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

G

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

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

GammaDistribution - Class in statalign.utils

Implementation of the Gamma distribution.

GammaDistribution(double, double) - Constructor for class statalign.utils.GammaDistribution

Creates a new gamma distribution with specified values of the shape and scale parameters.

GammaDistribution(double, double, double) - Constructor for class statalign.utils.GammaDistribution

Creates a new gamma distribution with specified values of the shape and scale parameters.

GammaDistribution(RandomGenerator, double, double, double) - Constructor for class statalign.utils.GammaDistribution

Creates a Gamma distribution.

GammaPrior - Class in statalign.mcmc

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

GammaProposal - Class in statalign.mcmc

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

GAPEXT - Variable in class statalign.base.TreeAlgo

GAPOPEN - Variable in class statalign.base.TreeAlgo

GaussianProposal - Class in statalign.mcmc

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

generator - Static variable in class statalign.base.Utils

The random number generator used throughout the program.

get(int) - Method in class statalign.base.CircularArray

Retrieves the element at the given key in the array or null if there is no element with that key.

get() - Method in interface statalign.mcmc.ParameterInterface

get() - Method in class statalign.model.ext.plugins.structalign.StructAlignParameterInterface.EpsilonInterface

get() - Method in class statalign.model.ext.plugins.structalign.StructAlignParameterInterface.NuInterface

get() - Method in class statalign.model.ext.plugins.structalign.StructAlignParameterInterface.Sigma2HInterface

get() - Method in class statalign.model.ext.plugins.structalign.StructAlignParameterInterface.Sigma2Interface

get() - Method in class statalign.model.ext.plugins.structalign.StructAlignParameterInterface.TauInterface

getAlpha() - Method in class statalign.utils.BetaDistribution

Access the first shape parameter, alpha.

getAlpha() - Method in class statalign.utils.GammaDistribution

Deprecated. as of version 3.1, GammaDistribution.getShape() should be preferred. This method will be removed in version 4.0.

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

getAverageLength(ArrayList<String>) - Static method in class statalign.postprocess.plugins.benchmarks.Benchmarks

getAvg() - Method in class statalign.utils.SimpleStats

getBaseFileName() - Method in class statalign.postprocess.PostprocessManager

getBasePairCountMatrix(String[]) - Static method in class statalign.postprocess.utils.RNAFoldingTools

Given an String array of dot-bracket structures, fills a matrix which counts the number of times a pair of nucleotides is base-paired in each structure.

getBeta() - Method in class statalign.utils.BetaDistribution

Access the second shape parameter, beta.

getBeta() - Method in class statalign.utils.GammaDistribution

Deprecated. as of version 3.1, GammaDistribution.getScale() should be preferred. This method will be removed in version 4.0.

getColor(char) - Method in class statalign.model.subst.plugins.AminoAcidModel

Returns the color of a character.

getColor(char) - Method in class statalign.model.subst.plugins.NucleotideModel

This function assigns colors to characters.

getColor(char) - Method in class statalign.model.subst.SubstitutionModel

Returns the colour associated with the character.

getColor(float) - Method in class statalign.postprocess.gui.ColorGradient

getCount() - Method in class statalign.postprocess.plugins.structalign.StructTrace

getCovariances() - Method in class statalign.model.ext.plugins.structalign.MultiNormCholesky

Gets the covariance matrix.

getDecodedTaxaName(String) - Static method in class statalign.postprocess.utils.NewickParser

A utility function to decode taxa names that have been encoded by NewickParser.getEncodedTaxaName(String).

getDependences() - Method in class statalign.postprocess.plugins.Entropy

getDependences() - Method in class statalign.postprocess.plugins.MpdAlignment

getDependences() - Method in class statalign.postprocess.plugins.PPFold

getDependences() - Method in class statalign.postprocess.plugins.structalign.RmsdTrace

getDependences() - Method in class statalign.postprocess.plugins.Structure

getDependences() - Method in class statalign.postprocess.plugins.VisualDistance

getDependences() - Method in class statalign.postprocess.Postprocess

Override this and return an array of full-qualified class names of the plugins this plugin depends on.

getDimension() - Method in class statalign.postprocess.gui.PPFoldGUI

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

getDotBracketStringFromPairedSites(int[]) - Static method in class statalign.postprocess.utils.RNAFoldingTools

Returns a dot bracket string representation given an array paired sites.

getDouble(double) - Static method in class statalign.postprocess.plugins.benchmarks.Benchmarks

getDoubleMatrix(float[][]) - Static method in class statalign.postprocess.utils.RNAFoldingTools

getEmitPatt2State() - Method in class statalign.base.hmm.Hmm

Abstract function returning an array A that helps identify the state with some emission pattern.

getEmitPatt2State() - Method in class statalign.base.hmm.HmmNonParam

Returns a conversion array from emission patterns (coded as integers) into state indices.

getEmitPatt2State() - Method in class statalign.base.hmm.HmmTkf92

Returns a conversion array from emission patterns (coded as integers) into state indices.

getEncodedTaxaName(String) - Static method in class statalign.postprocess.utils.NewickParser

A utility function to encode taxa names so they do not contain any of the Newick formats special characters, as specified in NewickParser.isSpecialChar(int).

getEnd() - Method in class statalign.base.hmm.Hmm

Returns the index of the end state.

getEnd() - Method in class statalign.base.hmm.HmmNonParam

Returns the index of the end state.

getEnd() - Method in class statalign.base.hmm.HmmTkf92

Returns the index of the end state.

getFileExtension() - Method in class statalign.postprocess.plugins.ConsensusNetwork

getFileExtension() - Method in class statalign.postprocess.plugins.ConsensusTreeVisualizer

getFileExtension() - Method in class statalign.postprocess.plugins.CurrentAlignment

getFileExtension() - Method in class statalign.postprocess.plugins.CurrentTreeVisualizer

getFileExtension() - Method in class statalign.postprocess.plugins.Entropy

getFileExtension() - Method in class statalign.postprocess.plugins.LogLikelihoodTrace

getFileExtension() - Method in class statalign.postprocess.plugins.MpdAlignment

getFileExtension() - Method in class statalign.postprocess.plugins.structalign.RmsdTrace

getFileExtension() - Method in class statalign.postprocess.plugins.structalign.StructTrace

getFileExtension() - Method in class statalign.postprocess.Postprocess

Returns default file extension that is to appended to the input file name to get the file this plugin is writing into.

getFilenameExtension() - Method in class statalign.model.ext.ModelExtension

getFilenameExtension() - Method in class statalign.model.ext.ModelExtManager

getFloatMatrix(double[][]) - Static method in class statalign.postprocess.utils.RNAFoldingTools

getFullAlign() - Method in class statalign.base.State

Returns the multiple alignment of all sequences, including ancestors.

getGappedToUngappedMapping(String) - Static method in class statalign.postprocess.utils.Mapping

getIcon() - Method in class statalign.base.Input

getIcon() - Method in class statalign.postprocess.plugins.ConsensusNetwork

It generates a new icon based on the figure in file icons/calignment.gif

getIcon() - Method in class statalign.postprocess.plugins.ConsensusTreeVisualizer

getIcon() - Method in class statalign.postprocess.plugins.CurrentAlignment

It generates a new icon based on the figure in file icons/calignment.gif

getIcon() - Method in class statalign.postprocess.plugins.CurrentTreeVisualizer

getIcon() - Method in class statalign.postprocess.plugins.Entropy

Returns the icon generated from the picture in file icons/loglikelihood1.gif.

getIcon() - Method in class statalign.postprocess.plugins.LogLikelihoodTrace

Returns the icon generated from the picture in file icons/loglikelihood1.gif.

getIcon() - Method in class statalign.postprocess.plugins.MpdAlignment

getIcon() - Method in class statalign.postprocess.plugins.PPFold

getIcon() - Method in class statalign.postprocess.plugins.structalign.RmsdTrace

getIcon() - Method in class statalign.postprocess.plugins.structalign.StructTrace

getIcon() - Method in class statalign.postprocess.plugins.Structure

getIcon() - Method in class statalign.postprocess.plugins.VisualDistance

getIcon() - Method in class statalign.postprocess.Postprocess

getIdentifier() - Method in class statalign.postprocess.gui.treeviews.TreeView

getIndex() - Method in class statalign.model.ext.plugins.structalign.StructAlignParameterInterface.Sigma2Interface

getInfoString() - Method in class statalign.base.Mcmc

Returns a string representation describing the acceptance ratios of the current MCMC run.

getIntProperty(String) - Method in class statalign.postprocess.plugins.TreeNode

Same as TreeNode.getProperty(String) but this method returns a value casted to an Integer.

getJPanel() - Method in class statalign.base.Input

getJPanel() - Method in class statalign.postprocess.plugins.ConsensusNetwork

It constructs a new JPanel, and returns with it

getJPanel() - Method in class statalign.postprocess.plugins.CurrentAlignment

It constructs a new JPanel, and returns with it

getJPanel() - Method in class statalign.postprocess.plugins.Entropy

It generates a panel and returns it.

getJPanel() - Method in class statalign.postprocess.plugins.LogLikelihoodTrace

It generates a panel and returns it.

getJPanel() - Method in class statalign.postprocess.plugins.MpdAlignment

getJPanel() - Method in class statalign.postprocess.plugins.PPFold

getJPanel() - Method in class statalign.postprocess.plugins.structalign.RmsdTrace

getJPanel() - Method in class statalign.postprocess.plugins.structalign.StructTrace

getJPanel() - Method in class statalign.postprocess.plugins.Structure

getJPanel() - Method in class statalign.postprocess.plugins.VisualDistance

getJPanel() - Method in class statalign.postprocess.Postprocess

getJPanel() - Method in class statalign.postprocess.TreeVisualizer

getLeafAlign() - Method in class statalign.base.State

Returns the multiple alignment of all leaf sequences.

getLeaves() - Method in class statalign.postprocess.plugins.TreeNode

Finds all of the leaves of the subtree of this node.

getLeaves(TreeNode) - Method in class statalign.postprocess.plugins.TreeNode

Same as TreeNode.getLeaves().

getLeft() - Method in class statalign.distance.Pair

getLeft() - Method in class statalign.postprocess.plugins.TreeNode

TODO: WHAT?

getLength() - Method in class statalign.base.Vertex

getLicenseFile() - Method in enum statalign.utils.Libraries

getLogChildDensity(ContinuousPositiveStructAlignMove) - Method in class statalign.model.ext.plugins.structalign.HierarchicalContinuousPositiveStructAlignMove

getLogLike() - Method in class statalign.base.Tree

getLogLike() - Method in class statalign.mcmc.McmcModule

getLogPrior() - Method in class statalign.base.Tree

getLogStationaryProb(int) - Method in class statalign.base.hmm.Hmm

Returns the logarithm of the stationary probability of generating a sequence of length characters under the HMM.

getLogStationaryProb(int) - Method in class statalign.base.hmm.HmmTkf92

getMax() - Method in class statalign.utils.SimpleStats

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

getMcmc() - Method in class statalign.model.ext.ModelExtManager

Allows access to the Mcmc class.

getMcmcInfo() - Method in class statalign.mcmc.McmcModule

getMcmcInfo() - Method in class statalign.model.ext.ModelExtManager

getMcmcMove(String) - Method in class statalign.mcmc.McmcModule

getMcmcMoves() - Method in class statalign.mcmc.McmcModule

getMean() - Method in class statalign.utils.NormalDistribution

Access the mean.

getMeans() - Method in class statalign.model.ext.plugins.structalign.MultiNormCholesky

Gets the mean vector.

getMedian(ArrayList<Double>) - Static method in class statalign.postprocess.plugins.benchmarks.Benchmarks

Returns the median from a list of values

getMenuName() - Method in class statalign.model.subst.SubstitutionModel

Retrieves the static field menuName of the class of the object the method is called on.

getMenuName(Class<? extends SubstitutionModel>) - Static method in class statalign.model.subst.SubstitutionModel

Retrieves menuName static field of a SubstitutionModel plug-in class.

getMessage() - Method in exception statalign.io.input.plugins.NewickReader.FormatException

getMessage() - Method in enum statalign.io.input.plugins.NewickReader.FormatExceptType

getMin() - Method in class statalign.utils.SimpleStats

getMinimumSize() - Method in class statalign.postprocess.gui.AlignmentGUI

This function tells the minimum size of the panel

getMinimumSize() - Method in class statalign.postprocess.gui.CNetworkView

Gives the minimum size of the component

getMinimumSize() - Method in class statalign.postprocess.gui.DistanceGUI

This function tells the minimum size of the panel

getMinimumSize() - Method in class statalign.postprocess.gui.EntropyGUI

This function tells the minimum size of the panel

getMinimumSize() - Method in class statalign.postprocess.gui.PPFoldGUI

This function tells the minimum size of the panel

getMinimumSize() - Method in class statalign.postprocess.gui.treeviews.HorizontalCladogramTreeView

Gives the minimum size of the component

getMinimumSize() - Method in class statalign.postprocess.gui.treeviews.HorizontalPhylogramTreeView

Gives the minimum size of the component

getMinimumSize() - Method in class statalign.postprocess.gui.treeviews.NetworkTreeView

Gives the minimum size of the component

getMinimumSize() - Method in class statalign.postprocess.gui.treeviews.VerticalPhylogramTreeView

getModelExtMan() - Method in class statalign.base.mcmc.CoreMcmcModule

getModExtPlugins() - Method in class statalign.postprocess.Postprocess

getN() - Method in class statalign.utils.SimpleStats

getName(int) - Method in class statalign.postprocess.plugins.contree.TaxaMap

getName() - Method in class statalign.utils.SimpleStats

getNewickString() - Method in class statalign.base.State

Returns the Newick string representation of the tree

getNewickStringWithLabels() - Method in class statalign.base.State

getNextPrime(int) - Static method in class statalign.postprocess.plugins.contree.hash.HashUtils

Determines the next prime above or equal to n.

getNextSection() - Method in class statalign.postprocess.utils.RNAFoldingTools.MultiThreadedPosteriorDecoding

Generates a sequence of coordinates of windows on which posterior-decoding can be performed independently in parallel.

getNumericalMean() - Method in class statalign.utils.BetaDistribution

For first shape parameter alpha and second shape parameter beta, the mean is alpha / (alpha + beta).

getNumericalMean() - Method in class statalign.utils.GammaDistribution

For shape parameter alpha and scale parameter beta, the mean is alpha * beta.

getNumericalMean() - Method in class statalign.utils.NormalDistribution

For mean parameter mu, the mean is mu.

getNumericalVariance() - Method in class statalign.utils.BetaDistribution

For first shape parameter alpha and second shape parameter beta, the variance is (alpha * beta) / [(alpha + beta)^2 * (alpha + beta + 1)].

getNumericalVariance() - Method in class statalign.utils.GammaDistribution

For shape parameter alpha and scale parameter beta, the variance is alpha * beta^2.

getNumericalVariance() - Method in class statalign.utils.NormalDistribution

For standard deviation parameter s, the variance is s^2.

getOwner() - Method in class statalign.mcmc.McmcCombinationMove

getOwner() - Method in class statalign.mcmc.McmcMove

getPairedSites(char[]) - Static method in class statalign.postprocess.plugins.benchmarks.Benchmarks

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

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

getPairedSitesFromDotBracketString(String) - Static method in class statalign.postprocess.utils.RNAFoldingTools

Given a dot bracket string representation, returns an array of paired sites.

getPairedSitesFromDotBracketString(String, char, char) - Static method in class statalign.postprocess.utils.RNAFoldingTools

Given a dot bracket string representation, returns an array of paired sites.

getPairwiseAlign(int) - Method in class statalign.base.State

Returns string representation of alignment between node and its parent.

getParam() - Method in class statalign.mcmc.McmcMove

getParamChangeWeight() - Method in class statalign.mcmc.McmcModule

getParamChangeWeight() - Method in class statalign.model.ext.ModelExtension

Returns the weight for choosing a parameter change for this model extension in the MCMC kernel.

getParamChangeWeight() - Method in class statalign.model.ext.ModelExtManager

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

getParameter(String) - Method in class statalign.postprocess.PluginParameters

Returns the corresponding parameter value or null if the parameter does not exist.

getParameterHistory() - Method in class statalign.postprocess.plugins.structalign.StructTrace

getPluginID() - Method in class statalign.model.ext.ModelExtension

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

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

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

getPluginList() - Method in class statalign.model.ext.ModelExtension

Returns the (unmodifiable) list of recognised ModelExtension plugins.

getPluginList() - Method in class statalign.model.ext.ModelExtManager

Returns the (unmodifiable) list of recognised ModelExtension plugins.

getPlugins() - Method in class statalign.postprocess.PostprocessManager

getPosteriorDecodingConsensusStructure(float[][]) - Static method in class statalign.postprocess.utils.RNAFoldingTools

getPosteriorDecodingConsensusStructure(double[][]) - Static method in class statalign.postprocess.utils.RNAFoldingTools

getPosteriorDecodingConsensusStructure(double[][], double[]) - Static method in class statalign.postprocess.utils.RNAFoldingTools

A single-threaded method for generating the posterior-decoding structure.

getPosteriorDecodingConsensusStructureMultiThreaded(double[][], double[]) - Method in class statalign.postprocess.utils.RNAFoldingTools

Returns the posterior-decoding consensus structure.

getPosteriorDecodingConsensusStructureMultiThreaded(float[][]) - Method in class statalign.postprocess.utils.RNAFoldingTools

getPosteriorDecodingConsensusStructureMultiThreaded(double[][]) - Method in class statalign.postprocess.utils.RNAFoldingTools

Returns the posterior-decoding consensus structure.

getPPfoldTree(Mcmc) - Static method in class statalign.postprocess.plugins.PPFold

getPreferredSize() - Method in class statalign.postprocess.gui.AlignmentGUI

This function tells the preferred size of the panel

getPreferredSize() - Method in class statalign.postprocess.gui.CNetworkView

It gives the preferred size of the component

getPreferredSize() - Method in class statalign.postprocess.gui.DistanceGUI

This function tells the preferred size of the panel

getPreferredSize() - Method in class statalign.postprocess.gui.EntropyGUI

This function tells the preferred size of the panel

getPreferredSize() - Method in class statalign.postprocess.gui.PPFoldGUI

getPreferredSize() - Method in class statalign.postprocess.gui.treeviews.HorizontalCladogramTreeView

It gives the preferred size of the component

getPreferredSize() - Method in class statalign.postprocess.gui.treeviews.HorizontalPhylogramTreeView

It gives the preferred size of the component

getPreferredSize() - Method in class statalign.postprocess.gui.treeviews.NetworkTreeView

It gives the preferred size of the component

getPreferredSize() - Method in class statalign.postprocess.gui.treeviews.VerticalPhylogramTreeView

getPrior() - Method in class statalign.model.subst.SubstitutionModel

Returns the prior for the substitution parameters.

getProjectionIndices(String, char) - Static method in class statalign.postprocess.utils.Mapping

getProperty(String) - Method in class statalign.postprocess.plugins.TreeNode

Return the value for a certain key property associated with this node.

getProxySimilarityFromAvgPosterior(double) - Static method in class statalign.postprocess.plugins.PPFold

getRealRotation() - Method in class statalign.model.ext.plugins.structalign.Transformation

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

getRefName() - Static method in class statalign.postprocess.plugins.PPFold

getResPercentage() - Method in class statalign.postprocess.plugins.contree.CTMain

getRight() - Method in class statalign.distance.Pair

getRight() - Method in class statalign.postprocess.plugins.TreeNode

getRoot() - Method in class statalign.postprocess.plugins.contree.CTree

getRowSub(double[][], ArrayList<Integer>) - Static method in class statalign.model.ext.plugins.structalign.Funcs

getSampleRateOfTheSpace(ArrayList<Double>, int) - Static method in class statalign.base.AutomateParameters

Looks either for major decline in theSpace or if we get very close to the average line.

getScale() - Method in class statalign.utils.GammaDistribution

Returns the scale parameter of this distribution.

getScrollMultiplier() - Method in class statalign.ui.ScrollAdapter

getSeed() - Method in class statalign.postprocess.plugins.contree.CTMain

getSeqName(int) - Method in class statalign.io.RawSequences

getSeqNamePadded(int) - Method in class statalign.io.RawSequences

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

getSeqs() - Method in class statalign.base.Tree

getSeqs() - Method in interface statalign.io.DataType

getSeqs() - Method in class statalign.io.ProteinSkeletons

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

getSequence(int) - Method in class statalign.io.RawSequences

getSequenceByName(String[][], String) - Static method in class statalign.postprocess.plugins.PPFold

getSequenceByName(String, List<String>, List<String>) - Static method in class statalign.postprocess.utils.RNAFoldingTools

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

getSequences() - Method in class statalign.postprocess.plugins.PPFold

getShape() - Method in class statalign.utils.GammaDistribution

Returns the shape parameter of this distribution.

getSilent() - Method in class statalign.base.hmm.HmmNonParam

Returns the index of the silent state.

getSilent() - Method in class statalign.base.hmm.HmmSilent

Returns the index of the silent state.

getSingleBaseCount(String[]) - Static method in class statalign.postprocess.utils.RNAFoldingTools

Given a String array of dot-bracket structures, fills a vector which counts the number of times a specific nucleotide position is unpaired.

getSingleBaseProb(double[][]) - Static method in class statalign.postprocess.utils.RNAFoldingTools

getSmallResult() - Method in class statalign.postprocess.plugins.RNAalifoldResult

getStandardDeviation() - Method in class statalign.utils.NormalDistribution

Access the standard deviation.

getStart() - Method in class statalign.base.hmm.Hmm

Returns the index of the start state.

getStart() - Method in class statalign.base.hmm.HmmNonParam

Returns the index of the start state.

getStart() - Method in class statalign.base.hmm.HmmTkf92

Returns the index of the start state.

getState() - Method in class statalign.base.Mcmc

Returns a State object that describes the current state of the MCMC.

getState() - Method in class statalign.base.Tree

Returns a State object representing the current state.

getStateEmit() - Method in class statalign.base.hmm.Hmm

Abstract function that specifies the emission of each state in the HMM in the form of an array A: A[s][i]=1 iff state i emits into sequence s (s=0 is the parent sequence; for pair-HMMs s=1 is the child sequence, for 3-seq HMMs s=1 is left and s=2 is right child).

getStateEmit() - Method in class statalign.base.hmm.HmmNonParam

Returns an array specifying the emission pattern of each state.

getStateEmit() - Method in class statalign.base.hmm.HmmTkf92

Returns an array specifying the emission pattern of each state.

getStdDev() - Method in class statalign.utils.SimpleStats

getSubMatrix(double[][], int[], int[]) - Static method in class statalign.model.ext.plugins.structalign.Funcs

getSubsetJoins(CNetworkEdge, int) - Method in class statalign.postprocess.plugins.contree.CNetworkSplit

Takes an input edge and finds the side of this split it occurs on and then returns the number of taxa on that side of this split.

getSubtreeLeaves(Tree, Vertex, int) - Static method in class statalign.model.ext.plugins.structalign.Subtree

getSummaryAssociatedWith(String) - Method in class statalign.base.Tree

getSummaryAssociatedWith(String) - Method in interface statalign.io.DataType

getSummaryAssociatedWith(String) - Method in class statalign.io.ProteinSkeletons

getSummaryAssociatedWith(String) - Method in class statalign.io.RawSequences

getSupportLowerBound() - Method in class statalign.utils.BetaDistribution

The lower bound of the support is always 0 no matter the parameters.

getSupportLowerBound() - Method in class statalign.utils.GammaDistribution

The lower bound of the support is always 0 no matter the parameters.

getSupportLowerBound() - Method in class statalign.utils.NormalDistribution

The lower bound of the support is always negative infinity no matter the parameters.

getSupportUpperBound() - Method in class statalign.utils.BetaDistribution

The upper bound of the support is always 1 no matter the parameters.

getSupportUpperBound() - Method in class statalign.utils.GammaDistribution

The upper bound of the support is always positive infinity no matter the parameters.

getSupportUpperBound() - Method in class statalign.utils.NormalDistribution

The upper bound of the support is always positive infinity no matter the parameters.

getTabName() - Method in class statalign.base.Input

getTabName() - Method in class statalign.postprocess.plugins.ConsensusNetwork

It returns with its tab name, 'Alignment'

getTabName() - Method in class statalign.postprocess.plugins.ConsensusTreeVisualizer

getTabName() - Method in class statalign.postprocess.plugins.CurrentAlignment

It returns with its tab name, 'Alignment'

getTabName() - Method in class statalign.postprocess.plugins.CurrentTreeVisualizer

getTabName() - Method in class statalign.postprocess.plugins.Entropy

Returns the name of the postprocess, 'Loglikelihood'.

getTabName() - Method in class statalign.postprocess.plugins.LogLikelihoodTrace

Returns the name of the postprocess, 'Loglikelihood'.

getTabName() - Method in class statalign.postprocess.plugins.MpdAlignment

getTabName() - Method in class statalign.postprocess.plugins.PPFold

getTabName() - Method in class statalign.postprocess.plugins.structalign.RmsdTrace

getTabName() - Method in class statalign.postprocess.plugins.structalign.StructTrace

getTabName() - Method in class statalign.postprocess.plugins.Structure

getTabName() - Method in class statalign.postprocess.plugins.VisualDistance

getTabName() - Method in class statalign.postprocess.Postprocess

getTabOrder() - Method in class statalign.base.Input

getTabOrder() - Method in class statalign.postprocess.plugins.ConsensusNetwork

getTabOrder() - Method in class statalign.postprocess.plugins.ConsensusTreeVisualizer

getTabOrder() - Method in class statalign.postprocess.plugins.CurrentAlignment

getTabOrder() - Method in class statalign.postprocess.plugins.CurrentTreeVisualizer

getTabOrder() - Method in class statalign.postprocess.plugins.Entropy

getTabOrder() - Method in class statalign.postprocess.plugins.LogLikelihoodTrace

getTabOrder() - Method in class statalign.postprocess.plugins.MpdAlignment

getTabOrder() - Method in class statalign.postprocess.plugins.PPFold

getTabOrder() - Method in class statalign.postprocess.plugins.structalign.StructTrace

getTabOrder() - Method in class statalign.postprocess.plugins.Structure

getTabOrder() - Method in class statalign.postprocess.plugins.VisualDistance

getTabOrder() - Method in class statalign.postprocess.Postprocess

Specifies the order of the tab for this plugin in the GUI.

getTime() - Method in class statalign.mcmc.McmcMove

getTip() - Method in class statalign.base.Input

getTip() - Method in class statalign.postprocess.plugins.ConsensusNetwork

It returns with the tip of the tabulated panel 'Current alignment in the Markov chain' (shown when mouse is moved over the panel)

getTip() - Method in class statalign.postprocess.plugins.ConsensusTreeVisualizer

getTip() - Method in class statalign.postprocess.plugins.CurrentAlignment

It returns with the tip of the tabulated panel 'Current alignment in the Markov chain' (shown when mouse is moved over the panel)

getTip() - Method in class statalign.postprocess.plugins.CurrentTreeVisualizer

getTip() - Method in class statalign.postprocess.plugins.Entropy

Returns the tip of the tabulated panel 'Log-likelihood trace' (shown when mouse is moved over the panel)

getTip() - Method in class statalign.postprocess.plugins.LogLikelihoodTrace

Returns the tip of the tabulated panel 'Log-likelihood trace' (shown when mouse is moved over the panel)

getTip() - Method in class statalign.postprocess.plugins.MpdAlignment

getTip() - Method in class statalign.postprocess.plugins.PPFold

getTip() - Method in class statalign.postprocess.plugins.structalign.RmsdTrace

getTip() - Method in class statalign.postprocess.plugins.structalign.StructTrace

getTip() - Method in class statalign.postprocess.plugins.Structure

getTip() - Method in class statalign.postprocess.plugins.VisualDistance

getTip() - Method in class statalign.postprocess.Postprocess

Returns with the tip information (shown when the mouse cursor is moved over the label of the tabulated panel)

getToolBarButton() - Method in class statalign.postprocess.gui.treeviews.HorizontalCladogramTreeView

getToolBarButton() - Method in class statalign.postprocess.gui.treeviews.HorizontalPhylogramTreeView

getToolBarButton() - Method in class statalign.postprocess.gui.treeviews.NetworkTreeView

getToolBarButton() - Method in class statalign.postprocess.gui.treeviews.TreeView

getToolBarButton() - Method in class statalign.postprocess.gui.treeviews.VerticalPhylogramTreeView

getToolBarItems() - Method in class statalign.model.ext.ModelExtension

Override this to return the list of toolbar items to be added.

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

getToolBarItems() - Method in class statalign.postprocess.plugins.Structure

getToolBarItems() - Method in class statalign.postprocess.Postprocess

Returns the toolbar that this plugin uses.

getToolBarItems() - Method in class statalign.postprocess.TreeVisualizer

getTopVertexId(int) - Method in class statalign.base.Tree

getTracks() - Method in class statalign.postprocess.Postprocess

The extra tracks to be plotted

getType() - Method in class statalign.model.subst.SubstitutionModel

Retrieves the static field type of the class of the object the method is called on.

getType(Class<? extends SubstitutionModel>) - Static method in class statalign.model.subst.SubstitutionModel

Retrieves the static field type of a SubstitutionModel plug-in class.

getUngappedPosition(String, int, char) - Static method in class statalign.postprocess.utils.Mapping

Returns the position in the sequence without gaps.

getUngappedToGappedMapping(String) - Static method in class statalign.postprocess.utils.Mapping

getUsageInfo() - Method in class statalign.model.ext.ModelExtension

Prints the usage information for this plugin.

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

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

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

getValue(String) - Static method in class statalign.postprocess.gui.ColorGradient

getValue(ArrayList<Double>, double) - Static method in class statalign.postprocess.plugins.benchmarks.Benchmarks

Returns a value at a given percentile.

getValues(int[], int[]) - Static method in class statalign.postprocess.plugins.benchmarks.Benchmarks

getWebPageURI() - Method in enum statalign.utils.Libraries

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

globalSigma - Variable in class statalign.postprocess.plugins.structalign.StructAlignTraceParameters

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

If globalSigma = false then this switches on a spike prior at sigma2Hier.