com.chemaxon.descriptors.vectors.binary

Class BvGeneratorImpl

java.lang.Object

com.chemaxon.descriptors.vectors.binary.BvGeneratorImpl

All Implemented Interfaces:

DescriptorGenerator<BinaryVectorDescriptor>, DescriptorSerializer<BinaryVectorDescriptor>, Guarded, BinaryVectorMetricFactory<DescriptorComparator<BinaryVectorDescriptor>>, MetricFactory<DescriptorComparator<BinaryVectorDescriptor>>, BvGenerator, Serializable

public class BvGeneratorImpl
extends Object
implements BvGenerator

Implementation for binary vectors.

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	BvGeneratorImpl.Service Class wrapping constructor for DI.

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

Guarded.EnsureThat, Guarded.New

Nested classes/interfaces inherited from interface com.chemaxon.descriptors.metrics.BinaryVectorMetricFactory

BinaryVectorMetricFactory.ToLinenote<C>

Method Summary

Modifier and Type	Method and Description
BinaryVectorComparisonContextFactory<long[]>	comparisonContextFactory() Get an unguarded context factory.
Linenote<DescriptorComparator<BinaryVectorDescriptor>>	comparisonLinenote() Gets the string based parameterization description.
DescriptorComparator<BinaryVectorDescriptor>	defaultComparison() Default comparator.
DescriptorComparator<BinaryVectorDescriptor>	forBinaryMetrics(BinaryMetrics metrics) Creates a new instance according to the given metric.
DescriptorComparator<BinaryVectorDescriptor>	forTversky(TverskyParameters tverskyParamaters) Creates a new Comparator instance according to the given Tversky metric parameters.
DescriptorComparator<BinaryVectorDescriptor>	forTverskyCoefficients(double coeffQuery, double coeffTarget) Creates a new Comparator instance according to the given Tversky metric parameters.
BinaryVectorDescriptor	fromBitSet(BitSet bits) Create a descriptor from a BitSet representation.
BinaryVectorDescriptor	fromByteArray(byte[] desc) Builds a descriptor from its byte array representation.
BinaryVectorDescriptor	fromString(String desc) Builds a descriptor from its string representation.
BinaryVectorDescriptor	generateDescriptor(Molecule mol) Calculates the associated descriptor for the given Molecule.
BinaryVectorDescriptor	getBareDescriptor(BinaryVectorDescriptor descriptor) Get bare-only form of a descriptor.
DescriptorComparator<BinaryVectorDescriptor>	getBinaryMetricsComparator(BinaryMetrics metrics) Deprecated comparison method kept for compatibility reasons.
DescriptorComparator<BinaryVectorDescriptor>	getDefaultComparator() Gets the default comparator object.
Object	getGuardObject() Gets the guard object associated to the generated descriptors/utilities.
DescriptorParameters	getParameters() Gets the parameter object.
DescriptorComparator<BinaryVectorDescriptor>	getTverskyComparator(double coeffQuery, double coeffTarget) Deprecated comparison method kept for compatibility reasons.
DescriptorComparator<BinaryVectorDescriptor>	getTverskyComparator(TverskyParameters tverskyParamaters) Deprecated comparison method kept for compatibility reasons.
boolean	serializerIsEqualWith(DescriptorSerializer other) Check strict equivalence of serializers.
byte[]	toByteArray(BinaryVectorDescriptor desc) Creates the byte array representation of a descriptor object.
String	toString()
String	toString(BinaryVectorDescriptor desc) Creates the String representation of a descriptor object.

Methods inherited from class java.lang.Object

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

Method Detail

generateDescriptor

public BinaryVectorDescriptor 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<BinaryVectorDescriptor>

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.

getBareDescriptor

public BinaryVectorDescriptor getBareDescriptor(BinaryVectorDescriptor descriptor)

Description copied from interface: DescriptorGenerator

Get bare-only form of a descriptor.

Specified by:

getBareDescriptor in interface DescriptorGenerator<BinaryVectorDescriptor>

Parameters:

descriptor - A descriptor's rich or bare form

Returns:

Bare-only representation of given descriptor

toByteArray

public byte[] toByteArray(BinaryVectorDescriptor 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<BinaryVectorDescriptor>

Parameters:

desc - Descriptor (only bare form is considered)

Returns:

Byte array representation of the descriptor

toString

public String toString(BinaryVectorDescriptor 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<BinaryVectorDescriptor>

Parameters:

desc - Descriptor (only bare form is considered)

Returns:

String representation of descriptor

fromString

public BinaryVectorDescriptor 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<BinaryVectorDescriptor>

Parameters:

desc - String representation

Returns:

Reconstructed descriptors bare form

fromByteArray

public BinaryVectorDescriptor 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<BinaryVectorDescriptor>

Parameters:

desc - Byte array of the descriptor

Returns:

Reconstructed descriptors bare form

getDefaultComparator

public DescriptorComparator<BinaryVectorDescriptor> getDefaultComparator()

Description copied from interface: DescriptorGenerator

Gets the default comparator object.

Specified by:

getDefaultComparator in interface DescriptorGenerator<BinaryVectorDescriptor>

Returns:

default comparator

forBinaryMetrics

public DescriptorComparator<BinaryVectorDescriptor> forBinaryMetrics(BinaryMetrics metrics)

Description copied from interface: BinaryVectorMetricFactory

Creates a new instance according to the given metric.

Specified by:

forBinaryMetrics in interface BinaryVectorMetricFactory<DescriptorComparator<BinaryVectorDescriptor>>

Parameters:

metrics - binary metric

Returns:

a comparator object

forTversky

public DescriptorComparator<BinaryVectorDescriptor> forTversky(TverskyParameters tverskyParamaters)

Description copied from interface: BinaryVectorMetricFactory

Creates a new Comparator instance according to the given Tversky metric parameters.

Specified by:

forTversky in interface BinaryVectorMetricFactory<DescriptorComparator<BinaryVectorDescriptor>>

Parameters:

tverskyParamaters - parameters for the comparator

Returns:

a comparator object

getParameters

public DescriptorParameters getParameters()

Description copied from interface: DescriptorGenerator

Gets the parameter object.

Specified by:

getParameters in interface DescriptorGenerator<BinaryVectorDescriptor>

Returns:

paramater obj

fromBitSet

public BinaryVectorDescriptor fromBitSet(BitSet bits)

Description copied from interface: BvGenerator

Create a descriptor from a BitSet representation.

Specified by:

fromBitSet in interface BvGenerator

Parameters:

bits - Values to represent.

Returns:

Descriptor representing the given values.

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

comparisonContextFactory

public BinaryVectorComparisonContextFactory<long[]> 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<BinaryVectorDescriptor>

Returns:

an unguarded context factory

forTverskyCoefficients

public DescriptorComparator<BinaryVectorDescriptor> forTverskyCoefficients(double coeffQuery,
                                                                           double coeffTarget)

Description copied from interface: BinaryVectorMetricFactory

Creates a new Comparator instance according to the given Tversky metric parameters.

Specified by:

forTverskyCoefficients in interface BinaryVectorMetricFactory<DescriptorComparator<BinaryVectorDescriptor>>

Parameters:

coeffQuery - Query side coefficient

coeffTarget - Target side coefficient

Returns:

a comparator object

defaultComparison

public DescriptorComparator<BinaryVectorDescriptor> defaultComparison()

Description copied from interface: DescriptorGenerator

Default comparator.

Specified by:

defaultComparison in interface DescriptorGenerator<BinaryVectorDescriptor>

Specified by:

defaultComparison in interface MetricFactory<DescriptorComparator<BinaryVectorDescriptor>>

Returns:

Default comparator

getBinaryMetricsComparator

public DescriptorComparator<BinaryVectorDescriptor> getBinaryMetricsComparator(BinaryMetrics metrics)

Description copied from interface: BvGenerator

Deprecated comparison method kept for compatibility reasons.

Specified by:

getBinaryMetricsComparator in interface BvGenerator

Parameters:

metrics - Metrics

Returns:

Comparator

getTverskyComparator

public DescriptorComparator<BinaryVectorDescriptor> getTverskyComparator(double coeffQuery,
                                                                         double coeffTarget)

Description copied from interface: BvGenerator

Deprecated comparison method kept for compatibility reasons.

Specified by:

getTverskyComparator in interface BvGenerator

Parameters:

coeffQuery - Metric parameter

coeffTarget - Metric parameter

Returns:

Comparator

getTverskyComparator

public DescriptorComparator<BinaryVectorDescriptor> getTverskyComparator(TverskyParameters tverskyParamaters)

Description copied from interface: BvGenerator

Deprecated comparison method kept for compatibility reasons.

Specified by:

getTverskyComparator in interface BvGenerator

Parameters:

tverskyParamaters - Metrics parameter

Returns:

Comparator

comparisonLinenote

public Linenote<DescriptorComparator<BinaryVectorDescriptor>> comparisonLinenote()

Description copied from interface: MetricFactory

Gets the string based parameterization description. This can be used to automatically compose user interfaces with rich parameterization. Please note that the represented APIs are under development.

Specified by:

comparisonLinenote in interface MetricFactory<DescriptorComparator<BinaryVectorDescriptor>>

Returns:

Parameterization description

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<BinaryVectorDescriptor>

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.