# Index

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
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

## A

A_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
A_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
abort - Enum constant in enum class jebl.evolution.io.IllegalCharacterPolicy
AbstractRateMatrix - Class in jebl.evolution.substmodel
  abstract base class for all rate matrices
AbstractRootedTree - Class in jebl.evolution.trees
AbstractRootedTree() - Constructor for class jebl.evolution.trees.AbstractRootedTree
add(Sequence) - Method in interface jebl.evolution.io.ImmediateSequenceImporter.Callback
add(RootedTree) - Method in class jebl.evolution.trees.CladeSystem
  adds all the clades in the tree
addCharacter(char, int) - Method in class jebl.evolution.align.ProfileCharacter
addChild(Node, Node) - Method in class jebl.evolution.trees.MutableRootedTree
  Insert a child node.
addCoalescentEvent(double) - Method in class jebl.evolution.coalescent.Intervals
addEdge(Node, Node, double) - Method in class jebl.evolution.trees.SimpleTree
  Add a new edge between two existing (non adjacent yet) nodes.
addFeedbackAction(String, String, SimpleListener) - Method in class jebl.util.CompositeProgressListener
addFeedbackAction(String, String, SimpleListener) - Method in class jebl.util.ProgressListener
  Adds an action that can choose to provide feedback.
addFeedbackAction(String, String, SimpleListener) - Method in class jebl.util.ProgressListener.Wrapper
addFeedbackAction(String, SimpleListener) - Method in class jebl.util.CompositeProgressListener
addFeedbackAction(String, SimpleListener) - Method in class jebl.util.ProgressListener
  Equivalent to `addFeedbackAction(label,"",listener)`
addFeedbackAction(String, SimpleListener) - Method in class jebl.util.ProgressListener.Wrapper
addGaps(int) - Method in class jebl.evolution.align.ProfileCharacter
addMigrationEvent(double, int) - Method in class jebl.evolution.coalescent.Intervals
addNode(Edge) - Method in class jebl.evolution.trees.SimpleRootedTree
  Adds a new node at the midpoint of the given edge
addNode(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
  Adds a new node at the midpoint of the edge connecting the given node to its parent.
addNothingEvent(double) - Method in class jebl.evolution.coalescent.Intervals
addProfileCharacter(ProfileCharacter) - Method in class jebl.evolution.align.ProfileCharacter
addProgress(double) - Method in class jebl.util.CompositeProgressListener
  Increments the progress of the current sub task by this much.
addProgressListener(ProgressListener) - Method in interface jebl.evolution.aligners.Aligner
addProgressListener(ProgressListener) - Method in class jebl.evolution.trees.ClusteringTreeBuilder
addProgressListener(ProgressListener) - Method in class jebl.evolution.trees.ConsensusTreeBuilder
addProgressListener(ProgressListener) - Method in interface jebl.evolution.trees.TreeBuilder
addSampleEvent(double) - Method in class jebl.evolution.coalescent.Intervals
addSequence(Sequence) - Method in class jebl.evolution.alignments.BasicAlignment
  Adds a sequence to this alignment
addTaxa(Set<Taxon>) - Method in class jebl.evolution.characters.ContinuousCharacter
  set the taxa for this character with a previously constructed Set<Taxon>
addTaxon(Taxon) - Method in interface jebl.evolution.characters.Character
  add a taxon with this character
addTaxon(Taxon) - Method in class jebl.evolution.characters.ContinuousCharacter
addTaxon(Taxon) - Method in class jebl.evolution.characters.DiscreteCharacter
addTreeToDensityMap(CalculateSplitRates.DensityMap, RootedTree) - Method in class jebl.evolution.trees.CalculateSplitRates
align(List<Sequence>, ProgressListener, boolean, boolean) - Method in class jebl.evolution.align.BartonSternberg
Align - Class in jebl.evolution.align
Align(Scores, float) - Constructor for class jebl.evolution.align.Align
AlignCommand - Class in jebl.evolution.align
  A command line interface for the algorithms in jebl.evolution.align.
AlignCommand() - Constructor for class jebl.evolution.align.AlignCommand
AlignCommand(String, String) - Constructor for class jebl.evolution.align.AlignCommand
Aligner - Interface in jebl.evolution.aligners
  As of 2006-12-06, this interface is not used anywhere in JEBL, and it doesn't have any implementing classes.
alignment - Variable in class jebl.evolution.align.PairwiseAligner.Result
Alignment - Interface in jebl.evolution.alignments
AlignmentExporter - Interface in jebl.evolution.io
AlignmentImporter - Interface in jebl.evolution.io
AlignmentTreeBuilderFactory - Class in jebl.evolution.align
AlignmentTreeBuilderFactory() - Constructor for class jebl.evolution.align.AlignmentTreeBuilderFactory
AlignmentTreeBuilderFactory.Result - Class in jebl.evolution.align
alignSequences(Collection<Sequence>) - Method in interface jebl.evolution.aligners.Aligner
allocateMatrices(int, int) - Method in class jebl.evolution.align.NeedlemanWunschAffine
allocateMatrices(int, int) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
ALT_YEAST - Static variable in class jebl.evolution.sequences.GeneticCode
AMINO_ACID - Static variable in interface jebl.evolution.sequences.SequenceType
AMINO_ACID_IDENTITY - Static variable in class jebl.evolution.align.scores.ScoresFactory
AminoAcidModel - Class in jebl.evolution.substmodel
  base class of rate matrices for amino acids
AminoAcids - Class in jebl.evolution.sequences
  Uninstantiable utility class with only static methods.
AminoAcidScores - Class in jebl.evolution.align.scores
AminoAcidScores() - Constructor for class jebl.evolution.align.scores.AminoAcidScores
AminoAcidScores(float, float) - Constructor for class jebl.evolution.align.scores.AminoAcidScores
AminoAcidState - Class in jebl.evolution.sequences
append(char) - Method in class jebl.evolution.io.ByteBuilder
  Appends an ASCII character (see `ByteBuilder.isCharacterAscii(char)`) to this ByteBuilder.
append(CharSequence) - Method in class jebl.evolution.io.ByteBuilder
  Appends an ASCII CharSequence to this ByteBuilder.
append(CharSequence, int, int) - Method in class jebl.evolution.io.ByteBuilder
appendMatch(AlignmentResult, AlignmentResult) - Method in class jebl.evolution.align.NeedlemanWunschAffine
appendSequences(Sequence, Sequence) - Static method in interface jebl.evolution.sequences.Sequence
  Append two sequences together to create a new sequence object.
ASCIDIAN_MT - Static variable in class jebl.evolution.sequences.GeneticCode
askUser - Enum constant in enum class jebl.evolution.io.IllegalCharacterPolicy
assertAllTreesHaveTheSameTaxa(List<? extends Tree>) - Static method in class jebl.evolution.trees.Utils
  Checks whether all of the trees passed in have the same taxa sets (ignoring order of taxa), and throws an IllegalArgumentException if this is not the case.
asText(Tree) - Static method in class jebl.evolution.trees.Utils
asText(Tree, int) - Static method in class jebl.evolution.trees.Utils
Attributable - Interface in jebl.util
  Interface for associating attributeNames with an object.
Attributable.Utils - Class in jebl.util
AttributableHelper - Class in jebl.util
AttributableHelper() - Constructor for class jebl.util.AttributableHelper
AttributedCladeSystem - Class in jebl.evolution.trees
  Stores a set of unique clades for a tree
AttributedCladeSystem(String) - Constructor for class jebl.evolution.trees.AttributedCladeSystem
AttributedCladeSystem(String, RootedTree) - Constructor for class jebl.evolution.trees.AttributedCladeSystem

## B

B_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
B_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
BACTERIAL - Static variable in class jebl.evolution.sequences.GeneticCode
BadFormatException() - Constructor for exception class jebl.evolution.io.ImportException.BadFormatException
BadFormatException(String) - Constructor for exception class jebl.evolution.io.ImportException.BadFormatException
BartonSternberg - Class in jebl.evolution.align
BartonSternberg(Scores, float, float, int, boolean, boolean) - Constructor for class jebl.evolution.align.BartonSternberg
BaseEdge - Class in jebl.evolution.trees
  Common implementation of Attributable interface used by Nodes.
BaseEdge() - Constructor for class jebl.evolution.trees.BaseEdge
BaseNode - Class in jebl.evolution.trees
  Common implementation of Attributable interface used by Nodes.
BaseNode() - Constructor for class jebl.evolution.trees.BaseNode
BasicAlignment - Class in jebl.evolution.alignments
  A basic implementation of the Alignment interface.
BasicAlignment() - Constructor for class jebl.evolution.alignments.BasicAlignment
  Constructs a basic alignment with no sequences.
BasicAlignment(Collection<? extends Sequence>) - Constructor for class jebl.evolution.alignments.BasicAlignment
  Constructs a basic alignment from a collection of sequences.
BasicAlignment(Sequence[]) - Constructor for class jebl.evolution.alignments.BasicAlignment
  Constructs a basic alignment from an array of sequences.
BasicDistanceMatrix - Class in jebl.evolution.distances
BasicDistanceMatrix(Collection<Taxon>, double[][]) - Constructor for class jebl.evolution.distances.BasicDistanceMatrix
BasicProgressListener - Class in jebl.util
  A basic `ProgressListener` implementation that allows the caller to set the canceled status.
BasicProgressListener() - Constructor for class jebl.util.BasicProgressListener
BasicSequence - Class in jebl.evolution.sequences
  A default implementation of the Sequence interface.
BasicSequence(SequenceType, Taxon, CharSequence) - Constructor for class jebl.evolution.sequences.BasicSequence
  Creates a sequence with a name corresponding to the taxon name.
BasicSequence(SequenceType, Taxon, State[]) - Constructor for class jebl.evolution.sequences.BasicSequence
  Creates a sequence with a name corresponding to the taxon name
beginNextSubtask() - Method in class jebl.util.CompositeProgressListener
  begins the next subtask.
beginNextSubtask(String) - Method in class jebl.util.CompositeProgressListener
  Convenience method to start the next operation AND set a new message.
beginSubtask() - Method in class jebl.util.CompositeProgressListener
  Used as an alternative to `CompositeProgressListener.beginNextSubtask()`.
beginSubtask(String) - Method in class jebl.util.CompositeProgressListener
  Used as an alternative to `CompositeProgressListener.beginNextSubtask()`.
BilleraMetric - Class in jebl.evolution.treemetrics
  Billera tree distance - sum of change in branch lengths required to transform one tree to the second Note that this interface is not optimal for a large set where all pairs are required.
BilleraMetric() - Constructor for class jebl.evolution.treemetrics.BilleraMetric
Binomial - Class in jebl.math
  Binomial coefficients
Binomial() - Constructor for class jebl.math.Binomial
bitCode - Variable in class jebl.evolution.sequences.NucleotideState
BLEPHARISMA_NUC - Static variable in class jebl.evolution.sequences.GeneticCode
BLOSUM_45 - Static variable in class jebl.evolution.align.scores.ScoresFactory
BLOSUM_50 - Static variable in class jebl.evolution.align.scores.ScoresFactory
BLOSUM_55 - Static variable in class jebl.evolution.align.scores.ScoresFactory
BLOSUM_60 - Static variable in class jebl.evolution.align.scores.ScoresFactory
BLOSUM_62 - Static variable in class jebl.evolution.align.scores.ScoresFactory
BLOSUM_65 - Static variable in class jebl.evolution.align.scores.ScoresFactory
BLOSUM_70 - Static variable in class jebl.evolution.align.scores.ScoresFactory
BLOSUM_75 - Static variable in class jebl.evolution.align.scores.ScoresFactory
BLOSUM_80 - Static variable in class jebl.evolution.align.scores.ScoresFactory
BLOSUM_85 - Static variable in class jebl.evolution.align.scores.ScoresFactory
BLOSUM_90 - Static variable in class jebl.evolution.align.scores.ScoresFactory
Blosum45 - Class in jebl.evolution.align.scores
Blosum45() - Constructor for class jebl.evolution.align.scores.Blosum45
Blosum50 - Class in jebl.evolution.align.scores
Blosum50() - Constructor for class jebl.evolution.align.scores.Blosum50
Blosum55 - Class in jebl.evolution.align.scores
Blosum55() - Constructor for class jebl.evolution.align.scores.Blosum55
Blosum60 - Class in jebl.evolution.align.scores
Blosum60() - Constructor for class jebl.evolution.align.scores.Blosum60
Blosum62 - Class in jebl.evolution.align.scores
Blosum62() - Constructor for class jebl.evolution.align.scores.Blosum62
Blosum65 - Class in jebl.evolution.align.scores
Blosum65() - Constructor for class jebl.evolution.align.scores.Blosum65
Blosum70 - Class in jebl.evolution.align.scores
Blosum70() - Constructor for class jebl.evolution.align.scores.Blosum70
Blosum75 - Class in jebl.evolution.align.scores
Blosum75() - Constructor for class jebl.evolution.align.scores.Blosum75
Blosum80 - Class in jebl.evolution.align.scores
Blosum80() - Constructor for class jebl.evolution.align.scores.Blosum80
Blosum85 - Class in jebl.evolution.align.scores
Blosum85() - Constructor for class jebl.evolution.align.scores.Blosum85
Blosum90 - Class in jebl.evolution.align.scores
Blosum90() - Constructor for class jebl.evolution.align.scores.Blosum90
booleanValue(MaybeBoolean) - Static method in enum class jebl.util.MaybeBoolean
BootstrappedAlignment - Class in jebl.evolution.alignments
  Date: 15/01/2006 Time: 10:13:50
BootstrappedAlignment(Alignment) - Constructor for class jebl.evolution.alignments.BootstrappedAlignment
BootstrappedAlignment(Alignment, long) - Constructor for class jebl.evolution.alignments.BootstrappedAlignment
BootstrappedAlignment(Alignment, Random) - Constructor for class jebl.evolution.alignments.BootstrappedAlignment
BOTH - Enum constant in enum class jebl.evolution.io.DistanceMatrixImporter.Triangle
build() - Method in class jebl.evolution.trees.ClusteringTreeBuilder
build() - Method in interface jebl.evolution.trees.TreeBuilder
build(List<Sequence>, TreeBuilderFactory.Method, MultipleAligner, ProgressListener, boolean) - Static method in class jebl.evolution.align.AlignmentTreeBuilderFactory
build(List<Sequence>, TreeBuilderFactory.Method, PairwiseAligner, ProgressListener) - Static method in class jebl.evolution.align.AlignmentTreeBuilderFactory
  Will use model F84 for nucleotides and Jukes-Cantor for amino acid
build(List<Sequence>, TreeBuilderFactory.Method, PairwiseAligner, ProgressListener, TreeBuilderFactory.DistanceModel) - Static method in class jebl.evolution.align.AlignmentTreeBuilderFactory
build(Alignment, TreeBuilderFactory.Method, TreeBuilderFactory.DistanceModel, ProgressListener) - Static method in class jebl.evolution.align.AlignmentTreeBuilderFactory
build(Alignment, TreeBuilderFactory.Method, TreeBuilderFactory.DistanceModel, ProgressListener, boolean) - Static method in class jebl.evolution.align.AlignmentTreeBuilderFactory
buildRooted(RootedTree[], double, TreeBuilderFactory.ConsensusMethod) - Static method in class jebl.evolution.trees.TreeBuilderFactory
buildRooted(Tree[], double, TreeBuilderFactory.ConsensusMethod) - Static method in class jebl.evolution.trees.TreeBuilderFactory
  convenience method.
buildUnRooted(Tree[], Taxon, double, TreeBuilderFactory.ConsensusMethod) - Static method in class jebl.evolution.trees.TreeBuilderFactory
ByteBuilder - Class in jebl.evolution.io
  Similar to a StringBuilder, but its internal buffer is a byte[] with one entry for each character, so it can only correctly append single-byte characters.
ByteBuilder(int) - Constructor for class jebl.evolution.io.ByteBuilder
  Constructs a ByteBuilder that will never grow beyond `maxCapacity` bytes in length.

## C

C_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
C_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
calculateAnalyticalLogLikelihood(IntervalList) - Static method in class jebl.evolution.coalescent.Coalescent
  Calculates the log likelihood of this set of coalescent intervals, using an analytical integration over theta.
calculateLogLikelihood() - Method in class jebl.evolution.coalescent.Coalescent
  Calculates the log likelihood of this set of coalescent intervals, given a demographic model.
calculateLogLikelihood(IntervalList, DemographicFunction) - Static method in class jebl.evolution.coalescent.Coalescent
  Calculates the log likelihood of this set of coalescent intervals, given a demographic model.
CalculateSplitRates - Class in jebl.evolution.trees
  Created by IntelliJ IDEA.
CalculateSplitRates(NexusImporter) - Constructor for class jebl.evolution.trees.CalculateSplitRates
cancel() - Method in class jebl.util.BasicProgressListener
  Sets this progress listener as cancel, so that `BasicProgressListener.isCanceled()` will return true.
Cancelable - Interface in jebl.util
  Checks whether some operation has been cancelled; This will typically be used as a callback because it can only query whether a task has been cancelled, rather than cancel it (there is no cancel() method).
CannotBuildDistanceMatrixException - Exception Class in jebl.evolution.distances
CannotBuildDistanceMatrixException(String) - Constructor for exception class jebl.evolution.distances.CannotBuildDistanceMatrixException
CannotBuildDistanceMatrixException(String, String, String) - Constructor for exception class jebl.evolution.distances.CannotBuildDistanceMatrixException
CANONICAL_STATE_COUNT - Static variable in class jebl.evolution.sequences.AminoAcids
CANONICAL_STATE_COUNT - Static variable in class jebl.evolution.sequences.Codons
CANONICAL_STATE_COUNT - Static variable in class jebl.evolution.sequences.Nucleotides
CANONICAL_STATES - Static variable in class jebl.evolution.sequences.AminoAcids
  Deprecated.
CANONICAL_STATES - Static variable in class jebl.evolution.sequences.Codons
CANONICAL_STATES - Static variable in class jebl.evolution.sequences.Nucleotides
  Deprecated.
CanonicalSequence - Class in jebl.evolution.sequences
  A default implementation of the Sequence interface that converts sequence characters to States such that calling getString() will always return uppercase residues with nucleotide U residues converted to T
CanonicalSequence(SequenceType, Taxon, CharSequence) - Constructor for class jebl.evolution.sequences.CanonicalSequence
  Creates a sequence with a name corresponding to the taxon name.
CanonicalSequence(SequenceType, Taxon, State[]) - Constructor for class jebl.evolution.sequences.CanonicalSequence
  Creates a sequence with a name corresponding to the taxon name
cardinality() - Method in class jebl.util.FixedBitSet
CataclysmicDemographic - Class in jebl.evolution.coalescent
  This class models an exponentially growing (or shrinking) population (Parameters: N0=present-day population size; r=growth rate).
CataclysmicDemographic() - Constructor for class jebl.evolution.coalescent.CataclysmicDemographic
  Construct demographic model with default settings
CataclysmicDemographic(double, double, double, double) - Constructor for class jebl.evolution.coalescent.CataclysmicDemographic
  Construct demographic model with given settings
Character - Interface in jebl.evolution.characters
CHARACTERS - Enum constant in enum class jebl.evolution.io.NexusImporter.NexusBlock
CharacterType - Interface in jebl.evolution.characters
charAt(int) - Method in class jebl.evolution.io.ByteBuilder
CHEMICAL_CLASSIFICATION - Static variable in class jebl.evolution.sequences.AminoAcids
choleskyFactor(double[][]) - Static method in class jebl.math.MatrixCalc
  Cholesky factorization (aka Cholesky Decomposition) This factorization can be used when square matrix is symmetric and positive definite.
choleskySolve(double[][], double[]) - Static method in class jebl.math.MatrixCalc
  Cholesky solve Once the matrix is decomposed with the above routine, one can solve the triangular factor with backsubstitution.
choose(double, double) - Static method in class jebl.math.Binomial
  Binomial coefficient n choose k
choose2(int) - Static method in class jebl.math.Binomial
  get n choose 2
CILIATE - Static variable in class jebl.evolution.sequences.GeneticCode
CladeHeightMetric - Class in jebl.evolution.treemetrics
  For each clade_j in treeB, find the MRCA_j of the taxa in clade_j in treeA.
CladeHeightMetric() - Constructor for class jebl.evolution.treemetrics.CladeHeightMetric
CladeHeightMetric(List<Taxon>) - Constructor for class jebl.evolution.treemetrics.CladeHeightMetric
CladeSystem - Class in jebl.evolution.trees
  Stores a set of unique clades for a tree
CladeSystem() - Constructor for class jebl.evolution.trees.CladeSystem
CladeSystem(RootedTree) - Constructor for class jebl.evolution.trees.CladeSystem
CLADOGRAM - Enum constant in enum class jebl.evolution.trees.TransformedRootedTree.Transform
cleanSequence(CharSequence, SequenceType) - Static method in class jebl.evolution.sequences.Utils
  Produce a clean sequence filtered of spaces and digits.
clear() - Method in class jebl.evolution.align.ProfileCharacter
clear(int) - Method in class jebl.util.FixedBitSet
clearAllProgress() - Method in class jebl.util.CompositeProgressListener
  Clear all progress, including that of previous subtasks.
clearLastMetaComment() - Method in class jebl.evolution.io.ImportHelper
close() - Method in class jebl.evolution.io.NewickExporter
close() - Method in class jebl.evolution.io.NexusExporter
close() - Method in class jebl.evolution.io.PHYLIPExporter
close() - Method in interface jebl.evolution.io.TreeExporter
closeBlock() - Method in class jebl.evolution.io.NexusExporter
  close an existing open trees block
closeReader() - Method in class jebl.evolution.io.ImportHelper
CLUSTALW - Static variable in class jebl.evolution.align.scores.NucleotideScores
ClusteringTreeBuilder<T> - Class in jebl.evolution.trees
  An abstract base class for clustering algorithms from pairwise distances
Coalescent - Class in jebl.evolution.coalescent
  A likelihood function for the coalescent.
Coalescent(IntervalList, DemographicFunction) - Constructor for class jebl.evolution.coalescent.Coalescent
Coalescent(RootedTree, DemographicFunction) - Constructor for class jebl.evolution.coalescent.Coalescent
COALESCENT - Enum constant in enum class jebl.evolution.coalescent.IntervalList.IntervalType
  Denotes an interval after which a coalescent event is observed (i.e.
CoalescentIntervalGenerator - Class in jebl.evolution.treesimulation
  This is a class that draws coalescent intervals under the given demographic function.
CoalescentIntervalGenerator(DemographicFunction) - Constructor for class jebl.evolution.treesimulation.CoalescentIntervalGenerator
CODON - Static variable in interface jebl.evolution.sequences.SequenceType
Codons - Class in jebl.evolution.sequences
Codons() - Constructor for class jebl.evolution.sequences.Codons
CodonSequence - Class in jebl.evolution.sequences
  A codon implementation of the Sequence interface.
CodonSequence(Taxon, State[]) - Constructor for class jebl.evolution.sequences.CodonSequence
  Creates a sequence with a name corresponding to the taxon name
CodonState - Class in jebl.evolution.sequences
  As of 2007-07-30, instances of this class are only constructed for non-ambigous nucleotide triplets - see `Codons`.
CompactRootedTree - Class in jebl.evolution.trees
  A memory efficient rooted tree.
CompactRootedTree(RootedTree) - Constructor for class jebl.evolution.trees.CompactRootedTree
  Do all the hard work.
compareTo(Object) - Method in class jebl.evolution.alignments.ConsensusSequence
  Sequences are compared by their taxa
compareTo(Object) - Method in class jebl.evolution.sequences.AminoAcidState
compareTo(Object) - Method in class jebl.evolution.sequences.BasicSequence
  Sequences are compared by their taxa
compareTo(Object) - Method in class jebl.evolution.sequences.CanonicalSequence
  Sequences are compared by their taxa
compareTo(Object) - Method in class jebl.evolution.sequences.CodonSequence
  Sequences are compared by their taxa
compareTo(Object) - Method in class jebl.evolution.sequences.FilteredSequence
compareTo(Object) - Method in class jebl.evolution.sequences.NucleotideState
compareTo(Object) - Method in class jebl.evolution.sequences.State
compareTo(Object) - Method in class jebl.evolution.taxa.Taxon
complement() - Method in class jebl.util.FixedBitSet
complement(NucleotideState[]) - Static method in class jebl.evolution.sequences.Utils
complement(FixedBitSet) - Static method in class jebl.util.FixedBitSet
COMPLEMENTARY_STATES - Static variable in class jebl.evolution.sequences.Nucleotides
  Deprecated.
CompositeProgressListener - Class in jebl.util
  A `ProgressListener` that is suitable for a task that consists of several subtasks.
CompositeProgressListener(ProgressListener, double...) - Constructor for class jebl.util.CompositeProgressListener
  construct a new composite ProgressListener.
CompositeProgressListener(ProgressListener, int) - Constructor for class jebl.util.CompositeProgressListener
  Construct a CompositeProgressListener with a number of evenly weighted subtasks.
conceptuallyUnrooted() - Method in class jebl.evolution.trees.CompactRootedTree
conceptuallyUnrooted() - Method in class jebl.evolution.trees.FilteredRootedTree
conceptuallyUnrooted() - Method in class jebl.evolution.trees.MutableRootedTree
conceptuallyUnrooted() - Method in class jebl.evolution.trees.ReRootedTree
conceptuallyUnrooted() - Method in class jebl.evolution.trees.RootedFromUnrooted
conceptuallyUnrooted() - Method in class jebl.evolution.trees.RootedSubtree
conceptuallyUnrooted() - Method in interface jebl.evolution.trees.RootedTree
  Due to current implementation limitations, trees store "branch" information in nodes.
conceptuallyUnrooted() - Method in class jebl.evolution.trees.SimpleRootedTree
consensus(boolean, boolean) - Static method in enum class jebl.util.MaybeBoolean
ConsensusSequence - Class in jebl.evolution.alignments
ConsensusSequence(Taxon, Alignment) - Constructor for class jebl.evolution.alignments.ConsensusSequence
  Creates a FilteredSequence wrapper to the given source sequence.
ConsensusSequence(Taxon, Alignment, boolean) - Constructor for class jebl.evolution.alignments.ConsensusSequence
  Creates a FilteredSequence wrapper to the given source sequence.
ConsensusTreeBuilder<T> - Class in jebl.evolution.trees
  A `TreeBuilder` that builds a consensus tree for a set of trees on identical leaf sets.
ConsensusTreeBuilder.Method - Enum Class in jebl.evolution.trees
  Supported consensus methods.
ConstantPopulation - Class in jebl.evolution.coalescent
  This class models coalescent intervals for a constant population (parameter: N0=present-day population size).
ConstantPopulation() - Constructor for class jebl.evolution.coalescent.ConstantPopulation
  Construct demographic model with default settings
ConstantPopulation(double) - Constructor for class jebl.evolution.coalescent.ConstantPopulation
  Construct demographic model with given settings
ConstExponential - Class in jebl.evolution.coalescent
  This class models exponential growth from an initial population size.
ConstExponential() - Constructor for class jebl.evolution.coalescent.ConstExponential
  Construct demographic model with default settings
ConstExponential(double, double, double) - Constructor for class jebl.evolution.coalescent.ConstExponential
  Construct demographic model with given settings
ConstLogistic - Class in jebl.evolution.coalescent
  This class models logistic growth from an initial population size.
ConstLogistic() - Constructor for class jebl.evolution.coalescent.ConstLogistic
  Construct demographic model with default settings
ConstLogistic(double, double, double, double) - Constructor for class jebl.evolution.coalescent.ConstLogistic
  Construct demographic model with given settings
constructConsensus(Alignment, boolean) - Static method in class jebl.evolution.alignments.ConsensusSequence
contains(int) - Method in class jebl.util.FixedBitSet
CONTINUOUS - Static variable in interface jebl.evolution.characters.CharacterType
ContinuousCharacter - Class in jebl.evolution.characters
ContinuousCharacter(String, String) - Constructor for class jebl.evolution.characters.ContinuousCharacter
  Constructs a basic ContinuousCharacter object with no taxa added yet
ContinuousCharacter(String, String, Set<Taxon>) - Constructor for class jebl.evolution.characters.ContinuousCharacter
  Constructs a basic ContinuousCharacter object with taxa added
copy(double[][], double[][]) - Static method in class jebl.util.Utils
  Copies all of source into dest - assumes dest to be large enough
copy(double[], double[]) - Static method in class jebl.math.MultivariateMinimum
  Copy source vector into target vector
copyIntervals(Intervals) - Method in class jebl.evolution.coalescent.Intervals
copyMatrix(double[][]) - Static method in class jebl.math.MatrixCalc
  copy one matrix into another
copyTree(RootedTree) - Static method in class jebl.evolution.trees.Utils
  This method creates an unattached copy of the given rooted tree such that changes to the copied tree do not affect the original tree.
createExternalNode(Taxon) - Method in class jebl.evolution.trees.MutableRootedTree
  Creates a new external node with the given taxon.
createExternalNode(Taxon) - Method in class jebl.evolution.trees.SimpleRootedTree
  Creates a new external node with the given taxon.
createExternalNode(Taxon) - Method in class jebl.evolution.trees.SimpleTree
  Creates a new external node with the given taxon.
createInternalNode(List<? extends Node>) - Method in class jebl.evolution.trees.MutableRootedTree
  Once a SimpleRootedTree has been created, the node stucture can be created by calling createExternalNode and createInternalNode.
createInternalNode(List<? extends Node>) - Method in class jebl.evolution.trees.SimpleRootedTree
  Once a SimpleRootedTree has been created, the node stucture can be created by calling createExternalNode and createInternalNode.
createInternalNode(List<Node>) - Method in class jebl.evolution.trees.SimpleTree
  Once a SimpleTree has been created, the node stucture can be created by calling createExternalNode and createInternalNode.
createNodeDensityComparator(RootedTree) - Static method in class jebl.evolution.trees.Utils
createNodeDensityMinNodeHeightComparator(RootedTree) - Static method in class jebl.evolution.trees.Utils
createNodes(RootedTree, Node) - Method in class jebl.evolution.trees.SimpleRootedTree
  Clones the entire tree structure from the given RootedTree.
createNodes(RootedTree, Node, Node) - Method in class jebl.evolution.trees.ReRootedTree
  Clones the entire tree structure from the given (unrooted) Tree.
createNodes(Tree, Node, Node) - Method in class jebl.evolution.trees.SimpleRootedTree
  Clones the entire tree structure from the given (unrooted) Tree.
createNullMonitor() - Static method in class jebl.math.MinimiserMonitor.Utils
  Creates a MinimiserMonitor that looses all output
createOrderEnumerator(int) - Method in interface jebl.math.OrderEnumerator.OEFactory
  For generating an ordering from 0..size-1.
createSimpleMonitor(PrintWriter) - Static method in class jebl.math.MinimiserMonitor.Utils
  Creates a MinimiserMonitor that outputs current minimum to a print stream
createSplitMonitor(MinimiserMonitor, MinimiserMonitor) - Static method in class jebl.math.MinimiserMonitor.Utils
  creates a monitor such that all information sent to monitor is based on two sub monitors
createStringMonitor() - Static method in class jebl.math.MinimiserMonitor.Utils
  Creates a MinimiserMonitor that Stores output (use toString() to access current results)
createSystemErrorMonitor() - Static method in class jebl.math.MinimiserMonitor.Utils
  Creates a MinimiserMonitor that outputs current minimum to a System.err
createSystemOuptutMonitor() - Static method in class jebl.math.MinimiserMonitor.Utils
  Creates a MinimiserMonitor that outputs current minimum to a System.out

## D

D_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
D_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
DATA - Enum constant in enum class jebl.evolution.io.NexusImporter.NexusBlock
DEBUGsubTreeRep(RootedTree, Node) - Static method in class jebl.evolution.trees.Utils
DECREASING_NODE_DENSITY - Enum constant in enum class jebl.evolution.trees.SortedRootedTree.BranchOrdering
Default(String, String[], State[][]) - Constructor for class jebl.evolution.sequences.StateClassification.Default
DEFAULT_SUPPORT_ATTRIBUTE_NAME - Static variable in class jebl.evolution.trees.ConsensusTreeBuilder
  Name of attribute specifing amount of support for branch
deleteInternalNode(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
  Removes an internal node in this tree.
deleteMatrixColumn(double[][], int) - Static method in class jebl.math.MatrixCalc
  takes a matrix and deletes a column
deleteMatrixRow(double[][], int) - Static method in class jebl.math.MatrixCalc
  takes a matrix and deletes a row
DemographicFunction - Interface in jebl.evolution.coalescent
  This interface provides methods that describe a demographic function.
DemographicFunction.Utils - Class in jebl.evolution.coalescent
description - Variable in enum class jebl.evolution.io.IllegalCharacterPolicy
descriptionPropertyName - Static variable in class jebl.evolution.io.FastaImporter
  Name of Jebl sequence property which stores sequence description (i.e.
detachChildren(Node, List<Integer>) - Method in class jebl.evolution.trees.MutableRootedTree
diagonalHessian(MultivariateFunction, double[]) - Static method in class jebl.math.NumericalDerivative
  determine diagonal of Hessian
DISCRETE - Static variable in interface jebl.evolution.characters.CharacterType
DiscreteCharacter - Class in jebl.evolution.characters
DiscreteCharacter(String, String, int) - Constructor for class jebl.evolution.characters.DiscreteCharacter
  Constructs a basic DiscreteCharacter object with no taxa added yet
DiscreteCharacter(String, String, int, Set<Taxon>) - Constructor for class jebl.evolution.characters.DiscreteCharacter
  Constructs a basic DiscreteCharacter object with taxa
displayIntervals() - Method in class jebl.evolution.trees.CalculateSplitRates
displayStatistics() - Method in class jebl.evolution.trees.CalculateSplitRates
distance - Variable in class jebl.evolution.align.AlignmentTreeBuilderFactory.Result
distance(TreeBiPartitionInfo, TreeBiPartitionInfo, TreeBiPartitionInfo.DistanceNorm) - Static method in class jebl.evolution.trees.TreeBiPartitionInfo
DistanceMatrix - Interface in jebl.evolution.distances
DistanceMatrixImporter - Interface in jebl.evolution.io
DistanceMatrixImporter.Triangle - Enum Class in jebl.evolution.io
DISTANCES - Enum constant in enum class jebl.evolution.io.NexusImporter.NexusBlock
doAlign(List<Sequence>, RootedTree, ProgressListener) - Method in class jebl.evolution.align.BartonSternberg
doAlign(List<Sequence>, RootedTree, ProgressListener) - Method in interface jebl.evolution.align.MultipleAligner
doAlign(Alignment, Alignment, ProgressListener) - Method in class jebl.evolution.align.BartonSternberg
doAlign(Alignment, Alignment, ProgressListener) - Method in interface jebl.evolution.align.MultipleAligner
doAlign(Alignment, Sequence, ProgressListener) - Method in class jebl.evolution.align.BartonSternberg
doAlign(Alignment, Sequence, ProgressListener) - Method in interface jebl.evolution.align.MultipleAligner
doAlignment(String, String) - Method in class jebl.evolution.align.Align
  Performs the alignment, abstract.
doAlignment(String, String) - Method in class jebl.evolution.align.MaximalSegmentPair
doAlignment(String, String) - Method in class jebl.evolution.align.NeedlemanWunsch
doAlignment(String, String) - Method in class jebl.evolution.align.NeedlemanWunschAffine
doAlignment(String, String) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpace
doAlignment(String, String) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
doAlignment(String, String) - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
doAlignment(String, String) - Method in class jebl.evolution.align.OldNeedlemanWunschAffine
doAlignment(String, String) - Method in class jebl.evolution.align.OverlapAlign
doAlignment(String, String) - Method in class jebl.evolution.align.SmithWaterman
doAlignment(String, String) - Method in class jebl.evolution.align.SmithWatermanLinearSpace
doAlignment(String, String) - Method in class jebl.evolution.align.SmithWatermanLinearSpaceAffine
doAlignment(String, String, int, int) - Method in class jebl.evolution.align.NeedlemanWunschAffine
doAlignment(String, String, ProgressListener) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
doAlignment(String, String, ProgressListener) - Method in class jebl.evolution.align.SmithWaterman
doAlignment(String, String, ProgressListener) - Method in class jebl.evolution.align.SmithWatermanLinearSpaceAffine
doAlignment(String, String, ProgressListener, boolean) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
doAlignment(Profile, Profile, int, int, int, int, int, int) - Method in class jebl.evolution.align.NeedlemanWunschAffine
doAlignment(Profile, Profile, int, int, int, int, int, int, boolean, boolean) - Method in class jebl.evolution.align.NeedlemanWunschAffine
doAlignment(Profile, Profile, ProgressListener, boolean) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
doAlignment(Sequence, Sequence, ProgressListener) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
doAlignment(Sequence, Sequence, ProgressListener) - Method in interface jebl.evolution.align.PairwiseAligner
doMatch(Output, String) - Method in class jebl.evolution.align.Align
  Print the score and the alignment
doMatch(Output, String, boolean) - Method in class jebl.evolution.align.Align
  Print the score, the F matrix, and the alignment
duplicate(Scores) - Static method in class jebl.evolution.align.scores.Scores
DuplicateFieldException() - Constructor for exception class jebl.evolution.io.ImportException.DuplicateFieldException
DuplicateFieldException(String) - Constructor for exception class jebl.evolution.io.ImportException.DuplicateFieldException
DuplicateTaxaException() - Constructor for exception class jebl.evolution.io.ImportException.DuplicateTaxaException
DuplicateTaxaException(String) - Constructor for exception class jebl.evolution.io.ImportException.DuplicateTaxaException

## E

E_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
ECHINODERM_MT - Static variable in class jebl.evolution.sequences.GeneticCode
Edge - Interface in jebl.evolution.graphs
  Represents a node in a graph or tree.
edgeFraction - Variable in class jebl.evolution.trees.CalculateSplitRates
EmpiricalDemographicFunction - Class in jebl.evolution.coalescent
EmpiricalDemographicFunction(double[], double[], boolean) - Constructor for class jebl.evolution.coalescent.EmpiricalDemographicFunction
EMPTY - Static variable in class jebl.util.ProgressListener
  A ProgressListener that ignores all events and always returns false from `ProgressListener.isCanceled()`.
EPSILON - Static variable in class jebl.math.MachineAccuracy
  machine accuracy constant
equal(RootedTree, RootedTree) - Static method in class jebl.evolution.trees.RootedTreeUtils
  Compares 2 trees and returns true if they have the same topology.
EQUAL_LENGTHS - Enum constant in enum class jebl.evolution.trees.TransformedRootedTree.Transform
equals(Object) - Method in class jebl.evolution.sequences.BasicSequence
equals(Object) - Method in class jebl.evolution.sequences.CodonSequence
equals(Object) - Method in class jebl.util.FixedBitSet
equals(Object) - Method in class jebl.util.HashPair
equals(Taxon) - Method in class jebl.evolution.taxa.Taxon
EUPLOTID_NUC - Static variable in class jebl.evolution.sequences.GeneticCode
evaluate(double) - Method in class jebl.math.OrthogonalLineFunction
evaluate(double) - Method in interface jebl.math.UnivariateFunction
  compute function value
evaluate(double[]) - Method in class jebl.evolution.coalescent.Coalescent
evaluate(double[]) - Method in interface jebl.math.MultivariateFunction
  compute function value
Expansion - Class in jebl.evolution.coalescent
  This class models exponential growth from an initial ancestral population size.
Expansion() - Constructor for class jebl.evolution.coalescent.Expansion
  Construct demographic model with default settings
Expansion(double, double, double) - Constructor for class jebl.evolution.coalescent.Expansion
  Construct demographic model with given settings
ExponentialGrowth - Class in jebl.evolution.coalescent
  This class models an exponentially growing (or shrinking) population (Parameters: N0=present-day population size; r=growth rate).
ExponentialGrowth() - Constructor for class jebl.evolution.coalescent.ExponentialGrowth
  Construct demographic model with default settings
ExponentialGrowth(double, double) - Constructor for class jebl.evolution.coalescent.ExponentialGrowth
  Construct demographic model with given settings
ExponentialLogistic - Class in jebl.evolution.coalescent
  This class models logistic growth from an initial exponential phase.
ExponentialLogistic() - Constructor for class jebl.evolution.coalescent.ExponentialLogistic
  Construct demographic model with default settings
ExponentialLogistic(double, double, double, double, double) - Constructor for class jebl.evolution.coalescent.ExponentialLogistic
  Construct demographic model with given settings
exportAlignment(Alignment) - Method in interface jebl.evolution.io.AlignmentExporter
  export one alignment.
exportAlignment(Alignment) - Method in class jebl.evolution.io.MEGAExporter
  Deprecated.
  Files created by this export method won't be importable by MEGA (because they don't have titles). Use `MEGAExporter.exportAlignment(jebl.evolution.alignments.Alignment, String)` instead.
exportAlignment(Alignment) - Method in class jebl.evolution.io.NexusExporter
  exportAlignment.
exportAlignment(Alignment) - Method in class jebl.evolution.io.PHYLIPExporter
exportAlignment(Alignment, String) - Method in class jebl.evolution.io.MEGAExporter
exportExcludeKeys - Static variable in class jebl.evolution.io.NexusExporter
exportMatrix(DistanceMatrix) - Method in class jebl.evolution.io.NexusExporter
exportSequence(Sequence) - Method in class jebl.evolution.io.FastaExporter
  export a sequence.
exportSequences(Collection<? extends Sequence>) - Method in class jebl.evolution.io.FastaExporter
  export alignment or set of sequences.
exportSequences(Collection<? extends Sequence>) - Method in class jebl.evolution.io.NexusExporter
  export alignment.
exportSequences(Collection<? extends Sequence>) - Method in interface jebl.evolution.io.SequenceExporter
  exportSequences.
exportTree(Tree) - Method in class jebl.evolution.io.NewickExporter
  Export a single tree
exportTree(Tree) - Method in class jebl.evolution.io.NexusExporter
  Export a single tree
exportTree(Tree) - Method in class jebl.evolution.io.PHYLIPExporter
exportTree(Tree) - Method in interface jebl.evolution.io.TreeExporter
  Export a single tree
exportTrees(Collection<? extends Tree>) - Method in class jebl.evolution.io.NewickExporter
  Export a collection of trees
exportTrees(Collection<? extends Tree>) - Method in class jebl.evolution.io.NexusExporter
exportTrees(Collection<? extends Tree>) - Method in class jebl.evolution.io.PHYLIPExporter
exportTrees(Collection<? extends Tree>) - Method in interface jebl.evolution.io.TreeExporter
  Export a collection of trees
exportTrees(Collection<? extends Tree>, boolean) - Method in class jebl.evolution.io.NexusExporter
exportTreesWithTranslation(Collection<? extends Tree>, Map<String, String>) - Method in class jebl.evolution.io.NexusExporter

## F

F_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
f2minx - Variable in class jebl.math.UnivariateMinimum
  curvature at minimum
F84 - Enum constant in enum class jebl.evolution.trees.TreeBuilderFactory.DistanceModel
F84DistanceMatrix - Class in jebl.evolution.distances
F84DistanceMatrix(Alignment) - Constructor for class jebl.evolution.distances.F84DistanceMatrix
F84DistanceMatrix(Alignment, ProgressListener) - Constructor for class jebl.evolution.distances.F84DistanceMatrix
False - Enum constant in enum class jebl.util.MaybeBoolean
FastaExporter - Class in jebl.evolution.io
  Class for exporting a fasta file format.
FastaExporter(Writer) - Constructor for class jebl.evolution.io.FastaExporter
  Constructor
FastaImporter - Class in jebl.evolution.io
  Class for importing Fasta sequential file format.
FastaImporter(File, SequenceType) - Constructor for class jebl.evolution.io.FastaImporter
  Use this constructor if you are reading from a file.
FastaImporter(Reader, SequenceType) - Constructor for class jebl.evolution.io.FastaImporter
  This constuctor takes a reader.
FilteredRootedTree - Class in jebl.evolution.trees
FilteredRootedTree(RootedTree) - Constructor for class jebl.evolution.trees.FilteredRootedTree
FilteredSequence - Class in jebl.evolution.sequences
FilteredSequence(Sequence) - Constructor for class jebl.evolution.sequences.FilteredSequence
  Creates a FilteredSequence wrapper to the given source sequence.
findEndBlock() - Method in class jebl.evolution.io.NexusImporter
  Read ahead to the end of the current block.
findMinimum(double, UnivariateFunction) - Method in class jebl.math.UnivariateMinimum
  Find minimum (first estimate given)
findMinimum(double, UnivariateFunction, int) - Method in class jebl.math.UnivariateMinimum
  Find minimum (first estimate given, desired number of fractional digits specified)
findMinimum(MultivariateFunction, double[]) - Method in class jebl.math.MultivariateMinimum
  Find minimum close to vector x
findMinimum(MultivariateFunction, double[], int, int) - Method in class jebl.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 jebl.math.MultivariateMinimum
  Find minimum close to vector x (desired fractional digits for each parameter is specified)
findMinimum(UnivariateFunction) - Method in class jebl.math.UnivariateMinimum
  Find minimum (no first estimate given)
findMinimum(UnivariateFunction, int) - Method in class jebl.math.UnivariateMinimum
  Find minimum (no first estimate given, desired number of fractional digits specified)
findNextBlock() - Method in class jebl.evolution.io.NexusImporter
  Read ahead to the next block in the input.
findTimeIntervals() - Method in class jebl.evolution.trees.CalculateSplitRates
finishedTraceBack() - Method in interface jebl.evolution.align.TracebackPlotter
fireSetProgress(double) - Method in class jebl.evolution.trees.ClusteringTreeBuilder
first - Variable in class jebl.util.HashPair
firstDerivative(UnivariateFunction, double) - Static method in class jebl.math.NumericalDerivative
  determine first derivative
FitchParsimony - Class in jebl.evolution.parsimony
  Class for reconstructing characters using Fitch parsimony.
FitchParsimony(List<Pattern>, boolean) - Constructor for class jebl.evolution.parsimony.FitchParsimony
FitchParsimony(Patterns, boolean) - Constructor for class jebl.evolution.parsimony.FitchParsimony
FixedBitSet - Class in jebl.util
  A bit-set of fixed size.
FixedBitSet(int) - Constructor for class jebl.util.FixedBitSet
FixedBitSet(FixedBitSet) - Constructor for class jebl.util.FixedBitSet
FLATWORM_MT - Static variable in class jebl.evolution.sequences.GeneticCode
fminx - Variable in class jebl.math.UnivariateMinimum
  function value at minimum
forFiles(ProgressListener, List<File>) - Static method in class jebl.util.CompositeProgressListener
forMatrix(ScoreMatrix) - Static method in class jebl.evolution.align.scores.Scores
formatScore(float) - Method in class jebl.evolution.align.Align
fractionEqual(State) - Method in class jebl.evolution.sequences.State
  Determine how much in common these potentially ambigous states have as a fraction between 0 and 1 2 non-ambiguous states will return 0.

## G

G_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
G_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
GammaFunction - Class in jebl.math
  gamma function
GammaFunction() - Constructor for class jebl.math.GammaFunction
GAP_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
GAP_STATE - Static variable in class jebl.evolution.sequences.Codons
GAP_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
gapFraction() - Method in class jebl.evolution.align.ProfileCharacter
GaplessSequence - Class in jebl.evolution.sequences
GaplessSequence(Sequence) - Constructor for class jebl.evolution.sequences.GaplessSequence
generateFactory(boolean) - Static method in class jebl.math.OrthogonalSearch
  Generate a MultivariateMinimum.Factory for an OrthogonalSearch
generateNewMinimiser() - Method in interface jebl.math.MultivariateMinimum.Factory
  Generate a new Multivariate Minimum
generateScores(String) - Static method in class jebl.evolution.align.scores.ScoresFactory
  For any matrix.
generateScores(String, float) - Static method in class jebl.evolution.align.scores.ScoresFactory
  For calculated nucleotide matrices.
generateScores(String, int) - Static method in class jebl.evolution.align.scores.ScoresFactory
  For Blosum and Pam matrices
GENETIC_CODES - Static variable in class jebl.evolution.sequences.GeneticCode
  Deprecated.
  use `GeneticCode.getGeneticCodes()` instead
GeneticCode - Class in jebl.evolution.sequences
  A set of standard genetic codes.
get(int, double) - Method in class jebl.evolution.trees.MostProbableTopology
  Get the most probable tree(s)
getAdjacencies(Node) - Method in interface jebl.evolution.graphs.Graph
  Returns a list of nodes connected to this node by an edge
getAdjacencies(Node) - Method in class jebl.evolution.trees.CompactRootedTree
getAdjacencies(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
getAdjacencies(Node) - Method in class jebl.evolution.trees.MutableRootedTree
getAdjacencies(Node) - Method in class jebl.evolution.trees.ReRootedTree
getAdjacencies(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
getAdjacencies(Node) - Method in class jebl.evolution.trees.RootedSubtree
getAdjacencies(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
getAdjacencies(Node) - Method in class jebl.evolution.trees.SimpleTree
getAdjusted(OrderEnumerator, int) - Static method in class jebl.math.OrderEnumerator.Utils
getAdjusted(OrthogonalHints, int) - Static method in class jebl.math.OrthogonalHints.Utils
getAdjustedFactory(OrderEnumerator.OEFactory, int) - Static method in class jebl.math.OrderEnumerator.Utils
getAlignments() - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
  The indices for these correspond to those for the getScoreMatrix() matrix.
getAllTaxa() - Static method in class jebl.evolution.taxa.Taxon
getAlphabet() - Method in class jebl.evolution.align.scores.AminoAcidScores
getAlphabet() - Method in class jebl.evolution.align.scores.NucleotideScores
getAlphabet() - Method in interface jebl.evolution.align.scores.ScoreMatrix
getAlphabet() - Method in class jebl.evolution.align.scores.SubstScoreMatrix
getAlphabet(SequenceType) - Static method in class jebl.evolution.sequences.SequenceType.Utils
getAlternating(OrderEnumerator, OrderEnumerator) - Static method in class jebl.math.OrderEnumerator.Utils
getAlternatingFactory(OrderEnumerator.OEFactory, OrderEnumerator.OEFactory) - Static method in class jebl.math.OrderEnumerator.Utils
getArgmax(double[]) - Static method in class jebl.util.Utils
  Find the maximum "argument" (of a double array).
getArgmax(int[]) - Static method in class jebl.util.Utils
  Find the maximum "argument".
getArgument(int) - Method in class jebl.evolution.coalescent.ConstantPopulation
getArgument(int) - Method in class jebl.evolution.coalescent.ConstExponential
getArgument(int) - Method in class jebl.evolution.coalescent.ConstLogistic
getArgument(int) - Method in interface jebl.evolution.coalescent.DemographicFunction
  Returns the value of the nth argument of this function.
getArgument(int) - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
  Returns the value of the nth argument of this function.
getArgument(int) - Method in class jebl.evolution.coalescent.Expansion
getArgument(int) - Method in class jebl.evolution.coalescent.ExponentialGrowth
getArgument(int) - Method in class jebl.evolution.coalescent.ExponentialLogistic
getArgumentCount() - Method in class jebl.evolution.coalescent.ConstantPopulation
getArgumentCount() - Method in class jebl.evolution.coalescent.ConstExponential
getArgumentCount() - Method in class jebl.evolution.coalescent.ConstLogistic
getArgumentCount() - Method in interface jebl.evolution.coalescent.DemographicFunction
  Returns the number of arguments for this function.
getArgumentCount() - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
  Returns the number of arguments for this function.
getArgumentCount() - Method in class jebl.evolution.coalescent.Expansion
getArgumentCount() - Method in class jebl.evolution.coalescent.ExponentialGrowth
getArgumentCount() - Method in class jebl.evolution.coalescent.ExponentialLogistic
getArgumentName(int) - Method in class jebl.evolution.coalescent.ConstantPopulation
getArgumentName(int) - Method in class jebl.evolution.coalescent.ConstExponential
getArgumentName(int) - Method in class jebl.evolution.coalescent.ConstLogistic
getArgumentName(int) - Method in interface jebl.evolution.coalescent.DemographicFunction
  Returns the name of the nth argument of this function.
getArgumentName(int) - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
  Returns the name of the nth argument of this function.
getArgumentName(int) - Method in class jebl.evolution.coalescent.Expansion
getArgumentName(int) - Method in class jebl.evolution.coalescent.ExponentialGrowth
getArgumentName(int) - Method in class jebl.evolution.coalescent.ExponentialLogistic
getAttribute(String) - Method in class jebl.evolution.alignments.ConsensusSequence
getAttribute(String) - Method in class jebl.evolution.sequences.BasicSequence
getAttribute(String) - Method in class jebl.evolution.sequences.CanonicalSequence
getAttribute(String) - Method in class jebl.evolution.sequences.CodonSequence
getAttribute(String) - Method in class jebl.evolution.sequences.FilteredSequence
getAttribute(String) - Method in class jebl.evolution.taxa.Taxon
getAttribute(String) - Method in class jebl.evolution.trees.CompactRootedTree
getAttribute(String) - Method in class jebl.evolution.trees.BaseEdge
getAttribute(String) - Method in class jebl.evolution.trees.BaseNode
getAttribute(String) - Method in class jebl.evolution.trees.FilteredRootedTree
getAttribute(String) - Method in class jebl.evolution.trees.MutableRootedTree
getAttribute(String) - Method in class jebl.evolution.trees.ReRootedTree
getAttribute(String) - Method in class jebl.evolution.trees.RootedFromUnrooted
getAttribute(String) - Method in class jebl.evolution.trees.RootedSubtree
getAttribute(String) - Method in class jebl.evolution.trees.SimpleRootedTree
getAttribute(String) - Method in class jebl.evolution.trees.SimpleTree
getAttribute(String) - Method in interface jebl.util.Attributable
getAttribute(String) - Method in class jebl.util.AttributableHelper
getAttributeMap() - Method in class jebl.evolution.alignments.ConsensusSequence
getAttributeMap() - Method in class jebl.evolution.sequences.BasicSequence
getAttributeMap() - Method in class jebl.evolution.sequences.CanonicalSequence
getAttributeMap() - Method in class jebl.evolution.sequences.CodonSequence
getAttributeMap() - Method in class jebl.evolution.sequences.FilteredSequence
getAttributeMap() - Method in class jebl.evolution.taxa.Taxon
getAttributeMap() - Method in class jebl.evolution.trees.CompactRootedTree
getAttributeMap() - Method in class jebl.evolution.trees.BaseEdge
getAttributeMap() - Method in class jebl.evolution.trees.BaseNode
getAttributeMap() - Method in class jebl.evolution.trees.FilteredRootedTree
getAttributeMap() - Method in class jebl.evolution.trees.MutableRootedTree
getAttributeMap() - Method in class jebl.evolution.trees.ReRootedTree
getAttributeMap() - Method in class jebl.evolution.trees.RootedFromUnrooted
getAttributeMap() - Method in class jebl.evolution.trees.RootedSubtree
getAttributeMap() - Method in class jebl.evolution.trees.SimpleRootedTree
getAttributeMap() - Method in class jebl.evolution.trees.SimpleTree
getAttributeMap() - Method in interface jebl.util.Attributable
  Gets the entire attribute map.
getAttributeMap() - Method in class jebl.util.AttributableHelper
getAttributeNames() - Method in class jebl.evolution.alignments.ConsensusSequence
getAttributeNames() - Method in class jebl.evolution.sequences.BasicSequence
getAttributeNames() - Method in class jebl.evolution.sequences.CanonicalSequence
getAttributeNames() - Method in class jebl.evolution.sequences.CodonSequence
getAttributeNames() - Method in class jebl.evolution.sequences.FilteredSequence
getAttributeNames() - Method in class jebl.evolution.taxa.Taxon
getAttributeNames() - Method in class jebl.evolution.trees.CompactRootedTree
getAttributeNames() - Method in class jebl.evolution.trees.BaseEdge
getAttributeNames() - Method in class jebl.evolution.trees.BaseNode
getAttributeNames() - Method in class jebl.evolution.trees.FilteredRootedTree
getAttributeNames() - Method in class jebl.evolution.trees.MutableRootedTree
getAttributeNames() - Method in class jebl.evolution.trees.ReRootedTree
getAttributeNames() - Method in class jebl.evolution.trees.RootedFromUnrooted
getAttributeNames() - Method in class jebl.evolution.trees.RootedSubtree
getAttributeNames() - Method in class jebl.evolution.trees.SimpleRootedTree
getAttributeNames() - Method in class jebl.evolution.trees.SimpleTree
getAttributeNames() - Method in interface jebl.util.Attributable
getAttributeNames() - Method in class jebl.util.AttributableHelper
getAvailableAminoAcidScores() - Static method in class jebl.evolution.align.scores.ScoresFactory
getAvailableNucleotideScores() - Static method in class jebl.evolution.align.scores.ScoresFactory
getAverageTipDistance(RootedTree, Node) - Static method in class jebl.evolution.trees.RootedTreeUtils
  returns the average distance from the given node to all the tips below it
getBiasAlternating(OrderEnumerator, OrderEnumerator) - Static method in class jebl.math.OrderEnumerator.Utils
getBiasAlternatingFactory(OrderEnumerator.OEFactory, OrderEnumerator.OEFactory) - Static method in class jebl.math.OrderEnumerator.Utils
getBuilder(TreeBuilderFactory.Method, DistanceMatrix) - Static method in class jebl.evolution.trees.ClusteringTreeBuilder
  A factory method to create a ClusteringTreeBuilder
getBuilder(TreeBuilderFactory.Method, DistanceMatrix) - Static method in class jebl.evolution.trees.TreeBuilderFactory
getCanonicalStateCount() - Static method in class jebl.evolution.sequences.AminoAcids
getCanonicalStateCount() - Static method in class jebl.evolution.sequences.Codons
getCanonicalStateCount() - Static method in class jebl.evolution.sequences.Nucleotides
getCanonicalStateCount() - Method in interface jebl.evolution.sequences.SequenceType
  Get number of canonical states
getCanonicalStates() - Static method in class jebl.evolution.sequences.AminoAcids
getCanonicalStates() - Static method in class jebl.evolution.sequences.Codons
getCanonicalStates() - Static method in class jebl.evolution.sequences.Nucleotides
getCanonicalStates() - Method in interface jebl.evolution.sequences.SequenceType
  Get a list of canonical states ordered by their indices.
getCanonicalStates() - Method in class jebl.evolution.sequences.State
getCataclysmTime() - Method in class jebl.evolution.coalescent.CataclysmicDemographic
getChildren(Node) - Method in class jebl.evolution.trees.CompactRootedTree
getChildren(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
getChildren(Node) - Method in class jebl.evolution.trees.MutableRootedTree
getChildren(Node) - Method in class jebl.evolution.trees.ReRootedTree
getChildren(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
getChildren(Node) - Method in class jebl.evolution.trees.RootedSubtree
getChildren(Node) - Method in interface jebl.evolution.trees.RootedTree
getChildren(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
getChildren(Node) - Method in class jebl.evolution.trees.SortedRootedTree
getClade(int) - Method in class jebl.evolution.trees.CladeSystem
getCladeCount() - Method in class jebl.evolution.trees.CladeSystem
  get number of unique clades
getCladeFrequency(int) - Method in class jebl.evolution.trees.CladeSystem
  get clade frequency
getCladeString(int) - Method in class jebl.evolution.trees.CladeSystem
getCleanString() - Method in class jebl.evolution.sequences.BasicSequence
getCleanString() - Method in class jebl.evolution.sequences.CanonicalSequence
getCleanString() - Method in class jebl.evolution.sequences.CodonSequence
getCoalescentEvents(int) - Method in interface jebl.evolution.coalescent.IntervalList
  Returns the number coalescent events in an interval
getCoalescentEvents(int) - Method in class jebl.evolution.coalescent.Intervals
getCode() - Method in class jebl.evolution.sequences.State
  Returns the 1 letter code for this state.
getCodeLength() - Method in interface jebl.evolution.sequences.SequenceType
getCodeTable() - Method in class jebl.evolution.sequences.GeneticCode
  Returns a length-64 string that for each nucleotide triplet contains the single-character amino acid code (see `AminoAcids` to which that triplet is translated in this genetic code.
getCodonsForAminoAcid(AminoAcidState) - Method in class jebl.evolution.sequences.GeneticCode
getColumn(double[][], int) - Static method in class jebl.math.MatrixCalc
  takes a matrix and gets a column, then returns it as a vector
getCombined(OrthogonalHints, int, OrthogonalHints, int) - Static method in class jebl.math.OrthogonalHints.Utils
getCommonAncestorNode(RootedTree, Set<Node>) - Static method in class jebl.evolution.trees.RootedTreeUtils
  Gets the most recent common ancestor (MRCA) node of a set of tip nodes.
getComplementaryState(NucleotideState) - Static method in class jebl.evolution.sequences.Nucleotides
getConstant(int) - Static method in class jebl.math.OrderEnumerator.Utils
getConstantFactory(int) - Static method in class jebl.math.OrderEnumerator.Utils
getCopy(boolean[][]) - Static method in class jebl.util.Utils
  Clones an array of booleans
getCopy(byte[]) - Static method in class jebl.util.Utils
  Clones an array of bytes
getCopy(byte[][]) - Static method in class jebl.util.Utils
  Clones an array of bytes
getCopy(double[]) - Static method in class jebl.util.Utils
  Clones an array of doubles
getCopy(double[][]) - Static method in class jebl.util.Utils
  Clones an array of doubles
getCopy(double[][][]) - Static method in class jebl.util.Utils
  Clones an array of doubles
getCopy(double[], int) - Static method in class jebl.util.Utils
  Clones an array of doubles from index start (inclusive) to end
getCopy(double[], int, int) - Static method in class jebl.util.Utils
  Clones an array of doubles from index start (inclusive) to index end (exclusive)
getCopy(int[]) - Static method in class jebl.util.Utils
  Clones an array of ints
getCopy(int[][]) - Static method in class jebl.util.Utils
  Clones a matrix of ints
getCopy(int[], int) - Static method in class jebl.util.Utils
  Clones an array of ints
getCopy(String[]) - Static method in class jebl.util.Utils
  Clones an array of Strings
getDecimalPlaces() - Method in class jebl.util.NumberFormatter
  Get the number of decimal places to display when formatted.
getDeclineRate() - Method in class jebl.evolution.coalescent.CataclysmicDemographic
  returns the positive-valued decline rate
getDefaultDistanceModel(List<Sequence>) - Static method in class jebl.evolution.align.SequenceAlignmentsDistanceMatrix
getDegree() - Method in interface jebl.evolution.graphs.Node
  Get the number of edges connected to this node.
getDegree(Graph, Node) - Static method in class jebl.evolution.graphs.Graph.Utils
getDemographic(double) - Method in class jebl.evolution.coalescent.CataclysmicDemographic
getDemographic(double) - Method in class jebl.evolution.coalescent.ConstantPopulation
getDemographic(double) - Method in class jebl.evolution.coalescent.ConstExponential
getDemographic(double) - Method in class jebl.evolution.coalescent.ConstLogistic
getDemographic(double) - Method in interface jebl.evolution.coalescent.DemographicFunction
  Gets the value of the demographic function N(t) at time t.
getDemographic(double) - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
  Gets the value of the demographic function N(t) at time t.
getDemographic(double) - Method in class jebl.evolution.coalescent.Expansion
getDemographic(double) - Method in class jebl.evolution.coalescent.ExponentialGrowth
getDemographic(double) - Method in class jebl.evolution.coalescent.ExponentialLogistic
getDemographic(double) - Method in class jebl.evolution.coalescent.LogisticGrowth
  Gets the value of the demographic function N(t) at time t.
getDesc() - Method in interface jebl.evolution.characters.Character
  return the description of the character
getDesc() - Method in class jebl.evolution.characters.ContinuousCharacter
getDesc() - Method in class jebl.evolution.characters.DiscreteCharacter
getDescendantTips(RootedTree, Node) - Static method in class jebl.evolution.trees.RootedTreeUtils
  Gets a set of tip nodes descended from the given node.
getDescription() - Method in class jebl.evolution.sequences.GeneticCode
  Returns the description of the genetic code
getDimension() - Method in class jebl.evolution.substmodel.AbstractRateMatrix
getDimension() - Method in class jebl.evolution.substmodel.MatrixExponential
getDimension() - Method in interface jebl.evolution.substmodel.RateMatrix
getDistance(int, int) - Method in class jebl.evolution.distances.BasicDistanceMatrix
  Gets the distance at a particular row and column
getDistance(int, int) - Method in interface jebl.evolution.distances.DistanceMatrix
  Gets the distance at a particular row and column
getDistance(Taxon, Taxon) - Method in class jebl.evolution.distances.BasicDistanceMatrix
  Gets the distance between 2 taxa
getDistance(Taxon, Taxon) - Method in interface jebl.evolution.distances.DistanceMatrix
  Gets the distance between 2 taxa
getDistances() - Method in class jebl.evolution.distances.BasicDistanceMatrix
  Gets a 2-dimensional array containing the distances
getDistances() - Method in interface jebl.evolution.distances.DistanceMatrix
  Gets a 2-dimensional array containing the distances
getEdge(Node, Node) - Method in interface jebl.evolution.graphs.Graph
  Returns the Edge that connects these two nodes
getEdge(Node, Node) - Method in class jebl.evolution.trees.CompactRootedTree
getEdge(Node, Node) - Method in class jebl.evolution.trees.FilteredRootedTree
getEdge(Node, Node) - Method in class jebl.evolution.trees.MutableRootedTree
  Returns the Edge that connects these two nodes
getEdge(Node, Node) - Method in class jebl.evolution.trees.ReRootedTree
  Returns the Edge that connects these two nodes
getEdge(Node, Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
getEdge(Node, Node) - Method in class jebl.evolution.trees.RootedSubtree
  Returns the Edge that connects these two nodes
getEdge(Node, Node) - Method in class jebl.evolution.trees.SimpleRootedTree
  Returns the Edge that connects these two nodes
getEdge(Node, Node) - Method in class jebl.evolution.trees.SimpleTree
  Returns the Edge that connects these two nodes
getEdgeLength(Node, Node) - Method in interface jebl.evolution.graphs.Graph
  Returns the length of the edge that connects these two nodes
getEdgeLength(Node, Node) - Method in class jebl.evolution.trees.CompactRootedTree
getEdgeLength(Node, Node) - Method in class jebl.evolution.trees.FilteredRootedTree
getEdgeLength(Node, Node) - Method in class jebl.evolution.trees.MutableRootedTree
getEdgeLength(Node, Node) - Method in class jebl.evolution.trees.ReRootedTree
getEdgeLength(Node, Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
getEdgeLength(Node, Node) - Method in class jebl.evolution.trees.RootedSubtree
getEdgeLength(Node, Node) - Method in class jebl.evolution.trees.SimpleRootedTree
getEdgeLength(Node, Node) - Method in class jebl.evolution.trees.SimpleTree
getEdges() - Method in interface jebl.evolution.graphs.Graph
getEdges() - Method in class jebl.evolution.trees.CompactRootedTree
getEdges() - Method in class jebl.evolution.trees.FilteredRootedTree
getEdges() - Method in class jebl.evolution.trees.MutableRootedTree
getEdges() - Method in class jebl.evolution.trees.ReRootedTree
getEdges() - Method in class jebl.evolution.trees.RootedFromUnrooted
getEdges() - Method in class jebl.evolution.trees.RootedSubtree
getEdges() - Method in class jebl.evolution.trees.SimpleRootedTree
getEdges() - Method in class jebl.evolution.trees.SimpleTree
getEdges(Node) - Method in interface jebl.evolution.graphs.Graph
  Returns a list of edges connected to this node
getEdges(Node) - Method in class jebl.evolution.trees.CompactRootedTree
getEdges(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
getEdges(Node) - Method in class jebl.evolution.trees.MutableRootedTree
  Returns a list of edges connected to this node
getEdges(Node) - Method in class jebl.evolution.trees.ReRootedTree
  Returns a list of edges connected to this node
getEdges(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
  Returns a list of edges connected to this node
getEdges(Node) - Method in class jebl.evolution.trees.RootedSubtree
  Returns a list of edges connected to this node
getEdges(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
  Returns a list of edges connected to this node
getEdges(Node) - Method in class jebl.evolution.trees.SimpleTree
  Returns a list of edges connected to this node
getEquilibriumFrequencies() - Method in class jebl.evolution.substmodel.AbstractRateMatrix
getEquilibriumFrequencies() - Method in interface jebl.evolution.substmodel.RateMatrix
getEquilibriumFrequency(int) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
getEquilibriumFrequency(int) - Method in interface jebl.evolution.substmodel.RateMatrix
getEstimatedScores() - Method in class jebl.evolution.align.BartonSternberg
getExternalEdges() - Method in class jebl.evolution.trees.CompactRootedTree
getExternalEdges() - Method in class jebl.evolution.trees.FilteredRootedTree
getExternalEdges() - Method in class jebl.evolution.trees.MutableRootedTree
  The set of external edges.
getExternalEdges() - Method in class jebl.evolution.trees.ReRootedTree
  The set of external edges.
getExternalEdges() - Method in class jebl.evolution.trees.RootedFromUnrooted
  The set of external edges.
getExternalEdges() - Method in class jebl.evolution.trees.RootedSubtree
  The set of external edges.
getExternalEdges() - Method in class jebl.evolution.trees.SimpleRootedTree
  The set of external edges.
getExternalEdges() - Method in class jebl.evolution.trees.SimpleTree
  The set of external edges.
getExternalEdges() - Method in interface jebl.evolution.trees.Tree
getExternalNodeCount(Node) - Method in class jebl.evolution.trees.AbstractRootedTree
getExternalNodeCount(Node) - Method in class jebl.evolution.trees.CompactRootedTree
getExternalNodeCount(Node) - Method in interface jebl.evolution.trees.RootedTree
getExternalNodeCount(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
getExternalNodeCount(RootedTree, Node) - Static method in class jebl.evolution.trees.Utils
  Return the number of external nodes under this node.
getExternalNodes() - Method in class jebl.evolution.trees.CompactRootedTree
getExternalNodes() - Method in class jebl.evolution.trees.FilteredRootedTree
getExternalNodes() - Method in class jebl.evolution.trees.MutableRootedTree
getExternalNodes() - Method in class jebl.evolution.trees.ReRootedTree
getExternalNodes() - Method in class jebl.evolution.trees.RootedFromUnrooted
getExternalNodes() - Method in class jebl.evolution.trees.RootedSubtree
getExternalNodes() - Method in class jebl.evolution.trees.SimpleRootedTree
getExternalNodes() - Method in class jebl.evolution.trees.SimpleTree
getExternalNodes() - Method in interface jebl.evolution.trees.Tree
getExternalNodes(Node) - Method in class jebl.evolution.trees.AbstractRootedTree
getExternalNodes(Node) - Method in class jebl.evolution.trees.CompactRootedTree
getExternalNodes(Node) - Method in interface jebl.evolution.trees.RootedTree
getExternalNodes(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
getFormattedValue(double) - Method in class jebl.util.NumberFormatter
  Returns a string containing the current value for this column with appropriate formatting.
getFractionCompleted() - Method in class jebl.util.BasicProgressListener
getFullName() - Method in class jebl.evolution.sequences.State
  A descriptive name for this state.
getGaplessLocation(Sequence, int) - Static method in class jebl.evolution.sequences.Utils
  Gets the site location index for this sequence excluding any gaps.
getGappedLocation(Sequence, int) - Static method in class jebl.evolution.sequences.Utils
  Gets the site location index for this sequence that corresponds to a location given excluding all gaps.
getGapState() - Static method in class jebl.evolution.sequences.AminoAcids
getGapState() - Static method in class jebl.evolution.sequences.Codons
getGapState() - Static method in class jebl.evolution.sequences.Nucleotides
getGapState() - Method in interface jebl.evolution.sequences.SequenceType
  Get state corresponding to a gap
getGeneticCodes() - Static method in class jebl.evolution.sequences.GeneticCode
  Returns an iterable that allows you to iterate over all the standard genetic codes
getGeneticCodesArray() - Static method in class jebl.evolution.sequences.GeneticCode
getGrowthRate() - Method in class jebl.evolution.coalescent.ExponentialGrowth
  returns growth rate.
getHeight(Node) - Method in class jebl.evolution.trees.CompactRootedTree
getHeight(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
getHeight(Node) - Method in class jebl.evolution.trees.MutableRootedTree
getHeight(Node) - Method in class jebl.evolution.trees.ReRootedTree
getHeight(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
getHeight(Node) - Method in class jebl.evolution.trees.RootedSubtree
getHeight(Node) - Method in interface jebl.evolution.trees.RootedTree
getHeight(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
getHeight(Node) - Method in class jebl.evolution.trees.TransformedRootedTree
getImmutableProfileCharacter(char) - Static method in class jebl.evolution.align.ProfileCharacter
  An immutable ProfileCharacter that uses less memory than a mutable profile character.
getIndex() - Method in class jebl.evolution.sequences.State
getIntegral(double, double) - Method in class jebl.evolution.coalescent.ConstantPopulation
  Calculates the integral 1/N(x) dx between start and finish.
getIntegral(double, double) - Method in class jebl.evolution.coalescent.ConstExponential
getIntegral(double, double) - Method in class jebl.evolution.coalescent.ConstLogistic
getIntegral(double, double) - Method in interface jebl.evolution.coalescent.DemographicFunction
  Calculates the integral 1/N(x) dx between start and finish
getIntegral(double, double) - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
getIntegral(double, double) - Method in class jebl.evolution.coalescent.Expansion
getIntegral(double, double) - Method in class jebl.evolution.coalescent.ExponentialLogistic
getIntegral(double, double) - Method in class jebl.evolution.coalescent.LogisticGrowth
getIntensity(double) - Method in class jebl.evolution.coalescent.CataclysmicDemographic
getIntensity(double) - Method in class jebl.evolution.coalescent.ConstantPopulation
getIntensity(double) - Method in class jebl.evolution.coalescent.ConstExponential
getIntensity(double) - Method in class jebl.evolution.coalescent.ConstLogistic
getIntensity(double) - Method in interface jebl.evolution.coalescent.DemographicFunction
  Returns value of demographic intensity function at time t (= integral 1/N(x) dx from 0 to t).
getIntensity(double) - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
  Returns value of demographic intensity function at time t (= integral 1/N(x) dx from 0 to t).
getIntensity(double) - Method in class jebl.evolution.coalescent.Expansion
getIntensity(double) - Method in class jebl.evolution.coalescent.ExponentialGrowth
getIntensity(double) - Method in class jebl.evolution.coalescent.ExponentialLogistic
getIntensity(double) - Method in class jebl.evolution.coalescent.LogisticGrowth
  Returns value of demographic intensity function at time t (= integral 1/N(x) dx from 0 to t).
getInternalEdges() - Method in class jebl.evolution.trees.CompactRootedTree
getInternalEdges() - Method in class jebl.evolution.trees.FilteredRootedTree
getInternalEdges() - Method in class jebl.evolution.trees.MutableRootedTree
  The set of internal edges.
getInternalEdges() - Method in class jebl.evolution.trees.ReRootedTree
  The set of internal edges.
getInternalEdges() - Method in class jebl.evolution.trees.RootedFromUnrooted
  The set of internal edges.
getInternalEdges() - Method in class jebl.evolution.trees.RootedSubtree
  The set of internal edges.
getInternalEdges() - Method in class jebl.evolution.trees.SimpleRootedTree
  The set of internal edges.
getInternalEdges() - Method in class jebl.evolution.trees.SimpleTree
  The set of internal edges.
getInternalEdges() - Method in interface jebl.evolution.trees.Tree
getInternalNodes() - Method in class jebl.evolution.trees.CompactRootedTree
getInternalNodes() - Method in class jebl.evolution.trees.FilteredRootedTree
getInternalNodes() - Method in class jebl.evolution.trees.MutableRootedTree
getInternalNodes() - Method in class jebl.evolution.trees.ReRootedTree
getInternalNodes() - Method in class jebl.evolution.trees.RootedFromUnrooted
getInternalNodes() - Method in class jebl.evolution.trees.RootedSubtree
getInternalNodes() - Method in class jebl.evolution.trees.SimpleRootedTree
getInternalNodes() - Method in class jebl.evolution.trees.SimpleTree
getInternalNodes() - Method in interface jebl.evolution.trees.Tree
getInternalParameterBoundaries(int, double[]) - Method in interface jebl.math.OrthogonalHints
  A boundary is a value of a parameter for which values lower than the boundary and values higher than the boundary are better treated as two separate functions (IE, they are only piecewise connected), and minimisation should be performed over both ranges individually (and then the true minimum taken as the minimuma of the ranges)
getInternalParameterBoundaries(OrthogonalHints, int) - Static method in class jebl.math.OrthogonalHints.Utils
getInterval(double, int, double) - Method in class jebl.evolution.treesimulation.CoalescentIntervalGenerator
  Calculates the waiting time to the next coalescent for a given critical value (an intensity).
getInterval(double, int, double) - Method in interface jebl.evolution.treesimulation.IntervalGenerator
  Calculates the waiting time to the next coalescent for a given critical value (an intensity).
getInterval(int) - Method in interface jebl.evolution.coalescent.IntervalList
  Gets an interval.
getInterval(int) - Method in class jebl.evolution.coalescent.Intervals
getIntervalCount() - Method in interface jebl.evolution.coalescent.IntervalList
  get number of intervals
getIntervalCount() - Method in class jebl.evolution.coalescent.Intervals
getIntervalType(int) - Method in interface jebl.evolution.coalescent.IntervalList
  Returns the type of interval observed.
getIntervalType(int) - Method in class jebl.evolution.coalescent.Intervals
getInverseIntensity(double) - Method in class jebl.evolution.coalescent.CataclysmicDemographic
getInverseIntensity(double) - Method in class jebl.evolution.coalescent.ConstantPopulation
getInverseIntensity(double) - Method in class jebl.evolution.coalescent.ConstExponential
getInverseIntensity(double) - Method in class jebl.evolution.coalescent.ConstLogistic
getInverseIntensity(double) - Method in interface jebl.evolution.coalescent.DemographicFunction
  Returns value of inverse demographic intensity function (returns time, needed for simulation of coalescent intervals).
getInverseIntensity(double) - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
  Returns value of inverse demographic intensity function (returns time, needed for simulation of coalescent intervals).
getInverseIntensity(double) - Method in class jebl.evolution.coalescent.Expansion
getInverseIntensity(double) - Method in class jebl.evolution.coalescent.ExponentialGrowth
getInverseIntensity(double) - Method in class jebl.evolution.coalescent.ExponentialLogistic
getInverseIntensity(double) - Method in class jebl.evolution.coalescent.LogisticGrowth
  Returns value of demographic intensity function at time t (= integral 1/N(x) dx from 0 to t).
getLabelCount() - Method in class jebl.evolution.trees.SplitSystem
  get number of labels
getLastDelimiter() - Method in class jebl.evolution.io.ImportHelper
getLastMetaComment() - Method in class jebl.evolution.io.ImportHelper
  Deprecated.
  use `ImportHelper.getMetaComments()` instead
getLength() - Method in class jebl.evolution.alignments.ConsensusSequence
  Returns the length of the sequence
getLength() - Method in interface jebl.evolution.alignments.Pattern
getLength() - Method in interface jebl.evolution.graphs.Edge
getLength() - Method in class jebl.evolution.sequences.BasicSequence
  Returns the length of the sequence
getLength() - Method in class jebl.evolution.sequences.CanonicalSequence
  Returns the length of the sequence
getLength() - Method in class jebl.evolution.sequences.CodonSequence
  Returns the length of the sequence
getLength() - Method in class jebl.evolution.sequences.FilteredSequence
  Returns the length of the sequence
getLength() - Method in interface jebl.evolution.sequences.Sequence
  Get the length of the sequence
getLength(Node) - Method in class jebl.evolution.trees.CompactRootedTree
getLength(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
getLength(Node) - Method in class jebl.evolution.trees.MutableRootedTree
getLength(Node) - Method in class jebl.evolution.trees.ReRootedTree
getLength(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
getLength(Node) - Method in class jebl.evolution.trees.RootedSubtree
getLength(Node) - Method in interface jebl.evolution.trees.RootedTree
getLength(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
getLength(Node) - Method in class jebl.evolution.trees.TransformedRootedTree
getLength(RootedTree) - Static method in class jebl.evolution.trees.Utils
getLength(Tree) - Static method in class jebl.evolution.trees.Utils
getLineageCount(int) - Method in interface jebl.evolution.coalescent.IntervalList
  Returns the number of uncoalesced lineages within this interval.
getLineageCount(int) - Method in class jebl.evolution.coalescent.Intervals
getLineageCount(IntervalList, double) - Static method in class jebl.evolution.coalescent.IntervalList.Utils
getLineNumber() - Method in class jebl.evolution.io.ImportHelper
getLowerBound() - Method in class jebl.math.OrthogonalLineFunction
getLowerBound() - Method in interface jebl.math.UnivariateFunction
  get lower bound of argument
getLowerBound(int) - Method in class jebl.evolution.coalescent.Coalescent
getLowerBound(int) - Method in class jebl.evolution.coalescent.ConstantPopulation
getLowerBound(int) - Method in class jebl.evolution.coalescent.ConstExponential
getLowerBound(int) - Method in class jebl.evolution.coalescent.ConstLogistic
getLowerBound(int) - Method in interface jebl.evolution.coalescent.DemographicFunction
  Returns the lower bound of the nth argument of this function.
getLowerBound(int) - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
  Returns the lower bound of the nth argument of this function.
getLowerBound(int) - Method in class jebl.evolution.coalescent.Expansion
getLowerBound(int) - Method in class jebl.evolution.coalescent.ExponentialGrowth
getLowerBound(int) - Method in class jebl.evolution.coalescent.ExponentialLogistic
getLowerBound(int) - Method in interface jebl.math.MultivariateFunction
  get lower bound of argument n
getMatch() - Method in class jebl.evolution.align.Align
getMatch() - Method in class jebl.evolution.align.NeedlemanWunschAffine
getMatch() - Method in class jebl.evolution.align.NeedlemanWunschLinearSpace
getMatch() - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
getMatch() - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
getMatch() - Method in class jebl.evolution.align.SmithWatermanLinearSpace
getMatch() - Method in class jebl.evolution.align.SmithWatermanLinearSpaceAffine
getMatch(char[], char[]) - Method in class jebl.evolution.align.NeedlemanWunschAffine
getMatchScores(int) - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
getMatrixString() - Method in class jebl.evolution.align.scores.Scores
getMax() - Method in class jebl.evolution.align.SequenceShuffler
getMax(double[]) - Static method in class jebl.util.Utils
  Calculate the max of an array
getMax(double[], int, int) - Static method in class jebl.util.Utils
  Calculate the max of an array
getMaxTipHeight(RootedTree, Node) - Static method in class jebl.evolution.trees.RootedTreeUtils
getMean() - Method in class jebl.evolution.align.SequenceShuffler
getMean(double[]) - Static method in class jebl.util.Utils
  Calculate the mean value of an array
getMemoryRequiredForAlignment(int) - Static method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
getMessage() - Method in class jebl.util.BasicProgressListener
getMetaComments() - Method in class jebl.evolution.io.ImportHelper
  This method has been introduced because this class previously skipped over consecutive comments and discarded all but the last.
getMethodDescription() - Method in class jebl.evolution.trees.ConsensusTreeBuilder
  Returns a human readable name of this consensus tree building method
getMetric(RootedTree, RootedTree) - Method in class jebl.evolution.treemetrics.BilleraMetric
getMetric(RootedTree, RootedTree) - Method in class jebl.evolution.treemetrics.CladeHeightMetric
getMetric(RootedTree, RootedTree) - Method in class jebl.evolution.treemetrics.RobinsonsFouldMetric
getMetric(RootedTree, RootedTree) - Method in interface jebl.evolution.treemetrics.RootedTreeMetric
  calculates the metric between two rooted trees
getMin() - Method in class jebl.evolution.align.SequenceShuffler
getMin(double[]) - Static method in class jebl.util.Utils
  Calculate the min of an array
getMinNodeHeight(RootedTree, Node) - Static method in class jebl.evolution.trees.Utils
getMinTipHeight(RootedTree, Node) - Static method in class jebl.evolution.trees.RootedTreeUtils
getMostFrequentState() - Method in interface jebl.evolution.alignments.Pattern
  Returns the most frequent state in this pattern
getMostFrequentState(boolean) - Method in interface jebl.evolution.alignments.Pattern
  Returns the most frequent state in this pattern, optionally including ambiguous states
getN0() - Method in class jebl.evolution.coalescent.ConstantPopulation
  returns initial population size.
getN1() - Method in class jebl.evolution.coalescent.ConstExponential
getN1() - Method in class jebl.evolution.coalescent.ConstLogistic
getN1() - Method in class jebl.evolution.coalescent.Expansion
getName() - Method in class jebl.evolution.align.scores.AminoAcidScores
getName() - Method in class jebl.evolution.align.scores.Blosum45
getName() - Method in class jebl.evolution.align.scores.Blosum50
getName() - Method in class jebl.evolution.align.scores.NucleotideScores
getName() - Method in interface jebl.evolution.align.scores.ScoreMatrix
getName() - Method in class jebl.evolution.align.scores.SubstScoreMatrix
getName() - Method in interface jebl.evolution.characters.Character
  return the name of the character
getName() - Method in interface jebl.evolution.characters.CharacterType
getName() - Method in class jebl.evolution.characters.ContinuousCharacter
getName() - Method in class jebl.evolution.characters.DiscreteCharacter
getName() - Method in class jebl.evolution.sequences.GeneticCode
  Returns the name of the genetic code
getName() - Method in class jebl.evolution.sequences.Nucleotides
getName() - Method in interface jebl.evolution.sequences.SequenceType
  name of data type
getName() - Method in class jebl.evolution.sequences.State
  Deprecated.
  you probably want to use `State.getFullName()` or `State.getCode()`.
getName() - Method in class jebl.evolution.sequences.StateClassification.Default
getName() - Method in interface jebl.evolution.sequences.StateClassification
getName() - Method in class jebl.evolution.taxa.Taxon
  get the name of the taxon
getName() - Method in class jebl.evolution.taxa.TaxonomicLevel
  get the name of the taxonomic level
getName() - Method in enum class jebl.evolution.trees.ConsensusTreeBuilder.Method
getName() - Method in enum class jebl.evolution.trees.TreeBuilderFactory.Method
getNcbiTranslationTableNumber() - Method in class jebl.evolution.sequences.GeneticCode
getNext() - Method in interface jebl.math.OrderEnumerator
  The next value in the enumeration
getNextBlockName() - Method in class jebl.evolution.io.NexusImporter
getNexusDataType() - Method in interface jebl.evolution.sequences.SequenceType
getNode(Taxon) - Method in class jebl.evolution.trees.CompactRootedTree
getNode(Taxon) - Method in class jebl.evolution.trees.FilteredRootedTree
getNode(Taxon) - Method in class jebl.evolution.trees.MutableRootedTree
getNode(Taxon) - Method in class jebl.evolution.trees.ReRootedTree
getNode(Taxon) - Method in class jebl.evolution.trees.RootedFromUnrooted
getNode(Taxon) - Method in class jebl.evolution.trees.RootedSubtree
getNode(Taxon) - Method in class jebl.evolution.trees.SimpleRootedTree
getNode(Taxon) - Method in class jebl.evolution.trees.SimpleTree
getNode(Taxon) - Method in interface jebl.evolution.trees.Tree
getNodes() - Method in interface jebl.evolution.graphs.Graph
getNodes() - Method in class jebl.evolution.trees.CompactRootedTree
getNodes() - Method in class jebl.evolution.trees.FilteredRootedTree
getNodes() - Method in class jebl.evolution.trees.MutableRootedTree
getNodes() - Method in class jebl.evolution.trees.ReRootedTree
getNodes() - Method in class jebl.evolution.trees.RootedFromUnrooted
getNodes() - Method in class jebl.evolution.trees.RootedSubtree
getNodes() - Method in class jebl.evolution.trees.SimpleRootedTree
getNodes() - Method in class jebl.evolution.trees.SimpleTree
getNodes(int) - Method in interface jebl.evolution.graphs.Graph
getNodes(int) - Method in class jebl.evolution.trees.CompactRootedTree
getNodes(int) - Method in class jebl.evolution.trees.FilteredRootedTree
getNodes(int) - Method in class jebl.evolution.trees.MutableRootedTree
getNodes(int) - Method in class jebl.evolution.trees.ReRootedTree
getNodes(int) - Method in class jebl.evolution.trees.RootedFromUnrooted
getNodes(int) - Method in class jebl.evolution.trees.RootedSubtree
getNodes(int) - Method in class jebl.evolution.trees.SimpleRootedTree
getNodes(int) - Method in class jebl.evolution.trees.SimpleTree
getNodes(Edge) - Method in interface jebl.evolution.graphs.Graph
  Returns an array of 2 nodes which are the nodes at either end of the edge.
getNodes(Edge) - Method in class jebl.evolution.trees.CompactRootedTree
getNodes(Edge) - Method in class jebl.evolution.trees.FilteredRootedTree
getNodes(Edge) - Method in class jebl.evolution.trees.MutableRootedTree
  Returns an array of 2 nodes which are the nodes at either end of the edge.
getNodes(Edge) - Method in class jebl.evolution.trees.ReRootedTree
  Returns an array of 2 nodes which are the nodes at either end of the edge.
getNodes(Edge) - Method in class jebl.evolution.trees.RootedFromUnrooted
getNodes(Edge) - Method in class jebl.evolution.trees.RootedSubtree
  Returns an array of 2 nodes which are the nodes at either end of the edge.
getNodes(Edge) - Method in class jebl.evolution.trees.SimpleRootedTree
  Returns an array of 2 nodes which are the nodes at either end of the edge.
getNodes(Edge) - Method in class jebl.evolution.trees.SimpleTree
  Returns an array of 2 nodes which are the nodes at either end of the edge.
getNodes(RootedTree, Node) - Static method in class jebl.evolution.trees.Utils
  All nodes in subtree - parents before children (pre - order).
getNormalized(double[]) - Static method in class jebl.math.Random
getNull() - Static method in class jebl.math.OrthogonalHints.Utils
getNumArguments() - Method in class jebl.evolution.coalescent.Coalescent
getNumArguments() - Method in interface jebl.math.MultivariateFunction
  get number of arguments
getNumOfStates() - Method in class jebl.evolution.characters.DiscreteCharacter
getOrdered(int) - Static method in class jebl.math.OrderEnumerator.Utils
getOrderedFactory() - Static method in class jebl.math.OrderEnumerator.Utils
getOriginalFrequencies() - Static method in class jebl.evolution.substmodel.WAG
getOriginalFrequencies(double[]) - Static method in class jebl.evolution.substmodel.WAG
  get the frequencies of the original data set that formed the basis for the estimation of the rate matrix
getOrthogonalHints() - Method in class jebl.evolution.coalescent.Coalescent
getOrthogonalHints() - Method in interface jebl.math.MultivariateFunction
getParent(Node) - Method in class jebl.evolution.trees.CompactRootedTree
getParent(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
getParent(Node) - Method in class jebl.evolution.trees.MutableRootedTree
getParent(Node) - Method in class jebl.evolution.trees.ReRootedTree
getParent(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
getParent(Node) - Method in class jebl.evolution.trees.RootedSubtree
getParent(Node) - Method in interface jebl.evolution.trees.RootedTree
getParent(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
getParentEdge(Node) - Method in class jebl.evolution.trees.CompactRootedTree
getParentEdge(Node) - Method in class jebl.evolution.trees.MutableRootedTree
getParentEdge(Node) - Method in class jebl.evolution.trees.ReRootedTree
getParentEdge(Node) - Method in class jebl.evolution.trees.RootedSubtree
getParentEdge(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
getPathLength(Tree, Node, Node) - Static method in class jebl.evolution.trees.Utils
getPatternCount() - Method in class jebl.evolution.alignments.BasicAlignment
getPatternCount() - Method in interface jebl.evolution.alignments.Patterns
getPatternCount() - Method in class jebl.evolution.alignments.ResampledAlignment
getPatternLength() - Method in class jebl.evolution.alignments.BasicAlignment
getPatternLength() - Method in interface jebl.evolution.alignments.Patterns
getPatternLength() - Method in class jebl.evolution.alignments.ResampledAlignment
getPatterns() - Method in class jebl.evolution.alignments.BasicAlignment
getPatterns() - Method in interface jebl.evolution.alignments.Patterns
  Get a list of all the patterns
getPatterns() - Method in class jebl.evolution.alignments.ResampledAlignment
getProgress() - Method in class jebl.evolution.io.ImportHelper
getR2() - Method in class jebl.evolution.coalescent.ExponentialLogistic
getRelativeRates() - Method in class jebl.evolution.substmodel.AbstractRateMatrix
getRelativeRates() - Method in interface jebl.evolution.substmodel.RateMatrix
getRestricted(OrderEnumerator, int, int) - Static method in class jebl.math.OrderEnumerator.Utils
getRestrictedFactory(OrderEnumerator.OEFactory, int, int) - Static method in class jebl.math.OrderEnumerator.Utils
getRootNode() - Method in class jebl.evolution.trees.CompactRootedTree
getRootNode() - Method in class jebl.evolution.trees.FilteredRootedTree
getRootNode() - Method in class jebl.evolution.trees.MutableRootedTree
  The root of the tree has the largest node height of all nodes in the tree.
getRootNode() - Method in class jebl.evolution.trees.ReRootedTree
  The root of the tree has the largest node height of all nodes in the tree.
getRootNode() - Method in class jebl.evolution.trees.RootedFromUnrooted
getRootNode() - Method in class jebl.evolution.trees.RootedSubtree
  The root of the tree has the largest node height of all nodes in the tree.
getRootNode() - Method in interface jebl.evolution.trees.RootedTree
  The root of the tree has the largest node height of all nodes in the tree.
getRootNode() - Method in class jebl.evolution.trees.SimpleRootedTree
  The root of the tree has the largest node height of all nodes in the tree.
getRootProgressListener() - Method in class jebl.util.CompositeProgressListener
getSampleCount() - Method in interface jebl.evolution.coalescent.IntervalList
  get the total number of sampling events.
getSampleCount() - Method in class jebl.evolution.coalescent.Intervals
getScore() - Method in class jebl.evolution.align.Align
getScore() - Method in class jebl.evolution.align.OldNeedlemanWunschAffine
getScore() - Method in class jebl.evolution.align.MaximalSegmentPair
getScore() - Method in class jebl.evolution.align.OverlapAlign
getScore() - Method in class jebl.evolution.align.SmithWaterman
getScore() - Method in class jebl.evolution.align.BartonSternberg
getScore() - Method in class jebl.evolution.align.NeedlemanWunsch
getScore() - Method in class jebl.evolution.align.NeedlemanWunschAffine
getScore() - Method in class jebl.evolution.align.NeedlemanWunschLinearSpace
getScore() - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
getScore() - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
getScore() - Method in class jebl.evolution.align.SmithWatermanLinearSpace
getScore() - Method in class jebl.evolution.align.SmithWatermanLinearSpaceAffine
getScore(char, char) - Method in interface jebl.evolution.align.scores.ScoreMatrix
getScore(char, char) - Method in class jebl.evolution.align.scores.Scores
getScore(Sequence, Sequence) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
getScore(Sequence, Sequence) - Method in interface jebl.evolution.align.PairwiseAligner
getScore(Tree) - Method in class jebl.evolution.parsimony.FitchParsimony
getScore(Tree) - Method in interface jebl.evolution.parsimony.ParsimonyCriterion
  Calculates the minimum number of steps for the parsimony reconstruction for the given tree.
getScores() - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
  The indices for these correspond to those for the getAlignments() matrix.
getSE(Taxon) - Method in class jebl.evolution.characters.ContinuousCharacter
getSelectedNodes() - Method in class jebl.evolution.trees.TreeSelectionChangeEvent
getSequence(Taxon) - Method in class jebl.evolution.alignments.BasicAlignment
getSequence(Taxon) - Method in class jebl.evolution.alignments.ResampledAlignment
getSequence(Taxon) - Method in interface jebl.evolution.sequences.Sequences
getSequenceCharacters() - Method in class jebl.evolution.sequences.BasicSequence
  Get the sequence characters representing the sequence.
getSequenceCharacters() - Method in class jebl.evolution.sequences.CodonSequence
  Get the sequence characters representing the sequence.
getSequenceList() - Method in interface jebl.evolution.alignments.Alignment
getSequenceList() - Method in class jebl.evolution.alignments.BasicAlignment
getSequenceList() - Method in class jebl.evolution.alignments.ResampledAlignment
getSequences() - Method in class jebl.evolution.alignments.BasicAlignment
getSequences() - Method in class jebl.evolution.alignments.ResampledAlignment
getSequences() - Method in interface jebl.evolution.sequences.Sequences
getSequenceType() - Method in class jebl.evolution.alignments.BasicAlignment
getSequenceType() - Method in class jebl.evolution.alignments.ConsensusSequence
getSequenceType() - Method in interface jebl.evolution.alignments.Pattern
getSequenceType() - Method in interface jebl.evolution.alignments.Patterns
getSequenceType() - Method in class jebl.evolution.alignments.ResampledAlignment
getSequenceType() - Method in class jebl.evolution.sequences.BasicSequence
getSequenceType() - Method in class jebl.evolution.sequences.CanonicalSequence
getSequenceType() - Method in class jebl.evolution.sequences.CodonSequence
getSequenceType() - Method in class jebl.evolution.sequences.FilteredSequence
getSequenceType() - Method in interface jebl.evolution.sequences.Sequence
getSequenceType() - Method in class jebl.evolution.sequences.TranslatedSequence
getSequenceType() - Method in class jebl.evolution.substmodel.AbstractRateMatrix
getSequenceType() - Method in interface jebl.evolution.substmodel.RateMatrix
  Get the data type of this rate matrix
getSetName(State) - Method in class jebl.evolution.sequences.StateClassification.Default
getSetName(State) - Method in interface jebl.evolution.sequences.StateClassification
getSetNames() - Method in class jebl.evolution.sequences.StateClassification.Default
getSetNames() - Method in interface jebl.evolution.sequences.StateClassification
getShape() - Method in class jebl.evolution.coalescent.LogisticGrowth
getShuffled(int) - Static method in class jebl.math.OrderEnumerator.Utils
getShuffledFactory() - Static method in class jebl.math.OrderEnumerator.Utils
getSignificantFigures() - Method in class jebl.util.NumberFormatter
  Get the number of significant figures to display when formatted.
getSiteCount() - Method in interface jebl.evolution.alignments.Alignment
getSiteCount() - Method in class jebl.evolution.alignments.BasicAlignment
getSiteCount() - Method in class jebl.evolution.alignments.ResampledAlignment
getSiteScores(Tree) - Method in class jebl.evolution.parsimony.FitchParsimony
  Calculates the minimum number of siteScores for the parsimony reconstruction of a a set of character patterns on a tree.
getSiteScores(Tree) - Method in interface jebl.evolution.parsimony.ParsimonyCriterion
  Calculates the minimum number of steps for the parsimony reconstruction for the given tree.
getSize() - Method in class jebl.evolution.distances.BasicDistanceMatrix
  Gets the size of the matrix (which is square), i.e., number of rows or columns.
getSize() - Method in interface jebl.evolution.distances.DistanceMatrix
  Gets the size of the matrix (which is square), i.e., number of rows or columns.
getSource() - Method in class jebl.evolution.alignments.ConsensusSequence
getSource() - Method in class jebl.evolution.trees.FilteredRootedTree
getSourceNode(Node) - Method in class jebl.evolution.trees.ReRootedTree
getSplit(int) - Method in class jebl.evolution.trees.SplitSystem
  get split
getSplit(List<Taxon>, Tree, Edge, boolean[]) - Static method in class jebl.evolution.trees.SplitUtils
  get split for branch associated with internal node
getSplitCount() - Method in class jebl.evolution.trees.SplitSystem
  get number of splits
getSplits(List<Taxon>, Tree) - Static method in class jebl.evolution.trees.SplitUtils
  creates a split system from a tree (using a pre-specified order of sequences)
getSplits(Tree) - Static method in class jebl.evolution.trees.SplitUtils
  creates a split system from a tree (using tree-induced order of sequences)
getSplitVector() - Method in class jebl.evolution.trees.SplitSystem
  get split vector
getStartCodons() - Method in class jebl.evolution.sequences.GeneticCode
getState(char) - Static method in class jebl.evolution.sequences.AminoAcids
getState(char) - Static method in class jebl.evolution.sequences.Nucleotides
getState(char) - Method in interface jebl.evolution.sequences.SequenceType
  Get state whose code is the one-character string consisting only of code.
getState(int) - Method in class jebl.evolution.alignments.ConsensusSequence
getState(int) - Method in interface jebl.evolution.alignments.Pattern
  Get the state for the ith taxon
getState(int) - Static method in class jebl.evolution.sequences.AminoAcids
getState(int) - Method in class jebl.evolution.sequences.BasicSequence
getState(int) - Method in class jebl.evolution.sequences.CanonicalSequence
getState(int) - Static method in class jebl.evolution.sequences.Codons
getState(int) - Method in class jebl.evolution.sequences.CodonSequence
getState(int) - Method in class jebl.evolution.sequences.FilteredSequence
getState(int) - Static method in class jebl.evolution.sequences.Nucleotides
getState(int) - Method in interface jebl.evolution.sequences.Sequence
getState(int) - Method in interface jebl.evolution.sequences.SequenceType
  Get state corresponding to a state index
getState(String) - Static method in class jebl.evolution.sequences.AminoAcids
getState(String) - Static method in class jebl.evolution.sequences.Codons
  Gets the state object for the given code.
getState(String) - Static method in class jebl.evolution.sequences.Nucleotides
getState(String) - Method in interface jebl.evolution.sequences.SequenceType
  Get state corresponding to a string code
getState(NucleotideState, NucleotideState, NucleotideState) - Static method in class jebl.evolution.sequences.Codons
getStateCount() - Static method in class jebl.evolution.sequences.AminoAcids
getStateCount() - Static method in class jebl.evolution.sequences.Codons
getStateCount() - Static method in class jebl.evolution.sequences.Nucleotides
getStateCount() - Method in interface jebl.evolution.sequences.SequenceType
  Get number of states including ambiguous states
getStateCount(Sequence, State) - Static method in interface jebl.evolution.sequences.Sequence
  Counts the number of occurances of a state
getStateCount(State) - Method in interface jebl.evolution.alignments.Pattern
  Returns the count of the given state in this pattern
getStateDesc() - Method in class jebl.evolution.characters.DiscreteCharacter
getStateDesc(int) - Method in class jebl.evolution.characters.DiscreteCharacter
getStateFrequency(State) - Method in interface jebl.evolution.alignments.Pattern
  Returns the frequent of the given state in this pattern
getStateIndices() - Method in class jebl.evolution.alignments.ConsensusSequence
getStateIndices() - Method in class jebl.evolution.sequences.BasicSequence
getStateIndices() - Method in class jebl.evolution.sequences.CanonicalSequence
getStateIndices() - Method in class jebl.evolution.sequences.CodonSequence
getStateIndices() - Method in class jebl.evolution.sequences.FilteredSequence
getStateIndices() - Method in interface jebl.evolution.sequences.Sequence
getStateIndices(State[]) - Static method in class jebl.evolution.sequences.Utils
getStates() - Method in class jebl.evolution.alignments.ConsensusSequence
getStates() - Method in interface jebl.evolution.alignments.Pattern
getStates() - Static method in class jebl.evolution.sequences.AminoAcids
getStates() - Method in class jebl.evolution.sequences.BasicSequence
getStates() - Method in class jebl.evolution.sequences.CanonicalSequence
getStates() - Static method in class jebl.evolution.sequences.Codons
getStates() - Method in class jebl.evolution.sequences.CodonSequence
getStates() - Method in class jebl.evolution.sequences.FilteredSequence
getStates() - Static method in class jebl.evolution.sequences.Nucleotides
getStates() - Method in interface jebl.evolution.sequences.Sequence
getStates() - Method in interface jebl.evolution.sequences.SequenceType
  Get a list of states ordered by their indices.
getStates(Tree, Node) - Method in class jebl.evolution.parsimony.FitchParsimony
  Returns the reconstructed character states for a given node in the tree.
getStates(Tree, Node) - Method in interface jebl.evolution.parsimony.ParsimonyCriterion
  Returns the reconstructed character states for a given node in the tree.
getStateSet() - Method in interface jebl.evolution.alignments.Pattern
getStateSet(String) - Method in class jebl.evolution.sequences.StateClassification.Default
getStateSet(String) - Method in interface jebl.evolution.sequences.StateClassification
getStdev() - Method in class jebl.evolution.align.SequenceShuffler
getStopCodonCount() - Method in class jebl.evolution.sequences.GeneticCode
  Returns the number of terminator amino acids.
getStopCodonCount(Sequence) - Static method in class jebl.evolution.sequences.Utils
  Counts the number of stop codons in an amino acid sequence
getStopCodons() - Method in class jebl.evolution.sequences.GeneticCode
getString() - Method in class jebl.evolution.alignments.ConsensusSequence
getString() - Method in class jebl.evolution.sequences.BasicSequence
getString() - Method in class jebl.evolution.sequences.CanonicalSequence
getString() - Method in class jebl.evolution.sequences.CodonSequence
getString() - Method in class jebl.evolution.sequences.FilteredSequence
getString() - Method in interface jebl.evolution.sequences.Sequence
getSubmatrix(Collection<Taxon>) - Method in class jebl.evolution.distances.BasicDistanceMatrix
  Gets a sub-matrix for only those taxa in the collection (all of which should be present in this matrix).
getSubmatrix(Collection<Taxon>) - Method in interface jebl.evolution.distances.DistanceMatrix
  Gets a sub-matrix for only those taxa in the collection (all of which should be present in this matrix).
getSubSequence(Sequence, int, int) - Static method in interface jebl.evolution.sequences.Sequence
  Returns a sub-sequence for states from, to (inclusive).
getSuggestedOrdering(OrderEnumerator) - Method in interface jebl.math.OrthogonalHints
  If there is a "best" ordering to use it can be specified here, if not should return null
getSum(double[]) - Static method in class jebl.util.Utils
  Calculate the total of an array
getSupportAttributeName() - Method in class jebl.evolution.trees.ConsensusTreeBuilder
getTaxa() - Method in class jebl.evolution.alignments.BasicAlignment
getTaxa() - Method in interface jebl.evolution.alignments.Pattern
getTaxa() - Method in interface jebl.evolution.alignments.Patterns
getTaxa() - Method in class jebl.evolution.alignments.ResampledAlignment
getTaxa() - Method in interface jebl.evolution.characters.Character
  get a Set<Taxon> of all the taxa for this character
getTaxa() - Method in class jebl.evolution.characters.ContinuousCharacter
getTaxa() - Method in class jebl.evolution.characters.DiscreteCharacter
getTaxa() - Method in class jebl.evolution.distances.BasicDistanceMatrix
getTaxa() - Method in interface jebl.evolution.distances.DistanceMatrix
getTaxa() - Method in class jebl.evolution.trees.CompactRootedTree
getTaxa() - Method in class jebl.evolution.trees.FilteredRootedTree
getTaxa() - Method in class jebl.evolution.trees.MutableRootedTree
getTaxa() - Method in class jebl.evolution.trees.ReRootedTree
getTaxa() - Method in class jebl.evolution.trees.RootedFromUnrooted
getTaxa() - Method in class jebl.evolution.trees.RootedSubtree
getTaxa() - Method in class jebl.evolution.trees.SimpleRootedTree
getTaxa() - Method in class jebl.evolution.trees.SimpleTree
getTaxa() - Method in class jebl.evolution.trees.SplitSystem
  get taxon list
getTaxa() - Method in interface jebl.evolution.trees.Tree
getTaxon() - Method in class jebl.evolution.alignments.ConsensusSequence
getTaxon() - Method in class jebl.evolution.sequences.BasicSequence
getTaxon() - Method in class jebl.evolution.sequences.CanonicalSequence
getTaxon() - Method in class jebl.evolution.sequences.CodonSequence
getTaxon() - Method in class jebl.evolution.sequences.FilteredSequence
getTaxon() - Method in interface jebl.evolution.sequences.Sequence
getTaxon(String) - Static method in class jebl.evolution.taxa.Taxon
  A static method that returns a Taxon object with the given name.
getTaxon(Node) - Method in class jebl.evolution.trees.CompactRootedTree
getTaxon(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
getTaxon(Node) - Method in class jebl.evolution.trees.MutableRootedTree
getTaxon(Node) - Method in class jebl.evolution.trees.ReRootedTree
getTaxon(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
getTaxon(Node) - Method in class jebl.evolution.trees.RootedSubtree
getTaxon(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
getTaxon(Node) - Method in class jebl.evolution.trees.SimpleTree
getTaxon(Node) - Method in interface jebl.evolution.trees.Tree
getTaxonomicLevel() - Method in class jebl.evolution.taxa.Taxon
  get the taxonomic level of the taxon
getTaxonomicLevel(String) - Static method in class jebl.evolution.taxa.TaxonomicLevel
  A static method that returns a TaxonomicLevel object with the given name.
getTaxonomicLevels() - Static method in class jebl.evolution.taxa.TaxonomicLevel
  Returns a Set containing all the currently created taxonomic levels.
getTestSequence1() - Static method in class jebl.evolution.sequences.SequenceTester
getTestSequence1(String[]) - Static method in class jebl.evolution.sequences.SequenceTester
getTestSequence2() - Static method in class jebl.evolution.sequences.SequenceTester
getTestSequence2(String[]) - Static method in class jebl.evolution.sequences.SequenceTester
getThreeLetterName() - Method in class jebl.evolution.sequences.AminoAcidState
getTime() - Method in class jebl.evolution.coalescent.ExponentialLogistic
getTipCount(RootedTree, Node) - Static method in class jebl.evolution.trees.RootedTreeUtils
  Return the number of leaves under this node.
getTipsForTaxa(RootedTree, Collection<Taxon>) - Static method in class jebl.evolution.trees.RootedTreeUtils
  Gets a set of external nodes that correspond to the given taxa.
getTotal(double[]) - Static method in class jebl.math.Random
getTotal(double[], int, int) - Static method in class jebl.math.Random
getTotalDuration() - Method in interface jebl.evolution.coalescent.IntervalList
  get the total duration of these intervals.
getTotalDuration() - Method in class jebl.evolution.coalescent.Intervals
getTransitionProbabilities(double[][]) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
  A utility method for speed, transfers trans prob information quickly into store
getTransitionProbabilities(double[][]) - Method in class jebl.evolution.substmodel.MatrixExponential
  A utility method for speed, transfers trans prob information quickly into store
getTransitionProbabilities(double[][]) - Method in interface jebl.evolution.substmodel.RateMatrix
  A utility method for speed, transfers trans prob information quickly into store.
getTransitionProbability(int, int) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
getTransitionProbability(int, int) - Method in class jebl.evolution.substmodel.MatrixExponential
getTransitionProbability(int, int) - Method in interface jebl.evolution.substmodel.RateMatrix
getTranslation(String) - Method in class jebl.evolution.sequences.GeneticCode
  Returns the state associated with AminoAcid represented by the three nucleotides.
getTranslation(CodonState) - Method in class jebl.evolution.sequences.GeneticCode
  Returns the state associated with AminoAcid represented by codonState.
getTranslation(NucleotideState, NucleotideState, NucleotideState) - Method in class jebl.evolution.sequences.GeneticCode
  Returns the state associated with AminoAcid represented by the three nucleotides.
getTree() - Method in class jebl.evolution.trees.TreeChangeEvent
getTripletCode(AminoAcidState) - Static method in class jebl.evolution.sequences.AminoAcids
getType() - Method in interface jebl.evolution.characters.Character
  return the CharacterType of the character
getType() - Method in class jebl.evolution.characters.ContinuousCharacter
getType() - Method in class jebl.evolution.characters.DiscreteCharacter
getType() - Method in class jebl.evolution.sequences.AminoAcidState
getType() - Method in class jebl.evolution.sequences.CodonState
getType() - Method in class jebl.evolution.sequences.NucleotideState
getType() - Method in class jebl.evolution.sequences.State
getUniqueName() - Method in interface jebl.evolution.substmodel.RateMatrix
getUniqueName() - Method in class jebl.evolution.substmodel.WAG
getUnknownState() - Static method in class jebl.evolution.sequences.AminoAcids
getUnknownState() - Static method in class jebl.evolution.sequences.Codons
getUnknownState() - Static method in class jebl.evolution.sequences.Nucleotides
getUnknownState() - Method in interface jebl.evolution.sequences.SequenceType
  Get state corresponding to an unknown
getUpperBound() - Method in class jebl.math.OrthogonalLineFunction
getUpperBound() - Method in interface jebl.math.UnivariateFunction
  get upper bound of argument
getUpperBound(int) - Method in class jebl.evolution.coalescent.Coalescent
getUpperBound(int) - Method in class jebl.evolution.coalescent.ConstantPopulation
getUpperBound(int) - Method in class jebl.evolution.coalescent.ConstExponential
getUpperBound(int) - Method in class jebl.evolution.coalescent.ConstLogistic
getUpperBound(int) - Method in interface jebl.evolution.coalescent.DemographicFunction
  Returns the upper bound of the nth argument of this function.
getUpperBound(int) - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
  Returns the upper bound of the nth argument of this function.
getUpperBound(int) - Method in class jebl.evolution.coalescent.Expansion
getUpperBound(int) - Method in class jebl.evolution.coalescent.ExponentialGrowth
getUpperBound(int) - Method in class jebl.evolution.coalescent.ExponentialLogistic
getUpperBound(int) - Method in interface jebl.math.MultivariateFunction
  get upper bound of argument n
getV() - Method in class jebl.evolution.align.NeedlemanWunschLinearSpace
getValue(Taxon) - Method in interface jebl.evolution.characters.Character
  get a value for a taxon containing the character
getValue(Taxon) - Method in class jebl.evolution.characters.ContinuousCharacter
getValue(Taxon) - Method in class jebl.evolution.characters.DiscreteCharacter
getWeight() - Method in interface jebl.evolution.alignments.Pattern
  Get the weight of this pattern
getX() - Method in class jebl.evolution.align.Traceback
getY() - Method in class jebl.evolution.align.Traceback
getZero() - Static method in class jebl.math.OrderEnumerator.Utils
getZeroFactory() - Static method in class jebl.math.OrderEnumerator.Utils
gradient(MultivariateFunction, double[]) - Static method in class jebl.math.NumericalDerivative
  determine gradient
gradient(MultivariateFunction, double[], double[]) - Static method in class jebl.math.NumericalDerivative
  determine gradient
Graph - Interface in jebl.evolution.graphs
Graph.NoEdgeException - Exception Class in jebl.evolution.graphs
  This class is thrown by getEdgeLength(node1, node2) if node1 and node2 are not directly connected by an edge.
Graph.Utils - Class in jebl.evolution.graphs
GREEDY - Enum constant in enum class jebl.evolution.trees.ConsensusTreeBuilder.Method
GREEDY - Enum constant in enum class jebl.evolution.trees.TreeBuilderFactory.ConsensusMethod
guessSequenceType(CharSequence) - Static method in class jebl.evolution.sequences.Utils
  Guess type of sequence from contents.

## H

H_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
H_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
Hamming - Class in jebl.evolution.align.scores
Hamming() - Constructor for class jebl.evolution.align.scores.Hamming
hashCode() - Method in class jebl.evolution.sequences.BasicSequence
hashCode() - Method in class jebl.evolution.sequences.CodonSequence
hashCode() - Method in class jebl.evolution.taxa.Taxon
hashCode() - Method in class jebl.util.FixedBitSet
hashCode() - Method in class jebl.util.HashPair
hasHeights() - Method in class jebl.evolution.trees.CompactRootedTree
hasHeights() - Method in class jebl.evolution.trees.FilteredRootedTree
hasHeights() - Method in class jebl.evolution.trees.MutableRootedTree
hasHeights() - Method in class jebl.evolution.trees.ReRootedTree
hasHeights() - Method in class jebl.evolution.trees.RootedFromUnrooted
hasHeights() - Method in class jebl.evolution.trees.RootedSubtree
hasHeights() - Method in interface jebl.evolution.trees.RootedTree
hasHeights() - Method in class jebl.evolution.trees.SimpleRootedTree
hasHeights() - Method in class jebl.evolution.trees.TransformedRootedTree
HashPair<T> - Class in jebl.util
  A pair suitable for use in a HashMap.
HashPair(T, T) - Constructor for class jebl.util.HashPair
hasIntegral() - Method in class jebl.evolution.coalescent.CataclysmicDemographic
hasIntegral() - Method in class jebl.evolution.coalescent.ConstantPopulation
hasIntegral() - Method in class jebl.evolution.coalescent.ConstExponential
hasIntegral() - Method in class jebl.evolution.coalescent.ConstLogistic
hasIntegral() - Method in interface jebl.evolution.coalescent.DemographicFunction
  returns whether an analytical expression for the integral is implemented
hasIntegral() - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
hasIntegral() - Method in class jebl.evolution.coalescent.Expansion
hasIntegral() - Method in class jebl.evolution.coalescent.ExponentialLogistic
hasIntegral() - Method in class jebl.evolution.coalescent.LogisticGrowth
hasLengths() - Method in class jebl.evolution.trees.CompactRootedTree
hasLengths() - Method in class jebl.evolution.trees.FilteredRootedTree
hasLengths() - Method in class jebl.evolution.trees.MutableRootedTree
hasLengths() - Method in class jebl.evolution.trees.ReRootedTree
hasLengths() - Method in class jebl.evolution.trees.RootedFromUnrooted
hasLengths() - Method in class jebl.evolution.trees.RootedSubtree
hasLengths() - Method in interface jebl.evolution.trees.RootedTree
hasLengths() - Method in class jebl.evolution.trees.SimpleRootedTree
hasLengths() - Method in class jebl.evolution.trees.TransformedRootedTree
hasMore() - Method in interface jebl.math.OrderEnumerator
  If hasMore returns false reset should be called
hasNextSubtask() - Method in class jebl.util.CompositeProgressListener
hasSplit(boolean[]) - Method in class jebl.evolution.trees.SplitSystem
  + test whether a split is contained in this split system (assuming the same leaf order)
hasTree() - Method in class jebl.evolution.io.NewickImporter
hasTree() - Method in class jebl.evolution.io.NexusImporter
  If not currently reading a TREES block then read ahead to the next TREES block, parsing TRANSLATE and TAXA blocks in the process if necessary.
hasTree() - Method in interface jebl.evolution.io.TreeImporter
  This can be used to read one tree at a time in a loop: `List<Tree> trees = new ArrayList<Tree>(); while (hasTree()) { trees.add(importNextTree()); }` return whether another tree is available.
HKY - Enum constant in enum class jebl.evolution.trees.TreeBuilderFactory.DistanceModel
HKYDistanceMatrix - Class in jebl.evolution.distances
  Compute HKY corrected distance matrix
HKYDistanceMatrix(Alignment, ProgressListener) - Constructor for class jebl.evolution.distances.HKYDistanceMatrix
HKYDistanceMatrix(Alignment, ProgressListener, boolean) - Constructor for class jebl.evolution.distances.HKYDistanceMatrix
HYDROPATHY_CLASSIFICATION - Static variable in class jebl.evolution.sequences.AminoAcids

## I

I_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
IllegalCharacterPolicy - Enum Class in jebl.evolution.io
  What to do when an imported document contains illegal characters
ImmediateSequenceImporter - Interface in jebl.evolution.io
  A sequence importer sending the sequences back one by one, which makes it possible to import larger documents if handled wisely on the other side.
ImmediateSequenceImporter.Callback - Interface in jebl.evolution.io
importAlignments() - Method in interface jebl.evolution.io.AlignmentImporter
  importAlignment.
importAlignments() - Method in class jebl.evolution.io.NexusImporter
  Import all alignments in the input from the current position.
importDistanceMatrices() - Method in interface jebl.evolution.io.DistanceMatrixImporter
  importDistances.
importDistanceMatrices() - Method in class jebl.evolution.io.NexusImporter
  Import all distance matrices from all DISTANCES blocks in the input form the current position.
importDistanceMatrices() - Method in class jebl.evolution.io.TabDelimitedImporter
  importDistances.
ImportException - Exception Class in jebl.evolution.io
ImportException() - Constructor for exception class jebl.evolution.io.ImportException
ImportException(String) - Constructor for exception class jebl.evolution.io.ImportException
ImportException(String, Throwable) - Constructor for exception class jebl.evolution.io.ImportException
ImportException.BadFormatException - Exception Class in jebl.evolution.io
ImportException.DuplicateFieldException - Exception Class in jebl.evolution.io
ImportException.DuplicateTaxaException - Exception Class in jebl.evolution.io
ImportException.MissingFieldException - Exception Class in jebl.evolution.io
ImportException.ShortSequenceException - Exception Class in jebl.evolution.io
ImportException.TooFewTaxaException - Exception Class in jebl.evolution.io
ImportException.UnknownTaxonException - Exception Class in jebl.evolution.io
ImportException.UnparsableDataException - Exception Class in jebl.evolution.io
ImportHelper - Class in jebl.evolution.io
  A helper class for phylogenetic file format importers
ImportHelper(Reader) - Constructor for class jebl.evolution.io.ImportHelper
  ATTENTION: The ImportHelper never closes the reader passed to the constructor.
ImportHelper(Reader, Writer) - Constructor for class jebl.evolution.io.ImportHelper
importNextTree() - Method in class jebl.evolution.io.NewickImporter
importNextTree() - Method in class jebl.evolution.io.NexusImporter
  If not currently reading a TREES block then read ahead to the next TREES block, parsing TRANSLATE and TAXA blocks in the process if necessary.
importNextTree() - Method in interface jebl.evolution.io.TreeImporter
  Import a single tree
importSequences() - Method in class jebl.evolution.io.FastaImporter
importSequences() - Method in class jebl.evolution.io.NexusImporter
  Import all sequences in the input from the current position
importSequences() - Method in class jebl.evolution.io.PhylipSequentialImporter
  importSequences.
importSequences() - Method in interface jebl.evolution.io.SequenceImporter
  importSequences.
importSequences(ImmediateSequenceImporter.Callback, ProgressListener) - Method in class jebl.evolution.io.FastaImporter
importSequences(ImmediateSequenceImporter.Callback, ProgressListener) - Method in interface jebl.evolution.io.ImmediateSequenceImporter
importTrees() - Method in class jebl.evolution.io.NewickImporter
importTrees() - Method in class jebl.evolution.io.NexusImporter
  Import all trees in the file from the current position.
importTrees() - Method in interface jebl.evolution.io.TreeImporter
  Import all the trees
includeAdditionalCharacters(Scores, String) - Static method in class jebl.evolution.align.scores.Scores
  includes additional characters in the score matrix which will all have scored zero when compared to other characters.
includeGaps(Scores, float, float) - Static method in class jebl.evolution.align.scores.Scores
incompleteGammaP(double, double) - Static method in class jebl.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 jebl.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 jebl.math.GammaFunction
  Incomplete Gamma function Q(a,x) (a cleanroom implementation of Numerical Recipes gammq(a,x); in Mathematica this function is called GammaRegularized)
INCREASING_NODE_DENSITY - Enum constant in enum class jebl.evolution.trees.SortedRootedTree.BranchOrdering
INDICATOR - Variable in class jebl.evolution.trees.CalculateSplitRates
init(Alignment, int[]) - Method in class jebl.evolution.alignments.ResampledAlignment
  Setup resampled alignment.
innerProduct(double[], double[], int) - Static method in class jebl.math.MatrixCalc
  innerProdect calculates inner product of two vectors from i down
instanceOf(String) - Static method in enum class jebl.evolution.io.IllegalCharacterPolicy
intersect(FixedBitSet) - Method in class jebl.util.FixedBitSet
intersectCardinality(FixedBitSet) - Method in class jebl.util.FixedBitSet
IntervalGenerator - Interface in jebl.evolution.treesimulation
IntervalList - Interface in jebl.evolution.coalescent
  An interface for a set of coalescent intevals.
IntervalList.IntervalType - Enum Class in jebl.evolution.coalescent
IntervalList.Utils - Class in jebl.evolution.coalescent
Intervals - Class in jebl.evolution.coalescent
  A concrete class for a set of coalescent intevals.
Intervals(int) - Constructor for class jebl.evolution.coalescent.Intervals
Intervals(RootedTree) - Constructor for class jebl.evolution.coalescent.Intervals
INVERTEBRATE_MT - Static variable in class jebl.evolution.sequences.GeneticCode
isAcyclical(Graph) - Method in class jebl.evolution.graphs.Utils
isAllGaps() - Method in class jebl.evolution.align.ProfileCharacter
isAmbiguous() - Method in class jebl.evolution.sequences.State
isATstate(State) - Static method in class jebl.evolution.sequences.Nucleotides
isBinary(RootedTree) - Static method in class jebl.evolution.trees.RootedTreeUtils
isBinary(RootedTree) - Static method in class jebl.evolution.trees.Utils
isBinaryCoalescent() - Method in interface jebl.evolution.coalescent.IntervalList
  Checks whether this set of coalescent intervals is fully resolved (i.e.
isBinaryCoalescent() - Method in class jebl.evolution.coalescent.Intervals
isCanceled() - Method in class jebl.util.BasicProgressListener
isCanceled() - Method in interface jebl.util.Cancelable
isCanceled() - Method in class jebl.util.CompositeProgressListener
isCanceled() - Method in class jebl.util.ProgressListener
  This method must be implemented by all subclasses.
isCanceled() - Method in class jebl.util.ProgressListener.Wrapper
isCharacterAscii(char) - Static method in class jebl.evolution.io.ByteBuilder
isCoalescentOnly() - Method in interface jebl.evolution.coalescent.IntervalList
  Checks whether this set of coalescent intervals coalescent only (i.e.
isCoalescentOnly() - Method in class jebl.evolution.coalescent.Intervals
isConnected(Graph) - Method in class jebl.evolution.graphs.Utils
isContains(String[], String) - Static method in class jebl.util.Utils
  Test if a string occurs within a set
isExternal(Edge) - Method in class jebl.evolution.trees.SimpleTree
isExternal(Node) - Method in class jebl.evolution.trees.CompactRootedTree
isExternal(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
isExternal(Node) - Method in class jebl.evolution.trees.MutableRootedTree
isExternal(Node) - Method in class jebl.evolution.trees.ReRootedTree
isExternal(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
isExternal(Node) - Method in class jebl.evolution.trees.RootedSubtree
isExternal(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
isExternal(Node) - Method in class jebl.evolution.trees.SimpleTree
isExternal(Node) - Method in interface jebl.evolution.trees.Tree
isGap() - Method in class jebl.evolution.sequences.AminoAcidState
isGap() - Method in class jebl.evolution.sequences.CodonState
isGap() - Method in class jebl.evolution.sequences.NucleotideState
isGap() - Method in class jebl.evolution.sequences.State
isGap(AminoAcidState) - Static method in class jebl.evolution.sequences.AminoAcids
isGap(CodonState) - Static method in class jebl.evolution.sequences.Codons
isGap(NucleotideState) - Static method in class jebl.evolution.sequences.Nucleotides
isGap(State) - Method in interface jebl.evolution.sequences.SequenceType
isGCstate(State) - Static method in class jebl.evolution.sequences.Nucleotides
isGeneratedTreeName(String) - Static method in class jebl.evolution.io.NexusExporter
isHeightsKnown() - Method in class jebl.evolution.trees.CompactRootedTree
isHeightsKnown() - Method in class jebl.evolution.trees.FilteredRootedTree
isHeightsKnown() - Method in class jebl.evolution.trees.MutableRootedTree
isHeightsKnown() - Method in class jebl.evolution.trees.ReRootedTree
isHeightsKnown() - Method in class jebl.evolution.trees.RootedFromUnrooted
isHeightsKnown() - Method in class jebl.evolution.trees.RootedSubtree
isHeightsKnown() - Method in interface jebl.evolution.trees.RootedTree
isHeightsKnown() - Method in class jebl.evolution.trees.SimpleRootedTree
isHeightsKnown() - Method in class jebl.evolution.trees.TransformedRootedTree
isIndeterminate() - Method in class jebl.util.BasicProgressListener
isLengthsKnown() - Method in class jebl.evolution.trees.CompactRootedTree
isLengthsKnown() - Method in class jebl.evolution.trees.FilteredRootedTree
isLengthsKnown() - Method in class jebl.evolution.trees.MutableRootedTree
isLengthsKnown() - Method in class jebl.evolution.trees.ReRootedTree
isLengthsKnown() - Method in class jebl.evolution.trees.RootedFromUnrooted
isLengthsKnown() - Method in class jebl.evolution.trees.RootedSubtree
isLengthsKnown() - Method in interface jebl.evolution.trees.RootedTree
isLengthsKnown() - Method in class jebl.evolution.trees.SimpleRootedTree
isLengthsKnown() - Method in class jebl.evolution.trees.TransformedRootedTree
isMonophyletic(RootedTree, Set<Node>) - Static method in class jebl.evolution.trees.RootedTreeUtils
  Performs the a monophyly test on a set of tip nodes.
isOrdered() - Method in class jebl.evolution.characters.DiscreteCharacter
isPossibleTransition(char, char) - Static method in class jebl.evolution.sequences.Nucleotides
isPossibleTransition(State, State) - Static method in class jebl.evolution.sequences.Nucleotides
isPossibleTransversion(char, char) - Static method in class jebl.evolution.sequences.Nucleotides
isPossibleTransversion(State, State) - Static method in class jebl.evolution.sequences.Nucleotides
isPredominantlyRNA(CharSequence, int) - Static method in class jebl.evolution.sequences.Utils
  Is the given NucleotideSequence predominantly RNA? (i.e the more occurrences of "U" than "T")
isPurine(State) - Static method in class jebl.evolution.sequences.Nucleotides
isPyrimidine(State) - Static method in class jebl.evolution.sequences.Nucleotides
isRoot(Node) - Method in class jebl.evolution.trees.CompactRootedTree
isRoot(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
isRoot(Node) - Method in class jebl.evolution.trees.MutableRootedTree
isRoot(Node) - Method in class jebl.evolution.trees.ReRootedTree
isRoot(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
isRoot(Node) - Method in class jebl.evolution.trees.RootedSubtree
isRoot(Node) - Method in interface jebl.evolution.trees.RootedTree
isRoot(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
isRootedMethod(TreeBuilderFactory.Method) - Static method in class jebl.evolution.trees.TreeBuilderFactory
isSame(boolean[], boolean[]) - Static method in class jebl.evolution.trees.SplitUtils
  Checks two splits for identity.
isStartCodon(CodonState) - Method in class jebl.evolution.sequences.GeneticCode
  Deprecated.
isStartCodonString(String) - Method in class jebl.evolution.sequences.GeneticCode
  Checks whether all possible disambiguations of a given nucleotide triplet string represents a start codon.
isStop() - Method in class jebl.evolution.sequences.AminoAcidState
isStopCodon(CodonState) - Method in class jebl.evolution.sequences.GeneticCode
  Deprecated.
isStopCodonString(String) - Method in class jebl.evolution.sequences.GeneticCode
  Checks whether a given String represents a stop codon.
isSupportAsPercent() - Method in class jebl.evolution.trees.ConsensusTreeBuilder
isTransition(State, State) - Static method in class jebl.evolution.sequences.Nucleotides
isTransversion(State, State) - Static method in class jebl.evolution.sequences.Nucleotides
isTree(Graph) - Method in class jebl.evolution.graphs.Utils
isUltrametric(RootedTree) - Static method in class jebl.evolution.trees.Utils
isUltrametric(RootedTree, double) - Static method in class jebl.evolution.trees.RootedTreeUtils
isUnknown(AminoAcidState) - Static method in class jebl.evolution.sequences.AminoAcids
isUnknown(CodonState) - Static method in class jebl.evolution.sequences.Codons
isUnknown(NucleotideState) - Static method in class jebl.evolution.sequences.Nucleotides
isUnknown(State) - Method in interface jebl.evolution.sequences.SequenceType
iterator() - Method in class jebl.evolution.io.NewickImporter
  Returns an iterator over a set of elements of type T.
iterator() - Method in class jebl.evolution.io.NexusImporter
IUB - Static variable in class jebl.evolution.align.scores.NucleotideScores

## J

J_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
JackknifedAlignment - Class in jebl.evolution.alignments
  Date: 17/01/2006 Time: 08:18:32
JackknifedAlignment(Alignment, double) - Constructor for class jebl.evolution.alignments.JackknifedAlignment
JackknifedAlignment(Alignment, double, long) - Constructor for class jebl.evolution.alignments.JackknifedAlignment
JackknifedAlignment(Alignment, double, Random) - Constructor for class jebl.evolution.alignments.JackknifedAlignment
jebl.evolution.align - package jebl.evolution.align
  Provides classes and interfaces for pairwise alignment of two sequences.
jebl.evolution.align.scores - package jebl.evolution.align.scores
jebl.evolution.aligners - package jebl.evolution.aligners
jebl.evolution.alignments - package jebl.evolution.alignments
jebl.evolution.characters - package jebl.evolution.characters
jebl.evolution.coalescent - package jebl.evolution.coalescent
jebl.evolution.distances - package jebl.evolution.distances
jebl.evolution.graphs - package jebl.evolution.graphs
jebl.evolution.io - package jebl.evolution.io
jebl.evolution.parsimony - package jebl.evolution.parsimony
jebl.evolution.sequences - package jebl.evolution.sequences
jebl.evolution.substmodel - package jebl.evolution.substmodel
jebl.evolution.taxa - package jebl.evolution.taxa
jebl.evolution.treemetrics - package jebl.evolution.treemetrics
jebl.evolution.trees - package jebl.evolution.trees
jebl.evolution.treesimulation - package jebl.evolution.treesimulation
jebl.math - package jebl.math
jebl.util - package jebl.util
JukesCantor - Class in jebl.evolution.align.scores
  Jukes Cantor assumes equal substitution frequencies and equal nucleotide equilibrium frequencies.
JukesCantor - Enum constant in enum class jebl.evolution.trees.TreeBuilderFactory.DistanceModel
JukesCantor(float) - Constructor for class jebl.evolution.align.scores.JukesCantor
JukesCantorDistanceMatrix - Class in jebl.evolution.distances
  Compute jukes-cantor corrected distance matrix for a set of aligned sequences.
JukesCantorDistanceMatrix(Alignment, ProgressListener) - Constructor for class jebl.evolution.distances.JukesCantorDistanceMatrix
JukesCantorDistanceMatrix(Alignment, ProgressListener, boolean) - Constructor for class jebl.evolution.distances.JukesCantorDistanceMatrix

## K

K_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
K_STATE - Static variable in class jebl.evolution.sequences.Nucleotides

## L

L_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
leftNb(RootedTree, Node) - Static method in class jebl.evolution.trees.Utils
  Left Neighbour of a tip (taxon).
length() - Method in class jebl.evolution.io.ByteBuilder
lnGamma(double) - Static method in class jebl.math.GammaFunction
  log Gamma function: ln(gamma(alpha)) for alpha>0, accurate to 10 decimal places
loadTrees(int, int) - Method in class jebl.evolution.trees.CalculateSplitRates
LogisticGrowth - Class in jebl.evolution.coalescent
  This class models logistic growth.
LogisticGrowth() - Constructor for class jebl.evolution.coalescent.LogisticGrowth
  Construct demographic model with default settings
LogisticGrowth(double, double, double) - Constructor for class jebl.evolution.coalescent.LogisticGrowth
  Construct demographic model with given settings
LOWER - Enum constant in enum class jebl.evolution.io.DistanceMatrixImporter.Triangle
lowerSolve(double[][], double[], double) - Static method in class jebl.math.MatrixCalc
  lower Solve forward elimination with (optional) default diagonal value

## M

M_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
M_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
MachineAccuracy - Class in jebl.math
  determines machine accuracy
MachineAccuracy() - Constructor for class jebl.math.MachineAccuracy
main(String[]) - Static method in class jebl.evolution.align.AlignCommand
main(String[]) - Static method in class jebl.evolution.align.BartonSternberg
main(String[]) - Static method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
main(String[]) - Static method in class jebl.evolution.trees.CalculateSplitRates
main(String[]) - Static method in class jebl.evolution.treesimulation.TreeSimulator
  A main() to test the tree simulation classes.
makeIntoAllowableIdentifier(String) - Static method in class jebl.evolution.io.NexusImporter
MatrixCalc - Class in jebl.math
MatrixCalc() - Constructor for class jebl.math.MatrixCalc
MatrixCalcException - Exception Class in jebl.math
MatrixCalcException() - Constructor for exception class jebl.math.MatrixCalcException
MatrixCalcException(String) - Constructor for exception class jebl.math.MatrixCalcException
MatrixCalcException.NotSquareMatrixException - Exception Class in jebl.math
MatrixCalcException.PositiveDefiniteException - Exception Class in jebl.math
MatrixExponential - Class in jebl.evolution.substmodel
  compute matrix exponential and, subsequently, transition probabilities for a given rate matrix
MatrixExponential(int) - Constructor for class jebl.evolution.substmodel.MatrixExponential
MatrixExponential(RateMatrix) - Constructor for class jebl.evolution.substmodel.MatrixExponential
  create module
MAX_ROW_LENGTH - Static variable in class jebl.evolution.io.NexusExporter
maxFun - Variable in class jebl.math.MultivariateMinimum
  maxFun is the maximum number of calls to fun allowed.
maxFun - Variable in class jebl.math.UnivariateMinimum
  maximum number of function evaluations (default 0 indicates no limit on calls)
MaximalSegmentPair - Class in jebl.evolution.align
MaximalSegmentPair(Scores) - Constructor for class jebl.evolution.align.MaximalSegmentPair
maxLevels(RootedTree) - Static method in class jebl.evolution.trees.Utils
Maybe - Enum constant in enum class jebl.util.MaybeBoolean
MaybeBoolean - Enum Class in jebl.util
  A tri-state boolean value that can also be "Maybe" besides True and False.
MEGAExporter - Class in jebl.evolution.io
  * Export to MEGA.
MEGAExporter(Writer, String) - Constructor for class jebl.evolution.io.MEGAExporter
MIGRATION - Enum constant in enum class jebl.evolution.coalescent.IntervalList.IntervalType
  Denotes an interval at the end of which a migration event occurs.
MinimiserMonitor - Interface in jebl.math
  interface for a classes that wish to monitor the progress of a Minimiser
MinimiserMonitor.Utils - Class in jebl.math
minx - Variable in class jebl.math.UnivariateMinimum
  last minimum
MissingBlockException() - Constructor for exception class jebl.evolution.io.NexusImporter.MissingBlockException
MissingBlockException(String) - Constructor for exception class jebl.evolution.io.NexusImporter.MissingBlockException
MissingFieldException() - Constructor for exception class jebl.evolution.io.ImportException.MissingFieldException
MissingFieldException(String) - Constructor for exception class jebl.evolution.io.ImportException.MissingFieldException
MissingTaxonException - Exception Class in jebl.evolution.taxa
MissingTaxonException(Taxon) - Constructor for exception class jebl.evolution.taxa.MissingTaxonException
ModelBasedDistanceMatrix - Class in jebl.evolution.distances
ModelBasedDistanceMatrix() - Constructor for class jebl.evolution.distances.ModelBasedDistanceMatrix
MOLD_PROTOZOAN_MT - Static variable in class jebl.evolution.sequences.GeneticCode
MostProbableTopology - Class in jebl.evolution.trees
  Given a set of trees determine the most probable trees, i.e.
MostProbableTopology(Collection<? extends Tree>) - Constructor for class jebl.evolution.trees.MostProbableTopology
MRCAC - Enum constant in enum class jebl.evolution.trees.ConsensusTreeBuilder.Method
MRCAC - Enum constant in enum class jebl.evolution.trees.TreeBuilderFactory.ConsensusMethod
MultipleAligner - Interface in jebl.evolution.align
MultivariateFunction - Interface in jebl.math
  interface for a function of several variables
MultivariateMinimum - Class in jebl.math
  abstract base class for minimisation of a multivariate function
MultivariateMinimum() - Constructor for class jebl.math.MultivariateMinimum
MultivariateMinimum.Factory - Interface in jebl.math
  A factory interface for MultivariateMinimums (because they aren't statefree)
MutableRootedTree - Class in jebl.evolution.trees
  A simple rooted tree providing some ability to manipulate the tree.
MutableRootedTree(RootedTree) - Constructor for class jebl.evolution.trees.MutableRootedTree
  Construct a rooted tree from an immutable rooted tree.
MutableRootedTree(Tree, Node) - Constructor for class jebl.evolution.trees.MutableRootedTree
  Construct a rooted tree from unrooted.
MYCOPLASMA - Static variable in class jebl.evolution.sequences.GeneticCode

## N

N_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
N_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
NAME - Static variable in class jebl.evolution.sequences.AminoAcids
NAME - Static variable in class jebl.evolution.sequences.Codons
NAME - Static variable in class jebl.evolution.sequences.Nucleotides
NeedlemanWunsch - Class in jebl.evolution.align
NeedlemanWunsch(Scores, float) - Constructor for class jebl.evolution.align.NeedlemanWunsch
NeedlemanWunschAffine - Class in jebl.evolution.align
NeedlemanWunschAffine(Scores, float, float) - Constructor for class jebl.evolution.align.NeedlemanWunschAffine
NeedlemanWunschLinearSpace - Class in jebl.evolution.align
NeedlemanWunschLinearSpace(Scores, float) - Constructor for class jebl.evolution.align.NeedlemanWunschLinearSpace
NeedlemanWunschLinearSpaceAffine - Class in jebl.evolution.align
NeedlemanWunschLinearSpaceAffine(Scores, float, float) - Constructor for class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
NeedlemanWunschLinearSpaceAffine(Scores, float, float, boolean) - Constructor for class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
NeedlemanWunschLinearSpaceAffine(Scores, float, float, boolean, boolean) - Constructor for class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
NEIGHBOR_JOINING - Enum constant in enum class jebl.evolution.trees.TreeBuilderFactory.Method
NeighborJoiningTreeBuilder - Class in jebl.evolution.trees
  Constructs an unrooted tree by neighbor-joining using pairwise distances.
NeighborJoiningTreeBuilder(DistanceMatrix) - Constructor for class jebl.evolution.trees.NeighborJoiningTreeBuilder
  construct NJ tree
NewickExporter - Class in jebl.evolution.io
NewickExporter(Writer) - Constructor for class jebl.evolution.io.NewickExporter
NewickImporter - Class in jebl.evolution.io
NewickImporter(Reader, boolean) - Constructor for class jebl.evolution.io.NewickImporter
  Constructor
newMinimum(double, double[], MultivariateFunction) - Method in interface jebl.math.MinimiserMonitor
  Inform monitor of a new minimum, along with the current arguments.
newTraceBack(String, String) - Method in interface jebl.evolution.align.TracebackPlotter
next() - Method in class jebl.evolution.io.ImportHelper
next(Traceback) - Method in class jebl.evolution.align.Align
  Get the next state in the traceback
next(Traceback) - Method in class jebl.evolution.align.NeedlemanWunschAffine
  Get the next state in the traceback
next(Traceback) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
  Get the next state in the traceback
next(Traceback) - Method in class jebl.evolution.align.OldNeedlemanWunschAffine
  Get the next state in the traceback
next(Traceback) - Method in class jebl.evolution.align.SmithWatermanLinearSpaceAffine
  Get the next state in the traceback
next(Traceback) - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
  Get the next state in the traceback
next(Traceback) - Method in class jebl.evolution.align.NeedlemanWunsch
  Get the next state in the traceback
next(Traceback) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpace
  Get the next state in the traceback
next(Traceback) - Method in class jebl.evolution.align.OverlapAlign
  Get the next state in the traceback
next(Traceback) - Method in class jebl.evolution.align.SmithWaterman
  Get the next state in the traceback
next(Traceback) - Method in class jebl.evolution.align.SmithWatermanLinearSpace
  Get the next state in the traceback
next(Traceback) - Method in class jebl.evolution.align.MaximalSegmentPair
nextBoolean() - Static method in class jebl.math.Random
  Access a default instance of this class, access is synchronized
nextByte() - Static method in class jebl.math.Random
  Access a default instance of this class, access is synchronized
nextBytes(byte[]) - Static method in class jebl.math.Random
  Access a default instance of this class, access is synchronized
nextChar() - Static method in class jebl.math.Random
  Access a default instance of this class, access is synchronized
nextCharacter() - Method in class jebl.evolution.io.ImportHelper
nextDouble() - Static method in class jebl.math.Random
  Access a default instance of this class, access is synchronized
nextFloat() - Static method in class jebl.math.Random
  Access a default instance of this class, access is synchronized
nextGaussian() - Static method in class jebl.math.Random
  Access a default instance of this class, access is synchronized
nextInt() - Static method in class jebl.math.Random
  Access a default instance of this class, access is synchronized
nextInt(int) - Static method in class jebl.math.Random
  Access a default instance of this class, access is synchronized
nextLong() - Static method in class jebl.math.Random
  Access a default instance of this class, access is synchronized
nextOnBit(int) - Method in class jebl.util.FixedBitSet
  Iteration helper.
nextShort() - Static method in class jebl.math.Random
  Access a default instance of this class, access is synchronized
NexusExporter - Class in jebl.evolution.io
  Export sequences and trees to Nexus format.
NexusExporter(Writer) - Constructor for class jebl.evolution.io.NexusExporter
NexusExporter(Writer, boolean) - Constructor for class jebl.evolution.io.NexusExporter
NexusExporter(Writer, boolean, boolean) - Constructor for class jebl.evolution.io.NexusExporter
NexusImporter - Class in jebl.evolution.io
  Class for importing NEXUS file format.
NexusImporter(Reader) - Constructor for class jebl.evolution.io.NexusImporter
NexusImporter(Reader, boolean) - Constructor for class jebl.evolution.io.NexusImporter
  Deprecated.
  Use NexusImporter(Reader reader, boolean compactTrees, long expectedInputLength)
NexusImporter(Reader, boolean, long) - Constructor for class jebl.evolution.io.NexusImporter
NexusImporter(Reader, long) - Constructor for class jebl.evolution.io.NexusImporter
NexusImporter.MissingBlockException - Exception Class in jebl.evolution.io
  Thrown when a block is missing that is required for importing a particular type of data from the nexus input.
NexusImporter.NexusBlock - Enum Class in jebl.evolution.io
  Represents the block types used in the nexus format
Node - Interface in jebl.evolution.graphs
  Represents a node in a graph or tree.
NoEdgeException() - Constructor for exception class jebl.evolution.graphs.Graph.NoEdgeException
NonOverlapMultipleLocalAffine - Class in jebl.evolution.align
  Performs recursive local alignments.
NonOverlapMultipleLocalAffine(Scores, float, float, int) - Constructor for class jebl.evolution.align.NonOverlapMultipleLocalAffine
NORM1 - Enum constant in enum class jebl.evolution.trees.TreeBiPartitionInfo.DistanceNorm
NORM2 - Enum constant in enum class jebl.evolution.trees.TreeBiPartitionInfo.DistanceNorm
NOTHING - Enum constant in enum class jebl.evolution.coalescent.IntervalList.IntervalType
  Denotes an interval at the end of which nothing is observed (i.e.
NotSquareMatrixException() - Constructor for exception class jebl.math.MatrixCalcException.NotSquareMatrixException
NotSquareMatrixException(String) - Constructor for exception class jebl.math.MatrixCalcException.NotSquareMatrixException
NUCLEOTIDE - Static variable in interface jebl.evolution.sequences.SequenceType
NUCLEOTIDE_51_PERCENT_SIMILARITY - Static variable in class jebl.evolution.align.scores.ScoresFactory
NUCLEOTIDE_65_PERCENT_SIMILARITY - Static variable in class jebl.evolution.align.scores.ScoresFactory
NUCLEOTIDE_70_PERCENT_SIMILARITY - Static variable in class jebl.evolution.align.scores.ScoresFactory
NUCLEOTIDE_93_PERCENT_SIMILARITY - Static variable in class jebl.evolution.align.scores.ScoresFactory
Nucleotides - Class in jebl.evolution.sequences
  Uninstantiable utility class with only static methods.
NucleotideScores - Class in jebl.evolution.align.scores
NucleotideScores(float, float) - Constructor for class jebl.evolution.align.scores.NucleotideScores
NucleotideScores(float, float, float) - Constructor for class jebl.evolution.align.scores.NucleotideScores
NucleotideScores(String, float, float) - Constructor for class jebl.evolution.align.scores.NucleotideScores
NucleotideScores(String, float, float, float) - Constructor for class jebl.evolution.align.scores.NucleotideScores
NucleotideScores(String, float, float, float, float, boolean) - Constructor for class jebl.evolution.align.scores.NucleotideScores
NucleotideScores(NucleotideScores) - Constructor for class jebl.evolution.align.scores.NucleotideScores
NucleotideScores(Scores, double) - Constructor for class jebl.evolution.align.scores.NucleotideScores
NucleotideState - Class in jebl.evolution.sequences
NumberFormatter - Class in jebl.util
  An interface for a numerical column in a log.
NumberFormatter(int) - Constructor for class jebl.util.NumberFormatter
NumericalDerivative - Class in jebl.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 jebl.math.NumericalDerivative
numFun - Variable in class jebl.math.MultivariateMinimum
  total number of function evaluations necessary
numFun - Variable in class jebl.math.UnivariateMinimum
  total number of function evaluations neccessary
numFuncStops - Variable in class jebl.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)
numRateBoxes - Variable in class jebl.evolution.trees.CalculateSplitRates
numTimeBoxes - Variable in class jebl.evolution.trees.CalculateSplitRates

## O

O_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
objectChanged() - Method in interface jebl.util.SimpleListener
OldNeedlemanWunschAffine - Class in jebl.evolution.align
OldNeedlemanWunschAffine(Scores, float, float) - Constructor for class jebl.evolution.align.OldNeedlemanWunschAffine
optimize(double, UnivariateFunction, double) - Method in class jebl.math.UnivariateMinimum
  The actual optimization routine (Brent's golden section method)
optimize(double, UnivariateFunction, double, double, double) - Method in class jebl.math.UnivariateMinimum
  The actual optimization routine (Brent's golden section method)
optimize(MultivariateFunction, double[], double, double) - Method in class jebl.math.MultivariateMinimum
  The actual optimization routine (needs to be implemented in a subclass of MultivariateMinimum).
optimize(MultivariateFunction, double[], double, double) - Method in class jebl.math.OrthogonalSearch
optimize(MultivariateFunction, double[], double, double, MinimiserMonitor) - Method in class jebl.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 jebl.math.OrthogonalSearch
optimize(UnivariateFunction, double) - Method in class jebl.math.UnivariateMinimum
  The actual optimization routine (Brent's golden section method)
optimize(UnivariateFunction, double, double, double) - Method in class jebl.math.UnivariateMinimum
  The actual optimization routine (Brent's golden section method)
OrderEnumerator - Interface in jebl.math
  A means for describing odering information, and Utilities for creating such Orderings
OrderEnumerator.OEFactory - Interface in jebl.math
OrderEnumerator.Utils - Class in jebl.math
OrthogonalHints - Interface in jebl.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 jebl.math
OrthogonalLineFunction - Class in jebl.math
  converts a multivariate function into a univariate function by keeping all but one argument constant
OrthogonalLineFunction(MultivariateFunction) - Constructor for class jebl.math.OrthogonalLineFunction
  construct univariate function from multivariate function
OrthogonalLineFunction(MultivariateFunction, int, double[]) - Constructor for class jebl.math.OrthogonalLineFunction
  construct univariate function from multivariate function
OrthogonalSearch - Class in jebl.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 jebl.math.OrthogonalSearch
  Initialization
OrthogonalSearch(boolean) - Constructor for class jebl.math.OrthogonalSearch
  Initialization
OrthogonalSearch(OrderEnumerator.OEFactory) - Constructor for class jebl.math.OrthogonalSearch
  Initialization
Output - Class in jebl.evolution.align
Output() - Constructor for class jebl.evolution.align.Output
OverlapAlign - Class in jebl.evolution.align
OverlapAlign(Scores, float) - Constructor for class jebl.evolution.align.OverlapAlign

## P

P_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
PairwiseAligner - Interface in jebl.evolution.align
PairwiseAligner.Result - Class in jebl.evolution.align
PAM_100 - Static variable in class jebl.evolution.align.scores.ScoresFactory
PAM_110 - Static variable in class jebl.evolution.align.scores.ScoresFactory
PAM_120 - Static variable in class jebl.evolution.align.scores.ScoresFactory
PAM_130 - Static variable in class jebl.evolution.align.scores.ScoresFactory
PAM_140 - Static variable in class jebl.evolution.align.scores.ScoresFactory
PAM_150 - Static variable in class jebl.evolution.align.scores.ScoresFactory
PAM_160 - Static variable in class jebl.evolution.align.scores.ScoresFactory
PAM_170 - Static variable in class jebl.evolution.align.scores.ScoresFactory
PAM_180 - Static variable in class jebl.evolution.align.scores.ScoresFactory
PAM_190 - Static variable in class jebl.evolution.align.scores.ScoresFactory
PAM_200 - Static variable in class jebl.evolution.align.scores.ScoresFactory
PAM_210 - Static variable in class jebl.evolution.align.scores.ScoresFactory
PAM_220 - Static variable in class jebl.evolution.align.scores.ScoresFactory
PAM_230 - Static variable in class jebl.evolution.align.scores.ScoresFactory
PAM_240 - Static variable in class jebl.evolution.align.scores.ScoresFactory
PAM_250 - Static variable in class jebl.evolution.align.scores.ScoresFactory
Pam100 - Class in jebl.evolution.align.scores
Pam100() - Constructor for class jebl.evolution.align.scores.Pam100
Pam110 - Class in jebl.evolution.align.scores
Pam110() - Constructor for class jebl.evolution.align.scores.Pam110
Pam120 - Class in jebl.evolution.align.scores
Pam120() - Constructor for class jebl.evolution.align.scores.Pam120
Pam130 - Class in jebl.evolution.align.scores
Pam130() - Constructor for class jebl.evolution.align.scores.Pam130
Pam140 - Class in jebl.evolution.align.scores
Pam140() - Constructor for class jebl.evolution.align.scores.Pam140
Pam150 - Class in jebl.evolution.align.scores
Pam150() - Constructor for class jebl.evolution.align.scores.Pam150
Pam160 - Class in jebl.evolution.align.scores
Pam160() - Constructor for class jebl.evolution.align.scores.Pam160
Pam170 - Class in jebl.evolution.align.scores
Pam170() - Constructor for class jebl.evolution.align.scores.Pam170
Pam180 - Class in jebl.evolution.align.scores
Pam180() - Constructor for class jebl.evolution.align.scores.Pam180
Pam190 - Class in jebl.evolution.align.scores
Pam190() - Constructor for class jebl.evolution.align.scores.Pam190
Pam200 - Class in jebl.evolution.align.scores
Pam200() - Constructor for class jebl.evolution.align.scores.Pam200
Pam210 - Class in jebl.evolution.align.scores
Pam210() - Constructor for class jebl.evolution.align.scores.Pam210
Pam220 - Class in jebl.evolution.align.scores
Pam220() - Constructor for class jebl.evolution.align.scores.Pam220
Pam230 - Class in jebl.evolution.align.scores
Pam230() - Constructor for class jebl.evolution.align.scores.Pam230
Pam240 - Class in jebl.evolution.align.scores
Pam240() - Constructor for class jebl.evolution.align.scores.Pam240
Pam250 - Class in jebl.evolution.align.scores
Pam250() - Constructor for class jebl.evolution.align.scores.Pam250
parseCharactersBlock(List<Taxon>) - Method in class jebl.evolution.io.NexusImporter
  Parse the next 'CHARACTERS' block encountered in the input.
parseDataBlock(List<Taxon>) - Method in class jebl.evolution.io.NexusImporter
  Parse the next 'DATA' block encountered in the input.
parseDistancesBlock(List<Taxon>) - Method in class jebl.evolution.io.NexusImporter
  Parse the next 'DISTANCES' block encountered in the input.
parseTaxaBlock() - Method in class jebl.evolution.io.NexusImporter
  Parse the next 'TAXA' block encountered in the input.
parseTreesBlock(List<Taxon>) - Method in class jebl.evolution.io.NexusImporter
  Parse the next 'TREES' block encountered in the input.
ParsimonyCriterion - Interface in jebl.evolution.parsimony
Pattern - Interface in jebl.evolution.alignments
  An interface representing a list of states for a list of taxa (e.g.
Patterns - Interface in jebl.evolution.alignments
  An interface representing a set of site patterns.
PHYLIPExporter - Class in jebl.evolution.io
  Export alignment to Phylip format.
PHYLIPExporter(Writer) - Constructor for class jebl.evolution.io.PHYLIPExporter
PhylipSequentialImporter - Class in jebl.evolution.io
  Class for importing PHYLIP sequential file format
PhylipSequentialImporter(Reader, SequenceType, int) - Constructor for class jebl.evolution.io.PhylipSequentialImporter
  Constructor
PositiveDefiniteException() - Constructor for exception class jebl.math.MatrixCalcException.PositiveDefiniteException
PositiveDefiniteException(String) - Constructor for exception class jebl.math.MatrixCalcException.PositiveDefiniteException
possiblyEqual(State) - Method in class jebl.evolution.sequences.NucleotideState
possiblyEqual(State) - Method in class jebl.evolution.sequences.State
prepareAlignment(String, String) - Method in class jebl.evolution.align.Align
  Initialises the matrices for the alignment.
prepareAlignment(String, String) - Method in class jebl.evolution.align.OldNeedlemanWunschAffine
prepareAlignment(String, String) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpace
prepareAlignment(String, String) - Method in class jebl.evolution.align.SmithWatermanLinearSpace
prepareAlignment(String, String) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
prepareAlignment(String, String) - Method in class jebl.evolution.align.SmithWatermanLinearSpaceAffine
prepareAlignment(String, String) - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
prepareAlignment(String, String) - Method in class jebl.evolution.align.MaximalSegmentPair
prepareAlignment(String, String) - Method in class jebl.evolution.align.NeedlemanWunsch
prepareAlignment(String, String) - Method in class jebl.evolution.align.OverlapAlign
prepareAlignment(String, String) - Method in class jebl.evolution.align.SmithWaterman
prepareAlignment(String, String) - Method in class jebl.evolution.align.NeedlemanWunschAffine
print() - Method in class jebl.evolution.align.ProfileCharacter
print(String) - Method in class jebl.evolution.align.Output
print(String) - Method in class jebl.evolution.align.SystemOut
printf(Output) - Method in class jebl.evolution.align.Align
  Print the matrix (matrices) used to compute the alignment
printf(Output) - Method in class jebl.evolution.align.NeedlemanWunschAffine
  Print matrix used to calculate this alignment.
printf(Output) - Method in class jebl.evolution.align.OldNeedlemanWunschAffine
  Print matrix used to calculate this alignment.
printf(Output) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpace
  Print matrix used to calculate this alignment.
printf(Output) - Method in class jebl.evolution.align.SmithWatermanLinearSpace
  Print matrix used to calculate this alignment.
printf(Output) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
  Print matrix used to calculate this alignment.
printf(Output) - Method in class jebl.evolution.align.SmithWatermanLinearSpaceAffine
  Print matrix used to calculate this alignment.
printf(Output) - Method in class jebl.evolution.align.MaximalSegmentPair
  Print matrix used to calculate this alignment.
printf(Output) - Method in class jebl.evolution.align.NeedlemanWunsch
  Print matrix used to calculate this alignment.
printf(Output) - Method in class jebl.evolution.align.OverlapAlign
  Print matrix used to calculate this alignment.
printf(Output) - Method in class jebl.evolution.align.SmithWaterman
  Print matrix used to calculate this alignment.
printf(Output) - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
  Print matrix used to calculate this alignment.
println() - Method in class jebl.evolution.align.Output
println() - Method in class jebl.evolution.align.SystemOut
println(String) - Method in class jebl.evolution.align.Output
println(String) - Method in class jebl.evolution.align.SystemOut
ProfileCharacter - Class in jebl.evolution.align
ProfileCharacter(int) - Constructor for class jebl.evolution.align.ProfileCharacter
ProgressListener - Class in jebl.util
ProgressListener() - Constructor for class jebl.util.ProgressListener
ProgressListener.Wrapper - Class in jebl.util
  A decorator progress listener which delegates all method calls to an internal progress listener.
PROPORTIONAL - Enum constant in enum class jebl.evolution.trees.TransformedRootedTree.Transform

## Q

Q_STATE - Static variable in class jebl.evolution.sequences.AminoAcids

## R

R_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
R_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
Random - Class in jebl.math
  Random number generation.
randomChoice(double[]) - Static method in class jebl.math.Random
RATE - Variable in class jebl.evolution.trees.CalculateSplitRates
RateMatrix - Interface in jebl.evolution.substmodel
  abstract base class for all rate matrices
read() - Method in class jebl.evolution.io.ImportHelper
  All read attempts pass through this function.
readCharacter() - Method in class jebl.evolution.io.ImportHelper
readDouble() - Method in class jebl.evolution.io.ImportHelper
  Attempts to read and parse a double delimited by whitespace.
readDouble(String) - Method in class jebl.evolution.io.ImportHelper
  Attempts to read and parse a double delimited by whitespace or by any character in delimiters.
readInteger() - Method in class jebl.evolution.io.ImportHelper
  Attempts to read and parse an integer delimited by whitespace.
readInteger(String) - Method in class jebl.evolution.io.ImportHelper
  Attempts to read and parse an integer delimited by whitespace or by any character in delimiters.
readLine() - Method in class jebl.evolution.io.ImportHelper
  Reads a line, skipping over any comments.
readSequence(String) - Static method in class jebl.evolution.sequences.SequenceTester
readSequence(StringBuilder, SequenceType, String, int, String, String, String, String) - Method in class jebl.evolution.io.ImportHelper
readSequence(StringBuilder, SequenceType, String, int, String, String, String, String, boolean) - Method in class jebl.evolution.io.ImportHelper
readSequence(StringBuilder, SequenceType, String, int, String, String, String, String, ProgressListener) - Method in class jebl.evolution.io.ImportHelper
readSequence(StringBuilder, SequenceType, String, int, String, String, String, String, ProgressListener, boolean) - Method in class jebl.evolution.io.ImportHelper
  Reads sequence, skipping over any comments and filtering using sequenceType.
readSequenceLine(StringBuffer, SequenceType, String, String, String, String, String) - Method in class jebl.evolution.io.ImportHelper
  Reads a line of sequence, skipping over any comments and filtering using sequenceType.
readToken() - Method in class jebl.evolution.io.ImportHelper
  Reads a token stopping when any whitespace or a comment is found.
readToken(String) - Method in class jebl.evolution.io.ImportHelper
  Reads a token stopping when any whitespace, a comment or when any character in delimiters is found.
rebuild() - Method in class jebl.evolution.substmodel.AbstractRateMatrix
recurseAlignment(String, int) - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
refineNode(Node, int[]) - Method in class jebl.evolution.trees.MutableRootedTree
removeAttribute(String) - Method in class jebl.evolution.alignments.ConsensusSequence
removeAttribute(String) - Method in class jebl.evolution.sequences.BasicSequence
removeAttribute(String) - Method in class jebl.evolution.sequences.CanonicalSequence
removeAttribute(String) - Method in class jebl.evolution.sequences.CodonSequence
removeAttribute(String) - Method in class jebl.evolution.sequences.FilteredSequence
removeAttribute(String) - Method in class jebl.evolution.taxa.Taxon
removeAttribute(String) - Method in class jebl.evolution.trees.CompactRootedTree
removeAttribute(String) - Method in class jebl.evolution.trees.BaseEdge
removeAttribute(String) - Method in class jebl.evolution.trees.BaseNode
removeAttribute(String) - Method in class jebl.evolution.trees.FilteredRootedTree
removeAttribute(String) - Method in class jebl.evolution.trees.MutableRootedTree
removeAttribute(String) - Method in class jebl.evolution.trees.ReRootedTree
removeAttribute(String) - Method in class jebl.evolution.trees.RootedFromUnrooted
removeAttribute(String) - Method in class jebl.evolution.trees.RootedSubtree
removeAttribute(String) - Method in class jebl.evolution.trees.SimpleRootedTree
removeAttribute(String) - Method in class jebl.evolution.trees.SimpleTree
removeAttribute(String) - Method in interface jebl.util.Attributable
removeAttribute(String) - Method in class jebl.util.AttributableHelper
removeChild(Node, Node) - Method in class jebl.evolution.trees.MutableRootedTree
  Remove a child node.
removeFeedbackAction(String) - Method in class jebl.util.CompositeProgressListener
removeFeedbackAction(String) - Method in class jebl.util.ProgressListener
  Removes a feedback action previously added using `ProgressListener.addFeedbackAction(String, jebl.util.SimpleListener)`.
removeFeedbackAction(String) - Method in class jebl.util.ProgressListener.Wrapper
removeInternalNode(Node) - Method in class jebl.evolution.trees.MutableRootedTree
  Remove internal node.
removeProfileCharacter(ProfileCharacter) - Method in class jebl.evolution.align.ProfileCharacter
removeProgressListener(ProgressListener) - Method in interface jebl.evolution.aligners.Aligner
removeProgressListener(ProgressListener) - Method in class jebl.evolution.trees.ClusteringTreeBuilder
removeProgressListener(ProgressListener) - Method in class jebl.evolution.trees.ConsensusTreeBuilder
  Stops a ProgressListener from receiving progress.
removeProgressListener(ProgressListener) - Method in interface jebl.evolution.trees.TreeBuilder
renameTaxa(Taxon, Taxon) - Method in class jebl.evolution.trees.CompactRootedTree
renameTaxa(Taxon, Taxon) - Method in class jebl.evolution.trees.FilteredRootedTree
renameTaxa(Taxon, Taxon) - Method in class jebl.evolution.trees.MutableRootedTree
renameTaxa(Taxon, Taxon) - Method in class jebl.evolution.trees.ReRootedTree
renameTaxa(Taxon, Taxon) - Method in class jebl.evolution.trees.RootedFromUnrooted
renameTaxa(Taxon, Taxon) - Method in class jebl.evolution.trees.RootedSubtree
renameTaxa(Taxon, Taxon) - Method in class jebl.evolution.trees.SimpleRootedTree
renameTaxa(Taxon, Taxon) - Method in class jebl.evolution.trees.SimpleTree
renameTaxa(Taxon, Taxon) - Method in interface jebl.evolution.trees.Tree
replaceStates(Sequence, List<State>, State) - Static method in interface jebl.evolution.sequences.Sequence
  Searchers and replaces a sequence of any states given
replaceStates(State[], List<State>, State) - Static method in class jebl.evolution.sequences.Utils
  Searchers and replaces a sequence of any states given
ReRootedTree - Class in jebl.evolution.trees
  A rooted tree concrete class that wraps another tree and provides a differently rooted view of that tree.
ReRootedTree(RootedTree, Node, Node, double) - Constructor for class jebl.evolution.trees.ReRootedTree
  Make a copy of the given unrooted tree
reRootWithOutgroup(Node, Set<String>) - Method in class jebl.evolution.trees.MutableRootedTree
  Re-root tree using an outgroup.
ResampledAlignment - Class in jebl.evolution.alignments
  Date: 17/01/2006 Time: 08:08:44
ResampledAlignment() - Constructor for class jebl.evolution.alignments.ResampledAlignment
reset() - Method in interface jebl.math.OrderEnumerator
  Reset back to starting state, may have a differnet number of values, and a different ordering after a reset!
resetEvents() - Method in class jebl.evolution.coalescent.Intervals
reverse(State[]) - Static method in class jebl.evolution.sequences.Utils
reverseComplement(String) - Static method in class jebl.evolution.sequences.Utils
reverseComplement(NucleotideState[]) - Static method in class jebl.evolution.sequences.Utils
reverseComplementWithGaps(String) - Static method in class jebl.evolution.sequences.Utils
reverseMatrix(double[][]) - Static method in class jebl.math.MatrixCalc
  reverse a matrix
reverseVector(double[]) - Static method in class jebl.math.MatrixCalc
  reverse a vector
rightNb(RootedTree, Node) - Static method in class jebl.evolution.trees.Utils
  Right Neighbour of a tip (taxon).
RobinsonsFouldMetric - Class in jebl.evolution.treemetrics
RobinsonsFouldMetric() - Constructor for class jebl.evolution.treemetrics.RobinsonsFouldMetric
RobinsonsFouldMetric(List<Taxon>) - Constructor for class jebl.evolution.treemetrics.RobinsonsFouldMetric
RootedFromUnrooted - Class in jebl.evolution.trees
  Root an unrooted tree.
RootedFromUnrooted(Tree, Node, boolean) - Constructor for class jebl.evolution.trees.RootedFromUnrooted
  Root tree at some internal node.
RootedFromUnrooted(Tree, Node, Node, double) - Constructor for class jebl.evolution.trees.RootedFromUnrooted
  Root source by creating a new internal node whose children are (the adjacent) left and right.
RootedSubtree - Class in jebl.evolution.trees
  A simple, immutable rooted tree implementation that is a subtree of an existing tree subtending a specified set of taxa..
RootedSubtree(RootedTree, Set<Taxon>) - Constructor for class jebl.evolution.trees.RootedSubtree
  Make a copy of the given rooted tree
RootedTree - Interface in jebl.evolution.trees
  A tree with a root (node with maximum height).
RootedTreeMetric - Interface in jebl.evolution.treemetrics
RootedTreeUtils - Class in jebl.evolution.trees
  Static utility functions for rooted trees.
rootTheTree(Tree) - Static method in class jebl.evolution.trees.Utils
  Return a rooted tree from any tree.
rootTreeAtCenter(RootedTree) - Static method in class jebl.evolution.trees.ReRootedTree
  Root any tree by locating the "center" of tree and adding a new root node at that point
rootTreeAtCenter(Tree) - Static method in class jebl.evolution.trees.Utils
  Root any tree by locating the "center" of tree and adding a new root node at that point

## S

S_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
S_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
safeNodeHeight(RootedTree, Node) - Static method in class jebl.evolution.trees.Utils
same(double, double) - Static method in class jebl.math.MachineAccuracy
SAMPLE - Enum constant in enum class jebl.evolution.coalescent.IntervalList.IntervalType
  Denotes an interval at the end of which a new sample addition is observed (i.e.
scale(double) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
score - Variable in class jebl.evolution.align.PairwiseAligner.Result
score - Variable in class jebl.evolution.align.scores.Scores
score(ProfileCharacter, ProfileCharacter, Scores) - Static method in class jebl.evolution.align.ProfileCharacter
ScoreMatrix - Interface in jebl.evolution.align.scores
Scores - Class in jebl.evolution.align.scores
  Base class for all score matrices in the package.
Scores() - Constructor for class jebl.evolution.align.scores.Scores
scoreSelf(ProfileCharacter, Scores) - Static method in class jebl.evolution.align.ProfileCharacter
ScoresFactory - Class in jebl.evolution.align.scores
ScoresFactory() - Constructor for class jebl.evolution.align.scores.ScoresFactory
second - Variable in class jebl.util.HashPair
secondDerivative(UnivariateFunction, double) - Static method in class jebl.math.NumericalDerivative
  determine second derivative
selectArgument(int) - Method in class jebl.math.OrthogonalLineFunction
  use only the specified argument in the constructed univariate function and keep all others constant
selectionChanged(TreeSelectionChangeEvent) - Method in class jebl.evolution.trees.TreeChangeListener
  The selected nodes in the tree have changed.
Sequence - Interface in jebl.evolution.sequences
  A biomolecular sequence.
SequenceAlignmentsDistanceMatrix - Class in jebl.evolution.align
  Builds a distance matrix by performing a series of pairwise alignments between the specified sequences (unlike the methods in jebl.evolution.distances, which extract the pairwise distances from a multiple sequence alignment).
SequenceAlignmentsDistanceMatrix(List<Sequence>, PairwiseAligner, ProgressListener) - Constructor for class jebl.evolution.align.SequenceAlignmentsDistanceMatrix
SequenceAlignmentsDistanceMatrix(List<Sequence>, PairwiseAligner, ProgressListener, TreeBuilderFactory.DistanceModel) - Constructor for class jebl.evolution.align.SequenceAlignmentsDistanceMatrix
SequenceExporter - Interface in jebl.evolution.io
SequenceImporter - Interface in jebl.evolution.io
  Interface for importers that do sequences
Sequences - Interface in jebl.evolution.sequences
  A set of sequence objects.
SequenceShuffler - Class in jebl.evolution.align
  Shuffles a sequence and aligns it again multiple times to give mean and variance of alignments on random sequences.
SequenceShuffler() - Constructor for class jebl.evolution.align.SequenceShuffler
SequenceStateException - Exception Class in jebl.evolution.sequences
SequenceStateException(String) - Constructor for exception class jebl.evolution.sequences.SequenceStateException
SequenceTester - Class in jebl.evolution.sequences
SequenceTester() - Constructor for class jebl.evolution.sequences.SequenceTester
SequenceType - Interface in jebl.evolution.sequences
  Interface for sequences data types.
SequenceType.Utils - Class in jebl.evolution.sequences
set(int) - Method in class jebl.util.FixedBitSet
setAllArguments(double[]) - Method in class jebl.math.OrthogonalLineFunction
  set (change) values of all arguments (start values)
setArgument(double) - Method in class jebl.math.OrthogonalLineFunction
  set (change) value of a single argument (the one currently active)
setArgument(int, double) - Method in class jebl.evolution.coalescent.ConstantPopulation
setArgument(int, double) - Method in class jebl.evolution.coalescent.ConstExponential
setArgument(int, double) - Method in class jebl.evolution.coalescent.ConstLogistic
setArgument(int, double) - Method in interface jebl.evolution.coalescent.DemographicFunction
  Sets the value of the nth argument of this function.
setArgument(int, double) - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
  Sets the value of the nth argument of this function.
setArgument(int, double) - Method in class jebl.evolution.coalescent.Expansion
setArgument(int, double) - Method in class jebl.evolution.coalescent.ExponentialGrowth
setArgument(int, double) - Method in class jebl.evolution.coalescent.ExponentialLogistic
setAttribute(String, Object) - Method in class jebl.evolution.alignments.ConsensusSequence
setAttribute(String, Object) - Method in class jebl.evolution.sequences.BasicSequence
setAttribute(String, Object) - Method in class jebl.evolution.sequences.CanonicalSequence
setAttribute(String, Object) - Method in class jebl.evolution.sequences.CodonSequence
setAttribute(String, Object) - Method in class jebl.evolution.sequences.FilteredSequence
setAttribute(String, Object) - Method in class jebl.evolution.taxa.Taxon
setAttribute(String, Object) - Method in class jebl.evolution.trees.CompactRootedTree
setAttribute(String, Object) - Method in class jebl.evolution.trees.BaseEdge
setAttribute(String, Object) - Method in class jebl.evolution.trees.BaseNode
setAttribute(String, Object) - Method in class jebl.evolution.trees.FilteredRootedTree
setAttribute(String, Object) - Method in class jebl.evolution.trees.MutableRootedTree
setAttribute(String, Object) - Method in class jebl.evolution.trees.ReRootedTree
setAttribute(String, Object) - Method in class jebl.evolution.trees.RootedFromUnrooted
setAttribute(String, Object) - Method in class jebl.evolution.trees.RootedSubtree
setAttribute(String, Object) - Method in class jebl.evolution.trees.SimpleRootedTree
setAttribute(String, Object) - Method in class jebl.evolution.trees.SimpleTree
setAttribute(String, Object) - Method in interface jebl.util.Attributable
  Sets an named attribute for this object.
setAttribute(String, Object) - Method in class jebl.util.AttributableHelper
setCataclysmTime(double) - Method in class jebl.evolution.coalescent.CataclysmicDemographic
setCommentDelimiters(char) - Method in class jebl.evolution.io.ImportHelper
setCommentDelimiters(char, char) - Method in class jebl.evolution.io.ImportHelper
setCommentDelimiters(char, char, char) - Method in class jebl.evolution.io.ImportHelper
setCommentDelimiters(char, char, char, char, char) - Method in class jebl.evolution.io.ImportHelper
setCommentWriter(Writer) - Method in class jebl.evolution.io.ImportHelper
setComplete() - Method in class jebl.util.CompositeProgressListener
setConceptuallyUnrooted(boolean) - Method in class jebl.evolution.trees.CompactRootedTree
setConceptuallyUnrooted(boolean) - Method in class jebl.evolution.trees.MutableRootedTree
setConceptuallyUnrooted(boolean) - Method in class jebl.evolution.trees.RootedSubtree
setConceptuallyUnrooted(boolean) - Method in class jebl.evolution.trees.SimpleRootedTree
setDebug(boolean) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
setDecimalPlaces(int) - Method in class jebl.util.NumberFormatter
  Set the number of decimal places to display when formatted.
setDeclineRate(double) - Method in class jebl.evolution.coalescent.CataclysmicDemographic
  sets the decline rate.
setDesc(String) - Method in interface jebl.evolution.characters.Character
  set the description of the character
setDesc(String) - Method in class jebl.evolution.characters.ContinuousCharacter
setDesc(String) - Method in class jebl.evolution.characters.DiscreteCharacter
setDistance(double) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
  Sets the distance (such as time/branch length) used when calculating the probabilities.
setDistance(double) - Method in class jebl.evolution.substmodel.MatrixExponential
  compute transition probabilities for a expected distance using the prespecified rate matrix
setDistance(double) - Method in interface jebl.evolution.substmodel.RateMatrix
  Sets the distance (such as time/branch length) used when calculating the probabilities.
setDistanceTranspose(double) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
  Sets the distance (such as time/branch length) used when calculating the probabilities.
setDistanceTranspose(double) - Method in class jebl.evolution.substmodel.MatrixExponential
  compute transition probabilities for a expected distance using the prespecified rate matrix.
setDoublingTime(double) - Method in class jebl.evolution.coalescent.ExponentialGrowth
  An alternative parameterization of this model.
setEdgeLength(Edge, double) - Method in class jebl.evolution.trees.SimpleTree
  Change length of an existing edge.
setEdgeLength(Node, Node, double) - Method in class jebl.evolution.trees.SimpleTree
  Set edge distance between two adjacent nodes.
setExpectedInputLength(long) - Method in class jebl.evolution.io.ImportHelper
setGapExtend(float) - Method in class jebl.evolution.align.NeedlemanWunschAffine
setGapExtend(float) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
setGapExtend(float) - Method in class jebl.evolution.align.OldNeedlemanWunschAffine
setGapExtend(float) - Method in class jebl.evolution.align.SmithWatermanLinearSpaceAffine
setGapExtend(float) - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
setGapOpen(float) - Method in class jebl.evolution.align.Align
setGrowthRate(double) - Method in class jebl.evolution.coalescent.ExponentialGrowth
  sets growth rate.
setHeight(Node, double) - Method in class jebl.evolution.trees.MutableRootedTree
setHeight(Node, double) - Method in class jebl.evolution.trees.ReRootedTree
setHeight(Node, double) - Method in class jebl.evolution.trees.RootedSubtree
setHeight(Node, double) - Method in class jebl.evolution.trees.SimpleRootedTree
setIgnoreNonMinimalUnivariateMinimisations(boolean) - Method in class jebl.math.OrthogonalSearch
  Should we ignore new minisations that are not as minimal as the current one?
setIllegalCharacterPolicy(IllegalCharacterPolicy) - Method in class jebl.evolution.io.FastaImporter
setImage(Image) - Method in class jebl.util.ProgressListener
  Set an image associated with the current progress.
setInclusion(FixedBitSet) - Method in class jebl.util.FixedBitSet
setIndeterminateProgress() - Method in class jebl.util.ProgressListener
  Sets indefinite progress (i.e.
setIsOrdered(boolean) - Method in class jebl.evolution.characters.DiscreteCharacter
setLength(Node, double) - Method in class jebl.evolution.trees.MutableRootedTree
setLength(Node, double) - Method in class jebl.evolution.trees.ReRootedTree
setLength(Node, double) - Method in class jebl.evolution.trees.RootedSubtree
setLength(Node, double) - Method in class jebl.evolution.trees.SimpleRootedTree
setMatrix(RateMatrix) - Method in class jebl.evolution.substmodel.MatrixExponential
  update rate matrix used in present module
setMessage(String) - Method in class jebl.util.ProgressListener
  Set visible user message.
setMinus(FixedBitSet) - Method in class jebl.util.FixedBitSet
setN0(double) - Method in class jebl.evolution.coalescent.ConstantPopulation
  sets initial population size.
setN1(double) - Method in class jebl.evolution.coalescent.ConstExponential
setN1(double) - Method in class jebl.evolution.coalescent.ConstLogistic
setN1(double) - Method in class jebl.evolution.coalescent.Expansion
setName(String) - Method in interface jebl.evolution.characters.Character
  set the name of the character
setName(String) - Method in class jebl.evolution.characters.ContinuousCharacter
setName(String) - Method in class jebl.evolution.characters.DiscreteCharacter
setNumOfStates(int) - Method in class jebl.evolution.characters.DiscreteCharacter
setParametersNoScale(double[]) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
setProgress(double) - Method in class jebl.util.ProgressListener
setProgress(int, int) - Method in class jebl.util.ProgressListener
  Same as calling `setProgress(((double)currentStep)/numberOfSteps)`
setProgress(long, long) - Method in class jebl.util.ProgressListener
  Same as calling `setProgress(((double)currentStep)/numberOfSteps)`
setProgressMonitor(ProgressMonitor) - Method in class jebl.evolution.align.SequenceShuffler
setProportion(double) - Method in class jebl.evolution.coalescent.ConstExponential
setProportion(double) - Method in class jebl.evolution.coalescent.Expansion
setR2(double) - Method in class jebl.evolution.coalescent.ExponentialLogistic
setRoot(Node) - Method in class jebl.evolution.trees.MutableRootedTree
  Set the root node.
setScores(Scores) - Method in class jebl.evolution.align.Align
setSeed(long) - Static method in class jebl.math.Random
  Access a default instance of this class, access is synchronized
setShape(double) - Method in class jebl.evolution.coalescent.LogisticGrowth
setSignificantFigures(int) - Method in class jebl.util.NumberFormatter
  Set the number of significant figures to display when formatted.
setSpikeFactor(double) - Method in class jebl.evolution.coalescent.CataclysmicDemographic
  An alternative parameterization of this model.
setStateDesc(Map<Integer, String>) - Method in class jebl.evolution.characters.DiscreteCharacter
setThreshold(int) - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
setTime(double) - Method in class jebl.evolution.coalescent.ExponentialLogistic
setTime50(double) - Method in class jebl.evolution.coalescent.LogisticGrowth
  An alternative parameterization of this model.
setTitle(String) - Method in class jebl.util.CompositeProgressListener
setTitle(String) - Method in class jebl.util.ProgressListener
  Sets a title associated with whatever is being done.
setTitle(String) - Method in class jebl.util.ProgressListener.Wrapper
setUseCurrentInUnivariateMinimisation(boolean) - Method in class jebl.math.OrthogonalSearch
ShortSequenceException() - Constructor for exception class jebl.evolution.io.ImportException.ShortSequenceException
ShortSequenceException(String) - Constructor for exception class jebl.evolution.io.ImportException.ShortSequenceException
shuffle(int[]) - Static method in class jebl.math.Random
  Shuffles an array.
shuffle(int[], int) - Static method in class jebl.math.Random
  Shuffles an array.
shuffle(Align, String, String, int) - Method in class jebl.evolution.align.SequenceShuffler
shuffled(int) - Static method in class jebl.math.Random
  Returns an array of shuffled indices of length l.
SimpleListener - Interface in jebl.util
SimpleRootedTree - Class in jebl.evolution.trees
  A simple, and initially immutable rooted tree implementation.
SimpleRootedTree() - Constructor for class jebl.evolution.trees.SimpleRootedTree
SimpleRootedTree(RootedTree) - Constructor for class jebl.evolution.trees.SimpleRootedTree
  Make a copy of the given rooted tree
SimpleRootedTree(RootedTree, Map<Node, Node>) - Constructor for class jebl.evolution.trees.SimpleRootedTree
  Make a copy of the given rooted tree
SimpleRootedTree(Tree, Node, Node, double) - Constructor for class jebl.evolution.trees.SimpleRootedTree
  Make a copy of the given unrooted tree
SimpleTree - Class in jebl.evolution.trees
  A basic implementation on an unrooted tree.
SimpleTree() - Constructor for class jebl.evolution.trees.SimpleTree
  Tree (to be constructed by subsequent calls).
SimpleTree(Tree) - Constructor for class jebl.evolution.trees.SimpleTree
  Duplicate a tree.
simulate(IntervalGenerator) - Method in class jebl.evolution.treesimulation.TreeSimulator
simulate(IntervalGenerator, boolean) - Method in class jebl.evolution.treesimulation.TreeSimulator
skipCharacters(String) - Method in class jebl.evolution.io.ImportHelper
  Skips over any contiguous characters in skip.
skipSpace() - Method in class jebl.evolution.io.ImportHelper
  Skips over any space (plus tabs and returns) in the file.
skipToEndOfLine() - Method in class jebl.evolution.io.ImportHelper
  Skips to the end of the line.
skipUntil(String) - Method in class jebl.evolution.io.ImportHelper
  Skips over the file until a character from delimiters is found.
skipWhile(String) - Method in class jebl.evolution.io.ImportHelper
  Skips char any contiguous characters in skip.
SmithWaterman - Class in jebl.evolution.align
SmithWaterman(Scores, float) - Constructor for class jebl.evolution.align.SmithWaterman
SmithWatermanLinearSpace - Class in jebl.evolution.align
SmithWatermanLinearSpace(Scores, float) - Constructor for class jebl.evolution.align.SmithWatermanLinearSpace
SmithWatermanLinearSpaceAffine - Class in jebl.evolution.align
SmithWatermanLinearSpaceAffine(Scores, float, float) - Constructor for class jebl.evolution.align.SmithWatermanLinearSpaceAffine
SortedRootedTree - Class in jebl.evolution.trees
SortedRootedTree(RootedTree, Comparator<Node>) - Constructor for class jebl.evolution.trees.SortedRootedTree
SortedRootedTree(RootedTree, SortedRootedTree.BranchOrdering) - Constructor for class jebl.evolution.trees.SortedRootedTree
SortedRootedTree.BranchOrdering - Enum Class in jebl.evolution.trees
SplitSystem - Class in jebl.evolution.trees
  data structure for a set of splits
SplitSystem(Collection<Taxon>, int) - Constructor for class jebl.evolution.trees.SplitSystem
SplitUtils - Class in jebl.evolution.trees
  utilities for split systems
SQRT_EPSILON - Static variable in class jebl.math.MachineAccuracy
SQRT_SQRT_EPSILON - Static variable in class jebl.math.MachineAccuracy
startReadingTrees() - Method in class jebl.evolution.io.NexusImporter
  Read nexus blocks until the next TREES block (or the end of the input) is encountered.
State - Class in jebl.evolution.sequences
STATE_COUNT - Static variable in class jebl.evolution.sequences.AminoAcids
STATE_COUNT - Static variable in class jebl.evolution.sequences.Codons
STATE_COUNT - Static variable in class jebl.evolution.sequences.Nucleotides
StateClassification - Interface in jebl.evolution.sequences
StateClassification.Default - Class in jebl.evolution.sequences
STATES - Static variable in class jebl.evolution.sequences.AminoAcids
  Deprecated.
STATES - Static variable in class jebl.evolution.sequences.Codons
STATES - Static variable in class jebl.evolution.sequences.Nucleotides
  Deprecated.
STOP_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
stopCondition(double, double[], double, double, boolean) - Method in class jebl.math.MultivariateMinimum
  Checks whether optimization should stop
strip - Enum constant in enum class jebl.evolution.io.IllegalCharacterPolicy
stripGaps(Sequence) - Static method in interface jebl.evolution.sequences.Sequence
  Strips a sequence of gaps
stripGaps(State[]) - Static method in class jebl.evolution.sequences.Utils
  Strips a sequence of gaps
stripStates(Sequence, List<State>) - Static method in interface jebl.evolution.sequences.Sequence
  Strips a sequence of any states given
stripStates(State[], List<State>) - Static method in class jebl.evolution.sequences.Utils
  Strips a sequence of any states given
subSequence(int, int) - Method in class jebl.evolution.io.ByteBuilder
SubstScoreMatrix - Class in jebl.evolution.align.scores
SubstScoreMatrix(RateMatrix) - Constructor for class jebl.evolution.align.scores.SubstScoreMatrix
sumVector(double[]) - Static method in class jebl.math.MatrixCalc
  sum a vector
swapNodes(Node, int, int) - Method in class jebl.evolution.trees.SimpleRootedTree
SystemOut - Class in jebl.evolution.align
SystemOut() - Constructor for class jebl.evolution.align.SystemOut

## T

T_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
T_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
TabDelimitedImporter - Class in jebl.evolution.io
TabDelimitedImporter(Reader, DistanceMatrixImporter.Triangle, boolean, boolean, boolean) - Constructor for class jebl.evolution.io.TabDelimitedImporter
  Constructor
TamuraNei - Enum constant in enum class jebl.evolution.trees.TreeBuilderFactory.DistanceModel
TamuraNeiDistanceMatrix - Class in jebl.evolution.distances
  Date: 22/01/2006 Time: 17:28:59
TamuraNeiDistanceMatrix(Alignment, ProgressListener) - Constructor for class jebl.evolution.distances.TamuraNeiDistanceMatrix
TamuraNeiDistanceMatrix(Alignment, ProgressListener, boolean) - Constructor for class jebl.evolution.distances.TamuraNeiDistanceMatrix
TAXA - Enum constant in enum class jebl.evolution.io.NexusImporter.NexusBlock
Taxon - Class in jebl.evolution.taxa
TaxonomicLevel - Class in jebl.evolution.taxa
testConsistency(DemographicFunction, int, double) - Static method in class jebl.evolution.coalescent.DemographicFunction.Utils
  This function tests the consistency of the getIntensity and getInverseIntensity methods of this demographic model.
toCodons(State[], int) - Static method in class jebl.evolution.sequences.Nucleotides
  Convert an array of nucleotide states into an array of codon states
toNewick(RootedTree) - Static method in class jebl.evolution.trees.Utils
toNucleotides(CodonState) - Static method in class jebl.evolution.sequences.Codons
toNucleotides(State[]) - Static method in class jebl.evolution.sequences.Codons
TooFewTaxaException() - Constructor for exception class jebl.evolution.io.ImportException.TooFewTaxaException
TooFewTaxaException(String) - Constructor for exception class jebl.evolution.io.ImportException.TooFewTaxaException
toStateArray(byte[]) - Static method in class jebl.evolution.sequences.AminoAcids
toStateArray(byte[]) - Static method in class jebl.evolution.sequences.Codons
toStateArray(byte[]) - Static method in class jebl.evolution.sequences.Nucleotides
toStateArray(byte[]) - Method in interface jebl.evolution.sequences.SequenceType
  Converts an array of state indices into an array of State objects for this SequenceType
toStateArray(String) - Static method in class jebl.evolution.sequences.AminoAcids
toStateArray(String) - Static method in class jebl.evolution.sequences.Codons
toStateArray(String) - Static method in class jebl.evolution.sequences.Nucleotides
toStateArray(String) - Method in interface jebl.evolution.sequences.SequenceType
  Converts a string of state codes into an array of State objects for this SequenceType
toString() - Method in class jebl.evolution.align.ProfileCharacter
toString() - Method in class jebl.evolution.align.scores.Hamming
toString() - Method in class jebl.evolution.align.scores.NucleotideScores
toString() - Method in class jebl.evolution.align.scores.Scores
toString() - Method in class jebl.evolution.align.Traceback
toString() - Method in enum class jebl.evolution.coalescent.IntervalList.IntervalType
toString() - Method in class jebl.evolution.io.ByteBuilder
toString() - Method in enum class jebl.evolution.io.IllegalCharacterPolicy
toString() - Method in class jebl.evolution.sequences.BasicSequence
toString() - Method in class jebl.evolution.sequences.CanonicalSequence
toString() - Method in class jebl.evolution.sequences.CodonSequence
toString() - Method in class jebl.evolution.sequences.FilteredSequence
toString() - Method in class jebl.evolution.sequences.GeneticCode
  Same as getDescription() (so that GeneticCode objects can be used e.g.
toString() - Method in class jebl.evolution.sequences.State
toString() - Method in class jebl.evolution.taxa.Taxon
toString() - Method in enum class jebl.evolution.trees.ConsensusTreeBuilder.Method
toString() - Method in enum class jebl.evolution.trees.SortedRootedTree.BranchOrdering
toString() - Method in class jebl.evolution.trees.SplitSystem
  print split system
toString() - Method in enum class jebl.evolution.trees.TransformedRootedTree.Transform
toString() - Method in enum class jebl.evolution.trees.TreeBuilderFactory.Method
toString() - Method in class jebl.util.FixedBitSet
toString(double[]) - Static method in class jebl.util.Utils
  A simple toString method for an array of doubles.
toString(double[][]) - Static method in class jebl.util.Utils
  A simple toString method for an array of doubles.
toString(double[], int) - Static method in class jebl.util.Utils
  A simple toString method for an array of doubles.
toString(int[]) - Static method in class jebl.util.Utils
  A simple toString method for an array of ints.
toString(int[][]) - Static method in class jebl.util.Utils
  A simple toString method for an array of ints.
toString(int[], int) - Static method in class jebl.util.Utils
toString(Object[]) - Static method in class jebl.util.Utils
  A simple toString method for an array of doubles.
toString(Object[], int) - Static method in class jebl.util.Utils
  A simple toString method for an array of objects.
toString(Object[], String) - Static method in class jebl.util.Utils
  A simple toString method for an array of objects.
toString(Object[], String, int) - Static method in class jebl.util.Utils
  A simple toString method for an array of objects.
toString(State[]) - Static method in class jebl.evolution.sequences.Utils
toUniqueNewick(RootedTree) - Static method in class jebl.evolution.trees.Utils
  Constructs a unique newick representation of a tree
toUniqueNewickByAttribute(RootedTree, String) - Static method in class jebl.evolution.trees.Utils
  Constructs a unique newick representation of a tree print only an attribute
traceback(TracebackPlotter) - Method in class jebl.evolution.align.Align
traceback(TracebackPlotter) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpace
traceback(TracebackPlotter) - Method in class jebl.evolution.align.SmithWatermanLinearSpace
traceback(TracebackPlotter) - Method in class jebl.evolution.align.SmithWatermanLinearSpaceAffine
traceback(TracebackPlotter, int, int, String, String) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpace
traceBack(Traceback) - Method in interface jebl.evolution.align.TracebackPlotter
Traceback - Class in jebl.evolution.align
Traceback() - Constructor for class jebl.evolution.align.Traceback
TracebackPlotter - Interface in jebl.evolution.align
TransformedRootedTree - Class in jebl.evolution.trees
  This RootedTree class wraps another RootedTree and transforms the branch lengths and node heights using various functions.
TransformedRootedTree(RootedTree, TransformedRootedTree.Transform) - Constructor for class jebl.evolution.trees.TransformedRootedTree
TransformedRootedTree.Transform - Enum Class in jebl.evolution.trees
translate(String, GeneticCode) - Static method in class jebl.evolution.sequences.Utils
  A wrapper for `Utils.translateCharSequence(CharSequence,GeneticCode)` that takes a nucleotide sequence as a String only rather than a CharSequence.
translate(Sequence, GeneticCode) - Static method in class jebl.evolution.sequences.Utils
  Translates a given `Sequence` to a corresponding `Sequence` under the given genetic code.
translate(Sequence, GeneticCode, int) - Static method in class jebl.evolution.sequences.Utils
  Translates a given `Sequence` to a corresponding `Sequence` under the given genetic code.
translate(State[], GeneticCode) - Static method in class jebl.evolution.sequences.Utils
  Translates each of a given sequence of `NucleotideState`s or `CodonState`s to the `AminoAcidState` corresponding to it under the given genetic code.
translate(State[], GeneticCode, int) - Static method in class jebl.evolution.sequences.Utils
  Translates each of a given sequence of `NucleotideState`s or `CodonState`s to the `AminoAcidState` corresponding to it under the given genetic code.
translateCharSequence(CharSequence, GeneticCode) - Static method in class jebl.evolution.sequences.Utils
  Translates the given nucleotideSequence into an amino acid sequence string, using the given geneticCode.
TranslatedSequence - Class in jebl.evolution.sequences
TranslatedSequence(Sequence, GeneticCode) - Constructor for class jebl.evolution.sequences.TranslatedSequence
  Create a TranslatedSequence from a source codon or nucleotide sequence
TranslatedSequence(Sequence, GeneticCode, int) - Constructor for class jebl.evolution.sequences.TranslatedSequence
  Create a TranslatedSequence from a source codon or nucleotide sequence
tree - Variable in class jebl.evolution.align.AlignmentTreeBuilderFactory.Result
Tree - Interface in jebl.evolution.trees
  A rooted or unrooted tree.
TreeBiPartitionInfo - Class in jebl.evolution.trees
  Work in progress
TreeBiPartitionInfo(RootedTree, List<Taxon>) - Constructor for class jebl.evolution.trees.TreeBiPartitionInfo
TreeBiPartitionInfo.DistanceNorm - Enum Class in jebl.evolution.trees
TreeBuilder<T> - Interface in jebl.evolution.trees
TreeBuilderFactory - Class in jebl.evolution.trees
  A meeting point for tree building from sequence data.
TreeBuilderFactory() - Constructor for class jebl.evolution.trees.TreeBuilderFactory
TreeBuilderFactory.ConsensusMethod - Enum Class in jebl.evolution.trees
  Supported consensus methods.
TreeBuilderFactory.DistanceModel - Enum Class in jebl.evolution.trees
  Supported pairwise distance methods
TreeBuilderFactory.Method - Enum Class in jebl.evolution.trees
  Supported methods for tree building
treeChanged(TreeChangeEvent) - Method in class jebl.evolution.trees.TreeChangeListener
  The tree has changed.
TreeChangeEvent - Class in jebl.evolution.trees
  Represents a change to a tree.
TreeChangeEvent(Tree) - Constructor for class jebl.evolution.trees.TreeChangeEvent
TreeChangeListener - Class in jebl.evolution.trees
  A listener for notifying about changes to a tree or to the selected nodes in a tree.
TreeChangeListener() - Constructor for class jebl.evolution.trees.TreeChangeListener
TreeExporter - Interface in jebl.evolution.io
TreeImporter - Interface in jebl.evolution.io
  Interface for importers that do trees
treeNameAttributeKey - Static variable in class jebl.evolution.io.NexusExporter
TREES - Enum constant in enum class jebl.evolution.io.NexusImporter.NexusBlock
TreeSelectionChangeEvent - Class in jebl.evolution.trees
  Represents a change to the selected nodes in a tree.
TreeSelectionChangeEvent(Set<Node>) - Constructor for class jebl.evolution.trees.TreeSelectionChangeEvent
TreeSimulator - Class in jebl.evolution.treesimulation
  This class provides the framework for (backwards-through-time) tree simulation.
TreeSimulator(String, double[]) - Constructor for class jebl.evolution.treesimulation.TreeSimulator
TreeSimulator(String, int) - Constructor for class jebl.evolution.treesimulation.TreeSimulator
  A constructor for a given number of taxa, all sampled at the same time
TreeSimulator(String, int[], double[]) - Constructor for class jebl.evolution.treesimulation.TreeSimulator
TreeSimulator(Collection<Taxon>, String) - Constructor for class jebl.evolution.treesimulation.TreeSimulator
  A constructor for a given collection of taxa.
trimSequence(Sequence, List<State>) - Static method in interface jebl.evolution.sequences.Sequence
True - Enum constant in enum class jebl.util.MaybeBoolean

## U

U_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
UNALIGNED - Enum constant in enum class jebl.evolution.io.NexusImporter.NexusBlock
union(FixedBitSet) - Method in class jebl.util.FixedBitSet
uniqueNewick(RootedTree, Node) - Static method in class jebl.evolution.trees.RootedTreeUtils
  Recursive function for constructing a newick tree representation in the given buffer.
UnivariateFunction - Interface in jebl.math
  interface for a function of one variable
UnivariateMinimum - Class in jebl.math
  minimization of a real-valued function of one variable without using derivatives.
UnivariateMinimum() - Constructor for class jebl.math.UnivariateMinimum
UNIVERSAL - Static variable in class jebl.evolution.sequences.GeneticCode
UNKNOWN - Enum constant in enum class jebl.evolution.io.NexusImporter.NexusBlock
UNKNOWN_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
UNKNOWN_STATE - Static variable in class jebl.evolution.sequences.Codons
UNKNOWN_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
UnknownTaxonException() - Constructor for exception class jebl.evolution.io.ImportException.UnknownTaxonException
UnknownTaxonException(String) - Constructor for exception class jebl.evolution.io.ImportException.UnknownTaxonException
UnparsableDataException() - Constructor for exception class jebl.evolution.io.ImportException.UnparsableDataException
UnparsableDataException(String) - Constructor for exception class jebl.evolution.io.ImportException.UnparsableDataException
unreadCharacter(char) - Method in class jebl.evolution.io.ImportHelper
updateByRelativeRates(double[][]) - Method in class jebl.evolution.substmodel.MatrixExponential
updateProgress(double) - Method in interface jebl.math.MinimiserMonitor
  Inform monitor of current progress (as a number between 0 and 1), or -1 to reset
UPGMA - Enum constant in enum class jebl.evolution.trees.TreeBuilderFactory.Method
UPPER - Enum constant in enum class jebl.evolution.io.DistanceMatrixImporter.Triangle
upperSolve(double[][], double[], double) - Static method in class jebl.math.MatrixCalc
  upperSolve back substitution with optional over-riding diagonal
userMessage() - Method in exception class jebl.evolution.io.ImportException.MissingFieldException
userMessage() - Method in exception class jebl.evolution.io.ImportException.ShortSequenceException
userMessage() - Method in exception class jebl.evolution.io.ImportException.TooFewTaxaException
userMessage() - Method in exception class jebl.evolution.io.ImportException
Utils - Class in jebl.evolution.graphs
  A collection of utility functions for graphs.
Utils - Class in jebl.evolution.sequences
Utils - Class in jebl.evolution.trees
  A collection of utility functions for trees.
Utils - Class in jebl.util
  Provides some miscellaneous methods.

## V

V_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
V_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
valueOf(boolean) - Static method in enum class jebl.util.MaybeBoolean
  Returns the enum constant of this class with the specified name.
valueOf(int) - Static method in class jebl.evolution.sequences.GeneticCode
valueOf(String) - Static method in enum class jebl.evolution.coalescent.IntervalList.IntervalType
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class jebl.evolution.io.DistanceMatrixImporter.Triangle
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class jebl.evolution.io.IllegalCharacterPolicy
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class jebl.evolution.io.NexusImporter.NexusBlock
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in class jebl.evolution.sequences.GeneticCode
valueOf(String) - Static method in enum class jebl.evolution.trees.ConsensusTreeBuilder.Method
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class jebl.evolution.trees.SortedRootedTree.BranchOrdering
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class jebl.evolution.trees.TransformedRootedTree.Transform
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class jebl.evolution.trees.TreeBiPartitionInfo.DistanceNorm
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class jebl.evolution.trees.TreeBuilderFactory.ConsensusMethod
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class jebl.evolution.trees.TreeBuilderFactory.DistanceModel
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class jebl.evolution.trees.TreeBuilderFactory.Method
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class jebl.util.MaybeBoolean
  Returns the enum constant of this class with the specified name.
values() - Static method in enum class jebl.evolution.coalescent.IntervalList.IntervalType
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class jebl.evolution.io.DistanceMatrixImporter.Triangle
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class jebl.evolution.io.IllegalCharacterPolicy
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class jebl.evolution.io.NexusImporter.NexusBlock
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class jebl.evolution.trees.ConsensusTreeBuilder.Method
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class jebl.evolution.trees.SortedRootedTree.BranchOrdering
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class jebl.evolution.trees.TransformedRootedTree.Transform
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class jebl.evolution.trees.TreeBiPartitionInfo.DistanceNorm
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class jebl.evolution.trees.TreeBuilderFactory.ConsensusMethod
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class jebl.evolution.trees.TreeBuilderFactory.DistanceModel
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class jebl.evolution.trees.TreeBuilderFactory.Method
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class jebl.util.MaybeBoolean
  Returns an array containing the constants of this enum class, in the order they are declared.
VERTEBRATE_MT - Static variable in class jebl.evolution.sequences.GeneticCode
VOLUME_CLASSIFICATION - Static variable in class jebl.evolution.sequences.AminoAcids

## W

W_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
W_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
WAG - Class in jebl.evolution.substmodel
  WAG model of amino acid evolution (S.
WAG(double[]) - Constructor for class jebl.evolution.substmodel.WAG
  constructor
Wrapper(ProgressListener) - Constructor for class jebl.util.ProgressListener.Wrapper

## X

X_STATE - Static variable in class jebl.evolution.sequences.AminoAcids

## Y

Y_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
Y_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
YEAST - Static variable in class jebl.evolution.sequences.GeneticCode

## Z

Z_STATE - Static variable in class jebl.evolution.sequences.AminoAcids

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