Uses of Class
statalign.base.Vertex

Packages that use Vertex

statalign.base
statalign.model.ext
statalign.model.ext.plugins
statalign.model.ext.plugins.structalign

Uses of Vertex in statalign.base

Fields in statalign.base declared as Vertex

Vertex	Vertex.left This reference points to the left child of the vertex.
Vertex	AlignColumn.owner The owner tells the tree vertex where this AlignColumn belongs to.
Vertex	Vertex.parent This reference points to the parent of the vertex
Vertex	Vertex.right This reference points to the right child of the vertex.
Vertex	Tree.root The root of the tree
Vertex[]	Tree.vertex The array of vertices of the tree.

Methods in statalign.base that return Vertex

Vertex

Vertex.brother()

Methods in statalign.base with parameters of type Vertex

static void	Vertex.printChildren(Vertex v)
static void	Vertex.printEdges(Vertex v)

Constructors in statalign.base with parameters of type Vertex

AlignColumn(Vertex owner)
It constructs a new AlignColumn.

Vertex(Vertex parent)

Uses of Vertex in statalign.model.ext

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

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.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.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.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)

Uses of Vertex in statalign.model.ext.plugins

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

void	StructAlign.afterAlignChange(Tree tree, Vertex selectRoot, 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.beforeEdgeLenChange(Tree tree, Vertex vertex)
void	StructAlign.beforeTreeChange(Tree tree, Vertex nephew)
int[]	StructAlign.calcDistanceMatrix(Vertex vertex, double[][] distMat)
int[]	StructAlign.calcDistanceMatrix(Vertex vertex, double[][] distMat, boolean unweighted) recursive algorithm to traverse tree and calculate distance matrix between leaves
int[]	StructAlign.calcUnweightedDistanceMatrix(Vertex vertex, double[][] distMat)
double	StructAlign.logLikeAlignChange(Tree tree, Vertex selectRoot)
double	StructAlign.logLikeEdgeLenChange(Tree tree, Vertex vertex)
double	StructAlign.logLikeTreeChange(Tree tree, Vertex nephew)
void	StructAlign.printTree(Vertex v, java.lang.String vname)

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

Methods in statalign.model.ext.plugins.structalign that return Vertex

static Vertex

Funcs.sampleVertex(Tree tree)

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

static java.util.ArrayList<java.lang.Integer>	Funcs.collectLeaves(Vertex v)
static java.util.ArrayList<java.lang.Integer>	Subtree.getSubtreeLeaves(Tree tree, Vertex subtreeRoot, int nLeaves)
static void	Funcs.moveDown(Vertex v, java.util.List<java.lang.Integer> inds)
static void	Funcs.moveUp(Vertex v, java.util.List<java.lang.Integer> inds)