Class IndelAligner<T>

java.lang.Object

ca.phon.alignment.IndelAligner<T>

Type Parameters:

T -

All Implemented Interfaces:

Aligner<T>

Direct Known Subclasses:

PhoneAligner, SyllableAligner

public abstract class IndelAligner<T>
extends Object
implements Aligner<T>

Constructor Summary

Constructors

Constructor	Description
IndelAligner()

Method Summary

Modifier and Type	Method	Description
AlignmentMap<T>	calculateAlignment(T[] top, T[] bottom)	Calculate the alignment.
protected abstract int	costSkip(T ele)
protected abstract int	costSubstitute(T ele1, T ele2)	Return the similarity between two elements
AlignmentMap<T>	getAlignmentMap()	Returns the AlignmentMap calculated during the last call to 'calculateAlignment'.
protected Integer[][]	retrieveAlignment(T[] top, T[] bottom, int i, int j, int tally, int[][] matrix, Stack<Integer> tp, Stack<Integer> ap, int score)	Get the alignment from the completed matrix

Methods inherited from class java.lang.Object

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

Constructor Details

IndelAligner

public IndelAligner()

Method Details

costSubstitute

protected abstract int costSubstitute(T ele1,
 T ele2)

Return the similarity between two elements

Parameters:

ele1 -

ele2 -

Returns:

costSkip

protected abstract int costSkip(T ele)

calculateAlignment

public AlignmentMap<T> calculateAlignment(T[] top,
 T[] bottom)

Description copied from interface: Aligner

Calculate the alignment. Alignment calculation is determined by implementation. See global vs local alignment.

Specified by:

calculateAlignment in interface Aligner<T>

Returns:

the alignment map

retrieveAlignment

protected Integer[][] retrieveAlignment(T[] top,
 T[] bottom,
 int i,
 int j,
 int tally,
 int[][] matrix,
 Stack<Integer> tp,
 Stack<Integer> ap,
 int score)

Get the alignment from the completed matrix

Parameters:

top - top elements

bottom - bottom elements

i - the width of the matrix

j - the height of the matrix

tally - the total score accumulated in at each setp of the recursion

tp - the stack used to store the target alignment

ap - the stack used to store the actual alignment

score -

Matrix - the completed dynamic algorithm

getAlignmentMap

public AlignmentMap<T> getAlignmentMap()

Description copied from interface: Aligner

Returns the AlignmentMap calculated during the last call to 'calculateAlignment'. Undefined if calculateAlignment was not called.

Specified by:

getAlignmentMap in interface Aligner<T>

Returns:

alignment map