com.chemaxon.descriptors.alignment.drshape

Class DRShapeGenerator

java.lang.Object

com.chemaxon.descriptors.alignment.drshape.DRShapeGenerator

All Implemented Interfaces:

DescriptorGenerator<DRShapeDescriptor>, DescriptorSerializer<DRShapeDescriptor>, Guarded, Serializable

public final class DRShapeGenerator
extends Object
implements DescriptorGenerator<DRShapeDescriptor>

See Also:

Serialized Form

Nested Class Summary

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

Guarded.EnsureThat, Guarded.New

Constructor Summary

Constructors

Constructor and Description
DRShapeGenerator(DRShapeGeneratorParameter parameters)

Method Summary

Modifier and Type	Method and Description
ComparisonContextFactory<ShapeComparator<DRShapeDescriptor>,DRShapeDescriptor,? extends Serializable>	comparisonContextFactory() Get an unguarded context factory.
ShapeComparator<DRShapeDescriptor>	defaultComparison() Default comparator.
boolean	equals(Object obj)
DRShapeDescriptor	fromByteArray(byte[] desc) Builds a descriptor from its byte array representation.
DRShapeDescriptor	fromString(String desc) Builds a descriptor from its string representation.
DRShapeDescriptor	generateDescriptor(Molecule mol) Calculates the associated descriptor for the given Molecule.
DRShapeDescriptor	getBareDescriptor(DRShapeDescriptor descriptor) Get bare-only form of a descriptor.
ShapeComparator<DRShapeDescriptor>	getDefaultComparator() Deprecated.
Object	getGuardObject() Gets the guard object associated to the generated descriptors/utilities.
DRShapeGeneratorParameter	getParameters() Gets the parameter object.
ShapeComparator<DRShapeDescriptor>	getShapeComparator(DRShapeComparatorParameter params)
int	hashCode()
boolean	serializerIsEqualWith(DescriptorSerializer other) Check strict equivalence of serializers.
byte[]	toByteArray(DRShapeDescriptor desc) Creates the byte array representation of a descriptor object.
String	toString()
String	toString(DRShapeDescriptor desc) Creates the String representation of a descriptor object.

Methods inherited from class java.lang.Object

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

Constructor Detail

DRShapeGenerator

public DRShapeGenerator(DRShapeGeneratorParameter parameters)

Method Detail

generateDescriptor

public DRShapeDescriptor 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).

Specified by:

generateDescriptor in interface DescriptorGenerator<DRShapeDescriptor>

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.

toByteArray

public byte[] toByteArray(DRShapeDescriptor desc)

Description copied from interface: DescriptorSerializer

Creates the byte array representation of a descriptor object. Note that implementations of this method must ensure the matching of associated guard objects.

The descriptors bare form can be reconstructed using DescriptorSerializer.fromByteArray(byte[]).

Specified by:

toByteArray in interface DescriptorSerializer<DRShapeDescriptor>

Parameters:

desc - Descriptor (only bare form is considered)

Returns:

Byte array representation of the descriptor

toString

public String toString(DRShapeDescriptor desc)

Description copied from interface: DescriptorSerializer

Creates the String representation of a descriptor object.

The descriptors bare form can be reconstructed using DescriptorSerializer.fromString(java.lang.String).

Specified by:

toString in interface DescriptorSerializer<DRShapeDescriptor>

Parameters:

desc - Descriptor (only bare form is considered)

Returns:

String representation of descriptor

fromString

public DRShapeDescriptor fromString(String desc)

Description copied from interface: DescriptorSerializer

Builds a descriptor from its string representation.

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

Specified by:

fromString in interface DescriptorSerializer<DRShapeDescriptor>

Parameters:

desc - String representation

Returns:

Reconstructed descriptors bare form

fromByteArray

public DRShapeDescriptor 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.

Specified by:

fromByteArray in interface DescriptorSerializer<DRShapeDescriptor>

Parameters:

desc - Byte array of the descriptor

Returns:

Reconstructed descriptors bare form

getParameters

public DRShapeGeneratorParameter getParameters()

Description copied from interface: DescriptorGenerator

Gets the parameter object.

Specified by:

getParameters in interface DescriptorGenerator<DRShapeDescriptor>

Returns:

paramater obj

getGuardObject

public Object getGuardObject()

Description copied from interface: Guarded

Gets the guard object associated to the generated descriptors/utilities. Note that serialization/deserialization must preserve guard object reference.

This method is intended to use only for ensuring the compatibility of manipulated objects.

Implementations might use the associated DescriptorGenerator or DescriptorParameters reference as the guard object, however it is a non recommended practice to use this method to access the associated generator to perform further operations on it.

Specified by:

getGuardObject in interface Guarded

Returns:

The guard object, can not be null.

toString

public String toString()

Overrides:

toString in class Object

getDefaultComparator

@Deprecated
public ShapeComparator<DRShapeDescriptor> getDefaultComparator()

Deprecated.

Description copied from interface: DescriptorGenerator

Gets the default comparator object.

Specified by:

getDefaultComparator in interface DescriptorGenerator<DRShapeDescriptor>

Returns:

default comparator

getShapeComparator

public ShapeComparator<DRShapeDescriptor> getShapeComparator(DRShapeComparatorParameter params)

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

getBareDescriptor

public DRShapeDescriptor getBareDescriptor(DRShapeDescriptor descriptor)

Description copied from interface: DescriptorGenerator

Get bare-only form of a descriptor.

Specified by:

getBareDescriptor in interface DescriptorGenerator<DRShapeDescriptor>

Parameters:

descriptor - A descriptor's rich or bare form

Returns:

Bare-only representation of given descriptor

comparisonContextFactory

public ComparisonContextFactory<ShapeComparator<DRShapeDescriptor>,DRShapeDescriptor,? 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.

Specified by:

comparisonContextFactory in interface DescriptorGenerator<DRShapeDescriptor>

Returns:

an unguarded context factory

defaultComparison

public ShapeComparator<DRShapeDescriptor> defaultComparison()

Description copied from interface: DescriptorGenerator

Default comparator.

Specified by:

defaultComparison in interface DescriptorGenerator<DRShapeDescriptor>

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.

Specified by:

serializerIsEqualWith in interface DescriptorSerializer<DRShapeDescriptor>

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.