Package com.actelion.research.util.datamodel

Class ByteVec

java.lang.Object

com.actelion.research.util.datamodel.ByteVec

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<ByteVec>

public class ByteVec
extends java.lang.Object
implements java.lang.Comparable<ByteVec>, java.io.Serializable

ByteVec:

Description: Vector with byte values

Author:

Modest von Korff 05.04.2005 start implementation

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static int	COSINE
static int	EUCLIDEAN
static int	EUCLIDEAN_FAST
static java.util.Random	RANDOM
static int	TANIMOTO
static int	TANIMOTO_INV

Constructor Summary

Constructors

Constructor	Description
ByteVec(byte[] arr)
ByteVec(int iSize)
ByteVec(int[] arr)
ByteVec(ByteVec v)	Deep copy
ByteVec(java.lang.String s)	Hash code is calculated.

Method Summary

Modifier and Type	Method	Description
ByteVec	add(ByteVec dvVec)
void	append(java.lang.String s)
int	compareTo(ByteVec o)
static double	Cosine(ByteVec dVec1, ByteVec dVec2)	Vectors have to be normed!
static double	cubicDistance(ByteVec dVec1, ByteVec dVec2)
static ByteVec	devide(ByteVec dVec1, ByteVec dVec2)
static double	distance(ByteVec dVec1, ByteVec dVec2, int metric)
boolean	equal(ByteVec dv)
boolean	equals(java.lang.Object o)
static double	euclideanDistance(ByteVec dVec1, ByteVec dVec2)	Euclidean distance
static double	EuclideanDistanceFast(ByteVec dVec1, ByteVec dVec2)	Euclidean distance without sqrt
byte[]	get()
byte	get(int col)
int	getBitsSet()
static int	getHashCode(byte[] a)
double	getNorm()
static double	getTanimotoDist(byte[] a1, byte[] a2)
static double	getTanimotoDist(ByteVec bv1, ByteVec bv2)	Calculates the Tanimoto coefficient
static double	getTanimotoDistBitWise(ByteVec bv1, ByteVec bv2)	Calculates the Tanimoto coefficient
static double	getTanimotoDistInv(ByteVec bv1, ByteVec bv2)	Byte wise inverse Tanimoto distance.
int	hashCode()	The hash code has to be calculated before.
void	initRND(byte min, byte max)
static java.util.List<ByteVec>	initRND(byte min, byte max, int lenByteVec, int numelements)
static double	manhattanBlockDistance(ByteVec dVec1, ByteVec dVec2)
static ByteVec	meanClust()
static ByteVec	minus(ByteVec dVec1, ByteVec dVec2)
static double	mult(byte[] a1, byte[] a2)
ByteVec	mult(double dFactor)
static double	mult(ByteVec bv1, ByteVec bv2)
static ByteVec	multEl(ByteVec dVec1, ByteVec dVec2)	Elementwise multiplication
void	norm2One()
static ByteVec	plus(ByteVec dVec1, ByteVec dVec2)
void	reduce(java.util.Vector<java.lang.Integer> vecIndices)
static byte[]	reverse(byte[] a)
void	set(byte dVal)
void	set(int col, byte val)	Hash value has to be recalculated!
void	setRNDvalue(double dRange)
void	setRNDvalue(double dCenter, double dRange)
int	size()
ByteVec	sub(ByteVec dvSub)	Substraction
static ByteVec	test01()
static ByteVec	testS1()
static ByteVec	testTakeda1()
byte[]	toArray()
java.lang.String	toBinaryString()
java.lang.String	toBinaryStringDense()
static byte[]	toByteArray(double[] data)
static byte[]	toByteArray(int data)
static byte[]	toByteArray(int[] data)
static byte[]	toByteArray(long data)
java.lang.String	toString()	Converts a byte into its decimal.
static java.lang.String	toString(byte[] a)
static java.lang.String	toString(byte[] a, java.lang.String seperator)
java.lang.String	toString(int iNumDigits)
java.lang.String	toStringString()	Converts the bytes into chars.

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

RANDOM

public static final java.util.Random RANDOM

COSINE

public static final int COSINE

See Also:

Constant Field Values

EUCLIDEAN

public static final int EUCLIDEAN

See Also:

Constant Field Values

EUCLIDEAN_FAST

public static final int EUCLIDEAN_FAST

See Also:

Constant Field Values

TANIMOTO

public static final int TANIMOTO

See Also:

Constant Field Values

TANIMOTO_INV

public static final int TANIMOTO_INV

See Also:

Constant Field Values

Constructor Detail

ByteVec

public ByteVec(ByteVec v)

Deep copy

Parameters:

v -

ByteVec

public ByteVec(java.lang.String s)

Hash code is calculated.

Parameters:

s -

ByteVec

public ByteVec(int iSize)

ByteVec

public ByteVec(byte[] arr)

ByteVec

public ByteVec(int[] arr)

Method Detail

add

public ByteVec add(ByteVec dvVec)

append

public void append(java.lang.String s)

compareTo

public int compareTo(ByteVec o)

Specified by:

compareTo in interface java.lang.Comparable<ByteVec>

Parameters:

o - ByteVec

Returns:

-1 if the first different value is smaller than the corresponding value in dv. 0 if bot vectors are equal. 1 if the first different value is bigger than the corresponding value in dv.

distance

public static double distance(ByteVec dVec1,
                              ByteVec dVec2,
                              int metric)
                       throws java.lang.Exception

Throws:

java.lang.Exception

devide

public static ByteVec devide(ByteVec dVec1,
                             ByteVec dVec2)

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

equal

public boolean equal(ByteVec dv)

euclideanDistance

public static double euclideanDistance(ByteVec dVec1,
                                       ByteVec dVec2)

Euclidean distance

Parameters:

dVec1 -

dVec2 -

Returns:

EuclideanDistanceFast

public static double EuclideanDistanceFast(ByteVec dVec1,
                                           ByteVec dVec2)
                                    throws java.lang.ArrayIndexOutOfBoundsException

Euclidean distance without sqrt

Parameters:

dVec1 -

dVec2 -

Returns:

Throws:

java.lang.ArrayIndexOutOfBoundsException

get

public byte[] get()

get

public byte get(int col)

getNorm

public double getNorm()

getHashCode

public static int getHashCode(byte[] a)

hashCode

public int hashCode()

The hash code has to be calculated before. Should be done automatically in any of the ByteVec functions changing a value, but please check.

Overrides:

hashCode in class java.lang.Object

Cosine

public static double Cosine(ByteVec dVec1,
                            ByteVec dVec2)

Vectors have to be normed!

Parameters:

dVec1 - normed vector1

dVec2 - normed vector2

Returns:

Cosine

cubicDistance

public static double cubicDistance(ByteVec dVec1,
                                   ByteVec dVec2)

initRND

public void initRND(byte min,
                    byte max)

initRND

public static java.util.List<ByteVec> initRND(byte min,
                                              byte max,
                                              int lenByteVec,
                                              int numelements)

manhattanBlockDistance

public static double manhattanBlockDistance(ByteVec dVec1,
                                            ByteVec dVec2)

mult

public ByteVec mult(double dFactor)

mult

public static final double mult(ByteVec bv1,
                                ByteVec bv2)

mult

public static final double mult(byte[] a1,
                                byte[] a2)

multEl

public static ByteVec multEl(ByteVec dVec1,
                             ByteVec dVec2)

Elementwise multiplication

Parameters:

dVec1 - input vector

dVec2 - input vector

Returns:

ByteVec

norm2One

public void norm2One()

minus

public static ByteVec minus(ByteVec dVec1,
                            ByteVec dVec2)

reduce

public void reduce(java.util.Vector<java.lang.Integer> vecIndices)

plus

public static ByteVec plus(ByteVec dVec1,
                           ByteVec dVec2)

set

public void set(byte dVal)

set

public void set(int col,
                byte val)

Hash value has to be recalculated!

Parameters:

col -

val -

setRNDvalue

public void setRNDvalue(double dCenter,
                        double dRange)

size

public int size()

setRNDvalue

public void setRNDvalue(double dRange)

sub

public ByteVec sub(ByteVec dvSub)

Substraction

Parameters:

dvSub -

Returns:

getTanimotoDistBitWise

public static double getTanimotoDistBitWise(ByteVec bv1,
                                            ByteVec bv2)

Calculates the Tanimoto coefficient

Parameters:

bv1 - vector1

bv2 - vector2

Returns:

Tanimoto: 0.0: maximum distance, 1.0: maximum similarity. Calculation according http://www.pnylab.com/pny/papers/nmet/nmet/ Congruent with DoubleVec

getBitsSet

public int getBitsSet()

getTanimotoDist

public static double getTanimotoDist(ByteVec bv1,
                                     ByteVec bv2)

Calculates the Tanimoto coefficient

Parameters:

bv1 - vector1

bv2 - vector2

Returns:

Tanimoto: 0.0: maximum distance, 1.0: maximum similarity.

getTanimotoDist

public static double getTanimotoDist(byte[] a1,
                                     byte[] a2)

getTanimotoDistInv

public static double getTanimotoDistInv(ByteVec bv1,
                                        ByteVec bv2)

Byte wise inverse Tanimoto distance.

Parameters:

bv1 -

bv2 -

Returns:

toString

public java.lang.String toString()

Converts a byte into its decimal.

Overrides:

toString in class java.lang.Object

toStringString

public java.lang.String toStringString()

Converts the bytes into chars. The original string is reconstructed.

Returns:

toBinaryString

public java.lang.String toBinaryString()

toBinaryStringDense

public java.lang.String toBinaryStringDense()

toString

public java.lang.String toString(int iNumDigits)

Parameters:

iNumDigits - number of decimal places

Returns:

String with doubles in 0.0 notation 16.10.2003 MvK

toArray

public byte[] toArray()

toByteArray

public static byte[] toByteArray(long data)

toByteArray

public static byte[] toByteArray(double[] data)

toByteArray

public static byte[] toByteArray(int[] data)

toByteArray

public static byte[] toByteArray(int data)

reverse

public static byte[] reverse(byte[] a)

toString

public static java.lang.String toString(byte[] a,
                                        java.lang.String seperator)

toString

public static java.lang.String toString(byte[] a)

testS1

public static ByteVec testS1()

testTakeda1

public static ByteVec testTakeda1()

test01

public static ByteVec test01()

meanClust

public static ByteVec meanClust()