Index

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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
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
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
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 jebl.evolution.io.ImportException.BadFormatException
 
BadFormatException(String) - Constructor for exception 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
beginSubtask(String) - Method in class jebl.util.CompositeProgressListener
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 in jebl.evolution.distances
 
CannotBuildDistanceMatrixException(String) - Constructor for exception jebl.evolution.distances.CannotBuildDistanceMatrixException
 
CannotBuildDistanceMatrixException(String, String, String) - Constructor for exception 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
 
closeReader() - Method in class jebl.evolution.io.ImportHelper
 
CLUSTALW - Static variable in class jebl.evolution.align.scores.NucleotideScores
 
ClusteringTreeBuilder<T extends Tree> - 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.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 extends Tree> - 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(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 jebl.evolution.io.ImportException.DuplicateFieldException
 
DuplicateFieldException(String) - Constructor for exception jebl.evolution.io.ImportException.DuplicateFieldException
 
DuplicateTaxaException() - Constructor for exception jebl.evolution.io.ImportException.DuplicateTaxaException
 
DuplicateTaxaException(String) - Constructor for exception 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
 
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.
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.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.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.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.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
 
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.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.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.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.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.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.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(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.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
 
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.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.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.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.
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.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
 
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.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.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.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.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.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.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.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.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
 
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 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.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.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 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.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.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 trees = new ArrayList(); 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 in jebl.evolution.io
 
ImportException() - Constructor for exception jebl.evolution.io.ImportException
 
ImportException(String) - Constructor for exception jebl.evolution.io.ImportException
 
ImportException(String, Throwable) - Constructor for exception jebl.evolution.io.ImportException
 
ImportException.BadFormatException - Exception in jebl.evolution.io
 
ImportException.DuplicateFieldException - Exception in jebl.evolution.io
 
ImportException.DuplicateTaxaException - Exception in jebl.evolution.io
 
ImportException.MissingFieldException - Exception in jebl.evolution.io
 
ImportException.ShortSequenceException - Exception in jebl.evolution.io
 
ImportException.TooFewTaxaException - Exception in jebl.evolution.io
 
ImportException.UnknownTaxonException - Exception in jebl.evolution.io
 
ImportException.UnparsableDataException - Exception 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.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
 
isIndeterminate() - Method in class jebl.util.BasicProgressListener
 
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.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
 
LEAST_SQUARES - Enum constant in enum class jebl.evolution.trees.ReRootedTree.RootingType
 
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 in jebl.math
 
MatrixCalcException() - Constructor for exception jebl.math.MatrixCalcException
 
MatrixCalcException(String) - Constructor for exception jebl.math.MatrixCalcException
 
MatrixCalcException.NotSquareMatrixException - Exception in jebl.math
 
MatrixCalcException.PositiveDefiniteException - Exception 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
 
MID_POINT - Enum constant in enum class jebl.evolution.trees.ReRootedTree.RootingType
 
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 jebl.evolution.io.NexusImporter.MissingBlockException
 
MissingBlockException(String) - Constructor for exception jebl.evolution.io.NexusImporter.MissingBlockException
 
MissingFieldException() - Constructor for exception jebl.evolution.io.ImportException.MissingFieldException
 
MissingFieldException(String) - Constructor for exception jebl.evolution.io.ImportException.MissingFieldException
 
MissingTaxonException - Class in jebl.evolution.taxa
 
MissingTaxonException(Taxon) - Constructor for 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.NonOverlapMultipleLocalAffine
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 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 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 jebl.math.MatrixCalcException.NotSquareMatrixException
 
NotSquareMatrixException(String) - Constructor for exception 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 jebl.math.MatrixCalcException.PositiveDefiniteException
 
PositiveDefiniteException(String) - Constructor for exception 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.SmithWatermanLinearSpace
 
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.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.SmithWatermanLinearSpace
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.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.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.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
 
ReRootedTree(RootedTree, ReRootedTree.RootingType) - Constructor for class jebl.evolution.trees.ReRootedTree
 
ReRootedTree.RootingType - Enum Class in jebl.evolution.trees
 
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(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
roundDouble(double, int) - Static method in class jebl.evolution.io.NexusExporter
 

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 in jebl.evolution.sequences
 
SequenceStateException(String) - Constructor for exception 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.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.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.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.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
setProgress(long, long) - Method in class jebl.util.ProgressListener
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 jebl.evolution.io.ImportException.ShortSequenceException
 
ShortSequenceException(String) - Constructor for exception 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 jebl.evolution.io.ImportException.TooFewTaxaException
 
TooFewTaxaException(String) - Constructor for exception 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.ReRootedTree.RootingType
 
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 NucleotideStates or CodonStates 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 NucleotideStates or CodonStates 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 extends Tree> - 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 jebl.evolution.io.ImportException.UnknownTaxonException
 
UnknownTaxonException(String) - Constructor for exception jebl.evolution.io.ImportException.UnknownTaxonException
 
UnparsableDataException() - Constructor for exception jebl.evolution.io.ImportException.UnparsableDataException
 
UnparsableDataException(String) - Constructor for exception 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 jebl.evolution.io.ImportException.MissingFieldException
 
userMessage() - Method in exception jebl.evolution.io.ImportException.ShortSequenceException
 
userMessage() - Method in exception jebl.evolution.io.ImportException.TooFewTaxaException
 
userMessage() - Method in exception 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.ReRootedTree.RootingType
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.ReRootedTree.RootingType
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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