Download mitcr-1.0-sources.jar
mitcr/mitcr-1.0-sources.jar.zip( 368 k)
The download jar file contains the following class files or Java source files.
META-INF/LICENSE-APACHE-2.0
META-INF/LICENSE-LGPL-3.0
META-INF/MANIFEST.MF
com.milaboratory.core.clone.Clone.java
com.milaboratory.core.clone.CloneCluster.java
com.milaboratory.core.clone.CloneClusterImpl.java
com.milaboratory.core.clone.CloneComparator.java
com.milaboratory.core.clone.CloneImpl.java
com.milaboratory.core.clone.CloneSet.java
com.milaboratory.core.clone.CloneSetClustered.java
com.milaboratory.core.clone.CloneSetClusteredImpl.java
com.milaboratory.core.clone.CloneSetClusteredImpl.java.orig
com.milaboratory.core.clone.CloneSetImpl.java
com.milaboratory.core.clone.package-info.java
com.milaboratory.core.io.AbstractBinaryContainerIO.java
com.milaboratory.core.io.BinaryContainerIO.java
com.milaboratory.core.io.BinaryContainerReader.java
com.milaboratory.core.io.BinaryContainerWriter.java
com.milaboratory.core.io.DataInputPositioned.java
com.milaboratory.core.io.DataOutputPositioned.java
com.milaboratory.core.io.FixedBlockSize.java
com.milaboratory.core.io.IOUtill.java
com.milaboratory.core.io.IndexedContainerInput.java
com.milaboratory.core.io.IndexedContainerOutput.java
com.milaboratory.core.io.SignatureCheckError.java
com.milaboratory.core.io.WrongStructureException.java
com.milaboratory.core.io.impl.AbstractIndexedContainerInput.java
com.milaboratory.core.io.impl.BBBackedLongArrayList.java
com.milaboratory.core.io.impl.ByteArrayIndexedContainerInput.java
com.milaboratory.core.io.impl.ByteBufferHolder.java
com.milaboratory.core.io.impl.ByteBufferHolderCache.java
com.milaboratory.core.io.impl.DataInputPositionedStream.java
com.milaboratory.core.io.impl.DataOutputPositionedStream.java
com.milaboratory.core.io.impl.FileIndexedContainerInput.java
com.milaboratory.core.io.impl.FileIndexedContainerOutput.java
com.milaboratory.core.io.impl.IByteArrayOutputStream.java
com.milaboratory.core.io.package-info.java
com.milaboratory.core.io.serializers.Bit2ArrayIO.java
com.milaboratory.core.io.serializers.BitArrayIO.java
com.milaboratory.core.io.serializers.NucleotideSQPairIO.java
com.milaboratory.core.io.serializers.NucleotideSequenceIO.java
com.milaboratory.core.io.serializers.SegmentGroupContainerIO.java
com.milaboratory.core.io.serializers.SequenceQualityIO.java
com.milaboratory.core.io.util.ClassUtils.java
com.milaboratory.core.io.util.PrimitiveArrayIO.java
com.milaboratory.core.io.util.PrimitiveIO.java
com.milaboratory.core.io.util.PrimitiveMapIO.java
com.milaboratory.core.segment.Allele.java
com.milaboratory.core.segment.AlleleSet.java
com.milaboratory.core.segment.CDR.java
com.milaboratory.core.segment.Chain.java
com.milaboratory.core.segment.DefaultSegmentLibrary.java
com.milaboratory.core.segment.Gene.java
com.milaboratory.core.segment.MD5ChecksumTestFail.java
com.milaboratory.core.segment.Molecule.java
com.milaboratory.core.segment.Segment.java
com.milaboratory.core.segment.SegmentFamily.java
com.milaboratory.core.segment.SegmentGroup.java
com.milaboratory.core.segment.SegmentGroupContainer.java
com.milaboratory.core.segment.SegmentGroupType.java
com.milaboratory.core.segment.SegmentLibrary.java
com.milaboratory.core.segment.SegmentSet.java
com.milaboratory.core.segment.SegmentUtils.java
com.milaboratory.core.segment.Species.java
com.milaboratory.core.segment.SpeciesSegmentGroup.java
com.milaboratory.core.segment.package-info.java
com.milaboratory.core.sequence.Alphabet.java
com.milaboratory.core.sequence.NucleotideSQPair.java
com.milaboratory.core.sequence.Sequence.java
com.milaboratory.core.sequence.SequenceBuilder.java
com.milaboratory.core.sequence.SequenceBuilderFactory.java
com.milaboratory.core.sequence.SequenceQuality.java
com.milaboratory.core.sequence.SequencingErrorType.java
com.milaboratory.core.sequence.aminoacid.AminoAcidAlphabet.java
com.milaboratory.core.sequence.aminoacid.AminoAcidSequence.java
com.milaboratory.core.sequence.aminoacid.AminoAcidSequenceImpl.java
com.milaboratory.core.sequence.aminoacid.CDRAminoAcidAlphabet.java
com.milaboratory.core.sequence.aminoacid.CDRAminoAcidSequence.java
com.milaboratory.core.sequence.aminoacid.CDRTriplet.java
com.milaboratory.core.sequence.motif.LowQualityIndicator.java
com.milaboratory.core.sequence.motif.LowQualityIndicatorProvider.java
com.milaboratory.core.sequence.motif.NucleotideMotif.java
com.milaboratory.core.sequence.motif.NucleotideMotifBuilder.java
com.milaboratory.core.sequence.motif.NucleotideMotifSearchAdvanced.java
com.milaboratory.core.sequence.motif.NucleotideMotifSearchAdvancedWrapper.java
com.milaboratory.core.sequence.motif.NucleotideMotifSearchParameters.java
com.milaboratory.core.sequence.motif.NucleotideSQPairProvider.java
com.milaboratory.core.sequence.motif.NucleotideWildcards.java
com.milaboratory.core.sequence.motif.SSequencingReadBindings.java
com.milaboratory.core.sequence.nucleotide.AbstarctNucleotideSequence.java
com.milaboratory.core.sequence.nucleotide.NucleotideAlphabet.java
com.milaboratory.core.sequence.nucleotide.NucleotideAlphabetWithN.java
com.milaboratory.core.sequence.nucleotide.NucleotideSequence.java
com.milaboratory.core.sequence.nucleotide.NucleotideSequenceBuilder.java
com.milaboratory.core.sequence.nucleotide.NucleotideSequenceImpl.java
com.milaboratory.core.sequence.package-info.java
com.milaboratory.core.sequence.quality.SequenceQualityPhred.java
com.milaboratory.core.sequence.tree.LinearMinPenalty.java
com.milaboratory.core.sequence.tree.NucleotideSQPairSet.java
com.milaboratory.core.sequence.tree.NucleotideSQPairSetEvent.java
com.milaboratory.core.sequence.tree.NucleotideSQPairSetEventType.java
com.milaboratory.core.sequence.tree.NucleotideSQPairSetListener.java
com.milaboratory.core.sequence.tree.NucleotideSequencePenaltyTreeSet.java
com.milaboratory.core.sequence.tree.Penalty.java
com.milaboratory.core.sequence.tree.SequenceTreeMap.java
com.milaboratory.core.sequence.util.NucleotideRCSequence.java
com.milaboratory.core.sequence.util.NucleotideSequenceGenerator.java
com.milaboratory.core.sequence.util.NucleotideSubSequence.java
com.milaboratory.core.sequence.util.SequenceMismatch.java
com.milaboratory.core.sequence.util.SequenceMismatchCollector.java
com.milaboratory.core.sequence.util.SequenceQualityUtils.java
com.milaboratory.core.sequence.util.SequencesUtils.java
com.milaboratory.core.sequence.util.SubSequenceQuality.java
com.milaboratory.core.sequence.util.Translator.java
com.milaboratory.core.sequencing.SequencingUtils.java
com.milaboratory.core.sequencing.io.PSequencingDataReader.java
com.milaboratory.core.sequencing.io.SSequencingDataReader.java
com.milaboratory.core.sequencing.io.SSequencingDataReaderWithFlowgram.java
com.milaboratory.core.sequencing.io.SequencingDataReader.java
com.milaboratory.core.sequencing.io.fasta.FastaItem.java
com.milaboratory.core.sequencing.io.fasta.FastaItemsReader.java
com.milaboratory.core.sequencing.io.fasta.FastaReader.java
com.milaboratory.core.sequencing.io.fasta.FastaWriter.java
com.milaboratory.core.sequencing.io.fastq.Casava18InfoProvider.java
com.milaboratory.core.sequencing.io.fastq.IlluminaInfoProvider.java
com.milaboratory.core.sequencing.io.fastq.IlluminaInfoProviderFactory.java
com.milaboratory.core.sequencing.io.fastq.IlluminaReadInfo.java
com.milaboratory.core.sequencing.io.fastq.IlluminaReadInfoImpl.java
com.milaboratory.core.sequencing.io.fastq.NucleotideSQPairTrimmer.java
com.milaboratory.core.sequencing.io.fastq.PFastqReader.java
com.milaboratory.core.sequencing.io.fastq.PFastqWriter.java
com.milaboratory.core.sequencing.io.fastq.PSequencingReadsTrimmer.java
com.milaboratory.core.sequencing.io.fastq.SFastqReader.java
com.milaboratory.core.sequencing.io.fastq.SFastqWriter.java
com.milaboratory.core.sequencing.io.fastq.SSequencingReadTrimmer.java
com.milaboratory.core.sequencing.io.fastq.quality.AbstractSequenceQualityFactory.java
com.milaboratory.core.sequencing.io.fastq.quality.PhredSequenceQualityFactory.java
com.milaboratory.core.sequencing.io.fastq.quality.QualityStringFormat.java
com.milaboratory.core.sequencing.io.fastq.quality.SequenceQualityFactory.java
com.milaboratory.core.sequencing.io.fastq.quality.WrongQualityStringException.java
com.milaboratory.core.sequencing.io.sff.SFFClipper.java
com.milaboratory.core.sequencing.io.sff.SFFHeader.java
com.milaboratory.core.sequencing.io.sff.SFFRAWRead.java
com.milaboratory.core.sequencing.io.sff.SFFReader.java
com.milaboratory.core.sequencing.package-info.java
com.milaboratory.core.sequencing.read.PDataSerRecord.java
com.milaboratory.core.sequencing.read.PSequencingRead.java
com.milaboratory.core.sequencing.read.PSequencingReadImpl.java
com.milaboratory.core.sequencing.read.SSequencingRead.java
com.milaboratory.core.sequencing.read.SSequencingReadImpl.java
com.milaboratory.core.sequencing.read.SSequencingReadWithFlowgram.java
com.milaboratory.core.sequencing.read.SSequencingReadWithFlowgramImpl.java
com.milaboratory.core.sequencing.read.SequencingRead.java
com.milaboratory.mitcr.SimpleTest.java
com.milaboratory.mitcr.SimpleTest.java.orig
com.milaboratory.mitcr.cdrextraction.CDR3ExtractionResult.java
com.milaboratory.mitcr.cdrextraction.CDR3ExtractionResultUtils.java
com.milaboratory.mitcr.cdrextraction.CDR3Extractor.java
com.milaboratory.mitcr.cdrextraction.CDR3ExtractorFactory.java
com.milaboratory.mitcr.cdrextraction.CDR3ExtractorFactoryFromSQPair.java
com.milaboratory.mitcr.cdrextraction.CDR3ExtractorFactoryFromSRead.java
com.milaboratory.mitcr.cdrextraction.CDR3ExtractorFromPRead.java
com.milaboratory.mitcr.cdrextraction.CDR3ExtractorFromSQPair.java
com.milaboratory.mitcr.cdrextraction.CDR3ExtractorFromSRead.java
com.milaboratory.mitcr.cdrextraction.CDR3ExtractorListener.java
com.milaboratory.mitcr.cdrextraction.CDR3ExtractorParameters.java
com.milaboratory.mitcr.cdrextraction.CoreCDR3Extractor.java
com.milaboratory.mitcr.cdrextraction.Strand.java
com.milaboratory.mitcr.cdrextraction.TargetRead.java
com.milaboratory.mitcr.cdrextraction.package-info.java
com.milaboratory.mitcr.cli.BuildInformation.java
com.milaboratory.mitcr.cli.BuildInformationProvider.java
com.milaboratory.mitcr.cli.ExportDetalizationLevel.java
com.milaboratory.mitcr.cli.Main.java
com.milaboratory.mitcr.cli.ParametersIO.java
com.milaboratory.mitcr.cli.ReportExporter.java
com.milaboratory.mitcr.cli.TabDelimitedExporter.java
com.milaboratory.mitcr.cli.TabDelimitedImporter.java
com.milaboratory.mitcr.clonegenerator.AccumulatorClone.java
com.milaboratory.mitcr.clonegenerator.BarcodeAggregator.java
com.milaboratory.mitcr.clonegenerator.BasicCloneGenerator.java
com.milaboratory.mitcr.clonegenerator.BasicCloneGeneratorParameters.java
com.milaboratory.mitcr.clonegenerator.CloneGenerator.java
com.milaboratory.mitcr.clonegenerator.CloneGeneratorFactory.java
com.milaboratory.mitcr.clonegenerator.CloneGeneratorListener.java
com.milaboratory.mitcr.clonegenerator.CloneGeneratorParameters.java
com.milaboratory.mitcr.clonegenerator.CloneGeneratorParametersDeserializer.java
com.milaboratory.mitcr.clonegenerator.InMemoryResultAccumulator.java
com.milaboratory.mitcr.clonegenerator.LQFilteringOffCloneGenerator.java
com.milaboratory.mitcr.clonegenerator.LQFilteringOffCloneGeneratorParameters.java
com.milaboratory.mitcr.clonegenerator.LQMappingCloneGenerator.java
com.milaboratory.mitcr.clonegenerator.LQMappingCloneGeneratorParameters.java
com.milaboratory.mitcr.clonegenerator.OnHDDResultAccumulator.java
com.milaboratory.mitcr.clonegenerator.ResultsAccumulator.java
com.milaboratory.mitcr.clonegenerator.SequencingReadLink.java
com.milaboratory.mitcr.clonegenerator.TreePackingInfo.java
com.milaboratory.mitcr.clonegenerator.package-info.java
com.milaboratory.mitcr.clsexport.AbstractCloneSetMetadata.java
com.milaboratory.mitcr.clsexport.AbstractCloneSetMetadataIO.java
com.milaboratory.mitcr.clsexport.CloneClusterData.java
com.milaboratory.mitcr.clsexport.CloneClusterDataIO.java
com.milaboratory.mitcr.clsexport.CloneIO.java
com.milaboratory.mitcr.clsexport.ClsExporter.java
com.milaboratory.mitcr.clsexport.DataSetMetadata.java
com.milaboratory.mitcr.clsexport.DataSetMetadataIO.java
com.milaboratory.mitcr.clsexport.SCloneSetMetadata.java
com.milaboratory.mitcr.clsexport.SCloneSetMetadataIO.java
com.milaboratory.mitcr.clusterization.CloneClusterizationType.java
com.milaboratory.mitcr.clusterization.CloneClusterizer.java
com.milaboratory.mitcr.clusterization.CloneClusterizerFactory.java
com.milaboratory.mitcr.clusterization.ClusterizationListener.java
com.milaboratory.mitcr.clusterization.DummyCloneClusterizer.java
com.milaboratory.mitcr.clusterization.MonolayerCluster.java
com.milaboratory.mitcr.clusterization.PenaltyBasedFastClusterizer.java
com.milaboratory.mitcr.clusterization.PenaltyCalculator.java
com.milaboratory.mitcr.clusterization.package-info.java
com.milaboratory.mitcr.clusterization.penalty.NoClusterizationPenalty.java
com.milaboratory.mitcr.clusterization.penalty.OneMismatchPenaltyCalculator.java
com.milaboratory.mitcr.clusterization.penalty.VDJExplicitPenalty.java
com.milaboratory.mitcr.clusterization.penalty.VJMismatchPenalty.java
com.milaboratory.mitcr.pipeline.AnalysisListener.java
com.milaboratory.mitcr.pipeline.AnalysisListenerCombiner.java
com.milaboratory.mitcr.pipeline.DefaultAnalysisListener.java
com.milaboratory.mitcr.pipeline.FullPipeline.java
com.milaboratory.mitcr.pipeline.ParameterPresets.java
com.milaboratory.mitcr.pipeline.Parameters.java
com.milaboratory.mitcr.pipeline.package-info.java
com.milaboratory.mitcr.qualitystrategy.DummyQualityInterpretationStrategy.java
com.milaboratory.mitcr.qualitystrategy.GBNSBothSidesNucleotideInfoProvider.java
com.milaboratory.mitcr.qualitystrategy.GBNSNucleotideInfoProvider.java
com.milaboratory.mitcr.qualitystrategy.GBNSUtils.java
com.milaboratory.mitcr.qualitystrategy.GoodBadNucleotideSequence.java
com.milaboratory.mitcr.qualitystrategy.GoodBadNucleotideSequenceProvider.java
com.milaboratory.mitcr.qualitystrategy.IlluminaQualityInterpretationStrategy.java
com.milaboratory.mitcr.qualitystrategy.QualityInterpretationStrategy.java
com.milaboratory.mitcr.qualitystrategy.QualityInterpretationStrategyDeserializer.java
com.milaboratory.mitcr.qualitystrategy.package-info.java
com.milaboratory.mitcr.statistics.AnalysisStatisticsAggregator.java
com.milaboratory.mitcr.statistics.CloneSetQualityControl.java
com.milaboratory.mitcr.util.evolver.AbstractGenerator.java
com.milaboratory.mitcr.util.evolver.ConditionsProvider.java
com.milaboratory.mitcr.util.evolver.Generator.java
com.milaboratory.mitcr.util.evolver.Reactor.java
com.milaboratory.mitcr.vdjmapping.AlignmentDirection.java
com.milaboratory.mitcr.vdjmapping.DSegmentMapper.java
com.milaboratory.mitcr.vdjmapping.DSegmentMapperFactory.java
com.milaboratory.mitcr.vdjmapping.DSegmentMapperParameters.java
com.milaboratory.mitcr.vdjmapping.PointSegmentMapper.java
com.milaboratory.mitcr.vdjmapping.SearchDirection.java
com.milaboratory.mitcr.vdjmapping.SegmentMapper.java
com.milaboratory.mitcr.vdjmapping.SegmentMappingResult.java
com.milaboratory.mitcr.vdjmapping.SimplestAlignment.java
com.milaboratory.mitcr.vdjmapping.VDJSegmentsMapper.java
com.milaboratory.mitcr.vdjmapping.VDJSegmentsMapperFactory.java
com.milaboratory.mitcr.vdjmapping.VDJSegmentsMappingResult.java
com.milaboratory.mitcr.vdjmapping.VJMapperListener.java
com.milaboratory.mitcr.vdjmapping.VJSegmentMapper.java
com.milaboratory.mitcr.vdjmapping.VJSegmentMapperFactory.java
com.milaboratory.mitcr.vdjmapping.VJSegmentMapperParameters.java
com.milaboratory.mitcr.vdjmapping.VJSegmentMappingResult.java
com.milaboratory.mitcr.vdjmapping.VJSegmentMappingResultFormatter.java
com.milaboratory.mitcr.vdjmapping.VJSegmentsMapperAdapter.java
com.milaboratory.mitcr.vdjmapping.ntree.NTreeNode.java
com.milaboratory.mitcr.vdjmapping.ntree.NTreeNodeGenerator.java
com.milaboratory.mitcr.vdjmapping.ntree.NTreeNodeGeneratorBadDeletion.java
com.milaboratory.mitcr.vdjmapping.ntree.NTreeNodeGeneratorBadMismatch.java
com.milaboratory.mitcr.vdjmapping.ntree.NTreeNodeGeneratorBadMismatch3B.java
com.milaboratory.mitcr.vdjmapping.ntree.NTreeNodeGeneratorMatchOnly.java
com.milaboratory.mitcr.vdjmapping.ntree.NTreeSlider.java
com.milaboratory.mitcr.vdjmapping.ntree.NucleotideInfo.java
com.milaboratory.mitcr.vdjmapping.ntree.NucleotideInfoProvider.java
com.milaboratory.mitcr.vdjmapping.package-info.java
com.milaboratory.mitcr.vdjmapping.tree.CoreVJSegmentMapper.java
com.milaboratory.mitcr.vdjmapping.tree.OneDirectionSegmentMapper.java
com.milaboratory.mitcr.vdjmapping.tree.STree.java
com.milaboratory.mitcr.vdjmapping.tree.STreeResultHolder.java
com.milaboratory.mitcr.vdjmapping.tree.SmartAlignmentSegmentMapper.java
com.milaboratory.mitcr.vdjmapping.tree.SmartAlignmentSegmentMapperV2.java
com.milaboratory.mitcr.vdjmapping.tree.UniDirectionSegmentMapper.java
com.milaboratory.mitcr.vdjmapping.trivial.OneSideAligner.java
com.milaboratory.mitcr.vdjmapping.trivial.OneSideAlignmentResult.java
com.milaboratory.mitcr.vdjmapping.trivial.TrivialSegmentMapper.java
com.milaboratory.mitcr.vdjmapping.trivial.TrivialSegmentMapperFactory.java
com.milaboratory.util.Bit2Array.java
com.milaboratory.util.BitArray.java
com.milaboratory.util.CanReportProgress.java
com.milaboratory.util.CanReportProgressAndStage.java
com.milaboratory.util.CompressionType.java
com.milaboratory.util.CoordProxy.java
com.milaboratory.util.Factory.java
com.milaboratory.util.HashFunctions.java
com.milaboratory.util.IndexRange.java
com.milaboratory.util.IntArrayList.java
com.milaboratory.util.LongArrayList.java
com.milaboratory.util.Math.java
com.milaboratory.util.NullOutputStream.java
com.milaboratory.util.ProgressReporter.java
com.milaboratory.util.ProgressReporterFactory.java
com.milaboratory.util.TablePrintStreamAdapter.java
com.milaboratory.util.XMLException.java
mitcr
segments.gsl
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