net.maizegenetics.util

Class SuperByteMatrixSingle

java.lang.Object

net.maizegenetics.util.SuperByteMatrixSingle

All Implemented Interfaces:

SuperByteMatrix

public class SuperByteMatrixSingle
extends Object
implements SuperByteMatrix

Author:

Terry Casstevens

Method Summary

Modifier and Type	Method and Description
void	arraycopy(int row, byte[] src, int startColumn) Sets values at given row and starting column.
byte	get(int row, int column) Gets value at given row and column.
byte[]	getAllColumns(int row) Get all values for given row.
byte[]	getAllRows(int column) Get all values for give column.
byte[]	getColumnRange(int row, int start, int end) Get values for given row from start column (inclusive) to end column (exclusive).
int	getNumColumns() Return number of columns.
int	getNumRows() Return number of rows.
boolean	isColumnInnerLoop() Returns true if the matrix stored for better performance when column loop inside row loop.
void	reorderColumns(int[] newIndices) Reorders columns of this matrix based on the given indices.
void	reorderRows(int[] newIndices) Reorders rows of this matrix based on the given indices.
void	set(int row, int column, byte value) Sets value at given row and column.
void	setAll(byte value) Sets value for all elements.
void	setHetsTo(byte value) Changes all heterozygous values to give value.
Spliterator<Byte>	spliterator()
Stream<Byte>	stream() Returns a Stream over the bytes of this matrix.
Stream<Byte>	stream(int row)
void	transpose()

Methods inherited from class java.lang.Object

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

Method Detail

set

public void set(int row,
                int column,
                byte value)

Description copied from interface: SuperByteMatrix

Sets value at given row and column.

Specified by:

set in interface SuperByteMatrix

Parameters:

row - row

column - column

value - value

arraycopy

public void arraycopy(int row,
                      byte[] src,
                      int startColumn)

Description copied from interface: SuperByteMatrix

Sets values at given row and starting column.

Specified by:

arraycopy in interface SuperByteMatrix

Parameters:

row - row

src - values

startColumn - start column

setAll

public void setAll(byte value)

Description copied from interface: SuperByteMatrix

Sets value for all elements.

Specified by:

setAll in interface SuperByteMatrix

Parameters:

value - value

get

public byte get(int row,
                int column)

Description copied from interface: SuperByteMatrix

Gets value at given row and column.

Specified by:

get in interface SuperByteMatrix

Parameters:

row - row

column - column

Returns:

value

getAllColumns

public byte[] getAllColumns(int row)

Description copied from interface: SuperByteMatrix

Get all values for given row.

Specified by:

getAllColumns in interface SuperByteMatrix

Parameters:

row - row

Returns:

values

getColumnRange

public byte[] getColumnRange(int row,
                             int start,
                             int end)

Description copied from interface: SuperByteMatrix

Get values for given row from start column (inclusive) to end column (exclusive).

Specified by:

getColumnRange in interface SuperByteMatrix

Parameters:

row - row

start - start

end - end

Returns:

values

getAllRows

public byte[] getAllRows(int column)

Description copied from interface: SuperByteMatrix

Get all values for give column.

Specified by:

getAllRows in interface SuperByteMatrix

Parameters:

column - column

Returns:

values

getNumRows

public int getNumRows()

Description copied from interface: SuperByteMatrix

Return number of rows.

Specified by:

getNumRows in interface SuperByteMatrix

Returns:

number of rows

getNumColumns

public int getNumColumns()

Description copied from interface: SuperByteMatrix

Return number of columns.

Specified by:

getNumColumns in interface SuperByteMatrix

Returns:

number of columns

isColumnInnerLoop

public boolean isColumnInnerLoop()

Description copied from interface: SuperByteMatrix

Returns true if the matrix stored for better performance when column loop inside row loop. False if matrix stored for better performance when row loop inside column loop.

Specified by:

isColumnInnerLoop in interface SuperByteMatrix

Returns:

true if the matrix stored for better performance when column loop inside row loop. False if matrix stored for better performance when row loop inside column loop.

transpose

public void transpose()

reorderRows

public void reorderRows(int[] newIndices)

Description copied from interface: SuperByteMatrix

Reorders rows of this matrix based on the given indices.

Specified by:

reorderRows in interface SuperByteMatrix

Parameters:

newIndices - new indices.

reorderColumns

public void reorderColumns(int[] newIndices)

Description copied from interface: SuperByteMatrix

Reorders columns of this matrix based on the given indices.

Specified by:

reorderColumns in interface SuperByteMatrix

Parameters:

newIndices - new indices.

setHetsTo

public void setHetsTo(byte value)

Description copied from interface: SuperByteMatrix

Changes all heterozygous values to give value.

Specified by:

setHetsTo in interface SuperByteMatrix

Parameters:

value - value

stream

public Stream<Byte> stream()

Description copied from interface: SuperByteMatrix

Returns a Stream over the bytes of this matrix.

Specified by:

stream in interface SuperByteMatrix

Returns:

Stream over the bytes of this matrix

stream

public Stream<Byte> stream(int row)

Specified by:

stream in interface SuperByteMatrix

spliterator

public Spliterator<Byte> spliterator()