com.chemaxon.descriptors.alignment.shape

Class ShapeGenerator

java.lang.Object

com.chemaxon.descriptors.alignment.AbstractShapeGenerator<ShapeDescriptor,ShapeGeneratorParameter>

com.chemaxon.descriptors.alignment.shape.ShapeGenerator

All Implemented Interfaces:

DescriptorGenerator<ShapeDescriptor>, DescriptorSerializer<ShapeDescriptor>, Guarded, Serializable

public final class ShapeGenerator
extends AbstractShapeGenerator<ShapeDescriptor,ShapeGeneratorParameter>

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface com.chemaxon.descriptors.common.Guarded

Guarded.EnsureThat, Guarded.New

Field Summary

Fields inherited from class com.chemaxon.descriptors.alignment.AbstractShapeGenerator

parameters

Constructor Summary

Constructors

Constructor and Description
ShapeGenerator(ShapeGeneratorParameter parameters)

Method Summary

Modifier and Type	Method and Description
ComparisonContextFactory<ShapeComparator<ShapeDescriptor>,ShapeDescriptor,? extends Serializable>	comparisonContextFactory() Get an unguarded context factory.
ShapeComparator<ShapeDescriptor>	defaultComparison() Default comparator.
Shape	fromByteArray(byte[] desc) Builds a descriptor from its byte array representation.
Shape	generateDescriptor(Molecule mol) Calculates the associated descriptor for the given Molecule.
ShapeComparator<ShapeDescriptor>	getDefaultComparator() Deprecated.
ShapeComparator<ShapeDescriptor>	getShapeComparator(ShapeComparatorParameter params)
boolean	serializerIsEqualWith(DescriptorSerializer other) Check strict equivalence of serializers.

Methods inherited from class com.chemaxon.descriptors.alignment.AbstractShapeGenerator

equals, fromString, getBareDescriptor, getGuardObject, getParameters, hashCode, toByteArray, toString, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

ShapeGenerator

public ShapeGenerator(ShapeGeneratorParameter parameters)

Method Detail

generateDescriptor

public Shape generateDescriptor(Molecule mol)

Description copied from interface: DescriptorGenerator

Calculates the associated descriptor for the given Molecule.

Note that different descriptors/application scenarios might need different structure standardization. Currently structure standardization is generally not in the scope of the responsibilities of DescriptorGenerator to the possible maximal extent.

Since the returned descriptor might contain additional data (reference to input Molecule, etc) if it is stored for later comparison it is recommended to use the bare-only representation returned by DescriptorGenerator.getBareDescriptor(com.chemaxon.descriptors.common.Descriptor).

Parameters:

mol - Input molecule

Returns:

The calculated descriptor. If the implementation discriminates between rich and bare types then the rich type is returned, otherwise the bare type. Note that the bare type is always available using DescriptorGenerator.getBareDescriptor(com.chemaxon.descriptors.common.Descriptor) on either the rich or the bare representation.

getDefaultComparator

@Deprecated
public ShapeComparator<ShapeDescriptor> getDefaultComparator()

Deprecated.

Description copied from interface: DescriptorGenerator

Gets the default comparator object.

Returns:

default comparator

getShapeComparator

public ShapeComparator<ShapeDescriptor> getShapeComparator(ShapeComparatorParameter params)

fromByteArray

public Shape fromByteArray(byte[] desc)

Description copied from interface: DescriptorSerializer

Builds a descriptor from its byte array representation.

Please note that the compatibility of this (the reconstructing) DescriptorGenerator, regarding to the serializing generator (on which DescriptorSerializer.toByteArray(com.chemaxon.descriptors.common.Descriptor) was called to construct the byte array form) is not checked; compatibility must be ensured by the user application.

Parameters:

desc - Byte array of the descriptor

Returns:

Reconstructed descriptors bare form

comparisonContextFactory

public ComparisonContextFactory<ShapeComparator<ShapeDescriptor>,ShapeDescriptor,? extends Serializable> comparisonContextFactory()

Description copied from interface: DescriptorGenerator

Get an unguarded context factory. Implementations are supposed to provide space/processing efficient unguarded representation if applicable. Otherwise it is possible to expose byte [] serialization based unguarded representation.

Implementations are expected to provide additional factory methods for unguarded and plain descriptor comparators for implemented metrics.

Returns:

an unguarded context factory

defaultComparison

public ShapeComparator<ShapeDescriptor> defaultComparison()

Description copied from interface: DescriptorGenerator

Default comparator.

Returns:

Default comparator

serializerIsEqualWith

public boolean serializerIsEqualWith(DescriptorSerializer other)

Description copied from interface: DescriptorSerializer

Check strict equivalence of serializers. Implementations are expected to be symmetric and transitive.

Parameters:

other - Other serializer

Returns:

true when and only when the two serializers (this and other) are the same thus interchangeable. Implementations typically check class equivalence, guard object match and parameter match.