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

List of Classes in the JAR:

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org/biojava/bio/program/xff/BasicXFFHelper
org/biojava/bio/program/xff/XFFPartHandlerFactory
org/biojava/bio/program/xff/LocationHandlerBase
org/biojava/bio/program/xff/XFFWriter
org/biojava/bio/program/xff/ElementRecognizer
org/biojava/bio/program/xff/XFFFeatureSetHandler
org/biojava/bio/program/xff/XFFHelper
org/biojava/bio/program/xff/PropertyWriter
org/biojava/bio/program/xff/StrandedFeatureHandler
org/biojava/bio/program/xff/XFFTools
org/biojava/bio/program/xff/PropDetailHandler
org/biojava/bio/program/xml/BaseXMLWriter
org/biojava/bio/program/xml/SimpleXMLEmitter
org/biojava/bio/program/blast2html/SimpleAlignmentStyler
org/biojava/bio/program/blast2html/HSPSummary
org/biojava/bio/program/blast2html/Sequence
org/biojava/bio/program/blast2html/DefaultURLGeneratorFactory
org/biojava/bio/program/blast2html/HitId
org/biojava/bio/program/blast2html/HitSummary
org/biojava/bio/program/blast2html/HTMLRenderer
org/biojava/bio/program/blast2html/DatabaseURLGenerator
org/biojava/bio/program/blast2html/BlastMatrixAlignmentStyler
org/biojava/bio/program/blast2html/AbstractAlignmentStyler
org/biojava/bio/program/blast2html/BlastLikeAlignment
org/biojava/bio/program/blast2html/URLGeneratorFactory
org/biojava/bio/program/blast2html/HSP
org/biojava/bio/program/blast2html/AlignmentMarker
org/biojava/bio/program/blast2html/ColourCommand
org/biojava/bio/program/blast2html/HitDescription
org/biojava/bio/program/blast2html/DetailHit
org/biojava/bio/program/blast2html/NcbiDatabaseURLGenerator
org/biojava/bio/program/blast2html/AlignmentStyler
org/biojava/bio/program/blast2html/Blast2HTMLHandler
org/biojava/bio/program/blast2html/EbiDatabaseURLGenerator
org/biojava/bio/program/homologene/AbstractOrthoPairSet
org/biojava/bio/program/homologene/DuplicateTaxonException
org/biojava/bio/program/homologene/HomologeneBuilder
org/biojava/bio/program/homologene/OrthoPairFilter
org/biojava/bio/program/homologene/SimpleOrthoPairSet
org/biojava/bio/program/homologene/SimpleHomologeneDB
org/biojava/bio/program/homologene/SimpleOrthoPair
org/biojava/bio/program/homologene/OrthologueSet
org/biojava/bio/program/homologene/SimilarityType
org/biojava/bio/program/homologene/OrthoPair
org/biojava/bio/program/homologene/HomologeneDB
org/biojava/bio/program/homologene/HomologeneTools
org/biojava/bio/program/homologene/SimpleOrthoPairCollection
org/biojava/bio/program/homologene/OrthologueFilter
org/biojava/bio/program/homologene/Taxon
org/biojava/bio/program/homologene/SimpleOrthologue
org/biojava/bio/program/homologene/OrthoPairSet
org/biojava/bio/program/homologene/OrthoPairSetFilter
org/biojava/bio/program/homologene/SimpleOrthologueSet
org/biojava/bio/program/homologene/SimpleHomologeneBuilder
org/biojava/bio/program/homologene/OrthoPairCollection
org/biojava/bio/program/homologene/AbstractOrthoPairCollection
org/biojava/bio/program/homologene/AbstractOrthologueSet
org/biojava/bio/program/homologene/Orthologue
org/biojava/bio/program/unigene/SQLUnigeneFactory
org/biojava/bio/program/unigene/UnigeneFactory
org/biojava/bio/program/unigene/UnigeneTools
org/biojava/bio/program/unigene/FlatFileUnigeneFactory
org/biojava/bio/program/unigene/SQLUnigeneDB
org/biojava/bio/program/unigene/UnigeneDB
org/biojava/bio/program/unigene/UnigeneCluster
org/biojava/bio/program/unigene/FlatFileUnigeneDB
org/biojava/bio/program/gff3/GFF3Parser
org/biojava/bio/program/gff3/GFF3DocumentHandler
org/biojava/bio/program/gff3/GFF3Record
org/biojava/bio/program/phred/PhredTools
org/biojava/bio/program/phred/PhredFormat
org/biojava/bio/program/phred/PhredSequence
org/biojava/bio/program/phred/Qualitative
org/biojava/bio/program/indexdb/SearchableFileAsList
org/biojava/bio/program/indexdb/BioStoreFactory
org/biojava/bio/program/indexdb/PrimaryIDList
org/biojava/bio/program/indexdb/IndexStore
org/biojava/bio/program/indexdb/Record
org/biojava/bio/program/indexdb/CacheList
org/biojava/bio/program/indexdb/SecondaryFileAsList
org/biojava/bio/program/indexdb/ConfigFile
org/biojava/bio/program/indexdb/SearchableList
org/biojava/bio/program/indexdb/BioStore
org/biojava/bio/program/indexdb/PropertiesAnnotation
org/biojava/bio/program/indexdb/IndexTools
org/biojava/bio/program/indexdb/KeyPair
org/biojava/bio/program/ssaha/MappedDataStore
org/biojava/bio/program/ssaha/CompactedDataStore
org/biojava/bio/program/ssaha/SearchException
org/biojava/bio/program/ssaha/CompactedDataStoreFactory
org/biojava/bio/program/ssaha/MappedDataStoreFactory
org/biojava/bio/program/ssaha/DataStore
org/biojava/bio/program/ssaha/NIODataStoreFactory
org/biojava/bio/program/ssaha/HitMerger
org/biojava/bio/program/ssaha/SequenceStreamer
org/biojava/bio/program/ssaha/SearchListener
org/biojava/bio/program/ssaha/DataStoreFactory
org/biojava/bio/program/ssaha/NIODataStore
org/biojava/bio/program/ssbind/AnnotationFactory
org/biojava/bio/program/gff/SequencesAsGFF
org/biojava/bio/program/gff/GFFWriter
org/biojava/bio/program/gff/GFFFilterer
org/biojava/bio/program/gff/GFFTools
org/biojava/bio/program/gff/GFFRecordFilter
org/biojava/bio/program/gff/GFFComparator
org/biojava/bio/program/gff/GFFDocumentHandler
org/biojava/bio/program/gff/GFFErrorHandler
org/biojava/bio/program/gff/GFFParser
org/biojava/bio/program/gff/SimpleGFFRecord
org/biojava/bio/program/gff/GFFRecord
org/biojava/bio/program/gff/GFFEntrySet
org/biojava/bio/program/gff/IgnoreRecordException
org/biojava/bio/AnnotationChanger
org/biojava/bio/AnnotationTools
org/biojava/bio/AnnotationType
org/biojava/bio/AnnotationRenamer
org/biojava/bio/BioError
org/biojava/bio/EcNumber
org/biojava/bio/alignment/SimpleAlignment
org/biojava/bio/alignment/Alignment
org/biojava/bio/AnyPropertyConstraint
org/biojava/bio/dp/State
org/biojava/bio/dp/HMMTrainer
org/biojava/bio/dp/WeightMatrix
org/biojava/bio/dp/StatePath
org/biojava/bio/dp/ModelTrainer
org/biojava/bio/dp/ProfileHMM
org/biojava/bio/dp/FlatModel
org/biojava/bio/dp/SimpleModelTrainer
org/biojava/bio/dp/SimpleWeightMatrix
org/biojava/bio/dp/SimpleDotState
org/biojava/bio/dp/MarkovModel
org/biojava/bio/dp/SimpleEmissionState
org/biojava/bio/dp/DotState
org/biojava/bio/dp/BaumWelchTrainer
org/biojava/bio/dp/SimpleHMMTrainer
org/biojava/bio/dp/WMAsMM
org/biojava/bio/dp/SimpleStatePath
org/biojava/bio/dp/WeightMatrixAnnotator
org/biojava/bio/dp/SimpleMarkovModel
org/biojava/bio/dp/onehead/SingleDP
org/biojava/bio/dp/onehead/SmallCursor
org/biojava/bio/dp/onehead/AbstractCursor
org/biojava/bio/dp/onehead/MatrixCursor
org/biojava/bio/dp/onehead/SingleDPMatrix
org/biojava/bio/dp/onehead/DPCursor
org/biojava/bio/dp/XmlMarkovModel
org/biojava/bio/dp/Trainable
org/biojava/bio/dp/TrainerTransition
org/biojava/bio/dp/twohead/CellCalculator
org/biojava/bio/dp/twohead/CellCalculatorFactory
org/biojava/bio/dp/twohead/LightPairDPCursor
org/biojava/bio/dp/twohead/PairDPCursor
org/biojava/bio/dp/twohead/BackMatrixPairDPCursor
org/biojava/bio/dp/twohead/DPInterpreter
org/biojava/bio/dp/twohead/PairwiseDP
org/biojava/bio/dp/twohead/CellCalculatorFactoryMaker
org/biojava/bio/dp/twohead/PairDPMatrix
org/biojava/bio/dp/twohead/MatrixPairDPCursor
org/biojava/bio/dp/twohead/DPCompiler
org/biojava/bio/dp/twohead/Cell
org/biojava/bio/dp/twohead/AbstractMatrixPairDPCursor
org/biojava/bio/dp/twohead/EmissionCache
org/biojava/bio/dp/Transition
org/biojava/bio/dp/MagicalState
org/biojava/bio/dp/SimpleModelInState
org/biojava/bio/dp/StoppingCriteria
org/biojava/bio/dp/DPMatrix
org/biojava/bio/dp/DPFactory
org/biojava/bio/dp/TransitionTrainer
org/biojava/bio/dp/AbstractTrainer
org/biojava/bio/dp/DP
org/biojava/bio/dp/IllegalTransitionException
org/biojava/bio/dp/ModelInState
org/biojava/bio/dp/ScoreType
org/biojava/bio/dp/TrainingAlgorithm
org/biojava/bio/dp/BaumWelchSampler
org/biojava/bio/dp/EmissionState
org/biojava/bio/dp/BackPointer
org/biojava/bio/NonePropertyConstraint
org/biojava/bio/BioRuntimeException
org/biojava/bio/symbol/SimpleGappedSymbolList
org/biojava/bio/symbol/SimpleTranslationTable
org/biojava/bio/symbol/WobbleDistribution
org/biojava/bio/symbol/SimpleAlphabet
org/biojava/bio/symbol/Edit
org/biojava/bio/symbol/SuffixTree
org/biojava/bio/symbol/UkkonenSuffixTree
org/biojava/bio/symbol/FuzzyLocation
org/biojava/bio/symbol/SimpleSymbolList
org/biojava/bio/symbol/SimpleManyToOneTranslationTable
org/biojava/bio/symbol/FullDnaAlphabetIndex
org/biojava/bio/symbol/EmptySymbolList
org/biojava/bio/symbol/InfiniteCrossProductAlphabet
org/biojava/bio/symbol/AbstractLocationDecorator
org/biojava/bio/symbol/SimpleWobbleDistribution
org/biojava/bio/symbol/IllegalSymbolException
org/biojava/bio/symbol/SimpleAtomicSymbol
org/biojava/bio/symbol/BetweenLocationTools
org/biojava/bio/symbol/SimpleGeneticCodeTable
org/biojava/bio/symbol/FuzzyPointLocation
org/biojava/bio/symbol/LocationTools
org/biojava/bio/symbol/MergeLocation
org/biojava/bio/symbol/TranslationTable
org/biojava/bio/symbol/RelabeledAlignment
org/biojava/bio/symbol/SymbolListFactory
org/biojava/bio/symbol/AbstractRangeLocation
org/biojava/bio/symbol/ManyToOneTranslationTable
org/biojava/bio/symbol/AlphabetIndex
org/biojava/bio/symbol/FundamentalAtomicSymbol
org/biojava/bio/symbol/CodonPrefFilter
org/biojava/bio/symbol/SubList
org/biojava/bio/symbol/SparseCrossProductAlphabet
org/biojava/bio/symbol/DNANoAmbPack
org/biojava/bio/symbol/DNAAmbPack
org/biojava/bio/symbol/PackingFactory
org/biojava/bio/symbol/SoftMaskedAlphabet
org/biojava/bio/symbol/AbstractAlphabet
org/biojava/bio/symbol/PackedSymbolListFactory
org/biojava/bio/symbol/DoubleAlphabet
org/biojava/bio/symbol/GappedSymbolList
org/biojava/bio/symbol/SimpleCodonPref
org/biojava/bio/symbol/MotifTools
org/biojava/bio/symbol/AbstractSymbol
org/biojava/bio/symbol/AbstractTranslationTable
org/biojava/bio/symbol/RangeLocation
org/biojava/bio/symbol/CodonPref
org/biojava/bio/symbol/AlphabetManager
org/biojava/bio/symbol/SimpleSymbolListFactory
org/biojava/bio/symbol/SimpleSymbol
org/biojava/bio/symbol/OrderNSymbolList
org/biojava/bio/symbol/CodonPrefTools
org/biojava/bio/symbol/Symbol
org/biojava/bio/symbol/ReverseSymbolList
org/biojava/bio/symbol/Alphabet
org/biojava/bio/symbol/AbstractReversibleTranslationTable
org/biojava/bio/symbol/IllegalAlphabetException
org/biojava/bio/symbol/SymbolListViews
org/biojava/bio/symbol/EmptyAlphabet
org/biojava/bio/symbol/AbstractSymbolList
org/biojava/bio/symbol/BetweenLocation
org/biojava/bio/symbol/LinearAlphabetIndex
org/biojava/bio/symbol/WindowedSymbolList
org/biojava/bio/symbol/IndexedNoAmbPack
org/biojava/bio/symbol/LocationComparator
org/biojava/bio/symbol/SimpleReversibleTranslationTable
org/biojava/bio/symbol/AbstractLocation
org/biojava/bio/symbol/CircularLocationTools
org/biojava/bio/symbol/CircularLocation
org/biojava/bio/symbol/AbstractSimpleBasisSymbol
org/biojava/bio/symbol/FiniteAlphabet
org/biojava/bio/symbol/CompoundLocation
org/biojava/bio/symbol/CrossProductAlphabetIndex
org/biojava/bio/symbol/IntegerAlphabet
org/biojava/bio/symbol/PackedSymbolList
org/biojava/bio/symbol/Location
org/biojava/bio/symbol/AbstractManyToOneTranslationTable
org/biojava/bio/symbol/SymbolPropertyTable
org/biojava/bio/symbol/AtomicSymbol
org/biojava/bio/symbol/DummySymbolList
org/biojava/bio/symbol/Packing
org/biojava/bio/symbol/ReversibleTranslationTable
org/biojava/bio/symbol/EmptyLocation
org/biojava/bio/symbol/SingletonAlphabet
org/biojava/bio/symbol/ChunkedSymbolList
org/biojava/bio/symbol/SimpleBasisSymbol
org/biojava/bio/symbol/BasisSymbol
org/biojava/bio/symbol/TranslatedSymbolList
org/biojava/bio/symbol/PointLocation
org/biojava/bio/symbol/HashedAlphabetIndex
org/biojava/bio/symbol/SimpleCrossProductAlphabet
org/biojava/bio/symbol/SimpleSymbolPropertyTable
org/biojava/bio/symbol/SymbolList
org/biojava/bio/BioException
org/biojava/bio/PropertyConstraint
org/biojava/bio/OverlayAnnotation
org/biojava/bio/molbio/DNAComposition
org/biojava/bio/molbio/Composition
org/biojava/bio/molbio/RestrictionEnzyme
org/biojava/bio/molbio/RestrictionSite
org/biojava/bio/molbio/RestrictionMapper
org/biojava/bio/molbio/RestrictionSiteFinder
org/biojava/bio/molbio/RestrictionEnzymeManager
org/biojava/bio/Annotation
org/biojava/bio/taxa/SimpleTaxonFactory
org/biojava/bio/taxa/Taxon
org/biojava/bio/taxa/SimpleTaxon
org/biojava/bio/taxa/EbiFormat
org/biojava/bio/taxa/TaxonFactory
org/biojava/bio/taxa/CircularReferenceException
org/biojava/bio/taxa/WeakTaxonFactory
org/biojava/bio/taxa/AbstractTaxon
org/biojava/bio/taxa/WeakTaxon
org/biojava/bio/taxa/TaxonParser
org/biojava/bio/SmallAnnotation
org/biojava/bio/Annotatable
org/biojava/bio/annodb/SimpleAnnotationDB
org/biojava/bio/annodb/IndexedAnnotationDB
org/biojava/bio/annodb/MergingAnnotationDB
org/biojava/bio/annodb/EmptyAnnotationDB
org/biojava/bio/annodb/LazyFilteredAnnotationDB
org/biojava/bio/annodb/LazySearchedAnnotationDB
org/biojava/bio/annodb/AnnotationDB
org/biojava/bio/SimpleAnnotation
org/biojava/bio/CollectionConstraint
org/biojava/bio/proteomics/Digest
org/biojava/bio/proteomics/ProteaseManager
org/biojava/bio/proteomics/Protease
org/biojava/bio/proteomics/aaindex/AAindex
org/biojava/bio/proteomics/aaindex/SymbolPropertyTableIterator
org/biojava/bio/proteomics/aaindex/SymbolPropertyTableDB
org/biojava/bio/proteomics/aaindex/AAindexStreamReader
org/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDB
org/biojava/bio/proteomics/StructureTools
org/biojava/bio/proteomics/IsoelectricPointCalc
org/biojava/bio/proteomics/MassCalc
org/biojava/bio/search/KnuthMorrisPrattSearch
org/biojava/bio/search/FilterTest
org/biojava/bio/search/SeqSimilaritySearchSubHit
org/biojava/bio/search/SimpleSeqSimilaritySearchHit
org/biojava/bio/search/SequenceDBSearchSubHit
org/biojava/bio/search/SeqSimilaritySearchResult
org/biojava/bio/search/MaxMismatchPattern
org/biojava/bio/search/SearchBuilder
org/biojava/bio/search/SequenceDBSearchHit
org/biojava/bio/search/SearchContentAdapter
org/biojava/bio/search/SeqSimilaritySearchHit
org/biojava/bio/search/SearchContentFilter
org/biojava/bio/search/MaxMismatchMatcher
org/biojava/bio/search/SearchContentHandlerDebugger
org/biojava/bio/search/SequenceDBSearchResult
org/biojava/bio/search/SearchContentHandler
org/biojava/bio/search/BioPattern
org/biojava/bio/search/SeqContentMatcher
org/biojava/bio/search/FilteringContentHandler
org/biojava/bio/search/SimpleSeqSimilaritySearchSubHit
org/biojava/bio/search/BlastLikeSearchFilter
org/biojava/bio/search/SimpleSeqSimilaritySearchResult
org/biojava/bio/search/SeqSimilaritySearcher
org/biojava/bio/search/SeqContentPattern
org/biojava/bio/search/BioMatcher
org/biojava/bio/EmptyAnnotation
org/biojava/bio/dist/SimpleDistribution
org/biojava/bio/dist/Count
org/biojava/bio/dist/DistributionTrainerContext
org/biojava/bio/dist/Distribution
org/biojava/bio/dist/SimpleDistributionTrainerContext
org/biojava/bio/dist/OrderNDistributionFactory
org/biojava/bio/dist/PairDistribution
org/biojava/bio/dist/TranslatedDistribution
org/biojava/bio/dist/IndexedNthOrderDistribution
org/biojava/bio/dist/AbstractOrderNDistribution
org/biojava/bio/dist/IndexedCount
org/biojava/bio/dist/DistributionTools
org/biojava/bio/dist/GapDistribution
org/biojava/bio/dist/XMLDistributionReader
org/biojava/bio/dist/GeneralNthOrderDistribution
org/biojava/bio/dist/SimpleDistributionTrainer
org/biojava/bio/dist/DistributionTrainer
org/biojava/bio/dist/DistributionFactory
org/biojava/bio/dist/XMLDistributionWriter
org/biojava/bio/dist/IgnoreCountsTrainer
org/biojava/bio/dist/UniformDistribution
org/biojava/bio/dist/UntrainableDistribution
org/biojava/bio/dist/AbstractDistribution
org/biojava/bio/dist/OrderNDistribution
org/biojava/bibliography/BibRefQuery
org/biojava/bibliography/BiblioEntryStatus
org/biojava/bibliography/BiblioProvider
org/biojava/bibliography/BiblioBook
org/biojava/bibliography/BibRefSupport
org/biojava/bibliography/BiblioWebResource
org/biojava/bibliography/BiblioBookArticle
org/biojava/bibliography/BiblioJournal
org/biojava/bibliography/BiblioArticle
org/biojava/bibliography/BiblioTechReport
org/biojava/bibliography/BiblioSubject
org/biojava/bibliography/BibRefException
org/biojava/bibliography/BiblioJournalArticle
org/biojava/bibliography/BiblioCriterion
org/biojava/bibliography/BiblioPatent
org/biojava/bibliography/BiblioProceeding
org/biojava/bibliography/BiblioOrganisation
org/biojava/bibliography/BiblioDescription
org/biojava/bibliography/BiblioThesis
org/biojava/bibliography/BibRef
org/biojava/bibliography/BiblioService
org/biojava/bibliography/BiblioScope
org/biojava/bibliography/BiblioPerson
org/biojava/ontology/Term
org/biojava/ontology/Triple
org/biojava/ontology/Variable
org/biojava/ontology/InvalidTermException
org/biojava/ontology/AlreadyExistsException
org/biojava/ontology/RemoteTerm
org/biojava/ontology/OntologyException
org/biojava/ontology/OntologyTerm
org/biojava/ontology/Ontology
org/biojava/ontology/OntoTools
org/biojava/ontology/io/TabDelimParser
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