A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
All Classes All Packages
All Classes All Packages
All Classes All Packages
A
- A_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
- A_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
- abort - jebl.evolution.io.IllegalCharacterPolicy
- AbstractRateMatrix - Class in jebl.evolution.substmodel
-
abstract base class for all rate matrices
- AbstractRootedTree - Class in jebl.evolution.trees
- AbstractRootedTree() - Constructor for class jebl.evolution.trees.AbstractRootedTree
- add(Sequence) - Method in interface jebl.evolution.io.ImmediateSequenceImporter.Callback
- add(RootedTree) - Method in class jebl.evolution.trees.CladeSystem
-
adds all the clades in the tree
- addCharacter(char, int) - Method in class jebl.evolution.align.ProfileCharacter
- addChild(Node, Node) - Method in class jebl.evolution.trees.MutableRootedTree
-
Insert a child node.
- addCoalescentEvent(double) - Method in class jebl.evolution.coalescent.Intervals
- addEdge(Node, Node, double) - Method in class jebl.evolution.trees.SimpleTree
-
Add a new edge between two existing (non adjacent yet) nodes.
- addFeedbackAction(String, String, SimpleListener) - Method in class jebl.util.CompositeProgressListener
- addFeedbackAction(String, String, SimpleListener) - Method in class jebl.util.ProgressListener
-
Adds an action that can choose to provide feedback.
- addFeedbackAction(String, String, SimpleListener) - Method in class jebl.util.ProgressListener.Wrapper
- addFeedbackAction(String, SimpleListener) - Method in class jebl.util.CompositeProgressListener
- addFeedbackAction(String, SimpleListener) - Method in class jebl.util.ProgressListener
-
Equivalent to
addFeedbackAction(label,"",listener)
- addFeedbackAction(String, SimpleListener) - Method in class jebl.util.ProgressListener.Wrapper
- addGaps(int) - Method in class jebl.evolution.align.ProfileCharacter
- addMigrationEvent(double, int) - Method in class jebl.evolution.coalescent.Intervals
- addNode(Edge) - Method in class jebl.evolution.trees.SimpleRootedTree
-
Adds a new node at the midpoint of the given edge
- addNode(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
-
Adds a new node at the midpoint of the edge connecting the given node to its parent.
- addNothingEvent(double) - Method in class jebl.evolution.coalescent.Intervals
- addProfileCharacter(ProfileCharacter) - Method in class jebl.evolution.align.ProfileCharacter
- addProgress(double) - Method in class jebl.util.CompositeProgressListener
-
Increments the progress of the current sub task by this much.
- addProgressListener(ProgressListener) - Method in interface jebl.evolution.aligners.Aligner
- addProgressListener(ProgressListener) - Method in class jebl.evolution.trees.ClusteringTreeBuilder
- addProgressListener(ProgressListener) - Method in class jebl.evolution.trees.ConsensusTreeBuilder
- addProgressListener(ProgressListener) - Method in interface jebl.evolution.trees.TreeBuilder
- addSampleEvent(double) - Method in class jebl.evolution.coalescent.Intervals
- addSequence(Sequence) - Method in class jebl.evolution.alignments.BasicAlignment
-
Adds a sequence to this alignment
- addTaxa(Set<Taxon>) - Method in class jebl.evolution.characters.ContinuousCharacter
-
set the taxa for this character with a previously constructed Set
- 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 - 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
-
Used as an alternative to
CompositeProgressListener.beginNextSubtask()
. - beginSubtask(String) - Method in class jebl.util.CompositeProgressListener
-
Used as an alternative to
CompositeProgressListener.beginNextSubtask()
. - BilleraMetric - Class in jebl.evolution.treemetrics
-
Billera tree distance - sum of change in branch lengths required to transform one tree to the second Note that this interface is not optimal for a large set where all pairs are required.
- BilleraMetric() - Constructor for class jebl.evolution.treemetrics.BilleraMetric
- Binomial - Class in jebl.math
-
Binomial coefficients
- Binomial() - Constructor for class jebl.math.Binomial
- bitCode - Variable in class jebl.evolution.sequences.NucleotideState
- BLEPHARISMA_NUC - Static variable in class jebl.evolution.sequences.GeneticCode
- BLOSUM_45 - Static variable in class jebl.evolution.align.scores.ScoresFactory
- BLOSUM_50 - Static variable in class jebl.evolution.align.scores.ScoresFactory
- BLOSUM_55 - Static variable in class jebl.evolution.align.scores.ScoresFactory
- BLOSUM_60 - Static variable in class jebl.evolution.align.scores.ScoresFactory
- BLOSUM_62 - Static variable in class jebl.evolution.align.scores.ScoresFactory
- BLOSUM_65 - Static variable in class jebl.evolution.align.scores.ScoresFactory
- BLOSUM_70 - Static variable in class jebl.evolution.align.scores.ScoresFactory
- BLOSUM_75 - Static variable in class jebl.evolution.align.scores.ScoresFactory
- BLOSUM_80 - Static variable in class jebl.evolution.align.scores.ScoresFactory
- BLOSUM_85 - Static variable in class jebl.evolution.align.scores.ScoresFactory
- BLOSUM_90 - Static variable in class jebl.evolution.align.scores.ScoresFactory
- Blosum45 - Class in jebl.evolution.align.scores
- Blosum45() - Constructor for class jebl.evolution.align.scores.Blosum45
- Blosum50 - Class in jebl.evolution.align.scores
- Blosum50() - Constructor for class jebl.evolution.align.scores.Blosum50
- Blosum55 - Class in jebl.evolution.align.scores
- Blosum55() - Constructor for class jebl.evolution.align.scores.Blosum55
- Blosum60 - Class in jebl.evolution.align.scores
- Blosum60() - Constructor for class jebl.evolution.align.scores.Blosum60
- Blosum62 - Class in jebl.evolution.align.scores
- Blosum62() - Constructor for class jebl.evolution.align.scores.Blosum62
- Blosum65 - Class in jebl.evolution.align.scores
- Blosum65() - Constructor for class jebl.evolution.align.scores.Blosum65
- Blosum70 - Class in jebl.evolution.align.scores
- Blosum70() - Constructor for class jebl.evolution.align.scores.Blosum70
- Blosum75 - Class in jebl.evolution.align.scores
- Blosum75() - Constructor for class jebl.evolution.align.scores.Blosum75
- Blosum80 - Class in jebl.evolution.align.scores
- Blosum80() - Constructor for class jebl.evolution.align.scores.Blosum80
- Blosum85 - Class in jebl.evolution.align.scores
- Blosum85() - Constructor for class jebl.evolution.align.scores.Blosum85
- Blosum90 - Class in jebl.evolution.align.scores
- Blosum90() - Constructor for class jebl.evolution.align.scores.Blosum90
- booleanValue(MaybeBoolean) - Static method in enum 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 - 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 - 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 - jebl.evolution.trees.TransformedRootedTree.Transform
- cleanSequence(CharSequence, SequenceType) - Static method in class jebl.evolution.sequences.Utils
-
Produce a clean sequence filtered of spaces and digits.
- clear() - Method in class jebl.evolution.align.ProfileCharacter
- clear(int) - Method in class jebl.util.FixedBitSet
- clearAllProgress() - Method in class jebl.util.CompositeProgressListener
-
Clear all progress, including that of previous subtasks.
- clearLastMetaComment() - Method in class jebl.evolution.io.ImportHelper
- close() - Method in class jebl.evolution.io.NewickExporter
- close() - Method in class jebl.evolution.io.NexusExporter
- close() - Method in class jebl.evolution.io.PHYLIPExporter
- close() - Method in interface jebl.evolution.io.TreeExporter
- closeBlock() - Method in class jebl.evolution.io.NexusExporter
-
close an existing open trees block
- closeReader() - Method in class jebl.evolution.io.ImportHelper
- CLUSTALW - Static variable in class jebl.evolution.align.scores.NucleotideScores
- ClusteringTreeBuilder<T 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 - jebl.evolution.coalescent.IntervalList.IntervalType
-
Denotes an interval after which a coalescent event is observed (i.e.
- CoalescentIntervalGenerator - Class in jebl.evolution.treesimulation
-
This is a class that draws coalescent intervals under the given demographic function.
- CoalescentIntervalGenerator(DemographicFunction) - Constructor for class jebl.evolution.treesimulation.CoalescentIntervalGenerator
- CODON - Static variable in interface jebl.evolution.sequences.SequenceType
- Codons - Class in jebl.evolution.sequences
- Codons() - Constructor for class jebl.evolution.sequences.Codons
- CodonSequence - Class in jebl.evolution.sequences
-
A codon implementation of the Sequence interface.
- CodonSequence(Taxon, State[]) - Constructor for class jebl.evolution.sequences.CodonSequence
-
Creates a sequence with a name corresponding to the taxon name
- CodonState - Class in jebl.evolution.sequences
-
As of 2007-07-30, instances of this class are only constructed for non-ambigous nucleotide triplets - see
Codons
. - CompactRootedTree - Class in jebl.evolution.trees
-
A memory efficient rooted tree.
- CompactRootedTree(RootedTree) - Constructor for class jebl.evolution.trees.CompactRootedTree
-
Do all the hard work.
- compareTo(Object) - Method in class jebl.evolution.alignments.ConsensusSequence
-
Sequences are compared by their taxa
- compareTo(Object) - Method in class jebl.evolution.sequences.AminoAcidState
- compareTo(Object) - Method in class jebl.evolution.sequences.BasicSequence
-
Sequences are compared by their taxa
- compareTo(Object) - Method in class jebl.evolution.sequences.CanonicalSequence
-
Sequences are compared by their taxa
- compareTo(Object) - Method in class jebl.evolution.sequences.CodonSequence
-
Sequences are compared by their taxa
- compareTo(Object) - Method in class jebl.evolution.sequences.FilteredSequence
- compareTo(Object) - Method in class jebl.evolution.sequences.NucleotideState
- compareTo(Object) - Method in class jebl.evolution.sequences.State
- compareTo(Object) - Method in class jebl.evolution.taxa.Taxon
- complement() - Method in class jebl.util.FixedBitSet
- complement(NucleotideState[]) - Static method in class jebl.evolution.sequences.Utils
- complement(FixedBitSet) - Static method in class jebl.util.FixedBitSet
- COMPLEMENTARY_STATES - Static variable in class jebl.evolution.sequences.Nucleotides
-
Deprecated.
- CompositeProgressListener - Class in jebl.util
-
A
ProgressListener
that is suitable for a task that consists of several subtasks. - CompositeProgressListener(ProgressListener, double...) - Constructor for class jebl.util.CompositeProgressListener
-
construct a new composite ProgressListener.
- CompositeProgressListener(ProgressListener, int) - Constructor for class jebl.util.CompositeProgressListener
-
Construct a CompositeProgressListener with a number of evenly weighted subtasks.
- conceptuallyUnrooted() - Method in class jebl.evolution.trees.CompactRootedTree
- conceptuallyUnrooted() - Method in class jebl.evolution.trees.FilteredRootedTree
- conceptuallyUnrooted() - Method in class jebl.evolution.trees.MutableRootedTree
- conceptuallyUnrooted() - Method in class jebl.evolution.trees.ReRootedTree
- conceptuallyUnrooted() - Method in class jebl.evolution.trees.RootedFromUnrooted
- conceptuallyUnrooted() - Method in class jebl.evolution.trees.RootedSubtree
- conceptuallyUnrooted() - Method in interface jebl.evolution.trees.RootedTree
-
Due to current implementation limitations, trees store "branch" information in nodes.
- conceptuallyUnrooted() - Method in class jebl.evolution.trees.SimpleRootedTree
- consensus(boolean, boolean) - Static method in enum 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 in jebl.evolution.trees
-
Supported consensus methods.
- ConstantPopulation - Class in jebl.evolution.coalescent
-
This class models coalescent intervals for a constant population (parameter: N0=present-day population size).
- ConstantPopulation() - Constructor for class jebl.evolution.coalescent.ConstantPopulation
-
Construct demographic model with default settings
- ConstantPopulation(double) - Constructor for class jebl.evolution.coalescent.ConstantPopulation
-
Construct demographic model with given settings
- ConstExponential - Class in jebl.evolution.coalescent
-
This class models exponential growth from an initial population size.
- ConstExponential() - Constructor for class jebl.evolution.coalescent.ConstExponential
-
Construct demographic model with default settings
- ConstExponential(double, double, double) - Constructor for class jebl.evolution.coalescent.ConstExponential
-
Construct demographic model with given settings
- ConstLogistic - Class in jebl.evolution.coalescent
-
This class models logistic growth from an initial population size.
- ConstLogistic() - Constructor for class jebl.evolution.coalescent.ConstLogistic
-
Construct demographic model with default settings
- ConstLogistic(double, double, double, double) - Constructor for class jebl.evolution.coalescent.ConstLogistic
-
Construct demographic model with given settings
- constructConsensus(Alignment, boolean) - Static method in class jebl.evolution.alignments.ConsensusSequence
- contains(int) - Method in class jebl.util.FixedBitSet
- CONTINUOUS - Static variable in interface jebl.evolution.characters.CharacterType
- ContinuousCharacter - Class in jebl.evolution.characters
- ContinuousCharacter(String, String) - Constructor for class jebl.evolution.characters.ContinuousCharacter
-
Constructs a basic ContinuousCharacter object with no taxa added yet
- ContinuousCharacter(String, String, Set<Taxon>) - Constructor for class jebl.evolution.characters.ContinuousCharacter
-
Constructs a basic ContinuousCharacter object with taxa added
- copy(double[][], double[][]) - Static method in class jebl.util.Utils
-
Copies all of source into dest - assumes dest to be large enough
- copy(double[], double[]) - Static method in class jebl.math.MultivariateMinimum
-
Copy source vector into target vector
- copyIntervals(Intervals) - Method in class jebl.evolution.coalescent.Intervals
- copyMatrix(double[][]) - Static method in class jebl.math.MatrixCalc
-
copy one matrix into another
- copyTree(RootedTree) - Static method in class jebl.evolution.trees.Utils
-
This method creates an unattached copy of the given rooted tree such that changes to the copied tree do not affect the original tree.
- createExternalNode(Taxon) - Method in class jebl.evolution.trees.MutableRootedTree
-
Creates a new external node with the given taxon.
- createExternalNode(Taxon) - Method in class jebl.evolution.trees.SimpleRootedTree
-
Creates a new external node with the given taxon.
- createExternalNode(Taxon) - Method in class jebl.evolution.trees.SimpleTree
-
Creates a new external node with the given taxon.
- createInternalNode(List<? extends Node>) - Method in class jebl.evolution.trees.MutableRootedTree
-
Once a SimpleRootedTree has been created, the node stucture can be created by calling createExternalNode and createInternalNode.
- createInternalNode(List<? extends Node>) - Method in class jebl.evolution.trees.SimpleRootedTree
-
Once a SimpleRootedTree has been created, the node stucture can be created by calling createExternalNode and createInternalNode.
- createInternalNode(List<Node>) - Method in class jebl.evolution.trees.SimpleTree
-
Once a SimpleTree has been created, the node stucture can be created by calling createExternalNode and createInternalNode.
- createNodeDensityComparator(RootedTree) - Static method in class jebl.evolution.trees.Utils
- createNodeDensityMinNodeHeightComparator(RootedTree) - Static method in class jebl.evolution.trees.Utils
- createNodes(RootedTree, Node) - Method in class jebl.evolution.trees.SimpleRootedTree
-
Clones the entire tree structure from the given RootedTree.
- createNodes(RootedTree, Node, Node) - Method in class jebl.evolution.trees.ReRootedTree
-
Clones the entire tree structure from the given (unrooted) Tree.
- createNodes(Tree, Node, Node) - Method in class jebl.evolution.trees.SimpleRootedTree
-
Clones the entire tree structure from the given (unrooted) Tree.
- createNullMonitor() - Static method in class jebl.math.MinimiserMonitor.Utils
-
Creates a MinimiserMonitor that looses all output
- createOrderEnumerator(int) - Method in interface jebl.math.OrderEnumerator.OEFactory
-
For generating an ordering from 0..size-1.
- createSimpleMonitor(PrintWriter) - Static method in class jebl.math.MinimiserMonitor.Utils
-
Creates a MinimiserMonitor that outputs current minimum to a print stream
- createSplitMonitor(MinimiserMonitor, MinimiserMonitor) - Static method in class jebl.math.MinimiserMonitor.Utils
-
creates a monitor such that all information sent to monitor is based on two sub monitors
- createStringMonitor() - Static method in class jebl.math.MinimiserMonitor.Utils
-
Creates a MinimiserMonitor that Stores output (use toString() to access current results)
- createSystemErrorMonitor() - Static method in class jebl.math.MinimiserMonitor.Utils
-
Creates a MinimiserMonitor that outputs current minimum to a System.err
- createSystemOuptutMonitor() - Static method in class jebl.math.MinimiserMonitor.Utils
-
Creates a MinimiserMonitor that outputs current minimum to a System.out
D
- D_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
- D_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
- DATA - jebl.evolution.io.NexusImporter.NexusBlock
- DEBUGsubTreeRep(RootedTree, Node) - Static method in class jebl.evolution.trees.Utils
- DECREASING_NODE_DENSITY - 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 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 in jebl.evolution.io
- DISTANCES - 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 - jebl.evolution.trees.TransformedRootedTree.Transform
- equals(Object) - Method in class jebl.evolution.sequences.BasicSequence
- equals(Object) - Method in class jebl.evolution.sequences.CodonSequence
- equals(Object) - Method in class jebl.util.FixedBitSet
- equals(Object) - Method in class jebl.util.HashPair
- equals(Taxon) - Method in class jebl.evolution.taxa.Taxon
- EUPLOTID_NUC - Static variable in class jebl.evolution.sequences.GeneticCode
- evaluate(double) - Method in class jebl.math.OrthogonalLineFunction
- evaluate(double) - Method in interface jebl.math.UnivariateFunction
-
compute function value
- evaluate(double[]) - Method in class jebl.evolution.coalescent.Coalescent
- evaluate(double[]) - Method in interface jebl.math.MultivariateFunction
-
compute function value
- Expansion - Class in jebl.evolution.coalescent
-
This class models exponential growth from an initial ancestral population size.
- Expansion() - Constructor for class jebl.evolution.coalescent.Expansion
-
Construct demographic model with default settings
- Expansion(double, double, double) - Constructor for class jebl.evolution.coalescent.Expansion
-
Construct demographic model with given settings
- ExponentialGrowth - Class in jebl.evolution.coalescent
-
This class models an exponentially growing (or shrinking) population (Parameters: N0=present-day population size; r=growth rate).
- ExponentialGrowth() - Constructor for class jebl.evolution.coalescent.ExponentialGrowth
-
Construct demographic model with default settings
- ExponentialGrowth(double, double) - Constructor for class jebl.evolution.coalescent.ExponentialGrowth
-
Construct demographic model with given settings
- ExponentialLogistic - Class in jebl.evolution.coalescent
-
This class models logistic growth from an initial exponential phase.
- ExponentialLogistic() - Constructor for class jebl.evolution.coalescent.ExponentialLogistic
-
Construct demographic model with default settings
- ExponentialLogistic(double, double, double, double, double) - Constructor for class jebl.evolution.coalescent.ExponentialLogistic
-
Construct demographic model with given settings
- exportAlignment(Alignment) - Method in interface jebl.evolution.io.AlignmentExporter
-
export one alignment.
- exportAlignment(Alignment) - Method in class jebl.evolution.io.MEGAExporter
-
Deprecated.Files created by this export method won't be importable by MEGA (because they don't have titles). Use
MEGAExporter.exportAlignment(jebl.evolution.alignments.Alignment, String)
instead. - exportAlignment(Alignment) - Method in class jebl.evolution.io.NexusExporter
-
exportAlignment.
- exportAlignment(Alignment) - Method in class jebl.evolution.io.PHYLIPExporter
- exportAlignment(Alignment, String) - Method in class jebl.evolution.io.MEGAExporter
- exportExcludeKeys - Static variable in class jebl.evolution.io.NexusExporter
- exportMatrix(DistanceMatrix) - Method in class jebl.evolution.io.NexusExporter
- exportSequence(Sequence) - Method in class jebl.evolution.io.FastaExporter
-
export a sequence.
- exportSequences(Collection<? extends Sequence>) - Method in class jebl.evolution.io.FastaExporter
-
export alignment or set of sequences.
- exportSequences(Collection<? extends Sequence>) - Method in class jebl.evolution.io.NexusExporter
-
export alignment.
- exportSequences(Collection<? extends Sequence>) - Method in interface jebl.evolution.io.SequenceExporter
-
exportSequences.
- exportTree(Tree) - Method in class jebl.evolution.io.NewickExporter
-
Export a single tree
- exportTree(Tree) - Method in class jebl.evolution.io.NexusExporter
-
Export a single tree
- exportTree(Tree) - Method in class jebl.evolution.io.PHYLIPExporter
- exportTree(Tree) - Method in interface jebl.evolution.io.TreeExporter
-
Export a single tree
- exportTrees(Collection<? extends Tree>) - Method in class jebl.evolution.io.NewickExporter
-
Export a collection of trees
- exportTrees(Collection<? extends Tree>) - Method in class jebl.evolution.io.NexusExporter
- exportTrees(Collection<? extends Tree>) - Method in class jebl.evolution.io.PHYLIPExporter
- exportTrees(Collection<? extends Tree>) - Method in interface jebl.evolution.io.TreeExporter
-
Export a collection of trees
- exportTrees(Collection<? extends Tree>, boolean) - Method in class jebl.evolution.io.NexusExporter
- exportTreesWithTranslation(Collection<? extends Tree>, Map<String, String>) - Method in class jebl.evolution.io.NexusExporter
F
- F_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
- f2minx - Variable in class jebl.math.UnivariateMinimum
-
curvature at minimum
- F84 - 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 - jebl.util.MaybeBoolean
- FastaExporter - Class in jebl.evolution.io
-
Class for exporting a fasta file format.
- FastaExporter(Writer) - Constructor for class jebl.evolution.io.FastaExporter
-
Constructor
- FastaImporter - Class in jebl.evolution.io
-
Class for importing Fasta sequential file format.
- FastaImporter(File, SequenceType) - Constructor for class jebl.evolution.io.FastaImporter
-
Use this constructor if you are reading from a file.
- FastaImporter(Reader, SequenceType) - Constructor for class jebl.evolution.io.FastaImporter
-
This constuctor takes a reader.
- FilteredRootedTree - Class in jebl.evolution.trees
- FilteredRootedTree(RootedTree) - Constructor for class jebl.evolution.trees.FilteredRootedTree
- FilteredSequence - Class in jebl.evolution.sequences
- FilteredSequence(Sequence) - Constructor for class jebl.evolution.sequences.FilteredSequence
-
Creates a FilteredSequence wrapper to the given source sequence.
- findEndBlock() - Method in class jebl.evolution.io.NexusImporter
-
Read ahead to the end of the current block.
- findMinimum(double, UnivariateFunction) - Method in class jebl.math.UnivariateMinimum
-
Find minimum (first estimate given)
- findMinimum(double, UnivariateFunction, int) - Method in class jebl.math.UnivariateMinimum
-
Find minimum (first estimate given, desired number of fractional digits specified)
- findMinimum(MultivariateFunction, double[]) - Method in class jebl.math.MultivariateMinimum
-
Find minimum close to vector x
- findMinimum(MultivariateFunction, double[], int, int) - Method in class jebl.math.MultivariateMinimum
-
Find minimum close to vector x (desired fractional digits for each parameter is specified)
- findMinimum(MultivariateFunction, double[], int, int, MinimiserMonitor) - Method in class jebl.math.MultivariateMinimum
-
Find minimum close to vector x (desired fractional digits for each parameter is specified)
- findMinimum(UnivariateFunction) - Method in class jebl.math.UnivariateMinimum
-
Find minimum (no first estimate given)
- findMinimum(UnivariateFunction, int) - Method in class jebl.math.UnivariateMinimum
-
Find minimum (no first estimate given, desired number of fractional digits specified)
- findNextBlock() - Method in class jebl.evolution.io.NexusImporter
-
Read ahead to the next block in the input.
- findTimeIntervals() - Method in class jebl.evolution.trees.CalculateSplitRates
- finishedTraceBack() - Method in interface jebl.evolution.align.TracebackPlotter
- fireSetProgress(double) - Method in class jebl.evolution.trees.ClusteringTreeBuilder
- first - Variable in class jebl.util.HashPair
- firstDerivative(UnivariateFunction, double) - Static method in class jebl.math.NumericalDerivative
-
determine first derivative
- FitchParsimony - Class in jebl.evolution.parsimony
-
Class for reconstructing characters using Fitch parsimony.
- FitchParsimony(List<Pattern>, boolean) - Constructor for class jebl.evolution.parsimony.FitchParsimony
- FitchParsimony(Patterns, boolean) - Constructor for class jebl.evolution.parsimony.FitchParsimony
- FixedBitSet - Class in jebl.util
-
A bit-set of fixed size.
- FixedBitSet(int) - Constructor for class jebl.util.FixedBitSet
- FixedBitSet(FixedBitSet) - Constructor for class jebl.util.FixedBitSet
- FLATWORM_MT - Static variable in class jebl.evolution.sequences.GeneticCode
- fminx - Variable in class jebl.math.UnivariateMinimum
-
function value at minimum
- forFiles(ProgressListener, List<File>) - Static method in class jebl.util.CompositeProgressListener
- forMatrix(ScoreMatrix) - Static method in class jebl.evolution.align.scores.Scores
- formatScore(float) - Method in class jebl.evolution.align.Align
- fractionEqual(State) - Method in class jebl.evolution.sequences.State
-
Determine how much in common these potentially ambigous states have as a fraction between 0 and 1 2 non-ambiguous states will return 0.
G
- G_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
- G_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
- GammaFunction - Class in jebl.math
-
gamma function
- GammaFunction() - Constructor for class jebl.math.GammaFunction
- GAP_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
- GAP_STATE - Static variable in class jebl.evolution.sequences.Codons
- GAP_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
- gapFraction() - Method in class jebl.evolution.align.ProfileCharacter
- GaplessSequence - Class in jebl.evolution.sequences
- GaplessSequence(Sequence) - Constructor for class jebl.evolution.sequences.GaplessSequence
- generateFactory(boolean) - Static method in class jebl.math.OrthogonalSearch
-
Generate a MultivariateMinimum.Factory for an OrthogonalSearch
- generateNewMinimiser() - Method in interface jebl.math.MultivariateMinimum.Factory
-
Generate a new Multivariate Minimum
- generateScores(String) - Static method in class jebl.evolution.align.scores.ScoresFactory
-
For any matrix.
- generateScores(String, float) - Static method in class jebl.evolution.align.scores.ScoresFactory
-
For calculated nucleotide matrices.
- generateScores(String, int) - Static method in class jebl.evolution.align.scores.ScoresFactory
-
For Blosum and Pam matrices
- GENETIC_CODES - Static variable in class jebl.evolution.sequences.GeneticCode
-
Deprecated.use
GeneticCode.getGeneticCodes()
instead - GeneticCode - Class in jebl.evolution.sequences
-
A set of standard genetic codes.
- get(int, double) - Method in class jebl.evolution.trees.MostProbableTopology
-
Get the most probable tree(s)
- getAdjacencies(Node) - Method in interface jebl.evolution.graphs.Graph
-
Returns a list of nodes connected to this node by an edge
- getAdjacencies(Node) - Method in class jebl.evolution.trees.CompactRootedTree
- getAdjacencies(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
- getAdjacencies(Node) - Method in class jebl.evolution.trees.MutableRootedTree
- getAdjacencies(Node) - Method in class jebl.evolution.trees.ReRootedTree
- getAdjacencies(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
- getAdjacencies(Node) - Method in class jebl.evolution.trees.RootedSubtree
- getAdjacencies(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
- getAdjacencies(Node) - Method in class jebl.evolution.trees.SimpleTree
- getAdjusted(OrderEnumerator, int) - Static method in class jebl.math.OrderEnumerator.Utils
- getAdjusted(OrthogonalHints, int) - Static method in class jebl.math.OrthogonalHints.Utils
- getAdjustedFactory(OrderEnumerator.OEFactory, int) - Static method in class jebl.math.OrderEnumerator.Utils
- getAlignments() - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
-
The indices for these correspond to those for the getScoreMatrix() matrix.
- getAllTaxa() - Static method in class jebl.evolution.taxa.Taxon
- getAlphabet() - Method in class jebl.evolution.align.scores.AminoAcidScores
- getAlphabet() - Method in class jebl.evolution.align.scores.NucleotideScores
- getAlphabet() - Method in interface jebl.evolution.align.scores.ScoreMatrix
- getAlphabet() - Method in class jebl.evolution.align.scores.SubstScoreMatrix
- getAlphabet(SequenceType) - Static method in class jebl.evolution.sequences.SequenceType.Utils
- getAlternating(OrderEnumerator, OrderEnumerator) - Static method in class jebl.math.OrderEnumerator.Utils
- getAlternatingFactory(OrderEnumerator.OEFactory, OrderEnumerator.OEFactory) - Static method in class jebl.math.OrderEnumerator.Utils
- getArgmax(double[]) - Static method in class jebl.util.Utils
-
Find the maximum "argument" (of a double array).
- getArgmax(int[]) - Static method in class jebl.util.Utils
-
Find the maximum "argument".
- getArgument(int) - Method in class jebl.evolution.coalescent.ConstantPopulation
- getArgument(int) - Method in class jebl.evolution.coalescent.ConstExponential
- getArgument(int) - Method in class jebl.evolution.coalescent.ConstLogistic
- getArgument(int) - Method in interface jebl.evolution.coalescent.DemographicFunction
-
Returns the value of the nth argument of this function.
- getArgument(int) - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
-
Returns the value of the nth argument of this function.
- getArgument(int) - Method in class jebl.evolution.coalescent.Expansion
- getArgument(int) - Method in class jebl.evolution.coalescent.ExponentialGrowth
- getArgument(int) - Method in class jebl.evolution.coalescent.ExponentialLogistic
- getArgumentCount() - Method in class jebl.evolution.coalescent.ConstantPopulation
- getArgumentCount() - Method in class jebl.evolution.coalescent.ConstExponential
- getArgumentCount() - Method in class jebl.evolution.coalescent.ConstLogistic
- getArgumentCount() - Method in interface jebl.evolution.coalescent.DemographicFunction
-
Returns the number of arguments for this function.
- getArgumentCount() - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
-
Returns the number of arguments for this function.
- getArgumentCount() - Method in class jebl.evolution.coalescent.Expansion
- getArgumentCount() - Method in class jebl.evolution.coalescent.ExponentialGrowth
- getArgumentCount() - Method in class jebl.evolution.coalescent.ExponentialLogistic
- getArgumentName(int) - Method in class jebl.evolution.coalescent.ConstantPopulation
- getArgumentName(int) - Method in class jebl.evolution.coalescent.ConstExponential
- getArgumentName(int) - Method in class jebl.evolution.coalescent.ConstLogistic
- getArgumentName(int) - Method in interface jebl.evolution.coalescent.DemographicFunction
-
Returns the name of the nth argument of this function.
- getArgumentName(int) - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
-
Returns the name of the nth argument of this function.
- getArgumentName(int) - Method in class jebl.evolution.coalescent.Expansion
- getArgumentName(int) - Method in class jebl.evolution.coalescent.ExponentialGrowth
- getArgumentName(int) - Method in class jebl.evolution.coalescent.ExponentialLogistic
- getAttribute(String) - Method in class jebl.evolution.alignments.ConsensusSequence
- getAttribute(String) - Method in class jebl.evolution.sequences.BasicSequence
- getAttribute(String) - Method in class jebl.evolution.sequences.CanonicalSequence
- getAttribute(String) - Method in class jebl.evolution.sequences.CodonSequence
- getAttribute(String) - Method in class jebl.evolution.sequences.FilteredSequence
- getAttribute(String) - Method in class jebl.evolution.taxa.Taxon
- getAttribute(String) - Method in class jebl.evolution.trees.BaseEdge
- getAttribute(String) - Method in class jebl.evolution.trees.BaseNode
- getAttribute(String) - Method in class jebl.evolution.trees.FilteredRootedTree
- getAttribute(String) - Method in class jebl.evolution.trees.MutableRootedTree
- getAttribute(String) - Method in class jebl.evolution.trees.ReRootedTree
- getAttribute(String) - Method in class jebl.evolution.trees.RootedFromUnrooted
- getAttribute(String) - Method in class jebl.evolution.trees.RootedSubtree
- getAttribute(String) - Method in class jebl.evolution.trees.SimpleRootedTree
- getAttribute(String) - Method in class jebl.evolution.trees.SimpleTree
- getAttribute(String) - Method in interface jebl.util.Attributable
- getAttribute(String) - Method in class jebl.util.AttributableHelper
- getAttributeMap() - Method in class jebl.evolution.alignments.ConsensusSequence
- getAttributeMap() - Method in class jebl.evolution.sequences.BasicSequence
- getAttributeMap() - Method in class jebl.evolution.sequences.CanonicalSequence
- getAttributeMap() - Method in class jebl.evolution.sequences.CodonSequence
- getAttributeMap() - Method in class jebl.evolution.sequences.FilteredSequence
- getAttributeMap() - Method in class jebl.evolution.taxa.Taxon
- getAttributeMap() - Method in class jebl.evolution.trees.BaseEdge
- getAttributeMap() - Method in class jebl.evolution.trees.BaseNode
- getAttributeMap() - Method in class jebl.evolution.trees.FilteredRootedTree
- getAttributeMap() - Method in class jebl.evolution.trees.MutableRootedTree
- getAttributeMap() - Method in class jebl.evolution.trees.ReRootedTree
- getAttributeMap() - Method in class jebl.evolution.trees.RootedFromUnrooted
- getAttributeMap() - Method in class jebl.evolution.trees.RootedSubtree
- getAttributeMap() - Method in class jebl.evolution.trees.SimpleRootedTree
- getAttributeMap() - Method in class jebl.evolution.trees.SimpleTree
- getAttributeMap() - Method in interface jebl.util.Attributable
-
Gets the entire attribute map.
- getAttributeMap() - Method in class jebl.util.AttributableHelper
- getAttributeNames() - Method in class jebl.evolution.alignments.ConsensusSequence
- getAttributeNames() - Method in class jebl.evolution.sequences.BasicSequence
- getAttributeNames() - Method in class jebl.evolution.sequences.CanonicalSequence
- getAttributeNames() - Method in class jebl.evolution.sequences.CodonSequence
- getAttributeNames() - Method in class jebl.evolution.sequences.FilteredSequence
- getAttributeNames() - Method in class jebl.evolution.taxa.Taxon
- getAttributeNames() - Method in class jebl.evolution.trees.BaseEdge
- getAttributeNames() - Method in class jebl.evolution.trees.BaseNode
- getAttributeNames() - Method in class jebl.evolution.trees.FilteredRootedTree
- getAttributeNames() - Method in class jebl.evolution.trees.MutableRootedTree
- getAttributeNames() - Method in class jebl.evolution.trees.ReRootedTree
- getAttributeNames() - Method in class jebl.evolution.trees.RootedFromUnrooted
- getAttributeNames() - Method in class jebl.evolution.trees.RootedSubtree
- getAttributeNames() - Method in class jebl.evolution.trees.SimpleRootedTree
- getAttributeNames() - Method in class jebl.evolution.trees.SimpleTree
- getAttributeNames() - Method in interface jebl.util.Attributable
- getAttributeNames() - Method in class jebl.util.AttributableHelper
- getAvailableAminoAcidScores() - Static method in class jebl.evolution.align.scores.ScoresFactory
- getAvailableNucleotideScores() - Static method in class jebl.evolution.align.scores.ScoresFactory
- getAverageTipDistance(RootedTree, Node) - Static method in class jebl.evolution.trees.RootedTreeUtils
-
returns the average distance from the given node to all the tips below it
- getBiasAlternating(OrderEnumerator, OrderEnumerator) - Static method in class jebl.math.OrderEnumerator.Utils
- getBiasAlternatingFactory(OrderEnumerator.OEFactory, OrderEnumerator.OEFactory) - Static method in class jebl.math.OrderEnumerator.Utils
- getBuilder(TreeBuilderFactory.Method, DistanceMatrix) - Static method in class jebl.evolution.trees.ClusteringTreeBuilder
-
A factory method to create a ClusteringTreeBuilder
- getBuilder(TreeBuilderFactory.Method, DistanceMatrix) - Static method in class jebl.evolution.trees.TreeBuilderFactory
- getCanonicalStateCount() - Static method in class jebl.evolution.sequences.AminoAcids
- getCanonicalStateCount() - Static method in class jebl.evolution.sequences.Codons
- getCanonicalStateCount() - Static method in class jebl.evolution.sequences.Nucleotides
- getCanonicalStateCount() - Method in interface jebl.evolution.sequences.SequenceType
-
Get number of canonical states
- getCanonicalStates() - Static method in class jebl.evolution.sequences.AminoAcids
- getCanonicalStates() - Static method in class jebl.evolution.sequences.Codons
- getCanonicalStates() - Static method in class jebl.evolution.sequences.Nucleotides
- getCanonicalStates() - Method in interface jebl.evolution.sequences.SequenceType
-
Get a list of canonical states ordered by their indices.
- getCanonicalStates() - Method in class jebl.evolution.sequences.State
- getCataclysmTime() - Method in class jebl.evolution.coalescent.CataclysmicDemographic
- getChildren(Node) - Method in class jebl.evolution.trees.CompactRootedTree
- getChildren(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
- getChildren(Node) - Method in class jebl.evolution.trees.MutableRootedTree
- getChildren(Node) - Method in class jebl.evolution.trees.ReRootedTree
- getChildren(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
- getChildren(Node) - Method in class jebl.evolution.trees.RootedSubtree
- getChildren(Node) - Method in interface jebl.evolution.trees.RootedTree
- getChildren(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
- getChildren(Node) - Method in class jebl.evolution.trees.SortedRootedTree
- getClade(int) - Method in class jebl.evolution.trees.CladeSystem
- getCladeCount() - Method in class jebl.evolution.trees.CladeSystem
-
get number of unique clades
- getCladeFrequency(int) - Method in class jebl.evolution.trees.CladeSystem
-
get clade frequency
- getCladeString(int) - Method in class jebl.evolution.trees.CladeSystem
- getCleanString() - Method in class jebl.evolution.sequences.BasicSequence
- getCleanString() - Method in class jebl.evolution.sequences.CanonicalSequence
- getCleanString() - Method in class jebl.evolution.sequences.CodonSequence
- getCoalescentEvents(int) - Method in interface jebl.evolution.coalescent.IntervalList
-
Returns the number coalescent events in an interval
- getCoalescentEvents(int) - Method in class jebl.evolution.coalescent.Intervals
- getCode() - Method in class jebl.evolution.sequences.State
-
Returns the 1 letter code for this state.
- getCodeLength() - Method in interface jebl.evolution.sequences.SequenceType
- getCodeTable() - Method in class jebl.evolution.sequences.GeneticCode
-
Returns a length-64 string that for each nucleotide triplet contains the single-character amino acid code (see
AminoAcids
to which that triplet is translated in this genetic code. - getCodonsForAminoAcid(AminoAcidState) - Method in class jebl.evolution.sequences.GeneticCode
- getColumn(double[][], int) - Static method in class jebl.math.MatrixCalc
-
takes a matrix and gets a column, then returns it as a vector
- getCombined(OrthogonalHints, int, OrthogonalHints, int) - Static method in class jebl.math.OrthogonalHints.Utils
- getCommonAncestorNode(RootedTree, Set<Node>) - Static method in class jebl.evolution.trees.RootedTreeUtils
-
Gets the most recent common ancestor (MRCA) node of a set of tip nodes.
- getComplementaryState(NucleotideState) - Static method in class jebl.evolution.sequences.Nucleotides
- getConstant(int) - Static method in class jebl.math.OrderEnumerator.Utils
- getConstantFactory(int) - Static method in class jebl.math.OrderEnumerator.Utils
- getCopy(boolean[][]) - Static method in class jebl.util.Utils
-
Clones an array of booleans
- getCopy(byte[]) - Static method in class jebl.util.Utils
-
Clones an array of bytes
- getCopy(byte[][]) - Static method in class jebl.util.Utils
-
Clones an array of bytes
- getCopy(double[]) - Static method in class jebl.util.Utils
-
Clones an array of doubles
- getCopy(double[][]) - Static method in class jebl.util.Utils
-
Clones an array of doubles
- getCopy(double[][][]) - Static method in class jebl.util.Utils
-
Clones an array of doubles
- getCopy(double[], int) - Static method in class jebl.util.Utils
-
Clones an array of doubles from index start (inclusive) to end
- getCopy(double[], int, int) - Static method in class jebl.util.Utils
-
Clones an array of doubles from index start (inclusive) to index end (exclusive)
- getCopy(int[]) - Static method in class jebl.util.Utils
-
Clones an array of ints
- getCopy(int[][]) - Static method in class jebl.util.Utils
-
Clones a matrix of ints
- getCopy(int[], int) - Static method in class jebl.util.Utils
-
Clones an array of ints
- getCopy(String[]) - Static method in class jebl.util.Utils
-
Clones an array of Strings
- getDecimalPlaces() - Method in class jebl.util.NumberFormatter
-
Get the number of decimal places to display when formatted.
- getDeclineRate() - Method in class jebl.evolution.coalescent.CataclysmicDemographic
-
returns the positive-valued decline rate
- getDefaultDistanceModel(List<Sequence>) - Static method in class jebl.evolution.align.SequenceAlignmentsDistanceMatrix
- getDegree() - Method in interface jebl.evolution.graphs.Node
-
Get the number of edges connected to this node.
- getDegree(Graph, Node) - Static method in class jebl.evolution.graphs.Graph.Utils
- getDemographic(double) - Method in class jebl.evolution.coalescent.CataclysmicDemographic
- getDemographic(double) - Method in class jebl.evolution.coalescent.ConstantPopulation
- getDemographic(double) - Method in class jebl.evolution.coalescent.ConstExponential
- getDemographic(double) - Method in class jebl.evolution.coalescent.ConstLogistic
- getDemographic(double) - Method in interface jebl.evolution.coalescent.DemographicFunction
-
Gets the value of the demographic function N(t) at time t.
- getDemographic(double) - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
-
Gets the value of the demographic function N(t) at time t.
- getDemographic(double) - Method in class jebl.evolution.coalescent.Expansion
- getDemographic(double) - Method in class jebl.evolution.coalescent.ExponentialGrowth
- getDemographic(double) - Method in class jebl.evolution.coalescent.ExponentialLogistic
- getDemographic(double) - Method in class jebl.evolution.coalescent.LogisticGrowth
-
Gets the value of the demographic function N(t) at time t.
- getDesc() - Method in interface jebl.evolution.characters.Character
-
return the description of the character
- getDesc() - Method in class jebl.evolution.characters.ContinuousCharacter
- getDesc() - Method in class jebl.evolution.characters.DiscreteCharacter
- getDescendantTips(RootedTree, Node) - Static method in class jebl.evolution.trees.RootedTreeUtils
-
Gets a set of tip nodes descended from the given node.
- getDescription() - Method in class jebl.evolution.sequences.GeneticCode
-
Returns the description of the genetic code
- getDimension() - Method in class jebl.evolution.substmodel.AbstractRateMatrix
- getDimension() - Method in class jebl.evolution.substmodel.MatrixExponential
- getDimension() - Method in interface jebl.evolution.substmodel.RateMatrix
- getDistance(int, int) - Method in class jebl.evolution.distances.BasicDistanceMatrix
-
Gets the distance at a particular row and column
- getDistance(int, int) - Method in interface jebl.evolution.distances.DistanceMatrix
-
Gets the distance at a particular row and column
- getDistance(Taxon, Taxon) - Method in class jebl.evolution.distances.BasicDistanceMatrix
-
Gets the distance between 2 taxa
- getDistance(Taxon, Taxon) - Method in interface jebl.evolution.distances.DistanceMatrix
-
Gets the distance between 2 taxa
- getDistances() - Method in class jebl.evolution.distances.BasicDistanceMatrix
-
Gets a 2-dimensional array containing the distances
- getDistances() - Method in interface jebl.evolution.distances.DistanceMatrix
-
Gets a 2-dimensional array containing the distances
- getEdge(Node, Node) - Method in interface jebl.evolution.graphs.Graph
-
Returns the Edge that connects these two nodes
- getEdge(Node, Node) - Method in class jebl.evolution.trees.CompactRootedTree
- getEdge(Node, Node) - Method in class jebl.evolution.trees.FilteredRootedTree
- getEdge(Node, Node) - Method in class jebl.evolution.trees.MutableRootedTree
-
Returns the Edge that connects these two nodes
- getEdge(Node, Node) - Method in class jebl.evolution.trees.ReRootedTree
-
Returns the Edge that connects these two nodes
- getEdge(Node, Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
- getEdge(Node, Node) - Method in class jebl.evolution.trees.RootedSubtree
-
Returns the Edge that connects these two nodes
- getEdge(Node, Node) - Method in class jebl.evolution.trees.SimpleRootedTree
-
Returns the Edge that connects these two nodes
- getEdge(Node, Node) - Method in class jebl.evolution.trees.SimpleTree
-
Returns the Edge that connects these two nodes
- getEdgeLength(Node, Node) - Method in interface jebl.evolution.graphs.Graph
-
Returns the length of the edge that connects these two nodes
- getEdgeLength(Node, Node) - Method in class jebl.evolution.trees.CompactRootedTree
- getEdgeLength(Node, Node) - Method in class jebl.evolution.trees.FilteredRootedTree
- getEdgeLength(Node, Node) - Method in class jebl.evolution.trees.MutableRootedTree
- getEdgeLength(Node, Node) - Method in class jebl.evolution.trees.ReRootedTree
- getEdgeLength(Node, Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
- getEdgeLength(Node, Node) - Method in class jebl.evolution.trees.RootedSubtree
- getEdgeLength(Node, Node) - Method in class jebl.evolution.trees.SimpleRootedTree
- getEdgeLength(Node, Node) - Method in class jebl.evolution.trees.SimpleTree
- getEdges() - Method in interface jebl.evolution.graphs.Graph
- getEdges() - Method in class jebl.evolution.trees.CompactRootedTree
- getEdges() - Method in class jebl.evolution.trees.FilteredRootedTree
- getEdges() - Method in class jebl.evolution.trees.MutableRootedTree
- getEdges() - Method in class jebl.evolution.trees.ReRootedTree
- getEdges() - Method in class jebl.evolution.trees.RootedFromUnrooted
- getEdges() - Method in class jebl.evolution.trees.RootedSubtree
- getEdges() - Method in class jebl.evolution.trees.SimpleRootedTree
- getEdges() - Method in class jebl.evolution.trees.SimpleTree
- getEdges(Node) - Method in interface jebl.evolution.graphs.Graph
-
Returns a list of edges connected to this node
- getEdges(Node) - Method in class jebl.evolution.trees.CompactRootedTree
- getEdges(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
- getEdges(Node) - Method in class jebl.evolution.trees.MutableRootedTree
-
Returns a list of edges connected to this node
- getEdges(Node) - Method in class jebl.evolution.trees.ReRootedTree
-
Returns a list of edges connected to this node
- getEdges(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
-
Returns a list of edges connected to this node
- getEdges(Node) - Method in class jebl.evolution.trees.RootedSubtree
-
Returns a list of edges connected to this node
- getEdges(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
-
Returns a list of edges connected to this node
- getEdges(Node) - Method in class jebl.evolution.trees.SimpleTree
-
Returns a list of edges connected to this node
- getEquilibriumFrequencies() - Method in class jebl.evolution.substmodel.AbstractRateMatrix
- getEquilibriumFrequencies() - Method in interface jebl.evolution.substmodel.RateMatrix
- getEquilibriumFrequency(int) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
- getEquilibriumFrequency(int) - Method in interface jebl.evolution.substmodel.RateMatrix
- getEstimatedScores() - Method in class jebl.evolution.align.BartonSternberg
- getExternalEdges() - Method in class jebl.evolution.trees.CompactRootedTree
- getExternalEdges() - Method in class jebl.evolution.trees.FilteredRootedTree
- getExternalEdges() - Method in class jebl.evolution.trees.MutableRootedTree
-
The set of external edges.
- getExternalEdges() - Method in class jebl.evolution.trees.ReRootedTree
-
The set of external edges.
- getExternalEdges() - Method in class jebl.evolution.trees.RootedFromUnrooted
-
The set of external edges.
- getExternalEdges() - Method in class jebl.evolution.trees.RootedSubtree
-
The set of external edges.
- getExternalEdges() - Method in class jebl.evolution.trees.SimpleRootedTree
-
The set of external edges.
- getExternalEdges() - Method in class jebl.evolution.trees.SimpleTree
-
The set of external edges.
- getExternalEdges() - Method in interface jebl.evolution.trees.Tree
- getExternalNodeCount(Node) - Method in class jebl.evolution.trees.AbstractRootedTree
- getExternalNodeCount(Node) - Method in class jebl.evolution.trees.CompactRootedTree
- getExternalNodeCount(Node) - Method in interface jebl.evolution.trees.RootedTree
- getExternalNodeCount(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
- getExternalNodeCount(RootedTree, Node) - Static method in class jebl.evolution.trees.Utils
-
Return the number of external nodes under this node.
- getExternalNodes() - Method in class jebl.evolution.trees.CompactRootedTree
- getExternalNodes() - Method in class jebl.evolution.trees.FilteredRootedTree
- getExternalNodes() - Method in class jebl.evolution.trees.MutableRootedTree
- getExternalNodes() - Method in class jebl.evolution.trees.ReRootedTree
- getExternalNodes() - Method in class jebl.evolution.trees.RootedFromUnrooted
- getExternalNodes() - Method in class jebl.evolution.trees.RootedSubtree
- getExternalNodes() - Method in class jebl.evolution.trees.SimpleRootedTree
- getExternalNodes() - Method in class jebl.evolution.trees.SimpleTree
- getExternalNodes() - Method in interface jebl.evolution.trees.Tree
- getExternalNodes(Node) - Method in class jebl.evolution.trees.AbstractRootedTree
- getExternalNodes(Node) - Method in class jebl.evolution.trees.CompactRootedTree
- getExternalNodes(Node) - Method in interface jebl.evolution.trees.RootedTree
- getExternalNodes(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
- getFormattedValue(double) - Method in class jebl.util.NumberFormatter
-
Returns a string containing the current value for this column with appropriate formatting.
- getFractionCompleted() - Method in class jebl.util.BasicProgressListener
- getFullName() - Method in class jebl.evolution.sequences.State
-
A descriptive name for this state.
- getGaplessLocation(Sequence, int) - Static method in class jebl.evolution.sequences.Utils
-
Gets the site location index for this sequence excluding any gaps.
- getGappedLocation(Sequence, int) - Static method in class jebl.evolution.sequences.Utils
-
Gets the site location index for this sequence that corresponds to a location given excluding all gaps.
- getGapState() - Static method in class jebl.evolution.sequences.AminoAcids
- getGapState() - Static method in class jebl.evolution.sequences.Codons
- getGapState() - Static method in class jebl.evolution.sequences.Nucleotides
- getGapState() - Method in interface jebl.evolution.sequences.SequenceType
-
Get state corresponding to a gap
- getGeneticCodes() - Static method in class jebl.evolution.sequences.GeneticCode
-
Returns an iterable that allows you to iterate over all the standard genetic codes
- getGeneticCodesArray() - Static method in class jebl.evolution.sequences.GeneticCode
- getGrowthRate() - Method in class jebl.evolution.coalescent.ExponentialGrowth
-
returns growth rate.
- getHeight(Node) - Method in class jebl.evolution.trees.CompactRootedTree
- getHeight(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
- getHeight(Node) - Method in class jebl.evolution.trees.MutableRootedTree
- getHeight(Node) - Method in class jebl.evolution.trees.ReRootedTree
- getHeight(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
- getHeight(Node) - Method in class jebl.evolution.trees.RootedSubtree
- getHeight(Node) - Method in interface jebl.evolution.trees.RootedTree
- getHeight(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
- getHeight(Node) - Method in class jebl.evolution.trees.TransformedRootedTree
- getImmutableProfileCharacter(char) - Static method in class jebl.evolution.align.ProfileCharacter
-
An immutable ProfileCharacter that uses less memory than a mutable profile character.
- getIndex() - Method in class jebl.evolution.sequences.State
- getIntegral(double, double) - Method in class jebl.evolution.coalescent.ConstantPopulation
-
Calculates the integral 1/N(x) dx between start and finish.
- getIntegral(double, double) - Method in class jebl.evolution.coalescent.ConstExponential
- getIntegral(double, double) - Method in class jebl.evolution.coalescent.ConstLogistic
- getIntegral(double, double) - Method in interface jebl.evolution.coalescent.DemographicFunction
-
Calculates the integral 1/N(x) dx between start and finish
- getIntegral(double, double) - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
- getIntegral(double, double) - Method in class jebl.evolution.coalescent.Expansion
- getIntegral(double, double) - Method in class jebl.evolution.coalescent.ExponentialLogistic
- getIntegral(double, double) - Method in class jebl.evolution.coalescent.LogisticGrowth
- getIntensity(double) - Method in class jebl.evolution.coalescent.CataclysmicDemographic
- getIntensity(double) - Method in class jebl.evolution.coalescent.ConstantPopulation
- getIntensity(double) - Method in class jebl.evolution.coalescent.ConstExponential
- getIntensity(double) - Method in class jebl.evolution.coalescent.ConstLogistic
- getIntensity(double) - Method in interface jebl.evolution.coalescent.DemographicFunction
-
Returns value of demographic intensity function at time t (= integral 1/N(x) dx from 0 to t).
- getIntensity(double) - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
-
Returns value of demographic intensity function at time t (= integral 1/N(x) dx from 0 to t).
- getIntensity(double) - Method in class jebl.evolution.coalescent.Expansion
- getIntensity(double) - Method in class jebl.evolution.coalescent.ExponentialGrowth
- getIntensity(double) - Method in class jebl.evolution.coalescent.ExponentialLogistic
- getIntensity(double) - Method in class jebl.evolution.coalescent.LogisticGrowth
-
Returns value of demographic intensity function at time t (= integral 1/N(x) dx from 0 to t).
- getInternalEdges() - Method in class jebl.evolution.trees.CompactRootedTree
- getInternalEdges() - Method in class jebl.evolution.trees.FilteredRootedTree
- getInternalEdges() - Method in class jebl.evolution.trees.MutableRootedTree
-
The set of internal edges.
- getInternalEdges() - Method in class jebl.evolution.trees.ReRootedTree
-
The set of internal edges.
- getInternalEdges() - Method in class jebl.evolution.trees.RootedFromUnrooted
-
The set of internal edges.
- getInternalEdges() - Method in class jebl.evolution.trees.RootedSubtree
-
The set of internal edges.
- getInternalEdges() - Method in class jebl.evolution.trees.SimpleRootedTree
-
The set of internal edges.
- getInternalEdges() - Method in class jebl.evolution.trees.SimpleTree
-
The set of internal edges.
- getInternalEdges() - Method in interface jebl.evolution.trees.Tree
- getInternalNodes() - Method in class jebl.evolution.trees.CompactRootedTree
- getInternalNodes() - Method in class jebl.evolution.trees.FilteredRootedTree
- getInternalNodes() - Method in class jebl.evolution.trees.MutableRootedTree
- getInternalNodes() - Method in class jebl.evolution.trees.ReRootedTree
- getInternalNodes() - Method in class jebl.evolution.trees.RootedFromUnrooted
- getInternalNodes() - Method in class jebl.evolution.trees.RootedSubtree
- getInternalNodes() - Method in class jebl.evolution.trees.SimpleRootedTree
- getInternalNodes() - Method in class jebl.evolution.trees.SimpleTree
- getInternalNodes() - Method in interface jebl.evolution.trees.Tree
- getInternalParameterBoundaries(int, double[]) - Method in interface jebl.math.OrthogonalHints
-
A boundary is a value of a parameter for which values lower than the boundary and values higher than the boundary are better treated as two separate functions (IE, they are only piecewise connected), and minimisation should be performed over both ranges individually (and then the true minimum taken as the minimuma of the ranges)
- getInternalParameterBoundaries(OrthogonalHints, int) - Static method in class jebl.math.OrthogonalHints.Utils
- getInterval(double, int, double) - Method in class jebl.evolution.treesimulation.CoalescentIntervalGenerator
-
Calculates the waiting time to the next coalescent for a given critical value (an intensity).
- getInterval(double, int, double) - Method in interface jebl.evolution.treesimulation.IntervalGenerator
-
Calculates the waiting time to the next coalescent for a given critical value (an intensity).
- getInterval(int) - Method in interface jebl.evolution.coalescent.IntervalList
-
Gets an interval.
- getInterval(int) - Method in class jebl.evolution.coalescent.Intervals
- getIntervalCount() - Method in interface jebl.evolution.coalescent.IntervalList
-
get number of intervals
- getIntervalCount() - Method in class jebl.evolution.coalescent.Intervals
- getIntervalType(int) - Method in interface jebl.evolution.coalescent.IntervalList
-
Returns the type of interval observed.
- getIntervalType(int) - Method in class jebl.evolution.coalescent.Intervals
- getInverseIntensity(double) - Method in class jebl.evolution.coalescent.CataclysmicDemographic
- getInverseIntensity(double) - Method in class jebl.evolution.coalescent.ConstantPopulation
- getInverseIntensity(double) - Method in class jebl.evolution.coalescent.ConstExponential
- getInverseIntensity(double) - Method in class jebl.evolution.coalescent.ConstLogistic
- getInverseIntensity(double) - Method in interface jebl.evolution.coalescent.DemographicFunction
-
Returns value of inverse demographic intensity function (returns time, needed for simulation of coalescent intervals).
- getInverseIntensity(double) - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
-
Returns value of inverse demographic intensity function (returns time, needed for simulation of coalescent intervals).
- getInverseIntensity(double) - Method in class jebl.evolution.coalescent.Expansion
- getInverseIntensity(double) - Method in class jebl.evolution.coalescent.ExponentialGrowth
- getInverseIntensity(double) - Method in class jebl.evolution.coalescent.ExponentialLogistic
- getInverseIntensity(double) - Method in class jebl.evolution.coalescent.LogisticGrowth
-
Returns value of demographic intensity function at time t (= integral 1/N(x) dx from 0 to t).
- getLabelCount() - Method in class jebl.evolution.trees.SplitSystem
-
get number of labels
- getLastDelimiter() - Method in class jebl.evolution.io.ImportHelper
- getLastMetaComment() - Method in class jebl.evolution.io.ImportHelper
-
Deprecated.use
ImportHelper.getMetaComments()
instead - getLength() - Method in class jebl.evolution.alignments.ConsensusSequence
-
Returns the length of the sequence
- getLength() - Method in interface jebl.evolution.alignments.Pattern
- getLength() - Method in interface jebl.evolution.graphs.Edge
- getLength() - Method in class jebl.evolution.sequences.BasicSequence
-
Returns the length of the sequence
- getLength() - Method in class jebl.evolution.sequences.CanonicalSequence
-
Returns the length of the sequence
- getLength() - Method in class jebl.evolution.sequences.CodonSequence
-
Returns the length of the sequence
- getLength() - Method in class jebl.evolution.sequences.FilteredSequence
-
Returns the length of the sequence
- getLength() - Method in interface jebl.evolution.sequences.Sequence
-
Get the length of the sequence
- getLength(Node) - Method in class jebl.evolution.trees.CompactRootedTree
- getLength(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
- getLength(Node) - Method in class jebl.evolution.trees.MutableRootedTree
- getLength(Node) - Method in class jebl.evolution.trees.ReRootedTree
- getLength(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
- getLength(Node) - Method in class jebl.evolution.trees.RootedSubtree
- getLength(Node) - Method in interface jebl.evolution.trees.RootedTree
- getLength(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
- getLength(Node) - Method in class jebl.evolution.trees.TransformedRootedTree
- getLength(RootedTree) - Static method in class jebl.evolution.trees.Utils
- getLength(Tree) - Static method in class jebl.evolution.trees.Utils
- getLineageCount(int) - Method in interface jebl.evolution.coalescent.IntervalList
-
Returns the number of uncoalesced lineages within this interval.
- getLineageCount(int) - Method in class jebl.evolution.coalescent.Intervals
- getLineageCount(IntervalList, double) - Static method in class jebl.evolution.coalescent.IntervalList.Utils
- getLineNumber() - Method in class jebl.evolution.io.ImportHelper
- getLowerBound() - Method in class jebl.math.OrthogonalLineFunction
- getLowerBound() - Method in interface jebl.math.UnivariateFunction
-
get lower bound of argument
- getLowerBound(int) - Method in class jebl.evolution.coalescent.Coalescent
- getLowerBound(int) - Method in class jebl.evolution.coalescent.ConstantPopulation
- getLowerBound(int) - Method in class jebl.evolution.coalescent.ConstExponential
- getLowerBound(int) - Method in class jebl.evolution.coalescent.ConstLogistic
- getLowerBound(int) - Method in interface jebl.evolution.coalescent.DemographicFunction
-
Returns the lower bound of the nth argument of this function.
- getLowerBound(int) - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
-
Returns the lower bound of the nth argument of this function.
- getLowerBound(int) - Method in class jebl.evolution.coalescent.Expansion
- getLowerBound(int) - Method in class jebl.evolution.coalescent.ExponentialGrowth
- getLowerBound(int) - Method in class jebl.evolution.coalescent.ExponentialLogistic
- getLowerBound(int) - Method in interface jebl.math.MultivariateFunction
-
get lower bound of argument n
- getMatch() - Method in class jebl.evolution.align.Align
- getMatch() - Method in class jebl.evolution.align.NeedlemanWunschAffine
- getMatch() - Method in class jebl.evolution.align.NeedlemanWunschLinearSpace
- getMatch() - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
- getMatch() - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
- getMatch() - Method in class jebl.evolution.align.SmithWatermanLinearSpace
- getMatch() - Method in class jebl.evolution.align.SmithWatermanLinearSpaceAffine
- getMatch(char[], char[]) - Method in class jebl.evolution.align.NeedlemanWunschAffine
- getMatchScores(int) - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
- getMatrixString() - Method in class jebl.evolution.align.scores.Scores
- getMax() - Method in class jebl.evolution.align.SequenceShuffler
- getMax(double[]) - Static method in class jebl.util.Utils
-
Calculate the max of an array
- getMax(double[], int, int) - Static method in class jebl.util.Utils
-
Calculate the max of an array
- getMaxTipHeight(RootedTree, Node) - Static method in class jebl.evolution.trees.RootedTreeUtils
- getMean() - Method in class jebl.evolution.align.SequenceShuffler
- getMean(double[]) - Static method in class jebl.util.Utils
-
Calculate the mean value of an array
- getMemoryRequiredForAlignment(int) - Static method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
- getMessage() - Method in class jebl.util.BasicProgressListener
- getMetaComments() - Method in class jebl.evolution.io.ImportHelper
-
This method has been introduced because this class previously skipped over consecutive comments and discarded all but the last.
- getMethodDescription() - Method in class jebl.evolution.trees.ConsensusTreeBuilder
-
Returns a human readable name of this consensus tree building method
- getMetric(RootedTree, RootedTree) - Method in class jebl.evolution.treemetrics.BilleraMetric
- getMetric(RootedTree, RootedTree) - Method in class jebl.evolution.treemetrics.CladeHeightMetric
- getMetric(RootedTree, RootedTree) - Method in class jebl.evolution.treemetrics.RobinsonsFouldMetric
- getMetric(RootedTree, RootedTree) - Method in interface jebl.evolution.treemetrics.RootedTreeMetric
-
calculates the metric between two rooted trees
- getMin() - Method in class jebl.evolution.align.SequenceShuffler
- getMin(double[]) - Static method in class jebl.util.Utils
-
Calculate the min of an array
- getMinNodeHeight(RootedTree, Node) - Static method in class jebl.evolution.trees.Utils
- getMinTipHeight(RootedTree, Node) - Static method in class jebl.evolution.trees.RootedTreeUtils
- getMostFrequentState() - Method in interface jebl.evolution.alignments.Pattern
-
Returns the most frequent state in this pattern
- getMostFrequentState(boolean) - Method in interface jebl.evolution.alignments.Pattern
-
Returns the most frequent state in this pattern, optionally including ambiguous states
- getN0() - Method in class jebl.evolution.coalescent.ConstantPopulation
-
returns initial population size.
- getN1() - Method in class jebl.evolution.coalescent.ConstExponential
- getN1() - Method in class jebl.evolution.coalescent.ConstLogistic
- getN1() - Method in class jebl.evolution.coalescent.Expansion
- getName() - Method in class jebl.evolution.align.scores.AminoAcidScores
- getName() - Method in class jebl.evolution.align.scores.Blosum45
- getName() - Method in class jebl.evolution.align.scores.Blosum50
- getName() - Method in class jebl.evolution.align.scores.NucleotideScores
- getName() - Method in interface jebl.evolution.align.scores.ScoreMatrix
- getName() - Method in class jebl.evolution.align.scores.SubstScoreMatrix
- getName() - Method in interface jebl.evolution.characters.Character
-
return the name of the character
- getName() - Method in interface jebl.evolution.characters.CharacterType
- getName() - Method in class jebl.evolution.characters.ContinuousCharacter
- getName() - Method in class jebl.evolution.characters.DiscreteCharacter
- getName() - Method in class jebl.evolution.sequences.GeneticCode
-
Returns the name of the genetic code
- getName() - Method in class jebl.evolution.sequences.Nucleotides
- getName() - Method in interface jebl.evolution.sequences.SequenceType
-
name of data type
- getName() - Method in class jebl.evolution.sequences.State
-
Deprecated.you probably want to use
State.getFullName()
orState.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 jebl.evolution.trees.ConsensusTreeBuilder.Method
- getName() - Method in enum jebl.evolution.trees.TreeBuilderFactory.Method
- getNcbiTranslationTableNumber() - Method in class jebl.evolution.sequences.GeneticCode
- getNext() - Method in interface jebl.math.OrderEnumerator
-
The next value in the enumeration
- getNextBlockName() - Method in class jebl.evolution.io.NexusImporter
- getNexusDataType() - Method in interface jebl.evolution.sequences.SequenceType
- getNode(Taxon) - Method in class jebl.evolution.trees.CompactRootedTree
- getNode(Taxon) - Method in class jebl.evolution.trees.FilteredRootedTree
- getNode(Taxon) - Method in class jebl.evolution.trees.MutableRootedTree
- getNode(Taxon) - Method in class jebl.evolution.trees.ReRootedTree
- getNode(Taxon) - Method in class jebl.evolution.trees.RootedFromUnrooted
- getNode(Taxon) - Method in class jebl.evolution.trees.RootedSubtree
- getNode(Taxon) - Method in class jebl.evolution.trees.SimpleRootedTree
- getNode(Taxon) - Method in class jebl.evolution.trees.SimpleTree
- getNode(Taxon) - Method in interface jebl.evolution.trees.Tree
- getNodes() - Method in interface jebl.evolution.graphs.Graph
- getNodes() - Method in class jebl.evolution.trees.CompactRootedTree
- getNodes() - Method in class jebl.evolution.trees.FilteredRootedTree
- getNodes() - Method in class jebl.evolution.trees.MutableRootedTree
- getNodes() - Method in class jebl.evolution.trees.ReRootedTree
- getNodes() - Method in class jebl.evolution.trees.RootedFromUnrooted
- getNodes() - Method in class jebl.evolution.trees.RootedSubtree
- getNodes() - Method in class jebl.evolution.trees.SimpleRootedTree
- getNodes() - Method in class jebl.evolution.trees.SimpleTree
- getNodes(int) - Method in interface jebl.evolution.graphs.Graph
- getNodes(int) - Method in class jebl.evolution.trees.CompactRootedTree
- getNodes(int) - Method in class jebl.evolution.trees.FilteredRootedTree
- getNodes(int) - Method in class jebl.evolution.trees.MutableRootedTree
- getNodes(int) - Method in class jebl.evolution.trees.ReRootedTree
- getNodes(int) - Method in class jebl.evolution.trees.RootedFromUnrooted
- getNodes(int) - Method in class jebl.evolution.trees.RootedSubtree
- getNodes(int) - Method in class jebl.evolution.trees.SimpleRootedTree
- getNodes(int) - Method in class jebl.evolution.trees.SimpleTree
- getNodes(Edge) - Method in interface jebl.evolution.graphs.Graph
-
Returns an array of 2 nodes which are the nodes at either end of the edge.
- getNodes(Edge) - Method in class jebl.evolution.trees.CompactRootedTree
- getNodes(Edge) - Method in class jebl.evolution.trees.FilteredRootedTree
- getNodes(Edge) - Method in class jebl.evolution.trees.MutableRootedTree
-
Returns an array of 2 nodes which are the nodes at either end of the edge.
- getNodes(Edge) - Method in class jebl.evolution.trees.ReRootedTree
-
Returns an array of 2 nodes which are the nodes at either end of the edge.
- getNodes(Edge) - Method in class jebl.evolution.trees.RootedFromUnrooted
- getNodes(Edge) - Method in class jebl.evolution.trees.RootedSubtree
-
Returns an array of 2 nodes which are the nodes at either end of the edge.
- getNodes(Edge) - Method in class jebl.evolution.trees.SimpleRootedTree
-
Returns an array of 2 nodes which are the nodes at either end of the edge.
- getNodes(Edge) - Method in class jebl.evolution.trees.SimpleTree
-
Returns an array of 2 nodes which are the nodes at either end of the edge.
- getNodes(RootedTree, Node) - Static method in class jebl.evolution.trees.Utils
-
All nodes in subtree - parents before children (pre - order).
- getNormalized(double[]) - Static method in class jebl.math.Random
- getNull() - Static method in class jebl.math.OrthogonalHints.Utils
- getNumArguments() - Method in class jebl.evolution.coalescent.Coalescent
- getNumArguments() - Method in interface jebl.math.MultivariateFunction
-
get number of arguments
- getNumOfStates() - Method in class jebl.evolution.characters.DiscreteCharacter
- getOrdered(int) - Static method in class jebl.math.OrderEnumerator.Utils
- getOrderedFactory() - Static method in class jebl.math.OrderEnumerator.Utils
- getOriginalFrequencies() - Static method in class jebl.evolution.substmodel.WAG
- getOriginalFrequencies(double[]) - Static method in class jebl.evolution.substmodel.WAG
-
get the frequencies of the original data set that formed the basis for the estimation of the rate matrix
- getOrthogonalHints() - Method in class jebl.evolution.coalescent.Coalescent
- getOrthogonalHints() - Method in interface jebl.math.MultivariateFunction
- getParent(Node) - Method in class jebl.evolution.trees.CompactRootedTree
- getParent(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
- getParent(Node) - Method in class jebl.evolution.trees.MutableRootedTree
- getParent(Node) - Method in class jebl.evolution.trees.ReRootedTree
- getParent(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
- getParent(Node) - Method in class jebl.evolution.trees.RootedSubtree
- getParent(Node) - Method in interface jebl.evolution.trees.RootedTree
- getParent(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
- getParentEdge(Node) - Method in class jebl.evolution.trees.CompactRootedTree
- getParentEdge(Node) - Method in class jebl.evolution.trees.MutableRootedTree
- getParentEdge(Node) - Method in class jebl.evolution.trees.ReRootedTree
- getParentEdge(Node) - Method in class jebl.evolution.trees.RootedSubtree
- getParentEdge(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
- getPathLength(Tree, Node, Node) - Static method in class jebl.evolution.trees.Utils
- getPatternCount() - Method in class jebl.evolution.alignments.BasicAlignment
- getPatternCount() - Method in interface jebl.evolution.alignments.Patterns
- getPatternCount() - Method in class jebl.evolution.alignments.ResampledAlignment
- getPatternLength() - Method in class jebl.evolution.alignments.BasicAlignment
- getPatternLength() - Method in interface jebl.evolution.alignments.Patterns
- getPatternLength() - Method in class jebl.evolution.alignments.ResampledAlignment
- getPatterns() - Method in class jebl.evolution.alignments.BasicAlignment
- getPatterns() - Method in interface jebl.evolution.alignments.Patterns
-
Get a list of all the patterns
- getPatterns() - Method in class jebl.evolution.alignments.ResampledAlignment
- getProgress() - Method in class jebl.evolution.io.ImportHelper
- getR2() - Method in class jebl.evolution.coalescent.ExponentialLogistic
- getRelativeRates() - Method in class jebl.evolution.substmodel.AbstractRateMatrix
- getRelativeRates() - Method in interface jebl.evolution.substmodel.RateMatrix
- getRestricted(OrderEnumerator, int, int) - Static method in class jebl.math.OrderEnumerator.Utils
- getRestrictedFactory(OrderEnumerator.OEFactory, int, int) - Static method in class jebl.math.OrderEnumerator.Utils
- getRootNode() - Method in class jebl.evolution.trees.CompactRootedTree
- getRootNode() - Method in class jebl.evolution.trees.FilteredRootedTree
- getRootNode() - Method in class jebl.evolution.trees.MutableRootedTree
-
The root of the tree has the largest node height of all nodes in the tree.
- getRootNode() - Method in class jebl.evolution.trees.ReRootedTree
-
The root of the tree has the largest node height of all nodes in the tree.
- getRootNode() - Method in class jebl.evolution.trees.RootedFromUnrooted
- getRootNode() - Method in class jebl.evolution.trees.RootedSubtree
-
The root of the tree has the largest node height of all nodes in the tree.
- getRootNode() - Method in interface jebl.evolution.trees.RootedTree
-
The root of the tree has the largest node height of all nodes in the tree.
- getRootNode() - Method in class jebl.evolution.trees.SimpleRootedTree
-
The root of the tree has the largest node height of all nodes in the tree.
- getRootProgressListener() - Method in class jebl.util.CompositeProgressListener
- getSampleCount() - Method in interface jebl.evolution.coalescent.IntervalList
-
get the total number of sampling events.
- getSampleCount() - Method in class jebl.evolution.coalescent.Intervals
- getScore() - Method in class jebl.evolution.align.Align
- getScore() - Method in class jebl.evolution.align.BartonSternberg
- getScore() - Method in class jebl.evolution.align.NeedlemanWunsch
- getScore() - Method in class jebl.evolution.align.NeedlemanWunschAffine
- getScore() - Method in class jebl.evolution.align.NeedlemanWunschLinearSpace
- getScore() - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
- getScore() - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
- getScore() - Method in class jebl.evolution.align.SmithWatermanLinearSpace
- getScore() - Method in class jebl.evolution.align.SmithWatermanLinearSpaceAffine
- getScore(char, char) - Method in interface jebl.evolution.align.scores.ScoreMatrix
- getScore(char, char) - Method in class jebl.evolution.align.scores.Scores
- getScore(Sequence, Sequence) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
- getScore(Sequence, Sequence) - Method in interface jebl.evolution.align.PairwiseAligner
- getScore(Tree) - Method in class jebl.evolution.parsimony.FitchParsimony
- getScore(Tree) - Method in interface jebl.evolution.parsimony.ParsimonyCriterion
-
Calculates the minimum number of steps for the parsimony reconstruction for the given tree.
- getScores() - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
-
The indices for these correspond to those for the getAlignments() matrix.
- getSE(Taxon) - Method in class jebl.evolution.characters.ContinuousCharacter
- getSelectedNodes() - Method in class jebl.evolution.trees.TreeSelectionChangeEvent
- getSequence(Taxon) - Method in class jebl.evolution.alignments.BasicAlignment
- getSequence(Taxon) - Method in class jebl.evolution.alignments.ResampledAlignment
- getSequence(Taxon) - Method in interface jebl.evolution.sequences.Sequences
- getSequenceCharacters() - Method in class jebl.evolution.sequences.BasicSequence
-
Get the sequence characters representing the sequence.
- getSequenceCharacters() - Method in class jebl.evolution.sequences.CodonSequence
-
Get the sequence characters representing the sequence.
- getSequenceList() - Method in interface jebl.evolution.alignments.Alignment
- getSequenceList() - Method in class jebl.evolution.alignments.BasicAlignment
- getSequenceList() - Method in class jebl.evolution.alignments.ResampledAlignment
- getSequences() - Method in class jebl.evolution.alignments.BasicAlignment
- getSequences() - Method in class jebl.evolution.alignments.ResampledAlignment
- getSequences() - Method in interface jebl.evolution.sequences.Sequences
- getSequenceType() - Method in class jebl.evolution.alignments.BasicAlignment
- getSequenceType() - Method in class jebl.evolution.alignments.ConsensusSequence
- getSequenceType() - Method in interface jebl.evolution.alignments.Pattern
- getSequenceType() - Method in interface jebl.evolution.alignments.Patterns
- getSequenceType() - Method in class jebl.evolution.alignments.ResampledAlignment
- getSequenceType() - Method in class jebl.evolution.sequences.BasicSequence
- getSequenceType() - Method in class jebl.evolution.sequences.CanonicalSequence
- getSequenceType() - Method in class jebl.evolution.sequences.CodonSequence
- getSequenceType() - Method in class jebl.evolution.sequences.FilteredSequence
- getSequenceType() - Method in interface jebl.evolution.sequences.Sequence
- getSequenceType() - Method in class jebl.evolution.sequences.TranslatedSequence
- getSequenceType() - Method in class jebl.evolution.substmodel.AbstractRateMatrix
- getSequenceType() - Method in interface jebl.evolution.substmodel.RateMatrix
-
Get the data type of this rate matrix
- getSetName(State) - Method in class jebl.evolution.sequences.StateClassification.Default
- getSetName(State) - Method in interface jebl.evolution.sequences.StateClassification
- getSetNames() - Method in class jebl.evolution.sequences.StateClassification.Default
- getSetNames() - Method in interface jebl.evolution.sequences.StateClassification
- getShape() - Method in class jebl.evolution.coalescent.LogisticGrowth
- getShuffled(int) - Static method in class jebl.math.OrderEnumerator.Utils
- getShuffledFactory() - Static method in class jebl.math.OrderEnumerator.Utils
- getSignificantFigures() - Method in class jebl.util.NumberFormatter
-
Get the number of significant figures to display when formatted.
- getSiteCount() - Method in interface jebl.evolution.alignments.Alignment
- getSiteCount() - Method in class jebl.evolution.alignments.BasicAlignment
- getSiteCount() - Method in class jebl.evolution.alignments.ResampledAlignment
- getSiteScores(Tree) - Method in class jebl.evolution.parsimony.FitchParsimony
-
Calculates the minimum number of siteScores for the parsimony reconstruction of a a set of character patterns on a tree.
- getSiteScores(Tree) - Method in interface jebl.evolution.parsimony.ParsimonyCriterion
-
Calculates the minimum number of steps for the parsimony reconstruction for the given tree.
- getSize() - Method in class jebl.evolution.distances.BasicDistanceMatrix
-
Gets the size of the matrix (which is square), i.e., number of rows or columns.
- getSize() - Method in interface jebl.evolution.distances.DistanceMatrix
-
Gets the size of the matrix (which is square), i.e., number of rows or columns.
- getSource() - Method in class jebl.evolution.alignments.ConsensusSequence
- getSource() - Method in class jebl.evolution.trees.FilteredRootedTree
- getSourceNode(Node) - Method in class jebl.evolution.trees.ReRootedTree
- getSplit(int) - Method in class jebl.evolution.trees.SplitSystem
-
get split
- getSplit(List<Taxon>, Tree, Edge, boolean[]) - Static method in class jebl.evolution.trees.SplitUtils
-
get split for branch associated with internal node
- getSplitCount() - Method in class jebl.evolution.trees.SplitSystem
-
get number of splits
- getSplits(List<Taxon>, Tree) - Static method in class jebl.evolution.trees.SplitUtils
-
creates a split system from a tree (using a pre-specified order of sequences)
- getSplits(Tree) - Static method in class jebl.evolution.trees.SplitUtils
-
creates a split system from a tree (using tree-induced order of sequences)
- getSplitVector() - Method in class jebl.evolution.trees.SplitSystem
-
get split vector
- getStartCodons() - Method in class jebl.evolution.sequences.GeneticCode
- getState(char) - Static method in class jebl.evolution.sequences.AminoAcids
- getState(char) - Static method in class jebl.evolution.sequences.Nucleotides
- getState(char) - Method in interface jebl.evolution.sequences.SequenceType
-
Get state whose code is the one-character string consisting only of code.
- getState(int) - Method in class jebl.evolution.alignments.ConsensusSequence
- getState(int) - Method in interface jebl.evolution.alignments.Pattern
-
Get the state for the ith taxon
- getState(int) - Static method in class jebl.evolution.sequences.AminoAcids
- getState(int) - Method in class jebl.evolution.sequences.BasicSequence
- getState(int) - Method in class jebl.evolution.sequences.CanonicalSequence
- getState(int) - Static method in class jebl.evolution.sequences.Codons
- getState(int) - Method in class jebl.evolution.sequences.CodonSequence
- getState(int) - Method in class jebl.evolution.sequences.FilteredSequence
- getState(int) - Static method in class jebl.evolution.sequences.Nucleotides
- getState(int) - Method in interface jebl.evolution.sequences.Sequence
- getState(int) - Method in interface jebl.evolution.sequences.SequenceType
-
Get state corresponding to a state index
- getState(String) - Static method in class jebl.evolution.sequences.AminoAcids
- getState(String) - Static method in class jebl.evolution.sequences.Codons
-
Gets the state object for the given code.
- getState(String) - Static method in class jebl.evolution.sequences.Nucleotides
- getState(String) - Method in interface jebl.evolution.sequences.SequenceType
-
Get state corresponding to a string code
- getState(NucleotideState, NucleotideState, NucleotideState) - Static method in class jebl.evolution.sequences.Codons
- getStateCount() - Static method in class jebl.evolution.sequences.AminoAcids
- getStateCount() - Static method in class jebl.evolution.sequences.Codons
- getStateCount() - Static method in class jebl.evolution.sequences.Nucleotides
- getStateCount() - Method in interface jebl.evolution.sequences.SequenceType
-
Get number of states including ambiguous states
- getStateCount(Sequence, State) - Static method in interface jebl.evolution.sequences.Sequence
-
Counts the number of occurances of a state
- getStateCount(State) - Method in interface jebl.evolution.alignments.Pattern
-
Returns the count of the given state in this pattern
- getStateDesc() - Method in class jebl.evolution.characters.DiscreteCharacter
- getStateDesc(int) - Method in class jebl.evolution.characters.DiscreteCharacter
- getStateFrequency(State) - Method in interface jebl.evolution.alignments.Pattern
-
Returns the frequent of the given state in this pattern
- getStateIndices() - Method in class jebl.evolution.alignments.ConsensusSequence
- getStateIndices() - Method in class jebl.evolution.sequences.BasicSequence
- getStateIndices() - Method in class jebl.evolution.sequences.CanonicalSequence
- getStateIndices() - Method in class jebl.evolution.sequences.CodonSequence
- getStateIndices() - Method in class jebl.evolution.sequences.FilteredSequence
- getStateIndices() - Method in interface jebl.evolution.sequences.Sequence
- getStateIndices(State[]) - Static method in class jebl.evolution.sequences.Utils
- getStates() - Method in class jebl.evolution.alignments.ConsensusSequence
- getStates() - Method in interface jebl.evolution.alignments.Pattern
- getStates() - Static method in class jebl.evolution.sequences.AminoAcids
- getStates() - Method in class jebl.evolution.sequences.BasicSequence
- getStates() - Method in class jebl.evolution.sequences.CanonicalSequence
- getStates() - Static method in class jebl.evolution.sequences.Codons
- getStates() - Method in class jebl.evolution.sequences.CodonSequence
- getStates() - Method in class jebl.evolution.sequences.FilteredSequence
- getStates() - Static method in class jebl.evolution.sequences.Nucleotides
- getStates() - Method in interface jebl.evolution.sequences.Sequence
- getStates() - Method in interface jebl.evolution.sequences.SequenceType
-
Get a list of states ordered by their indices.
- getStates(Tree, Node) - Method in class jebl.evolution.parsimony.FitchParsimony
-
Returns the reconstructed character states for a given node in the tree.
- getStates(Tree, Node) - Method in interface jebl.evolution.parsimony.ParsimonyCriterion
-
Returns the reconstructed character states for a given node in the tree.
- getStateSet() - Method in interface jebl.evolution.alignments.Pattern
- getStateSet(String) - Method in class jebl.evolution.sequences.StateClassification.Default
- getStateSet(String) - Method in interface jebl.evolution.sequences.StateClassification
- getStdev() - Method in class jebl.evolution.align.SequenceShuffler
- getStopCodonCount() - Method in class jebl.evolution.sequences.GeneticCode
-
Returns the number of terminator amino acids.
- getStopCodonCount(Sequence) - Static method in class jebl.evolution.sequences.Utils
-
Counts the number of stop codons in an amino acid sequence
- getStopCodons() - Method in class jebl.evolution.sequences.GeneticCode
- getString() - Method in class jebl.evolution.alignments.ConsensusSequence
- getString() - Method in class jebl.evolution.sequences.BasicSequence
- getString() - Method in class jebl.evolution.sequences.CanonicalSequence
- getString() - Method in class jebl.evolution.sequences.CodonSequence
- getString() - Method in class jebl.evolution.sequences.FilteredSequence
- getString() - Method in interface jebl.evolution.sequences.Sequence
- getSubmatrix(Collection<Taxon>) - Method in class jebl.evolution.distances.BasicDistanceMatrix
-
Gets a sub-matrix for only those taxa in the collection (all of which should be present in this matrix).
- getSubmatrix(Collection<Taxon>) - Method in interface jebl.evolution.distances.DistanceMatrix
-
Gets a sub-matrix for only those taxa in the collection (all of which should be present in this matrix).
- getSubSequence(Sequence, int, int) - Static method in interface jebl.evolution.sequences.Sequence
-
Returns a sub-sequence for states from, to (inclusive).
- getSuggestedOrdering(OrderEnumerator) - Method in interface jebl.math.OrthogonalHints
-
If there is a "best" ordering to use it can be specified here, if not should return null
- getSum(double[]) - Static method in class jebl.util.Utils
-
Calculate the total of an array
- getSupportAttributeName() - Method in class jebl.evolution.trees.ConsensusTreeBuilder
- getTaxa() - Method in class jebl.evolution.alignments.BasicAlignment
- getTaxa() - Method in interface jebl.evolution.alignments.Pattern
- getTaxa() - Method in interface jebl.evolution.alignments.Patterns
- getTaxa() - Method in class jebl.evolution.alignments.ResampledAlignment
- getTaxa() - Method in interface jebl.evolution.characters.Character
-
get a Set
of all the taxa for this character - getTaxa() - Method in class jebl.evolution.characters.ContinuousCharacter
- getTaxa() - Method in class jebl.evolution.characters.DiscreteCharacter
- getTaxa() - Method in class jebl.evolution.distances.BasicDistanceMatrix
- getTaxa() - Method in interface jebl.evolution.distances.DistanceMatrix
- getTaxa() - Method in class jebl.evolution.trees.CompactRootedTree
- getTaxa() - Method in class jebl.evolution.trees.FilteredRootedTree
- getTaxa() - Method in class jebl.evolution.trees.MutableRootedTree
- getTaxa() - Method in class jebl.evolution.trees.ReRootedTree
- getTaxa() - Method in class jebl.evolution.trees.RootedFromUnrooted
- getTaxa() - Method in class jebl.evolution.trees.RootedSubtree
- getTaxa() - Method in class jebl.evolution.trees.SimpleRootedTree
- getTaxa() - Method in class jebl.evolution.trees.SimpleTree
- getTaxa() - Method in class jebl.evolution.trees.SplitSystem
-
get taxon list
- getTaxa() - Method in interface jebl.evolution.trees.Tree
- getTaxon() - Method in class jebl.evolution.alignments.ConsensusSequence
- getTaxon() - Method in class jebl.evolution.sequences.BasicSequence
- getTaxon() - Method in class jebl.evolution.sequences.CanonicalSequence
- getTaxon() - Method in class jebl.evolution.sequences.CodonSequence
- getTaxon() - Method in class jebl.evolution.sequences.FilteredSequence
- getTaxon() - Method in interface jebl.evolution.sequences.Sequence
- getTaxon(String) - Static method in class jebl.evolution.taxa.Taxon
-
A static method that returns a Taxon object with the given name.
- getTaxon(Node) - Method in class jebl.evolution.trees.CompactRootedTree
- getTaxon(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
- getTaxon(Node) - Method in class jebl.evolution.trees.MutableRootedTree
- getTaxon(Node) - Method in class jebl.evolution.trees.ReRootedTree
- getTaxon(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
- getTaxon(Node) - Method in class jebl.evolution.trees.RootedSubtree
- getTaxon(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
- getTaxon(Node) - Method in class jebl.evolution.trees.SimpleTree
- getTaxon(Node) - Method in interface jebl.evolution.trees.Tree
- getTaxonomicLevel() - Method in class jebl.evolution.taxa.Taxon
-
get the taxonomic level of the taxon
- getTaxonomicLevel(String) - Static method in class jebl.evolution.taxa.TaxonomicLevel
-
A static method that returns a TaxonomicLevel object with the given name.
- getTaxonomicLevels() - Static method in class jebl.evolution.taxa.TaxonomicLevel
-
Returns a Set containing all the currently created taxonomic levels.
- getTestSequence1() - Static method in class jebl.evolution.sequences.SequenceTester
- getTestSequence1(String[]) - Static method in class jebl.evolution.sequences.SequenceTester
- getTestSequence2() - Static method in class jebl.evolution.sequences.SequenceTester
- getTestSequence2(String[]) - Static method in class jebl.evolution.sequences.SequenceTester
- getThreeLetterName() - Method in class jebl.evolution.sequences.AminoAcidState
- getTime() - Method in class jebl.evolution.coalescent.ExponentialLogistic
- getTipCount(RootedTree, Node) - Static method in class jebl.evolution.trees.RootedTreeUtils
-
Return the number of leaves under this node.
- getTipsForTaxa(RootedTree, Collection<Taxon>) - Static method in class jebl.evolution.trees.RootedTreeUtils
-
Gets a set of external nodes that correspond to the given taxa.
- getTotal(double[]) - Static method in class jebl.math.Random
- getTotal(double[], int, int) - Static method in class jebl.math.Random
- getTotalDuration() - Method in interface jebl.evolution.coalescent.IntervalList
-
get the total duration of these intervals.
- getTotalDuration() - Method in class jebl.evolution.coalescent.Intervals
- getTransitionProbabilities(double[][]) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
-
A utility method for speed, transfers trans prob information quickly into store
- getTransitionProbabilities(double[][]) - Method in class jebl.evolution.substmodel.MatrixExponential
-
A utility method for speed, transfers trans prob information quickly into store
- getTransitionProbabilities(double[][]) - Method in interface jebl.evolution.substmodel.RateMatrix
-
A utility method for speed, transfers trans prob information quickly into store.
- getTransitionProbability(int, int) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
- getTransitionProbability(int, int) - Method in class jebl.evolution.substmodel.MatrixExponential
- getTransitionProbability(int, int) - Method in interface jebl.evolution.substmodel.RateMatrix
- getTranslation(String) - Method in class jebl.evolution.sequences.GeneticCode
-
Returns the state associated with AminoAcid represented by the three nucleotides.
- getTranslation(CodonState) - Method in class jebl.evolution.sequences.GeneticCode
-
Returns the state associated with AminoAcid represented by codonState.
- getTranslation(NucleotideState, NucleotideState, NucleotideState) - Method in class jebl.evolution.sequences.GeneticCode
-
Returns the state associated with AminoAcid represented by the three nucleotides.
- getTree() - Method in class jebl.evolution.trees.TreeChangeEvent
- getTripletCode(AminoAcidState) - Static method in class jebl.evolution.sequences.AminoAcids
- getType() - Method in interface jebl.evolution.characters.Character
-
return the CharacterType of the character
- getType() - Method in class jebl.evolution.characters.ContinuousCharacter
- getType() - Method in class jebl.evolution.characters.DiscreteCharacter
- getType() - Method in class jebl.evolution.sequences.AminoAcidState
- getType() - Method in class jebl.evolution.sequences.CodonState
- getType() - Method in class jebl.evolution.sequences.NucleotideState
- getType() - Method in class jebl.evolution.sequences.State
- getUniqueName() - Method in interface jebl.evolution.substmodel.RateMatrix
- getUniqueName() - Method in class jebl.evolution.substmodel.WAG
- getUnknownState() - Static method in class jebl.evolution.sequences.AminoAcids
- getUnknownState() - Static method in class jebl.evolution.sequences.Codons
- getUnknownState() - Static method in class jebl.evolution.sequences.Nucleotides
- getUnknownState() - Method in interface jebl.evolution.sequences.SequenceType
-
Get state corresponding to an unknown
- getUpperBound() - Method in class jebl.math.OrthogonalLineFunction
- getUpperBound() - Method in interface jebl.math.UnivariateFunction
-
get upper bound of argument
- getUpperBound(int) - Method in class jebl.evolution.coalescent.Coalescent
- getUpperBound(int) - Method in class jebl.evolution.coalescent.ConstantPopulation
- getUpperBound(int) - Method in class jebl.evolution.coalescent.ConstExponential
- getUpperBound(int) - Method in class jebl.evolution.coalescent.ConstLogistic
- getUpperBound(int) - Method in interface jebl.evolution.coalescent.DemographicFunction
-
Returns the upper bound of the nth argument of this function.
- getUpperBound(int) - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
-
Returns the upper bound of the nth argument of this function.
- getUpperBound(int) - Method in class jebl.evolution.coalescent.Expansion
- getUpperBound(int) - Method in class jebl.evolution.coalescent.ExponentialGrowth
- getUpperBound(int) - Method in class jebl.evolution.coalescent.ExponentialLogistic
- getUpperBound(int) - Method in interface jebl.math.MultivariateFunction
-
get upper bound of argument n
- getV() - Method in class jebl.evolution.align.NeedlemanWunschLinearSpace
- getValue(Taxon) - Method in interface jebl.evolution.characters.Character
-
get a value for a taxon containing the character
- getValue(Taxon) - Method in class jebl.evolution.characters.ContinuousCharacter
- getValue(Taxon) - Method in class jebl.evolution.characters.DiscreteCharacter
- getWeight() - Method in interface jebl.evolution.alignments.Pattern
-
Get the weight of this pattern
- getX() - Method in class jebl.evolution.align.Traceback
- getY() - Method in class jebl.evolution.align.Traceback
- getZero() - Static method in class jebl.math.OrderEnumerator.Utils
- getZeroFactory() - Static method in class jebl.math.OrderEnumerator.Utils
- gradient(MultivariateFunction, double[]) - Static method in class jebl.math.NumericalDerivative
-
determine gradient
- gradient(MultivariateFunction, double[], double[]) - Static method in class jebl.math.NumericalDerivative
-
determine gradient
- Graph - Interface in jebl.evolution.graphs
- Graph.NoEdgeException - Exception 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 - jebl.evolution.trees.ConsensusTreeBuilder.Method
- GREEDY - jebl.evolution.trees.TreeBuilderFactory.ConsensusMethod
- guessSequenceType(CharSequence) - Static method in class jebl.evolution.sequences.Utils
-
Guess type of sequence from contents.
H
- H_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
- H_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
- Hamming - Class in jebl.evolution.align.scores
- Hamming() - Constructor for class jebl.evolution.align.scores.Hamming
- hashCode() - Method in class jebl.evolution.sequences.BasicSequence
- hashCode() - Method in class jebl.evolution.sequences.CodonSequence
- hashCode() - Method in class jebl.evolution.taxa.Taxon
- hashCode() - Method in class jebl.util.FixedBitSet
- hashCode() - Method in class jebl.util.HashPair
- hasHeights() - Method in class jebl.evolution.trees.CompactRootedTree
- hasHeights() - Method in class jebl.evolution.trees.FilteredRootedTree
- hasHeights() - Method in class jebl.evolution.trees.MutableRootedTree
- hasHeights() - Method in class jebl.evolution.trees.ReRootedTree
- hasHeights() - Method in class jebl.evolution.trees.RootedFromUnrooted
- hasHeights() - Method in class jebl.evolution.trees.RootedSubtree
- hasHeights() - Method in interface jebl.evolution.trees.RootedTree
- hasHeights() - Method in class jebl.evolution.trees.SimpleRootedTree
- hasHeights() - Method in class jebl.evolution.trees.TransformedRootedTree
- HashPair<T> - Class in jebl.util
-
A pair suitable for use in a HashMap.
- HashPair(T, T) - Constructor for class jebl.util.HashPair
- hasIntegral() - Method in class jebl.evolution.coalescent.CataclysmicDemographic
- hasIntegral() - Method in class jebl.evolution.coalescent.ConstantPopulation
- hasIntegral() - Method in class jebl.evolution.coalescent.ConstExponential
- hasIntegral() - Method in class jebl.evolution.coalescent.ConstLogistic
- hasIntegral() - Method in interface jebl.evolution.coalescent.DemographicFunction
-
returns whether an analytical expression for the integral is implemented
- hasIntegral() - Method in class jebl.evolution.coalescent.EmpiricalDemographicFunction
- hasIntegral() - Method in class jebl.evolution.coalescent.Expansion
- hasIntegral() - Method in class jebl.evolution.coalescent.ExponentialLogistic
- hasIntegral() - Method in class jebl.evolution.coalescent.LogisticGrowth
- hasLengths() - Method in class jebl.evolution.trees.CompactRootedTree
- hasLengths() - Method in class jebl.evolution.trees.FilteredRootedTree
- hasLengths() - Method in class jebl.evolution.trees.MutableRootedTree
- hasLengths() - Method in class jebl.evolution.trees.ReRootedTree
- hasLengths() - Method in class jebl.evolution.trees.RootedFromUnrooted
- hasLengths() - Method in class jebl.evolution.trees.RootedSubtree
- hasLengths() - Method in interface jebl.evolution.trees.RootedTree
- hasLengths() - Method in class jebl.evolution.trees.SimpleRootedTree
- hasLengths() - Method in class jebl.evolution.trees.TransformedRootedTree
- hasMore() - Method in interface jebl.math.OrderEnumerator
-
If hasMore returns false reset should be called
- hasNextSubtask() - Method in class jebl.util.CompositeProgressListener
- hasSplit(boolean[]) - Method in class jebl.evolution.trees.SplitSystem
-
+ test whether a split is contained in this split system (assuming the same leaf order)
- hasTree() - Method in class jebl.evolution.io.NewickImporter
- hasTree() - Method in class jebl.evolution.io.NexusImporter
-
If not currently reading a TREES block then read ahead to the next TREES block, parsing TRANSLATE and TAXA blocks in the process if necessary.
- hasTree() - Method in interface jebl.evolution.io.TreeImporter
-
This can be used to read one tree at a time in a loop:
List
return whether another tree is available.trees = new ArrayList (); while (hasTree()) { trees.add(importNextTree()); } - HKY - 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 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 - 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 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 in jebl.evolution.coalescent
- IntervalList.Utils - Class in jebl.evolution.coalescent
- Intervals - Class in jebl.evolution.coalescent
-
A concrete class for a set of coalescent intevals.
- Intervals(int) - Constructor for class jebl.evolution.coalescent.Intervals
- Intervals(RootedTree) - Constructor for class jebl.evolution.coalescent.Intervals
- INVERTEBRATE_MT - Static variable in class jebl.evolution.sequences.GeneticCode
- isAcyclical(Graph) - Method in class jebl.evolution.graphs.Utils
- isAllGaps() - Method in class jebl.evolution.align.ProfileCharacter
- isAmbiguous() - Method in class jebl.evolution.sequences.State
- isATstate(State) - Static method in class jebl.evolution.sequences.Nucleotides
- isBinary(RootedTree) - Static method in class jebl.evolution.trees.RootedTreeUtils
- isBinary(RootedTree) - Static method in class jebl.evolution.trees.Utils
- isBinaryCoalescent() - Method in interface jebl.evolution.coalescent.IntervalList
-
Checks whether this set of coalescent intervals is fully resolved (i.e.
- isBinaryCoalescent() - Method in class jebl.evolution.coalescent.Intervals
- isCanceled() - Method in class jebl.util.BasicProgressListener
- isCanceled() - Method in interface jebl.util.Cancelable
- isCanceled() - Method in class jebl.util.CompositeProgressListener
- isCanceled() - Method in class jebl.util.ProgressListener
-
This method must be implemented by all subclasses.
- isCanceled() - Method in class jebl.util.ProgressListener.Wrapper
- isCharacterAscii(char) - Static method in class jebl.evolution.io.ByteBuilder
- isCoalescentOnly() - Method in interface jebl.evolution.coalescent.IntervalList
-
Checks whether this set of coalescent intervals coalescent only (i.e.
- isCoalescentOnly() - Method in class jebl.evolution.coalescent.Intervals
- isConnected(Graph) - Method in class jebl.evolution.graphs.Utils
- isContains(String[], String) - Static method in class jebl.util.Utils
-
Test if a string occurs within a set
- isExternal(Edge) - Method in class jebl.evolution.trees.SimpleTree
- isExternal(Node) - Method in class jebl.evolution.trees.CompactRootedTree
- isExternal(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
- isExternal(Node) - Method in class jebl.evolution.trees.MutableRootedTree
- isExternal(Node) - Method in class jebl.evolution.trees.ReRootedTree
- isExternal(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
- isExternal(Node) - Method in class jebl.evolution.trees.RootedSubtree
- isExternal(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
- isExternal(Node) - Method in class jebl.evolution.trees.SimpleTree
- isExternal(Node) - Method in interface jebl.evolution.trees.Tree
- isGap() - Method in class jebl.evolution.sequences.AminoAcidState
- isGap() - Method in class jebl.evolution.sequences.CodonState
- isGap() - Method in class jebl.evolution.sequences.NucleotideState
- isGap() - Method in class jebl.evolution.sequences.State
- isGap(AminoAcidState) - Static method in class jebl.evolution.sequences.AminoAcids
- isGap(CodonState) - Static method in class jebl.evolution.sequences.Codons
- isGap(NucleotideState) - Static method in class jebl.evolution.sequences.Nucleotides
- isGap(State) - Method in interface jebl.evolution.sequences.SequenceType
- isGCstate(State) - Static method in class jebl.evolution.sequences.Nucleotides
- isGeneratedTreeName(String) - Static method in class jebl.evolution.io.NexusExporter
- isHeightsKnown() - Method in class jebl.evolution.trees.CompactRootedTree
- isHeightsKnown() - Method in class jebl.evolution.trees.FilteredRootedTree
- isHeightsKnown() - Method in class jebl.evolution.trees.MutableRootedTree
- isHeightsKnown() - Method in class jebl.evolution.trees.ReRootedTree
- isHeightsKnown() - Method in class jebl.evolution.trees.RootedFromUnrooted
- isHeightsKnown() - Method in class jebl.evolution.trees.RootedSubtree
- isHeightsKnown() - Method in interface jebl.evolution.trees.RootedTree
- isHeightsKnown() - Method in class jebl.evolution.trees.SimpleRootedTree
- isHeightsKnown() - Method in class jebl.evolution.trees.TransformedRootedTree
- isIndeterminate() - Method in class jebl.util.BasicProgressListener
- isLengthsKnown() - Method in class jebl.evolution.trees.CompactRootedTree
- isLengthsKnown() - Method in class jebl.evolution.trees.FilteredRootedTree
- isLengthsKnown() - Method in class jebl.evolution.trees.MutableRootedTree
- isLengthsKnown() - Method in class jebl.evolution.trees.ReRootedTree
- isLengthsKnown() - Method in class jebl.evolution.trees.RootedFromUnrooted
- isLengthsKnown() - Method in class jebl.evolution.trees.RootedSubtree
- isLengthsKnown() - Method in interface jebl.evolution.trees.RootedTree
- isLengthsKnown() - Method in class jebl.evolution.trees.SimpleRootedTree
- isLengthsKnown() - Method in class jebl.evolution.trees.TransformedRootedTree
- isMonophyletic(RootedTree, Set<Node>) - Static method in class jebl.evolution.trees.RootedTreeUtils
-
Performs the a monophyly test on a set of tip nodes.
- isOrdered() - Method in class jebl.evolution.characters.DiscreteCharacter
- isPossibleTransition(char, char) - Static method in class jebl.evolution.sequences.Nucleotides
- isPossibleTransition(State, State) - Static method in class jebl.evolution.sequences.Nucleotides
- isPossibleTransversion(char, char) - Static method in class jebl.evolution.sequences.Nucleotides
- isPossibleTransversion(State, State) - Static method in class jebl.evolution.sequences.Nucleotides
- isPredominantlyRNA(CharSequence, int) - Static method in class jebl.evolution.sequences.Utils
-
Is the given NucleotideSequence predominantly RNA? (i.e the more occurrences of "U" than "T")
- isPurine(State) - Static method in class jebl.evolution.sequences.Nucleotides
- isPyrimidine(State) - Static method in class jebl.evolution.sequences.Nucleotides
- isRoot(Node) - Method in class jebl.evolution.trees.CompactRootedTree
- isRoot(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
- isRoot(Node) - Method in class jebl.evolution.trees.MutableRootedTree
- isRoot(Node) - Method in class jebl.evolution.trees.ReRootedTree
- isRoot(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
- isRoot(Node) - Method in class jebl.evolution.trees.RootedSubtree
- isRoot(Node) - Method in interface jebl.evolution.trees.RootedTree
- isRoot(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
- isRootedMethod(TreeBuilderFactory.Method) - Static method in class jebl.evolution.trees.TreeBuilderFactory
- isSame(boolean[], boolean[]) - Static method in class jebl.evolution.trees.SplitUtils
-
Checks two splits for identity.
- isStartCodon(CodonState) - Method in class jebl.evolution.sequences.GeneticCode
-
Deprecated.
- isStartCodonString(String) - Method in class jebl.evolution.sequences.GeneticCode
-
Checks whether all possible disambiguations of a given nucleotide triplet string represents a start codon.
- isStop() - Method in class jebl.evolution.sequences.AminoAcidState
- isStopCodon(CodonState) - Method in class jebl.evolution.sequences.GeneticCode
-
Deprecated.
- isStopCodonString(String) - Method in class jebl.evolution.sequences.GeneticCode
-
Checks whether a given String represents a stop codon.
- isSupportAsPercent() - Method in class jebl.evolution.trees.ConsensusTreeBuilder
- isTransition(State, State) - Static method in class jebl.evolution.sequences.Nucleotides
- isTransversion(State, State) - Static method in class jebl.evolution.sequences.Nucleotides
- isTree(Graph) - Method in class jebl.evolution.graphs.Utils
- isUltrametric(RootedTree) - Static method in class jebl.evolution.trees.Utils
- isUltrametric(RootedTree, double) - Static method in class jebl.evolution.trees.RootedTreeUtils
- isUnknown(AminoAcidState) - Static method in class jebl.evolution.sequences.AminoAcids
- isUnknown(CodonState) - Static method in class jebl.evolution.sequences.Codons
- isUnknown(NucleotideState) - Static method in class jebl.evolution.sequences.Nucleotides
- isUnknown(State) - Method in interface jebl.evolution.sequences.SequenceType
- iterator() - Method in class jebl.evolution.io.NewickImporter
-
Returns an iterator over a set of elements of type T.
- iterator() - Method in class jebl.evolution.io.NexusImporter
- IUB - Static variable in class jebl.evolution.align.scores.NucleotideScores
J
- J_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
- JackknifedAlignment - Class in jebl.evolution.alignments
-
Date: 17/01/2006 Time: 08:18:32
- JackknifedAlignment(Alignment, double) - Constructor for class jebl.evolution.alignments.JackknifedAlignment
- JackknifedAlignment(Alignment, double, long) - Constructor for class jebl.evolution.alignments.JackknifedAlignment
- JackknifedAlignment(Alignment, double, Random) - Constructor for class jebl.evolution.alignments.JackknifedAlignment
- jebl.evolution.align - package jebl.evolution.align
-
Provides classes and interfaces for pairwise alignment of two sequences.
- jebl.evolution.align.scores - package jebl.evolution.align.scores
- jebl.evolution.aligners - package jebl.evolution.aligners
- jebl.evolution.alignments - package jebl.evolution.alignments
- jebl.evolution.characters - package jebl.evolution.characters
- jebl.evolution.coalescent - package jebl.evolution.coalescent
- jebl.evolution.distances - package jebl.evolution.distances
- jebl.evolution.graphs - package jebl.evolution.graphs
- jebl.evolution.io - package jebl.evolution.io
- jebl.evolution.parsimony - package jebl.evolution.parsimony
- jebl.evolution.sequences - package jebl.evolution.sequences
- jebl.evolution.substmodel - package jebl.evolution.substmodel
- jebl.evolution.taxa - package jebl.evolution.taxa
- jebl.evolution.treemetrics - package jebl.evolution.treemetrics
- jebl.evolution.trees - package jebl.evolution.trees
- jebl.evolution.treesimulation - package jebl.evolution.treesimulation
- jebl.math - package jebl.math
- jebl.util - package jebl.util
- JukesCantor - Class in jebl.evolution.align.scores
-
Jukes Cantor assumes equal substitution frequencies and equal nucleotide equilibrium frequencies.
- JukesCantor - jebl.evolution.trees.TreeBuilderFactory.DistanceModel
- JukesCantor(float) - Constructor for class jebl.evolution.align.scores.JukesCantor
- JukesCantorDistanceMatrix - Class in jebl.evolution.distances
-
Compute jukes-cantor corrected distance matrix for a set of aligned sequences.
- JukesCantorDistanceMatrix(Alignment, ProgressListener) - Constructor for class jebl.evolution.distances.JukesCantorDistanceMatrix
- JukesCantorDistanceMatrix(Alignment, ProgressListener, boolean) - Constructor for class jebl.evolution.distances.JukesCantorDistanceMatrix
K
- K_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
- K_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
L
- L_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
- leftNb(RootedTree, Node) - Static method in class jebl.evolution.trees.Utils
-
Left Neighbour of a tip (taxon).
- length() - Method in class jebl.evolution.io.ByteBuilder
- lnGamma(double) - Static method in class jebl.math.GammaFunction
-
log Gamma function: ln(gamma(alpha)) for alpha>0, accurate to 10 decimal places
- loadTrees(int, int) - Method in class jebl.evolution.trees.CalculateSplitRates
- LogisticGrowth - Class in jebl.evolution.coalescent
-
This class models logistic growth.
- LogisticGrowth() - Constructor for class jebl.evolution.coalescent.LogisticGrowth
-
Construct demographic model with default settings
- LogisticGrowth(double, double, double) - Constructor for class jebl.evolution.coalescent.LogisticGrowth
-
Construct demographic model with given settings
- LOWER - 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 - jebl.util.MaybeBoolean
- MaybeBoolean - Enum in jebl.util
-
A tri-state boolean value that can also be "Maybe" besides True and False.
- MEGAExporter - Class in jebl.evolution.io
-
* Export to MEGA.
- MEGAExporter(Writer, String) - Constructor for class jebl.evolution.io.MEGAExporter
- MIGRATION - 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 - jebl.evolution.trees.ConsensusTreeBuilder.Method
- MRCAC - 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 - 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.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 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 - jebl.evolution.trees.TreeBiPartitionInfo.DistanceNorm
- NORM2 - jebl.evolution.trees.TreeBiPartitionInfo.DistanceNorm
- NOTHING - 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.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.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 - 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.BaseEdge
- removeAttribute(String) - Method in class jebl.evolution.trees.BaseNode
- removeAttribute(String) - Method in class jebl.evolution.trees.FilteredRootedTree
- removeAttribute(String) - Method in class jebl.evolution.trees.MutableRootedTree
- removeAttribute(String) - Method in class jebl.evolution.trees.ReRootedTree
- removeAttribute(String) - Method in class jebl.evolution.trees.RootedFromUnrooted
- removeAttribute(String) - Method in class jebl.evolution.trees.RootedSubtree
- removeAttribute(String) - Method in class jebl.evolution.trees.SimpleRootedTree
- removeAttribute(String) - Method in class jebl.evolution.trees.SimpleTree
- removeAttribute(String) - Method in interface jebl.util.Attributable
- removeAttribute(String) - Method in class jebl.util.AttributableHelper
- removeChild(Node, Node) - Method in class jebl.evolution.trees.MutableRootedTree
-
Remove a child node.
- removeFeedbackAction(String) - Method in class jebl.util.CompositeProgressListener
- removeFeedbackAction(String) - Method in class jebl.util.ProgressListener
-
Removes a feedback action previously added using
ProgressListener.addFeedbackAction(String, jebl.util.SimpleListener)
. - removeFeedbackAction(String) - Method in class jebl.util.ProgressListener.Wrapper
- removeInternalNode(Node) - Method in class jebl.evolution.trees.MutableRootedTree
-
Remove internal node.
- removeProfileCharacter(ProfileCharacter) - Method in class jebl.evolution.align.ProfileCharacter
- removeProgressListener(ProgressListener) - Method in interface jebl.evolution.aligners.Aligner
- removeProgressListener(ProgressListener) - Method in class jebl.evolution.trees.ClusteringTreeBuilder
- removeProgressListener(ProgressListener) - Method in class jebl.evolution.trees.ConsensusTreeBuilder
-
Stops a ProgressListener from receiving progress.
- removeProgressListener(ProgressListener) - Method in interface jebl.evolution.trees.TreeBuilder
- renameTaxa(Taxon, Taxon) - Method in class jebl.evolution.trees.CompactRootedTree
- renameTaxa(Taxon, Taxon) - Method in class jebl.evolution.trees.FilteredRootedTree
- renameTaxa(Taxon, Taxon) - Method in class jebl.evolution.trees.MutableRootedTree
- renameTaxa(Taxon, Taxon) - Method in class jebl.evolution.trees.ReRootedTree
- renameTaxa(Taxon, Taxon) - Method in class jebl.evolution.trees.RootedFromUnrooted
- renameTaxa(Taxon, Taxon) - Method in class jebl.evolution.trees.RootedSubtree
- renameTaxa(Taxon, Taxon) - Method in class jebl.evolution.trees.SimpleRootedTree
- renameTaxa(Taxon, Taxon) - Method in class jebl.evolution.trees.SimpleTree
- renameTaxa(Taxon, Taxon) - Method in interface jebl.evolution.trees.Tree
- replaceStates(Sequence, List<State>, State) - Static method in interface jebl.evolution.sequences.Sequence
-
Searchers and replaces a sequence of any states given
- replaceStates(State[], List<State>, State) - Static method in class jebl.evolution.sequences.Utils
-
Searchers and replaces a sequence of any states given
- ReRootedTree - Class in jebl.evolution.trees
-
A rooted tree concrete class that wraps another tree and provides a differently rooted view of that tree.
- ReRootedTree(RootedTree, Node, Node, double) - Constructor for class jebl.evolution.trees.ReRootedTree
-
Make a copy of the given unrooted tree
- reRootWithOutgroup(Node, Set<String>) - Method in class jebl.evolution.trees.MutableRootedTree
-
Re-root tree using an outgroup.
- ResampledAlignment - Class in jebl.evolution.alignments
-
Date: 17/01/2006 Time: 08:08:44
- ResampledAlignment() - Constructor for class jebl.evolution.alignments.ResampledAlignment
- reset() - Method in interface jebl.math.OrderEnumerator
-
Reset back to starting state, may have a differnet number of values, and a different ordering after a reset!
- resetEvents() - Method in class jebl.evolution.coalescent.Intervals
- reverse(State[]) - Static method in class jebl.evolution.sequences.Utils
- reverseComplement(String) - Static method in class jebl.evolution.sequences.Utils
- reverseComplement(NucleotideState[]) - Static method in class jebl.evolution.sequences.Utils
- reverseComplementWithGaps(String) - Static method in class jebl.evolution.sequences.Utils
- reverseMatrix(double[][]) - Static method in class jebl.math.MatrixCalc
-
reverse a matrix
- reverseVector(double[]) - Static method in class jebl.math.MatrixCalc
-
reverse a vector
- rightNb(RootedTree, Node) - Static method in class jebl.evolution.trees.Utils
-
Right Neighbour of a tip (taxon).
- RobinsonsFouldMetric - Class in jebl.evolution.treemetrics
- RobinsonsFouldMetric() - Constructor for class jebl.evolution.treemetrics.RobinsonsFouldMetric
- RobinsonsFouldMetric(List<Taxon>) - Constructor for class jebl.evolution.treemetrics.RobinsonsFouldMetric
- RootedFromUnrooted - Class in jebl.evolution.trees
-
Root an unrooted tree.
- RootedFromUnrooted(Tree, Node, boolean) - Constructor for class jebl.evolution.trees.RootedFromUnrooted
-
Root tree at some internal node.
- RootedFromUnrooted(Tree, Node, Node, double) - Constructor for class jebl.evolution.trees.RootedFromUnrooted
-
Root source by creating a new internal node whose children are (the adjacent) left and right.
- RootedSubtree - Class in jebl.evolution.trees
-
A simple, immutable rooted tree implementation that is a subtree of an existing tree subtending a specified set of taxa..
- RootedSubtree(RootedTree, Set<Taxon>) - Constructor for class jebl.evolution.trees.RootedSubtree
-
Make a copy of the given rooted tree
- RootedTree - Interface in jebl.evolution.trees
-
A tree with a root (node with maximum height).
- RootedTreeMetric - Interface in jebl.evolution.treemetrics
- RootedTreeUtils - Class in jebl.evolution.trees
-
Static utility functions for rooted trees.
- rootTheTree(Tree) - Static method in class jebl.evolution.trees.Utils
-
Return a rooted tree from any tree.
- rootTreeAtCenter(RootedTree) - Static method in class jebl.evolution.trees.ReRootedTree
-
Root any tree by locating the "center" of tree and adding a new root node at that point
- rootTreeAtCenter(Tree) - Static method in class jebl.evolution.trees.Utils
-
Root any tree by locating the "center" of tree and adding a new root node at that point
S
- S_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
- S_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
- safeNodeHeight(RootedTree, Node) - Static method in class jebl.evolution.trees.Utils
- same(double, double) - Static method in class jebl.math.MachineAccuracy
- SAMPLE - 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.BaseEdge
- setAttribute(String, Object) - Method in class jebl.evolution.trees.BaseNode
- setAttribute(String, Object) - Method in class jebl.evolution.trees.FilteredRootedTree
- setAttribute(String, Object) - Method in class jebl.evolution.trees.MutableRootedTree
- setAttribute(String, Object) - Method in class jebl.evolution.trees.ReRootedTree
- setAttribute(String, Object) - Method in class jebl.evolution.trees.RootedFromUnrooted
- setAttribute(String, Object) - Method in class jebl.evolution.trees.RootedSubtree
- setAttribute(String, Object) - Method in class jebl.evolution.trees.SimpleRootedTree
- setAttribute(String, Object) - Method in class jebl.evolution.trees.SimpleTree
- setAttribute(String, Object) - Method in interface jebl.util.Attributable
-
Sets an named attribute for this object.
- setAttribute(String, Object) - Method in class jebl.util.AttributableHelper
- setCataclysmTime(double) - Method in class jebl.evolution.coalescent.CataclysmicDemographic
- setCommentDelimiters(char) - Method in class jebl.evolution.io.ImportHelper
- setCommentDelimiters(char, char) - Method in class jebl.evolution.io.ImportHelper
- setCommentDelimiters(char, char, char) - Method in class jebl.evolution.io.ImportHelper
- setCommentDelimiters(char, char, char, char, char) - Method in class jebl.evolution.io.ImportHelper
- setCommentWriter(Writer) - Method in class jebl.evolution.io.ImportHelper
- setComplete() - Method in class jebl.util.CompositeProgressListener
- setConceptuallyUnrooted(boolean) - Method in class jebl.evolution.trees.CompactRootedTree
- setConceptuallyUnrooted(boolean) - Method in class jebl.evolution.trees.MutableRootedTree
- setConceptuallyUnrooted(boolean) - Method in class jebl.evolution.trees.RootedSubtree
- setConceptuallyUnrooted(boolean) - Method in class jebl.evolution.trees.SimpleRootedTree
- setDebug(boolean) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
- setDecimalPlaces(int) - Method in class jebl.util.NumberFormatter
-
Set the number of decimal places to display when formatted.
- setDeclineRate(double) - Method in class jebl.evolution.coalescent.CataclysmicDemographic
-
sets the decline rate.
- setDesc(String) - Method in interface jebl.evolution.characters.Character
-
set the description of the character
- setDesc(String) - Method in class jebl.evolution.characters.ContinuousCharacter
- setDesc(String) - Method in class jebl.evolution.characters.DiscreteCharacter
- setDistance(double) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
-
Sets the distance (such as time/branch length) used when calculating the probabilities.
- setDistance(double) - Method in class jebl.evolution.substmodel.MatrixExponential
-
compute transition probabilities for a expected distance using the prespecified rate matrix
- setDistance(double) - Method in interface jebl.evolution.substmodel.RateMatrix
-
Sets the distance (such as time/branch length) used when calculating the probabilities.
- setDistanceTranspose(double) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
-
Sets the distance (such as time/branch length) used when calculating the probabilities.
- setDistanceTranspose(double) - Method in class jebl.evolution.substmodel.MatrixExponential
-
compute transition probabilities for a expected distance using the prespecified rate matrix.
- setDoublingTime(double) - Method in class jebl.evolution.coalescent.ExponentialGrowth
-
An alternative parameterization of this model.
- setEdgeLength(Edge, double) - Method in class jebl.evolution.trees.SimpleTree
-
Change length of an existing edge.
- setEdgeLength(Node, Node, double) - Method in class jebl.evolution.trees.SimpleTree
-
Set edge distance between two adjacent nodes.
- setExpectedInputLength(long) - Method in class jebl.evolution.io.ImportHelper
- setGapOpen(float) - Method in class jebl.evolution.align.Align
- setGrowthRate(double) - Method in class jebl.evolution.coalescent.ExponentialGrowth
-
sets growth rate.
- setHeight(Node, double) - Method in class jebl.evolution.trees.MutableRootedTree
- setHeight(Node, double) - Method in class jebl.evolution.trees.ReRootedTree
- setHeight(Node, double) - Method in class jebl.evolution.trees.RootedSubtree
- setHeight(Node, double) - Method in class jebl.evolution.trees.SimpleRootedTree
- setIgnoreNonMinimalUnivariateMinimisations(boolean) - Method in class jebl.math.OrthogonalSearch
-
Should we ignore new minisations that are not as minimal as the current one?
- setIllegalCharacterPolicy(IllegalCharacterPolicy) - Method in class jebl.evolution.io.FastaImporter
- setImage(Image) - Method in class jebl.util.ProgressListener
-
Set an image associated with the current progress.
- setInclusion(FixedBitSet) - Method in class jebl.util.FixedBitSet
- setIndeterminateProgress() - Method in class jebl.util.ProgressListener
-
Sets indefinite progress (i.e.
- setIsOrdered(boolean) - Method in class jebl.evolution.characters.DiscreteCharacter
- setLength(Node, double) - Method in class jebl.evolution.trees.MutableRootedTree
- setLength(Node, double) - Method in class jebl.evolution.trees.ReRootedTree
- setLength(Node, double) - Method in class jebl.evolution.trees.RootedSubtree
- setLength(Node, double) - Method in class jebl.evolution.trees.SimpleRootedTree
- setMatrix(RateMatrix) - Method in class jebl.evolution.substmodel.MatrixExponential
-
update rate matrix used in present module
- setMessage(String) - Method in class jebl.util.ProgressListener
-
Set visible user message.
- setMinus(FixedBitSet) - Method in class jebl.util.FixedBitSet
- setN0(double) - Method in class jebl.evolution.coalescent.ConstantPopulation
-
sets initial population size.
- setN1(double) - Method in class jebl.evolution.coalescent.ConstExponential
- setN1(double) - Method in class jebl.evolution.coalescent.ConstLogistic
- setN1(double) - Method in class jebl.evolution.coalescent.Expansion
- setName(String) - Method in interface jebl.evolution.characters.Character
-
set the name of the character
- setName(String) - Method in class jebl.evolution.characters.ContinuousCharacter
- setName(String) - Method in class jebl.evolution.characters.DiscreteCharacter
- setNumOfStates(int) - Method in class jebl.evolution.characters.DiscreteCharacter
- setParametersNoScale(double[]) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
- setProgress(double) - Method in class jebl.util.ProgressListener
- setProgress(int, int) - Method in class jebl.util.ProgressListener
-
Same as calling
setProgress(((double)currentStep)/numberOfSteps)
- setProgress(long, long) - Method in class jebl.util.ProgressListener
-
Same as calling
setProgress(((double)currentStep)/numberOfSteps)
- setProgressMonitor(ProgressMonitor) - Method in class jebl.evolution.align.SequenceShuffler
- setProportion(double) - Method in class jebl.evolution.coalescent.ConstExponential
- setProportion(double) - Method in class jebl.evolution.coalescent.Expansion
- setR2(double) - Method in class jebl.evolution.coalescent.ExponentialLogistic
- setRoot(Node) - Method in class jebl.evolution.trees.MutableRootedTree
-
Set the root node.
- setScores(Scores) - Method in class jebl.evolution.align.Align
- setSeed(long) - Static method in class jebl.math.Random
-
Access a default instance of this class, access is synchronized
- setShape(double) - Method in class jebl.evolution.coalescent.LogisticGrowth
- setSignificantFigures(int) - Method in class jebl.util.NumberFormatter
-
Set the number of significant figures to display when formatted.
- setSpikeFactor(double) - Method in class jebl.evolution.coalescent.CataclysmicDemographic
-
An alternative parameterization of this model.
- setStateDesc(Map<Integer, String>) - Method in class jebl.evolution.characters.DiscreteCharacter
- 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 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 - 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 - 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 - 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 jebl.evolution.coalescent.IntervalList.IntervalType
- toString() - Method in class jebl.evolution.io.ByteBuilder
- toString() - Method in enum 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 jebl.evolution.trees.ConsensusTreeBuilder.Method
- toString() - Method in enum jebl.evolution.trees.SortedRootedTree.BranchOrdering
- toString() - Method in class jebl.evolution.trees.SplitSystem
-
print split system
- toString() - Method in enum jebl.evolution.trees.TransformedRootedTree.Transform
- toString() - Method in enum 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 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
- translate(Sequence, GeneticCode, int) - Static method in class jebl.evolution.sequences.Utils
- translate(State[], GeneticCode) - Static method in class jebl.evolution.sequences.Utils
-
Translates each of a given sequence of
NucleotideState
s orCodonState
s to theAminoAcidState
corresponding to it under the given genetic code. - translate(State[], GeneticCode, int) - Static method in class jebl.evolution.sequences.Utils
-
Translates each of a given sequence of
NucleotideState
s orCodonState
s to theAminoAcidState
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 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 in jebl.evolution.trees
-
Supported consensus methods.
- TreeBuilderFactory.DistanceModel - Enum in jebl.evolution.trees
-
Supported pairwise distance methods
- TreeBuilderFactory.Method - Enum 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 - 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 - jebl.util.MaybeBoolean
U
- U_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
- UNALIGNED - 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 - 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 - jebl.evolution.trees.TreeBuilderFactory.Method
- UPPER - 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 jebl.util.MaybeBoolean
-
Returns the enum constant of this type with the specified name.
- valueOf(int) - Static method in class jebl.evolution.sequences.GeneticCode
- valueOf(String) - Static method in enum jebl.evolution.coalescent.IntervalList.IntervalType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum jebl.evolution.io.DistanceMatrixImporter.Triangle
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum jebl.evolution.io.IllegalCharacterPolicy
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum jebl.evolution.io.NexusImporter.NexusBlock
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in class jebl.evolution.sequences.GeneticCode
- valueOf(String) - Static method in enum jebl.evolution.trees.ConsensusTreeBuilder.Method
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum jebl.evolution.trees.SortedRootedTree.BranchOrdering
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum jebl.evolution.trees.TransformedRootedTree.Transform
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum jebl.evolution.trees.TreeBiPartitionInfo.DistanceNorm
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum jebl.evolution.trees.TreeBuilderFactory.ConsensusMethod
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum jebl.evolution.trees.TreeBuilderFactory.DistanceModel
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum jebl.evolution.trees.TreeBuilderFactory.Method
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum jebl.util.MaybeBoolean
-
Returns the enum constant of this type with the specified name.
- values() - Static method in enum jebl.evolution.coalescent.IntervalList.IntervalType
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum jebl.evolution.io.DistanceMatrixImporter.Triangle
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum jebl.evolution.io.IllegalCharacterPolicy
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum jebl.evolution.io.NexusImporter.NexusBlock
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum jebl.evolution.trees.ConsensusTreeBuilder.Method
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum jebl.evolution.trees.SortedRootedTree.BranchOrdering
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum jebl.evolution.trees.TransformedRootedTree.Transform
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum jebl.evolution.trees.TreeBiPartitionInfo.DistanceNorm
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum jebl.evolution.trees.TreeBuilderFactory.ConsensusMethod
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum jebl.evolution.trees.TreeBuilderFactory.DistanceModel
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum jebl.evolution.trees.TreeBuilderFactory.Method
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum jebl.util.MaybeBoolean
-
Returns an array containing the constants of this enum type, 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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