statalign.base
Class AlignColumn

java.lang.Object
  statalign.base.AlignColumn

public class AlignColumn
extends java.lang.Object

An AlignColumn is an object that represents an observed or a hidden character and stores a double array storing the Felsenstein likelihoods. AlignColumns are double chained to form an observed or hidden sequence. There are also links to their parent. If the character that AlignColumn represents is aligned to an ancestral characters, then the alignColumn is not orphan otherwise it is, and then its parent represents the first ancestral character to the right in the alignment column.

Author:

miklos, novak, herman

Field Summary

int[]	aligned Vector indicating which characters are aligned to this column at the leaves below.
int[]	alignedUpp Vector indicating which characters are aligned to the parent of this column.
AlignColumn	left This reference points to the left child of this AlignColumn
AlignColumn	next This reference points to the next AlignColumn in the alignment
boolean	orphan If true, then this AlignColumn is inserted, and its parent is the first ancestral character to the right in the alignment If it is false, then this AlignColumn is aligned to its parent
Vertex	owner The owner tells the tree vertex where this AlignColumn belongs to.
AlignColumn	parent This reference points to the parent of this AlignColumn
AlignColumn	prev This reference points to the previous AlignColumn in the alignment
AlignColumn	right This reference points to the right child of this Aligncolumn
double[]	seq This double array contains the Felsenstein Likelihoods
double[]	upp This double array contains the upper Likelihoods

Constructor Summary

AlignColumn(AlignColumn next)

AlignColumn(AlignColumn next, boolean newSeq)
It creates a new AlignColumn, chains it to the next column (namely, it is used to generate a new ancestral sequence built in a traceback phase of a dynamic programming).

AlignColumn(Vertex owner)
It constructs a new AlignColumn.

Method Summary

AlignColumn

clone() Creates a new column as a clone of the this, copying (or cloning) all fields except prev and next.

Methods inherited from class java.lang.Object

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

Field Detail

owner

public Vertex owner

The owner tells the tree vertex where this AlignColumn belongs to.

parent

public AlignColumn parent

This reference points to the parent of this AlignColumn

orphan

public boolean orphan

If true, then this AlignColumn is inserted, and its parent is the first ancestral character to the right in the alignment

If it is false, then this AlignColumn is aligned to its parent

prev

public AlignColumn prev

This reference points to the previous AlignColumn in the alignment

next

public AlignColumn next

This reference points to the next AlignColumn in the alignment

left

public AlignColumn left

This reference points to the left child of this AlignColumn

right

public AlignColumn right

This reference points to the right child of this Aligncolumn

seq

public double[] seq

This double array contains the Felsenstein Likelihoods

upp

public double[] upp

This double array contains the upper Likelihoods

aligned

public int[] aligned

Vector indicating which characters are aligned to this column at the leaves below.

alignedUpp

public int[] alignedUpp

Vector indicating which characters are aligned to the parent of this column.

Constructor Detail

AlignColumn

public AlignColumn(Vertex owner)

It constructs a new AlignColumn. Sets only the owner, other fields are filled in outside of the constructor

Parameters:

owner - The vertex where this AlignColumn belongs to.

AlignColumn

public AlignColumn(AlignColumn next,
                   boolean newSeq)

It creates a new AlignColumn, chains it to the next column (namely, it is used to generate a new ancestral sequence built in a traceback phase of a dynamic programming). the owner is set to the same vertex as the owner of the next AlignColumn.

Parameters:

next - The next AlignColumn in the sequence that is being generated

newSeq - If true, then the constructor allocates memory for the seq[] array that contains the Felsenstein likelihoods. If false, then the seq[] array of other AlignColumn is associated to this Aligncolumn and reused. For speeding-up purposes.

AlignColumn

public AlignColumn(AlignColumn next)

Method Detail

clone

public AlignColumn clone()

Creates a new column as a clone of the this, copying (or cloning) all fields except prev and next.

Overrides:

clone in class java.lang.Object