umcg.genetica.math.matrix

Class SymmetricShortDistanceMatrix

java.lang.Object

umcg.genetica.math.matrix.SymmetricShortDistanceMatrix

public class SymmetricShortDistanceMatrix
extends Object

Symmetric Short 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
static int	MAX_VALUE

Constructor Summary

Constructors

Constructor and Description
SymmetricShortDistanceMatrix(int size) Creates a new instance of SymmetricShortDistancaMatrix Defines a new Symmetric matrix, with a predefined size Initially all values will be Short.MAX_Value (65535) All data is stored in memory efficient one dimensional array, which costs size * (size + 1) bytes
SymmetricShortDistanceMatrix(int size, boolean setMaxDistance)

Method Summary

Modifier and Type	Method and Description
int	get(int x, int y)
void	getAllPairsShortestPath()
double	getCorrelationFromDistance(int distance)
int	getDistance(double pValue)
int	getDistanceFromCorrelation(double correlation) The distance measure in short ranges from 0 to 65.000.
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

Constructor Detail

SymmetricShortDistanceMatrix

public SymmetricShortDistanceMatrix(int size)

Creates a new instance of SymmetricShortDistancaMatrix Defines a new Symmetric matrix, with a predefined size Initially all values will be Short.MAX_Value (65535) All data is stored in memory efficient one dimensional array, which costs size * (size + 1) bytes

SymmetricShortDistanceMatrix

public SymmetricShortDistanceMatrix(int size,
                                    boolean setMaxDistance)

Method Detail

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)

getDistanceFromCorrelation

public int getDistanceFromCorrelation(double correlation)

The distance measure in short ranges from 0 to 65.000. The distance in correlation (Pearson, Spearman, whatever) ranges from -1 to 1. This method translates correlationdistance into short distance.

getCorrelationFromDistance

public double getCorrelationFromDistance(int distance)

save

public void save(File fileName)

load

public void load(File fileName)