net.maizegenetics.analysis.gbs.neobio

Class OutMatrix

net.maizegenetics.analysis.gbs.neobio.OutMatrix

All Implemented Interfaces:

Matrix

public class OutMatrix
implements Matrix

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

See Also:

class CrochemoreLandauZivUkelson, class AlignmentBlock, class CrochemoreLandauZivUkelson, class CrochemoreLandauZivUkelsonGlobalAlignment, class CrochemoreLandauZivUkelsonLocalAlignment, class AlignmentBlock, class Smawk

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 kotlin.Array[] dist

The DIST matrix of a block.

input_border

protected kotlin.Array[] 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.

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(kotlin.Array[] dist,
                    kotlin.Array[] 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.

Parameters:

row - row index

col - column index

Returns:

org.jetbrains.dokka.NodeRenderContent@561158c2: the value at row row, column col of this OUT matrix

numRows

public int numRows()

Returns the number of rows of this OUT matrix.

Returns:

org.jetbrains.dokka.NodeRenderContent@1ac7acff: the number of rows of this OUT matrix

numColumns

public int numColumns()

Returns the number of columns of this OUT matrix.

Returns:

org.jetbrains.dokka.NodeRenderContent@11bc2aed: the number of columns of this OUT matrix