Download biojava-core JAR 6.0.4 with all dependencies

Files of the artifact biojava-core version 6.0.4 from the group org.biojava.

Artifact biojava-core
Group org.biojava
Version 6.0.4
Last update 05. January 2022
Tags: development common data parsers analytical routines formats statistical open allows file dedicated processing biojava application facilitate sequences provides providing rapid framework manipulation goal structures project biological source java bioinformatics
Organization BioJava
URL http://www.biojava.org
License GNU LGPL v2
Dependencies amount 4
Dependencies slf4j-api, log4j-slf4j-impl, log4j-api, log4j-core,
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14 downloads

Source code of biojava-core version 6.0.4

META-INF

META-INF.META-INF.MANIFEST.MF

META-INF.maven.org.biojava.biojava-core

META-INF.maven.org.biojava.biojava-core.META-INF.maven.org.biojava.biojava-core.pom.properties

META-INF.maven.org.biojava.biojava-core.META-INF.maven.org.biojava.biojava-core.pom.xml

META-INF.services

META-INF.services.META-INF.services.org.biojava.nbio.core.search.io.ResultFactory

demo

demo.demo.DemoSixFrameTranslation

demo.demo.ParseFastaFileDemo

demo.demo.UncompressFile

.log4j2.xml

matrices

matrices.matrices.AAINDEX.txt

matrices.matrices.blosum100.txt

matrices.matrices.blosum30.txt

matrices.matrices.blosum35.txt

matrices.matrices.blosum40.txt

matrices.matrices.blosum45.txt

matrices.matrices.blosum50.txt

matrices.matrices.blosum55.txt

matrices.matrices.blosum60.txt

matrices.matrices.blosum62.txt

matrices.matrices.blosum65.txt

matrices.matrices.blosum70.txt

matrices.matrices.blosum75.txt

matrices.matrices.blosum80.txt

matrices.matrices.blosum85.txt

matrices.matrices.blosum90.txt

matrices.matrices.gonnet250.txt

matrices.matrices.identity.txt

matrices.matrices.nuc-4_2.txt

matrices.matrices.nuc-4_4.txt

matrices.matrices.pam250.txt

org.biojava.nbio.core.alignment

org.biojava.nbio.core.alignment.org.biojava.nbio.core.alignment.SimpleAlignedSequence

org.biojava.nbio.core.alignment.org.biojava.nbio.core.alignment.SimpleProfile

org.biojava.nbio.core.alignment.org.biojava.nbio.core.alignment.SimpleProfilePair

org.biojava.nbio.core.alignment.org.biojava.nbio.core.alignment.SimpleSequencePair

org.biojava.nbio.core.alignment.matrices

org.biojava.nbio.core.alignment.matrices.org.biojava.nbio.core.alignment.matrices.AAIndexFileParser

org.biojava.nbio.core.alignment.matrices.org.biojava.nbio.core.alignment.matrices.AAIndexProvider

org.biojava.nbio.core.alignment.matrices.org.biojava.nbio.core.alignment.matrices.AAindexFactory

org.biojava.nbio.core.alignment.matrices.org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProvider

org.biojava.nbio.core.alignment.matrices.org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix

org.biojava.nbio.core.alignment.matrices.org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix

org.biojava.nbio.core.alignment.matrices.org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper

org.biojava.nbio.core.alignment.template

org.biojava.nbio.core.alignment.template.org.biojava.nbio.core.alignment.template.AlignedSequence

org.biojava.nbio.core.alignment.template.org.biojava.nbio.core.alignment.template.MutableAlignedSequence

org.biojava.nbio.core.alignment.template.org.biojava.nbio.core.alignment.template.MutableProfile

org.biojava.nbio.core.alignment.template.org.biojava.nbio.core.alignment.template.MutableProfilePair

org.biojava.nbio.core.alignment.template.org.biojava.nbio.core.alignment.template.MutableSequencePair

org.biojava.nbio.core.alignment.template.org.biojava.nbio.core.alignment.template.Profile

org.biojava.nbio.core.alignment.template.org.biojava.nbio.core.alignment.template.ProfilePair

org.biojava.nbio.core.alignment.template.org.biojava.nbio.core.alignment.template.ProfileView

org.biojava.nbio.core.alignment.template.org.biojava.nbio.core.alignment.template.SequencePair

org.biojava.nbio.core.alignment.template.org.biojava.nbio.core.alignment.template.SubstitutionMatrix

org.biojava.nbio.core.exceptions

org.biojava.nbio.core.exceptions.org.biojava.nbio.core.exceptions.CompoundNotFoundException

org.biojava.nbio.core.exceptions.org.biojava.nbio.core.exceptions.Messages

org.biojava.nbio.core.exceptions.org.biojava.nbio.core.exceptions.ParserException

org.biojava.nbio.core.exceptions.org.biojava.nbio.core.exceptions.TranslationException

org.biojava.nbio.core.search.io

org.biojava.nbio.core.search.io.org.biojava.nbio.core.search.io.Hit

org.biojava.nbio.core.search.io.org.biojava.nbio.core.search.io.Hsp

org.biojava.nbio.core.search.io.org.biojava.nbio.core.search.io.Result

org.biojava.nbio.core.search.io.org.biojava.nbio.core.search.io.ResultFactory

org.biojava.nbio.core.search.io.org.biojava.nbio.core.search.io.SearchIO

org.biojava.nbio.core.search.io.blast

org.biojava.nbio.core.search.io.blast.org.biojava.nbio.core.search.io.blast.BlastHitBuilder

org.biojava.nbio.core.search.io.blast.org.biojava.nbio.core.search.io.blast.BlastHspBuilder

org.biojava.nbio.core.search.io.blast.org.biojava.nbio.core.search.io.blast.BlastResult

org.biojava.nbio.core.search.io.blast.org.biojava.nbio.core.search.io.blast.BlastResultBuilder

org.biojava.nbio.core.search.io.blast.org.biojava.nbio.core.search.io.blast.BlastTabularParser

org.biojava.nbio.core.search.io.blast.org.biojava.nbio.core.search.io.blast.BlastXMLParser

org.biojava.nbio.core.sequence

org.biojava.nbio.core.sequence.org.biojava.nbio.core.sequence.AccessionID

org.biojava.nbio.core.sequence.org.biojava.nbio.core.sequence.BasicSequence

org.biojava.nbio.core.sequence.org.biojava.nbio.core.sequence.CDSComparator

org.biojava.nbio.core.sequence.org.biojava.nbio.core.sequence.CDSSequence

org.biojava.nbio.core.sequence.org.biojava.nbio.core.sequence.ChromosomeSequence

org.biojava.nbio.core.sequence.org.biojava.nbio.core.sequence.DNASequence

org.biojava.nbio.core.sequence.org.biojava.nbio.core.sequence.DataSource

org.biojava.nbio.core.sequence.org.biojava.nbio.core.sequence.ExonComparator

org.biojava.nbio.core.sequence.org.biojava.nbio.core.sequence.ExonSequence

org.biojava.nbio.core.sequence.org.biojava.nbio.core.sequence.GeneSequence

org.biojava.nbio.core.sequence.org.biojava.nbio.core.sequence.IntronSequence

org.biojava.nbio.core.sequence.org.biojava.nbio.core.sequence.MultipleSequenceAlignment

org.biojava.nbio.core.sequence.org.biojava.nbio.core.sequence.ProteinSequence

org.biojava.nbio.core.sequence.org.biojava.nbio.core.sequence.RNASequence

org.biojava.nbio.core.sequence.org.biojava.nbio.core.sequence.SequenceComparator

org.biojava.nbio.core.sequence.org.biojava.nbio.core.sequence.SequenceOptimizationHints

org.biojava.nbio.core.sequence.org.biojava.nbio.core.sequence.StartCodonSequence

org.biojava.nbio.core.sequence.org.biojava.nbio.core.sequence.StopCodonSequence

org.biojava.nbio.core.sequence.org.biojava.nbio.core.sequence.Strand

org.biojava.nbio.core.sequence.org.biojava.nbio.core.sequence.TaxonomyID

org.biojava.nbio.core.sequence.org.biojava.nbio.core.sequence.TranscriptSequence

org.biojava.nbio.core.sequence.compound

org.biojava.nbio.core.sequence.compound.org.biojava.nbio.core.sequence.compound.ABITracerCompoundSet

org.biojava.nbio.core.sequence.compound.org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundSet

org.biojava.nbio.core.sequence.compound.org.biojava.nbio.core.sequence.compound.AmbiguityDNARNAHybridCompoundSet

org.biojava.nbio.core.sequence.compound.org.biojava.nbio.core.sequence.compound.AmbiguityRNACompoundSet

org.biojava.nbio.core.sequence.compound.org.biojava.nbio.core.sequence.compound.AminoAcidCompound

org.biojava.nbio.core.sequence.compound.org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet

org.biojava.nbio.core.sequence.compound.org.biojava.nbio.core.sequence.compound.CodonCompound

org.biojava.nbio.core.sequence.compound.org.biojava.nbio.core.sequence.compound.DNACompoundSet

org.biojava.nbio.core.sequence.compound.org.biojava.nbio.core.sequence.compound.NucleotideCompound

org.biojava.nbio.core.sequence.compound.org.biojava.nbio.core.sequence.compound.RNACompoundSet

org.biojava.nbio.core.sequence.edits

org.biojava.nbio.core.sequence.edits.org.biojava.nbio.core.sequence.edits.Edit

org.biojava.nbio.core.sequence.features

org.biojava.nbio.core.sequence.features.org.biojava.nbio.core.sequence.features.AbstractFeature

org.biojava.nbio.core.sequence.features.org.biojava.nbio.core.sequence.features.DBReferenceInfo

org.biojava.nbio.core.sequence.features.org.biojava.nbio.core.sequence.features.DatabaseReferenceInterface

org.biojava.nbio.core.sequence.features.org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo

org.biojava.nbio.core.sequence.features.org.biojava.nbio.core.sequence.features.FeatureInterface

org.biojava.nbio.core.sequence.features.org.biojava.nbio.core.sequence.features.FeatureRetriever

org.biojava.nbio.core.sequence.features.org.biojava.nbio.core.sequence.features.FeaturesKeyWordInterface

org.biojava.nbio.core.sequence.features.org.biojava.nbio.core.sequence.features.Qualifier

org.biojava.nbio.core.sequence.features.org.biojava.nbio.core.sequence.features.QualityFeature

org.biojava.nbio.core.sequence.features.org.biojava.nbio.core.sequence.features.QuantityFeature

org.biojava.nbio.core.sequence.features.org.biojava.nbio.core.sequence.features.TextFeature

org.biojava.nbio.core.sequence.io

org.biojava.nbio.core.sequence.io.org.biojava.nbio.core.sequence.io.ABITrace

org.biojava.nbio.core.sequence.io.org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead

org.biojava.nbio.core.sequence.io.org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator

org.biojava.nbio.core.sequence.io.org.biojava.nbio.core.sequence.io.DNASequenceCreator

org.biojava.nbio.core.sequence.io.org.biojava.nbio.core.sequence.io.FastaGeneWriter

org.biojava.nbio.core.sequence.io.org.biojava.nbio.core.sequence.io.FastaReader

org.biojava.nbio.core.sequence.io.org.biojava.nbio.core.sequence.io.FastaReaderHelper

org.biojava.nbio.core.sequence.io.org.biojava.nbio.core.sequence.io.FastaSequenceParser

org.biojava.nbio.core.sequence.io.org.biojava.nbio.core.sequence.io.FastaWriter

org.biojava.nbio.core.sequence.io.org.biojava.nbio.core.sequence.io.FastaWriterHelper

org.biojava.nbio.core.sequence.io.org.biojava.nbio.core.sequence.io.FileProxyDNASequenceCreator

org.biojava.nbio.core.sequence.io.org.biojava.nbio.core.sequence.io.FileProxyProteinSequenceCreator

org.biojava.nbio.core.sequence.io.org.biojava.nbio.core.sequence.io.FileProxyRNASequenceCreator

org.biojava.nbio.core.sequence.io.org.biojava.nbio.core.sequence.io.GenbankReader

org.biojava.nbio.core.sequence.io.org.biojava.nbio.core.sequence.io.GenbankReaderHelper

org.biojava.nbio.core.sequence.io.org.biojava.nbio.core.sequence.io.GenbankSequenceParser

org.biojava.nbio.core.sequence.io.org.biojava.nbio.core.sequence.io.GenbankWriter

org.biojava.nbio.core.sequence.io.org.biojava.nbio.core.sequence.io.GenbankWriterHelper

org.biojava.nbio.core.sequence.io.org.biojava.nbio.core.sequence.io.GenericFastaHeaderFormat

org.biojava.nbio.core.sequence.io.org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser

org.biojava.nbio.core.sequence.io.org.biojava.nbio.core.sequence.io.GenericGenbankHeaderFormat

org.biojava.nbio.core.sequence.io.org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser

org.biojava.nbio.core.sequence.io.org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat

org.biojava.nbio.core.sequence.io.org.biojava.nbio.core.sequence.io.IUPACParser

org.biojava.nbio.core.sequence.io.org.biojava.nbio.core.sequence.io.PlainFastaHeaderParser

org.biojava.nbio.core.sequence.io.org.biojava.nbio.core.sequence.io.ProteinSequenceCreator

org.biojava.nbio.core.sequence.io.org.biojava.nbio.core.sequence.io.RNASequenceCreator

org.biojava.nbio.core.sequence.io.embl

org.biojava.nbio.core.sequence.io.embl.org.biojava.nbio.core.sequence.io.embl.EmblId

org.biojava.nbio.core.sequence.io.embl.org.biojava.nbio.core.sequence.io.embl.EmblReader

org.biojava.nbio.core.sequence.io.embl.org.biojava.nbio.core.sequence.io.embl.EmblRecord

org.biojava.nbio.core.sequence.io.embl.org.biojava.nbio.core.sequence.io.embl.EmblReference

org.biojava.nbio.core.sequence.io.template

org.biojava.nbio.core.sequence.io.template.org.biojava.nbio.core.sequence.io.template.FastaHeaderFormatInterface

org.biojava.nbio.core.sequence.io.template.org.biojava.nbio.core.sequence.io.template.GenbankHeaderFormatInterface

org.biojava.nbio.core.sequence.io.template.org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface

org.biojava.nbio.core.sequence.io.template.org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface

org.biojava.nbio.core.sequence.io.template.org.biojava.nbio.core.sequence.io.template.SequenceParserInterface

org.biojava.nbio.core.sequence.io.util

org.biojava.nbio.core.sequence.io.util.org.biojava.nbio.core.sequence.io.util.ClasspathResource

org.biojava.nbio.core.sequence.io.util.org.biojava.nbio.core.sequence.io.util.IOUtils

org.biojava.nbio.core.sequence

org.biojava.nbio.core.sequence.org.biojava.nbio.core.sequence.iupac.txt

org.biojava.nbio.core.sequence.loader

org.biojava.nbio.core.sequence.loader.org.biojava.nbio.core.sequence.loader.ArrayListProxySequenceReader

org.biojava.nbio.core.sequence.loader.org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader

org.biojava.nbio.core.sequence.loader.org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader

org.biojava.nbio.core.sequence.loader.org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

org.biojava.nbio.core.sequence.loader.org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader

org.biojava.nbio.core.sequence.location

org.biojava.nbio.core.sequence.location.org.biojava.nbio.core.sequence.location.FuzzyPoint

org.biojava.nbio.core.sequence.location.org.biojava.nbio.core.sequence.location.InsdcLocations

org.biojava.nbio.core.sequence.location.org.biojava.nbio.core.sequence.location.InsdcParser

org.biojava.nbio.core.sequence.location.org.biojava.nbio.core.sequence.location.LocationHelper

org.biojava.nbio.core.sequence.location.org.biojava.nbio.core.sequence.location.SequenceLocation

org.biojava.nbio.core.sequence.location.org.biojava.nbio.core.sequence.location.SimpleLocation

org.biojava.nbio.core.sequence.location.org.biojava.nbio.core.sequence.location.SimplePoint

org.biojava.nbio.core.sequence.location.template

org.biojava.nbio.core.sequence.location.template.org.biojava.nbio.core.sequence.location.template.AbstractLocation

org.biojava.nbio.core.sequence.location.template.org.biojava.nbio.core.sequence.location.template.AccesionedLocation

org.biojava.nbio.core.sequence.location.template.org.biojava.nbio.core.sequence.location.template.Location

org.biojava.nbio.core.sequence.location.template.org.biojava.nbio.core.sequence.location.template.Point

org.biojava.nbio.core.sequence.reference

org.biojava.nbio.core.sequence.reference.org.biojava.nbio.core.sequence.reference.AbstractReference

org.biojava.nbio.core.sequence.reference.org.biojava.nbio.core.sequence.reference.GenbankReference

org.biojava.nbio.core.sequence.reference.org.biojava.nbio.core.sequence.reference.ReferenceInterface

org.biojava.nbio.core.sequence.storage

org.biojava.nbio.core.sequence.storage.org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader

org.biojava.nbio.core.sequence.storage.org.biojava.nbio.core.sequence.storage.BitSequenceReader

org.biojava.nbio.core.sequence.storage.org.biojava.nbio.core.sequence.storage.FourBitSequenceReader

org.biojava.nbio.core.sequence.storage.org.biojava.nbio.core.sequence.storage.JoiningSequenceReader

org.biojava.nbio.core.sequence.storage.org.biojava.nbio.core.sequence.storage.SequenceAsStringHelper

org.biojava.nbio.core.sequence.storage.org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader

org.biojava.nbio.core.sequence.storage.org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader

org.biojava.nbio.core.sequence.template

org.biojava.nbio.core.sequence.template.org.biojava.nbio.core.sequence.template.AbstractCompound

org.biojava.nbio.core.sequence.template.org.biojava.nbio.core.sequence.template.AbstractCompoundSet

org.biojava.nbio.core.sequence.template.org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator

org.biojava.nbio.core.sequence.template.org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet

org.biojava.nbio.core.sequence.template.org.biojava.nbio.core.sequence.template.AbstractSequence

org.biojava.nbio.core.sequence.template.org.biojava.nbio.core.sequence.template.Accessioned

org.biojava.nbio.core.sequence.template.org.biojava.nbio.core.sequence.template.ComplementCompound

org.biojava.nbio.core.sequence.template.org.biojava.nbio.core.sequence.template.Compound

org.biojava.nbio.core.sequence.template.org.biojava.nbio.core.sequence.template.CompoundSet

org.biojava.nbio.core.sequence.template.org.biojava.nbio.core.sequence.template.CompoundTranslator

org.biojava.nbio.core.sequence.template.org.biojava.nbio.core.sequence.template.LightweightProfile

org.biojava.nbio.core.sequence.template.org.biojava.nbio.core.sequence.template.ProxySequenceReader

org.biojava.nbio.core.sequence.template.org.biojava.nbio.core.sequence.template.Sequence

org.biojava.nbio.core.sequence.template.org.biojava.nbio.core.sequence.template.SequenceMixin

org.biojava.nbio.core.sequence.template.org.biojava.nbio.core.sequence.template.SequenceProxyView

org.biojava.nbio.core.sequence.template.org.biojava.nbio.core.sequence.template.SequenceReader

org.biojava.nbio.core.sequence.template.org.biojava.nbio.core.sequence.template.SequenceView

org.biojava.nbio.core.sequence.transcription

org.biojava.nbio.core.sequence.transcription.org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound

org.biojava.nbio.core.sequence.transcription.org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator

org.biojava.nbio.core.sequence.transcription.org.biojava.nbio.core.sequence.transcription.Frame

org.biojava.nbio.core.sequence.transcription.org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator

org.biojava.nbio.core.sequence.transcription.org.biojava.nbio.core.sequence.transcription.Table

org.biojava.nbio.core.sequence.transcription.org.biojava.nbio.core.sequence.transcription.TranscriptionEngine

org.biojava.nbio.core.sequence.views

org.biojava.nbio.core.sequence.views.org.biojava.nbio.core.sequence.views.ComplementSequenceView

org.biojava.nbio.core.sequence.views.org.biojava.nbio.core.sequence.views.ReversedSequenceView

org.biojava.nbio.core.sequence.views.org.biojava.nbio.core.sequence.views.RnaSequenceView

org.biojava.nbio.core.sequence.views.org.biojava.nbio.core.sequence.views.WindowedSequence

org.biojava.nbio.core.util

org.biojava.nbio.core.util.org.biojava.nbio.core.util.CRC64Checksum

org.biojava.nbio.core.util.org.biojava.nbio.core.util.ConcurrencyTools

org.biojava.nbio.core.util.org.biojava.nbio.core.util.Equals

org.biojava.nbio.core.util.org.biojava.nbio.core.util.FileDownloadUtils

org.biojava.nbio.core.util.org.biojava.nbio.core.util.FlatFileCache

org.biojava.nbio.core.util.org.biojava.nbio.core.util.Hashcoder

org.biojava.nbio.core.util.org.biojava.nbio.core.util.InputStreamProvider

org.biojava.nbio.core.util.org.biojava.nbio.core.util.PrettyXMLWriter

org.biojava.nbio.core.util.org.biojava.nbio.core.util.SequenceTools

org.biojava.nbio.core.util.org.biojava.nbio.core.util.SingleLinkageClusterer

org.biojava.nbio.core.util.org.biojava.nbio.core.util.SoftHashMap

org.biojava.nbio.core.util.org.biojava.nbio.core.util.StringManipulationHelper

org.biojava.nbio.core.util.org.biojava.nbio.core.util.UncompressInputStream

org.biojava.nbio.core.util.org.biojava.nbio.core.util.XMLHelper

org.biojava.nbio.core.util.org.biojava.nbio.core.util.XMLWriter