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.

biojava3-core.jar is the Core module of BioJava 3.

JAR File Size and Download Location:

File name: biojava3-core.jar, biojava3-core-3.0.2.jar
File size: 257635 bytes
Date modified: 02-Sep-2011
Download: BioJava 3.0 - Core

Manifest of the JAR:

Archiver-Version: Plexus Archiver
Built-By: andreas
Build-Jdk: 1.7.0

List of Classes in the JAR:

org/biojava3/core/exceptions/TranslationException
org/biojava3/core/exceptions/CompoundNotFoundError
org/biojava3/core/exceptions/HeaderParseException
org/biojava3/core/exceptions/FileAccessError
org/biojava3/core/exceptions/SequenceLengthError
org/biojava3/core/exceptions/ParserException
org/biojava3/core/sequence/AccessionID
org/biojava3/core/sequence/ChromosomeSequence
org/biojava3/core/sequence/Strand
org/biojava3/core/sequence/RNASequence
org/biojava3/core/sequence/transcription/Table
org/biojava3/core/sequence/transcription/Frame
org/biojava3/core/sequence/transcription/CaseInsensitiveCompound
org/biojava3/core/sequence/transcription/DNAToRNATranslator
org/biojava3/core/sequence/transcription/RNAToAminoAcidTranslator
org/biojava3/core/sequence/transcription/TranscriptionEngine
org/biojava3/core/sequence/edits/Edit
org/biojava3/core/sequence/compound/CodonCompound
org/biojava3/core/sequence/compound/AmbiguityRNACompoundSet
org/biojava3/core/sequence/compound/DNACompoundSet
org/biojava3/core/sequence/compound/RNACompoundSet
org/biojava3/core/sequence/compound/NucleotideCompound
org/biojava3/core/sequence/compound/AminoAcidCompound
org/biojava3/core/sequence/compound/AmbiguityDNACompoundSet
org/biojava3/core/sequence/compound/AminoAcidCompoundSet
org/biojava3/core/sequence/ExonSequence
org/biojava3/core/sequence/views/ComplementSequenceView
org/biojava3/core/sequence/views/WindowedSequence
org/biojava3/core/sequence/views/RnaSequenceView
org/biojava3/core/sequence/views/ReversedSequenceView
org/biojava3/core/sequence/features/TextFeature
org/biojava3/core/sequence/features/FeatureInterface
org/biojava3/core/sequence/features/FeaturesKeyWordInterface
org/biojava3/core/sequence/features/DBReferenceInfo
org/biojava3/core/sequence/features/DatabaseReferenceInterface
org/biojava3/core/sequence/features/QuantityFeature
org/biojava3/core/sequence/features/AbstractFeature
org/biojava3/core/sequence/ProteinSequence
org/biojava3/core/sequence/TaxonomyID
org/biojava3/core/sequence/MultipleSequenceAlignment
org/biojava3/core/sequence/StopCodonSequence
org/biojava3/core/sequence/BasicSequence
org/biojava3/core/sequence/DNASequence
org/biojava3/core/sequence/IntronSequence
org/biojava3/core/sequence/storage/FourBitSequenceReader
org/biojava3/core/sequence/storage/TwoBitSequenceReader
org/biojava3/core/sequence/storage/BitSequenceReader
org/biojava3/core/sequence/storage/SequenceAsStringHelper
org/biojava3/core/sequence/storage/SingleCompoundSequenceReader
org/biojava3/core/sequence/storage/ArrayListSequenceReader
org/biojava3/core/sequence/storage/JoiningSequenceReader
org/biojava3/core/sequence/SequenceComparator
org/biojava3/core/sequence/SequenceOptimizationHints
org/biojava3/core/sequence/GeneSequence
org/biojava3/core/sequence/CDSComparator
org/biojava3/core/sequence/DataSource
org/biojava3/core/sequence/StartCodonSequence
org/biojava3/core/sequence/io/DNASequenceCreator
org/biojava3/core/sequence/io/RNASequenceCreator
org/biojava3/core/sequence/io/FastaReaderHelper
org/biojava3/core/sequence/io/FileProxyDNASequenceCreator
org/biojava3/core/sequence/io/ProteinSequenceCreator
org/biojava3/core/sequence/io/GenericFastaHeaderFormat
org/biojava3/core/sequence/io/FastaWriterHelper
org/biojava3/core/sequence/io/FastaWriter
org/biojava3/core/sequence/io/BufferedReaderBytesRead
org/biojava3/core/sequence/io/FileProxyProteinSequenceCreator
org/biojava3/core/sequence/io/FastaGeneWriter
org/biojava3/core/sequence/io/IUPACParser
org/biojava3/core/sequence/io/util/IOUtils
org/biojava3/core/sequence/io/util/ClasspathResource
org/biojava3/core/sequence/io/GenericFastaHeaderParser
org/biojava3/core/sequence/io/FastaReader
org/biojava3/core/sequence/io/FastaSequenceParser
org/biojava3/core/sequence/io/template/SequenceCreatorInterface
org/biojava3/core/sequence/io/template/SequenceParserInterface
org/biojava3/core/sequence/io/template/FastaHeaderFormatInterface
org/biojava3/core/sequence/io/template/FastaHeaderParserInterface
org/biojava3/core/sequence/TranscriptSequence
org/biojava3/core/sequence/loader/UniprotProxySequenceReader
org/biojava3/core/sequence/loader/StringProxySequenceReader
org/biojava3/core/sequence/loader/SequenceFileProxyLoader
org/biojava3/core/sequence/loader/ArrayListProxySequenceReader
org/biojava3/core/sequence/ExonComparator
org/biojava3/core/sequence/location/SimplePoint
org/biojava3/core/sequence/location/FuzzyPoint
org/biojava3/core/sequence/location/InsdcParser
org/biojava3/core/sequence/location/InsdcLocations
org/biojava3/core/sequence/location/SimpleLocation
org/biojava3/core/sequence/location/LocationHelper
org/biojava3/core/sequence/location/SequenceLocation
org/biojava3/core/sequence/location/template/AbstractLocation
org/biojava3/core/sequence/location/template/Point
org/biojava3/core/sequence/location/template/Location
org/biojava3/core/sequence/location/template/AccesionedLocation
org/biojava3/core/sequence/CDSSequence
org/biojava3/core/sequence/template/AbstractNucleotideCompoundSet
org/biojava3/core/sequence/template/CompoundTranslator
org/biojava3/core/sequence/template/AbstractCompound
org/biojava3/core/sequence/template/SequenceProxyView
org/biojava3/core/sequence/template/LightweightProfile
org/biojava3/core/sequence/template/Sequence
org/biojava3/core/sequence/template/SequenceMixin
org/biojava3/core/sequence/template/SequenceReader
org/biojava3/core/sequence/template/AbstractSequence
org/biojava3/core/sequence/template/Compound
org/biojava3/core/sequence/template/Accessioned
org/biojava3/core/sequence/template/AbstractCompoundTranslator
org/biojava3/core/sequence/template/AbstractCompoundSet
org/biojava3/core/sequence/template/CompoundSet
org/biojava3/core/sequence/template/ProxySequenceReader
org/biojava3/core/sequence/template/SequenceView
org/biojava3/core/sequence/template/ComplementCompound
org/biojava3/core/util/FlatFileCache
org/biojava3/core/util/ConcurrencyTools
org/biojava3/core/util/CRC64Checksum
org/biojava3/core/util/Hashcoder
org/biojava3/core/util/PrettyXMLWriter
org/biojava3/core/util/SoftHashMap
org/biojava3/core/util/XMLHelper
org/biojava3/core/util/SequenceTools
org/biojava3/core/util/Equals
org/biojava3/core/util/XMLWriter
org/biojava3/core/util/InputStreamProvider
org/biojava3/core/util/UncompressInputStream