jklustor-overlap-0.0.2-20140619012940 (ChemAxon)


Serialized Form


Package com.chemaxon.descriptors.fingerprints.ecfp

Class com.chemaxon.descriptors.fingerprints.ecfp.EcfpComparatorImpl extends com.chemaxon.descriptors.common.binary.SimpleBinaryVectorComparator implements Serializable

Class com.chemaxon.descriptors.fingerprints.ecfp.EcfpGeneratorImpl extends Object implements Serializable

Serialized Fields

parameters

com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters parameters

Class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters extends Object implements Serializable

serialVersionUID: 0L

Serialized Fields

diameter

int diameter

length

int length

atomTypizer

com.chemaxon.descriptors.fingerprints.ecfp.EcfpAtomTypizers atomTypizer

Class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpGenerator extends Object implements Serializable

serialVersionUID: 0L

Serialization Methods

readObject

private void readObject(ObjectInputStream stream)
                 throws InvalidObjectException
This method dies because SerializedForm is used through ThreadLocalizedEcfpGenerator.writeReplace().

Throws:
InvalidObjectException - This method should not be called

writeReplace

private Object writeReplace()
Part of Java serialization mechanism.

See Also:
http://docs.oracle.com/javase/6/docs/platform/serialization/spec/output.html#5324

Class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters extends Object implements Serializable

serialVersionUID: 0L

Serialized Fields

diameter

int diameter
Represented diameter.


Package com.chemaxon.descriptors.fingerprints.pf2d

Class com.chemaxon.descriptors.fingerprints.pf2d.PfComparatorImpl extends com.chemaxon.descriptors.common.realvector.SimpleFloatVectorComparator implements Serializable

Class com.chemaxon.descriptors.fingerprints.pf2d.PfGeneratorImpl extends Object implements Serializable

Serialized Fields

parameters

com.chemaxon.descriptors.fingerprints.pf2d.PfParameters parameters

Class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters extends Object implements Serializable

Serialized Fields

xmlConfig

Optional<T> xmlConfig

Class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfGenerator extends Object implements Serializable

serialVersionUID: 0L

Serialization Methods

readObject

private void readObject(ObjectInputStream stream)
                 throws InvalidObjectException
This method dies because SerializedForm is used through ThreadLocalizedPfGenerator.writeReplace().

Throws:
InvalidObjectException - This method should not be called

writeReplace

private Object writeReplace()
Part of Java serialization mechanism.

See Also:
http://docs.oracle.com/javase/6/docs/platform/serialization/spec/output.html#5324

Class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfParameters extends Object implements Serializable

serialVersionUID: 0L

Serialized Fields

xmlConfig

Optional<T> xmlConfig
XML configuration string.


Package com.chemaxon.overlap

Class com.chemaxon.overlap.KnnResultsImpl extends Object implements Serializable

serialVersionUID: 0L

Serialized Fields

k

int k
Number of nearest neighbor IDs stored.


queries

int[] queries
Array of query IDs.


targets

int[] targets
Concatenated kNN lists.

First item is the nearest neighbor of the first query (having index [0] and ID KnnResultsImpl.queries[0]; Item n+1 (having index n]) is the nearest neighbor of the second query (having index [1] and ID KnnResultsImpl.queries[1])


dissimilarities

double[] dissimilarities
Array of dissimilarities.

Items are associate to the contents of KnnResultsImpl.targets array.

Class com.chemaxon.overlap.OverlapAnalysisContext extends Object implements Serializable

serialVersionUID: 0L

Serialized Fields

standardizer

StandardizerWrapper standardizer
Represented Standardizer which can not be null.


generator

com.chemaxon.descriptors.common.DescriptorGenerator<B extends com.chemaxon.descriptors.common.Descriptor> generator
Represented descriptor generator which can not be null.


comparator

com.chemaxon.descriptors.common.DescriptorComparator<D extends com.chemaxon.descriptors.common.Descriptor> comparator
Represented descriptor comparator which can not be null.


pagesize

int pagesize
Represented page size.


unguardedFormExtractor

Function<F,T> unguardedFormExtractor
Extractor function which can not be null.


unguardedDissimCalc

UnguardedDissimilarityCalculator<T> unguardedDissimCalc
Unguarded dissimilarity calculation used for searches which can not be null.

Class com.chemaxon.overlap.SimilarityResultsImpl extends Object implements Serializable

serialVersionUID: 0L

Serialized Fields

queries

int[] queries
Array of queries.


targets

int[] targets
Array of targets.


dissimilarities

double[] dissimilarities
Array of dissimilarities.


Package com.chemaxon.overlap.bruteforce

Class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap extends Object implements Serializable

serialVersionUID: 0L

Serialized Fields

pages

ImmutableList<E> pages
Page storage.

All but the last page is expected to have the same size.


comparator

UnguardedDissimilarityCalculator<T> comparator
Descriptor comparator to use.


size

int size
Total number of descriptors stored.


Package com.chemaxon.overlap.io

Class com.chemaxon.overlap.io.CompactStringStorage extends Object implements Serializable

serialVersionUID: 0L

Serialized Fields

pagesize

int pagesize
Number of master entities stored on one page.

All but the last page is expected to contain the given entity count.


absentCount

int absentCount
Total number of absent master entities, including skippeds.


size

int size
Total number of covered master entities, including absents (and skippeds).


skips

int skips
Number of initial skips.

The given number of master entities are all absent, they are not stored.


starts

int[][] starts
Index of the first byte of the i * pagesize + j-th non-skipped structure.


storage

byte[][] storage
Storage array.

Class com.chemaxon.overlap.io.MasterMoleculeStorage extends Object implements Serializable

serialVersionUID: 0L

Serialized Fields

sources

CompactStringStorage sources
Structure sources which can be imported with MolImporter.

Since ImmutableList does not permit null elements missing structures are represented as a special String literal stored in


Package com.chemaxon.overlap.unguarded

Class com.chemaxon.overlap.unguarded.ExtractFloatFp extends Object implements Serializable

serialVersionUID: 0L

Class com.chemaxon.overlap.unguarded.ExtractIntFp extends Object implements Serializable

serialVersionUID: 0L

Class com.chemaxon.overlap.unguarded.ExtractLongFp extends Object implements Serializable

serialVersionUID: 0L

Class com.chemaxon.overlap.unguarded.UnguardedBinaryIntManhattan extends Object implements Serializable

serialVersionUID: 0L

Class com.chemaxon.overlap.unguarded.UnguardedBinaryIntTanimoto extends Object implements Serializable

serialVersionUID: 0L

Class com.chemaxon.overlap.unguarded.UnguardedBinaryLongManhattan extends Object implements Serializable

serialVersionUID: 0L

Class com.chemaxon.overlap.unguarded.UnguardedBinaryLongTanimoto extends Object implements Serializable

serialVersionUID: 0L

Class com.chemaxon.overlap.unguarded.UnguardedBinaryLongTversky extends Object implements Serializable

serialVersionUID: 0L

Serialized Fields

coeffQuery

double coeffQuery
Query side coefficient.


coeffTarget

double coeffTarget
Target side coefficient.

Class com.chemaxon.overlap.unguarded.UnguardedFloatVectorEuclidSqr extends Object implements Serializable

serialVersionUID: 0L

Class com.chemaxon.overlap.unguarded.UnguardedFloatVectorManhattan extends Object implements Serializable

serialVersionUID: 0L

Class com.chemaxon.overlap.unguarded.UnguardedFloatVectorMaxDiff extends Object implements Serializable

serialVersionUID: 0L

Class com.chemaxon.overlap.unguarded.UnguardedFloatVectorTanimoto extends Object implements Serializable

serialVersionUID: 0L


jklustor-overlap-0.0.2-20140619012940 (ChemAxon)