statalign.base
Class Vertex

java.lang.Object
  statalign.base.Vertex

public class Vertex
extends java.lang.Object

This is a vertex of the tree. The 'hardcore' functions are implemented in this class, developers are suggested not change functions in it. The implemented functions are quite unreadable, since we opted for efficiency and not readability. You should be able to develop novel functionality of the software package (postprocessing, substitution models, etc.) without touching this class.

Author:

miklos, novak, herman

Field Summary

double	edgeLength The length of the edge that connects this vertex with its parent.
AlignColumn	first
double	indelLogLike The log-sum of the cumulative insertion-deletion loglikelihoods up to this vertex (ie. summed over the subtree below this vertex.).
int	index Index of this vertex in the Tree.vertex array
int	leafCount
Vertex	left This reference points to the left child of the vertex.
java.lang.String	name The name of the sequence associated to the vertex.
int	nSilentIndels
double	orphanLogLike The log-sum of the Felsenstein's likelihoods of characters that are inserted into the sequence of this vertex.
Vertex	parent This reference points to the parent of the vertex
Vertex	right This reference points to the right child of the vertex.
boolean	selected

Constructor Summary

Vertex(Tree tree)

Vertex(Vertex parent)

Method Summary

void	alignRestore() Restores all the changes an alignment resampling on the currently selected subtree has produced.
Vertex	brother()
void	calcAllUp() Calculates Felsenstein and indel likelihoods up to root, starting from `parent'
void	calcFelsen()
void	calcFelsenRecursively() This function calculates the Felsenstein likelihood for the subtree below this.
void	calcIndelLogLike()
void	calcIndelLogLikeRecursively()
void	calcOrphan()
void	calcOrphanRecursively()
void	calcUpperFromRoot()
void	calcUpperRecursively() This function calculates the upper probability vectors, which contain the partial likelihoods for everything except this subtree.
void	calcUpperRecursivelyWithCheck()
double	calcSumOfEdges() Calculate the sum of branch lengths below on this vertex.
void	checkPointers() this function checks if the pointers are all right...
void	computeWeights(statalign.base.Vertex.Neighbours curr, double[] logProbs) Computes the probability of all the possible imputations for parent and grandpa given the neighbouring AlignColumn objects.
void	edgeChangeUpdate()
void	exciseAllSilentIndels()
double	exciseSilentIndel()
double	exciseSilentIndel(AlignColumn c)
double	exciseSilentIndel(AlignColumn c, boolean remove)
double	exciseSilentIndelBlock(AlignColumn insert, boolean remove)
void	fastSwapBackUncle() Restores the exact state just before the call of fastSwapWithUncle().
double	fastSwapWithUncle() Swaps this with its uncle, but keeps alignment columns where this, its parent, the uncle node and its parent are all aligned unchanged with a given probability, and only proposes new alignments between these selected alignment anchors columns.
int	favouredDestination(int state)
int	getLength()
double	hmm2AlignWithSave() Samples a new alignment between `this' & `this.parent', taking window sizes into account.
double	hmm2AlignWithSave(double heat)
double	insertSilentIndel()
double	insertSilentIndel(AlignColumn c)
double	insertSilentIndelBlock(AlignColumn c)
double	maxDepth() Calculate the maximum depth below on this vertex.
double	modifySilentIndel(boolean insert)
double	nephewUncleSwapFixedColumns()
double	nephewUncleSwapFixedColumns2()
double	nephewUncleSwapFixedColumns3()
java.lang.String	print(int digits)
void	print(java.lang.StringBuffer b)
void	print(java.lang.StringBuffer b, boolean withNumbers)
static void	printChildren(Vertex v)
java.lang.String[]	printedAlignment()
java.lang.String[]	printedAlignment(boolean inWindow)
static void	printEdges(Vertex v)
void	printPointers()
void	printToScreenAlignment(int windowStart, int windowEnd)
void	printToScreenAlignment(int windowStart, int windowEnd, boolean printAll)
void	printWithNumbers(java.lang.StringBuffer b)
double	realignToParent()
double	realignToParent(boolean useCurrentWin)
double	realignToParent(boolean useCurrentWin, double heat) Samples a new alignment between the subtree rooted at this vertex and the rest of the sequences.
double	realignToParent(double heat)
void	recomputeCheckLogLike()
void	recomputeLogLike()
void	recomputeLogLikeSelected()
void	recursivelyUpdateHmm2Matrices()
void	recursivelyUpdateHmm3Matrices()
void	recursivelyUpdateHmmMatrices()
void	restoreData()
void	restoreFiveWay()
void	restoreFiveWay(boolean swapNephewUncle)
void	saveData()
double	selectAndResampleAlignment() This function cuts out a window and realigns in the selected subtree.
void	selectSubtree(double[] weights, int level) Selects a subtree
void	setEdgeLength(double x)
void	swapBackUncleAlignToParent() Restores the exact state just before the call to swapWithUncleAlignToParent().
double	swapWithUncleAlignToParent() Swaps this with its uncle, but proposes new alignments only between this node and its parent, and the uncle node and its parent, every other alignment is kept fixed.
void	undoExciseSilentIndel()
void	undoInsertSilentIndel()
void	updateAligned()
void	updateAlignedInWindow()
void	updateAlignedParent()
void	updateAlignedParentInWindow()
void	updateAlignedRecursively()
void	updateAlignedRecursivelyInWindow()
void	updateAlignedRecursivelyInWindowWithCheck()
void	updateAlignedRecursivelyWithCheck()
void	updateHmm2Matrices()
void	updateHmm2Matrix(double[] params)
void	updateHmmMatrices()
void	updateTransitionMatrix()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

name

public java.lang.String name

The name of the sequence associated to the vertex. Used only if the vertex is a leaf of the tree.

index

public int index

Index of this vertex in the Tree.vertex array

parent

public Vertex parent

This reference points to the parent of the vertex

left

public Vertex left

This reference points to the left child of the vertex. If the vertex is a leaf, it is set to null.

right

public Vertex right

This reference points to the right child of the vertex. If the vertex is a leaf, it is set to null.

nSilentIndels

public int nSilentIndels

first

public AlignColumn first

selected

public boolean selected

edgeLength

public double edgeLength

The length of the edge that connects this vertex with its parent.

orphanLogLike

public double orphanLogLike

The log-sum of the Felsenstein's likelihoods of characters that are inserted into the sequence of this vertex.

indelLogLike

public double indelLogLike

The log-sum of the cumulative insertion-deletion loglikelihoods up to this vertex (ie. summed over the subtree below this vertex.).

leafCount

public int leafCount

Constructor Detail

Vertex

public Vertex(Tree tree)

Vertex

public Vertex(Vertex parent)

Method Detail

brother

public Vertex brother()

Returns:

the "brother" of this node, i.e. the other descendant of its parent

updateTransitionMatrix

public void updateTransitionMatrix()

updateHmm2Matrix

public void updateHmm2Matrix(double[] params)

updateHmmMatrices

public void updateHmmMatrices()

recursivelyUpdateHmmMatrices

public void recursivelyUpdateHmmMatrices()

updateHmm2Matrices

public void updateHmm2Matrices()

recursivelyUpdateHmm2Matrices

public void recursivelyUpdateHmm2Matrices()

recursivelyUpdateHmm3Matrices

public void recursivelyUpdateHmm3Matrices()

setEdgeLength

public void setEdgeLength(double x)

printChildren

public static void printChildren(Vertex v)

printEdges

public static void printEdges(Vertex v)

edgeChangeUpdate

public void edgeChangeUpdate()

printWithNumbers

public void printWithNumbers(java.lang.StringBuffer b)

print

public void print(java.lang.StringBuffer b)

print

public void print(java.lang.StringBuffer b,
                  boolean withNumbers)

print

public java.lang.String print(int digits)

recomputeLogLike

public void recomputeLogLike()

recomputeLogLikeSelected

public void recomputeLogLikeSelected()

recomputeCheckLogLike

public void recomputeCheckLogLike()

calcUpperFromRoot

public void calcUpperFromRoot()

calcUpperRecursively

public void calcUpperRecursively()

This function calculates the upper probability vectors, which contain the partial likelihoods for everything except this subtree. Requires the felsenstein partial likelihoods to have already been computed for everything below.

calcUpperRecursivelyWithCheck

public void calcUpperRecursivelyWithCheck()

calcFelsenRecursively

public void calcFelsenRecursively()

This function calculates the Felsenstein likelihood for the subtree below this. When called from the root, the result is stored in orphanLogLike at the root.

calcFelsen

public void calcFelsen()

calcOrphan

public void calcOrphan()

calcOrphanRecursively

public void calcOrphanRecursively()

calcIndelLogLikeRecursively

public void calcIndelLogLikeRecursively()

calcIndelLogLike

public void calcIndelLogLike()

hmm2AlignWithSave

public double hmm2AlignWithSave()

Samples a new alignment between `this' & `this.parent', taking window sizes into account. Updates all Vertex-stored suppl. data, saving old data for restoration into oldVertex.

Returns:

log of 1/proposal

hmm2AlignWithSave

public double hmm2AlignWithSave(double heat)

selectSubtree

public void selectSubtree(double[] weights,
                          int level)

Selects a subtree

selectAndResampleAlignment

public double selectAndResampleAlignment()

This function cuts out a window and realigns in the selected subtree.

realignToParent

public double realignToParent(double heat)

realignToParent

public double realignToParent()

realignToParent

public double realignToParent(boolean useCurrentWin)

realignToParent

public double realignToParent(boolean useCurrentWin,
                              double heat)

Samples a new alignment between the subtree rooted at this vertex and the rest of the sequences. Only the alignment between this vertex and its parent is changed.

Parameters:

useCurrentWin - if true then keeps the current window selection for this node (backproposal and proposal for window selection must be computed by the caller)

Returns:

the ratio between backproposal and proposal probabilities

updateAligned

public void updateAligned()

updateAlignedInWindow

public void updateAlignedInWindow()

updateAlignedParentInWindow

public void updateAlignedParentInWindow()

updateAlignedParent

public void updateAlignedParent()

updateAlignedRecursively

public void updateAlignedRecursively()

updateAlignedRecursivelyInWindow

public void updateAlignedRecursivelyInWindow()

updateAlignedRecursivelyInWindowWithCheck

public void updateAlignedRecursivelyInWindowWithCheck()

updateAlignedRecursivelyWithCheck

public void updateAlignedRecursivelyWithCheck()

alignRestore

public void alignRestore()

Restores all the changes an alignment resampling on the currently selected subtree has produced. Must be called on selected subtree root.

restoreFiveWay

public void restoreFiveWay()

restoreFiveWay

public void restoreFiveWay(boolean swapNephewUncle)

computeWeights

public void computeWeights(statalign.base.Vertex.Neighbours curr,
                           double[] logProbs)

Computes the probability of all the possible imputations for parent and grandpa given the neighbouring AlignColumn objects.

Parameters:

curr - Neighbours struct corresponding to current state

old - Neighbours struct corresponding to original state

favouredDestination

public int favouredDestination(int state)

saveData

public void saveData()

restoreData

public void restoreData()

insertSilentIndel

public double insertSilentIndel()

insertSilentIndel

public double insertSilentIndel(AlignColumn c)

insertSilentIndelBlock

public double insertSilentIndelBlock(AlignColumn c)

undoInsertSilentIndel

public void undoInsertSilentIndel()

undoExciseSilentIndel

public void undoExciseSilentIndel()

exciseSilentIndel

public double exciseSilentIndel()

exciseSilentIndel

public double exciseSilentIndel(AlignColumn c)

exciseSilentIndel

public double exciseSilentIndel(AlignColumn c,
                                boolean remove)

exciseAllSilentIndels

public void exciseAllSilentIndels()

modifySilentIndel

public double modifySilentIndel(boolean insert)

exciseSilentIndelBlock

public double exciseSilentIndelBlock(AlignColumn insert,
                                     boolean remove)

nephewUncleSwapFixedColumns3

public double nephewUncleSwapFixedColumns3()

nephewUncleSwapFixedColumns2

public double nephewUncleSwapFixedColumns2()

nephewUncleSwapFixedColumns

public double nephewUncleSwapFixedColumns()

swapWithUncleAlignToParent

public double swapWithUncleAlignToParent()

Swaps this with its uncle, but proposes new alignments only between this node and its parent, and the uncle node and its parent, every other alignment is kept fixed. Slow because full sequence alignment is done. Assumes this has a non-null grandparent.

Returns:

log-quotient of backproposal and proposal

swapBackUncleAlignToParent

public void swapBackUncleAlignToParent()

Restores the exact state just before the call to swapWithUncleAlignToParent(). Must be called on ex-uncle node. Assumes this has a non-null grandparent.

fastSwapWithUncle

public double fastSwapWithUncle()

Swaps this with its uncle, but keeps alignment columns where this, its parent, the uncle node and its parent are all aligned unchanged with a given probability, and only proposes new alignments between these selected alignment anchors columns. Alignments between other sequences than the above mentioned four are kept unchanged. Assumes this has a non-null grandparent.

Returns:

log-quotient of backproposal and proposal

fastSwapBackUncle

public void fastSwapBackUncle()

Restores the exact state just before the call of fastSwapWithUncle(). Must be called on ex-uncle node. Assumes this has a non-null grandparent.

calcAllUp

public void calcAllUp()

Calculates Felsenstein and indel likelihoods up to root, starting from `parent'

printedAlignment

public java.lang.String[] printedAlignment(boolean inWindow)

printedAlignment

public java.lang.String[] printedAlignment()

printPointers

public void printPointers()

printToScreenAlignment

public void printToScreenAlignment(int windowStart,
                                   int windowEnd)

printToScreenAlignment

public void printToScreenAlignment(int windowStart,
                                   int windowEnd,
                                   boolean printAll)

calcSumOfEdges

public double calcSumOfEdges()

Calculate the sum of branch lengths below on this vertex. Used to generate the prior for the whole state.

Returns:

sum of branchlengths below this node.

maxDepth

public double maxDepth()

Calculate the maximum depth below on this vertex. Used in tree visualisation.

Returns:

maximum depth below this vertex.

checkPointers

public void checkPointers()

this function checks if the pointers are all right...

getLength

public int getLength()