Package de.uni_trier.wi2.procake.similarity.nest.sequence.utils.impl

Class ScoringMatrixImpl

java.lang.Object

de.uni_trier.wi2.procake.similarity.nest.sequence.utils.impl.ScoringMatrixImpl

All Implemented Interfaces:

ScoringMatrix

public class ScoringMatrixImpl
extends Object
implements ScoringMatrix

Field Summary

Fields inherited from interface de.uni_trier.wi2.procake.similarity.nest.sequence.utils.ScoringMatrix

DIAGONAL, HORIZONTAL, NO_STEP, VERTICAL

Constructor Summary

Constructors

Constructor	Description
ScoringMatrixImpl(DataObject[] queryObjects, DataObject[] caseObjects)

Method Summary

Modifier and Type	Method	Description
MatrixPath	backtrackFrom(int queryIdx, int caseIdx)	Create the alignment path of this scoring matrix.
MatrixPath	backtrackFrom(MatrixPath.MatrixCellPair cell)	Create the alignment path of this scoring matrix.
double	get(int queryIdx, int caseIdx)	Get the value of a cell.
double	get(MatrixPath.MatrixCellPair pair)	Get the value of a cell.
double	getHighestScore()	Get the highest score in the last row of the matrix.
MatrixPath.MatrixCellPair	getPair(int queryIdx, int caseIdx)	Get the NESTTaskPair object at the specified position.
MatrixPath.MatrixCellPair	getSourceOf(int queryIdx, int caseIdx)	Get the source of a cell.
int	getSourceStepOf(int queryIdx, int caseIdx)	Get the source step of a cell.
MatrixPath.MatrixCellPair	getStartCell(boolean onlyLastRow)	Get the start cell of the alignment path.
void	initialize()	Initialize the first row and first column to value zero.
boolean	isInBounds(int queryIdx, int caseIdx)	Whether or not the indices are in bounds.
void	set(int queryIdx, int caseIdx, int stepToSource, double value)	Set a cell of the matrix to a given value and also provide the direction to the source cell.
void	set(int queryIdx, int caseIdx, MatrixPath.MatrixCellPair sourceCell, double value)	Set a cell of the matrix to a given value and also provide a reference to the source cell.
void	set(MatrixPath.MatrixCellPair pair)	Set a cell of the matrix to the given pair.

Methods inherited from class java.lang.Object

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

Constructor Detail

ScoringMatrixImpl

public ScoringMatrixImpl(DataObject[] queryObjects,
                         DataObject[] caseObjects)

Method Detail

initialize

public void initialize()

Description copied from interface: ScoringMatrix

Initialize the first row and first column to value zero.

Specified by:

initialize in interface ScoringMatrix

set

public void set(int queryIdx,
                int caseIdx,
                int stepToSource,
                double value)

Description copied from interface: ScoringMatrix

Set a cell of the matrix to a given value and also provide the direction to the source cell.

Specified by:

set in interface ScoringMatrix

Parameters:

queryIdx - Index of the query task to set.

caseIdx - Index of the case task to set.

stepToSource - Either DIAGONAL, VERTICAL or HORIZONTAL.

value - The value to set this cell to.

set

public void set(int queryIdx,
                int caseIdx,
                MatrixPath.MatrixCellPair sourceCell,
                double value)

Description copied from interface: ScoringMatrix

Set a cell of the matrix to a given value and also provide a reference to the source cell.

Specified by:

set in interface ScoringMatrix

Parameters:

queryIdx - Index of the query task to set.

caseIdx - Index of the case task to set.

sourceCell - The source cell.

value - The value to set this cell to.

set

public void set(MatrixPath.MatrixCellPair pair)

Description copied from interface: ScoringMatrix

Set a cell of the matrix to the given pair.

Specified by:

set in interface ScoringMatrix

Parameters:

pair - The new cell entry containing also the indices.

get

public double get(int queryIdx,
                  int caseIdx)

Description copied from interface: ScoringMatrix

Get the value of a cell.

Specified by:

get in interface ScoringMatrix

Parameters:

queryIdx - The query task index.

caseIdx - The case task index.

Returns:

The value at the given position.

get

public double get(MatrixPath.MatrixCellPair pair)

Description copied from interface: ScoringMatrix

Get the value of a cell.

Specified by:

get in interface ScoringMatrix

Parameters:

pair - Specifies the cell's position in the matrix.

Returns:

The value at the given position.

getPair

public MatrixPath.MatrixCellPair getPair(int queryIdx,
                                         int caseIdx)

Description copied from interface: ScoringMatrix

Get the NESTTaskPair object at the specified position.

Specified by:

getPair in interface ScoringMatrix

Returns:

getSourceOf

public MatrixPath.MatrixCellPair getSourceOf(int queryIdx,
                                             int caseIdx)

Description copied from interface: ScoringMatrix

Get the source of a cell.

Specified by:

getSourceOf in interface ScoringMatrix

Parameters:

queryIdx - The query task index of the cell.

caseIdx - The case task index of the dell.

Returns:

A pair representing the source cell.

getSourceStepOf

public int getSourceStepOf(int queryIdx,
                           int caseIdx)

Description copied from interface: ScoringMatrix

Get the source step of a cell.

Specified by:

getSourceStepOf in interface ScoringMatrix

Parameters:

queryIdx - The query task index of the cell.

caseIdx - The case task index of the dell.

Returns:

Either DIAGONAL, VERTICAL or HORIZONTAL.

getHighestScore

public double getHighestScore()

Description copied from interface: ScoringMatrix

Get the highest score in the last row of the matrix.

Specified by:

getHighestScore in interface ScoringMatrix

Returns:

The score.

getStartCell

public MatrixPath.MatrixCellPair getStartCell(boolean onlyLastRow)

Description copied from interface: ScoringMatrix

Get the start cell of the alignment path. Always returns the cell with the highest value in the last row of the matrix.

Specified by:

getStartCell in interface ScoringMatrix

Parameters:

onlyLastRow - Depicts whether only to search in last row of matrix.

Returns:

A pair representing the start cell.

backtrackFrom

public MatrixPath backtrackFrom(MatrixPath.MatrixCellPair cell)

Description copied from interface: ScoringMatrix

Create the alignment path of this scoring matrix. Backtracks to a cell of value 0 (not included).

Specified by:

backtrackFrom in interface ScoringMatrix

Parameters:

cell - The cell to start the backtrack from.

Returns:

The found path.

backtrackFrom

public MatrixPath backtrackFrom(int queryIdx,
                                int caseIdx)

Description copied from interface: ScoringMatrix

Create the alignment path of this scoring matrix. Backtracks to a cell of value 0 (not included).

Specified by:

backtrackFrom in interface ScoringMatrix

Parameters:

queryIdx - The query task index of the starting cell.

caseIdx - The case task index of the starting cell.

Returns:

The found path.

isInBounds

public boolean isInBounds(int queryIdx,
                          int caseIdx)

Description copied from interface: ScoringMatrix

Whether or not the indices are in bounds.

Specified by:

isInBounds in interface ScoringMatrix

Returns:

True, if the indices are in bounds.