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Hierarchy For All Packages
Package Hierarchies:
pal.alignment
,
pal.coalescent
,
pal.datatype
,
pal.distance
,
pal.eval
,
pal.gui
,
pal.io
,
pal.math
,
pal.mep
,
pal.misc
,
pal.popgen
,
pal.statistics
,
pal.substmodel
,
pal.tree
,
pal.util
,
pal.xml
Class Hierarchy
class java.lang.Object
class pal.alignment.
AbstractAlignment
(implements pal.alignment.
Alignment
, pal.misc.
IdGroup
, pal.misc.
Report
, java.io.Serializable)
class pal.alignment.
AminoAcidAlignment
class pal.alignment.
BootstrappedAlignment
class pal.alignment.
CodonAlignment
class pal.alignment.
ConcatenatedAlignment
class pal.alignment.
ConcatenatedAnnotatedAlignment
(implements pal.alignment.
AnnotationAlignment
)
class pal.alignment.
GapBalancedAlignment
(implements java.io.Serializable)
class pal.alignment.
IndelAlignment
class pal.alignment.
IndelAnnotatedAlignment
(implements pal.alignment.
AnnotationAlignment
)
class pal.alignment.
JumbledAlignment
class pal.alignment.
ReadAlignment
class pal.alignment.
SimpleAlignment
class pal.alignment.
MultiLocusAnnotatedAlignment
(implements pal.alignment.
AnnotationAlignment
)
class pal.alignment.
SimpleAnnotatedAlignment
(implements pal.alignment.
AnnotationAlignment
)
class pal.tree.
SimulatedAlignment
class pal.alignment.
SitePattern
class pal.alignment.
StrippedAlignment
class pal.alignment.
StrippedAnnotatedAlignment
(implements pal.alignment.
AnnotationAlignment
)
class pal.substmodel.
AbstractRateMatrix
(implements pal.substmodel.
RateMatrix
)
class pal.substmodel.
AminoAcidModel
(implements pal.substmodel.
RateMatrix
)
class pal.substmodel.
BLOSUM62
(implements pal.util.
XMLConstants
)
class pal.substmodel.
CPREV
(implements pal.util.
XMLConstants
)
class pal.substmodel.
Dayhoff
(implements pal.util.
XMLConstants
)
class pal.substmodel.
JTT
(implements pal.util.
XMLConstants
)
class pal.substmodel.
MTREV24
(implements pal.util.
XMLConstants
)
class pal.substmodel.
VT
(implements pal.util.
XMLConstants
)
class pal.substmodel.
WAG
(implements pal.util.
XMLConstants
)
class pal.substmodel.
CodonModel
(implements pal.substmodel.
RateMatrix
, java.io.Serializable)
class pal.substmodel.
YangCodonModel
(implements java.io.Serializable, pal.util.
XMLConstants
)
class pal.substmodel.
NucleotideModel
(implements pal.substmodel.
RateMatrix
, java.io.Serializable)
class pal.substmodel.
F81
(implements java.io.Serializable, pal.util.
XMLConstants
)
class pal.substmodel.
F84
(implements java.io.Serializable, pal.util.
XMLConstants
)
class pal.substmodel.
GTR
(implements java.io.Serializable, pal.util.
XMLConstants
)
class pal.substmodel.
HKY
(implements java.io.Serializable, pal.util.
XMLConstants
)
class pal.substmodel.
TN
(implements pal.util.
XMLConstants
)
class pal.substmodel.
TwoStateModel
(implements pal.substmodel.
RateMatrix
, pal.util.
XMLConstants
)
class pal.alignment.
AlignmentUtils
class pal.misc.
Attribute
class pal.math.
Binomial
(implements java.io.Serializable)
class pal.statistics.
BootstrapStatistics
class pal.math.
BoundsCheckedFunction
(implements pal.math.
MultivariateFunction
)
class pal.substmodel.
CachedRateMatrix
(implements pal.misc.
PalObjectListener
, pal.substmodel.
RateMatrix
)
class pal.statistics.
ChiSquareTest
class pal.eval.
ChiSquareValue
(implements pal.math.
MultivariateFunction
)
class pal.gui.
CircularGraphics
class pal.coalescent.
CoalescentIntervals
(implements pal.misc.
Report
, java.io.Serializable, pal.misc.
Units
)
class pal.coalescent.
CoalescentSimulator
class pal.datatype.
CodonTableFactory
class pal.datatype.
CodonTableUtils
class pal.util.
ComparableDouble
(implements pal.util.
Comparable
)
class java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
class pal.gui.
LinkageDisequilibriumComponent
(implements java.awt.print.Printable)
class pal.gui.
TreeComponent
class pal.statistics.
ContigencyTable
class pal.datatype.
DataTypeUtils
(implements java.io.Serializable)
class pal.util.
DefaultCache
(implements pal.util.
DoubleKeyCache
)
class pal.coalescent.
DemographicModel
(implements java.lang.Cloneable, pal.misc.
Parameterized
, pal.misc.
Report
, java.io.Serializable, pal.misc.
Summarizable
, pal.misc.
Units
)
class pal.coalescent.
ConstantPopulation
(implements pal.misc.
Parameterized
, pal.misc.
Report
, java.io.Serializable, pal.misc.
Summarizable
)
class pal.coalescent.
ExponentialGrowth
(implements pal.misc.
Parameterized
, pal.misc.
Report
, java.io.Serializable, pal.misc.
Summarizable
)
class pal.coalescent.
ConstExpGrowth
(implements pal.misc.
Parameterized
, pal.misc.
Report
, java.io.Serializable)
class pal.coalescent.
ExpandingPopulation
(implements pal.misc.
Parameterized
, pal.misc.
Report
, java.io.Serializable)
class pal.eval.
DemographicValue
(implements pal.math.
MultivariateFunction
)
class pal.statistics.
DiscreteStatistics
class pal.distance.
DistanceMatrix
(implements pal.misc.
IdGroup
, java.io.Serializable)
class pal.distance.
AlignmentDistanceMatrix
(implements java.io.Serializable)
class pal.distance.
JukesCantorDistanceMatrix
class pal.distance.
ReadDistanceMatrix
class pal.distance.
SUPGMADistanceMatrix
class pal.tree.
TreeDistanceMatrix
class pal.distance.
DistanceMatrixUtils
(implements java.io.Serializable)
class pal.xml.
ElementFactory
(implements pal.util.
XMLConstants
)
class pal.xml.
ElementParser
(implements pal.util.
XMLConstants
)
class pal.math.
ErrorFunction
class java.util.EventObject (implements java.io.Serializable)
class pal.misc.
PalObjectEvent
class pal.misc.
ParameterEvent
class pal.eval.
FastLikelihoodCalculator
(implements pal.eval.
LikelihoodCalculator
, pal.misc.
PalObjectListener
)
class pal.statistics.
FisherExact
class pal.io.
FormattedInput
(implements java.io.Serializable)
class pal.io.
FormattedOutput
(implements java.io.Serializable)
class pal.statistics.
GammaDistribution
class pal.statistics.
ChiSquareDistribution
class pal.statistics.
ExponentialDistribution
class pal.math.
GammaFunction
class pal.alignment.
Genotype
class pal.util.
HeapSort
class pal.misc.
Identifier
(implements pal.util.
Comparable
, pal.misc.
Nameable
, java.io.Serializable)
class pal.misc.
IdGenerator
class pal.coalescent.
IntervalsExtractor
(implements pal.misc.
Units
)
class pal.datatype.
IUPACNucleotides
(implements pal.datatype.
DataType
)
class pal.datatype.
IUPACPenaltyTable
(implements pal.datatype.
TransitionPenaltyTable
)
class pal.statistics.
KishinoHasegawaTest
(implements pal.misc.
Report
)
class pal.misc.
LabelMapping
(implements java.io.Serializable)
class pal.gui.
LayoutTracker
class pal.statistics.
LikelihoodRatioTest
class pal.eval.
LikelihoodValue
class pal.eval.
DemographicLikelihoodValue
class pal.math.
LineFunction
(implements pal.math.
UnivariateFunction
)
class pal.tree.
Local
class pal.util.
Log
(implements pal.util.
Logger
)
class pal.math.
MachineAccuracy
class pal.math.
MathUtils
class pal.substmodel.
MatrixExponential
(implements java.lang.Cloneable, java.io.Serializable)
class pal.math.
MersenneTwisterFast
(implements java.io.Serializable)
class pal.eval.
ModelParameters
(implements pal.math.
MultivariateFunction
)
class pal.statistics.
ModelSupport
(implements pal.misc.
Report
)
class pal.math.
MultivariateMinimum
class pal.math.
ConjugateDirectionSearch
class pal.math.
ConjugateGradientSearch
class pal.math.
DifferentialEvolution
class pal.math.
GeneralizedDEOptimizer
class pal.math.
OrthogonalSearch
class pal.math.
StochasticOSearch
class pal.mep.
MutationRateModel
(implements java.lang.Cloneable, pal.misc.
Parameterized
, pal.misc.
Report
, java.io.Serializable, pal.misc.
Summarizable
, pal.misc.
Units
)
class pal.mep.
ConstantMutationRate
(implements pal.misc.
Parameterized
, pal.misc.
Report
, java.io.Serializable, pal.misc.
Summarizable
)
class pal.mep.
SteppedMutationRate
(implements pal.misc.
Parameterized
, pal.misc.
Report
, java.io.Serializable, pal.misc.
Summarizable
)
class pal.mep.
WindowedMutationRate
(implements pal.misc.
Parameterized
, pal.misc.
Report
, java.io.Serializable, pal.misc.
Summarizable
)
class pal.gui.
NameColouriser
(implements java.io.Serializable)
class pal.tree.
NodeFactory
class pal.tree.
NodeUtils
class pal.statistics.
NormalDistribution
class pal.math.
NumericalDerivative
class pal.math.
OrthogonalLineFunction
(implements pal.math.
UnivariateFunction
)
class pal.distance.
PairwiseDistance
(implements java.io.Serializable)
class pal.misc.
PalEventMulticaster
class pal.misc.
ParameterizedDouble
(implements pal.misc.
Parameterized
, java.io.Serializable)
class pal.tree.
ParameterizedTree
(implements pal.misc.
Parameterized
, pal.tree.
Tree
)
class pal.tree.
ClockTree
class pal.coalescent.
DemographicClockTree
(implements pal.coalescent.
DemographicTree
)
class pal.tree.
DatedTipsClockTree
(implements pal.misc.
ExternalParameterListener
, java.io.Serializable)
class pal.tree.
LogParameterizedTree
class pal.tree.
MutationRateModelTree
class pal.tree.
UnconstrainedTree
class pal.statistics.
ParetoDistribution
class pal.statistics.
PenalizedLikelihood
class pal.substmodel.
RateDistribution
(implements java.lang.Cloneable, pal.misc.
Parameterized
, pal.misc.
Report
, java.io.Serializable)
class pal.substmodel.
GammaRates
class pal.substmodel.
InvariableSites
(implements java.io.Serializable)
class pal.substmodel.
UniformRate
(implements java.io.Serializable)
class pal.substmodel.
RateMatrixUtils
class java.io.Reader
class java.io.FilterReader
class java.io.PushbackReader
class pal.io.
InputSource
class pal.misc.
ReleaseInfo
class pal.tree.
RootedTreeUtils
class pal.distance.
SequencePairLikelihood
(implements pal.math.
UnivariateFunction
)
class pal.coalescent.
SerialCoalescentSimulator
(implements java.io.Serializable)
class pal.statistics.
ShimodairaHasegawaTest
(implements pal.misc.
Report
)
class pal.alignment.
SimpleCharacterAlignment
(implements pal.alignment.
CharacterAlignment
, pal.misc.
IdGroup
, pal.misc.
Report
, java.io.Serializable)
class pal.datatype.
SimpleDataType
(implements pal.datatype.
DataType
)
class pal.datatype.
AminoAcids
class pal.datatype.
Codons
class pal.datatype.
GeneralizedCodons
(implements java.io.Serializable)
class pal.datatype.
Nucleotides
class pal.datatype.
NumericDataType
class pal.datatype.
StateRemover
(implements java.io.Serializable)
class pal.datatype.
TwoStates
class pal.misc.
SimpleIdGroup
(implements pal.misc.
IdGroup
, pal.misc.
Nameable
, java.io.Serializable)
class pal.eval.
SimpleLikelihoodCalculator
(implements pal.eval.
LikelihoodCalculator
)
class pal.tree.
SimpleNode
(implements pal.tree.
AttributeNode
)
class pal.gui.
PositionedNode
class pal.substmodel.
SimpleSubstitutionModel
(implements pal.substmodel.
SubstitutionModel
)
class pal.misc.
SimpleSummarizable
(implements java.io.Serializable, pal.misc.
Summarizable
)
class pal.tree.
SimpleTree
(implements pal.misc.
Report
, java.io.Serializable, pal.tree.
Tree
, pal.misc.
Units
)
class pal.tree.
NeighborJoiningTree
class pal.tree.
ReadTree
class pal.tree.
UPGMATree
class pal.tree.
SUPGMATree
class pal.coalescent.
SkylinePlot
(implements pal.misc.
Report
, java.io.Serializable, pal.misc.
Units
)
class pal.tree.
SplitSystem
class pal.tree.
SplitUtils
class java.lang.Thread (implements java.lang.Runnable)
class pal.popgen.
LinkageDisequilibrium
(implements java.io.Serializable, pal.misc.
TableReport
)
class pal.util.
ThreeNumberSort
class java.lang.Throwable (implements java.io.Serializable)
class java.lang.Exception
class pal.alignment.
AlignmentParseException
class pal.coalescent.
CoalescentException
class pal.distance.
DistanceParseException
class pal.tree.
TreeParseException
class pal.xml.
XmlParseException
class pal.misc.
TimeOrderCharacterData
(implements pal.misc.
BranchLimits
, pal.misc.
IdGroup
, java.io.Serializable)
class pal.misc.
TimeStamp
class pal.gui.
TreePainter
(implements pal.gui.
Painter
)
class pal.gui.
TreePainterCircular
class pal.gui.
TreePainterNormal
class pal.tree.
TreeUtils
class pal.math.
UnivariateMinimum
class pal.math.
UrnModel
(implements java.io.Serializable)
class pal.misc.
Utils
class pal.util.
Version
class java.io.Writer
class java.io.PrintWriter
class pal.io.
OutputTarget
Interface Hierarchy
interface pal.misc.
BranchLimits
interface java.lang.Cloneable
interface pal.substmodel.
RateMatrix
(also extends pal.misc.
NamedParameterized
, pal.misc.
Report
, java.io.Serializable)
interface pal.coalescent.
CoalescentTree
interface java.lang.Comparable
interface pal.util.
DoubleKey
interface pal.util.
Comparable
interface pal.util.
Comparator
interface pal.coalescent.
DemographicTree
interface pal.util.
DoubleKeyCache
interface pal.misc.
ExternalParameterListener
interface pal.eval.
LikelihoodCalculator
interface pal.util.
Logger
interface pal.math.
MultivariateFunction
interface pal.math.
MFWithGradient
interface pal.misc.
Nameable
interface pal.gui.
Painter
interface pal.misc.
PalObjectListener
interface pal.misc.
Parameterized
interface pal.misc.
NamedParameterized
interface pal.substmodel.
RateMatrix
(also extends java.lang.Cloneable, pal.misc.
Report
, java.io.Serializable)
interface pal.substmodel.
SubstitutionModel
(also extends pal.misc.
Report
, java.io.Serializable)
interface pal.misc.
Report
interface pal.alignment.
AnnotationAlignment
(also extends pal.alignment.
Alignment
)
interface pal.alignment.
CharacterAlignment
(also extends pal.misc.
IdGroup
, java.io.Serializable, pal.misc.
TableReport
)
interface pal.substmodel.
RateMatrix
(also extends java.lang.Cloneable, pal.misc.
NamedParameterized
, java.io.Serializable)
interface pal.substmodel.
SubstitutionModel
(also extends pal.misc.
Parameterized
, java.io.Serializable)
interface java.io.Serializable
interface pal.alignment.
Alignment
(also extends pal.misc.
IdGroup
)
interface pal.alignment.
AnnotationAlignment
(also extends pal.misc.
Report
)
interface pal.substmodel.
AminoAcidModelID
interface pal.alignment.
CharacterAlignment
(also extends pal.misc.
IdGroup
, pal.misc.
Report
, pal.misc.
TableReport
)
interface pal.datatype.
CodonTable
interface pal.datatype.
DataType
interface pal.misc.
IdGroup
interface pal.alignment.
Alignment
(also extends java.io.Serializable)
interface pal.alignment.
AnnotationAlignment
(also extends pal.misc.
Report
)
interface pal.alignment.
CharacterAlignment
(also extends pal.misc.
Report
, java.io.Serializable, pal.misc.
TableReport
)
interface pal.tree.
Node
interface pal.tree.
AttributeNode
interface pal.substmodel.
NucleotideModelID
interface pal.substmodel.
RateMatrix
(also extends java.lang.Cloneable, pal.misc.
NamedParameterized
, pal.misc.
Report
)
interface pal.substmodel.
SubstitutionModel
(also extends pal.misc.
Parameterized
, pal.misc.
Report
)
interface pal.misc.
Summarizable
interface pal.tree.
Tree
(also extends pal.misc.
Units
)
interface pal.misc.
TableReport
interface pal.alignment.
CharacterAlignment
(also extends pal.misc.
IdGroup
, pal.misc.
Report
, java.io.Serializable)
interface pal.datatype.
TransitionPenaltyTable
interface pal.misc.
Units
interface pal.tree.
Tree
(also extends java.io.Serializable)
interface pal.math.
UnivariateFunction
interface pal.util.
XMLConstants
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