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/ontology/io/GOParser
org/biojava/ontology/io/OboParser
org/biojava/ontology/DefaultOps
org/biojava/ontology/OntologyOps
org/biojava/ontology/obo/NestedValue
org/biojava/ontology/obo/OboFileEventListener
org/biojava/ontology/obo/OboFileParser
org/biojava/ontology/obo/OboFileHandler
org/biojava/ontology/Synonym
org/biojava/ontology/IntegerOntology
org/biojava/ontology/OntologyFactory
org/biojava/ontology/AbstractTerm
org/biojava/utils/process/ReaderWriterPipe
org/biojava/utils/process/ReaderInputHandler
org/biojava/utils/process/InputHandler
org/biojava/utils/process/ExternalProcess
org/biojava/utils/process/SimpleOutputHandler
org/biojava/utils/process/SimpleInputHandler
org/biojava/utils/process/WriterOutputHandler
org/biojava/utils/process/StreamPipe
org/biojava/utils/process/OutputHandler
org/biojava/utils/TriState
org/biojava/utils/ChangeListener
org/biojava/utils/ThreadPool
org/biojava/utils/ListTools
org/biojava/utils/ActivityListener
org/biojava/utils/StaticMemberPlaceHolder
org/biojava/utils/math/BinarySearch
org/biojava/utils/math/ComputeObject
org/biojava/utils/cache/WeakCacheMap
org/biojava/utils/cache/WeakValueHashMap
org/biojava/utils/cache/Cache
org/biojava/utils/cache/KeyedWeakReference
org/biojava/utils/cache/ChangeableCache
org/biojava/utils/cache/SoftReferenceCache
org/biojava/utils/cache/FixedSizeMap
org/biojava/utils/cache/FixedSizeCache
org/biojava/utils/cache/CacheMap
org/biojava/utils/cache/CacheReference
org/biojava/utils/Constants
org/biojava/utils/ParseErrorSource
org/biojava/utils/Commitable
org/biojava/utils/lsid/Identifiable
org/biojava/utils/lsid/LifeScienceIdentifier
org/biojava/utils/lsid/LifeScienceIdentifierParseException
org/biojava/utils/ParseErrorEvent
org/biojava/utils/CommitFailure
org/biojava/utils/ProcessTimeoutException
org/biojava/utils/MergingSet
org/biojava/utils/MergingIterator
org/biojava/utils/Services
org/biojava/utils/xml/XMLBeans
org/biojava/utils/xml/PrettyXMLWriter
org/biojava/utils/xml/XMLWritable
org/biojava/utils/xml/XMLWriter
org/biojava/utils/xml/AppEntry
org/biojava/utils/xml/AppBeanRunner
org/biojava/utils/xml/FastXMLWriter
org/biojava/utils/xml/Initializable
org/biojava/utils/xml/AppException
org/biojava/utils/xml/ResourceEntityResolver
org/biojava/utils/Unchangeable
org/biojava/utils/walker/Visitor
org/biojava/utils/walker/Walker
org/biojava/utils/walker/WalkerFactory
org/biojava/utils/JDBCPooledDataSource
org/biojava/utils/SmallMap
org/biojava/utils/ParseErrorListener
org/biojava/utils/io/CountedBufferedReader
org/biojava/utils/io/UncompressInputStream
org/biojava/utils/io/RandomAccessReader
org/biojava/utils/io/SoftHashMap
org/biojava/utils/io/RAF
org/biojava/utils/io/LargeBuffer
org/biojava/utils/io/Seekable
org/biojava/utils/io/InputStreamProvider
org/biojava/utils/io/FlatFileCache
org/biojava/utils/io/CachingInputStream
org/biojava/utils/OverlayMap
org/biojava/utils/ExecRunner
org/biojava/utils/ParserException
org/biojava/utils/ChangeAdapter
org/biojava/utils/IndexedChangeHub
org/biojava/utils/BeanAsMap
org/biojava/utils/ProcessTools
org/biojava/utils/JDBCConnectionPool
org/biojava/utils/SingletonList
org/biojava/utils/StreamGobbler
org/biojava/utils/AbstractChangeable
org/biojava/utils/SimpleThreadPool
org/biojava/utils/RepeatedCharSequence
org/biojava/utils/stax/IntElementHandlerBase
org/biojava/utils/stax/DelegationManager
org/biojava/utils/stax/SAX2StAXAdaptor
org/biojava/utils/stax/DoubleElementHandlerBase
org/biojava/utils/stax/CharElementHandlerBase
org/biojava/utils/stax/StringElementHandlerBase
org/biojava/utils/stax/ByteElementHandlerBase
org/biojava/utils/stax/FloatElementHandlerBase
org/biojava/utils/stax/BooleanElementHandlerBase
org/biojava/utils/stax/StAXContentHandler
org/biojava/utils/stax/StAXContentHandlerBase
org/biojava/utils/stax/LongElementHandlerBase
org/biojava/utils/ChangeSupport
org/biojava/utils/regex/PatternChecker
org/biojava/utils/regex/RegexException
org/biojava/utils/regex/Matcher
org/biojava/utils/regex/Search
org/biojava/utils/regex/Pattern
org/biojava/utils/regex/PatternFactory
org/biojava/utils/AssertionFailure
org/biojava/utils/candy/CandyException
org/biojava/utils/candy/CandyVocabulary
org/biojava/utils/candy/CandyEntry
org/biojava/utils/candy/CandyFinder
org/biojava/utils/ChangeForwarder
org/biojava/utils/FileAsList
org/biojava/utils/ChangeEvent
org/biojava/utils/SmallSet
org/biojava/utils/ObjectUtil
org/biojava/utils/ChangeType
org/biojava/utils/ClassTools
org/biojava/utils/ChangeHub
org/biojava/utils/ChangeVetoException
org/biojava/utils/automata/StateMachineFactory
org/biojava/utils/automata/ArrayStateMachineToolkit
org/biojava/utils/automata/NfaBuilder
org/biojava/utils/automata/DfaBuilder
org/biojava/utils/automata/Nfa
org/biojava/utils/automata/FiniteAutomaton
org/biojava/utils/automata/PatternBlitz
org/biojava/utils/automata/PatternMaker
org/biojava/utils/automata/PatternListener
org/biojava/utils/automata/NfaSubModel
org/biojava/utils/automata/StateMachineInstance
org/biojava/utils/automata/AutomatonException
org/biojava/utils/automata/StateMachineToolkit
org/biojava/utils/Changeable
org/biojava/utils/TypedProperties
org/biojava/utils/net/URLFactory
org/biojavax/SimpleRichObjectBuilder
org/biojavax/ga/GAStoppingCriteria
org/biojavax/ga/GeneticAlgorithm
org/biojavax/ga/impl/SimplePopulation
org/biojavax/ga/impl/SimpleGeneticAlgorithm
org/biojavax/ga/impl/AbstractOrganism
org/biojavax/ga/impl/AbstractGeneticAlgorithm
org/biojavax/ga/impl/AbstractPopulation
org/biojavax/ga/impl/SimpleOrganism
org/biojavax/ga/exception/IllegalOrganismException
org/biojavax/ga/functions/ProportionalSelection
org/biojavax/ga/functions/MutationFunction
org/biojavax/ga/functions/SelectionFunction
org/biojavax/ga/functions/OrderCrossover
org/biojavax/ga/functions/SwapMutationFunction
org/biojavax/ga/functions/SimpleCrossOverFunction
org/biojavax/ga/functions/GACrossResult
org/biojavax/ga/functions/AbstractCrossOverFunction
org/biojavax/ga/functions/FitnessFunction
org/biojavax/ga/functions/GACross
org/biojavax/ga/functions/AbstractMutationFunction
org/biojavax/ga/functions/SimpleGACrossResult
org/biojavax/ga/functions/CrossOverFunction
org/biojavax/ga/functions/TournamentSelection
org/biojavax/ga/functions/SimpleMutationFunction
org/biojavax/ga/util/WeightedSet
org/biojavax/ga/util/GATools
org/biojavax/ga/Population
org/biojavax/ga/Organism
org/biojavax/RichObjectBuilder
org/biojavax/SimpleDocRef
org/biojavax/SimpleDocRefAuthor
org/biojavax/Namespace
org/biojavax/Comment
org/biojavax/RichAnnotation
org/biojavax/bio/seq/RichFeatureRelationship
org/biojavax/bio/seq/RichLocation
org/biojavax/bio/seq/SimpleRichSequence
org/biojavax/bio/seq/SimpleRichFeatureRelationship
org/biojavax/bio/seq/SimpleRichLocation
org/biojavax/bio/seq/EmptyRichLocation
org/biojavax/bio/seq/CompoundRichLocation
org/biojavax/bio/seq/InfinitelyAmbiguousSymbolList
org/biojavax/bio/seq/ThinRichSequence
org/biojavax/bio/seq/DummyRichSequenceHandler
org/biojavax/bio/seq/RichSequence
org/biojavax/bio/seq/RichFeatureRelationshipHolder
org/biojavax/bio/seq/io/EMBLFormat
org/biojavax/bio/seq/io/GenbankLocationParser
org/biojavax/bio/seq/io/FastaHeader
org/biojavax/bio/seq/io/RichSeqIOListener
org/biojavax/bio/seq/io/SimpleRichSequenceBuilder
org/biojavax/bio/seq/io/GenbankFormat
org/biojavax/bio/seq/io/MyRichSeqIOListener
org/biojavax/bio/seq/io/UniProtXMLFormat
org/biojavax/bio/seq/io/RichStreamWriter
org/biojavax/bio/seq/io/FastaFormat
org/biojavax/bio/seq/io/EMBLxmlFormat
org/biojavax/bio/seq/io/INSDseqFormat
org/biojavax/bio/seq/io/DebuggingRichSeqIOListener
org/biojavax/bio/seq/io/SimpleRichSequenceBuilderFactory
org/biojavax/bio/seq/io/UniProtFormat
org/biojavax/bio/seq/io/UniProtLocationParser
org/biojavax/bio/seq/io/RichSequenceFormat
org/biojavax/bio/seq/io/UniProtCommentParser
org/biojavax/bio/seq/io/RichSequenceBuilderFactory
org/biojavax/bio/seq/io/HashedFastaIterator
org/biojavax/bio/seq/io/RichSequenceBuilder
org/biojavax/bio/seq/io/RichStreamReader
org/biojavax/bio/seq/io/RichSeqIOAdapter
org/biojavax/bio/seq/SimpleRichFeature
org/biojavax/bio/seq/PositionResolver
org/biojavax/bio/seq/MultiSourceCompoundRichLocation
org/biojavax/bio/seq/RichSequenceIterator
org/biojavax/bio/seq/Position
org/biojavax/bio/seq/RichFeature
org/biojavax/bio/seq/SimplePosition
org/biojavax/bio/seq/RichSequenceHandler
org/biojavax/bio/BioEntryIterator
org/biojavax/bio/alignment/blast/RemoteQBlastOutputFormat
org/biojavax/bio/alignment/blast/RemoteQBlastAlignmentProperties
org/biojavax/bio/alignment/blast/RemoteQBlastOutputProperties
org/biojavax/bio/alignment/blast/RemoteQBlastService
org/biojavax/bio/alignment/RemotePairwiseAlignmentService
org/biojavax/bio/alignment/RemotePairwiseAlignmentOutputProperties
org/biojavax/bio/alignment/RemotePairwiseAlignmentProperties
org/biojavax/bio/taxa/SimpleNCBITaxon
org/biojavax/bio/taxa/SimpleNCBITaxonName
org/biojavax/bio/taxa/NCBITaxon
org/biojavax/bio/taxa/io/SimpleNCBITaxonomyLoader
org/biojavax/bio/taxa/io/NCBITaxonomyLoader
org/biojavax/bio/db/AbstractRichSequenceDB
org/biojavax/bio/db/HashRichSequenceDB
org/biojavax/bio/db/ncbi/GenbankRichSequenceDB
org/biojavax/bio/db/ncbi/GenpeptRichSequenceDB
org/biojavax/bio/db/BioEntryDBLite
org/biojavax/bio/db/BioEntryDB
org/biojavax/bio/db/RichSequenceDB
org/biojavax/bio/db/HashBioEntryDB
org/biojavax/bio/db/AbstractBioEntryDB
org/biojavax/bio/db/RichSequenceDBLite
org/biojavax/bio/SimpleBioEntryRelationship
org/biojavax/bio/BioEntry
org/biojavax/bio/BioEntryRelationship
org/biojavax/bio/SimpleBioEntry
org/biojavax/RankedDocRef
org/biojavax/DocRefAuthor
org/biojavax/DummyCrossReferenceResolver
org/biojavax/RichObjectFactory
org/biojavax/ontology/SimpleComparableTriple
org/biojavax/ontology/ComparableOntology
org/biojavax/ontology/ComparableTerm
org/biojavax/ontology/SimpleComparableTerm
org/biojavax/ontology/SimpleComparableOntology
org/biojavax/ontology/ComparableTriple
org/biojavax/utils/XMLTools
org/biojavax/utils/CRC64Checksum
org/biojavax/utils/StringTools
org/biojavax/CrossRef
org/biojavax/SimpleNote
org/biojavax/SimpleRankedDocRef
org/biojavax/RankedCrossRef
org/biojavax/SimpleRankedCrossRef
org/biojavax/SimpleCrossRef
org/biojavax/RichAnnotatable
org/biojavax/SimpleRichAnnotation
org/biojavax/DocRef
org/biojavax/RankedCrossRefable
org/biojavax/SimpleComment
org/biojavax/EmptyRichAnnotation
org/biojavax/CrossReferenceResolutionException
org/biojavax/Note
org/biojavax/SimpleNamespace
org/biojavax/CrossReferenceResolver