Deprecated API

Contents

• Deprecated Interfaces
• Deprecated Classes
• Deprecated Fields
• Deprecated Methods
• Deprecated Constructors

Deprecated Interfaces

Interface and Description
com.chemaxon.calculations.io.Sink Use Consumer instead.
com.chemaxon.calculations.common.SubProgressObserver Use ProgressObserver instead. Will be removed.

Deprecated Classes

Class and Description
com.chemaxon.overlap.servlets.MetaServlet Use MetaResource instead.
com.chemaxon.overlap.servlets.MolsContext Use unified context
com.chemaxon.overlap.servlets.MolsServlet

Deprecated Fields

Field and Description
com.chemaxon.overlap.wui.dto.KnnInfo.k Use KnnInfo.maxneighborcount

Deprecated Methods

Method and Description
com.chemaxon.descriptors.metrics.FloatVectorComparator.calculateFloatVectorSimilarity(float[], float[]) In various cases (euclid, euclid sqr, manhattan) this has no practical interpretation
com.chemaxon.calculations.common.ProgressObservers.createForgivingNullObserver() Use ProgressObservers.nullProgressObserver() instead.
com.chemaxon.calculations.common.ProgressObservers.createNoCancelObserver() Use ProgressObservers.noCanceller()
com.chemaxon.calculations.common.ProgressObservers.createNullObserver(String) Use ProgressObservers.createStrictNullObserver().
com.chemaxon.overlap.cli.PagedDescriptorImport.generatorToString(DescriptorGenerator<?>)
com.chemaxon.descriptors.vectors.binary.BvGenerator.getBinaryMetricsComparator(BinaryMetrics) Use BinaryVectorMetricFactory.forBinaryMetrics(com.chemaxon.descriptors.metrics.BinaryMetrics).
com.chemaxon.descriptors.fingerprints.cfp.CfpGenerator.getBinaryMetricsComparator(BinaryMetrics) Use BinaryVectorMetricFactory.forBinaryMetrics(com.chemaxon.descriptors.metrics.BinaryMetrics)
com.chemaxon.descriptors.fingerprints.ecfp.EcfpGenerator.getBinaryMetricsComparator(BinaryMetrics) Use BinaryVectorMetricFactory.forBinaryMetrics(com.chemaxon.descriptors.metrics.BinaryMetrics)
com.chemaxon.descriptors.fingerprints.maccs.MaccsGenerator.getBinaryMetricsComparator(BinaryMetrics) Use BinaryVectorMetricFactory.forBinaryMetrics(com.chemaxon.descriptors.metrics.BinaryMetrics)
com.chemaxon.descriptors.alignment.shape.ShapeGenerator.getDefaultComparator()
com.chemaxon.descriptors.alignment.drshape.DRShapeGenerator.getDefaultComparator()
com.chemaxon.descriptors.fingerprints.cfp.CfpGenerator.getDefaultComparator()
com.chemaxon.descriptors.fingerprints.ecfp.EcfpGenerator.getDefaultComparator()
com.chemaxon.descriptors.fingerprints.maccs.MaccsGenerator.getDefaultComparator()
com.chemaxon.descriptors.fingerprints.pf2d.PfGenerator.getDefaultComparator()
com.chemaxon.descriptors.common.DescriptorGenerator.getDefaultComparator() This method is kept for compatibility reason. Use ComparisonContext#descriptorComparator() on the instance returned by MetricFactory.defaultComparison() from DescriptorGenerator.comparisonContextFactory()
com.chemaxon.descriptors.alignment.ShapeDescriptor.getDescriptorGenerator() Use Guarded.getGuardObject()
com.chemaxon.descriptors.vectors.floats.FvGenerator.getFloatMetricsComparator(FloatVectorMetrics) Use FloatVectorMetricFactory.forFloatMetrics(com.chemaxon.descriptors.metrics.FloatVectorMetrics).
com.chemaxon.descriptors.vectors.floats.FvGeneratorImpl.getFloatMetricsComparator(FloatVectorMetrics)
com.chemaxon.descriptors.fingerprints.pf2d.PfGenerator.getFloatVectorComparator(FloatVectorMetrics) Use FloatVectorMetricFactory.forFloatMetrics(com.chemaxon.descriptors.metrics.FloatVectorMetrics)
com.chemaxon.overlap.result.KnnResults.getK() Use KnnResults.getMinNeighborCount() and KnnResults.getMaxNeighborCount()
com.chemaxon.descriptors.vectors.binary.BvGenerator.getTverskyComparator(double, double) Use #forTversky(double, double).
com.chemaxon.descriptors.fingerprints.cfp.CfpGenerator.getTverskyComparator(double, double) Use BinaryVectorMetricFactory.forTverskyCoefficients(double, double)
com.chemaxon.descriptors.fingerprints.ecfp.EcfpGenerator.getTverskyComparator(double, double) Use BinaryVectorMetricFactory.forTverskyCoefficients(double, double)
com.chemaxon.descriptors.fingerprints.maccs.MaccsGenerator.getTverskyComparator(double, double) Use BinaryVectorMetricFactory.forTverskyCoefficients(double, double)
com.chemaxon.descriptors.vectors.binary.BvGenerator.getTverskyComparator(TverskyParameters) Use BinaryVectorMetricFactory.forBinaryMetrics(com.chemaxon.descriptors.metrics.BinaryMetrics).
com.chemaxon.descriptors.fingerprints.cfp.CfpGenerator.getTverskyComparator(TverskyParameters) Use BinaryVectorMetricFactory.forTversky(com.chemaxon.descriptors.metrics.TverskyParameters)
com.chemaxon.descriptors.fingerprints.ecfp.EcfpGenerator.getTverskyComparator(TverskyParameters) Use BinaryVectorMetricFactory.forTversky(com.chemaxon.descriptors.metrics.TverskyParameters)
com.chemaxon.descriptors.fingerprints.maccs.MaccsGenerator.getTverskyComparator(TverskyParameters) Use BinaryVectorMetricFactory.forTversky(com.chemaxon.descriptors.metrics.TverskyParameters)
com.chemaxon.descriptors.metrics.FloatVectorComparator.getUpperBoundForFloatVectors() In various cases (euclid, euclid sqr, manhattan) this has no practical interpretation
com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorImpl.serialize() Use BinaryVectorDescriptorImpl.getFpAsBytes()
com.chemaxon.calculations.common.ProgressObserver.subTask(String, long) Will be removed.
com.chemaxon.overlap.storage.PagedDescriptorStorage.toBytes(ObjectOutputStream, SubProgressObserver) Use PagedDescriptorStorage.toBytes(java.io.ObjectOutputStream, com.chemaxon.calculations.common.SubProgressObserver, long) with a sound reset interval.
com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorImpl.toDecimalString() Use BinaryVectorDescriptorImpl.toIntDecimalString()
com.chemaxon.calculations.io.CloseableIterators.transform(CloseableIterator<T>, Function<T, U>) CloseableIterator.transform(java.util.function.Function) provides default method making this utility not necessary

Deprecated Constructors

Constructor and Description
com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorImpl(byte[], Object, int) Use BinaryVectorDescriptorImpl.BinaryVectorDescriptorImpl(byte[], java.lang.Object, int, com.chemaxon.descriptors.common.BinaryVectors.Endianness)
com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorImpl(int[], Object, int) Use BinaryVectorDescriptorImpl.BinaryVectorDescriptorImpl(int[], java.lang.Object, int, com.chemaxon.descriptors.common.BinaryVectors.Endianness)
com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorImpl(long[], Object, int) Use BinaryVectorDescriptorImpl.BinaryVectorDescriptorImpl(long[], java.lang.Object, int, com.chemaxon.descriptors.common.BinaryVectors.Endianness) with explicit endianness specification
com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorImpl(byte[], Object) use FloatVectorDescriptorImpl.FloatVectorDescriptorImpl(byte[], java.lang.Object, int) with explicit expected vector length instead
com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorImpl(float[], Object) Use FloatVectorDescriptorImpl.FloatVectorDescriptorImpl(float[], Object, int) with explicit expected vector length parameter
com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorImpl(String, Object) Use FloatVectorDescriptorImpl.FloatVectorDescriptorImpl(java.lang.String, Object, int) with explicit expected vector length instead
com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap(UnguardedDissimilarityCalculator<T>, ImmutableList<ImmutableList<T>>, int) Use UnguardedPagedOverlap.UnguardedPagedOverlap(com.chemaxon.descriptors.common.unguarded.UnguardedDissimilarityCalculator, com.google.common.collect.ImmutableList)