Hierarchy For All Packages

Package Hierarchies:

alun.gchap, alun.genapps, alun.genepi, alun.genio, alun.graph, alun.linkage, alun.markov, alun.mcld, alun.util, alun.view, alun.viewgraph, alun.zeroloop

Class Hierarchy

• java.lang.Object
  • java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    • java.util.AbstractList<E> (implements java.util.List<E>)
      • java.util.ArrayList<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.RandomAccess, java.io.Serializable)
        • alun.util.RandomBag<V>
  • alun.graph.AbstractGraph<V,E> (implements alun.graph.MutableGraph<V,E>)
    • alun.graph.Network<V,E> (implements alun.graph.MutableGraph<V,E>)
      • alun.graph.CarefulNetwork<V,E>
      • alun.graph.DirectedNetwork<V,E>
        • alun.graph.Decomposition<V>
        • alun.genio.MarriageNodeMap
      • alun.mcld.JunctionTree
  • alun.viewgraph.AbstractMappable (implements alun.viewgraph.Mappable)
    • alun.viewgraph.LabelledBlob
      • alun.mcld.Locus (implements java.lang.Comparable<T>, alun.util.Interval, alun.viewgraph.Mappable, alun.markov.Variable)
  • alun.markov.AbstractTable (implements alun.markov.Table)
    • alun.markov.DenseTable
    • alun.markov.SparseTable
  • alun.genepi.AlleleErrorPenetrance (implements alun.markov.Function)
  • alun.genapps.AlleleSharing
    • HGS
      • SimHGS
    • SGS
      • SimSGS
  • alun.mcld.AllelesToGenotype (implements alun.markov.Function)
  • alun.gchap.ApproxGCHap
    • ApproxGCHap
  • alun.util.BasicInterval (implements alun.util.Interval)
  • alun.markov.BasicVariable (implements alun.markov.Variable)
    • alun.zeroloop.Edge
    • alun.genepi.GeneticVariable
      • alun.genepi.Allele
      • alun.genepi.AuxiliaryVariable
        • alun.genepi.AuxOneGenHalvesVariable
        • alun.genepi.AuxOneGenVariable
        • alun.genepi.AuxThreeGenVariable
      • alun.genepi.Error
      • alun.genepi.Genotype
        • alun.genepi.UnorderedGenotype
      • alun.genepi.Inheritance
      • alun.genepi.Theta
        • alun.genepi.OneTheta
  • CheckFormat
  • CheckParameters
  • CheckPedigree
  • CheckTriplets
  • alun.markov.Clique
    • alun.markov.BasicClique
      • alun.genepi.TripletClique
  • cMorgansToTheta
  • java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    • java.awt.Canvas (implements javax.accessibility.Accessible)
      • alun.view.BufferedCanvas
        • alun.view.ActiveCanvas
          • alun.view.PrintActiveCanvas
    • java.awt.Container
      • java.awt.Panel (implements javax.accessibility.Accessible)
        • java.applet.Applet
          • alun.view.ViewingApplet (implements alun.view.Paintable, alun.util.SafeRunnable)
            • alun.view.PrintingApplet
              • alun.viewgraph.MapViewer
                • alun.viewgraph.MapEditor
                  • alun.mcld.HaploGUI
                    • alun.mcld.DiploGUI
    • java.awt.Scrollbar (implements javax.accessibility.Accessible, java.awt.Adjustable)
      • alun.view.ScrollWidget (implements java.awt.event.AdjustmentListener)
  • alun.mcld.ComponentMarker
  • alun.mcld.DecomposableSearch (implements alun.mcld.GraphMHScheme)
    • alun.mcld.LocalizedDecomposableSearch
  • alun.util.DoubleValue (implements java.lang.Comparable<T>)
  • DownCodeAlleles
  • alun.zeroloop.EdgeConstraint (implements alun.markov.Function)
    • alun.zeroloop.MonogamyConstraint
    • alun.zeroloop.OneParentalMarriageConstraint
    • alun.zeroloop.TwoParentConstraint
  • alun.markov.EqualityFunction (implements alun.markov.Function)
  • alun.genepi.ErrorPrior (implements alun.markov.Function)
  • alun.genio.Family
  • alun.gchap.GCHap
    • GCHap
  • GeneCountAlleles
  • alun.genapps.GeneCounter
  • alun.genapps.GeneDropper
  • alun.genepi.GeneticFunction (implements alun.markov.Function)
    • alun.genepi.AuxiliaryFunction
      • alun.genepi.AuxLinkFunction
      • alun.genepi.AuxLocusFunction
    • alun.genepi.ErrorPenetrance
    • alun.genepi.FixedRecombination
    • alun.genepi.GenotypePrior
      • alun.genepi.UnorderedPrior
    • alun.genepi.MaternalInheritance
    • alun.genepi.MendelianTransmission
      • alun.genepi.UnorderedTransmission
    • alun.genepi.PaternalInheritance
    • alun.genepi.Penetrance
    • alun.genepi.Recombination
    • alun.genepi.TrivialFunction
    • alun.genepi.VariableRecombination
  • alun.gchap.GeneticTrait
    • alun.gchap.Marker
      • alun.gchap.SNP
    • alun.gchap.MultiLocusTrait
  • alun.gchap.Genotype
  • alun.genepi.GenotypeOnlyDropSampler
  • GetPolymorphisms
  • alun.util.GoldenSection
  • alun.graph.GraphFunction
  • alun.markov.GraphicalModel
    • alun.genepi.AuxiliaryModel
    • alun.genepi.GenotypeModel
  • alun.gchap.HapFormatter
  • alun.util.HashOfHash
  • HetCutOff
  • Heterozygosities
  • alun.zeroloop.Individual (implements alun.zeroloop.PedNode)
  • alun.util.InputFormatter
    • alun.linkage.LinkageFormatter
  • alun.util.IntArray
  • alun.mcld.IntervalSearch (implements alun.mcld.GraphMHScheme)
    • alun.mcld.TiedIntervalSearch
  • alun.util.IntervalTree<V>
    • alun.util.IntervalTreeGraph<V,E> (implements alun.graph.Graph<V,E>)
  • alun.util.IntValue (implements java.lang.Comparable<T>)
  • alun.markov.IteratorFunction (implements alun.markov.Function, alun.markov.Iterable)
  • alun.mcld.JointScheme
    • alun.mcld.WindowingScheme
  • alun.util.Lattice<E>
  • alun.mcld.LikelihoodCalculator
    • alun.mcld.DataCalculator
  • alun.mcld.LimitedIntervalSearch (implements alun.mcld.GraphMHScheme)
  • alun.viewgraph.Line
    • alun.viewgraph.Arrow
  • alun.linkage.LinkageDataSet
  • alun.linkage.LinkageIndividual (implements alun.linkage.LinkConstants)
  • alun.linkage.LinkageInterface (implements alun.genio.GeneticDataSource)
  • alun.linkage.LinkageLocus
    • alun.linkage.AffectionStatusLocus
    • alun.linkage.NumberedAlleleLocus
    • alun.linkage.QuantitativeLocus
  • alun.linkage.LinkageParameterData
  • alun.linkage.LinkagePedigreeData (implements alun.linkage.LinkConstants)
  • alun.linkage.LinkagePhenotype
    • alun.linkage.AffectionStatusPhenotype
    • alun.linkage.NumberedAllelePhenotype
    • alun.linkage.QuantitativePhenotype
  • alun.genepi.LinkageSampler
    • alun.genepi.IndependentLocusSampler
      • alun.mcld.LDSampler (implements alun.mcld.DataHaplotypeSource)
      • alun.genepi.LinkedLocusSampler
        • alun.genepi.LocusMeiosisSampler
          • alun.genepi.ExtendedLMSampler
    • alun.genepi.UnconditionalMeiosisSampler
  • LinkageToFastPhase
  • LinkageToPhase
  • alun.genepi.LociVariables
    • alun.genepi.LinkageVariables
  • alun.gchap.Locus
    • alun.gchap.MultiLocus
  • alun.genepi.LocusVariables
  • alun.mcld.LogLikelihood
  • alun.util.Main
    • GeneDrop
    • GeneDrops
    • HapGraph
    • HetLods
    • IntervalLD
    • McLinkLD
    • TwoPointLods
  • MakeProbands
  • alun.viewgraph.Map<V> (implements alun.viewgraph.MappableGraph)
    • alun.viewgraph.DynamicMap<V>
    • alun.viewgraph.DynamicMappableMap<V> (implements alun.viewgraph.MappableGraph)
    • alun.viewgraph.StaticMap<V>
  • alun.util.MapAsCollection<K,V> (implements java.util.Collection<E>)
  • alun.viewgraph.MapCoordinator
    • alun.viewgraph.EditingCoordinator
  • alun.viewgraph.MapMover
    • alun.viewgraph.DagMover
      • alun.viewgraph.NewerDagMover
    • alun.viewgraph.LocalMover
      • alun.viewgraph.AnnealMover
        • alun.mcld.DistanceAnnealMover
      • alun.viewgraph.GlobalMover
      • alun.viewgraph.NewerLocalMover
  • alun.zeroloop.Marriage (implements alun.zeroloop.PedNode)
  • alun.graph.MaskedNetwork<V,E> (implements alun.graph.MutableGraph<V,E>)
  • alun.genepi.MaxLoder (implements alun.util.Curve)
  • MaxTwoPointLods
  • McLink
  • alun.view.MouseKey (implements java.awt.event.KeyListener, java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
    • alun.view.Mouser
      • alun.viewgraph.MapMouser
        • alun.viewgraph.EditingMouser
        • alun.viewgraph.MovingMouser
  • alun.genapps.ObligatoryErrors
    • alun.genapps.FindErrorProbs
      • CheckErrors
        • GMCheck
    • ObligateErrors
  • alun.gchap.Observation
    • alun.gchap.MarkerObservation
    • alun.gchap.MultiLocusObservation
  • alun.mcld.Observation (implements alun.markov.Function)
  • OnePoints
  • alun.view.OutputFileListener (implements java.awt.event.ActionListener)
  • alun.view.PageType
  • alun.util.Pair<E,F>
    • alun.util.Triplet<E,F,G>
  • alun.genio.Pedigree
  • alun.mcld.PerfectHaplotypes (implements alun.mcld.DataHaplotypeSource)
    • alun.mcld.ImperfectHaplotypes
      • alun.mcld.Diplotypes
      • alun.mcld.Haplotypes
    • alun.mcld.TransposedPerfectHaplotypes
  • alun.gchap.Phenotype
    • alun.gchap.MarkerPhenotype
    • alun.gchap.MultiLocusPhenotype
  • alun.markov.Product (implements alun.graph.Graph<V,E>)
    • alun.mcld.LDModel
  • alun.util.RadixPlaneSorter<E>
  • alun.zeroloop.RandomBipartiteTree<V,E>
    • alun.zeroloop.RandomPedTree<V,E>
  • SelectKindreds
    • SelectPedigrees
  • SelectLoci
  • alun.util.Sorter
  • alun.util.StringFormatter
  • alun.markov.TableMaker
  • java.lang.Thread (implements java.lang.Runnable)
    • alun.util.SafeThread
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • java.lang.RuntimeException
        • alun.linkage.LinkageException
  • alun.genepi.Tlods
  • TrimPed
  • alun.markov.VerySparseTable (implements alun.markov.Table)
  • ViewGraph
  • ViewLinkPed
  • ViewPed
  • java.awt.event.WindowAdapter (implements java.awt.event.WindowFocusListener, java.awt.event.WindowListener, java.awt.event.WindowStateListener)
    • alun.view.FrameQuitter
  • alun.util.XYPair (implements alun.util.CartesianPoint)
  • ZeroLoopPed
  • alun.zeroloop.ZeroLoopPedGenerator

Interface Hierarchy

• alun.util.CartesianPoint
  • alun.viewgraph.Mappable
• alun.util.Curve
• alun.markov.Function
  • alun.markov.Table (also extends alun.markov.Iterable)
• alun.graph.Graph<V,E>
  • alun.graph.MutableGraph<V,E>
• alun.mcld.GraphMHScheme
• alun.mcld.HaplotypeSource
  • alun.mcld.DataHaplotypeSource
• alun.util.Interval
• alun.markov.Iterable
  • alun.markov.Table (also extends alun.markov.Function)
  • alun.markov.Variable
• alun.linkage.LinkConstants
• alun.viewgraph.MappableGraph
• alun.view.Paintable
• alun.genio.ParameterData
  • alun.genio.BasicGeneticData (also extends alun.genio.PedigreeData)
    • alun.genio.GeneticDataSource
  • alun.genio.GeneticDataSource
• alun.genio.PedigreeData
  • alun.genio.BasicGeneticData (also extends alun.genio.ParameterData)
    • alun.genio.GeneticDataSource
  • alun.genio.GeneticDataSource
• alun.zeroloop.PedNode
• alun.util.SafeRunnable