com.chemaxon.clustering.common
Class MolInput<D extends Descriptor>

Object
  com.chemaxon.clustering.common.MolInput<D>

Type Parameters:

D - Used descriptors bare type

Please note that this class is marked with @Beta annotation, so it can be subject of incompatible changes or removal in later releases.

All Implemented Interfaces:

DissimilarityInput

@Beta
public class MolInput<D extends Descriptor>
extends Object
implements DissimilarityInput

Dissimilarity input implementation over Molecule objects and descriptors.

Author:

Gabor Imre

Constructor Summary

MolInput(List<? extends chemaxon.struc.Molecule> mols, DescriptorGenerator<D> gen, DescriptorComparator<D> comp)
Construct over Molecules.

Method Summary

double	dissimilarity(int targetIndex, int queryIndex) Dissimilarity/distance between an ordered pair of input items.
MetricMetadata	getMetricMetadata() Metadata about the underlying metric.
chemaxon.struc.Molecule	getMolecule(int index) Retrieve a structure.
int	size() Item count to be considered.

Methods inherited from class Object

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

Constructor Detail

MolInput

public MolInput(List<? extends chemaxon.struc.Molecule> mols,
                DescriptorGenerator<D> gen,
                DescriptorComparator<D> comp)

Construct over Molecules.

Parameters:

mols - Molecules to represent

gen - Descriptor generator

comp - Associated comparator

Method Detail

size

public int size()

Description copied from interface: DissimilarityInput

Item count to be considered.

Specified by:

size in interface DissimilarityInput

Returns:

Item count

dissimilarity

public double dissimilarity(int targetIndex,
                            int queryIndex)

Description copied from interface: DissimilarityInput

Dissimilarity/distance between an ordered pair of input items.

Please note that the represented input is not necessarily a metric space; only the satisfactions of criteria described by the results of DissimilarityInput.getMetricMetadata() is guaranteed.

Note that parameter naming discriminates query and target indexes to be consistent with the usage of non symmetric underlying comparison metrics.

Specified by:

dissimilarity in interface DissimilarityInput

Parameters:

targetIndex - Index of first item to be compared

queryIndex - Index of second item to be compared

Returns:

Dissimilarity of the two compared items

getMetricMetadata

public MetricMetadata getMetricMetadata()

Description copied from interface: DissimilarityInput

Metadata about the underlying metric.

Specified by:

getMetricMetadata in interface DissimilarityInput

Returns:

Metadata of the comparison of dissimilarity calculations

getMolecule

public chemaxon.struc.Molecule getMolecule(int index)

Retrieve a structure.

Parameters:

index - Structure index

Returns:

Represented structure