- C_RETURN - Static variable in class pal.io.NexusTokenizer
-
- 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 in pal.substmodel
-
a cached rate matrix.
- CachedRateMatrix(RateMatrix, DoubleKeyCache) - Constructor for class pal.substmodel.CachedRateMatrix
-
- CachedRateMatrix(RateMatrix, int) - Constructor for class pal.substmodel.CachedRateMatrix
-
- CachedRateMatrix(CachedRateMatrix) - 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.
- calculateAscendentExtendedConditionals(double, double, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.MolecularClockLikelihoodModel.Internal
-
- calculateAscendentFlatConditionals(PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.MolecularClockLikelihoodModel.Internal
-
- calculateCategoryPatternConditionalProbabilities(double[], double[], int) - Method in class pal.eval.ConditionalProbabilityStore
-
Calculate the conditional probabilities for each ancestral state at each site pattern, multiplied by related equilibrium frequencies
- calculateCategoryPatternProbabilities(double, SubstitutionModel, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore, ConditionalProbabilityStore, double[][]) - Method in class pal.eval.LHCalculator.AbstractExternal
-
- calculateCategoryPatternProbabilities(SubstitutionModel, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore, double[][]) - Method in class pal.eval.LHCalculator.AbstractExternal
-
- calculateCladeProbabilities(Tree, CladeSystem[]) - Static method in class pal.tree.CladeSystem
-
- calculatedLogLikelihood() - Method in class pal.treesearch.GeneralLikelihoodSearcher
-
- calculateExtended(double, SubstitutionModel, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.LHCalculator.External
-
- calculateExtended(double, SubstitutionModel, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore, boolean) - Method in interface pal.eval.LHCalculator.Internal
-
- calculateExtended(double, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in class pal.eval.SimpleUnconstrainedLikelihoodModel.InternalImpl
-
- calculateExtended(double, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.UnconstrainedLikelihoodModel.External
-
- calculateExtended(double, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.UnconstrainedLikelihoodModel.Internal
-
- calculateExtendedConditionals(double, double, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.MolecularClockLikelihoodModel.External
-
- calculateExtendedConditionals(double, double, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.MolecularClockLikelihoodModel.Internal
-
- calculateExtendedConditionals(double, double) - Method in interface pal.eval.MolecularClockLikelihoodModel.Leaf
-
- calculateFlat(PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.LHCalculator.External
-
- calculateFlat(PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.LHCalculator.Internal
-
calculate flat probability information (not extended over a branch).
- calculateFlat(PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in class pal.eval.SimpleUnconstrainedLikelihoodModel.InternalImpl
-
- calculateFlat(PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.UnconstrainedLikelihoodModel.External
-
- calculateFlat(PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.UnconstrainedLikelihoodModel.Internal
-
calculate flat probability information (not extended over a branch).
- calculateFlatConditionals(double, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.MolecularClockLikelihoodModel.External
-
- calculateFlatConditionals(PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.MolecularClockLikelihoodModel.Internal
-
- calculateFlatConditionals(double) - Method in interface pal.eval.MolecularClockLikelihoodModel.Leaf
-
- calculateLikelihood(Tree, Alignment) - Method in interface pal.statistics.LikelihoodEvaluator
-
- calculateLikelihoodScore() - Method in interface pal.treesearch.GeneralConstraintGroupManager.LikelihoodScoreAccess
-
The likelihood score doesn't exactly have to be the likelihood (well, it should be, but it may be the optimised likelihood)
- calculateLogLikelihood(double[], double[], int[], int) - Method in class pal.eval.ConditionalProbabilityStore
-
- calculateLogLikelihood(double[], double[], int) - Method in class pal.eval.ConditionalProbabilityStore
-
- calculateLogLikelihood() - Method in class pal.eval.FastLikelihoodCalculator
-
- calculateLogLikelihood() - Method in class pal.eval.GeneralLikelihoodCalculator
-
- calculateLogLikelihood(double, SubstitutionModel, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.LHCalculator.External
-
Calculate the likelihood given two sub trees (left, right) and their flat (unextend) likeihood probabilities
- calculateLogLikelihood(SubstitutionModel, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.LHCalculator.External
-
Calculate the likelihood given two sub trees (left, right) and their extended likeihood probabilities
- calculateLogLikelihood() - Method in interface pal.eval.LikelihoodCalculator
-
- calculateLogLikelihood(Tree, Alignment, SubstitutionModel) - Static method in class pal.eval.LikelihoodTool
-
Calculate the log likelihood of a particular set of phylogenetic data
- calculateLogLikelihood(double, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.MolecularClockLikelihoodModel.External
-
Calculate the likelihood given two sub trees (left, right) and their extended likeihood probabilities
- calculateLogLikelihood() - Method in class pal.eval.SimpleLikelihoodCalculator
-
compute log-likelihood for current tree (fixed branch lengths and model)
return log-likelihood
- calculateLogLikelihood(double, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.UnconstrainedLikelihoodModel.External
-
Calculate the likelihood given two sub trees (left, right) and their flat (unextend) likeihood probabilities
- calculateLogLikelihood(PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.UnconstrainedLikelihoodModel.External
-
Calculate the likelihood given two sub trees (left, right) and their extended likeihood probabilities
- calculateLogLikelihood(GeneralConstructionTool) - Method in class pal.treesearch.ConstrainedInternalNode
-
- calculateLogLikelihood(GeneralConstructionTool) - Method in class pal.treesearch.FreeBranch
-
- calculateLogLikelihood(GeneralConstructionTool) - Method in class pal.treesearch.PivotNode
-
- calculateLogLikelihood(GeneralConstructionTool) - Method in interface pal.treesearch.RootAccess
-
- calculateLogLikelihood(Tree, Alignment, SubstitutionModel) - Static method in class pal.treesearch.TreeSearchTool
-
Calculate the log likelihood of a particular set of phylogenetic data
- calculateLogLikelihood() - Method in class pal.treesearch.UnrootedMLSearcher
-
Likelihood calculation method (not optimisation)
- calculateLogLikelihood2(GeneralConstructionTool) - Method in class pal.treesearch.FreeBranch
-
- calculateLogLikelihood2() - Method in class pal.treesearch.UnrootedMLSearcher
-
An alternative likelihood calculation method (should give same results as other method, and in same time)
- calculateLogLikelihoodNonRoot(double, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.MolecularClockLikelihoodModel.External
-
Calculate the likelihood given a non root node
- calculateLogLikelihoodSingle(SubstitutionModel, int[], int, ConditionalProbabilityStore) - Method in interface pal.eval.LHCalculator.External
-
Calculate the likelihood given the conditional probabilites at the root
- calculateLogLikelihoodSingle(double, PatternInfo, ConditionalProbabilityStore) - Method in interface pal.eval.MolecularClockLikelihoodModel.External
-
- calculateLogLikelihoodSingle(int[], int, ConditionalProbabilityStore) - Method in interface pal.eval.UnconstrainedLikelihoodModel.External
-
Calculate the likelihood given the conditional probabilites at the root
- calculateLogLikelihoodSummary() - Method in class pal.eval.GeneralLikelihoodCalculator
-
- calculatePatternLogLikelihoods(double[], double[], int) - Method in class pal.eval.ConditionalProbabilityStore
-
- calculatePositions() - Method in class pal.gui.PositionedNode
-
- calculatePostExtendedFlat(double, SubstitutionModel, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore, boolean) - Method in interface pal.eval.LHCalculator.Internal
-
- calculatePostExtendedFlatConditionals(double, double, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.MolecularClockLikelihoodModel.Internal
-
Extends left and right conditionals by type and then calculates flat conditionals
- calculateRFromLx() - Method in class pal.coalescent.ConstExpGrowth
-
- calculateSingleAscendentExtendedConditionalsDirect(double, double, PatternInfo, ConditionalProbabilityStore) - Method in interface pal.eval.MolecularClockLikelihoodModel.External
-
- calculateSingleAscendentExtendedConditionalsIndirect(double, double, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.MolecularClockLikelihoodModel.External
-
- calculateSingleDescendentExtendedConditionals(double, double, PatternInfo, ConditionalProbabilityStore) - Method in interface pal.eval.MolecularClockLikelihoodModel.External
-
- calculateSingleExtendedDirect(double, SubstitutionModel, int, ConditionalProbabilityStore) - Method in interface pal.eval.LHCalculator.External
-
Extend the conditionals back in time by some distance, with some model
- calculateSingleExtendedDirect(double, int, ConditionalProbabilityStore) - Method in interface pal.eval.UnconstrainedLikelihoodModel.External
-
Extend the conditionals back in time by some distance
- calculateSingleExtendedIndirect(double, SubstitutionModel, int, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.LHCalculator.External
-
Extend the conditionals back in time by some distance, with some model
- calculateSingleExtendedIndirect(double, int, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.UnconstrainedLikelihoodModel.External
-
Extend the conditionals back in time by some distance
- calculateSiteDetails(double, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.MolecularClockLikelihoodModel.External
-
- calculateSiteDetails(UnconstrainedLikelihoodModel.External, GeneralConstructionTool) - Method in class pal.treesearch.FreeBranch
-
- calculateSiteDetails() - Method in class pal.treesearch.UnrootedMLSearcher
-
- calculateSiteDetailsRooted(SubstitutionModel, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in class pal.eval.LHCalculator.AbstractExternal
-
- calculateSiteDetailsRooted(SubstitutionModel, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.LHCalculator.External
-
Calculate the conditional probabilities of each pattern for each category
- calculateSiteDetailsRooted(PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.UnconstrainedLikelihoodModel.External
-
Calculate the conditional probabilities of each pattern for each category
- calculateSiteDetailsUnrooted(double, SubstitutionModel, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in class pal.eval.LHCalculator.AbstractExternal
-
- calculateSiteDetailsUnrooted(double, SubstitutionModel, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.LHCalculator.External
-
Calculate the conditional probabilities of each pattern for each category
- calculateSiteDetailsUnrooted(double, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.UnconstrainedLikelihoodModel.External
-
Calculate the conditional probabilities of each pattern for each category
- canGenerateAlternativeTreeRepresentation() - Method in interface pal.mep.DeltaModel
-
- canGenerateDemogrpahicModel() - Method in interface pal.supgma.ThetaHandler
-
- cdf(double, double) - Static method in class pal.statistics.ChiSquareDistribution
-
cumulative density function of the chi-square distribution
- 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[]) - 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) - Static method in class pal.statistics.ExponentialDistribution
-
cumulative density function of the exponential distribution
- 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 in pal.alignment
-
This interface is designed to hold quantitative character states.
- checkDirection(double[], double[]) - Method in class pal.math.LineFunction
-
check direction vector.
- checkMuChanges(boolean, double[], boolean, double[], boolean) - Static method in class pal.mep.SteppedMutationRate
-
Checks if mu changes are valid for a particular set of sample times.
- 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 in pal.statistics
-
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 in pal.statistics
-
chi-square test
- ChiSquareTest() - Constructor for class pal.statistics.ChiSquareTest
-
- ChiSquareValue - Class in pal.eval
-
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.IndelAnnotatedAlignment
-
used to designate chromosome
- chromosome - Variable in class pal.alignment.MultiLocusAnnotatedAlignment
-
used to designate chromosome
- chromosome - Variable in class pal.alignment.SimpleAnnotatedAlignment
-
used to designate chromosome
- chromosomePosition - Variable in class pal.alignment.IndelAnnotatedAlignment
-
used to designate position along 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
- CILATE - Static variable in interface pal.datatype.CodonTable
-
TypeID for Cilate
- 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 in pal.gui
-
- 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
-
- CladeSystem - Class in pal.tree
-
data structure for a set of splits
- CladeSystem(IdGroup, int) - Constructor for class pal.tree.CladeSystem
-
- ClassDistribution - Interface in pal.substmodel
-
- clear() - Method in class pal.alignment.AlignmentReceiver.BucketReceiver
-
- clearAll() - Method in class pal.alignment.AlignmentBuilder
-
Remove all currently stored sequences.
- clearCache() - Method in class pal.util.DefaultCache
-
- clearCache() - Method in interface pal.util.DoubleKeyCache
-
- clearProgress() - Method in interface pal.util.AlgorithmCallback
-
- ClockTree - Class in pal.tree
-
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.coalescent.ConstantPopulation
-
- clone() - Method in class pal.coalescent.ConstExpConst
-
Makes a copy of this demographic model.
- clone() - Method in class pal.coalescent.ConstExpGrowth
-
- clone() - Method in class pal.coalescent.DemographicModel
-
- clone() - Method in class pal.coalescent.ExpandingPopulation
-
- clone() - Method in class pal.coalescent.ExponentialGrowth
-
- clone() - Method in class pal.mep.ConstantMutationRate
-
- clone() - Method in class pal.mep.MutationRateModel
-
- clone() - Method in class pal.mep.SteppedMutationRate
-
- clone() - Method in class pal.mep.WindowedMutationRate
-
- clone(TimeOrderCharacterData) - Static method in class pal.misc.TimeOrderCharacterData
-
Returns a clone of the specified TimeOrderCharacterData
- clone() - Method in class pal.substmodel.AbstractRateMatrix
-
- clone() - Method in class pal.substmodel.CachedRateMatrix
-
A non shallow implementation of clone()
- clone() - Method in class pal.substmodel.GeneralRateDistributionSubstitutionModel
-
- clone() - Method in class pal.substmodel.GTR
-
- clone() - Method in class pal.substmodel.HKY
-
- clone() - Method in class pal.substmodel.RateDistribution
-
- clone() - Method in interface pal.substmodel.RateMatrix
-
- clone() - Method in class pal.substmodel.SingleClassSubstitutionModel
-
- clone() - Method in interface pal.substmodel.SubstitutionModel
-
- clone() - Method in class pal.substmodel.YangCodonModel.SimpleNeutralSelection
-
- clone() - Method in class pal.substmodel.YangCodonModel.SimplePositiveSelection
-
- clone() - Method in class pal.tree.MutationRateModelTree
-
- clone() - Method in class pal.util.DefaultCache
-
- clone() - Method in interface pal.util.DoubleKeyCache
-
- ClusterTree - Class in pal.tree
-
- ClusterTree(DistanceMatrix, ClusterTree.ClusteringMethod) - Constructor for class pal.tree.ClusterTree
-
- ClusterTree.ClusteringMethod - Interface in pal.tree
-
An interface for describing Clustering methods
To be updated to cope with Ward's method and others...
- COALESCENT - Static variable in class pal.coalescent.CoalescentIntervals
-
Denotes and interval after which a coalescent event is observed
(i.e.
- COALESCENT - Static variable in interface pal.util.XMLConstants
-
- CoalescentException - Exception in pal.coalescent
-
Exceptions to do with coalescent models et cetera.
- CoalescentException() - Constructor for exception pal.coalescent.CoalescentException
-
Parameterless constructor.
- CoalescentException(String) - Constructor for exception pal.coalescent.CoalescentException
-
Constructor taking message.
- CoalescentIntervals - Class in pal.coalescent
-
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 in pal.coalescent
-
Simulates a set of coalescent intervals given a demographic model.
- CoalescentSimulator() - Constructor for class pal.coalescent.CoalescentSimulator
-
- CoalescentTree - Interface in pal.coalescent
-
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)
- CodonModel - Class in pal.substmodel
-
base class for nucleotide rate matrices
- CodonModel(double[]) - Constructor for class pal.substmodel.CodonModel
-
- Codons - Class in pal.datatype
-
implements DataType for all Codons (including terminators).
- Codons() - Constructor for class pal.datatype.Codons
-
- CODONS - Static variable in interface pal.datatype.DataType
-
- CodonTable - Interface in pal.datatype
-
Describes a device for translating Nucleotide triplets
or codon indices into amino acid codes.
- CodonTableFactory - Class in pal.datatype
-
Generates CodonTables
- CodonTableFactory() - Constructor for class pal.datatype.CodonTableFactory
-
- CodonTableUtils - Class in pal.datatype
-
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.
- COLON - Static variable in class pal.io.NexusTokenizer
-
- combine(Parameterized[]) - Static method in class pal.misc.Parameterized.Utils
-
Combine multiple parameterized objects into one
- combine(Parameterized, Parameterized) - Static method in class pal.misc.Parameterized.Utils
-
Combine multiple parameterized objects into one
- 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.
- COMMA - Static variable in class pal.io.NexusTokenizer
-
- Comparable - Interface in pal.util
-
interface for an object that is comparable.
- ComparableDouble - Class in pal.util
-
This class is unfortunate but necessary to conform to JDK 1.1
- ComparableDouble(double) - Constructor for class pal.util.ComparableDouble
-
- Comparator - Interface in pal.util
-
interface for an object that can compare other objects for the
purposes of ordering them.
- compare(double[], int[]) - Static method in class pal.statistics.ChiSquareTest
-
chi square test
- 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.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[], 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[], 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(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 interface pal.util.Comparable
-
Returns a number representing the ordering relationship that
the object has with the given object.
- compareTo(Object) - Method in class pal.util.ComparableDouble
-
- complementSequence(int[]) - Static method in class pal.datatype.Nucleotides
-
Complement of a sequence of nucleotides (or IUPACNucleotides - but IUPAC ness is lost)
- COMPLETE_LINKAGE - Static variable in class pal.tree.ClusterTree
-
- 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.DemographicLikelihoodValue
-
compute log-likelihood
for current branch lengths and model
return negative log-likelihood
- compute() - Method in class pal.eval.DemographicValue
-
compute log-likelihood
for current model
return negative log-likelihood
- compute() - Method in class pal.eval.LikelihoodValue
-
compute log-likelihood for current tree (fixed branch lengths and model)
return 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 class pal.coalescent.DemographicClockTree
-
Returns the likelihood of the current demographic model, given
the current branch lengths.
- computeDemoLogLikelihood() - Method in interface pal.coalescent.DemographicTree
-
- computeDistance(int, int, double, int, double) - Method in interface pal.tree.ClusterTree.ClusteringMethod
-
- computeDistance(Tree, int, int) - Static method in class pal.tree.TreeUtils
-
compute distance between two external nodes
- 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
- computeHeight(int, int, double) - Method in interface pal.tree.ClusterTree.ClusteringMethod
-
- 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.
- computeLogLikelihood() - Method in class pal.eval.DemographicValue
-
- 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 in pal.alignment
-
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 in pal.alignment
-
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
- ConditionalProbabilityStore - Class in pal.eval
-
Title: ConditionalProbabilityStore (was ConditionalLikelihoodStore)
- ConditionalProbabilityStore(int, int) - Constructor for class pal.eval.ConditionalProbabilityStore
-
- ConditionalProbabilityStore(int, int, ConditionalProbabilityStore.ExtraProcessor) - Constructor for class pal.eval.ConditionalProbabilityStore
-
- ConditionalProbabilityStore.ExtraProcessor - Interface in pal.eval
-
- ConjugateDirectionSearch - Class in pal.math
-
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 in pal.math
-
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_CONST - Static variable in interface pal.util.XMLConstants
-
- 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
- ConstantIndependentSingleSplitDistribution - Class in pal.substmodel
-
Title: ConstantIndependentSingleSplitDistribution
- ConstantIndependentSingleSplitDistribution(int) - Constructor for class pal.substmodel.ConstantIndependentSingleSplitDistribution
-
- ConstantIndependentSingleSplitDistribution(int, double[]) - Constructor for class pal.substmodel.ConstantIndependentSingleSplitDistribution
-
- ConstantMutationRate - Class in pal.mep
-
This class models a constant mutation rate
(parameter: mu = mutation rate).
- ConstantMutationRate(int, double) - Constructor for class pal.mep.ConstantMutationRate
-
Construct demographic model with default settings
- ConstantMutationRate(double, int, double) - Constructor for class pal.mep.ConstantMutationRate
-
Construct mutation rate model of a give rate in given units
- ConstantMutationRate(double, int, double, double) - Constructor for class pal.mep.ConstantMutationRate
-
Construct mutation rate model of a give rate in given units, with a given range of possible values
- ConstantMutationRate(ConstantMutationRate) - Constructor for class pal.mep.ConstantMutationRate
-
- ConstantPopulation - Class in pal.coalescent
-
This class models coalescent intervals for a constant population
(parameter: N0=present-day population size).
- ConstantPopulation(int) - Constructor for class pal.coalescent.ConstantPopulation
-
Construct demographic model with default settings
- ConstantPopulation(double, int) - Constructor for class pal.coalescent.ConstantPopulation
-
Construct demographic model of a constant population size.
- Constants - Interface in pal.treesearch
-
Title: Constants
- ConstExpConst - Class in pal.coalescent
-
This class models a population that grows exponentially from an
initial population size alpha N0 at time y to a size N0
at time x until the present-day.
- ConstExpConst(int, int) - Constructor for class pal.coalescent.ConstExpConst
-
Construct demographic model with default settings.
- ConstExpConst(double, double, double, double, int, int) - Constructor for class pal.coalescent.ConstExpConst
-
Construct demographic model of constexpconst population.
- ConstExpGrowth - Class in pal.coalescent
-
This class models a population that grows
exponentially from an inital population size alpha N0 to a present-day size N0.
- ConstExpGrowth(int, int) - Constructor for class pal.coalescent.ConstExpGrowth
-
Construct demographic model with default settings.
- ConstExpGrowth(double, double, double, int, int) - Constructor for class pal.coalescent.ConstExpGrowth
-
Construct demographic model of an expanding population.
- CONSTRAINED_LEAF_COMPONENT_TYPE - Static variable in interface pal.treesearch.Constants
-
- CONSTRAINED_NODE_COMPONENT_TYPE - Static variable in interface pal.treesearch.Constants
-
- ConstrainedInternalNode - Class in pal.treesearch
-
- ConstrainedInternalNode(Node, ParentableConstrainedNode, GeneralConstructionTool, GeneralConstraintGroupManager.Store, GeneralConstraintGroupManager) - Constructor for class pal.treesearch.ConstrainedInternalNode
-
- ConstrainedLeafNode - Class in pal.treesearch
-
- ConstrainedLeafNode(ParentableConstrainedNode, Node, double, GeneralConstructionTool, ConstraintModel.GroupManager) - Constructor for class pal.treesearch.ConstrainedLeafNode
-
- ConstrainedNode - Interface in pal.treesearch
-
- ConstrainedNode.HeightAdjustment - Interface in pal.treesearch
-
- ConstraintModel - Interface in pal.treesearch
-
- ConstraintModel.GroupManager - Interface in pal.treesearch
-
- construct(Node, String[], boolean, boolean) - Method in class pal.tree.TreeRestricter
-
- CONSTRUCTED_BRANCH_LENGTH - Static variable in interface pal.treesearch.Constants
-
- constructEvolutionaryDistances(Alignment, SubstitutionModel) - Static method in class pal.distance.DistanceTool
-
Construct a distance matrix object such that the distance between sequence A, and sequence B, is the
evolutionary distance by a given substitution model.
- constructFreshPatternInfo(boolean) - Method in class pal.treesearch.GeneralConstructionTool
-
- 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 in pal.statistics
-
Class for permuting contigency tables and determining the likelihood of the table.
- ContigencyTable(int) - Constructor for class pal.statistics.ContigencyTable
-
constructor for Contigency table
- convertNegativeBranchLengthsToZeroLength(Node) - Static method in class pal.tree.NodeUtils
-
If the given node or the sub tree defined by that node have negative branch lengths, they'll have
zeron branch lengths after a call to this function!
- convertNewLine() - Method in class pal.io.NexusTokenizer
-
Gets the flag indicating whether this parser instance should convert
newline characters.
- convertNucleotideToAminoAcid(String, int, int, boolean, CodonTable) - Static method in class pal.datatype.CodonTableUtils
-
Translates a Nucleotide sequence into a Amino Acid sequence
- convertNucleotideToAminoAcid(char[], int, int, boolean, CodonTable) - Static method in class pal.datatype.CodonTableUtils
-
Translates a Nucleotide sequence into a Amino Acid sequence
- convertToUniversalAminoAcids(Alignment, int) - Static method in class pal.alignment.AlignmentTool
-
Convert an alignment to one of amino acids (using Universal Translation)
- copy(double[], double[]) - Static method in class pal.math.MultivariateMinimum
-
Copy source vector into target vector
- copy(double[][], double[][]) - Static method in class pal.misc.Utils
-
Copies all of source into dest - assumes dest to be large enough
- countParameters(Parameterized[]) - Static method in class pal.misc.MultiParameterized
-
- 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 - Static variable in interface pal.substmodel.AminoAcidModelID
-
- CPREV - Class in pal.substmodel
-
CPREV model of amino acid evolution (J.Adachi et al.
- CPREV(double[]) - Constructor for class pal.substmodel.CPREV
-
constructor
- CPREV - Static variable in interface pal.util.XMLConstants
-
- CR - Variable in class pal.math.DifferentialEvolution
-
Crossing over factor (default 0.9)
- create(double[][], boolean, SubstitutionModel, int, int[], int, double[]) - Static method in class pal.eval.SiteDetails.Utils
-
Create a Postriors object
- create(double[][], boolean, int, int[], int, double[]) - Static method in class pal.eval.SiteDetails.Utils
-
Create a Postriors object with no related substitution model
- createAlignmentElement(Alignment, Document) - Static method in class pal.xml.ElementFactory
-
- createAppropriateConditionalProbabilityStore(boolean) - Method in interface pal.eval.LHCalculator.Generator
-
- createAppropriateConditionalProbabilityStore(boolean) - Method in interface pal.eval.MolecularClockLikelihoodModel.Instance
-
- createAppropriateConditionalProbabilityStore(boolean) - Method in interface pal.eval.UnconstrainedLikelihoodModel.Instance
-
- createAppropriateConditionalProbabilityStore(boolean) - Method in interface pal.treesearch.ConstraintModel
-
- createAppropriateConditionalProbabilityStore(boolean) - Method in class pal.treesearch.FixedBSRDTGlobalClockModel
-
- createAppropriateConditionalProbabilityStore(boolean) - Method in class pal.treesearch.FixedSRDTGlobalClockModel
-
- createAppropriateConditionalProbabilityStore(boolean) - Method in class pal.treesearch.GlobalClockModel
-
- createAppropriateConditionalProbabilityStore(boolean) - Method in class pal.treesearch.MRDTGlobalClockModel
-
- createAppropriateConditionalProbabilityStore(boolean) - Method in class pal.treesearch.SRDTGlobalClockModel
-
- createAppropriateConditionalProbabilityStore(boolean) - Method in class pal.treesearch.UnconstrainedModel
-
- createAttributeElement(Attribute, Document) - Static method in class pal.xml.ElementFactory
-
- createBase() - Method in interface pal.tree.UnrootedTreeInterface
-
- createBootstrapGenerator(Alignment) - Static method in class pal.alignment.AlignmentGenerator.Utils
-
- createBootstrapReplicate(Alignment) - Static method in class pal.alignment.AlignmentTool
-
A simple approach to creating a bootstrap replicate
- createConstrainedNode(Node, ParentableConstrainedNode, GeneralConstraintGroupManager.Store, GeneralConstraintGroupManager) - Method in class pal.treesearch.GeneralConstructionTool
-
Create an appropriate constrained node given a peer, and it's parent node
- 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
-
- createEvolutionary(Alignment, SubstitutionModel) - Static method in class pal.distance.DistanceMatrixAccess.Utils
-
- createEvolutionary(Alignment, SubstitutionModel) - Static method in class pal.distance.DistanceMatrixGenerator.Utils
-
- createF81Matrix(double[]) - Static method in class pal.substmodel.SubstitutionTool
-
Create an F81 model of substitution
- createF81Model(double[]) - Static method in class pal.substmodel.SubstitutionTool
-
Create an F81 model of substitution
- createF84Matrix(double, double[]) - Static method in class pal.substmodel.SubstitutionTool
-
Create an F84 model of substitution
- createF84Model(double, double[]) - Static method in class pal.substmodel.SubstitutionTool
-
Create an F84 model of substitution
- createFixed(double, int) - Static method in class pal.mep.ConstantMutationRate
-
- createFreeNode(Node, FreeBranch, GeneralConstraintGroupManager.Store) - Method in class pal.treesearch.GeneralConstructionTool
-
Create an appropriate free node given a peer, and it's parent branch
- 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.
- createGapBalanced(Alignment, int) - Static method in class pal.alignment.AlignmentTool
-
Create a gap balanced alignment.
- createGTR() - Static method in class pal.substmodel.GeneralREVRateMatrix
-
Create a rate matrix equivalent to the GTR model
- createGTR(double[]) - Static method in class pal.substmodel.GeneralREVRateMatrix
-
Create a rate matrix equivalent to the GTR model
- createGTR(double, double, double, double, double) - Static method in class pal.substmodel.GeneralREVRateMatrix
-
Create a rate matrix equivalent to the GTR model
Parameters laid out
*
-> + A C G T
A * a b c
C * * d e
G * * * 1
T * * * *
- createGTRMatrix(double, double, double, double, double, double[]) - Static method in class pal.substmodel.SubstitutionTool
-
Create an GTR model of substitution
- createGTRModel(double, double, double, double, double, double[]) - Static method in class pal.substmodel.SubstitutionTool
-
Create an GTR model of substitution
- createHKY() - Static method in class pal.substmodel.GeneralREVRateMatrix
-
Create a rate matrix equivalent to the HKY model, the one parameter will be kappa
- createHKY(double) - Static method in class pal.substmodel.GeneralREVRateMatrix
-
Create a rate matrix equivalent to the HKY model, the one parameter will be kappa
- createIdGroup(int) - Static method in class pal.misc.IdGenerator
-
generates a group of unique identifiers numbered from zero.
- createInstance(LHCalculator.Factory, SubstitutionModel) - Static method in class pal.eval.SimpleMolecularClockLikelihoodModel
-
- createInstance(SubstitutionModel) - Static method in class pal.eval.SimpleMolecularClockLikelihoodModel
-
- createInstance(LHCalculator.Generator, SubstitutionModel) - Static method in class pal.eval.SimpleUnconstrainedLikelihoodModel
-
Create a SimpleUnconstrainedLikelihoodModel instance
- createInstance(LHCalculator.Factory, SubstitutionModel) - Static method in class pal.eval.SimpleUnconstrainedLikelihoodModel
-
Create a SimpleUnconstrainedLikelihoodModel instance
- createInstance(RateMatrixGroup, RateMatrixGroup, NeoParameterized, SingleSplitDistribution, LHCalculator.Factory, double) - Static method in class pal.eval.SingleSplitMolecularClockLikelihoodModel
-
- createInstance(RateMatrixGroup, RateMatrixGroup, NeoParameterized, SingleSplitDistribution, double) - Static method in class pal.eval.SingleSplitMolecularClockLikelihoodModel
-
- createInstance(RateMatrixGroup, RateMatrixGroup, NeoParameterized, double) - Static method in class pal.eval.SingleSplitMolecularClockLikelihoodModel
-
- createInstance(RateMatrixGroup, RateMatrixGroup, NeoParameterized, double[], double) - Static method in class pal.eval.SingleSplitMolecularClockLikelihoodModel
-
- createJC69Matrix() - Static method in class pal.substmodel.SubstitutionTool
-
Create a Jukes-cantor model of substitution
- createJC69Model() - Static method in class pal.substmodel.SubstitutionTool
-
Create a Jukes-cantor model of substitution
- createKappaStore(double) - Static method in class pal.substmodel.YangCodonModel
-
- createKappaStore(double, String) - Static method in class pal.substmodel.YangCodonModel
-
- createM0YangCodonModel(double, double, double[]) - Static method in class pal.substmodel.SubstitutionTool
-
Create an base Yang Codon model (M0) of substitution
- createM1YangCodonModel(double, double, double[]) - Static method in class pal.substmodel.SubstitutionTool
-
Create an neutral Yang Codon model (M1) of substitution
- createM2YangCodonModel(double, double, double, double, double[]) - Static method in class pal.substmodel.SubstitutionTool
-
Create an Positive Yang Codon model (M2) of substitution
- createMatchups(int, int, int[], int[], int[]) - Static method in class pal.treesearch.SearcherUtils
-
Fill in matchup arrays
- createMutationRateModelElement(MutationRateModel, Document) - Static method in class pal.xml.ElementFactory
-
Creates an XML element representing a mutation rate model.
- createNeighbourJoiningGenerator(DistanceMatrixGenerator, String[]) - Static method in class pal.tree.TreeGenerator.Utils
-
- createNeighbourJoiningTree(DistanceMatrix) - Static method in class pal.tree.TreeTool
-
Neighbour-joining tree construction based on a distance matrix
- createNeighbourJoiningTree(double[][], String[]) - Static method in class pal.tree.TreeTool
-
Neighbour-joining tree construction based on a distance matrix
- createNewClockExternal() - Method in interface pal.treesearch.ConstraintModel.GroupManager
-
- createNewClockExternal() - Method in class pal.treesearch.FixedBSRDTGlobalClockModel
-
- createNewClockExternal() - Method in class pal.treesearch.FixedSRDTGlobalClockModel
-
- createNewClockExternal() - Method in class pal.treesearch.GlobalClockModel
-
- createNewClockExternal() - Method in class pal.treesearch.MRDTGlobalClockModel
-
- createNewClockExternal() - Method in class pal.treesearch.SRDTGlobalClockModel
-
- createNewClockInternal() - Method in interface pal.treesearch.ConstraintModel.GroupManager
-
- createNewClockInternal() - Method in class pal.treesearch.FixedBSRDTGlobalClockModel
-
- createNewClockInternal() - Method in class pal.treesearch.FixedSRDTGlobalClockModel
-
- createNewClockInternal() - Method in class pal.treesearch.GlobalClockModel
-
- createNewClockInternal() - Method in class pal.treesearch.MRDTGlobalClockModel
-
- createNewClockInternal() - Method in class pal.treesearch.SRDTGlobalClockModel
-
- createNewClockLeaf(PatternInfo, int[]) - Method in interface pal.treesearch.ConstraintModel.GroupManager
-
- createNewClockLeaf(PatternInfo, int[]) - Method in class pal.treesearch.FixedBSRDTGlobalClockModel
-
- createNewClockLeaf(PatternInfo, int[]) - Method in class pal.treesearch.FixedSRDTGlobalClockModel
-
- createNewClockLeaf(PatternInfo, int[]) - Method in class pal.treesearch.GlobalClockModel
-
- createNewClockLeaf(PatternInfo, int[]) - Method in class pal.treesearch.MRDTGlobalClockModel
-
- createNewClockLeaf(PatternInfo, int[]) - Method in class pal.treesearch.SRDTGlobalClockModel
-
- createNewConstrainedLeafCalculator(ConstraintModel.GroupManager) - Method in class pal.treesearch.AbstractLeafNode
-
- createNewExternal() - Method in interface pal.eval.LHCalculator.Generator
-
- createNewExternal(LHCalculator.Generator) - Method in interface pal.eval.LHCalculator.Generator
-
An obscure method, primarily used by the High Accuracy calculator
- createNewExternal(MolecularClockLikelihoodModel.HeightConverter) - Method in interface pal.eval.MolecularClockLikelihoodModel.Instance
-
- createNewExternal() - Method in interface pal.eval.UnconstrainedLikelihoodModel.Instance
-
- createNewFreeExternal() - Method in interface pal.treesearch.ConstraintModel
-
- createNewFreeExternal() - Method in class pal.treesearch.FixedBSRDTGlobalClockModel
-
- createNewFreeExternal() - Method in class pal.treesearch.FixedSRDTGlobalClockModel
-
- createNewFreeExternal() - Method in class pal.treesearch.GlobalClockModel
-
- createNewFreeExternal() - Method in class pal.treesearch.MRDTGlobalClockModel
-
- createNewFreeExternal() - Method in class pal.treesearch.SRDTGlobalClockModel
-
- createNewFreeExternal() - Method in class pal.treesearch.UnconstrainedModel
-
- createNewFreeInternal() - Method in interface pal.treesearch.ConstraintModel
-
- createNewFreeInternal() - Method in class pal.treesearch.FixedBSRDTGlobalClockModel
-
- createNewFreeInternal() - Method in class pal.treesearch.FixedSRDTGlobalClockModel
-
- createNewFreeInternal() - Method in class pal.treesearch.GlobalClockModel
-
- createNewFreeInternal() - Method in class pal.treesearch.MRDTGlobalClockModel
-
- createNewFreeInternal() - Method in class pal.treesearch.SRDTGlobalClockModel
-
- createNewFreeInternal() - Method in class pal.treesearch.UnconstrainedModel
-
- createNewFreeLeaf(int[], int) - Method in interface pal.treesearch.ConstraintModel
-
- createNewFreeLeaf(int[], int) - Method in class pal.treesearch.FixedBSRDTGlobalClockModel
-
- createNewFreeLeaf(int[], int) - Method in class pal.treesearch.FixedSRDTGlobalClockModel
-
- createNewFreeLeaf(int[], int) - Method in class pal.treesearch.GlobalClockModel
-
- createNewFreeLeaf(int[], int) - Method in class pal.treesearch.MRDTGlobalClockModel
-
- createNewFreeLeaf(int[], int) - Method in class pal.treesearch.SRDTGlobalClockModel
-
- createNewFreeLeaf(int[], int) - Method in class pal.treesearch.UnconstrainedModel
-
- createNewFreeLeafCalculator(GeneralConstructionTool) - Method in class pal.treesearch.AbstractLeafNode
-
- createNewFreeLeafCalculator(int[], int) - Method in class pal.treesearch.GeneralConstructionTool
-
- createNewInternal() - Method in interface pal.eval.LHCalculator.Generator
-
- createNewInternal(LHCalculator.Generator) - Method in interface pal.eval.LHCalculator.Generator
-
An obscure method, primarily used by the High Accuracy calculator
- createNewInternal(MolecularClockLikelihoodModel.HeightConverter) - Method in interface pal.eval.MolecularClockLikelihoodModel.Instance
-
- createNewInternal() - Method in interface pal.eval.UnconstrainedLikelihoodModel.Instance
-
- createNewLeaf(int[], int) - Method in interface pal.eval.LHCalculator.Generator
-
Create anew leaf calculator
- createNewLeaf(int[], int, LHCalculator.Generator) - Method in interface pal.eval.LHCalculator.Generator
-
- createNewLeaf(MolecularClockLikelihoodModel.HeightConverter, PatternInfo, int[]) - Method in interface pal.eval.MolecularClockLikelihoodModel.Instance
-
- createNewLeaf(int[], int) - Method in interface pal.eval.UnconstrainedLikelihoodModel.Instance
-
Create anew leaf calculator
- createNode() - Static method in class pal.tree.NodeFactory
-
create a node
- createNode(Identifier) - Static method in class pal.tree.NodeFactory
-
create a node, with a specified identifier
- createNode(Identifier, double) - Static method in class pal.tree.NodeFactory
-
create a node, with a specified identifier
- createNode(Node) - Static method in class pal.tree.NodeFactory
-
constructor used to clone a node and all children
- createNode(Node[]) - Static method in class pal.tree.NodeFactory
-
- createNode(Node[], double) - Static method in class pal.tree.NodeFactory
-
Create a node with the specified children, and the specified branch height
- createNodeBranchLength(double, Identifier) - Static method in class pal.tree.NodeFactory
-
create a node, with a specified identifier
- createNodeBranchLength(double, Node[]) - Static method in class pal.tree.NodeFactory
-
Create a node with the specified children, and the specified branch length
- 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.ParameterizedTreeBase
-
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.
- createNodeList() - Method in class pal.tree.Tree.TreeBase
-
count and list external and internal nodes and
compute heights of each node
- createNullMonitor() - Static method in class pal.math.MinimiserMonitor.Utils
-
Creates a MinimiserMonitor that looses all output
- createNullMonitor() - Static method in class pal.treesearch.SearchMonitor.Utils
-
- createOmegaStore(double) - Static method in class pal.substmodel.YangCodonModel
-
- createOmegaStore(double, String) - Static method in class pal.substmodel.YangCodonModel
-
- createOrderEnumerator(int) - Method in interface pal.math.OrderEnumerator.OEFactory
-
For generating an ordering from 0..size-1.
- createParameterElement(String, double, Document) - Static method in class pal.xml.ElementFactory
-
Creates an XML element representing a parameter.
- createParametizedWrapper(double[], double[], double[], double[]) - Static method in class pal.misc.Parameterized.Utils
-
Create a wrapper around a set of double arrays to create a parameterized object
(changes to parameterized object change given arrays)
- createParametizedWrapper(double[], double[], double[], double[], double[]) - Static method in class pal.misc.Parameterized.Utils
-
Create a wrapper around a set of double arrays to create a parameterized object
(changes to parameterized object change given arrays)
- createParametric(Tree, SubstitutionModel, int) - Static method in class pal.distance.DistanceMatrixGenerator.Utils
-
Silly idea stuff
- createPipeline(TreeOperation, TreeOperation) - Static method in class pal.tree.TreeOperation.Utils
-
Creates a tree operation that first applies one tree operation and then applies a second operation to get it's result
- createRateMatrixElement(RateMatrix, Document) - Static method in class pal.xml.ElementFactory
-
- createRChild() - Method in interface pal.tree.RootedTreeInterface.RNode
-
Create a child that is further from the base
- createRelativeRates(double[][], double[], int) - Method in class pal.substmodel.GeneralPoissonRateMatrix
-
- createRelativeRates(double[][], double[], int) - Method in class pal.substmodel.GeneralREVRateMatrix
-
- createRelativeRates(double[][], double[], int) - Method in interface pal.substmodel.NeoRateMatrix
-
Create the relative rates array
- createRELLEvaluator(SubstitutionModel) - Static method in class pal.statistics.ReplicateLikelihoodEvaluator.Utils
-
Create a ReplicateLikelihoodEvaluator that based likelihood on original tree (does no optimisation)
- createRoot() - Method in interface pal.tree.RootedTreeInterface
-
- createRootAccess(Node, GeneralConstraintGroupManager.Store) - Method in class pal.treesearch.GeneralConstructionTool
-
- createSampleInformation(String[]) - Method in interface pal.misc.SampleInformation.Factory
-
- createScale(double, int) - Static method in class pal.tree.TreeOperation.Utils
-
Create a tree operation that scales the input tree and changes the units
- createSequenceElement(Identifier, String, Document) - Static method in class pal.xml.ElementFactory
-
- createSeries(int, DataType) - Method in interface pal.eval.LHCalculator.Factory
-
- createSimple(DistanceMatrix) - Static method in class pal.distance.DistanceMatrixAccess.Utils
-
- createSimple(Parameterized, int) - Static method in class pal.misc.IndividualParameterHandler.Utils
-
- createSimple(Parameterized[]) - Static method in class pal.misc.IndividualParameterHandler.Utils
-
- createSimple(Parameterized, int, IndividualParameterHandler.Listener) - Static method in class pal.misc.IndividualParameterHandler.Utils
-
- createSimpleEvaluator(SubstitutionModel) - Static method in class pal.statistics.LikelihoodEvaluator.Utils
-
Create a simple evaluator that uses UnrootedTreeSearch
- createSimpleMonitor(PrintWriter) - Static method in class pal.math.MinimiserMonitor.Utils
-
Creates a MinimiserMonitor that outputs current minimum to a print stream
- createSplitMonitor(MinimiserMonitor, MinimiserMonitor) - Static method in class pal.math.MinimiserMonitor.Utils
-
- createStringMonitor() - Static method in class pal.math.MinimiserMonitor.Utils
-
Creates a MinimiserMonitor that Stores output (use toString() to access current results)
- createSubgroup(int) - Method in class pal.misc.TimeOrderCharacterData
-
Creates a TimeOrderCharacterData which is a subset of this sub group.
- createSubstitutionModel(RateMatrix) - Static method in class pal.substmodel.SubstitutionModel.Utils
-
- createSubstitutionModel(NeoRateMatrix, DataType, double[]) - Static method in class pal.substmodel.SubstitutionModel.Utils
-
- createSubstitutionModel(RateMatrix, RateDistribution) - Static method in class pal.substmodel.SubstitutionModel.Utils
-
- createSubstitutionModel(RateMatrix, RateDistribution, boolean) - Static method in class pal.substmodel.SubstitutionModel.Utils
-
- createSystemErrorMonitor() - Static method in class pal.math.MinimiserMonitor.Utils
-
Creates a MinimiserMonitor that outputs current minimum to a System.err
- createSystemOuptutMonitor() - Static method in class pal.math.MinimiserMonitor.Utils
-
Creates a MinimiserMonitor that outputs current minimum to a System.out
- createTimeDataElement(TimeOrderCharacterData, Document) - Static method in class pal.xml.ElementFactory
-
- createTNMatrix(double, double, double[]) - Static method in class pal.substmodel.SubstitutionTool
-
Create an Tamura-Nei model of substitution
- createTNModel(double, double, double[]) - Static method in class pal.substmodel.SubstitutionTool
-
Create an Tamura-Nei model of substitution
- 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
-
- createUChild() - Method in interface pal.tree.UnrootedTreeInterface.UNode
-
Create a child that is further from the base
- createUniversalTranslator() - Static method in class pal.datatype.CodonTableFactory
-
- createUPGMA(DistanceMatrix) - Static method in class pal.tree.TreeTool
-
UPGMA tree construction based on a distance matrix
- createUPGMATree(double[][], String[]) - Static method in class pal.tree.TreeTool
-
UPGMA tree construction based on a distance matrix
- CURRENT_POP_SIZE_DURATION - Static variable in interface pal.util.XMLConstants
-
- G_STATE - Static variable in class pal.datatype.Nucleotides
-
- G_THAN - Static variable in class pal.io.NexusTokenizer
-
- G_TO_T - Static variable in interface pal.util.XMLConstants
-
- GAMMA_ALPHA - Static variable in interface pal.util.XMLConstants
-
- GAMMA_DISTRIBUTION - Static variable in interface pal.util.XMLConstants
-
- GammaDistribution - Class in pal.statistics
-
gamma distribution.
- GammaDistribution() - Constructor for class pal.statistics.GammaDistribution
-
- GammaFunction - Class in pal.math
-
gamma function
- GammaFunction() - Constructor for class pal.math.GammaFunction
-
- GammaRates - Class in pal.substmodel
-
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
- GAP_BALANCED - Static variable in interface pal.datatype.DataType
-
- GAP_BALANCED_DESCRIPTION - Static variable in interface pal.datatype.DataType
-
generalized codon name (for XML and human readability)
- GAP_TLA - Static variable in interface pal.alignment.Alignment
-
A three letter acronym version of a gap.
- GapBalanced - Class in pal.datatype
-
implements a ResidueDataType for GapBalanced notation.
- GapBalanced(CodonTable) - Constructor for class pal.datatype.GapBalanced
-
- GapBalancedAlignment - Class in pal.alignment
-
Creates a "Gap-Balanced" alignment.
- GapBalancedAlignment(Alignment, int, boolean) - Constructor for class pal.alignment.GapBalancedAlignment
-
The standard GapBalanced constructor
- GapBalancedAlignment(Alignment, int, int) - Constructor for class pal.alignment.GapBalancedAlignment
-
GapBalanced power user constructor
- GapBalancedAlignment(Alignment, int, boolean, int) - Constructor for class pal.alignment.GapBalancedAlignment
-
GapBalanced power user constructor
- GAPS - Static variable in interface pal.alignment.Alignment
-
Characters that might be used as gaps
- GENERAL_OPTIMISABLE_TYPE - Static variable in interface pal.treesearch.Constants
-
- GeneralConstraintGroupManager - Class in pal.treesearch
-
- GeneralConstraintGroupManager(ConstraintModel.GroupManager) - Constructor for class pal.treesearch.GeneralConstraintGroupManager
-
- GeneralConstraintGroupManager.LikelihoodScoreAccess - Interface in pal.treesearch
-
- GeneralConstraintGroupManager.Store - Class in pal.treesearch
-
- GeneralConstraintGroupManager.Store() - Constructor for class pal.treesearch.GeneralConstraintGroupManager.Store
-
- GeneralConstructionTool - Class in pal.treesearch
-
- GeneralConstructionTool(ConstraintModel, Alignment) - Constructor for class pal.treesearch.GeneralConstructionTool
-
The constructor
- GeneralizedDEOptimizer - Class in pal.math
-
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
-
- GeneralizedDEOptimizer(int) - Constructor for class pal.math.GeneralizedDEOptimizer
-
- GeneralLikelihoodCalculator - Class in pal.eval
-
Title: General Likelihood Calculator
Description: A General likelihood calculator
This calculates the likelihood of an topologically invariant tree
(on an unchanging alignment) quickly by remembering partial likelihoods of invariant subtrees, and
by essentially generating site patterns for each sub tree.
- GeneralLikelihoodCalculator(Alignment, Tree, RateMatrix) - Constructor for class pal.eval.GeneralLikelihoodCalculator
-
Constructor taking site pattern, tree and a rate matrix.
- GeneralLikelihoodCalculator(Alignment, Tree, RateMatrix, RateDistribution) - Constructor for class pal.eval.GeneralLikelihoodCalculator
-
Constructor taking site pattern, tree rate matrix, and a rate distribution
- GeneralLikelihoodCalculator(Alignment, Tree, SubstitutionModel) - Constructor for class pal.eval.GeneralLikelihoodCalculator
-
Constructor taking site pattern, tree and a general substitution model.
- GeneralLikelihoodSearcher - Class in pal.treesearch
-
- GeneralLikelihoodSearcher(Node, Alignment, ConstraintModel) - Constructor for class pal.treesearch.GeneralLikelihoodSearcher
-
- GeneralObjectState - Class in pal.algorithmics
-
Title:
- GeneralObjectState(UndoableAction, StateProvider, boolean) - Constructor for class pal.algorithmics.GeneralObjectState
-
- GeneralOptimisable - Interface in pal.treesearch
-
- GeneralPoissonRateMatrix - Class in pal.substmodel
-
A general rate matrix class for JC69/F81 style rate matrices (but for all data types)
- GeneralPoissonRateMatrix(int) - Constructor for class pal.substmodel.GeneralPoissonRateMatrix
-
- GeneralRateDistributionSubstitutionModel - Class in pal.substmodel
-
- GeneralRateDistributionSubstitutionModel(NeoRateMatrix, RateDistribution, DataType, double[]) - Constructor for class pal.substmodel.GeneralRateDistributionSubstitutionModel
-
- GeneralREVRateMatrix - Class in pal.substmodel
-
A general rate matrix class for REV style rate matrices (GTR but for all data types)
Includes the ability for arbitarily constraints
- GeneralREVRateMatrix(int) - Constructor for class pal.substmodel.GeneralREVRateMatrix
-
The general constructor for a fully specified REV model
- GeneralREVRateMatrix(int, double[]) - Constructor for class pal.substmodel.GeneralREVRateMatrix
-
The general constructor for a fully specified REV model
- GeneralREVRateMatrix(int, int[]) - Constructor for class pal.substmodel.GeneralREVRateMatrix
-
The general constructor
Constraint ordering example, for nucleotide data
-> + A C G T
A * 0 1 2
C * * 3 4
G * * * 5
T * * * *
if constraints were {0,1,1,0,0,1} then would be constrained so a-c = c-g = c-t and a-g = a-t = g-t (and there would be only one parameter)
- GeneralREVRateMatrix(int, int[], double[]) - Constructor for class pal.substmodel.GeneralREVRateMatrix
-
The general constructor
Constraint ordering example, for nucleotide data
-> + A C G T
A * 0 1 2
C * * 3 4
G * * * 5
T * * * *
if constraints were {0,1,1,0,0,1} then would be constrained so a-c = c-g = c-t and a-g = a-t = g-t (and there would be only one parameter)
- GeneralREVRateMatrix(int, int[], double[], int) - Constructor for class pal.substmodel.GeneralREVRateMatrix
-
The general constructor
Constraint ordering example, for nucleotide data
-> + A C G T
A * 0 1 2
C * * 3 4
G * * * 5
T * * * *
if constraints were {0,1,1,0,0,1} then would be constrained so a-c = c-g = c-t and a-g = a-t = g-t (and there would be only one parameter)
- GeneralTopologyPool - Class in pal.statistics
-
- GeneralTopologyPool(Tree[], LikelihoodEvaluator, ReplicateLikelihoodEvaluator, Alignment, AlignmentGenerator) - Constructor for class pal.statistics.GeneralTopologyPool
-
- GeneralTreeComponent - Interface in pal.treesearch
-
- generateAlignment(DataType) - Method in class pal.alignment.AlignmentBuilder
-
Build an alignment based on sequences stored.
- generateAlignment(Tree) - Method in class pal.tree.SimulatedAlignment.Factory
-
Generate a simulated alignment based on input tree
- generateAlignmentBootstrappedSUPGMATree(AlgorithmCallback, ClusterTree.ClusteringMethod, SUPGMABase.PopulationParameters, int, LMSSolver) - Method in class pal.supgma.SUPGMABase
-
- generateAlignments(Tree[], AlgorithmCallback) - Method in class pal.tree.SimulatedAlignment.Factory
-
Generate an array of simulated alignments based on an array of input trees
- generateAlternativeRepresentation(Tree) - Method in interface pal.mep.DeltaModel.Instance
-
- generateAnalyser() - Method in class pal.supgma.SUPGMABase
-
Generates a suitable analyser.
- generateCategoryRanking(int) - Method in class pal.eval.LikelihoodSummary
-
- generateCategoryRankings() - Method in class pal.eval.LikelihoodSummary
-
- generateDemographicModel(double[], double[], TimeOrderCharacterData) - Method in interface pal.supgma.ThetaHandler
-
May return null if not possible to infer demographic model
- generateDummyTimedTOCD(double[]) - Method in class pal.misc.TimeOrderCharacterData
-
- generateExpectedSubsitutionsTimedTOCD(double[]) - Method in class pal.misc.TimeOrderCharacterData
-
Given an array of rates between samples (matching exactly the samples in order) then
produces a TimeOrderCharacterData object that is timed by Expected Substitutions.
- generateFactory() - Static method in class pal.math.ConjugateDirectionSearch
-
Generate a MultivariateMinimum.Factory for a ConjugateDirectionSearch
- generateFactory(int) - Static method in class pal.math.GeneralizedDEOptimizer
-
Generate a MultivariateMinimum.Factory for an GeneralizedDEOptimiser with a set population size
- generateFactory() - Static method in class pal.math.GeneralizedDEOptimizer
-
Generate a MultivariateMinimum.Factory for an GeneralizedDEOptimiser with a population size proportional to the size of the problem
- generateFactory(boolean) - Static method in class pal.math.OrthogonalSearch
-
Generate a MultivariateMinimum.Factory for an OrthogonalSearch
- generateFactory() - Method in class pal.mep.ConstantMutationRate
-
- generateFactory() - Method in class pal.mep.MutationRateModel
-
- generateFactory() - Method in class pal.mep.SteppedMutationRate
-
- generateFactory() - Method in class pal.mep.WindowedMutationRate
-
- generateHTML() - Method in interface pal.supgma.SUPGMABase.PopulationParameters
-
- generateInstance(TimeOrderCharacterData) - Method in interface pal.mep.DeltaModel
-
- generateNewMinimiser() - Method in interface pal.math.MultivariateMinimum.Factory
-
Generate a new Multivariate Minimum
- generateNewModel() - Method in interface pal.mep.MutationRateModel.Factory
-
Request a new MutationRateModel instance
- generateNewTree(Tree) - Method in interface pal.tree.ParameterizedTree.Factory
-
Generate a new parameterized tree wrapped around base
- generateNextMatrix(AlgorithmCallback) - Method in interface pal.distance.DistanceMatrixGenerator
-
- generateNode() - Method in class pal.tree.TreeRestricter
-
- generateOrthogonalRoundOptimiser(MultivariateFunction) - Method in class pal.math.OrthogonalSearch
-
- generateRateModelFactory(double[], TimeOrderCharacterData) - Method in interface pal.supgma.RateHandler
-
- generateResults(AlgorithmCallback) - Method in class pal.coalescent.SerialCoalescentGenerator
-
- generateRoot(double) - Method in interface pal.eval.MolecularClockLikelihoodModel.Simulator
-
- generateRoot() - Method in class pal.substmodel.SequenceSimulator
-
- generateSiteLikelihoods(int) - Method in class pal.eval.LikelihoodSummary
-
- generateSitePosteriors(int) - Method in class pal.eval.LikelihoodSummary
-
- generateSUPGMATree(ClusterTree.ClusteringMethod) - Method in interface pal.supgma.SUPGMABase.PopulationParameters
-
- generateSUPGMATree(AlgorithmCallback, ClusterTree.ClusteringMethod, DistanceMatrixGenerator, int, LMSSolver) - Method in interface pal.supgma.SUPGMABase.PopulationParameters
-
- generateTransitionProbabilityTables(SubstitutionModel) - Static method in class pal.substmodel.SubstitutionModel.Utils
-
- generateTree() - Method in class pal.coalescent.SerialCoalescentGenerator
-
- generateTree() - Method in class pal.tree.TreeRestricter
-
- generateTrees(AlgorithmCallback) - Method in class pal.coalescent.SerialCoalescentGenerator
-
If callback request stop then returns trees creating thus far
- generateUnivariateMinimum() - Method in class pal.math.OrthogonalSearch
-
- 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 in pal.alignment
-
This class provides from genotype to be constructed from separate but paired
alignments.
- Genotype(Alignment, Alignment) - Constructor for class pal.alignment.Genotype
-
- getAccessToBranches() - Method in class pal.treesearch.UnrootedMLSearcher
-
- getAccessToNodes() - Method in class pal.treesearch.UnrootedMLSearcher
-
- getAdjusted(OrderEnumerator, int) - Static method in class pal.math.OrderEnumerator.Utils
-
- getAdjusted(OrthogonalHints, int) - Static method in class pal.math.OrthogonalHints.Utils
-
- getAdjustedFactory(OrderEnumerator.OEFactory, int) - Static method in class pal.math.OrderEnumerator.Utils
-
- getAdjustedHeight(Object, double) - Method in interface pal.treesearch.ConstrainedNode.HeightAdjustment
-
- getAICC() - Method in class pal.coalescent.SkylinePlot
-
Compute AICC-corrected log-likelihood
- getAlignedSequenceIndices(Alignment, int, int[], DataType, int) - 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 interface pal.alignment.Alignment
-
Returns string representation of single sequence in
alignment with gap characters included.
- getAlignedSequenceString(int) - Method in class pal.alignment.SimpleAlignment
-
Returns a string representing a single sequence (including gaps)
from this alignment.
- getAlignedStates(Alignment) - Static method in class pal.alignment.AlignmentUtils
-
Unknown characters are given the state of -1
- getAlignedStates(Alignment, int) - Static method in class pal.alignment.AlignmentUtils
-
- getAlignment(int) - Method in class pal.alignment.Genotype
-
- 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.
- 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.
- getAlignments() - Method in class pal.coalescent.SerialCoalescentGenerator.Results
-
- getAllComponents(ArrayList, Class) - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
- getAllComponents(ArrayList, Class) - Method in class pal.treesearch.ConstrainedLeafNode
-
- getAllComponents(ArrayList, Class) - Method in class pal.treesearch.FreeBranch
-
- getAllComponents(ArrayList, Class, FreeNode) - Method in class pal.treesearch.FreeBranch
-
- getAllComponents(ArrayList, Class) - Method in class pal.treesearch.FreeInternalNode
-
- getAllComponents(ArrayList, Class, FreeBranch) - Method in class pal.treesearch.FreeInternalNode
-
- getAllComponents(ArrayList, Class, FreeBranch) - Method in class pal.treesearch.FreeLeafNode
-
- getAllComponents(ArrayList, Class) - Method in class pal.treesearch.FreeLeafNode
-
- getAllComponents(ArrayList, Class, FreeBranch) - Method in interface pal.treesearch.FreeNode
-
Recurse to all neighbours but caller
- getAllComponents(ArrayList, Class) - Method in interface pal.treesearch.GeneralTreeComponent
-
- getAllComponents(ArrayList, Class, FreeBranch) - Method in class pal.treesearch.PivotNode
-
- getAllComponents(ArrayList, Class) - Method in interface pal.treesearch.RootAccess
-
- getAllConnections(ArrayList, FreeBranch) - Method in class pal.treesearch.FreeLeafNode
-
- getAllGroupRelatedParameterAccess() - Method in interface pal.treesearch.ConstraintModel.GroupManager
-
- getAllGroupRelatedParameterAccess() - Method in class pal.treesearch.FixedBSRDTGlobalClockModel
-
- getAllGroupRelatedParameterAccess() - Method in class pal.treesearch.FixedSRDTGlobalClockModel
-
- getAllGroupRelatedParameterAccess() - Method in class pal.treesearch.GlobalClockModel
-
- getAllGroupRelatedParameterAccess() - Method in class pal.treesearch.MRDTGlobalClockModel
-
- getAllGroupRelatedParameterAccess() - Method in class pal.treesearch.SRDTGlobalClockModel
-
- getAllParameters() - Method in class pal.misc.Parameterized.ParameterizedUser
-
Obtain a fresh array containing the current parameter values
- getAllRootedBy(String[]) - Method in class pal.tree.TreeManipulator
-
- getAllRootingsBy(Tree, String[]) - Static method in class pal.tree.TreeManipulator
-
Roots a tree by an outgroup
- getAllTreesRootedBy(String[]) - Method in class pal.tree.TreeManipulator
-
- getAlternating(OrderEnumerator, OrderEnumerator) - Static method in class pal.math.OrderEnumerator.Utils
-
- getAlternatingFactory(OrderEnumerator.OEFactory, OrderEnumerator.OEFactory) - Static method in class pal.math.OrderEnumerator.Utils
-
- getAmbiguity(int, boolean[]) - Method in interface pal.datatype.AmbiguousDataType
-
Attempts to "resolve" the ambiguity in a state with regard to the specific data type.
- getAmbiguity(int, double[]) - Method in interface pal.datatype.AmbiguousDataType
-
A more accurate attempt to "resolve" the ambiguity in a state with regard to the specific data type.
- getAmbiguity(int, boolean[]) - Method in class pal.datatype.IUPACNucleotides
-
Attempts to "resolve" the ambiguity in a state with regard to the specific data type.
- getAmbiguity(int, double[]) - Method in class pal.datatype.IUPACNucleotides
-
A more accurate attempt to "resolve" the ambiguity in a state with regard to the specific data type.
- getAmbiguousVersion() - Method in interface pal.datatype.DataType
-
- getAmbiguousVersion() - Method in class pal.datatype.IUPACNucleotides
-
- getAmbiguousVersion() - Method in class pal.datatype.SimpleDataType
-
- 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
- getAminoAcidStateFromStates(int[]) - Method in interface pal.datatype.CodonTable
-
- 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
- getAnnotation() - Method in class pal.tree.TreeManipulator.PALBranchWrapper
-
- getAnnotation() - Method in class pal.tree.TreeManipulator.PALNodeWrapper
-
- getAnnotation() - Method in interface pal.treesearch.BranchAccess
-
- getAnnotation() - Method in interface pal.treesearch.NodeAccess
-
- getAppendedHorizontally(Matrix) - Method in class pal.math.Matrix
-
- getAppendedVertically(Matrix) - Method in class pal.math.Matrix
-
- getArbitaryIntervalCount(double[], double) - Static method in class pal.supgma.RateHandler.Utils
-
- getArbitaryIntervalHandler(double[]) - Static method in class pal.supgma.RateHandler.Utils
-
- getArgmax(int[]) - Static method in class pal.misc.Utils
-
Find the maximum "argument"
- getArgmax(double[]) - Static method in class pal.misc.Utils
-
Find the maximum "argument" (of a double array)
- getAscendentExtended(double, ConstrainedNode, GeneralConstructionTool, boolean) - Method in class pal.treesearch.ConstrainedInternalNode
-
- getAscendentExtended(double, ConstrainedNode, GeneralConstructionTool, boolean) - Method in interface pal.treesearch.ParentableConstrainedNode
-
- getAscendentExtended(double, ConstrainedNode, GeneralConstructionTool, boolean) - Method in class pal.treesearch.PivotNode
-
- getAscendentFlat(ConstrainedNode, GeneralConstructionTool, boolean) - Method in class pal.treesearch.ConstrainedInternalNode
-
- getAscendentFlat(ConstrainedNode, GeneralConstructionTool, boolean) - Method in interface pal.treesearch.ParentableConstrainedNode
-
- getAscendentFlat(ConstrainedNode, GeneralConstructionTool, boolean) - Method in class pal.treesearch.PivotNode
-
- getAscendentPatternInfo(ConstrainedNode, GeneralConstructionTool) - Method in class pal.treesearch.ConstrainedInternalNode
-
- getAscendentPatternInfo(ConstrainedNode, GeneralConstructionTool) - Method in interface pal.treesearch.ParentableConstrainedNode
-
- getAscendentPatternInfo(ConstrainedNode, GeneralConstructionTool) - Method in class pal.treesearch.PivotNode
-
- getAsInputRooting() - Method in class pal.tree.TreeManipulator
-
A method for recovering the input (construction) tree (with the EXPANSION/MIMIC/REDUCED differences)
- getAsInputRootingTree() - Method in class pal.tree.TreeManipulator
-
A method for recovering the input (construction) tree (with the EXPANSION/MIMIC/REDUCED differences)
- getAttribute(String) - Method in interface pal.tree.AttributeNode
-
- getAttribute(Node, String) - Method in class pal.tree.ParameterizedTree.ParameterizedTreeBase
-
- getAttribute(String) - Method in class pal.tree.SimpleNode
-
- getAttribute(Node, String) - Method in class pal.tree.SimpleTree
-
- getAttribute(Node, String) - Method in interface pal.tree.Tree
-
- getAttribute(Node, String) - Method in class pal.tree.Tree.TreeBase
-
- getAttributeNames() - Method in interface pal.tree.AttributeNode
-
- getAttributeNames() - Method in class pal.tree.SimpleNode
-
- getBaseHeight(double) - Method in interface pal.treesearch.ConstraintModel.GroupManager
-
- getBaseHeight(double) - Method in class pal.treesearch.FixedBSRDTGlobalClockModel
-
- getBaseHeight(double) - Method in class pal.treesearch.FixedSRDTGlobalClockModel
-
- getBaseHeight(double) - Method in class pal.treesearch.GlobalClockModel
-
- getBaseHeight(double) - Method in class pal.treesearch.MRDTGlobalClockModel
-
- getBaseHeight(double) - Method in class pal.treesearch.SRDTGlobalClockModel
-
- getBaseHeightUnits() - Method in interface pal.treesearch.ConstraintModel.GroupManager
-
- getBaseHeightUnits() - Method in class pal.treesearch.FixedBSRDTGlobalClockModel
-
- getBaseHeightUnits() - Method in class pal.treesearch.FixedSRDTGlobalClockModel
-
- getBaseHeightUnits() - Method in class pal.treesearch.GlobalClockModel
-
- getBaseHeightUnits() - Method in class pal.treesearch.MRDTGlobalClockModel
-
- getBaseHeightUnits() - Method in class pal.treesearch.SRDTGlobalClockModel
-
- getBaseParameters(Parameterized) - Method in class pal.misc.MultiParameterized
-
- getBaseParameters(int) - Method in class pal.misc.MultiParameterized
-
- getBaseTree() - Method in class pal.tree.ParameterizedTree.ParameterizedTreeBase
-
- getBestObject() - Method in class pal.algorithmics.Ranker
-
- getBestScore() - Method in class pal.algorithmics.Ranker
-
Obtain the best score which may be the highest score (if maximising), or the lowest score (if minimising)
- getBiasAlternating(OrderEnumerator, OrderEnumerator) - Static method in class pal.math.OrderEnumerator.Utils
-
- getBiasAlternatingFactory(OrderEnumerator.OEFactory, OrderEnumerator.OEFactory) - Static method in class pal.math.OrderEnumerator.Utils
-
- getBoltzman(double, double, int) - Static method in class pal.algorithmics.ProbabilityIterator.Utils
-
- getBootstrapSupportByCladeTree(String, Tree, Tree[]) - Static method in class pal.tree.TreeUtils
-
Deprecated.
Use getReplicateCladeSupport instead
- getBootstrapValue(PositionedNode) - Method in class pal.gui.TreePainter
-
Returns -1 if no
trap value available
- getBounds(String) - Method in class pal.gui.LayoutTracker
-
- getBounds(Identifier) - Method in class pal.gui.LayoutTracker
-
- getBranchAccess() - Method in class pal.tree.TreeManipulator
-
Obtain access to individual branches
- getBranchLength() - Method in interface pal.tree.Node
-
Get the length of the branch attaching this node to its parent.
- getBranchLength() - Method in class pal.tree.SimpleNode
-
Get the length of the branch attaching this node to its parent.
- getBranchLength() - Method in class pal.tree.TreeManipulator.PALBranchWrapper
-
- getBranchLength() - Method in class pal.treesearch.FreeBranch
-
- getBranchLengthOptimiseAction(StoppingCriteria.Factory) - Method in class pal.treesearch.UnrootedMLSearcher
-
- getBranchLengthSE() - Method in interface pal.tree.Node
-
Get the length SE 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.
- getBranchLengthWithModelOptimiseAction(StoppingCriteria.Factory, MultivariateMinimum, int, int) - Method in class pal.treesearch.UnrootedMLSearcher
-
- getByteStates(String, DataType) - Static method in class pal.datatype.DataType.Utils
-
For converting a sequence to an array of bytes where each byte represents the
state of the corresponding character in sequence
- getByteStates(char[], DataType) - Static method in class pal.datatype.DataType.Utils
-
For converting a sequence to an array of bytes where each byte represents the
state of the corresponding character in sequence
- getCategoryProbabilities() - Method in class pal.substmodel.RateDistribution
-
The non direct access method
- getCategoryProbability(int) - Method in class pal.substmodel.RateDistribution
-
- getCenterPattern(GeneralConstructionTool) - Method in class pal.treesearch.ConstrainedInternalNode
-
For center pattern, left is ascendent component, right is descendent component
- getCenterPatternInfo(GeneralConstructionTool) - Method in class pal.treesearch.FreeBranch
-
- getCenterPatternInfo(GeneralConstructionTool, PatternInfo) - Method in class pal.treesearch.FreeBranch
-
- 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.
- getChangeHeight(double[]) - Method in interface pal.substmodel.TemporalModelChange
-
- getChar(int) - Method in class pal.alignment.AbstractAlignment
-
Same as getDataType().getChar(state)
- getChar(int) - Method in interface pal.datatype.DataType
-
get character corresponding to a given state
- getChar(int) - Method in class pal.datatype.SimpleDataType
-
Handles gap state and then passes on to getStateImpl
- getCharImpl(int) - Method in class pal.datatype.AminoAcids
-
- getCharImpl(int) - Method in class pal.datatype.Codons
-
Get character corresponding to a given state
- getCharImpl(int) - Method in class pal.datatype.GapBalanced
-
- getCharImpl(int) - Method in class pal.datatype.IUPACNucleotides
-
- getCharImpl(int) - Method in class pal.datatype.Nucleotides
-
Get character corresponding to a given state
- getCharImpl(int) - Method in class pal.datatype.NumericDataType
-
Get character corresponding to a given state
- getCharImpl(int) - Method in class pal.datatype.SimpleDataType
-
- getCharImpl(int) - Method in class pal.datatype.StateRemover
-
Get character corresponding to a given state
- getCharImpl(int) - Method in class pal.datatype.TwoStates
-
- getChars(int[][], char, char, DataType) - Static method in class pal.datatype.DataType.Utils
-
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, char, DataType) - Static method in class pal.datatype.DataType.Utils
-
For converting a sequence of ints representing states to an array of chars
- getChars(int[], DataType) - Static method in class pal.datatype.DataType.Utils
-
For converting a sequence of ints representing states to an array of chars
- getChild(int) - Method in interface pal.tree.Node
-
get child node
- getChild(int) - Method in class pal.tree.SimpleNode
-
get child node
- getChild(int) - Method in class pal.tree.TreeManipulator.PALNodeWrapper
-
- getChildCount() - Method in interface pal.tree.Node
-
Returns the number of children this node has.
- getChildCount() - Method in class pal.tree.SimpleNode
-
Returns the number of children this node has.
- getChildNode() - Method in class pal.tree.TreeManipulator.PALBranchWrapper
-
- getChromosome(int) - Method in interface pal.alignment.AnnotationAlignment
-
Returns chromosome
- getChromosome(int) - Method in class pal.alignment.ConcatenatedAnnotatedAlignment
-
Returns chromosome
- getChromosome(int) - Method in class pal.alignment.IndelAnnotatedAlignment
-
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 class pal.alignment.StrippedAnnotatedAlignment
-
Returns chromosome
- getChromosomePosition(int) - Method in interface pal.alignment.AnnotationAlignment
-
Return the position along chromosome
- getChromosomePosition(int) - Method in class pal.alignment.ConcatenatedAnnotatedAlignment
-
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.MultiLocusAnnotatedAlignment
-
Return the position along chromosome
- getChromosomePosition(int) - Method in class pal.alignment.SimpleAnnotatedAlignment
-
Return the position along chromosome
- getChromosomePosition(int) - Method in class pal.alignment.StrippedAnnotatedAlignment
-
Return the position along chromosome
- getClade(int) - Method in class pal.tree.CladeSystem
-
get clade
- getClade(IdGroup, Node, boolean[]) - Static method in class pal.tree.CladeSystem
-
get clade for internal node
- getClade(Node, Node) - Static method in class pal.tree.RootedTreeUtils
-
- getCladeArray() - Method in class pal.tree.CladeSystem
-
get clade array
- getCladeConstraints(String[]) - Method in interface pal.treesearch.ConstraintModel
-
Obtain the permanent clade sets.
- getCladeConstraints(String[]) - Method in class pal.treesearch.FixedBSRDTGlobalClockModel
-
- getCladeConstraints(String[]) - Method in class pal.treesearch.FixedSRDTGlobalClockModel
-
- getCladeConstraints(String[]) - Method in class pal.treesearch.GlobalClockModel
-
- getCladeConstraints(String[]) - Method in class pal.treesearch.MRDTGlobalClockModel
-
- getCladeConstraints(String[]) - Method in class pal.treesearch.SRDTGlobalClockModel
-
- getCladeConstraints(String[]) - Method in class pal.treesearch.UnconstrainedModel
-
- getCladeCount() - Method in class pal.tree.CladeSystem
-
get number of clades
- getClades(IdGroup, Tree) - Static method in class pal.tree.CladeSystem
-
creates a clade system from a tree
(using a pre-specified order of sequences)
- getClades(Tree) - Static method in class pal.tree.CladeSystem
-
creates a clade system from a tree
(using tree-induced order of sequences)
- getCladeSystems(Tree[]) - Static method in class pal.tree.CladeSystem
-
- getClonedDistances() - Method in class pal.distance.DistanceMatrix
-
Returns the distances as a 2-dimensional array of doubles.
- getCloserNode() - Method in interface pal.tree.UnrootedTreeInterface.UBranch
-
- getClosestIndex(String, String[]) - Method in class pal.distance.DistanceMatrix
-
- getClosestIndex(int, int[]) - Method in class pal.distance.DistanceMatrix
-
- getCoalescentEvents(int) - Method in class pal.coalescent.CoalescentIntervals
-
Returns the number coalescent events in an interval
- getCoalescentIntervals() - Method in interface pal.coalescent.CoalescentTree
-
- getCoalescentIntervals() - Method in class pal.eval.DemographicValue
-
Returns the coalescent tree of this likelihood value.
- getCodonIndexFromIUPACNucleotideStates(int[]) - Static method in class pal.datatype.Codons
-
The codon index is a number between 0 and 64 assigned to each different codon type
- getCodonIndexFromIUPACNucleotideStates(int[], int) - Static method in class pal.datatype.Codons
-
The codon index is a number between 0 and 64 assigned to each different codon type
- getCodonIndexFromNucleotides(char[]) - Static method in class pal.datatype.Codons
-
The codon index is a number between 0 and 64 assigned to each different codon type
- getCodonIndexFromNucleotideStates(int[]) - Static method in class pal.datatype.Codons
-
The codon index is a number between 0 and 64 assigned to each different codon type
- getCodonIndexFromNucleotideStates(int[], int) - Static method in class pal.datatype.Codons
-
The codon index is a number between 0 and 64 assigned to each different codon type
- getCodonsFromAminoAcidChar(char) - Method in interface pal.datatype.CodonTable
-
- getCodonsFromAminoAcidState(int) - Method in interface pal.datatype.CodonTable
-
- getCol() - Method in class pal.io.NexusTokenizer
-
Gets the current column position of the cursor.
- getCombined(StoppingCriteria.Factory[]) - Static method in class pal.algorithmics.StoppingCriteria.Utils
-
A stopping criteria that is a composite of a set of criteria, stops when at least one
sub criteria wants to stop
- getCombined(UndoableAction[]) - Static method in class pal.algorithmics.UndoableAction.Utils
-
Create an action that combines multiple actions
- getCombined(OrthogonalHints, int, OrthogonalHints, int) - Static method in class pal.math.OrthogonalHints.Utils
-
- getComplementState(int) - Static method in class pal.datatype.Nucleotides
-
Obtain the complement state
- getConditionalProbabilityAccess(int, boolean) - Method in class pal.eval.ConditionalProbabilityStore
-
Use this when access the internal conditional likelihood store for the purpose
of changing the contents.
- getConditionalProbabilityAccessNoChangeData(int, boolean) - Method in class pal.eval.ConditionalProbabilityStore
-
Use this when access the internal conditional likelihood store for the purpose
of changing the contents.
- getConsistency(Alignment, Alignment) - Static method in class pal.alignment.AlignmentUtils
-
- getConstant(double) - Static method in class pal.algorithmics.ProbabilityIterator.Utils
-
- getConstant(int) - Static method in class pal.math.OrderEnumerator.Utils
-
- getConstantFactory(int) - Static method in class pal.math.OrderEnumerator.Utils
-
- getConstrainedInternal() - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
- getConstraintGroupManager(String[], ConstraintModel) - Method in class pal.treesearch.GeneralConstraintGroupManager.Store
-
- getConstraintGroupManager(ConstraintModel.GroupManager) - Method in class pal.treesearch.GeneralConstraintGroupManager.Store
-
- getConstraintGroupManagers() - Method in class pal.treesearch.GeneralConstraintGroupManager.Store
-
- getCopy() - Method in interface pal.eval.ConditionalProbabilityStore.ExtraProcessor
-
- getCopy() - Method in class pal.eval.ConditionalProbabilityStore
-
Cloning
- getCopy() - Method in interface pal.eval.LHCalculator.Leaf
-
Create a new Leaf calculator that has exactly the same properties as this one (but is different such that it may be used independently)
- getCopy() - Method in class pal.eval.PatternInfo
-
Obtain an exact copy of this pattern info
- getCopy() - Method in class pal.eval.SimpleLeafCalculator
-
- getCopy() - Method in class pal.eval.SimpleUnconstrainedLikelihoodModel.LeafImpl
-
- getCopy() - Method in interface pal.eval.UnconstrainedLikelihoodModel.Leaf
-
Create a new Leaf calculator that has exactly the same properties as this one (but is different such that it may be used independently)
- getCopy() - Method in class pal.mep.ConstantMutationRate
-
- getCopy() - Method in class pal.mep.MutationRateModel
-
- getCopy() - Method in class pal.mep.SteppedMutationRate
-
- getCopy() - Method in class pal.mep.WindowedMutationRate
-
- getCopy(double[]) - Static method in class pal.misc.Utils
-
Clones an array of doubles
- getCopy(double[], int, int) - Static method in class pal.misc.Utils
-
Clones an array of doubles from index start (inclusive) to index end (exclusive)
- getCopy(double[], int) - Static method in class pal.misc.Utils
-
Clones an array of doubles from index start (inclusive) to end
- getCopy(byte[]) - Static method in class pal.misc.Utils
-
Clones an array of bytes
- getCopy(String[]) - Static method in class pal.misc.Utils
-
Clones an array of Strings
- getCopy(double[][]) - Static method in class pal.misc.Utils
-
Clones an array of doubles
- getCopy(int[][]) - Static method in class pal.misc.Utils
-
Clones a matrix of ints
- getCopy(double[][][]) - Static method in class pal.misc.Utils
-
Clones an array of doubles
- getCopy(byte[][]) - Static method in class pal.misc.Utils
-
Clones an array of bytes
- getCopy(boolean[][]) - Static method in class pal.misc.Utils
-
Clones an array of booleans
- getCopy(int[]) - Static method in class pal.misc.Utils
-
Clones an array of ints
- getCopy(int[], int) - Static method in class pal.misc.Utils
-
Clones an array of ints
- getCopy() - Method in class pal.substmodel.GeneralRateDistributionSubstitutionModel
-
- getCopy() - Method in class pal.substmodel.MultiRateMatrixHandler
-
- getCopy() - Method in class pal.substmodel.RateMatrixHandler
-
- getCopy(RateMatrix[]) - Static method in class pal.substmodel.RateMatrixUtils
-
- getCopy() - Method in class pal.substmodel.SingleClassSubstitutionModel
-
- getCopy() - Method in class pal.substmodel.YangCodonModel.SimpleNeutralSelection
-
- getCopy() - Method in class pal.substmodel.YangCodonModel.SimplePositiveSelection
-
- getCopy(YangCodonModel[]) - Static method in class pal.substmodel.YangCodonModel.Utils
-
Probably of no use to anyone else (is used by internal code though)
- getCopy() - Method in class pal.tree.ClockTree
-
- getCopy() - Method in class pal.tree.MutationRateModelTree
-
- getCopy() - Method in class pal.tree.ParameterizedTree.ParameterizedTreeBase
-
The cheapy copy that just creates a SimpleTree
- getCopy() - Method in class pal.tree.SimpleTree
-
- getCopy() - Method in interface pal.tree.Tree
-
- getCopy() - Method in class pal.tree.UnconstrainedTree
-
- 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
- getCurrentConditionalProbabilities() - Method in class pal.eval.ConditionalProbabilityStore
-
Used for getting access to the internal conditional probability store when
the data is not to be directly changed.
- getCurrentConditionalProbabilities(int) - Method in class pal.eval.ConditionalProbabilityStore
-
Used for getting access to the internal conditional probability store when
the data is not to be directly changed.
- getCurrentValue() - Method in interface pal.algorithmics.Assessor
-
- getData(int, int) - Method in class pal.alignment.AbstractAlignment
-
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.BootstrappedAlignment
-
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.alignment.GapBalancedAlignment
-
sequence alignment at (sequence, site)
- getData(int, int, int) - Method in class pal.alignment.Genotype
-
sequence alignment at (sequence, site, allele)
- getData(int, int) - Method in class pal.alignment.IndelAlignment
-
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.ReadAlignment
-
sequence alignment at (sequence, site)
- getData(int, int) - Method in class pal.alignment.ReadAlignmentOld
-
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.SitePattern
-
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.tree.SimulatedAlignment
-
sequence alignment at (sequence, site)
- 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(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.ConcatenatedAnnotatedAlignment
-
Return the datatype for a given site, which can differ between source alignments
- getDataType(int) - Method in class pal.alignment.IndelAnnotatedAlignment
-
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 class pal.alignment.StrippedAnnotatedAlignment
-
Returns the datatype
- getDataType() - Method in class pal.datatype.IUPACPenaltyTable
-
- getDataType() - Method in interface pal.datatype.TransitionPenaltyTable
-
- getDataType() - Method in class pal.substmodel.AbstractRateMatrix
-
- getDataType() - Method in class pal.substmodel.CachedRateMatrix
-
- getDataType() - Method in class pal.substmodel.GeneralRateDistributionSubstitutionModel
-
- getDataType() - Method in class pal.substmodel.NeutralSelectionRateMatrixGroup
-
- getDataType() - Method in class pal.substmodel.PositiveSelectionRateMatrixGroup
-
- getDataType() - Method in interface pal.substmodel.RateMatrix
-
Get the data type of this rate matrix
- getDataType() - Method in interface pal.substmodel.RateMatrixGroup
-
- getDataType() - Method in class pal.substmodel.SimpleRateMatrixGroup
-
- getDataType() - Method in class pal.substmodel.SingleClassSubstitutionModel
-
- getDataType() - Method in interface pal.substmodel.SubstitutionModel
-
- getDataType() - Method in class pal.substmodel.YangCodonModel.SimpleNeutralSelection
-
- getDataType() - Method in class pal.substmodel.YangCodonModel.SimplePositiveSelection
-
- getDataType() - Method in class pal.treesearch.GeneralConstructionTool
-
- 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
-
- getDefaultRateParameters(double[], int) - Method in class pal.substmodel.GeneralPoissonRateMatrix
-
- getDefaultRateParameters(double[], int) - Method in class pal.substmodel.GeneralREVRateMatrix
-
- getDefaultRateParameters(double[], int) - Method in interface pal.substmodel.NeoRateMatrix
-
- getDefaultRoot() - Method in class pal.tree.TreeManipulator
-
- getDefaultRootTree() - Method in class pal.tree.TreeManipulator
-
- getDefaultValue(int) - Method in class pal.coalescent.ConstantPopulation
-
- getDefaultValue(int) - Method in class pal.coalescent.ConstExpConst
-
- getDefaultValue(int) - Method in class pal.coalescent.ConstExpGrowth
-
- getDefaultValue(int) - Method in class pal.coalescent.ExpandingPopulation
-
- getDefaultValue(int) - Method in class pal.coalescent.ExponentialGrowth
-
- getDefaultValue(int) - Method in class pal.mep.ConstantMutationRate
-
- getDefaultValue(int) - Method in class pal.mep.SteppedMutationRate
-
- getDefaultValue(int) - Method in class pal.mep.WindowedMutationRate
-
- getDefaultValue() - Method in interface pal.misc.IndividualParameterHandler
-
- getDefaultValue(int) - Method in class pal.misc.MultiParameterized
-
- getDefaultValue() - Method in class pal.misc.MutableDouble
-
- getDefaultValue(int) - Method in interface pal.misc.Parameterized
-
get default value of parameter
- getDefaultValue(int) - Method in class pal.misc.Parameterized.Null
-
- getDefaultValue(int) - Method in class pal.misc.Parameterized.ParameterizedBase
-
- getDefaultValue(int) - Method in class pal.misc.Parameterized.ParameterizedUser
-
- getDefaultValue(int) - Method in class pal.substmodel.AminoAcidModel
-
- getDefaultValue(int) - Method in class pal.substmodel.CachedRateMatrix
-
- getDefaultValue(int) - Method in class pal.substmodel.F81
-
- getDefaultValue(int) - Method in class pal.substmodel.F84
-
- getDefaultValue(int) - Method in class pal.substmodel.GammaRates
-
- getDefaultValue(int) - Method in class pal.substmodel.GTR
-
- getDefaultValue(int) - Method in class pal.substmodel.HKY
-
- getDefaultValue(int) - Method in class pal.substmodel.InvariableSites
-
- getDefaultValue(int) - Method in class pal.substmodel.MultiRateMatrixHandler
-
- getDefaultValue(int) - Method in class pal.substmodel.RateMatrixHandler
-
- getDefaultValue(int) - Method in class pal.substmodel.SimpleRateMatrixGroup
-
- getDefaultValue(int) - Method in class pal.substmodel.TN
-
- getDefaultValue(int) - Method in class pal.substmodel.TwoStateModel
-
- getDefaultValue(int) - Method in class pal.substmodel.UniformRate
-
- getDefaultValue(int) - Method in class pal.substmodel.YangCodonModel
-
- getDefaultValue(int) - Method in class pal.substmodel.YangCodonModel.SimpleNeutralSelection
-
- getDefaultValue(int) - Method in class pal.substmodel.YangCodonModel.SimplePositiveSelection
-
- getDefaultValue(int) - Method in class pal.tree.ClockTree
-
- getDefaultValue(int) - Method in class pal.tree.LogParameterizedTree
-
- getDefaultValue(int) - Method in class pal.tree.MutationRateModelTree
-
- getDefaultValue(int) - Method in class pal.tree.UnconstrainedTree
-
- getDefaultValues(double[], int) - Method in interface pal.misc.NeoParameterized
-
get default value parameter values
- getDefaultValues(double[], int) - Method in class pal.misc.ParameterizedDoubleBundle
-
- getDefaultValues(double[], int) - Method in class pal.misc.ParameterizedNeoWrapper
-
- getDefaultValues(double[], int) - Method in class pal.substmodel.ConstantIndependentSingleSplitDistribution
-
- getDefaultValues(double[], int) - Method in class pal.substmodel.MultiRateMatrixHandler
-
- getDefaultValues(double[], int) - Method in class pal.substmodel.SaturatedSingleSplitDistribution
-
- getDefaultValues(double[], int) - Method in class pal.substmodel.VariableIndependentSingleSplitDistribution
-
- getDefaultValues(double[], int) - Method in class pal.treesearch.FixedBSRDTGlobalClockModel
-
- getDefaultValues(double[], int) - Method in class pal.treesearch.GlobalClockModel
-
- getDefaultValues(double[], int) - Method in class pal.treesearch.MRDTGlobalClockModel
-
- getDefaultValues(double[], int) - Method in class pal.treesearch.SRDTGlobalClockModel
-
- getDeltas(double[]) - Method in class pal.mep.SteppedMutationRate
-
- getDemographic(double) - Method in class pal.coalescent.ConstantPopulation
-
- getDemographic(double) - Method in class pal.coalescent.ConstExpConst
-
- getDemographic(double) - Method in class pal.coalescent.ConstExpGrowth
-
- 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.ExpandingPopulation
-
- getDemographic(double) - Method in class pal.coalescent.ExponentialGrowth
-
- getDemographicModel() - Method in class pal.coalescent.DemographicClockTree
-
Return the demographic model being used to optimize the
likelihood of this tree.
- getDemographicModel() - Method in interface pal.coalescent.DemographicTree
-
- getDemographicModel() - Method in class pal.eval.DemographicValue
-
Returns the demographic model of this likelihood value
- getDescendentExtendedConditionals(double, GeneralConstructionTool, boolean) - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
- getDescendentExtendedConditionals(double, GeneralConstructionTool, boolean) - Method in class pal.treesearch.ConstrainedLeafNode
-
- getDescendentExtendedConditionals(double, GeneralConstructionTool, boolean) - Method in interface pal.treesearch.ConstrainedNode
-
- getDescendentExtendedConditionalsWithAdjustedInternalHeights(double, GeneralConstructionTool, ConstrainedNode.HeightAdjustment, boolean) - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
- getDescendentExtendedConditionalsWithAdjustedInternalHeights(double, GeneralConstructionTool, ConstrainedNode.HeightAdjustment, boolean) - Method in class pal.treesearch.ConstrainedLeafNode
-
- getDescendentExtendedConditionalsWithAdjustedInternalHeights(double, GeneralConstructionTool, ConstrainedNode.HeightAdjustment, boolean) - Method in interface pal.treesearch.ConstrainedNode
-
- getDescendentFlatConditionals(GeneralConstructionTool, boolean) - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
- getDescendentFlatConditionals(GeneralConstructionTool, boolean) - Method in class pal.treesearch.ConstrainedLeafNode
-
- getDescendentFlatConditionals(GeneralConstructionTool, boolean) - Method in interface pal.treesearch.ConstrainedNode
-
- getDescendentLogLikelihood(GeneralConstructionTool, boolean) - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
- getDescendentPatternInfo(GeneralConstructionTool) - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
- getDescendentPatternInfo(GeneralConstructionTool) - Method in class pal.treesearch.ConstrainedLeafNode
-
- getDescendentPatternInfo(GeneralConstructionTool) - Method in interface pal.treesearch.ConstrainedNode
-
- getDescription() - Method in class pal.datatype.AminoAcids
-
- getDescription() - Method in class pal.datatype.Codons
-
- getDescription() - Method in interface pal.datatype.DataType
-
description of data type
- getDescription() - Method in class pal.datatype.GapBalanced
-
- getDescription() - Method in class pal.datatype.IUPACNucleotides
-
- getDescription() - Method in class pal.datatype.Nucleotides
-
- 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.TwoStates
-
- getDimension() - Method in class pal.substmodel.AbstractRateMatrix
-
- getDimension() - Method in class pal.substmodel.CachedRateMatrix
-
- getDimension() - Method in class pal.substmodel.GeneralPoissonRateMatrix
-
- getDimension() - Method in class pal.substmodel.GeneralREVRateMatrix
-
- getDimension() - Method in class pal.substmodel.MatrixExponential
-
- getDimension() - Method in interface pal.substmodel.NeoRateMatrix
-
- getDimension() - Method in interface pal.substmodel.RateMatrix
-
- getDisjointBased(DeltaModel, DeltaModel, TimeOrderCharacterData) - Static method in class pal.mep.DeltaModel.Utils
-
- getDisplay(String, LabelDisplayer) - Method in class pal.gui.NameColouriser
-
- getDisplay(Identifier, LabelDisplayer) - Method in class pal.gui.NameColouriser
-
- getDistance(int, int) - Method in class pal.distance.DistanceMatrix
-
- getDistance(int, int) - Method in class pal.distance.PairwiseDistance
-
compute distance between two sequences in the given alignment
- 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)
- getDistances() - Method in class pal.distance.DistanceMatrix
-
Returns the distances as a 2-dimensional array of doubles (in the actual array used to store the distances)
- getDistanceToRoot(Node) - Static method in class pal.tree.NodeUtils
-
determine distance to root
- getDistributedSelection(UndoableAction[], double[]) - Static method in class pal.algorithmics.UndoableAction.Utils
-
Create an action that selects uniformly from a number of sub actions
- getDistribution() - Method in class pal.substmodel.ConstantIndependentSingleSplitDistribution
-
- getDistribution() - Method in class pal.substmodel.SaturatedSingleSplitDistribution
-
- getDistribution() - Method in class pal.substmodel.VariableIndependentSingleSplitDistribution
-
- getDistributionInfo() - Method in class pal.substmodel.ConstantIndependentSingleSplitDistribution
-
- getDistributionInfo() - Method in class pal.substmodel.SaturatedSingleSplitDistribution
-
- getDistributionInfo() - Method in interface pal.substmodel.SingleSplitDistribution
-
Obtain the distribution information stored in the following format: [beforeclass][afterclass]
For example, the probability of evolving in class 0 before the split, and class 1 after the split - [0][1]
- getDistributionInfo() - Method in class pal.substmodel.VariableIndependentSingleSplitDistribution
-
- 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
- getEndTime(double, double) - Method in class pal.mep.ConstantMutationRate
-
- getEndTime(double, double) - Method in class pal.mep.MutationRateModel
-
Return the end time at which expected substitutions has occurred, given we start at start time
- getEndTime(double, double) - Method in class pal.mep.SteppedMutationRate
-
- getEndTime(double, double) - Method in class pal.mep.WindowedMutationRate
-
Window must not span zero!
- 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 class pal.substmodel.GeneralRateDistributionSubstitutionModel
-
- getEquilibriumFrequencies() - Method in class pal.substmodel.MultiRateMatrixHandler
-
- getEquilibriumFrequencies() - Method in class pal.substmodel.NeutralSelectionRateMatrixGroup
-
- getEquilibriumFrequencies() - Method in class pal.substmodel.PositiveSelectionRateMatrixGroup
-
- getEquilibriumFrequencies() - Method in interface pal.substmodel.RateMatrix
-
- getEquilibriumFrequencies() - Method in interface pal.substmodel.RateMatrixGroup
-
- getEquilibriumFrequencies() - Method in class pal.substmodel.RateMatrixHandler
-
- getEquilibriumFrequencies() - Method in class pal.substmodel.SimpleRateMatrixGroup
-
- getEquilibriumFrequencies() - Method in class pal.substmodel.SingleClassSubstitutionModel
-
- getEquilibriumFrequencies() - Method in interface pal.substmodel.SubstitutionModel
-
Should return a double[] array of the related equilibrium frequencies.
- getEquilibriumFrequencies() - Method in class pal.substmodel.YangCodonModel.SimpleNeutralSelection
-
- getEquilibriumFrequencies() - Method in class pal.substmodel.YangCodonModel.SimplePositiveSelection
-
- getEquilibriumFrequency(int) - Method in class pal.substmodel.AbstractRateMatrix
-
- getEquilibriumFrequency(int) - Method in class pal.substmodel.CachedRateMatrix
-
- getEquilibriumFrequency(int) - Method in interface pal.substmodel.RateMatrix
-
- getEquilibriumProbabilities() - Method in class pal.substmodel.YangCodonModel.SimpleNeutralSelection
-
- getEvaluationCount() - Method in class pal.math.EvaluationCounter
-
- getEveryRoot() - Method in class pal.tree.TreeManipulator
-
- getEveryRoot(Tree) - Static method in class pal.tree.TreeManipulator
-
Obtains every rooting of a base tree
- getEveryRootIterator() - Method in class pal.tree.TreeManipulator
-
- getEveryRootIterator(Tree) - Static method in class pal.tree.TreeManipulator
-
Obtains every rooting of a base tree
- getExpectedSubstitutionDistance(double, double) - Method in interface pal.eval.MolecularClockLikelihoodModel.HeightConverter
-
- getExpectedSubstitutionDistance(double, double) - Method in class pal.treesearch.FixedBSRDTGlobalClockModel
-
- getExpectedSubstitutionDistance(double, double) - Method in class pal.treesearch.FixedSRDTGlobalClockModel
-
- getExpectedSubstitutionDistance(double, double) - Method in class pal.treesearch.GlobalClockModel
-
- getExpectedSubstitutionDistance(double, double) - Method in class pal.treesearch.MRDTGlobalClockModel
-
- getExpectedSubstitutionDistance(double, double) - Method in class pal.treesearch.SRDTGlobalClockModel
-
- getExpectedSubstitutionHeight(double) - Method in interface pal.eval.MolecularClockLikelihoodModel.HeightConverter
-
- getExpectedSubstitutionHeight(double) - Method in interface pal.treesearch.ConstraintModel.GroupManager
-
- getExpectedSubstitutionHeight(double) - Method in class pal.treesearch.FixedBSRDTGlobalClockModel
-
- getExpectedSubstitutionHeight(double) - Method in class pal.treesearch.FixedSRDTGlobalClockModel
-
- getExpectedSubstitutionHeight(double) - Method in class pal.treesearch.GlobalClockModel
-
- getExpectedSubstitutionHeight(double) - Method in class pal.treesearch.MRDTGlobalClockModel
-
- getExpectedSubstitutionHeight(double) - Method in class pal.treesearch.SRDTGlobalClockModel
-
- getExpectedSubstitutions(double) - Method in class pal.mep.ConstantMutationRate
-
- getExpectedSubstitutions(int) - Method in interface pal.mep.DeltaModel.Instance
-
- getExpectedSubstitutions(double) - Method in class pal.mep.MutationRateModel
-
Returns integral of mutation rate function
(= integral mu(x) dx from 0 to t).
- getExpectedSubstitutions(double, double) - Method in class pal.mep.MutationRateModel
-
Calculates the integral 1/mu(x) dx between start and finish.
- getExpectedSubstitutions(double) - Method in class pal.mep.SteppedMutationRate
-
- getExpectedSubstitutions(double) - Method in class pal.mep.WindowedMutationRate
-
Window must not span zero!
- getExpectedSubstitutionsToTime(double) - Method in interface pal.mep.DeltaModel.Instance
-
- getExtendedConditionalProbabilities(double, SubstitutionModel, boolean) - Method in interface pal.eval.LHCalculator.Leaf
-
- getExtendedConditionalProbabilities(double, SubstitutionModel, boolean) - Method in class pal.eval.SimpleLeafCalculator
-
- getExtendedConditionalProbabilities(double) - Method in class pal.eval.SimpleUnconstrainedLikelihoodModel.LeafImpl
-
- getExtendedConditionalProbabilities(double) - Method in interface pal.eval.UnconstrainedLikelihoodModel.Leaf
-
- getExtendedConditionalProbabilities(FreeNode, GeneralConstructionTool) - Method in class pal.treesearch.FreeBranch
-
- getExtendedConditionalProbabilities(FreeNode, UnconstrainedLikelihoodModel.External, ConditionalProbabilityStore, GeneralConstructionTool) - Method in class pal.treesearch.FreeBranch
-
- getExtendedConditionalProbabilities(double, FreeBranch, UnconstrainedLikelihoodModel.External, ConditionalProbabilityStore, GeneralConstructionTool) - Method in class pal.treesearch.FreeInternalNode
-
- getExtendedConditionalProbabilities(double, FreeBranch, GeneralConstructionTool) - Method in class pal.treesearch.FreeInternalNode
-
- getExtendedConditionalProbabilities(double, FreeBranch, UnconstrainedLikelihoodModel.External, ConditionalProbabilityStore, GeneralConstructionTool) - Method in class pal.treesearch.FreeLeafNode
-
- getExtendedConditionalProbabilities(double, FreeBranch, GeneralConstructionTool) - Method in class pal.treesearch.FreeLeafNode
-
- getExtendedConditionalProbabilities(double, FreeBranch, GeneralConstructionTool) - Method in interface pal.treesearch.FreeNode
-
- getExtendedConditionalProbabilities(double, FreeBranch, UnconstrainedLikelihoodModel.External, ConditionalProbabilityStore, GeneralConstructionTool) - Method in interface pal.treesearch.FreeNode
-
- getExtendedConditionalProbabilities(double, FreeBranch, GeneralConstructionTool) - Method in class pal.treesearch.PivotNode
-
- getExtendedConditionalProbabilities(double, FreeBranch, UnconstrainedLikelihoodModel.External, ConditionalProbabilityStore, GeneralConstructionTool) - Method in class pal.treesearch.PivotNode
-
- getExternalNode(int) - Method in class pal.tree.ParameterizedTree.ParameterizedTreeBase
-
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
-
- getExternalNode(int) - Method in class pal.tree.Tree.TreeBase
-
Returns the ith external node.
- getExternalNodeCount() - Method in class pal.tree.ParameterizedTree.ParameterizedTreeBase
-
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
-
- getExternalNodeCount() - Method in class pal.tree.Tree.TreeBase
-
Returns the number of external nodes.
- getExternalNodes(Node, Vector) - Static method in class pal.tree.NodeUtils
-
Appends all external nodes from tree defined by root to Vector store
- getExternalNodes(Node) - Static method in class pal.tree.NodeUtils
-
Obtains all external nodes from tree defined by root and returns as an array
- getExtraProcessor() - Method in class pal.eval.ConditionalProbabilityStore
-
- getF1X4CodonFrequencies(double[]) - Static method in class pal.datatype.Codons
-
- getF3X4CodonFrequencies(double[][]) - Static method in class pal.datatype.Codons
-
- getFactory(LHCalculator.Factory) - Static method in class pal.eval.FastFourStateLHCalculator
-
- getFactory() - Static method in class pal.eval.FastFourStateLHCalculator
-
- getFactory() - Static method in class pal.eval.SimpleLHCalculator
-
- getFactory(LHCalculator.Factory) - Static method in class pal.eval.SimpleModelFastFourStateLHCalculator
-
- getFactory() - Static method in class pal.eval.SimpleModelFastFourStateLHCalculator
-
- getFactory(double[], int, double) - Static method in class pal.mep.SteppedMutationRate
-
Generate a MutationRateModel.Factory class for a SteppedMutationRate
- getFactory(double[], double[], int, double) - Static method in class pal.mep.SteppedMutationRate
-
Generate a MutationRateModel.Factory class for a SteppedMutationRate
- getFactory(double[], TimeOrderCharacterData) - Static method in class pal.mep.SteppedMutationRate
-
Generate a MutationRateModel.Factory class for a SteppedMutationRate
- getFactory(double, double, double, double, int, double) - Static method in class pal.mep.WindowedMutationRate
-
Generate a MutationRateModel.Factory class for a WindowedMutationRate
- getFartherNode() - Method in interface pal.tree.UnrootedTreeInterface.UBranch
-
- 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)
- getFixedFactory(double, int) - Static method in class pal.mep.ConstantMutationRate
-
Generate a MutationRateModel.Factory class for a ConstantMutationRate
- getFlatConditionalProbabilities() - Method in interface pal.eval.LHCalculator.Leaf
-
- getFlatConditionalProbabilities() - Method in class pal.eval.SimpleLeafCalculator
-
- getFlatConditionalProbabilities() - Method in class pal.eval.SimpleUnconstrainedLikelihoodModel.LeafImpl
-
- getFlatConditionalProbabilities() - Method in interface pal.eval.UnconstrainedLikelihoodModel.Leaf
-
- getFlatConditionalProbabilities(FreeBranch, UnconstrainedLikelihoodModel.External, ConditionalProbabilityStore, GeneralConstructionTool) - Method in class pal.treesearch.FreeInternalNode
-
- getFlatConditionalProbabilities(FreeBranch, GeneralConstructionTool) - Method in class pal.treesearch.FreeInternalNode
-
- getFlatConditionalProbabilities(FreeBranch, UnconstrainedLikelihoodModel.External, ConditionalProbabilityStore, GeneralConstructionTool) - Method in class pal.treesearch.FreeLeafNode
-
- getFlatConditionalProbabilities(FreeBranch, GeneralConstructionTool) - Method in class pal.treesearch.FreeLeafNode
-
- getFlatConditionalProbabilities(FreeBranch, GeneralConstructionTool) - Method in interface pal.treesearch.FreeNode
-
- getFlatConditionalProbabilities(FreeBranch, GeneralConstructionTool) - Method in class pal.treesearch.PivotNode
-
- getFreeFactory(int, double) - Static method in class pal.mep.ConstantMutationRate
-
Generate a MutationRateModel.Factory class for a ConstantMutationRate
- getFreeFactory(double, int, double) - Static method in class pal.mep.ConstantMutationRate
-
Generate a MutationRateModel.Factory class for a ConstantMutationRate
- getFreeFactory(double, int, double, double) - Static method in class pal.mep.ConstantMutationRate
-
Generate a MutationRateModel.Factory class for a ConstantMutationRate
- getFrequencies(MolecularDataType, int) - Method in class pal.alignment.DataTranslator
-
- getFrequencies() - Method in class pal.substmodel.AbstractRateMatrix
-
- getFullSweepSPRAction(StoppingCriteria.Factory) - Method in class pal.treesearch.UnrootedMLSearcher
-
- getGlobalClockConstraintGrouping(String[]) - Method in interface pal.treesearch.ConstraintModel
-
Enquire about the clock constraint grouping of the leaf
- getGlobalClockConstraintGrouping(String[]) - Method in class pal.treesearch.FixedBSRDTGlobalClockModel
-
- getGlobalClockConstraintGrouping(String[]) - Method in class pal.treesearch.FixedSRDTGlobalClockModel
-
- getGlobalClockConstraintGrouping(String[]) - Method in class pal.treesearch.GlobalClockModel
-
- getGlobalClockConstraintGrouping(String[]) - Method in class pal.treesearch.MRDTGlobalClockModel
-
- getGlobalClockConstraintGrouping(String[]) - Method in class pal.treesearch.SRDTGlobalClockModel
-
- getGlobalClockConstraintGrouping(String[]) - Method in class pal.treesearch.UnconstrainedModel
-
- getGlobalParameterAccess() - Method in interface pal.treesearch.ConstraintModel
-
- getGlobalParameterAccess() - Method in class pal.treesearch.FixedBSRDTGlobalClockModel
-
- getGlobalParameterAccess() - Method in class pal.treesearch.FixedSRDTGlobalClockModel
-
- getGlobalParameterAccess() - Method in class pal.treesearch.GlobalClockModel
-
- getGlobalParameterAccess() - Method in class pal.treesearch.MRDTGlobalClockModel
-
- getGlobalParameterAccess() - Method in class pal.treesearch.SRDTGlobalClockModel
-
- getGlobalParameterAccess() - Method in class pal.treesearch.UnconstrainedModel
-
- getGrowthParam() - Method in class pal.coalescent.ConstExpGrowth
-
- getGrowthPhaseDuration() - Method in class pal.coalescent.ConstExpConst
-
- getGrowthPhaseDuration() - Method in class pal.coalescent.ConstExpGrowth
-
- getGrowthRate() - Method in class pal.coalescent.ConstExpGrowth
-
This method overrides superclass to check parameterization.
- getGrowthRate() - Method in class pal.coalescent.ExponentialGrowth
-
returns growth rate.
- getHeight() - Method in class pal.math.Matrix
-
- getHeight(int) - Method in interface pal.misc.SampleInformation
-
- getHeight(int, double) - Method in class pal.misc.TimeOrderCharacterData
-
NOTE: currently assumes times exist!
- getHeight(int) - Method in class pal.misc.TOCDSampleInformation
-
- getHeights() - Method in class pal.treesearch.HeightInformationUser
-
- getHeightUnits() - Method in interface pal.misc.SampleInformation
-
- getHeightUnits() - Method in class pal.misc.TOCDSampleInformation
-
- getHillClimb() - Static method in class pal.algorithmics.ProbabilityIterator.Utils
-
- getHTMLInfo() - Method in interface pal.mep.DeltaModel.Instance
-
- getIdCount() - Method in class pal.alignment.AbstractAlignment
-
- getIdCount() - Method in class pal.alignment.SimpleCharacterAlignment
-
- getIdCount() - Method in class pal.distance.DistanceMatrix
-
- getIdCount() - Method in interface pal.misc.IdGroup
-
Returns the number of identifiers in this group
- getIdCount() - Method in class pal.misc.SimpleIdGroup
-
Returns the number of identifiers in this group
- getIdCount() - Method in class pal.misc.TimeOrderCharacterData
-
- getIdCount() - Method in class pal.tree.ParameterizedTree.ParameterizedTreeBase
-
- getIdCount() - Method in class pal.tree.SimpleTree
-
- getIdCount() - Method in class pal.tree.Tree.TreeBase
-
- 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 interface pal.misc.IdGroup
-
Returns the ith identifier.
- getIdentifier(int) - Method in class pal.misc.SimpleIdGroup
-
Returns the ith identifier.
- getIdentifier(int) - Method in class pal.misc.TimeOrderCharacterData
-
- getIdentifier() - Method in interface pal.tree.Node
-
Returns the identifier for this node.
- getIdentifier(int) - Method in class pal.tree.ParameterizedTree.ParameterizedTreeBase
-
- getIdentifier() - Method in class pal.tree.SimpleNode
-
Returns the identifier for this node.
- getIdentifier(int) - Method in class pal.tree.SimpleTree
-
- getIdentifier(int) - Method in class pal.tree.Tree.TreeBase
-
- getIdentifiers(String[]) - Static method in class pal.misc.Identifier
-
Translates an an array of strings into an array of identifiers
- getIdentifiers(IdGroup) - Static method in class pal.misc.Identifier
-
Translates an IdGroup into an array of identifiers
- 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.CladeSystem
-
get idGroup
- getIdGroup() - Method in class pal.tree.SplitSystem
-
get idGroup
- getIncompleteConditionalProbabilityAccess(int, boolean, boolean) - Method in class pal.eval.ConditionalProbabilityStore
-
Use this when access the internal conditional likelihood store for the purpose
of changing the contents.
- getIndex(Parameterized) - Method in class pal.misc.MultiParameterized
-
Get the index of a base parameterized object
- 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
- getInfo() - Method in interface pal.supgma.RateHandler
-
- getInfo() - Method in interface pal.supgma.ThetaHandler
-
- getInstance(int) - Static method in class pal.datatype.DataType.Utils
-
create object according to this code
- 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() - 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(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.CodonModel
-
Create codon substitution 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, int, double[], double[]) - Static method in class pal.substmodel.RateMatrixUtils
-
Create rate matrix given model and data type codes
- getInstance(double[]) - Static method in class pal.substmodel.TwoStateModel
-
create object using an instance method
- getIntegerValue(Element) - Static method in class pal.xml.ElementParser
-
- 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.ConstantPopulation
-
- getIntensity(double) - Method in class pal.coalescent.ConstExpConst
-
- getIntensity(double) - Method in class pal.coalescent.ConstExpGrowth
-
- 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.ExpandingPopulation
-
- getIntensity(double) - Method in class pal.coalescent.ExponentialGrowth
-
- getInternalNode(int) - Method in class pal.tree.ParameterizedTree.ParameterizedTreeBase
-
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
-
- getInternalNode(int) - Method in class pal.tree.Tree.TreeBase
-
Returns the ith internal node.
- getInternalNodeCount(Node) - Static method in class pal.tree.NodeUtils
-
- getInternalNodeCount() - Method in class pal.tree.ParameterizedTree.ParameterizedTreeBase
-
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
-
- getInternalNodeCount() - Method in class pal.tree.Tree.TreeBase
-
Returns the number of internal nodes.
- getInternalNodes(Node, Vector) - Static method in class pal.tree.NodeUtils
-
Appends all internal nodes from tree defined by root to Vector store
- getInternalNodes(Node, boolean) - Static method in class pal.tree.NodeUtils
-
Obtains all internal nodes from tree defined by root and returns as an array
- getInternalParameterBoundaries(int, double[]) - Method in interface pal.math.OrthogonalHints
-
A boundary is a value of a parameter for which values lower than the boundary and values
higher than the boundary are better treated as two separate functions (IE, they
are only piecewise connected), and minimisation should be performed over both ranges
individually (and then the true minimum taken as the minimuma of the ranges)
- getInternalParameterBoundaries(OrthogonalHints, int) - Static method in class pal.math.OrthogonalHints.Utils
-
- getInternalParameterBoundaries(int, double[]) - Method in class pal.tree.MutationRateModelTree
-
- 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.
- getInverse() - Method in class pal.math.Matrix
-
Obtains the inverse of a matrix by appending identity and doing row reduction.
- getInverseIntensity(double) - Method in class pal.coalescent.ConstantPopulation
-
- getInverseIntensity(double) - Method in class pal.coalescent.ConstExpConst
-
- getInverseIntensity(double) - Method in class pal.coalescent.ConstExpGrowth
-
- 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.ExpandingPopulation
-
- getInverseIntensity(double) - Method in class pal.coalescent.ExponentialGrowth
-
- getIterationCount(int) - Static method in class pal.algorithmics.StoppingCriteria.Utils
-
A stopping criteria that stops after a set number of iterations
- getIUPACState(int) - Static method in class pal.datatype.IUPACNucleotides
-
- getIUPACState(boolean, boolean, boolean, boolean) - Static method in class pal.datatype.IUPACNucleotides
-
- getIUPACStatesFromAminoAcidState(int) - Method in interface pal.datatype.CodonTable
-
- getKappa() - Method in class pal.substmodel.YangCodonModel
-
- getKappaDefaultValue() - Method in class pal.substmodel.YangCodonModel
-
- getKappaLowerLimit() - Method in class pal.substmodel.YangCodonModel
-
- getKappaUpperLimit() - Method in class pal.substmodel.YangCodonModel
-
- getKey() - Method in interface pal.util.DoubleKey
-
- getLabel(String, String) - Method in class pal.misc.LabelMapping
-
- getLabel(Identifier, String) - Method in class pal.misc.LabelMapping
-
- getLabel(Identifier) - Method in class pal.misc.LabelMapping
-
- getLabel() - Method in class pal.tree.TreeManipulator.PALNodeWrapper
-
- getLabel() - Method in class pal.treesearch.AbstractLeafNode
-
- getLabel() - Method in interface pal.treesearch.NodeAccess
-
- getLabelCount() - Method in class pal.tree.CladeSystem
-
get number of labels
- getLabelCount() - Method in class pal.tree.SplitSystem
-
get number of labels
- getLabelFont() - Method in class pal.gui.TreePainter
-
- getLabelIdentifier(Identifier) - Method in class pal.misc.LabelMapping
-
- getLabels() - Method in class pal.treesearch.HeightInformationUser
-
- getLabelSplit() - Method in interface pal.tree.TreeManipulator.BranchAccess
-
Obtain the split of the labels around this branch.
- getLargestNumber() - Method in class pal.util.ThreeNumberSort
-
get largest number
- getLastReadToken() - Method in class pal.io.NexusTokenizer
-
Returns the last read token.
- getLastReceivedAlignment() - Method in class pal.alignment.AlignmentReceiver.SingleReceiver
-
- getLastTokenType() - Method in class pal.io.NexusTokenizer
-
Determine the type of the last read token.
- getLeadingIncompleteCodonsStripped(Alignment) - Static method in class pal.alignment.AlignmentUtils
-
Creates a new nucleotide alignment based on the input that has any leading incomplete
codons (that is, the first codon of the sequence that is not a gap/unknown but is not complete - has
a nucleotide unknown) replaced by a triplet of unknowns
- getLeafBaseHeight(String) - Method in interface pal.treesearch.ConstraintModel.GroupManager
-
- getLeafBaseHeight(String) - Method in class pal.treesearch.FixedBSRDTGlobalClockModel
-
- getLeafBaseHeight(String) - Method in class pal.treesearch.FixedSRDTGlobalClockModel
-
- getLeafBaseHeight(String) - Method in class pal.treesearch.GlobalClockModel
-
- getLeafBaseHeight(String) - Method in class pal.treesearch.MRDTGlobalClockModel
-
- getLeafBaseHeight(String) - Method in class pal.treesearch.SRDTGlobalClockModel
-
- 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
- getLeafLabelSet(Node) - Method in class pal.treesearch.GeneralConstructionTool
-
A horibly inefficient way of doing things.
- getLeafLabelSet(Node, ArrayList) - Method in class pal.treesearch.GeneralConstructionTool
-
- getLeft() - Method in class pal.treesearch.FreeBranch
-
- getLeftBranch(FreeBranch) - Method in class pal.treesearch.FreeInternalNode
-
- getLeftBranch(FreeBranch) - Method in class pal.treesearch.FreeLeafNode
-
- getLeftBranch(FreeBranch) - Method in interface pal.treesearch.FreeNode
-
- getLeftBranch(FreeBranch) - Method in class pal.treesearch.PivotNode
-
- getLeftChild() - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
- getLeftChild() - Method in class pal.treesearch.ConstrainedLeafNode
-
Returns null as we can't have children...
- getLeftChild() - Method in interface pal.treesearch.ConstrainedNode
-
- getLeftChildPatternInfo(GeneralConstructionTool) - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
- getLeftDescendentExtendedConditionals(GeneralConstructionTool, boolean) - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
Obtain conditionals by extended left child conditionals to height of this node
- getLeftDescendentExtendedConditionals(double, GeneralConstructionTool, boolean) - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
Obtain conditionals by extended left child conditionals to a particular height
- getLeftExtendedConditionalProbabilities(FreeBranch, UnconstrainedLikelihoodModel.External, ConditionalProbabilityStore, GeneralConstructionTool) - Method in class pal.treesearch.FreeInternalNode
-
- getLeftExtendedConditionalProbabilities(FreeBranch, UnconstrainedLikelihoodModel.External, ConditionalProbabilityStore) - Method in class pal.treesearch.FreeLeafNode
-
- getLeftFlatConditionalProbabilities(GeneralConstructionTool) - Method in class pal.treesearch.FreeBranch
-
- getLeftLeafNames() - Method in interface pal.treesearch.BranchAccess
-
Obtain the leaf names to the "left" of this branch (left/right is an arbitary name to either end of branch - the only guarantee is that left is not right)
- getLeftLeftBranch() - Method in class pal.treesearch.FreeBranch
-
- getLeftNode() - Method in interface pal.tree.UnrootedTreeInterface.BaseBranch
-
- getLeftPatternInfo(GeneralConstructionTool) - Method in class pal.treesearch.FreeBranch
-
- getLeftPatternInfo(GeneralConstructionTool, FreeBranch) - Method in class pal.treesearch.FreeInternalNode
-
- getLeftPatternInfo(GeneralConstructionTool, FreeBranch) - Method in class pal.treesearch.FreeLeafNode
-
- getLeftPatternInfo(GeneralConstructionTool, FreeBranch) - Method in interface pal.treesearch.FreeNode
-
- getLeftPatternInfo(GeneralConstructionTool, FreeBranch) - Method in class pal.treesearch.PivotNode
-
- getLeftRightBranch() - Method in class pal.treesearch.FreeBranch
-
- 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
- getLessRecentNode() - Method in interface pal.tree.RootedTreeInterface.RBranch
-
- getLnL() - Method in class pal.tree.MutationRateModelTree
-
- getLocusName(int) - Method in interface pal.alignment.AnnotationAlignment
-
Returns the name of the locus
- getLocusName(int) - Method in class pal.alignment.ConcatenatedAnnotatedAlignment
-
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.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 class pal.alignment.StrippedAnnotatedAlignment
-
Returns the name of the locus
- getLocusPosition(int) - Method in interface pal.alignment.AnnotationAlignment
-
Return the position along the locus (ignores gaps)
- getLocusPosition(int) - Method in class pal.alignment.ConcatenatedAnnotatedAlignment
-
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.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 class pal.alignment.StrippedAnnotatedAlignment
-
Return the position along the locus (ignores gaps)
- getLoggedDifferenceFromLogged(double, double) - Static method in class pal.math.MathUtils
-
Calculate the logged difference in two values = x - y, where the log of x and y are given.
- getLogL() - Method in class pal.coalescent.DemographicModel
-
returns log-likelihood.
- getLogLikelihood() - Method in class pal.coalescent.SkylinePlot
-
Compute log-likelihood
- getLogLikelihood() - Method in interface pal.statistics.LikelihoodEvaluator.MLResult
-
- getLogLikelihood() - Method in class pal.statistics.LikelihoodEvaluator.SimpleMLResult
-
- getLongestIdentifierPixelWidth(FontMetrics) - Method in class pal.gui.TreePainter
-
- getLowerBound() - Method in class pal.distance.SequencePairLikelihood
-
- getLowerBound(int) - Method in class pal.eval.ChiSquareValue
-
- getLowerBound(int) - Method in class pal.eval.DemographicValue
-
- getLowerBound(int) - Method in class pal.eval.ModelParameters
-
- getLowerBound(int) - Method in class pal.math.BoundsCheckedFunction
-
- getLowerBound(int) - Method in class pal.math.EvaluationCounter
-
- getLowerBound() - Method in class pal.math.LineFunction
-
- getLowerBound(int) - Method in interface pal.math.MultivariateFunction
-
get lower bound of argument n
- getLowerBound() - Method in class pal.math.OrthogonalLineFunction
-
- getLowerBound() - Method in interface pal.math.UnivariateFunction
-
get lower bound of argument
- getLowerBoundParameter() - Method in class pal.math.LineFunction
-
get parameter that limits the lower bound
- getLowerLimit(int) - Method in class pal.coalescent.ConstantPopulation
-
- getLowerLimit(int) - Method in class pal.coalescent.ConstExpConst
-
- getLowerLimit(int) - Method in class pal.coalescent.ConstExpGrowth
-
- getLowerLimit(int) - Method in class pal.coalescent.ExpandingPopulation
-
- getLowerLimit(int) - Method in class pal.coalescent.ExponentialGrowth
-
- getLowerLimit(int) - Method in class pal.mep.ConstantMutationRate
-
- getLowerLimit(int) - Method in class pal.mep.SteppedMutationRate
-
- getLowerLimit(int) - Method in class pal.mep.WindowedMutationRate
-
- getLowerLimit() - Method in interface pal.misc.IndividualParameterHandler
-
- getLowerLimit(int) - Method in class pal.misc.MultiParameterized
-
- getLowerLimit() - Method in class pal.misc.MutableDouble
-
- getLowerLimit(int) - Method in interface pal.misc.NeoParameterized
-
get lower parameter limit
- getLowerLimit(int) - Method in interface pal.misc.Parameterized
-
get lower parameter limit
- getLowerLimit(int) - Method in class pal.misc.Parameterized.Null
-
- getLowerLimit(int) - Method in class pal.misc.Parameterized.ParameterizedBase
-
- getLowerLimit(int) - Method in class pal.misc.Parameterized.ParameterizedUser
-
- getLowerLimit(int) - Method in class pal.misc.ParameterizedDoubleBundle
-
- getLowerLimit(int) - Method in class pal.misc.ParameterizedNeoWrapper
-
- getLowerLimit(int) - Method in class pal.substmodel.AminoAcidModel
-
- getLowerLimit(int) - Method in class pal.substmodel.CachedRateMatrix
-
- getLowerLimit(int) - Method in class pal.substmodel.ConstantIndependentSingleSplitDistribution
-
- getLowerLimit(int) - Method in class pal.substmodel.F81
-
- getLowerLimit(int) - Method in class pal.substmodel.F84
-
- getLowerLimit(int) - Method in class pal.substmodel.GammaRates
-
- getLowerLimit(int) - Method in class pal.substmodel.GTR
-
- getLowerLimit(int) - Method in class pal.substmodel.HKY
-
- getLowerLimit(int) - Method in class pal.substmodel.InvariableSites
-
- getLowerLimit(int) - Method in class pal.substmodel.MultiRateMatrixHandler
-
- getLowerLimit(int) - Method in class pal.substmodel.RateMatrixHandler
-
- getLowerLimit(int) - Method in class pal.substmodel.SaturatedSingleSplitDistribution
-
- getLowerLimit(int) - Method in class pal.substmodel.SimpleRateMatrixGroup
-
- getLowerLimit(int) - Method in class pal.substmodel.TN
-
- getLowerLimit(int) - Method in class pal.substmodel.TwoStateModel
-
- getLowerLimit(int) - Method in class pal.substmodel.UniformRate
-
- getLowerLimit(int) - Method in class pal.substmodel.VariableIndependentSingleSplitDistribution
-
- getLowerLimit(int) - Method in class pal.substmodel.YangCodonModel
-
- getLowerLimit(int) - Method in class pal.substmodel.YangCodonModel.SimpleNeutralSelection
-
- getLowerLimit(int) - Method in class pal.substmodel.YangCodonModel.SimplePositiveSelection
-
- getLowerLimit(int) - Method in class pal.tree.ClockTree
-
- getLowerLimit(int) - Method in class pal.tree.LogParameterizedTree
-
- getLowerLimit(int) - Method in class pal.tree.MutationRateModelTree
-
Returns lower limit of parameter estimate.
- getLowerLimit(int) - Method in class pal.tree.UnconstrainedTree
-
- getLowerLimit(int) - Method in class pal.treesearch.FixedBSRDTGlobalClockModel
-
- getLowerLimit(int) - Method in class pal.treesearch.GlobalClockModel
-
- getLowerLimit(int) - Method in class pal.treesearch.MRDTGlobalClockModel
-
- getLowerLimit(int) - Method in class pal.treesearch.SRDTGlobalClockModel
-
- getMapped(IdGroup) - Method in class pal.misc.LabelMapping
-
- getMatching(BranchAccess[], BranchAccess) - Static method in class pal.treesearch.BranchAccess.Utils
-
- getMatching(BranchAccess[], String[], String[]) - Static method in class pal.treesearch.BranchAccess.Utils
-
- getMatchingDataType(Alignment, SubstitutionModel) - Static method in class pal.eval.LikelihoodTool
-
Creates a new alignment that has a compatible data type with a substution model (needed for likelihood stuff)
- getMatchingDataType(Alignment, SubstitutionModel) - Static method in class pal.treesearch.TreeSearchTool
-
Creates a new alignment that has a compatible data type with a substution model (needed for likelihood stuff)
- getMatrixCopy() - Method in class pal.math.Matrix
-
Cloning
- getMatrixParameters() - Method in class pal.substmodel.GeneralRateDistributionSubstitutionModel
-
- getMax(double[]) - Static method in class pal.misc.Utils
-
Calculate the max of an array
- getMax(double[], int, int) - Static method in class pal.misc.Utils
-
Calculate the max of an array
- getMaxCacheSize() - Method in class pal.util.DefaultCache
-
- getMaxChildHeight() - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
- getMaxHeight() - Method in interface pal.misc.SampleInformation
-
- getMaxHeight() - Method in class pal.misc.TOCDSampleInformation
-
- getMaximum(double[]) - Static method in class pal.math.MathUtils
-
- getMaximum(double[], int, int) - Static method in class pal.math.MathUtils
-
- getMaximumMutationRate() - Method in class pal.mep.MutationRateModel
-
- getMaximumPathLengthLengthToLeaf(Node) - Static method in class pal.tree.NodeUtils
-
- getMaximumTime() - Method in class pal.misc.TimeOrderCharacterData
-
- getMaxLeafTime(Node) - Static method in class pal.gui.TreePainter
-
- getMaxNodeDepth(Node) - Static method in class pal.tree.NodeUtils
-
- getMaxOriginalDescendentLeafHeight() - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
- getMaxOriginalDescendentLeafHeight() - Method in class pal.treesearch.ConstrainedLeafNode
-
- getMaxOriginalDescendentLeafHeight() - Method in interface pal.treesearch.ConstrainedNode
-
- getMaxPopulationSize() - Method in class pal.coalescent.SkylinePlot
-
Returns the largest estimate of population size.
- getMaxTime() - Method in class pal.coalescent.SkylinePlot
-
Returns the largest value of time defined in this plot
(= maximum value for epsilon)
- getMean(double[]) - Static method in class pal.misc.Utils
-
Calculate the mean value of an array
- getMeanCladeHeight(Node, Vector) - Static method in class pal.tree.RootedTreeUtils
-
- getMeanSubtreeHeight(Node, Vector) - Static method in class pal.tree.RootedTreeUtils
-
- getMethodName() - Method in interface pal.tree.ClusterTree.ClusteringMethod
-
- getMidPointRooted() - Method in class pal.tree.TreeManipulator
-
- getMidpointRooted(Tree) - Static method in class pal.tree.TreeManipulator
-
Returns the mid point rooting of a tree.
- getMidPointRooted(Tree) - Static method in class pal.tree.TreeTool
-
Root a tree around it's midpoint.
- getMidPointRootedTree() - Method in class pal.tree.TreeManipulator
-
- getMin(double[]) - Static method in class pal.misc.Utils
-
Calculate the min of an array
- getMinimum(double[], int, int) - Static method in class pal.math.MathUtils
-
- getMinimum(double[]) - Static method in class pal.math.MathUtils
-
- getMinimumChildSeperation() - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
- getMinimumChildSeperation(double) - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
- getMinimumChildSeperation(double) - Method in class pal.treesearch.ConstrainedLeafNode
-
- getMinimumChildSeperation(double) - Method in interface pal.treesearch.ConstrainedNode
-
- getMinimumDirectChildDistance() - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
- getMinimumDirectChildDistance() - Method in class pal.treesearch.ConstrainedLeafNode
-
- getMinimumDirectChildDistance() - Method in interface pal.treesearch.ConstrainedNode
-
- getMinimumLeafChildSeperation() - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
- getMinimumLeafChildSeperation(double) - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
- getMinimumLeafChildSeperation(double) - Method in class pal.treesearch.ConstrainedLeafNode
-
- getMinimumLeafChildSeperation(double) - Method in interface pal.treesearch.ConstrainedNode
-
- getMinimumPathLengthLengthToLeaf(Node) - Static method in class pal.tree.NodeUtils
-
- getMinimumSize() - Method in class pal.gui.TreeComponent
-
- getMinimumTime() - Method in class pal.misc.TimeOrderCharacterData
-
- getMinOriginalDescendentLeafHeight() - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
- getMinOriginalDescendentLeafHeight() - Method in class pal.treesearch.ConstrainedLeafNode
-
- getMinOriginalDescendentLeafHeight() - Method in interface pal.treesearch.ConstrainedNode
-
- getMLOptimised(Tree, Alignment, AlgorithmCallback) - Method in interface pal.statistics.LikelihoodEvaluator
-
- 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.BLOSUM62
-
- getModelID() - Method in class pal.substmodel.CachedRateMatrix
-
- getModelID() - Method in class pal.substmodel.CPREV
-
- getModelID() - Method in class pal.substmodel.Dayhoff
-
- getModelID() - Method in class pal.substmodel.F81
-
- getModelID() - Method in class pal.substmodel.F84
-
- getModelID() - Method in class pal.substmodel.GTR
-
- getModelID() - Method in class pal.substmodel.HKY
-
- getModelID() - Method in class pal.substmodel.JTT
-
- getModelID() - Method in class pal.substmodel.MTREV24
-
- getModelID() - Method in interface pal.substmodel.RateMatrix
-
get numerical code describing the model type
- getModelID() - Method in class pal.substmodel.TN
-
- getModelID() - Method in class pal.substmodel.TwoStateModel
-
get numerical code describing the model type
- getModelID() - Method in class pal.substmodel.VT
-
- getModelID() - Method in class pal.substmodel.WAG
-
- getModelID() - Method in class pal.substmodel.YangCodonModel
-
- getModelOptimiseAction(MultivariateMinimum, int, int) - Method in class pal.treesearch.UnrootedMLSearcher
-
- getModelOptimiseAction(MultivariateMinimum, MinimiserMonitor, int, int) - Method in class pal.treesearch.UnrootedMLSearcher
-
- getMolecularDataType(DataType) - Static method in class pal.datatype.MolecularDataType.Utils
-
Converts (if possible) a DataType into a MolecularDataType.
- getMolecularStatesFromIUPACNucleotides(int[], int) - Method in class pal.datatype.Codons
-
- getMolecularStatesFromIUPACNucleotides(int[], int) - Method in class pal.datatype.GapBalanced
-
Currently converts ambiguous states to a simple version (IE takes the first possible simple state for the ambiguous state)
- getMolecularStatesFromIUPACNucleotides(int[], int) - Method in class pal.datatype.IUPACNucleotides
-
- getMolecularStatesFromIUPACNucleotides(int[], int) - Method in interface pal.datatype.MolecularDataType
-
- getMolecularStatesFromIUPACNucleotides(int[], int) - Method in class pal.datatype.Nucleotides
-
- getMolecularStatesFromIUPACNucleotides(int[], int) - Method in class pal.datatype.SpecificAminoAcids
-
- getMolecularStatesFromSimpleNucleotides(int[], int) - Method in class pal.datatype.Codons
-
- getMolecularStatesFromSimpleNucleotides(int[], int) - Method in class pal.datatype.GapBalanced
-
- getMolecularStatesFromSimpleNucleotides(int[], int) - Method in class pal.datatype.IUPACNucleotides
-
- getMolecularStatesFromSimpleNucleotides(int[], int) - Method in interface pal.datatype.MolecularDataType
-
- getMolecularStatesFromSimpleNucleotides(int[], int) - Method in class pal.datatype.Nucleotides
-
- getMolecularStatesFromSimpleNucleotides(int[], int) - Method in class pal.datatype.SpecificAminoAcids
-
- getMoreRecentNode() - Method in interface pal.tree.RootedTreeInterface.RBranch
-
- getMu() - Method in class pal.mep.ConstantMutationRate
-
returns initial population size.
- getMu() - Method in class pal.mep.SteppedMutationRate
-
returns current day mutation rate.
- getMu() - Method in class pal.mep.WindowedMutationRate
-
returns current day mutation rate.
- getMuChanges() - Method in class pal.mep.SteppedMutationRate
-
- getMultiplied(Matrix) - Method in class pal.math.Matrix
-
Multiply as in [this][other]
- getMultiplied(double) - Method in class pal.math.Matrix
-
- getMus(double[]) - Method in class pal.mep.SteppedMutationRate
-
- getMus() - Method in class pal.mep.SteppedMutationRate
-
- getMutationRate(double) - Method in class pal.mep.ConstantMutationRate
-
- 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.SteppedMutationRate
-
- getMutationRate(double) - Method in class pal.mep.WindowedMutationRate
-
- getMutationRateModel() - Method in class pal.tree.MutationRateModelTree
-
returns mu
- getMutationRateModelBased(MutationRateModel.Factory) - Static method in class pal.mep.DeltaModel.Utils
-
For interfacing with time based mutation rate models
- 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.Attribute
-
- getName() - Method in class pal.misc.Identifier
-
- getName() - Method in class pal.misc.MutableDouble
-
- 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
- getName() - Method in class pal.misc.SimpleIdGroup
-
Return the name of this IdGroup.
- getName() - Method in class pal.misc.TimeOrderCharacterData
-
Returns a name for this character data.
- 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
- 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(DoubleKey, 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
- getNewLabel(String) - Method in interface pal.misc.LabelMapping.Relabeller
-
- getNewReplicateLogLikelihoods(AlgorithmCallback) - Method in class pal.statistics.GeneralTopologyPool
-
- getNewReplicateLogLikelihoods(AlgorithmCallback) - Method in class pal.statistics.RELLTopologyPool
-
- getNewReplicateLogLikelihoods(AlgorithmCallback) - Method in interface pal.statistics.TopologyTestEngine.TopologyPool
-
- getNext() - Method in interface pal.math.OrderEnumerator
-
The next value in the enumeration
- getNextAlignment(AlgorithmCallback) - Method in interface pal.alignment.AlignmentGenerator
-
- 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
- getNextProbability(double, double, boolean) - Method in interface pal.algorithmics.ProbabilityIterator
-
- getNextShort() - Static method in class pal.math.MersenneTwisterFast
-
Access a default instance of this class, access is synchronized
- getNextTree(AlgorithmCallback) - Method in interface pal.tree.TreeGenerator
-
- getNNIAction(StoppingCriteria.Factory) - Method in class pal.treesearch.UnrootedMLSearcher
-
- getNNIBranchLengthOptimiseAction(StoppingCriteria.Factory) - Method in class pal.treesearch.UnrootedMLSearcher
-
- getNodeByName(Tree, String) - Static method in class pal.tree.TreeUtils
-
- getNodeByName(Node, String) - Static method in class pal.tree.TreeUtils
-
- getNodeCount() - Method in class pal.tree.ParameterizedTree.ParameterizedTreeBase
-
- getNodeDisplay(Node, LabelDisplayer) - Method in class pal.gui.TreePainter
-
- getNodeHeight() - Method in interface pal.tree.Node
-
Get the height of this node relative to the most recent node.
- getNodeHeight() - Method in class pal.tree.SimpleNode
-
Get the height of this node relative to the most recent node.
- getNodeHeight() - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
- getNodeHeight() - Method in class pal.treesearch.ConstrainedLeafNode
-
- getNodeHeight() - Method in interface pal.treesearch.ConstrainedNode
-
- getNodeHeight() - Method in interface pal.treesearch.ParentableConstrainedNode
-
- getNodeName(Node) - Method in class pal.gui.TreePainter
-
- getNonExactUnchangedScore(int, boolean, double) - Static method in class pal.algorithmics.StoppingCriteria.Utils
-
A stopping criteria that works by counting how many iterations occur at a given score (either the best score or the
current score) and stopping when score does not change after a set number of generations
- getNonSubTreeComponents(ArrayList, Class) - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
- getNonSubTreeComponents(ArrayList, Class) - Method in class pal.treesearch.ConstrainedInternalNode
-
- getNonSubTreeComponents(ArrayList, Class) - Method in class pal.treesearch.ConstrainedLeafNode
-
- getNonSubTreeComponents(ArrayList, Class) - Method in interface pal.treesearch.ConstrainedNode
-
- getNonSubTreeComponents(ArrayList, Class) - Method in class pal.treesearch.PivotNode
-
- getNonSubTreeOfChildComponents(ArrayList, Class, ConstrainedNode) - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
- getNonSubTreeOfChildComponents(ArrayList, Class, ConstrainedNode) - Method in interface pal.treesearch.ParentableConstrainedNode
-
- getNoOperation() - Static method in class pal.tree.TreeOperation.Utils
-
- getNormalized(double[]) - Static method in class pal.math.MathUtils
-
- getNucleotideLength() - Method in class pal.datatype.Codons
-
- getNucleotideLength() - Method in class pal.datatype.GapBalanced
-
- getNucleotideLength() - Method in class pal.datatype.IUPACNucleotides
-
- getNucleotideLength() - Method in interface pal.datatype.MolecularDataType
-
- getNucleotideLength() - Method in class pal.datatype.Nucleotides
-
- getNucleotideLength() - Method in class pal.datatype.SpecificAminoAcids
-
- getNucleotides() - Static method in class pal.datatype.DataTypeTool
-
A set access point for a data type object describing nucleotides (DNA)
- getNucleotidesFromCodonIndex(int) - Static method in class pal.datatype.Codons
-
Translates an index into a codon
- getNucleotideStates(int[]) - Method in class pal.datatype.Codons
-
- getNucleotideStates(int[]) - Method in class pal.datatype.GapBalanced
-
- getNucleotideStates(int[]) - Method in class pal.datatype.IUPACNucleotides
-
- getNucleotideStates(int[]) - Method in interface pal.datatype.MolecularDataType
-
- getNucleotideStates(int[]) - Method in class pal.datatype.Nucleotides
-
- getNucleotideStates(int[]) - Method in class pal.datatype.SpecificAminoAcids
-
- getNucleotideStatesFromCodonIndex(int) - Static method in class pal.datatype.Codons
-
Translates an index into a codon
- getNull() - Static method in class pal.math.OrthogonalHints.Utils
-
- getNullCallback() - Static method in class pal.util.AlgorithmCallback.Utils
-
- 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.eval.ModelParameters
-
- getNumArguments() - Method in class pal.math.BoundsCheckedFunction
-
- getNumArguments() - Method in class pal.math.EvaluationCounter
-
- getNumArguments() - Method in interface pal.math.MultivariateFunction
-
get number of arguments
- getNumber() - Method in interface pal.tree.Node
-
return the index of this node
- getNumber() - Method in class pal.tree.SimpleNode
-
- getNumberOfBaseTransitionCategories() - Method in class pal.substmodel.ConstantIndependentSingleSplitDistribution
-
- getNumberOfBaseTransitionCategories() - Method in class pal.substmodel.SaturatedSingleSplitDistribution
-
- getNumberOfBaseTransitionCategories() - Method in interface pal.substmodel.SingleSplitDistribution
-
- getNumberOfBaseTransitionCategories() - Method in class pal.substmodel.VariableIndependentSingleSplitDistribution
-
- getNumberOfChildren() - Method in class pal.tree.TreeManipulator.PALNodeWrapper
-
- getNumberOfOptimisationTypes() - Method in class pal.treesearch.ConstrainedInternalNode
-
- getNumberOfOptimisationTypes() - Method in class pal.treesearch.FreeBranch
-
- getNumberOfOptimisationTypes() - Method in interface pal.treesearch.GeneralOptimisable
-
- getNumberOfOptimisationTypes() - Method in class pal.treesearch.PivotNode
-
- getNumberOfParameters() - Method in interface pal.misc.NeoParameterized
-
get number of parameters
- getNumberOfParameters() - Method in class pal.misc.ParameterizedDoubleBundle
-
- getNumberOfParameters() - Method in class pal.misc.ParameterizedNeoWrapper
-
- getNumberOfParameters() - Method in class pal.substmodel.ConstantIndependentSingleSplitDistribution
-
- getNumberOfParameters() - Method in class pal.substmodel.MultiRateMatrixHandler
-
- getNumberOfParameters() - Method in class pal.substmodel.SaturatedSingleSplitDistribution
-
- getNumberOfParameters() - Method in class pal.substmodel.SimpleRateMatrixGroup
-
- getNumberOfParameters() - Method in class pal.substmodel.VariableIndependentSingleSplitDistribution
-
- getNumberOfParameters(TimeOrderCharacterData) - Method in interface pal.supgma.RateHandler
-
- getNumberOfParameters(TimeOrderCharacterData) - Method in interface pal.supgma.ThetaHandler
-
- getNumberOfParameters() - Method in class pal.treesearch.FixedBSRDTGlobalClockModel
-
- getNumberOfParameters() - Method in class pal.treesearch.GlobalClockModel
-
- getNumberOfParameters() - Method in class pal.treesearch.MRDTGlobalClockModel
-
- getNumberOfParameters() - Method in class pal.treesearch.SRDTGlobalClockModel
-
- getNumberOfPatterns() - Method in class pal.alignment.SitePattern
-
Accessor method for numPatterns
- getNumberOfPatterns() - Method in class pal.eval.PatternInfo
-
- getNumberOfPatterns() - Method in class pal.treesearch.AbstractLeafNode
-
- getNumberOfPopulations() - Method in class pal.coalescent.SerialCoalescentGenerator.Results
-
- getNumberOfRateParameters() - Method in class pal.substmodel.GeneralPoissonRateMatrix
-
- getNumberOfRateParameters() - Method in class pal.substmodel.GeneralREVRateMatrix
-
- getNumberOfRateParameters() - Method in interface pal.substmodel.NeoRateMatrix
-
- getNumberOfRates() - Method in class pal.substmodel.RateDistribution
-
- getNumberOfSamples() - Method in interface pal.misc.SampleInformation
-
- getNumberOfSamples() - Method in class pal.misc.TOCDSampleInformation
-
- getNumberOfSites() - Method in class pal.eval.PatternInfo
-
- getNumberOfSites() - Method in class pal.treesearch.GeneralConstructionTool
-
- getNumberOfStates() - Method in class pal.treesearch.GeneralConstructionTool
-
- getNumberOfSubgroups() - Method in class pal.misc.TimeOrderCharacterData
-
- getNumberOfSubstitutionClasses() - Method in class pal.substmodel.MultiRateMatrixHandler
-
- getNumberOfTerminatorIndexes() - Method in interface pal.datatype.CodonTable
-
Returns the number of terminator amino acids.
- getNumberOfTopologies() - Method in class pal.statistics.GeneralTopologyPool
-
- getNumberOfTopologies() - Method in class pal.statistics.RELLTopologyPool
-
- getNumberOfTopologies() - Method in interface pal.statistics.TopologyTestEngine.TopologyPool
-
- getNumberOfTransitionCategories() - Method in class pal.substmodel.GeneralRateDistributionSubstitutionModel
-
- getNumberOfTransitionCategories() - Method in class pal.substmodel.NeutralSelectionRateMatrixGroup
-
- getNumberOfTransitionCategories() - Method in class pal.substmodel.PositiveSelectionRateMatrixGroup
-
- getNumberOfTransitionCategories() - Method in interface pal.substmodel.RateMatrixGroup
-
- getNumberOfTransitionCategories() - Method in class pal.substmodel.SimpleRateMatrixGroup
-
- getNumberOfTransitionCategories() - Method in class pal.substmodel.SingleClassSubstitutionModel
-
- getNumberOfTransitionCategories() - Method in interface pal.substmodel.SubstitutionModel
-
- getNumberOfTransitionCategories() - Method in class pal.substmodel.YangCodonModel.SimpleNeutralSelection
-
- getNumberOfTransitionCategories() - Method in class pal.substmodel.YangCodonModel.SimplePositiveSelection
-
- getNumberRelabelledTree(Tree, IdGroup) - Static method in class pal.tree.TreeUtils
-
Create a new tree such that the labels are redifined from a base tree in such a manner:
For each leaf label
If the base label is not a number the new label is just the original label
If the base label is a number the new label appropriately index label from a set identifiers
- 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.coalescent.ConstantPopulation
-
- getNumParameters() - Method in class pal.coalescent.ConstExpConst
-
- getNumParameters() - Method in class pal.coalescent.ConstExpGrowth
-
- getNumParameters() - Method in class pal.coalescent.DemographicClockTree
-
- getNumParameters() - Method in class pal.coalescent.ExpandingPopulation
-
- getNumParameters() - Method in class pal.coalescent.ExponentialGrowth
-
- getNumParameters() - Method in class pal.mep.ConstantMutationRate
-
- getNumParameters() - Method in class pal.mep.SteppedMutationRate
-
- getNumParameters() - Method in class pal.mep.WindowedMutationRate
-
- getNumParameters() - Method in class pal.misc.MultiParameterized
-
- getNumParameters() - Method in interface pal.misc.Parameterized
-
get number of parameters
- getNumParameters() - Method in class pal.misc.Parameterized.Null
-
- getNumParameters() - Method in class pal.misc.Parameterized.ParameterizedBase
-
- getNumParameters() - Method in class pal.misc.Parameterized.ParameterizedUser
-
- getNumParameters() - Method in class pal.substmodel.AminoAcidModel
-
- getNumParameters() - Method in class pal.substmodel.CachedRateMatrix
-
- getNumParameters() - Method in class pal.substmodel.F81
-
- getNumParameters() - Method in class pal.substmodel.F84
-
- getNumParameters() - Method in class pal.substmodel.GammaRates
-
- getNumParameters() - Method in class pal.substmodel.GTR
-
- getNumParameters() - Method in class pal.substmodel.HKY
-
- getNumParameters() - Method in class pal.substmodel.InvariableSites
-
- getNumParameters() - Method in class pal.substmodel.RateMatrixHandler
-
- getNumParameters() - Method in class pal.substmodel.TN
-
- getNumParameters() - Method in class pal.substmodel.TwoStateModel
-
- getNumParameters() - Method in class pal.substmodel.UniformRate
-
- getNumParameters() - Method in class pal.substmodel.YangCodonModel
-
- getNumParameters() - Method in class pal.substmodel.YangCodonModel.SimpleNeutralSelection
-
Two parameters, kappa, p,
- getNumParameters() - Method in class pal.substmodel.YangCodonModel.SimplePositiveSelection
-
Five parameters, three proportions, kappa, omega.
- getNumParameters() - Method in class pal.tree.ClockTree
-
- getNumParameters() - Method in class pal.tree.LogParameterizedTree
-
- getNumParameters() - Method in class pal.tree.MutationRateModelTree
-
- getNumParameters() - Method in class pal.tree.UnconstrainedTree
-
- getNumStates() - Method in class pal.datatype.AminoAcids
-
- getNumStates() - Method in class pal.datatype.Codons
-
- getNumStates() - Method in interface pal.datatype.DataType
-
get number of unique states
- getNumStates() - Method in class pal.datatype.GapBalanced
-
- getNumStates() - Method in class pal.datatype.IUPACNucleotides
-
Get number of states.
- getNumStates() - Method in class pal.datatype.Nucleotides
-
- getNumStates() - Method in class pal.datatype.NumericDataType
-
- getNumStates() - Method in class pal.datatype.StateRemover
-
- getNumStates() - Method in class pal.datatype.TwoStates
-
- getObjects() - Method in class pal.algorithmics.Ranker
-
Obtain the objects in this ranker
- getOmega() - Method in class pal.substmodel.YangCodonModel
-
- getOmegaDefaultValue() - Method in class pal.substmodel.YangCodonModel
-
- getOmegaLowerLimit() - Method in class pal.substmodel.YangCodonModel
-
- getOmegaUpperLimit() - Method in class pal.substmodel.YangCodonModel
-
- getOneRatePerIntervalHandler() - Static method in class pal.supgma.RateHandler.Utils
-
- getOneThetaPerSampleHandler() - Static method in class pal.supgma.ThetaHandler.Utils
-
- getOptimisedTree() - Method in interface pal.statistics.LikelihoodEvaluator.MLResult
-
- getOptimisedTree() - Method in class pal.statistics.LikelihoodEvaluator.SimpleMLResult
-
- getOrdered(int) - Static method in class pal.math.OrderEnumerator.Utils
-
- getOrderedFactory() - Static method in class pal.math.OrderEnumerator.Utils
-
- getOrdinalCount() - Method in class pal.misc.TimeOrderCharacterData
-
- getOrdinals() - Method in class pal.misc.TimeOrderCharacterData
-
Gets ordinals.
- getOrdinalTime(int) - Method in class pal.misc.TimeOrderCharacterData
-
Obtain the time of a particular ordinal
- getOrganismTypeID() - Method in interface pal.datatype.CodonTable
-
- getOrganismTypeID() - Method in class pal.datatype.SpecificAminoAcids
-
- 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() - Static method in class pal.substmodel.BLOSUM62
-
- 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() - Static method in class pal.substmodel.CPREV
-
- 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() - Static method in class pal.substmodel.Dayhoff
-
- 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() - Static method in class pal.substmodel.JTT
-
- 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() - Static method in class pal.substmodel.MTREV24
-
- 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
- getOriginalFrequencies() - Static method in class pal.substmodel.VT
-
- 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() - Static method in class pal.substmodel.WAG
-
- getOriginalOptimisedLogLikelihoods() - Method in class pal.statistics.GeneralTopologyPool
-
- getOriginalOptimisedLogLikelihoods() - Method in class pal.statistics.RELLTopologyPool
-
- getOriginalOptimisedLogLikelihoods() - Method in interface pal.statistics.TopologyTestEngine.TopologyPool
-
- getOriginalOptimisedTrees() - Method in class pal.statistics.GeneralTopologyPool
-
- getOriginalTestStatistics(double[], int) - Method in class pal.statistics.ShimodairaHasegawaStatistics
-
- getOriginalTestStatistics(double[], int) - Method in interface pal.statistics.TopologyTestEngine.StatisticsHandler
-
- getOrthogonalHints() - Method in class pal.eval.ChiSquareValue
-
- getOrthogonalHints() - Method in class pal.eval.DemographicValue
-
- getOrthogonalHints() - Method in class pal.eval.ModelParameters
-
- getOrthogonalHints() - Method in class pal.math.BoundsCheckedFunction
-
- getOrthogonalHints() - Method in class pal.math.EvaluationCounter
-
- getOrthogonalHints() - Method in interface pal.math.MultivariateFunction
-
- getOrthogonalHints() - Method in interface pal.mep.DeltaModel.Instance
-
- getOrthogonalHints() - Method in class pal.mep.MutationRateModel
-
Overide if there is any orthogonal hint information available
- getOrthogonalHints() - Method in class pal.substmodel.AbstractRateMatrix
-
- getOrthogonalHints() - Method in class pal.substmodel.CachedRateMatrix
-
- getOrthogonalHints() - Method in class pal.substmodel.GeneralRateDistributionSubstitutionModel
-
- getOrthogonalHints() - Method in interface pal.substmodel.RateMatrix
-
- getOrthogonalHints() - Method in class pal.substmodel.SingleClassSubstitutionModel
-
- getOrthogonalHints() - Method in interface pal.substmodel.SubstitutionModel
-
May return null
- getOrthogonalHints() - Method in class pal.substmodel.YangCodonModel.SimpleNeutralSelection
-
- getOrthogonalHints() - Method in class pal.substmodel.YangCodonModel.SimplePositiveSelection
-
- getOrthogonalHints() - Method in class pal.tree.MutationRateModelTree
-
- getOrthogonalHints() - Method in interface pal.tree.ParameterizedTree
-
- getOrthogonalHints() - Method in class pal.tree.ParameterizedTree.ParameterizedTreeBase
-
- getOther(FreeNode) - Method in class pal.treesearch.FreeBranch
-
- getOverallLogLikelihood() - Method in class pal.eval.LikelihoodSummary
-
- 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
- getPALPeer() - Method in class pal.tree.TreeManipulator.PALNodeWrapper
-
- getParameter(int) - Method in class pal.coalescent.ConstantPopulation
-
- getParameter(int) - Method in class pal.coalescent.ConstExpConst
-
- getParameter(int) - Method in class pal.coalescent.ConstExpGrowth
-
- getParameter(int) - Method in class pal.coalescent.ExpandingPopulation
-
- getParameter(int) - Method in class pal.coalescent.ExponentialGrowth
-
- getParameter(int) - Method in class pal.mep.ConstantMutationRate
-
- getParameter(int) - Method in class pal.mep.SteppedMutationRate
-
- getParameter(int) - Method in class pal.mep.WindowedMutationRate
-
- getParameter() - Method in interface pal.misc.IndividualParameterHandler
-
- getParameter(int) - Method in class pal.misc.MultiParameterized
-
- getParameter(int) - Method in interface pal.misc.Parameterized
-
get model parameter
- getParameter(int) - Method in class pal.misc.Parameterized.Null
-
- getParameter(int) - Method in class pal.misc.Parameterized.ParameterizedBase
-
- getParameter(int) - Method in class pal.misc.Parameterized.ParameterizedUser
-
- getParameter(int) - Method in class pal.substmodel.AbstractRateMatrix
-
- getParameter(int) - Method in class pal.substmodel.CachedRateMatrix
-
- getParameter(int) - Method in class pal.substmodel.GammaRates
-
- getParameter(int) - Method in class pal.substmodel.InvariableSites
-
- getParameter(int) - Method in class pal.substmodel.RateMatrixHandler
-
- getParameter(int) - Method in class pal.substmodel.UniformRate
-
- getParameter(int) - Method in class pal.substmodel.YangCodonModel.SimpleNeutralSelection
-
- getParameter(int) - Method in class pal.substmodel.YangCodonModel.SimplePositiveSelection
-
- getParameter(int) - Method in class pal.tree.ClockTree
-
- getParameter(int) - Method in class pal.tree.LogParameterizedTree
-
- getParameter(int) - Method in class pal.tree.MutationRateModelTree
-
- getParameter(int) - Method in class pal.tree.UnconstrainedTree
-
- getParameterAccess() - Method in interface pal.eval.MolecularClockLikelihoodModel.Instance
-
- getParameterAccess() - Method in interface pal.eval.UnconstrainedLikelihoodModel.Instance
-
- getParameterCount() - Method in class pal.coalescent.SkylinePlot
-
Returns the number of composite intervals (=number of parameters).
- getParameterization() - Method in class pal.coalescent.ConstExpGrowth
-
- getParameterizationInfo() - Method in class pal.tree.ClockTree
-
- getParameterizationInfo() - Method in class pal.tree.LogParameterizedTree
-
- getParameterizationInfo() - Method in class pal.tree.MutationRateModelTree
-
- getParameterizationInfo() - Method in interface pal.tree.ParameterizedTree
-
- getParameterizationInfo() - Method in class pal.tree.UnconstrainedTree
-
- getParameterizedTreeFactory() - Static method in class pal.tree.ClockTree
-
Obtain a ParameterizedTree.Factory for generating Clock trees
- getParameterizedTreeFactory(MutationRateModel.Factory, TimeOrderCharacterData) - Static method in class pal.tree.MutationRateModelTree
-
Obtain a ParameterizedTree.Factory for generating Unconstrained trees
- getParameterizedTreeFactory() - Static method in class pal.tree.UnconstrainedTree
-
Obtain a ParameterizedTree.Factory for generating Unconstrained trees
- 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.F81
-
- getParameterName(int) - Method in class pal.substmodel.F84
-
- getParameterName(int) - Method in class pal.substmodel.GTR
-
- getParameterName(int) - Method in class pal.substmodel.HKY
-
- getParameterName(int) - Method in class pal.substmodel.TN
-
- getParameterName(int) - Method in class pal.substmodel.TwoStateModel
-
- getParameterName(int) - Method in class pal.substmodel.YangCodonModel
-
- getParameters(double[], int) - Method in interface pal.misc.NeoParameterized
-
get model parameter
- getParameters(Parameterized) - Static method in class pal.misc.Parameterized.Utils
-
- getParameters(double[], int) - Method in class pal.misc.ParameterizedDoubleBundle
-
- getParameters(double[], int) - Method in class pal.misc.ParameterizedNeoWrapper
-
- getParameters(double[], int) - Method in class pal.substmodel.ConstantIndependentSingleSplitDistribution
-
- getParameters(double[], int) - Method in class pal.substmodel.MultiRateMatrixHandler
-
- getParameters(double[], int) - Method in class pal.substmodel.SaturatedSingleSplitDistribution
-
- getParameters(double[], int) - Method in class pal.substmodel.VariableIndependentSingleSplitDistribution
-
- getParameters(double[], int) - Method in class pal.treesearch.FixedBSRDTGlobalClockModel
-
- getParameters(double[], int) - Method in class pal.treesearch.GlobalClockModel
-
- getParameters(double[], int) - Method in class pal.treesearch.MRDTGlobalClockModel
-
- getParameters(double[], int) - Method in class pal.treesearch.SRDTGlobalClockModel
-
- getParametersSE() - Method in class pal.misc.Parameterized.ParameterizedBase
-
- getParent() - Method in interface pal.tree.Node
-
Returns the parent node of this node.
- getParent() - Method in class pal.tree.SimpleNode
-
Returns the parent node of this node.
- getParentBranch() - Method in class pal.tree.TreeManipulator.PALNodeWrapper
-
- getParentBranchLength() - Method in class pal.tree.TreeManipulator.PALNodeWrapper
-
- getParentNode() - Method in class pal.tree.TreeManipulator.PALBranchWrapper
-
- getParentRBranch() - Method in interface pal.tree.RootedTreeInterface.RNode
-
Get the parent branch (or null if the root)
- getParentUBranch() - Method in interface pal.tree.UnrootedTreeInterface.UNode
-
Get the branch closest to the base (or maybe even the base)
- getPartial(Node) - Method in class pal.eval.SimpleLikelihoodCalculator
-
get partial likelihood of a branch
- getPathLengthInfo(Node) - Static method in class pal.tree.NodeUtils
-
Calculates max/min lengths of paths from root to leaf, taking into account branch lengths
- getPatternCapacity() - Method in class pal.eval.ConditionalProbabilityStore
-
- getPatternData(int, int) - Method in class pal.alignment.SitePattern
-
- getPatternInfo() - Method in class pal.treesearch.AbstractLeafNode
-
- getPatternInfo(GeneralConstructionTool, FreeNode) - Method in class pal.treesearch.FreeBranch
-
- getPatternInfo(GeneralConstructionTool, FreeBranch) - Method in class pal.treesearch.FreeInternalNode
-
- getPatternInfo(GeneralConstructionTool, FreeBranch) - Method in class pal.treesearch.FreeLeafNode
-
- getPatternInfo(GeneralConstructionTool, FreeBranch) - Method in interface pal.treesearch.FreeNode
-
- getPatternInfo(GeneralConstructionTool, FreeBranch) - Method in class pal.treesearch.PivotNode
-
- getPatternLookup() - Method in class pal.eval.PatternInfo
-
- getPatternState(int, int) - Method in class pal.alignment.SitePattern
-
- getPatternWeights() - Method in class pal.eval.PatternInfo
-
- getPeer() - Method in class pal.gui.PositionedNode
-
- getPenWidth() - Method in class pal.gui.TreePainter
-
- getPoint(PositionedNode, int, int) - Method in class pal.gui.TreePainterNormal
-
- 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)
- getPopulationSize(int) - Method in class pal.coalescent.SkylinePlot
-
Returns the population size in interval i.
- getPositionMisalignmentInfo(Alignment, PrintWriter, int, CodonTable, boolean) - Static method in class pal.alignment.AlignmentUtils
-
- getPositionMisalignmentInfo(Alignment, PrintWriter, int) - Static method in class pal.alignment.AlignmentUtils
-
- getPositionType(int) - Method in interface pal.alignment.AnnotationAlignment
-
Returns position type (eg.
- getPositionType(int) - Method in class pal.alignment.ConcatenatedAnnotatedAlignment
-
Returns position type (eg.
- getPositionType(int) - Method in class pal.alignment.IndelAnnotatedAlignment
-
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 class pal.alignment.StrippedAnnotatedAlignment
-
Returns position type (eg.
- getPreferredChar(char) - Method in interface pal.datatype.DataType
-
get the preferred version of a particular character (eg a -> A)
Should not always assume that a DataType only uses Upper case characters!
- getPreferredChar(char) - Method in class pal.datatype.SimpleDataType
-
Automatically handles Gaps for sub classes
- getPreferredCharImpl(char) - Method in class pal.datatype.SimpleDataType
-
Can be overidden by subclasses.
- getPreferredChars(char[], DataType) - Static method in class pal.datatype.DataType.Utils
-
Converts a sequence of characters to the preferred form for a data type
- getPreferredChars(char[], DataType, boolean) - Static method in class pal.datatype.DataType.Utils
-
Converts a sequence of characters to the preferred form for a data type
- getPreferredChars(String, DataType) - Static method in class pal.datatype.DataType.Utils
-
Converts a sequence of characters to the preferred form for a data type (using Strings)
- getPreferredChars(String, DataType, boolean) - Static method in class pal.datatype.DataType.Utils
-
Converts a sequence of characters to the preferred form for a data type (using Strings) * @param specialDots if true then the dot (period) '.' is used even if it is not the prefered character by the data type
- getPreferredSize() - Method in interface pal.gui.Painter
-
- getPreferredSize() - Method in class pal.gui.TreeComponent
-
- getPreferredSize() - Method in class pal.gui.TreePainterCircular
-
Returns the preferred size for drawing
(that is the size that will show everything nicely)
- getPreferredSize() - Method in class pal.gui.TreePainterNormal
-
Returns the preferred size for drawing
(that is the size that will show everything nicely)
- getPrimaryGroupRelatedParameterAccess() - Method in interface pal.treesearch.ConstraintModel.GroupManager
-
- getPrimaryGroupRelatedParameterAccess() - Method in class pal.treesearch.FixedBSRDTGlobalClockModel
-
- getPrimaryGroupRelatedParameterAccess() - Method in class pal.treesearch.FixedSRDTGlobalClockModel
-
- getPrimaryGroupRelatedParameterAccess() - Method in class pal.treesearch.GlobalClockModel
-
- getPrimaryGroupRelatedParameterAccess() - Method in class pal.treesearch.MRDTGlobalClockModel
-
- getPrimaryGroupRelatedParameterAccess() - Method in class pal.treesearch.SRDTGlobalClockModel
-
- getPrintWriterCallback(PrintWriter) - Static method in class pal.util.AlgorithmCallback.Utils
-
Construct an algorithm callback that redirects status reports to a print writer
- getPValue(int) - Method in interface pal.statistics.TopologyTestEngine.TestResult
-
- getPValues(double[], double[][], int, int) - Method in class pal.statistics.ShimodairaHasegawaStatistics
-
The pValue in this case represents the alpha value ( CI 1-alpha) when topology becomes significantly different from the ML topology (or stops being not significantly different)
- getPValues(double[], double[][], int, int) - Method in interface pal.statistics.TopologyTestEngine.StatisticsHandler
-
- 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.
- getRandomParameterValue(int) - Method in class pal.misc.Parameterized.ParameterizedUser
-
- getRate(int) - Method in class pal.substmodel.RateDistribution
-
- getRateDistributionParameters() - Method in class pal.substmodel.GeneralRateDistributionSubstitutionModel
-
- getRateModelSummary() - Method in interface pal.treesearch.ConstraintModel
-
- getRateModelSummary() - Method in class pal.treesearch.FixedBSRDTGlobalClockModel
-
- getRateModelSummary() - Method in class pal.treesearch.FixedSRDTGlobalClockModel
-
- getRateModelSummary() - Method in class pal.treesearch.GlobalClockModel
-
- getRateModelSummary() - Method in class pal.treesearch.MRDTGlobalClockModel
-
- getRateModelSummary() - Method in class pal.treesearch.SRDTGlobalClockModel
-
- getRateModelSummary() - Method in class pal.treesearch.UnconstrainedModel
-
- getRateParameterLowerBound(int) - Method in class pal.substmodel.GeneralPoissonRateMatrix
-
- getRateParameterLowerBound(int) - Method in class pal.substmodel.GeneralREVRateMatrix
-
- getRateParameterLowerBound(int) - Method in interface pal.substmodel.NeoRateMatrix
-
- getRateParameterUpperBound(int) - Method in class pal.substmodel.GeneralPoissonRateMatrix
-
- getRateParameterUpperBound(int) - Method in class pal.substmodel.GeneralREVRateMatrix
-
- getRateParameterUpperBound(int) - Method in interface pal.substmodel.NeoRateMatrix
-
- getRates() - Method in class pal.substmodel.RateDistribution
-
- getRatio() - Method in class pal.coalescent.ExpandingPopulation
-
returns ratio of population sizes
- getReceivedAlignments() - Method in class pal.alignment.AlignmentReceiver.BucketReceiver
-
- getRecommendedGapState() - Method in interface pal.datatype.DataType
-
- getRecommendedGapState() - Method in class pal.datatype.SimpleDataType
-
- getRecommendedUnknownState() - Method in interface pal.datatype.DataType
-
- getRecommendedUnknownState() - Method in class pal.datatype.IUPACNucleotides
-
- getRecommendedUnknownState() - Method in class pal.datatype.SimpleDataType
-
- getRelabeled(LabelMapping.Relabeller) - Method in class pal.misc.LabelMapping
-
- getRelatedGroup() - Method in class pal.treesearch.GeneralConstraintGroupManager
-
- getRelatedModel() - Method in interface pal.eval.SiteDetails
-
- 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.
- getRelativeStoppingRatio() - Method in interface pal.algorithmics.StoppingCriteria
-
Get an indication of how close to stopping we currently are
- getRelavantLength(int) - Method in class pal.datatype.Nucleotides
-
- getReordered(IdGroup) - Method in class pal.misc.TimeOrderCharacterData
-
Creates a new TimeOrderCharacterData object with the same properites as this one
but the identifier positions match that of base (ie whichIdNumber(Name) returns the same as for base)
- getReplicateCladeSupport(String, Tree, TreeGenerator, int, AlgorithmCallback) - 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 replicate
support by clade (that is the proportion of replicates that produce the sub clade under that node)
- getReplicateLogLikelihood(Tree, Alignment) - Method in interface pal.statistics.ReplicateLikelihoodEvaluator
-
- getRestricted(OrderEnumerator, int, int) - Static method in class pal.math.OrderEnumerator.Utils
-
- getRestrictedFactory(OrderEnumerator.OEFactory, int, int) - Static method in class pal.math.OrderEnumerator.Utils
-
- getRight() - Method in class pal.treesearch.FreeBranch
-
- getRightBranch(FreeBranch) - Method in class pal.treesearch.FreeInternalNode
-
- getRightBranch(FreeBranch) - Method in class pal.treesearch.FreeLeafNode
-
- getRightBranch(FreeBranch) - Method in interface pal.treesearch.FreeNode
-
- getRightBranch(FreeBranch) - Method in class pal.treesearch.PivotNode
-
- getRightChild() - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
- getRightChild() - Method in class pal.treesearch.ConstrainedLeafNode
-
- getRightChild() - Method in interface pal.treesearch.ConstrainedNode
-
- getRightChildPatternInfo(GeneralConstructionTool) - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
- getRightDescendentExtendedConditionals(GeneralConstructionTool, boolean) - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
Obtain conditionals by extended right child conditionals to height of this node
- getRightDescendentExtendedConditionals(double, GeneralConstructionTool, boolean) - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
Obtain conditionals by extended left child conditionals to a particular height
- getRightExtendedConditionalProbabilities(FreeBranch, UnconstrainedLikelihoodModel.External, ConditionalProbabilityStore, GeneralConstructionTool) - Method in class pal.treesearch.FreeInternalNode
-
- getRightExtendedConditionalProbabilities(FreeBranch, UnconstrainedLikelihoodModel.External, ConditionalProbabilityStore) - Method in class pal.treesearch.FreeLeafNode
-
- getRightFlatConditionalProbabilities(GeneralConstructionTool) - Method in class pal.treesearch.FreeBranch
-
- getRightLeafNames() - Method in interface pal.treesearch.BranchAccess
-
Obtain the leaf names to the "right" of this branch (left/right is an arbitary name to either end of branch - the only guarantee is that left is not right)
- getRightLeftBranch() - Method in class pal.treesearch.FreeBranch
-
- getRightNode() - Method in interface pal.tree.UnrootedTreeInterface.BaseBranch
-
- getRightPatternInfo(GeneralConstructionTool) - Method in class pal.treesearch.FreeBranch
-
- getRightPatternInfo(GeneralConstructionTool, FreeBranch) - Method in class pal.treesearch.FreeInternalNode
-
- getRightPatternInfo(GeneralConstructionTool, FreeBranch) - Method in class pal.treesearch.FreeLeafNode
-
- getRightPatternInfo(GeneralConstructionTool, FreeBranch) - Method in interface pal.treesearch.FreeNode
-
- getRightPatternInfo(GeneralConstructionTool, FreeBranch) - Method in class pal.treesearch.PivotNode
-
- getRightRightBranch() - Method in class pal.treesearch.FreeBranch
-
- getRNANucleotides() - Static method in class pal.datatype.DataTypeTool
-
A set access point for a data type object describing nucleotides (RNA)
- getRobinsonFouldsDistance(Tree, Tree) - Static method in class pal.tree.TreeUtils
-
computes Robinson-Foulds (1981) distance between two trees
- getRobinsonFouldsDistance(SplitSystem, Tree) - Static method in class pal.tree.TreeUtils
-
computes Robinson-Foulds (1981) distance between two trees
- 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
- 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
- getRoot() - Method in class pal.tree.ParameterizedTree.ParameterizedTreeBase
-
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
-
- getRoot() - Method in class pal.tree.Tree.TreeBase
-
Returns the root node of this tree.
- getRooted(Tree, String[]) - Static method in class pal.tree.TreeTool
-
Root a tree by an outgroup.
- getRootedAbove(Node) - Method in class pal.tree.TreeManipulator
-
- getRootedBy(String[]) - Method in class pal.tree.TreeManipulator
-
- getRootedBy(String[], double) - Method in class pal.tree.TreeManipulator
-
- getRootedBy(Tree, String[]) - Static method in class pal.tree.TreeManipulator
-
Roots a tree by an outgroup
- getRootedBy(Tree, String[], double) - Static method in class pal.tree.TreeManipulator
-
Roots a tree by an outgroup
- getRow() - Method in class pal.io.NexusTokenizer
-
Gets the current row position of the cursor.
- getRowReduced() - Method in class pal.math.Matrix
-
Peforms a simple row reduction tramsformation
- 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
-
Deprecated.
Use getOrdinalCount()
- getSampleLinked(int) - Static method in class pal.substmodel.TemporalModelChange.Utils
-
- getSampleOrdinal(String) - Method in interface pal.misc.SampleInformation
-
- getSampleOrdinal(String) - Method in class pal.misc.TOCDSampleInformation
-
- getScaled(Tree, double) - Static method in class pal.tree.TreeUtils
-
Takes a tree and returns a scaled version of it.
- getScaled(Tree, double, int) - Static method in class pal.tree.TreeUtils
-
Takes a tree and returns a scaled version of it.
- getScaled(Tree, MutationRateModel) - Static method in class pal.tree.TreeUtils
-
Takes a tree and returns a scaled version of it.
- getScaled(Tree, MutationRateModel, int) - Static method in class pal.tree.TreeUtils
-
Takes a tree and returns a scaled version of it.
- 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.MutableDouble
-
- getSecondaryGroupRelatedParameterAccess() - Method in interface pal.treesearch.ConstraintModel.GroupManager
-
- getSecondaryGroupRelatedParameterAccess() - Method in class pal.treesearch.FixedBSRDTGlobalClockModel
-
- getSecondaryGroupRelatedParameterAccess() - Method in class pal.treesearch.FixedSRDTGlobalClockModel
-
- getSecondaryGroupRelatedParameterAccess() - Method in class pal.treesearch.GlobalClockModel
-
- getSecondaryGroupRelatedParameterAccess() - Method in class pal.treesearch.MRDTGlobalClockModel
-
- getSecondaryGroupRelatedParameterAccess() - Method in class pal.treesearch.SRDTGlobalClockModel
-
- getSequence() - Method in interface pal.tree.Node
-
Returns the sequence at this node, in the form an array of bytes.
- getSequence() - Method in class pal.tree.SimpleNode
-
Returns the sequence at this node, in the form of an array of bytes.
- getSequence(String) - Method in class pal.treesearch.GeneralConstructionTool
-
Get the sequence data for a particular OTU
- getSequenceCharArray(Alignment, int) - Static method in class pal.alignment.AlignmentUtils
-
Returns a particular sequence of an alignment as a char array
- getSequenceComplement(int[]) - Static method in class pal.datatype.Nucleotides
-
Obtain the complement of a sequence of nucleotides (or IUPACNucleotides - but IUPAC ness is lost)
- getSequenceCount() - Method in class pal.alignment.AbstractAlignment
-
Return number of sequences in this alignment
- getSequenceCount() - Method in interface pal.alignment.Alignment
-
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 class pal.alignment.SimpleCharacterAlignment
-
Return number of taxa or sequences in this alignment
- getSequenceString(Alignment, int) - Static method in class pal.alignment.AlignmentUtils
-
Returns a particular sequence of an alignment as a String
- getSequenceString() - Method in class pal.tree.SimpleNode
-
Returns the sequence at this node, in the form of a String.
- getSetRateHandler(double, int) - Static method in class pal.supgma.RateHandler.Utils
-
- getSetRateHandler(MutationRateModel) - Static method in class pal.supgma.RateHandler.Utils
-
- getSetThetaHandler(double) - Static method in class pal.supgma.ThetaHandler.Utils
-
- getSetThetaHandler(double, boolean) - Static method in class pal.supgma.ThetaHandler.Utils
-
- getSFString(double[], int, String) - Method in class pal.io.FormattedOutput
-
- getSFString(double, int) - Method in class pal.io.FormattedOutput
-
- getShuffled(int) - Static method in class pal.math.OrderEnumerator.Utils
-
- getShuffledFactory() - Static method in class pal.math.OrderEnumerator.Utils
-
- getSignificance(double, int) - Static method in class pal.statistics.LikelihoodRatioTest
-
compute significance level for the differences
in log-likelihood (based on chi-square distribution)
- getSignificantTopologyIndex(double) - Method in interface pal.statistics.TopologyTestEngine.TestResult
-
- getSimpleAssessor(StoppingCriteria.Factory) - Method in class pal.treesearch.UnrootedMLSearcher
-
- getSimpleDesparation(UndoableAction, UndoableAction, double, int) - Static method in class pal.algorithmics.UndoableAction.Utils
-
A simple tool for change actions when things get desparate
- getSimpleSolver() - Static method in class pal.math.LMSSolver.Utils
-
Obtain a simple LMSSolver that uses the "traditional" method for LMS stuff (IE, using row reduction to find the inverse, with poor numerical accuracy)
- getSimpleState(int) - Static method in class pal.datatype.IUPACNucleotides
-
Converts an IUPAC State to either a A,T,G,C state (eg.
- getSimpleStates(int[]) - Static method in class pal.datatype.IUPACNucleotides
-
Converts an IUPAC State array to either a A,T,G,C state (eg.
- getSimpleStates(int[], int) - Static method in class pal.datatype.IUPACNucleotides
-
Converts an IUPAC State array to either a A,T,G,C state (eg.
- getSimpleUniformSelection(UndoableAction[]) - Static method in class pal.algorithmics.UndoableAction.Utils
-
Create an action that selects uniformly from a number of sub actions
- getSimulated(int[], double, double) - Method in interface pal.eval.MolecularClockLikelihoodModel.Simulator
-
- getSimulated(int[], double) - Method in class pal.substmodel.SequenceSimulator
-
- getSimulatedInterval(int, double) - Method in class pal.coalescent.DemographicModel
-
Returns an random interval size selected from the Kingman prior of the demographic model.
- getSingleRateHandler() - Static method in class pal.supgma.RateHandler.Utils
-
- getSingleThetaHandler() - Static method in class pal.supgma.ThetaHandler.Utils
-
- getSingleThetaHandler(boolean) - Static method in class pal.supgma.ThetaHandler.Utils
-
- getSiteCategoryDistribution() - Method in class pal.substmodel.SequenceSimulator
-
- 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
- getSiteLikelihoods() - Method in interface pal.eval.SiteDetails
-
Get the likelihoods for each site (not the log likelihoods)
- getSiteLogLikelihoods() - Method in interface pal.eval.SiteDetails
-
Get the likelihoods for each site (logged)
- getSitePattern(Alignment) - Static method in class pal.alignment.SitePattern
-
- getSitePattern() - Method in class pal.eval.LikelihoodValue
-
Returns the site pattern of this likelihood value
- getSitePattern() - Method in class pal.eval.SimpleLikelihoodCalculator
-
- getSitePatternMatchup() - Method in class pal.eval.PatternInfo
-
- getSitePosteriors(int) - Method in interface pal.eval.SiteDetails
-
- getSiteWeights() - Method in class pal.alignment.SitePattern
-
Accessor method for weight
- getSize() - Method in class pal.coalescent.SkylinePlot
-
Returns the number of intervals in this skyline plot.
- getSize() - Method in class pal.distance.DistanceMatrix
-
Returns the number of rows and columns that the distance matrix has.
- 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).
- getSorted(double[]) - Static method in class pal.util.HeapSort
-
- getSpecificDataType() - Method in interface pal.datatype.AmbiguousDataType
-
- getSpecificDataType() - Method in class pal.datatype.IUPACNucleotides
-
- getSpecificHeight(double) - Static method in class pal.substmodel.TemporalModelChange.Utils
-
- getSpecificStates(int) - Method in interface pal.datatype.AmbiguousDataType
-
returns an array containing the non-ambiguous states that this state represents.
- getSpecificStates(int) - Method in class pal.datatype.IUPACNucleotides
-
returns an array containing the non-ambiguous states
that this state represents.
- getSpecificTime(double, TimeOrderCharacterData) - Static method in class pal.substmodel.TemporalModelChange.Utils
-
- getSplit(int) - Method in class pal.tree.SplitSystem
-
get split
- getSplit(IdGroup, Node, boolean[]) - Static method in class pal.tree.SplitUtils
-
get split for branch associated with internal node
- getSplitCount() - Method in class pal.tree.SplitSystem
-
get number of splits
- getSplitInformation(String[]) - Method in interface pal.treesearch.BranchAccess
-
Constructe an array detailing the split information
- 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
- getSPRAction(StoppingCriteria.Factory) - Method in class pal.treesearch.UnrootedMLSearcher
-
- getState(char) - Method in class pal.alignment.AbstractAlignment
-
Same as getDataType().getState(char)
- getState(char) - Method in interface pal.datatype.DataType
-
get state corresponding to a character
- getState(char) - Method in class pal.datatype.SimpleDataType
-
Handles gap char and then passes on to getStateImpl
- getStateImpl(char) - Method in class pal.datatype.AminoAcids
-
- getStateImpl(char) - Method in class pal.datatype.Codons
-
- getStateImpl(char) - Method in class pal.datatype.GapBalanced
-
- getStateImpl(char) - Method in class pal.datatype.IUPACNucleotides
-
- getStateImpl(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!
- It relies on the fact that all the states for 'ACGTU' are between [0, 3]
- getStateImpl(char) - Method in class pal.datatype.NumericDataType
-
get state corresponding to a character
- getStateImpl(char) - Method in class pal.datatype.SimpleDataType
-
For sub classes to implement main functionality of getState.
- getStateImpl(char) - Method in class pal.datatype.StateRemover
-
- getStateImpl(char) - Method in class pal.datatype.TwoStates
-
- getStateReference() - Method in class pal.algorithmics.GeneralObjectState
-
- getStateReference() - Method in interface pal.algorithmics.ObjectState
-
- getStateReference() - Method in interface pal.algorithmics.StateProvider
-
- getStateReference() - Method in class pal.treesearch.UnrootedMLSearcher
-
- getStates() - Method in class pal.alignment.AbstractAlignment
-
Fills a [numsequences][length] matrix with indices.
- getStates(char[][], int, int, DataType) - Static method in class pal.datatype.DataType.Utils
-
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, int, DataType) - Static method in class pal.datatype.DataType.Utils
-
For converting a sequence to an array of ints where each int represents the
state of the corresponding character in sequence
Allows user selection of unknown and gap states
- getStates(char[][], DataType) - Static method in class pal.datatype.DataType.Utils
-
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.DataType.Utils
-
For converting a sequence to an array of ints where each int represents the
state of the corresponding character in sequence
- getStatesFromAminoAcidState(int) - Method in interface pal.datatype.CodonTable
-
- getString() - Method in class pal.io.OutputTarget
-
get string corresponding to current stream created by openString()
- getSubCallback(AlgorithmCallback, String, double, double) - Static method in class pal.util.AlgorithmCallback.Utils
-
- getSubgroupMembers(int) - Method in class pal.misc.TimeOrderCharacterData
-
- getSubsetColumns(int, int) - Method in class pal.math.Matrix
-
Returns a new Matrix that is formed from a subset of the colums of this matrix
- getSubstitutionClassDefaultValue() - Method in class pal.substmodel.MultiRateMatrixHandler
-
- getSubstitutionClassLowerLimit() - Method in class pal.substmodel.MultiRateMatrixHandler
-
- getSubstitutionClassUpperLimit() - Method in class pal.substmodel.MultiRateMatrixHandler
-
- getSubstitutionModelSummary() - Method in interface pal.eval.MolecularClockLikelihoodModel.Instance
-
- getSubstitutionModelSummary() - Method in interface pal.eval.UnconstrainedLikelihoodModel.Instance
-
- getSubstitutionRate() - Method in class pal.treesearch.FixedBSRDTGlobalClockModel
-
- getSubstitutionRate() - Method in class pal.treesearch.FixedSRDTGlobalClockModel
-
- getSubstitutionRate() - Method in class pal.treesearch.SRDTGlobalClockModel
-
- getSubtree(Node, Node) - Static method in class pal.tree.RootedTreeUtils
-
- getSubTreeComponents(ArrayList, Class) - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
- getSubTreeComponents(ArrayList, Class) - Method in class pal.treesearch.ConstrainedLeafNode
-
- getSubTreeComponents(ArrayList, Class) - Method in interface pal.treesearch.ConstrainedNode
-
- getSuggestedMaximumMutationRate() - Method in class pal.misc.TimeOrderCharacterData
-
A simple utility method for generating a maximu mutation rate based
on times.
- getSuggestedOrdering(OrderEnumerator) - Method in interface pal.math.OrthogonalHints
-
If there is a "best" ordering to use it can be specified here,
if not should return null
- getSuggestedOrdering(OrderEnumerator) - Method in class pal.tree.MutationRateModelTree
-
- getSuitableInstance(Alignment) - Static method in class pal.alignment.AlignmentUtils
-
guess data type suitable for a given sequence data set
- getSuitableInstance(String[]) - Static method in class pal.alignment.AlignmentUtils
-
guess data type suitable for a given sequence data set
- getSuitableInstance(char[][]) - 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
- getSum(double[]) - Static method in class pal.misc.Utils
-
Calculate the total of an array
- getSummary(double[]) - Method in class pal.substmodel.NeutralSelectionRateMatrixGroup
-
- getSummary(double[]) - Method in class pal.substmodel.PositiveSelectionRateMatrixGroup
-
- getSummary(double[]) - Method in interface pal.substmodel.RateMatrixGroup
-
- getSummary(double[], double[]) - Method in class pal.substmodel.SimpleRateMatrixGroup
-
- getSummaryTypes() - Method in class pal.coalescent.ConstantPopulation
-
- getSummaryTypes() - Method in class pal.coalescent.ExponentialGrowth
-
- getSummaryTypes() - Method in class pal.mep.ConstantMutationRate
-
- getSummaryTypes() - Method in class pal.mep.SteppedMutationRate
-
- getSummaryTypes() - Method in class pal.mep.WindowedMutationRate
-
- getSummaryTypes() - Method in class pal.misc.SimpleSummarizable
-
- getSummaryTypes() - Method in interface pal.misc.Summarizable
-
- getSummaryValue(int) - Method in class pal.coalescent.ConstantPopulation
-
- getSummaryValue(int) - Method in class pal.coalescent.ExponentialGrowth
-
- getSummaryValue(int) - Method in class pal.mep.ConstantMutationRate
-
- getSummaryValue(int) - Method in class pal.mep.SteppedMutationRate
-
- getSummaryValue(int) - Method in class pal.mep.WindowedMutationRate
-
- getSummaryValue(int) - Method in class pal.misc.SimpleSummarizable
-
- getSummaryValue(int) - Method in interface pal.misc.Summarizable
-
- getSweepSPRAction(StoppingCriteria.Factory) - Method in class pal.treesearch.UnrootedMLSearcher
-
- getSystemOutCallback() - Static method in class pal.util.AlgorithmCallback.Utils
-
- 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
-
- getTime(double) - Method in class pal.mep.MutationRateModel
-
Return the time at which expected substitutions has occurred.
- getTime(int) - Method in class pal.misc.TimeOrderCharacterData
-
- getTime(String) - Method in class pal.misc.TimeOrderCharacterData
-
- getTimeIntervals(double[], double, double) - Static method in class pal.mep.SteppedMutationRate
-
- getTimeOrderCharacterData() - Method in class pal.gui.TreePainter
-
- getTimeOrdinal(int) - Method in class pal.misc.TimeOrderCharacterData
-
- getTimeOrdinal(String) - Method in class pal.misc.TimeOrderCharacterData
-
- getTimeOrdinal(Identifier) - Method in class pal.misc.TimeOrderCharacterData
-
- getTimeX() - Method in class pal.coalescent.ConstExpConst
-
- getTitle() - Method in class pal.gui.TreeComponent
-
- getTitle() - Method in class pal.gui.TreePainter
-
- getTLA(int) - Static method in class pal.datatype.AminoAcids
-
- getTLA(int) - Static method in class pal.datatype.Codons
-
- getTotal(double[], int, int) - Static method in class pal.math.MathUtils
-
- getTotal(double[]) - 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.
- getTotalNumberOfParameters(Parameterized[]) - Static method in class pal.misc.Parameterized.Utils
-
- 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
- getTransitionCategoryProbabilities() - Method in class pal.substmodel.GeneralRateDistributionSubstitutionModel
-
- getTransitionCategoryProbabilities() - Method in class pal.substmodel.SingleClassSubstitutionModel
-
- getTransitionCategoryProbabilities() - Method in interface pal.substmodel.SubstitutionModel
-
- getTransitionCategoryProbabilities() - Method in class pal.substmodel.YangCodonModel.SimpleNeutralSelection
-
- getTransitionCategoryProbabilities() - Method in class pal.substmodel.YangCodonModel.SimplePositiveSelection
-
- getTransitionCategoryProbability(int) - Method in class pal.substmodel.GeneralRateDistributionSubstitutionModel
-
- getTransitionCategoryProbability(int) - Method in class pal.substmodel.SingleClassSubstitutionModel
-
- getTransitionCategoryProbability(int) - Method in interface pal.substmodel.SubstitutionModel
-
- getTransitionCategoryProbability(int) - Method in class pal.substmodel.YangCodonModel.SimpleNeutralSelection
-
- getTransitionCategoryProbability(int) - Method in class pal.substmodel.YangCodonModel.SimplePositiveSelection
-
- 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.CachedRateMatrix
-
- getTransitionProbabilities(double, double[][][]) - Method in class pal.substmodel.GeneralRateDistributionSubstitutionModel
-
- getTransitionProbabilities(double, int, double[][]) - Method in class pal.substmodel.GeneralRateDistributionSubstitutionModel
-
- getTransitionProbabilities(double[][]) - Method in class pal.substmodel.MatrixExponential
-
A utility method for speed, transfers trans prob information quickly
into store
- getTransitionProbabilities(double, double[][][]) - Method in class pal.substmodel.MultiRateMatrixHandler
-
- getTransitionProbabilities(double, int, double[][]) - Method in class pal.substmodel.MultiRateMatrixHandler
-
- getTransitionProbabilities(double, double[][][]) - Method in class pal.substmodel.NeutralSelectionRateMatrixGroup
-
- getTransitionProbabilities(double, int, double[][]) - Method in class pal.substmodel.NeutralSelectionRateMatrixGroup
-
- getTransitionProbabilities(double, double[][][]) - Method in class pal.substmodel.PositiveSelectionRateMatrixGroup
-
- getTransitionProbabilities(double, int, double[][]) - Method in class pal.substmodel.PositiveSelectionRateMatrixGroup
-
- getTransitionProbabilities(double[][]) - Method in interface pal.substmodel.RateMatrix
-
A utility method for speed, transfers trans prob information quickly
into store
- getTransitionProbabilities(double, double[][][]) - Method in interface pal.substmodel.RateMatrixGroup
-
- getTransitionProbabilities(double, int, double[][]) - Method in interface pal.substmodel.RateMatrixGroup
-
- getTransitionProbabilities(double, double[][]) - Method in class pal.substmodel.RateMatrixHandler
-
- getTransitionProbabilities(double, double[][][]) - Method in class pal.substmodel.SimpleRateMatrixGroup
-
- getTransitionProbabilities(double, int, double[][]) - Method in class pal.substmodel.SimpleRateMatrixGroup
-
- getTransitionProbabilities(double, double[][][]) - Method in class pal.substmodel.SingleClassSubstitutionModel
-
- getTransitionProbabilities(double, int, double[][]) - Method in class pal.substmodel.SingleClassSubstitutionModel
-
- getTransitionProbabilities(double, double[][][]) - Method in interface pal.substmodel.SubstitutionModel
-
Table is organized as [transition_group][from][to]
- getTransitionProbabilities(double, int, double[][]) - Method in interface pal.substmodel.SubstitutionModel
-
Table is organized as [transition_group][from][to]
- getTransitionProbabilities(double, double[][][]) - Method in class pal.substmodel.YangCodonModel.SimpleNeutralSelection
-
Table is organized as [tree_group][from][to]
- getTransitionProbabilities(double, int, double[][]) - Method in class pal.substmodel.YangCodonModel.SimpleNeutralSelection
-
- getTransitionProbabilities(double, double[][][]) - Method in class pal.substmodel.YangCodonModel.SimplePositiveSelection
-
- getTransitionProbabilities(double, int, double[][]) - Method in class pal.substmodel.YangCodonModel.SimplePositiveSelection
-
Table is organized as [tree_group][from][to]
- getTransitionProbabilitiesTranspose(double, double[][][]) - Method in class pal.substmodel.GeneralRateDistributionSubstitutionModel
-
- getTransitionProbabilitiesTranspose(double, int, double[][]) - Method in class pal.substmodel.GeneralRateDistributionSubstitutionModel
-
- getTransitionProbabilitiesTranspose(double, double[][][]) - Method in class pal.substmodel.MultiRateMatrixHandler
-
- getTransitionProbabilitiesTranspose(double, int, double[][]) - Method in class pal.substmodel.MultiRateMatrixHandler
-
- getTransitionProbabilitiesTranspose(double, double[][][]) - Method in class pal.substmodel.NeutralSelectionRateMatrixGroup
-
- getTransitionProbabilitiesTranspose(double, int, double[][]) - Method in class pal.substmodel.NeutralSelectionRateMatrixGroup
-
- getTransitionProbabilitiesTranspose(double, double[][][]) - Method in class pal.substmodel.PositiveSelectionRateMatrixGroup
-
- getTransitionProbabilitiesTranspose(double, int, double[][]) - Method in class pal.substmodel.PositiveSelectionRateMatrixGroup
-
- getTransitionProbabilitiesTranspose(double, double[][][]) - Method in interface pal.substmodel.RateMatrixGroup
-
- getTransitionProbabilitiesTranspose(double, int, double[][]) - Method in interface pal.substmodel.RateMatrixGroup
-
- getTransitionProbabilitiesTranspose(double, double[][]) - Method in class pal.substmodel.RateMatrixHandler
-
- getTransitionProbabilitiesTranspose(double, double[][][]) - Method in class pal.substmodel.SimpleRateMatrixGroup
-
- getTransitionProbabilitiesTranspose(double, int, double[][]) - Method in class pal.substmodel.SimpleRateMatrixGroup
-
- getTransitionProbabilitiesTranspose(double, double[][][]) - Method in class pal.substmodel.SingleClassSubstitutionModel
-
- getTransitionProbabilitiesTranspose(double, int, double[][]) - Method in class pal.substmodel.SingleClassSubstitutionModel
-
- getTransitionProbabilitiesTranspose(double, double[][][]) - Method in interface pal.substmodel.SubstitutionModel
-
Table is organized as [transition_group][to][from]
- getTransitionProbabilitiesTranspose(double, int, double[][]) - Method in interface pal.substmodel.SubstitutionModel
-
Table is organized as [transition_group][to][from]
- getTransitionProbabilitiesTranspose(double, double[][][]) - Method in class pal.substmodel.YangCodonModel.SimpleNeutralSelection
-
- getTransitionProbabilitiesTranspose(double, int, double[][]) - Method in class pal.substmodel.YangCodonModel.SimpleNeutralSelection
-
- getTransitionProbabilitiesTranspose(double, double[][][]) - Method in class pal.substmodel.YangCodonModel.SimplePositiveSelection
-
Table is organized as [tree_group][to][from]
- getTransitionProbabilitiesTranspose(double, int, double[][]) - Method in class pal.substmodel.YangCodonModel.SimplePositiveSelection
-
Table is organized as [to][from]
- 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.CachedRateMatrix
-
get transition probability for the preselected model and
the previously specified distance
- getTransitionProbability(int, int) - Method in class pal.substmodel.MatrixExponential
-
- getTransitionProbability(int, int) - Method in interface pal.substmodel.RateMatrix
-
- getTransitionTime() - Method in class pal.coalescent.ConstExpConst
-
Gets the time of transition from initial constant phase to exponential phase.
- getTransitionTime() - Method in class pal.coalescent.ConstExpGrowth
-
Gets the time of transition from ancestral constant phase to exponential phase.
- getTranspose() - Method in class pal.math.Matrix
-
- getTree() - Method in class pal.coalescent.SerialCoalescentSimulator
-
- getTree() - Method in class pal.eval.ChiSquareValue
-
Returns the (parameterized) tree of this likelihood value.
- getTree() - Method in class pal.eval.LikelihoodValue
-
Returns the (potentially parameterized) tree of this likelihood value.
- getTree() - Method in class pal.eval.SimpleLikelihoodCalculator
-
- getTree() - Method in class pal.gui.TreePainter
-
- getTreeRootedAbove(Node) - Method in class pal.tree.TreeManipulator
-
- getTreeRootedBy(String[]) - Method in class pal.tree.TreeManipulator
-
- getTreeRootedBy(String[], double) - Method in class pal.tree.TreeManipulator
-
- getTrees() - Method in class pal.coalescent.SerialCoalescentGenerator.Results
-
- getTypeID() - Method in class pal.datatype.AminoAcids
-
- getTypeID() - Method in class pal.datatype.Codons
-
- getTypeID() - Method in interface pal.datatype.DataType
-
get numerical code describing the data type
- getTypeID() - Method in class pal.datatype.GapBalanced
-
- getTypeID() - Method in class pal.datatype.IUPACNucleotides
-
- getTypeID() - Method in class pal.datatype.Nucleotides
-
- 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.TwoStates
-
- 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
- getUnchangedScore(int, boolean) - Static method in class pal.algorithmics.StoppingCriteria.Utils
-
A stopping criteria that works by counting how many iterations occur at a given score (either the best score or the
current score) and stopping when score does not change after a set number of generations
- getUniqueName() - Method in class pal.substmodel.BLOSUM62
-
- getUniqueName() - Method in class pal.substmodel.CachedRateMatrix
-
- getUniqueName() - Method in class pal.substmodel.CPREV
-
- getUniqueName() - Method in class pal.substmodel.Dayhoff
-
- getUniqueName() - Method in class pal.substmodel.F81
-
- getUniqueName() - Method in class pal.substmodel.F84
-
- getUniqueName() - Method in class pal.substmodel.GeneralPoissonRateMatrix
-
- getUniqueName() - Method in class pal.substmodel.GeneralREVRateMatrix
-
- getUniqueName() - Method in class pal.substmodel.GTR
-
- getUniqueName() - Method in class pal.substmodel.HKY
-
- getUniqueName() - Method in class pal.substmodel.JTT
-
- getUniqueName() - Method in class pal.substmodel.MTREV24
-
- getUniqueName() - Method in interface pal.substmodel.NeoRateMatrix
-
- getUniqueName() - Method in interface pal.substmodel.RateMatrix
-
- getUniqueName() - Method in class pal.substmodel.TN
-
- getUniqueName() - Method in class pal.substmodel.TwoStateModel
-
- getUniqueName() - Method in class pal.substmodel.VT
-
- getUniqueName() - Method in class pal.substmodel.WAG
-
- getUniqueName() - Method in class pal.substmodel.YangCodonModel
-
- 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.
- getUniquifiedMappings() - Method in class pal.misc.LabelMapping
-
If a mapping occurs more than once will rename instance to "x 1", "x 2"...
- getUnits() - Method in class pal.coalescent.CoalescentIntervals
-
Returns the units these coalescent intervals are
measured 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.mep.MutationRateModel
-
returns units of measurement.
- getUnits() - Method in class pal.misc.TimeOrderCharacterData
-
- getUnits() - Method in interface pal.misc.UnitsProvider
-
- getUnits() - Method in class pal.tree.ParameterizedTree.ParameterizedTreeBase
-
- 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.tree.Tree.TreeBase
-
Return the units that this tree is expressed in.
- getUnitsAttr(Element) - Static method in class pal.xml.ElementParser
-
- getUniverisalAminoAcids() - Static method in class pal.datatype.DataTypeTool
-
A set access point for a data type object describing amino acids (used with relation to the Universal codon table)
- getUnrooted() - Method in class pal.tree.TreeManipulator
-
return unrooted node
- getUnrooted(Tree) - Static method in class pal.tree.TreeManipulator
-
Unroots a tree
- getUnrooted(Tree) - Static method in class pal.tree.TreeTool
-
Unroot a tree (makes the base of the tree a trification).
- getUnrootedBranchCount(Node) - Static method in class pal.tree.NodeUtils
-
returns number of branches centered around an internal node in an unrooted tree
- getUnrootedTree() - Method in class pal.tree.TreeManipulator
-
return unrooted node
- getUnsignificantTopologyIndex(double) - Method in interface pal.statistics.TopologyTestEngine.TestResult
-
- getUntimedBased() - Static method in class pal.mep.DeltaModel.Utils
-
For serial sampled analysis when no time information is available.
- getUntimedBased(double[]) - Static method in class pal.mep.DeltaModel.Utils
-
For serial sampled analysis when no time information is available.
- getUpperBound() - Method in class pal.distance.SequencePairLikelihood
-
- getUpperBound(int) - Method in class pal.eval.ChiSquareValue
-
- getUpperBound(int) - Method in class pal.eval.DemographicValue
-
- getUpperBound(int) - Method in class pal.eval.ModelParameters
-
- getUpperBound(int) - Method in class pal.math.BoundsCheckedFunction
-
- getUpperBound(int) - Method in class pal.math.EvaluationCounter
-
- getUpperBound() - Method in class pal.math.LineFunction
-
- getUpperBound(int) - Method in interface pal.math.MultivariateFunction
-
get upper bound of argument n
- getUpperBound() - Method in class pal.math.OrthogonalLineFunction
-
- getUpperBound() - Method in interface pal.math.UnivariateFunction
-
get upper bound of argument
- getUpperBoundParameter() - Method in class pal.math.LineFunction
-
get parameter that limits the upper bound
- getUpperLimit(int) - Method in class pal.coalescent.ConstantPopulation
-
- getUpperLimit(int) - Method in class pal.coalescent.ConstExpConst
-
- getUpperLimit(int) - Method in class pal.coalescent.ConstExpGrowth
-
- getUpperLimit(int) - Method in class pal.coalescent.ExpandingPopulation
-
- getUpperLimit(int) - Method in class pal.coalescent.ExponentialGrowth
-
- getUpperLimit(int) - Method in class pal.mep.ConstantMutationRate
-
- getUpperLimit(int) - Method in class pal.mep.SteppedMutationRate
-
- getUpperLimit(int) - Method in class pal.mep.WindowedMutationRate
-
- getUpperLimit() - Method in interface pal.misc.IndividualParameterHandler
-
- getUpperLimit(int) - Method in class pal.misc.MultiParameterized
-
- getUpperLimit() - Method in class pal.misc.MutableDouble
-
- getUpperLimit(int) - Method in interface pal.misc.NeoParameterized
-
get upper parameter limit
- getUpperLimit(int) - Method in interface pal.misc.Parameterized
-
get upper parameter limit
- getUpperLimit(int) - Method in class pal.misc.Parameterized.Null
-
- getUpperLimit(int) - Method in class pal.misc.Parameterized.ParameterizedBase
-
- getUpperLimit(int) - Method in class pal.misc.Parameterized.ParameterizedUser
-
- getUpperLimit(int) - Method in class pal.misc.ParameterizedDoubleBundle
-
- getUpperLimit(int) - Method in class pal.misc.ParameterizedNeoWrapper
-
- getUpperLimit(int) - Method in class pal.substmodel.AminoAcidModel
-
- getUpperLimit(int) - Method in class pal.substmodel.CachedRateMatrix
-
- getUpperLimit(int) - Method in class pal.substmodel.ConstantIndependentSingleSplitDistribution
-
- getUpperLimit(int) - Method in class pal.substmodel.F81
-
- getUpperLimit(int) - Method in class pal.substmodel.F84
-
- getUpperLimit(int) - Method in class pal.substmodel.GammaRates
-
- getUpperLimit(int) - Method in class pal.substmodel.GTR
-
- getUpperLimit(int) - Method in class pal.substmodel.HKY
-
- getUpperLimit(int) - Method in class pal.substmodel.InvariableSites
-
- getUpperLimit(int) - Method in class pal.substmodel.MultiRateMatrixHandler
-
- getUpperLimit(int) - Method in class pal.substmodel.RateMatrixHandler
-
- getUpperLimit(int) - Method in class pal.substmodel.SaturatedSingleSplitDistribution
-
- getUpperLimit(int) - Method in class pal.substmodel.SimpleRateMatrixGroup
-
- getUpperLimit(int) - Method in class pal.substmodel.TN
-
- getUpperLimit(int) - Method in class pal.substmodel.TwoStateModel
-
- getUpperLimit(int) - Method in class pal.substmodel.UniformRate
-
- getUpperLimit(int) - Method in class pal.substmodel.VariableIndependentSingleSplitDistribution
-
- getUpperLimit(int) - Method in class pal.substmodel.YangCodonModel
-
- getUpperLimit(int) - Method in class pal.substmodel.YangCodonModel.SimpleNeutralSelection
-
- getUpperLimit(int) - Method in class pal.substmodel.YangCodonModel.SimplePositiveSelection
-
- getUpperLimit(int) - Method in class pal.tree.ClockTree
-
- getUpperLimit(int) - Method in class pal.tree.LogParameterizedTree
-
- getUpperLimit(int) - Method in class pal.tree.MutationRateModelTree
-
- getUpperLimit(int) - Method in class pal.tree.UnconstrainedTree
-
- getUpperLimit(int) - Method in class pal.treesearch.FixedBSRDTGlobalClockModel
-
- getUpperLimit(int) - Method in class pal.treesearch.GlobalClockModel
-
- getUpperLimit(int) - Method in class pal.treesearch.MRDTGlobalClockModel
-
- getUpperLimit(int) - Method in class pal.treesearch.SRDTGlobalClockModel
-
- getValue(int, int) - Method in class pal.math.Matrix
-
- getValue() - Method in class pal.misc.Attribute
-
- getValue() - Method in class pal.misc.MutableDouble
-
Get the current value of this double
- getVersionString() - Static method in class pal.util.Version
-
- getWeightedLocusPosition(int) - Method in interface pal.alignment.AnnotationAlignment
-
Return the weighted position along the locus (handles gaps)
- getWeightedLocusPosition(int) - Method in class pal.alignment.ConcatenatedAnnotatedAlignment
-
Return the weighted position along the gene (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.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 class pal.alignment.StrippedAnnotatedAlignment
-
Return the weighted position along the gene (handles gaps)
- getWidth() - Method in class pal.math.Matrix
-
- getWordModification() - Method in class pal.io.NexusTokenizer
-
Gets the word modification flag currently in use
- getX() - Method in class pal.gui.PositionedNode
-
- getZero() - Static method in class pal.math.OrderEnumerator.Utils
-
- getZeroFactory() - Static method in class pal.math.OrderEnumerator.Utils
-
- GlobalClockModel - Class in pal.treesearch
-
- GlobalClockModel(MolecularClockLikelihoodModel.Instance) - Constructor for class pal.treesearch.GlobalClockModel
-
- 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.
- GroupLeader - Interface in pal.treesearch
-
Title: GroupLeader
- GROWTH_PHASE_DURATION - Static variable in interface pal.util.XMLConstants
-
- GROWTH_RATE - Static variable in interface pal.util.XMLConstants
-
- GTR - Class in pal.substmodel
-
GTR (general time reversible) model of nucleotide evolution
Lanave, C., G.
- GTR(double, double, double, double, double, double[]) - Constructor for class pal.substmodel.GTR
-
constructor 1
- GTR(double[], double[]) - Constructor for class pal.substmodel.GTR
-
constructor 2
- GTR - Static variable in interface pal.substmodel.NucleotideModelID
-
- GTR - Static variable in interface pal.util.XMLConstants
-
- guessDataType() - Method in class pal.alignment.AbstractAlignment
-
Guess data type
- P_DEFAULT_VALUE - Static variable in class pal.substmodel.YangCodonModel.SimpleNeutralSelection
-
- P_LOWER_LIMIT - Static variable in class pal.substmodel.YangCodonModel.SimpleNeutralSelection
-
- P_UPPER_LIMIT - Static variable in class pal.substmodel.YangCodonModel.SimpleNeutralSelection
-
- P_VALUE - Static variable in class pal.gui.LinkageDisequilibriumComponent
-
- paint(Graphics) - Method in class pal.gui.LinkageDisequilibriumComponent
-
- paint(Graphics, int, int) - Method in interface pal.gui.Painter
-
- paint(Graphics, int, int, LayoutTracker) - Method in interface pal.gui.Painter
-
- paint(Graphics) - Method in class pal.gui.TreeComponent
-
- paint(PositionedNode, CircularGraphics) - Method in class pal.gui.TreePainterCircular
-
- paint(Graphics, int, int) - Method in class pal.gui.TreePainterCircular
-
- paint(Graphics, int, int, LayoutTracker) - 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(PositionedNode, Graphics, int, int, LayoutTracker, boolean) - Method in class pal.gui.TreePainterNormal
-
- paint(Graphics, int, int) - Method in class pal.gui.TreePainterNormal
-
- paint(Graphics, int, int, LayoutTracker) - Method in class pal.gui.TreePainterNormal
-
- paintComponent(Graphics) - Method in class pal.gui.LinkageDisequilibriumComponent
-
- Painter - Interface in pal.gui
-
An interface for objects which are used for painting themselves in a
general Graphics object
- PairwiseDistance - Class in pal.distance
-
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.algorithmics - package pal.algorithmics
-
- 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.
- pal.supgma - package pal.supgma
-
- 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.treesearch - package pal.treesearch
-
- 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 in pal.misc
-
A utility class for accomodating Pal listeners
- PalEventMulticaster() - Constructor for class pal.misc.PalEventMulticaster
-
- PalObjectEvent - Class in pal.misc
-
An event used by PalObjectListeners
- PalObjectEvent(Object) - Constructor for class pal.misc.PalObjectEvent
-
- PalObjectEvent() - Constructor for class pal.misc.PalObjectEvent
-
- PalObjectListener - Interface in pal.misc
-
Defines objects that monitor certain PalObjects for changes
- PalObjectListener.EventGenerator - Class in pal.misc
-
A base class for classes that fire PalObject events
- PalObjectListener.EventGenerator() - Constructor for class pal.misc.PalObjectListener.EventGenerator
-
- parameter - Variable in class pal.tree.ClockTree
-
- PARAMETER - Static variable in interface pal.util.XMLConstants
-
- parameterChanged(ParameterEvent) - Method in interface pal.misc.ExternalParameterListener
-
- parameterChanged(Parameterized, int, double) - Method in interface pal.misc.IndividualParameterHandler.Listener
-
- parameterChanged(ParameterEvent) - Method in class pal.substmodel.AbstractRateMatrix
-
For the external parameter interface.
- ParameterEvent - Class in pal.misc
-
An event used by ExternalParameterListeners
- ParameterEvent(Object) - Constructor for class pal.misc.ParameterEvent
-
- parameterization - Variable in class pal.coalescent.ConstExpGrowth
-
parameterization bit string:
first bit: 0 = ALPHA, 1 = N1
second bit: 0 = GROWTH RATE, 1 = LX
- Parameterized - Interface in pal.misc
-
interface for class with (optimizable) parameters
- Parameterized.Null - Class in pal.misc
-
NullParameterized Object
Can be used by subclasses to implement parameterized without actually having paramters
- Parameterized.Null() - Constructor for class pal.misc.Parameterized.Null
-
- Parameterized.ParameterizedBase - Class in pal.misc
-
A Utility class for using as the superclass to subclasses which are based on double arrays
- Parameterized.ParameterizedBase(double[], double[], double[], double[]) - Constructor for class pal.misc.Parameterized.ParameterizedBase
-
Builds a parameterized objects around a set of double arrays
- Parameterized.ParameterizedBase(double[], double[], double[], double[], double[]) - Constructor for class pal.misc.Parameterized.ParameterizedBase
-
Builds a parameterized objects around a set of double arrays
- Parameterized.ParameterizedBase() - Constructor for class pal.misc.Parameterized.ParameterizedBase
-
Builds a parameterized objects around a set of double arrays.
- Parameterized.ParameterizedUser - Class in pal.misc
-
A Utility class for using as the superclass to subclasses which work by adding functionality to
a general Parameterized object (the base Parameterized object)
- Parameterized.ParameterizedUser(Parameterized) - Constructor for class pal.misc.Parameterized.ParameterizedUser
-
- Parameterized.ParameterizedUser() - Constructor for class pal.misc.Parameterized.ParameterizedUser
-
Sub class should call setParameterizedBase() at some point if using this constructor...
- Parameterized.Utils - Class in pal.misc
-
- Parameterized.Utils() - Constructor for class pal.misc.Parameterized.Utils
-
- ParameterizedDoubleBundle - Class in pal.misc
-
Title: ParameterizedDoubleBundle
- ParameterizedDoubleBundle(MutableDouble[]) - Constructor for class pal.misc.ParameterizedDoubleBundle
-
- ParameterizedNeoWrapper - Class in pal.misc
-
Title: ParameterizedNeoWrapper
- ParameterizedNeoWrapper(Parameterized) - Constructor for class pal.misc.ParameterizedNeoWrapper
-
- ParameterizedTree - Interface in pal.tree
-
abstract base class for a tree with an Parameterized interface
- ParameterizedTree.Factory - Interface in pal.tree
-
Factory interface
- ParameterizedTree.ParameterizedTreeBase - Class in pal.tree
-
For parameterisations that work by adjusting a base tree (that is, they aren't really
tree's themselves...)
- ParameterizedTree.ParameterizedTreeBase(ParameterizedTree.ParameterizedTreeBase) - Constructor for class pal.tree.ParameterizedTree.ParameterizedTreeBase
-
Cloning constructor
- ParameterizedTree.ParameterizedTreeBase() - Constructor for class pal.tree.ParameterizedTree.ParameterizedTreeBase
-
- ParameterizedTree.ParameterizedTreeBase(Tree) - Constructor for class pal.tree.ParameterizedTree.ParameterizedTreeBase
-
- parameters2Heights() - Method in class pal.coalescent.DemographicClockTree
-
- parameters2Heights() - Method in class pal.tree.ClockTree
-
- parameters2Heights() - Method in class pal.tree.MutationRateModelTree
-
- parametersChanged(PalObjectEvent) - Method in class pal.eval.FastLikelihoodCalculator
-
- parametersChanged(PalObjectEvent) - Method in class pal.eval.GeneralLikelihoodCalculator
-
- 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
-
- parameterSet(Parameterized, double, int) - Method in interface pal.misc.MultiParameterized.ParameterAccessWatcher
-
- ParentableConstrainedNode - Interface in pal.treesearch
-
- ParetoDistribution - Class in pal.statistics
-
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
-
- parseRateDistribution(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]
- PatternInfo - Class in pal.eval
-
Title: PatternInfo
- PatternInfo(int, boolean) - Constructor for class pal.eval.PatternInfo
-
- PatternInfo(int[], int[], int[], int) - Constructor for class pal.eval.PatternInfo
-
- PatternInfo(int[], int) - Constructor for class pal.eval.PatternInfo
-
- PatternInfo(int[], int[], int) - Constructor for class pal.eval.PatternInfo
-
- pdf(double, double) - Static method in class pal.statistics.ChiSquareDistribution
-
probability density function of the chi-square distribution
- pdf(double, double) - Static method in class pal.statistics.ExponentialDistribution
-
probability density function of the exponential distribution
(mean = 1/lambda)
- 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 in pal.statistics
-
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
-
- performTest(TopologyTestEngine.TopologyPool, int, AlgorithmCallback) - Method in class pal.statistics.TopologyTestEngine
-
- PERIOD - Static variable in class pal.io.NexusTokenizer
-
- PIVOT_COMPONENT_TYPE - Static variable in interface pal.treesearch.Constants
-
- PivotNode - Class in pal.treesearch
-
- PivotNode(Node, FreeBranch, GeneralConstructionTool, GeneralConstraintGroupManager, GeneralConstraintGroupManager.Store) - Constructor for class pal.treesearch.PivotNode
-
The subtree constructor with a connection to the rest of the tree
- PivotNode(Node, GeneralConstructionTool, GeneralConstraintGroupManager, GeneralConstraintGroupManager.Store) - Constructor for class pal.treesearch.PivotNode
-
The root constructor, only used when the whole tree is constrained
- POLAK_RIBIERE_UPDATE - Static variable in class pal.math.ConjugateGradientSearch
-
- poolIntervals(boolean[]) - Method in class pal.coalescent.CoalescentIntervals
-
Starting at time zero (i.e.
- poolSmallIntervals(double) - Method in class pal.coalescent.CoalescentIntervals
-
Starting at time zero (i.e.
- POPULATION_SIZE - Static variable in interface pal.util.XMLConstants
-
- PositionedNode - Class in pal.gui
-
A tree node that has a scalar position for the purposes of drawing the tree.
- PositionedNode(Node, Node) - Constructor for class pal.gui.PositionedNode
-
Builds a tree based on node, but highlights highlightNode
- PositionedNode(Node) - Constructor for class pal.gui.PositionedNode
-
- positionType - Variable in class pal.alignment.IndelAnnotatedAlignment
-
used to designate position Type
- positionType - Variable in class pal.alignment.MultiLocusAnnotatedAlignment
-
used to designate position Type
- positionType - Variable in class pal.alignment.SimpleAnnotatedAlignment
-
used to designate position Type
- PositiveSelectionRateMatrixGroup - Class in pal.substmodel
-
- PositiveSelectionRateMatrixGroup(MutableDouble, MutableDouble, double[], CodonTable) - Constructor for class pal.substmodel.PositiveSelectionRateMatrixGroup
-
- 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
- postSetupNotify(ConstraintModel.GroupManager) - Method in interface pal.treesearch.GroupLeader
-
Tell the group leader that the groupConstraints have been set up (parameter wise),
and that internal node heights for example may be calculated
- postSetupNotify(ConstraintModel.GroupManager) - Method in class pal.treesearch.PivotNode
-
- preorderSuccessor(Node) - Static method in class pal.tree.NodeUtils
-
determine preorder successor of this node
- PRIMARY_SUGGESTED_GAP_CHARACTER - Static variable in interface pal.datatype.DataType
-
A suggested Gap character
- 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.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
- 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)
- 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.CodonModel
-
- printFrequencies(PrintWriter) - Method in class pal.substmodel.NucleotideModel
-
- printInterleaved(Alignment, PrintWriter) - Static method in class pal.alignment.AlignmentUtils
-
print alignment (in PHYLIP 3.4 INTERLEAVED format)
- printNH(PrintWriter, Node, boolean, boolean) - Static method in class pal.tree.NodeUtils
-
prints node in New Hamshire format.
- printNH(PrintWriter, Node, boolean, boolean, int, boolean) - Static method in class pal.tree.NodeUtils
-
- 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.CodonModel
-
- printRatios(PrintWriter) - Method in class pal.substmodel.NucleotideModel
-
- 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
- ProbabilityIterator - Interface in pal.algorithmics
-
A function for obtaining probabilities (that may change over time)
- ProbabilityIterator.Factory - Interface in pal.algorithmics
-
- ProbabilityIterator.Utils - Class in pal.algorithmics
-
- ProbabilityIterator.Utils() - Constructor for class pal.algorithmics.ProbabilityIterator.Utils
-
- process(DistanceMatrixAccess, AlgorithmCallback, LMSSolver) - Method in class pal.supgma.SUPGMABase
-
- process(AlgorithmCallback, LMSSolver) - Method in class pal.supgma.SUPGMABase
-
- productPartials(Node) - Method in class pal.eval.SimpleLikelihoodCalculator
-
multiply partials into the neighbour of branch
- PUNCTUATION_TOKEN - Static variable in class pal.io.NexusTokenizer
-
Flag indicating last token read was a punctuation symbol
- pval - Variable in class pal.statistics.KishinoHasegawaTest
-
corresponding p-value (two-sided test on normal distribution)
- pval - Variable in class pal.statistics.ShimodairaHasegawaTest
-
corresponding p-value
- PYRIMIDINE_PURINE_RATIO - Static variable in interface pal.util.XMLConstants
-
- S_QUOTE - Static variable in class pal.io.NexusTokenizer
-
- same(double, double) - Static method in class pal.math.MachineAccuracy
-
- sameTaxa(Node, Node) - Static method in class pal.tree.RootedTreeUtils
-
- SAMPLE - Static variable in interface pal.misc.Units
-
- SampleInformation - Interface in pal.misc
-
Title: SampleInformation
- SampleInformation.Factory - Interface in pal.misc
-
- SaturatedSingleSplitDistribution - Class in pal.substmodel
-
Title: SaturatedSingleSplitDistribution
- SaturatedSingleSplitDistribution(int) - Constructor for class pal.substmodel.SaturatedSingleSplitDistribution
-
- SaturatedSingleSplitDistribution(int, double[]) - Constructor for class pal.substmodel.SaturatedSingleSplitDistribution
-
- scale(double) - Method in class pal.mep.ConstantMutationRate
-
Linearly scales this mutation rate model.
- scale(double) - Method in class pal.mep.MutationRateModel
-
Linearly scales this mutation rate model.
- scale(TimeOrderCharacterData) - Method in class pal.mep.MutationRateModel
-
- scale(double) - Method in class pal.mep.SteppedMutationRate
-
Linearly scales this mutation rate model.
- scale(double) - Method in class pal.mep.WindowedMutationRate
-
Linearly scales this mutation rate model.
- scale(double, int) - Method in class pal.misc.TimeOrderCharacterData
-
- scale(double) - Method in class pal.substmodel.AbstractRateMatrix
-
- scale(double) - Method in interface pal.substmodel.RateMatrix
-
- scale(Tree, double, int) - Static method in class pal.tree.TreeUtils
-
Deprecated.
use getScaled()
- scale(Tree, MutationRateModel) - Static method in class pal.tree.TreeUtils
-
Deprecated.
use getScaled()
- scale(Tree, MutationRateModel, int) - Static method in class pal.tree.TreeUtils
-
Deprecated.
use getScaled()
- scbd - Variable in class pal.math.ConjugateDirectionSearch
-
scbd is a scaling parameter.
- screenCentreX - Variable in class pal.gui.CircularGraphics
-
- screenCentreY - Variable in class pal.gui.CircularGraphics
-
- screenRadius - Variable in class pal.gui.CircularGraphics
-
- SearchEngine - Class in pal.algorithmics
-
A simplistic class (most of the work is done elsewhere) that handles basic search algorithms
- SearchEngine(ProbabilityIterator.Factory) - Constructor for class pal.algorithmics.SearchEngine
-
- SearcherUtils - Class in pal.treesearch
-
- SearcherUtils() - Constructor for class pal.treesearch.SearcherUtils
-
- SearchMonitor - Interface in pal.treesearch
-
Title: SearchMonitor
- SearchMonitor.Utils - Class in pal.treesearch
-
- SearchMonitor.Utils() - Constructor for class pal.treesearch.SearchMonitor.Utils
-
- searchStepComplete(double) - Method in interface pal.treesearch.SearchMonitor
-
When this method is called, it should be safe to access the tree search methods (for example, to build a pal tree)
- 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
- seek(int) - Method in class pal.io.NexusTokenizer
-
Seeks through the stream to find the next token of the specified type.
- seek(String) - Method in class pal.io.NexusTokenizer
-
Seeks through the stream to find the token argument.
- selectArgument(int) - Method in class pal.math.OrthogonalLineFunction
-
use only the specified argument in the
constructed univariate function
and keep all others constant
- SEMI_COLON - Static variable in class pal.io.NexusTokenizer
-
- SEQUENCE - Static variable in interface pal.util.XMLConstants
-
- SequencePairLikelihood - Class in pal.distance
-
computation of the (negative) log-likelihood for a pair of sequences
- SequencePairLikelihood(SitePattern, SubstitutionModel) - Constructor for class pal.distance.SequencePairLikelihood
-
initialisation
- SequenceSimulator - Class in pal.substmodel
-
- SequenceSimulator(SubstitutionModel, int, boolean) - Constructor for class pal.substmodel.SequenceSimulator
-
A constructor (with no provided random number generator - a fresh one is created)
- SequenceSimulator(SubstitutionModel, int, MersenneTwisterFast, boolean) - Constructor for class pal.substmodel.SequenceSimulator
-
A constructor (with no provided random number generator - a fresh one is created)
- SerialCoalescentGenerator - Class in pal.coalescent
-
- SerialCoalescentGenerator(TimeOrderCharacterData, DemographicModel, int) - Constructor for class pal.coalescent.SerialCoalescentGenerator
-
Results will not contain alignments
- SerialCoalescentGenerator(TimeOrderCharacterData, DemographicModel, int, TreeOperation) - Constructor for class pal.coalescent.SerialCoalescentGenerator
-
Results will not contain alignments
- SerialCoalescentGenerator(TimeOrderCharacterData, DemographicModel, TreeOperation, SimulatedAlignment.Factory) - Constructor for class pal.coalescent.SerialCoalescentGenerator
-
- SerialCoalescentGenerator(TimeOrderCharacterData, DemographicModel, int, TreeOperation, SimulatedAlignment.Factory) - Constructor for class pal.coalescent.SerialCoalescentGenerator
-
- SerialCoalescentGenerator.Results - Class in pal.coalescent
-
A simple wrapper class for containing the results which may either be
a number of trees, or a number of trees and alignments (in parallel arrays)
- SerialCoalescentGenerator.Results(Tree[]) - Constructor for class pal.coalescent.SerialCoalescentGenerator.Results
-
- SerialCoalescentGenerator.Results(Tree[], Alignment[]) - Constructor for class pal.coalescent.SerialCoalescentGenerator.Results
-
- SerialCoalescentSimulator - Class in pal.coalescent
-
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)
- setAllParameters(double[], double[]) - Method in class pal.substmodel.MultiRateMatrixHandler
-
- setAncestral(double) - Method in class pal.coalescent.ConstExpGrowth
-
Sets the ancestral parameter.
- setAnnotation(Object) - Method in interface pal.tree.RootedTreeInterface.RBranch
-
- setAnnotation(Object) - Method in interface pal.tree.RootedTreeInterface.RNode
-
- setAnnotation(Object) - Method in interface pal.tree.TreeManipulator.BranchAccess
-
Set the annotation for this branch (will be used when instructing a TreeInterface
- setAnnotation(Object) - Method in interface pal.tree.UnrootedTreeInterface.GeneralBranch
-
- setAnnotation(Object) - Method in interface pal.tree.UnrootedTreeInterface.UNode
-
- setAnnotation(Object) - Method in interface pal.treesearch.BranchAccess
-
Set the annotation for this branch (will be used when instructing TreeInterfaces
- setAnnotation(Object) - Method in class pal.treesearch.FreeBranch
-
- setAnnotation(Object) - Method in interface pal.treesearch.NodeAccess
-
Set the annotation for this branch (will be used when instructing TreeInterfaces
- setArgument(double) - Method in class pal.math.OrthogonalLineFunction
-
set (change) value of a single argument
(the one currently active)
- setAttribute(String, Object) - Method in interface pal.tree.AttributeNode
-
Sets a named attribute to the given value.
- setAttribute(Node, String, Object) - Method in class pal.tree.ParameterizedTree.ParameterizedTreeBase
-
- setAttribute(String, Object) - Method in class pal.tree.SimpleNode
-
Sets a named attribute to the given value.
- 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(Node, String, Object) - Method in class pal.tree.Tree.TreeBase
-
Sets an named attribute for a given node.
- setAttributeName(String) - Method in class pal.gui.TreeComponent
-
- setAttributeName(String) - Method in class pal.gui.TreePainter
-
- setBasedOnCachedData(boolean) - Method in class pal.eval.ConditionalProbabilityStore
-
- setBaseTree(Tree) - Method in class pal.tree.ParameterizedTree.ParameterizedTreeBase
-
- setBranchLength(double) - Method in interface pal.tree.Node
-
Set the length of the branch attaching this node to its parent.
- setBranchLength(double) - Method in class pal.tree.SimpleNode
-
Set the length of the branch attaching this node to its parent.
- setBranchLength(double) - Method in class pal.treesearch.FreeBranch
-
- setBranchLengthSE(double) - Method in interface pal.tree.Node
-
Set the length SE 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.
- setChild(int, Node) - Method in interface pal.tree.Node
-
set child node
- setChild(int, Node) - Method in class pal.tree.SimpleNode
-
set child node
- setChromosome(int) - Method in class pal.alignment.IndelAnnotatedAlignment
-
Sets chromosome
- setChromosome(int, int) - Method in class pal.alignment.MultiLocusAnnotatedAlignment
-
Sets chromosome
- setChromosome(int) - Method in class pal.alignment.SimpleAnnotatedAlignment
-
Sets 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
- setChromosomePosition(float) - Method in class pal.alignment.SimpleAnnotatedAlignment
-
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.TreeComponent
-
- setColouriser(NameColouriser) - Method in class pal.gui.TreePainter
-
- setConnectingBranches(FreeBranch[], int) - Method in class pal.treesearch.FreeInternalNode
-
- setConnectingBranches(FreeBranch[], int) - Method in class pal.treesearch.FreeLeafNode
-
- setConnectingBranches(FreeBranch[], int) - Method in interface pal.treesearch.FreeNode
-
- setConnectingBranches(FreeBranch[], int) - Method in class pal.treesearch.PivotNode
-
- setConvertNewLine(boolean) - Method in class pal.io.NexusTokenizer
-
Sets the convertNL
flag.
- setDataType(DataType) - Method in class pal.alignment.AbstractAlignment
-
Sets the datatype of this alignment
- setDataType(DataType) - Method in class pal.substmodel.AbstractRateMatrix
-
- 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(int, int, double) - Method in class pal.distance.DistanceMatrix
-
Sets both upper and lower triangles.
- 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.CachedRateMatrix
-
set distance and corresponding computation transition 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 interface pal.substmodel.RateMatrix
-
Sets the distance (such as time/branch length) used when calculating
the probabilities.
- setDistances(double[][]) - Method in class pal.distance.DistanceMatrix
-
- setDistanceTranspose(double) - Method in class pal.substmodel.AbstractRateMatrix
-
Sets the distance (such as time/branch length) used when calculating
the probabilities.
- setDistanceTranspose(double) - Method in class pal.substmodel.CachedRateMatrix
-
- setDistanceTranspose(double) - Method in class pal.substmodel.MatrixExponential
-
compute transition probabilities for a expected distance
using the prespecified rate matrix
- setDistanceTranspose(double) - Method in interface pal.substmodel.RateMatrix
-
Sets the distance (such as time/branch length) used when calculating
the probabilities.
- setFont(Font) - Method in class pal.gui.CircularGraphics
-
- setFrequencies(double[]) - Method in class pal.substmodel.AbstractRateMatrix
-
- setGrowthParam(double) - Method in class pal.coalescent.ConstExpGrowth
-
Sets the growth parameter.
- setGrowthPhaseDuration(double) - Method in class pal.coalescent.ConstExpGrowth
-
Sets the length of the growth phase.
- 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 interface pal.misc.IdGroup
-
Sets the ith identifier.
- setIdentifier(int, Identifier) - Method in class pal.misc.SimpleIdGroup
-
Sets the ith identifier.
- setIdentifier(int, Identifier) - Method in class pal.misc.TimeOrderCharacterData
-
- setIdentifier(Identifier) - Method in interface pal.tree.Node
-
Set identifier for this node.
- setIdentifier(int, Identifier) - Method in class pal.tree.ParameterizedTree.ParameterizedTreeBase
-
- setIdentifier(Identifier) - Method in class pal.tree.SimpleNode
-
Set identifier for this node.
- setIdentifier(int, Identifier) - Method in class pal.tree.SimpleTree
-
- setIdentifier(int, Identifier) - Method in class pal.tree.Tree.TreeBase
-
- setIdGroup(IdGroup) - Method in class pal.distance.DistanceMatrix
-
- setIgnoreComments(boolean) - Method in class pal.io.NexusTokenizer
-
Sets the ignoreComments
flag.
- setIgnoreNonMinimalUnivariateMinimisations(boolean) - Method in class pal.math.OrthogonalSearch
-
Should we ignore new minisations that are not as minimal as the current one?
- setInterval(int, double) - Method in class pal.coalescent.CoalescentIntervals
-
Sets interval.
- setInvertCircular(boolean) - Method in class pal.gui.TreeComponent
-
- setKappa(double) - Method in class pal.substmodel.YangCodonModel
-
- setKappaSE(double) - Method in class pal.substmodel.YangCodonModel
-
- setLabel(String) - Method in interface pal.tree.RootedTreeInterface.RNode
-
- setLabel(String) - Method in interface pal.tree.UnrootedTreeInterface.UNode
-
- setLabelFont(Font) - Method in class pal.gui.TreePainter
-
Set the font used to display labels
- setLabelFontSize(int) - Method in class pal.gui.TreePainter
-
Set the font used to display labels
- setLabelMapping(LabelMapping) - Method in class pal.gui.TreeComponent
-
- setLabelMapping(LabelMapping) - Method in class pal.gui.TreePainter
-
- setLength(double) - Method in interface pal.tree.RootedTreeInterface.RBranch
-
- setLength(double) - Method in interface pal.tree.UnrootedTreeInterface.GeneralBranch
-
- setLnL(double) - Method in class pal.tree.MutationRateModelTree
-
- 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
- setLocusName(String) - Method in class pal.alignment.SimpleAnnotatedAlignment
-
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
-
- setMaxHeight(double) - Method in class pal.gui.TreeComponent
-
- setMaxHeight(double) - Method in class pal.gui.TreePainter
-
sets the maximum height of plot.
- setMaxRelativeHeight(double) - Method in class pal.tree.MutationRateModelTree
-
Sets the maximum distance between ancestor and latest descendant.
- setMode(int) - Method in class pal.gui.TreeComponent
-
Sets the mode of display for this component.
- 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.Identifier
-
- setName(String) - Method in interface pal.misc.Nameable
-
set the name of this object.
- 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.
- setNewLineChar(char) - Method in class pal.io.NexusTokenizer
-
Sets the character to be convert newline characters into
- setNewNumberOfPatterns(int) - Method in interface pal.eval.ConditionalProbabilityStore.ExtraProcessor
-
- setNodeHeight(double) - Method in interface pal.tree.Node
-
Set the height of this node relative to the most recent node.
- setNodeHeight(double, boolean) - Method in interface pal.tree.Node
-
Set the height of this node relative to the most recent node.
- setNodeHeight(double) - Method in class pal.tree.SimpleNode
-
Set the height of this node relative to the most recent node.
- setNodeHeight(double, boolean) - Method in class pal.tree.SimpleNode
-
Set the height of this node relative to the most recent node.
- setNodeHeight(double) - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
- setNodes(FreeNode, FreeNode) - Method in class pal.treesearch.FreeBranch
-
Does nothing to fix up tree structure
- setNumber(int) - Method in interface pal.tree.Node
-
set the index of this node
- setNumber(int) - Method in class pal.tree.SimpleNode
-
- setNumberOfPatterns(int) - Method in class pal.eval.PatternInfo
-
- setNumLineages(int, int) - Method in class pal.coalescent.CoalescentIntervals
-
set the number lineages for this particular interval.
- setOmega(double) - Method in class pal.substmodel.YangCodonModel
-
- setOmegaSE(double) - Method in class pal.substmodel.YangCodonModel
-
- 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.coalescent.ConstantPopulation
-
- setParameter(double, int) - Method in class pal.coalescent.ConstExpConst
-
- setParameter(double, int) - Method in class pal.coalescent.ConstExpGrowth
-
- setParameter(double, int) - Method in class pal.coalescent.ExpandingPopulation
-
- setParameter(double, int) - Method in class pal.coalescent.ExponentialGrowth
-
- setParameter(double, int) - Method in class pal.mep.ConstantMutationRate
-
- setParameter(double, int) - Method in class pal.mep.SteppedMutationRate
-
- setParameter(double, int) - Method in class pal.mep.WindowedMutationRate
-
- setParameter(double) - Method in interface pal.misc.IndividualParameterHandler
-
- setParameter(double, int) - Method in class pal.misc.MultiParameterized
-
- setParameter(double, int) - Method in class pal.misc.Parameterized.Null
-
- setParameter(double, int) - Method in class pal.misc.Parameterized.ParameterizedBase
-
- setParameter(double, int) - Method in class pal.misc.Parameterized.ParameterizedUser
-
- setParameter(double, int) - Method in interface pal.misc.Parameterized
-
set model parameter
- setParameter(double, int) - Method in class pal.substmodel.AbstractRateMatrix
-
- setParameter(double, int) - Method in class pal.substmodel.CachedRateMatrix
-
- setParameter(double, int) - Method in class pal.substmodel.GammaRates
-
- setParameter(double, int) - Method in class pal.substmodel.InvariableSites
-
- setParameter(double, int) - Method in class pal.substmodel.RateMatrixHandler
-
- setParameter(double, int) - Method in class pal.substmodel.UniformRate
-
- setParameter(double, int) - Method in class pal.substmodel.YangCodonModel.SimpleNeutralSelection
-
- setParameter(double, int) - Method in class pal.substmodel.YangCodonModel.SimplePositiveSelection
-
- setParameter(double, int) - Method in class pal.tree.ClockTree
-
- setParameter(double, int) - Method in class pal.tree.LogParameterizedTree
-
- setParameter(double, int) - Method in class pal.tree.MutationRateModelTree
-
- setParameter(double, int) - Method in class pal.tree.UnconstrainedTree
-
- setParameterization(int) - Method in class pal.coalescent.ConstExpGrowth
-
Sets the parameterization.
- setParameterizedBase(Parameterized) - Method in class pal.misc.Parameterized.ParameterizedUser
-
Set's the base parameterized object...
- setParameters(double[], int) - Method in interface pal.misc.NeoParameterized
-
set model parameter
- setParameters(double[], int) - Method in class pal.misc.ParameterizedDoubleBundle
-
- setParameters(double[], int) - Method in class pal.misc.ParameterizedNeoWrapper
-
- setParameters(double[]) - Method in class pal.substmodel.AbstractRateMatrix
-
- setParameters(double[], int) - Method in class pal.substmodel.ConstantIndependentSingleSplitDistribution
-
- setParameters(double[], int) - Method in class pal.substmodel.MultiRateMatrixHandler
-
- setParameters(double[], int) - Method in class pal.substmodel.SaturatedSingleSplitDistribution
-
- setParameters(double[], double[]) - Method in class pal.substmodel.SimpleRateMatrixGroup
-
- setParameters(double[], int) - Method in class pal.substmodel.VariableIndependentSingleSplitDistribution
-
- setParameters(double[], int) - Method in class pal.treesearch.FixedBSRDTGlobalClockModel
-
- setParameters(double[], int) - Method in class pal.treesearch.GlobalClockModel
-
- setParameters(double[], int) - Method in class pal.treesearch.MRDTGlobalClockModel
-
- setParameters(double[], int) - Method in class pal.treesearch.SRDTGlobalClockModel
-
- setParameterSE(double, int) - Method in class pal.coalescent.ConstantPopulation
-
- setParameterSE(double, int) - Method in class pal.coalescent.ConstExpConst
-
- setParameterSE(double, int) - Method in class pal.coalescent.ConstExpGrowth
-
- setParameterSE(double, int) - Method in class pal.coalescent.ExpandingPopulation
-
- setParameterSE(double, int) - Method in class pal.coalescent.ExponentialGrowth
-
- setParameterSE(double, int) - Method in class pal.mep.ConstantMutationRate
-
- setParameterSE(double, int) - Method in class pal.mep.SteppedMutationRate
-
- setParameterSE(double, int) - Method in class pal.mep.WindowedMutationRate
-
- setParameterSE(double) - Method in interface pal.misc.IndividualParameterHandler
-
- setParameterSE(double, int) - Method in class pal.misc.MultiParameterized
-
- setParameterSE(double, int) - Method in class pal.misc.Parameterized.Null
-
- setParameterSE(double, int) - Method in class pal.misc.Parameterized.ParameterizedBase
-
- setParameterSE(double, int) - Method in class pal.misc.Parameterized.ParameterizedUser
-
- 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.CachedRateMatrix
-
- setParameterSE(double, int) - Method in class pal.substmodel.F81
-
- setParameterSE(double, int) - Method in class pal.substmodel.F84
-
- setParameterSE(double, int) - Method in class pal.substmodel.GammaRates
-
- setParameterSE(double, int) - Method in class pal.substmodel.GTR
-
- setParameterSE(double, int) - Method in class pal.substmodel.HKY
-
- setParameterSE(double, int) - Method in class pal.substmodel.InvariableSites
-
- setParameterSE(double, int) - Method in class pal.substmodel.RateMatrixHandler
-
- setParameterSE(double, int) - Method in class pal.substmodel.TN
-
- setParameterSE(double, int) - Method in class pal.substmodel.TwoStateModel
-
- setParameterSE(double, int) - Method in class pal.substmodel.UniformRate
-
- setParameterSE(double, int) - Method in class pal.substmodel.YangCodonModel
-
- setParameterSE(double, int) - Method in class pal.substmodel.YangCodonModel.SimpleNeutralSelection
-
- setParameterSE(double, int) - Method in class pal.substmodel.YangCodonModel.SimplePositiveSelection
-
- setParameterSE(double, int) - Method in class pal.tree.ClockTree
-
- setParameterSE(double, int) - Method in class pal.tree.LogParameterizedTree
-
- setParameterSE(double, int) - Method in class pal.tree.MutationRateModelTree
-
- setParameterSE(double, int) - Method in class pal.tree.UnconstrainedTree
-
- setParametersNoScale(double[]) - Method in class pal.substmodel.AbstractRateMatrix
-
- setParametersNoScale(double[]) - Method in interface pal.substmodel.RateMatrix
-
- setParent(ConditionalProbabilityStore) - Method in interface pal.eval.ConditionalProbabilityStore.ExtraProcessor
-
- setParent(Node) - Method in interface pal.tree.Node
-
Set the parent node of this node.
- setParent(Node) - Method in class pal.tree.SimpleNode
-
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.
- setRateHandler(RateHandler) - Method in class pal.supgma.SUPGMABase
-
Makes no difference if no time info available
- setRateMatrix(RateMatrix) - Method in class pal.eval.FastLikelihoodCalculator
-
- setRateMatrix(RateMatrix) - Method in class pal.eval.SimpleLikelihoodCalculator
-
define model
(a site pattern must have been set before calling this method)
- setReadWhiteSpace(boolean) - Method in class pal.io.NexusTokenizer
-
Sets the readWS
flag.
- setRoot(Node) - Method in class pal.tree.ParameterizedTree.ParameterizedTreeBase
-
- 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.
- setRoot(Node) - Method in class pal.tree.Tree.TreeBase
-
Called by subclasses that can't give root at time of construction (of this class)
- 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.MutableDouble
-
- setSeed(long) - Method in class pal.math.MersenneTwisterFast
-
Initalize the pseudo random number generator.
- setSequence(byte[]) - Method in interface pal.tree.Node
-
Sets the sequence using an array of bytes.
- setSequence(byte[]) - Method in class pal.tree.SimpleNode
-
Sets the sequence at this node, in the form of an array of bytes.
- setSequences(int, int) - Method in class pal.distance.SequencePairLikelihood
-
specification of two sequences in the given alignment
- 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)
- setSetupLengthsAndHeights(boolean) - Method in class pal.tree.Tree.TreeBase
-
Set whether or not this class should call methods to adjust
either heights or lengths automatically
- setShowingNodeHeights(boolean) - Method in class pal.gui.TreePainter
-
- setShowSchematic(boolean) - Method in class pal.gui.LinkageDisequilibriumComponent
-
This sets whether a schematic is displayed.
- setSource(double[], double[], double[], double[]) - Method in class pal.misc.Parameterized.ParameterizedBase
-
Set's the base arrays...
- setSource(double[], double[], double[], double[], double[]) - Method in class pal.misc.Parameterized.ParameterizedBase
-
Set's the base arrays...
- setSubgroup(int[]) - Method in class pal.misc.TimeOrderCharacterData
-
A means for define a subgroup.
- setSubgroup(String[]) - Method in class pal.misc.TimeOrderCharacterData
-
A means for define a subgroup.
- setSubgroups(int[][]) - Method in class pal.misc.TimeOrderCharacterData
-
A means for define a subgroup.
- setSubgroups(String[][]) - Method in class pal.misc.TimeOrderCharacterData
-
A means for define subgroups.
- setSubstitutionClassProbabilities(double[]) - Method in class pal.substmodel.MultiRateMatrixHandler
-
- setSubstitutionClassProbabilities(double[], int) - Method in class pal.substmodel.MultiRateMatrixHandler
-
- setSubstitutionRate(double) - Method in class pal.treesearch.SRDTGlobalClockModel
-
- setThetaHandler(ThetaHandler) - Method in class pal.supgma.SUPGMABase
-
- 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
-
- setTimeX(double) - Method in class pal.coalescent.ConstExpConst
-
- setTitle(String) - Method in class pal.gui.TreeComponent
-
- setTitle(String) - Method in class pal.gui.TreePainter
-
- setTransitionCategoryProbabilities(double, double, double) - Method in class pal.substmodel.YangCodonModel.SimplePositiveSelection
-
We use three parameters instead of two to make opimisation easier (there are effectively only *two* parameters though)
- setTree(Tree) - Method in class pal.eval.ChiSquareValue
-
define (parameterized) tree
- setTree(Tree) - Method in class pal.eval.FastLikelihoodCalculator
-
- 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.SimpleLikelihoodCalculator
-
define tree
,(must only be called only after a site pattern has been defined).
- setTree(Tree) - Method in class pal.gui.TreeComponent
-
- setTree(Tree) - Method in class pal.gui.TreePainter
-
- setTreeImpl(Tree) - Method in class pal.gui.TreePainter
-
may be implemented by sub classes
- setTreeImpl(Tree) - Method in class pal.gui.TreePainterCircular
-
- setUnits(int) - Method in class pal.coalescent.CoalescentIntervals
-
Sets the units these coalescent intervals are
measured in.
- setUnits(int) - Method in class pal.coalescent.DemographicModel
-
sets units of measurement.
- setUnits(int, double) - Method in class pal.mep.MutationRateModel
-
sets units of measurement.
- setUnits(int) - Method in class pal.tree.SimpleTree
-
Sets the units that this tree is expressed in.
- setUnits(int) - Method in class pal.tree.Tree.TreeBase
-
Sets the units that this tree is expressed in.
- setup(Tree, SubstitutionModel) - Method in class pal.eval.GeneralLikelihoodCalculator
-
- setup(Parameterized[], int[], int[]) - Static method in class pal.misc.MultiParameterized
-
- setup() - Method in class pal.treesearch.GeneralConstraintGroupManager
-
- setupConstraintGroupManagers() - Method in class pal.treesearch.GeneralConstraintGroupManager.Store
-
- setupInternalNodeHeights(ConstraintModel.GroupManager) - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
- setupInternalNodeHeights(ConstraintModel.GroupManager) - Method in class pal.treesearch.ConstrainedLeafNode
-
- setupInternalNodeHeights(ConstraintModel.GroupManager) - Method in interface pal.treesearch.ConstrainedNode
-
- setupLookups(Parameterized[], int[], int[], int) - Static method in class pal.misc.Parameterized.Utils
-
- setUpperCorner(int) - Method in class pal.gui.LinkageDisequilibriumComponent
-
This determines what is displayed in the upper right corner.
- setUseCurrentInUnivariateMinimisation(boolean) - Method in class pal.math.OrthogonalSearch
-
- 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(int, int, double) - Method in class pal.math.Matrix
-
- setValue(double) - Method in class pal.misc.MutableDouble
-
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)
- setWordModification(int) - Method in class pal.io.NexusTokenizer
-
Sets the flag value for word modification.
- ShimodairaHasegawaStatistics - Class in pal.statistics
-
Title: ShimodairaHasegawaStatistics
- ShimodairaHasegawaStatistics() - Constructor for class pal.statistics.ShimodairaHasegawaStatistics
-
- ShimodairaHasegawaTest - Class in pal.statistics
-
Shimodaira-Hasegawa-Test (1999) to
compare a set of evolutionary hypotheses
- ShimodairaHasegawaTest() - Constructor for class pal.statistics.ShimodairaHasegawaTest
-
- SHORT_UNIT_NAMES - Static variable in interface pal.misc.Units
-
- 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(Object[]) - Method in class pal.math.MersenneTwisterFast
-
Shuffles an array of objects.
- shuffle(int[], int) - Method in class pal.math.MersenneTwisterFast
-
Shuffles an array by repeatedly choosing two random members and swapping them.
- shuffled(int) - Method in class pal.math.MersenneTwisterFast
-
Generates an array of ints that are shuffled
- shuffleSubset(int, int, Object[]) - Method in class pal.math.MersenneTwisterFast
-
Shuffles an array of objects.
- shuffleTimes() - Method in class pal.misc.TimeOrderCharacterData
-
- SimpleAlignment - Class in pal.alignment
-
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, LabelMapping) - Constructor for class pal.alignment.SimpleAlignment
-
Clone constructor.
- SimpleAlignment(Alignment, int) - Constructor for class pal.alignment.SimpleAlignment
-
Clone constructor.
- SimpleAlignment(Identifier[], String[], String, DataType) - Constructor for class pal.alignment.SimpleAlignment
-
- SimpleAlignment(IdGroup, String[], DataType) - Constructor for class pal.alignment.SimpleAlignment
-
- SimpleAlignment(IdGroup, String[], String, DataType) - Constructor for class pal.alignment.SimpleAlignment
-
- SimpleAlignment(Identifier[], String[], DataType) - Constructor for class pal.alignment.SimpleAlignment
-
- SimpleAlignment(IdGroup, char[][], DataType) - Constructor for class pal.alignment.SimpleAlignment
-
- SimpleAlignment(IdGroup, DataType, int[][]) - Constructor for class pal.alignment.SimpleAlignment
-
- SimpleAlignment(IdGroup, char[][], String, DataType) - Constructor for class pal.alignment.SimpleAlignment
-
- SimpleAlignment(Identifier, String, DataType) - Constructor for class pal.alignment.SimpleAlignment
-
Constructor taking single identifier and sequence.
- SimpleAlignment(Alignment, Alignment, String, String, char) - Constructor for class pal.alignment.SimpleAlignment
-
This constructor combines to alignments given two guide strings.
- SimpleAnnotatedAlignment - Class in pal.alignment
-
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, DataType) - Constructor for class pal.alignment.SimpleAnnotatedAlignment
-
This constructor creates a basic SimpleAnnotatedAlignment.
- SimpleAnnotatedAlignment(IdGroup, String[], DataType) - Constructor for class pal.alignment.SimpleAnnotatedAlignment
-
This constructor creates a basic SimpleAnnotatedAlignment.
- SimpleAnnotatedAlignment(IdGroup, String[], String, DataType) - Constructor for class pal.alignment.SimpleAnnotatedAlignment
-
This constructor creates a basic SimpleAnnotatedAlignment.
- SimpleCharacterAlignment - Class in pal.alignment
-
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 in pal.datatype
-
interface for sequence data types
- SimpleDataType() - Constructor for class pal.datatype.SimpleDataType
-
- SimpleIdGroup - Class in pal.misc
-
Default implementation of IdGroup interface.
- SimpleIdGroup(int) - 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.
- SimpleIdGroup(int, boolean) - Constructor for class pal.misc.SimpleIdGroup
-
Constructor taking the size of the group.
- SimpleIdGroup(Identifier[]) - Constructor for class pal.misc.SimpleIdGroup
-
Constructor taking an array of identifiers.
- SimpleIdGroup(IdGroup, IdGroup) - Constructor for class pal.misc.SimpleIdGroup
-
Constructor taking two separate id groups and merging them.
- SimpleIdGroup(IdGroup) - Constructor for class pal.misc.SimpleIdGroup
-
Impersonating Constructor.
- SimpleIdGroup(IdGroup, int) - Constructor for class pal.misc.SimpleIdGroup
-
Impersonating Constructor.
- SimpleLeafCalculator - Class in pal.eval
-
- SimpleLeafCalculator(int[], int, int, int, LHCalculator.Generator) - Constructor for class pal.eval.SimpleLeafCalculator
-
- SimpleLHCalculator - Class in pal.eval
-
- SimpleLHCalculator() - Constructor for class pal.eval.SimpleLHCalculator
-
- SimpleLikelihoodCalculator - Class in pal.eval
-
- 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, RateMatrix) - Constructor for class pal.eval.SimpleLikelihoodCalculator
-
- SimpleModelFastFourStateLHCalculator - Class in pal.eval
-
- SimpleModelFastFourStateLHCalculator() - Constructor for class pal.eval.SimpleModelFastFourStateLHCalculator
-
- SimpleMolecularClockLikelihoodModel - Class in pal.eval
-
- SimpleMolecularClockLikelihoodModel() - Constructor for class pal.eval.SimpleMolecularClockLikelihoodModel
-
- SimpleNode - Class in pal.tree
-
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(String, double) - Constructor for class pal.tree.SimpleNode
-
- SimpleNode(Node[], double) - Constructor for class pal.tree.SimpleNode
-
Constructor
- SimpleNode(Node[]) - Constructor for class pal.tree.SimpleNode
-
- 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
-
- simpleOptimiseLikelihood(double, AlgorithmCallback) - Method in class pal.treesearch.UnrootedMLSearcher
-
Optimise the branch lengths of the tree to obtain the maximum likelihood.
- simpleOptimiseLikelihood(StoppingCriteria, AlgorithmCallback) - Method in class pal.treesearch.UnrootedMLSearcher
-
Optimise the branch lengths of the tree to obtain the maximum likelihood.
- SimpleRateMatrixGroup - Class in pal.substmodel
-
- SimpleRateMatrixGroup(NeoRateMatrix[], double[], double[], DataType) - Constructor for class pal.substmodel.SimpleRateMatrixGroup
-
- SimpleSummarizable - Class in pal.misc
-
- 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 in pal.tree
-
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
- SimpleUnconstrainedLikelihoodModel - Class in pal.eval
-
- SimpleUnconstrainedLikelihoodModel() - Constructor for class pal.eval.SimpleUnconstrainedLikelihoodModel
-
- SimpleUnconstrainedLikelihoodModel.InternalImpl - Class in pal.eval
-
- SimpleUnconstrainedLikelihoodModel.InternalImpl(LHCalculator.Internal, SubstitutionModel) - Constructor for class pal.eval.SimpleUnconstrainedLikelihoodModel.InternalImpl
-
- SimpleUnconstrainedLikelihoodModel.LeafImpl - Class in pal.eval
-
- SimpleUnconstrainedLikelihoodModel.LeafImpl(LHCalculator.Leaf, SubstitutionModel) - Constructor for class pal.eval.SimpleUnconstrainedLikelihoodModel.LeafImpl
-
- simulate(int[], double, int[]) - Method in class pal.substmodel.SequenceSimulator
-
- simulate() - Method in class pal.tree.SimulatedAlignment
-
generate new artificial data set (random root sequence)
- simulate(String) - 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)
- simulated(int[], double, double, int[]) - Method in interface pal.eval.MolecularClockLikelihoodModel.Simulator
-
- SimulatedAlignment - Class in pal.tree
-
generates an artificial data set
- SimulatedAlignment(int, Tree, SubstitutionModel) - Constructor for class pal.tree.SimulatedAlignment
-
Inititalisation
- SimulatedAlignment.Factory - Class in pal.tree
-
A utility class that can be used to generate Simulated alignments based on
a tree with predefined sequence length and substitution model
- SimulatedAlignment.Factory(int, SubstitutionModel) - Constructor for class pal.tree.SimulatedAlignment.Factory
-
- 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.
- simulateTree() - Method in interface pal.supgma.SUPGMABase.PopulationParameters
-
- simulateTrees(int, AlgorithmCallback, LMSSolver) - Method in interface pal.supgma.SUPGMABase.PopulationParameters
-
- SINGLE_LINKAGE - Static variable in class pal.tree.ClusterTree
-
- SingleClassSubstitutionModel - Class in pal.substmodel
-
- SingleClassSubstitutionModel(NeoRateMatrix, DataType, double[]) - Constructor for class pal.substmodel.SingleClassSubstitutionModel
-
- SingleSplitDistribution - Interface in pal.substmodel
-
- SingleSplitMolecularClockLikelihoodModel - Class in pal.eval
-
- SingleSplitMolecularClockLikelihoodModel() - Constructor for class pal.eval.SingleSplitMolecularClockLikelihoodModel
-
- siteDataType - Variable in class pal.alignment.MultiLocusAnnotatedAlignment
-
provides datatype for each locus separately
- SiteDetails - Interface in pal.eval
-
- SiteDetails.Utils - Class in pal.eval
-
- SiteDetails.Utils() - Constructor for class pal.eval.SiteDetails.Utils
-
- siteLogL - Variable in class pal.eval.LikelihoodValue
-
log-likelihood for each site pattern
- SitePattern - Class in pal.alignment
-
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
- sitePatternMatchupToString() - Method in class pal.eval.PatternInfo
-
- 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 in pal.coalescent
-
Skyline plot derived from a strictly bifurcating tree
or a coalescent interval.
- SkylinePlot(Tree, double) - Constructor for class pal.coalescent.SkylinePlot
-
Construct skyline plot from tree
- SkylinePlot(CoalescentIntervals, double) - Constructor for class pal.coalescent.SkylinePlot
-
Construct skyline plot from given coalescent intervals
- solve(double[][], double[]) - Method in interface pal.math.LMSSolver
-
- solve(AlgorithmCallback, ClusterTree.ClusteringMethod, LMSSolver) - Method in class pal.supgma.SUPGMABase
-
- sort(Vector, int[]) - Static method in class pal.util.HeapSort
-
Sorts an array of indices to vector of comparable objects
into increasing order.
- sort(Vector) - Static method in class pal.util.HeapSort
-
Sorts a vector of comparable objects into increasing order.
- sort(Comparable[]) - Static method in class pal.util.HeapSort
-
Sorts an array of comparable objects into increasing order.
- sort(Object[], Comparator) - Static method in class pal.util.HeapSort
-
Sorts an array of objects into increasing order given a comparator.
- 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
- 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.
- SPACE - Static variable in class pal.io.NexusTokenizer
-
- SPACES_PER_LEVEL - Static variable in interface pal.util.XMLConstants
-
- SpecificAminoAcids - Class in pal.datatype
-
implements a MolecularDataType for amino acids, where we specifiy the Codon Table basis of amino acid by
supplying the CodonTable which is/was used for converting Nucleotide sequences to Amino Acids.
- SpecificAminoAcids() - Constructor for class pal.datatype.SpecificAminoAcids
-
Creates with Universal Codon Table
- SpecificAminoAcids(CodonTable) - Constructor for class pal.datatype.SpecificAminoAcids
-
- SpecificAminoAcids(int) - Constructor for class pal.datatype.SpecificAminoAcids
-
- split(String[], MersenneTwisterFast) - Static method in class pal.treesearch.SearcherUtils
-
- SplitSystem - Class in pal.tree
-
data structure for a set of splits
- SplitSystem(IdGroup, int) - Constructor for class pal.tree.SplitSystem
-
- SplitUtils - Class in pal.tree
-
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.
- SRDTGlobalClockModel - Class in pal.treesearch
-
- SRDTGlobalClockModel(SampleInformation, MolecularClockLikelihoodModel.Instance) - Constructor for class pal.treesearch.SRDTGlobalClockModel
-
- SRDTGlobalClockModel(SampleInformation, MolecularClockLikelihoodModel.Instance, boolean) - Constructor for class pal.treesearch.SRDTGlobalClockModel
-
- 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.
- StateProvider - Interface in pal.algorithmics
-
Title:
- StateRemover - Class in pal.datatype
-
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.
- STEPPED_MUTATION_RATE - Static variable in interface pal.util.XMLConstants
-
- SteppedMutationRate - Class in pal.mep
-
This class models a step-wise mutation rate.
- SteppedMutationRate(double[], int, double) - Constructor for class pal.mep.SteppedMutationRate
-
Construct demographic model with default settings
- SteppedMutationRate(double[], double[], int, double) - Constructor for class pal.mep.SteppedMutationRate
-
Construct mutation rate model of a give rate in given units.
- SteppedMutationRate(double[], double[], int, boolean, double) - Constructor for class pal.mep.SteppedMutationRate
-
Construct mutation rate model of a give rate in given units.
- SteppedMutationRate(double[], TimeOrderCharacterData) - Constructor for class pal.mep.SteppedMutationRate
-
Construct mutation rate model of a give rate in given units.
- SteppedMutationRate(double[], TimeOrderCharacterData, boolean) - Constructor for class pal.mep.SteppedMutationRate
-
Construct mutation rate model of a give rate in given units.
- stochasticNNI(Tree) - Static method in class pal.tree.Local
-
- 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
- StoppingCriteria - Interface in pal.algorithmics
-
- StoppingCriteria.Factory - Interface in pal.algorithmics
-
- StoppingCriteria.Utils - Class in pal.algorithmics
-
- StoppingCriteria.Utils() - Constructor for class pal.algorithmics.StoppingCriteria.Utils
-
- STRING - Static variable in class pal.misc.Attribute
-
- StrippedAlignment - Class in pal.alignment
-
takes an alignment and repeatedly removes sites
- StrippedAlignment(Alignment) - Constructor for class pal.alignment.StrippedAlignment
-
Constructor
- StrippedAnnotatedAlignment - Class in pal.alignment
-
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 class pal.eval.GeneralLikelihoodCalculator
-
- 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
-
- subgroups_ - Variable in class pal.misc.TimeOrderCharacterData
-
- subset(IdGroup) - Method in class pal.misc.TimeOrderCharacterData
-
Extracts a subset of a TimeOrderCharacterData.
- SubstitutionModel - Interface in pal.substmodel
-
model of sequence substitution (rate matrix + rate variation).
- SubstitutionModel.Utils - Class in pal.substmodel
-
A small Utility class for things relating to Substitution Models in general
- SubstitutionModel.Utils() - Constructor for class pal.substmodel.SubstitutionModel.Utils
-
- SubstitutionTool - Class in pal.substmodel
-
- SubstitutionTool() - Constructor for class pal.substmodel.SubstitutionTool
-
- 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
-
- SUGGESTED_GAP_CHARACTERS - Static variable in interface pal.datatype.DataType
-
- SUGGESTED_GAP_STATE - Static variable in interface pal.datatype.DataType
-
The gap state that should generally be used (-2),
though the DataType specification makes no requirement that this be the gap state
- SUGGESTED_UNKNOWN_STATE - Static variable in interface pal.datatype.DataType
-
The gap state that should generally be used (-1).
- sum4(double[]) - Static method in class pal.eval.GeneralLikelihoodCalculator
-
- Summarizable - Interface in pal.misc
-
interface for classes that can provide summaries
- SUPGMABase - Class in pal.supgma
-
- SUPGMABase(DistanceMatrixAccess, DistanceMatrixGenerator, TimeOrderCharacterData) - Constructor for class pal.supgma.SUPGMABase
-
- SUPGMABase.CISummary - Interface in pal.supgma
-
- SUPGMABase.PopulationParameters - Interface in pal.supgma
-
- SUPGMADistanceMatrix - Class in pal.supgma
-
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, DeltaModel) - Constructor for class pal.supgma.SUPGMADistanceMatrix
-
Uses date/time information and a constant rate to correct distance matrices.
- SUPGMATree - Class in pal.supgma
-
constructs an SUPGMA tree from pairwise distances.
- SUPGMATree(DistanceMatrix, TimeOrderCharacterData, double, ClusterTree.ClusteringMethod) - Constructor for class pal.supgma.SUPGMATree
-
constructor SUPGMA tree
- SUPGMATree(DistanceMatrix, TimeOrderCharacterData, DeltaModel, boolean, ClusterTree.ClusteringMethod) - Constructor for class pal.supgma.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
- swapConnection(FreeBranch, FreeNode, FreeBranch) - Method in class pal.treesearch.FreeInternalNode
-
- swapConnection(FreeBranch, FreeBranch) - Method in class pal.treesearch.FreeInternalNode
-
- swapConnection(FreeBranch, FreeBranch) - Method in class pal.treesearch.FreeLeafNode
-
- swapConnection(FreeBranch, FreeNode, FreeBranch) - Method in class pal.treesearch.FreeLeafNode
-
- swapConnection(FreeBranch, FreeBranch) - Method in interface pal.treesearch.FreeNode
-
Should not do anything but swap branches around
- swapConnection(FreeBranch, FreeNode, FreeBranch) - Method in interface pal.treesearch.FreeNode
-
Should preserve tree integrity
- swapConnection(FreeBranch, FreeBranch) - Method in class pal.treesearch.PivotNode
-
Should not do anything but swap branches around
- swapConnection(FreeBranch, FreeNode, FreeBranch) - Method in class pal.treesearch.PivotNode
-
Should preserve tree integrity
- swapNode(FreeNode, FreeNode) - Method in class pal.treesearch.FreeBranch
-