallbackItf
org/biojava/bio/seq/io/agave/AGAVEAnnotationsHandler
org/biojava/bio/seq/io/agave/AGAVEFragmentOrderHandler
org/biojava/bio/seq/io/agave/AGAVEIdAlias
org/biojava/bio/seq/io/agave/AGAVEDbId
org/biojava/bio/seq/io/agave/SequenceHandler
org/biojava/bio/seq/io/agave/AGAVERelatedAnnot
org/biojava/bio/seq/io/agave/AGAVEDbIdPropHandler
org/biojava/bio/seq/io/agave/AGAVEResultPropertyPropHandler
org/biojava/bio/seq/io/agave/AGAVEFeatureCallbackItf
org/biojava/bio/seq/io/agave/AGAVEComputationHandler
org/biojava/bio/seq/io/agave/AGAVEMapPositionPropHandler
org/biojava/bio/seq/io/agave/AgaveWriter
org/biojava/bio/seq/io/agave/SimpleAnnotFilter
org/biojava/bio/seq/io/agave/AGAVEContigCallbackItf
org/biojava/bio/seq/io/agave/AGAVEContigHandler
org/biojava/bio/seq/io/agave/AGAVEFragmentOrientationHandler
org/biojava/bio/seq/io/agave/UtilHelper
org/biojava/bio/seq/io/agave/StAXFeatureHandler
org/biojava/bio/seq/io/agave/AGAVEProperty
org/biojava/bio/seq/io/agave/AGAVENotePropHandler
org/biojava/bio/seq/io/agave/AGAVEXrefCallbackItf
org/biojava/bio/seq/io/agave/StAXContentHandler
org/biojava/bio/seq/io/agave/AGAVEXrefPropPropHandler
org/biojava/bio/seq/io/agave/StAXPropertyHandler
org/biojava/bio/seq/io/agave/AGAVEMatchDescPropHandler
org/biojava/bio/seq/io/agave/AGAVESeqFeatureHandler
org/biojava/bio/seq/io/agave/AGAVEMapPosition
org/biojava/bio/seq/io/agave/StAXContentHandlerBase
org/biojava/bio/seq/io/agave/AGAVEAnnotFilter
org/biojava/bio/seq/io/agave/AGAVEDbIdCallbackItf
org/biojava/bio/seq/io/agave/AGAVEIdAliasCallbackItf
org/biojava/bio/seq/io/agave/AGAVEAnnotFilterFactory
org/biojava/bio/seq/io/agave/AGAVEDbIdPropCallbackItf
org/biojava/bio/seq/io/agave/AGAVETranscriptHandler
org/biojava/bio/seq/io/agave/AGAVEMapLocationPropHandler
org/biojava/bio/seq/io/agave/AGAVEElementIdPropHandler
org/biojava/bio/seq/io/agave/AGAVEXrefsPropHandler
org/biojava/bio/seq/io/GenpeptFileFormer
org/biojava/bio/seq/io/FastaFormat
org/biojava/bio/seq/io/DoubleTokenization
org/biojava/bio/seq/io/StreamParser
org/biojava/bio/seq/io/SeqIOTools
org/biojava/bio/seq/io/ChunkedSymbolListFactory
org/biojava/bio/seq/io/SeqIOFilter
org/biojava/bio/seq/io/SeqIOConstants
org/biojava/bio/seq/io/ReferenceAnnotation
org/biojava/bio/seq/io/AlignmentFormat
org/biojava/bio/seq/io/EmblFileFormer
org/biojava/bio/seq/io/CharacterTokenization
org/biojava/bio/seq/io/ProteinRefSeqProcessor
org/biojava/bio/seq/io/SeqIOAdapter
org/biojava/bio/seq/io/GenEmblPropertyComparator
org/biojava/bio/seq/io/filterxml/XMLFilterHandler
org/biojava/bio/seq/io/filterxml/XMLFilterWriter
org/biojava/bio/seq/io/filterxml/QName
org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeWriter
org/biojava/bio/seq/io/filterxml/XMLAnnotationTypeHandler
org/biojava/bio/seq/io/MSFAlignmentFormat
org/biojava/bio/seq/io/GenbankFileFormer
org/biojava/bio/seq/io/WordTokenization
org/biojava/bio/seq/io/SeqIOEventEmitter
org/biojava/bio/seq/io/AlignIOConstants
org/biojava/bio/seq/io/GenEmblFeatureComparator
org/biojava/bio/seq/io/SymbolTokenization
org/biojava/bio/seq/io/SwissprotFeatureTableParser
org/biojava/bio/seq/io/FastaAlignmentFormat
org/biojava/bio/seq/io/StreamReader
org/biojava/bio/seq/io/FastaDescriptionLineParser
org/biojava/bio/seq/io/ProteinRefSeqFileFormer
org/biojava/bio/seq/io/ParseException
org/biojava/bio/seq/io/GenbankXmlFormat
org/biojava/bio/seq/io/SimpleAssemblyBuilder
org/biojava/bio/seq/io/CrossProductTokenization
org/biojava/bio/seq/io/GAMEFormat
org/biojava/bio/seq/io/SubIntegerTokenization
org/biojava/bio/seq/io/SeqIOListener
org/biojava/bio/seq/io/EmblReferenceComparator
org/biojava/bio/seq/io/GenbankProcessor
org/biojava/bio/seq/io/AbstractGenEmblFileFormer
org/biojava/bio/seq/io/GenpeptFormat
org/biojava/bio/seq/io/game/StAXHandlerFactory
org/biojava/bio/seq/io/game/GAMEFeatureCallbackItf
org/biojava/bio/seq/io/game/GAMETypePropHandler
org/biojava/bio/seq/io/game/SequenceContentHandlerBase
org/biojava/bio/seq/io/game/GAMEResiduesPropHandler
org/biojava/bio/seq/io/game/GAMENamePropHandler
org/biojava/bio/seq/io/game/GAMEAspectPropHandler
org/biojava/bio/seq/io/game/GAMEFeatureSetHandler
org/biojava/bio/seq/io/game/ElementRecognizer
org/biojava/bio/seq/io/game/GAMEDescriptionPropHandler
org/biojava/bio/seq/io/game/GAMETranscriptCallbackItf
org/biojava/bio/seq/io/game/GAMEFeatureSpanHandler
org/biojava/bio/seq/io/game/GAMEFeatureSetPropHandler
org/biojava/bio/seq/io/game/GAMESeqPropHandler
org/biojava/bio/seq/io/game/GAMEHandler
org/biojava/bio/seq/io/game/GAMEDbxrefPropHandler
org/biojava/bio/seq/io/game/StAXFeatureHandler
org/biojava/bio/seq/io/game/GAMEMapPosPropHandler
org/biojava/bio/seq/io/game/GAMESpanPropHandler
org/biojava/bio/seq/io/game/StAXPropertyHandler
org/biojava/bio/seq/io/game/GAMEGenePropHandler
org/biojava/bio/seq/io/game/GAMEAnnotationHandler
org/biojava/bio/seq/io/game/GAMENameCallbackItf
org/biojava/bio/seq/io/game/GAMESeqRelPropHandler
org/biojava/bio/seq/io/SwissprotProcessor
org/biojava/bio/seq/io/SmartSequenceBuilder
org/biojava/bio/seq/io/IntegerTokenization
org/biojava/bio/seq/io/SwissprotFileFormer
org/biojava/bio/seq/io/game12/StAXHandlerFactory
org/biojava/bio/seq/io/game12/GAMEFeatureSetHandler
org/biojava/bio/seq/io/game12/GAMESeqRelHandler
org/biojava/bio/seq/io/game12/GAMEAspectHandler
org/biojava/bio/seq/io/game12/GAMEFeatureSpanHandler
org/biojava/bio/seq/io/game12/GAMESpanHandler
org/biojava/bio/seq/io/game12/GAMEHandler
org/biojava/bio/seq/io/game12/StAXFeatureHandler
org/biojava/bio/seq/io/game12/GAMEPropertyHandler
org/biojava/bio/seq/io/game12/GAMEAnnotationHandler
org/biojava/bio/seq/io/game12/GAMESeqHandler
org/biojava/bio/seq/io/game12/GAMEDbxrefHandler
org/biojava/bio/seq/io/game12/GAMEGeneHandler
org/biojava/bio/seq/io/AlternateTokenization
org/biojava/bio/seq/io/SymbolListCharSequence
org/biojava/bio/seq/ByLocationMinMaxFeatureComparator
org/biojava/bio/seq/CircularView
org/biojava/bio/seq/Down
org/biojava/bio/seq/IsTopLevel
org/biojava/bio/seq/Frame
org/biojava/bio/seq/FeatureHolder
org/biojava/bio/seq/DNATools
org/biojava/bio/seq/OptimizableFilter
org/biojava/bio/seq/filter/FilterTransformer
org/biojava/bio/seq/SimpleFeatureHolder
org/biojava/bio/seq/StrandParser
org/biojava/bio/seq/IsLeaf
org/biojava/bio/seq/FeatureTypes
org/biojava/bio/seq/FeatureRealizer
org/biojava/bio/seq/AcceptAllFilter
org/biojava/bio/seq/db/FetchURL
org/biojava/bio/seq/db/Index
org/biojava/bio/seq/db/WebSequenceDB
org/biojava/bio/seq/db/HashSequenceDB
org/biojava/bio/seq/db/ViewingSequenceDB
org/biojava/bio/seq/db/AbstractSequenceDB
org/biojava/bio/seq/db/SequenceDBInstallation
org/biojava/bio/seq/db/DummySequenceDB
org/biojava/bio/seq/db/IndexStore
org/biojava/bio/seq/db/SequenceDB
org/biojava/bio/seq/db/biofetch/BioFetchSequenceDBProvider
org/biojava/bio/seq/db/biofetch/BioFetchSequenceDB
org/biojava/bio/seq/db/SimpleIndex
org/biojava/bio/seq/db/SubSequenceDB
org/biojava/bio/seq/db/GenbankSequenceDB
org/biojava/bio/seq/db/emblcd/EntryNamIdxReader
org/biojava/bio/seq/db/emblcd/EntryNamRandomAccess
org/biojava/bio/seq/db/emblcd/EmblCDROMRandomAccess
org/biojava/bio/seq/db/emblcd/RecordParser
org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader
org/biojava/bio/seq/db/emblcd/AcnumTrgReader
org/biojava/bio/seq/db/emblcd/DivisionLkpReader
org/biojava/bio/seq/db/emblcd/AcnumHitReader
org/biojava/bio/seq/db/BioIndex
org/biojava/bio/seq/db/GenpeptSequenceDB
org/biojava/bio/seq/db/IDMaker
org/biojava/bio/seq/db/IllegalIDException
org/biojava/bio/seq/db/flat/FlatSequenceDBProvider
org/biojava/bio/seq/db/flat/FlatSequenceDB
org/biojava/bio/seq/db/SimpleSequenceDBInstallation
org/biojava/bio/seq/db/SequenceDBWrapper
org/biojava/bio/seq/db/AnnotatedSequenceDB
org/biojava/bio/seq/db/EmblCDROMIndexStore
org/biojava/bio/seq/db/TabIndexStore
org/biojava/bio/seq/db/SwissprotSequenceDB
org/biojava/bio/seq/db/SequenceDBLite
org/biojava/bio/seq/db/IndexedSequenceDB
org/biojava/bio/seq/db/DummySequenceDBInstallation
org/biojava/bio/seq/db/NCBISequenceDB
org/biojava/bio/seq/db/CachingSequenceDB
org/biojava/bio/seq/SimpleFeatureRealizer
org/biojava/bio/seq/ComponentFeature
org/biojava/bio/seq/GappedSequence
org/biojava/bio/seq/NewSimpleAssembly
org/biojava/bio/seq/ByLocationMinMaxComparator
org/biojava/bio/seq/SequenceAnnotator
org/biojava/bio/seq/RemoteFeature
org/biojava/bio/seq/GeneticCodes
org/biojava/bio/seq/RealizingFeatureHolder
org/biojava/bio/seq/ProteinTools
org/biojava/bio/seq/homol/SimilarityPairFeature
org/biojava/bio/seq/homol/HomologyFeature
org/biojava/bio/seq/homol/HomologyDB
org/biojava/bio/seq/homol/Homology
org/biojava/bio/seq/homol/SimpleHomology
org/biojava/bio/seq/StrandedFeature
org/biojava/bio/seq/distributed/SequenceDBDataSource
org/biojava/bio/seq/distributed/GFFDataSource
org/biojava/bio/seq/distributed/DistProjectionContext
org/biojava/bio/seq/distributed/DistDataSource
org/biojava/bio/seq/distributed/DistComponentFeature
org/biojava/bio/seq/distributed/DistributedSequenceDB
org/biojava/bio/seq/distributed/DistributedSequence
org/biojava/bio/seq/projection/TranslateFlipContext
org/biojava/bio/seq/projection/ReparentContext
org/biojava/bio/seq/projection/Projection
org/biojava/bio/seq/projection/ProjectedFeatureHolder
org/biojava/bio/seq/projection/ProjectedFeature
org/biojava/bio/seq/projection/ProjectionContext
org/biojava/bio/seq/projection/ProjectionUtils
org/biojava/bio/seq/projection/ProjectionEngine
org/biojava/bio/seq/AbstractFeatureHolder
org/biojava/bio/seq/SimpleAssembly
org/biojava/bio/seq/MergeFeatureHolder
org/biojava/bio/seq/Feature
org/biojava/bio/seq/NucleotideTools
org/biojava/bio/BeanAsAnnotation
org/biojava/bio/MergeAnnotation
org/biojava/bio/CardinalityConstraint
org/biojava/bio/program/hmmer/HmmerProfileHMM
org/biojava/bio/program/hmmer/ProfileEmissionState
org/biojava/bio/program/hmmer/HmmerProfileParser
org/biojava/bio/program/hmmer/FullHmmerProfileHMM
org/biojava/bio/program/formats/Embl
org/biojava/bio/program/formats/Format
org/biojava/bio/program/formats/Ligand
org/biojava/bio/program/formats/Swissprot
org/biojava/bio/program/formats/Enzyme
org/biojava/bio/program/formats/FormatTools
org/biojava/bio/program/Meme
org/biojava/bio/program/tagvalue/TagValue
org/biojava/bio/program/tagvalue/Echo
org/biojava/bio/program/tagvalue/Aggregator
org/biojava/bio/program/tagvalue/RegexSplitter
org/biojava/bio/program/tagvalue/TagValueWrapper
org/biojava/bio/program/tagvalue/SimpleTagValueWrapper
org/biojava/bio/program/tagvalue/TagDelegator
org/biojava/bio/program/tagvalue/TagRenamer
org/biojava/bio/program/tagvalue/RegexFieldFinder
org/biojava/bio/program/tagvalue/ParserListener
org/biojava/bio/program/tagvalue/Indexer
org/biojava/bio/program/tagvalue/Formats
org/biojava/bio/program/tagvalue/PropertyChanger
org/biojava/bio/program/tagvalue/ChangeTable
org/biojava/bio/program/tagvalue/ValueChanger
org/biojava/bio/program/tagvalue/BoundaryFinder
org/biojava/bio/program/tagvalue/Parser
org/biojava/bio/program/tagvalue/AbstractWrapper
org/biojava/bio/program/tagvalue/Indexer2
org/biojava/bio/program/tagvalue/TagMapper
org/biojava/bio/program/tagvalue/TagValueContext
org/biojava/bio/program/tagvalue/TagDropper
org/biojava/bio/program/tagvalue/TagValueParser
org/biojava/bio/program/tagvalue/RegexParser
org/biojava/bio/program/tagvalue/RegexChanger
org/biojava/bio/program/tagvalue/MultiTagger
org/biojava/bio/program/tagvalue/LineSplitParser
org/biojava/bio/program/tagvalue/Index2Model
org/biojava/bio/program/tagvalue/AnnotationBuilder
org/biojava/bio/program/tagvalue/StateMachine
org/biojava/bio/program/tagvalue/TagValueListener
org/biojava/bio/program/xff/FeatureHandler
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