View Java Class Source Code in JAR file
- Download JD-GUI to open JAR file and explore Java source code file (.class .java)
- Click menu "File → Open File..." or just drag-and-drop the JAR file in the JD-GUI window jillion-5.3.3.jar file.
Once you open a JAR file, all the java classes in the JAR file will be displayed.
org.jcvi.jillion.core.pos
├─ org.jcvi.jillion.core.pos.DefaultPositionCodec.class - [JAR]
├─ org.jcvi.jillion.core.pos.DefaultPositionSequence.class - [JAR]
├─ org.jcvi.jillion.core.pos.Position.class - [JAR]
├─ org.jcvi.jillion.core.pos.PositionSequence.class - [JAR]
├─ org.jcvi.jillion.core.pos.PositionSequenceBuilder.class - [JAR]
org.jcvi.jillion.internal.core.residue
├─ org.jcvi.jillion.internal.core.residue.AbstractResidueSequence.class - [JAR]
org.jcvi.jillion.internal.core.util
├─ org.jcvi.jillion.internal.core.util.AbstractFOQueue.class - [JAR]
├─ org.jcvi.jillion.internal.core.util.ArrayUtil.class - [JAR]
├─ org.jcvi.jillion.internal.core.util.BoundedPriorityQueue.class - [JAR]
├─ org.jcvi.jillion.internal.core.util.Caches.class - [JAR]
├─ org.jcvi.jillion.internal.core.util.ComparableComparator.class - [JAR]
├─ org.jcvi.jillion.internal.core.util.FIFOQueue.class - [JAR]
├─ org.jcvi.jillion.internal.core.util.GrowableBitArray.class - [JAR]
├─ org.jcvi.jillion.internal.core.util.GrowableByteArray.class - [JAR]
├─ org.jcvi.jillion.internal.core.util.GrowableCharArray.class - [JAR]
├─ org.jcvi.jillion.internal.core.util.GrowableIntArray.class - [JAR]
├─ org.jcvi.jillion.internal.core.util.GrowableLongArray.class - [JAR]
├─ org.jcvi.jillion.internal.core.util.GrowableShortArray.class - [JAR]
├─ org.jcvi.jillion.internal.core.util.JillionUtil.class - [JAR]
├─ org.jcvi.jillion.internal.core.util.LIFOQueue.class - [JAR]
├─ org.jcvi.jillion.internal.core.util.RunLength.class - [JAR]
├─ org.jcvi.jillion.internal.core.util.Sneak.class - [JAR]
├─ org.jcvi.jillion.internal.core.util.ValidationException.class - [JAR]
├─ org.jcvi.jillion.internal.core.util.Validator.class - [JAR]
org.jcvi.jillion.internal.core
├─ org.jcvi.jillion.internal.core.EncodedSequence.class - [JAR]
├─ org.jcvi.jillion.internal.core.GlyphCodec.class - [JAR]
org.jcvi.jillion.trace
├─ org.jcvi.jillion.trace.Trace.class - [JAR]
├─ org.jcvi.jillion.trace.TraceDataStore.class - [JAR]
├─ org.jcvi.jillion.trace.TraceNucleotideDataStoreAdapter.class - [JAR]
├─ org.jcvi.jillion.trace.TraceQualityDataStoreAdapter.class - [JAR]
org.jcvi.jillion.testutils
├─ org.jcvi.jillion.testutils.NucleotideSequenceTestUtil.class - [JAR]
├─ org.jcvi.jillion.testutils.ProteinSequenceTestUtil.class - [JAR]
org.jcvi.jillion.fasta
├─ org.jcvi.jillion.fasta.AbstractFastaRecordVisitor.class - [JAR]
├─ org.jcvi.jillion.fasta.FastaCollectors.class - [JAR]
├─ org.jcvi.jillion.fasta.FastaDataStore.class - [JAR]
├─ org.jcvi.jillion.fasta.FastaFileParser.class - [JAR]
├─ org.jcvi.jillion.fasta.FastaParser.class - [JAR]
├─ org.jcvi.jillion.fasta.FastaRecord.class - [JAR]
├─ org.jcvi.jillion.fasta.FastaRecordVisitor.class - [JAR]
├─ org.jcvi.jillion.fasta.FastaVisitor.class - [JAR]
├─ org.jcvi.jillion.fasta.FastaVisitorCallback.class - [JAR]
├─ org.jcvi.jillion.fasta.FastaWriter.class - [JAR]
├─ org.jcvi.jillion.fasta.FastaWriterAdapterImpl.class - [JAR]
├─ org.jcvi.jillion.fasta.SplitFastaWriter.class - [JAR]
org.jcvi.jillion.experimental.plate
├─ org.jcvi.jillion.experimental.plate.PlateFormat.class - [JAR]
├─ org.jcvi.jillion.experimental.plate.PlatePopulator.class - [JAR]
├─ org.jcvi.jillion.experimental.plate.Well.class - [JAR]
org.jcvi.jillion.fasta.aa
├─ org.jcvi.jillion.fasta.aa.AbstractProteinFastaRecordVisitor.class - [JAR]
├─ org.jcvi.jillion.fasta.aa.ProteinFastaDataStore.class - [JAR]
├─ org.jcvi.jillion.fasta.aa.ProteinFastaFileDataStore.class - [JAR]
├─ org.jcvi.jillion.fasta.aa.ProteinFastaFileDataStoreBuilder.class - [JAR]
├─ org.jcvi.jillion.fasta.aa.ProteinFastaRecord.class - [JAR]
├─ org.jcvi.jillion.fasta.aa.ProteinFastaRecordBuilder.class - [JAR]
├─ org.jcvi.jillion.fasta.aa.ProteinFastaWriter.class - [JAR]
├─ org.jcvi.jillion.fasta.aa.ProteinFastaWriterBuilder.class - [JAR]
org.jcvi.jillion.trace.chromat.scf
├─ org.jcvi.jillion.trace.chromat.scf.PrivateData.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.scf.ScfChromatogram.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.scf.ScfChromatogramBuilder.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.scf.ScfChromatogramFileVisitor.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.scf.ScfChromatogramParser.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.scf.ScfChromatogramWriterBuilder.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.scf.ScfDecoderException.class - [JAR]
org.jcvi.jillion.sam.index
├─ org.jcvi.jillion.sam.index.BamIndex.class - [JAR]
├─ org.jcvi.jillion.sam.index.BamIndexFileWriterBuilder.class - [JAR]
├─ org.jcvi.jillion.sam.index.Bin.class - [JAR]
├─ org.jcvi.jillion.sam.index.Chunk.class - [JAR]
├─ org.jcvi.jillion.sam.index.ReferenceIndex.class - [JAR]
org.jcvi.jillion.trace.chromat
├─ org.jcvi.jillion.trace.chromat.Channel.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.ChannelGroup.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.Chromatogram.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.ChromatogramFactory.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.ChromatogramFileVisitor.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.ChromatogramWriter.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.EncodedShortData.class - [JAR]
org.jcvi.jillion.core.datastore
├─ org.jcvi.jillion.core.datastore.DataStore.class - [JAR]
├─ org.jcvi.jillion.core.datastore.DataStoreClosedException.class - [JAR]
├─ org.jcvi.jillion.core.datastore.DataStoreEntry.class - [JAR]
├─ org.jcvi.jillion.core.datastore.DataStoreException.class - [JAR]
├─ org.jcvi.jillion.core.datastore.DataStoreFilter.class - [JAR]
├─ org.jcvi.jillion.core.datastore.DataStoreFilters.class - [JAR]
├─ org.jcvi.jillion.core.datastore.DataStoreProviderHint.class - [JAR]
├─ org.jcvi.jillion.core.datastore.DataStoreUtil.class - [JAR]
org.jcvi.jillion.assembly.clc.cas
├─ org.jcvi.jillion.assembly.clc.cas.AbstractAlignedReadCasVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.AbstractCasFileVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.AbstractReadCasVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.CasAlignment.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.CasAlignmentRegion.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.CasAlignmentRegionType.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.CasAlignmentScore.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.CasAlignmentScoreBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.CasAlignmentType.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.CasColorSpaceAlignmentScore.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.CasContigPair.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.CasFileInfo.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.CasFileInfoValidator.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.CasFileParser.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.CasFileVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.CasFileVisitorAdapter.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.CasGappedReferenceDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.CasGappedReferenceDataStoreBuilderVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.CasMatch.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.CasMatchVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.CasMatchVisitorAdapter.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.CasParser.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.CasReferenceDescription.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.CasScoreType.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.CasScoringScheme.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.CasUtil.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.CasValidator.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.DefaultCasAlignment.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.DefaultCasAlignmentRegion.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.DefaultCasAlignmentScore.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.DefaultCasColorSpaceAlignmentScore.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.DefaultCasFileInfo.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.DefaultCasMatch.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.DefaultCasReferenceDescription.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.DefaultCasScoringScheme.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.PhaseChangeCasAlignmentRegion.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.ReAlignReads.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.ReadFileType.class - [JAR]
org.jcvi.jillion.sam.cigar
├─ org.jcvi.jillion.sam.cigar.Cigar.class - [JAR]
├─ org.jcvi.jillion.sam.cigar.CigarElement.class - [JAR]
├─ org.jcvi.jillion.sam.cigar.CigarOperation.class - [JAR]
org.jcvi.jillion.internal.trace.chromat.abi.tag
├─ org.jcvi.jillion.internal.trace.chromat.abi.tag.AbstractTaggedDataRecord.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.abi.tag.DefaultAsciiTaggedDataRecord.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.abi.tag.DefaultDateTaggedDataRecord.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.abi.tag.DefaultFloatTaggedDataRecord.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.abi.tag.DefaultIntegerArrayTaggedDataRecord.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.abi.tag.DefaultPascalStringTaggedDataRecord.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.abi.tag.DefaultShortArrayTaggedDataRecord.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.abi.tag.DefaultTaggedDataRecord.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.abi.tag.DefaultTimeTaggedDataRecord.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.abi.tag.DefaultUserDefinedTaggedDataRecord.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.abi.tag.TaggedDataRecordBuilder.class - [JAR]
org.jcvi.jillion.internal.trace.chromat.ztr.data
├─ org.jcvi.jillion.internal.trace.chromat.ztr.data.DataFactory.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.ztr.data.DataHeader.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.ztr.data.DeltaEncodedData.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.ztr.data.DeltaStrategy.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.ztr.data.FollowData.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.ztr.data.RawData.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.ztr.data.RunLengthEncodedData.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.ztr.data.ShrinkToEightBitData.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.ztr.data.ZLibData.class - [JAR]
org.jcvi.jillion.internal.trace.chromat.scf
├─ org.jcvi.jillion.internal.trace.chromat.scf.PrivateDataImpl.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.scf.SCFCodec.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.scf.SCFCodecs.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.scf.SCFUtils.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.scf.ScfChromatogramImpl.class - [JAR]
org.jcvi.jillion.internal.core.io
├─ org.jcvi.jillion.internal.core.io.BlockingAccumulator.class - [JAR]
├─ org.jcvi.jillion.internal.core.io.ByteBufferInputStream.class - [JAR]
├─ org.jcvi.jillion.internal.core.io.LineParser.class - [JAR]
├─ org.jcvi.jillion.internal.core.io.MagicNumberInputStream.class - [JAR]
├─ org.jcvi.jillion.internal.core.io.OpenAwareInputStream.class - [JAR]
├─ org.jcvi.jillion.internal.core.io.OutputStreamFactory.class - [JAR]
├─ org.jcvi.jillion.internal.core.io.PositionlessLineParser.class - [JAR]
├─ org.jcvi.jillion.internal.core.io.RandomAccessFileInputStream.class - [JAR]
├─ org.jcvi.jillion.internal.core.io.StreamUtil.class - [JAR]
├─ org.jcvi.jillion.internal.core.io.TextLineParser.class - [JAR]
├─ org.jcvi.jillion.internal.core.io.ValueSizeStrategy.class - [JAR]
org.jcvi.jillion.assembly.tigr.tasm
├─ org.jcvi.jillion.assembly.tigr.tasm.AbstractTasmContigBuilderVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.tasm.DefaultTasmAssembledRead.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.tasm.DefaultTasmFileContigDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.tasm.IndexedTasmFileDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.tasm.LargeTasmContigFileDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.tasm.TasmAssembledRead.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.tasm.TasmAssembledReadAdapter.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.tasm.TasmAssembledReadBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.tasm.TasmContig.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.tasm.TasmContigAttribute.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.tasm.TasmContigBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.tasm.TasmContigDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.tasm.TasmContigFileContigIterator.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.tasm.TasmContigFileDataStoreBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.tasm.TasmContigReadVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.tasm.TasmContigVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.tasm.TasmFileParser.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.tasm.TasmFileWriterBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.tasm.TasmFileWriterUtil.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.tasm.TasmParser.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.tasm.TasmReadAttribute.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.tasm.TasmUtil.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.tasm.TasmVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.tasm.TasmWriter.class - [JAR]
org.jcvi.jillion.trace.chromat.abi.tag.rate
├─ org.jcvi.jillion.trace.chromat.abi.tag.rate.ScanRate.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.abi.tag.rate.ScanRateTaggedDataType.class - [JAR]
org.jcvi.jillion.internal.trace.chromat
├─ org.jcvi.jillion.internal.trace.chromat.BasicChromatogram.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.BasicChromatogramBuilder.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.ChromatogramUtil.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.DefaultChannel.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.DefaultChannelGroup.class - [JAR]
org.jcvi.jillion.fasta.qual
├─ org.jcvi.jillion.fasta.qual.AbstractQualityFastaRecordVisitor.class - [JAR]
├─ org.jcvi.jillion.fasta.qual.CommentedQualityFastaRecord.class - [JAR]
├─ org.jcvi.jillion.fasta.qual.DefaultQualityFastaFileDataStore.class - [JAR]
├─ org.jcvi.jillion.fasta.qual.QualityFastaDataStore.class - [JAR]
├─ org.jcvi.jillion.fasta.qual.QualityFastaFileDataStoreBuilder.class - [JAR]
├─ org.jcvi.jillion.fasta.qual.QualityFastaRecord.class - [JAR]
├─ org.jcvi.jillion.fasta.qual.QualityFastaRecordBuilder.class - [JAR]
├─ org.jcvi.jillion.fasta.qual.QualityFastaWriter.class - [JAR]
├─ org.jcvi.jillion.fasta.qual.QualityFastaWriterBuilder.class - [JAR]
├─ org.jcvi.jillion.fasta.qual.UncommentedQualityFastaRecord.class - [JAR]
org.jcvi.jillion.core.util.streams
├─ org.jcvi.jillion.core.util.streams.ThrowingBiConsumer.class - [JAR]
├─ org.jcvi.jillion.core.util.streams.ThrowingConsumer.class - [JAR]
├─ org.jcvi.jillion.core.util.streams.ThrowingFunction.class - [JAR]
├─ org.jcvi.jillion.core.util.streams.ThrowingIndexedConsumer.class - [JAR]
├─ org.jcvi.jillion.core.util.streams.ThrowingIntIndexedBooleanConsumer.class - [JAR]
├─ org.jcvi.jillion.core.util.streams.ThrowingIntIndexedByteConsumer.class - [JAR]
├─ org.jcvi.jillion.core.util.streams.ThrowingIntIndexedCharConsumer.class - [JAR]
├─ org.jcvi.jillion.core.util.streams.ThrowingIntIndexedConsumer.class - [JAR]
├─ org.jcvi.jillion.core.util.streams.ThrowingIntIndexedIntConsumer.class - [JAR]
├─ org.jcvi.jillion.core.util.streams.ThrowingIntIndexedLongConsumer.class - [JAR]
├─ org.jcvi.jillion.core.util.streams.ThrowingIntIndexedShortConsumer.class - [JAR]
org.jcvi.jillion.align
├─ org.jcvi.jillion.align.AbstractSubstitutionMatrixFileParser.class - [JAR]
├─ org.jcvi.jillion.align.AminoAcidSubstitutionMatrix.class - [JAR]
├─ org.jcvi.jillion.align.AminoAcidSubstitutionMatrixFileParser.class - [JAR]
├─ org.jcvi.jillion.align.BlosumMatrices.class - [JAR]
├─ org.jcvi.jillion.align.NucleotidePropertyFileScoringMatrixParser.class - [JAR]
├─ org.jcvi.jillion.align.NucleotideSequenceAlignment.class - [JAR]
├─ org.jcvi.jillion.align.NucleotideSubstitutionMatrices.class - [JAR]
├─ org.jcvi.jillion.align.NucleotideSubstitutionMatrix.class - [JAR]
├─ org.jcvi.jillion.align.NucleotideSubstitutionMatrixBuilder.class - [JAR]
├─ org.jcvi.jillion.align.ProteinSequenceAlignment.class - [JAR]
├─ org.jcvi.jillion.align.SequenceAlignment.class - [JAR]
├─ org.jcvi.jillion.align.SubstitutionMatrix.class - [JAR]
org.jcvi.jillion.assembly
├─ org.jcvi.jillion.assembly.AbstractAssemblyTransformer.class - [JAR]
├─ org.jcvi.jillion.assembly.AbstractContigBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.AssembledRead.class - [JAR]
├─ org.jcvi.jillion.assembly.AssembledReadBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.AssemblyTransformationService.class - [JAR]
├─ org.jcvi.jillion.assembly.AssemblyTransformer.class - [JAR]
├─ org.jcvi.jillion.assembly.AssemblyUtil.class - [JAR]
├─ org.jcvi.jillion.assembly.Contig.class - [JAR]
├─ org.jcvi.jillion.assembly.ContigBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.ContigDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.ContigDataStoreTransfomationService.class - [JAR]
├─ org.jcvi.jillion.assembly.DefaultPlacedContig.class - [JAR]
├─ org.jcvi.jillion.assembly.DefaultScaffold.class - [JAR]
├─ org.jcvi.jillion.assembly.DefaultScaffoldDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.GappedReferenceBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.PlacedContig.class - [JAR]
├─ org.jcvi.jillion.assembly.ReadInfo.class - [JAR]
├─ org.jcvi.jillion.assembly.Scaffold.class - [JAR]
├─ org.jcvi.jillion.assembly.ScaffoldBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.ScaffoldDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.ScaffoldDataStoreBuilder.class - [JAR]
org.jcvi.jillion.internal.trace.chromat.scf.header
├─ org.jcvi.jillion.internal.trace.chromat.scf.header.DefaultSCFHeader.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.scf.header.DefaultSCFHeaderCodec.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.scf.header.SCFHeader.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.scf.header.SCFHeaderCodec.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.scf.header.SCFHeaderDecoder.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.scf.header.SCFHeaderDecoderException.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.scf.header.SCFHeaderEncoder.class - [JAR]
org.jcvi.jillion.assembly.consed.transform
├─ org.jcvi.jillion.assembly.consed.transform.ConsedTransformationService.class - [JAR]
org.jcvi.jillion.experimental.align.blast.btab
├─ org.jcvi.jillion.experimental.align.blast.btab.BtabWriter.class - [JAR]
├─ org.jcvi.jillion.experimental.align.blast.btab.BtabWriterBuilder.class - [JAR]
org.jcvi.jillion.internal.fasta.qual
├─ org.jcvi.jillion.internal.fasta.qual.DefaultQualityFastaFileDataStoreBuilder.class - [JAR]
├─ org.jcvi.jillion.internal.fasta.qual.IndexedQualityFastaFileDataStore.class - [JAR]
├─ org.jcvi.jillion.internal.fasta.qual.LargeQualityFastaFileDataStore.class - [JAR]
├─ org.jcvi.jillion.internal.fasta.qual.QualitySequenceFastaDataStoreIteratorImpl.class - [JAR]
org.jcvi.jillion.internal
├─ org.jcvi.jillion.internal.ResourceHelper.class - [JAR]
org.jcvi.jillion.internal.trace.chromat.scf.header.pos
├─ org.jcvi.jillion.internal.trace.chromat.scf.header.pos.BytePositionStrategy.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.scf.header.pos.PositionStrategy.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.scf.header.pos.PositionStrategyFactory.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.scf.header.pos.ShortPositionStrategy.class - [JAR]
org.jcvi.jillion.core.residue
├─ org.jcvi.jillion.core.residue.Frame.class - [JAR]
├─ org.jcvi.jillion.core.residue.Kmer.class - [JAR]
├─ org.jcvi.jillion.core.residue.KmerSpliterator.class - [JAR]
├─ org.jcvi.jillion.core.residue.Residue.class - [JAR]
├─ org.jcvi.jillion.core.residue.ResidueSequence.class - [JAR]
├─ org.jcvi.jillion.core.residue.ResidueSequenceBuilder.class - [JAR]
├─ org.jcvi.jillion.core.residue.ResidueTypeGuesser.class - [JAR]
org.jcvi.jillion.internal.sam.index
├─ org.jcvi.jillion.internal.sam.index.BaiBin.class - [JAR]
├─ org.jcvi.jillion.internal.sam.index.BaiRefIndex.class - [JAR]
├─ org.jcvi.jillion.internal.sam.index.BamIndexer.class - [JAR]
├─ org.jcvi.jillion.internal.sam.index.BinBuilder.class - [JAR]
├─ org.jcvi.jillion.internal.sam.index.IndexUtil.class - [JAR]
├─ org.jcvi.jillion.internal.sam.index.ReferenceIndexBuilder.class - [JAR]
org.jcvi.jillion.assembly.ca.asm
├─ org.jcvi.jillion.assembly.ca.asm.AbstractAsmContigBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.asm.AbstractAsmUnitigBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.asm.AsmAssembledRead.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.asm.AsmAssembledReadBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.asm.AsmContig.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.asm.AsmContigBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.asm.AsmContigDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.asm.AsmContigVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.asm.AsmFileContigDataStoreBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.asm.AsmFileParser.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.asm.AsmFileUnitigDataStoreBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.asm.AsmParser.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.asm.AsmScaffoldVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.asm.AsmUnitig.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.asm.AsmUnitigBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.asm.AsmUnitigDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.asm.AsmUnitigVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.asm.AsmUtil.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.asm.AsmVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.asm.DefaultAsmAssembledRead.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.asm.DefaultAsmContig.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.asm.DefaultAsmContigDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.asm.DefaultAsmUnitig.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.asm.DefaultAsmUnitigDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.asm.IndexedAsmFileContigDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.asm.IndexedAsmFileUnitigDataStore.class - [JAR]
org.jcvi.jillion.core
├─ org.jcvi.jillion.core.Defline.class - [JAR]
├─ org.jcvi.jillion.core.DeflineImpl.class - [JAR]
├─ org.jcvi.jillion.core.DirectedRange.class - [JAR]
├─ org.jcvi.jillion.core.Direction.class - [JAR]
├─ org.jcvi.jillion.core.Range.class - [JAR]
├─ org.jcvi.jillion.core.Rangeable.class - [JAR]
├─ org.jcvi.jillion.core.Ranges.class - [JAR]
├─ org.jcvi.jillion.core.Sequence.class - [JAR]
├─ org.jcvi.jillion.core.SequenceBuilder.class - [JAR]
org.jcvi.jillion.internal.trace.chromat.abi
├─ org.jcvi.jillion.internal.trace.chromat.abi.AbiUtil.class - [JAR]
org.jcvi.jillion.core.residue.aa
├─ org.jcvi.jillion.core.residue.aa.AbstractProteinSequence.class - [JAR]
├─ org.jcvi.jillion.core.residue.aa.AminoAcid.class - [JAR]
├─ org.jcvi.jillion.core.residue.aa.AminoAcidCodec.class - [JAR]
├─ org.jcvi.jillion.core.residue.aa.Codon.class - [JAR]
├─ org.jcvi.jillion.core.residue.aa.CompactProteinSequence.class - [JAR]
├─ org.jcvi.jillion.core.residue.aa.CompactProteinSequenceCodec.class - [JAR]
├─ org.jcvi.jillion.core.residue.aa.IupacTranslationTables.class - [JAR]
├─ org.jcvi.jillion.core.residue.aa.ProteinSequence.class - [JAR]
├─ org.jcvi.jillion.core.residue.aa.ProteinSequenceBuilder.class - [JAR]
├─ org.jcvi.jillion.core.residue.aa.ProteinSequenceDataStore.class - [JAR]
├─ org.jcvi.jillion.core.residue.aa.TranslationTable.class - [JAR]
├─ org.jcvi.jillion.core.residue.aa.TranslationVisitor.class - [JAR]
├─ org.jcvi.jillion.core.residue.aa.UnCompressedGappedProteinSequence.class - [JAR]
├─ org.jcvi.jillion.core.residue.aa.UnCompressedUngappedProteinSequence.class - [JAR]
├─ org.jcvi.jillion.core.residue.aa.UngappedProteinSequence.class - [JAR]
org.jcvi.jillion.internal.core.util.iter
├─ org.jcvi.jillion.internal.core.util.iter.AbstractBlockingStreamingIterator.class - [JAR]
├─ org.jcvi.jillion.internal.core.util.iter.MergedSortedRecordIterator.class - [JAR]
├─ org.jcvi.jillion.internal.core.util.iter.PrimitiveArrayIterators.class - [JAR]
├─ org.jcvi.jillion.internal.core.util.iter.PushBackIterator.class - [JAR]
org.jcvi.jillion.assembly.clc.cas.consed
├─ org.jcvi.jillion.assembly.clc.cas.consed.Cas2Consed.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.consed.ChromatDirFastaConsedPhdAdaptedIterator.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.consed.FastaConsedPhdAdaptedIterator.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.consed.FastqConsedPhdAdaptedIterator.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.consed.FlowgramConsedPhdAdaptedIterator.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.consed.PhdReadRecord.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.consed.QualFastaConsedPhdAdaptedIterator.class - [JAR]
org.jcvi.jillion.internal.assembly
├─ org.jcvi.jillion.internal.assembly.DefaultAssembledRead.class - [JAR]
├─ org.jcvi.jillion.internal.assembly.DefaultContig.class - [JAR]
org.jcvi.jillion.internal.core.seq.trace.sanger.chromat.ztr.data
├─ org.jcvi.jillion.internal.core.seq.trace.sanger.chromat.ztr.data.Data.class - [JAR]
org.jcvi.jillion.shared.fasta
├─ org.jcvi.jillion.shared.fasta.AbstractFastaFileDataStoreBuilder.class - [JAR]
├─ org.jcvi.jillion.shared.fasta.AbstractFastaRecordBuilder.class - [JAR]
├─ org.jcvi.jillion.shared.fasta.AbstractFastaRecordWriter.class - [JAR]
├─ org.jcvi.jillion.shared.fasta.AbstractResidueFastaWriter.class - [JAR]
org.jcvi.jillion.internal.fasta.nt
├─ org.jcvi.jillion.internal.fasta.nt.AdaptedNucleotideFastaDataStore.class - [JAR]
org.jcvi.jillion.core.qual
├─ org.jcvi.jillion.core.qual.DefaultQualitySymbolCodec.class - [JAR]
├─ org.jcvi.jillion.core.qual.EncodedQualitySequence.class - [JAR]
├─ org.jcvi.jillion.core.qual.PhredQuality.class - [JAR]
├─ org.jcvi.jillion.core.qual.QualitySequence.class - [JAR]
├─ org.jcvi.jillion.core.qual.QualitySequenceBuilder.class - [JAR]
├─ org.jcvi.jillion.core.qual.QualitySequenceDataStore.class - [JAR]
├─ org.jcvi.jillion.core.qual.QualitySymbolCodec.class - [JAR]
├─ org.jcvi.jillion.core.qual.RunLengthEncodedQualityCodec.class - [JAR]
├─ org.jcvi.jillion.core.qual.RunLengthEncodedQualitySequence.class - [JAR]
org.jcvi.jillion.internal.trace.fastq
├─ org.jcvi.jillion.internal.trace.fastq.CommentedParsedFastqRecord.class - [JAR]
├─ org.jcvi.jillion.internal.trace.fastq.ParsedFastqRecord.class - [JAR]
├─ org.jcvi.jillion.internal.trace.fastq.ParsedQualitySequence.class - [JAR]
org.jcvi.jillion.sam.header
├─ org.jcvi.jillion.sam.header.SamHeader.class - [JAR]
├─ org.jcvi.jillion.sam.header.SamHeaderBuilder.class - [JAR]
├─ org.jcvi.jillion.sam.header.SamHeaderTag.class - [JAR]
├─ org.jcvi.jillion.sam.header.SamHeaderTagKey.class - [JAR]
├─ org.jcvi.jillion.sam.header.SamProgram.class - [JAR]
├─ org.jcvi.jillion.sam.header.SamProgramBuilder.class - [JAR]
├─ org.jcvi.jillion.sam.header.SamReadGroup.class - [JAR]
├─ org.jcvi.jillion.sam.header.SamReadGroupBuilder.class - [JAR]
├─ org.jcvi.jillion.sam.header.SamReferenceSequence.class - [JAR]
├─ org.jcvi.jillion.sam.header.SamReferenceSequenceBuilder.class - [JAR]
├─ org.jcvi.jillion.sam.header.SamVersion.class - [JAR]
org.jcvi.jillion.internal.trace.chromat.ztr.chunk
├─ org.jcvi.jillion.internal.trace.chromat.ztr.chunk.Chunk.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.ztr.chunk.ChunkException.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.ztr.chunk.ChunkType.class - [JAR]
org.jcvi.jillion.assembly.ca.frg
├─ org.jcvi.jillion.assembly.ca.frg.AbstractFragmentDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.frg.DefaultFragment.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.frg.DefaultFragmentDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.frg.DefaultLibrary.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.frg.Distance.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.frg.Fragment.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.frg.FragmentDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.frg.FragmentUtil.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.frg.Frg2Parser.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.frg.Frg2Visitor.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.frg.IndexedFragmentDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.frg.Library.class - [JAR]
├─ org.jcvi.jillion.assembly.ca.frg.MateOrientation.class - [JAR]
org.jcvi.jillion.assembly.consed.nav
├─ org.jcvi.jillion.assembly.consed.nav.AbstractNavigationElement.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.nav.ConsedNavigationParser.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.nav.ConsedNavigationVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.nav.ConsedNavigationWriter.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.nav.ConsensusNavigationElement.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.nav.NavigationElement.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.nav.ReadNavigationElement.class - [JAR]
org.jcvi.jillion.fasta.pos
├─ org.jcvi.jillion.fasta.pos.AbstractPositionSequenceFastaRecordVisitor.class - [JAR]
├─ org.jcvi.jillion.fasta.pos.DefaultPositionFastaFileDataStore.class - [JAR]
├─ org.jcvi.jillion.fasta.pos.LargePositionFastaFileDataStore.class - [JAR]
├─ org.jcvi.jillion.fasta.pos.LargePositionFastaIterator.class - [JAR]
├─ org.jcvi.jillion.fasta.pos.PositionFastaDataStore.class - [JAR]
├─ org.jcvi.jillion.fasta.pos.PositionFastaFileDataStoreBuilder.class - [JAR]
├─ org.jcvi.jillion.fasta.pos.PositionFastaRecord.class - [JAR]
├─ org.jcvi.jillion.fasta.pos.PositionFastaWriter.class - [JAR]
├─ org.jcvi.jillion.fasta.pos.PositionFastaWriterBuilder.class - [JAR]
├─ org.jcvi.jillion.fasta.pos.PositionSequenceDataStore.class - [JAR]
org.jcvi.jillion.assembly.util.slice
├─ org.jcvi.jillion.assembly.util.slice.CodonSliceMapBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.util.slice.SingleNucleotideSlice.class - [JAR]
├─ org.jcvi.jillion.assembly.util.slice.SingleNucleotideSliceElement.class - [JAR]
├─ org.jcvi.jillion.assembly.util.slice.SingleNucleotideSliceMap.class - [JAR]
├─ org.jcvi.jillion.assembly.util.slice.VariableWidthNucleotideSlice.class - [JAR]
├─ org.jcvi.jillion.assembly.util.slice.VariableWidthNucleotideSliceElement.class - [JAR]
├─ org.jcvi.jillion.assembly.util.slice.VariableWidthNucleotideSliceMap.class - [JAR]
├─ org.jcvi.jillion.assembly.util.slice.VariableWidthSlice.class - [JAR]
├─ org.jcvi.jillion.assembly.util.slice.VariableWidthSliceElement.class - [JAR]
├─ org.jcvi.jillion.assembly.util.slice.VariableWidthSliceMap.class - [JAR]
org.jcvi.jillion.assembly.util.consensus
├─ org.jcvi.jillion.assembly.util.consensus.AbstractChurchillWatermanConsensusCaller.class - [JAR]
├─ org.jcvi.jillion.assembly.util.consensus.AcgtnConsensusCaller.class - [JAR]
├─ org.jcvi.jillion.assembly.util.consensus.ChurchillWatermanConsensusCaller.class - [JAR]
├─ org.jcvi.jillion.assembly.util.consensus.ConicConsensusCaller.class - [JAR]
├─ org.jcvi.jillion.assembly.util.consensus.ConsensusCaller.class - [JAR]
├─ org.jcvi.jillion.assembly.util.consensus.ConsensusCollectors.class - [JAR]
├─ org.jcvi.jillion.assembly.util.consensus.ConsensusCombiner.class - [JAR]
├─ org.jcvi.jillion.assembly.util.consensus.ConsensusProbabilities.class - [JAR]
├─ org.jcvi.jillion.assembly.util.consensus.ConsensusResult.class - [JAR]
├─ org.jcvi.jillion.assembly.util.consensus.ConsensusUtil.class - [JAR]
├─ org.jcvi.jillion.assembly.util.consensus.DefaultConsensusResult.class - [JAR]
├─ org.jcvi.jillion.assembly.util.consensus.MostFrequentBasecallConsensusCaller.class - [JAR]
├─ org.jcvi.jillion.assembly.util.consensus.NextGenReferenceConsensusRecaller.class - [JAR]
├─ org.jcvi.jillion.assembly.util.consensus.NoAmbiguityConsensusCaller.class - [JAR]
├─ org.jcvi.jillion.assembly.util.consensus.TigrAnnotationConsensusCaller.class - [JAR]
org.jcvi.jillion.experimental.trace.archive2
├─ org.jcvi.jillion.experimental.trace.archive2.DefaultTraceArchiveInfo.class - [JAR]
├─ org.jcvi.jillion.experimental.trace.archive2.DefaultTraceArchiveRecord.class - [JAR]
├─ org.jcvi.jillion.experimental.trace.archive2.TraceArchiveInfo.class - [JAR]
├─ org.jcvi.jillion.experimental.trace.archive2.TraceArchiveRecord.class - [JAR]
├─ org.jcvi.jillion.experimental.trace.archive2.TraceArchiveRecordBuilder.class - [JAR]
├─ org.jcvi.jillion.experimental.trace.archive2.TraceArchiveWriter.class - [JAR]
├─ org.jcvi.jillion.experimental.trace.archive2.TraceInfoField.class - [JAR]
├─ org.jcvi.jillion.experimental.trace.archive2.TraceInfoWriterUtil.class - [JAR]
├─ org.jcvi.jillion.experimental.trace.archive2.XmlTraceArchiveInfoFactory.class - [JAR]
org.jcvi.jillion.trace.chromat.abi.tag
├─ org.jcvi.jillion.trace.chromat.abi.tag.Ab1LocalDate.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.abi.tag.Ab1LocalTime.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.abi.tag.AsciiTaggedDataRecord.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.abi.tag.ByteArrayTaggedDataRecord.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.abi.tag.DateTaggedDataRecord.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.abi.tag.FloatArrayTaggedDataRecord.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.abi.tag.IntArrayTaggedDataRecord.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.abi.tag.PascalStringTaggedDataRecord.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.abi.tag.ShortArrayTaggedDataRecord.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.abi.tag.StringTaggedDataRecord.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.abi.tag.TaggedDataName.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.abi.tag.TaggedDataRecord.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.abi.tag.TaggedDataType.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.abi.tag.TimeTaggedDataRecord.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.abi.tag.UserDefinedTaggedDataRecord.class - [JAR]
org.jcvi.jillion.internal.sam
├─ org.jcvi.jillion.internal.sam.IndexerCallback.class - [JAR]
├─ org.jcvi.jillion.internal.sam.SamUtil.class - [JAR]
org.jcvi.jillion.internal.trace.chromat.ztr
├─ org.jcvi.jillion.internal.trace.chromat.ztr.DefaultZTRChromatogramWriterBuilder.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.ztr.IOLibLikeZtrChromatogramWriter.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.ztr.ZTRChromatogramImpl.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.ztr.ZTRUtil.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.ztr.ZtrChromatogramWriter.class - [JAR]
org.jcvi.jillion.core.io
├─ org.jcvi.jillion.core.io.AbstractFileInputStreamSupplier.class - [JAR]
├─ org.jcvi.jillion.core.io.BasicZipInputStreamSupplier.class - [JAR]
├─ org.jcvi.jillion.core.io.BufferSize.class - [JAR]
├─ org.jcvi.jillion.core.io.FileUtil.class - [JAR]
├─ org.jcvi.jillion.core.io.FileVisitor.class - [JAR]
├─ org.jcvi.jillion.core.io.GZipInputStreamSupplier.class - [JAR]
├─ org.jcvi.jillion.core.io.IOUtil.class - [JAR]
├─ org.jcvi.jillion.core.io.InputStreamSupplier.class - [JAR]
├─ org.jcvi.jillion.core.io.OutputStreams.class - [JAR]
├─ org.jcvi.jillion.core.io.PushBackBufferedReader.class - [JAR]
├─ org.jcvi.jillion.core.io.RawFileInputStreamSupplier.class - [JAR]
├─ org.jcvi.jillion.core.io.SubLengthInputStream.class - [JAR]
├─ org.jcvi.jillion.core.io.TextFileVisitor.class - [JAR]
org.jcvi.jillion.trim.trimmomatic
├─ org.jcvi.jillion.trim.trimmomatic.AbstractEdgeQualityTrimmer.class - [JAR]
├─ org.jcvi.jillion.trim.trimmomatic.LeadingQualityTrimmer.class - [JAR]
├─ org.jcvi.jillion.trim.trimmomatic.MaxInfoTrimmer.class - [JAR]
├─ org.jcvi.jillion.trim.trimmomatic.SlidingWindowQualityTrimmer.class - [JAR]
├─ org.jcvi.jillion.trim.trimmomatic.TrailingQualityTrimmer.class - [JAR]
org.jcvi.jillion.internal.align
├─ org.jcvi.jillion.internal.align.AbstractSequenceAlignmentBuilder.class - [JAR]
├─ org.jcvi.jillion.internal.align.NucleotideSequenceAlignmentBuilder.class - [JAR]
├─ org.jcvi.jillion.internal.align.ProteinSequenceAlignmentBuilder.class - [JAR]
├─ org.jcvi.jillion.internal.align.SequenceAlignmentBuilder.class - [JAR]
org.jcvi.jillion.align.exonerate
├─ org.jcvi.jillion.align.exonerate.Exonerate.class - [JAR]
├─ org.jcvi.jillion.align.exonerate.Exonerate2.class - [JAR]
├─ org.jcvi.jillion.align.exonerate.package-info.class - [JAR]
org.jcvi.jillion.fasta.nt
├─ org.jcvi.jillion.fasta.nt.AbstractNucleotideFastaRecordVisitor.class - [JAR]
├─ org.jcvi.jillion.fasta.nt.CommentedNucleotideSequenceFastaRecord.class - [JAR]
├─ org.jcvi.jillion.fasta.nt.DefaultNucleotideFastaFileDataStore.class - [JAR]
├─ org.jcvi.jillion.fasta.nt.FaiNucleotideFastaFileDataStore.class - [JAR]
├─ org.jcvi.jillion.fasta.nt.FaiNucleotideFastaWriter.class - [JAR]
├─ org.jcvi.jillion.fasta.nt.FaiNucleotideWriterBuilder.class - [JAR]
├─ org.jcvi.jillion.fasta.nt.IndexedNucleotideSequenceFastaFileDataStore.class - [JAR]
├─ org.jcvi.jillion.fasta.nt.LargeNucleotideSequenceFastaFileDataStore.class - [JAR]
├─ org.jcvi.jillion.fasta.nt.LargeNucleotideSequenceFastaIterator.class - [JAR]
├─ org.jcvi.jillion.fasta.nt.NucleotideFastaDataStore.class - [JAR]
├─ org.jcvi.jillion.fasta.nt.NucleotideFastaFileDataStore.class - [JAR]
├─ org.jcvi.jillion.fasta.nt.NucleotideFastaFileDataStoreBuilder.class - [JAR]
├─ org.jcvi.jillion.fasta.nt.NucleotideFastaFileReader.class - [JAR]
├─ org.jcvi.jillion.fasta.nt.NucleotideFastaRecord.class - [JAR]
├─ org.jcvi.jillion.fasta.nt.NucleotideFastaRecordBuilder.class - [JAR]
├─ org.jcvi.jillion.fasta.nt.NucleotideFastaWriter.class - [JAR]
├─ org.jcvi.jillion.fasta.nt.NucleotideFastaWriterBuilder.class - [JAR]
├─ org.jcvi.jillion.fasta.nt.UnCommentedNucleotideSequenceFastaRecord.class - [JAR]
org.jcvi.jillion.maq.bfq
├─ org.jcvi.jillion.maq.bfq.BfqFileDataStoreBuilder.class - [JAR]
├─ org.jcvi.jillion.maq.bfq.BfqFileParser.class - [JAR]
├─ org.jcvi.jillion.maq.bfq.BfqFileWriterBuilder.class - [JAR]
org.jcvi.jillion.internal.fasta.aa
├─ org.jcvi.jillion.internal.fasta.aa.CommentedProteinFastaRecord.class - [JAR]
├─ org.jcvi.jillion.internal.fasta.aa.DefaultProteinFastaDataStore.class - [JAR]
├─ org.jcvi.jillion.internal.fasta.aa.IndexedProteinFastaFileDataStore.class - [JAR]
├─ org.jcvi.jillion.internal.fasta.aa.LargeProteinFastaFileDataStore.class - [JAR]
├─ org.jcvi.jillion.internal.fasta.aa.LargeProteinFastaIterator.class - [JAR]
├─ org.jcvi.jillion.internal.fasta.aa.UnCommentedProteinFastaRecord.class - [JAR]
org.jcvi.jillion.sam.transform
├─ org.jcvi.jillion.sam.transform.PaddedSamTransformationService.class - [JAR]
├─ org.jcvi.jillion.sam.transform.SamGappedReferenceBuilderVisitor.class - [JAR]
├─ org.jcvi.jillion.sam.transform.SamTransformationService.class - [JAR]
org.jcvi.jillion.assembly.tigr.contig
├─ org.jcvi.jillion.assembly.tigr.contig.AbstractTigrContigBuilderVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.contig.CtgContigDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.contig.DefaultTigrContigFileDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.contig.IndexedTigrContigFileDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.contig.LargeTigrContigFileDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.contig.TigrContig.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.contig.TigrContigBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.contig.TigrContigDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.contig.TigrContigFileContigIterator.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.contig.TigrContigFileDataStoreBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.contig.TigrContigFileParser.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.contig.TigrContigFileVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.contig.TigrContigFileWriter.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.contig.TigrContigParser.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.contig.TigrContigRead.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.contig.TigrContigReadBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.contig.TigrContigReadVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.tigr.contig.TigrContigVisitor.class - [JAR]
org.jcvi.jillion.sam
├─ org.jcvi.jillion.sam.AbstractSamFileParser.class - [JAR]
├─ org.jcvi.jillion.sam.AbstractSamVisitor.class - [JAR]
├─ org.jcvi.jillion.sam.BamFileParser.class - [JAR]
├─ org.jcvi.jillion.sam.BgzfInputStream.class - [JAR]
├─ org.jcvi.jillion.sam.BgzfOutputStream.class - [JAR]
├─ org.jcvi.jillion.sam.DefaultSamFileDataStore.class - [JAR]
├─ org.jcvi.jillion.sam.Encoding.class - [JAR]
├─ org.jcvi.jillion.sam.IndexedBamFileParser.class - [JAR]
├─ org.jcvi.jillion.sam.NullSamAttributeValidator.class - [JAR]
├─ org.jcvi.jillion.sam.PresortedBamFileWriter.class - [JAR]
├─ org.jcvi.jillion.sam.PresortedSamFileWriter.class - [JAR]
├─ org.jcvi.jillion.sam.QuerySortedSamFileDataStore.class - [JAR]
├─ org.jcvi.jillion.sam.ReSortSamFileWriter.class - [JAR]
├─ org.jcvi.jillion.sam.SamAttributed.class - [JAR]
├─ org.jcvi.jillion.sam.SamFileDataStore.class - [JAR]
├─ org.jcvi.jillion.sam.SamFileDataStoreBuilder.class - [JAR]
├─ org.jcvi.jillion.sam.SamFileParser.class - [JAR]
├─ org.jcvi.jillion.sam.SamFileWriterBuilder.class - [JAR]
├─ org.jcvi.jillion.sam.SamParser.class - [JAR]
├─ org.jcvi.jillion.sam.SamParserFactory.class - [JAR]
├─ org.jcvi.jillion.sam.SamRecord.class - [JAR]
├─ org.jcvi.jillion.sam.SamRecordBuilder.class - [JAR]
├─ org.jcvi.jillion.sam.SamRecordFlag.class - [JAR]
├─ org.jcvi.jillion.sam.SamRecordFlags.class - [JAR]
├─ org.jcvi.jillion.sam.SamRecordImpl.class - [JAR]
├─ org.jcvi.jillion.sam.SamValidationException.class - [JAR]
├─ org.jcvi.jillion.sam.SamVisitor.class - [JAR]
├─ org.jcvi.jillion.sam.SamWriter.class - [JAR]
├─ org.jcvi.jillion.sam.SortOrder.class - [JAR]
├─ org.jcvi.jillion.sam.VirtualFileOffset.class - [JAR]
org.jcvi.jillion.maq.bfa
├─ org.jcvi.jillion.maq.bfa.BfaParser.class - [JAR]
├─ org.jcvi.jillion.maq.bfa.BfaWriterBuilder.class - [JAR]
org.jcvi.jillion.orf
├─ org.jcvi.jillion.orf.Orf.class - [JAR]
├─ org.jcvi.jillion.orf.OrfFinder.class - [JAR]
org.jcvi.jillion.assembly.clc.cas.read
├─ org.jcvi.jillion.assembly.clc.cas.read.CasPlacedRead.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.read.DefaultCasPlacedRead.class - [JAR]
org.jcvi.jillion.internal.trace.chromat.abi.tag.rate
├─ org.jcvi.jillion.internal.trace.chromat.abi.tag.rate.DefaultScanRate.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.abi.tag.rate.DefaultScanRateTaggedDataType.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.abi.tag.rate.ScanRateUtils.class - [JAR]
org.jcvi.jillion.profile
├─ org.jcvi.jillion.profile.BaseCount.class - [JAR]
├─ org.jcvi.jillion.profile.DisplayCountStrategy.class - [JAR]
├─ org.jcvi.jillion.profile.MostFrequentTieBreakerRule.class - [JAR]
├─ org.jcvi.jillion.profile.ProfileWriter.class - [JAR]
├─ org.jcvi.jillion.profile.ProfileWriterBuilder.class - [JAR]
├─ org.jcvi.jillion.profile.SimpleProfileWriter.class - [JAR]
org.jcvi.jillion.sam.attribute
├─ org.jcvi.jillion.sam.attribute.ChainedSamAttributeValidatorBuilder.class - [JAR]
├─ org.jcvi.jillion.sam.attribute.InvalidAttributeException.class - [JAR]
├─ org.jcvi.jillion.sam.attribute.InvalidValueTypeException.class - [JAR]
├─ org.jcvi.jillion.sam.attribute.NoDuplicateAttributeValidator.class - [JAR]
├─ org.jcvi.jillion.sam.attribute.ReservedAttributeValidator.class - [JAR]
├─ org.jcvi.jillion.sam.attribute.ReservedSamAttributeKeys.class - [JAR]
├─ org.jcvi.jillion.sam.attribute.SamAttribute.class - [JAR]
├─ org.jcvi.jillion.sam.attribute.SamAttributeKey.class - [JAR]
├─ org.jcvi.jillion.sam.attribute.SamAttributeKeyFactory.class - [JAR]
├─ org.jcvi.jillion.sam.attribute.SamAttributeType.class - [JAR]
├─ org.jcvi.jillion.sam.attribute.SamAttributeValidator.class - [JAR]
org.jcvi.jillion.internal.trace.chromat.scf.section
├─ org.jcvi.jillion.internal.trace.chromat.scf.section.AbstractBasesSectionCodec.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.scf.section.AbstractSampleSectionCodec.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.scf.section.CommentSectionCodec.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.scf.section.DefaultSectionCodecFactory.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.scf.section.EncodedSection.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.scf.section.NullSectionCodec.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.scf.section.PrivateDataCodec.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.scf.section.Section.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.scf.section.SectionCodec.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.scf.section.SectionCodecFactory.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.scf.section.SectionDecoder.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.scf.section.SectionDecoderException.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.scf.section.SectionEncoder.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.scf.section.Version2BasesSectionCodec.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.scf.section.Version2SampleSectionCodec.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.scf.section.Version3BasesSectionCodec.class - [JAR]
├─ org.jcvi.jillion.internal.trace.chromat.scf.section.Version3SampleSectionCodec.class - [JAR]
org.jcvi.jillion.align.exonerate.vulgar
├─ org.jcvi.jillion.align.exonerate.vulgar.VulgarElement.class - [JAR]
├─ org.jcvi.jillion.align.exonerate.vulgar.VulgarOperation.class - [JAR]
├─ org.jcvi.jillion.align.exonerate.vulgar.VulgarProtein2Genome.class - [JAR]
├─ org.jcvi.jillion.align.exonerate.vulgar.VulgarProtein2Genome2.class - [JAR]
├─ org.jcvi.jillion.align.exonerate.vulgar.package-info.class - [JAR]
org.jcvi.jillion.core.residue.nt
├─ org.jcvi.jillion.core.residue.nt.AbstractNucleotideCodec.class - [JAR]
├─ org.jcvi.jillion.core.residue.nt.AbstractTwoBitEncodedNucleotideCodec.class - [JAR]
├─ org.jcvi.jillion.core.residue.nt.AcgtGapNucleotideCodec.class - [JAR]
├─ org.jcvi.jillion.core.residue.nt.AcgtnNucloetideCodec.class - [JAR]
├─ org.jcvi.jillion.core.residue.nt.BasicNucleotideCodec.class - [JAR]
├─ org.jcvi.jillion.core.residue.nt.DefaultNucleotideSequence.class - [JAR]
├─ org.jcvi.jillion.core.residue.nt.DefaultReferenceEncodedNucleotideSequence.class - [JAR]
├─ org.jcvi.jillion.core.residue.nt.Nucleotide.class - [JAR]
├─ org.jcvi.jillion.core.residue.nt.NucleotideCodec.class - [JAR]
├─ org.jcvi.jillion.core.residue.nt.NucleotideSequence.class - [JAR]
├─ org.jcvi.jillion.core.residue.nt.NucleotideSequenceBuilder.class - [JAR]
├─ org.jcvi.jillion.core.residue.nt.NucleotideSequenceDataStore.class - [JAR]
├─ org.jcvi.jillion.core.residue.nt.NucleotideSequencePermuter.class - [JAR]
├─ org.jcvi.jillion.core.residue.nt.ReferenceMappedNucleotideSequence.class - [JAR]
├─ org.jcvi.jillion.core.residue.nt.SimpleNucleotideSequence.class - [JAR]
├─ org.jcvi.jillion.core.residue.nt.Triplet.class - [JAR]
├─ org.jcvi.jillion.core.residue.nt.UandTNucleotideCodec.class - [JAR]
org.jcvi.jillion.core.util
├─ org.jcvi.jillion.core.util.Builder.class - [JAR]
├─ org.jcvi.jillion.core.util.DateUtil.class - [JAR]
├─ org.jcvi.jillion.core.util.FileIterator.class - [JAR]
├─ org.jcvi.jillion.core.util.GenomeStatistics.class - [JAR]
├─ org.jcvi.jillion.core.util.JillionCollectors.class - [JAR]
├─ org.jcvi.jillion.core.util.JoinedStringBuilder.class - [JAR]
├─ org.jcvi.jillion.core.util.MapUtil.class - [JAR]
├─ org.jcvi.jillion.core.util.MapValueComparator.class - [JAR]
├─ org.jcvi.jillion.core.util.MemoizedSupplier.class - [JAR]
├─ org.jcvi.jillion.core.util.MultipleFileFilter.class - [JAR]
├─ org.jcvi.jillion.core.util.MultipleWrapper.class - [JAR]
├─ org.jcvi.jillion.core.util.ObjectsUtil.class - [JAR]
├─ org.jcvi.jillion.core.util.Pair.class - [JAR]
├─ org.jcvi.jillion.core.util.SingleThreadAdder.class - [JAR]
├─ org.jcvi.jillion.core.util.ThrowingStream.class - [JAR]
├─ org.jcvi.jillion.core.util.ThrowingStreamImpl.class - [JAR]
├─ org.jcvi.jillion.core.util.UnsignedByteArray.class - [JAR]
├─ org.jcvi.jillion.core.util.UnsignedIntArray.class - [JAR]
├─ org.jcvi.jillion.core.util.UnsignedShortArray.class - [JAR]
org.jcvi.jillion.assembly.consed.phd
├─ org.jcvi.jillion.assembly.consed.phd.AbstractPhdBallVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.AbstractPhdReadTagVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.AbstractPhdVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.ArtificialPhd.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.DefaultPhd.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.DefaultPhdDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.DefaultPhdReadTag.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.DefaultPhdWholeReadItem.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.IndexedPhdDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.LargePhdballDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.Phd.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.PhdBallFileParser.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.PhdBallIdIterator.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.PhdBallIterator.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.PhdBallParser.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.PhdBallVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.PhdBallVisitorCallback.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.PhdBallWriter.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.PhdBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.PhdDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.PhdDirDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.PhdFileDataStoreBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.PhdReadTag.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.PhdReadTagVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.PhdUtil.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.PhdVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.PhdWholeReadItem.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.PhdWholeReadItemVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.PhdWriter.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.ReadPhdFileFilter.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.SinglePhdWriter.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.phd.TraceDirPhdDataStoreBuilder.class - [JAR]
org.jcvi.jillion.experimental.assembly.agp
├─ org.jcvi.jillion.experimental.assembly.agp.AgpFileVisitor.class - [JAR]
├─ org.jcvi.jillion.experimental.assembly.agp.AgpParser.class - [JAR]
├─ org.jcvi.jillion.experimental.assembly.agp.AgpWriter.class - [JAR]
├─ org.jcvi.jillion.experimental.assembly.agp.DefaultAgpScaffoldDataStore.class - [JAR]
├─ org.jcvi.jillion.experimental.assembly.agp.ScaffoldDataStoreBuilderAgpVisitor.class - [JAR]
org.jcvi.jillion.experimental.align
├─ org.jcvi.jillion.experimental.align.AlnFileParser.class - [JAR]
├─ org.jcvi.jillion.experimental.align.AlnFileWriter.class - [JAR]
├─ org.jcvi.jillion.experimental.align.AlnGroupVisitor.class - [JAR]
├─ org.jcvi.jillion.experimental.align.AlnParser.class - [JAR]
├─ org.jcvi.jillion.experimental.align.AlnUtil.class - [JAR]
├─ org.jcvi.jillion.experimental.align.AlnVisitor.class - [JAR]
├─ org.jcvi.jillion.experimental.align.AlnWriter.class - [JAR]
├─ org.jcvi.jillion.experimental.align.GappedNucleotideAlignmentDataStore.class - [JAR]
org.jcvi.jillion.experimental.ncbi.submit.assemblyArchive
├─ org.jcvi.jillion.experimental.ncbi.submit.assemblyArchive.AssemblyArchiveConformation.class - [JAR]
├─ org.jcvi.jillion.experimental.ncbi.submit.assemblyArchive.AssemblyArchiveMetaData.class - [JAR]
├─ org.jcvi.jillion.experimental.ncbi.submit.assemblyArchive.AssemblyArchiveType.class - [JAR]
├─ org.jcvi.jillion.experimental.ncbi.submit.assemblyArchive.AssemblyArchiveWriter.class - [JAR]
├─ org.jcvi.jillion.experimental.ncbi.submit.assemblyArchive.AssemblyArchiveWriterBuilder.class - [JAR]
org.jcvi.jillion.internal.fasta
├─ org.jcvi.jillion.internal.fasta.AbstractLargeFastaFileDataStore.class - [JAR]
├─ org.jcvi.jillion.internal.fasta.AbstractResuseableFastaRecordVisitor.class - [JAR]
├─ org.jcvi.jillion.internal.fasta.AdaptedFastaDataStore.class - [JAR]
├─ org.jcvi.jillion.internal.fasta.DefaultFastaIndex.class - [JAR]
├─ org.jcvi.jillion.internal.fasta.FastaIndex.class - [JAR]
├─ org.jcvi.jillion.internal.fasta.FastaIndexRecord.class - [JAR]
├─ org.jcvi.jillion.internal.fasta.FastaUtil.class - [JAR]
├─ org.jcvi.jillion.internal.fasta.InMemorySortedFastaWriter.class - [JAR]
├─ org.jcvi.jillion.internal.fasta.LargeFastaIdIterator.class - [JAR]
├─ org.jcvi.jillion.internal.fasta.TmpDirSortedFastaWriter.class - [JAR]
org.jcvi.jillion.assembly.clc.cas.transform
├─ org.jcvi.jillion.assembly.clc.cas.transform.CasFileTransformationService.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.transform.ChromatDirFastaReadDataAdaptedIterator.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.transform.FastaReadDataAdaptedIterator.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.transform.FastqReadDatadAdaptedIterator.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.transform.FlowgramReadDataAdaptedIterator.class - [JAR]
├─ org.jcvi.jillion.assembly.clc.cas.transform.ReadData.class - [JAR]
org.jcvi.jillion.trim
├─ org.jcvi.jillion.trim.BwaQualityTrimmer.class - [JAR]
├─ org.jcvi.jillion.trim.NucleotideTrimmer.class - [JAR]
├─ org.jcvi.jillion.trim.QualityTrimmer.class - [JAR]
├─ org.jcvi.jillion.trim.Trimmer.class - [JAR]
├─ org.jcvi.jillion.trim.TrimmerPipeline.class - [JAR]
├─ org.jcvi.jillion.trim.TrimmerPipelineBuilder.class - [JAR]
org.jcvi.jillion.trace.chromat.abi
├─ org.jcvi.jillion.trace.chromat.abi.AbiChromatogram.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.abi.AbiChromatogramBuilder.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.abi.AbiChromatogramFileVisitor.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.abi.AbiChromatogramParser.class - [JAR]
org.jcvi.jillion.align.pairwise
├─ org.jcvi.jillion.align.pairwise.AbstractNeedlemanWunschAligner.class - [JAR]
├─ org.jcvi.jillion.align.pairwise.AbstractPairwiseAligner.class - [JAR]
├─ org.jcvi.jillion.align.pairwise.AbstractPairwiseSequenceAlignment.class - [JAR]
├─ org.jcvi.jillion.align.pairwise.AbstractSmithWatermanAligner.class - [JAR]
├─ org.jcvi.jillion.align.pairwise.NucleotideNeedlemanWunschAligner.class - [JAR]
├─ org.jcvi.jillion.align.pairwise.NucleotidePairwiseSequenceAlignment.class - [JAR]
├─ org.jcvi.jillion.align.pairwise.NucleotidePairwiseSequenceAlignmentImpl.class - [JAR]
├─ org.jcvi.jillion.align.pairwise.NucleotideSmithWatermanAligner.class - [JAR]
├─ org.jcvi.jillion.align.pairwise.PairwiseAlignmentBuilder.class - [JAR]
├─ org.jcvi.jillion.align.pairwise.PairwiseSequenceAlignment.class - [JAR]
├─ org.jcvi.jillion.align.pairwise.PairwiseSequenceAlignmentWrapper.class - [JAR]
├─ org.jcvi.jillion.align.pairwise.ProteinNeedlemanWunschAligner.class - [JAR]
├─ org.jcvi.jillion.align.pairwise.ProteinPairwiseSequenceAlignment.class - [JAR]
├─ org.jcvi.jillion.align.pairwise.ProteinPairwiseSequenceAlignmentImpl.class - [JAR]
├─ org.jcvi.jillion.align.pairwise.ProteinSmithWatermanAligner.class - [JAR]
├─ org.jcvi.jillion.align.pairwise.ResiduePairwiseStrategy.class - [JAR]
org.jcvi.jillion.assembly.consed
├─ org.jcvi.jillion.assembly.consed.AceAssemblyTransformerPostProcessor.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ConsedAssemblyTransformerBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ConsedUtil.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.IndividualPhdConsedTransformerHelper.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.PhdBallConsedTransformerHelper.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.PhdConsedTransformerHelper.class - [JAR]
org.jcvi.jillion.assembly.consed.ace
├─ org.jcvi.jillion.assembly.consed.ace.AbstractAceConsensusTagVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.AbstractAceContigBuilderVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.AbstractAceContigReadVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.AbstractAceContigVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.AbstractAceFileVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.AbstractAceFileWriter.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.AbstractDefaultAceTag.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.AbstractDefaultPlacedAceTag.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.AceAssembledRead.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.AceAssembledReadAdapter.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.AceAssembledReadBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.AceBaseSegment.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.AceConsensusTagVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.AceContig.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.AceContigBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.AceContigReadVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.AceContigVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.AceContigVisitorAdapter.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.AceFileDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.AceFileDataStoreBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.AceFileParser.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.AceFileUtil.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.AceFileVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.AceFileVisitorCallback.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.AceFileWriter.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.AceFileWriterBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.AceParser.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.AceTag.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.AlignedReadInfo.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.BaseSegmentUtil.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.ConsedConsensusQualityComputer.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.ConsensusAceTag.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.ConsensusAceTagBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.DefaultAceAssembledRead.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.DefaultAceBaseSegment.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.DefaultAceFileDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.HighLowAceContigPhdDatastore.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.HighLowPhdAceContigVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.IndexedAceFileDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.LargeAceFileDataStore.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.MultiAceFileVisitorAdapter.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.MultipleAceContigReadVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.MultipleAceContigVisitor.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.PhdInfo.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.RangeableAceTag.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.ReadAceTag.class - [JAR]
├─ org.jcvi.jillion.assembly.consed.ace.WholeAssemblyAceTag.class - [JAR]
org.jcvi.jillion.internal.core.datastore
├─ org.jcvi.jillion.internal.core.datastore.AbstractDataStore.class - [JAR]
├─ org.jcvi.jillion.internal.core.datastore.AbstractMapBackedDataStore.class - [JAR]
├─ org.jcvi.jillion.internal.core.datastore.DataStoreIterator.class - [JAR]
├─ org.jcvi.jillion.internal.core.datastore.DataStoreStreamingIterator.class - [JAR]
org.jcvi.jillion.assembly.util
├─ org.jcvi.jillion.assembly.util.AbstractCoverageMapBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.util.ContigCoverageMapBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.util.CoverageMap.class - [JAR]
├─ org.jcvi.jillion.assembly.util.CoverageMapBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.util.CoverageMapCollectors.class - [JAR]
├─ org.jcvi.jillion.assembly.util.CoverageMapFactory.class - [JAR]
├─ org.jcvi.jillion.assembly.util.CoverageMapStats.class - [JAR]
├─ org.jcvi.jillion.assembly.util.CoverageMapStatsCollector.class - [JAR]
├─ org.jcvi.jillion.assembly.util.CoverageRegion.class - [JAR]
├─ org.jcvi.jillion.assembly.util.CoverageRegionBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.util.CoverageStatsCombiner.class - [JAR]
├─ org.jcvi.jillion.assembly.util.DefaultCoverageRegion.class - [JAR]
├─ org.jcvi.jillion.assembly.util.GapQualityValueStrategy.class - [JAR]
├─ org.jcvi.jillion.assembly.util.ReadFilter.class - [JAR]
├─ org.jcvi.jillion.assembly.util.Slice.class - [JAR]
├─ org.jcvi.jillion.assembly.util.SliceBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.util.SliceCombiner.class - [JAR]
├─ org.jcvi.jillion.assembly.util.SliceElement.class - [JAR]
├─ org.jcvi.jillion.assembly.util.SliceMap.class - [JAR]
├─ org.jcvi.jillion.assembly.util.SliceMapBuilder.class - [JAR]
├─ org.jcvi.jillion.assembly.util.SliceMapCollector.class - [JAR]
org.jcvi.jillion.experimental.align.blast
├─ org.jcvi.jillion.experimental.align.blast.BlastHit.class - [JAR]
├─ org.jcvi.jillion.experimental.align.blast.BlastHitImpl.class - [JAR]
├─ org.jcvi.jillion.experimental.align.blast.BlastParser.class - [JAR]
├─ org.jcvi.jillion.experimental.align.blast.BlastVisitor.class - [JAR]
├─ org.jcvi.jillion.experimental.align.blast.Hsp.class - [JAR]
├─ org.jcvi.jillion.experimental.align.blast.HspBuilder.class - [JAR]
├─ org.jcvi.jillion.experimental.align.blast.TabularBlastParser.class - [JAR]
├─ org.jcvi.jillion.experimental.align.blast.XmlFileBlastParser.class - [JAR]
org.jcvi.jillion.internal.assembly.util
├─ org.jcvi.jillion.internal.assembly.util.CompactedSliceElement.class - [JAR]
├─ org.jcvi.jillion.internal.assembly.util.CompactedSliceMap.class - [JAR]
├─ org.jcvi.jillion.internal.assembly.util.ConsensusCompactedSlice.class - [JAR]
├─ org.jcvi.jillion.internal.assembly.util.NoConsensusCompactedSlice.class - [JAR]
org.jcvi.jillion.experimental.primer
├─ org.jcvi.jillion.experimental.primer.OptimalMeltingTemperatureEstimator.class - [JAR]
├─ org.jcvi.jillion.experimental.primer.PrimerDetector.class - [JAR]
├─ org.jcvi.jillion.experimental.primer.PrimerUtil.class - [JAR]
├─ org.jcvi.jillion.experimental.primer.SaltCorrectionStrategy.class - [JAR]
org.jcvi.jillion.trace.sff
├─ org.jcvi.jillion.trace.sff.CompletelyParsedIndexedSffFileDataStore.class - [JAR]
├─ org.jcvi.jillion.trace.sff.DefaultSFFCommonHeaderDecoder.class - [JAR]
├─ org.jcvi.jillion.trace.sff.DefaultSffCommonHeader.class - [JAR]
├─ org.jcvi.jillion.trace.sff.DefaultSffFileDataStore.class - [JAR]
├─ org.jcvi.jillion.trace.sff.DefaultSffReadData.class - [JAR]
├─ org.jcvi.jillion.trace.sff.DefaultSffReadDataDecoder.class - [JAR]
├─ org.jcvi.jillion.trace.sff.DefaultSffReadHeader.class - [JAR]
├─ org.jcvi.jillion.trace.sff.DefaultSffReadHeaderDecoder.class - [JAR]
├─ org.jcvi.jillion.trace.sff.LargeSffFileDataStore.class - [JAR]
├─ org.jcvi.jillion.trace.sff.ManifestIndexed454SffFileDataStore.class - [JAR]
├─ org.jcvi.jillion.trace.sff.Sff454NameUtil.class - [JAR]
├─ org.jcvi.jillion.trace.sff.SffCommonHeader.class - [JAR]
├─ org.jcvi.jillion.trace.sff.SffCommonHeaderDecoder.class - [JAR]
├─ org.jcvi.jillion.trace.sff.SffDataStoreBuilder.class - [JAR]
├─ org.jcvi.jillion.trace.sff.SffDecoderException.class - [JAR]
├─ org.jcvi.jillion.trace.sff.SffFileDataStore.class - [JAR]
├─ org.jcvi.jillion.trace.sff.SffFileDataStoreBuilder.class - [JAR]
├─ org.jcvi.jillion.trace.sff.SffFileIterator.class - [JAR]
├─ org.jcvi.jillion.trace.sff.SffFileParser.class - [JAR]
├─ org.jcvi.jillion.trace.sff.SffFileReadVisitor.class - [JAR]
├─ org.jcvi.jillion.trace.sff.SffFlowgram.class - [JAR]
├─ org.jcvi.jillion.trace.sff.SffFlowgramImpl.class - [JAR]
├─ org.jcvi.jillion.trace.sff.SffParser.class - [JAR]
├─ org.jcvi.jillion.trace.sff.SffReadData.class - [JAR]
├─ org.jcvi.jillion.trace.sff.SffReadDataDecoder.class - [JAR]
├─ org.jcvi.jillion.trace.sff.SffReadHeader.class - [JAR]
├─ org.jcvi.jillion.trace.sff.SffReadHeaderDecoder.class - [JAR]
├─ org.jcvi.jillion.trace.sff.SffUtil.class - [JAR]
├─ org.jcvi.jillion.trace.sff.SffVisitor.class - [JAR]
├─ org.jcvi.jillion.trace.sff.SffVisitorCallback.class - [JAR]
├─ org.jcvi.jillion.trace.sff.SffWriter.class - [JAR]
├─ org.jcvi.jillion.trace.sff.SffWriterBuilder.class - [JAR]
├─ org.jcvi.jillion.trace.sff.SffWriterUtil.class - [JAR]
org.jcvi.jillion.trace.chromat.ztr
├─ org.jcvi.jillion.trace.chromat.ztr.ZtrChromatogram.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.ztr.ZtrChromatogramBuilder.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.ztr.ZtrChromatogramFileVisitor.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.ztr.ZtrChromatogramParser.class - [JAR]
├─ org.jcvi.jillion.trace.chromat.ztr.ZtrChromatogramWriterBuilder.class - [JAR]
org.jcvi.jillion.trim.lucy
├─ org.jcvi.jillion.trim.lucy.LucyQualityTrimmerBuilder.class - [JAR]
├─ org.jcvi.jillion.trim.lucy.LucyVectorSpliceTrimmerBuilder.class - [JAR]
org.jcvi.jillion.core.util.iter
├─ org.jcvi.jillion.core.util.iter.ArrayIterator.class - [JAR]
├─ org.jcvi.jillion.core.util.iter.ChainedIterator.class - [JAR]
├─ org.jcvi.jillion.core.util.iter.ChainedIteratorOfSuppliers.class - [JAR]
├─ org.jcvi.jillion.core.util.iter.ChainedStreamingIterator.class - [JAR]
├─ org.jcvi.jillion.core.util.iter.ChainedStreamingIteratorFromSuppliers.class - [JAR]
├─ org.jcvi.jillion.core.util.iter.IteratorUtil.class - [JAR]
├─ org.jcvi.jillion.core.util.iter.PeekableIterator.class - [JAR]
├─ org.jcvi.jillion.core.util.iter.PeekableStreamingIterator.class - [JAR]
├─ org.jcvi.jillion.core.util.iter.RollOverListIterator.class - [JAR]
├─ org.jcvi.jillion.core.util.iter.SingleElementIterator.class - [JAR]
├─ org.jcvi.jillion.core.util.iter.StreamingIterator.class - [JAR]
├─ org.jcvi.jillion.core.util.iter.StreamingIteratorAdapter.class - [JAR]
org.jcvi.jillion.testutils.assembly.cas
├─ org.jcvi.jillion.testutils.assembly.cas.CasParserTestDouble.class - [JAR]
├─ org.jcvi.jillion.testutils.assembly.cas.CasTestUtil.class - [JAR]
├─ org.jcvi.jillion.testutils.assembly.cas.DefaultCasAlignment.class - [JAR]
├─ org.jcvi.jillion.testutils.assembly.cas.DefaultCasAlignmentRegion.class - [JAR]
├─ org.jcvi.jillion.testutils.assembly.cas.FastaRecordWriter.class - [JAR]
├─ org.jcvi.jillion.testutils.assembly.cas.FastqRecordWriter.class - [JAR]
├─ org.jcvi.jillion.testutils.assembly.cas.RecordWriter.class - [JAR]
├─ org.jcvi.jillion.testutils.assembly.cas.SffRecordWriter.class - [JAR]
org.jcvi.jillion.trace.fastq
├─ org.jcvi.jillion.trace.fastq.AbstractFastqRecordVisitor.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.AbstractFastqVisitor.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.CommentedFastqRecord.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.DefaultFastqFileDataStore.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.FastqCollectors.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.FastqDataStore.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.FastqFileDataStore.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.FastqFileDataStoreBuilder.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.FastqFileDataStoreImpl.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.FastqFileParser.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.FastqFileParserBuilder.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.FastqFileReader.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.FastqParser.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.FastqQualityCodec.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.FastqRecord.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.FastqRecordBuilder.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.FastqRecordBuilderImpl.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.FastqRecordVisitor.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.FastqUtil.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.FastqVisitor.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.FastqWriter.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.FastqWriterAdapter.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.FastqWriterBuilder.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.IlluminaUtil.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.InMemorySortedFastqWriter.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.IndexedFastqFileDataStore.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.LargeFastqFileDataStore.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.SolexaUtil.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.SplitFastqWriter.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.TmpDirSortedFastqWriter.class - [JAR]
├─ org.jcvi.jillion.trace.fastq.UncommentedFastqRecord.class - [JAR]
