Hierarchy For All Packages
Package Hierarchies:Class Hierarchy
- java.lang.Object
- Accuracy.AccuracyCalculator
- Accuracy.AccuracyStats
- Executable.Available
- org.apache.commons.configuration2.event.BaseEventSource (implements org.apache.commons.configuration2.event.EventSource)
- org.apache.commons.configuration2.AbstractConfiguration (implements org.apache.commons.configuration2.Configuration)
- org.apache.commons.configuration2.AbstractHierarchicalConfiguration<T> (implements java.lang.Cloneable, org.apache.commons.configuration2.HierarchicalConfiguration<T>, org.apache.commons.configuration2.tree.NodeKeyResolver<T>)
- org.apache.commons.configuration2.BaseHierarchicalConfiguration (implements java.lang.Cloneable, org.apache.commons.configuration2.tree.InMemoryNodeModelSupport)
- org.apache.commons.configuration2.XMLConfiguration (implements org.apache.commons.configuration2.FileBasedConfiguration, org.apache.commons.configuration2.io.FileLocatorAware, org.apache.commons.configuration2.io.InputStreamSupport)
- Executable.ExtendedXMLConfiguration
- org.apache.commons.configuration2.XMLConfiguration (implements org.apache.commons.configuration2.FileBasedConfiguration, org.apache.commons.configuration2.io.FileLocatorAware, org.apache.commons.configuration2.io.InputStreamSupport)
- org.apache.commons.configuration2.BaseHierarchicalConfiguration (implements java.lang.Cloneable, org.apache.commons.configuration2.tree.InMemoryNodeModelSupport)
- org.apache.commons.configuration2.AbstractHierarchicalConfiguration<T> (implements java.lang.Cloneable, org.apache.commons.configuration2.HierarchicalConfiguration<T>, org.apache.commons.configuration2.tree.NodeKeyResolver<T>)
- org.apache.commons.configuration2.AbstractConfiguration (implements org.apache.commons.configuration2.Configuration)
- VCF.ByteToGeno
- Callers.Caller
- Callers.BiasedBinomialCaller
- Callers.BinomialCaller
- Callers.LogBiasedBinomialCaller
- Callers.LogBinomialCaller
- Callers.BiasedBinomialCaller
- Executable.Case
- Executable.ClassList<X,Y>
- Executable.CombinerOption
- Utils.Distribution.ComparableDistributionCollector<V> (implements java.util.stream.Collector<T,A,R>)
- Utils.Correlation.Correlation
- Utils.Distribution.CountMap<V>
- VCF.Mappers.DepthMapper (implements VCF.Mappers.Mapper<M>)
- Accuracy.DepthMask
- Accuracy.DepthMaskFactory
- Utils.Optimize.Descent
- Utils.Distribution.Distribution<V>
- Utils.Distribution.ComparableDistribution<V>
- Utils.Distribution.DistributionCollector<V> (implements java.util.stream.Collector<T,A,R>)
- Utils.Progress.DotsProgress (implements Utils.Progress.Progress)
- VCF.Mappers.GenoToByte (implements VCF.Mappers.ByteMapper)
- VCF.Genotype
- Utils.Optimize.GoldenSection
- Executable.ImputationOption
- Executable.Input
- Imputers.KnniLDProb (implements Imputers.Imputer)
- Imputers.KnniLDProbOptimizedCalls (implements Imputers.OptimizeImputer<I>)
- Executable.LinkImputeR
- Utils.Log
- Utils.MAFCalculator
- Utils.Matrix
- Combiner.MaxDepthCombiner (implements Combiner.Combiner)
- Combiner.MaxDepthCombinerOptimizedCalls (implements Combiner.OptimizeCombiner<C>)
- VCF.Changers.MaxDepthNoReadsChanger (implements VCF.Changers.GenotypeChanger)
- VCF.Meta
- VCF.Changers.MinDepthMissingChanger (implements VCF.Changers.GenotypeChanger)
- Utils.Optimize.MultipleTest
- Executable.Output
- VCF.Position
- VCF.Filters.PositionFilter (implements VCF.Filters.VCFFilter)
- VCF.Filters.BiallelicFilter
- VCF.Filters.HasDepthFilter
- VCF.Filters.MAFFilter
- VCF.Filters.ParalogHWFilter
- VCF.Filters.PositionMissing
- VCF.PositionMeta
- Executable.PrintStats
- Utils.ProbToCall
- Utils.ProbToCallMinDepth
- Utils.Progress.ProgressFactory
- VCF.Changers.RenameFormatChanger (implements VCF.Changers.PositionChanger)
- VCF.Sample
- VCF.Filters.SampleFilter (implements VCF.Filters.VCFFilter)
- VCF.Filters.SampleMissing
- Utils.Progress.SilentProgress (implements Utils.Progress.Progress)
- Utils.SingleGenotype.SingleGenotypePosition
- Utils.SingleGenotype.SingleGenotypeCall
- Utils.SingleGenotype.SingleGenotypeMasked
- Utils.SingleGenotype.SingleGenotypeProbability
- Utils.SingleGenotype.SingleGenotypeReads
- Utils.SortByIndexDouble (implements java.util.Comparator<T>)
- VCF.Changers.StandardizeCountsFormatChanger (implements VCF.Changers.PositionChanger)
- Utils.Progress.TextBarProgress (implements Utils.Progress.Progress)
- Utils.Progress.TextProgress (implements Utils.Progress.Progress)
- java.lang.Throwable (implements java.io.Serializable)
- java.lang.Exception
- Exceptions.AlgorithmException
- Exceptions.NotEnoughMaskableGenotypesException
- Exceptions.INIException
- Exceptions.OutputException
- java.lang.RuntimeException
- Exceptions.ProgrammerException
- VCF.Exceptions.VCFException
- VCF.Exceptions.VCFDataException
- VCF.Exceptions.VCFMissingFormatException
- VCF.Exceptions.VCFNoDataException
- VCF.Exceptions.VCFUnexpectedDataException
- VCF.Exceptions.VCFInputException
- VCF.Exceptions.VCFDataLineException
- VCF.Exceptions.VCFHeaderLineException
- VCF.Exceptions.VCFDataException
- Exceptions.XMLException
- Exceptions.AlgorithmException
- java.lang.Exception
- Utils.TopQueue
- VCF.VCF
Interface Hierarchy
- VCF.Mappers.ByteMapper
- Combiner.Combiner
- VCF.Mappers.DoubleMapper
- VCF.Changers.GenotypeChanger
- Imputers.Imputer
- VCF.Mappers.IntegerMapper
- VCF.Mappers.Mapper<M>
- Utils.Optimize.MultipleIntegerValue
- Combiner.OptimizeCombiner<C>
- Imputers.OptimizeImputer<I>
- VCF.Changers.PositionChanger
- Utils.Progress.Progress
- Utils.Optimize.SingleDoubleValue
- VCF.Filters.VCFFilter
Enum Hierarchy
- java.lang.Object
- java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
- Accuracy.AccuracyCalculator.AccuracyMethod
- Accuracy.DepthMask.Method
- Utils.Log.Level
- Utils.Progress.ProgressFactory.ProgressType
- java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)