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

Interface ScoringMatrix

All Known Implementing Classes:

ScoringMatrixImpl

public interface ScoringMatrix

Representation of the scoring matrix of an dp algorithm.

Field Summary

Fields

Modifier and Type	Field	Description
static int	DIAGONAL
static int	HORIZONTAL
static int	NO_STEP
static int	VERTICAL

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 source, 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.

Field Detail

DIAGONAL

static final int DIAGONAL

See Also:

Constant Field Values

VERTICAL

static final int VERTICAL

See Also:

Constant Field Values

HORIZONTAL

static final int HORIZONTAL

See Also:

Constant Field Values

NO_STEP

static final int NO_STEP

See Also:

Constant Field Values

Method Detail

initialize

void initialize()

Initialize the first row and first column to value zero.

set

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.

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

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

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

Parameters:

queryIdx - Index of the query task to set.

caseIdx - Index of the case task to set.

source - The source cell.

value - The value to set this cell to.

set

void set(MatrixPath.MatrixCellPair pair)

Set a cell of the matrix to the given pair.

Parameters:

pair - The new cell entry containing also the indices.

get

double get(int queryIdx,
           int caseIdx)

Get the value of a cell.

Parameters:

queryIdx - The query task index.

caseIdx - The case task index.

Returns:

The value at the given position.

get

double get(MatrixPath.MatrixCellPair pair)

Get the value of a cell.

Parameters:

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

Returns:

The value at the given position.

getPair

MatrixPath.MatrixCellPair getPair(int queryIdx,
                                  int caseIdx)

Get the NESTTaskPair object at the specified position.

Parameters:

queryIdx -

caseIdx -

Returns:

getSourceOf

MatrixPath.MatrixCellPair getSourceOf(int queryIdx,
                                      int caseIdx)

Get the source of a cell.

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

int getSourceStepOf(int queryIdx,
                    int caseIdx)

Get the source step of a cell.

Parameters:

queryIdx - The query task index of the cell.

caseIdx - The case task index of the dell.

Returns:

Either DIAGONAL, VERTICAL or HORIZONTAL.

getHighestScore

double getHighestScore()

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

Returns:

The score.

getStartCell

MatrixPath.MatrixCellPair getStartCell(boolean onlyLastRow)

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

Parameters:

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

Returns:

A pair representing the start cell.

backtrackFrom

MatrixPath backtrackFrom(MatrixPath.MatrixCellPair cell)

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

Parameters:

cell - The cell to start the backtrack from.

Returns:

The found path.

backtrackFrom

MatrixPath backtrackFrom(int queryIdx,
                         int caseIdx)

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

Parameters:

queryIdx - The query task index of the starting cell.

caseIdx - The case task index of the starting cell.

Returns:

The found path.

isInBounds

boolean isInBounds(int queryIdx,
                   int caseIdx)

Whether or not the indices are in bounds.

Parameters:

queryIdx -

caseIdx -

Returns:

True, if the indices are in bounds.