chemaxon.descriptors

Class MDSetParameters

java.lang.Object

chemaxon.descriptors.MDSetParameters

@PublicAPI
public class MDSetParameters
extends java.lang.Object

Parameters settings for MDSet-s. The main purpose of this class is the support for dissimilarity calculations over MDSet objects. The dissimilarity coefficient of two MDSet objects is defined as the weighted sum of component-wise dissimilarity coefficients. Weights of components are stored in this class, along with the metric indices used as default metric. This is allows by MDSet.getDissimilarity( final Object other ) perform calculations with the required metric (not only the default one).

Since:

JChem 2.0

Author:

Miklos Vargyas

Field Summary

Fields

Modifier and Type	Field and Description
protected int[]	metricIndex metric index by component
protected float[]	userDataWeights user data weights
protected float[]	weights component weights

Constructor Summary

Constructors

Constructor and Description
MDSetParameters() Crates an empty object.
MDSetParameters(float[] weights, float[] userDataWeights, int[] metricIndex) Creates and initializes an object with the given weights and metric indices.
MDSetParameters(float[] weights, int[] metricIndex) Creates and initializes an object with the given weights and metric indices.
MDSetParameters(int nComponents) Creates an object of the given size.
MDSetParameters(int nComponents, int nUserData) Creates an object of the given size.

Method Summary

Modifier and Type	Method and Description
int	getMetricIndex(int index) Gets the index of the metric used by a component to calculate the dissimilarity coefficient.
float	getUserDataWeight(int index) Gets the weight of a userData component.
float	getWeight(int index) Gets the weight of a component.
void	setMetricIndex(int componentIndex, int mi) Sets the index of metric used in the dissimilarity calculation by an individual component.
void	setMetricIndices(int[] metricIndices) Sets the index of metric of components.
void	setSize(int nComponents) Sets the size, number of components of an empty MDSetParameters object.
void	setSize(int nComponents, int nUserData) Sets the size, number of components and number of userData values of an empty MDSetParameters object.
void	setUserDataWeight(int index, float w) Sets the weight of an individual user data component.
void	setUserDataWeights(float[] weights) Sets the weights for userData.
void	setWeight(int componentIndex, float w) Sets the weight of an individual component.
void	setWeights(float[] weights) Sets the weights.
int	size() Get the size of the associated MDSet instance.

Methods inherited from class java.lang.Object

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

Field Detail

weights

protected float[] weights

component weights

userDataWeights

protected float[] userDataWeights

user data weights

metricIndex

protected int[] metricIndex

metric index by component

Constructor Detail

MDSetParameters

public MDSetParameters()

Crates an empty object.

MDSetParameters

public MDSetParameters(int nComponents)

Creates an object of the given size.

Parameters:

nComponents - number of components in the MDSet

MDSetParameters

public MDSetParameters(int nComponents,
                       int nUserData)

Creates an object of the given size.

Parameters:

nComponents - number of components in the MDSet

nUserData - number of further floating point values

MDSetParameters

public MDSetParameters(float[] weights,
                       int[] metricIndex)

Creates and initializes an object with the given weights and metric indices.

Parameters:

weights - weights of every components used in MDSet.getDissimilarity( final Object other )

metricIndex - index of metrices of components to be used in MDSet.getDissimilarity( final Object other )

MDSetParameters

public MDSetParameters(float[] weights,
                       float[] userDataWeights,
                       int[] metricIndex)

Creates and initializes an object with the given weights and metric indices.

Parameters:

weights - weights of every components used in MDSet.getDissimilarity( final Object other )

userDataWeights - weights of every components of user data

metricIndex - index of metrices of components to be used in MDSet.getDissimilarity( final Object other )

Method Detail

setSize

public void setSize(int nComponents)

Sets the size, number of components of an empty MDSetParameters object.

Parameters:

nComponents - number of components in the MDSet

setSize

public void setSize(int nComponents,
                    int nUserData)

Sets the size, number of components and number of userData values of an empty MDSetParameters object.

Parameters:

nComponents - number of components in the MDSet

nUserData - number of further floating point values

setWeights

public void setWeights(float[] weights)

Sets the weights.

Parameters:

weights - weights of every components used in MDSet.getDissimilarity( final Object other )

setUserDataWeights

public void setUserDataWeights(float[] weights)

Sets the weights for userData.

Parameters:

weights - weights of every components used in MDSet.getDissimilarity( final Object other )

setMetricIndices

public void setMetricIndices(int[] metricIndices)

Sets the index of metric of components.

Parameters:

metricIndices - index of metrices of components to be used in MDSet.getDissimilarity( final Object other )

setWeight

public void setWeight(int componentIndex,
                      float w)

Sets the weight of an individual component.

Parameters:

componentIndex - index of the component

w - the weight of this component in MDSet.getDissimilarity( final Object other )

setUserDataWeight

public void setUserDataWeight(int index,
                              float w)

Sets the weight of an individual user data component.

Parameters:

index - index of the component

w - the weight of this user data component

setMetricIndex

public void setMetricIndex(int componentIndex,
                           int mi)

Sets the index of metric used in the dissimilarity calculation by an individual component.

Parameters:

componentIndex - index of the component

mi - index of the metric of this component in MDSet.getDissimilarity( final Object other )

size

public int size()

Get the size of the associated MDSet instance.

Returns:

number of components in the MDSet

getWeight

public float getWeight(int index)

Gets the weight of a component.

Parameters:

index - index of a component

Returns:

the weight of the component

getUserDataWeight

public float getUserDataWeight(int index)

Gets the weight of a userData component.

Parameters:

index - index of a component

Returns:

the weight of the component

getMetricIndex

public int getMetricIndex(int index)

Gets the index of the metric used by a component to calculate the dissimilarity coefficient.

Parameters:

index - index of a component

Returns:

the index of the metric used by the specified component