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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
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