A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
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All Classes All Packages
All Classes All Packages
A
- A_STATE - Static variable in class pal.datatype.Nucleotides
- A_TO_C - Static variable in interface pal.util.XMLConstants
- A_TO_G - Static variable in interface pal.util.XMLConstants
- A_TO_T - Static variable in interface pal.util.XMLConstants
- absoluteDistance(DistanceMatrix) - Method in class pal.distance.DistanceMatrix
-
compute absolute distance to second distance matrix
- ABSTOL - Static variable in interface pal.misc.BranchLimits
-
maximum tolerated error when determining branch lengths
- AbstractAlignment - Class in pal.alignment
-
abstract base class for any alignment data.
- AbstractAlignment() - Constructor for class pal.alignment.AbstractAlignment
- AbstractExternal() - Constructor for class pal.eval.LHCalculator.AbstractExternal
- AbstractLeafNode - Class in pal.treesearch
- AbstractLeafNode(String, GeneralConstructionTool) - Constructor for class pal.treesearch.AbstractLeafNode
- AbstractParentableConstrainedNode - Class in pal.treesearch
- AbstractParentableConstrainedNode(Node, GeneralConstructionTool, GeneralConstraintGroupManager.Store, GeneralConstraintGroupManager) - Constructor for class pal.treesearch.AbstractParentableConstrainedNode
- AbstractRateMatrix - Class in pal.substmodel
-
abstract base class for all rate matrices
- AbstractRateMatrix(int) - Constructor for class pal.substmodel.AbstractRateMatrix
- add(Object, double, boolean) - Method in class pal.algorithmics.Ranker
-
Add in (if it's good enough) a new object based on a score If an object has equality with an object already in the store that object is replaced by the new version
- add(ExternalParameterListener, ExternalParameterListener) - Static method in class pal.misc.PalEventMulticaster
-
For managing ExternalParamterListeners Usage: ExternalParamterListener current = null; ...
- add(PalObjectListener, PalObjectListener) - Static method in class pal.misc.PalEventMulticaster
-
For managing PalObjectListeners Usage: PalObjectListener current = null; ...
- addChild(Node) - Method in interface pal.tree.Node
-
add new child node
- addChild(Node) - Method in class pal.tree.SimpleNode
-
add new child node
- addDistance(int, int, double) - Method in class pal.distance.DistanceMatrix
-
Adds a delta to both upper and lower triangle distances.
- addDoubleKey(double, Object) - Method in class pal.util.DefaultCache
- addDoubleKey(double, Object) - Method in interface pal.util.DoubleKeyCache
- addDoubleKey(DoubleKey) - Method in class pal.util.DefaultCache
- addGroupLeader(GroupLeader) - Method in class pal.treesearch.GeneralConstraintGroupManager
- addHeight(String, double) - Method in class pal.treesearch.HeightInformationUser
- ADDITION - Static variable in class pal.io.NexusTokenizer
- addMapping(String, Color) - Method in class pal.gui.NameColouriser
- addMapping(String, Color, int) - Method in class pal.gui.NameColouriser
- addMapping(String, Rectangle) - Method in class pal.gui.LayoutTracker
- addMapping(String, String) - Method in class pal.misc.LabelMapping
- addMapping(String, LabelDisplayer) - Method in class pal.gui.NameColouriser
- addMapping(Identifier, Color) - Method in class pal.gui.NameColouriser
- addMapping(Identifier, Rectangle) - Method in class pal.gui.LayoutTracker
- addMapping(Identifier, String) - Method in class pal.misc.LabelMapping
- addMappings(String[], Color[]) - Method in class pal.gui.NameColouriser
- addMappings(String[], String[]) - Method in class pal.misc.LabelMapping
- addPalObjectListener(PalObjectListener) - Method in interface pal.mep.DeltaModel.Instance
- addPalObjectListener(PalObjectListener) - Method in class pal.misc.PalObjectListener.EventGenerator
- addPalObjectListener(PalObjectListener) - Method in class pal.substmodel.AbstractRateMatrix
- addPalObjectListener(PalObjectListener) - Method in class pal.substmodel.CachedRateMatrix
- addPalObjectListener(PalObjectListener) - Method in class pal.substmodel.GeneralRateDistributionSubstitutionModel
- addPalObjectListener(PalObjectListener) - Method in interface pal.substmodel.RateMatrix
-
Add a PalObjectListener to be notified of changes to the model.
- addPalObjectListener(PalObjectListener) - Method in class pal.substmodel.SingleClassSubstitutionModel
- addPalObjectListener(PalObjectListener) - Method in interface pal.substmodel.SubstitutionModel
- addSequence(int[], String) - Method in class pal.alignment.AlignmentBuilder
-
Add sequence data to store
- adjustDistances(double[][], TimeOrderCharacterData) - Method in interface pal.supgma.RateHandler
- adjustDistances(double[][], TimeOrderCharacterData) - Method in interface pal.supgma.ThetaHandler
- adjustNodeHeight(double) - Method in class pal.treesearch.AbstractParentableConstrainedNode
- AIC(double, int) - Static method in class pal.statistics.PenalizedLikelihood
-
Akaike (AIC) correction (Akaike 1974)
- AICC(double, int, int) - Static method in class pal.statistics.PenalizedLikelihood
-
Second-order Akaike (AICC) correction (Hurvich and Tsai 1989)
- AlgorithmCallback - Interface in pal.util
- AlgorithmCallback.Utils - Class in pal.util
-
A Utility class that provides some simple implementations of AlgorithmCallback that can be used for manipulating callback results
- alias - Variable in class pal.alignment.SitePattern
-
site -> site pattern
- alias - Variable in class pal.alignment.StrippedAlignment
- Alignment - Interface in pal.alignment
-
interface for any alignment data.
- ALIGNMENT - Static variable in interface pal.util.XMLConstants
- AlignmentBuilder - Class in pal.alignment
-
A class for the gradual construction of an alignment.
- AlignmentBuilder(int) - Constructor for class pal.alignment.AlignmentBuilder
-
The constructor
- AlignmentDistanceMatrix - Class in pal.distance
-
compute distance matrix (observed and ML) from alignment (SitePattern)
- AlignmentDistanceMatrix(SitePattern) - Constructor for class pal.distance.AlignmentDistanceMatrix
-
compute observed distances
- AlignmentDistanceMatrix(SitePattern, SubstitutionModel) - Constructor for class pal.distance.AlignmentDistanceMatrix
-
compute maximum-likelihood distances
- AlignmentDistanceMatrix(SitePattern, SubstitutionModel, AlgorithmCallback) - Constructor for class pal.distance.AlignmentDistanceMatrix
-
compute maximum-likelihood distances
- AlignmentDistanceMatrix(SitePattern, AlgorithmCallback) - Constructor for class pal.distance.AlignmentDistanceMatrix
-
compute observed distances
- AlignmentGenerator - Interface in pal.alignment
-
A AlignmentGenerator is an object that can generate alignments! (most probably replicates for statistical tests)
- AlignmentGenerator.Utils - Class in pal.alignment
- AlignmentParseException - Exception in pal.alignment
-
Exception thrown by ReadAlignment
- AlignmentParseException() - Constructor for exception pal.alignment.AlignmentParseException
- AlignmentParseException(String) - Constructor for exception pal.alignment.AlignmentParseException
- AlignmentReaders - Class in pal.alignment
-
Temporary class for reading alignments...
- AlignmentReaders() - Constructor for class pal.alignment.AlignmentReaders
- AlignmentReaders.PhylipClustalAlignment - Class in pal.alignment
- AlignmentReaders.UnalignedAlignment - Class in pal.alignment
- AlignmentReceiver - Interface in pal.alignment
- AlignmentReceiver.BucketReceiver - Class in pal.alignment
-
The SingleReceiver only keeps track of one alignment, the last one it received
- AlignmentReceiver.SingleReceiver - Class in pal.alignment
-
The SingleReceiver only keeps track of one alignment, the last one it received
- AlignmentTool - Class in pal.alignment
-
Simple access for alignment functions.
- AlignmentTool() - Constructor for class pal.alignment.AlignmentTool
- AlignmentUtils - Class in pal.alignment
-
Helper utilities for alignments.
- AlignmentUtils() - Constructor for class pal.alignment.AlignmentUtils
- all - Static variable in class pal.datatype.IUPACPenaltyTable
- allocateNewFreeInternalCalculator() - Method in class pal.treesearch.GeneralConstructionTool
- allocateNextConnectionIndex() - Method in class pal.treesearch.GeneralConstructionTool
- alpha - Variable in class pal.coalescent.ConstExpGrowth
-
ratio of pop.
- alpha - Variable in class pal.coalescent.ExpandingPopulation
-
ratio of pop.
- ALPHA - Static variable in interface pal.util.XMLConstants
- ALPHA_PARAMETERIZATION - Static variable in class pal.coalescent.ConstExpGrowth
-
use alpha instead of N1 parameterization
- alphaSE - Variable in class pal.coalescent.ConstExpGrowth
-
standard error of time alpha
- alphaSE - Variable in class pal.coalescent.ExpandingPopulation
-
standard error of time alpha
- ALTERNATIVE_YEAST - Static variable in interface pal.datatype.CodonTable
-
TypeID for Alternative Yeast
- AmbiguousDataType - Interface in pal.datatype
-
Additional interface information for data types which represent ambiguity in sub types.
- AMINO_ACID_DESCRIPTION - Static variable in interface pal.datatype.DataType
-
amino acid name (for XML and human readability)
- AminoAcidModel - Class in pal.substmodel
-
base class of rate matrices for amino acids
- AminoAcidModel(double[]) - Constructor for class pal.substmodel.AminoAcidModel
- AminoAcidModelID - Interface in pal.substmodel
-
interface for IDs of amino acid models
- AminoAcids - Class in pal.datatype
-
implements DataType for amino acids
- AminoAcids() - Constructor for class pal.datatype.AminoAcids
- AMINOACIDS - Static variable in interface pal.datatype.DataType
- ANCESTRAL_MU_RATE - Static variable in interface pal.util.XMLConstants
- ANCESTRAL_POP_SIZE - Static variable in interface pal.util.XMLConstants
- AnnotationAlignment - Interface in pal.alignment
-
The AnnotationAlignment interface is designed to provide annotation for an alignment.
- ANONYMOUS - Static variable in class pal.misc.Identifier
- argmax(double[]) - Static method in class pal.misc.Utils
-
Deprecated.
- argmax(int[]) - Static method in class pal.misc.Utils
-
Deprecated.
- ASCIDIAN_MITOCHONDRIAL - Static variable in interface pal.datatype.CodonTable
-
TypeID for Ascidian Mitochondrial
- Assessor - Interface in pal.algorithmics
-
Title:
- ASTERIX - Static variable in class pal.io.NexusTokenizer
- attach(String, Alignment) - Method in interface pal.treesearch.BranchAccess
-
Create a new Tree Searcher with a new sub tree attached
- attach(String, Alignment, SubstitutionModel) - Method in interface pal.treesearch.BranchAccess
-
Create a new Tree Searcher with a new sub tree attached
- attach(Node, Alignment) - Method in interface pal.treesearch.BranchAccess
-
Create a new Tree Searcher with a new sub tree attached
- attach(Node, Alignment, SubstitutionModel) - Method in interface pal.treesearch.BranchAccess
-
Create a new Tree Searcher with a new sub tree attached
- attachSubTree(Node, int) - Method in interface pal.tree.TreeManipulator.BranchAccess
-
Create a new TreeManipulator object that has sub grafted on (half way across this branch)
- attachTo(FreeBranch, FreeBranch[]) - Method in class pal.treesearch.FreeBranch
- attName - Variable in class pal.gui.TreePainter
- Attribute - Class in pal.misc
-
An immutable attribute has a name and value.
- Attribute(String, Object) - Constructor for class pal.misc.Attribute
- Attribute(String, String, String) - Constructor for class pal.misc.Attribute
- ATTRIBUTE - Static variable in interface pal.util.XMLConstants
- AttributeNode - Interface in pal.tree
-
interface for a node (includes branch) in a binary/non-binary rooted/unrooted tree.
B
- B_SLASH - Static variable in class pal.io.NexusTokenizer
- B_TICK - Static variable in class pal.io.NexusTokenizer
- BACKGROUND - Static variable in class pal.gui.TreePainter
- BACKWARDS - Static variable in interface pal.util.XMLConstants
- BACTERIAL - Static variable in interface pal.datatype.CodonTable
-
TypeID for Bacterial
- basicUnrootedTreeMLSearch(Alignment, SubstitutionModel, boolean) - Method in class pal.treesearch.TreeSearchTool
-
Do a basic tree search using maximum likelihood on an unrooted tree space, without a given starting tree
- basicUnrootedTreeMLSearch(Alignment, SubstitutionModel, boolean, AlgorithmCallback) - Method in class pal.treesearch.TreeSearchTool
-
Do a basic tree search using maximum likelihood on an unrooted tree space, without a given starting tree
- basicUnrootedTreeMLSearch(Tree, Alignment, SubstitutionModel, boolean) - Method in class pal.treesearch.TreeSearchTool
-
Do a basic tree search using maximum likelihood on an unrooted tree space, with a given starting tree
- basicUnrootedTreeMLSearch(Tree, Alignment, SubstitutionModel, boolean, AlgorithmCallback) - Method in class pal.treesearch.TreeSearchTool
-
Do a basic tree search using maximum likelihood on an unrooted tree space, with a given starting tree
- BEALE_SORENSON_HESTENES_STIEFEL_UPDATE - Static variable in class pal.math.ConjugateGradientSearch
- bestH - Variable in class pal.statistics.KishinoHasegawaTest
-
number of maximum likelihood hypothesis
- bestH - Variable in class pal.statistics.ShimodairaHasegawaTest
-
number of maximum likelihood hypothesis
- biasCorrectedEstimate(double, double[]) - Static method in class pal.statistics.BootstrapStatistics
-
correct a statistic thetaHat for its bias
- BIC(double, int, int) - Static method in class pal.statistics.PenalizedLikelihood
-
BIC correction (Schwarz 1978)
- Binomial - Class in pal.math
-
Binomial coefficients
- Binomial() - Constructor for class pal.math.Binomial
- BLEPHARISMA_NUCLEAR - Static variable in interface pal.datatype.CodonTable
-
TypeID for Blepharisma Nuclear
- BLOSUM62 - Class in pal.substmodel
-
BLOSUM62 model of amino acid evolution
- BLOSUM62 - Static variable in interface pal.substmodel.AminoAcidModelID
- BLOSUM62 - Static variable in interface pal.util.XMLConstants
- BLOSUM62(double[]) - Constructor for class pal.substmodel.BLOSUM62
-
constructor
- BOOLEAN - Static variable in class pal.misc.Attribute
- bootstrap() - Method in class pal.alignment.BootstrappedAlignment
-
bootstrap alignment
- BOOTSTRAP_ATTRIBUTE_NAME - Static variable in class pal.gui.TreePainter
- BOOTSTRAP_SUPPORT_COLOUR - Static variable in class pal.gui.TreePainter
- BootstrappedAlignment - Class in pal.alignment
-
generates bootstrapped alignments from a raw alignment
- BootstrappedAlignment(Alignment) - Constructor for class pal.alignment.BootstrappedAlignment
-
Constructor
- BootstrapStatistics - Class in pal.statistics
-
computation of bootstrap estimators (BIAS, SD, VAR, CI) given a statistic theta and corresponding bootstrap replicates.
- BootstrapStatistics() - Constructor for class pal.statistics.BootstrapStatistics
- BOTTOMBORDER - Static variable in class pal.gui.TreePainterCircular
- BOTTOMBORDER - Static variable in class pal.gui.TreePainterNormal
- BoundsCheckedFunction - Class in pal.math
-
returns a very large number instead of the function value if arguments are out of bound (useful for minimization with minimizers that don't check argument boundaries)
- BoundsCheckedFunction(MultivariateFunction) - Constructor for class pal.math.BoundsCheckedFunction
-
construct bound-checked multivariate function (a large number will be returned on function evaluation if argument is out of bounds; default is 1000000)
- BoundsCheckedFunction(MultivariateFunction, double) - Constructor for class pal.math.BoundsCheckedFunction
-
construct constrained multivariate function
- BranchAccess - Interface in pal.treesearch
- BranchAccess.Utils - Class in pal.treesearch
- BranchLimits - Interface in pal.misc
-
limits for branch lengths
- BucketReceiver() - Constructor for class pal.alignment.AlignmentReceiver.BucketReceiver
- build(PatternInfo, PatternInfo, int) - Method in class pal.eval.PatternInfo
- build(PatternInfo, PatternInfo, PatternInfo) - Method in class pal.treesearch.GeneralConstructionTool
- buildConstraintModel(SampleInformation, MolecularClockLikelihoodModel.Instance) - Method in interface pal.mep.DeltaModel
- buildConstraintModel(SampleInformation, MolecularClockLikelihoodModel.Instance) - Method in interface pal.mep.MutationRateModel.Factory
- buildDescendentPALNodeBase() - Method in class pal.treesearch.AbstractParentableConstrainedNode
- buildDescendentPALNodeBase() - Method in class pal.treesearch.ConstrainedLeafNode
- buildDescendentPALNodeBase() - Method in interface pal.treesearch.ConstrainedNode
-
Build node model base units (eg years)
- buildDescendentPALNodeES(ConstraintModel.GroupManager) - Method in class pal.treesearch.AbstractParentableConstrainedNode
- buildDescendentPALNodeES(ConstraintModel.GroupManager) - Method in class pal.treesearch.ConstrainedLeafNode
- buildDescendentPALNodeES(ConstraintModel.GroupManager) - Method in interface pal.treesearch.ConstrainedNode
-
Build node with Expected Substitution Units
- buildDisplay(Color) - Static method in class pal.gui.LabelDisplayer.Utils
- buildDisplay(Color, int) - Static method in class pal.gui.LabelDisplayer.Utils
- buildLeftDecendentPALNodeBase() - Method in class pal.treesearch.AbstractParentableConstrainedNode
- buildPALNode() - Method in class pal.treesearch.UnrootedMLSearcher
- buildPALNode(double, FreeBranch) - Method in class pal.treesearch.FreeLeafNode
- buildPALNodeBase() - Method in class pal.treesearch.FreeBranch
- buildPALNodeBase() - Method in class pal.treesearch.GeneralLikelihoodSearcher
- buildPALNodeBase() - Method in class pal.treesearch.PivotNode
- buildPALNodeBase() - Method in interface pal.treesearch.RootAccess
- buildPALNodeBase(double, FreeBranch) - Method in class pal.treesearch.FreeInternalNode
- buildPALNodeBase(double, FreeBranch) - Method in class pal.treesearch.FreeLeafNode
- buildPALNodeBase(double, FreeBranch) - Method in interface pal.treesearch.FreeNode
- buildPALNodeBase(double, FreeBranch) - Method in class pal.treesearch.PivotNode
- buildPALNodeBase(FreeNode) - Method in class pal.treesearch.FreeBranch
- buildPALNodeES() - Method in class pal.treesearch.FreeBranch
- buildPALNodeES() - Method in class pal.treesearch.GeneralLikelihoodSearcher
- buildPALNodeES() - Method in class pal.treesearch.PivotNode
- buildPALNodeES() - Method in interface pal.treesearch.RootAccess
- buildPALNodeES(double, FreeBranch) - Method in class pal.treesearch.FreeInternalNode
- buildPALNodeES(double, FreeBranch) - Method in class pal.treesearch.FreeLeafNode
- buildPALNodeES(double, FreeBranch) - Method in interface pal.treesearch.FreeNode
- buildPALNodeES(double, FreeBranch) - Method in class pal.treesearch.PivotNode
- buildPALNodeES(FreeNode) - Method in class pal.treesearch.FreeBranch
- buildPALTree() - Method in class pal.treesearch.UnrootedMLSearcher
- buildPALTreeBase() - Method in class pal.treesearch.GeneralLikelihoodSearcher
- buildPALTreeES() - Method in class pal.treesearch.GeneralLikelihoodSearcher
- buildRightDecendentPALNodeBase() - Method in class pal.treesearch.AbstractParentableConstrainedNode
C
- 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(CachedRateMatrix) - Constructor for class pal.substmodel.CachedRateMatrix
- CachedRateMatrix(RateMatrix, int) - Constructor for class pal.substmodel.CachedRateMatrix
- CachedRateMatrix(RateMatrix, DoubleKeyCache) - 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, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in class pal.eval.SimpleUnconstrainedLikelihoodModel.InternalImpl
- calculateExtended(double, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.UnconstrainedLikelihoodModel.Internal
- calculateExtended(double, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.UnconstrainedLikelihoodModel.External
- calculateExtended(double, SubstitutionModel, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore, boolean) - Method in interface pal.eval.LHCalculator.Internal
- calculateExtended(double, SubstitutionModel, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.LHCalculator.External
- calculateExtendedConditionals(double, double) - Method in interface pal.eval.MolecularClockLikelihoodModel.Leaf
- calculateExtendedConditionals(double, double, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.MolecularClockLikelihoodModel.Internal
- calculateExtendedConditionals(double, double, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.MolecularClockLikelihoodModel.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) - Method in interface pal.eval.UnconstrainedLikelihoodModel.Internal
-
calculate flat probability information (not extended over a branch).
- calculateFlat(PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.LHCalculator.External
- calculateFlat(PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.UnconstrainedLikelihoodModel.External
- calculateFlatConditionals(double) - Method in interface pal.eval.MolecularClockLikelihoodModel.Leaf
- calculateFlatConditionals(double, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.MolecularClockLikelihoodModel.External
- calculateFlatConditionals(PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.MolecularClockLikelihoodModel.Internal
- 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() - Method in class pal.eval.FastLikelihoodCalculator
- calculateLogLikelihood() - Method in class pal.eval.GeneralLikelihoodCalculator
- calculateLogLikelihood() - Method in interface pal.eval.LikelihoodCalculator
- calculateLogLikelihood() - Method in class pal.eval.SimpleLikelihoodCalculator
-
compute log-likelihood for current tree (fixed branch lengths and model) return log-likelihood
- calculateLogLikelihood() - Method in class pal.treesearch.UnrootedMLSearcher
-
Likelihood calculation method (not optimisation)
- calculateLogLikelihood(double[], double[], int) - Method in class pal.eval.ConditionalProbabilityStore
- calculateLogLikelihood(double[], double[], int[], int) - Method in class pal.eval.ConditionalProbabilityStore
- 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(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(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(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(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(Tree, Alignment, SubstitutionModel) - Static method in class pal.eval.LikelihoodTool
-
Calculate the log likelihood of a particular set of phylogenetic data
- calculateLogLikelihood(Tree, Alignment, SubstitutionModel) - Static method in class pal.treesearch.TreeSearchTool
-
Calculate the log likelihood of a particular set of phylogenetic data
- 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
- calculateLogLikelihood2() - Method in class pal.treesearch.UnrootedMLSearcher
-
An alternative likelihood calculation method (should give same results as other method, and in same time)
- calculateLogLikelihood2(GeneralConstructionTool) - Method in class pal.treesearch.FreeBranch
- calculateLogLikelihoodNonRoot(double, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.MolecularClockLikelihoodModel.External
-
Calculate the likelihood given a non root node
- 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
- calculateLogLikelihoodSingle(SubstitutionModel, int[], int, ConditionalProbabilityStore) - Method in interface pal.eval.LHCalculator.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, int, ConditionalProbabilityStore) - Method in interface pal.eval.UnconstrainedLikelihoodModel.External
-
Extend the conditionals back in time by some distance
- calculateSingleExtendedDirect(double, SubstitutionModel, int, 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
- 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
- calculateSiteDetails() - Method in class pal.treesearch.UnrootedMLSearcher
- calculateSiteDetails(double, PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.MolecularClockLikelihoodModel.External
- calculateSiteDetails(UnconstrainedLikelihoodModel.External, GeneralConstructionTool) - Method in class pal.treesearch.FreeBranch
- calculateSiteDetailsRooted(PatternInfo, ConditionalProbabilityStore, ConditionalProbabilityStore) - Method in interface pal.eval.UnconstrainedLikelihoodModel.External
-
Calculate the conditional probabilities of each pattern for each category
- 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
- calculateSiteDetailsUnrooted(double, PatternInfo, ConditionalProbabilityStore, 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
- 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) - Static method in class pal.statistics.ExponentialDistribution
-
cumulative density function of the exponential distribution
- cdf(double, double[]) - Static method in class pal.statistics.DiscreteStatistics
-
compute the cumulative probability Pr(x <= z) for a given z and a distribution of x
- cdf(double, double[], int[]) - Static method in class pal.statistics.DiscreteStatistics
-
compute the cumulative probability Pr(x <= z) for a given z and a distribution of x
- cdf(double, double, double) - Static method in class pal.statistics.GammaDistribution
-
cumulative density function of the Gamma distribution
- cdf(double, double, double) - Static method in class pal.statistics.NormalDistribution
-
cumulative density function
- cdf(double, double, double) - Static method in class pal.statistics.ParetoDistribution
-
cumulative density function of the Pareto distribution
- CharacterAlignment - Interface 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() - 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
- clone(TimeOrderCharacterData) - Static method in class pal.misc.TimeOrderCharacterData
-
Returns a clone of the specified TimeOrderCharacterData
- 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[][]) - Method in class pal.statistics.KishinoHasegawaTest
-
Compare all given hypotheses to the best (ML) hypothesis and store results in public arrays delta, deltaSE, pval (which will automatically be created by this procedure).
- compare(double[][], int) - Method in class pal.statistics.ModelSupport
-
Determine posterior probabilties and support values for each hypothesis and store results in public arrays posterior, support etc which will automatically be created by this procedure.
- compare(double[][], int) - Method in class pal.statistics.ShimodairaHasegawaTest
-
Compare all given hypotheses to the best (ML) hypothesis and store results in public arrays delta, pval (which will automatically be created by this procedure).
- compare(double[][], int[]) - Method in class pal.statistics.KishinoHasegawaTest
-
Compare all given hypotheses to the best (ML) hypothesis and store results in public arrays delta, deltaSE, pval (which will automatically be created by this procedure).
- compare(double[][], int[], int) - Method in class pal.statistics.ModelSupport
-
Determine posterior probabilties and support values for each hypothesis and store results in public arrays posterior, support etc which will automatically be created by this procedure.
- compare(double[][], int[], int) - Method in class pal.statistics.ShimodairaHasegawaTest
-
Compare all given hypotheses to the best (ML) hypothesis and store results in public arrays delta, pval (which will automatically be created by this procedure).
- compare(double[], int[]) - Static method in class pal.statistics.ChiSquareTest
-
chi square test
- compare(Object, Object) - Method in interface pal.util.Comparator
-
Returns a number representing the ordering relationship that the two objects have.
- compareTo(Object) - Method in class pal.misc.Identifier
- compareTo(Object) - Method in 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() - Method in class pal.eval.DemographicValue
- 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(DemographicModel) - Method in class pal.coalescent.CoalescentIntervals
-
Returns the log likelihood of this set of coalescent intervals, given a demographic model.
- 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(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(int, double) - Constructor for class pal.mep.ConstantMutationRate
-
Construct demographic model with default settings
- 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(double, int) - Constructor for class pal.coalescent.ConstantPopulation
-
Construct demographic model of a constant population size.
- ConstantPopulation(int) - Constructor for class pal.coalescent.ConstantPopulation
-
Construct demographic model with default settings
- 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(double, double, double, double, int, int) - Constructor for class pal.coalescent.ConstExpConst
-
Construct demographic model of constexpconst population.
- ConstExpConst(int, int) - Constructor for class pal.coalescent.ConstExpConst
-
Construct demographic model with default settings.
- 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(double, double, double, int, int) - Constructor for class pal.coalescent.ConstExpGrowth
-
Construct demographic model of an expanding population.
- ConstExpGrowth(int, int) - Constructor for class pal.coalescent.ConstExpGrowth
-
Construct demographic model with default settings.
- 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(char[], int, int, boolean, CodonTable) - Static method in class pal.datatype.CodonTableUtils
-
Translates a Nucleotide sequence into a Amino Acid sequence
- convertNucleotideToAminoAcid(String, int, int, boolean, CodonTable) - Static method in class pal.datatype.CodonTableUtils
-
Translates a Nucleotide sequence into a Amino Acid sequence
- 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.misc.Utils
-
Copies all of source into dest - assumes dest to be large enough
- copy(double[], double[]) - Static method in class pal.math.MultivariateMinimum
-
Copy source vector into target vector
- 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 - Class in pal.substmodel
-
CPREV model of amino acid evolution (J.Adachi et al.
- CPREV - Static variable in interface pal.substmodel.AminoAcidModelID
- CPREV - Static variable in interface pal.util.XMLConstants
- CPREV(double[]) - Constructor for class pal.substmodel.CPREV
-
constructor
- CR - Variable in class pal.math.DifferentialEvolution
-
Crossing over factor (default 0.9)
- create(double[][], boolean, int, int[], int, double[]) - Static method in class pal.eval.SiteDetails.Utils
-
Create a Postriors object with no related substitution model
- create(double[][], boolean, SubstitutionModel, int, int[], int, double[]) - Static method in class pal.eval.SiteDetails.Utils
-
Create a Postriors object
- 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(LHCalculator.Factory, SubstitutionModel) - Static method in class pal.eval.SimpleUnconstrainedLikelihoodModel
-
Create a SimpleUnconstrainedLikelihoodModel instance
- createInstance(LHCalculator.Generator, SubstitutionModel) - Static method in class pal.eval.SimpleUnconstrainedLikelihoodModel
-
Create a SimpleUnconstrainedLikelihoodModel instance
- 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
- createInstance(RateMatrixGroup, RateMatrixGroup, NeoParameterized, SingleSplitDistribution, double) - Static method in class pal.eval.SingleSplitMolecularClockLikelihoodModel
- createInstance(RateMatrixGroup, RateMatrixGroup, NeoParameterized, SingleSplitDistribution, LHCalculator.Factory, double) - Static method in class pal.eval.SingleSplitMolecularClockLikelihoodModel
- createInstance(SubstitutionModel) - Static method in class pal.eval.SimpleMolecularClockLikelihoodModel
- 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(double[][], String[]) - Static method in class pal.tree.TreeTool
-
Neighbour-joining tree construction based on a distance matrix
- createNeighbourJoiningTree(DistanceMatrix) - 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() - Method in interface pal.eval.UnconstrainedLikelihoodModel.Instance
- 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
- 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(int[], int) - Method in class pal.treesearch.GeneralConstructionTool
- createNewFreeLeafCalculator(GeneralConstructionTool) - Method in class pal.treesearch.AbstractLeafNode
- createNewInternal() - Method in interface pal.eval.LHCalculator.Generator
- createNewInternal() - Method in interface pal.eval.UnconstrainedLikelihoodModel.Instance
- 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
- createNewLeaf(int[], int) - Method in interface pal.eval.LHCalculator.Generator
-
Create anew leaf calculator
- createNewLeaf(int[], int) - Method in interface pal.eval.UnconstrainedLikelihoodModel.Instance
-
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
- 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[]) - Static method in class pal.misc.IndividualParameterHandler.Utils
- createSimple(Parameterized, int) - 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(NeoRateMatrix, DataType, double[]) - Static method in class pal.substmodel.SubstitutionModel.Utils
- createSubstitutionModel(RateMatrix) - 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
D
- D_QUOTE - Static variable in class pal.io.NexusTokenizer
- DASH - Static variable in class pal.io.NexusTokenizer
- DATA_TYPE - Static variable in interface pal.util.XMLConstants
- DATA_TYPE_ID - Static variable in interface pal.util.XMLConstants
- DataTranslator - Class in pal.alignment
- DataTranslator(int[][]) - Constructor for class pal.alignment.DataTranslator
-
Base DataType is assumed to be IUPAC
- DataTranslator(int[][], MolecularDataType) - Constructor for class pal.alignment.DataTranslator
- DataTranslator(int[][], MolecularDataType, IdGroup) - Constructor for class pal.alignment.DataTranslator
- DataTranslator(Alignment) - Constructor for class pal.alignment.DataTranslator
- DataTranslator(MolecularDataType, char[][]) - Constructor for class pal.alignment.DataTranslator
- DataType - Interface in pal.datatype
-
interface for sequence data types History: 21 March 2003, Added gap stuff, to counter frustration and not being able to differentiat unknowns from gaps.
- DataType.Utils - Class in pal.datatype
-
Some useful methods for implmenting classes and for DataType users
- DataTypeTool - Class in pal.datatype
-
Simple access for data type functions.
- DataTypeTool() - Constructor for class pal.datatype.DataTypeTool
- Dayhoff - Class in pal.substmodel
-
Dayhoff model for amino acid evolution Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C.
- Dayhoff(double[]) - Constructor for class pal.substmodel.Dayhoff
-
constructor
- DAYHOFF - Static variable in interface pal.substmodel.AminoAcidModelID
- DAYHOFF - Static variable in interface pal.util.XMLConstants
- DAYS - Static variable in interface pal.misc.Units
- DAYS - Static variable in interface pal.util.XMLConstants
- debug(Object) - Method in class pal.math.OrthogonalSearch
- debug(Object) - Method in class pal.util.Log
- debug(Object) - Method in interface pal.util.Logger
- DEFAULT_FONT - Static variable in class pal.gui.TreePainter
- DEFAULT_FONT_NAME - Static variable in class pal.gui.TreePainter
- DEFAULT_FONT_SIZE - Static variable in class pal.gui.TreePainter
- DEFAULT_FONT_STYLE - Static variable in class pal.gui.TreePainter
- DEFAULT_INSTANCE - Static variable in class pal.datatype.AminoAcids
- DEFAULT_INSTANCE - Static variable in class pal.datatype.Codons
- DEFAULT_INSTANCE - Static variable in class pal.datatype.GapBalanced
- DEFAULT_INSTANCE - Static variable in class pal.datatype.IUPACNucleotides
- DEFAULT_INSTANCE - Static variable in class pal.datatype.Nucleotides
- DEFAULT_INSTANCE - Static variable in class pal.datatype.NumericDataType
- DEFAULT_INSTANCE - Static variable in class pal.datatype.TwoStates
- DEFAULT_KAPPA - Static variable in class pal.substmodel.YangCodonModel
- DEFAULT_LENGTH - Static variable in interface pal.misc.BranchLimits
-
default branch length
- DEFAULT_OMEGA - Static variable in class pal.substmodel.YangCodonModel
- DefaultCache - Class in pal.util
- DefaultCache() - Constructor for class pal.util.DefaultCache
- DefaultCache(int) - Constructor for class pal.util.DefaultCache
- defaultStep - Variable in class pal.math.ConjugateGradientSearch
-
defaultStep is a steplength parameter and should be set equal to the expected distance from the solution (in a line search) exceptionally small or large values of defaultStep lead to slower convergence on the first few iterations (the step length itself is adapted during search), the default value is 1.0
- delta - Variable in class pal.statistics.KishinoHasegawaTest
-
log-likelihood difference to maximum likelihood hypothesis
- delta - Variable in class pal.statistics.ShimodairaHasegawaTest
-
log-likelihood difference to maximum likelihood hypothesis
- deltaL - Variable in class pal.statistics.ModelSupport
-
log-likelihood differences to the best tree
- DeltaModel - Interface in pal.mep
- DeltaModel.Instance - Interface in pal.mep
- DeltaModel.Utils - Class in pal.mep
- deltaSE - Variable in class pal.statistics.KishinoHasegawaTest
-
estimated error of log-likelihood differences
- DEMOGRAPHIC_MODEL - Static variable in interface pal.util.XMLConstants
- DemographicClockTree - Class in pal.coalescent
-
Provides parameter interface to a clock-like genealogy which is assumed to have some demographic pattern of theta (diversity) as well as branch parameters (the minimal node height differences at each internal node).
- DemographicClockTree(Tree, DemographicModel) - Constructor for class pal.coalescent.DemographicClockTree
-
take any tree and afford it with an interface suitable for a clock-like genealogy, under a certain demographic assumption.
- DemographicLikelihoodValue - Class in pal.eval
-
Estimates the likelihood for a tree using a specified model of sequence evolution and a sequence alignment and a specific demographic model as a prior on coalescent intervals.
- DemographicLikelihoodValue(SitePattern) - Constructor for class pal.eval.DemographicLikelihoodValue
-
Parameter taking a site pattern.
- DemographicModel - Class in pal.coalescent
-
This abstract class contains methods that are of general use for modelling coalescent intervals given a demographic model.
- DemographicModel() - Constructor for class pal.coalescent.DemographicModel
- DemographicTree - Interface in pal.coalescent
-
interface defining a parameterized tree that includes demographic information.
- DemographicValue - Class in pal.eval
-
estimates demographic parameters by maximising the coalescent prior for a tree with given branch lengths.
- DemographicValue() - Constructor for class pal.eval.DemographicValue
- diagonalHessian(MultivariateFunction, double[]) - Static method in class pal.math.NumericalDerivative
-
determine diagonal of Hessian
- DifferentialEvolution - Class in pal.math
-
global minimization of a real-valued function of several variables without using derivatives using a genetic algorithm (Differential Evolution)
- DifferentialEvolution(int) - Constructor for class pal.math.DifferentialEvolution
-
construct DE optimization modul (population size is selected automatically)
- DifferentialEvolution(int, int) - Constructor for class pal.math.DifferentialEvolution
-
construct optimization modul
- DIRECTION - Static variable in interface pal.util.XMLConstants
- directProduct4(double[], double[], double[]) - Static method in class pal.eval.GeneralLikelihoodCalculator
- DiscreteStatistics - Class in pal.statistics
-
simple discrete statistics (mean, variance, cumulative probability, quantiles etc.)
- DiscreteStatistics() - Constructor for class pal.statistics.DiscreteStatistics
- display(Graphics, String, int, int) - Method in interface pal.gui.LabelDisplayer
- displayDecimal(PrintWriter, double, int) - Method in class pal.io.FormattedOutput
-
print decimal number with a prespecified number of digits after the point
- displayInteger(PrintWriter, int, int) - Method in class pal.io.FormattedOutput
-
print integer, aligned to a reference number, (introducing space at the left side)
- displayIntegerWhite(PrintWriter, int) - Method in class pal.io.FormattedOutput
-
print whitespace of length of a string displaying a given integer
- displayLabel(PrintWriter, String, int) - Method in class pal.io.FormattedOutput
-
print label with a prespecified length (label will be shortened or spaces will introduced, if necessary)
- displayLabel(PrintWriter, String, int, boolean) - Static method in class pal.tree.Local
-
print label with a prespecified length (label will be shortened or spaces will introduced, if necessary)
- distance - Variable in class pal.distance.PairwiseDistance
-
last estimated distance
- DistanceMatrix - Class in pal.distance
-
storage for pairwise distance matrices.
- DistanceMatrix() - Constructor for class pal.distance.DistanceMatrix
-
constructor
- DistanceMatrix(double[][], IdGroup) - Constructor for class pal.distance.DistanceMatrix
-
constructor taking distances array and IdGroup
- DistanceMatrix(DistanceMatrix) - Constructor for class pal.distance.DistanceMatrix
-
constructor that takes a distance matrix and clones the distances but uses the same idGroup.
- DistanceMatrix(DistanceMatrix, IdGroup) - Constructor for class pal.distance.DistanceMatrix
-
constructor that takes a distance matrix and clones the distances, of a the identifiers in idGroup.
- DistanceMatrixAccess - Interface in pal.distance
- DistanceMatrixAccess.Utils - Class in pal.distance
- DistanceMatrixGenerator - Interface in pal.distance
- DistanceMatrixGenerator.Utils - Class in pal.distance
- DistanceMatrixUtils - Class in pal.distance
-
Auxillary functions for distance matrices
- DistanceMatrixUtils() - Constructor for class pal.distance.DistanceMatrixUtils
- DistanceParseException - Exception in pal.distance
-
exception thrown by ReadDistanceMatrix
- DistanceParseException() - Constructor for exception pal.distance.DistanceParseException
- DistanceParseException(String) - Constructor for exception pal.distance.DistanceParseException
- distanceSE - Variable in class pal.distance.PairwiseDistance
-
last estimate standard error of a distance
- DistanceTool - Class in pal.distance
- DistanceTool() - Constructor for class pal.distance.DistanceTool
- DNA_INSTANCE - Static variable in class pal.datatype.IUPACNucleotides
- doAction(double, double) - Method in class pal.algorithmics.GeneralObjectState
-
Perform an action
- doAction(double, double) - Method in interface pal.algorithmics.ObjectState
-
Perform an action
- doAction(double, double) - Method in interface pal.algorithmics.UndoableAction
-
Perform an action
- doNNI(boolean, boolean) - Method in class pal.treesearch.FreeBranch
-
Does not reconstruct patterns
- doNNI(MersenneTwisterFast) - Method in class pal.treesearch.FreeBranch
- doRound(double[], UnivariateMinimum, double, double, MinimiserMonitor) - Method in interface pal.math.OrthogonalSearch.RoundOptimiser
- doScale(Graphics, double, int, int) - Method in class pal.gui.TreePainter
- doTitle(Graphics, int, int) - Method in class pal.gui.TreePainter
- dotProduct4(double[], double[]) - Static method in class pal.eval.GeneralLikelihoodCalculator
- dotProduct4(double[], double[], double[]) - Static method in class pal.eval.GeneralLikelihoodCalculator
- DOUBLE - Static variable in class pal.misc.Attribute
- DoubleKey - Interface in pal.util
- DoubleKeyCache - Interface in pal.util
- doubleValue() - Method in class pal.util.ComparableDouble
- DPRIME - Static variable in class pal.gui.LinkageDisequilibriumComponent
- drawArc(double, double, double) - Method in class pal.gui.CircularGraphics
-
For drawing arbitary lines
- drawDontPutBack() - Method in class pal.math.UrnModel
-
draw a number without putting back
- drawLine(double, double, double) - Method in class pal.gui.CircularGraphics
-
For drawing arbitary lines
- drawLine(double, double, double, double) - Method in class pal.gui.CircularGraphics
-
For drawing arbitary lines
- drawLineDegreeAlign(double, double, double) - Method in class pal.gui.CircularGraphics
-
For drawing arbitary lines
- drawPoint(double, double, int) - Method in class pal.gui.CircularGraphics
- drawPutBack() - Method in class pal.math.UrnModel
-
draws a number with putting back
- drawString(String, double, double) - Method in class pal.gui.CircularGraphics
- drawString(String, double, double, int) - Method in class pal.gui.CircularGraphics
- drawSymbol(double, double, int, int, int) - Method in class pal.gui.CircularGraphics
- drawSymbol(Graphics, int, int, int, int) - Static method in class pal.gui.TreePainter
- dropSite(int) - Method in class pal.alignment.StrippedAlignment
-
drop a site
E
- ECHINODERM_MITOCHONDRIAL - Static variable in interface pal.datatype.CodonTable
-
TypeID for Echinoderm Mitochondrial
- EDGE - Static variable in interface pal.util.XMLConstants
- efronCI(double, double[]) - Static method in class pal.statistics.BootstrapStatistics
-
compute approximate central confidence interval for thetaHat (Efron percentile method)
- efronCI(double, double[], int[]) - Static method in class pal.statistics.BootstrapStatistics
-
compute approximate central confidence interval for thetaHat (Efron percentile method)
- ElementFactory - Class in pal.xml
-
This class provides static methods for creating DOM Elements from PAL Objects.
- ElementFactory() - Constructor for class pal.xml.ElementFactory
- ElementParser - Class in pal.xml
-
This class provides static methods for parsing PAL objects from DOM Elements.
- ElementParser() - Constructor for class pal.xml.ElementParser
- ensureBounded(double, double, double) - Static method in class pal.math.MathUtils
-
Ensure a value of x is actaully bounded between two values.
- ensureUnknownState(int[], int) - Method in class pal.alignment.DataTranslator
-
Ensures that all states that are "unknown" get set to the value of 'unknownState'
- ensureUnknownState(DataType, int[], int) - Static method in class pal.alignment.DataTranslator
-
Ensures that all states that are "unknown" (according to a certain DataType) get set to the value of 'unknownState'
- environmentNames - Variable in class pal.alignment.SimpleCharacterAlignment
-
names of the traits
- EPSILON - Static variable in class pal.math.MachineAccuracy
-
machine accuracy constant
- equal(Node, Node) - Static method in class pal.tree.RootedTreeUtils
- equals(Object) - Method in class pal.misc.Identifier
- equals(Object) - Method in class pal.treesearch.UnrootedMLSearcher.StateObject
- equals(Object) - Method in interface pal.util.Comparable
-
Returns true if this object is equal to the given object.
- equals(Object) - Method in class pal.util.ComparableDouble
- equals(Object, Object) - Method in interface pal.util.Comparator
-
Returns true if the two objects are equal.
- EQUALS - Static variable in class pal.io.NexusTokenizer
- erf(double) - Static method in class pal.math.ErrorFunction
-
error function
- erfc(double) - Static method in class pal.math.ErrorFunction
-
complementary error function = 1-erf(x)
- ErrorFunction - Class in pal.math
-
error function and related stuff
- ErrorFunction() - Constructor for class pal.math.ErrorFunction
- estimate() - Method in class pal.eval.ModelParameters
-
estimate (approximate) values for the model parameters from the data using a neighbor-joining tree
- estimateCodonFrequenciesF1X4(Alignment) - Static method in class pal.alignment.AlignmentUtils
-
Estimate the frequencies of codons, calculated from the average nucleotide frequencies.
- estimateCodonFrequenciesF3X4(Alignment) - Static method in class pal.alignment.AlignmentUtils
-
Estimate the frequencies of codons, calculated from the average nucleotide frequencies at the three codon positions.
- estimateFrequencies(Alignment) - Static method in class pal.alignment.AlignmentUtils
-
count states
- estimateFromTree(ParameterizedTree) - Method in class pal.eval.ModelParameters
-
estimate (approximate) values for the model parameters from the data using a given (parameterized) tree
- estimateTupletFrequencies(Alignment, int) - Static method in class pal.alignment.AlignmentUtils
-
Estimates frequencies via tuplets.
- EUPLOTID_NUCLEAR - Static variable in interface pal.datatype.CodonTable
-
TypeID for Euplotid Nuclear
- evaluate(double) - Method in class pal.distance.SequencePairLikelihood
- evaluate(double) - Method in class pal.math.LineFunction
-
evaluate f(start+lambda*dir)
- evaluate(double) - Method in class pal.math.OrthogonalLineFunction
- evaluate(double) - Method in interface pal.math.UnivariateFunction
-
compute function value
- evaluate(double[]) - Method in class pal.eval.ChiSquareValue
-
compute (weighted) least-squares value
- evaluate(double[]) - Method in class pal.eval.DemographicValue
- evaluate(double[]) - Method in class pal.eval.ModelParameters
- evaluate(double[]) - Method in class pal.math.BoundsCheckedFunction
-
computes function value, taking into account the constraints on the argument
- evaluate(double[]) - Method in class pal.math.EvaluationCounter
- evaluate(double[]) - Method in interface pal.math.MultivariateFunction
-
compute function value
- evaluate(double[], double[]) - Method in interface pal.math.MFWithGradient
-
compute both function value and gradient at a point
- EvaluationCounter - Class in pal.math
-
A utiltity class that can be used to track the number of evaluations of a general function
- EvaluationCounter(MultivariateFunction) - Constructor for class pal.math.EvaluationCounter
- EventGenerator() - Constructor for class pal.misc.PalObjectListener.EventGenerator
- exchangeInfo(Node, Node) - Static method in class pal.tree.NodeUtils
-
Exchange field info between two nodes.
- EXPAND_CONSTRUCTION - Static variable in class pal.tree.TreeManipulator
-
Construct tree, but convert general multifications to a series of bifications
- EXPANDING_POPULATION - Static variable in interface pal.util.XMLConstants
- ExpandingPopulation - 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.
- ExpandingPopulation(double, double, double, int) - Constructor for class pal.coalescent.ExpandingPopulation
-
Construct demographic model of an expanding population
- ExpandingPopulation(int) - Constructor for class pal.coalescent.ExpandingPopulation
-
Construct demographic model with default settings
- EXPECTED_SUBSTITUTIONS - Static variable in interface pal.misc.Units
- EXPECTED_TS_TV_PARAMETER_INDEX - Static variable in class pal.substmodel.F84
- EXPONENTIAL_GROWTH - Static variable in interface pal.util.XMLConstants
- ExponentialDistribution - Class in pal.statistics
-
exponential distribution.
- ExponentialDistribution() - Constructor for class pal.statistics.ExponentialDistribution
- ExponentialGrowth - Class in pal.coalescent
-
This class models an exponentially growing (or shrinking) population (Parameters: N0=present-day population size; r=growth rate).
- ExponentialGrowth(double, double, int) - Constructor for class pal.coalescent.ExponentialGrowth
-
Construct demographic model of an exponentially growing population
- ExponentialGrowth(int) - Constructor for class pal.coalescent.ExponentialGrowth
-
Construct demographic model with default settings
- ExternalParameterListener - Interface in pal.misc
-
Defines objects that listen to exteneral ParameterEvents
- extract(FreeBranch) - Method in class pal.treesearch.FreeInternalNode
- extract(FreeBranch) - Method in class pal.treesearch.FreeLeafNode
- extract(FreeBranch) - Method in interface pal.treesearch.FreeNode
-
Instruct the node to extract itself from the two connections that aren't the caller One of the other two connections will become redunant.
- extract(FreeBranch) - Method in class pal.treesearch.PivotNode
-
We can't extract
- extractAlignment(Tree) - Static method in class pal.tree.TreeUtils
-
Extracts an alignment from a tree.
- extractAlignment(Tree, boolean) - Static method in class pal.tree.TreeUtils
-
Extracts an alignment from a tree.
- extractFromClockTree(Tree) - Static method in class pal.coalescent.IntervalsExtractor
-
extracts intervals from clock tree.
- extractFromClockTree(Tree, double) - Static method in class pal.coalescent.IntervalsExtractor
-
extracts intervals from clock tree.
- extractFromTree(Tree) - Static method in class pal.coalescent.IntervalsExtractor
-
extracts intervals from serial clock tree.
- extractFromTree(Tree, MutationRateModel) - Static method in class pal.coalescent.IntervalsExtractor
-
extracts intervals in generation times from serial clock tree (in mutation times) after taking into account mutation rate model.
- extractTimeOrderCharacterData(Tree, int) - Static method in class pal.tree.TreeUtils
-
Extracts a time order character data from a tree.
F
- F - Variable in class pal.math.DifferentialEvolution
-
weight factor (default 0.7)
- F_SLASH - Static variable in class pal.io.NexusTokenizer
- f2minx - Variable in class pal.math.UnivariateMinimum
-
curvature at minimum
- F81 - Class in pal.substmodel
-
Felsenstein 1981 model of nucleotide evolution
- F81 - Static variable in interface pal.substmodel.NucleotideModelID
- F81 - Static variable in interface pal.util.XMLConstants
- F81(double[]) - Constructor for class pal.substmodel.F81
-
constructor
- F84 - Class in pal.substmodel
-
Felsenstein 1984 (PHYLIP) model of nucleotide evolution
- F84 - Static variable in interface pal.substmodel.NucleotideModelID
- F84 - Static variable in interface pal.util.XMLConstants
- F84(double[], double[]) - Constructor for class pal.substmodel.F84
-
Constructor 2
- F84(double, double[]) - Constructor for class pal.substmodel.F84
-
constructor 1
- Factory(int, SubstitutionModel) - Constructor for class pal.tree.SimulatedAlignment.Factory
- FastFourStateLHCalculator - Class in pal.eval
- FastFourStateLHCalculator() - Constructor for class pal.eval.FastFourStateLHCalculator
- FastLikelihoodCalculator - Class in pal.eval
-
Title: Fast Likelihood Calculator
Description: A fast likelihood calculator
Original code by Matthew Goode. - FastLikelihoodCalculator(SitePattern) - Constructor for class pal.eval.FastLikelihoodCalculator
-
Constructor taking only site pattern.
- FastLikelihoodCalculator(SitePattern, Tree, RateMatrix) - Constructor for class pal.eval.FastLikelihoodCalculator
-
Constructor taking site pattern, tree and model.
- fillInLSInfo(double[], int, int, int) - Method in interface pal.supgma.ThetaHandler
- fillInLSInfo(double[], int, int, int, double[]) - Method in interface pal.supgma.RateHandler
- fillPoint(double, double, int) - Method in class pal.gui.CircularGraphics
- findByIdentifier(Node, String) - Static method in class pal.tree.NodeUtils
-
Returns the first node in this tree that has the required identifier.
- findByIdentifier(Node, String[]) - Static method in class pal.tree.NodeUtils
-
Returns the first nodes in this tree that has the required identifiers.
- findByIdentifier(Node, Identifier) - Static method in class pal.tree.NodeUtils
-
Returns the first node in this tree that has the required identifier.
- findByIdentifier(Node, Identifier[]) - Static method in class pal.tree.NodeUtils
-
Returns the first nodes in this tree that has the required identifiers.
- findInterval(double) - Method in class pal.coalescent.SkylinePlot
-
Find interval corresponding to a specific time
- findLargestChild(Node) - Static method in class pal.tree.NodeUtils
-
Finds the largest child (in terms of node height).
- findMinimum() - Method in class pal.math.LineFunction
-
find parameter lambda within the given bounds that minimizes the univariate function (due to numerical inaccuaries it may happen that getPoint for the returned lambda produces a point that lies slightly out of bounds)
- findMinimum(double, UnivariateFunction) - Method in class pal.math.UnivariateMinimum
-
Find minimum (first estimate given)
- findMinimum(double, UnivariateFunction, int) - Method in class pal.math.UnivariateMinimum
-
Find minimum (first estimate given, desired number of fractional digits specified)
- findMinimum(MultivariateFunction, double[]) - Method in class pal.math.MultivariateMinimum
-
Find minimum close to vector x
- findMinimum(MultivariateFunction, double[], int, int) - Method in class pal.math.MultivariateMinimum
-
Find minimum close to vector x (desired fractional digits for each parameter is specified)
- findMinimum(MultivariateFunction, double[], int, int, MinimiserMonitor) - Method in class pal.math.MultivariateMinimum
-
Find minimum close to vector x (desired fractional digits for each parameter is specified)
- findMinimum(UnivariateFunction) - Method in class pal.math.UnivariateMinimum
-
Find minimum (no first estimate given)
- findMinimum(UnivariateFunction, int) - Method in class pal.math.UnivariateMinimum
-
Find minimum (no first estimate given, desired number of fractional digits specified)
- findNode(int) - Method in class pal.tree.SimpleTree
-
return node with number num (as displayed in ASCII tree)
- findNode(int) - Method in class pal.tree.Tree.TreeBase
-
return node with number num (as displayed in ASCII tree)
- fireParametersChangedEvent() - Method in class pal.misc.PalObjectListener.EventGenerator
-
Called by subclasses to fire the default Event on all listeners
- fireParametersChangedEvent() - Method in class pal.substmodel.AbstractRateMatrix
- fireParametersChangedEvent(PalObjectEvent) - Method in class pal.misc.PalObjectListener.EventGenerator
-
Called by subclasses to fire a specific PalObjectEvent on all listeners
- fireParametersChangedEvent(PalObjectEvent) - Method in class pal.substmodel.AbstractRateMatrix
- fireStructureChangedEvent() - Method in class pal.misc.PalObjectListener.EventGenerator
-
Called by subclasses to fire the default Event on all listeners
- fireStructureChangedEvent(PalObjectEvent) - Method in class pal.misc.PalObjectListener.EventGenerator
-
Called by subclasses to fire a specific PalObjectEvent on all listeners
- first - Variable in class pal.util.ThreeNumberSort
-
order of the numbers (0-2)
- firstDerivative(UnivariateFunction, double) - Static method in class pal.math.NumericalDerivative
-
determine first derivative
- firstSite - Variable in class pal.alignment.StrippedAnnotatedAlignment
- FisherExact - Class in pal.statistics
-
This does a one tail fisher exact test.
- FisherExact(int) - Constructor for class pal.statistics.FisherExact
-
constructor for FisherExact table
- FixedBSRDTGlobalClockModel - Class in pal.treesearch
- FixedBSRDTGlobalClockModel(SampleInformation, MolecularClockLikelihoodModel.Instance, double) - Constructor for class pal.treesearch.FixedBSRDTGlobalClockModel
- FixedSRDTGlobalClockModel - Class in pal.treesearch
- FixedSRDTGlobalClockModel(SampleInformation, MolecularClockLikelihoodModel.Instance, double) - Constructor for class pal.treesearch.FixedSRDTGlobalClockModel
- FLATWORM_MITOCHONDRIAL - Static variable in interface pal.datatype.CodonTable
-
TypeID for Flatworm Mitochondrial
- FLETCHER_REEVES_UPDATE - Static variable in class pal.math.ConjugateGradientSearch
- FLOAT - Static variable in class pal.misc.Attribute
- fminx - Variable in class pal.math.UnivariateMinimum
-
function value at minimum
- fo - Variable in class pal.coalescent.DemographicModel
- fo - Variable in class pal.mep.MutationRateModel
- FONT_SIZE - Static variable in class pal.gui.TreePainterNormal
- FOREGROUND - Static variable in class pal.gui.TreePainter
- format - Variable in class pal.substmodel.AbstractRateMatrix
- format - Variable in class pal.substmodel.RateDistribution
- FormattedInput - Class in pal.io
-
tools to simplify formatted input from an input stream
- FormattedOutput - Class in pal.io
-
tools to simplify formatted output to a stream
- FRACDIGITS - Static variable in class pal.eval.ModelParameters
-
fractional digits desired for parameters
- FRACDIGITS - Static variable in interface pal.misc.BranchLimits
-
desired fractional digits when determining branch lengths
- FREE_BRANCH_COMPONENT_TYPE - Static variable in interface pal.treesearch.Constants
- FREE_LEAF_COMPONENT_TYPE - Static variable in interface pal.treesearch.Constants
- FREE_NODE_COMPONENT_TYPE - Static variable in interface pal.treesearch.Constants
- FreeBranch - Class in pal.treesearch
- FreeBranch(Node, FreeNode, GeneralConstructionTool, GeneralConstraintGroupManager.Store) - Constructor for class pal.treesearch.FreeBranch
-
Continuing recurison constructor for a given tree
- FreeBranch(Node, GeneralConstructionTool, GeneralConstraintGroupManager.Store) - Constructor for class pal.treesearch.FreeBranch
-
The starting constructor for building from a given tree
- FreeBranch(FreeNode, FreeNode, double, GeneralConstructionTool) - Constructor for class pal.treesearch.FreeBranch
-
A generic constructor given two already defined left and right children
- FreeInternalNode - Class in pal.treesearch
- FreeInternalNode(Node, FreeBranch, GeneralConstructionTool, GeneralConstraintGroupManager.Store) - Constructor for class pal.treesearch.FreeInternalNode
- FreeLeafNode - Class in pal.treesearch
- FreeLeafNode(FreeBranch, String, GeneralConstructionTool) - Constructor for class pal.treesearch.FreeLeafNode
- FreeNode - Interface in pal.treesearch
- FREQUENCIES - Static variable in interface pal.util.XMLConstants
G
- 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, boolean, int) - Constructor for class pal.alignment.GapBalancedAlignment
-
GapBalanced power user constructor
- GapBalancedAlignment(Alignment, int, int) - Constructor for class pal.alignment.GapBalancedAlignment
-
GapBalanced power user constructor
- 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
- 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() - 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() - 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
- generateFactory(boolean) - Static method in class pal.math.OrthogonalSearch
-
Generate a MultivariateMinimum.Factory for an OrthogonalSearch
- generateFactory(int) - Static method in class pal.math.GeneralizedDEOptimizer
-
Generate a MultivariateMinimum.Factory for an GeneralizedDEOptimiser with a set population size
- 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() - Method in class pal.substmodel.SequenceSimulator
- generateRoot(double) - Method in interface pal.eval.MolecularClockLikelihoodModel.Simulator
- 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, DataType, TransitionPenaltyTable, double, double, boolean) - Static method in class pal.alignment.AlignmentUtils
-
Returns total sum of pairs alignment distance using gap creation and extension penalties and transition penalties as defined in the TransitionPenaltyTable provided.
- getAlignmentPenalty(Alignment, TransitionPenaltyTable, double, double) - Static method in class pal.alignment.AlignmentUtils
-
Returns total sum of pairs alignment penalty using gap creation and extension penalties and transition penalties in the TransitionPenaltyTable provided.
- 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) - Method in class pal.treesearch.FreeInternalNode
- getAllComponents(ArrayList, Class) - Method in class pal.treesearch.FreeLeafNode
- getAllComponents(ArrayList, Class) - Method in interface pal.treesearch.GeneralTreeComponent
- getAllComponents(ArrayList, Class) - Method in interface pal.treesearch.RootAccess
- getAllComponents(ArrayList, Class, FreeBranch) - Method in class pal.treesearch.FreeInternalNode
- getAllComponents(ArrayList, Class, FreeBranch) - 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, FreeBranch) - Method in class pal.treesearch.PivotNode
- getAllComponents(ArrayList, Class, FreeNode) - Method in class pal.treesearch.FreeBranch
- 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, 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 interface pal.datatype.AmbiguousDataType
-
A more accurate attempt 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(double[]) - Static method in class pal.misc.Utils
-
Find the maximum "argument" (of a double array)
- getArgmax(int[]) - Static method in class pal.misc.Utils
-
Find the maximum "argument"
- 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(String) - Method in class pal.tree.SimpleNode
- getAttribute(Node, String) - Method in class pal.tree.ParameterizedTree.ParameterizedTreeBase
- 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(int) - Method in class pal.misc.MultiParameterized
- getBaseParameters(Parameterized) - 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(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
- 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
- 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(int, int[]) - Method in class pal.distance.DistanceMatrix
- getClosestIndex(String, String[]) - 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() - Method in class pal.substmodel.GeneralRateDistributionSubstitutionModel
- getCopy() - Method in class pal.substmodel.MultiRateMatrixHandler
- getCopy() - Method in class pal.substmodel.RateMatrixHandler
- getCopy() - Method in class pal.substmodel.SingleClassSubstitutionModel
- getCopy() - Method in class pal.substmodel.YangCodonModel.SimpleNeutralSelection
- getCopy() - Method in class pal.substmodel.YangCodonModel.SimplePositiveSelection
- 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
- getCopy(boolean[][]) - Static method in class pal.misc.Utils
-
Clones an array of booleans
- getCopy(byte[]) - Static method in class pal.misc.Utils
-
Clones an array of bytes
- getCopy(byte[][]) - Static method in class pal.misc.Utils
-
Clones an array of bytes
- getCopy(double[]) - Static method in class pal.misc.Utils
-
Clones an array of doubles
- getCopy(double[][]) - Static method in class pal.misc.Utils
-
Clones an array of doubles
- getCopy(double[][][]) - Static method in class pal.misc.Utils
-
Clones an array of doubles
- getCopy(double[], int) - Static method in class pal.misc.Utils
-
Clones an array of doubles from index start (inclusive) to end
- 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(int[]) - Static method in class pal.misc.Utils
-
Clones an array of ints
- getCopy(int[][]) - Static method in class pal.misc.Utils
-
Clones a matrix of ints
- getCopy(int[], int) - Static method in class pal.misc.Utils
-
Clones an array of ints
- getCopy(String[]) - Static method in class pal.misc.Utils
-
Clones an array of Strings
- getCopy(RateMatrix[]) - Static method in class pal.substmodel.RateMatrixUtils
- getCopy(YangCodonModel[]) - Static method in class pal.substmodel.YangCodonModel.Utils
-
Probably of no use to anyone else (is used by internal code though)
- 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) - 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)
- getData(int, int, int) - Method in class pal.alignment.Genotype
-
sequence alignment at (sequence, site, allele)
- getDataType() - Method in class pal.alignment.AbstractAlignment
-
Returns the datatype of this alignment
- getDataType() - Method in interface pal.alignment.Alignment
-
Return DataType of this alignment.
- getDataType() - Method in class pal.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
- 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
- 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() - Method in interface pal.misc.IndividualParameterHandler
- getDefaultValue() - Method in class pal.misc.MutableDouble
- 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(int) - Method in class pal.misc.MultiParameterized
- 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
- getDimension() - Method in interface pal.substmodel.TransitionProbability
- 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(byte[], byte[]) - Method in class pal.distance.PairwiseDistance
-
compute distance between two sequences (not necessarly in the given alignment but with the same weights in the site pattern)
- getDistance(int, int) - Method in class pal.distance.DistanceMatrix
- getDistance(int, int) - Method in class pal.distance.PairwiseDistance
-
compute distance between two sequences in the given alignment
- getDistances() - Method in class pal.distance.DistanceMatrix
-
Returns the distances as a 2-dimensional array of doubles (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(double) - Method in class pal.mep.MutationRateModel
-
Returns integral of mutation rate function (= integral mu(x) dx from 0 to t).
- getExpectedSubstitutions(double) - Method in class pal.mep.SteppedMutationRate
- getExpectedSubstitutions(double) - Method in class pal.mep.WindowedMutationRate
-
Window must not span zero!
- getExpectedSubstitutions(double, double) - Method in class pal.mep.MutationRateModel
-
Calculates the integral 1/mu(x) dx between start and finish.
- getExpectedSubstitutions(int) - Method in interface pal.mep.DeltaModel.Instance
- getExpectedSubstitutionsToTime(double) - Method in interface pal.mep.DeltaModel.Instance
- getExtendedConditionalProbabilities(double) - Method in class pal.eval.SimpleUnconstrainedLikelihoodModel.LeafImpl
- getExtendedConditionalProbabilities(double) - Method in interface pal.eval.UnconstrainedLikelihoodModel.Leaf
- getExtendedConditionalProbabilities(double, SubstitutionModel, boolean) - Method in interface pal.eval.LHCalculator.Leaf
- getExtendedConditionalProbabilities(double, SubstitutionModel, boolean) - Method in class pal.eval.SimpleLeafCalculator
- getExtendedConditionalProbabilities(double, FreeBranch, UnconstrainedLikelihoodModel.External, ConditionalProbabilityStore, GeneralConstructionTool) - Method in class pal.treesearch.FreeInternalNode
- getExtendedConditionalProbabilities(double, FreeBranch, UnconstrainedLikelihoodModel.External, ConditionalProbabilityStore, GeneralConstructionTool) - Method in class pal.treesearch.FreeLeafNode
- getExtendedConditionalProbabilities(double, FreeBranch, UnconstrainedLikelihoodModel.External, ConditionalProbabilityStore, GeneralConstructionTool) - Method in interface pal.treesearch.FreeNode
- getExtendedConditionalProbabilities(double, FreeBranch, UnconstrainedLikelihoodModel.External, ConditionalProbabilityStore, GeneralConstructionTool) - Method in class pal.treesearch.PivotNode
- getExtendedConditionalProbabilities(double, FreeBranch, GeneralConstructionTool) - Method in class pal.treesearch.FreeInternalNode
- getExtendedConditionalProbabilities(double, FreeBranch, GeneralConstructionTool) - Method in class pal.treesearch.FreeLeafNode
- getExtendedConditionalProbabilities(double, FreeBranch, GeneralConstructionTool) - Method in interface pal.treesearch.FreeNode
- getExtendedConditionalProbabilities(double, FreeBranch, GeneralConstructionTool) - Method in class pal.treesearch.PivotNode
- getExtendedConditionalProbabilities(FreeNode, UnconstrainedLikelihoodModel.External, ConditionalProbabilityStore, GeneralConstructionTool) - Method in class pal.treesearch.FreeBranch
- getExtendedConditionalProbabilities(FreeNode, GeneralConstructionTool) - Method in class pal.treesearch.FreeBranch
- 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) - Static method in class pal.tree.NodeUtils
-
Obtains all external nodes from tree defined by root and returns as an array
- getExternalNodes(Node, Vector) - Static method in class pal.tree.NodeUtils
-
Appends all external nodes from tree defined by root to Vector store
- 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() - Static method in class pal.eval.FastFourStateLHCalculator
- getFactory() - Static method in class pal.eval.SimpleLHCalculator
- getFactory() - Static method in class pal.eval.SimpleModelFastFourStateLHCalculator
- getFactory(double[], double[], int, double) - Static method in class pal.mep.SteppedMutationRate
-
Generate a MutationRateModel.Factory class for a SteppedMutationRate
- getFactory(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
- getFactory(LHCalculator.Factory) - Static method in class pal.eval.FastFourStateLHCalculator
- getFactory(LHCalculator.Factory) - Static method in class pal.eval.SimpleModelFastFourStateLHCalculator
- 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, UnconstrainedLikelihoodModel.External, ConditionalProbabilityStore, GeneralConstructionTool) - Method in class pal.treesearch.FreeLeafNode
- getFlatConditionalProbabilities(FreeBranch, GeneralConstructionTool) - Method in class pal.treesearch.FreeInternalNode
- 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(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
- getFreeFactory(int, double) - Static method in class pal.mep.ConstantMutationRate
-
Generate a MutationRateModel.Factory class for a ConstantMutationRate
- getFrequencies() - Method in class pal.substmodel.AbstractRateMatrix
- getFrequencies(MolecularDataType, int) - Method in class pal.alignment.DataTranslator
- 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) - Method in class pal.misc.TOCDSampleInformation
- getHeight(int, double) - Method in class pal.misc.TimeOrderCharacterData
-
NOTE: currently assumes times exist!
- 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() - Method in interface pal.tree.Node
-
Returns the identifier for this node.
- getIdentifier() - Method in class pal.tree.SimpleNode
-
Returns the identifier for this node.
- getIdentifier(int) - Method in class pal.alignment.AbstractAlignment
- getIdentifier(int) - Method in class pal.alignment.SimpleCharacterAlignment
- getIdentifier(int) - Method in class pal.distance.DistanceMatrix
- getIdentifier(int) - Method in 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(int) - Method in class pal.tree.ParameterizedTree.ParameterizedTreeBase
- 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() - 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(double[]) - Static method in class pal.substmodel.TwoStateModel
-
create object using an instance method
- getInstance(int) - Static method in class pal.datatype.DataType.Utils
-
create object according to this code
- getInstance(int, double[]) - Static method in class pal.substmodel.AminoAcidModel
-
Create amino acid model according to model type
- getInstance(int, double[], double[]) - Static method in class pal.substmodel.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
- 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() - 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.
- getInternalNodeCount(Node) - Static method in class pal.tree.NodeUtils
- getInternalNodes(Node, boolean) - Static method in class pal.tree.NodeUtils
-
Obtains all internal nodes from tree defined by root and returns as an array
- getInternalNodes(Node, Vector) - Static method in class pal.tree.NodeUtils
-
Appends all internal nodes from tree defined by root to Vector store
- 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(int, double[]) - Method in class pal.tree.MutationRateModelTree
- getInternalParameterBoundaries(OrthogonalHints, int) - Static method in class pal.math.OrthogonalHints.Utils
- 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(boolean, boolean, boolean, boolean) - Static method in class pal.datatype.IUPACNucleotides
- getIUPACState(int) - 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() - Method in class pal.tree.TreeManipulator.PALNodeWrapper
- getLabel() - Method in class pal.treesearch.AbstractLeafNode
- getLabel() - Method in interface pal.treesearch.NodeAccess
- getLabel(String, String) - Method in class pal.misc.LabelMapping
- getLabel(Identifier) - Method in class pal.misc.LabelMapping
- getLabel(Identifier, String) - Method in class pal.misc.LabelMapping
- 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(double, GeneralConstructionTool, boolean) - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
Obtain conditionals by extended left child conditionals to a particular height
- getLeftDescendentExtendedConditionals(GeneralConstructionTool, boolean) - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
Obtain conditionals by extended left child conditionals to height of this node
- getLeftExtendedConditionalProbabilities(FreeBranch, UnconstrainedLikelihoodModel.External, ConditionalProbabilityStore) - Method in class pal.treesearch.FreeLeafNode
- getLeftExtendedConditionalProbabilities(FreeBranch, UnconstrainedLikelihoodModel.External, ConditionalProbabilityStore, GeneralConstructionTool) - Method in class pal.treesearch.FreeInternalNode
- 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() - Method in class pal.math.LineFunction
- getLowerBound() - Method in class pal.math.OrthogonalLineFunction
- getLowerBound() - Method in interface pal.math.UnivariateFunction
-
get lower bound of argument
- 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(int) - Method in interface pal.math.MultivariateFunction
-
get lower bound of argument n
- getLowerBoundParameter() - Method in class pal.math.LineFunction
-
get parameter that limits the lower bound
- getLowerLimit() - Method in interface pal.misc.IndividualParameterHandler
- getLowerLimit() - Method in class pal.misc.MutableDouble
- 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(int) - Method in class pal.misc.MultiParameterized
- 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[], String[], String[]) - Static method in class pal.treesearch.BranchAccess.Utils
- getMatching(BranchAccess[], BranchAccess) - 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(Tree) - Static method in class pal.tree.TreeManipulator
-
Returns the mid point rooting of a tree.
- getMidPointRooted() - Method in class pal.tree.TreeManipulator
- 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[]) - Static method in class pal.math.MathUtils
- getMinimum(double[], int, int) - 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(double) - Method in class pal.math.Matrix
- getMultiplied(Matrix) - Method in class pal.math.Matrix
-
Multiply as in [this][other]
- getMus() - Method in class pal.mep.SteppedMutationRate
- getMus(double[]) - 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() - 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.
- getName(int) - Method in class pal.misc.SimpleIdGroup
-
Convenience method to return the name of identifier i
- getNameAttr(Element) - Static method in class pal.xml.ElementParser
- getNames(Identifier[]) - Static method in class pal.misc.Identifier
-
Translates an array of identifiers into an array of strings
- getNames(Identifier[], int) - Static method in class pal.misc.Identifier
-
Translates an array of identifiers into an array of strings, with optional removal of particular identifier
- getNames(IdGroup) - Static method in class pal.misc.Identifier
-
Translates an IdGroup into an array of strings
- getNames(IdGroup, int) - Static method in class pal.misc.Identifier
-
Translates an IDgroup into an array of strings, with optional removal of particular identifier
- getNames(IdGroup, int[]) - Static method in class pal.misc.Identifier
-
Translates an IDgroup into an array of strings, with optional removal of particular identifier
- getNChoose2(int) - Method in class pal.math.Binomial
-
get (precomputed) n choose 2
- getNearest(double, double) - Method in class pal.util.DefaultCache
- getNearest(double, double) - Method in interface pal.util.DoubleKeyCache
-
retrieves the object with the key nearest to given value
- getNearest(DoubleKey, double) - Method in class pal.util.DefaultCache
- 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(Node, String) - Static method in class pal.tree.TreeUtils
- getNodeByName(Tree, 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() - 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
- getNumberOfParameters(TimeOrderCharacterData) - Method in interface pal.supgma.RateHandler
- getNumberOfParameters(TimeOrderCharacterData) - Method in interface pal.supgma.ThetaHandler
- 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() - Static method in class pal.substmodel.BLOSUM62
- getOriginalFrequencies() - Static method in class pal.substmodel.CPREV
- getOriginalFrequencies() - Static method in class pal.substmodel.Dayhoff
- getOriginalFrequencies() - Static method in class pal.substmodel.JTT
- getOriginalFrequencies() - Static method in class pal.substmodel.MTREV24
- getOriginalFrequencies() - Static method in class pal.substmodel.VT
- getOriginalFrequencies() - Static method in class pal.substmodel.WAG
- getOriginalFrequencies(double[]) - Static method in class pal.substmodel.BLOSUM62
-
get the frequencies of the original data set that formed the basis for the estimation of the rate matrix
- getOriginalFrequencies(double[]) - Static method in class pal.substmodel.CPREV
-
get the frequencies of the original data set that formed the basis for the estimation of the rate matrix
- getOriginalFrequencies(double[]) - Static method in class pal.substmodel.Dayhoff
-
get the frequencies of the original data set that formed the basis for the estimation of the rate matrix
- getOriginalFrequencies(double[]) - Static method in class pal.substmodel.JTT
-
get the frequencies of the original data set that formed the basis for the estimation of the rate matrix
- getOriginalFrequencies(double[]) - Static method in class pal.substmodel.MTREV24
-
get the frequencies of the original data set that formed the basis for the estimation of the rate matrix
- getOriginalFrequencies(double[]) - Static method in class pal.substmodel.VT
-
get the frequencies of the original data set that formed the basis for the estimation of the rate matrix
- getOriginalFrequencies(double[]) - Static method in class pal.substmodel.WAG
-
get the frequencies of the original data set that formed the basis for the estimation of the rate matrix
- 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() - Method in interface pal.misc.IndividualParameterHandler
- 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(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() - Static method in class pal.tree.UnconstrainedTree
-
Obtain a ParameterizedTree.Factory for generating Unconstrained trees
- getParameterizedTreeFactory(MutationRateModel.Factory, TimeOrderCharacterData) - Static method in class pal.tree.MutationRateModelTree
-
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(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
- getParameters(Parameterized) - Static method in class pal.misc.Parameterized.Utils
- 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, 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
- getPatternInfo(GeneralConstructionTool, FreeNode) - Method in class pal.treesearch.FreeBranch
- 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(double, double[]) - Method in class pal.math.LineFunction
-
get point associated with the one-dimensional parameter (bounds of of multivariate function are NOT checked)
- getPoint(PositionedNode, int, int) - Method in class pal.gui.TreePainterNormal
- getPopulationSize(int) - Method in class pal.coalescent.SkylinePlot
-
Returns the population size in interval i.
- getPositionMisalignmentInfo(Alignment, PrintWriter, int) - Static method in class pal.alignment.AlignmentUtils
- getPositionMisalignmentInfo(Alignment, PrintWriter, int, CodonTable, boolean) - Static method in class pal.alignment.AlignmentUtils
- getPositionType(int) - Method in 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(double, GeneralConstructionTool, boolean) - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
Obtain conditionals by extended left child conditionals to a particular height
- getRightDescendentExtendedConditionals(GeneralConstructionTool, boolean) - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
Obtain conditionals by extended right child conditionals to height of this node
- getRightExtendedConditionalProbabilities(FreeBranch, UnconstrainedLikelihoodModel.External, ConditionalProbabilityStore) - Method in class pal.treesearch.FreeLeafNode
- getRightExtendedConditionalProbabilities(FreeBranch, UnconstrainedLikelihoodModel.External, ConditionalProbabilityStore, GeneralConstructionTool) - Method in class pal.treesearch.FreeInternalNode
- 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(SplitSystem, Tree) - Static method in class pal.tree.TreeUtils
-
computes Robinson-Foulds (1981) distance between two trees
- getRobinsonFouldsDistance(Tree, Tree) - Static method in class pal.tree.TreeUtils
-
computes Robinson-Foulds (1981) distance between two trees
- getRobinsonFouldsRescaledDistance(SplitSystem, Tree) - Static method in class pal.tree.TreeUtils
-
computes Robinson-Foulds (1981) distance between two trees rescaled to a number between 0 and 1
- getRobinsonFouldsRescaledDistance(Tree, Tree) - Static method in class pal.tree.TreeUtils
-
computes Robinson-Foulds (1981) distance between two trees rescaled to a number between 0 and 1
- getRoot() - Method in class pal.tree.ParameterizedTree.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() - Method in class pal.tree.SimpleNode
-
Returns the sequence at this node, in the form of a String.
- getSequenceString(Alignment, int) - Static method in class pal.alignment.AlignmentUtils
-
Returns a particular sequence of an alignment as a String
- 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) - Method in class pal.substmodel.SequenceSimulator
- getSimulated(int[], double, double) - Method in interface pal.eval.MolecularClockLikelihoodModel.Simulator
- 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() - Method in class pal.eval.LikelihoodValue
-
Returns the site pattern of this likelihood value
- getSitePattern() - Method in class pal.eval.SimpleLikelihoodCalculator
- getSitePattern(Alignment) - Static method in class pal.alignment.SitePattern
- 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[][], 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 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(char[][]) - 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(Alignment) - Static method in class pal.alignment.AlignmentUtils
-
guess data type suitable for a given sequence data set
- getSuitableModelID(double[]) - Static method in class pal.substmodel.AminoAcidModel
-
get numerical code of amino acid model that would probably be suitable for a given sequence data set
- 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[]) - Static method in class pal.math.MathUtils
- getTotal(double[], int, int) - Static method in class pal.math.MathUtils
- getTotalHeight() - Method in class pal.coalescent.CoalescentIntervals
-
get the total height of the genealogy represented by these intervals.
- 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[][]) - Method in class pal.substmodel.MatrixExponential
-
A utility method for speed, transfers trans prob information quickly into store
- 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 class pal.substmodel.RateMatrixHandler
- getTransitionProbabilities(double, double[][][]) - Method in class pal.substmodel.GeneralRateDistributionSubstitutionModel
- getTransitionProbabilities(double, double[][][]) - Method in class pal.substmodel.MultiRateMatrixHandler
- getTransitionProbabilities(double, double[][][]) - Method in class pal.substmodel.NeutralSelectionRateMatrixGroup
- getTransitionProbabilities(double, double[][][]) - Method in class pal.substmodel.PositiveSelectionRateMatrixGroup
- getTransitionProbabilities(double, double[][][]) - Method in interface pal.substmodel.RateMatrixGroup
- getTransitionProbabilities(double, double[][][]) - Method in class pal.substmodel.SimpleRateMatrixGroup
- getTransitionProbabilities(double, 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, double[][][]) - Method in class pal.substmodel.YangCodonModel.SimpleNeutralSelection
-
Table is organized as [tree_group][from][to]
- getTransitionProbabilities(double, double[][][]) - Method in class pal.substmodel.YangCodonModel.SimplePositiveSelection
- getTransitionProbabilities(double, int, double[][]) - Method in class pal.substmodel.GeneralRateDistributionSubstitutionModel
- getTransitionProbabilities(double, int, double[][]) - Method in class pal.substmodel.MultiRateMatrixHandler
- getTransitionProbabilities(double, int, double[][]) - Method in class pal.substmodel.NeutralSelectionRateMatrixGroup
- getTransitionProbabilities(double, int, double[][]) - Method in class pal.substmodel.PositiveSelectionRateMatrixGroup
- getTransitionProbabilities(double, int, double[][]) - Method in interface pal.substmodel.RateMatrixGroup
- getTransitionProbabilities(double, int, double[][]) - Method in class pal.substmodel.SimpleRateMatrixGroup
- getTransitionProbabilities(double, int, double[][]) - Method in class pal.substmodel.SingleClassSubstitutionModel
- getTransitionProbabilities(double, int, double[][]) - Method in interface pal.substmodel.SubstitutionModel
-
Table is organized as [transition_group][from][to]
- getTransitionProbabilities(double, int, double[][]) - Method in class pal.substmodel.YangCodonModel.SimpleNeutralSelection
- 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.RateMatrixHandler
- getTransitionProbabilitiesTranspose(double, double[][][]) - Method in class pal.substmodel.GeneralRateDistributionSubstitutionModel
- getTransitionProbabilitiesTranspose(double, double[][][]) - Method in class pal.substmodel.MultiRateMatrixHandler
- getTransitionProbabilitiesTranspose(double, double[][][]) - Method in class pal.substmodel.NeutralSelectionRateMatrixGroup
- getTransitionProbabilitiesTranspose(double, double[][][]) - Method in class pal.substmodel.PositiveSelectionRateMatrixGroup
- getTransitionProbabilitiesTranspose(double, double[][][]) - Method in interface pal.substmodel.RateMatrixGroup
- getTransitionProbabilitiesTranspose(double, double[][][]) - Method in class pal.substmodel.SimpleRateMatrixGroup
- getTransitionProbabilitiesTranspose(double, 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, 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.GeneralRateDistributionSubstitutionModel
- getTransitionProbabilitiesTranspose(double, int, double[][]) - Method in class pal.substmodel.MultiRateMatrixHandler
- getTransitionProbabilitiesTranspose(double, int, double[][]) - Method in class pal.substmodel.NeutralSelectionRateMatrixGroup
- getTransitionProbabilitiesTranspose(double, int, double[][]) - Method in class pal.substmodel.PositiveSelectionRateMatrixGroup
- getTransitionProbabilitiesTranspose(double, int, double[][]) - Method in interface pal.substmodel.RateMatrixGroup
- getTransitionProbabilitiesTranspose(double, int, double[][]) - Method in class pal.substmodel.SimpleRateMatrixGroup
- getTransitionProbabilitiesTranspose(double, int, double[][]) - Method in class pal.substmodel.SingleClassSubstitutionModel
- getTransitionProbabilitiesTranspose(double, int, double[][]) - Method in interface pal.substmodel.SubstitutionModel
-
Table is organized as [transition_group][to][from]
- getTransitionProbabilitiesTranspose(double, int, double[][]) - Method in class pal.substmodel.YangCodonModel.SimpleNeutralSelection
- 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
- getTransitionProbability(int, int) - Method in interface pal.substmodel.TransitionProbability
-
Returns the transition probability for changing from startState into endState
- 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() - Method in class pal.math.LineFunction
- getUpperBound() - Method in class pal.math.OrthogonalLineFunction
- getUpperBound() - Method in interface pal.math.UnivariateFunction
-
get upper bound of argument
- 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(int) - Method in interface pal.math.MultivariateFunction
-
get upper bound of argument n
- getUpperBoundParameter() - Method in class pal.math.LineFunction
-
get parameter that limits the upper bound
- getUpperLimit() - Method in interface pal.misc.IndividualParameterHandler
- getUpperLimit() - Method in class pal.misc.MutableDouble
- 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(int) - Method in class pal.misc.MultiParameterized
- 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() - Method in class pal.misc.Attribute
- getValue() - Method in class pal.misc.MutableDouble
-
Get the current value of this double
- getValue(int, int) - Method in class pal.math.Matrix
- 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 - Static variable in interface pal.substmodel.NucleotideModelID
- GTR - Static variable in interface pal.util.XMLConstants
- GTR(double[], double[]) - Constructor for class pal.substmodel.GTR
-
constructor 2
- GTR(double, double, double, double, double, double[]) - Constructor for class pal.substmodel.GTR
-
constructor 1
- guessDataType() - Method in class pal.alignment.AbstractAlignment
-
Guess data type
H
- hallCI(double, double, double[]) - Static method in class pal.statistics.BootstrapStatistics
-
compute approximate central confidence interval for thetaHat (Hall percentile method)
- hallCI(double, double, double[], int[]) - Static method in class pal.statistics.BootstrapStatistics
-
compute approximate central confidence interval for thetaHat (Hall percentile method)
- hasAlignments() - Method in class pal.coalescent.SerialCoalescentGenerator.Results
- hasAttribute(Element, String) - Static method in class pal.xml.ElementParser
-
This method allows the removeal of e.hasAttribute which is DOM Level 2.
- hasChildren() - Method in class pal.tree.SimpleNode
-
check whether this node is an internal node
- hasClade(boolean[]) - Method in class pal.tree.CladeSystem
-
+ test whether a clade is contained in this clade system (assuming the same leaf order)
- hasConnection(FreeBranch, FreeBranch) - Method in class pal.treesearch.FreeInternalNode
- hasConnection(FreeBranch, FreeBranch) - Method in class pal.treesearch.FreeLeafNode
- hasConnection(FreeBranch, FreeBranch) - Method in interface pal.treesearch.FreeNode
- hasConnection(FreeBranch, FreeBranch) - Method in class pal.treesearch.PivotNode
- hasConnection(FreeBranch, FreeNode) - Method in class pal.treesearch.FreeBranch
- hasDirectConnection(FreeBranch) - Method in class pal.treesearch.FreeInternalNode
- hasDirectConnection(FreeBranch) - Method in class pal.treesearch.FreeLeafNode
- hasDirectConnection(FreeBranch) - Method in interface pal.treesearch.FreeNode
- hasDirectConnection(FreeBranch) - Method in class pal.treesearch.PivotNode
- hasGap() - Method in interface pal.datatype.DataType
- hasGap() - Method in class pal.datatype.SimpleDataType
- HASH - Static variable in class pal.io.NexusTokenizer
- hasMore() - Method in interface pal.math.OrderEnumerator
-
If hasMore returns false reset should be called
- hasSource() - Method in class pal.misc.PalObjectEvent
- hasSplit(boolean[]) - Method in class pal.tree.SplitSystem
-
+ test whether a split is contained in this split system (assuming the same leaf order)
- hasSubgroups() - Method in class pal.misc.TimeOrderCharacterData
- hasTimes() - Method in class pal.misc.TimeOrderCharacterData
- HEADER_TOKEN - Static variable in class pal.io.NexusTokenizer
-
Flag indicating last token read was the header token #NEXUS
- HeapSort - Class in pal.util
-
sorts numbers and comparable objects by treating contents of array as a binary tree.
- HeapSort() - Constructor for class pal.util.HeapSort
- HEIGHT - Static variable in interface pal.util.XMLConstants
- HeightInformationUser - Class in pal.treesearch
-
Title: HeightInformationUser
- HeightInformationUser() - Constructor for class pal.treesearch.HeightInformationUser
- heights2Lengths(Node) - Static method in class pal.tree.NodeUtils
-
determines branch lengths of this and all descendent nodes from heights
- heights2Lengths(Node, boolean) - Static method in class pal.tree.NodeUtils
-
determines branch lengths of this and all descendent nodes from heights
- heights2parameters() - Method in class pal.coalescent.DemographicClockTree
- heights2parameters() - Method in class pal.tree.ClockTree
- heights2parameters() - Method in class pal.tree.MutationRateModelTree
- HILITED_LABEL_DISPLAY - Static variable in class pal.gui.TreePainter
- HKY - Class in pal.substmodel
-
Hasegawa-Kishino-Yano model of nucleotide evolution Hasegawa, M., H.
- HKY - Static variable in interface pal.substmodel.NucleotideModelID
- HKY - Static variable in interface pal.util.XMLConstants
- HKY(double[], double[]) - Constructor for class pal.substmodel.HKY
-
Constructor 2
- HKY(double, double[]) - Constructor for class pal.substmodel.HKY
-
Constructor 1
I
- ID - Static variable in interface pal.util.XMLConstants
- Identifier - Class in pal.misc
-
An identifier for some sampled data.
- Identifier() - Constructor for class pal.misc.Identifier
- Identifier(String) - Constructor for class pal.misc.Identifier
- IdGenerator - Class in pal.misc
-
Generates IdGroup objects given certain parameters.
- IdGenerator() - Constructor for class pal.misc.IdGenerator
- idGroup - Variable in class pal.alignment.AbstractAlignment
-
sequence identifiers
- idGroup - Variable in class pal.alignment.SimpleCharacterAlignment
-
sequence identifiers
- IdGroup - Interface in pal.misc
-
An indexed group of identifiers.
- IdGroup.Utils - Class in pal.misc
- illc - Variable in class pal.math.ConjugateDirectionSearch
-
illc should be set to true if the problem is known to be ill-conditioned.
- incompleteGammaP(double, double) - Static method in class pal.math.GammaFunction
-
Incomplete Gamma function P(a,x) = 1-Q(a,x) (a cleanroom implementation of Numerical Recipes gammp(a,x); in Mathematica this function is 1-GammaRegularized)
- incompleteGammaP(double, double, double) - Static method in class pal.math.GammaFunction
-
Incomplete Gamma function P(a,x) = 1-Q(a,x) (a cleanroom implementation of Numerical Recipes gammp(a,x); in Mathematica this function is 1-GammaRegularized)
- incompleteGammaQ(double, double) - Static method in class pal.math.GammaFunction
-
Incomplete Gamma function Q(a,x) (a cleanroom implementation of Numerical Recipes gammq(a,x); in Mathematica this function is called GammaRegularized)
- IndelAlignment - Class in pal.alignment
-
This class extracts indels (insertion/deletion) out of an alignment, and creates an alignment of indel polymorphisms.
- IndelAlignment(Alignment, boolean) - Constructor for class pal.alignment.IndelAlignment
-
Basic constructor.
- IndelAnnotatedAlignment - Class in pal.alignment
-
an extension of the IndelAlignment that includes annotation.
- IndelAnnotatedAlignment(AnnotationAlignment, boolean) - Constructor for class pal.alignment.IndelAnnotatedAlignment
-
Basic constructor.
- IndividualParameterHandler - Interface in pal.misc
-
Title:
- IndividualParameterHandler.Listener - Interface in pal.misc
- IndividualParameterHandler.Utils - Class in pal.misc
- inferCI(AlgorithmCallback, int, SimulatedAlignment.Factory, SubstitutionModel, LMSSolver) - Method in interface pal.supgma.SUPGMABase.PopulationParameters
- init(IdGroup, String[]) - Method in class pal.alignment.MultiLocusAnnotatedAlignment
- init(Node) - Method in class pal.tree.SimpleNode
- init(Node, boolean) - Method in class pal.tree.SimpleNode
-
Initialized node instance variables based on given Node.
- init(Node, boolean, LabelMapping) - Method in class pal.tree.SimpleNode
-
Initialized node instance variables based on given Node.
- initialiseParameters(String[], double[]) - Method in interface pal.treesearch.ConstraintModel.GroupManager
- initialiseParameters(String[], double[]) - Method in class pal.treesearch.FixedBSRDTGlobalClockModel
- initialiseParameters(String[], double[]) - Method in class pal.treesearch.FixedSRDTGlobalClockModel
- initialiseParameters(String[], double[]) - Method in class pal.treesearch.GlobalClockModel
- initialiseParameters(String[], double[]) - Method in class pal.treesearch.MRDTGlobalClockModel
- initialiseParameters(String[], double[]) - Method in class pal.treesearch.SRDTGlobalClockModel
- initMatrices() - Method in class pal.alignment.MultiLocusAnnotatedAlignment
- InputSource - Class in pal.io
-
convenience class to open input streams linked to files, stdin, and strings
- insertChild(Node, int) - Method in interface pal.tree.Node
-
add new child node (insertion at a specific position)
- insertChild(Node, int) - Method in class pal.tree.SimpleNode
-
add new child node (insertion at a specific position)
- instruct(Node, RootedTreeInterface) - Static method in class pal.tree.RootedTreeInterface.Utils
-
Build a tree display based on a normal pal node.
- instruct(Node, UnrootedTreeInterface) - Static method in class pal.tree.UnrootedTreeInterface.Utils
-
Build a tree display based on a normal pal node.
- instruct(RootedTreeInterface) - Method in interface pal.tree.RootedTreeInterface.Instructee
- instruct(RootedTreeInterface) - Method in class pal.tree.TreeManipulator
- instruct(UnrootedTreeInterface) - Method in class pal.tree.TreeManipulator
- instruct(UnrootedTreeInterface) - Method in interface pal.tree.UnrootedTreeInterface.Instructee
- instruct(UnrootedTreeInterface) - Method in class pal.treesearch.UnrootedMLSearcher
- instructRootedBy(RootedTreeInterface, String[]) - Method in class pal.tree.TreeManipulator
- INTEGER - Static variable in class pal.misc.Attribute
- InternalImpl(LHCalculator.Internal, SubstitutionModel) - Constructor for class pal.eval.SimpleUnconstrainedLikelihoodModel.InternalImpl
- intervals - Variable in class pal.eval.DemographicValue
- IntervalsExtractor - Class in pal.coalescent
-
A series of coalescent intervals representing the time order information contained in a (serial) clock-constrained tree.
- IntervalsExtractor() - Constructor for class pal.coalescent.IntervalsExtractor
- INVALID_INTERVALS_TEXT - Static variable in class pal.mep.SteppedMutationRate
- InvariableSites - Class in pal.substmodel
-
invariable sites model (two-rate model with mean rate = 1.0)
- InvariableSites(double) - Constructor for class pal.substmodel.InvariableSites
-
construct discrete rate distribution with two rates (one invariable and one variable)
- inverseErf(double) - Static method in class pal.math.ErrorFunction
-
inverse error function
- INVERTEBRATE_MITOCHONDRIAL - Static variable in interface pal.datatype.CodonTable
-
TypeID for Invertebrate Mitochondrial
- isActionDeterministic() - Method in interface pal.algorithmics.UndoableAction
-
Was the last action deterministic? That is, if it wasn't chosen and state is still as before is it worth doing it again?
- isActionSuccessful() - Method in interface pal.algorithmics.UndoableAction
-
Was the last call to doAction() succesful?
- isAllowCaching() - Method in interface pal.eval.LHCalculator.Generator
- isAllowCaching() - Method in interface pal.eval.UnconstrainedLikelihoodModel.Instance
-
If true, then user can assume that areas of trees that haven't changed, and the model parameters haven't be altered, can have their conditionals cached.
- isAmbiguous() - Method in interface pal.datatype.DataType
- isAmbiguous() - Method in class pal.datatype.IUPACNucleotides
- isAmbiguous() - Method in class pal.datatype.SimpleDataType
- isAncestor(Node, Node) - Static method in class pal.tree.NodeUtils
-
For two nodes in the tree true if the first node is the ancestor of the second
- isBasedOnCachedData() - Method in class pal.eval.ConditionalProbabilityStore
- isBinaryCoalescent() - Method in class pal.coalescent.CoalescentIntervals
-
Checks whether this set of coalescent intervals is fully resolved (i.e.
- isCICompatible() - Method in interface pal.supgma.RateHandler
- isCICompatible() - Method in interface pal.supgma.SUPGMABase.PopulationParameters
- isCICompatible() - Method in interface pal.supgma.ThetaHandler
- isCoalescentOnly() - Method in class pal.coalescent.CoalescentIntervals
-
Checks whether this set of coalescent intervals coalescent only (i.e.
- isContained(String[], String[]) - Static method in class pal.treesearch.BranchAccess.Utils
- isContainedWithin(IdGroup, IdGroup) - Static method in class pal.misc.IdGroup.Utils
- isContains(String[], String) - Static method in class pal.misc.Utils
-
Test if a string occurs within a set
- isCreatesIUPACNuecleotides() - Method in class pal.datatype.Codons
- isCreatesIUPACNuecleotides() - Method in class pal.datatype.GapBalanced
- isCreatesIUPACNuecleotides() - Method in class pal.datatype.IUPACNucleotides
- isCreatesIUPACNuecleotides() - Method in interface pal.datatype.MolecularDataType
- isCreatesIUPACNuecleotides() - Method in class pal.datatype.Nucleotides
- isCreatesIUPACNuecleotides() - Method in class pal.datatype.SpecificAminoAcids
- isDataTypeCompatible(DataType) - Method in class pal.substmodel.GeneralPoissonRateMatrix
-
Check the compatibility of a data type to be used with the rate matrix
- isDataTypeCompatible(DataType) - Method in class pal.substmodel.GeneralREVRateMatrix
-
Check the compatibility of a data type to be used with the rate matrix
- isDataTypeCompatible(DataType) - Method in interface pal.substmodel.NeoRateMatrix
-
Check the compatibility of a data type to be used with the rate matrix
- isDebug() - Method in class pal.math.OrthogonalSearch
- isDebugging() - Method in class pal.util.Log
- isDistributionIndependentlyMutable() - Method in class pal.substmodel.InvariableSites
- isEqualIgnoringOrder(IdGroup, IdGroup) - Static method in class pal.misc.IdGroup.Utils
- isFrequentMonitoring() - Method in class pal.math.OrthogonalSearch
- isGap(int, int) - Method in class pal.alignment.AbstractAlignment
-
returns true if there is a gap in the give position.
- isGap(Alignment, int, int) - Static method in class pal.alignment.AlignmentUtils
-
Returns true if the alignment has a gap at the site in the sequence specified.
- isGap(DataType, char) - Static method in class pal.datatype.DataType.Utils
-
Deprecated.use DataType.isGapChar()
- isGapChar(char) - Method in interface pal.datatype.DataType
- isGapChar(char) - Method in class pal.datatype.SimpleDataType
- isGapState(int) - Method in interface pal.datatype.DataType
- isGapState(int) - Method in class pal.datatype.SimpleDataType
- isHasExtraProcessor() - Method in class pal.eval.ConditionalProbabilityStore
- isHighlighted() - Method in class pal.gui.PositionedNode
- isIgnoreNonMinimalUnivariateMinimisations() - Method in class pal.math.OrthogonalSearch
-
Should we ignore new minisations that are not as minimal as the current one?
- isIntersection(String[], String[]) - Static method in class pal.treesearch.BranchAccess.Utils
- isLeaf() - Method in interface pal.tree.Node
-
check whether this node is an external node
- isLeaf() - Method in class pal.tree.SimpleNode
-
check whether this node is an external node
- isLeaf() - Method in class pal.tree.TreeManipulator.PALNodeWrapper
- isLeaf() - Method in interface pal.treesearch.NodeAccess
- isLeafBranch(String) - Method in interface pal.treesearch.BranchAccess
-
Test if this branch leads directly to a leaf of a particular label
- isLeftChild(ConstrainedNode) - Method in class pal.treesearch.AbstractParentableConstrainedNode
-
Investigate if given node is left node (and not right)
- isLxParameterized() - Method in class pal.coalescent.ConstExpGrowth
- isMatching(BranchAccess, String[], String[]) - Static method in class pal.treesearch.BranchAccess.Utils
- isMaximiseScore() - Method in class pal.algorithmics.GeneralObjectState
- isMaximiseScore() - Method in interface pal.algorithmics.ObjectState
-
If true, than a bigger score is better, otherwise a smaller score is better
- isMoreTrees() - Method in interface pal.tree.TreeIterator
- isN1Parameterized() - Method in class pal.coalescent.ConstExpGrowth
- isNucleotideState(int, int) - Static method in class pal.datatype.IUPACNucleotides
- isOptimisable() - Method in class pal.treesearch.GeneralConstraintGroupManager
- isPleaseStop() - Method in interface pal.util.AlgorithmCallback
-
Should be called intermittedly to check if algorithm should stop (should return null if has output)
- isPrimaryOptimisable() - Method in class pal.treesearch.GeneralConstraintGroupManager
- isReversible() - Method in class pal.substmodel.GeneralPoissonRateMatrix
- isReversible() - Method in class pal.substmodel.GeneralREVRateMatrix
- isReversible() - Method in interface pal.substmodel.NeoRateMatrix
-
Is the relative rate matrix described by this rate matrix meant to represent a reversible process? If true only the upper part of the rate matrix needs to be filled in (eg in matrix[i][j], for all where j > i );
- isRoot() - Method in interface pal.tree.Node
-
check whether this node is a root node
- isRoot() - Method in class pal.tree.SimpleNode
-
check whether this node is a root node
- isSame(boolean[], boolean[]) - Static method in class pal.tree.CladeSystem
-
checks whether two clades are identical (assuming they are of the same length and use the same leaf order)
- isSame(boolean[], boolean[]) - Static method in class pal.tree.SplitUtils
-
checks whether two splits are identical (assuming they are of the same length and use the same leaf order)
- isSameGroup(ConstraintModel.GroupManager) - Method in class pal.treesearch.GeneralConstraintGroupManager
- isSecondarOptimisable() - Method in class pal.treesearch.GeneralConstraintGroupManager
- isShowingInternalLabels() - Method in class pal.gui.TreePainter
- isShowingNodeHeights() - Method in class pal.gui.TreePainter
- isShowTitle() - Method in class pal.gui.TreePainter
- isSiteRedundant(Alignment, int) - Static method in class pal.alignment.AlignmentUtils
- isSquare() - Method in class pal.math.Matrix
- isStablised() - Method in interface pal.algorithmics.ProbabilityIterator
- isSuggestedGap(char) - Static method in class pal.datatype.DataType.Utils
-
Useful for implementing classes to check if a character is a suggest gap character Users of datatypes should query the datatype to see if a character is a gap - not use this method.
- isSymmetric() - Method in class pal.distance.DistanceMatrix
-
test whether this matrix is a symmetric distance matrix
- isSynonymous(int, int) - Method in interface pal.datatype.CodonTable
- isTimeToStop() - Method in interface pal.algorithmics.StoppingCriteria
- isTransitionByChar(char, char) - Method in class pal.datatype.Nucleotides
- isTransitionByState(int, int) - Method in class pal.datatype.Nucleotides
- isUnknownChar(char) - Method in interface pal.datatype.DataType
- isUnknownChar(char) - Method in class pal.datatype.SimpleDataType
- isUnknownState(int) - Method in class pal.alignment.AbstractAlignment
-
Same as getDataType().isUnknownState(state)
- isUnknownState(int) - Method in interface pal.datatype.DataType
- isUnknownState(int) - Method in class pal.datatype.SimpleDataType
-
Checks if state is a gap state (then returns true), otherwise passes on to isUnknownStateImpl
- isUnknownStateImpl(int) - Method in class pal.datatype.AminoAcids
- isUnknownStateImpl(int) - Method in class pal.datatype.Codons
- isUnknownStateImpl(int) - Method in class pal.datatype.GapBalanced
- isUnknownStateImpl(int) - Method in class pal.datatype.IUPACNucleotides
- isUnknownStateImpl(int) - Method in class pal.datatype.Nucleotides
- isUnknownStateImpl(int) - Method in class pal.datatype.NumericDataType
- isUnknownStateImpl(int) - Method in class pal.datatype.SimpleDataType
-
For subclasses to handle, without regard for gaps
- isUnknownStateImpl(int) - Method in class pal.datatype.StateRemover
- isUnknownStateImpl(int) - Method in class pal.datatype.TwoStates
- isUseCurrentInUnivariateMinimisation() - Method in class pal.math.OrthogonalSearch
- isUsingColor() - Method in class pal.gui.TreePainter
- isUsingSymbols() - Method in class pal.gui.TreePainter
- isWorthAdding(double, boolean) - Method in class pal.algorithmics.Ranker
-
Enquire to the merits of adding an object with a particular score
- IUPAC_NUCELOTIDES_DESCRIPTION - Static variable in interface pal.datatype.DataType
-
iupac nucleotide name (for XML and human readability)
- IUPACNucleotides - Class in pal.datatype
-
implements DataType for nucleotides with ambiguous characters
- IUPACNucleotides() - Constructor for class pal.datatype.IUPACNucleotides
- IUPACNucleotides(boolean) - Constructor for class pal.datatype.IUPACNucleotides
- IUPACNUCLEOTIDES - Static variable in interface pal.datatype.DataType
- IUPACPenalties - Variable in class pal.datatype.IUPACPenaltyTable
- IUPACPenaltyTable - Class in pal.datatype
-
Implements a table of transition penalties for a DNA states and IUPAC ambiguous states.
- IUPACPenaltyTable() - Constructor for class pal.datatype.IUPACPenaltyTable
J
- JC - Static variable in interface pal.util.XMLConstants
- JC69_MATRIX - Static variable in class pal.substmodel.F81
- JC69_MODEL - Static variable in class pal.substmodel.F81
- joinChilds(Node, int, int) - Static method in class pal.tree.NodeUtils
-
join two childs, introducing a new node/branch in the tree that replaces the first child
- JTT - Class in pal.substmodel
-
JTT model of amino acid evolution Jones, D.
- JTT - Static variable in interface pal.substmodel.AminoAcidModelID
- JTT - Static variable in interface pal.util.XMLConstants
- JTT(double[]) - Constructor for class pal.substmodel.JTT
-
constructor
- JukesCantorDistanceMatrix - Class in pal.distance
-
compute jukes-cantor corrected distance matrix
- JukesCantorDistanceMatrix(Alignment) - Constructor for class pal.distance.JukesCantorDistanceMatrix
-
compute jukes-cantor corrected distances
- JukesCantorDistanceMatrix(SitePattern) - Constructor for class pal.distance.JukesCantorDistanceMatrix
-
compute jukes-cantor corrected distances
- JukesCantorDistanceMatrix(DistanceMatrix) - Constructor for class pal.distance.JukesCantorDistanceMatrix
-
compute jukes-cantor corrected distances (assumes nucleotides as underlying data)
- JukesCantorDistanceMatrix(DistanceMatrix, int) - Constructor for class pal.distance.JukesCantorDistanceMatrix
-
compute jukes-cantor corrected distances
- jumble() - Method in class pal.alignment.JumbledAlignment
-
jumble sequences (rearrange input order)
- JumbledAlignment - Class in pal.alignment
-
generates jumbled alignments (randomizing input order of sequences)
- JumbledAlignment(Alignment) - Constructor for class pal.alignment.JumbledAlignment
K
- KAPPA - Static variable in interface pal.util.XMLConstants
- KAPPA_PARAMETER - Static variable in class pal.substmodel.YangCodonModel
- KAPPA_PARAMETER_INDEX - Static variable in class pal.substmodel.HKY
- KAPPA_PARAMETER_INDEX - Static variable in class pal.substmodel.TN
- KishinoHasegawaTest - Class in pal.statistics
-
Kishino-Hasegawa-(Templeton)-Test (1989, 1983) to compare a set of evolutionary hypotheses
- KishinoHasegawaTest() - Constructor for class pal.statistics.KishinoHasegawaTest
L
- L_BRACE - Static variable in class pal.io.NexusTokenizer
- L_BRACKET - Static variable in class pal.io.NexusTokenizer
- L_FEED - Static variable in class pal.io.NexusTokenizer
- L_PARENTHESIS - Static variable in class pal.io.NexusTokenizer
- L_THAN - Static variable in class pal.io.NexusTokenizer
- LabelDisplayer - Interface in pal.gui
-
A Label display object displays a label at a particular location on a graphics object.
- LabelDisplayer.Utils - Class in pal.gui
- labelInternalNodes(Tree) - Static method in class pal.tree.TreeUtils
-
Labels the internal nodes of the tree using numbers starting from 0.
- LabelMapping - Class in pal.misc
- LabelMapping() - Constructor for class pal.misc.LabelMapping
- LabelMapping.Relabeller - Interface in pal.misc
- lastSite - Variable in class pal.alignment.StrippedAnnotatedAlignment
- LayoutTracker - Class in pal.gui
- LayoutTracker() - Constructor for class pal.gui.LayoutTracker
- LeafImpl(LHCalculator.Leaf, SubstitutionModel) - Constructor for class pal.eval.SimpleUnconstrainedLikelihoodModel.LeafImpl
- leftAlignSequence(int[], DataType) - Static method in class pal.datatype.DataType.Utils
-
Realigns a sequence of states so that there are no gaps at the beggining (shifts to the left if necessary)
- LEFTBORDER - Static variable in class pal.gui.TreePainterCircular
- LEFTBORDER - Static variable in class pal.gui.TreePainterNormal
- LENGTH - Static variable in interface pal.util.XMLConstants
- lengths2Heights(Node) - Static method in class pal.tree.NodeUtils
-
Converts lengths to heights, *without* assuming contemporaneous tips.
- lengths2HeightsContemp() - Method in class pal.tree.SimpleNode
-
determines the height of this node and its descendants from branch lengths, assuming contemporaneous tips.
- lengths2HeightsKeepTips(Node, boolean) - Static method in class pal.tree.NodeUtils
-
Converts lengths to heights, but maintains tip heights.
- LHCalculator - Interface in pal.eval
- LHCalculator.AbstractExternal - Class in pal.eval
- LHCalculator.External - Interface in pal.eval
-
The External calculator does not maintain any state and is approapriate for calculation where a store is provided
- LHCalculator.Factory - Interface in pal.eval
- LHCalculator.Generator - Interface in pal.eval
- LHCalculator.Internal - Interface in pal.eval
-
The Internal calculator may maintain state and is approapriate permanent attachment to internal nodes of the tree structure
- LHCalculator.Leaf - Interface in pal.eval
-
A LHCalculator.Leaf object is attached to each leaf node and can be used to calculated conditional probabilities across the related branch.
- LikelihoodCalculator - Interface in pal.eval
-
classes that calculate likelihoods should implement this interface.
- LikelihoodEvaluator - Interface in pal.statistics
- LikelihoodEvaluator.MLResult - Interface in pal.statistics
- LikelihoodEvaluator.SimpleMLResult - Class in pal.statistics
- LikelihoodEvaluator.Utils - Class in pal.statistics
- LikelihoodOptimiser - Class in pal.eval
- LikelihoodOptimiser(Tree, Alignment, SubstitutionModel) - Constructor for class pal.eval.LikelihoodOptimiser
- likelihoodOrder - Variable in class pal.statistics.ModelSupport
-
likelhood order of the tree hypotheses
- LikelihoodRatioTest - Class in pal.statistics
-
Likelihood ratio test based on chi-square statistics
- LikelihoodRatioTest() - Constructor for class pal.statistics.LikelihoodRatioTest
- LikelihoodSummary - Class in pal.eval
- LikelihoodSummary(DataType, double, double[], double[][], int[]) - Constructor for class pal.eval.LikelihoodSummary
- LikelihoodTool - Class in pal.eval
- LikelihoodTool() - Constructor for class pal.eval.LikelihoodTool
- LikelihoodValue - Class in pal.eval
-
Computes the likelihood for a tree given a model of sequence evolution and a sequence alignment; also optimises tree parameters such as branch lengths by maximising the likelihood (for optimal performance special optimisation procedures are employed for UnconstrainedTree, ClockTree and DatedTipsClockTree; a general optimisation precedure is used for another ParameterizedTree).
- LikelihoodValue(SitePattern) - Constructor for class pal.eval.LikelihoodValue
-
initialization
- LineFunction - Class in pal.math
-
converts a multivariate function into a univariate function
- LineFunction(MultivariateFunction) - Constructor for class pal.math.LineFunction
-
construct univariate function from multivariate function
- LinkageDisequilibrium - Class in pal.popgen
-
This class calculates D' and r^2 estimates of linkage disequilibrium.
- LinkageDisequilibrium(Alignment) - Constructor for class pal.popgen.LinkageDisequilibrium
-
compute LD based on an alignment.
- LinkageDisequilibrium(Alignment, boolean, int) - Constructor for class pal.popgen.LinkageDisequilibrium
-
compute LD based on an alignment
- LinkageDisequilibriumComponent - Class in pal.gui
-
An AWT Component for displaying information on linkage disequilibrium.
- LinkageDisequilibriumComponent(LinkageDisequilibrium, boolean, boolean) - Constructor for class pal.gui.LinkageDisequilibriumComponent
- LMSSolver - Interface in pal.math
-
Title: LMSSolver
- LMSSolver.Utils - Class in pal.math
-
Title: Utils
- lnGamma(double) - Static method in class pal.math.GammaFunction
-
log Gamma function: ln(gamma(alpha)) for alpha>0, accurate to 10 decimal places
- local(Tree) - Static method in class pal.tree.Local
- local(Tree, double) - Static method in class pal.tree.Local
-
This method does a local interchange on the given tree: Note the original tree is modified.
- Local - Class in pal.tree
-
Implements LOCAL (Larget and Simon, 1999) and stochastic NNI moves for unrooted trees.
- Local() - Constructor for class pal.tree.Local
- localHeights2Lengths(Node, boolean) - Static method in class pal.tree.NodeUtils
-
determines branch lengths of this node and its immediate descendent nodes from heights.
- locusName - Variable in class pal.alignment.IndelAnnotatedAlignment
-
used to designate locus name
- locusName - Variable in class pal.alignment.MultiLocusAnnotatedAlignment
-
used to designate locus name
- locusName - Variable in class pal.alignment.SimpleAnnotatedAlignment
-
used to designate locus name
- locusPosition - Variable in class pal.alignment.IndelAnnotatedAlignment
-
used to designate position; do not account for gaps
- locusPosition - Variable in class pal.alignment.MultiLocusAnnotatedAlignment
-
used to designate position; do not account for gaps
- log(Object) - Method in class pal.util.Log
- log(Object) - Method in interface pal.util.Logger
- Log - Class in pal.util
-
Log provides a mechanism for logging and debugging to the standard output stream.
- Log() - Constructor for class pal.util.Log
- Logger - Interface in pal.util
-
Interface for all objects that provide a logging facility.
- logL - Variable in class pal.eval.DemographicValue
-
Log-Likelihood
- logL - Variable in class pal.eval.LikelihoodValue
-
Log-Likelihood
- LogParameterizedTree - Class in pal.tree
-
This class logarithmically transforms tree parameters.
- LogParameterizedTree(ParameterizedTree) - Constructor for class pal.tree.LogParameterizedTree
-
Takes a parameterized object and transforms the parameters logarithmically.
- LX_PARAMETERIZATION - Static variable in class pal.coalescent.ConstExpGrowth
-
use lx instead of growth parameterization
M
- MachineAccuracy - Class in pal.math
-
determines machine accuracy
- MachineAccuracy() - Constructor for class pal.math.MachineAccuracy
- main(String[]) - Static method in class pal.coalescent.ConstExpConst
- main(String[]) - Static method in class pal.datatype.CodonTableFactory
- main(String[]) - Static method in class pal.eval.SingleSplitMolecularClockLikelihoodModel
- main(String[]) - Static method in class pal.tree.Local
- main(String[]) - Static method in class pal.util.HeapSort
-
test harness for heapsort algorithm
- mapExternalIdentifiers(IdGroup, Tree) - Static method in class pal.tree.TreeUtils
-
map external identifiers in the tree to a set of given identifiers (which can be larger than the set of external identifiers but must contain all of them) NOTE: for efficiency it is assumed that the node lists of the tree are correctly maintained.
- mark() - Method in interface pal.algorithmics.Markable
- mark() - Method in class pal.treesearch.FreeBranch
-
Mark this node, or in other words store information on left and right nodes and branch length for later retreival (via undoToMark())
- mark() - Method in class pal.treesearch.FreeInternalNode
- mark() - Method in class pal.treesearch.FreeLeafNode
- mark() - Method in class pal.treesearch.UnrootedMLSearcher
- Markable - Interface in pal.algorithmics
-
Title: Markable
- MathUtils - Class in pal.math
-
Handy utility functions which have some Mathematical relavance.
- MathUtils() - Constructor for class pal.math.MathUtils
- Matrix - Class in pal.math
-
Title: Matrix
- Matrix(double[][]) - Constructor for class pal.math.Matrix
- Matrix(int, boolean) - Constructor for class pal.math.Matrix
- Matrix(int, int) - Constructor for class pal.math.Matrix
- MatrixExponential - Class in pal.substmodel
-
compute matrix exponential and, subsequently, transition probabilities for a given rate matrix
- MatrixExponential(int) - Constructor for class pal.substmodel.MatrixExponential
-
create module
- MatrixExponential(RateMatrix) - Constructor for class pal.substmodel.MatrixExponential
-
create module
- MAX_TIME_IS_TEXT - Static variable in class pal.mep.SteppedMutationRate
- MAXARC - Static variable in interface pal.misc.BranchLimits
-
maximum branch length
- maxFun - Variable in class pal.math.MultivariateMinimum
-
maxFun is the maximum number of calls to fun allowed.
- maxFun - Variable in class pal.math.UnivariateMinimum
-
maximum number of function evaluations (default 0 indicates no limit on calls)
- MAXIMUM_BRANCH_LENGTH - Static variable in interface pal.treesearch.Constants
- MAXIMUM_KAPPA - Static variable in class pal.substmodel.YangCodonModel
- MAXIMUM_OMEGA - Static variable in class pal.substmodel.YangCodonModel
- mean(double) - Static method in class pal.statistics.ChiSquareDistribution
-
mean of the chi-square distribution
- mean(double) - Static method in class pal.statistics.ExponentialDistribution
-
mean of the exponential distribution
- mean(double[]) - Static method in class pal.statistics.DiscreteStatistics
-
compute mean
- mean(double, double) - Static method in class pal.statistics.GammaDistribution
-
mean of the Gamma distribution
- mean(double, double) - Static method in class pal.statistics.NormalDistribution
-
mean
- mean(double, double) - Static method in class pal.statistics.ParetoDistribution
-
mean of the Pareto distribution
- MEAN_CLADE_HEIGHT - Static variable in interface pal.tree.AttributeNode
-
attribute name for the mean height of this clade in a group of trees.
- meanDistance() - Method in class pal.distance.DistanceMatrix
-
Returns the mean pairwise distance of this matrix
- MersenneTwisterFast - Class in pal.math
-
MersenneTwisterFast: A simulation quality fast random number generator (MT19937) with the same public methods as java.util.Random.
- MersenneTwisterFast() - Constructor for class pal.math.MersenneTwisterFast
-
Constructor using the time of day as default seed.
- MersenneTwisterFast(long) - Constructor for class pal.math.MersenneTwisterFast
-
Constructor using a given seed.
- MFWithGradient - Interface in pal.math
-
interface for a function of several variables with a gradient
- MIMIC_CONSTRUCTION - Static variable in class pal.tree.TreeManipulator
-
Construct tree with same multification as original
- MINARC - Static variable in interface pal.misc.BranchLimits
-
minimum branch length
- MinimiserMonitor - Interface in pal.math
-
interface for a classes that wish to monitor the progress of a Minimiser
- MinimiserMonitor.Utils - Class in pal.math
- MINIMUM_BRANCH_LENGTH - Static variable in interface pal.treesearch.Constants
- MINIMUM_KAPPA - Static variable in class pal.substmodel.YangCodonModel
- MINIMUM_OMEGA - Static variable in class pal.substmodel.YangCodonModel
- minimumCount - Variable in class pal.alignment.StrippedAnnotatedAlignment
- minimumProportion - Variable in class pal.alignment.StrippedAnnotatedAlignment
- minus(DistanceMatrix, int) - Static method in class pal.distance.DistanceMatrixUtils
-
Returns a distance matrix with the specified taxa removed.
- minx - Variable in class pal.math.UnivariateMinimum
-
last minimum
- MISSING - Static variable in interface pal.alignment.CharacterAlignment
- MISSING - Static variable in interface pal.util.XMLConstants
- MODE_NAMES - Static variable in class pal.gui.TreeComponent
- model - Variable in class pal.eval.DemographicValue
- MODEL - Static variable in interface pal.util.XMLConstants
- MODELCOUNT - Static variable in interface pal.substmodel.AminoAcidModelID
- MODELCOUNT - Static variable in interface pal.substmodel.NucleotideModelID
- ModelParameters - Class in pal.eval
-
estimates substitution model parameters from the data
- ModelParameters(SitePattern, SubstitutionModel) - Constructor for class pal.eval.ModelParameters
-
Constructor
- ModelSupport - Class in pal.statistics
-
Computes Akaike weights and expected Akaike weights (relative evidence, expected relative evidence) for a set of models and computes corresponding confidence sets
- ModelSupport() - Constructor for class pal.statistics.ModelSupport
- modelUpdated() - Method in class pal.eval.SimpleLikelihoodCalculator
- MOLD_PROTOZOAN_MITOCHONDRIAL - Static variable in interface pal.datatype.CodonTable
-
TypeID for Mold Protozoan Mitochondrial
- MolecularClockLikelihoodModel - Interface in pal.eval
- MolecularClockLikelihoodModel.External - Interface in pal.eval
-
The External calculator does not maintain any state and is approapriate for calculation where a store is provided
- MolecularClockLikelihoodModel.HeightConverter - Interface in pal.eval
- MolecularClockLikelihoodModel.Instance - Interface in pal.eval
- MolecularClockLikelihoodModel.Internal - Interface in pal.eval
-
The Internal calculator may maintain state and is approapriate permanent attachment to internal nodes of the tree structure
- MolecularClockLikelihoodModel.Leaf - Interface in pal.eval
-
A ConstrainedLHCalculator.Leaf object is attached to each leaf node and can be used to calculated conditional probabilities across the related branch.
- MolecularClockLikelihoodModel.Simulator - Interface in pal.eval
- MolecularDataType - Interface in pal.datatype
-
An extension to the generic DataType class for DataTypes related to genetic residues (by this it is meant Nucleotides, AminoAcids, and Codons).
- MolecularDataType.Utils - Class in pal.datatype
-
Utilities relating to MolecularDataType stuff
- moment(int, double, double) - Static method in class pal.statistics.ParetoDistribution
-
moments E(X^n) of the Pareto distribution
- MONTHS - Static variable in interface pal.misc.Units
- MONTHS - Static variable in interface pal.util.XMLConstants
- MRDTGlobalClockModel - Class in pal.treesearch
- MRDTGlobalClockModel(SampleInformation, MolecularClockLikelihoodModel.Instance) - Constructor for class pal.treesearch.MRDTGlobalClockModel
- MRDTGlobalClockModel(SampleInformation, MolecularClockLikelihoodModel.Instance, double[]) - Constructor for class pal.treesearch.MRDTGlobalClockModel
- MTREV24 - Class in pal.substmodel
-
MTREV24 model of amino acid evolution
- MTREV24 - Static variable in interface pal.substmodel.AminoAcidModelID
- MTREV24 - Static variable in interface pal.util.XMLConstants
- MTREV24(double[]) - Constructor for class pal.substmodel.MTREV24
-
constructor
- MU_STEP_TIME - Static variable in interface pal.util.XMLConstants
- MultiLocusAnnotatedAlignment - Class in pal.alignment
-
MultiLocusAnnotatedAlignment is an extension of the SimpleAlignment that includes Annotation, and is designed for multiple loci.
- MultiLocusAnnotatedAlignment() - Constructor for class pal.alignment.MultiLocusAnnotatedAlignment
-
null constructor.
- MultiLocusAnnotatedAlignment(Alignment) - Constructor for class pal.alignment.MultiLocusAnnotatedAlignment
-
Basic constructor.
- MultiLocusAnnotatedAlignment(AnnotationAlignment) - Constructor for class pal.alignment.MultiLocusAnnotatedAlignment
-
Clone constructor for Annotated alignment
- MultiLocusAnnotatedAlignment(AnnotationAlignment, IdGroup) - Constructor for class pal.alignment.MultiLocusAnnotatedAlignment
-
This constructor will subset the alignment based on the taxa in IdGroup
- MultiLocusAnnotatedAlignment(Identifier[], String[], String, DataType) - Constructor for class pal.alignment.MultiLocusAnnotatedAlignment
- MultiLocusAnnotatedAlignment(IdGroup, String[], String, DataType) - Constructor for class pal.alignment.MultiLocusAnnotatedAlignment
- MultiLocusAnnotatedAlignment(IdGroup, String[], DataType) - Constructor for class pal.alignment.MultiLocusAnnotatedAlignment
- MultiParameterized - Class in pal.misc
-
Title: MultiParameterized
- MultiParameterized(Parameterized[]) - Constructor for class pal.misc.MultiParameterized
- MultiParameterized(Parameterized[], MultiParameterized.ParameterAccessWatcher) - Constructor for class pal.misc.MultiParameterized
- MultiParameterized(Parameterized, Parameterized) - Constructor for class pal.misc.MultiParameterized
- MultiParameterized.ParameterAccessWatcher - Interface in pal.misc
-
An interface for classes that wish to find out about particular parameter access
- multiplePrint(PrintWriter, char, int) - Method in class pal.io.FormattedOutput
-
repeatedly print a character
- multiply(double) - Method in class pal.math.Matrix
- MultiRateMatrixHandler - Class in pal.substmodel
- MultiRateMatrixHandler(NeoRateMatrix[], double[], double[]) - Constructor for class pal.substmodel.MultiRateMatrixHandler
- MultivariateFunction - Interface in pal.math
-
interface for a function of several variables
- MultivariateMinimum - Class in pal.math
-
abstract base class for minimisation of a multivariate function
- MultivariateMinimum() - Constructor for class pal.math.MultivariateMinimum
- MultivariateMinimum.Factory - Interface in pal.math
-
A factory interface for MultivariateMinimums (because they aren't statefree)
- MutableDouble - Class in pal.misc
- MutableDouble(double, double, double, double, String) - Constructor for class pal.misc.MutableDouble
-
The default value is also the initial value.
- MUTATION_RATE - Static variable in interface pal.util.XMLConstants
- MUTATION_RATE_MODEL - Static variable in interface pal.util.XMLConstants
- MutationRateModel - Class in pal.mep
-
This abstract class contains methods that are of general use for modelling mutation rate changes over time.
- MutationRateModel(int, double) - Constructor for class pal.mep.MutationRateModel
- MutationRateModel(MutationRateModel) - Constructor for class pal.mep.MutationRateModel
- MutationRateModel.Factory - Interface in pal.mep
-
An interface for objects which generate fresh MutationRAteModels
- MutationRateModelTree - Class in pal.tree
-
Provides parameter interface to any clock-like tree with serially sampled tips (parameters are the minimal node height differences at each internal node).
- MutationRateModelTree(MutationRateModelTree) - Constructor for class pal.tree.MutationRateModelTree
-
Cloning constructor
- MutationRateModelTree(Tree, TimeOrderCharacterData, MutationRateModel) - Constructor for class pal.tree.MutationRateModelTree
-
take any tree and afford it with an interface suitable for a clock-like tree (parameters are the minimal node height differences at each internal node).
- MutationRateModelTree(Tree, TimeOrderCharacterData, MutationRateModel, boolean) - Constructor for class pal.tree.MutationRateModelTree
-
take any tree and afford it with an interface suitable for a clock-like tree (parameters are the minimal node height differences at each internal node).
- MUTATIONS - Static variable in interface pal.util.XMLConstants
- mutationsToGenerations(Tree, MutationRateModel) - Static method in class pal.tree.TreeUtils
-
Takes a tree (in mutation units) and returns a scaled version of it (in generation units).
- MYCOPLASMA - Static variable in interface pal.datatype.CodonTable
-
TypeID for Mycoplasma
N
- N0 - Variable in class pal.coalescent.ConstantPopulation
-
population size
- N0SE - Variable in class pal.coalescent.ConstantPopulation
-
standard error of population size
- N1 - Variable in class pal.coalescent.ConstExpGrowth
-
ancestral pop.
- N1_PARAMETERIZATION - Static variable in class pal.coalescent.ConstExpGrowth
-
use N1 instead of alpha parameterization
- N1SE - Variable in class pal.coalescent.ConstExpGrowth
-
standard error of ancestral pop.
- NAME - Static variable in interface pal.util.XMLConstants
- Nameable - Interface in pal.misc
-
interface for classes that can be named.
- NameColouriser - Class in pal.gui
- NameColouriser() - Constructor for class pal.gui.NameColouriser
- NameColouriser(String[], Color) - Constructor for class pal.gui.NameColouriser
- NameColouriser(String, Color) - Constructor for class pal.gui.NameColouriser
- NameColouriser(Identifier, Color) - Constructor for class pal.gui.NameColouriser
- NamedParameterized - Interface in pal.misc
-
interface for class with (optimizable) named parameters
- NEGATIVE_VALUES_TEXT - Static variable in class pal.mep.SteppedMutationRate
- NeighborJoiningTree - Class in pal.tree
-
constructs a neighbor-joining tree from pairwise distances
Saitou, N., and Nei, M., (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. - NeighborJoiningTree(DistanceMatrix) - Constructor for class pal.tree.NeighborJoiningTree
-
construct NJ tree
- NeoParameterized - Interface in pal.misc
-
interface for class with (optimizable) parameters.
- NeoRateMatrix - Interface in pal.substmodel
-
The new RateMatrix class.
- NeutralSelectionRateMatrixGroup - Class in pal.substmodel
- NeutralSelectionRateMatrixGroup(MutableDouble, double[], CodonTable) - Constructor for class pal.substmodel.NeutralSelectionRateMatrixGroup
- NEW_SAMPLE - Static variable in class pal.coalescent.CoalescentIntervals
-
Denotes an interval at the end of which a new sample addition is observed (i.e.
- newAlignment(Alignment) - Method in class pal.alignment.AlignmentReceiver.BucketReceiver
- newAlignment(Alignment) - Method in interface pal.alignment.AlignmentReceiver
- newAlignment(Alignment) - Method in class pal.alignment.AlignmentReceiver.SingleReceiver
- newConditionalProbabilityStore(boolean) - Method in class pal.treesearch.GeneralConstructionTool
- newInstance() - Method in interface pal.algorithmics.ProbabilityIterator.Factory
- newInstance() - Method in interface pal.algorithmics.StoppingCriteria.Factory
- newIteration(double, double, boolean, boolean, AlgorithmCallback) - Method in interface pal.algorithmics.StoppingCriteria
- NEWLINE_TOKEN - Static variable in class pal.io.NexusTokenizer
-
Flag indicating last token read was a newline symbol/word
- newMinimum(double, double[], MultivariateFunction) - Method in interface pal.math.MinimiserMonitor
-
Inform monitor of a new minimum, along with the current arguments.
- nextBoolean() - Method in class pal.math.MersenneTwisterFast
- nextByte() - Method in class pal.math.MersenneTwisterFast
- nextBytes(byte[]) - Method in class pal.math.MersenneTwisterFast
- nextChar() - Method in class pal.math.MersenneTwisterFast
- nextDouble() - Method in class pal.math.MersenneTwisterFast
- nextFloat() - Method in class pal.math.MersenneTwisterFast
- nextGaussian() - Method in class pal.math.MersenneTwisterFast
- nextInt() - Method in class pal.math.MersenneTwisterFast
- nextInt(int) - Method in class pal.math.MersenneTwisterFast
-
Returns an integer drawn uniformly from 0 to n-1.
- nextLine(PushbackReader) - Method in class pal.io.FormattedInput
-
go to the beginning of the next line.
- nextLong() - Method in class pal.math.MersenneTwisterFast
- nextShort() - Method in class pal.math.MersenneTwisterFast
- NexusParseException - Exception in pal.io
-
Exception class for the NexusParser.
- NexusParseException() - Constructor for exception pal.io.NexusParseException
-
Constructor for the
NexusParseException
object - NexusParseException(String) - Constructor for exception pal.io.NexusParseException
-
Constructor for the
NexusParseException
object - NexusTokenizer - Class in pal.io
-
Comments
- NexusTokenizer(PushbackReader) - Constructor for class pal.io.NexusTokenizer
-
Constructor for a
NexusTokenParser
- NexusTokenizer(String) - Constructor for class pal.io.NexusTokenizer
-
Constructor for a
NexusTokenParser
- NO_OPTIMISE - Static variable in class pal.treesearch.GeneralLikelihoodSearcher
- NO_SOURCE - Static variable in class pal.misc.PalObjectEvent
- Node - Interface in pal.tree
-
interface for a node (includes branch) in a binary/non-binary rooted/unrooted tree
- NODE - Static variable in interface pal.util.XMLConstants
- NODE_HEIGHT_SE - Static variable in interface pal.tree.AttributeNode
-
attribute name for the standard error on a node's height.
- NodeAccess - Interface in pal.treesearch
- NodeFactory - Class in pal.tree
- NodeFactory() - Constructor for class pal.tree.NodeFactory
- NodeUtils - Class in pal.tree
-
Helper routines for dealing with nodes.
- NodeUtils() - Constructor for class pal.tree.NodeUtils
- NORMAL_BW - Static variable in class pal.gui.TreeComponent
- NORMAL_COLOR - Static variable in class pal.gui.TreeComponent
- NORMAL_LABEL_COLOR - Static variable in class pal.gui.TreePainter
- NORMAL_LABEL_DISPLAY - Static variable in class pal.gui.TreePainter
- NormalDistribution - Class in pal.statistics
-
normal distribution (pdf, cdf, quantile)
- NormalDistribution() - Constructor for class pal.statistics.NormalDistribution
- notDropped - Variable in class pal.alignment.StrippedAlignment
- NOTHING - Static variable in class pal.coalescent.CoalescentIntervals
-
Denotes an interval at the end of which nothing is observed (i.e.
- NUCLEOTIDE_DESCRIPTION - Static variable in interface pal.datatype.DataType
-
Name of nucleotide data type.
- NucleotideModel - Class in pal.substmodel
-
base class for nucleotide rate matrices
- NucleotideModel(double[]) - Constructor for class pal.substmodel.NucleotideModel
- NucleotideModelID - Interface in pal.substmodel
-
interface for IDs of nucleotide models
- Nucleotides - Class in pal.datatype
-
implements DataType for nucleotides
- Nucleotides() - Constructor for class pal.datatype.Nucleotides
- Nucleotides(boolean) - Constructor for class pal.datatype.Nucleotides
-
If isRNA is true than getChar(state) will return a U instead of a T
- NUCLEOTIDES - Static variable in interface pal.datatype.DataType
- Null() - Constructor for class pal.misc.Parameterized.Null
- NUMBER_CATEGORIES - Static variable in interface pal.util.XMLConstants
- numbers - Variable in class pal.util.ThreeNumberSort
-
the three numbers
- numBootstraps - Variable in class pal.statistics.ModelSupport
-
number of bootstrap replicates
- numBootstraps - Variable in class pal.statistics.ShimodairaHasegawaTest
-
number of bootstrap replicates
- NUMERIC - Static variable in interface pal.datatype.DataType
- NumericalDerivative - Class in pal.math
-
approximates numerically the first and second derivatives of a function of a single variable and approximates gradient and diagonal of Hessian for multivariate functions
- NumericalDerivative() - Constructor for class pal.math.NumericalDerivative
- NumericDataType - Class in pal.datatype
-
This datatype stores numeric values.
- NumericDataType() - Constructor for class pal.datatype.NumericDataType
- NumericDataType(int) - Constructor for class pal.datatype.NumericDataType
- numFun - Variable in class pal.math.MultivariateMinimum
-
total number of function evaluations necessary
- numFun - Variable in class pal.math.UnivariateMinimum
-
total number of function evaluations neccessary
- numFuncStops - Variable in class pal.math.MultivariateMinimum
-
numFuncStops is the number of consecutive positive evaluations of the stop criterion based on function evaluation necessary to cause the abortion of the optimization (default is 4)
- numPatterns - Variable in class pal.alignment.SitePattern
-
number of site patterns
- numRates - Variable in class pal.substmodel.RateDistribution
-
number of rate categories
- numSeqs - Variable in class pal.alignment.AbstractAlignment
-
number of sequences
- numSeqs - Variable in class pal.alignment.SimpleCharacterAlignment
-
number of sequences
- numSites - Variable in class pal.alignment.AbstractAlignment
-
length of each sequence
- numTraits - Variable in class pal.alignment.SimpleCharacterAlignment
-
number of traits
O
- ObjectState - Interface in pal.algorithmics
-
Title: Object State
- obtainConstrainedExternalCalculator() - Method in class pal.treesearch.AbstractParentableConstrainedNode
- obtainConstrainedExternalCalculator() - Method in class pal.treesearch.GeneralConstraintGroupManager
- obtainFreeExternalCalculator() - Method in class pal.treesearch.GeneralConstructionTool
- obtainLeafInformation(HeightInformationUser) - Method in class pal.treesearch.AbstractParentableConstrainedNode
- obtainLeafInformation(HeightInformationUser) - Method in class pal.treesearch.ConstrainedLeafNode
- obtainLeafInformation(HeightInformationUser) - Method in interface pal.treesearch.ConstrainedNode
-
Obtain information regarding the current state of the leaf heights (called when first constructed).
- obtainLeafInformation(HeightInformationUser) - Method in interface pal.treesearch.GroupLeader
- obtainMatrix(AlgorithmCallback) - Method in interface pal.distance.DistanceMatrixAccess
- obtainTempConditionalProbabilityStore() - Method in class pal.treesearch.GeneralConstructionTool
- OMEGA - Static variable in interface pal.util.XMLConstants
- OMEGA_PARAMETER - Static variable in class pal.substmodel.YangCodonModel
- openFile(String) - Static method in class pal.io.InputSource
-
open file for reading
- openFile(String) - Static method in class pal.io.OutputTarget
-
open file for writing
- openStdIn() - Static method in class pal.io.InputSource
-
open standard input
- openStdOut() - Static method in class pal.io.OutputTarget
-
open standard out
- openString() - Static method in class pal.io.OutputTarget
-
"open" string to write into
- openString(String) - Static method in class pal.io.InputSource
-
"open" string for reading
- operateOn(Tree) - Method in interface pal.tree.TreeOperation
-
Operates on input tree.
- optimise(int, UnivariateMinimum, GeneralConstructionTool, int) - Method in class pal.treesearch.ConstrainedInternalNode
- optimise(int, UnivariateMinimum, GeneralConstructionTool, int) - Method in class pal.treesearch.FreeBranch
- optimise(int, UnivariateMinimum, GeneralConstructionTool, int) - Method in interface pal.treesearch.GeneralOptimisable
- optimise(int, UnivariateMinimum, GeneralConstructionTool, int) - Method in class pal.treesearch.PivotNode
- OPTIMISE_ALL - Static variable in class pal.treesearch.GeneralLikelihoodSearcher
- OPTIMISE_PRIMARY - Static variable in class pal.treesearch.GeneralLikelihoodSearcher
- OPTIMISE_SECONDARY - Static variable in class pal.treesearch.GeneralLikelihoodSearcher
- optimiseAllFullHeirarchy(StoppingCriteria, StoppingCriteria, MultivariateMinimum, int, int, AlgorithmCallback, SearchMonitor, MinimiserMonitor) - Method in class pal.treesearch.GeneralLikelihoodSearcher
- optimiseAllGlobalClockConstraints(MultivariateMinimum, GeneralConstraintGroupManager.LikelihoodScoreAccess, int, int, MinimiserMonitor) - Method in class pal.treesearch.GeneralConstraintGroupManager
-
Optimise all the global clock parameters related to this group
- optimiseAllPlusSubstitutionModel(StoppingCriteria, MultivariateMinimum, MultivariateMinimum, int, int, AlgorithmCallback, SearchMonitor, int, MinimiserMonitor, MinimiserMonitor) - Method in class pal.treesearch.GeneralLikelihoodSearcher
- optimiseAllSimple(StoppingCriteria, MultivariateMinimum, int, int, AlgorithmCallback) - Method in class pal.treesearch.GeneralLikelihoodSearcher
- optimiseAllSimple(StoppingCriteria, MultivariateMinimum, int, int, AlgorithmCallback, SearchMonitor, MinimiserMonitor) - Method in class pal.treesearch.GeneralLikelihoodSearcher
- optimiseAllSimple(StoppingCriteria, MultivariateMinimum, int, int, AlgorithmCallback, SearchMonitor, MinimiserMonitor, int) - Method in class pal.treesearch.GeneralLikelihoodSearcher
- optimiseAllSimpleHeirarchy(StoppingCriteria, MultivariateMinimum, int, int, AlgorithmCallback, SearchMonitor, MinimiserMonitor) - Method in class pal.treesearch.GeneralLikelihoodSearcher
- optimiseAlternate(ParameterizedTree, Alignment, SubstitutionModel, MultivariateMinimum, int, int) - Static method in class pal.eval.LikelihoodOptimiser
-
Optimise parameters to acheive maximum likelihood using an alternating stategy.
- optimiseAlternate(ParameterizedTree, Alignment, SubstitutionModel, MultivariateMinimum, int, int, MinimiserMonitor) - Static method in class pal.eval.LikelihoodOptimiser
-
Optimise parameters to acheive maximum likelihood using an alternating stategy.
- optimiseClockConstrained(Tree, Alignment, SubstitutionModel, boolean) - Static method in class pal.eval.LikelihoodTool
-
Optimise the branches of a tree with regard to maximum likelihood, with a molecular clock assumption, that is, constrained such that all tips are contemporaneous, the tree is treated as rooted.
- optimiseClockConstrainedFixed(Tree, Alignment, SubstitutionModel, boolean, AlgorithmCallback) - Static method in class pal.treesearch.TreeSearchTool
-
Optimise the branches of a tree with regard to maximum likelihood, with the contraints of a global molecular clock - that is, all the tips terminate at the same point.
- optimiseCombined(ParameterizedTree, Alignment, SubstitutionModel, MultivariateMinimum, int, int) - Static method in class pal.eval.LikelihoodOptimiser
-
Optimise parameters to acheive maximum likelihood using a combined stategy.
- optimiseCombined(ParameterizedTree, Alignment, SubstitutionModel, MultivariateMinimum, int, int, MinimiserMonitor) - Static method in class pal.eval.LikelihoodOptimiser
-
Optimise parameters to acheive maximum likelihood using a combined stategy.
- optimiseConstraintRateModels(MultivariateMinimum, int, int, MinimiserMonitor) - Method in class pal.treesearch.GeneralLikelihoodSearcher
- optimiseGeneral(StoppingCriteria, int, AlgorithmCallback) - Method in class pal.treesearch.GeneralLikelihoodSearcher
- optimiseGeneral(StoppingCriteria, int, AlgorithmCallback, SearchMonitor) - Method in class pal.treesearch.GeneralLikelihoodSearcher
- optimiseLogLikelihood(Parameterized, MultivariateMinimum, int, int) - Method in class pal.eval.LikelihoodOptimiser
- optimiseLogLikelihood(Parameterized, MultivariateMinimum, int, int, MinimiserMonitor) - Method in class pal.eval.LikelihoodOptimiser
- optimiseModel(Tree, Alignment, SubstitutionModel, MultivariateMinimum, int, int, MinimiserMonitor) - Static method in class pal.eval.LikelihoodOptimiser
-
Optimise model parameters only to acheive maximum likelihood using a combined stategy.
- optimiseMRDT(Tree, Alignment, SubstitutionModel, TimeOrderCharacterData, boolean, double[]) - Static method in class pal.eval.LikelihoodTool
-
Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and multiple mutation rate parameters, mu - one for each sampling interval.
- optimiseMRDT(Tree, Alignment, SubstitutionModel, TimeOrderCharacterData, boolean, double[], double[]) - Static method in class pal.eval.LikelihoodTool
-
Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and multiple mutation rate parameters, mu, over general time intervals.
- optimiseOriginalTopologies(AlgorithmCallback) - Method in class pal.statistics.GeneralTopologyPool
- optimiseParameters() - Method in class pal.eval.ChiSquareValue
-
optimise parameters of a tree by minimising its chi-square value (tree must be a ParameterizedTree)
- optimiseParameters() - Method in class pal.eval.LikelihoodValue
-
optimise parameters of tree by maximising its likelihood (this assumes that tree is a ParameterizedTree)
- optimiseParameters(MultivariateMinimum) - Method in class pal.eval.ChiSquareValue
-
optimise parameters of a tree by minimising its chi-square value (tree must be a ParameterizedTree)
- optimiseParameters(MultivariateMinimum) - Method in class pal.eval.LikelihoodValue
-
optimise parameters of tree by maximising its likelihood (this assumes that tree is a ParameterizedTree)
- optimisePrimaryGlobalClockConstraints(MultivariateMinimum, GeneralConstraintGroupManager.LikelihoodScoreAccess, int, int, MinimiserMonitor) - Method in class pal.treesearch.GeneralConstraintGroupManager
-
Optimise the global clock parameters marked as primary related to this group
- optimiseSecondaryGlobalClockConstraints(MultivariateMinimum, GeneralConstraintGroupManager.LikelihoodScoreAccess, int, int, MinimiserMonitor) - Method in class pal.treesearch.GeneralConstraintGroupManager
-
Optimise the global clock parameters marked as secondary related to this group
- optimiseSRDT(Tree, Alignment, SubstitutionModel, TimeOrderCharacterData, boolean, double[]) - Static method in class pal.eval.LikelihoodTool
-
Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and a single mutation rate parameter.
- optimiseSubstitutionModels(MultivariateMinimum, int, int, MinimiserMonitor) - Method in class pal.treesearch.GeneralLikelihoodSearcher
- optimiseTree(ParameterizedTree, Alignment, SubstitutionModel, MultivariateMinimum, int, int) - Static method in class pal.eval.LikelihoodOptimiser
-
Optimise tree branchlengths only to acheive maximum likelihood using a combined stategy.
- optimiseTree(ParameterizedTree, Alignment, SubstitutionModel, MultivariateMinimum, int, int, MinimiserMonitor) - Static method in class pal.eval.LikelihoodOptimiser
-
Optimise tree branchlengths only to acheive maximum likelihood using a combined stategy.
- optimiseUnrooted(Tree, Alignment, SubstitutionModel, boolean) - Static method in class pal.eval.LikelihoodTool
-
Optimise the branches of a tree with regard to maximum likelihood, with no constraints on the branchlengths (as for an unrooted tree).
- optimiseUnrootedFixed(Tree, Alignment, SubstitutionModel, boolean) - Static method in class pal.treesearch.TreeSearchTool
-
Optimise the branches of a tree with regard to maximum likelihood, with no constraints on the branchlengths (as for an unrooted tree).
- optimiseUnrootedFixed(Tree, Alignment, SubstitutionModel, boolean, AlgorithmCallback) - Static method in class pal.treesearch.TreeSearchTool
-
Optimise the branches of a tree with regard to maximum likelihood, with no constraints on the branchlengths (as for an unrooted tree).
- optimize() - Method in class pal.coalescent.SkylinePlot
-
Optimize generalized skyline plot
- optimize() - Method in class pal.eval.DemographicValue
-
optimize log-likelihood using default optimizer return minimum negative log-likelihood
- optimize(double, UnivariateFunction, double) - Method in class pal.math.UnivariateMinimum
-
The actual optimization routine (Brent's golden section method)
- optimize(double, UnivariateFunction, double, double, double) - Method in class pal.math.UnivariateMinimum
-
The actual optimization routine (Brent's golden section method)
- optimize(MultivariateFunction, double[], double, double) - Method in class pal.math.ConjugateDirectionSearch
- optimize(MultivariateFunction, double[], double, double) - Method in class pal.math.ConjugateGradientSearch
- optimize(MultivariateFunction, double[], double, double) - Method in class pal.math.DifferentialEvolution
- optimize(MultivariateFunction, double[], double, double) - Method in class pal.math.GeneralizedDEOptimizer
-
The actual optimization routine It finds a minimum close to vector x when the absolute tolerance for each parameter is specified.
- optimize(MultivariateFunction, double[], double, double) - Method in class pal.math.MultivariateMinimum
-
The actual optimization routine (needs to be implemented in a subclass of MultivariateMinimum).
- optimize(MultivariateFunction, double[], double, double) - Method in class pal.math.OrthogonalSearch
- optimize(MultivariateFunction, double[], double, double, MinimiserMonitor) - Method in class pal.math.ConjugateDirectionSearch
- optimize(MultivariateFunction, double[], double, double, MinimiserMonitor) - Method in class pal.math.ConjugateGradientSearch
- optimize(MultivariateFunction, double[], double, double, MinimiserMonitor) - Method in class pal.math.DifferentialEvolution
- optimize(MultivariateFunction, double[], double, double, MinimiserMonitor) - Method in class pal.math.GeneralizedDEOptimizer
-
The actual optimization routine It finds a minimum close to vector x when the absolute tolerance for each parameter is specified.
- optimize(MultivariateFunction, double[], double, double, MinimiserMonitor) - Method in class pal.math.MultivariateMinimum
-
The actual optimization routine It finds a minimum close to vector x when the absolute tolerance for each parameter is specified.
- optimize(MultivariateFunction, double[], double, double, MinimiserMonitor) - Method in class pal.math.OrthogonalSearch
- optimize(MultivariateMinimum) - Method in class pal.eval.DemographicValue
-
optimize log-likelihood value and compute corresponding SEs given an optimizer
- optimize(UnivariateFunction, double) - Method in class pal.math.UnivariateMinimum
-
The actual optimization routine (Brent's golden section method)
- optimize(UnivariateFunction, double, double, double) - Method in class pal.math.UnivariateMinimum
-
The actual optimization routine (Brent's golden section method)
- OrderEnumerator - Interface in pal.math
-
A means for describing odering information, and Utilities for creating such Orderings
- OrderEnumerator.OEFactory - Interface in pal.math
- OrderEnumerator.Utils - Class in pal.math
- ORGANISM_TYPE_NAMES - Static variable in interface pal.datatype.CodonTable
-
A textual version of an organism type - type is index into array
- ORIGIN - Static variable in interface pal.util.XMLConstants
- OrthogonalHints - Interface in pal.math
-
Provides a means for giving an Orthogonal base optimiser (IE, OrthognalMinimum) hints about the function that may alow it to optimise better.
- OrthogonalHints.Utils - Class in pal.math
- OrthogonalLineFunction - Class in pal.math
-
converts a multivariate function into a univariate function by keeping all but one argument constant
- OrthogonalLineFunction(MultivariateFunction) - Constructor for class pal.math.OrthogonalLineFunction
-
construct univariate function from multivariate function
- OrthogonalLineFunction(MultivariateFunction, int, double[]) - Constructor for class pal.math.OrthogonalLineFunction
-
construct univariate function from multivariate function
- OrthogonalSearch - Class in pal.math
-
minimization of a real-valued function of several variables without using derivatives, using the simple strategy of optimizing variables one by one.
- OrthogonalSearch() - Constructor for class pal.math.OrthogonalSearch
-
Initialization
- OrthogonalSearch(boolean) - Constructor for class pal.math.OrthogonalSearch
-
Initialization
- OrthogonalSearch(OrderEnumerator.OEFactory) - Constructor for class pal.math.OrthogonalSearch
-
Initialization
- OrthogonalSearch.RoundOptimiser - Interface in pal.math
- OutputTarget - Class in pal.io
-
convenience class to create output streams linked to files, stdout, and strings
P
- 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) - Method in class pal.gui.TreeComponent
- paint(Graphics, int, int) - Method in interface pal.gui.Painter
- paint(Graphics, int, int) - Method in class pal.gui.TreePainterCircular
- paint(Graphics, int, int) - Method in class pal.gui.TreePainterNormal
- paint(Graphics, int, int, boolean) - Method in class pal.gui.TreePainterCircular
- paint(Graphics, int, int, boolean, LayoutTracker) - Method in class pal.gui.TreePainterCircular
- paint(Graphics, int, int, LayoutTracker) - Method in interface pal.gui.Painter
- paint(Graphics, int, int, LayoutTracker) - Method in class pal.gui.TreePainterCircular
- paint(Graphics, int, int, LayoutTracker) - Method in class pal.gui.TreePainterNormal
- paint(PositionedNode, Graphics, int, int, LayoutTracker, boolean) - Method in class pal.gui.TreePainterNormal
- paint(PositionedNode, CircularGraphics) - Method in class pal.gui.TreePainterCircular
- 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.
- PALBranchWrapper(TreeManipulator.PALNodeWrapper, TreeManipulator.PALNodeWrapper, double) - Constructor for class pal.tree.TreeManipulator.PALBranchWrapper
- PalEventMulticaster - Class in pal.misc
-
A utility class for accomodating Pal listeners
- PalEventMulticaster() - Constructor for class pal.misc.PalEventMulticaster
- PALNodeWrapper(Node) - Constructor for class pal.tree.TreeManipulator.PALNodeWrapper
- PALNodeWrapper(Node, TreeManipulator.PALNodeWrapper) - Constructor for class pal.tree.TreeManipulator.PALNodeWrapper
- PalObjectEvent - Class in pal.misc
-
An event used by PalObjectListeners
- PalObjectEvent() - Constructor for class pal.misc.PalObjectEvent
- PalObjectEvent(Object) - 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
- parameter - Variable in class pal.tree.ClockTree
- PARAMETER - Static variable in interface pal.util.XMLConstants
- parameterChanged(ParameterEvent) - Method in interface pal.misc.ExternalParameterListener
- parameterChanged(ParameterEvent) - Method in class pal.substmodel.AbstractRateMatrix
-
For the external parameter interface.
- parameterChanged(Parameterized, int, double) - Method in interface pal.misc.IndividualParameterHandler.Listener
- 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.ParameterizedBase - Class in pal.misc
-
A Utility class for using as the superclass to subclasses which are based on 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.Utils - Class in pal.misc
- ParameterizedBase() - Constructor for class pal.misc.Parameterized.ParameterizedBase
-
Builds a parameterized objects around a set of double arrays.
- ParameterizedBase(double[], double[], double[], double[]) - Constructor for class pal.misc.Parameterized.ParameterizedBase
-
Builds a parameterized objects around a set of double arrays
- ParameterizedBase(double[], double[], double[], double[], double[]) - Constructor for class pal.misc.Parameterized.ParameterizedBase
-
Builds a parameterized objects around a set of double arrays
- 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...)
- ParameterizedTreeBase() - Constructor for class pal.tree.ParameterizedTree.ParameterizedTreeBase
- ParameterizedTreeBase(ParameterizedTree.ParameterizedTreeBase) - Constructor for class pal.tree.ParameterizedTree.ParameterizedTreeBase
-
Cloning constructor
- ParameterizedTreeBase(Tree) - Constructor for class pal.tree.ParameterizedTree.ParameterizedTreeBase
- ParameterizedUser() - Constructor for class pal.misc.Parameterized.ParameterizedUser
-
Sub class should call setParameterizedBase() at some point if using this constructor...
- ParameterizedUser(Parameterized) - Constructor for class pal.misc.Parameterized.ParameterizedUser
- 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[], int) - Constructor for class pal.eval.PatternInfo
- PatternInfo(int[], int[], int) - Constructor for class pal.eval.PatternInfo
- PatternInfo(int[], int[], int[], int) - Constructor for class pal.eval.PatternInfo
- PatternInfo(int, boolean) - 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
- PhylipClustalAlignment(String[], String[], DataType) - Constructor for class pal.alignment.AlignmentReaders.PhylipClustalAlignment
- 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) - Constructor for class pal.gui.PositionedNode
- PositionedNode(Node, Node) - Constructor for class pal.gui.PositionedNode
-
Builds a tree based on node, but highlights highlightNode
- positionType - Variable in class pal.alignment.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(Graphics, PageFormat, int) - Method in class pal.gui.LinkageDisequilibriumComponent
- print(Alignment, PrintWriter) - Static method in class pal.alignment.AlignmentUtils
-
print alignment (default format: INTERLEAVED)
- 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
- 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
Q
- quantile(double, double) - Static method in class pal.statistics.ChiSquareDistribution
-
quantile (inverse cumulative density function) of the chi-square distribution
- quantile(double, double) - Static method in class pal.statistics.ExponentialDistribution
-
quantile (inverse cumulative density function) of the exponential distribution
- quantile(double, double[]) - Static method in class pal.statistics.DiscreteStatistics
-
compute the q-th quantile for a distribution of x (= inverse cdf)
- quantile(double, double[], int[]) - Static method in class pal.statistics.DiscreteStatistics
-
compute the q-th quantile for a distribution of x (= inverse cdf)
- quantile(double, double, double) - Static method in class pal.statistics.GammaDistribution
-
quantile (inverse cumulative density function) of the Gamma distribution
- quantile(double, double, double) - Static method in class pal.statistics.NormalDistribution
-
quantiles (=inverse cumulative density function)
- quantile(double, double, double) - Static method in class pal.statistics.ParetoDistribution
-
quantile (inverse cumulative density function) of the Pareto distribution
R
- r - Variable in class pal.coalescent.ExponentialGrowth
-
growth rate r
- R_BRACE - Static variable in class pal.io.NexusTokenizer
- R_BRACKET - Static variable in class pal.io.NexusTokenizer
- R_PARAMETER_INDEX - Static variable in class pal.substmodel.TN
- R_PARENTHESIS - Static variable in class pal.io.NexusTokenizer
- random - Static variable in class pal.math.MathUtils
-
A random number generator that is initialized with the clock when this class is loaded into the JVM.
- randomiseParameters() - Method in class pal.misc.Parameterized.ParameterizedUser
- Ranker - Class in pal.algorithmics
-
Title: Ranker Description: Maintains a list of ranked objects
- Ranker(int) - Constructor for class pal.algorithmics.Ranker
- rate - Variable in class pal.substmodel.RateDistribution
-
rates of each rate category
- RATE_DISTRIBUTION - Static variable in interface pal.util.XMLConstants
- RATE_MATRIX - Static variable in interface pal.util.XMLConstants
- rateAtSite - Variable in class pal.eval.LikelihoodValue
-
map estimation of rate at site pattern
- RateDistribution - Class in pal.substmodel
-
abstract base class for models of rate variation over sites employing a discrete rate distribution
- RateDistribution(int) - Constructor for class pal.substmodel.RateDistribution
-
construct discrete distribution
- RateHandler - Interface in pal.supgma
- RateHandler.Utils - Class in pal.supgma
- RateMatrix - Interface in pal.substmodel
-
abstract base class for all rate matrices
- RateMatrixGroup - Interface in pal.substmodel
- RateMatrixHandler - Class in pal.substmodel
- RateMatrixHandler(NeoRateMatrix, double[]) - Constructor for class pal.substmodel.RateMatrixHandler
- RateMatrixUtils - Class in pal.substmodel
- RateMatrixUtils() - Constructor for class pal.substmodel.RateMatrixUtils
- rawAlignment - Variable in class pal.alignment.StrippedAlignment
- rawNumSites - Variable in class pal.alignment.StrippedAlignment
- readAlignment(Reader, DataType) - Static method in class pal.alignment.AlignmentTool
-
Attempt to read a file from a reader object
- ReadAlignment - Class in pal.alignment
-
reads aligned sequence data from plain text files.
- ReadAlignment(PushbackReader) - Constructor for class pal.alignment.ReadAlignment
-
read from stream
- ReadAlignment(String) - Constructor for class pal.alignment.ReadAlignment
-
read from file
- ReadAlignmentOld - Class in pal.alignment
-
reads aligned sequence data from plain text files.
- ReadAlignmentOld(PushbackReader) - Constructor for class pal.alignment.ReadAlignmentOld
-
read from stream
- ReadAlignmentOld(String) - Constructor for class pal.alignment.ReadAlignmentOld
-
read from file
- readAllPhylipClustalAlignments(Reader, DataType) - Static method in class pal.alignment.AlignmentReaders
-
Read an alignment in phylip/clustal/simple format.
- ReadDistanceMatrix - Class in pal.distance
-
reads pairwise distance matrices in PHYLIP format (full matrix)
- ReadDistanceMatrix(PushbackReader) - Constructor for class pal.distance.ReadDistanceMatrix
-
read from stream
- ReadDistanceMatrix(String) - Constructor for class pal.distance.ReadDistanceMatrix
-
read from file
- readDouble(PushbackReader) - Method in class pal.io.FormattedInput
-
read next number from stream and convert it to a double (newline/cr are treated as separators)
- readDouble(PushbackReader, boolean) - Method in class pal.io.FormattedInput
-
read next number from stream and convert it to a double
- readFastaSequences(Reader, DataType) - Static method in class pal.alignment.AlignmentReaders
-
Read an a set of unaligned Fasta sequences
- readInt(PushbackReader) - Method in class pal.io.FormattedInput
-
read next number from stream and convert it to a int (newline/cr are treated as separators)
- readInt(PushbackReader, boolean) - Method in class pal.io.FormattedInput
-
read next number from stream and convert it to a int
- readLabel(PushbackReader, int) - Method in class pal.io.FormattedInput
-
read sequence label from stream A sequence label is not allowed to contain whitespace and either of :,;()[]{}.
- readLine(PushbackReader, boolean) - Method in class pal.io.FormattedInput
-
read a whole line
- readNewLineSeperatedSequences(Reader, DataType) - Static method in class pal.alignment.AlignmentReaders
-
Read an a set of unaligned Fasta sequences
- readNextChar(PushbackReader) - Method in class pal.io.FormattedInput
-
read next character from stream (EOF does not count as character but will throw exception)
- readNumber(PushbackReader, boolean) - Method in class pal.io.FormattedInput
- readPhylipClustalAlignment(Reader, DataType) - Static method in class pal.alignment.AlignmentReaders
-
Read an alignment in phylip/clustal/simple format.
- readPhylipClustalAlignment(Reader, DataType, AlignmentReceiver) - Static method in class pal.alignment.AlignmentReaders
-
Read an alignment in phylip/clustal/simple format.
- readToken() - Method in class pal.io.NexusTokenizer
-
Reads a token in from the underlying stream.
- readTree(Reader) - Static method in class pal.tree.TreeTool
-
Read a tree from an input source.
- ReadTree - Class in pal.tree
-
constructs a tree reading in a New Hampshire treefile, taking care for internal labels and branch lengths and binary/nonbinary and rooted/unrooted trees
- ReadTree(PushbackReader) - Constructor for class pal.tree.ReadTree
-
read tree from input stream
- ReadTree(String) - Constructor for class pal.tree.ReadTree
-
read tree from file
- readWhiteSpace() - Method in class pal.io.NexusTokenizer
-
Get the flag indicating whether or not this parser object is reading (and returning) whitespace
- readWord(PushbackReader) - Method in class pal.io.FormattedInput
-
read word from stream
- rebuild() - Method in class pal.substmodel.AbstractRateMatrix
- rebuildConnectionPatterns(GeneralConstructionTool, FreeBranch) - Method in class pal.treesearch.FreeLeafNode
- rebuildDescendentPattern(GeneralConstructionTool) - Method in class pal.treesearch.AbstractParentableConstrainedNode
- rebuildDescendentPattern(GeneralConstructionTool) - Method in class pal.treesearch.ConstrainedLeafNode
- rebuildRateMatrix(double[][], double[]) - Method in class pal.substmodel.AbstractRateMatrix
- rebuildRateMatrix(double[][], double[]) - Method in class pal.substmodel.BLOSUM62
- rebuildRateMatrix(double[][], double[]) - Method in class pal.substmodel.CPREV
- rebuildRateMatrix(double[][], double[]) - Method in class pal.substmodel.Dayhoff
- rebuildRateMatrix(double[][], double[]) - Method in class pal.substmodel.F81
- rebuildRateMatrix(double[][], double[]) - Method in class pal.substmodel.F84
- rebuildRateMatrix(double[][], double[]) - Method in class pal.substmodel.GTR
- rebuildRateMatrix(double[][], double[]) - Method in class pal.substmodel.HKY
- rebuildRateMatrix(double[][], double[]) - Method in class pal.substmodel.JTT
- rebuildRateMatrix(double[][], double[]) - Method in class pal.substmodel.MTREV24
- rebuildRateMatrix(double[][], double[]) - Method in class pal.substmodel.TN
- rebuildRateMatrix(double[][], double[]) - Method in class pal.substmodel.TwoStateModel
- rebuildRateMatrix(double[][], double[]) - Method in class pal.substmodel.VT
- rebuildRateMatrix(double[][], double[]) - Method in class pal.substmodel.WAG
- rebuildRateMatrix(double[][], double[]) - Method in class pal.substmodel.YangCodonModel
- rebuildTree(UnrootedMLSearcher.Connection[], UnrootedMLSearcher.UNode[]) - Method in class pal.treesearch.UnrootedMLSearcher.StateObject
- recompute(SitePattern, SubstitutionModel) - Method in class pal.distance.AlignmentDistanceMatrix
-
recompute maximum-likelihood distances under new site pattern
- recompute(SitePattern, SubstitutionModel, AlgorithmCallback) - Method in class pal.distance.AlignmentDistanceMatrix
-
recompute maximum-likelihood distances under new site pattern
- recompute(SitePattern, AlgorithmCallback) - Method in class pal.distance.AlignmentDistanceMatrix
-
recompute observed distances under new site pattern
- recompute(Tree) - Method in class pal.tree.TreeDistanceMatrix
- recursivelyAdjustNodeHeight(ConstrainedNode.HeightAdjustment) - Method in class pal.treesearch.AbstractParentableConstrainedNode
- recursivelyAdjustNodeHeight(ConstrainedNode.HeightAdjustment) - Method in class pal.treesearch.ConstrainedLeafNode
- recursivelyAdjustNodeHeight(ConstrainedNode.HeightAdjustment) - Method in interface pal.treesearch.ConstrainedNode
- recursivelySetChildrenParentPivot(PivotNode) - Method in class pal.treesearch.AbstractParentableConstrainedNode
- recursivelySetParentPivot(PivotNode) - Method in class pal.treesearch.ConstrainedInternalNode
- recursivelySetParentPivot(PivotNode) - Method in class pal.treesearch.ConstrainedLeafNode
- recursivelySetParentPivot(PivotNode) - Method in interface pal.treesearch.ConstrainedNode
- redirectRebuildPattern(GeneralConstructionTool) - Method in class pal.treesearch.FreeLeafNode
-
This should only be called by another leaf node on the other end of the connection.
- REDUCE_CONSTRUCTION - Static variable in class pal.tree.TreeManipulator
-
Construct tree, but convert bificating nodes that appear as multifications (due to very short branchlengths) to multifications
- release() - Method in class pal.eval.FastLikelihoodCalculator
- release() - Method in class pal.eval.GeneralLikelihoodCalculator
- release() - Method in interface pal.eval.LikelihoodCalculator
-
This method should be called when the user is through using this calculator to inform it to release any resources it has allocated.
- release() - Method in class pal.eval.SimpleLikelihoodCalculator
-
Doesn't do anything...
- RELEASE_DATE - Static variable in class pal.misc.ReleaseInfo
-
release date
- ReleaseInfo - Class in pal.misc
-
release information
- ReleaseInfo() - Constructor for class pal.misc.ReleaseInfo
- RELLTopologyPool - Class in pal.statistics
- RELLTopologyPool(SiteDetails[], int) - Constructor for class pal.statistics.RELLTopologyPool
- remove(ExternalParameterListener, ExternalParameterListener) - Static method in class pal.misc.PalEventMulticaster
-
For managing ExternalParamterListeners Usage: ExternalParamterListener current = null; ...
- remove(PalObjectListener, PalObjectListener) - Static method in class pal.misc.PalEventMulticaster
-
For managing PalObjectListeners Usage: PalObjectListener current = null; ...
- removeBranch(Node) - Static method in class pal.tree.NodeUtils
-
remove internal branch (collapse node with its parent)
- removeChild(int) - Method in interface pal.tree.Node
-
remove child
- removeChild(int) - Method in class pal.tree.SimpleNode
-
remove child
- removeChild(Node, Node) - Static method in class pal.tree.NodeUtils
-
remove child
- removeConstantSites() - Method in class pal.alignment.StrippedAlignment
-
remove constant sites
- removeConstantSitesIgnoreGapsMissing() - Method in class pal.alignment.StrippedAnnotatedAlignment
-
remove constant sites but ignore gaps and missing data (- and ?)
- removeGaps() - Method in class pal.alignment.StrippedAlignment
-
remove sites with gaps
- removeNoninformativeSites() - Method in class pal.alignment.StrippedAlignment
-
remove noninformative sites
- removePalObjectListener(PalObjectListener) - Method in interface pal.mep.DeltaModel.Instance
- removePalObjectListener(PalObjectListener) - Method in class pal.misc.PalObjectListener.EventGenerator
- removePalObjectListener(PalObjectListener) - Method in class pal.substmodel.AbstractRateMatrix
- removePalObjectListener(PalObjectListener) - Method in class pal.substmodel.CachedRateMatrix
- removePalObjectListener(PalObjectListener) - Method in class pal.substmodel.GeneralRateDistributionSubstitutionModel
- removePalObjectListener(PalObjectListener) - Method in interface pal.substmodel.RateMatrix
- removePalObjectListener(PalObjectListener) - Method in class pal.substmodel.SingleClassSubstitutionModel
- removePalObjectListener(PalObjectListener) - Method in interface pal.substmodel.SubstitutionModel
- removeParent() - Method in class pal.tree.SimpleNode
-
removes parent.
- removeRedundantSites(Alignment) - Static method in class pal.alignment.AlignmentUtils
- removeSites(char) - Method in class pal.alignment.StrippedAlignment
-
remove site that contain a specified character
- removeSitesBasedOnFreqIgnoreGapsMissing(double, int) - Method in class pal.alignment.StrippedAnnotatedAlignment
-
remove sites based on minimum frequency (the count of good bases) and based on the proportion of good sites different from consensus
- removeSitesOutsideRange(int, int) - Method in class pal.alignment.StrippedAnnotatedAlignment
-
Remove sites based on site position (excluded sites are
lastSite) This not effect any prior exclusions. - removeTimes() - Method in class pal.misc.TimeOrderCharacterData
-
Remove time character data.
- removeUnknowns() - Method in class pal.alignment.StrippedAlignment
-
remove sites with unknowns
- renameNodes(Tree, Hashtable) - Static method in class pal.tree.TreeUtils
-
Given a translation table where the keys are the current identifier names and the values are the new identifier names, this method replaces the current identifiers in the tree with new identifiers.
- renewSitePattern(SitePattern) - Method in class pal.eval.LikelihoodValue
-
Set new site pattern (while keeping tree and model)
- REPEATED_TIMES_TEXT - Static variable in class pal.mep.SteppedMutationRate
- ReplicateLikelihoodEvaluator - Interface in pal.statistics
- ReplicateLikelihoodEvaluator.Utils - Class in pal.statistics
- report(PrintWriter) - Method in class pal.alignment.AbstractAlignment
- report(PrintWriter) - Method in interface pal.alignment.AnnotationAlignment
-
Returns a report for the alignment
- report(PrintWriter) - Method in class pal.alignment.ConcatenatedAnnotatedAlignment
- report(PrintWriter) - Method in class pal.alignment.SimpleAnnotatedAlignment
- report(PrintWriter) - Method in class pal.alignment.SimpleCharacterAlignment
- report(PrintWriter) - Method in class pal.alignment.StrippedAnnotatedAlignment
- report(PrintWriter) - Method in class pal.coalescent.CoalescentIntervals
- report(PrintWriter) - Method in class pal.coalescent.ConstantPopulation
- report(PrintWriter) - Method in class pal.coalescent.ConstExpConst
- report(PrintWriter) - Method in class pal.coalescent.ConstExpGrowth
- report(PrintWriter) - Method in class pal.coalescent.ExpandingPopulation
- report(PrintWriter) - Method in class pal.coalescent.ExponentialGrowth
- report(PrintWriter) - Method in class pal.coalescent.SkylinePlot
- report(PrintWriter) - Method in class pal.mep.ConstantMutationRate
- report(PrintWriter) - Method in class pal.mep.SteppedMutationRate
- report(PrintWriter) - Method in class pal.mep.WindowedMutationRate
- report(PrintWriter) - Method in interface pal.misc.Report
-
print human readable report (e.g., on parameters and associated model)
- report(PrintWriter) - Method in class pal.misc.TimeStamp
-
report on runtime
- report(PrintWriter) - Method in class pal.statistics.KishinoHasegawaTest
- report(PrintWriter) - Method in class pal.statistics.ModelSupport
- report(PrintWriter) - Method in class pal.statistics.ShimodairaHasegawaTest
- report(PrintWriter) - Method in class pal.substmodel.AminoAcidModel
- report(PrintWriter) - Method in class pal.substmodel.BLOSUM62
- report(PrintWriter) - Method in class pal.substmodel.CachedRateMatrix
- report(PrintWriter) - Method in class pal.substmodel.CPREV
- report(PrintWriter) - Method in class pal.substmodel.Dayhoff
- report(PrintWriter) - Method in class pal.substmodel.F81
- report(PrintWriter) - Method in class pal.substmodel.F84
- report(PrintWriter) - Method in class pal.substmodel.GammaRates
- report(PrintWriter) - Method in class pal.substmodel.GeneralRateDistributionSubstitutionModel
- report(PrintWriter) - Method in class pal.substmodel.GTR
- report(PrintWriter) - Method in class pal.substmodel.HKY
- report(PrintWriter) - Method in class pal.substmodel.InvariableSites
- report(PrintWriter) - Method in class pal.substmodel.JTT
- report(PrintWriter) - Method in class pal.substmodel.MTREV24
- report(PrintWriter) - Method in class pal.substmodel.MultiRateMatrixHandler
-
Reporting stuff
- report(PrintWriter) - Method in class pal.substmodel.RateMatrixHandler
-
Reporting stuff
- report(PrintWriter) - Method in class pal.substmodel.SingleClassSubstitutionModel
- report(PrintWriter) - Method in class pal.substmodel.TN
- report(PrintWriter) - Method in class pal.substmodel.TwoStateModel
- report(PrintWriter) - Method in class pal.substmodel.UniformRate
- report(PrintWriter) - Method in class pal.substmodel.VT
- report(PrintWriter) - Method in class pal.substmodel.WAG
- report(PrintWriter) - Method in class pal.substmodel.YangCodonModel
- report(PrintWriter) - Method in class pal.substmodel.YangCodonModel.SimpleNeutralSelection
- report(PrintWriter) - Method in class pal.substmodel.YangCodonModel.SimplePositiveSelection
- report(PrintWriter) - Method in class pal.tree.SimpleTree
- report(PrintWriter) - Method in class pal.tree.Tree.TreeBase
- report(Alignment, PrintWriter) - Static method in class pal.alignment.AlignmentUtils
-
Report number of sequences, sites, and data type
- report(Tree, PrintWriter) - Static method in class pal.tree.TreeUtils
- Report - Interface in pal.misc
-
interface for classes that can print out a human readable report of itself
- reroot(int) - Method in class pal.tree.SimpleTree
-
make node with number num to root node
- reroot(int) - Method in class pal.tree.Tree.TreeBase
-
make node with number num to root node
- reroot(Node) - Method in class pal.tree.SimpleTree
-
make provided node the root node
- reroot(Node) - Method in class pal.tree.Tree.TreeBase
-
make provided node the root node
- reroot(Tree, Node) - Static method in class pal.tree.TreeUtils
- reset() - Method in interface pal.algorithmics.StoppingCriteria
- reset() - Method in class pal.gui.LayoutTracker
- reset() - Method in class pal.math.EvaluationCounter
- reset() - Method in interface pal.math.OrderEnumerator
-
Reset back to starting state, may have a differnet number of values, and a different ordering after a reset!
- reset() - Method in class pal.math.UrnModel
-
refill urn
- reset() - Method in class pal.tree.SimpleNode
- resetChildren() - Method in interface pal.tree.RootedTreeInterface.RNode
- resetChildren() - Method in interface pal.tree.UnrootedTreeInterface.UNode
- resetDistributions() - Method in interface pal.eval.MolecularClockLikelihoodModel.Simulator
- resetSiteCategoryDistribution(boolean) - Method in class pal.substmodel.SequenceSimulator
-
Reassigns model classes to each site (a site belongs to a particular class/category of the model)
- resetSiteCategoryDistribution(double[][]) - Method in class pal.substmodel.SequenceSimulator
- resetSiteCategoryDistribution(double[][], int[]) - Method in class pal.substmodel.SequenceSimulator
- resetSiteCategoryDistribution(double[][], SequenceSimulator) - Method in class pal.substmodel.SequenceSimulator
- resetSiteCategoryDistribution(double[], boolean) - Method in class pal.substmodel.SequenceSimulator
- restoreBranch(Node) - Static method in class pal.tree.NodeUtils
-
restore internal branch
- restoreState(Object) - Method in class pal.algorithmics.GeneralObjectState
- restoreState(Object) - Method in interface pal.algorithmics.ObjectState
-
Used to restore the state of the this object to that of a previous time point
- restoreState(Object) - Method in interface pal.algorithmics.StateProvider
- restoreState(Object) - Method in class pal.treesearch.UnrootedMLSearcher
- Results(Tree[]) - Constructor for class pal.coalescent.SerialCoalescentGenerator.Results
- Results(Tree[], Alignment[]) - Constructor for class pal.coalescent.SerialCoalescentGenerator.Results
- reverseSequence(int[]) - Static method in class pal.datatype.DataType.Utils
-
Reverses an array of states
- RIGHTBORDER - Static variable in class pal.gui.TreePainterCircular
- RIGHTBORDER - Static variable in class pal.gui.TreePainterNormal
- RNA_INSTANCE - Static variable in class pal.datatype.IUPACNucleotides
- RootAccess - Interface in pal.treesearch
- RootedTreeInterface - Interface in pal.tree
-
Title: RootedTreeInterface
- RootedTreeInterface.Instructee - Interface in pal.tree
- RootedTreeInterface.RBranch - Interface in pal.tree
- RootedTreeInterface.RNode - Interface in pal.tree
- RootedTreeInterface.Utils - Class in pal.tree
- RootedTreeUtils - Class in pal.tree
-
This class contains utility methods.
- RootedTreeUtils() - Constructor for class pal.tree.RootedTreeUtils
- rotateByLeafCount(Tree) - Static method in class pal.tree.TreeUtils
-
Rotates branches by leaf count.
- rowReduce() - Method in class pal.math.Matrix
- rSE - Variable in class pal.coalescent.ExponentialGrowth
-
standard error of growth rate r
- RSQUARE - Static variable in class pal.gui.LinkageDisequilibriumComponent
- run() - Method in class pal.popgen.LinkageDisequilibrium
-
starts the thread to calculate LD
- run(AlgorithmCallback, double, ObjectState, StoppingCriteria.Factory, Ranker) - Method in class pal.algorithmics.SearchEngine
S
- 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(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) - Method in class pal.substmodel.AbstractRateMatrix
- scale(double) - Method in interface pal.substmodel.RateMatrix
- scale(double, int) - Method in class pal.misc.TimeOrderCharacterData
- scale(TimeOrderCharacterData) - Method in class pal.mep.MutationRateModel
- 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
- 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, int, TreeOperation, SimulatedAlignment.Factory) - Constructor for class pal.coalescent.SerialCoalescentGenerator
- SerialCoalescentGenerator(TimeOrderCharacterData, DemographicModel, 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)
- 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(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.ParameterizedTree.ParameterizedTreeBase
- 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) - Method in class pal.alignment.SimpleAnnotatedAlignment
-
Sets chromosome
- setChromosome(int, int) - Method in class pal.alignment.MultiLocusAnnotatedAlignment
-
Sets chromosome
- setChromosomePosition(float) - Method in class pal.alignment.IndelAnnotatedAlignment
-
Set the position along chromosome
- setChromosomePosition(float) - Method in class pal.alignment.SimpleAnnotatedAlignment
-
Set the position along chromosome
- setChromosomePosition(float, int) - Method in class pal.alignment.MultiLocusAnnotatedAlignment
-
Set the position along chromosome
- setCoalescentIntervals(CoalescentIntervals) - Method in class pal.eval.DemographicValue
-
define coalescent tree.
- setColor(Color) - Method in class pal.gui.CircularGraphics
- setColouriser(NameColouriser) - Method in class pal.gui.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(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.
- setDistance(double) - Method in interface pal.substmodel.TransitionProbability
-
compute transition probabilities for a expected distance using the prespecified rate matrix
- setDistance(int, int, double) - Method in class pal.distance.DistanceMatrix
-
Sets both upper and lower triangles.
- 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(int, Identifier) - Method in class pal.tree.ParameterizedTree.ParameterizedTreeBase
- setIdentifier(int, Identifier) - Method in class pal.tree.SimpleTree
- setIdentifier(int, Identifier) - Method in class pal.tree.Tree.TreeBase
- setIdentifier(Identifier) - Method in interface pal.tree.Node
-
Set identifier for this node.
- setIdentifier(Identifier) - Method in class pal.tree.SimpleNode
-
Set identifier for this node.
- 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) - Method in class pal.alignment.SimpleAnnotatedAlignment
-
Sets the name of the locus
- setLocusName(String, int) - Method in class pal.alignment.MultiLocusAnnotatedAlignment
-
Sets the name of the locus
- setLocusPosition(int, int) - Method in class pal.alignment.MultiLocusAnnotatedAlignment
-
Set the position within the locus
- setLogL(double) - Method in class pal.coalescent.DemographicModel
-
sets log likelihood
- setLowerCorner(int) - Method in class pal.gui.LinkageDisequilibriumComponent
-
This determines what is displayed in the lower left corner.
- setMatrix(int[][]) - Method in class pal.statistics.ContigencyTable
-
sets the data for the contigency table, must be set before other methods are called.
- setMatrix(RateMatrix) - Method in class pal.substmodel.MatrixExponential
-
update rate matrix used in present module
- setMax(int) - Method in class pal.math.Binomial
-
set capacity and precompute the n choose 2 values
- setMaxCacheSize(int) - Method in class pal.util.DefaultCache
- 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) - 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
- setNodeHeight(double, boolean) - Method in interface pal.tree.Node
-
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.
- 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) - Method in interface pal.misc.IndividualParameterHandler
- 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, 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[]) - Method in class pal.substmodel.AbstractRateMatrix
- setParameters(double[], double[]) - Method in class pal.substmodel.SimpleRateMatrixGroup
- 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[], 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[], 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) - Method in interface pal.misc.IndividualParameterHandler
- 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, 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(byte[], byte[]) - Method in class pal.distance.SequencePairLikelihood
-
specification of two sequences (not necessarily in the given alignment but with the same weights in the site pattern)
- setSequences(int, int) - Method in class pal.distance.SequencePairLikelihood
-
specification of two sequences in the given alignment
- 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
- setTime(double, double) - Method in interface pal.substmodel.TransitionProbability
-
compute transition probabilities for a expected time span using the prespecified rate matrix
- 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) - 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.
- setUnits(int, double) - Method in class pal.mep.MutationRateModel
-
sets units of measurement.
- setup() - Method in class pal.treesearch.GeneralConstraintGroupManager
- setup(Parameterized[], int[], int[]) - Static method in class pal.misc.MultiParameterized
- setup(Tree, SubstitutionModel) - Method in class pal.eval.GeneralLikelihoodCalculator
- 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(double) - Method in class pal.misc.MutableDouble
-
Set the current value of this double
- setValue(int, int, double) - Method in class pal.math.Matrix
- 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(int[], int) - Method in class pal.math.MersenneTwisterFast
-
Shuffles an array by repeatedly choosing two random members and swapping them.
- shuffle(Object[]) - Method in class pal.math.MersenneTwisterFast
-
Shuffles an array of objects.
- 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, int) - Constructor for class pal.alignment.SimpleAlignment
-
Clone constructor.
- SimpleAlignment(Alignment, Alignment, String, String, char) - Constructor for class pal.alignment.SimpleAlignment
-
This constructor combines to alignments given two guide strings.
- SimpleAlignment(Alignment, LabelMapping) - Constructor for class pal.alignment.SimpleAlignment
-
Clone constructor.
- SimpleAlignment(Identifier[], String[], String, DataType) - Constructor for class pal.alignment.SimpleAlignment
- SimpleAlignment(Identifier[], 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(IdGroup, char[][], String, DataType) - Constructor for class pal.alignment.SimpleAlignment
- SimpleAlignment(IdGroup, char[][], DataType) - Constructor for class pal.alignment.SimpleAlignment
- SimpleAlignment(IdGroup, String[], String, DataType) - Constructor for class pal.alignment.SimpleAlignment
- SimpleAlignment(IdGroup, String[], DataType) - Constructor for class pal.alignment.SimpleAlignment
- SimpleAlignment(IdGroup, DataType, int[][]) - Constructor for class pal.alignment.SimpleAlignment
- 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[], 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.
- 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(int, boolean) - Constructor for class pal.misc.SimpleIdGroup
-
Constructor taking the size of the group.
- SimpleIdGroup(String[]) - Constructor for class pal.misc.SimpleIdGroup
-
Constructor taking an array of strings.
- SimpleIdGroup(Identifier[]) - Constructor for class pal.misc.SimpleIdGroup
-
Constructor taking an array of identifiers.
- SimpleIdGroup(IdGroup) - Constructor for class pal.misc.SimpleIdGroup
-
Impersonating Constructor.
- SimpleIdGroup(IdGroup, int) - Constructor for class pal.misc.SimpleIdGroup
-
Impersonating Constructor.
- SimpleIdGroup(IdGroup, IdGroup) - Constructor for class pal.misc.SimpleIdGroup
-
Constructor taking two separate id groups and merging them.
- 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
- SimpleMLResult(double, Tree) - Constructor for class pal.statistics.LikelihoodEvaluator.SimpleMLResult
- SimpleModelFastFourStateLHCalculator - Class in pal.eval
- SimpleModelFastFourStateLHCalculator() - Constructor for class pal.eval.SimpleModelFastFourStateLHCalculator
- SimpleMolecularClockLikelihoodModel - Class in pal.eval
- SimpleMolecularClockLikelihoodModel() - Constructor for class pal.eval.SimpleMolecularClockLikelihoodModel
- SimpleNeutralSelection(CodonTable, double[], double) - Constructor for class pal.substmodel.YangCodonModel.SimpleNeutralSelection
- SimpleNeutralSelection(CodonTable, double[], double, double) - Constructor for class pal.substmodel.YangCodonModel.SimpleNeutralSelection
- 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) - Constructor for class pal.tree.SimpleNode
-
constructor used to clone a node and all children
- SimpleNode(Node[]) - Constructor for class pal.tree.SimpleNode
- SimpleNode(Node[], double) - Constructor for class pal.tree.SimpleNode
-
Constructor
- 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.
- SimplePositiveSelection(CodonTable, double[], double, double) - Constructor for class pal.substmodel.YangCodonModel.SimplePositiveSelection
- SimplePositiveSelection(CodonTable, double[], double, double, double, double) - Constructor for class pal.substmodel.YangCodonModel.SimplePositiveSelection
- SimplePositiveSelection(CodonTable, double[], double, double, double, double, double) - Constructor for class pal.substmodel.YangCodonModel.SimplePositiveSelection
- SimplePositiveSelection(YangCodonModel.SimplePositiveSelection) - Constructor for class pal.substmodel.YangCodonModel.SimplePositiveSelection
- 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.LeafImpl - Class in pal.eval
- simulate() - Method in class pal.tree.SimulatedAlignment
-
generate new artificial data set (random root sequence)
- simulate(byte[]) - Method in class pal.tree.SimulatedAlignment
-
generate new artificial data set (specified root sequence)
- simulate(int[], double, int[]) - Method in class pal.substmodel.SequenceSimulator
- simulate(String) - Method in class pal.tree.SimulatedAlignment
-
generate new artificial data set (random 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
- 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
- SingleReceiver() - Constructor for class pal.alignment.AlignmentReceiver.SingleReceiver
- 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
- 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(CoalescentIntervals, double) - Constructor for class pal.coalescent.SkylinePlot
-
Construct skyline plot from given coalescent intervals
- SkylinePlot(Tree, double) - Constructor for class pal.coalescent.SkylinePlot
-
Construct skyline plot from tree
- solve(double[][], double[]) - Method in interface pal.math.LMSSolver
- solve(AlgorithmCallback, ClusterTree.ClusteringMethod, LMSSolver) - Method in class pal.supgma.SUPGMABase
- sort(double[]) - Static method in class pal.util.HeapSort
-
Sorts an array of doubles into increasing order.
- sort(double[], int[]) - Static method in class pal.util.HeapSort
-
Sorts an array of indices into an array of doubles into increasing order.
- sort(double, double, double) - Method in class pal.util.ThreeNumberSort
-
sort three doubles
- sort(Object[], Comparator) - Static method in class pal.util.HeapSort
-
Sorts an array of objects into increasing order given a comparator.
- sort(Vector) - Static method in class pal.util.HeapSort
-
Sorts a vector of comparable objects into increasing order.
- sort(Vector, int[]) - Static method in class pal.util.HeapSort
-
Sorts an array of indices to vector of comparable objects into increasing order.
- sort(Comparable[]) - Static method in class pal.util.HeapSort
-
Sorts an array of comparable objects into increasing order.
- sortAbs(double[]) - Static method in class pal.util.HeapSort
-
Sorts an array of doubles into increasing order, ingoring sign.
- sortSites() - Method in class pal.alignment.ConcatenatedAnnotatedAlignment
-
sort the sites by chromosome, then by chromosomal location, and final locusPosition
- space(int, char) - Static method in class pal.io.FormattedOutput
-
returns of string of a given length of a single character.
- 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(int) - Constructor for class pal.datatype.SpecificAminoAcids
- SpecificAminoAcids(CodonTable) - 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.
- StateObject(UnrootedMLSearcher.Connection[]) - Constructor for class pal.treesearch.UnrootedMLSearcher.StateObject
- 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[], double[], int, boolean, double) - Constructor for class pal.mep.SteppedMutationRate
-
Construct mutation rate model of a give rate in given units.
- SteppedMutationRate(double[], double[], int, double) - Constructor for class pal.mep.SteppedMutationRate
-
Construct mutation rate model of a give rate in given units.
- SteppedMutationRate(double[], int, double) - Constructor for class pal.mep.SteppedMutationRate
-
Construct demographic model with default settings
- 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
- Store() - Constructor for class pal.treesearch.GeneralConstraintGroupManager.Store
- 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
- 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, FreeBranch) - Method in class pal.treesearch.FreeInternalNode
- swapConnection(FreeBranch, 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, FreeBranch) - Method in class pal.treesearch.PivotNode
-
Should not do anything but swap branches around
- swapConnection(FreeBranch, FreeNode, FreeBranch) - Method in class pal.treesearch.FreeInternalNode
- swapConnection(FreeBranch, FreeNode, FreeBranch) - Method in class pal.treesearch.FreeLeafNode
- swapConnection(FreeBranch, FreeNode, FreeBranch) - Method in interface pal.treesearch.FreeNode
-
Should preserve tree integrity
- swapConnection(FreeBranch, FreeNode, FreeBranch) - Method in class pal.treesearch.PivotNode
-
Should preserve tree integrity
- swapNode(FreeNode, FreeNode) - Method in class pal.treesearch.FreeBranch
T
- TAB - Static variable in class pal.io.NexusTokenizer
- TableReport - Interface in pal.misc
-
interface for classes with data that can be presented in tables
- taxa - Variable in class pal.misc.TimeOrderCharacterData
-
the identifier group
- TemporalModelChange - Interface in pal.substmodel
- TemporalModelChange.Utils - Class in pal.substmodel
- TERMINATE_CHARACTER - Static variable in class pal.datatype.AminoAcids
- TERMINATE_STATE - Static variable in class pal.datatype.AminoAcids
- testConsistency(int, double) - Method in class pal.coalescent.DemographicModel
-
This function tests the consistency of the getIntensity and getInverseIntensity methods of this demographic model.
- testLikelihood() - Method in class pal.treesearch.GeneralLikelihoodSearcher
- testLikelihood(FreeBranch, GeneralConstructionTool) - Method in class pal.treesearch.FreeInternalNode
- testLikelihood(FreeBranch, GeneralConstructionTool) - Method in class pal.treesearch.FreeLeafNode
- testLikelihood(FreeBranch, GeneralConstructionTool) - Method in interface pal.treesearch.FreeNode
- testLikelihood(FreeBranch, GeneralConstructionTool) - Method in class pal.treesearch.PivotNode
- testLikelihood(FreeNode, GeneralConstructionTool) - Method in class pal.treesearch.FreeBranch
- testLikelihood(GeneralConstructionTool) - Method in class pal.treesearch.ConstrainedInternalNode
- testLikelihood(GeneralConstructionTool) - Method in class pal.treesearch.ConstrainedLeafNode
- testLikelihood(GeneralConstructionTool) - Method in interface pal.treesearch.ConstrainedNode
- testLikelihood(GeneralConstructionTool) - Method in class pal.treesearch.FreeBranch
- testLikelihood(GeneralConstructionTool) - Method in class pal.treesearch.PivotNode
- testLikelihood(GeneralConstructionTool) - Method in interface pal.treesearch.RootAccess
- testLiklihood() - Method in class pal.treesearch.UnrootedMLSearcher
- theAlignment - Variable in class pal.popgen.LinkageDisequilibrium
- theAnnotationAlignment - Variable in class pal.popgen.LinkageDisequilibrium
- ThetaHandler - Interface in pal.supgma
- ThetaHandler.Utils - Class in pal.supgma
- third - Variable in class pal.util.ThreeNumberSort
-
order of the numbers (0-2)
- ThreeNumberSort - Class in pal.util
-
sorts three numbers (doubles) and choose randomly among the minimum/maximum values
- ThreeNumberSort() - Constructor for class pal.util.ThreeNumberSort
-
constructor
- TIME - Static variable in interface pal.util.XMLConstants
- TIME_DATA - Static variable in interface pal.util.XMLConstants
- TimeOrderCharacterData - Class in pal.misc
-
Character data that expresses an order through time.
- TimeOrderCharacterData() - Constructor for class pal.misc.TimeOrderCharacterData
-
Parameterless constructor for superclasses.
- TimeOrderCharacterData(int, int, double, int) - Constructor for class pal.misc.TimeOrderCharacterData
-
Constructs a TimeOrderCharacterData with a number of equal-sized, evenly-spaced sampling times.
- TimeOrderCharacterData(IdGroup, int) - Constructor for class pal.misc.TimeOrderCharacterData
-
Constructor taking only IdGroup.
- TimeOrderCharacterData(IdGroup, int, boolean) - Constructor for class pal.misc.TimeOrderCharacterData
-
Constructor taking only IdGroup.
- timeOrdinals - Variable in class pal.misc.TimeOrderCharacterData
-
Order of times
- times - Variable in class pal.misc.TimeOrderCharacterData
-
Actual times of each sample
- TimeStamp - Class in pal.misc
-
keeps track of program runtime
- TimeStamp() - Constructor for class pal.misc.TimeStamp
-
create object and start timer
- title_ - Variable in class pal.gui.TreePainter
- TN - Class in pal.substmodel
-
Tamura-Nei model of nucleotide evolution Tamura, K.
- TN - Static variable in interface pal.substmodel.NucleotideModelID
- TN - Static variable in interface pal.util.XMLConstants
- TN(double[], double[]) - Constructor for class pal.substmodel.TN
-
constructor 2
- TN(double, double, double[]) - Constructor for class pal.substmodel.TN
-
constructor 1
- toAlignment(MolecularDataType, int) - Method in class pal.alignment.DataTranslator
- toArray() - Method in class pal.math.Matrix
- TOCDSampleInformation - Class in pal.misc
-
Title: TOCDSampleInformation
- TOCDSampleInformation(TimeOrderCharacterData) - Constructor for class pal.misc.TOCDSampleInformation
- toChars(int[][], DataType) - Static method in class pal.alignment.DataTranslator
-
Converts an state matrix to a char matrix Stored as [sequnce][site]
- toChars(MolecularDataType, int) - Method in class pal.alignment.DataTranslator
- toLeftAlignedReverseComplementNucleotides(int) - Method in class pal.alignment.DataTranslator
- toNucleotides(int[][], MolecularDataType) - Static method in class pal.alignment.DataTranslator
-
Converts an alignment to a state matrix Stored as [sequnce][site]
- TOPBORDER - Static variable in class pal.gui.TreePainterCircular
- TOPBORDER - Static variable in class pal.gui.TreePainterNormal
- TopologyTestEngine - Class in pal.statistics
- TopologyTestEngine(TopologyTestEngine.StatisticsHandler) - Constructor for class pal.statistics.TopologyTestEngine
- TopologyTestEngine.StatisticsHandler - Interface in pal.statistics
- TopologyTestEngine.TestResult - Interface in pal.statistics
- TopologyTestEngine.TopologyPool - Interface in pal.statistics
- toReverseComplementNucleotides(int) - Method in class pal.alignment.DataTranslator
- toSingleLine() - Method in class pal.mep.ConstantMutationRate
- toSingleLine() - Method in class pal.mep.MutationRateModel
- toSingleLine() - Method in class pal.mep.SteppedMutationRate
- toSingleLine() - Method in class pal.mep.WindowedMutationRate
- toStates(char[][], DataType) - Static method in class pal.alignment.DataTranslator
-
Converts an alignment to a state matrix Stored as [sequnce][site]
- toStates(Alignment) - Static method in class pal.alignment.DataTranslator
-
Converts an alignment to a state matrix Stored as [sequnce][site]
- toStates(Alignment, int) - Static method in class pal.alignment.DataTranslator
-
Converts an alignment to a state matrix Stored as [sequnce][site]
- toStates(MolecularDataType, int) - Method in class pal.alignment.DataTranslator
- toString() - Method in class pal.algorithmics.Ranker
- toString() - Method in class pal.alignment.AbstractAlignment
-
returns representation of this alignment as a string
- toString() - Method in class pal.alignment.SimpleCharacterAlignment
-
returns representation of this alignment as a string
- toString() - Method in class pal.coalescent.CoalescentIntervals
- toString() - Method in class pal.coalescent.ConstantPopulation
- toString() - Method in class pal.coalescent.ConstExpConst
- toString() - Method in class pal.coalescent.ConstExpGrowth
- toString() - Method in class pal.coalescent.ExpandingPopulation
- toString() - Method in class pal.coalescent.ExponentialGrowth
- toString() - Method in class pal.coalescent.SkylinePlot
- toString() - Method in class pal.datatype.IUPACNucleotides
- toString() - Method in class pal.datatype.SimpleDataType
- toString() - Method in class pal.distance.DistanceMatrix
-
returns representation of this alignment as a string
- toString() - Method in class pal.eval.ConditionalProbabilityStore
- toString() - Method in class pal.eval.LikelihoodSummary
- toString() - Method in class pal.eval.PatternInfo
- toString() - Method in class pal.math.Matrix
- toString() - Method in class pal.mep.ConstantMutationRate
- toString() - Method in class pal.mep.SteppedMutationRate
- toString() - Method in class pal.mep.WindowedMutationRate
- toString() - Method in class pal.misc.Identifier
- toString() - Method in class pal.misc.MultiParameterized
- toString() - Method in class pal.misc.MutableDouble
- toString() - Method in class pal.misc.ParameterizedDoubleBundle
- toString() - Method in class pal.misc.SimpleIdGroup
-
Returns a string representation of this IdGroup in the form of a bracketed list.
- toString() - Method in class pal.misc.TimeOrderCharacterData
-
Returns a string representation of this time order character data.
- toString() - Method in class pal.popgen.LinkageDisequilibrium
-
returns representation of the LD results as a string
- toString() - Method in class pal.substmodel.CachedRateMatrix
-
Return string representation of substitution model.
- toString() - Method in class pal.substmodel.ConstantIndependentSingleSplitDistribution
- toString() - Method in class pal.substmodel.F84
- toString() - Method in class pal.substmodel.GeneralRateDistributionSubstitutionModel
- toString() - Method in class pal.substmodel.SaturatedSingleSplitDistribution
- toString() - Method in class pal.substmodel.SingleClassSubstitutionModel
- toString() - Method in class pal.substmodel.VariableIndependentSingleSplitDistribution
- toString() - Method in class pal.substmodel.YangCodonModel.SimpleNeutralSelection
- toString() - Method in class pal.substmodel.YangCodonModel.SimplePositiveSelection
- toString() - Method in class pal.substmodel.YangCodonModel
- toString() - Method in class pal.supgma.SUPGMABase
- toString() - Method in class pal.tree.CladeSystem
-
print clade system
- toString() - Method in class pal.tree.ParameterizedTree.ParameterizedTreeBase
- toString() - Method in class pal.tree.SimpleNode
- toString() - Method in class pal.tree.SimpleTree
- toString() - Method in class pal.tree.SplitSystem
-
print split system
- toString() - Method in class pal.tree.Tree.TreeBase
- toString() - Method in class pal.treesearch.FreeBranch
- toString() - Method in class pal.treesearch.PivotNode
- toString() - Method in class pal.util.ComparableDouble
- toString(double[]) - Static method in class pal.misc.Utils
-
A simple toString method for an array of doubles.
- toString(double[][]) - Static method in class pal.misc.Utils
-
A simple toString method for an array of doubles.
- toString(double[], int) - Static method in class pal.misc.Utils
-
A simple toString method for an array of doubles.
- toString(int) - Method in class pal.eval.ConditionalProbabilityStore
- toString(int[]) - Static method in class pal.misc.Utils
-
A simple toString method for an array of ints.
- toString(int[][]) - Static method in class pal.misc.Utils
-
A simple toString method for an array of ints.
- toString(int[], int) - Static method in class pal.misc.Utils
- toString(Object[]) - Static method in class pal.misc.Utils
-
A simple toString method for an array of doubles.
- toString(Object[], int) - Static method in class pal.misc.Utils
-
A simple toString method for an array of objects.
- toString(Object[], String) - Static method in class pal.misc.Utils
-
A simple toString method for an array of objects.
- toString(Object[], String, int) - Static method in class pal.misc.Utils
-
A simple toString method for an array of objects.
- toString(DataType, int[]) - Static method in class pal.datatype.DataType.Utils
-
For converting an array of states into a String of characters, based on a DataType
- toString(FreeBranch) - Method in class pal.treesearch.ConstrainedLeafNode
- toString(FreeBranch) - Method in class pal.treesearch.FreeInternalNode
- toString(FreeBranch) - Method in class pal.treesearch.FreeLeafNode
- toString(FreeBranch) - Method in interface pal.treesearch.FreeNode
- toString(FreeBranch) - Method in class pal.treesearch.PivotNode
- toString(FreeNode) - Method in class pal.treesearch.FreeBranch
- toStringHeights() - Method in class pal.treesearch.AbstractParentableConstrainedNode
- toStringHeights() - Method in class pal.treesearch.ConstrainedLeafNode
- toStringHeights() - Method in interface pal.treesearch.ConstrainedNode
- toStringLengths() - Method in class pal.treesearch.AbstractParentableConstrainedNode
- toStringLengths(double) - Method in class pal.treesearch.AbstractParentableConstrainedNode
- toStringLengths(double) - Method in class pal.treesearch.ConstrainedLeafNode
- toStringLengths(double) - Method in interface pal.treesearch.ConstrainedNode
- toSummary(double) - Method in interface pal.supgma.SUPGMABase.CISummary
- traitNames - Variable in class pal.alignment.SimpleCharacterAlignment
-
names of the traits
- traitValues - Variable in class pal.alignment.SimpleCharacterAlignment
-
trait values
- transferAnnotation(String[], String[], Object, BranchAccess[]) - Static method in class pal.treesearch.BranchAccess.Utils
- transferAnnotation(BranchAccess[], BranchAccess[]) - Static method in class pal.treesearch.BranchAccess.Utils
-
Transfers the annotation across two independent sets of BranchAccess objects.
- transferAnnotation(BranchAccess, BranchAccess[]) - Static method in class pal.treesearch.BranchAccess.Utils
- TransitionPenaltyTable - Interface in pal.datatype
-
Implements a table of transition penalties for a particular datatype.
- TransitionProbability - Interface in pal.substmodel
-
For objects that represent a source of transition probabilities TransitionProbability.java,v 1.3 2000/08/08 22:58:29 alexi Exp $
- transpose() - Method in class pal.math.Matrix
- Tree - Interface in pal.tree
-
Interface for a phylogenetic or genealogical tree.
- TREE - Static variable in interface pal.util.XMLConstants
- Tree.TreeBase - Class in pal.tree
- TreeBase() - Constructor for class pal.tree.Tree.TreeBase
-
constructor
- TreeBase(Node) - Constructor for class pal.tree.Tree.TreeBase
-
constructor
- TreeBase(Tree.TreeBase, Node) - Constructor for class pal.tree.Tree.TreeBase
-
clone constructor
- TreeComponent - Class in pal.gui
-
An AWT Component for displaying a tree.
- TreeComponent(Tree) - Constructor for class pal.gui.TreeComponent
- TreeComponent(Tree, boolean) - Constructor for class pal.gui.TreeComponent
- TreeComponent(Tree, String) - Constructor for class pal.gui.TreeComponent
- TreeComponent(Tree, String, boolean) - Constructor for class pal.gui.TreeComponent
- TreeComponent(Tree, TimeOrderCharacterData, boolean) - Constructor for class pal.gui.TreeComponent
- TreeDistanceMatrix - Class in pal.tree
-
computes distance matrix induced by a tree (needs only O(n^2) time, following algorithm DistanceInTree by D.Bryant and P.
- TreeDistanceMatrix(Tree) - Constructor for class pal.tree.TreeDistanceMatrix
-
compute induced distance matrix using actual branch lengths (using tree-induced order of sequences)
- TreeDistanceMatrix(Tree, boolean, double) - Constructor for class pal.tree.TreeDistanceMatrix
-
compute induced distance matrix (using tree-induced order of sequences)
- TreeDistanceMatrix(Tree, IdGroup) - Constructor for class pal.tree.TreeDistanceMatrix
-
compute induced distance matrix using actual branch lengths
- TreeDistanceMatrix(Tree, IdGroup, boolean, double) - Constructor for class pal.tree.TreeDistanceMatrix
-
compute induced distance matrix
- TreeGenerator - Interface in pal.tree
- TreeGenerator.Utils - Class in pal.tree
- TreeIterator - Interface in pal.tree
- TreeManipulator - Class in pal.tree
- TreeManipulator(Node) - Constructor for class pal.tree.TreeManipulator
-
Units will be Units.UNKNOWN
- TreeManipulator(Node, int) - Constructor for class pal.tree.TreeManipulator
-
Construct a TreeManipulator based around a normal tree
- TreeManipulator(Node, int, int) - Constructor for class pal.tree.TreeManipulator
-
Construct a TreeManipulator based around a normal tree
- TreeManipulator(RootedTreeInterface.Instructee, int, int) - Constructor for class pal.tree.TreeManipulator
- TreeManipulator(Tree) - Constructor for class pal.tree.TreeManipulator
-
Construct a TreeManipulator based around a normal tree
- TreeManipulator(Tree, int) - Constructor for class pal.tree.TreeManipulator
-
Construct a TreeManipulator based around a normal tree
- TreeManipulator(UnrootedTreeInterface.Instructee, int, int) - Constructor for class pal.tree.TreeManipulator
- TreeManipulator.BranchAccess - Interface in pal.tree
-
The branch access objects allow specific operations on a particular branch (refered to as connections internally to confuse and bewilder)
- TreeManipulator.PALBranchWrapper - Class in pal.tree
- TreeManipulator.PALNodeWrapper - Class in pal.tree
- treeNode - Variable in class pal.gui.TreePainter
- TreeOperation - Interface in pal.tree
-
Title: TreeOperation
- TreeOperation.Utils - Class in pal.tree
-
Utility class
- TreePainter - Class in pal.gui
-
A class that can paint a tree into a Graphics object.
- TreePainter(Tree, String, boolean) - Constructor for class pal.gui.TreePainter
- TreePainterCircular - Class in pal.gui
-
A class that can paint a tree (in a circular fashion) into a Graphics object .
- TreePainterCircular(Tree, String, boolean) - Constructor for class pal.gui.TreePainterCircular
- TreePainterNormal - Class in pal.gui
-
A class that can paint a tree into a Graphics object.
- TreePainterNormal(Tree, String, boolean) - Constructor for class pal.gui.TreePainterNormal
- TreeParseException - Exception in pal.tree
-
exception thrown by ReadTree
- TreeParseException() - Constructor for exception pal.tree.TreeParseException
- TreeParseException(String) - Constructor for exception pal.tree.TreeParseException
- TreeRestricter - Class in pal.tree
- TreeRestricter(Node, int, String[], boolean) - Constructor for class pal.tree.TreeRestricter
- TreeRestricter(Tree, String[], boolean) - Constructor for class pal.tree.TreeRestricter
- TreeSearchTool - Class in pal.treesearch
-
Title: TreeSearchTool
- TreeSearchTool() - Constructor for class pal.treesearch.TreeSearchTool
- TreeTool - Class in pal.tree
- TreeTool() - Constructor for class pal.tree.TreeTool
- treeUpdated() - Method in class pal.eval.SimpleLikelihoodCalculator
- TreeUtils - Class in pal.tree
-
various utility functions on trees.
- TreeUtils() - Constructor for class pal.tree.TreeUtils
- TS_TV_RATIO - Static variable in interface pal.util.XMLConstants
- TWO_STATE - Static variable in interface pal.util.XMLConstants
- TWO_STATE_DESCRIPTION - Static variable in interface pal.datatype.DataType
-
two state name (for XML and human readability)
- TwoStateModel - Class in pal.substmodel
-
implements the most general reversible rate matrix for two-state data
- TwoStateModel(double[]) - Constructor for class pal.substmodel.TwoStateModel
-
constructor
- TwoStates - Class in pal.datatype
-
implements DataType for two-state data
- TwoStates() - Constructor for class pal.datatype.TwoStates
- TWOSTATES - Static variable in interface pal.datatype.DataType
- tx - Variable in class pal.coalescent.ConstExpConst
-
time of end of exponential growth
- txSE - Variable in class pal.coalescent.ConstExpConst
-
standard error of time of growth
- TYPE - Static variable in interface pal.util.XMLConstants
U
- UnalignedAlignment(String[], String[], DataType) - Constructor for class pal.alignment.AlignmentReaders.UnalignedAlignment
- UnconstrainedLikelihoodModel - Interface in pal.eval
- UnconstrainedLikelihoodModel.External - Interface in pal.eval
-
The External calculator does not maintain any state and is approapriate for calculation where a store is provided
- UnconstrainedLikelihoodModel.Instance - Interface in pal.eval
- UnconstrainedLikelihoodModel.Internal - Interface in pal.eval
-
The Internal calculator may maintain state and is approapriate permanent attachment to internal nodes of the tree structure
- UnconstrainedLikelihoodModel.Leaf - Interface in pal.eval
-
A LHCalculator.Leaf object is attached to each leaf node and can be used to calculated conditional probabilities across the related branch.
- UnconstrainedModel - Class in pal.treesearch
- UnconstrainedModel(UnconstrainedLikelihoodModel.Instance) - Constructor for class pal.treesearch.UnconstrainedModel
- UnconstrainedTree - Class in pal.tree
-
provides parameter interface to an unconstrained tree (parameters are all available branch lengths)
- UnconstrainedTree(Tree) - Constructor for class pal.tree.UnconstrainedTree
-
take any tree and afford it with an interface suitable for an unconstrained tree (parameters are all available branch lengths)
- UnconstrainedTree(UnconstrainedTree) - Constructor for class pal.tree.UnconstrainedTree
- UNDEFINED_TOKEN - Static variable in class pal.io.NexusTokenizer
-
Flag indicating last token read was undefined
- UndoableAction - Interface in pal.algorithmics
- UndoableAction.Utils - Class in pal.algorithmics
- undoAction() - Method in class pal.algorithmics.GeneralObjectState
- undoAction() - Method in interface pal.algorithmics.ObjectState
-
Undo the last action (if it was successful) Users of an ObjectState should accept that sometimes undoing an action isn't possible.
- undoAction() - Method in interface pal.algorithmics.UndoableAction
-
Undo the last action (if it was successful) Users of undoable actions should accept that sometimes it isn't possible.
- undoToMark() - Method in interface pal.algorithmics.Markable
- undoToMark() - Method in class pal.treesearch.FreeBranch
- undoToMark() - Method in class pal.treesearch.FreeInternalNode
- undoToMark() - Method in class pal.treesearch.FreeLeafNode
- undoToMark() - Method in class pal.treesearch.UnrootedMLSearcher
- UNIFORM - Static variable in interface pal.util.XMLConstants
- UNIFORM_RATE_DISTRIBUTION - Static variable in interface pal.util.XMLConstants
- UniformRate - Class in pal.substmodel
-
uniform rate distribution
- UniformRate() - Constructor for class pal.substmodel.UniformRate
-
construct uniform rate distribution
- UNIT_NAMES - Static variable in interface pal.misc.Units
- units - Variable in class pal.misc.TimeOrderCharacterData
- Units - Interface in pal.misc
-
interface holding unit constants
- UNITS - Static variable in interface pal.util.XMLConstants
- UnitsProvider - Interface in pal.misc
-
interface for classes that can provide the related Units used, (as
- UnivariateFunction - Interface in pal.math
-
interface for a function of one variable
- UnivariateMinimum - Class in pal.math
-
minimization of a real-valued function of one variable without using derivatives.
- UnivariateMinimum() - Constructor for class pal.math.UnivariateMinimum
- UNIVERSAL - Static variable in interface pal.datatype.CodonTable
-
TypeID for Universal
- UNKNOWN - Static variable in interface pal.alignment.Alignment
-
character used to designate unknown characters
- UNKNOWN - Static variable in interface pal.datatype.DataType
- UNKNOWN - Static variable in interface pal.misc.Units
- UNKNOWN - Static variable in interface pal.util.XMLConstants
- UNKNOWN_CHARACTER - Static variable in interface pal.datatype.DataType
- UNKNOWN_TLA - Static variable in interface pal.alignment.Alignment
-
character used to designate unknown characters
- UNKNOWN_TLA - Static variable in interface pal.datatype.DataType
- UnrootedMLSearcher - Class in pal.treesearch
- UnrootedMLSearcher(Alignment, SubstitutionModel) - Constructor for class pal.treesearch.UnrootedMLSearcher
-
Build an unconstrained optimiser based on a randomly generated tree.
- UnrootedMLSearcher(Alignment, SubstitutionModel, LHCalculator.Factory) - Constructor for class pal.treesearch.UnrootedMLSearcher
- UnrootedMLSearcher(Node) - Constructor for class pal.treesearch.UnrootedMLSearcher
-
Create a searcher based on a given tree, that has no alignment , or model, specified (useful as backbone tree for attaching new nodes)
- UnrootedMLSearcher(Node, Alignment, SubstitutionModel) - Constructor for class pal.treesearch.UnrootedMLSearcher
- UnrootedMLSearcher(Node, Alignment, SubstitutionModel, LHCalculator.Factory) - Constructor for class pal.treesearch.UnrootedMLSearcher
- UnrootedMLSearcher(Node, SubstitutionModel) - Constructor for class pal.treesearch.UnrootedMLSearcher
-
Create a searcher based on a given tree, that has no alignment specified (useful as backbone tree for attaching new nodes)
- UnrootedMLSearcher(Tree, Alignment, SubstitutionModel) - Constructor for class pal.treesearch.UnrootedMLSearcher
- UnrootedMLSearcher.StateObject - Class in pal.treesearch
- UnrootedTreeInterface - Interface in pal.tree
-
Title: UnrootedTreeInterface
- UnrootedTreeInterface.BaseBranch - Interface in pal.tree
- UnrootedTreeInterface.GeneralBranch - Interface in pal.tree
- UnrootedTreeInterface.Instructee - Interface in pal.tree
- UnrootedTreeInterface.UBranch - Interface in pal.tree
- UnrootedTreeInterface.UNode - Interface in pal.tree
- UnrootedTreeInterface.Utils - Class in pal.tree
- update() - Method in class pal.tree.ClockTree
-
make clocktree consistent with branch lengths
- update(double[], double[]) - Method in class pal.math.LineFunction
-
update start point and direction (bounds and search direction are NOT checked)
- updateByRelativeRates(double[][]) - Method in class pal.substmodel.MatrixExponential
- updateMatrixExp() - Method in class pal.substmodel.AbstractRateMatrix
- updateModel(SubstitutionModel) - Method in class pal.distance.PairwiseDistance
-
update model of substitution
- updateModel(SubstitutionModel) - Method in class pal.distance.SequencePairLikelihood
-
update model of substitution
- updateParameters(double[]) - Method in class pal.substmodel.NeutralSelectionRateMatrixGroup
- updateParameters(double[]) - Method in class pal.substmodel.PositiveSelectionRateMatrixGroup
- updateParameters(double[]) - Method in interface pal.substmodel.RateMatrixGroup
-
Update internal representation based on any parameters (that are specified externally) and the given category probablitilies.
- updateProgress(double) - Method in interface pal.math.MinimiserMonitor
-
Inform monitor of current progress (as a number between 0 and 1), or -1 to reset
- updateProgress(double) - Method in interface pal.util.AlgorithmCallback
- updateSitePattern(SitePattern) - Method in class pal.distance.PairwiseDistance
-
update site pattern
- updateSitePattern(SitePattern) - Method in class pal.distance.SequencePairLikelihood
-
update site pattern
- updateSitePattern(SitePattern) - Method in class pal.eval.FastLikelihoodCalculator
- updateStatus(String) - Method in interface pal.util.AlgorithmCallback
-
Inform caller of current status
- UPGMA - Static variable in class pal.tree.ClusterTree
- UPGMATree - Class in pal.tree
-
Deprecated.Use ClusterTree
- UPGMATree(DistanceMatrix) - Constructor for class pal.tree.UPGMATree
-
Deprecated.constructor UPGMA tree
- UrnModel - Class in pal.math
-
class for drawing numbers from an urn with and without laying back
- UrnModel(int) - Constructor for class pal.math.UrnModel
-
create urn model
- UT_STATE - Static variable in class pal.datatype.Nucleotides
- Utils - Class in pal.misc
-
Provides some miscellaneous methods.
- Utils() - Constructor for class pal.algorithmics.ProbabilityIterator.Utils
- Utils() - Constructor for class pal.algorithmics.StoppingCriteria.Utils
- Utils() - Constructor for class pal.algorithmics.UndoableAction.Utils
- Utils() - Constructor for class pal.alignment.AlignmentGenerator.Utils
- Utils() - Constructor for class pal.datatype.DataType.Utils
- Utils() - Constructor for class pal.datatype.MolecularDataType.Utils
- Utils() - Constructor for class pal.distance.DistanceMatrixAccess.Utils
- Utils() - Constructor for class pal.distance.DistanceMatrixGenerator.Utils
- Utils() - Constructor for class pal.eval.SiteDetails.Utils
- Utils() - Constructor for class pal.gui.LabelDisplayer.Utils
- Utils() - Constructor for class pal.math.LMSSolver.Utils
- Utils() - Constructor for class pal.math.MinimiserMonitor.Utils
- Utils() - Constructor for class pal.math.OrderEnumerator.Utils
- Utils() - Constructor for class pal.math.OrthogonalHints.Utils
- Utils() - Constructor for class pal.mep.DeltaModel.Utils
- Utils() - Constructor for class pal.misc.IdGroup.Utils
- Utils() - Constructor for class pal.misc.IndividualParameterHandler.Utils
- Utils() - Constructor for class pal.misc.Parameterized.Utils
- Utils() - Constructor for class pal.misc.Utils
- Utils() - Constructor for class pal.statistics.LikelihoodEvaluator.Utils
- Utils() - Constructor for class pal.statistics.ReplicateLikelihoodEvaluator.Utils
- Utils() - Constructor for class pal.substmodel.SubstitutionModel.Utils
- Utils() - Constructor for class pal.substmodel.TemporalModelChange.Utils
- Utils() - Constructor for class pal.substmodel.YangCodonModel.Utils
- Utils() - Constructor for class pal.supgma.RateHandler.Utils
- Utils() - Constructor for class pal.supgma.ThetaHandler.Utils
- Utils() - Constructor for class pal.tree.RootedTreeInterface.Utils
- Utils() - Constructor for class pal.tree.TreeGenerator.Utils
- Utils() - Constructor for class pal.tree.TreeOperation.Utils
- Utils() - Constructor for class pal.tree.UnrootedTreeInterface.Utils
- Utils() - Constructor for class pal.treesearch.BranchAccess.Utils
- Utils() - Constructor for class pal.treesearch.SearchMonitor.Utils
- Utils() - Constructor for class pal.util.AlgorithmCallback.Utils
V
- validateTagName(Element, String) - Static method in class pal.xml.ElementParser
-
Throws a runtime exception if the element does not have the given name.
- VALUE - Static variable in interface pal.util.XMLConstants
- VariableIndependentSingleSplitDistribution - Class in pal.substmodel
-
Title: VariableIndependentSingleSplitDistribution
- VariableIndependentSingleSplitDistribution(int) - Constructor for class pal.substmodel.VariableIndependentSingleSplitDistribution
- VariableIndependentSingleSplitDistribution(int, double[]) - Constructor for class pal.substmodel.VariableIndependentSingleSplitDistribution
- variance(double) - Static method in class pal.statistics.ChiSquareDistribution
-
variance of the chi-square distribution
- variance(double) - Static method in class pal.statistics.ExponentialDistribution
-
variance of the exponential distribution
- variance(double[]) - Static method in class pal.statistics.DiscreteStatistics
-
compute variance (ML estimator)
- variance(double[], double) - Static method in class pal.statistics.DiscreteStatistics
-
compute variance (ML estimator)
- variance(double, double) - Static method in class pal.statistics.GammaDistribution
-
variance of the Gamma distribution
- variance(double, double) - Static method in class pal.statistics.NormalDistribution
-
variance
- variance(double, double) - Static method in class pal.statistics.ParetoDistribution
-
variance of the Pareto distribution
- varianceSampleMean(double[]) - Static method in class pal.statistics.DiscreteStatistics
-
compute variance of sample mean (ML estimator)
- varianceSampleMean(double[], double) - Static method in class pal.statistics.DiscreteStatistics
-
compute variance of sample mean (ML estimator)
- Version - Class in pal.util
-
This class provides a mechanism for returning the version number of the pal library.
- Version() - Constructor for class pal.util.Version
- VERSION - Static variable in class pal.misc.ReleaseInfo
-
version
- VERTEBRATE_MITOCHONDRIAL - Static variable in interface pal.datatype.CodonTable
-
TypeID for Vertebrate Mitochondrial
- VT - Class in pal.substmodel
-
VT (variable time matrix) model of amino acid evolution Modeling Amino Acid Replacement Mueller, T.
- VT - Static variable in interface pal.substmodel.AminoAcidModelID
- VT - Static variable in interface pal.util.XMLConstants
- VT(double[]) - Constructor for class pal.substmodel.VT
-
constructor
W
- WAG - Class in pal.substmodel
-
WAG model of amino acid evolution (S.
- WAG - Static variable in interface pal.substmodel.AminoAcidModelID
- WAG - Static variable in interface pal.util.XMLConstants
- WAG(double[]) - Constructor for class pal.substmodel.WAG
-
constructor
- weight - Variable in class pal.alignment.SitePattern
-
weights of each site pattern
- weightedLocusPosition - Variable in class pal.alignment.IndelAnnotatedAlignment
-
used to designate weighted position; accounts for gaps
- weightedPosition - Variable in class pal.alignment.MultiLocusAnnotatedAlignment
-
used to designate weighted position; accounts for gaps
- weightedPosition - Variable in class pal.alignment.SimpleAnnotatedAlignment
-
used to designate weighted position; accounts for gaps
- whichIdNumber(String) - Method in class pal.alignment.AbstractAlignment
- whichIdNumber(String) - Method in class pal.alignment.SimpleCharacterAlignment
- whichIdNumber(String) - Method in class pal.distance.DistanceMatrix
- whichIdNumber(String) - Method in interface pal.misc.IdGroup
-
returns the index of the identifier with the given name.
- whichIdNumber(String) - Method in class pal.misc.SimpleIdGroup
-
Return index of identifier with name or -1 if not found
- whichIdNumber(String) - Method in class pal.misc.TimeOrderCharacterData
- whichIdNumber(String) - Method in class pal.tree.ParameterizedTree.ParameterizedTreeBase
- whichIdNumber(String) - Method in class pal.tree.SimpleTree
- whichIdNumber(String) - Method in class pal.tree.Tree.TreeBase
- whichIdNumber(IdGroup, String) - Static method in class pal.misc.IdGroup.Utils
-
A convenience implementation of whichIdNumber that can be used by IdGroup implementations
- WHITESPACE_TOKEN - Static variable in class pal.io.NexusTokenizer
-
Flag indicating last token read was whitespace
- WindowedMutationRate - Class in pal.mep
-
This class models a windowed mutation rate (parameter: mu = mutation rate).
- WindowedMutationRate(double, double, double, double, int, boolean, double) - Constructor for class pal.mep.WindowedMutationRate
-
Construct mutation rate model of a give rate in given units.
- WindowedMutationRate(double, double, double, double, int, double) - Constructor for class pal.mep.WindowedMutationRate
-
Construct mutation rate model of a give rate in given units.
- WindowedMutationRate(double, double, double, int, double) - Constructor for class pal.mep.WindowedMutationRate
-
Construct mutation rate model of a give rate in given units.
- WindowedMutationRate(double, double, int, double) - Constructor for class pal.mep.WindowedMutationRate
-
Construct mutation model with default settings
- WindowedMutationRate(WindowedMutationRate) - Constructor for class pal.mep.WindowedMutationRate
- WORD_LOWERCASE - Static variable in class pal.io.NexusTokenizer
-
Flag indicating words should be converted to lowercase
- WORD_TOKEN - Static variable in class pal.io.NexusTokenizer
-
Flag indicating last token read was a word
- WORD_UNMODIFIED - Static variable in class pal.io.NexusTokenizer
-
Flag indicating words should be untouched
- WORD_UPPERCASE - Static variable in class pal.io.NexusTokenizer
-
Flag indicating words should be converted to uppercase
- WPGMA - Static variable in class pal.tree.ClusterTree
X
- x - Variable in class pal.gui.PositionedNode
- XMLConstants - Interface in pal.util
-
constants (strings and numbers) relating to reading and writing XML.
- XmlParseException - Exception in pal.xml
-
exception thrown by ElementParser.
- XmlParseException() - Constructor for exception pal.xml.XmlParseException
- XmlParseException(String) - Constructor for exception pal.xml.XmlParseException
- XSPACER - Static variable in class pal.gui.TreePainterCircular
- XSPACER - Static variable in class pal.gui.TreePainterNormal
Y
- YANG_CODON_MODEL - Static variable in interface pal.util.XMLConstants
- YangCodonModel - Class in pal.substmodel
-
Yang's model of codon evolution More advanced codon Substitution Models (of Neilson and Yang) are now included (the M1, and M2 models).
- YangCodonModel(double[], double[]) - Constructor for class pal.substmodel.YangCodonModel
-
constructor 4 (universal codon table)
- YangCodonModel(double[], double[], CodonTable) - Constructor for class pal.substmodel.YangCodonModel
-
constructor 3
- YangCodonModel(double, double, double[]) - Constructor for class pal.substmodel.YangCodonModel
-
constructor 2 (universal codon table)
- YangCodonModel(double, double, double[], CodonTable) - Constructor for class pal.substmodel.YangCodonModel
-
constructor 1
- YangCodonModel.SimpleNeutralSelection - Class in pal.substmodel
-
A Substitution Model which can be used to implment the Neutral Model (with out continuous rate stuff) Codon model of [1] which uses the weighted sum of trwo base YangCodon models where omega=0, omega=1 repectively
[1] Nielsen, R., Yang Z., 1998 Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene. - YangCodonModel.SimplePositiveSelection - Class in pal.substmodel
-
A Substitution Model which can be used to implment the Postitive Selection (with out continuous rate stuff) Codon model of [1] which uses the weighted sum of a three base Codon model where omega=0, omega=1 and omega=free
[1] Nielsen, R., Yang Z., 1998 Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene. - YangCodonModel.Utils - Class in pal.substmodel
-
A Utility class
- YEARS - Static variable in interface pal.misc.Units
- YEARS - Static variable in interface pal.util.XMLConstants
- YEAST - Static variable in interface pal.datatype.CodonTable
-
TypeID for Yeast
- YSPACER - Static variable in class pal.gui.TreePainterCircular
- YSPACER - Static variable in class pal.gui.TreePainterNormal
Z
- ZERO_TIME_TEXT - Static variable in class pal.mep.SteppedMutationRate
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