Uses of Class
statalign.base.Tree

Packages that use Tree

statalign.base
statalign.base.mcmc
statalign.io.input.plugins
statalign.mcmc
statalign.model.ext
statalign.model.ext.plugins
statalign.model.ext.plugins.structalign

Uses of Tree in statalign.base

Fields in statalign.base declared as Tree

Tree	Mcmc.tree Current tree in the MCMC chain.
Tree	InputData.tree The initial tree, if given, which is optionally fixed for the whole analysis

Methods in statalign.base that return Tree

Tree	TreeAlgo.buildNJTree(java.lang.String[] sequences, java.lang.String[] names, SubstitutionModel model, java.lang.String filename)
Tree	TreeAlgo.rearrangeTree(Tree tree, java.lang.String[] names)

Methods in statalign.base with parameters of type Tree

void	TreeAlgo.addAlignSeqsToTree(Tree tree, java.lang.String[] sequences, java.lang.String[] names, SubstitutionModel model, java.lang.String filename)
Tree	TreeAlgo.rearrangeTree(Tree tree, java.lang.String[] names)

Constructors in statalign.base with parameters of type Tree

Mcmc(Tree tree, MCMCPars pars, PostprocessManager ppm, ModelExtManager modelExtMan)

Mcmc(Tree tree, MCMCPars pars, PostprocessManager ppm, ModelExtManager modelExtMan, int noOfProcesses, int rank, double heat)

Vertex(Tree tree)

Uses of Tree in statalign.base.mcmc

Methods in statalign.base.mcmc with parameters of type Tree

double	CoreMcmcModule.logLikeFactor(Tree tree)
boolean	CoreMcmcModule.proposeParamChange(Tree tree)
double	CoreMcmcModule.totalLogPrior(Tree tree)

Uses of Tree in statalign.io.input.plugins

Methods in statalign.io.input.plugins that return Tree

Tree	NewickReader.read(java.io.Reader reader) Parses tree.

Uses of Tree in statalign.mcmc

Methods in statalign.mcmc with parameters of type Tree

void	McmcModule.beforeSampling(Tree tree) Called before the start of MCMC sampling, but after the initial tree, alignment etc. have been generated.
abstract double	McmcModule.logLikeFactor(Tree tree) 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.
double	McmcModule.logPrior(Tree tree) This should return the log of the total prior calculated for the model parameters.
boolean	McmcModule.proposeParamChange(Tree tree)

Uses of Tree in statalign.model.ext

Methods in statalign.model.ext with parameters of type Tree

void	ModelExtManager.afterAlignChange(Tree tree, Vertex selectRoot, boolean accepted)
void	ModelExtension.afterAlignChange(Tree tree, Vertex selectRoot, boolean accepted) Called after an alignment change proposal (accepted or rejected).
void	ModelExtManager.afterEdgeLenChange(Tree tree, Vertex vertex, boolean accepted)
void	ModelExtension.afterEdgeLenChange(Tree tree, Vertex vertex, boolean accepted) Called after a proposed edge length change (accepted or rejected).
void	ModelExtManager.afterIndelParamChange(Tree tree, Hmm hmm, McmcMove m, boolean accepted)
void	ModelExtension.afterIndelParamChange(Tree tree, Hmm hmm, McmcMove m, boolean accepted) Called after a proposed indel parameter change (accepted or rejected).
void	ModelExtManager.afterModExtParamChange(Tree tree, boolean accepted)
void	ModelExtension.afterModExtParamChange(Tree tree, ModelExtension ext, boolean accepted) Called after a proposed model extension parameter change (accepted or rejected).
void	ModelExtManager.afterSubstParamChange(Tree tree, SubstitutionModel model, int ind, boolean accepted)
void	ModelExtension.afterSubstParamChange(Tree tree, SubstitutionModel model, int ind, boolean accepted) Called after a proposed indel parameter change (accepted or rejected).
void	ModelExtManager.afterTreeChange(Tree tree, Vertex nephew, boolean accepted)
void	ModelExtension.afterTreeChange(Tree tree, Vertex nephew, boolean accepted) Called after a proposed topology change (accepted or rejected).
void	ModelExtManager.beforeAlignChange(Tree tree, Vertex selectRoot)
void	ModelExtension.beforeAlignChange(Tree tree, Vertex selectRoot) Called before an alignment change is proposed, but after the affected subtree has been selected.
void	ModelExtManager.beforeEdgeLenChange(Tree tree, Vertex vertex)
void	ModelExtension.beforeEdgeLenChange(Tree tree, Vertex vertex) Called before an edge length change is proposed, but after the affected edge is selected.
void	ModelExtManager.beforeIndelParamChange(Tree tree, Hmm hmm, McmcMove m)
void	ModelExtension.beforeIndelParamChange(Tree tree, Hmm hmm, McmcMove m) Called before an indel parameter change is proposed, but after the affected parameter is selected.
void	ModelExtManager.beforeModExtParamChange(Tree tree)
void	ModelExtension.beforeModExtParamChange(Tree tree, ModelExtension ext) Called when a model extension plugin is to propose a parameter change.
void	ModelExtManager.beforeSampling(Tree tree) Calls McmcModule.beforeSampling(Tree) on each active plugin.
void	ModelExtManager.beforeSubstParamChange(Tree tree, SubstitutionModel model, int ind)
void	ModelExtension.beforeSubstParamChange(Tree tree, SubstitutionModel model, int ind) Called before a substitution parameter change is proposed.
void	ModelExtManager.beforeTreeChange(Tree tree, Vertex nephew)
void	ModelExtension.beforeTreeChange(Tree tree, Vertex nephew) Called before a topology change is proposed, but after the affected branches are selected.
double	ModelExtManager.logLikeAlignChange(Tree tree, Vertex selectRoot) 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.
double	ModelExtension.logLikeAlignChange(Tree tree, Vertex selectRoot)
double	ModelExtManager.logLikeEdgeLenChange(Tree tree, Vertex vertex) 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.
double	ModelExtension.logLikeEdgeLenChange(Tree tree, Vertex vertex)
double	ModelExtManager.logLikeIndelParamChange(Tree tree, Hmm hmm, McmcMove m) 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.
double	ModelExtension.logLikeIndelParamChange(Tree tree, Hmm hmm, McmcMove m)
double	ModelExtManager.logLikeModExtParamChange(Tree tree) 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.
double	ModelExtension.logLikeModExtParamChange(Tree tree, ModelExtension ext) Computes the change in likelihood to this ModelExtension, after a change to ext.
double	ModelExtManager.logLikeSubstParamChange(Tree tree, SubstitutionModel model, int ind) 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.
double	ModelExtension.logLikeSubstParamChange(Tree tree, SubstitutionModel model, int ind)
double	ModelExtManager.logLikeTreeChange(Tree tree, Vertex nephew) 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.
double	ModelExtension.logLikeTreeChange(Tree tree, Vertex nephew)
boolean	ModelExtManager.proposeParamChange(Tree tree)
double	ModelExtManager.totalLogLike(Tree tree) 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.
double	ModelExtManager.totalLogPrior(Tree tree) Calculates the log of total prior probability by including contributions from model extension plugins.

Uses of Tree in statalign.model.ext.plugins

Methods in statalign.model.ext.plugins with parameters of type Tree

void	StructAlign.afterAlignChange(Tree tree, Vertex selectRoot, boolean accepted)
void	StructAlign.afterContinuousParamChange(Tree tree, boolean accepted)
void	StructAlign.afterEdgeLenChange(Tree tree, Vertex vertex, boolean accepted)
void	StructAlign.afterTreeChange(Tree tree, Vertex nephew, boolean accepted)
void	StructAlign.beforeAlignChange(Tree tree, Vertex selectRoot)
void	StructAlign.beforeContinuousParamChange(Tree tree)
void	StructAlign.beforeEdgeLenChange(Tree tree, Vertex vertex)
void	StructAlign.beforeSampling(Tree tree)
void	StructAlign.beforeTreeChange(Tree tree, Vertex nephew)
double[][]	StructAlign.calcFullCovar(Tree tree) return the full covariance matrix for the tree topology and branch lengths
double	StructAlign.computeLogLikeFactor(Tree tree)
double	StructAlign.logLikeAlignChange(Tree tree, Vertex selectRoot)
double	StructAlign.logLikeContinuousParamChange(Tree tree)
double	StructAlign.logLikeEdgeLenChange(Tree tree, Vertex vertex)
double	StructAlign.logLikeFactor(Tree tree)
double	RNAAliFold.logLikeFactor(Tree tree)
double	PPFold.logLikeFactor(Tree tree)
double	StructAlign.logLikeIndelParamChange(Tree tree, Hmm hmm, McmcMove m)
double	StructAlign.logLikeModExtParamChange(Tree tree, ModelExtension ext)
double	StructAlign.logLikeSubstParamChange(Tree tree, SubstitutionModel model, int ind)
double	StructAlign.logLikeTreeChange(Tree tree, Vertex nephew)

Uses of Tree in statalign.model.ext.plugins.structalign

Methods in statalign.model.ext.plugins.structalign with parameters of type Tree

static java.util.ArrayList<java.lang.Integer>	Funcs.findRefSubtrees(Tree tree, int refInd)
static java.util.ArrayList<java.lang.Integer>	Subtree.getSubtreeLeaves(Tree tree, Vertex subtreeRoot, int nLeaves)
static void	Funcs.initLSRotations(Tree tree, double[][][] coords, double[][] xlats, double[][] axes, double[] angles)
static Vertex	Funcs.sampleVertex(Tree tree)
static void	Funcs.writeRotationFiles(Tree tree, double[][][] coords, double[][] xlats, double[][] axes, double[] angles)