jklustor-all-api-0.0.7-20140619012755 (ChemAxon)


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

Object
  extended by 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

jklustor-all-api-0.0.7-20140619012755 (ChemAxon)