A B C D E F G H I J K L M N O P Q R S T U V W X Y

A

A_STATE - Static variable in class pal.datatype.Nucleotides
 
A_TO_C - Static variable in interface pal.util.XMLConstants
 
A_TO_G - Static variable in interface pal.util.XMLConstants
 
A_TO_T - Static variable in interface pal.util.XMLConstants
 
absoluteDistance(DistanceMatrix) - Method in class pal.distance.DistanceMatrix
compute absolute distance to second distance matrix
ABSTOL - Static variable in interface pal.misc.BranchLimits
maximum tolerated error when determining branch lengths
AbstractAlignment - class pal.alignment.AbstractAlignment.
abstract base class for any alignment data.
AbstractAlignment() - Constructor for class pal.alignment.AbstractAlignment
 
AbstractRateMatrix - class pal.substmodel.AbstractRateMatrix.
abstract base class for all rate matrices
AbstractRateMatrix(int) - Constructor for class pal.substmodel.AbstractRateMatrix
 
add(ExternalParameterListener, ExternalParameterListener) - Static method in class pal.misc.PalEventMulticaster
For managing ExternalParamterListeners Usage: ExternalParamterListener current = null; ...
add(PalObjectListener, PalObjectListener) - Static method in class pal.misc.PalEventMulticaster
For managing PalObjectListeners Usage: PalObjectListener current = null; ...
addChild(Node) - Method in class pal.tree.SimpleNode
add new child node
addChild(Node) - Method in interface pal.tree.Node
add new child node
addDistance(int, int, double) - Method in class pal.distance.DistanceMatrix
Adds a delta to both upper and lower triangle distances.
addDoubleKey(DoubleKey) - Method in class pal.util.DefaultCache
 
addDoubleKey(double, Object) - Method in class pal.util.DefaultCache
 
addDoubleKey(double, Object) - Method in interface pal.util.DoubleKeyCache
 
addExternalParameterListener(ExternalParameterListener) - Method in class pal.misc.ParameterizedDouble
 
addMapping(Identifier, Color) - Method in class pal.gui.NameColouriser
 
addMapping(Identifier, Rectangle) - Method in class pal.gui.LayoutTracker
 
addMapping(Identifier, String) - Method in class pal.misc.LabelMapping
 
addMapping(String, Color) - Method in class pal.gui.NameColouriser
 
addMapping(String, Rectangle) - Method in class pal.gui.LayoutTracker
 
addMapping(String, String) - Method in class pal.misc.LabelMapping
 
addMappings(String[], Color[]) - Method in class pal.gui.NameColouriser
 
addMappings(String[], String[]) - Method in class pal.misc.LabelMapping
 
addPalObjectListener(PalObjectListener) - Method in class pal.substmodel.AbstractRateMatrix
 
addPalObjectListener(PalObjectListener) - Method in class pal.substmodel.SimpleSubstitutionModel
Add a PalObjectListener to be notified of changes to the model.
addPalObjectListener(PalObjectListener) - Method in class pal.substmodel.CachedRateMatrix
 
addPalObjectListener(PalObjectListener) - Method in interface pal.substmodel.RateMatrix
Add a PalObjectListener to be notified of changes to the model.
addPalObjectListener(PalObjectListener) - Method in interface pal.substmodel.SubstitutionModel
Add a PalObjectListener to be notified of changes to the model.
AIC(double, int) - Static method in class pal.statistics.PenalizedLikelihood
Akaike (AIC) correction (Akaike 1974)
AICC(double, int, int) - Static method in class pal.statistics.PenalizedLikelihood
Second-order Akaike (AICC) correction (Hurvich and Tsai 1989)
alias - Variable in class pal.alignment.StrippedAlignment
 
alias - Variable in class pal.alignment.SitePattern
site -> site pattern
Alignment - interface pal.alignment.Alignment.
interface for any alignment data.
ALIGNMENT - Static variable in interface pal.util.XMLConstants
 
AlignmentDistanceMatrix - class pal.distance.AlignmentDistanceMatrix.
compute distance matrix (observed and ML) from alignment (SitePattern)
AlignmentDistanceMatrix(SitePattern) - Constructor for class pal.distance.AlignmentDistanceMatrix
compute observed distances
AlignmentDistanceMatrix(SitePattern, boolean) - Constructor for class pal.distance.AlignmentDistanceMatrix
compute observed distances
AlignmentDistanceMatrix(SitePattern, SubstitutionModel) - Constructor for class pal.distance.AlignmentDistanceMatrix
compute maximum-likelihood distances
AlignmentDistanceMatrix(SitePattern, SubstitutionModel, boolean) - Constructor for class pal.distance.AlignmentDistanceMatrix
compute maximum-likelihood distances
AlignmentParseException - exception pal.alignment.AlignmentParseException.
Exception thrown by ReadAlignment
AlignmentParseException() - Constructor for class pal.alignment.AlignmentParseException
 
AlignmentParseException(String) - Constructor for class pal.alignment.AlignmentParseException
 
AlignmentUtils - class pal.alignment.AlignmentUtils.
Helper utilities for alignments.
AlignmentUtils() - Constructor for class pal.alignment.AlignmentUtils
 
all - Static variable in class pal.datatype.IUPACPenaltyTable
 
alpha - Variable in class pal.coalescent.ConstExpGrowth
ratio of pop. sizes
alpha - Variable in class pal.coalescent.ExpandingPopulation
ratio of pop. sizes
ALPHA - Static variable in interface pal.util.XMLConstants
 
ALPHA_PARAMETERIZATION - Static variable in class pal.coalescent.ConstExpGrowth
Constants for different parameterizations
alphaSE - Variable in class pal.coalescent.ConstExpGrowth
standard error of time alpha
alphaSE - Variable in class pal.coalescent.ExpandingPopulation
standard error of time alpha
AMINO_ACID_DESCRIPTION - Static variable in interface pal.datatype.DataType
amino acid name (for XML and human readability)
AminoAcidAlignment - class pal.alignment.AminoAcidAlignment.
generates an amino acid alignment from a nucleotide alignment.
AminoAcidAlignment(Alignment) - Constructor for class pal.alignment.AminoAcidAlignment
Constructs an AminoAcidAlignment from a given alignment (which should be a nucleotide alignment), from codon position 0.
AminoAcidAlignment(Alignment, int) - Constructor for class pal.alignment.AminoAcidAlignment
Constructor
AminoAcidAlignment(Alignment, int, CodonTable) - Constructor for class pal.alignment.AminoAcidAlignment
Constructor
AminoAcidModel - class pal.substmodel.AminoAcidModel.
base class of rate matrices for amino acids
AminoAcidModel(double[]) - Constructor for class pal.substmodel.AminoAcidModel
 
AminoAcidModelID - interface pal.substmodel.AminoAcidModelID.
interface for IDs of amino acid models
AminoAcids - class pal.datatype.AminoAcids.
implements DataType for amino acids
AMINOACIDS - Static variable in interface pal.datatype.DataType
 
AminoAcids() - Constructor for class pal.datatype.AminoAcids
 
ANCESTRAL_MU_RATE - Static variable in interface pal.util.XMLConstants
 
ANCESTRAL_POP_SIZE - Static variable in interface pal.util.XMLConstants
 
AnnotationAlignment - interface pal.alignment.AnnotationAlignment.
The AnnotationAlignment interface is designed to provide annotation for an alignment.
ANONYMOUS - Static variable in class pal.misc.Identifier
 
attName - Variable in class pal.gui.TreePainter
 
Attribute - class pal.misc.Attribute.
An immutable attribute has a name and value.
ATTRIBUTE - Static variable in interface pal.util.XMLConstants
 
Attribute(String, Object) - Constructor for class pal.misc.Attribute
 
Attribute(String, String, String) - Constructor for class pal.misc.Attribute
 
AttributeNode - interface pal.tree.AttributeNode.
interface for a node (includes branch) in a binary/non-binary rooted/unrooted tree.

B

BACKGROUND - Static variable in class pal.gui.TreePainter
 
backgroundFixed - Variable in class pal.mep.WindowedMutationRate
 
BACKWARDS - Static variable in interface pal.util.XMLConstants
 
BEALE_SORENSON_HESTENES_STIEFEL_UPDATE - Static variable in class pal.math.ConjugateGradientSearch
 
bestH - Variable in class pal.statistics.ShimodairaHasegawaTest
number of maximum likelihood hypothesis
bestH - Variable in class pal.statistics.KishinoHasegawaTest
number of maximum likelihood hypothesis
biasCorrectedEstimate(double, double[]) - Static method in class pal.statistics.BootstrapStatistics
correct a statistic thetaHat for its bias
BIC(double, int, int) - Static method in class pal.statistics.PenalizedLikelihood
BIC correction (Schwarz 1978)
Binomial - class pal.math.Binomial.
Binomial coefficients
Binomial() - Constructor for class pal.math.Binomial
 
BLOSUM62 - class pal.substmodel.BLOSUM62.
BLOSUM62 model of amino acid evolution
BLOSUM62 - Static variable in interface pal.substmodel.AminoAcidModelID
 
BLOSUM62 - Static variable in interface pal.util.XMLConstants
 
BLOSUM62(double[]) - Constructor for class pal.substmodel.BLOSUM62
constructor
BOOLEAN - Static variable in class pal.misc.Attribute
 
BOOTSTRAP_SUPPORT_COLOUR - Static variable in class pal.gui.TreePainter
 
bootstrap() - Method in class pal.alignment.BootstrappedAlignment
bootstrap alignment
BootstrappedAlignment - class pal.alignment.BootstrappedAlignment.
generates bootstrapped alignments from a raw alignment
BootstrappedAlignment(Alignment) - Constructor for class pal.alignment.BootstrappedAlignment
Constructor
BootstrapStatistics - class pal.statistics.BootstrapStatistics.
computation of bootstrap estimators (BIAS, SD, VAR, CI) given a statistic theta and corresponding bootstrap replicates.
BootstrapStatistics() - Constructor for class pal.statistics.BootstrapStatistics
 
BOTTOMBORDER - Static variable in class pal.gui.TreePainterNormal
 
BOTTOMBORDER - Static variable in class pal.gui.TreePainterCircular
 
BoundsCheckedFunction - class pal.math.BoundsCheckedFunction.
returns a very large number instead of the function value if arguments are out of bound (useful for minimization with minimizers that don't check argument boundaries)
BoundsCheckedFunction(MultivariateFunction) - Constructor for class pal.math.BoundsCheckedFunction
construct bound-checked multivariate function (a large number will be returned on function evaluation if argument is out of bounds; default is 1000000)
BoundsCheckedFunction(MultivariateFunction, double) - Constructor for class pal.math.BoundsCheckedFunction
construct constrained multivariate function
BranchLimits - interface pal.misc.BranchLimits.
limits for branch lengths

C

C_STATE - Static variable in class pal.datatype.Nucleotides
 
C_TO_G - Static variable in interface pal.util.XMLConstants
 
C_TO_T - Static variable in interface pal.util.XMLConstants
 
CachedRateMatrix - class pal.substmodel.CachedRateMatrix.
a cached rate matrix.
CachedRateMatrix(CachedRateMatrix) - Constructor for class pal.substmodel.CachedRateMatrix
 
CachedRateMatrix(RateMatrix, DoubleKeyCache) - Constructor for class pal.substmodel.CachedRateMatrix
 
CachedRateMatrix(RateMatrix, int) - Constructor for class pal.substmodel.CachedRateMatrix
 
calcContigencyChiSquare(int) - Method in class pal.statistics.ContigencyTable
This calculates the probability in the normal approach, using the Chi Square as the test statistic.
calcMonteCarloExactTest(int) - Method in class pal.statistics.ContigencyTable
This calculates the probability in the normal permutation approach, using the method described by Weir, B.
calcRapidContigencyChiSquare(int) - Method in class pal.statistics.ContigencyTable
This calculates the probability in a rapid approach, using the Chi Square as the test statistic.
calcRapidMonteCarloExactTest(int) - Method in class pal.statistics.ContigencyTable
This calculates the probability in the rapid permutational approach, using the method described by Weir, B.
calculateLogLikelihood() - Method in class pal.eval.SimpleLikelihoodCalculator
compute log-likelihood for current tree (fixed branch lengths and model) return log-likelihood
calculateLogLikelihood() - Method in interface pal.eval.LikelihoodCalculator
 
calculateLogLikelihood() - Method in class pal.eval.FastLikelihoodCalculator
 
calculatePositions() - Method in class pal.gui.PositionedNode
 
cdf(double, double) - Static method in class pal.statistics.ExponentialDistribution
cumulative density function of the exponential distribution
cdf(double, double) - Static method in class pal.statistics.ChiSquareDistribution
cumulative density function of the chi-square distribution
cdf(double, double[]) - Static method in class pal.statistics.DiscreteStatistics
compute the cumulative probability Pr(x <= z) for a given z and a distribution of x
cdf(double, double[], int[]) - Static method in class pal.statistics.DiscreteStatistics
compute the cumulative probability Pr(x <= z) for a given z and a distribution of x
cdf(double, double, double) - Static method in class pal.statistics.GammaDistribution
cumulative density function of the Gamma distribution
cdf(double, double, double) - Static method in class pal.statistics.NormalDistribution
cumulative density function
cdf(double, double, double) - Static method in class pal.statistics.ParetoDistribution
cumulative density function of the Pareto distribution
CharacterAlignment - interface pal.alignment.CharacterAlignment.
This interface is designed to hold quantitative character states.
checkDirection(double[], double[]) - Method in class pal.math.LineFunction
check direction vector.
checkPoint(double[]) - Method in class pal.math.LineFunction
check (and modify, if necessary) whether a point lies properly within the predefined bounds
checkVariables(double[], double[], boolean[]) - Method in class pal.math.LineFunction
determine active variables at a point p and corresponding gradient grad (if a component of p lies on a border and the corresponding component of the gradient points out of the border the variable is considered inactive)
ChiSquareDistribution - class pal.statistics.ChiSquareDistribution.
chi-square distribution (distribution of sum of squares of n uniform random variables) (Parameter: n; mean: n; variance: 2*n) The chi-square distribution is a special case of the Gamma distribution (shape parameter = n/2.0, scale = 2.0).
ChiSquareDistribution() - Constructor for class pal.statistics.ChiSquareDistribution
 
ChiSquareTest - class pal.statistics.ChiSquareTest.
chi-square test
ChiSquareTest() - Constructor for class pal.statistics.ChiSquareTest
 
ChiSquareValue - class pal.eval.ChiSquareValue.
computes chi-square value of a (parameterized) tree for its set of parameters (e.g., branch lengths) and a given distance matrix
ChiSquareValue(DistanceMatrix, boolean) - Constructor for class pal.eval.ChiSquareValue
initialization
choose(double, double) - Method in class pal.math.Binomial
Binomial coefficient n choose k
chromosome - Variable in class pal.alignment.MultiLocusAnnotatedAlignment
used to designate chromosome
chromosome - Variable in class pal.alignment.SimpleAnnotatedAlignment
used to designate chromosome
chromosome - Variable in class pal.alignment.IndelAnnotatedAlignment
used to designate chromosome
chromosomePosition - Variable in class pal.alignment.MultiLocusAnnotatedAlignment
used to designate position along chromosome
chromosomePosition - Variable in class pal.alignment.SimpleAnnotatedAlignment
used to designate position along chromosome
chromosomePosition - Variable in class pal.alignment.IndelAnnotatedAlignment
used to designate position along chromosome
circleString(String, double, double, int) - Method in class pal.gui.CircularGraphics
 
CIRCULAR_BW - Static variable in class pal.gui.TreeComponent
 
CIRCULAR_COLOR - Static variable in class pal.gui.TreeComponent
 
CircularGraphics - class pal.gui.CircularGraphics.
 
CircularGraphics(Graphics, double, double, int, int, int, int) - Constructor for class pal.gui.CircularGraphics
 
CircularGraphics(Graphics, double, double, int, int, int, int, boolean) - Constructor for class pal.gui.CircularGraphics
 
CLADE_PROBABILITY - Static variable in interface pal.tree.AttributeNode
attribute name for the probability of the clade defined by an internal node.
cladeCount(Node, Vector) - Static method in class pal.tree.RootedTreeUtils
 
clearCache() - Method in class pal.util.DefaultCache
 
clearCache() - Method in interface pal.util.DoubleKeyCache
 
ClockTree - class pal.tree.ClockTree.
provides parameter interface to a clock tree (parameters are the minimal node height differences at each internal node)
ClockTree() - Constructor for class pal.tree.ClockTree
 
ClockTree(Tree) - Constructor for class pal.tree.ClockTree
take any tree and afford it with an interface suitable for a clock-like tree (parameters are the minimal node height differences at each internal node).
clone() - Method in class pal.mep.MutationRateModel
 
clone() - Method in class pal.mep.ConstantMutationRate
 
clone() - Method in class pal.mep.WindowedMutationRate
 
clone() - Method in class pal.mep.SteppedMutationRate
 
clone() - Method in class pal.substmodel.AbstractRateMatrix
 
clone() - Method in class pal.substmodel.SimpleSubstitutionModel
A non shallow implementation of clone()
clone() - Method in class pal.substmodel.RateDistribution
 
clone() - Method in class pal.substmodel.CachedRateMatrix
A non shallow implementation of clone()
clone() - Method in class pal.substmodel.HKY
 
clone() - Method in interface pal.substmodel.RateMatrix
 
clone() - Method in class pal.substmodel.GTR
 
clone() - Method in interface pal.substmodel.SubstitutionModel
A non shallow implementation of clone()
clone() - Method in class pal.util.DefaultCache
 
clone() - Method in interface pal.util.DoubleKeyCache
 
clone() - Method in class pal.coalescent.DemographicModel
 
clone() - Method in class pal.coalescent.ConstantPopulation
 
clone() - Method in class pal.coalescent.ExponentialGrowth
 
clone() - Method in class pal.coalescent.ConstExpGrowth
 
clone() - Method in class pal.coalescent.ExpandingPopulation
 
clone(TimeOrderCharacterData) - Static method in class pal.misc.TimeOrderCharacterData
Returns a clone of the specified TimeOrderCharacterData
COALESCENT - Static variable in interface pal.util.XMLConstants
 
COALESCENT - Static variable in class pal.coalescent.CoalescentIntervals
Denotes and interval after which a coalescent event is observed (i.e. the number of lineages is smaller in the next interval)
CoalescentException - exception pal.coalescent.CoalescentException.
Exceptions to do with coalescent models et cetera.
CoalescentException() - Constructor for class pal.coalescent.CoalescentException
Parameterless constructor.
CoalescentException(String) - Constructor for class pal.coalescent.CoalescentException
Constructor taking message.
CoalescentIntervals - class pal.coalescent.CoalescentIntervals.
A series of coalescent intervals representing the time order information contained in a (serial) clock-constrained tree.
CoalescentIntervals() - Constructor for class pal.coalescent.CoalescentIntervals
Parameterless constructor.
CoalescentIntervals(int) - Constructor for class pal.coalescent.CoalescentIntervals
Constructor taking a number of intervals.
CoalescentSimulator - class pal.coalescent.CoalescentSimulator.
Simulates a set of coalescent intervals given a demographic model.
CoalescentSimulator() - Constructor for class pal.coalescent.CoalescentSimulator
 
CoalescentTree - interface pal.coalescent.CoalescentTree.
interface defining a parameterized tree that includes demographic information.
CODON_DESCRIPTION - Static variable in interface pal.datatype.DataType
codon name (for XML and human readability)
CodonAlignment - class pal.alignment.CodonAlignment.
generates an codon alignment from a nucleotide alignment.
CodonAlignment(Alignment) - Constructor for class pal.alignment.CodonAlignment
Constructs an CodonAlignment from a given alignment (which should be a nucleotide alignment), from codon position 0.
CodonAlignment(Alignment, int) - Constructor for class pal.alignment.CodonAlignment
Constructor
CodonAlignment(Alignment, int, GeneralizedCodons) - Constructor for class pal.alignment.CodonAlignment
Constructor
CodonModel - class pal.substmodel.CodonModel.
base class for nucleotide rate matrices
CodonModel(double[]) - Constructor for class pal.substmodel.CodonModel
 
Codons - class pal.datatype.Codons.
implements DataType for all Codons (including terminators).
CODONS - Static variable in interface pal.datatype.DataType
 
Codons() - Constructor for class pal.datatype.Codons
 
CodonTable - interface pal.datatype.CodonTable.
Describes a device for translating Nucleotide triplets or codon indices into amino acid codes
CodonTableFactory - class pal.datatype.CodonTableFactory.
Generates CodonTables
CodonTableFactory() - Constructor for class pal.datatype.CodonTableFactory
 
CodonTableUtils - class pal.datatype.CodonTableUtils.
Nucleotide Translating Utilities
CodonTableUtils() - Constructor for class pal.datatype.CodonTableUtils
 
collectProportions(Tree, Vector) - Static method in class pal.tree.RootedTreeUtils
 
collectTaxa(Node, Hashtable) - Static method in class pal.tree.RootedTreeUtils
Collects all of the names of the taxa in the tree into a hashtable.
combineMultivariateFunction(MultivariateFunction, Parameterized[]) - Static method in class pal.misc.Utils
Creates an interface between a parameterised object to allow it to act as a multivariate minimum.
Comparable - interface pal.util.Comparable.
interface for an object that is comparable.
ComparableDouble - class pal.util.ComparableDouble.
This class is unfortunate but necessary to conform to JDK 1.1
ComparableDouble(double) - Constructor for class pal.util.ComparableDouble
 
Comparator - interface pal.util.Comparator.
interface for an object that can compare other objects for the purposes of ordering them.
compare(double[][]) - Method in class pal.statistics.KishinoHasegawaTest
Compare all given hypotheses to the best (ML) hypothesis and store results in public arrays delta, deltaSE, pval (which will automatically be created by this procedure).
compare(double[][], int) - Method in class pal.statistics.ModelSupport
Determine posterior probabilties and support values for each hypothesis and store results in public arrays posterior, support etc which will automatically be created by this procedure.
compare(double[][], int) - Method in class pal.statistics.ShimodairaHasegawaTest
Compare all given hypotheses to the best (ML) hypothesis and store results in public arrays delta, pval (which will automatically be created by this procedure).
compare(double[][], int[]) - Method in class pal.statistics.KishinoHasegawaTest
Compare all given hypotheses to the best (ML) hypothesis and store results in public arrays delta, deltaSE, pval (which will automatically be created by this procedure).
compare(double[][], int[], int) - Method in class pal.statistics.ModelSupport
Determine posterior probabilties and support values for each hypothesis and store results in public arrays posterior, support etc which will automatically be created by this procedure.
compare(double[][], int[], int) - Method in class pal.statistics.ShimodairaHasegawaTest
Compare all given hypotheses to the best (ML) hypothesis and store results in public arrays delta, pval (which will automatically be created by this procedure).
compare(double[], int[]) - Static method in class pal.statistics.ChiSquareTest
chi square test
compare(Object, Object) - Method in interface pal.util.Comparator
Returns a number representing the ordering relationship that the two objects have.
compareTo(Object) - Method in class pal.misc.Identifier
 
compareTo(Object) - Method in class pal.util.ComparableDouble
 
compareTo(Object) - Method in interface pal.util.Comparable
Returns a number representing the ordering relationship that the object has with the given object.
compute() - Method in class pal.eval.LikelihoodValue
compute log-likelihood for current tree (fixed branch lengths and model) return log-likelihood
compute() - Method in class pal.eval.DemographicLikelihoodValue
compute log-likelihood for current branch lengths and model return negative log-likelihood
compute() - Method in class pal.eval.ChiSquareValue
compute (weighted) least-square value for current tree (fixed branch lengths) return chi-square value
compute() - Method in class pal.eval.DemographicValue
compute log-likelihood for current model return negative log-likelihood
computeAllDistances(Tree, int, double[], double[], boolean, double) - Static method in class pal.tree.TreeUtils
 
computeBIAS(double, double[]) - Static method in class pal.statistics.BootstrapStatistics
compute bias of a statistic thetaHat in estimating the true theta
computeClassic() - Method in class pal.coalescent.SkylinePlot
Compute classic skyline plot
computeDemoLogLikelihood() - Method in interface pal.coalescent.DemographicTree
 
computeDemoLogLikelihood() - Method in class pal.coalescent.DemographicClockTree
Returns the likelihood of the current demographic model, given the current branch lengths.
computeDistance(Tree, int, int) - Static method in class pal.tree.TreeUtils
compute distance between two external nodes
computeDistances() - Method in class pal.tree.TreeDistanceMatrix
recompute distances (actual branch lengths)
computeDistances(boolean, double) - Method in class pal.tree.TreeDistanceMatrix
recompute distances
computeEpsilon() - Static method in class pal.math.MachineAccuracy
compute EPSILON from scratch
computeGeneralized(double) - Method in class pal.coalescent.SkylinePlot
Compute generalized skyline plot
computeGradient(double[], double[]) - Method in interface pal.math.MFWithGradient
compute gradient at a point
computeLogLikelihood() - Method in class pal.eval.DemographicValue
 
computeLogLikelihood(DemographicModel) - Method in class pal.coalescent.CoalescentIntervals
Returns the log likelihood of this set of coalescent intervals, given a demographic model.
computeLogLikelihood(double, double, int) - Method in class pal.coalescent.DemographicModel
Returns the likelihood of a given *coalescent* interval
computeLogLikelihood(double, double, int, int) - Method in class pal.coalescent.DemographicModel
Returns the likelihood of a given interval,coalescent or otherwise.
computeSD(double[]) - Static method in class pal.statistics.BootstrapStatistics
compute standard error (accuracy) of a statistic thetaHat
computeVAR(double[]) - Static method in class pal.statistics.BootstrapStatistics
compute variance of a statistic thetaHat
concatAlignments(Alignment[], DataType) - Static method in class pal.alignment.AlignmentUtils
Concatenates an array of alignments such that the resulting alignment is all of the sub alignments place along side each other
ConcatenatedAlignment - class pal.alignment.ConcatenatedAlignment.
concatenates a list of alignments to one single alignment, increasing the number of sites
ConcatenatedAlignment(Alignment[]) - Constructor for class pal.alignment.ConcatenatedAlignment
concatenate alignments
ConcatenatedAnnotatedAlignment - class pal.alignment.ConcatenatedAnnotatedAlignment.
This is an annotation version of the ConcatenatedAlignment Unlike normal ConcatenatedAlignment, it permits for merges with different numbers of sequences.
ConcatenatedAnnotatedAlignment(AnnotationAlignment[], boolean, boolean) - Constructor for class pal.alignment.ConcatenatedAnnotatedAlignment
concatenate alignments
ConjugateDirectionSearch - class pal.math.ConjugateDirectionSearch.
methods for minimization of a real-valued function of several variables without using derivatives (Brent's modification of a conjugate direction search method proposed by Powell)
ConjugateDirectionSearch() - Constructor for class pal.math.ConjugateDirectionSearch
constructor
ConjugateGradientSearch - class pal.math.ConjugateGradientSearch.
minimization of a real-valued function of several variables using a the nonlinear conjugate gradient method where several variants of the direction update are available (Fletcher-Reeves, Polak-Ribiere, Beale-Sorenson, Hestenes-Stiefel) and bounds are respected.
ConjugateGradientSearch() - Constructor for class pal.math.ConjugateGradientSearch
 
ConjugateGradientSearch(int) - Constructor for class pal.math.ConjugateGradientSearch
 
conjugateGradientStyle - Variable in class pal.math.ConjugateGradientSearch
conjugateGradientStyle determines the method for the conjugate gradient direction update update (0 -> Fletcher-Reeves, 1 -> Polak-Ribiere, 2 -> Beale-Sorenson, Hestenes-Stiefel), the default is 2.
CONST_EXP_GROWTH - Static variable in interface pal.util.XMLConstants
 
CONSTANT_MUTATION_RATE - Static variable in interface pal.util.XMLConstants
 
CONSTANT_POPULATION - Static variable in interface pal.util.XMLConstants
constant population demographic model type
ConstantMutationRate - class pal.mep.ConstantMutationRate.
This class models a constant mutation rate (parameter: mu = mutation rate).
ConstantMutationRate(double, int) - Constructor for class pal.mep.ConstantMutationRate
Construct mutation rate model of a give rate in given units.
ConstantMutationRate(int) - Constructor for class pal.mep.ConstantMutationRate
Construct demographic model with default settings
ConstantPopulation - class pal.coalescent.ConstantPopulation.
This class models coalescent intervals for a constant population (parameter: N0=present-day population size).
ConstantPopulation(double, int) - Constructor for class pal.coalescent.ConstantPopulation
Construct demographic model of a constant population size.
ConstantPopulation(int) - Constructor for class pal.coalescent.ConstantPopulation
Construct demographic model with default settings
ConstExpGrowth - class pal.coalescent.ConstExpGrowth.
This class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.
ConstExpGrowth(double, double, double, int, int) - Constructor for class pal.coalescent.ConstExpGrowth
Construct demographic model of an expanding population
ConstExpGrowth(int, int) - Constructor for class pal.coalescent.ConstExpGrowth
Construct demographic model with default settings
containsClade(Node, Node) - Static method in class pal.tree.RootedTreeUtils
 
containsNovelTaxa(Node, Hashtable) - Static method in class pal.tree.RootedTreeUtils
 
containsSubtree(Node, Node) - Static method in class pal.tree.RootedTreeUtils
 
ContigencyTable - class pal.statistics.ContigencyTable.
Class for permuting contigency tables and determining the likelihood of the table.
ContigencyTable(int) - Constructor for class pal.statistics.ContigencyTable
constructor for Contigency table
convertNucleotideToAminoAcid(char[], int, int, boolean, CodonTable) - Static method in class pal.datatype.CodonTableUtils
Translates a Nucleotide sequence into a Amino Acid sequence
convertNucleotideToAminoAcid(String, int, int, boolean, CodonTable) - Static method in class pal.datatype.CodonTableUtils
Translates a Nucleotide sequence into a Amino Acid sequence
convertNucleotideToCodon(char[], int, int, boolean) - Method in class pal.datatype.GeneralizedCodons
Translates a Nucleotide sequence into a Codon sequence
convertNucleotideToCodon(String, int, int, boolean) - Method in class pal.datatype.GeneralizedCodons
Translates a Nucleotide sequence into a Codon sequence
copy(double[][], double[][]) - Static method in class pal.misc.Utils
Copies all of source into dest - assumes dest to be large enough
copy(double[], double[]) - Method in class pal.math.MultivariateMinimum
Copy source vector into target vector
countUnknowns(Alignment, DataType) - Static method in class pal.alignment.AlignmentUtils
Tests the characters of an alignment to see if there are any characters that are not within a data type.
CPREV - class pal.substmodel.CPREV.
CPREV model of amino acid evolution (J.Adachi et al. 2000)
CPREV - Static variable in interface pal.substmodel.AminoAcidModelID
 
CPREV - Static variable in interface pal.util.XMLConstants
 
CPREV(double[]) - Constructor for class pal.substmodel.CPREV
constructor
CR - Variable in class pal.math.DifferentialEvolution
Crossing over factor (default 0.9)
createAlignmentElement(Alignment, Document) - Static method in class pal.xml.ElementFactory
 
createAttributeElement(Attribute, Document) - Static method in class pal.xml.ElementFactory
 
createDemographicModelElement(DemographicModel, Document) - Static method in class pal.xml.ElementFactory
Creates an XML element representing a demographic model.
createEdgeNodeElement(Node, Document) - Static method in class pal.xml.ElementFactory
 
createFrequenciesElement(double[], Document) - Static method in class pal.xml.ElementFactory
Creates a DOM element associated with the given document representing the given equilibrium frequencies of a rate matrix.
createIdGroup(int) - Static method in class pal.misc.IdGenerator
generates a group of unique identifiers numbered from zero.
createMutationRateModelElement(MutationRateModel, Document) - Static method in class pal.xml.ElementFactory
Creates an XML element representing a mutation rate model.
createNode() - Static method in class pal.tree.NodeFactory
create a node
createNode(Node) - Static method in class pal.tree.NodeFactory
constructor used to clone a node and all children
createNodeElement(Node, Document) - Static method in class pal.xml.ElementFactory
 
createNodeElement(Node, Document, boolean) - Static method in class pal.xml.ElementFactory
 
createNodeList() - Method in class pal.tree.ParameterizedTree
This method is called to ensure that the calls to other methods in this interface are valid.
createNodeList() - Method in class pal.tree.SimpleTree
count and list external and internal nodes and compute heights of each node
createNodeList() - Method in interface pal.tree.Tree
This method is called to ensure that the calls to other methods in this interface are valid.
createParameterElement(String, double, Document) - Static method in class pal.xml.ElementFactory
Creates an XML element representing a parameter.
createRateMatrixElement(RateMatrix, Document) - Static method in class pal.xml.ElementFactory
 
createSequenceElement(Identifier, String, Document) - Static method in class pal.xml.ElementFactory
 
createTimeDataElement(TimeOrderCharacterData, Document) - Static method in class pal.xml.ElementFactory
 
createTranslator(int) - Static method in class pal.datatype.CodonTableFactory
Creates a translator of a given types
createTreeElement(Tree, Document, boolean) - Static method in class pal.xml.ElementFactory
 
createUniversalTranslator() - Static method in class pal.datatype.CodonTableFactory
 

D

DATA_TYPE - Static variable in interface pal.util.XMLConstants
 
DATA_TYPE_ID - Static variable in interface pal.util.XMLConstants
 
dataType - Variable in class pal.alignment.AbstractAlignment
data type
dataType - Variable in class pal.substmodel.AbstractRateMatrix
data type
DataType - interface pal.datatype.DataType.
interface for sequence data types
DataTypeUtils - class pal.datatype.DataTypeUtils.
helper class for sequence data types.
DataTypeUtils() - Constructor for class pal.datatype.DataTypeUtils
 
DatedTipsClockTree - class pal.tree.DatedTipsClockTree.
provides parameter interface to a clock tree with dated tips, following A.
DatedTipsClockTree(Tree) - Constructor for class pal.tree.DatedTipsClockTree
Constructor without TimeOrderCharacterData.
DatedTipsClockTree(Tree, ParameterizedDouble, TimeOrderCharacterData, int, int) - Constructor for class pal.tree.DatedTipsClockTree
take any tree and afford it with an interface suitable for a clock-like tree with dated tips (parameters are the minimal node height differences at each internal node and the rate).
DatedTipsClockTree(Tree, TimeOrderCharacterData, boolean) - Constructor for class pal.tree.DatedTipsClockTree
take any tree and afford it with an interface suitable for a clock-like tree with dated tips (parameters are the minimal node height differences at each internal node and the rate).
Dayhoff - class pal.substmodel.Dayhoff.
Dayhoff model for amino acid evolution
DAYHOFF - Static variable in interface pal.substmodel.AminoAcidModelID
 
DAYHOFF - Static variable in interface pal.util.XMLConstants
 
Dayhoff(double[]) - Constructor for class pal.substmodel.Dayhoff
constructor
DAYS - Static variable in interface pal.misc.Units
 
DAYS - Static variable in interface pal.util.XMLConstants
 
debug(Object) - Method in class pal.util.Log
 
debug(Object) - Method in interface pal.util.Logger
 
DEFAULT_CODON_TRANSLATOR - Static variable in class pal.alignment.CodonAlignment
 
DEFAULT_INSTANCE - Static variable in class pal.datatype.GeneralizedCodons
An instance for Nucleotides because what is the point of reconstructing this class
DEFAULT_INSTANCE - Static variable in class pal.datatype.AminoAcids
 
DEFAULT_INSTANCE - Static variable in class pal.datatype.Nucleotides
 
DEFAULT_LENGTH - Static variable in interface pal.misc.BranchLimits
default branch length
DefaultCache - class pal.util.DefaultCache.
 
DefaultCache() - Constructor for class pal.util.DefaultCache
 
DefaultCache(int) - Constructor for class pal.util.DefaultCache
 
defaultStep - Variable in class pal.math.ConjugateGradientSearch
defaultStep is a steplength parameter and should be set equal to the expected distance from the solution (in a line search) exceptionally small or large values of defaultStep lead to slower convergence on the first few iterations (the step length itself is adapted during search), the default value is 1.0
delta - Variable in class pal.statistics.ShimodairaHasegawaTest
log-likelihood difference to maximum likelihood hypothesis
delta - Variable in class pal.statistics.KishinoHasegawaTest
log-likelihood difference to maximum likelihood hypothesis
deltaL - Variable in class pal.statistics.ModelSupport
log-likelihood differences to the best tree
deltaSE - Variable in class pal.statistics.KishinoHasegawaTest
estimated error of log-likelihood differences
DEMOGRAPHIC_MODEL - Static variable in interface pal.util.XMLConstants
 
DemographicClockTree - class pal.coalescent.DemographicClockTree.
Provides parameter interface to a clock-like genealogy which is assumed to have some demographic pattern of theta (diversity) as well as branch parameters (the minimal node height differences at each internal node).
DemographicClockTree(Tree, DemographicModel) - Constructor for class pal.coalescent.DemographicClockTree
take any tree and afford it with an interface suitable for a clock-like genealogy, under a certain demographic assumption.
DemographicLikelihoodValue - class pal.eval.DemographicLikelihoodValue.
Estimates the likelihood for a tree using a specified model of sequence evolution and a sequence alignment and a specific demographic model as a prior on coalescent intervals.
DemographicLikelihoodValue(SitePattern) - Constructor for class pal.eval.DemographicLikelihoodValue
Parameter taking a site pattern.
DemographicModel - class pal.coalescent.DemographicModel.
This abstract class contains methods that are of general use for modelling coalescent intervals given a demographic model.
DemographicModel() - Constructor for class pal.coalescent.DemographicModel
 
DemographicTree - interface pal.coalescent.DemographicTree.
interface defining a parameterized tree that includes demographic information.
DemographicValue - class pal.eval.DemographicValue.
estimates demographic parameters by maximising the coalescent prior for a tree with given branch lengths.
DemographicValue() - Constructor for class pal.eval.DemographicValue
 
diagonalHessian(MultivariateFunction, double[]) - Static method in class pal.math.NumericalDerivative
determine diagonal of Hessian
DifferentialEvolution - class pal.math.DifferentialEvolution.
global minimization of a real-valued function of several variables without using derivatives using a genetic algorithm (Differential Evolution)
DifferentialEvolution(int) - Constructor for class pal.math.DifferentialEvolution
construct DE optimization modul (population size is selected automatically) DE web page: http://www.icsi.berkeley.edu/~storn/code.html
DifferentialEvolution(int, int) - Constructor for class pal.math.DifferentialEvolution
construct optimization modul
dimension - Variable in class pal.substmodel.AbstractRateMatrix
dimension
dimension - Variable in class pal.substmodel.MatrixExponential
dimension of rate matrix
DIRECTION - Static variable in interface pal.util.XMLConstants
 
DiscreteStatistics - class pal.statistics.DiscreteStatistics.
simple discrete statistics (mean, variance, cumulative probability, quantiles etc.)
DiscreteStatistics() - Constructor for class pal.statistics.DiscreteStatistics
 
displayDecimal(PrintWriter, double, int) - Method in class pal.io.FormattedOutput
print decimal number with a prespecified number of digits after the point
displayInteger(PrintWriter, int, int) - Method in class pal.io.FormattedOutput
print integer, aligned to a reference number, (introducing space at the left side)
displayIntegerWhite(PrintWriter, int) - Method in class pal.io.FormattedOutput
print whitespace of length of a string displaying a given integer
displayLabel(PrintWriter, String, int) - Method in class pal.io.FormattedOutput
print label with a prespecified length (label will be shortened or spaces will introduced, if necessary)
displayLabel(PrintWriter, String, int, boolean) - Static method in class pal.tree.Local
print label with a prespecified length (label will be shortened or spaces will introduced, if necessary)
distance - Variable in class pal.distance.DistanceMatrix
distances [seq1][seq2]
distance - Variable in class pal.distance.PairwiseDistance
last estimated distance
DistanceMatrix - class pal.distance.DistanceMatrix.
storage for pairwise distance matrices. features: - printing in in PHYLIP format, - computation of (weighted) squared distance to other distance matrix - Fills in all of array...
DistanceMatrix() - Constructor for class pal.distance.DistanceMatrix
constructor
DistanceMatrix(DistanceMatrix) - Constructor for class pal.distance.DistanceMatrix
constructor that takes a distance matrix and clones the distances but uses the same idGroup.
DistanceMatrix(DistanceMatrix, IdGroup) - Constructor for class pal.distance.DistanceMatrix
constructor that takes a distance matrix and clones the distances, of a the identifiers in idGroup.
DistanceMatrix(double[][], IdGroup) - Constructor for class pal.distance.DistanceMatrix
constructor taking distances array and IdGroup
DistanceMatrixUtils - class pal.distance.DistanceMatrixUtils.
Auxillary functions for distance matrices
DistanceMatrixUtils() - Constructor for class pal.distance.DistanceMatrixUtils
 
DistanceParseException - exception pal.distance.DistanceParseException.
exception thrown by ReadDistanceMatrix
DistanceParseException() - Constructor for class pal.distance.DistanceParseException
 
DistanceParseException(String) - Constructor for class pal.distance.DistanceParseException
 
distanceSE - Variable in class pal.distance.PairwiseDistance
last estimate standard error of a distance
doScale(Graphics, double, int, int) - Method in class pal.gui.TreePainter
 
doTitle(Graphics, int, int) - Method in class pal.gui.TreePainter
 
DOUBLE - Static variable in class pal.misc.Attribute
 
DoubleKey - interface pal.util.DoubleKey.
 
DoubleKeyCache - interface pal.util.DoubleKeyCache.
 
doubleValue() - Method in class pal.util.ComparableDouble
 
DPRIME - Static variable in class pal.gui.LinkageDisequilibriumComponent
 
drawArc(double, double, double) - Method in class pal.gui.CircularGraphics
For drawing arbitary lines
drawDontPutBack() - Method in class pal.math.UrnModel
draw a number without putting back
drawLine(double, double, double) - Method in class pal.gui.CircularGraphics
For drawing arbitary lines
drawLine(double, double, double, double) - Method in class pal.gui.CircularGraphics
For drawing arbitary lines
drawLineDegreeAlign(double, double, double) - Method in class pal.gui.CircularGraphics
For drawing arbitary lines
drawPoint(double, double, int) - Method in class pal.gui.CircularGraphics
 
drawPutBack() - Method in class pal.math.UrnModel
draws a number with putting back
drawString(String, double, double) - Method in class pal.gui.CircularGraphics
 
drawString(String, double, double, int) - Method in class pal.gui.CircularGraphics
 
drawSymbol(double, double, int, int, int) - Method in class pal.gui.CircularGraphics
 
drawSymbol(Graphics, int, int, int, int) - Static method in class pal.gui.TreePainter
 
dropSite(int) - Method in class pal.alignment.StrippedAlignment
drop a site

E

EDGE - Static variable in interface pal.util.XMLConstants
 
efronCI(double, double[]) - Static method in class pal.statistics.BootstrapStatistics
compute approximate central confidence interval for thetaHat (Efron percentile method)
efronCI(double, double[], int[]) - Static method in class pal.statistics.BootstrapStatistics
compute approximate central confidence interval for thetaHat (Efron percentile method)
ElementFactory - class pal.xml.ElementFactory.
This class provides static methods for creating DOM Elements from PAL Objects.
ElementFactory() - Constructor for class pal.xml.ElementFactory
 
ElementParser - class pal.xml.ElementParser.
This class provides static methods for parsing PAL objects from DOM Elements.
ElementParser() - Constructor for class pal.xml.ElementParser
 
environmentNames - Variable in class pal.alignment.SimpleCharacterAlignment
names of the traits
EPSILON - Static variable in class pal.math.MachineAccuracy
machine accuracy constant
equal(Node, Node) - Static method in class pal.tree.RootedTreeUtils
 
equals(Object) - Method in class pal.misc.Identifier
 
equals(Object) - Method in class pal.util.ComparableDouble
 
equals(Object) - Method in interface pal.util.Comparable
Returns true if this object is equal to the given object.
equals(Object, Object) - Method in interface pal.util.Comparator
Returns true if the two objects are equal.
erf(double) - Static method in class pal.math.ErrorFunction
error function
erfc(double) - Static method in class pal.math.ErrorFunction
complementary error function = 1-erf(x)
ErrorFunction - class pal.math.ErrorFunction.
error function and related stuff
ErrorFunction() - Constructor for class pal.math.ErrorFunction
 
estimate() - Method in class pal.eval.ModelParameters
estimate (approximate) values for the model parameters from the data using a neighbor-joining tree
estimateFrequencies(Alignment) - Static method in class pal.alignment.AlignmentUtils
count states (creates dataType if not yet specified)
estimateFromTree(ParameterizedTree) - Method in class pal.eval.ModelParameters
estimate (approximate) values for the model parameters from the data using a given (parameterized) tree
evaluate(double) - Method in class pal.distance.SequencePairLikelihood
compute (negative) log-likelihood for a given distance between the two sequences
evaluate(double) - Method in class pal.math.OrthogonalLineFunction
 
evaluate(double) - Method in interface pal.math.UnivariateFunction
compute function value
evaluate(double) - Method in class pal.math.LineFunction
evaluate f(start+lambda*dir)
evaluate(double[]) - Method in class pal.eval.ModelParameters
 
evaluate(double[]) - Method in class pal.eval.ChiSquareValue
compute (weighted) least-squares value
evaluate(double[]) - Method in class pal.eval.DemographicValue
 
evaluate(double[]) - Method in class pal.math.BoundsCheckedFunction
computes function value, taking into account the constraints on the argument
evaluate(double[]) - Method in interface pal.math.MultivariateFunction
compute function value
evaluate(double[], double[]) - Method in interface pal.math.MFWithGradient
compute both function value and gradient at a point
exchangeInfo(Node, Node) - Static method in class pal.tree.NodeUtils
Exchange field info between two nodes.
ExpandingPopulation - class pal.coalescent.ExpandingPopulation.
This class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.
ExpandingPopulation(double, double, double, int) - Constructor for class pal.coalescent.ExpandingPopulation
Construct demographic model of an expanding population
ExpandingPopulation(int) - Constructor for class pal.coalescent.ExpandingPopulation
Construct demographic model with default settings
EXPECTED_SUBSTITUTIONS - Static variable in interface pal.misc.Units
 
EXPONENTIAL_GROWTH - Static variable in interface pal.util.XMLConstants
 
ExponentialDistribution - class pal.statistics.ExponentialDistribution.
exponential distribution.
ExponentialDistribution() - Constructor for class pal.statistics.ExponentialDistribution
 
ExponentialGrowth - class pal.coalescent.ExponentialGrowth.
This class models an exponentially growing (or shrinking) population (Parameters: N0=present-day population size; r=growth rate).
ExponentialGrowth(double, double, int) - Constructor for class pal.coalescent.ExponentialGrowth
Construct demographic model of an exponentially growing population
ExponentialGrowth(int) - Constructor for class pal.coalescent.ExponentialGrowth
Construct demographic model with default settings
ExternalParameterListener - interface pal.misc.ExternalParameterListener.
Defines objects that listen to exteneral ParameterEvents
extractAlignment(Tree) - Static method in class pal.tree.TreeUtils
Extracts an alignment from a tree.
extractAlignment(Tree, boolean) - Static method in class pal.tree.TreeUtils
Extracts an alignment from a tree.
extractFromClockTree(Tree) - Static method in class pal.coalescent.IntervalsExtractor
extracts intervals from clock tree.
extractFromClockTree(Tree, double) - Static method in class pal.coalescent.IntervalsExtractor
extracts intervals from clock tree.
extractFromTree(Tree) - Static method in class pal.coalescent.IntervalsExtractor
extracts intervals from serial clock tree.
extractFromTree(Tree, MutationRateModel) - Static method in class pal.coalescent.IntervalsExtractor
extracts intervals in generation times from serial clock tree (in mutation times) after taking into account mutation rate model.
extractTimeOrderCharacterData(Tree, int) - Static method in class pal.tree.TreeUtils
Extracts a time order character data from a tree.

F

F - Variable in class pal.math.DifferentialEvolution
weight factor (default 0.7)
f2minx - Variable in class pal.math.UnivariateMinimum
curvature at minimum
F81 - class pal.substmodel.F81.
Felsenstein 1981 model of nucleotide evolution
F81 - Static variable in interface pal.substmodel.NucleotideModelID
 
F81 - Static variable in interface pal.util.XMLConstants
 
F81(double[]) - Constructor for class pal.substmodel.F81
constructor
F84 - class pal.substmodel.F84.
Felsenstein 1984 (PHYLIP) model of nucleotide evolution
F84 - Static variable in interface pal.substmodel.NucleotideModelID
 
F84 - Static variable in interface pal.util.XMLConstants
 
F84(double[], double[]) - Constructor for class pal.substmodel.F84
Constructor 2
F84(double, double[]) - Constructor for class pal.substmodel.F84
constructor 1
FastLikelihoodCalculator - class pal.eval.FastLikelihoodCalculator.
Title: Fast Likelihood Calculator
Description: A fast likelihood calculator
Original code by Matthew Goode.
FastLikelihoodCalculator(SitePattern) - Constructor for class pal.eval.FastLikelihoodCalculator
Constructor taking only site pattern.
FastLikelihoodCalculator(SitePattern, Tree, RateMatrix) - Constructor for class pal.eval.FastLikelihoodCalculator
Constructor taking site pattern, tree and model.
fillPoint(double, double, int) - Method in class pal.gui.CircularGraphics
 
findByIdentifier(Node, Identifier) - Static method in class pal.tree.NodeUtils
Returns the first node in this tree that has the required identifier.
findByIdentifier(Node, Identifier[]) - Static method in class pal.tree.NodeUtils
Returns the first nodes in this tree that has the required identifiers.
findByIdentifier(Node, String) - Static method in class pal.tree.NodeUtils
Returns the first node in this tree that has the required identifier.
findByIdentifier(Node, String[]) - Static method in class pal.tree.NodeUtils
Returns the first nodes in this tree that has the required identifiers.
findInterval(double) - Method in class pal.coalescent.SkylinePlot
Find interval corresponding to a specific time
findLargestChild(Node) - Static method in class pal.tree.NodeUtils
Finds the largest child (in terms of node height).
findMinimum() - Method in class pal.math.LineFunction
find parameter lambda within the given bounds that minimizes the univariate function (due to numerical inaccuaries it may happen that getPoint for the returned lambda produces a point that lies slightly out of bounds)
findMinimum(double, UnivariateFunction) - Method in class pal.math.UnivariateMinimum
Find minimum (first estimate given)
findMinimum(double, UnivariateFunction, int) - Method in class pal.math.UnivariateMinimum
Find minimum (first estimate given, desired number of fractional digits specified)
findMinimum(MultivariateFunction, double[]) - Method in class pal.math.MultivariateMinimum
Find minimum close to vector x
findMinimum(MultivariateFunction, double[], int, int) - Method in class pal.math.MultivariateMinimum
Find minimum close to vector x (desired fractional digits for each parameter is specified)
findMinimum(UnivariateFunction) - Method in class pal.math.UnivariateMinimum
Find minimum (no first estimate given)
findMinimum(UnivariateFunction, int) - Method in class pal.math.UnivariateMinimum
Find minimum (no first estimate given, desired number of fractional digits specified)
findNode(int) - Method in class pal.tree.SimpleTree
return node with number num (as displayed in ASCII tree)
fireParametersChangedEvent() - Method in class pal.substmodel.AbstractRateMatrix
 
fireParametersChangedEvent(PalObjectEvent) - Method in class pal.substmodel.AbstractRateMatrix
 
first - Variable in class pal.util.ThreeNumberSort
order of the numbers (0-2)
firstDerivative(UnivariateFunction, double) - Static method in class pal.math.NumericalDerivative
determine first derivative
firstSite - Variable in class pal.alignment.StrippedAnnotatedAlignment
 
FisherExact - class pal.statistics.FisherExact.
This does a one tail fisher exact test.
FisherExact(int) - Constructor for class pal.statistics.FisherExact
constructor for FisherExact table
fixedMus - Variable in class pal.mep.SteppedMutationRate
whether or not the mu values are optimizable
FLETCHER_REEVES_UPDATE - Static variable in class pal.math.ConjugateGradientSearch
 
FLOAT - Static variable in class pal.misc.Attribute
 
fminx - Variable in class pal.math.UnivariateMinimum
function value at minimum
fo - Variable in class pal.mep.MutationRateModel
 
fo - Variable in class pal.coalescent.DemographicModel
 
FONT_SIZE - Static variable in class pal.gui.TreePainterNormal
 
FONT_SIZE - Static variable in class pal.gui.TreePainterCircular
 
FOREGROUND - Static variable in class pal.gui.TreePainter
 
format - Variable in class pal.substmodel.AbstractRateMatrix
 
format - Variable in class pal.substmodel.RateDistribution
 
FormattedInput - class pal.io.FormattedInput.
tools to simplify formatted input from an input stream
FormattedOutput - class pal.io.FormattedOutput.
tools to simplify formatted output to a stream
FRACDIGITS - Static variable in class pal.eval.ModelParameters
fractional digits desired for parameters
FRACDIGITS - Static variable in interface pal.misc.BranchLimits
desired fractional digits when determining branch lengths
FREQUENCIES - Static variable in interface pal.util.XMLConstants
 
frequency - Variable in class pal.alignment.AbstractAlignment
frequencies of the allowed states (scaled to sum to 1.0 and suitable for RateMatrix)
frequency - Variable in class pal.substmodel.AbstractRateMatrix
stationary frequencies (sum = 1.0)
fromQToR() - Method in class pal.substmodel.AbstractRateMatrix
Computes normalized rate matrix from Q matrix (general reversible model) - Q_ii = 0 - Q_ij = Q_ji - Q_ij is stored in R_ij (rate) - only upper triangular is used Also updates related MatrixExponential

G

G_STATE - Static variable in class pal.datatype.Nucleotides
 
G_TO_T - Static variable in interface pal.util.XMLConstants
 
GammaDistribution - class pal.statistics.GammaDistribution.
gamma distribution.
GammaDistribution() - Constructor for class pal.statistics.GammaDistribution
 
GammaFunction - class pal.math.GammaFunction.
gamma function
GammaFunction() - Constructor for class pal.math.GammaFunction
 
GammaRates - class pal.substmodel.GammaRates.
discrete Gamma distribution (Z.
GammaRates(int, double) - Constructor for class pal.substmodel.GammaRates
construct discrete Gamma distribution (mean = 1.0)
GAP - Static variable in interface pal.alignment.Alignment
character used to designate gaps
GapBalancedAlignment - class pal.alignment.GapBalancedAlignment.
Creates a "Gap-Balanced" alignment.
GapBalancedAlignment(Alignment, int, boolean) - Constructor for class pal.alignment.GapBalancedAlignment
The standard GapBalanced constructor
GapBalancedAlignment(Alignment, int, boolean, int) - Constructor for class pal.alignment.GapBalancedAlignment
GapBalanced power user constructor
GapBalancedAlignment(Alignment, int, int) - Constructor for class pal.alignment.GapBalancedAlignment
GapBalanced power user constructor
GENERALIZED_CODONS_DESCRIPTION - Static variable in interface pal.datatype.DataType
generalized codon name (for XML and human readability)
GeneralizedCodons - class pal.datatype.GeneralizedCodons.
Used for mapping an exact codon to an exact state, and vice versa Can also be used as a DataType (exactly as for Codons, but more versatile).
GENERALIZEDCODONS - Static variable in interface pal.datatype.DataType
 
GeneralizedCodons() - Constructor for class pal.datatype.GeneralizedCodons
The Biologists, what else do we need, constructor (nucleode character types, codon length 3)
GeneralizedCodons(DataType, int) - Constructor for class pal.datatype.GeneralizedCodons
The Computer Scientist's want of abstraction consturctor
GeneralizedDEOptimizer - class pal.math.GeneralizedDEOptimizer.
Provides an general interface to the DifferentialEvolution class that is not tied to a certain number of parameters (as DifferentialEvolution is).
GeneralizedDEOptimizer() - Constructor for class pal.math.GeneralizedDEOptimizer
 
GENERATIONS - Static variable in interface pal.misc.Units
 
GENERATIONS - Static variable in interface pal.util.XMLConstants
 
generationsToMutations(Tree, MutationRateModel) - Static method in class pal.tree.TreeUtils
Takes a tree (in generation units) and returns a scaled version of it (in mutation units).
generationsToMutations(Tree, MutationRateModel, double) - Static method in class pal.tree.TreeUtils
Takes a tree (in generation units) and returns a scaled version of it (in mutation units).
Genotype - class pal.alignment.Genotype.
This class provides from genotype to be constructed from separate but paired alignments.
Genotype(Alignment, Alignment) - Constructor for class pal.alignment.Genotype
 
getAICC() - Method in class pal.coalescent.SkylinePlot
Compute AICC-corrected log-likelihood
getAlignedSequenceIndices(Alignment, int, int[], DataType) - Static method in class pal.alignment.AlignmentUtils
Returns state indices for a sequence.
getAlignedSequenceString(int) - Method in class pal.alignment.AbstractAlignment
Returns a string representing a single sequence (including gaps) from this alignment.
getAlignedSequenceString(int) - Method in class pal.alignment.SimpleAlignment
Returns a string representing a single sequence (including gaps) from this alignment.
getAlignedSequenceString(int) - Method in interface pal.alignment.Alignment
Returns string representation of single sequence in alignment with gap characters included.
getAlignment(int) - Method in class pal.alignment.Genotype
 
getAlignmentPenalty(Alignment, DataType, TransitionPenaltyTable, double, double, boolean) - Static method in class pal.alignment.AlignmentUtils
Returns total sum of pairs alignment distance using gap creation and extension penalties and transition penalties as defined in the TransitionPenaltyTable provided.
getAlignmentPenalty(Alignment, TransitionPenaltyTable, double, double) - Static method in class pal.alignment.AlignmentUtils
Returns total sum of pairs alignment penalty using gap creation and extension penalties and transition penalties in the TransitionPenaltyTable provided.
getAminoAcidChar(char[]) - Method in interface pal.datatype.CodonTable
Returns the char associated with AminoAcid represented by 'codon'
getAminoAcidCharFromCodonIndex(int) - Method in interface pal.datatype.CodonTable
Returns the amino acid char at the corresponding codonIndex
getAminoAcidState(char[]) - Method in interface pal.datatype.CodonTable
Returns the state associated with AminoAcid represented by 'codon'
getAminoAcidStateFromCodonIndex(int) - Method in interface pal.datatype.CodonTable
Returns the amino acid state at the corresponding codonIndex
getAncestral() - Method in class pal.coalescent.ConstExpGrowth
returns ancestral parameter
getAncestralN0() - Method in class pal.coalescent.ConstExpGrowth
returns ancestral population size
getAnnotatedAlignment() - Method in class pal.popgen.LinkageDisequilibrium
Returns an annotated aligment if one was used for this LD this could be used to access information of locus position
getAttribute(Node, String) - Method in class pal.tree.ParameterizedTree
 
getAttribute(Node, String) - Method in class pal.tree.SimpleTree
 
getAttribute(Node, String) - Method in interface pal.tree.Tree
 
getAttribute(String) - Method in class pal.tree.SimpleNode
 
getAttribute(String) - Method in interface pal.tree.AttributeNode
 
getAttributeNames() - Method in class pal.tree.SimpleNode
 
getAttributeNames() - Method in interface pal.tree.AttributeNode
 
getBaseStatesFromCodonState(int) - Method in class pal.datatype.GeneralizedCodons
Translates an index into a codon
getBaseTree() - Method in class pal.tree.ParameterizedTree
 
getBootstrapSupportByCladeTree(String, Tree, Tree[]) - Static method in class pal.tree.TreeUtils
Generates a tree which is identical to baseTree but has attributes (defined by attributeName) at all internal nodes excluding the root node signifying (as a value between 0 and 100) the bootstrap support by clade (that is the proportion of replicates that produce the sub clade under that node)
getBootstrapValue(PositionedNode) - Method in class pal.gui.TreePainter
Returns -1 if no bootstrap value available
getBounds(Identifier) - Method in class pal.gui.LayoutTracker
 
getBounds(String) - Method in class pal.gui.LayoutTracker
 
getBranchLength() - Method in class pal.tree.SimpleNode
Get the length of the branch attaching this node to its parent.
getBranchLength() - Method in interface pal.tree.Node
Get the length of the branch attaching this node to its parent.
getBranchLengthSE() - Method in class pal.tree.SimpleNode
Get the length SE of the branch attaching this node to its parent.
getBranchLengthSE() - Method in interface pal.tree.Node
Get the length SE of the branch attaching this node to its parent.
getByteStates(char[], DataType) - Static method in class pal.datatype.DataTypeUtils
For converting a sequence to an array of bytes where each byte represents the state of the corresponding character in sequence
getByteStates(String, DataType) - Static method in class pal.datatype.DataTypeUtils
For converting a sequence to an array of bytes where each byte represents the state of the corresponding character in sequence
getChangedDataType(Alignment, DataType) - Static method in class pal.alignment.AlignmentUtils
Returns an alignment which follows the pattern of the input alignment except that all sites which do not contain states in dt (excluding the gap character) are removed.
getChar(int) - Method in class pal.datatype.TwoStates
 
getChar(int) - Method in class pal.datatype.GeneralizedCodons
Get character corresponding to a given state
getChar(int) - Method in interface pal.datatype.DataType
get character corresponding to a given state
getChar(int) - Method in class pal.datatype.AminoAcids
 
getChar(int) - Method in class pal.datatype.NumericDataType
Get character corresponding to a given state
getChar(int) - Method in class pal.datatype.StateRemover
Get character corresponding to a given state
getChar(int) - Method in class pal.datatype.Nucleotides
Get character corresponding to a given state
getChar(int) - Method in class pal.datatype.IUPACNucleotides
 
getChar(int) - Method in class pal.datatype.Codons
Get character corresponding to a given state
getChars(int[][], char, DataType) - Static method in class pal.datatype.DataTypeUtils
For converting an array of sequence to arrays of ints where each int represents the state of the corresponding character in sequence
getChars(int[], char, DataType) - Static method in class pal.datatype.DataTypeUtils
For converting a sequence of ints representing states to an array of chars
getChild(int) - Method in class pal.tree.SimpleNode
get child node
getChild(int) - Method in interface pal.tree.Node
get child node
getChildCount() - Method in class pal.tree.SimpleNode
Returns the number of children this node has.
getChildCount() - Method in interface pal.tree.Node
Returns the number of children this node has.
getChromosome(int) - Method in class pal.alignment.StrippedAnnotatedAlignment
Returns chromosome
getChromosome(int) - Method in class pal.alignment.MultiLocusAnnotatedAlignment
Returns chromosome
getChromosome(int) - Method in class pal.alignment.SimpleAnnotatedAlignment
Returns chromosome
getChromosome(int) - Method in interface pal.alignment.AnnotationAlignment
Returns chromosome
getChromosome(int) - Method in class pal.alignment.IndelAnnotatedAlignment
Returns chromosome
getChromosome(int) - Method in class pal.alignment.ConcatenatedAnnotatedAlignment
Returns chromosome
getChromosomePosition(int) - Method in class pal.alignment.StrippedAnnotatedAlignment
Return the position along chromosome
getChromosomePosition(int) - Method in class pal.alignment.MultiLocusAnnotatedAlignment
Return the position along chromosome
getChromosomePosition(int) - Method in class pal.alignment.SimpleAnnotatedAlignment
Return the position along chromosome
getChromosomePosition(int) - Method in interface pal.alignment.AnnotationAlignment
Return the position along chromosome
getChromosomePosition(int) - Method in class pal.alignment.IndelAnnotatedAlignment
Return the position along chromosome
getChromosomePosition(int) - Method in class pal.alignment.ConcatenatedAnnotatedAlignment
Return the position along chromosome
getClade(Node, Node) - Static method in class pal.tree.RootedTreeUtils
 
getCoalescentEvents(int) - Method in class pal.coalescent.CoalescentIntervals
Returns the number coalescent events in an interval
getCoalescentIntervals() - Method in class pal.eval.DemographicValue
Returns the coalescent tree of this likelihood value.
getCoalescentIntervals() - Method in interface pal.coalescent.CoalescentTree
 
getCodonCharFromCodon(char[]) - Method in class pal.datatype.GeneralizedCodons
Returns a unique ascii character for any given codon
getCodonCharFromCodonIndex(int) - Method in class pal.datatype.GeneralizedCodons
Returns a unique ascii character for any given codon index
getCodonCharFromCodonStates(int[]) - Method in class pal.datatype.GeneralizedCodons
Returns a unique ascii character for any given codon
getCodonFrequencies(double[]) - Method in class pal.datatype.GeneralizedCodons
 
getCodonFromCodonChar(char) - Method in class pal.datatype.GeneralizedCodons
Translates an index into a codon
getCodonFromCodonIndex(int) - Method in class pal.datatype.GeneralizedCodons
Translates an index into a codon
getCodonIndexFromCodon(char[]) - Method in class pal.datatype.GeneralizedCodons
Returns -1 if the codon has unknowns, or gaps in it, or is less than length length!
getCodonIndexFromCodonChar(char) - Method in class pal.datatype.GeneralizedCodons
Returns a unique ascii character for any given codon index
getCodonIndexFromCodonStates(int[]) - Method in class pal.datatype.GeneralizedCodons
Returns -1 if the codon has unknowns, or gaps in it, or is less than length length!
getCodonsFromAminoAcidChar(char) - Method in interface pal.datatype.CodonTable
 
getCodonsFromAminoAcidState(int) - Method in interface pal.datatype.CodonTable
 
getColour(Identifier, Color) - Method in class pal.gui.NameColouriser
 
getColour(String, Color) - Method in class pal.gui.NameColouriser
 
getCopy(double[]) - Static method in class pal.misc.Utils
Clones an array of doubles
getCopy(double[][]) - Static method in class pal.misc.Utils
Clones an array of doubles
getCopy(int[]) - Static method in class pal.misc.Utils
Clones an array of ints
getCopy(RateMatrix[]) - Static method in class pal.substmodel.RateMatrixUtils
 
getCopyOfTimes() - Method in class pal.misc.TimeOrderCharacterData
Returns a copy of the times in the form of an array.
getCumlativeP(int, int, int, int) - Method in class pal.statistics.FisherExact
calculates the one tail P-value for the Fisher Exact test This
getData(int, int) - Method in class pal.alignment.AbstractAlignment
sequence alignment at (sequence, site)
getData(int, int) - Method in class pal.alignment.StrippedAlignment
sequence alignment at (sequence, site)
getData(int, int) - Method in class pal.alignment.SimpleAlignment
sequence alignment at (sequence, site)
getData(int, int) - Method in class pal.alignment.ReadAlignment
sequence alignment at (sequence, site)
getData(int, int) - Method in class pal.alignment.AminoAcidAlignment
sequence alignment at (sequence, site)
getData(int, int) - Method in class pal.alignment.IndelAlignment
sequence alignment at (sequence, site)
getData(int, int) - Method in class pal.alignment.BootstrappedAlignment
sequence alignment at (sequence, site)
getData(int, int) - Method in class pal.alignment.JumbledAlignment
sequence alignment at (sequence, site)
getData(int, int) - Method in class pal.alignment.GapBalancedAlignment
sequence alignment at (sequence, site)
getData(int, int) - Method in class pal.alignment.SitePattern
sequence alignment at (sequence, site)
getData(int, int) - Method in class pal.alignment.CodonAlignment
sequence alignment at (sequence, site)
getData(int, int) - Method in interface pal.alignment.Alignment
sequence alignment at (sequence, site)
getData(int, int) - Method in class pal.alignment.ConcatenatedAlignment
sequence alignment at (sequence, site)
getData(int, int) - Method in class pal.alignment.ConcatenatedAnnotatedAlignment
sequence alignment at (sequence, site)
getData(int, int) - Method in class pal.tree.SimulatedAlignment
sequence alignment at (sequence, site)
getData(int, int, int) - Method in class pal.alignment.Genotype
sequence alignment at (sequence, site, allele)
getDataType() - Method in class pal.alignment.AbstractAlignment
Returns the datatype of this alignment
getDataType() - Method in interface pal.alignment.Alignment
Return DataType of this alignment.
getDataType() - Method in class pal.substmodel.AbstractRateMatrix
 
getDataType() - Method in class pal.substmodel.SimpleSubstitutionModel
 
getDataType() - Method in class pal.substmodel.CachedRateMatrix
 
getDataType() - Method in interface pal.substmodel.RateMatrix
Get the data type of this rate matrix
getDataType() - Method in interface pal.substmodel.SubstitutionModel
 
getDataType() - Method in class pal.datatype.IUPACPenaltyTable
 
getDataType() - Method in interface pal.datatype.TransitionPenaltyTable
 
getDataType(int) - Method in class pal.alignment.StrippedAnnotatedAlignment
Returns the datatype
getDataType(int) - Method in class pal.alignment.MultiLocusAnnotatedAlignment
Returns the datatype
getDataType(int) - Method in class pal.alignment.SimpleAnnotatedAlignment
Returns the datatype (for SimpleAnnotatedAlignment there is only one datatype)
getDataType(int) - Method in interface pal.alignment.AnnotationAlignment
Returns the datatype for a specific site, which could differ by site in complex alignments
getDataType(int) - Method in class pal.alignment.IndelAnnotatedAlignment
Returns the datatype
getDataType(int) - Method in class pal.alignment.ConcatenatedAnnotatedAlignment
Return the datatype for a given site, which can differ between source alignments
getDatedTipsClockTree() - Method in class pal.tree.SUPGMATree
 
getDecimalString(double, int) - Method in class pal.io.FormattedOutput
Returns a decimal string representation of a number with constrained width.
getDefaultLogger() - Static method in class pal.util.Log
 
getDefaultValue() - Method in class pal.misc.ParameterizedDouble
 
getDefaultValue(int) - Method in class pal.mep.ConstantMutationRate
 
getDefaultValue(int) - Method in class pal.mep.WindowedMutationRate
 
getDefaultValue(int) - Method in class pal.mep.SteppedMutationRate
 
getDefaultValue(int) - Method in class pal.misc.ParameterizedDouble
get default value of parameter
getDefaultValue(int) - Method in interface pal.misc.Parameterized
get default value of parameter
getDefaultValue(int) - Method in class pal.substmodel.AminoAcidModel
 
getDefaultValue(int) - Method in class pal.substmodel.SimpleSubstitutionModel
 
getDefaultValue(int) - Method in class pal.substmodel.GammaRates
 
getDefaultValue(int) - Method in class pal.substmodel.CachedRateMatrix
 
getDefaultValue(int) - Method in class pal.substmodel.HKY
 
getDefaultValue(int) - Method in class pal.substmodel.GTR
 
getDefaultValue(int) - Method in class pal.substmodel.F81
 
getDefaultValue(int) - Method in class pal.substmodel.InvariableSites
 
getDefaultValue(int) - Method in class pal.substmodel.YangCodonModel
 
getDefaultValue(int) - Method in class pal.substmodel.TN
 
getDefaultValue(int) - Method in class pal.substmodel.F84
 
getDefaultValue(int) - Method in class pal.substmodel.UniformRate
 
getDefaultValue(int) - Method in class pal.substmodel.TwoStateModel
 
getDefaultValue(int) - Method in class pal.tree.UnconstrainedTree
 
getDefaultValue(int) - Method in class pal.tree.LogParameterizedTree
 
getDefaultValue(int) - Method in class pal.tree.DatedTipsClockTree
 
getDefaultValue(int) - Method in class pal.tree.MutationRateModelTree
 
getDefaultValue(int) - Method in class pal.tree.ClockTree
 
getDefaultValue(int) - Method in class pal.coalescent.ConstantPopulation
 
getDefaultValue(int) - Method in class pal.coalescent.ExponentialGrowth
 
getDefaultValue(int) - Method in class pal.coalescent.ConstExpGrowth
 
getDefaultValue(int) - Method in class pal.coalescent.ExpandingPopulation
 
getDeltas(double[]) - Method in class pal.mep.SteppedMutationRate
 
getDemographic(double) - Method in class pal.coalescent.DemographicModel
Gets the value of the demographic function N(t) at time t.
getDemographic(double) - Method in class pal.coalescent.ConstantPopulation
 
getDemographic(double) - Method in class pal.coalescent.ExponentialGrowth
 
getDemographic(double) - Method in class pal.coalescent.ConstExpGrowth
 
getDemographic(double) - Method in class pal.coalescent.ExpandingPopulation
 
getDemographicModel() - Method in class pal.eval.DemographicValue
Returns the demographic model of this likelihood value
getDemographicModel() - Method in interface pal.coalescent.DemographicTree
 
getDemographicModel() - Method in class pal.coalescent.DemographicClockTree
Return the demographic model being used to optimize the likelihood of this tree.
getDescription() - Method in class pal.datatype.TwoStates
 
getDescription() - Method in class pal.datatype.GeneralizedCodons
String describing the data type
getDescription() - Method in interface pal.datatype.DataType
description of data type
getDescription() - Method in class pal.datatype.AminoAcids
 
getDescription() - Method in class pal.datatype.NumericDataType
String describing the data type
getDescription() - Method in class pal.datatype.StateRemover
 
getDescription() - Method in class pal.datatype.Nucleotides
 
getDescription() - Method in class pal.datatype.IUPACNucleotides
 
getDescription() - Method in class pal.datatype.Codons
 
getDimension() - Method in class pal.substmodel.AbstractRateMatrix
 
getDimension() - Method in class pal.substmodel.MatrixExponential
 
getDimension() - Method in class pal.substmodel.SimpleSubstitutionModel
 
getDimension() - Method in class pal.substmodel.CachedRateMatrix
 
getDimension() - Method in interface pal.substmodel.RateMatrix
 
getDimension() - Method in interface pal.substmodel.SubstitutionModel
Deprecated.  
getDistance(byte[], byte[]) - Method in class pal.distance.PairwiseDistance
compute distance between two sequences (not necessarly in the given alignment but with the same weights in the site pattern)
getDistance(int, int) - Method in class pal.distance.PairwiseDistance
compute distance between two sequences in the given alignment
getDistances() - Method in class pal.distance.DistanceMatrix
Returns the distances as a 2-dimensional array of doubles.
getDistanceToRoot(Node) - Static method in class pal.tree.NodeUtils
determine distance to root
getDoubleValue(Element) - Static method in class pal.xml.ElementParser
 
getDPrime(int, int) - Method in class pal.popgen.LinkageDisequilibrium
Returns D' estimate for a given pair of sites
getEnvironmentName(int) - Method in interface pal.alignment.CharacterAlignment
Return name of the environments for this trait number
getEnvironmentName(int) - Method in class pal.alignment.SimpleCharacterAlignment
Return name of the environments for this trait number
getEpsilon() - Method in class pal.coalescent.SkylinePlot
Returns epsilon
getEquilibriumFrequencies() - Method in class pal.substmodel.AbstractRateMatrix
 
getEquilibriumFrequencies() - Method in class pal.substmodel.CachedRateMatrix
 
getEquilibriumFrequencies() - Method in interface pal.substmodel.RateMatrix
 
getEquilibriumFrequency(int) - Method in class pal.substmodel.AbstractRateMatrix
 
getEquilibriumFrequency(int) - Method in class pal.substmodel.CachedRateMatrix
 
getEquilibriumFrequency(int) - Method in interface pal.substmodel.RateMatrix
 
getEveryRoot(Tree, Vector) - Static method in class pal.tree.TreeUtils
Makes a copy of this tree for every possible rooting and fills a vector with all possible rootings of the given tree.
getExpectedSubstitutions(double) - Method in class pal.mep.MutationRateModel
Returns integral of mutation rate function (= integral mu(x) dx from 0 to t).
getExpectedSubstitutions(double) - Method in class pal.mep.ConstantMutationRate
 
getExpectedSubstitutions(double) - Method in class pal.mep.WindowedMutationRate
Window must not span zero!
getExpectedSubstitutions(double) - Method in class pal.mep.SteppedMutationRate
 
getExpectedSubstitutions(double, double) - Method in class pal.mep.MutationRateModel
Calculates the integral 1/mu(x) dx between start and finish.
getExternalNode(int) - Method in class pal.tree.ParameterizedTree
returns the ith external node in the tree.
getExternalNode(int) - Method in class pal.tree.SimpleTree
Returns the ith external node.
getExternalNode(int) - Method in interface pal.tree.Tree
 
getExternalNodeCount() - Method in class pal.tree.ParameterizedTree
returns a count of the number of external nodes (tips) in this tree.
getExternalNodeCount() - Method in class pal.tree.SimpleTree
Returns the number of external nodes.
getExternalNodeCount() - Method in interface pal.tree.Tree
 
getFirstByName(Element, String) - Static method in class pal.xml.ElementParser
 
getFirstCommonAncestor(Node[]) - Static method in class pal.tree.NodeUtils
For a set of nodes in the tree returns the common ancestor closest to all nodes (most recent common ancestor)
getFirstCommonAncestor(Node, Node) - Static method in class pal.tree.NodeUtils
For two nodes in the tree returns the common ancestor closest to both nodes (most recent common ancestor)
getFrequency() - Method in class pal.alignment.AbstractAlignment
 
getFrequency() - Method in interface pal.alignment.Alignment
Returns frequency of character states.
getGrowthRate() - Method in class pal.coalescent.ExponentialGrowth
returns growth rate.
getHeight(int, double) - Method in class pal.misc.TimeOrderCharacterData
NOTE: currently assumes times exist!
getIdCount() - Method in class pal.alignment.AbstractAlignment
 
getIdCount() - Method in class pal.alignment.SimpleCharacterAlignment
 
getIdCount() - Method in class pal.distance.DistanceMatrix
 
getIdCount() - Method in class pal.misc.SimpleIdGroup
Returns the number of identifiers in this group
getIdCount() - Method in interface pal.misc.IdGroup
Returns the number of identifiers in this group
getIdCount() - Method in class pal.misc.TimeOrderCharacterData
 
getIdentifier() - Method in class pal.tree.SimpleNode
Returns the identifier for this node.
getIdentifier() - Method in interface pal.tree.Node
Returns the identifier for this node.
getIdentifier(int) - Method in class pal.alignment.AbstractAlignment
 
getIdentifier(int) - Method in class pal.alignment.SimpleCharacterAlignment
 
getIdentifier(int) - Method in class pal.distance.DistanceMatrix
 
getIdentifier(int) - Method in class pal.misc.SimpleIdGroup
Returns the ith identifier.
getIdentifier(int) - Method in interface pal.misc.IdGroup
Returns the ith identifier.
getIdentifier(int) - Method in class pal.misc.TimeOrderCharacterData
 
getIdGroup() - Method in class pal.distance.DistanceMatrix
Deprecated. distance matrix now implements IdGroup
getIdGroup() - Method in class pal.misc.TimeOrderCharacterData
Deprecated. TimeOrderCharacterData now implements IdGroup
getIdGroup() - Method in class pal.tree.SplitSystem
get idGroup
getIndexOfLargestNumber() - Method in class pal.util.ThreeNumberSort
get input index of largest number
getIndexOfSmallestNumber() - Method in class pal.util.ThreeNumberSort
get input index of smallest number
getInstance() - Static method in class pal.io.FormattedOutput
create instance of this class (note that there is no public constructor as this class is a singleton)
getInstance() - Static method in class pal.io.FormattedInput
create new instance of this object (note that there is no public constructor because this class is a singleton!)
getInstance(double[]) - Static method in class pal.substmodel.TwoStateModel
create object using an instance method
getInstance(int) - Static method in class pal.datatype.DataTypeUtils
create object according to this code
getInstance(int, double[]) - Static method in class pal.substmodel.AminoAcidModel
Create amino acid model according to model type
getInstance(int, double[], double[]) - Static method in class pal.substmodel.NucleotideModel
Create nucleotide substitution model according to model type
getInstance(int, double[], double[]) - Static method in class pal.substmodel.CodonModel
Create codon substitution model according to model type
getInstance(int, int, double[], double[]) - Static method in class pal.substmodel.RateMatrixUtils
Create rate matrix given model and data type codes
getIntegral(double, double) - Method in class pal.coalescent.DemographicModel
Calculates the integral 1/N(x) dx between start and finish.
getIntensity(double) - Method in class pal.coalescent.DemographicModel
Returns value of demographic intensity function at time t (= integral 1/N(x) dx from 0 to t).
getIntensity(double) - Method in class pal.coalescent.ConstantPopulation
 
getIntensity(double) - Method in class pal.coalescent.ExponentialGrowth
 
getIntensity(double) - Method in class pal.coalescent.ConstExpGrowth
 
getIntensity(double) - Method in class pal.coalescent.ExpandingPopulation
 
getInternalNode(int) - Method in class pal.tree.ParameterizedTree
returns the ith internal node in the tree.
getInternalNode(int) - Method in class pal.tree.SimpleTree
Returns the ith internal node.
getInternalNode(int) - Method in interface pal.tree.Tree
 
getInternalNodeCount() - Method in class pal.tree.ParameterizedTree
returns a count of the number of internal nodes (and hence clades) in this tree.
getInternalNodeCount() - Method in class pal.tree.SimpleTree
Returns the number of internal nodes.
getInternalNodeCount() - Method in interface pal.tree.Tree
 
getInterval(int) - Method in class pal.coalescent.CoalescentIntervals
Gets an interval.
getIntervalCount() - Method in class pal.coalescent.CoalescentIntervals
get number of intervals
getIntervals() - Method in class pal.coalescent.SkylinePlot
Returns the coalescent intervals in this skyline plot.
getIntervalType(int) - Method in class pal.coalescent.CoalescentIntervals
Returns the type of interval observed.
getInverseIntensity(double) - Method in class pal.coalescent.DemographicModel
Returns value of inverse demographic intensity function (returns time, needed for simulation of coalescent intervals).
getInverseIntensity(double) - Method in class pal.coalescent.ConstantPopulation
 
getInverseIntensity(double) - Method in class pal.coalescent.ExponentialGrowth
 
getInverseIntensity(double) - Method in class pal.coalescent.ConstExpGrowth
 
getInverseIntensity(double) - Method in class pal.coalescent.ExpandingPopulation
 
getKey() - Method in interface pal.util.DoubleKey
 
getLabel(Identifier) - Method in class pal.misc.LabelMapping
 
getLabel(Identifier, String) - Method in class pal.misc.LabelMapping
 
getLabel(String, String) - Method in class pal.misc.LabelMapping
 
getLabelCount() - Method in class pal.tree.SplitSystem
get number of labels
getLabelIdentifier(Identifier) - Method in class pal.misc.LabelMapping
 
getLargestNumber() - Method in class pal.util.ThreeNumberSort
get largest number
getLeafCount(Node) - Static method in class pal.tree.NodeUtils
Return the number of terminal leaves below this node or 1 if this is a terminal leaf.
getLeafIdGroup(Tree) - Static method in class pal.tree.TreeUtils
get list of the identifiers of the external nodes
getLength() - Method in class pal.alignment.AbstractAlignment
Return number of sites in this alignment
getLength() - Method in class pal.alignment.SimpleCharacterAlignment
Return number of traits in this alignment
getLnL() - Method in class pal.tree.MutationRateModelTree
 
getLocusName(int) - Method in class pal.alignment.StrippedAnnotatedAlignment
Returns the name of the locus
getLocusName(int) - Method in class pal.alignment.MultiLocusAnnotatedAlignment
Returns the name of the locus
getLocusName(int) - Method in class pal.alignment.SimpleAnnotatedAlignment
Returns the name of the locus
getLocusName(int) - Method in interface pal.alignment.AnnotationAlignment
Returns the name of the locus
getLocusName(int) - Method in class pal.alignment.IndelAnnotatedAlignment
Returns the name of the locus
getLocusName(int) - Method in class pal.alignment.ConcatenatedAnnotatedAlignment
Returns the name of the locus
getLocusPosition(int) - Method in class pal.alignment.StrippedAnnotatedAlignment
Return the position along the locus (ignores gaps)
getLocusPosition(int) - Method in class pal.alignment.MultiLocusAnnotatedAlignment
Return the position along the locus (ignores gaps)
getLocusPosition(int) - Method in class pal.alignment.SimpleAnnotatedAlignment
Return the position along the locus (ignores gaps)
getLocusPosition(int) - Method in interface pal.alignment.AnnotationAlignment
Return the position along the locus (ignores gaps)
getLocusPosition(int) - Method in class pal.alignment.IndelAnnotatedAlignment
Return the position along the locus (ignores gaps)
getLocusPosition(int) - Method in class pal.alignment.ConcatenatedAnnotatedAlignment
Return the position along the locus (ignores gaps)
getLogL() - Method in class pal.coalescent.DemographicModel
returns log-likelihood.
getLogLikelihood() - Method in class pal.coalescent.SkylinePlot
Compute log-likelihood
getLowerBound() - Method in class pal.distance.SequencePairLikelihood
 
getLowerBound() - Method in class pal.math.OrthogonalLineFunction
 
getLowerBound() - Method in interface pal.math.UnivariateFunction
get lower bound of argument
getLowerBound() - Method in class pal.math.LineFunction
 
getLowerBound(int) - Method in class pal.eval.ModelParameters
 
getLowerBound(int) - Method in class pal.eval.ChiSquareValue
 
getLowerBound(int) - Method in class pal.eval.DemographicValue
 
getLowerBound(int) - Method in class pal.math.BoundsCheckedFunction
 
getLowerBound(int) - Method in interface pal.math.MultivariateFunction
get lower bound of argument n
getLowerBoundParameter() - Method in class pal.math.LineFunction
get parameter that limits the lower bound
getLowerLimit() - Method in class pal.misc.ParameterizedDouble
 
getLowerLimit(int) - Method in class pal.mep.ConstantMutationRate
 
getLowerLimit(int) - Method in class pal.mep.WindowedMutationRate
 
getLowerLimit(int) - Method in class pal.mep.SteppedMutationRate
 
getLowerLimit(int) - Method in class pal.misc.ParameterizedDouble
get lower parameter limit
getLowerLimit(int) - Method in interface pal.misc.Parameterized
get lower parameter limit
getLowerLimit(int) - Method in class pal.substmodel.AminoAcidModel
 
getLowerLimit(int) - Method in class pal.substmodel.SimpleSubstitutionModel
 
getLowerLimit(int) - Method in class pal.substmodel.GammaRates
 
getLowerLimit(int) - Method in class pal.substmodel.CachedRateMatrix
 
getLowerLimit(int) - Method in class pal.substmodel.HKY
 
getLowerLimit(int) - Method in class pal.substmodel.GTR
 
getLowerLimit(int) - Method in class pal.substmodel.F81
 
getLowerLimit(int) - Method in class pal.substmodel.InvariableSites
 
getLowerLimit(int) - Method in class pal.substmodel.YangCodonModel
 
getLowerLimit(int) - Method in class pal.substmodel.TN
 
getLowerLimit(int) - Method in class pal.substmodel.F84
 
getLowerLimit(int) - Method in class pal.substmodel.UniformRate
 
getLowerLimit(int) - Method in class pal.substmodel.TwoStateModel
 
getLowerLimit(int) - Method in class pal.tree.UnconstrainedTree
 
getLowerLimit(int) - Method in class pal.tree.LogParameterizedTree
 
getLowerLimit(int) - Method in class pal.tree.DatedTipsClockTree
 
getLowerLimit(int) - Method in class pal.tree.MutationRateModelTree
Returns lower limit of parameter estimate.
getLowerLimit(int) - Method in class pal.tree.ClockTree
 
getLowerLimit(int) - Method in class pal.coalescent.ConstantPopulation
 
getLowerLimit(int) - Method in class pal.coalescent.ExponentialGrowth
 
getLowerLimit(int) - Method in class pal.coalescent.ConstExpGrowth
 
getLowerLimit(int) - Method in class pal.coalescent.ExpandingPopulation
 
getMaxCacheSize() - Method in class pal.util.DefaultCache
 
getMaxLeafTime(Node) - Static method in class pal.gui.TreePainter
 
getMaxPopulationSize() - Method in class pal.coalescent.SkylinePlot
Returns the largest estimate of population size.
getMaxRate() - Method in class pal.tree.DatedTipsClockTree
find max. rate (for setRate) allowed by current node heights
getMaxTime() - Method in class pal.coalescent.SkylinePlot
Returns the largest value of time defined in this plot (= maximum value for epsilon)
getMeanCladeHeight(Node, Vector) - Static method in class pal.tree.RootedTreeUtils
 
getMeanSubtreeHeight(Node, Vector) - Static method in class pal.tree.RootedTreeUtils
 
getMinimumSize() - Method in class pal.gui.TreeComponent
 
getModel() - Method in class pal.eval.LikelihoodValue
Returns the model of this likelihood value.
getModelID() - Method in class pal.substmodel.AbstractRateMatrix
get numerical code describing the model type
getModelID() - Method in class pal.substmodel.Dayhoff
 
getModelID() - Method in class pal.substmodel.BLOSUM62
 
getModelID() - Method in class pal.substmodel.CachedRateMatrix
 
getModelID() - Method in class pal.substmodel.HKY
 
getModelID() - Method in interface pal.substmodel.RateMatrix
get numerical code describing the model type
getModelID() - Method in class pal.substmodel.CPREV
 
getModelID() - Method in class pal.substmodel.GTR
 
getModelID() - Method in class pal.substmodel.MTREV24
 
getModelID() - Method in class pal.substmodel.F81
 
getModelID() - Method in class pal.substmodel.YangCodonModel
 
getModelID() - Method in class pal.substmodel.JTT
 
getModelID() - Method in class pal.substmodel.WAG
 
getModelID() - Method in class pal.substmodel.TN
 
getModelID() - Method in class pal.substmodel.F84
 
getModelID() - Method in class pal.substmodel.VT
 
getModelID() - Method in class pal.substmodel.TwoStateModel
get numerical code describing the model type
getMu() - Method in class pal.mep.ConstantMutationRate
returns initial population size.
getMu() - Method in class pal.mep.WindowedMutationRate
returns current day mutation rate.
getMu() - Method in class pal.mep.SteppedMutationRate
returns current day mutation rate.
getMus() - Method in class pal.mep.SteppedMutationRate
 
getMutationRate(double) - Method in class pal.mep.MutationRateModel
Gets the mutation rate, value of mu(t) at time t.
getMutationRate(double) - Method in class pal.mep.ConstantMutationRate
 
getMutationRate(double) - Method in class pal.mep.WindowedMutationRate
 
getMutationRate(double) - Method in class pal.mep.SteppedMutationRate
 
getMutationRateModel() - Method in class pal.tree.MutationRateModelTree
returns mu
getN(int, int) - Method in class pal.popgen.LinkageDisequilibrium
Get number of gametes included in LD calculations (after missing data was excluded)
getN0() - Method in class pal.coalescent.ConstantPopulation
returns initial population size.
getName() - Method in class pal.misc.SimpleIdGroup
Return the name of this IdGroup.
getName() - Method in class pal.misc.Attribute
 
getName() - Method in class pal.misc.TimeOrderCharacterData
Returns a name for this character data.
getName() - Method in class pal.misc.Identifier
 
getName() - Method in interface pal.misc.Nameable
get the name of this object.
getName(int) - Method in class pal.misc.SimpleIdGroup
Convenience method to return the name of identifier i
getNameAttr(Element) - Static method in class pal.xml.ElementParser
 
getNames(Identifier[]) - Static method in class pal.misc.Identifier
Translates an array of identifiers into an array of strings
getNames(Identifier[], int) - Static method in class pal.misc.Identifier
Translates an array of identifiers into an array of strings, with optional removal of particular identifier
getNames(IdGroup) - Static method in class pal.misc.Identifier
Translates an IdGroup into an array of strings
getNames(IdGroup, int) - Static method in class pal.misc.Identifier
Translates an IDgroup into an array of strings, with optional removal of particular identifier
getNChoose2(int) - Method in class pal.math.Binomial
get (precomputed) n choose 2
getNearest(double, double) - Method in class pal.util.DefaultCache
 
getNearest(double, double) - Method in interface pal.util.DoubleKeyCache
retrieves the object with the key nearest to given value
getNearest(DoubleKey, double) - Method in class pal.util.DefaultCache
 
getNextBoolean() - Static method in class pal.math.MersenneTwisterFast
Access a default instance of this class, access is synchronized
getNextBranch(Node, Node) - Method in class pal.eval.SimpleLikelihoodCalculator
get next branch around a center node (center may be root, but root is never returned)
getNextByte() - Static method in class pal.math.MersenneTwisterFast
Access a default instance of this class, access is synchronized
getNextBytes(byte[]) - Static method in class pal.math.MersenneTwisterFast
Access a default instance of this class, access is synchronized
getNextChar() - Static method in class pal.math.MersenneTwisterFast
Access a default instance of this class, access is synchronized
getNextDouble() - Static method in class pal.math.MersenneTwisterFast
Access a default instance of this class, access is synchronized
getNextFloat() - Static method in class pal.math.MersenneTwisterFast
Access a default instance of this class, access is synchronized
getNextInt() - Static method in class pal.math.MersenneTwisterFast
Access a default instance of this class, access is synchronized
getNextLong() - Static method in class pal.math.MersenneTwisterFast
Access a default instance of this class, access is synchronized
getNextShort() - Static method in class pal.math.MersenneTwisterFast
Access a default instance of this class, access is synchronized
getNodeByName(Node, String) - Static method in class pal.tree.TreeUtils
 
getNodeByName(Tree, String) - Static method in class pal.tree.TreeUtils
 
getNodeHeight() - Method in class pal.tree.SimpleNode
Get the height of this node relative to the most recent node.
getNodeHeight() - Method in interface pal.tree.Node
Get the height of this node relative to the most recent node.
getNodeLabelColour(Node, Color) - Method in class pal.gui.TreePainter
 
getNodeName(Node) - Method in class pal.gui.TreePainter
 
getNormalized(double[]) - Static method in class pal.math.MathUtils
 
getNucleotideAlignment(Alignment) - Static method in class pal.alignment.AlignmentUtils
Translates an alignment to an alignment using Nucleotide characters.
getNucleotideAlignment(char[][], DataType) - Static method in class pal.alignment.AlignmentUtils
Translates an alignment (as a char array) to an alignment (as a char arrayusing Nucleotide characters.
getNucleotideFrequencies(double[]) - Method in class pal.datatype.GeneralizedCodons
 
getNumArguments() - Method in class pal.eval.ModelParameters
 
getNumArguments() - Method in class pal.eval.ChiSquareValue
get number of parameters in tree
getNumArguments() - Method in class pal.eval.DemographicValue
 
getNumArguments() - Method in class pal.math.BoundsCheckedFunction
 
getNumArguments() - Method in interface pal.math.MultivariateFunction
get number of arguments
getNumber() - Method in class pal.tree.SimpleNode
 
getNumber() - Method in interface pal.tree.Node
return the index of this node
getNumberOfTerminatorIndexes() - Method in interface pal.datatype.CodonTable
Returns the number of terminator amino acids.
getNumChars() - Method in class pal.misc.TimeOrderCharacterData
Returns the number of characters per identifier
getNumericCharFromNumericIndex(int) - Method in class pal.datatype.NumericDataType
Returns a unique ascii character for any given numeric size
getNumericIndexFromNumericChar(char) - Method in class pal.datatype.NumericDataType
Returns numeric index (size) from a unique ascii character
getNumLineages(int) - Method in class pal.coalescent.CoalescentIntervals
Returns the number of uncoalesced lineages within this interval.
getNumParameters() - Method in class pal.mep.ConstantMutationRate
 
getNumParameters() - Method in class pal.mep.WindowedMutationRate
 
getNumParameters() - Method in class pal.mep.SteppedMutationRate
 
getNumParameters() - Method in class pal.misc.ParameterizedDouble
 
getNumParameters() - Method in interface pal.misc.Parameterized
get number of parameters
getNumParameters() - Method in class pal.substmodel.AminoAcidModel
 
getNumParameters() - Method in class pal.substmodel.SimpleSubstitutionModel
 
getNumParameters() - Method in class pal.substmodel.GammaRates
 
getNumParameters() - Method in class pal.substmodel.CachedRateMatrix
 
getNumParameters() - Method in class pal.substmodel.HKY
 
getNumParameters() - Method in class pal.substmodel.GTR
 
getNumParameters() - Method in class pal.substmodel.F81
 
getNumParameters() - Method in class pal.substmodel.InvariableSites
 
getNumParameters() - Method in class pal.substmodel.YangCodonModel
 
getNumParameters() - Method in class pal.substmodel.TN
 
getNumParameters() - Method in class pal.substmodel.F84
 
getNumParameters() - Method in class pal.substmodel.UniformRate
 
getNumParameters() - Method in class pal.substmodel.TwoStateModel
 
getNumParameters() - Method in class pal.tree.UnconstrainedTree
 
getNumParameters() - Method in class pal.tree.LogParameterizedTree
 
getNumParameters() - Method in class pal.tree.DatedTipsClockTree
 
getNumParameters() - Method in class pal.tree.MutationRateModelTree
 
getNumParameters() - Method in class pal.tree.ClockTree
 
getNumParameters() - Method in class pal.coalescent.ConstantPopulation
 
getNumParameters() - Method in class pal.coalescent.ExponentialGrowth
 
getNumParameters() - Method in class pal.coalescent.DemographicClockTree
 
getNumParameters() - Method in class pal.coalescent.ConstExpGrowth
 
getNumParameters() - Method in class pal.coalescent.ExpandingPopulation
 
getNumSimpleStates() - Method in class pal.datatype.SimpleDataType
get number of unique non-ambiguous states
getNumSimpleStates() - Method in interface pal.datatype.DataType
get number of unique non-ambiguous states
getNumSimpleStates() - Method in class pal.datatype.IUPACNucleotides
returns the number of true non-ambiguous states.
getNumStates() - Method in class pal.datatype.TwoStates
 
getNumStates() - Method in class pal.datatype.GeneralizedCodons
get number of unique states
getNumStates() - Method in interface pal.datatype.DataType
get number of unique states
getNumStates() - Method in class pal.datatype.AminoAcids
 
getNumStates() - Method in class pal.datatype.NumericDataType
 
getNumStates() - Method in class pal.datatype.StateRemover
 
getNumStates() - Method in class pal.datatype.Nucleotides
 
getNumStates() - Method in class pal.datatype.IUPACNucleotides
Get number of states.
getNumStates() - Method in class pal.datatype.Codons
 
getOrdinals() - Method in class pal.misc.TimeOrderCharacterData
Gets ordinals.
getOriginalFrequencies(double[]) - Static method in class pal.substmodel.Dayhoff
get the frequencies of the original data set that formed the basis for the estimation of the rate matrix
getOriginalFrequencies(double[]) - Static method in class pal.substmodel.BLOSUM62
get the frequencies of the original data set that formed the basis for the estimation of the rate matrix
getOriginalFrequencies(double[]) - Static method in class pal.substmodel.CPREV
get the frequencies of the original data set that formed the basis for the estimation of the rate matrix
getOriginalFrequencies(double[]) - Static method in class pal.substmodel.MTREV24
get the frequencies of the original data set that formed the basis for the estimation of the rate matrix
getOriginalFrequencies(double[]) - Static method in class pal.substmodel.JTT
get the frequencies of the original data set that formed the basis for the estimation of the rate matrix
getOriginalFrequencies(double[]) - Static method in class pal.substmodel.WAG
get the frequencies of the original data set that formed the basis for the estimation of the rate matrix
getOriginalFrequencies(double[]) - Static method in class pal.substmodel.VT
get the frequencies of the original data set that formed the basis for the estimation of the rate matrix
getP(int, int) - Method in class pal.popgen.LinkageDisequilibrium
Returns P-value estimate for a given pair of sites.
getP(int, int, int, int) - Method in class pal.statistics.FisherExact
calculates the P-value for this specific state
getParameter(int) - Method in class pal.mep.ConstantMutationRate
 
getParameter(int) - Method in class pal.mep.WindowedMutationRate
 
getParameter(int) - Method in class pal.mep.SteppedMutationRate
 
getParameter(int) - Method in class pal.misc.ParameterizedDouble
get model parameter
getParameter(int) - Method in interface pal.misc.Parameterized
get model parameter
getParameter(int) - Method in class pal.substmodel.AminoAcidModel
 
getParameter(int) - Method in class pal.substmodel.SimpleSubstitutionModel
 
getParameter(int) - Method in class pal.substmodel.GammaRates
 
getParameter(int) - Method in class pal.substmodel.CachedRateMatrix
 
getParameter(int) - Method in class pal.substmodel.HKY
 
getParameter(int) - Method in class pal.substmodel.GTR
 
getParameter(int) - Method in class pal.substmodel.F81
 
getParameter(int) - Method in class pal.substmodel.InvariableSites
 
getParameter(int) - Method in class pal.substmodel.YangCodonModel
 
getParameter(int) - Method in class pal.substmodel.TN
 
getParameter(int) - Method in class pal.substmodel.F84
 
getParameter(int) - Method in class pal.substmodel.UniformRate
 
getParameter(int) - Method in class pal.substmodel.TwoStateModel
 
getParameter(int) - Method in class pal.tree.UnconstrainedTree
 
getParameter(int) - Method in class pal.tree.LogParameterizedTree
 
getParameter(int) - Method in class pal.tree.DatedTipsClockTree
 
getParameter(int) - Method in class pal.tree.MutationRateModelTree
 
getParameter(int) - Method in class pal.tree.ClockTree
 
getParameter(int) - Method in class pal.coalescent.ConstantPopulation
 
getParameter(int) - Method in class pal.coalescent.ExponentialGrowth
 
getParameter(int) - Method in class pal.coalescent.ConstExpGrowth
 
getParameter(int) - Method in class pal.coalescent.ExpandingPopulation
 
getParameterCount() - Method in class pal.coalescent.SkylinePlot
Returns the number of composite intervals (=number of parameters).
getParameterization() - Method in class pal.coalescent.ConstExpGrowth
returns parameterization
getParameterName(int) - Method in interface pal.misc.NamedParameterized
 
getParameterName(int) - Method in class pal.substmodel.AminoAcidModel
 
getParameterName(int) - Method in class pal.substmodel.CachedRateMatrix
 
getParameterName(int) - Method in class pal.substmodel.HKY
 
getParameterName(int) - Method in class pal.substmodel.GTR
 
getParameterName(int) - Method in class pal.substmodel.F81
 
getParameterName(int) - Method in class pal.substmodel.YangCodonModel
 
getParameterName(int) - Method in class pal.substmodel.TN
 
getParameterName(int) - Method in class pal.substmodel.F84
 
getParameterName(int) - Method in class pal.substmodel.TwoStateModel
 
getParameterSE(int) - Method in class pal.tree.DatedTipsClockTree
return standard error of parameter
getParent() - Method in class pal.tree.SimpleNode
Returns the parent node of this node.
getParent() - Method in interface pal.tree.Node
Returns the parent node of this node.
getPartial(Node) - Method in class pal.eval.SimpleLikelihoodCalculator
get partial likelihood of a branch
getPeer() - Method in class pal.gui.PositionedNode
 
getPenWidth() - Method in class pal.gui.TreePainter
 
getPoint(double, double[]) - Method in class pal.math.LineFunction
get point associated with the one-dimensional parameter (bounds of of multivariate function are NOT checked)
getPoint(PositionedNode, int, int) - Method in class pal.gui.TreePainterNormal
 
getPopulationSize(int) - Method in class pal.coalescent.SkylinePlot
Returns the population size in interval i.
getPositionMisalignmentInfo(Alignment, PrintWriter, int) - Static method in class pal.alignment.AlignmentUtils
 
getPositionMisalignmentInfo(Alignment, PrintWriter, int, CodonTable, boolean) - Static method in class pal.alignment.AlignmentUtils
 
getPositionType(int) - Method in class pal.alignment.StrippedAnnotatedAlignment
Returns position type (eg.
getPositionType(int) - Method in class pal.alignment.MultiLocusAnnotatedAlignment
Returns position type (eg.
getPositionType(int) - Method in class pal.alignment.SimpleAnnotatedAlignment
Returns position type (eg.
getPositionType(int) - Method in interface pal.alignment.AnnotationAlignment
Returns position type (eg.
getPositionType(int) - Method in class pal.alignment.IndelAnnotatedAlignment
Returns position type (eg.
getPositionType(int) - Method in class pal.alignment.ConcatenatedAnnotatedAlignment
Returns position type (eg.
getPreferredSize() - Method in class pal.gui.TreeComponent
 
getPreferredSize() - Method in interface pal.gui.Painter
 
getPreferredSize() - Method in class pal.gui.TreePainterNormal
Returns the preferred size for drawing (that is the size that will show everything nicely)
getPreferredSize() - Method in class pal.gui.TreePainterCircular
Returns the preferred size for drawing (that is the size that will show everything nicely)
getProgress() - Method in class pal.distance.AlignmentDistanceMatrix
Returns -1 if not doing anything, or a number between 0 and 1
getRandomArguments(MultivariateFunction) - Static method in class pal.math.MathUtils
 
getRandomNode(Tree) - Static method in class pal.tree.TreeUtils
Returns a uniformly distributed random node from the tree, including both internal and external nodes.
getRate() - Method in class pal.tree.DatedTipsClockTree
get rate
getRateDistribution() - Method in class pal.substmodel.SimpleSubstitutionModel
 
getRateDistribution() - Method in interface pal.substmodel.SubstitutionModel
 
getRateMatrix() - Method in class pal.substmodel.SimpleSubstitutionModel
 
getRateMatrix() - Method in interface pal.substmodel.SubstitutionModel
 
getRatio() - Method in class pal.coalescent.ExpandingPopulation
returns ratio of population sizes
getRelativeRates() - Method in class pal.substmodel.AbstractRateMatrix
 
getRelativeRates() - Method in class pal.substmodel.CachedRateMatrix
 
getRelativeRates() - Method in interface pal.substmodel.RateMatrix
Deprecated. try not to use.
getRobinsonFouldsDistance(SplitSystem, Tree) - Static method in class pal.tree.TreeUtils
computes Robinson-Foulds (1981) distance between two trees
getRobinsonFouldsDistance(Tree, Tree) - Static method in class pal.tree.TreeUtils
computes Robinson-Foulds (1981) distance between two trees
getRobinsonFouldsRescaledDistance(SplitSystem, Tree) - Static method in class pal.tree.TreeUtils
computes Robinson-Foulds (1981) distance between two trees rescaled to a number between 0 and 1
getRobinsonFouldsRescaledDistance(Tree, Tree) - Static method in class pal.tree.TreeUtils
computes Robinson-Foulds (1981) distance between two trees rescaled to a number between 0 and 1
getRoot() - Method in class pal.tree.ParameterizedTree
Returns the root node of this tree.
getRoot() - Method in class pal.tree.SimpleTree
Returns the root node of this tree.
getRoot() - Method in interface pal.tree.Tree
 
getRSqr(int, int) - Method in class pal.popgen.LinkageDisequilibrium
Returns r^2 estimate for a given pair of sites
getSampleCount() - Method in class pal.misc.TimeOrderCharacterData
Returns the number of unique times in this data.
getScreenDeltaX(double, double) - Method in class pal.gui.CircularGraphics
 
getScreenDeltaY(double, double) - Method in class pal.gui.CircularGraphics
 
getScreenX(double, double) - Method in class pal.gui.CircularGraphics
 
getScreenX(double, double, int) - Method in class pal.gui.CircularGraphics
 
getScreenY(double, double) - Method in class pal.gui.CircularGraphics
 
getScreenY(double, double, int) - Method in class pal.gui.CircularGraphics
 
getSE() - Method in class pal.misc.ParameterizedDouble
 
getSequence() - Method in class pal.tree.SimpleNode
Returns the sequence at this node, in the form of an array of bytes.
getSequence() - Method in interface pal.tree.Node
Returns the sequence at this node, in the form an array of bytes.
getSequenceCharArray(Alignment, int) - Static method in class pal.alignment.AlignmentUtils
Returns a particular sequence of an alignment as a char array
getSequenceCount() - Method in class pal.alignment.AbstractAlignment
Return number of sequences in this alignment
getSequenceCount() - Method in interface pal.alignment.CharacterAlignment
Return number of sequences(taxa) in this alignment
getSequenceCount() - Method in interface pal.alignment.Alignment
Return number of sequences in this alignment
getSequenceCount() - Method in class pal.alignment.SimpleCharacterAlignment
Return number of taxa or sequences in this alignment
getSequenceStates(DataType, String) - Static method in class pal.datatype.DataTypeUtils
Return states of a sequence.
getSequenceString() - Method in class pal.tree.SimpleNode
Returns the sequence at this node, in the form of a String.
getSequenceString(Alignment, int) - Static method in class pal.alignment.AlignmentUtils
Returns a particular sequence of an alignment as a String
getSFString(double, int) - Method in class pal.io.FormattedOutput
An alternative version of getSFString which works on the actual string Returns a string representing the given number to the number of significant figures requested.
getSignificance(double, int) - Static method in class pal.statistics.LikelihoodRatioTest
compute significance level for the differences in log-likelihood (based on chi-square distribution)
getSimpleStates(int) - Method in class pal.datatype.SimpleDataType
returns an array containing the non-ambiguous states that this state represents.
getSimpleStates(int) - Method in interface pal.datatype.DataType
returns an array containing the non-ambiguous states that this state represents.
getSimpleStates(int) - Method in class pal.datatype.IUPACNucleotides
returns an array containing the non-ambiguous states that this state represents.
getSimulatedInterval(int, double) - Method in class pal.coalescent.DemographicModel
Returns an random interval size selected from the Kingman prior of the demographic model.
getSiteCount() - Method in class pal.alignment.AbstractAlignment
Return number of sites for each sequence in this alignment
getSiteCount() - Method in interface pal.alignment.Alignment
 
getSiteCount() - Method in class pal.popgen.LinkageDisequilibrium
Returns the counts of the sites in the alignment
getSitePattern() - Method in class pal.eval.SimpleLikelihoodCalculator
 
getSitePattern() - Method in class pal.eval.LikelihoodValue
Returns the site pattern of this likelihood value
getSitePattern(Alignment) - Static method in class pal.alignment.SitePattern
 
getSize() - Method in class pal.distance.DistanceMatrix
Returns the number of rows and columns that the distance matrix has.
getSize() - Method in class pal.coalescent.SkylinePlot
Returns the number of intervals in this skyline plot.
getSizeOfScale(double) - Method in class pal.gui.TreePainter
 
getSmallestNumber() - Method in class pal.util.ThreeNumberSort
get smallest number
getSmallIntervals(double, boolean[]) - Method in class pal.coalescent.CoalescentIntervals
Returns a list stating which of the intervals are <= minSize (and thus should be pooled).
getSplit(IdGroup, Node, boolean[]) - Static method in class pal.tree.SplitUtils
get split for branch associated with internal node
getSplit(int) - Method in class pal.tree.SplitSystem
get split
getSplitCount() - Method in class pal.tree.SplitSystem
get number of splits
getSplits(IdGroup, Tree) - Static method in class pal.tree.SplitUtils
creates a split system from a tree (using a pre-specified order of sequences)
getSplits(Tree) - Static method in class pal.tree.SplitUtils
creates a split system from a tree (using tree-induced order of sequences)
getSplitVector() - Method in class pal.tree.SplitSystem
get split vector
getState(char) - Method in class pal.datatype.TwoStates
 
getState(char) - Method in class pal.datatype.GeneralizedCodons
get state corresponding to a character
getState(char) - Method in interface pal.datatype.DataType
get state corresponding to a character
getState(char) - Method in class pal.datatype.AminoAcids
 
getState(char) - Method in class pal.datatype.NumericDataType
get state corresponding to a character
getState(char) - Method in class pal.datatype.StateRemover
 
getState(char) - Method in class pal.datatype.Nucleotides
Get state corresponding to character c
NOTE: IF YOU CHANGE THIS IT MAY STOP THE NUCLEOTIDE TRANSLATOR FROM WORKING!
getState(char) - Method in class pal.datatype.IUPACNucleotides
 
getState(char) - Method in class pal.datatype.Codons
 
getStates() - Method in class pal.alignment.AbstractAlignment
Fills a [numsequences][length] matrix with indices.
getStates(char[][], DataType) - Static method in class pal.datatype.DataTypeUtils
For converting an array of sequence to arrays of ints where each int represents the state of the corresponding character in sequence
getStates(char[][], int, DataType) - Static method in class pal.datatype.DataTypeUtils
For converting an array of sequence to arrays of ints where each int represents the state of the corresponding character in sequence
getStates(char[], DataType) - Static method in class pal.datatype.DataTypeUtils
For converting a sequence to an array of ints where each int represents the state of the corresponding character in sequence
getStates(char[], int, DataType) - Static method in class pal.datatype.DataTypeUtils
For converting a sequence to an array of ints where each int represents the state of the corresponding character in sequence
getString() - Method in class pal.io.OutputTarget
get string corresponding to current stream created by openString()
getSubtree(Node, Node) - Static method in class pal.tree.RootedTreeUtils
 
getSuitableInstance(Alignment) - Static method in class pal.alignment.AlignmentUtils
guess data type suitable for a given sequence data set
getSuitableModelID(double[]) - Static method in class pal.substmodel.AminoAcidModel
get numerical code of amino acid model that would probably be suitable for a given sequence data set
getSummaryTypes() - Method in class pal.mep.ConstantMutationRate
 
getSummaryTypes() - Method in class pal.mep.WindowedMutationRate
 
getSummaryTypes() - Method in class pal.mep.SteppedMutationRate
 
getSummaryTypes() - Method in interface pal.misc.Summarizable
 
getSummaryTypes() - Method in class pal.misc.SimpleSummarizable
 
getSummaryTypes() - Method in class pal.coalescent.ConstantPopulation
 
getSummaryTypes() - Method in class pal.coalescent.ExponentialGrowth
 
getSummaryValue(int) - Method in class pal.mep.ConstantMutationRate
 
getSummaryValue(int) - Method in class pal.mep.WindowedMutationRate
 
getSummaryValue(int) - Method in class pal.mep.SteppedMutationRate
 
getSummaryValue(int) - Method in interface pal.misc.Summarizable
 
getSummaryValue(int) - Method in class pal.misc.SimpleSummarizable
 
getSummaryValue(int) - Method in class pal.coalescent.ConstantPopulation
 
getSummaryValue(int) - Method in class pal.coalescent.ExponentialGrowth
 
getTableColumnNames() - Method in class pal.alignment.SimpleCharacterAlignment
Return column names for the table
getTableColumnNames() - Method in interface pal.misc.TableReport
get the names of the columns
getTableColumnNames() - Method in class pal.popgen.LinkageDisequilibrium
 
getTableData() - Method in class pal.alignment.SimpleCharacterAlignment
Return data for the table
getTableData() - Method in interface pal.misc.TableReport
get the data elements
getTableData() - Method in class pal.popgen.LinkageDisequilibrium
 
getTableTitle() - Method in class pal.alignment.SimpleCharacterAlignment
Return the name for the title of the ANOVA
getTableTitle() - Method in interface pal.misc.TableReport
get the title of the table
getTableTitle() - Method in class pal.popgen.LinkageDisequilibrium
 
getTerminatorIndexes() - Method in interface pal.datatype.CodonTable
Returns the codon indexes of terminator amino acids.
getTime(double) - Method in class pal.mep.MutationRateModel
Return the time at which expected substitutions has occurred.
getTime(double) - Method in class pal.mep.ConstantMutationRate
 
getTime(double) - Method in class pal.mep.WindowedMutationRate
Window must not span zero!
getTime(double) - Method in class pal.mep.SteppedMutationRate
 
getTime(int) - Method in class pal.misc.TimeOrderCharacterData
 
getTimeIntervals(double[], double, double) - Static method in class pal.mep.SteppedMutationRate
 
getTimeOrderCharacterData() - Method in class pal.gui.TreePainter
 
getTimeOrderCharacterData() - Method in class pal.tree.DatedTipsClockTree
Gets the TimeOrderCharacterData
getTimeOrdinal(int) - Method in class pal.misc.TimeOrderCharacterData
 
getTitle() - Method in class pal.gui.TreePainter
 
getTitle() - Method in class pal.gui.TreeComponent
 
getTotal(double[]) - Static method in class pal.math.MathUtils
 
getTotal(double[], int, int) - Static method in class pal.math.MathUtils
 
getTotalHeight() - Method in class pal.coalescent.CoalescentIntervals
get the total height of the genealogy represented by these intervals.
getTrait(int, int) - Method in interface pal.alignment.CharacterAlignment
Return the trait value for a given sequence (taxon) and trait number
getTrait(int, int) - Method in class pal.alignment.SimpleCharacterAlignment
Return the trait value for a given sequence (taxon) and trait number
getTraitCount() - Method in interface pal.alignment.CharacterAlignment
Return number of traits for each sequence in this alignment
getTraitCount() - Method in class pal.alignment.SimpleCharacterAlignment
Return number of trait for each taxon in this alignment
getTraitName(int) - Method in interface pal.alignment.CharacterAlignment
Return name of the trait for this trait number
getTraitName(int) - Method in class pal.alignment.SimpleCharacterAlignment
Return name of the trait for this trait number
getTransitionProbabilities(double[][]) - Method in class pal.substmodel.AbstractRateMatrix
A utility method for speed, transfers trans prob information quickly into store
getTransitionProbabilities(double[][]) - Method in class pal.substmodel.MatrixExponential
A utility method for speed, transfers trans prob information quickly into store
getTransitionProbabilities(double[][]) - Method in class pal.substmodel.CachedRateMatrix
 
getTransitionProbabilities(double[][]) - Method in interface pal.substmodel.RateMatrix
A utility method for speed, transfers trans prob information quickly into store
getTransitionProbability(int, int) - Method in class pal.substmodel.AbstractRateMatrix
Returns the probability of going from one state to another given the current distance
getTransitionProbability(int, int) - Method in class pal.substmodel.MatrixExponential
 
getTransitionProbability(int, int) - Method in class pal.substmodel.CachedRateMatrix
get transition probability for the preselected model and the previously specified distance
getTransitionProbability(int, int) - Method in interface pal.substmodel.RateMatrix
 
getTransitionTime() - Method in class pal.coalescent.ConstExpGrowth
Gets the time of transition from constant phase to exponential phase.
getTree() - Method in class pal.eval.SimpleLikelihoodCalculator
 
getTree() - Method in class pal.eval.LikelihoodValue
Returns the (potentially parameterized) tree of this likelihood value.
getTree() - Method in class pal.eval.ChiSquareValue
Returns the (parameterized) tree of this likelihood value.
getTree() - Method in class pal.gui.TreePainter
 
getTree() - Method in class pal.coalescent.SerialCoalescentSimulator
 
getTypeID() - Method in class pal.substmodel.AbstractRateMatrix
get numerical code describing the data type
getTypeID() - Method in class pal.substmodel.CachedRateMatrix
 
getTypeID() - Method in interface pal.substmodel.RateMatrix
get numerical code describing the data type
getTypeID() - Method in class pal.datatype.TwoStates
 
getTypeID() - Method in class pal.datatype.GeneralizedCodons
Get numerical code describing the data type
getTypeID() - Method in interface pal.datatype.DataType
get numerical code describing the data type
getTypeID() - Method in class pal.datatype.AminoAcids
 
getTypeID() - Method in class pal.datatype.NumericDataType
Get numerical code describing the data type
getTypeID() - Method in class pal.datatype.StateRemover
 
getTypeID() - Method in class pal.datatype.Nucleotides
 
getTypeID() - Method in class pal.datatype.IUPACNucleotides
 
getTypeID() - Method in class pal.datatype.Codons
 
getUniqueName() - Method in class pal.substmodel.Dayhoff
 
getUniqueName() - Method in class pal.substmodel.BLOSUM62
 
getUniqueName() - Method in class pal.substmodel.CachedRateMatrix
 
getUniqueName() - Method in class pal.substmodel.HKY
 
getUniqueName() - Method in interface pal.substmodel.RateMatrix
 
getUniqueName() - Method in class pal.substmodel.CPREV
 
getUniqueName() - Method in class pal.substmodel.GTR
 
getUniqueName() - Method in class pal.substmodel.MTREV24
 
getUniqueName() - Method in class pal.substmodel.F81
 
getUniqueName() - Method in class pal.substmodel.YangCodonModel
 
getUniqueName() - Method in class pal.substmodel.JTT
 
getUniqueName() - Method in class pal.substmodel.WAG
 
getUniqueName() - Method in class pal.substmodel.TN
 
getUniqueName() - Method in class pal.substmodel.F84
 
getUniqueName() - Method in class pal.substmodel.VT
 
getUniqueName() - Method in class pal.substmodel.TwoStateModel
 
getUniqueTimeArray() - Method in class pal.misc.TimeOrderCharacterData
Returns an ordered vector of unique times in this time order character data.
getUniqueTimeMatrix() - Method in class pal.misc.TimeOrderCharacterData
Returns a matrix of times between samples.
getUnits() - Method in class pal.mep.MutationRateModel
returns units of measurement.
getUnits() - Method in class pal.misc.TimeOrderCharacterData
 
getUnits() - Method in class pal.tree.ParameterizedTree
 
getUnits() - Method in class pal.tree.SimpleTree
Return the units that this tree is expressed in.
getUnits() - Method in interface pal.tree.Tree
Gets the units that this tree's branch lengths and node heights are expressed in.
getUnits() - Method in class pal.coalescent.DemographicModel
returns units of measurement.
getUnits() - Method in class pal.coalescent.SkylinePlot
Returns unit of time.
getUnits() - Method in class pal.coalescent.CoalescentIntervals
Returns the units these coalescent intervals are measured in.
getUnitsAttr(Element) - Static method in class pal.xml.ElementParser
 
getUnrooted(Node) - Static method in class pal.tree.NodeUtils
Attempts to remove the root of a tree by making it polyficating (as opposed to bificating).
getUnrootedBranchCount(Node) - Static method in class pal.tree.NodeUtils
returns number of branches centered around an internal node in an unrooted tree
getUnrootedTree(Tree) - Static method in class pal.tree.TreeUtils
Creates an unrooted copy of a tree.
getUpperBound() - Method in class pal.distance.SequencePairLikelihood
 
getUpperBound() - Method in class pal.math.OrthogonalLineFunction
 
getUpperBound() - Method in interface pal.math.UnivariateFunction
get upper bound of argument
getUpperBound() - Method in class pal.math.LineFunction
 
getUpperBound(int) - Method in class pal.eval.ModelParameters
 
getUpperBound(int) - Method in class pal.eval.ChiSquareValue
 
getUpperBound(int) - Method in class pal.eval.DemographicValue
 
getUpperBound(int) - Method in class pal.math.BoundsCheckedFunction
 
getUpperBound(int) - Method in interface pal.math.MultivariateFunction
get upper bound of argument n
getUpperBoundParameter() - Method in class pal.math.LineFunction
get parameter that limits the upper bound
getUpperLimit() - Method in class pal.misc.ParameterizedDouble
 
getUpperLimit(int) - Method in class pal.mep.ConstantMutationRate
 
getUpperLimit(int) - Method in class pal.mep.WindowedMutationRate
 
getUpperLimit(int) - Method in class pal.mep.SteppedMutationRate
 
getUpperLimit(int) - Method in class pal.misc.ParameterizedDouble
get upper parameter limit
getUpperLimit(int) - Method in interface pal.misc.Parameterized
get upper parameter limit
getUpperLimit(int) - Method in class pal.substmodel.AminoAcidModel
 
getUpperLimit(int) - Method in class pal.substmodel.SimpleSubstitutionModel
 
getUpperLimit(int) - Method in class pal.substmodel.GammaRates
 
getUpperLimit(int) - Method in class pal.substmodel.CachedRateMatrix
 
getUpperLimit(int) - Method in class pal.substmodel.HKY
 
getUpperLimit(int) - Method in class pal.substmodel.GTR
 
getUpperLimit(int) - Method in class pal.substmodel.F81
 
getUpperLimit(int) - Method in class pal.substmodel.InvariableSites
 
getUpperLimit(int) - Method in class pal.substmodel.YangCodonModel
 
getUpperLimit(int) - Method in class pal.substmodel.TN
 
getUpperLimit(int) - Method in class pal.substmodel.F84
 
getUpperLimit(int) - Method in class pal.substmodel.UniformRate
 
getUpperLimit(int) - Method in class pal.substmodel.TwoStateModel
 
getUpperLimit(int) - Method in class pal.tree.UnconstrainedTree
 
getUpperLimit(int) - Method in class pal.tree.LogParameterizedTree
 
getUpperLimit(int) - Method in class pal.tree.DatedTipsClockTree
 
getUpperLimit(int) - Method in class pal.tree.MutationRateModelTree
 
getUpperLimit(int) - Method in class pal.tree.ClockTree
 
getUpperLimit(int) - Method in class pal.coalescent.ConstantPopulation
 
getUpperLimit(int) - Method in class pal.coalescent.ExponentialGrowth
 
getUpperLimit(int) - Method in class pal.coalescent.ConstExpGrowth
 
getUpperLimit(int) - Method in class pal.coalescent.ExpandingPopulation
 
getValue() - Method in class pal.misc.ParameterizedDouble
Get the current value of this double
getValue() - Method in class pal.misc.Attribute
 
getVersionString() - Static method in class pal.util.Version
 
getWeightedLocusPosition(int) - Method in class pal.alignment.StrippedAnnotatedAlignment
Return the weighted position along the gene (handles gaps)
getWeightedLocusPosition(int) - Method in class pal.alignment.MultiLocusAnnotatedAlignment
Return the weighted position along the gene (handles gaps)
getWeightedLocusPosition(int) - Method in class pal.alignment.SimpleAnnotatedAlignment
Return the weighted position along the gene (handles gaps)
getWeightedLocusPosition(int) - Method in interface pal.alignment.AnnotationAlignment
Return the weighted position along the locus (handles gaps)
getWeightedLocusPosition(int) - Method in class pal.alignment.IndelAnnotatedAlignment
Return the weighted position along the gene (handles gaps)
getWeightedLocusPosition(int) - Method in class pal.alignment.ConcatenatedAnnotatedAlignment
Return the weighted position along the gene (handles gaps)
getX() - Method in class pal.gui.PositionedNode
 
gradient(MultivariateFunction, double[]) - Static method in class pal.math.NumericalDerivative
determine gradient
gradient(MultivariateFunction, double[], double[]) - Static method in class pal.math.NumericalDerivative
determine gradient
groupIntervals(CoalescentIntervals) - Method in class pal.coalescent.CoalescentIntervals
Group intervals following a given (compatible) reference.
GROWTH_RATE - Static variable in interface pal.util.XMLConstants
 
GTR - class pal.substmodel.GTR.
GTR (general time reversible) model of nucleotide evolution
GTR - Static variable in interface pal.substmodel.NucleotideModelID
 
GTR - Static variable in interface pal.util.XMLConstants
 
GTR(double[], double[]) - Constructor for class pal.substmodel.GTR
constructor 2
GTR(double, double, double, double, double, double[]) - Constructor for class pal.substmodel.GTR
constructor 1
guessDataType() - Method in class pal.alignment.AbstractAlignment
Guess data type

H

hallCI(double, double, double[]) - Static method in class pal.statistics.BootstrapStatistics
compute approximate central confidence interval for thetaHat (Hall percentile method)
hallCI(double, double, double[], int[]) - Static method in class pal.statistics.BootstrapStatistics
compute approximate central confidence interval for thetaHat (Hall percentile method)
hasAttribute(Element, String) - Static method in class pal.xml.ElementParser
This method allows the removeal of e.hasAttribute which is DOM Level 2.
hasChildren() - Method in class pal.tree.SimpleNode
check whether this node is an internal node
hasSplit(boolean[]) - Method in class pal.tree.SplitSystem
+ test whether a split is contained in this split system (assuming the same leaf order)
hasTimes() - Method in class pal.misc.TimeOrderCharacterData
 
HeapSort - class pal.util.HeapSort.
sorts numbers and comparable objects by treating contents of array as a binary tree.
HeapSort() - Constructor for class pal.util.HeapSort
 
HEIGHT - Static variable in interface pal.util.XMLConstants
 
heights2Lengths(Node) - Static method in class pal.tree.NodeUtils
determines branch lengths of this and all descendent nodes from heights
heights2Lengths(Node, boolean) - Static method in class pal.tree.NodeUtils
determines branch lengths of this and all descendent nodes from heights
heights2parameters() - Method in class pal.tree.MutationRateModelTree
 
heights2parameters() - Method in class pal.tree.ClockTree
 
heights2parameters() - Method in class pal.coalescent.DemographicClockTree
 
HILITED_LABEL_COLOR - Static variable in class pal.gui.TreePainter
 
HKY - class pal.substmodel.HKY.
Hasegawa-Kishino-Yano model of nucleotide evolution
HKY - Static variable in interface pal.substmodel.NucleotideModelID
 
HKY - Static variable in interface pal.util.XMLConstants
 
HKY(double[], double[]) - Constructor for class pal.substmodel.HKY
Constructor 2
HKY(double, double[]) - Constructor for class pal.substmodel.HKY
Constructor 1

I

ID - Static variable in interface pal.util.XMLConstants
 
Identifier - class pal.misc.Identifier.
An identifier for some sampled data.
Identifier() - Constructor for class pal.misc.Identifier
 
Identifier(String) - Constructor for class pal.misc.Identifier
 
IdGenerator - class pal.misc.IdGenerator.
Generates IdGroup objects given certain parameters.
IdGenerator() - Constructor for class pal.misc.IdGenerator
 
idGroup - Variable in class pal.alignment.AbstractAlignment
sequence identifiers
idGroup - Variable in class pal.alignment.SimpleCharacterAlignment
sequence identifiers
idGroup - Variable in class pal.distance.DistanceMatrix
sequence identifiers
IdGroup - interface pal.misc.IdGroup.
An indexed group of identifiers.
illc - Variable in class pal.math.ConjugateDirectionSearch
illc should be set to true if the problem is known to be ill-conditioned. the default is false. this variable is automatically set, when the problem is found to to be ill-conditioned during iterations.
incompleteGammaP(double, double) - Static method in class pal.math.GammaFunction
Incomplete Gamma function P(a,x) = 1-Q(a,x) (a cleanroom implementation of Numerical Recipes gammp(a,x); in Mathematica this function is 1-GammaRegularized)
incompleteGammaP(double, double, double) - Static method in class pal.math.GammaFunction
Incomplete Gamma function P(a,x) = 1-Q(a,x) (a cleanroom implementation of Numerical Recipes gammp(a,x); in Mathematica this function is 1-GammaRegularized)
incompleteGammaQ(double, double) - Static method in class pal.math.GammaFunction
Incomplete Gamma function Q(a,x) (a cleanroom implementation of Numerical Recipes gammq(a,x); in Mathematica this function is called GammaRegularized)
IndelAlignment - class pal.alignment.IndelAlignment.
This class extracts indels (insertion/deletion) out of an alignment, and creates an alignment of indel polymorphisms.
IndelAlignment(Alignment, boolean) - Constructor for class pal.alignment.IndelAlignment
Basic constructor.
IndelAnnotatedAlignment - class pal.alignment.IndelAnnotatedAlignment.
an extension of the IndelAlignment that includes annotation.
IndelAnnotatedAlignment(AnnotationAlignment, boolean) - Constructor for class pal.alignment.IndelAnnotatedAlignment
Basic constructor.
init(IdGroup, String[]) - Method in class pal.alignment.MultiLocusAnnotatedAlignment
 
init(Node) - Method in class pal.tree.SimpleNode
 
init(Node, boolean) - Method in class pal.tree.SimpleNode
Initialized node instance variables based on given Node. children are ignored.
init(Node, boolean, LabelMapping) - Method in class pal.tree.SimpleNode
Initialized node instance variables based on given Node. children are ignored.
initMatrices() - Method in class pal.alignment.MultiLocusAnnotatedAlignment
 
InputSource - class pal.io.InputSource.
convenience class to open input streams linked to files, stdin, and strings
insertChild(Node, int) - Method in class pal.tree.SimpleNode
add new child node (insertion at a specific position)
insertChild(Node, int) - Method in interface pal.tree.Node
add new child node (insertion at a specific position)
INTEGER - Static variable in class pal.misc.Attribute
 
intervals - Variable in class pal.eval.DemographicValue
 
IntervalsExtractor - class pal.coalescent.IntervalsExtractor.
A series of coalescent intervals representing the time order information contained in a (serial) clock-constrained tree.
IntervalsExtractor() - Constructor for class pal.coalescent.IntervalsExtractor
 
InvariableSites - class pal.substmodel.InvariableSites.
invariable sites model (two-rate model with mean rate = 1.0)
InvariableSites(double) - Constructor for class pal.substmodel.InvariableSites
construct discrete rate distribution with two rates (one invariable and one variable)
inverseErf(double) - Static method in class pal.math.ErrorFunction
inverse error function
isAmbiguousState(int) - Method in class pal.datatype.SimpleDataType
returns true if this state is an ambiguous state.
isAmbiguousState(int) - Method in interface pal.datatype.DataType
returns true if this state is an ambiguous state.
isAmbiguousState(int) - Method in class pal.datatype.IUPACNucleotides
returns true if this state is an ambiguous state.
isAncestor(Node, Node) - Static method in class pal.tree.NodeUtils
For two nodes in the tree true if the first node is the ancestor of the second
isBinaryCoalescent() - Method in class pal.coalescent.CoalescentIntervals
Checks whether this set of coalescent intervals is fully resolved (i.e. whether is has exactly one coalescent event in each subsequent interval)
isCoalescentOnly() - Method in class pal.coalescent.CoalescentIntervals
Checks whether this set of coalescent intervals coalescent only (i.e. whether is has exactly one or more coalescent event in each subsequent interval)
isDebugging() - Method in class pal.util.Log
 
isGap(Alignment, int, int) - Static method in class pal.alignment.AlignmentUtils
Returns true if the alignment has a gap at the site in the sequence specified.
isGap(DataType, char) - Static method in class pal.datatype.DataTypeUtils
returns true if the character represents a gap in the sequence.
isGap(int, int) - Method in class pal.alignment.AbstractAlignment
returns true if there is a gap in the give position.
isGapChar(char) - Method in class pal.datatype.SimpleDataType
 
isHighlighted() - Method in class pal.gui.PositionedNode
 
isLeaf() - Method in class pal.tree.SimpleNode
check whether this node is an external node
isLeaf() - Method in interface pal.tree.Node
check whether this node is an external node
isRoot() - Method in class pal.tree.SimpleNode
check whether this node is a root node
isRoot() - Method in interface pal.tree.Node
check whether this node is a root node
isSame(boolean[], boolean[]) - Static method in class pal.tree.SplitUtils
checks whether two splits are identical (assuming they are of the same length and use the same leaf order)
isShowingInternalLabels() - Method in class pal.gui.TreePainter
 
isShowingNodeHeights() - Method in class pal.gui.TreePainter
 
isShowTitle() - Method in class pal.gui.TreePainter
 
isSimpleJukesCantor() - Method in class pal.substmodel.SimpleSubstitutionModel
 
isSiteRedundant(Alignment, int) - Static method in class pal.alignment.AlignmentUtils
 
isSymmetric() - Method in class pal.distance.DistanceMatrix
test whether this matrix is a symmetric distance matrix
isTransistionByChar(char, char) - Method in class pal.datatype.Nucleotides
 
isTransistionByState(int, int) - Method in class pal.datatype.Nucleotides
 
isUnknownChar(char) - Method in class pal.datatype.SimpleDataType
 
isUnknownChar(char) - Method in interface pal.datatype.DataType
 
isUnknownChar(char) - Method in class pal.datatype.IUPACNucleotides
 
isUnknownState(int) - Method in class pal.datatype.SimpleDataType
 
isUnknownState(int) - Method in class pal.datatype.TwoStates
 
isUnknownState(int) - Method in class pal.datatype.GeneralizedCodons
 
isUnknownState(int) - Method in interface pal.datatype.DataType
 
isUnknownState(int) - Method in class pal.datatype.AminoAcids
 
isUnknownState(int) - Method in class pal.datatype.NumericDataType
 
isUnknownState(int) - Method in class pal.datatype.StateRemover
 
isUnknownState(int) - Method in class pal.datatype.Nucleotides
 
isUnknownState(int) - Method in class pal.datatype.IUPACNucleotides
 
isUnknownState(int) - Method in class pal.datatype.Codons
 
isUsingColor() - Method in class pal.gui.TreePainter
 
isUsingSymbols() - Method in class pal.gui.TreePainter
 
IUPAC_NUCELOTIDES_DESCRIPTION - Static variable in interface pal.datatype.DataType
iupac nucleotide name (for XML and human readability)
IUPACNucleotides - class pal.datatype.IUPACNucleotides.
implements DataType for nucleotides with ambiguous characters
IUPACNUCLEOTIDES - Static variable in interface pal.datatype.DataType
 
IUPACNucleotides() - Constructor for class pal.datatype.IUPACNucleotides
 
IUPACPenalties - Variable in class pal.datatype.IUPACPenaltyTable
 
IUPACPenaltyTable - class pal.datatype.IUPACPenaltyTable.
Implements a table of transition penalties for a DNA states and IUPAC ambiguous states.
IUPACPenaltyTable() - Constructor for class pal.datatype.IUPACPenaltyTable
 

J

JC - Static variable in interface pal.util.XMLConstants
 
joinChilds(Node, int, int) - Static method in class pal.tree.NodeUtils
join two childs, introducing a new node/branch in the tree that replaces the first child
JTT - class pal.substmodel.JTT.
JTT model of amino acid evolution
JTT - Static variable in interface pal.substmodel.AminoAcidModelID
 
JTT - Static variable in interface pal.util.XMLConstants
 
JTT(double[]) - Constructor for class pal.substmodel.JTT
constructor
JukesCantorDistanceMatrix - class pal.distance.JukesCantorDistanceMatrix.
compute jukes-cantor corrected distance matrix
JukesCantorDistanceMatrix(Alignment) - Constructor for class pal.distance.JukesCantorDistanceMatrix
compute jukes-cantor corrected distances
JukesCantorDistanceMatrix(DistanceMatrix) - Constructor for class pal.distance.JukesCantorDistanceMatrix
compute jukes-cantor corrected distances (assumes nucleotides as underlying data)
JukesCantorDistanceMatrix(DistanceMatrix, int) - Constructor for class pal.distance.JukesCantorDistanceMatrix
compute jukes-cantor corrected distances
JukesCantorDistanceMatrix(SitePattern) - Constructor for class pal.distance.JukesCantorDistanceMatrix
compute jukes-cantor corrected distances
jumble() - Method in class pal.alignment.JumbledAlignment
jumble sequences (rearrange input order)
JumbledAlignment - class pal.alignment.JumbledAlignment.
generates jumbled alignments (randomizing input order of sequences)
JumbledAlignment(Alignment) - Constructor for class pal.alignment.JumbledAlignment
 

K

KAPPA - Static variable in interface pal.util.XMLConstants
 
KishinoHasegawaTest - class pal.statistics.KishinoHasegawaTest.
Kishino-Hasegawa-(Templeton)-Test (1989, 1983) to compare a set of evolutionary hypotheses
KishinoHasegawaTest() - Constructor for class pal.statistics.KishinoHasegawaTest
 

L

labelInternalNodes(Tree) - Static method in class pal.tree.TreeUtils
Labels the internal nodes of the tree using numbers starting from 0.
LabelMapping - class pal.misc.LabelMapping.
 
LabelMapping() - Constructor for class pal.misc.LabelMapping
 
lastSite - Variable in class pal.alignment.StrippedAnnotatedAlignment
 
LayoutTracker - class pal.gui.LayoutTracker.
 
LayoutTracker() - Constructor for class pal.gui.LayoutTracker
 
LEFTBORDER - Static variable in class pal.gui.TreePainterNormal
 
LEFTBORDER - Static variable in class pal.gui.TreePainterCircular
 
LENGTH - Static variable in interface pal.util.XMLConstants
 
lengths2Heights(Node) - Static method in class pal.tree.NodeUtils
Converts lengths to heights, *without* assuming contemporaneous tips.
lengths2HeightsContemp() - Method in class pal.tree.SimpleNode
determines the height of this node and its descendants from branch lengths, assuming contemporaneous tips.
lengths2HeightsKeepTips(Node, boolean) - Static method in class pal.tree.NodeUtils
Converts lengths to heights, but maintains tip heights.
LikelihoodCalculator - interface pal.eval.LikelihoodCalculator.
classes that calculate likelihoods should implement this interface.
likelihoodOrder - Variable in class pal.statistics.ModelSupport
likelhood order of the tree hypotheses
LikelihoodRatioTest - class pal.statistics.LikelihoodRatioTest.
Likelihood ratio test based on chi-square statistics
LikelihoodRatioTest() - Constructor for class pal.statistics.LikelihoodRatioTest
 
LikelihoodValue - class pal.eval.LikelihoodValue.
Computes the likelihood for a tree given a model of sequence evolution and a sequence alignment; also optimises tree parameters such as branch lengths by maximising the likelihood (for optimal performance special optimisation procedures are employed for UnconstrainedTree, ClockTree and DatedTipsClockTree; a general optimisation precedure is used for another ParameterizedTree).
LikelihoodValue(SitePattern) - Constructor for class pal.eval.LikelihoodValue
initialization
LineFunction - class pal.math.LineFunction.
converts a multivariate function into a univariate function
LineFunction(MultivariateFunction) - Constructor for class pal.math.LineFunction
construct univariate function from multivariate function
LinkageDisequilibrium - class pal.popgen.LinkageDisequilibrium.
This class calculates D' and r^2 estimates of linkage disequilibrium.
LinkageDisequilibrium(Alignment) - Constructor for class pal.popgen.LinkageDisequilibrium
compute LD based on an alignment.
LinkageDisequilibrium(Alignment, boolean, int) - Constructor for class pal.popgen.LinkageDisequilibrium
compute LD based on an alignment
LinkageDisequilibriumComponent - class pal.gui.LinkageDisequilibriumComponent.
An AWT Component for displaying information on linkage disequilibrium.
LinkageDisequilibriumComponent(LinkageDisequilibrium, boolean, boolean) - Constructor for class pal.gui.LinkageDisequilibriumComponent
 
lnGamma(double) - Static method in class pal.math.GammaFunction
log Gamma function: ln(gamma(alpha)) for alpha>0, accurate to 10 decimal places
Local - class pal.tree.Local.
Implements LOCAL (Larget and Simon, 1999) and stochastic NNI moves for unrooted trees.
Local() - Constructor for class pal.tree.Local
 
local(Tree) - Static method in class pal.tree.Local
 
local(Tree, double) - Static method in class pal.tree.Local
This method does a local interchange on the given tree: Note the original tree is modified.
localHeights2Lengths(Node, boolean) - Static method in class pal.tree.NodeUtils
determines branch lengths of this node and its immediate descendent nodes from heights.
locusName - Variable in class pal.alignment.MultiLocusAnnotatedAlignment
used to designate locus name
locusName - Variable in class pal.alignment.SimpleAnnotatedAlignment
used to designate locus name
locusName - Variable in class pal.alignment.IndelAnnotatedAlignment
used to designate locus name
locusPosition - Variable in class pal.alignment.MultiLocusAnnotatedAlignment
used to designate position; do not account for gaps
locusPosition - Variable in class pal.alignment.IndelAnnotatedAlignment
used to designate position; do not account for gaps
Log - class pal.util.Log.
Log provides a mechanism for logging and debugging to the standard output stream.
Log() - Constructor for class pal.util.Log
 
log(Object) - Method in class pal.util.Log
 
log(Object) - Method in interface pal.util.Logger
 
Logger - interface pal.util.Logger.
Interface for all objects that provide a logging facility.
logL - Variable in class pal.eval.LikelihoodValue
Log-Likelihood
logL - Variable in class pal.eval.DemographicValue
Log-Likelihood
LogParameterizedTree - class pal.tree.LogParameterizedTree.
This class logarithmically transforms tree parameters.
LogParameterizedTree(ParameterizedTree) - Constructor for class pal.tree.LogParameterizedTree
Takes a parameterized object and transforms the parameters logarithmically.

M

M_VERTEBRATE - Static variable in class pal.datatype.CodonTableFactory
Mitochondrial Vertebrate type
MachineAccuracy - class pal.math.MachineAccuracy.
determines machine accuracy
MachineAccuracy() - Constructor for class pal.math.MachineAccuracy
 
main(String[]) - Static method in class pal.tree.Local
 
main(String[]) - Static method in class pal.util.HeapSort
test harness for heapsort algorithm
makeMTREV24() - Method in class pal.substmodel.MTREV24
 
mapExternalIdentifiers(IdGroup, Tree) - Static method in class pal.tree.TreeUtils
map external identifiers in the tree to a set of given identifiers (which can be larger than the set of external identifiers but must contain all of them) NOTE: for efficiency it is assumed that the node lists of the tree are correctly maintained.
MathUtils - class pal.math.MathUtils.
Handy utility functions which have some Mathematical relavance.
MathUtils() - Constructor for class pal.math.MathUtils
 
MatrixExponential - class pal.substmodel.MatrixExponential.
compute matrix exponential and, subsequently, transition probabilities for a given rate matrix
MatrixExponential(RateMatrix) - Constructor for class pal.substmodel.MatrixExponential
create module
MAXARC - Static variable in interface pal.misc.BranchLimits
maximum branch length
maxFun - Variable in class pal.math.MultivariateMinimum
maxFun is the maximum number of calls to fun allowed. the default value of 0 indicates no limit on the number of calls.
maxFun - Variable in class pal.math.UnivariateMinimum
maximum number of function evaluations (default 0 indicates no limit on calls)
MEAN_CLADE_HEIGHT - Static variable in interface pal.tree.AttributeNode
attribute name for the mean height of this clade in a group of trees.
mean(double) - Static method in class pal.statistics.ExponentialDistribution
mean of the exponential distribution
mean(double) - Static method in class pal.statistics.ChiSquareDistribution
mean of the chi-square distribution
mean(double[]) - Static method in class pal.statistics.DiscreteStatistics
compute mean
mean(double, double) - Static method in class pal.statistics.GammaDistribution
mean of the Gamma distribution
mean(double, double) - Static method in class pal.statistics.NormalDistribution
mean
mean(double, double) - Static method in class pal.statistics.ParetoDistribution
mean of the Pareto distribution
meanDistance() - Method in class pal.distance.DistanceMatrix
Returns the mean pairwise distance of this matrix
MersenneTwisterFast - class pal.math.MersenneTwisterFast.
MersenneTwisterFast: A simulation quality fast random number generator (MT19937) with the same public methods as java.util.Random.
MersenneTwisterFast() - Constructor for class pal.math.MersenneTwisterFast
Constructor using the time of day as default seed.
MersenneTwisterFast(long) - Constructor for class pal.math.MersenneTwisterFast
Constructor using a given seed.
MFWithGradient - interface pal.math.MFWithGradient.
interface for a function of several variables with a gradient
MINARC - Static variable in interface pal.misc.BranchLimits
minimum branch length
minimumCount - Variable in class pal.alignment.StrippedAnnotatedAlignment
 
minimumProportion - Variable in class pal.alignment.StrippedAnnotatedAlignment
 
minus(DistanceMatrix, int) - Static method in class pal.distance.DistanceMatrixUtils
Returns a distance matrix with the specified taxa removed.
minx - Variable in class pal.math.UnivariateMinimum
last minimum
MISSING - Static variable in interface pal.alignment.CharacterAlignment
 
MISSING - Static variable in interface pal.util.XMLConstants
 
MODE_NAMES - Static variable in class pal.gui.TreeComponent
 
model - Variable in class pal.eval.DemographicValue
 
MODEL - Static variable in interface pal.util.XMLConstants
 
MODELCOUNT - Static variable in interface pal.substmodel.NucleotideModelID
 
MODELCOUNT - Static variable in interface pal.substmodel.AminoAcidModelID
 
ModelParameters - class pal.eval.ModelParameters.
estimates substitution model parameters from the data
ModelParameters(SitePattern, SubstitutionModel) - Constructor for class pal.eval.ModelParameters
Constructor
ModelSupport - class pal.statistics.ModelSupport.
Computes Akaike weights and expected Akaike weights (relative evidence, expected relative evidence) for a set of models and computes corresponding confidence sets
ModelSupport() - Constructor for class pal.statistics.ModelSupport
 
modelUpdated() - Method in class pal.eval.SimpleLikelihoodCalculator
 
moment(int, double, double) - Static method in class pal.statistics.ParetoDistribution
moments E(X^n) of the Pareto distribution
MONTHS - Static variable in interface pal.misc.Units
 
MONTHS - Static variable in interface pal.util.XMLConstants
 
MTREV24 - class pal.substmodel.MTREV24.
MTREV24 model of amino acid evolution
MTREV24 - Static variable in interface pal.substmodel.AminoAcidModelID
 
MTREV24 - Static variable in interface pal.util.XMLConstants
 
MTREV24(double[]) - Constructor for class pal.substmodel.MTREV24
constructor
MU_STEP_TIME - Static variable in interface pal.util.XMLConstants
 
muBackground - Variable in class pal.mep.WindowedMutationRate
mutation rates
muBackgroundSE - Variable in class pal.mep.WindowedMutationRate
mutation rate SEs
muChanges - Variable in class pal.mep.SteppedMutationRate
mutation rate change times
MultiLocusAnnotatedAlignment - class pal.alignment.MultiLocusAnnotatedAlignment.
MultiLocusAnnotatedAlignment is an extension of the SimpleAlignment that includes Annotation, and is designed for multiple loci.
MultiLocusAnnotatedAlignment() - Constructor for class pal.alignment.MultiLocusAnnotatedAlignment
null constructor.
MultiLocusAnnotatedAlignment(Alignment) - Constructor for class pal.alignment.MultiLocusAnnotatedAlignment
Basic constructor.
MultiLocusAnnotatedAlignment(AnnotationAlignment) - Constructor for class pal.alignment.MultiLocusAnnotatedAlignment
Clone constructor for Annotated alignment
MultiLocusAnnotatedAlignment(AnnotationAlignment, IdGroup) - Constructor for class pal.alignment.MultiLocusAnnotatedAlignment
This constructor will subset the alignment based on the taxa in IdGroup
MultiLocusAnnotatedAlignment(Identifier[], String[], String) - Constructor for class pal.alignment.MultiLocusAnnotatedAlignment
 
MultiLocusAnnotatedAlignment(IdGroup, String[]) - Constructor for class pal.alignment.MultiLocusAnnotatedAlignment
 
MultiLocusAnnotatedAlignment(IdGroup, String[], String) - Constructor for class pal.alignment.MultiLocusAnnotatedAlignment
 
multiplePrint(PrintWriter, char, int) - Method in class pal.io.FormattedOutput
repeatedly print a character
MultivariateFunction - interface pal.math.MultivariateFunction.
interface for a function of several variables
MultivariateMinimum - class pal.math.MultivariateMinimum.
abstract base class for minimisation of a multivariate function
MultivariateMinimum() - Constructor for class pal.math.MultivariateMinimum
 
mus - Variable in class pal.mep.SteppedMutationRate
mutation rates
muSEs - Variable in class pal.mep.SteppedMutationRate
mutation rate SEs
MUTATION_RATE - Static variable in interface pal.util.XMLConstants
 
MUTATION_RATE_MODEL - Static variable in interface pal.util.XMLConstants
 
MutationRateModel - class pal.mep.MutationRateModel.
This abstract class contains methods that are of general use for modelling mutation rate changes over time.
MutationRateModel() - Constructor for class pal.mep.MutationRateModel
 
MutationRateModelTree - class pal.tree.MutationRateModelTree.
Provides parameter interface to any clock-like tree with serially sampled tips (parameters are the minimal node height differences at each internal node).
MutationRateModelTree(Tree, TimeOrderCharacterData, MutationRateModel) - Constructor for class pal.tree.MutationRateModelTree
take any tree and afford it with an interface suitable for a clock-like tree (parameters are the minimal node height differences at each internal node).
MUTATIONS - Static variable in interface pal.util.XMLConstants
 
mutationsToGenerations(Tree, MutationRateModel) - Static method in class pal.tree.TreeUtils
Takes a tree (in mutation units) and returns a scaled version of it (in generation units).
muWindow - Variable in class pal.mep.WindowedMutationRate
 
muWindowSE - Variable in class pal.mep.WindowedMutationRate
 

N

N0 - Variable in class pal.coalescent.ConstantPopulation
population size
N0SE - Variable in class pal.coalescent.ConstantPopulation
standard error of population size
N1 - Variable in class pal.coalescent.ConstExpGrowth
ancestral pop. size
N1_PARAMETERIZATION - Static variable in class pal.coalescent.ConstExpGrowth
 
N1SE - Variable in class pal.coalescent.ConstExpGrowth
standard error of ancestral pop. size
NAME - Static variable in interface pal.util.XMLConstants
 
Nameable - interface pal.misc.Nameable.
interface for classes that can be named.
NameColouriser - class pal.gui.NameColouriser.
 
NameColouriser() - Constructor for class pal.gui.NameColouriser
 
NameColouriser(Identifier, Color) - Constructor for class pal.gui.NameColouriser
 
NameColouriser(String, Color) - Constructor for class pal.gui.NameColouriser
 
NamedParameterized - interface pal.misc.NamedParameterized.
interface for class with (optimizable) named parameters
NeighborJoiningTree - class pal.tree.NeighborJoiningTree.
constructs a neighbor-joining tree from pairwise distances
NeighborJoiningTree(DistanceMatrix) - Constructor for class pal.tree.NeighborJoiningTree
construct NJ tree
NEW_SAMPLE - Static variable in class pal.coalescent.CoalescentIntervals
Denotes an interval at the end of which a new sample addition is observed (i.e. the number of lineages is larger in the next interval).
nextBoolean() - Method in class pal.math.MersenneTwisterFast
 
nextByte() - Method in class pal.math.MersenneTwisterFast
 
nextBytes(byte[]) - Method in class pal.math.MersenneTwisterFast
 
nextChar() - Method in class pal.math.MersenneTwisterFast
 
nextDouble() - Method in class pal.math.MersenneTwisterFast
 
nextFloat() - Method in class pal.math.MersenneTwisterFast
 
nextGaussian() - Method in class pal.math.MersenneTwisterFast
 
nextInt() - Method in class pal.math.MersenneTwisterFast
 
nextInt(int) - Method in class pal.math.MersenneTwisterFast
Returns an integer drawn uniformly from 0 to n-1.
nextLine(PushbackReader) - Method in class pal.io.FormattedInput
go to the beginning of the next line.
nextLong() - Method in class pal.math.MersenneTwisterFast
 
nextShort() - Method in class pal.math.MersenneTwisterFast
 
NO_PARAMETRIZE - Static variable in class pal.tree.DatedTipsClockTree
 
Node - interface pal.tree.Node.
interface for a node (includes branch) in a binary/non-binary rooted/unrooted tree
NODE - Static variable in interface pal.util.XMLConstants
 
NODE_HEIGHT_SE - Static variable in interface pal.tree.AttributeNode
attribute name for the standard error on a node's height.
NodeFactory - class pal.tree.NodeFactory.
Creates nodes The purpose of this class is to decouple the creation of a class of type "Node" from its actual implementation.
NodeFactory() - Constructor for class pal.tree.NodeFactory
 
NodeUtils - class pal.tree.NodeUtils.
Helper routines for dealing with nodes.
NodeUtils() - Constructor for class pal.tree.NodeUtils
 
NORMAL_BW - Static variable in class pal.gui.TreeComponent
 
NORMAL_COLOR - Static variable in class pal.gui.TreeComponent
 
NORMAL_LABEL_COLOR - Static variable in class pal.gui.TreePainter
 
NormalDistribution - class pal.statistics.NormalDistribution.
normal distribution (pdf, cdf, quantile)
NormalDistribution() - Constructor for class pal.statistics.NormalDistribution
 
notDropped - Variable in class pal.alignment.StrippedAlignment
 
NOTHING - Static variable in class pal.coalescent.CoalescentIntervals
Denotes an interval at the end of which nothing is observed (i.e. the number of lineages is the same in the next interval).
NUCLEOTIDE_DESCRIPTION - Static variable in interface pal.datatype.DataType
Name of nucleotide data type.
NucleotideModel - class pal.substmodel.NucleotideModel.
base class for nucleotide rate matrices
NucleotideModel(double[]) - Constructor for class pal.substmodel.NucleotideModel
 
NucleotideModelID - interface pal.substmodel.NucleotideModelID.
interface for IDs of nucleotide models
Nucleotides - class pal.datatype.Nucleotides.
implements DataType for nucleotides
NUCLEOTIDES - Static variable in interface pal.datatype.DataType
 
Nucleotides() - Constructor for class pal.datatype.Nucleotides
 
Nucleotides(boolean) - Constructor for class pal.datatype.Nucleotides
If isRNA is true than getChar(state) will return a U instead of a T
numbers - Variable in class pal.util.ThreeNumberSort
the three numbers
numBootstraps - Variable in class pal.statistics.ModelSupport
number of bootstrap replicates
numBootstraps - Variable in class pal.statistics.ShimodairaHasegawaTest
number of bootstrap replicates
NumericalDerivative - class pal.math.NumericalDerivative.
approximates numerically the first and second derivatives of a function of a single variable and approximates gradient and diagonal of Hessian for multivariate functions
NumericalDerivative() - Constructor for class pal.math.NumericalDerivative
 
NumericDataType - class pal.datatype.NumericDataType.
This datatype stores numeric values.
NumericDataType() - Constructor for class pal.datatype.NumericDataType
 
numFun - Variable in class pal.math.MultivariateMinimum
total number of function evaluations necessary
numFun - Variable in class pal.math.UnivariateMinimum
total number of function evaluations neccessary
numFuncStops - Variable in class pal.math.MultivariateMinimum
numFuncStops is the number of consecutive positive evaluations of the stop criterion based on function evaluation necessary to cause the abortion of the optimization (default is 4)
numPatterns - Variable in class pal.alignment.SitePattern
number of site patterns
numRates - Variable in class pal.substmodel.RateDistribution
number of rate categories
numSeqs - Variable in class pal.alignment.AbstractAlignment
number of sequences
numSeqs - Variable in class pal.alignment.SimpleCharacterAlignment
number of sequences
numSeqs - Variable in class pal.distance.DistanceMatrix
number of sequences.
numSites - Variable in class pal.alignment.AbstractAlignment
length of each sequence
numTraits - Variable in class pal.alignment.SimpleCharacterAlignment
number of traits

O

OMEGA - Static variable in interface pal.util.XMLConstants
 
openFile(String) - Static method in class pal.io.InputSource
open file for reading
openFile(String) - Static method in class pal.io.OutputTarget
open file for writing
openStdIn() - Static method in class pal.io.InputSource
open standard input
openStdOut() - Static method in class pal.io.OutputTarget
open standard out
openString() - Static method in class pal.io.OutputTarget
"open" string to write into
openString(String) - Static method in class pal.io.InputSource
"open" string for reading
optimiseParameters() - Method in class pal.eval.LikelihoodValue
optimise parameters of tree by maximising its likelihood (this assumes that tree is a ParameterizedTree)
optimiseParameters() - Method in class pal.eval.ChiSquareValue
optimise parameters of a tree by minimising its chi-square value (tree must be a ParameterizedTree)
optimiseParameters(MultivariateMinimum) - Method in class pal.eval.LikelihoodValue
optimise parameters of tree by maximising its likelihood (this assumes that tree is a ParameterizedTree)
optimiseParameters(MultivariateMinimum) - Method in class pal.eval.ChiSquareValue
optimise parameters of a tree by minimising its chi-square value (tree must be a ParameterizedTree)
optimize() - Method in class pal.eval.DemographicValue
optimize log-likelihood using default optimizer return minimum negative log-likelihood
optimize() - Method in class pal.coalescent.SkylinePlot
Optimize generalized skyline plot
optimize(double, UnivariateFunction, double) - Method in class pal.math.UnivariateMinimum
The actual optimization routine (Brent's golden section method)
optimize(MultivariateFunction, double[], double, double) - Method in class pal.math.MultivariateMinimum
The actual optimization routine (needs to be implemented in a subclass of MultivariateMinimum).
optimize(MultivariateFunction, double[], double, double) - Method in class pal.math.ConjugateDirectionSearch
 
optimize(MultivariateFunction, double[], double, double) - Method in class pal.math.GeneralizedDEOptimizer
The actual optimization routine It finds a minimum close to vector x when the absolute tolerance for each parameter is specified.
optimize(MultivariateFunction, double[], double, double) - Method in class pal.math.DifferentialEvolution
 
optimize(MultivariateFunction, double[], double, double) - Method in class pal.math.OrthogonalSearch
 
optimize(MultivariateFunction, double[], double, double) - Method in class pal.math.StochasticOSearch
 
optimize(MultivariateFunction, double[], double, double) - Method in class pal.math.ConjugateGradientSearch
 
optimize(MultivariateMinimum) - Method in class pal.eval.DemographicValue
optimize log-likelihood value and compute corresponding SEs given an optimizer
optimize(UnivariateFunction, double) - Method in class pal.math.UnivariateMinimum
The actual optimization routine (Brent's golden section method)
ORIGIN - Static variable in interface pal.util.XMLConstants
 
OrthogonalLineFunction - class pal.math.OrthogonalLineFunction.
converts a multivariate function into a univariate function by keeping all but one argument constant
OrthogonalLineFunction(MultivariateFunction) - Constructor for class pal.math.OrthogonalLineFunction
construct univariate function from multivariate function
OrthogonalSearch - class pal.math.OrthogonalSearch.
minimization of a real-valued function of several variables without using derivatives, using the simple strategy of optimizing variables one by one.
OrthogonalSearch() - Constructor for class pal.math.OrthogonalSearch
Initialization
OutputTarget - class pal.io.OutputTarget.
convenience class to create output streams linked to files, stdout, and strings

P

P_VALUE - Static variable in class pal.gui.LinkageDisequilibriumComponent
 
paint(Graphics) - Method in class pal.gui.TreeComponent
 
paint(Graphics) - Method in class pal.gui.LinkageDisequilibriumComponent
 
paint(Graphics, int, int) - Method in interface pal.gui.Painter
 
paint(Graphics, int, int) - Method in class pal.gui.TreePainterNormal
 
paint(Graphics, int, int) - Method in class pal.gui.TreePainterCircular
 
paint(Graphics, int, int, boolean) - Method in class pal.gui.TreePainterCircular
 
paint(Graphics, int, int, boolean, LayoutTracker) - Method in class pal.gui.TreePainterCircular
 
paint(Graphics, int, int, LayoutTracker) - Method in interface pal.gui.Painter
 
paint(Graphics, int, int, LayoutTracker) - Method in class pal.gui.TreePainterNormal
 
paint(Graphics, int, int, LayoutTracker) - Method in class pal.gui.TreePainterCircular
 
paint(PositionedNode, CircularGraphics) - Method in class pal.gui.TreePainterCircular
 
paint(PositionedNode, Graphics, int, int, LayoutTracker) - Method in class pal.gui.TreePainterNormal
 
paintComponent(Graphics) - Method in class pal.gui.LinkageDisequilibriumComponent
 
Painter - interface pal.gui.Painter.
An interface for objects which are used for painting themselves in a general Graphics object
PairwiseDistance - class pal.distance.PairwiseDistance.
determines the (observed and ML) distance between a pair of sequences
PairwiseDistance(SitePattern) - Constructor for class pal.distance.PairwiseDistance
Constructor 1 (estimate observed distances only)
PairwiseDistance(SitePattern, SubstitutionModel) - Constructor for class pal.distance.PairwiseDistance
Constructor 2 (uses evolutionary model)
pal.alignment - package pal.alignment
Classes dealing with sequence alignments, including methods for reading and printing in several possible formats, as well as rearranging and concatenating.
pal.coalescent - package pal.coalescent
Classes to model population genetic processes using the coalescent.
pal.datatype - package pal.datatype
Classes describing data types (nucleotides, amino acids, codons, codon tables etc.)
pal.distance - package pal.distance
Classes for reading and generating distance matrices, including computation of pairwise distances for sequence data (maximum-likelihood and observed distances).
pal.eval - package pal.eval
Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters.
pal.gui - package pal.gui
GUI components for some special objects (e.g., trees).
pal.io - package pal.io
Classes for simple (formatted) input/output from/to files, strings and standard-in/out streams.
pal.math - package pal.math
Classes for math stuff such as optimisation, numerical derivatives, matrix exponentials, random numbers, special function etc.
pal.mep - package pal.mep
Classes for the analysis of "measurably evolving populations" (mep).
pal.misc - package pal.misc
Classes that don't fit elsewhere ;^)
pal.popgen - package pal.popgen
Classes for providing 'classical' population genetics analyses.
pal.statistics - package pal.statistics
Classes with useful for statistics (normal distribution, Gamma distribution, chi-square distribution, exponential distribution, likelihood-ratio test, chi-square test, descriptive statistics, bootstrap estimators etc.)
pal.substmodel - package pal.substmodel
Classes describing substitution models, i.e. rate matrices (e.g., the HKY matrix) and rate heterogeneity distributions (e.g., the discrete Gamma distribution), as well as a class for conveniently computing transition probabilities.
pal.tree - package pal.tree
Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint).
pal.util - package pal.util
Utility classes for sorting etc.
pal.xml - package pal.xml
Utility classes for converting PAL objects to and from XML documents.
PalEventMulticaster - class pal.misc.PalEventMulticaster.
A utility class for accomodating Pal listeners
PalEventMulticaster() - Constructor for class pal.misc.PalEventMulticaster
 
PalObjectEvent - class pal.misc.PalObjectEvent.
An event used by PalObjectListeners
PalObjectEvent(Object) - Constructor for class pal.misc.PalObjectEvent
 
PalObjectListener - interface pal.misc.PalObjectListener.
Defines objects that monitor certain PalObjects for changes
parameter - Variable in class pal.tree.ClockTree
 
PARAMETER - Static variable in interface pal.util.XMLConstants
 
parameterChanged(ParameterEvent) - Method in interface pal.misc.ExternalParameterListener
 
parameterChanged(ParameterEvent) - Method in class pal.tree.DatedTipsClockTree
The rate was changed externally
ParameterEvent - class pal.misc.ParameterEvent.
An event used by ExternalParameterListeners
ParameterEvent(Object) - Constructor for class pal.misc.ParameterEvent
 
parameterization - Variable in class pal.coalescent.ConstExpGrowth
parameterization
PARAMETERIZE_WITH_DEFAULTS - Static variable in class pal.tree.DatedTipsClockTree
 
PARAMETERIZE_WITH_GIVEN - Static variable in class pal.tree.DatedTipsClockTree
 
Parameterized - interface pal.misc.Parameterized.
interface for class with (optimizable) parameters
ParameterizedDouble - class pal.misc.ParameterizedDouble.
 
ParameterizedDouble(double, double, double) - Constructor for class pal.misc.ParameterizedDouble
The default value is also the initial value.
ParameterizedTree - class pal.tree.ParameterizedTree.
abstract base class for a tree with an Parameterized interface
ParameterizedTree() - Constructor for class pal.tree.ParameterizedTree
 
parameters2Heights() - Method in class pal.tree.MutationRateModelTree
 
parameters2Heights() - Method in class pal.tree.ClockTree
 
parameters2Heights() - Method in class pal.coalescent.DemographicClockTree
 
parametersChanged(PalObjectEvent) - Method in class pal.eval.FastLikelihoodCalculator
 
parametersChanged(PalObjectEvent) - Method in interface pal.misc.PalObjectListener
Signifies that parametric valued governing the state of this Object have changed.
parametersChanged(PalObjectEvent) - Method in class pal.substmodel.CachedRateMatrix
 
ParetoDistribution - class pal.statistics.ParetoDistribution.
Pareto distribution (scale-free distribution without characteristic length scale).
ParetoDistribution() - Constructor for class pal.statistics.ParetoDistribution
 
parseAlignmentElement(Element) - Static method in class pal.xml.ElementParser
Parses an alignment element and returns an alignment object.
parseAttributeElement(Element) - Static method in class pal.xml.ElementParser
parses an attribute element.
parseDemographicModel(Element) - Static method in class pal.xml.ElementParser
Parses an element from an DOM document into a DemographicModel.
parseEdgeNodeElement(Element) - Static method in class pal.xml.ElementParser
 
parseFrequencies(Element) - Static method in class pal.xml.ElementParser
reads XML format of frequencies.
parseMutationRateModel(Element) - Static method in class pal.xml.ElementParser
Reads a mutation rate model from a DOM Document element.
parseNodeElement(Element) - Static method in class pal.xml.ElementParser
 
parseRateMatrix(Element) - Static method in class pal.xml.ElementParser
Reads a rate matrix from a DOM Document element.
parseRateMatrix(Element, Alignment) - Static method in class pal.xml.ElementParser
Reads a rate matrix from a DOM Document element.
parseTimeDataElement(Element) - Static method in class pal.xml.ElementParser
 
parseTreeElement(Element) - Static method in class pal.xml.ElementParser
 
partialsExternal(Node) - Method in class pal.eval.SimpleLikelihoodCalculator
compute partials for external branch
partialsInternal(Node) - Method in class pal.eval.SimpleLikelihoodCalculator
compute partials for branch around center node (it is assumed that multiplied partials are available in the neighbor branch)
pattern - Variable in class pal.alignment.SitePattern
site patterns [sequence][site pattern]
pdf(double, double) - Static method in class pal.statistics.ExponentialDistribution
probability density function of the exponential distribution (mean = 1/lambda)
pdf(double, double) - Static method in class pal.statistics.ChiSquareDistribution
probability density function of the chi-square distribution
pdf(double, double, double) - Static method in class pal.statistics.GammaDistribution
probability density function of the Gamma distribution
pdf(double, double, double) - Static method in class pal.statistics.NormalDistribution
probability density function
pdf(double, double, double) - Static method in class pal.statistics.ParetoDistribution
probability density function of the Pareto distribution
PenalizedLikelihood - class pal.statistics.PenalizedLikelihood.
Penalized likelihood criteria
PenalizedLikelihood() - Constructor for class pal.statistics.PenalizedLikelihood
 
penalty(int, int) - Method in class pal.datatype.IUPACPenaltyTable
 
penalty(int, int) - Method in interface pal.datatype.TransitionPenaltyTable
 
POLAK_RIBIERE_UPDATE - Static variable in class pal.math.ConjugateGradientSearch
 
poolIntervals(boolean[]) - Method in class pal.coalescent.CoalescentIntervals
Starting at time zero (i.e. with the interval with largest number of lineages), the specified small intervals are pooled with the next non-small interval (if this does not exist then with the previous non-small interval)
poolSmallIntervals(double) - Method in class pal.coalescent.CoalescentIntervals
Starting at time zero (i.e. with the interval with largest number of lineages), small intervals (<= minSize) are pooled with the next non-small interval (if this does not exist then with the previous non-small interval)
POPULATION_SIZE - Static variable in interface pal.util.XMLConstants
 
PositionedNode - class pal.gui.PositionedNode.
A tree node that has a scalar position for the purposes of drawing the tree.
PositionedNode(Node) - Constructor for class pal.gui.PositionedNode
 
PositionedNode(Node, Node) - Constructor for class pal.gui.PositionedNode
Builds a tree based on node, but highlights highlightNode
positionType - Variable in class pal.alignment.MultiLocusAnnotatedAlignment
used to designate position Type
positionType - Variable in class pal.alignment.SimpleAnnotatedAlignment
used to designate position Type
positionType - Variable in class pal.alignment.IndelAnnotatedAlignment
used to designate position Type
posterior - Variable in class pal.statistics.ModelSupport
posterior probabilities for each hypothesis
postorderSuccessor(Node) - Static method in class pal.tree.NodeUtils
determine postorder successor of a node
preorderSuccessor(Node) - Static method in class pal.tree.NodeUtils
determine preorder successor of this node
prin - Variable in class pal.math.ConjugateDirectionSearch
controls the printed output from the routine (0 -> no output, 1 -> print only starting and final values, 2 -> detailed map of the minimization process, 3 -> print also eigenvalues and vectors of the search directions), the default value is 0
prin - Variable in class pal.math.DifferentialEvolution
variable controlling print out, default value = 0 (0 -> no output, 1 -> print final value, 2 -> detailed map of optimization process)
prin - Variable in class pal.math.ConjugateGradientSearch
controls the printed output from the routine (0 -> no output, 1 -> print only starting and final values, 2 -> detailed map of the minimisation process), the default value is 0
print(Alignment, PrintWriter) - Static method in class pal.alignment.AlignmentUtils
print alignment (default format: INTERLEAVED)
print(Graphics, PageFormat, int) - Method in class pal.gui.LinkageDisequilibriumComponent
 
print(LinkageDisequilibrium, PrintWriter) - Method in class pal.popgen.LinkageDisequilibrium
print the LD to the PrintWrite
print4TaxonTree(Tree, PrintWriter) - Static method in class pal.tree.Local
 
printCLUSTALW(Alignment, PrintWriter) - Static method in class pal.alignment.AlignmentUtils
Print alignment (in CLUSTAL W format)
printFrequencies(PrintWriter) - Method in class pal.substmodel.AbstractRateMatrix
 
printFrequencies(PrintWriter) - Method in class pal.substmodel.AminoAcidModel
 
printFrequencies(PrintWriter) - Method in class pal.substmodel.NucleotideModel
 
printFrequencies(PrintWriter) - Method in class pal.substmodel.CodonModel
 
printInterleaved(Alignment, PrintWriter) - Static method in class pal.alignment.AlignmentUtils
print alignment (in PHYLIP 3.4 INTERLEAVED format)
printNH(Tree, PrintWriter) - Static method in class pal.tree.TreeUtils
print a this tree in New Hampshire format (including distances and internal labels)
printNH(Tree, PrintWriter, boolean, boolean) - Static method in class pal.tree.TreeUtils
print this tree in New Hampshire format
printPHYLIP(PrintWriter) - Method in class pal.distance.DistanceMatrix
print alignment (PHYLIP format)
printPlain(Alignment, PrintWriter) - Static method in class pal.alignment.AlignmentUtils
print alignment (in plain format)
printPlain(Alignment, PrintWriter, boolean) - Static method in class pal.alignment.AlignmentUtils
print alignment (in plain format)
printRates(PrintWriter) - Method in class pal.substmodel.RateDistribution
 
printRatios(PrintWriter) - Method in class pal.substmodel.NucleotideModel
 
printRatios(PrintWriter) - Method in class pal.substmodel.CodonModel
 
printSequential(Alignment, PrintWriter) - Static method in class pal.alignment.AlignmentUtils
print alignment (in PHYLIP SEQUENTIAL format)
probability - Variable in class pal.substmodel.RateDistribution
probability of each rate
productPartials(Node) - Method in class pal.eval.SimpleLikelihoodCalculator
multiply partials into the neighbour of branch
pval - Variable in class pal.statistics.ShimodairaHasegawaTest
corresponding p-value
pval - Variable in class pal.statistics.KishinoHasegawaTest
corresponding p-value (two-sided test on normal distribution)
PYRIMIDINE_PURINE_RATIO - Static variable in interface pal.util.XMLConstants
 

Q

quantile(double, double) - Static method in class pal.statistics.ExponentialDistribution
quantile (inverse cumulative density function) of the exponential distribution
quantile(double, double) - Static method in class pal.statistics.ChiSquareDistribution
quantile (inverse cumulative density function) of the chi-square distribution
quantile(double, double[]) - Static method in class pal.statistics.DiscreteStatistics
compute the q-th quantile for a distribution of x (= inverse cdf)
quantile(double, double[], int[]) - Static method in class pal.statistics.DiscreteStatistics
compute the q-th quantile for a distribution of x (= inverse cdf)
quantile(double, double, double) - Static method in class pal.statistics.GammaDistribution
quantile (inverse cumulative density function) of the Gamma distribution
quantile(double, double, double) - Static method in class pal.statistics.NormalDistribution
quantiles (=inverse cumulative density function)
quantile(double, double, double) - Static method in class pal.statistics.ParetoDistribution
quantile (inverse cumulative density function) of the Pareto distribution

R

r - Variable in class pal.coalescent.ExponentialGrowth
growth rate r
random - Static variable in class pal.math.MathUtils
A random number generator that is initialized with the clock when this class is loaded into the JVM.
rate - Variable in class pal.substmodel.AbstractRateMatrix
rate matrix (transition: from 1st index to 2nd index)
rate - Variable in class pal.substmodel.RateDistribution
rates of each rate category
RATE_MATRIX - Static variable in interface pal.util.XMLConstants
 
rateAtSite - Variable in class pal.eval.LikelihoodValue
map estimation of rate at site pattern
RateDistribution - class pal.substmodel.RateDistribution.
abstract base class for models of rate variation over sites employing a discrete rate distribution
RateDistribution(int) - Constructor for class pal.substmodel.RateDistribution
construct discrete distribution
RateMatrix - interface pal.substmodel.RateMatrix.
abstract base class for all rate matrices
RateMatrixUtils - class pal.substmodel.RateMatrixUtils.
 
RateMatrixUtils() - Constructor for class pal.substmodel.RateMatrixUtils
 
rawAlignment - Variable in class pal.alignment.StrippedAlignment
 
rawNumSites - Variable in class pal.alignment.StrippedAlignment
 
ReadAlignment - class pal.alignment.ReadAlignment.
reads aligned sequence data from plain text files. recognizes PHYLIP 3.4 INTERLEAVED, PHYLIP SEQUENTIAL, CLUSTAL and derived formats. Other features: - the dot as "copy character" is recognized, - all base characters are capitalized, - automatic data type estimation - determination of corresponding base frequencies.
ReadAlignment(PushbackReader) - Constructor for class pal.alignment.ReadAlignment
read from stream
ReadAlignment(String) - Constructor for class pal.alignment.ReadAlignment
read from file
ReadDistanceMatrix - class pal.distance.ReadDistanceMatrix.
reads pairwise distance matrices in PHYLIP format (full matrix)
ReadDistanceMatrix(PushbackReader) - Constructor for class pal.distance.ReadDistanceMatrix
read from stream
ReadDistanceMatrix(String) - Constructor for class pal.distance.ReadDistanceMatrix
read from file
readDouble(PushbackReader) - Method in class pal.io.FormattedInput
read next number from stream and convert it to a double (newline/cr are treated as separators)
readDouble(PushbackReader, boolean) - Method in class pal.io.FormattedInput
read next number from stream and convert it to a double
readInt(PushbackReader) - Method in class pal.io.FormattedInput
read next number from stream and convert it to a int (newline/cr are treated as separators)
readInt(PushbackReader, boolean) - Method in class pal.io.FormattedInput
read next number from stream and convert it to a int
readLabel(PushbackReader, int) - Method in class pal.io.FormattedInput
read sequence label from stream A sequence label is not allowed to contain whitespace and either of :,;()[]{}.
readLine(PushbackReader, boolean) - Method in class pal.io.FormattedInput
read a whole line
readNextChar(PushbackReader) - Method in class pal.io.FormattedInput
read next character from stream (EOF does not count as character but will throw exception)
readNumber(PushbackReader, boolean) - Method in class pal.io.FormattedInput
 
ReadTree - class pal.tree.ReadTree.
constructs a tree reading in a New Hampshire treefile, taking care for internal labels and branch lengths and binary/nonbinary and rooted/unrooted trees
ReadTree(PushbackReader) - Constructor for class pal.tree.ReadTree
read tree from input stream
ReadTree(String) - Constructor for class pal.tree.ReadTree
read tree from file
readWord(PushbackReader) - Method in class pal.io.FormattedInput
read word from stream
recompute(SitePattern) - Method in class pal.distance.AlignmentDistanceMatrix
recompute maximum-likelihood distances under new site pattern
recompute(SubstitutionModel) - Method in class pal.distance.AlignmentDistanceMatrix
recompute maximum-likelihood distances under new model
RELEASE_DATE - Static variable in class pal.misc.ReleaseInfo
release date
ReleaseInfo - class pal.misc.ReleaseInfo.
release information
ReleaseInfo() - Constructor for class pal.misc.ReleaseInfo
 
remove(ExternalParameterListener, ExternalParameterListener) - Static method in class pal.misc.PalEventMulticaster
For managing ExternalParamterListeners Usage: ExternalParamterListener current = null; ...
remove(PalObjectListener, PalObjectListener) - Static method in class pal.misc.PalEventMulticaster
For managing PalObjectListeners Usage: PalObjectListener current = null; ...
removeBranch(Node) - Static method in class pal.tree.NodeUtils
remove internal branch (collapse node with its parent)
removeChild(int) - Method in class pal.tree.SimpleNode
remove child
removeChild(int) - Method in interface pal.tree.Node
remove child
removeChild(Node, Node) - Static method in class pal.tree.NodeUtils
remove child
removeConstantSites() - Method in class pal.alignment.StrippedAlignment
remove constant sites
removeConstantSitesIgnoreGapsMissing() - Method in class pal.alignment.StrippedAnnotatedAlignment
remove constant sites but ignore gaps and missing data (- and ?)
removeExternalParameterListener(ExternalParameterListener) - Method in class pal.misc.ParameterizedDouble
 
removeGaps() - Method in class pal.alignment.StrippedAlignment
remove sites with gaps
removeNoninformativeSites() - Method in class pal.alignment.StrippedAlignment
remove noninformative sites
removePalObjectListener(PalObjectListener) - Method in class pal.substmodel.AbstractRateMatrix
 
removePalObjectListener(PalObjectListener) - Method in class pal.substmodel.SimpleSubstitutionModel
Currently passes request on to rateMatrix
removePalObjectListener(PalObjectListener) - Method in class pal.substmodel.CachedRateMatrix
 
removePalObjectListener(PalObjectListener) - Method in interface pal.substmodel.RateMatrix
 
removePalObjectListener(PalObjectListener) - Method in interface pal.substmodel.SubstitutionModel
 
removeParent() - Method in class pal.tree.SimpleNode
removes parent.
removeRedundantSites(Alignment) - Static method in class pal.alignment.AlignmentUtils
 
removeSites(char) - Method in class pal.alignment.StrippedAlignment
remove site that contain a specified character
removeSitesBasedOnFreqIgnoreGapsMissing(double, int) - Method in class pal.alignment.StrippedAnnotatedAlignment
remove sites based on minimum frequency (the count of good bases) and based on the proportion of good sites different from consensus
removeSitesOutsideRange(int, int) - Method in class pal.alignment.StrippedAnnotatedAlignment
Remove sites based on site position (excluded sites are lastSite) This not effect any prior exclusions.
removeTimes() - Method in class pal.misc.TimeOrderCharacterData
Remove time character data.
removeUnknowns() - Method in class pal.alignment.StrippedAlignment
remove sites with unknowns
renameNodes(Tree, Hashtable) - Static method in class pal.tree.TreeUtils
Given a translation table where the keys are the current identifier names and the values are the new identifier names, this method replaces the current identifiers in the tree with new identifiers.
renewSitePattern(SitePattern) - Method in class pal.eval.LikelihoodValue
Set new site pattern (while keeping tree and model)
Report - interface pal.misc.Report.
interface for classes that can print out a human readable report of itself
report(Alignment, PrintWriter) - Static method in class pal.alignment.AlignmentUtils
report number of sequences, sites, and data type
report(PrintWriter) - Method in class pal.alignment.AbstractAlignment
 
report(PrintWriter) - Method in class pal.alignment.StrippedAnnotatedAlignment
 
report(PrintWriter) - Method in class pal.alignment.SimpleAnnotatedAlignment
 
report(PrintWriter) - Method in interface pal.alignment.AnnotationAlignment
Returns a report for the alignment
report(PrintWriter) - Method in class pal.alignment.ConcatenatedAnnotatedAlignment
 
report(PrintWriter) - Method in class pal.alignment.SimpleCharacterAlignment
 
report(PrintWriter) - Method in class pal.mep.ConstantMutationRate
 
report(PrintWriter) - Method in class pal.mep.WindowedMutationRate
 
report(PrintWriter) - Method in class pal.mep.SteppedMutationRate
 
report(PrintWriter) - Method in interface pal.misc.Report
print human readable report (e.g., on parameters and associated model)
report(PrintWriter) - Method in class pal.misc.TimeStamp
report on runtime
report(PrintWriter) - Method in class pal.statistics.ModelSupport
 
report(PrintWriter) - Method in class pal.statistics.ShimodairaHasegawaTest
 
report(PrintWriter) - Method in class pal.statistics.KishinoHasegawaTest
 
report(PrintWriter) - Method in class pal.substmodel.AminoAcidModel
 
report(PrintWriter) - Method in class pal.substmodel.Dayhoff
 
report(PrintWriter) - Method in class pal.substmodel.SimpleSubstitutionModel
 
report(PrintWriter) - Method in class pal.substmodel.BLOSUM62
 
report(PrintWriter) - Method in class pal.substmodel.GammaRates
 
report(PrintWriter) - Method in class pal.substmodel.CachedRateMatrix
 
report(PrintWriter) - Method in class pal.substmodel.HKY
 
report(PrintWriter) - Method in class pal.substmodel.CPREV
 
report(PrintWriter) - Method in class pal.substmodel.GTR
 
report(PrintWriter) - Method in class pal.substmodel.MTREV24
 
report(PrintWriter) - Method in class pal.substmodel.F81
 
report(PrintWriter) - Method in class pal.substmodel.InvariableSites
 
report(PrintWriter) - Method in class pal.substmodel.YangCodonModel
 
report(PrintWriter) - Method in class pal.substmodel.JTT
 
report(PrintWriter) - Method in class pal.substmodel.WAG
 
report(PrintWriter) - Method in class pal.substmodel.TN
 
report(PrintWriter) - Method in class pal.substmodel.F84
 
report(PrintWriter) - Method in class pal.substmodel.VT
 
report(PrintWriter) - Method in class pal.substmodel.UniformRate
 
report(PrintWriter) - Method in class pal.substmodel.TwoStateModel
 
report(PrintWriter) - Method in class pal.tree.SimpleTree
 
report(PrintWriter) - Method in class pal.coalescent.ConstantPopulation
 
report(PrintWriter) - Method in class pal.coalescent.SkylinePlot
 
report(PrintWriter) - Method in class pal.coalescent.ExponentialGrowth
 
report(PrintWriter) - Method in class pal.coalescent.ConstExpGrowth
 
report(PrintWriter) - Method in class pal.coalescent.CoalescentIntervals
 
report(PrintWriter) - Method in class pal.coalescent.ExpandingPopulation
 
report(Tree, PrintWriter) - Static method in class pal.tree.TreeUtils
 
reroot(int) - Method in class pal.tree.SimpleTree
make node with number num to root node
reroot(Node) - Method in class pal.tree.SimpleTree
make provided node the root node
reroot(Tree, Node) - Static method in class pal.tree.TreeUtils
 
reset() - Method in class pal.gui.LayoutTracker
 
reset() - Method in class pal.math.UrnModel
refill urn
reset() - Method in class pal.tree.SimpleNode
 
restoreBranch(Node) - Static method in class pal.tree.NodeUtils
restore internal branch
RIGHTBORDER - Static variable in class pal.gui.TreePainterNormal
 
RIGHTBORDER - Static variable in class pal.gui.TreePainterCircular
 
root(Node) - Static method in class pal.tree.NodeUtils
Root tree at this node.
rootAbove(Identifier, Node) - Static method in class pal.tree.NodeUtils
Root the tree above the node with this identifier.
rootAbove(Node) - Static method in class pal.tree.NodeUtils
Root tree above this node;
RootedTreeUtils - class pal.tree.RootedTreeUtils.
This class contains utility methods.
RootedTreeUtils() - Constructor for class pal.tree.RootedTreeUtils
 
rotateByLeafCount(Tree) - Static method in class pal.tree.TreeUtils
Rotates branches by leaf count.
rSE - Variable in class pal.coalescent.ExponentialGrowth
standard error of growth rate r
RSQUARE - Static variable in class pal.gui.LinkageDisequilibriumComponent
 
run() - Method in class pal.popgen.LinkageDisequilibrium
starts the thread to calculate LD

S

same(double, double) - Static method in class pal.math.MachineAccuracy
 
sameTaxa(Node, Node) - Static method in class pal.tree.RootedTreeUtils
 
scale(double) - Method in class pal.mep.MutationRateModel
Linearly scales this mutation rate model.
scale(double) - Method in class pal.mep.ConstantMutationRate
Linearly scales this mutation rate model.
scale(double) - Method in class pal.mep.WindowedMutationRate
Linearly scales this mutation rate model.
scale(double) - Method in class pal.mep.SteppedMutationRate
Linearly scales this mutation rate model.
scale(double, int) - Method in class pal.misc.TimeOrderCharacterData
 
scale(Tree, double, int) - Static method in class pal.tree.TreeUtils
Takes a tree and returns a scaled version of it.
scbd - Variable in class pal.math.ConjugateDirectionSearch
scbd is a scaling parameter. 1.0 is the default and indicates no scaling. if the scales for the different parameters are very different, scbd should be set to a value of about 10.0.
screenCentreX - Variable in class pal.gui.CircularGraphics
 
screenCentreY - Variable in class pal.gui.CircularGraphics
 
screenRadius - Variable in class pal.gui.CircularGraphics
 
second - Variable in class pal.util.ThreeNumberSort
order of the numbers (0-2)
secondDerivative(UnivariateFunction, double) - Static method in class pal.math.NumericalDerivative
determine second derivative
selectArgument(int) - Method in class pal.math.OrthogonalLineFunction
use only the specified argument in the constructed univariate function and keep all others constant
SEQUENCE - Static variable in interface pal.util.XMLConstants
 
SequencePairLikelihood - class pal.distance.SequencePairLikelihood.
computation of the (negative) log-likelihood for a pair of sequences
SequencePairLikelihood(SitePattern, SubstitutionModel) - Constructor for class pal.distance.SequencePairLikelihood
initialisation
SerialCoalescentSimulator - class pal.coalescent.SerialCoalescentSimulator.
Simulates a set of coalescent intervals given a demographic model.
SerialCoalescentSimulator() - Constructor for class pal.coalescent.SerialCoalescentSimulator
 
setAllArguments(double[]) - Method in class pal.math.OrthogonalLineFunction
set (change) values of all arguments (start values)
setAncestral(double) - Method in class pal.coalescent.ConstExpGrowth
 
setArgument(double) - Method in class pal.math.OrthogonalLineFunction
set (change) value of a single argument (the one currently active)
setAttribute(Node, String, Object) - Method in class pal.tree.ParameterizedTree
 
setAttribute(Node, String, Object) - Method in class pal.tree.SimpleTree
Sets an named attribute for a given node.
setAttribute(Node, String, Object) - Method in interface pal.tree.Tree
Sets an named attribute for a given node.
setAttribute(String, Object) - Method in class pal.tree.SimpleNode
Sets a named attribute to the given value.
setAttribute(String, Object) - Method in interface pal.tree.AttributeNode
Sets a named attribute to the given value.
setAttributeName(String) - Method in class pal.gui.TreePainter
 
setAttributeName(String) - Method in class pal.gui.TreeComponent
 
setBaseTree(Tree) - Method in class pal.tree.ParameterizedTree
 
setBranchLength(double) - Method in class pal.tree.SimpleNode
Set the length of the branch attaching this node to its parent.
setBranchLength(double) - Method in interface pal.tree.Node
Set the length of the branch attaching this node to its parent.
setBranchLengthSE(double) - Method in class pal.tree.SimpleNode
Set the length SE of the branch attaching this node to its parent.
setBranchLengthSE(double) - Method in interface pal.tree.Node
Set the length SE of the branch attaching this node to its parent.
setChild(int, Node) - Method in class pal.tree.SimpleNode
set child node
setChild(int, Node) - Method in interface pal.tree.Node
set child node
setChromosome(int) - Method in class pal.alignment.SimpleAnnotatedAlignment
Sets chromosome
setChromosome(int) - Method in class pal.alignment.IndelAnnotatedAlignment
Sets chromosome
setChromosome(int, int) - Method in class pal.alignment.MultiLocusAnnotatedAlignment
Sets chromosome
setChromosomePosition(float) - Method in class pal.alignment.SimpleAnnotatedAlignment
Set the position along chromosome
setChromosomePosition(float) - Method in class pal.alignment.IndelAnnotatedAlignment
Set the position along chromosome
setChromosomePosition(float, int) - Method in class pal.alignment.MultiLocusAnnotatedAlignment
Set the position along chromosome
setCoalescentIntervals(CoalescentIntervals) - Method in class pal.eval.DemographicValue
define coalescent tree.
setColor(Color) - Method in class pal.gui.CircularGraphics
 
setColouriser(NameColouriser) - Method in class pal.gui.TreePainter
 
setColouriser(NameColouriser) - Method in class pal.gui.TreeComponent
 
setDataType(DataType) - Method in class pal.alignment.AbstractAlignment
Sets the datatype of this alignment
setDataType(DataType) - Method in interface pal.alignment.Alignment
Sets the dataType of this alignment.
setDebug(boolean) - Method in class pal.util.Log
 
setDefaultLogger(Logger) - Static method in class pal.util.Log
 
setDemographicModel(DemographicModel) - Method in class pal.eval.DemographicValue
define model
setDistance(double) - Method in class pal.substmodel.AbstractRateMatrix
Sets the distance (such as time/branch length) used when calculating the probabilities.
setDistance(double) - Method in class pal.substmodel.MatrixExponential
compute transition probabilities for a expected distance using the prespecified rate matrix
setDistance(double) - Method in class pal.substmodel.SimpleSubstitutionModel
set distance and corresponding computation transition probabilities
setDistance(double) - Method in class pal.substmodel.CachedRateMatrix
set distance and corresponding computation transition probabilities
setDistance(double) - Method in interface pal.substmodel.RateMatrix
Sets the distance (such as time/branch length) used when calculating the probabilities.
setDistance(double) - Method in interface pal.substmodel.SubstitutionModel
set distance and corresponding computation transition probabilities
setDistance(int, int, double) - Method in class pal.distance.DistanceMatrix
Sets both upper and lower triangles.
setFont(Font) - Method in class pal.gui.CircularGraphics
 
setFrequencies(double[]) - Method in class pal.substmodel.AbstractRateMatrix
 
setFrequency(double[]) - Method in class pal.alignment.AbstractAlignment
 
setFrequency(double[]) - Method in interface pal.alignment.Alignment
Sets frequency of character states.
setIdentifier(Identifier) - Method in class pal.tree.SimpleNode
Set identifier for this node.
setIdentifier(Identifier) - Method in interface pal.tree.Node
Set identifier for this node.
setIdentifier(int, Identifier) - Method in class pal.alignment.AbstractAlignment
 
setIdentifier(int, Identifier) - Method in class pal.alignment.SimpleCharacterAlignment
 
setIdentifier(int, Identifier) - Method in class pal.distance.DistanceMatrix
 
setIdentifier(int, Identifier) - Method in class pal.misc.SimpleIdGroup
Sets the ith identifier.
setIdentifier(int, Identifier) - Method in interface pal.misc.IdGroup
Sets the ith identifier.
setIdentifier(int, Identifier) - Method in class pal.misc.TimeOrderCharacterData
 
setInterval(int, double) - Method in class pal.coalescent.CoalescentIntervals
Sets interval.
setInvertCircular(boolean) - Method in class pal.gui.TreeComponent
 
setLabelMapping(LabelMapping) - Method in class pal.gui.TreePainter
 
setLabelMapping(LabelMapping) - Method in class pal.gui.TreeComponent
 
setLnL(double) - Method in class pal.tree.MutationRateModelTree
 
setLocusName(String) - Method in class pal.alignment.SimpleAnnotatedAlignment
Sets the name of the locus
setLocusName(String) - Method in class pal.alignment.IndelAnnotatedAlignment
Sets the name of the locus
setLocusName(String, int) - Method in class pal.alignment.MultiLocusAnnotatedAlignment
Sets the name of the locus
setLocusPosition(int, int) - Method in class pal.alignment.MultiLocusAnnotatedAlignment
Set the position within the locus
setLogL(double) - Method in class pal.coalescent.DemographicModel
sets log likelihood
setLowerCorner(int) - Method in class pal.gui.LinkageDisequilibriumComponent
This determines what is displayed in the lower left corner.
setMatrix(int[][]) - Method in class pal.statistics.ContigencyTable
sets the data for the contigency table, must be set before other methods are called.
setMatrix(RateMatrix) - Method in class pal.substmodel.MatrixExponential
update rate matrix used in present module
setMax(int) - Method in class pal.math.Binomial
set capacity and precompute the n choose 2 values
setMaxCacheSize(int) - Method in class pal.util.DefaultCache
 
setMaximumValue(double) - Method in class pal.misc.ParameterizedDouble
 
setMinimumValue(double) - Method in class pal.misc.ParameterizedDouble
 
setMode(int) - Method in class pal.gui.TreeComponent
Sets the mode of display for this component.
setModel(SubstitutionModel) - Method in class pal.eval.SimpleLikelihoodCalculator
define model (a site pattern must have been set before calling this method)
setModel(SubstitutionModel) - Method in class pal.eval.LikelihoodValue
define model (a site pattern must have been set before calling this method)
setMu(double) - Method in class pal.mep.ConstantMutationRate
 
setMu(double) - Method in class pal.mep.SteppedMutationRate
 
setName(String) - Method in class pal.misc.SimpleIdGroup
Sets the name of this IdGroup.
setName(String) - Method in class pal.misc.TimeOrderCharacterData
Sets the name of this character data.
setName(String) - Method in class pal.misc.Identifier
 
setName(String) - Method in interface pal.misc.Nameable
set the name of this object.
setNodeHeight(double) - Method in class pal.tree.SimpleNode
Set the height of this node relative to the most recent node.
setNodeHeight(double) - Method in interface pal.tree.Node
Set the height of this node relative to the most recent node.
setNumber(int) - Method in class pal.tree.SimpleNode
 
setNumber(int) - Method in interface pal.tree.Node
set the index of this node
setNumLineages(int, int) - Method in class pal.coalescent.CoalescentIntervals
set the number lineages for this particular interval.
setOrdinals(int[]) - Method in class pal.misc.TimeOrderCharacterData
Sets ordinals.
setOrdinals(TimeOrderCharacterData) - Method in class pal.misc.TimeOrderCharacterData
Set time ordinals from another TimeOrderCharacterData.
setOrdinals(TimeOrderCharacterData, IdGroup, boolean) - Method in class pal.misc.TimeOrderCharacterData
Set time ordinals from another TimeOrderCharacterData.
setParameter(double, int) - Method in class pal.mep.ConstantMutationRate
 
setParameter(double, int) - Method in class pal.mep.WindowedMutationRate
 
setParameter(double, int) - Method in class pal.mep.SteppedMutationRate
 
setParameter(double, int) - Method in class pal.misc.ParameterizedDouble
set model parameter
setParameter(double, int) - Method in interface pal.misc.Parameterized
set model parameter
setParameter(double, int) - Method in class pal.substmodel.AminoAcidModel
 
setParameter(double, int) - Method in class pal.substmodel.SimpleSubstitutionModel
 
setParameter(double, int) - Method in class pal.substmodel.GammaRates
 
setParameter(double, int) - Method in class pal.substmodel.CachedRateMatrix
 
setParameter(double, int) - Method in class pal.substmodel.HKY
 
setParameter(double, int) - Method in class pal.substmodel.GTR
 
setParameter(double, int) - Method in class pal.substmodel.F81
 
setParameter(double, int) - Method in class pal.substmodel.InvariableSites
 
setParameter(double, int) - Method in class pal.substmodel.YangCodonModel
 
setParameter(double, int) - Method in class pal.substmodel.TN
 
setParameter(double, int) - Method in class pal.substmodel.F84
 
setParameter(double, int) - Method in class pal.substmodel.UniformRate
 
setParameter(double, int) - Method in class pal.substmodel.TwoStateModel
 
setParameter(double, int) - Method in class pal.tree.UnconstrainedTree
 
setParameter(double, int) - Method in class pal.tree.LogParameterizedTree
 
setParameter(double, int) - Method in class pal.tree.DatedTipsClockTree
 
setParameter(double, int) - Method in class pal.tree.MutationRateModelTree
 
setParameter(double, int) - Method in class pal.tree.ClockTree
 
setParameter(double, int) - Method in class pal.coalescent.ConstantPopulation
 
setParameter(double, int) - Method in class pal.coalescent.ExponentialGrowth
 
setParameter(double, int) - Method in class pal.coalescent.ConstExpGrowth
 
setParameter(double, int) - Method in class pal.coalescent.ExpandingPopulation
 
setParameterization(int) - Method in class pal.coalescent.ConstExpGrowth
Sets the parameterization.
setParameterSE(double, int) - Method in class pal.mep.ConstantMutationRate
 
setParameterSE(double, int) - Method in class pal.mep.WindowedMutationRate
 
setParameterSE(double, int) - Method in class pal.mep.SteppedMutationRate
 
setParameterSE(double, int) - Method in class pal.misc.ParameterizedDouble
set standard errors for model parameter
setParameterSE(double, int) - Method in interface pal.misc.Parameterized
set standard errors for model parameter
setParameterSE(double, int) - Method in class pal.substmodel.AminoAcidModel
 
setParameterSE(double, int) - Method in class pal.substmodel.SimpleSubstitutionModel
 
setParameterSE(double, int) - Method in class pal.substmodel.GammaRates
 
setParameterSE(double, int) - Method in class pal.substmodel.CachedRateMatrix
 
setParameterSE(double, int) - Method in class pal.substmodel.HKY
 
setParameterSE(double, int) - Method in class pal.substmodel.GTR
 
setParameterSE(double, int) - Method in class pal.substmodel.F81
 
setParameterSE(double, int) - Method in class pal.substmodel.InvariableSites
 
setParameterSE(double, int) - Method in class pal.substmodel.YangCodonModel
 
setParameterSE(double, int) - Method in class pal.substmodel.TN
 
setParameterSE(double, int) - Method in class pal.substmodel.F84
 
setParameterSE(double, int) - Method in class pal.substmodel.UniformRate
 
setParameterSE(double, int) - Method in class pal.substmodel.TwoStateModel
 
setParameterSE(double, int) - Method in class pal.tree.UnconstrainedTree
 
setParameterSE(double, int) - Method in class pal.tree.LogParameterizedTree
 
setParameterSE(double, int) - Method in class pal.tree.DatedTipsClockTree
 
setParameterSE(double, int) - Method in class pal.tree.MutationRateModelTree
 
setParameterSE(double, int) - Method in class pal.tree.ClockTree
 
setParameterSE(double, int) - Method in class pal.coalescent.ConstantPopulation
 
setParameterSE(double, int) - Method in class pal.coalescent.ExponentialGrowth
 
setParameterSE(double, int) - Method in class pal.coalescent.ConstExpGrowth
 
setParameterSE(double, int) - Method in class pal.coalescent.ExpandingPopulation
 
setParent(Node) - Method in class pal.tree.SimpleNode
Set the parent node of this node.
setParent(Node) - Method in interface pal.tree.Node
Set the parent node of this node.
setPenWidth(int) - Method in class pal.gui.TreePainter
 
setPositionType(int, char) - Method in class pal.alignment.MultiLocusAnnotatedAlignment
Set thes position type (eg.
setPositionType(int, char) - Method in class pal.alignment.SimpleAnnotatedAlignment
Set thes position type (eg.
setRate(double) - Method in class pal.tree.DatedTipsClockTree
set rate (and thus node heights and branch lengths of leaves) without changing all other node heights and branch lengths
setRateMatrix(RateMatrix) - Method in class pal.eval.SimpleLikelihoodCalculator
define model (a site pattern must have been set before calling this method)
setRateMatrix(RateMatrix) - Method in class pal.eval.FastLikelihoodCalculator
 
setRateSE(double) - Method in class pal.tree.DatedTipsClockTree
set rate SE
setRoot(Node) - Method in class pal.tree.ParameterizedTree
 
setRoot(Node) - Method in class pal.tree.SimpleTree
Set a new node as root node.
setRoot(Node) - Method in interface pal.tree.Tree
This method constructs a tree from the given root node.
setScaleOfView(boolean) - Method in class pal.gui.LinkageDisequilibriumComponent
This sets the scale of the LD view, either sites are organized by chromosomes if chromosomalScale is true, otherwise they are organized by genes
setSE(double) - Method in class pal.misc.ParameterizedDouble
 
setSeed(long) - Method in class pal.math.MersenneTwisterFast
Initalize the pseudo random number generator.
setSequence(byte[]) - Method in class pal.tree.SimpleNode
Sets the sequence at this node, in the form of an array of bytes.
setSequence(byte[]) - Method in interface pal.tree.Node
Sets the sequence using an array of bytes.
setSequences(byte[], byte[]) - Method in class pal.distance.SequencePairLikelihood
specification of two sequences (not necessarily in the given alignment but with the same weights in the site pattern)
setSequences(int, int) - Method in class pal.distance.SequencePairLikelihood
specification of two sequences in the given alignment
setShowingNodeHeights(boolean) - Method in class pal.gui.TreePainter
 
setShowSchematic(boolean) - Method in class pal.gui.LinkageDisequilibriumComponent
This sets whether a schematic is displayed.
setSpan(double, double) - Method in class pal.substmodel.MatrixExponential
compute transition probabilities for a expected distance using the prespecified rate matrix
setTime(double, double) - Method in class pal.substmodel.SimpleSubstitutionModel
 
setTimeOrderCharacterData(TimeOrderCharacterData) - Method in class pal.gui.TreePainter
 
setTimes(double[], int) - Method in class pal.misc.TimeOrderCharacterData
Sets the times, and works out what the ordinals should be.
setTimes(double[], int, boolean) - Method in class pal.misc.TimeOrderCharacterData
Sets the times.
setTimesAndOrdinals(TimeOrderCharacterData) - Method in class pal.misc.TimeOrderCharacterData
 
setTitle(String) - Method in class pal.gui.TreePainter
 
setTitle(String) - Method in class pal.gui.TreeComponent
 
setTree(Tree) - Method in class pal.eval.SimpleLikelihoodCalculator
define tree ,(must only be called only after a site pattern has been defined).
setTree(Tree) - Method in class pal.eval.LikelihoodValue
define (parameterized) tree ,(must only be called only after a site pattern has been defined).
setTree(Tree) - Method in class pal.eval.FastLikelihoodCalculator
 
setTree(Tree) - Method in class pal.eval.ChiSquareValue
define (parameterized) tree
setTree(Tree) - Method in class pal.gui.TreePainter
 
setTree(Tree) - Method in class pal.gui.TreeComponent
 
setUnits(int) - Method in class pal.mep.MutationRateModel
sets units of measurement.
setUnits(int) - Method in class pal.tree.ParameterizedTree
 
setUnits(int) - Method in class pal.tree.SimpleTree
Sets the units that this tree is expressed in.
setUnits(int) - Method in interface pal.tree.Tree
Sets the units that this tree's branch lengths and node heights are expressed in.
setUnits(int) - Method in class pal.coalescent.DemographicModel
sets units of measurement.
setUnits(int) - Method in class pal.coalescent.CoalescentIntervals
Sets the units these coalescent intervals are measured in.
setUpperCorner(int) - Method in class pal.gui.LinkageDisequilibriumComponent
This determines what is displayed in the upper right corner.
setUsingColor(boolean) - Method in class pal.gui.TreePainter
 
setUsingSymbols(boolean) - Method in class pal.gui.TreePainter
Sets whether the tree is painted with symbols.
setValue(double) - Method in class pal.misc.ParameterizedDouble
Set the current value of this double
setWeightedLocusPosition(int, float) - Method in class pal.alignment.MultiLocusAnnotatedAlignment
Sets the weighted position along the gene (handles gaps)
setWeightedLocusPosition(int, float) - Method in class pal.alignment.SimpleAnnotatedAlignment
Sets the weighted position along the gene (handles gaps)
ShimodairaHasegawaTest - class pal.statistics.ShimodairaHasegawaTest.
Shimodaira-Hasegawa-Test (1999) to compare a set of evolutionary hypotheses
ShimodairaHasegawaTest() - Constructor for class pal.statistics.ShimodairaHasegawaTest
 
showingInternalLabels - Variable in class pal.gui.TreePainter
determines whether internal nodes are labelled
shuffle(int[]) - Method in class pal.math.MersenneTwisterFast
Shuffles an array.
shuffle(int[], int) - Method in class pal.math.MersenneTwisterFast
Shuffles an array.
shuffled(int) - Method in class pal.math.MersenneTwisterFast
Returns an array of shuffled indices of length l.
shuffleTimes() - Method in class pal.misc.TimeOrderCharacterData
 
SimpleAlignment - class pal.alignment.SimpleAlignment.
An alignment class that can be efficiently constructed from an array of strings.
SimpleAlignment() - Constructor for class pal.alignment.SimpleAlignment
parameterless constructor.
SimpleAlignment(Alignment) - Constructor for class pal.alignment.SimpleAlignment
Clone constructor.
SimpleAlignment(Alignment, Alignment, String, String, char) - Constructor for class pal.alignment.SimpleAlignment
This constructor combines to alignments given two guide strings.
SimpleAlignment(Alignment, int) - Constructor for class pal.alignment.SimpleAlignment
Clone constructor.
SimpleAlignment(Identifier[], String[], String) - Constructor for class pal.alignment.SimpleAlignment
 
SimpleAlignment(Identifier, String, DataType) - Constructor for class pal.alignment.SimpleAlignment
Constructor taking single identifier and sequence.
SimpleAlignment(Identifier, String, DataType, boolean) - Constructor for class pal.alignment.SimpleAlignment
Constructor taking single identifier and sequence.
SimpleAlignment(IdGroup, char[][]) - Constructor for class pal.alignment.SimpleAlignment
 
SimpleAlignment(IdGroup, char[][], String) - Constructor for class pal.alignment.SimpleAlignment
 
SimpleAlignment(IdGroup, char[][], String, DataType) - Constructor for class pal.alignment.SimpleAlignment
 
SimpleAlignment(IdGroup, String[]) - Constructor for class pal.alignment.SimpleAlignment
 
SimpleAlignment(IdGroup, String[], String) - Constructor for class pal.alignment.SimpleAlignment
 
SimpleAnnotatedAlignment - class pal.alignment.SimpleAnnotatedAlignment.
This is the basic implementation of the Annotation interface, which is designed to provide annotation for an alignment.
SimpleAnnotatedAlignment(Alignment) - Constructor for class pal.alignment.SimpleAnnotatedAlignment
Clone constructor from an unannotated alignment.
SimpleAnnotatedAlignment(AnnotationAlignment) - Constructor for class pal.alignment.SimpleAnnotatedAlignment
Clone constructor.
SimpleAnnotatedAlignment(AnnotationAlignment, IdGroup) - Constructor for class pal.alignment.SimpleAnnotatedAlignment
This constructor will subset the alignment based on the taxa in IdGroup
SimpleAnnotatedAlignment(Identifier[], String[], String) - Constructor for class pal.alignment.SimpleAnnotatedAlignment
This constructor creates a basic SimpleAnnotatedAlignment.
SimpleAnnotatedAlignment(IdGroup, String[]) - Constructor for class pal.alignment.SimpleAnnotatedAlignment
This constructor creates a basic SimpleAnnotatedAlignment.
SimpleAnnotatedAlignment(IdGroup, String[], String) - Constructor for class pal.alignment.SimpleAnnotatedAlignment
This constructor creates a basic SimpleAnnotatedAlignment.
SimpleCharacterAlignment - class pal.alignment.SimpleCharacterAlignment.
This provides a basic implementation of CharacterAlignment.
SimpleCharacterAlignment() - Constructor for class pal.alignment.SimpleCharacterAlignment
 
SimpleCharacterAlignment(Identifier[], double[][], String[]) - Constructor for class pal.alignment.SimpleCharacterAlignment
Constructor for SimpleCharacterAlignment.
SimpleCharacterAlignment(IdGroup, double[][], String[]) - Constructor for class pal.alignment.SimpleCharacterAlignment
Constructor for SimpleCharacterAlignment.
SimpleCharacterAlignment(IdGroup, double[][], String[], String[]) - Constructor for class pal.alignment.SimpleCharacterAlignment
Constructor for SimpleCharacterAlignment
SimpleCharacterAlignment(IdGroup, double[], String) - Constructor for class pal.alignment.SimpleCharacterAlignment
Constructor for SimpleCharacterAlignment when there is only a single trait.
SimpleDataType - class pal.datatype.SimpleDataType.
interface for sequence data types
SimpleDataType() - Constructor for class pal.datatype.SimpleDataType
 
SimpleIdGroup - class pal.misc.SimpleIdGroup.
Default implementation of IdGroup interface.
SimpleIdGroup(Identifier[]) - Constructor for class pal.misc.SimpleIdGroup
Constructor taking an array of identifiers.
SimpleIdGroup(IdGroup) - Constructor for class pal.misc.SimpleIdGroup
Impersonating Constructor.
SimpleIdGroup(IdGroup, IdGroup) - Constructor for class pal.misc.SimpleIdGroup
Constructor taking two separate id groups and merging them.
SimpleIdGroup(IdGroup, int) - Constructor for class pal.misc.SimpleIdGroup
Impersonating Constructor.
SimpleIdGroup(int) - Constructor for class pal.misc.SimpleIdGroup
Constructor taking the size of the group.
SimpleIdGroup(int, boolean) - Constructor for class pal.misc.SimpleIdGroup
Constructor taking the size of the group.
SimpleIdGroup(String[]) - Constructor for class pal.misc.SimpleIdGroup
Constructor taking an array of strings.
SimpleLikelihoodCalculator - class pal.eval.SimpleLikelihoodCalculator.
Only to be used by one thread.
SimpleLikelihoodCalculator(SitePattern) - Constructor for class pal.eval.SimpleLikelihoodCalculator
Need to use setTree(), and setModel() before using compute() if you use this constructor
SimpleLikelihoodCalculator(SitePattern, Tree, SubstitutionModel) - Constructor for class pal.eval.SimpleLikelihoodCalculator
 
SimpleNode - class pal.tree.SimpleNode.
data structure for a node (includes branch) in a binary/non-binary rooted/unrooted tree
SimpleNode() - Constructor for class pal.tree.SimpleNode
constructor default node
SimpleNode(Node) - Constructor for class pal.tree.SimpleNode
constructor used to clone a node and all children
SimpleNode(Node, boolean) - Constructor for class pal.tree.SimpleNode
 
SimpleNode(Node, LabelMapping) - Constructor for class pal.tree.SimpleNode
 
SimpleNode(String, double) - Constructor for class pal.tree.SimpleNode
 
SimpleSubstitutionModel - class pal.substmodel.SimpleSubstitutionModel.
model of sequence substitution (rate matrix + rate variation). provides a convenient interface for the computation of transition probabilities
SimpleSubstitutionModel(RateMatrix) - Constructor for class pal.substmodel.SimpleSubstitutionModel
constructor 1 (uniform rate distribution)
SimpleSubstitutionModel(RateMatrix, int, double) - Constructor for class pal.substmodel.SimpleSubstitutionModel
constructor 2 (gamma rate distribution)
SimpleSubstitutionModel(RateMatrix, RateDistribution) - Constructor for class pal.substmodel.SimpleSubstitutionModel
constructor 3 (arbitrary rate distribution)
SimpleSubstitutionModel(SubstitutionModel) - Constructor for class pal.substmodel.SimpleSubstitutionModel
Return a copy of this substitution model.
SimpleSummarizable - class pal.misc.SimpleSummarizable.
 
SimpleSummarizable(String[], double[]) - Constructor for class pal.misc.SimpleSummarizable
The simple constructor
SimpleSummarizable(Summarizable) - Constructor for class pal.misc.SimpleSummarizable
The Imitation constructor - for immitating another Summarizable object with minimum memory requirements
SimpleTree - class pal.tree.SimpleTree.
data structure for a binary/non-binary rooted/unrooted trees
SimpleTree() - Constructor for class pal.tree.SimpleTree
constructor tree consisting solely of root node
SimpleTree(Node) - Constructor for class pal.tree.SimpleTree
constructor taking a root node
SimpleTree(Tree) - Constructor for class pal.tree.SimpleTree
clone constructor
SimpleTree(Tree, boolean) - Constructor for class pal.tree.SimpleTree
clone constructor
SimpleTree(Tree, LabelMapping) - Constructor for class pal.tree.SimpleTree
clone constructor
simulate() - Method in class pal.tree.SimulatedAlignment
generate new artificial data set (random root sequence)
simulate(byte[]) - Method in class pal.tree.SimulatedAlignment
generate new artificial data set (specified root sequence)
simulate(String) - Method in class pal.tree.SimulatedAlignment
generate new artificial data set (random root sequence)
SimulatedAlignment - class pal.tree.SimulatedAlignment.
generates an artificial data set
SimulatedAlignment(int, Tree, SubstitutionModel) - Constructor for class pal.tree.SimulatedAlignment
Inititalisation
simulateIntervals(int, DemographicModel) - Method in class pal.coalescent.CoalescentSimulator
Simulates a set of CoalescentIntervals from a genealogy assuming contemporaneous tips.
simulateIntervals(TimeOrderCharacterData, DemographicModel, boolean) - Method in class pal.coalescent.SerialCoalescentSimulator
Simulates a set of CoalescentIntervals from a genealogy.
siteDataType - Variable in class pal.alignment.MultiLocusAnnotatedAlignment
provides datatype for each locus separately
siteLogL - Variable in class pal.eval.LikelihoodValue
log-likelihood for each site pattern
SitePattern - class pal.alignment.SitePattern.
takes an Alignment and determines its site patterns
SitePattern(Alignment) - Constructor for class pal.alignment.SitePattern
infer site patterns for a given alignment
SitePattern(DataType, int, int, IdGroup, int, int[], int[], byte[][]) - Constructor for class pal.alignment.SitePattern
construct SitePattern from scratch
skewness(double[]) - Static method in class pal.statistics.DiscreteStatistics
compute fisher skewness
skipWhiteSpace(PushbackReader) - Method in class pal.io.FormattedInput
go to first non-whitespace character
SkylinePlot - class pal.coalescent.SkylinePlot.
Skyline plot derived from a strictly bifurcating tree or a coalescent interval.
SkylinePlot(CoalescentIntervals, double) - Constructor for class pal.coalescent.SkylinePlot
Construct skyline plot from given coalescent intervals
SkylinePlot(Tree, double) - Constructor for class pal.coalescent.SkylinePlot
Construct skyline plot from tree
sort(Comparable[]) - Static method in class pal.util.HeapSort
Sorts an array of comparable objects into increasing order.
sort(double[]) - Static method in class pal.util.HeapSort
Sorts an array of doubles into increasing order.
sort(double[], int[]) - Static method in class pal.util.HeapSort
Sorts an array of indices into an array of doubles into increasing order.
sort(double, double, double) - Method in class pal.util.ThreeNumberSort
sort three doubles
sort(Object[], Comparator) - Static method in class pal.util.HeapSort
Sorts an array of objects into increasing order given a comparator.
sort(Vector) - Static method in class pal.util.HeapSort
Sorts a vector of comparable objects into increasing order.
sort(Vector, int[]) - Static method in class pal.util.HeapSort
Sorts an array of indices to vector of comparable objects into increasing order.
sortAbs(double[]) - Static method in class pal.util.HeapSort
Sorts an array of doubles into increasing order, ingoring sign.
sortSites() - Method in class pal.alignment.ConcatenatedAnnotatedAlignment
sort the sites by chromosome, then by chromosomal location, and final locusPosition
space(int, char) - Static method in class pal.io.FormattedOutput
returns of string of a given length of a single character.
SPACES_PER_LEVEL - Static variable in interface pal.util.XMLConstants
 
SplitSystem - class pal.tree.SplitSystem.
data structure for a set of splits
SplitSystem(IdGroup, int) - Constructor for class pal.tree.SplitSystem
 
SplitUtils - class pal.tree.SplitUtils.
utilities for split systems
SplitUtils() - Constructor for class pal.tree.SplitUtils
 
SQRT_EPSILON - Static variable in class pal.math.MachineAccuracy
 
SQRT_SQRT_EPSILON - Static variable in class pal.math.MachineAccuracy
 
squaredDistance(DistanceMatrix, boolean) - Method in class pal.distance.DistanceMatrix
compute squared distance to second distance matrix
squaredDistance(DistanceMatrix, DistanceMatrix, boolean) - Static method in class pal.distance.DistanceMatrixUtils
compute squared distance to second distance matrix.
standardTreePrep() - Method in class pal.gui.TreePainter
Rotates the tree by leaf count, creates a positioned node version of the trees root and calculates postions and width and height information.
StateRemover - class pal.datatype.StateRemover.
A standard data type, but with characters removed
StateRemover(DataType, int[]) - Constructor for class pal.datatype.StateRemover
A translation array -> originalToAdjusted_["adjusted State"] = "original state"
stdev(double[]) - Static method in class pal.statistics.DiscreteStatistics
compute standard deviation
step - Variable in class pal.math.ConjugateDirectionSearch
step is a steplength parameter and should be set equal to the expected distance from the solution. exceptionally small or large values of step lead to slower convergence on the first few iterations the default value for step is 1.0
STEPPED_MUTATION_RATE - Static variable in interface pal.util.XMLConstants
 
SteppedMutationRate - class pal.mep.SteppedMutationRate.
This class models a step-wise mutation rate.
SteppedMutationRate(double[], double[], int) - Constructor for class pal.mep.SteppedMutationRate
Construct mutation rate model of a give rate in given units.
SteppedMutationRate(double[], double[], int, boolean) - Constructor for class pal.mep.SteppedMutationRate
Construct mutation rate model of a give rate in given units.
SteppedMutationRate(double[], int) - Constructor for class pal.mep.SteppedMutationRate
Construct demographic model with default settings
stochasticNNI(Tree) - Static method in class pal.tree.Local
 
StochasticOSearch - class pal.math.StochasticOSearch.
minimization of a real-valued function of several variables without using derivatives, using the simple strategy of optimizing variables one by one.
StochasticOSearch() - Constructor for class pal.math.StochasticOSearch
Initialization
stop() - Method in class pal.misc.TimeStamp
stop timer
stopCondition(double, double[], double, double, boolean) - Method in class pal.math.MultivariateMinimum
Checks whether optimization should stop
STRING - Static variable in class pal.misc.Attribute
 
StrippedAlignment - class pal.alignment.StrippedAlignment.
takes an alignment and repeatedly removes sites
StrippedAlignment(Alignment) - Constructor for class pal.alignment.StrippedAlignment
Constructor
StrippedAnnotatedAlignment - class pal.alignment.StrippedAnnotatedAlignment.
This is the stripped implementation of the Annotation interface, which is designed to provide stripped and annotated alignments.
StrippedAnnotatedAlignment(AnnotationAlignment) - Constructor for class pal.alignment.StrippedAnnotatedAlignment
Simple constructor
structureChanged(PalObjectEvent) - Method in class pal.eval.FastLikelihoodCalculator
 
structureChanged(PalObjectEvent) - Method in interface pal.misc.PalObjectListener
Signifies that the structure of the object has changed (for example in trees to topology has changed)
structureChanged(PalObjectEvent) - Method in class pal.substmodel.CachedRateMatrix
 
subset(IdGroup) - Method in class pal.misc.TimeOrderCharacterData
Extracts a subset of a TimeOrderCharacterData.
SubstitutionModel - interface pal.substmodel.SubstitutionModel.
model of sequence substitution (rate matrix + rate variation). provides a convenient interface for the computation of transition probabilities
SUBTREE_PROBABILITY - Static variable in interface pal.tree.AttributeNode
attribute name for the probability of the subtree defined by an internal node.
subtreeCount(Node, Vector) - Static method in class pal.tree.RootedTreeUtils
 
Summarizable - interface pal.misc.Summarizable.
interface for classes that can provide summaries
SUPGMADistanceMatrix - class pal.distance.SUPGMADistanceMatrix.
Corrects distances in a distance matrix such that all tips appear contemporaneous, given a time/date and rate information for the taxa.
SUPGMADistanceMatrix(DistanceMatrix, TimeOrderCharacterData, double) - Constructor for class pal.distance.SUPGMADistanceMatrix
Uses date/time information and a constant rate to correct distance matrices.
SUPGMATree - class pal.tree.SUPGMATree.
constructs an SUPGMA tree from pairwise distances.
SUPGMATree(DistanceMatrix, TimeOrderCharacterData, double) - Constructor for class pal.tree.SUPGMATree
constructor SUPGMA tree
SUPGMATree(DistanceMatrix, TimeOrderCharacterData, double, boolean) - Constructor for class pal.tree.SUPGMATree
constructor SUPGMA tree
support - Variable in class pal.statistics.ModelSupport
support in each hypothesis
supportOrder - Variable in class pal.statistics.ModelSupport
support order of the tree hypotheses

T

TableReport - interface pal.misc.TableReport.
interface for classes with data that can be presented in tables
taxa - Variable in class pal.misc.TimeOrderCharacterData
the identifier group
TERMINATE_CHARACTER - Static variable in class pal.datatype.AminoAcids
 
TERMINATE_STATE - Static variable in class pal.datatype.AminoAcids
 
theAlignment - Variable in class pal.popgen.LinkageDisequilibrium
 
theAnnotationAlignment - Variable in class pal.popgen.LinkageDisequilibrium
 
third - Variable in class pal.util.ThreeNumberSort
order of the numbers (0-2)
ThreeNumberSort - class pal.util.ThreeNumberSort.
sorts three numbers (doubles) and choose randomly among the minimum/maximum values
ThreeNumberSort() - Constructor for class pal.util.ThreeNumberSort
constructor
TIME - Static variable in interface pal.util.XMLConstants
 
TIME_DATA - Static variable in interface pal.util.XMLConstants
 
TimeOrderCharacterData - class pal.misc.TimeOrderCharacterData.
Character data that expresses an order through time.
TimeOrderCharacterData() - Constructor for class pal.misc.TimeOrderCharacterData
Parameterless constructor for superclasses.
TimeOrderCharacterData(IdGroup, int) - Constructor for class pal.misc.TimeOrderCharacterData
Constructor taking only IdGroup.
TimeOrderCharacterData(int, int, double, int) - Constructor for class pal.misc.TimeOrderCharacterData
Constructs a TimeOrderCharacterData.
timeOrdinals - Variable in class pal.misc.TimeOrderCharacterData
Order of times
times - Variable in class pal.misc.TimeOrderCharacterData
Actual times of each sample
TimeStamp - class pal.misc.TimeStamp.
keeps track of program runtime
TimeStamp() - Constructor for class pal.misc.TimeStamp
create object and start timer
title_ - Variable in class pal.gui.TreePainter
 
TN - class pal.substmodel.TN.
Tamura-Nei model of nucleotide evolution
TN - Static variable in interface pal.substmodel.NucleotideModelID
 
TN - Static variable in interface pal.util.XMLConstants
 
TN(double[], double[]) - Constructor for class pal.substmodel.TN
constructor 2
TN(double, double, double[]) - Constructor for class pal.substmodel.TN
constructor 1
TOPBORDER - Static variable in class pal.gui.TreePainterNormal
 
TOPBORDER - Static variable in class pal.gui.TreePainterCircular
 
toSingleLine() - Method in class pal.mep.MutationRateModel
 
toSingleLine() - Method in class pal.mep.ConstantMutationRate
 
toSingleLine() - Method in class pal.mep.WindowedMutationRate
 
toSingleLine() - Method in class pal.mep.SteppedMutationRate
 
toString() - Method in class pal.alignment.AbstractAlignment
returns representation of this alignment as a string
toString() - Method in class pal.alignment.SimpleCharacterAlignment
returns representation of this alignment as a string
toString() - Method in class pal.distance.DistanceMatrix
returns representation of this alignment as a string
toString() - Method in class pal.mep.ConstantMutationRate
 
toString() - Method in class pal.mep.WindowedMutationRate
 
toString() - Method in class pal.mep.SteppedMutationRate
 
toString() - Method in class pal.misc.SimpleIdGroup
Returns a string representation of this IdGroup in the form of a bracketed list.
toString() - Method in class pal.misc.ParameterizedDouble
 
toString() - Method in class pal.misc.TimeOrderCharacterData
Returns a string representation of this time order character data.
toString() - Method in class pal.misc.Identifier
 
toString() - Method in class pal.popgen.LinkageDisequilibrium
returns representation of the LD results as a string
toString() - Method in class pal.substmodel.SimpleSubstitutionModel
Return string representation of substitution model.
toString() - Method in class pal.substmodel.CachedRateMatrix
Return string representation of substitution model.
toString() - Method in class pal.substmodel.F84
 
toString() - Method in class pal.tree.SimpleNode
 
toString() - Method in class pal.tree.ParameterizedTree
 
toString() - Method in class pal.tree.SimpleTree
 
toString() - Method in class pal.tree.SplitSystem
print split system
toString() - Method in class pal.util.ComparableDouble
 
toString() - Method in class pal.coalescent.ConstantPopulation
 
toString() - Method in class pal.coalescent.SkylinePlot
 
toString() - Method in class pal.coalescent.ExponentialGrowth
 
toString() - Method in class pal.coalescent.ConstExpGrowth
 
toString() - Method in class pal.coalescent.CoalescentIntervals
 
toString() - Method in class pal.coalescent.ExpandingPopulation
 
toString(double[]) - Static method in class pal.misc.Utils
A simple toString method for an array of doubles.
toString(double[][]) - Static method in class pal.misc.Utils
A simple toString method for an array of doubles.
toString(int[]) - Static method in class pal.misc.Utils
A simple toString method for an array of ints.
traitNames - Variable in class pal.alignment.SimpleCharacterAlignment
names of the traits
traitValues - Variable in class pal.alignment.SimpleCharacterAlignment
trait values
TransitionPenaltyTable - interface pal.datatype.TransitionPenaltyTable.
Implements a table of transition penalties for a particular datatype.
transProb - Variable in class pal.substmodel.MatrixExponential
transition probability matrix
transProb(int, int, int) - Method in class pal.substmodel.SimpleSubstitutionModel
get transition probability for the preselected model and the previously specified distance
transProb(int, int, int) - Method in interface pal.substmodel.SubstitutionModel
get transition probability for the preselected model and the previously specified distance
Tree - interface pal.tree.Tree.
Interface for a phylogenetic or genealogical tree.
TREE - Static variable in interface pal.util.XMLConstants
 
TreeComponent - class pal.gui.TreeComponent.
An AWT Component for displaying a tree.
TreeComponent(Tree) - Constructor for class pal.gui.TreeComponent
 
TreeComponent(Tree, boolean) - Constructor for class pal.gui.TreeComponent
 
TreeComponent(Tree, String) - Constructor for class pal.gui.TreeComponent
 
TreeComponent(Tree, String, boolean) - Constructor for class pal.gui.TreeComponent
 
TreeComponent(Tree, TimeOrderCharacterData, boolean) - Constructor for class pal.gui.TreeComponent
 
TreeDistanceMatrix - class pal.tree.TreeDistanceMatrix.
computes distance matrix induced by a tree (needs only O(n^2) time, following algorithm DistanceInTree by D.Bryant and P.
TreeDistanceMatrix(IdGroup, Tree) - Constructor for class pal.tree.TreeDistanceMatrix
compute induced distance matrix using actual branch lengths
TreeDistanceMatrix(IdGroup, Tree, boolean, double) - Constructor for class pal.tree.TreeDistanceMatrix
compute induced distance matrix
TreeDistanceMatrix(Tree) - Constructor for class pal.tree.TreeDistanceMatrix
compute induced distance matrix using actual branch lengths (using tree-induced order of sequences)
TreeDistanceMatrix(Tree, boolean, double) - Constructor for class pal.tree.TreeDistanceMatrix
compute induced distance matrix (using tree-induced order of sequences)
treeNode - Variable in class pal.gui.TreePainter
 
TreePainter - class pal.gui.TreePainter.
A class that can paint a tree into a Graphics object.
TreePainter(Tree, String, boolean) - Constructor for class pal.gui.TreePainter
 
TreePainterCircular - class pal.gui.TreePainterCircular.
A class that can paint a tree (in a circular fashion) into a Graphics object .
TreePainterCircular(Tree, String, boolean) - Constructor for class pal.gui.TreePainterCircular
 
TreePainterNormal - class pal.gui.TreePainterNormal.
A class that can paint a tree into a Graphics object.
TreePainterNormal(Tree, String, boolean) - Constructor for class pal.gui.TreePainterNormal
 
TreeParseException - exception pal.tree.TreeParseException.
exception thrown by ReadTree
TreeParseException() - Constructor for class pal.tree.TreeParseException
 
TreeParseException(String) - Constructor for class pal.tree.TreeParseException
 
treeUpdated() - Method in class pal.eval.SimpleLikelihoodCalculator
 
TreeUtils - class pal.tree.TreeUtils.
various utility functions on trees.
TreeUtils() - Constructor for class pal.tree.TreeUtils
 
TS_TV_RATIO - Static variable in interface pal.util.XMLConstants
 
TWO_STATE - Static variable in interface pal.util.XMLConstants
 
TWO_STATE_DESCRIPTION - Static variable in interface pal.datatype.DataType
two state name (for XML and human readability)
TwoStateModel - class pal.substmodel.TwoStateModel.
implements the most general reversible rate matrix for two-state data
TwoStateModel(double[]) - Constructor for class pal.substmodel.TwoStateModel
constructor
TwoStates - class pal.datatype.TwoStates.
implements DataType for two-state data
TWOSTATES - Static variable in interface pal.datatype.DataType
 
TwoStates() - Constructor for class pal.datatype.TwoStates
 
TYPE - Static variable in interface pal.util.XMLConstants
 
TYPE_NAMES - Static variable in class pal.datatype.CodonTableFactory
 

U

UnconstrainedTree - class pal.tree.UnconstrainedTree.
provides parameter interface to an unconstrained tree (parameters are all available branch lengths)
UnconstrainedTree(Tree) - Constructor for class pal.tree.UnconstrainedTree
take any tree and afford it with an interface suitable for an unconstrained tree (parameters are all available branch lengths)
UNIFORM - Static variable in interface pal.util.XMLConstants
 
UniformRate - class pal.substmodel.UniformRate.
uniform rate distribution
UniformRate() - Constructor for class pal.substmodel.UniformRate
construct uniform rate distribution
units - Variable in class pal.misc.TimeOrderCharacterData
 
Units - interface pal.misc.Units.
interface holding unit constants
UNITS - Static variable in interface pal.util.XMLConstants
 
UnivariateFunction - interface pal.math.UnivariateFunction.
interface for a function of one variable
UnivariateMinimum - class pal.math.UnivariateMinimum.
minimization of a real-valued function of one variable without using derivatives.
UnivariateMinimum() - Constructor for class pal.math.UnivariateMinimum
 
UNIVERSAL - Static variable in class pal.datatype.CodonTableFactory
Universal type
UNKNOWN - Static variable in interface pal.util.XMLConstants
 
UNKNOWN_CHARACTER - Static variable in interface pal.datatype.DataType
 
update() - Method in class pal.tree.DatedTipsClockTree
make parameters consistent with branch lengths and rate parameter
update() - Method in class pal.tree.ClockTree
make clocktree consistent with branch lengths
update(double[], double[]) - Method in class pal.math.LineFunction
update start point and direction (bounds and search direction are NOT checked)
updateMatrixExp() - Method in class pal.substmodel.AbstractRateMatrix
 
updateModel(SubstitutionModel) - Method in class pal.distance.SequencePairLikelihood
update model of substitution
updateModel(SubstitutionModel) - Method in class pal.distance.PairwiseDistance
update model of substitution
updateSitePattern(SitePattern) - Method in class pal.distance.SequencePairLikelihood
update site pattern
updateSitePattern(SitePattern) - Method in class pal.distance.PairwiseDistance
update site pattern
updateSitePattern(SitePattern) - Method in class pal.eval.FastLikelihoodCalculator
 
UPGMATree - class pal.tree.UPGMATree.
constructs a UPGMA tree from pairwise distances
UPGMATree(DistanceMatrix) - Constructor for class pal.tree.UPGMATree
constructor UPGMA tree
UrnModel - class pal.math.UrnModel.
class for drawing numbers from an urn with and without laying back
UrnModel(int) - Constructor for class pal.math.UrnModel
create urn model
UT_STATE - Static variable in class pal.datatype.Nucleotides
 
Utils - class pal.misc.Utils.
Provides some miscellaneous methods.
Utils() - Constructor for class pal.misc.Utils
 

V

validateTagName(Element, String) - Static method in class pal.xml.ElementParser
Throws a runtime exception if the element does not have the given name.
VALUE - Static variable in interface pal.util.XMLConstants
 
variance(double) - Static method in class pal.statistics.ExponentialDistribution
variance of the exponential distribution
variance(double) - Static method in class pal.statistics.ChiSquareDistribution
variance of the chi-square distribution
variance(double[]) - Static method in class pal.statistics.DiscreteStatistics
compute variance (ML estimator)
variance(double[], double) - Static method in class pal.statistics.DiscreteStatistics
compute variance (ML estimator)
variance(double, double) - Static method in class pal.statistics.GammaDistribution
variance of the Gamma distribution
variance(double, double) - Static method in class pal.statistics.NormalDistribution
variance
variance(double, double) - Static method in class pal.statistics.ParetoDistribution
variance of the Pareto distribution
varianceSampleMean(double[]) - Static method in class pal.statistics.DiscreteStatistics
compute variance of sample mean (ML estimator)
varianceSampleMean(double[], double) - Static method in class pal.statistics.DiscreteStatistics
compute variance of sample mean (ML estimator)
Version - class pal.util.Version.
This class provides a mechanism for returning the version number of the pal library.
VERSION - Static variable in class pal.misc.ReleaseInfo
version
Version() - Constructor for class pal.util.Version
 
VT - class pal.substmodel.VT.
VT (variable time matrix) model of amino acid evolution
VT - Static variable in interface pal.substmodel.AminoAcidModelID
 
VT - Static variable in interface pal.util.XMLConstants
 
VT(double[]) - Constructor for class pal.substmodel.VT
constructor

W

WAG - class pal.substmodel.WAG.
WAG model of amino acid evolution (S.
WAG - Static variable in interface pal.substmodel.AminoAcidModelID
 
WAG - Static variable in interface pal.util.XMLConstants
 
WAG(double[]) - Constructor for class pal.substmodel.WAG
constructor
weight - Variable in class pal.alignment.SitePattern
weights of each site pattern
weightedLocusPosition - Variable in class pal.alignment.IndelAnnotatedAlignment
used to designate weighted position; accounts for gaps
weightedPosition - Variable in class pal.alignment.MultiLocusAnnotatedAlignment
used to designate weighted position; accounts for gaps
weightedPosition - Variable in class pal.alignment.SimpleAnnotatedAlignment
used to designate weighted position; accounts for gaps
whichIdNumber(String) - Method in class pal.alignment.AbstractAlignment
 
whichIdNumber(String) - Method in class pal.alignment.SimpleCharacterAlignment
 
whichIdNumber(String) - Method in class pal.distance.DistanceMatrix
 
whichIdNumber(String) - Method in class pal.misc.SimpleIdGroup
Return index of identifier with name or -1 if not found
whichIdNumber(String) - Method in interface pal.misc.IdGroup
returns the index of the identifier with the given name.
whichIdNumber(String) - Method in class pal.misc.TimeOrderCharacterData
 
windowCenter - Variable in class pal.mep.WindowedMutationRate
mutation rate change times
WindowedMutationRate - class pal.mep.WindowedMutationRate.
This class models a windowed mutation rate (parameter: mu = mutation rate).
WindowedMutationRate(double, double, double, double, int) - Constructor for class pal.mep.WindowedMutationRate
Construct mutation rate model of a give rate in given units.
WindowedMutationRate(double, double, double, double, int, boolean) - Constructor for class pal.mep.WindowedMutationRate
Construct mutation rate model of a give rate in given units.
WindowedMutationRate(double, double, double, int) - Constructor for class pal.mep.WindowedMutationRate
Construct mutation rate model of a give rate in given units.
WindowedMutationRate(double, double, int) - Constructor for class pal.mep.WindowedMutationRate
Construct demographic model with default settings
windowWidth - Variable in class pal.mep.WindowedMutationRate
 

X

x - Variable in class pal.gui.PositionedNode
 
XMLConstants - interface pal.util.XMLConstants.
constants (strings and numbers) relating to reading and writing XML.
XmlParseException - exception pal.xml.XmlParseException.
exception thrown by ElementParser.
XmlParseException() - Constructor for class pal.xml.XmlParseException
 
XmlParseException(String) - Constructor for class pal.xml.XmlParseException
 
XSPACER - Static variable in class pal.gui.TreePainterNormal
 
XSPACER - Static variable in class pal.gui.TreePainterCircular
 

Y

YANG_CODON_MODEL - Static variable in interface pal.util.XMLConstants
 
YangCodonModel - class pal.substmodel.YangCodonModel.
Yang's model of codon evolution
YangCodonModel(double[], double[]) - Constructor for class pal.substmodel.YangCodonModel
constructor 4 (universal codon table)
YangCodonModel(double[], double[], CodonTable) - Constructor for class pal.substmodel.YangCodonModel
constructor 3
YangCodonModel(double, double, double[]) - Constructor for class pal.substmodel.YangCodonModel
constructor 2 (universal codon table)
YangCodonModel(double, double, double[], CodonTable) - Constructor for class pal.substmodel.YangCodonModel
constructor 1
YEARS - Static variable in interface pal.misc.Units
 
YEARS - Static variable in interface pal.util.XMLConstants
 
YSPACER - Static variable in class pal.gui.TreePainterNormal
 
YSPACER - Static variable in class pal.gui.TreePainterCircular
 

A B C D E F G H I J K L M N O P Q R S T U V W X Y