umcg.genetica.math.matrix

Class SymmetricByteDistanceMatrix

java.lang.Object

umcg.genetica.math.matrix.SymmetricByteDistanceMatrix

public class SymmetricByteDistanceMatrix
extends Object

Symmetric Byte Distance Matrix: A memory efficient matrix capable of performing calculations on all genes x all genes:

Author:

Lude Franke

Field Summary

Fields

Modifier and Type	Field and Description
boolean	loadSuccess
static int	MAX_VALUE

Constructor Summary

Constructors

Constructor and Description
SymmetricByteDistanceMatrix(int size) Creates a new instance of SymmetricByteDistancaMatrix Defines a new Symmetric matrix, with a predefined size Initially all values will be Byte.MAX_Value (127) All data is stored in memory efficient one dimensional array, which costs size * (size + 1) / 2 bytes
SymmetricByteDistanceMatrix(int size, boolean setMaxDistance)

Method Summary

Modifier and Type	Method and Description
void	dispose()
int	get(int x, int y)
void	getAllPairsShortestPath()
int	getDistance(double pValue)
double	getPValue(int distance)
Vector	getShortestPath(int x, int y)
void	load(File fileName)
int	maxValue()
void	save(File fileName)
void	set(int x, int y, int value)
void	setAllElements(int value)
int	size()

Methods inherited from class java.lang.Object

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

Field Detail

MAX_VALUE

public static final int MAX_VALUE

See Also:

Constant Field Values

loadSuccess

public boolean loadSuccess

Constructor Detail

SymmetricByteDistanceMatrix

public SymmetricByteDistanceMatrix(int size)

Creates a new instance of SymmetricByteDistancaMatrix Defines a new Symmetric matrix, with a predefined size Initially all values will be Byte.MAX_Value (127) All data is stored in memory efficient one dimensional array, which costs size * (size + 1) / 2 bytes

SymmetricByteDistanceMatrix

public SymmetricByteDistanceMatrix(int size,
                                   boolean setMaxDistance)

Method Detail

dispose

public void dispose()

setAllElements

public void setAllElements(int value)

set

public void set(int x,
                int y,
                int value)

get

public int get(int x,
               int y)

size

public int size()

maxValue

public int maxValue()

getAllPairsShortestPath

public void getAllPairsShortestPath()

getShortestPath

public Vector getShortestPath(int x,
                              int y)

getDistance

public int getDistance(double pValue)

getPValue

public double getPValue(int distance)

save

public void save(File fileName)

load

public void load(File fileName)