neobio.alignment
Class OutMatrix

java.lang.Object
  |
  +--neobio.alignment.OutMatrix

All Implemented Interfaces:

Matrix

public class OutMatrix

extends java.lang.Object

implements Matrix

Implements an interface to the OUT matrix of a block. This class is used by the CrochemoreLandauZivUkelson and subclasses to enconde the OUT matrix from the input border and DIST matrix of an AlignmentBlock.

The OUT matrix defined as OUT[i,j] = I[i] + DIST[i,j] where I is the input border array and DIST is the DIST matrix.

The output border of a block is computed from the OUT matrix by taking the maximum value of each column. Note that this class does not compute the OUT matrix, it just stores the necessary information to retrieve a value at any position of the matrix.

It implements the Matrix interface so that the SMAWK algorithm can be used to compute its column maxima.

For more information on how this class is used, please refer to the specification of the CrochemoreLandauZivUkelson and its subclasses.

Author:

Sergio A. de Carvalho Jr.

See Also:

CrochemoreLandauZivUkelson, CrochemoreLandauZivUkelsonGlobalAlignment, CrochemoreLandauZivUkelsonLocalAlignment, AlignmentBlock, Smawk

Field Summary

protected int	dim The dimension of the OUT matrix.
protected int[][]	dist The DIST matrix of a block.
protected int[]	input_border The input border of a block.
protected int	lc The number of columns of the block.
protected int	max_length The length of the longest sequence (number of characters) being aligned.
protected int	max_score The maximum absolute score that the current scoring scheme can return.

Constructor Summary

OutMatrix()

Method Summary

void	init(int max_length, int max_score) Initialised this OUT matrix interface.
int	numColumns() Returns the number of columns of this OUT matrix.
int	numRows() Returns the number of rows of this OUT matrix.
void	setData(int[][] dist, int[] input_border, int dim, int lc) Sets this interface's data to represent an OUT matrix for a block.
int	valueAt(int row, int col) Returns the value at a given position of the matrix.

Methods inherited from class java.lang.Object

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

Field Detail

max_length

protected int max_length

The length of the longest sequence (number of characters) being aligned. It needs to be set only once per alignment.

max_score

protected int max_score

The maximum absolute score that the current scoring scheme can return. It needs to be set only once per alignment.

dist

protected int[][] dist

The DIST matrix of a block.

input_border

protected int[] input_border

The input border of a block.

dim

protected int dim

The dimension of the OUT matrix.

lc

protected int lc

The number of columns of the block.

Constructor Detail

OutMatrix

public OutMatrix()

Method Detail

init

public void init(int max_length,
                 int max_score)

Initialised this OUT matrix interface. This method needs to be executed only once per alignment.

Parameters:

max_length - the length of the longest sequence (number of characters) being aligned

max_score - the maximum absolute score that the current scoring scheme can return

setData

public void setData(int[][] dist,
                    int[] input_border,
                    int dim,
                    int lc)

Sets this interface's data to represent an OUT matrix for a block. This method is typically executed once for each block being aligned.

Parameters:

dist - the DIST matrix

input_border - the input border

dim - the dimension of the OUT matrix

lc - the number of columns of the block

valueAt

public int valueAt(int row,
                   int col)

Returns the value at a given position of the matrix. In general it returns the value of DIST[col][row] + input_border[row]. However, special cases occur for its upper right and lower left triangular parts.

Specified by:

valueAt in interface Matrix

Parameters:

row - row index

col - column index

Returns:

the value at row row, column col of this OUT matrix

numRows

public int numRows()

Returns the number of rows of this OUT matrix.

Specified by:

numRows in interface Matrix

Returns:

the number of rows of this OUT matrix

numColumns

public int numColumns()

Returns the number of columns of this OUT matrix.

Specified by:

numColumns in interface Matrix

Returns:

the number of columns of this OUT matrix