Package net.sf.okapi.steps.gcaligner

Class DpMatrix<T>

java.lang.Object

net.sf.okapi.steps.gcaligner.DpMatrix<T>

public class DpMatrix<T>
extends Object

DpMatrix is a matrix used in dynamic programming. Two sequences to be aligned are passed to this class in a form of List of Object. Each cell (DpMatrixCell) of the matrix records the alignment score of the two elements. The score is calculated by DpFunction class that is passed to the constructor. The alignment result is returned as a List of DpMatrixCell.

Constructor Summary

Constructors

Constructor	Description
DpMatrix(List<T> sequenceX, List<T> sequenceY, DpFunction<T> p_dpFunction)

Method Summary

Modifier and Type	Method	Description
List<DpMatrixCell>	align()	Align the two sequences.
List<T>	getAlignmentElementsX(int p_xFromIdx, int p_xToIdx)	Returns a List of X sequence elements starting at p_xFromIdx (inclusive) and ending at p_xToIdx (exclusive).
List<T>	getAlignmentElementsY(int p_yFromIdx, int p_yToIdx)	Returns a List of Y sequence elements starting at p_yFromIdx (inclusive) and ending at p_yToIdx (exclusive).
T	getAlignmentElementX(int p_xIdx)	Returns an element of X sequence.
T	getAlignmentElementY(int p_yIdx)	Returns an element of Y sequence.
DpMatrixCell	getCell(int p_xIdx, int p_yIdx)	Return a cell of the matrix.
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

DpMatrix

public DpMatrix(List<T> sequenceX,
                List<T> sequenceY,
                DpFunction<T> p_dpFunction)

Method Detail

align

public List<DpMatrixCell> align()

Align the two sequences. The result is returned as a List of DpMatrixCell in order from the start to the end. Each DpMatrixCell may indicate the match, insertion or deletion of the elements. Some may even indicate the 1:n, n:1 or n:n match. The match state should be queried to DpMatrixCell.

Returns:

List of DpMatrixCell

getAlignmentElementX

public T getAlignmentElementX(int p_xIdx)

Returns an element of X sequence.

Parameters:

p_xIdx - index of X sequence. The index starts with 1. The rule of sum is to specify the same index as the cell's X index, then you'll get what you want. If 0 is specified, IndexOutOfBoundsException will be thrown.

Returns:

DpMatrix

getAlignmentElementY

public T getAlignmentElementY(int p_yIdx)

Returns an element of Y sequence.

Parameters:

p_yIdx - index of Y sequence. The index starts with 1. The rule of sum is to specify the same index as the cell's Y index, then you'll get what you want. If 0 is specified, IndexOutOfBoundsException will be thrown.

Returns:

DpMatrix

getAlignmentElementsX

public List<T> getAlignmentElementsX(int p_xFromIdx,
                                     int p_xToIdx)

Returns a List of X sequence elements starting at p_xFromIdx (inclusive) and ending at p_xToIdx (exclusive).

Parameters:

p_xFromIdx - start index of X sequence (inclusive). The index starts with 1. Usually, a return value of DpMatrixCell#getMultiMatchXIndexBegin() is specified.

p_xToIdx - end index of X sequence (exclusive). The index starts with 1. Usually, a return value of DpMatrixCell#getMultiMatchXIndexEnd() is specified.

Returns:

List of X sequence elements

getAlignmentElementsY

public List<T> getAlignmentElementsY(int p_yFromIdx,
                                     int p_yToIdx)

Returns a List of Y sequence elements starting at p_yFromIdx (inclusive) and ending at p_yToIdx (exclusive).

Parameters:

p_yFromIdx - start index of Y sequence (inclusive). The index starts with 1. Usually, a return value of DpMatrixCell#getMultiMatchYIndexBegin() is specified.

p_yToIdx - end index of Y sequence (exclusive). The index starts with 1. Usually, a return value of DpMatrixCell#getMultiMatchYIndexEnd() is specified.

Returns:

List of Y sequence elements

getCell

public DpMatrixCell getCell(int p_xIdx,
                            int p_yIdx)

Return a cell of the matrix.

Parameters:

p_xIdx - Index of X axis. The index starts with 0.

p_yIdx - Index of Y axis. The index starts with 0.

Returns:

DpMatrixCell object

toString

public String toString()

Overrides:

toString in class Object