statalign.base
Class State

java.lang.Object
  statalign.base.State

public class State
extends java.lang.Object

Objects of this class completely describe the state of the MCMC at a certain time. The state space that the chain explores comprises:

• a phylogenetic tree (topology + edge lengths)
• alignments between neighbouring nodes in the tree (implicitly lengths of the ancestral sequences)
• parameters of the insertion-deletion model (TKF92) and the user-selected substitution model

Apart from the above listed components State objects also store the Felsenstein likelihoods calculated for each character of each sequence and the full likelihood of the state to facilitate postprocessing based on these values (e.g. ancestral sequence estimation, loglikelihood trace etc.).

Tree node representation assumption: first nl nodes are the leaves, then come the ancestral nodes.

Author:

novak

Field Summary

int[][]	align Alignment: for each sequence and each character in the sequence the index of the ancestral character that it is aligned to, or -i-1 if it is not homologous to any character in the ancestor (gap) and the next character in the ancestor sequence (to the right) has index i
double[]	edgeLen Edge length to parent, for each node (first nl are leaves)
double[][][]	felsen Felsenstein likelihoods for each sequence and each character therein
double[]	indelParams Indel model parameters (in the order: R, lambda, mu)
boolean	isBurnin true if this state comes from the burnin.
int[]	left Tree representation: left descendant of each node (first nl are leaves), -1 for none
double	logLike Log-likelihood of the state, excluding model extension factors
java.lang.String[]	name Names of the leaf sequences
int	nl Number of leaves (input sequences)
int	nn Number of nodes
int[]	parent Tree representation: parent of each node (first nl are leaves), -1 for none
int[]	right Tree representation: right descendant of each node (first nl are leaves), -1 for none
int	root Root node of the tree
java.lang.String[]	seq All sequences as strings, including most likely ancestral characters
double[]	substParams Substitution model parameters, as given by the substitution plugin

Constructor Summary

State(int nn)
Constructs a new State object, filling the given parameter and pre-allocating arrays (first dimensions only).

Method Summary

java.lang.String[]	getFullAlign() Returns the multiple alignment of all sequences, including ancestors.
java.lang.String[]	getLeafAlign() Returns the multiple alignment of all leaf sequences.
java.lang.String	getNewickString() Returns the Newick string representation of the tree
java.lang.String	getNewickStringWithLabels()
java.lang.String[]	getPairwiseAlign(int node) Returns string representation of alignment between node and its parent.
static void	main(java.lang.String[] args)
void	updateNewickStringWithLabels()

Methods inherited from class java.lang.Object

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

Field Detail

nn

public int nn

Number of nodes

nl

public int nl

Number of leaves (input sequences)

root

public int root

Root node of the tree

left

public int[] left

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

right

public int[] right

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

parent

public int[] parent

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

edgeLen

public double[] edgeLen

Edge length to parent, for each node (first nl are leaves)

align

public int[][] align

Alignment: for each sequence and each character in the sequence the index of the ancestral character that it is aligned to, or -i-1 if it is not homologous to any character in the ancestor (gap) and the next character in the ancestor sequence (to the right) has index i

felsen

public double[][][] felsen

Felsenstein likelihoods for each sequence and each character therein

seq

public java.lang.String[] seq

All sequences as strings, including most likely ancestral characters

name

public java.lang.String[] name

Names of the leaf sequences

indelParams

public double[] indelParams

Indel model parameters (in the order: R, lambda, mu)

substParams

public double[] substParams

Substitution model parameters, as given by the substitution plugin

logLike

public double logLike

Log-likelihood of the state, excluding model extension factors

isBurnin

public boolean isBurnin

true if this state comes from the burnin.

Constructor Detail

State

public State(int nn)

Constructs a new State object, filling the given parameter and pre-allocating arrays (first dimensions only). Does not create parameter arrays.

Parameters:

nn - number of nodes total (including leaves)

Method Detail

getPairwiseAlign

public java.lang.String[] getPairwiseAlign(int node)

Returns string representation of alignment between node and its parent. Uses characters in seq to construct the strings, - is printed for gaps. Don't call for root, it will produce array bounds errors.

Parameters:

node - the node to get the alignment for

Returns:

String array of two elements, parent comes first

getLeafAlign

public java.lang.String[] getLeafAlign()

Returns the multiple alignment of all leaf sequences.

getFullAlign

public java.lang.String[] getFullAlign()

Returns the multiple alignment of all sequences, including ancestors.

getNewickString

public java.lang.String getNewickString()

Returns the Newick string representation of the tree

getNewickStringWithLabels

public java.lang.String getNewickStringWithLabels()

updateNewickStringWithLabels

public void updateNewickStringWithLabels()

main

public static void main(java.lang.String[] args)