Download biojava-core-5.0.0.jar file

Introduction

You can download biojava-core-5.0.0.jar in this page.

License

GNU LGPL v2

Type List

biojava-core-5.0.0.jar file has the following types.

META-INF/MANIFEST.MF
META-INF/services/org.biojava.nbio.core.search.io.ResultFactory
log4j2.xml
matrices/AAINDEX.txt
matrices/blosum100.txt
matrices/blosum30.txt
matrices/blosum35.txt
matrices/blosum40.txt
matrices/blosum45.txt
matrices/blosum50.txt
matrices/blosum55.txt
matrices/blosum60.txt
matrices/blosum62.txt
matrices/blosum65.txt
matrices/blosum70.txt
matrices/blosum75.txt
matrices/blosum80.txt
matrices/blosum85.txt
matrices/blosum90.txt
matrices/gonnet250.txt
matrices/identity.txt
matrices/nuc-4_2.txt
matrices/nuc-4_4.txt
matrices/pam250.txt
org.biojava.nbio.core.alignment.SimpleAlignedSequence.class
org.biojava.nbio.core.alignment.SimpleProfile.class
org.biojava.nbio.core.alignment.SimpleProfilePair.class
org.biojava.nbio.core.alignment.SimpleSequencePair.class
org.biojava.nbio.core.alignment.matrices.AAIndexFileParser.class
org.biojava.nbio.core.alignment.matrices.AAIndexProvider.class
org.biojava.nbio.core.alignment.matrices.AAindexFactory.class
org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProvider.class
org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix.class
org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix.class
org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper.class
org.biojava.nbio.core.alignment.template.AlignedSequence.class
org.biojava.nbio.core.alignment.template.MutableAlignedSequence.class
org.biojava.nbio.core.alignment.template.MutableProfile.class
org.biojava.nbio.core.alignment.template.MutableProfilePair.class
org.biojava.nbio.core.alignment.template.MutableSequencePair.class
org.biojava.nbio.core.alignment.template.Profile.class
org.biojava.nbio.core.alignment.template.ProfilePair.class
org.biojava.nbio.core.alignment.template.ProfileView.class
org.biojava.nbio.core.alignment.template.SequencePair.class
org.biojava.nbio.core.alignment.template.SubstitutionMatrix.class
org.biojava.nbio.core.exceptions.CompoundNotFoundException.class
org.biojava.nbio.core.exceptions.Messages.class
org.biojava.nbio.core.exceptions.ParserException.class
org.biojava.nbio.core.exceptions.TranslationException.class
org.biojava.nbio.core.search.io.Hit.class
org.biojava.nbio.core.search.io.Hsp.class
org.biojava.nbio.core.search.io.Result.class
org.biojava.nbio.core.search.io.ResultFactory.class
org.biojava.nbio.core.search.io.SearchIO.class
org.biojava.nbio.core.search.io.blast.BlastHit.class
org.biojava.nbio.core.search.io.blast.BlastHitBuilder.class
org.biojava.nbio.core.search.io.blast.BlastHsp.class
org.biojava.nbio.core.search.io.blast.BlastHspBuilder.class
org.biojava.nbio.core.search.io.blast.BlastResult.class
org.biojava.nbio.core.search.io.blast.BlastResultBuilder.class
org.biojava.nbio.core.search.io.blast.BlastTabularParser.class
org.biojava.nbio.core.search.io.blast.BlastXMLParser.class
org.biojava.nbio.core.sequence.AccessionID.class
org.biojava.nbio.core.sequence.BasicSequence.class
org.biojava.nbio.core.sequence.CDSComparator.class
org.biojava.nbio.core.sequence.CDSSequence.class
org.biojava.nbio.core.sequence.ChromosomeSequence.class
org.biojava.nbio.core.sequence.DNASequence.class
org.biojava.nbio.core.sequence.DataSource.class
org.biojava.nbio.core.sequence.ExonComparator.class
org.biojava.nbio.core.sequence.ExonSequence.class
org.biojava.nbio.core.sequence.GeneSequence.class
org.biojava.nbio.core.sequence.IntronSequence.class
org.biojava.nbio.core.sequence.MultipleSequenceAlignment.class
org.biojava.nbio.core.sequence.ProteinSequence.class
org.biojava.nbio.core.sequence.RNASequence.class
org.biojava.nbio.core.sequence.SequenceComparator.class
org.biojava.nbio.core.sequence.SequenceOptimizationHints.class
org.biojava.nbio.core.sequence.StartCodonSequence.class
org.biojava.nbio.core.sequence.StopCodonSequence.class
org.biojava.nbio.core.sequence.Strand.class
org.biojava.nbio.core.sequence.TaxonomyID.class
org.biojava.nbio.core.sequence.TranscriptSequence.class
org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundSet.class
org.biojava.nbio.core.sequence.compound.AmbiguityDNARNAHybridCompoundSet.class
org.biojava.nbio.core.sequence.compound.AmbiguityRNACompoundSet.class
org.biojava.nbio.core.sequence.compound.AminoAcidCompound.class
org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet.class
org.biojava.nbio.core.sequence.compound.CodonCompound.class
org.biojava.nbio.core.sequence.compound.DNACompoundSet.class
org.biojava.nbio.core.sequence.compound.NucleotideCompound.class
org.biojava.nbio.core.sequence.compound.RNACompoundSet.class
org.biojava.nbio.core.sequence.edits.Edit.class
org.biojava.nbio.core.sequence.features.AbstractFeature.class
org.biojava.nbio.core.sequence.features.DBReferenceInfo.class
org.biojava.nbio.core.sequence.features.DatabaseReferenceInterface.class
org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo.class
org.biojava.nbio.core.sequence.features.FeatureInterface.class
org.biojava.nbio.core.sequence.features.FeatureRetriever.class
org.biojava.nbio.core.sequence.features.FeaturesKeyWordInterface.class
org.biojava.nbio.core.sequence.features.Qualifier.class
org.biojava.nbio.core.sequence.features.QualityFeature.class
org.biojava.nbio.core.sequence.features.QuantityFeature.class
org.biojava.nbio.core.sequence.features.TextFeature.class
org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead.class
org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator.class
org.biojava.nbio.core.sequence.io.DNASequenceCreator.class
org.biojava.nbio.core.sequence.io.FastaGeneWriter.class
org.biojava.nbio.core.sequence.io.FastaReader.class
org.biojava.nbio.core.sequence.io.FastaReaderHelper.class
org.biojava.nbio.core.sequence.io.FastaSequenceParser.class
org.biojava.nbio.core.sequence.io.FastaWriter.class
org.biojava.nbio.core.sequence.io.FastaWriterHelper.class
org.biojava.nbio.core.sequence.io.FileProxyDNASequenceCreator.class
org.biojava.nbio.core.sequence.io.FileProxyProteinSequenceCreator.class
org.biojava.nbio.core.sequence.io.FileProxyRNASequenceCreator.class
org.biojava.nbio.core.sequence.io.GenbankReader.class
org.biojava.nbio.core.sequence.io.GenbankReaderHelper.class
org.biojava.nbio.core.sequence.io.GenbankSequenceParser.class
org.biojava.nbio.core.sequence.io.GenbankWriter.class
org.biojava.nbio.core.sequence.io.GenbankWriterHelper.class
org.biojava.nbio.core.sequence.io.GenericFastaHeaderFormat.class
org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser.class
org.biojava.nbio.core.sequence.io.GenericGenbankHeaderFormat.class
org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser.class
org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat.class
org.biojava.nbio.core.sequence.io.IUPACParser.class
org.biojava.nbio.core.sequence.io.PlainFastaHeaderParser.class
org.biojava.nbio.core.sequence.io.ProteinSequenceCreator.class
org.biojava.nbio.core.sequence.io.RNASequenceCreator.class
org.biojava.nbio.core.sequence.io.embl.EmblId.class
org.biojava.nbio.core.sequence.io.embl.EmblReader.class
org.biojava.nbio.core.sequence.io.embl.EmblRecord.class
org.biojava.nbio.core.sequence.io.embl.EmblReference.class
org.biojava.nbio.core.sequence.io.template.FastaHeaderFormatInterface.class
org.biojava.nbio.core.sequence.io.template.GenbankHeaderFormatInterface.class
org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface.class
org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface.class
org.biojava.nbio.core.sequence.io.template.SequenceParserInterface.class
org.biojava.nbio.core.sequence.io.util.ClasspathResource.class
org.biojava.nbio.core.sequence.io.util.IOUtils.class
org.biojava.nbio.core.sequence.loader.ArrayListProxySequenceReader.class
org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader.class
org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader.class
org.biojava.nbio.core.sequence.loader.StringProxySequenceReader.class
org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader.class
org.biojava.nbio.core.sequence.location.FuzzyPoint.class
org.biojava.nbio.core.sequence.location.InsdcLocations.class
org.biojava.nbio.core.sequence.location.InsdcParser.class
org.biojava.nbio.core.sequence.location.LocationHelper.class
org.biojava.nbio.core.sequence.location.SequenceLocation.class
org.biojava.nbio.core.sequence.location.SimpleLocation.class
org.biojava.nbio.core.sequence.location.SimplePoint.class
org.biojava.nbio.core.sequence.location.template.AbstractLocation.class
org.biojava.nbio.core.sequence.location.template.AccesionedLocation.class
org.biojava.nbio.core.sequence.location.template.Location.class
org.biojava.nbio.core.sequence.location.template.Point.class
org.biojava.nbio.core.sequence.reference.AbstractReference.class
org.biojava.nbio.core.sequence.reference.GenbankReference.class
org.biojava.nbio.core.sequence.reference.ReferenceInterface.class
org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader.class
org.biojava.nbio.core.sequence.storage.BitSequenceReader.class
org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.class
org.biojava.nbio.core.sequence.storage.JoiningSequenceReader.class
org.biojava.nbio.core.sequence.storage.SequenceAsStringHelper.class
org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader.class
org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.class
org.biojava.nbio.core.sequence.template.AbstractCompound.class
org.biojava.nbio.core.sequence.template.AbstractCompoundSet.class
org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator.class
org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet.class
org.biojava.nbio.core.sequence.template.AbstractSequence.class
org.biojava.nbio.core.sequence.template.Accessioned.class
org.biojava.nbio.core.sequence.template.ComplementCompound.class
org.biojava.nbio.core.sequence.template.Compound.class
org.biojava.nbio.core.sequence.template.CompoundSet.class
org.biojava.nbio.core.sequence.template.CompoundTranslator.class
org.biojava.nbio.core.sequence.template.LightweightProfile.class
org.biojava.nbio.core.sequence.template.ProxySequenceReader.class
org.biojava.nbio.core.sequence.template.Sequence.class
org.biojava.nbio.core.sequence.template.SequenceMixin.class
org.biojava.nbio.core.sequence.template.SequenceProxyView.class
org.biojava.nbio.core.sequence.template.SequenceReader.class
org.biojava.nbio.core.sequence.template.SequenceView.class
org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound.class
org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator.class
org.biojava.nbio.core.sequence.transcription.Frame.class
org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator.class
org.biojava.nbio.core.sequence.transcription.Table.class
org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.class
org.biojava.nbio.core.sequence.views.ComplementSequenceView.class
org.biojava.nbio.core.sequence.views.ReversedSequenceView.class
org.biojava.nbio.core.sequence.views.RnaSequenceView.class
org.biojava.nbio.core.sequence.views.WindowedSequence.class
org.biojava.nbio.core.util.CRC64Checksum.class
org.biojava.nbio.core.util.ConcurrencyTools.class
org.biojava.nbio.core.util.Equals.class
org.biojava.nbio.core.util.FileDownloadUtils.class
org.biojava.nbio.core.util.FlatFileCache.class
org.biojava.nbio.core.util.Hashcoder.class
org.biojava.nbio.core.util.InputStreamProvider.class
org.biojava.nbio.core.util.PrettyXMLWriter.class
org.biojava.nbio.core.util.SequenceTools.class
org.biojava.nbio.core.util.SingleLinkageClusterer.class
org.biojava.nbio.core.util.SoftHashMap.class
org.biojava.nbio.core.util.StringManipulationHelper.class
org.biojava.nbio.core.util.UncompressInputStream.class
org.biojava.nbio.core.util.XMLHelper.class
org.biojava.nbio.core.util.XMLWriter.class
org/biojava/nbio/core/sequence/iupac.txt

Pom

biojava-core-5.0.0.pom file content.

<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
	<parent>
		<artifactId>biojava</artifactId>
		<groupId>org.biojava</groupId>
		<version>5.0.0</version>
	</parent>
	<modelVersion>4.0.0</modelVersion>
	<artifactId>biojava-core</artifactId>
	<name>biojava-core</name>
	<url>http://www.biojava.org</url>
	<organization>
		<name>BioJava</name>
		<url>http://www.biojava.org</url>
	</organization>

	<licenses>
		<license>
			<name>GNU LGPL v2</name>
			<url>http://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt</url>
			<distribution>repo</distribution>
		</license>
	</licenses>

	<build>
		<plugins>

			<!-- Excluding demo package is required for avoiding namespace clashes (demo package is in all modules) for signing the jar. See issue #387 -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-jar-plugin</artifactId>
                <configuration>
                    <excludes>
                        <exclude>demo/**</exclude>
                    </excludes>
                </configuration>
            </plugin>		
		
		</plugins>
	</build>
	<dependencies>
		<dependency>
			<groupId>junit</groupId>
			<artifactId>junit</artifactId>
			<scope>test</scope>
		</dependency>
		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
		<dependency>
        	<groupId>org.slf4j</groupId>
        	<artifactId>slf4j-api</artifactId>
    	</dependency>
    	<!-- binding for log4j2, scope=runTime set in parent pom -->
 		<dependency>
    		<groupId>org.apache.logging.log4j</groupId>
    		<artifactId>log4j-slf4j-impl</artifactId>
  		</dependency>
  		<dependency>
    		<groupId>org.apache.logging.log4j</groupId>
    		<artifactId>log4j-api</artifactId>
  		</dependency>
  		<dependency>
    		<groupId>org.apache.logging.log4j</groupId>
    		<artifactId>log4j-core</artifactId>
  		</dependency>
	</dependencies>
</project>

POM Entry

<dependency>
   <groupId>org.biojava</groupId>
   <artifactId>biojava-core</artifactId>
   <version>5.0.0</version>
</dependency>

Download

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Download biojava-core-5.0.0.jar file

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