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

L

label - Variable in class statalign.postprocess.utils.DisplayString

LambdaMove - Class in statalign.base.mcmc

LambdaMove(McmcModule, PriorDistribution<Double>, ProposalDistribution<Double>, String) - Constructor for class statalign.base.mcmc.LambdaMove

lastMoveAccepted - Variable in class statalign.mcmc.McmcMove

LEAF_COUNT_POW - Static variable in class statalign.base.Utils

Power determining how much we favour realigning the larger subtree first when doing a nearest-neighbour interchange move.

leafAlignment - Variable in class statalign.postprocess.plugins.CurrentAlignment

leafCount - Variable in class statalign.base.Vertex

leafCount - Variable in class statalign.postprocess.plugins.TreeNode

The number of leaves in this subtree.

leaflabel - Variable in class statalign.postprocess.gui.CNetworkView

leaflabel - Variable in class statalign.postprocess.gui.treeviews.NetworkTreeView

leaveOutColumns(double[][], List<Integer>) - Static method in class statalign.postprocess.plugins.PPFold

leaves - Variable in class statalign.postprocess.plugins.contree.hash.HashEntry

left - Variable in class statalign.base.AlignColumn

This reference points to the left child of this AlignColumn

left - Variable in class statalign.base.State

Tree representation: left descendant of each node (first nl are leaves), -1 for none

left - Variable in class statalign.base.Vertex

This reference points to the left child of the vertex.

len() - Method in class statalign.io.RawSequences

Returns the common length of the aligned sequences or -1 if sequences are unaligned (have different length).

length() - Method in class statalign.base.CircularArray

Difference between the highest and lowest key of elements in the array plus 1.

Libraries - Enum in statalign.utils

libraryLogDensity(int, Transformation) - Method in class statalign.model.ext.plugins.structalign.RotationProposal

LibraryMove - Class in statalign.model.ext.plugins.structalign

LibraryMove(StructAlign, String) - Constructor for class statalign.model.ext.plugins.structalign.LibraryMove

linearizerWeight(int, MuDouble, double) - Static method in class statalign.base.Utils

This function selects a random integer with expected value given by expectedLength.

linearizerWeightProb(int, int, double) - Static method in class statalign.base.Utils

This function returns the probability of choosing a particular index with linearizerWeight.

LinearLink - Class in statalign.model.ext.plugins.structalign

LinearLink() - Constructor for class statalign.model.ext.plugins.structalign.LinearLink

LinearPrior - Class in statalign.mcmc

LinearPrior() - Constructor for class statalign.mcmc.LinearPrior

LinearPrior(double) - Constructor for class statalign.mcmc.LinearPrior

lines - Variable in class statalign.postprocess.gui.CNetworkView

lines - Variable in class statalign.postprocess.gui.treeviews.NetworkTreeView

LinkFunction<T> - Interface in statalign.utils

linkType - Variable in class statalign.model.ext.plugins.StructAlign

list - Variable in class statalign.postprocess.plugins.LogLikelihoodTrace

ListToAdd(CNetworkEdge, boolean, ArrayList<CNetworkEdge>) - Method in class statalign.postprocess.plugins.contree.CNetworkNode

Function returns joined up ArrayList if must be joined in a certain order...

loadAlignments(File) - Static method in class statalign.distance.AlignmentSample

loadAlignments(File) - Static method in class statalign.postprocess.plugins.benchmarks.AlignmentSample

Loads an alignment sample object from a file.

loadBasePairProbMatrix(File, int) - Static method in class statalign.postprocess.utils.RNAalifold

loadDatasetResult(File) - Static method in class statalign.postprocess.plugins.benchmarks.Dataset

loadDotBracketStructure(File) - Static method in class statalign.postprocess.utils.RNAalifold

loadExperimentalStructure(File) - Static method in class statalign.postprocess.plugins.benchmarks.Benchmarks

Loads the experimentally-derived secondary structures and alignments.

loadFastaSequences(File, ArrayList<String>, ArrayList<String>) - Static method in class statalign.postprocess.utils.RNAFoldingTools

loadFastaSequences(File, ArrayList<String>, ArrayList<String>, int) - Static method in class statalign.postprocess.utils.RNAFoldingTools

loadFolds(File, int) - Static method in class statalign.postprocess.plugins.PPFold

loadMatrix(File) - Static method in class statalign.postprocess.utils.RNAFoldingTools

loadOptions() - Method in class statalign.ui.RNASettingsDlg

loadStatAlignResultFile(File) - Static method in class statalign.postprocess.plugins.benchmarks.Benchmarks

localEpsilon - Variable in class statalign.model.ext.plugins.StructAlign

LOCALTopologyMove - Class in statalign.base.mcmc

LOCALTopologyMove(McmcModule, PriorDistribution<Double>, double, double, String) - Constructor for class statalign.base.mcmc.LOCALTopologyMove

log0 - Static variable in class statalign.base.Utils

log(0) is set to Double.NEGATIVE_INFINITY.

logAdd(double, double) - Static method in class statalign.base.Utils

Logarithmically add two numbers

logBetaDensity(double, double, double) - Static method in class statalign.base.Utils

logDensity(Double) - Method in class statalign.mcmc.BetaPrior

logDensity(Double) - Method in class statalign.mcmc.GammaPrior

logDensity(Double) - Method in class statalign.mcmc.GammaProposal

logDensity(Double) - Method in class statalign.mcmc.GaussianProposal

logDensity(Double) - Method in class statalign.mcmc.HyperbolicPrior

logDensity(Double) - Method in class statalign.mcmc.InverseGammaPrior

logDensity(Double) - Method in class statalign.mcmc.LinearPrior

logDensity(Double) - Method in class statalign.mcmc.LogisticProposal

Computes the logDensity of proposing a value x, adding on the term from the Jacobian of the transformation from x to logit(x).

logDensity(Double) - Method in class statalign.mcmc.LogNormalPrior

logDensity(Double) - Method in class statalign.mcmc.MultiplicativeProposal

Computes the logDensity of proposing a value x, adding on the term from the Jacobian of the transformation from x to log x.

logDensity(Double) - Method in interface statalign.mcmc.PriorDistribution

logDensity(T) - Method in class statalign.mcmc.ProposalDistribution

logDensity(Double) - Method in class statalign.mcmc.UniformPrior

logDensity(Double) - Method in class statalign.mcmc.UniformProposal

logDensity(double[]) - Method in class statalign.model.ext.plugins.structalign.MultiNormCholesky

logDensity(double) - Method in class statalign.utils.NormalDistribution

logDensityUnnormalised(Double) - Method in class statalign.mcmc.BetaPrior

logDensityUnnormalised(Double) - Method in class statalign.mcmc.GammaPrior

logDensityUnnormalised(Double) - Method in class statalign.mcmc.HyperbolicPrior

logDensityUnnormalised(Double) - Method in class statalign.mcmc.InverseGammaPrior

logDensityUnnormalised(Double) - Method in class statalign.mcmc.LinearPrior

logDensityUnnormalised(Double) - Method in class statalign.mcmc.LogNormalPrior

logDensityUnnormalised(Double) - Method in interface statalign.mcmc.PriorDistribution

logDensityUnnormalised(Double) - Method in class statalign.mcmc.UniformPrior

logFile - Variable in class statalign.postprocess.PostprocessManager

This is the log-file writer

logGammaDensity(double, double, double) - Static method in class statalign.base.Utils

LogisticProposal - Class in statalign.mcmc

Proposal distribution for variables whose support is [0,1].

LogisticProposal() - Constructor for class statalign.mcmc.LogisticProposal

logLike - Variable in class statalign.base.State

Log-likelihood of the state, excluding model extension factors

logLikeAlignChange(Tree, Vertex) - Method in class statalign.model.ext.ModelExtension

logLikeAlignChange(Tree, Vertex) - Method in class statalign.model.ext.ModelExtManager

Calculates the total log-likelihood of the state by adding the log-likelihood factor contributions from all model extension plugins to the log-likelihood of the tree.

logLikeAlignChange(Tree, Vertex) - Method in class statalign.model.ext.plugins.StructAlign

logLikeContinuousParamChange(Tree) - Method in class statalign.model.ext.plugins.StructAlign

logLikeEdgeLenChange(Tree, Vertex) - Method in class statalign.model.ext.ModelExtension

logLikeEdgeLenChange(Tree, Vertex) - Method in class statalign.model.ext.ModelExtManager

Calculates the total log-likelihood of the state by adding the log-likelihood factor contributions from all model extension plugins to the log-likelihood of the tree.

logLikeEdgeLenChange(Tree, Vertex) - Method in class statalign.model.ext.plugins.StructAlign

logLikeFactor(Tree) - Method in class statalign.base.mcmc.CoreMcmcModule

logLikeFactor(Tree) - Method in class statalign.mcmc.McmcModule

This should return the log of the model's contribution to the likelihood, it will be added on to the log-likelihood of the current point in the MCMC state space.

logLikeFactor(Tree) - Method in class statalign.model.ext.plugins.PPFold

logLikeFactor(Tree) - Method in class statalign.model.ext.plugins.RNAAliFold

logLikeFactor(Tree) - Method in class statalign.model.ext.plugins.StructAlign

logLikeIndelParamChange(Tree, Hmm, McmcMove) - Method in class statalign.model.ext.ModelExtension

logLikeIndelParamChange(Tree, Hmm, McmcMove) - Method in class statalign.model.ext.ModelExtManager

Calculates the total log-likelihood of the state by adding the log-likelihood factor contributions from all model extension plugins to the log-likelihood of the tree.

logLikeIndelParamChange(Tree, Hmm, McmcMove) - Method in class statalign.model.ext.plugins.StructAlign

loglikelihood - Variable in class statalign.postprocess.utils.LogLikelihoodTraceContainer

The log-likelihood value

logLikelihoods - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

LogLikelihoodTrace - Class in statalign.postprocess.plugins

This is the implementation of the postprocess that handles loglikelihoods.

LogLikelihoodTrace() - Constructor for class statalign.postprocess.plugins.LogLikelihoodTrace

It constructs a postprocess handler that is screenable (=can be shown on the GUI), outputable (= can be written into the log file) and postprocessable (= can generate its own output file).

LogLikelihoodTraceContainer - Class in statalign.postprocess.utils

A container class that stores a loglikelihood value and a logical value if the sample comes from the burn-in period or not.

LogLikelihoodTraceContainer(double, boolean) - Constructor for class statalign.postprocess.utils.LogLikelihoodTraceContainer

This constructor sets the values in the container.

LogLikelihoodTraceGUI - Class in statalign.postprocess.gui

This class implements the graphical interface for showing the log-likelihood plot.

LogLikelihoodTraceGUI(JPanel, LogLikelihoodTrace) - Constructor for class statalign.postprocess.gui.LogLikelihoodTraceGUI

Constructor to initialise the GUI for loglikelihood trace

logLikeModExtParamChange(Tree, ModelExtension) - Method in class statalign.model.ext.ModelExtension

Computes the change in likelihood to this ModelExtension, after a change to ext.

logLikeModExtParamChange(Tree) - Method in class statalign.model.ext.ModelExtManager

Calculates the total log-likelihood of the state by adding the log-likelihood factor contributions from all model extension plugins to the log-likelihood of the tree.

logLikeModExtParamChange(Tree, ModelExtension) - Method in class statalign.model.ext.plugins.StructAlign

logLikeSubstParamChange(Tree, SubstitutionModel, int) - Method in class statalign.model.ext.ModelExtension

logLikeSubstParamChange(Tree, SubstitutionModel, int) - Method in class statalign.model.ext.ModelExtManager

Calculates the total log-likelihood of the state by adding the log-likelihood factor contributions from all model extension plugins to the log-likelihood of the tree.

logLikeSubstParamChange(Tree, SubstitutionModel, int) - Method in class statalign.model.ext.plugins.StructAlign

logLikeTreeChange(Tree, Vertex) - Method in class statalign.model.ext.ModelExtension

logLikeTreeChange(Tree, Vertex) - Method in class statalign.model.ext.ModelExtManager

Calculates the total log-likelihood of the state by adding the log-likelihood factor contributions from all model extension plugins to the log-likelihood of the tree.

logLikeTreeChange(Tree, Vertex) - Method in class statalign.model.ext.plugins.StructAlign

LogNormalPrior - Class in statalign.mcmc

LogNormalPrior(double, double) - Constructor for class statalign.mcmc.LogNormalPrior

logPrior(Tree) - Method in class statalign.mcmc.McmcModule

This should return the log of the total prior calculated for the model parameters.

logPriorDensity(Object) - Method in class statalign.base.mcmc.AlignmentMove

logPriorDensity(Object) - Method in class statalign.base.mcmc.AllEdgeMove

logPriorDensity(Object) - Method in class statalign.base.mcmc.LOCALTopologyMove

logPriorDensity(Object) - Method in class statalign.base.mcmc.SilentIndelMove

logPriorDensity(Object) - Method in class statalign.base.mcmc.SubstMove

logPriorDensity(Object) - Method in class statalign.base.mcmc.TopologyMove

logPriorDensity(Object) - Method in class statalign.mcmc.ContinuousPositiveParameterMove

logPriorDensity(Object) - Method in class statalign.mcmc.McmcCombinationMove

logPriorDensity(Object) - Method in class statalign.mcmc.McmcMove

logPriorDensity(Object) - Method in class statalign.model.ext.plugins.structalign.AlignmentMove

logPriorDensity(Object) - Method in class statalign.model.ext.plugins.structalign.ContinuousPositiveStructAlignMove

logPriorDensity(Object) - Method in class statalign.model.ext.plugins.structalign.RotationOrTranslationMove

logWeightedChoose(double[], MuDouble) - Static method in class statalign.base.Utils

Equivalent to weightedChoose(weights, selectLogLike) where logWeights[i] = Math.log(weights[i]), but avoids overflows that might result from exponentiation.

logWeightedChoose(double[]) - Static method in class statalign.base.Utils

longName - Variable in enum statalign.utils.Libraries

LOW_COUNT_MULTIPLIER - Static variable in class statalign.base.Utils

LOW_COUNT_THRESHOLD - Static variable in class statalign.base.Utils

lowCounts - Variable in class statalign.mcmc.McmcMove

Number of times that the acceptance rate has been recorded as being below the minimum.

lsTrans(RealMatrix, RealMatrix) - Method in class statalign.model.ext.plugins.structalign.Transformation