jklustor-overlap-0.0.2-20140619012940 (ChemAxon)

A B C D E F G H I J K L M N O P Q R S T U V W X

A

add(double) - Method in class com.chemaxon.calculations.util.Histo
Add a value to the histogram.
add(int, String) - Method in class com.chemaxon.overlap.io.CompactStringStorage.Builder
 
add(int, T) - Method in interface com.chemaxon.overlap.io.MasterStorages.MasterStorageBuilder
Add next represented data.
addAll(InputStream, String, int, int, StandardizerWrapper, SubProgressObserver, ExecutorService, MoleculeCallback) - Method in interface com.chemaxon.overlap.io.Updater
Read all molecules from a structure file into the similarity subsystem.
addAll(InputStream, String, int, int, StandardizerWrapper, SubProgressObserver, ExecutorService, MoleculeCallback) - Method in class com.chemaxon.overlap.storage.PagedDescriptorStorage
 
addAll(Iterator<StructureRecord>, StandardizerWrapper, ProgressObserver, ExecutorService, MoleculeCallback) - Method in class com.chemaxon.overlap.storage.PagedDescriptorStorage
Import from an input iterator.
addDescriptor(D) - Method in interface com.chemaxon.overlap.io.Updater
Add a single descriptor to the similarity subsystem.
addDescriptor(D) - Method in class com.chemaxon.overlap.storage.PagedDescriptorStorage
 
addError(int) - Method in class com.chemaxon.overlap.io.IdProjectors.IdProjectorBuilder
Report master ID for which no client ID.
addMissing(int) - Method in class com.chemaxon.overlap.io.CompactStringStorage.Builder
 
addMissing(int) - Method in interface com.chemaxon.overlap.io.MasterStorages.MasterStorageBuilder
Add missing data.
addMolecule(Molecule) - Method in interface com.chemaxon.overlap.io.Updater
Add a single molecule to the similarity subsystem.
addMolecule(Molecule) - Method in class com.chemaxon.overlap.storage.PagedDescriptorStorage
 
addOk(int, int) - Method in class com.chemaxon.overlap.io.IdProjectors.IdProjectorBuilder
Report new master-client mapping.
addPropertyChangeListener(PropertyChangeListener) - Method in class com.chemaxon.calculations.common.ConsolePO
 
align(List<String>, CharLayout.HA) - Static method in class com.chemaxon.calculations.util.CharLayout
Align lines.
apply(ImmutableList<T>) - Method in class com.chemaxon.overlap.bruteforce.FullMatrix.Calc
 
apply(ImmutableList<T>) - Method in class com.chemaxon.overlap.bruteforce.SelfKnn.Calc
 
apply(FloatVectorDescriptor) - Method in class com.chemaxon.overlap.unguarded.ExtractFloatFp
 
apply(BinaryVectorDescriptor) - Method in class com.chemaxon.overlap.unguarded.ExtractIntFp
 
apply(BinaryVectorDescriptor) - Method in class com.chemaxon.overlap.unguarded.ExtractLongFp
 
arrayAwareToString(Object) - Static method in class com.chemaxon.overlap.io.Util
Array aware toString.
AsyncResult<T> - Interface in com.chemaxon.overlap
Result handler for long running asynchronous calculations where partial return values are provided.
AutoThrottle - Class in com.chemaxon.calculations.common
Throttles interactive periodic events.
AutoThrottle(long, boolean) - Constructor for class com.chemaxon.calculations.common.AutoThrottle
Construct an autothrottle which targets a time delay.

B

BatchedPagedProcessor - Class in com.chemaxon.overlap.concurrent
Lightweight wrapper to provide batched paged processing.
bestdissims - Variable in class com.chemaxon.overlap.bruteforce.BruteForcePagedSimilarity.DissimResult
 
bestEffortConvert(Molecule) - Static method in class com.chemaxon.overlap.io.MasterMoleculeStorage
Convert Molecule to String multiple formats.
bestids - Variable in class com.chemaxon.overlap.bruteforce.BruteForcePagedSimilarity.DissimResult
 
BppFrontend<S,T> - Class in com.chemaxon.overlap.concurrent
Batched paged processor frontend.
BppFrontend(SubProgressObserver, Iterator<S>, Function<S, T>, ErrorHandler<S>, ResultHandler<S, T>) - Constructor for class com.chemaxon.overlap.concurrent.BppFrontend
Construct new instance.
BppManager - Class in com.chemaxon.overlap.concurrent
Management bean implementation.
BppManager(ManagedBpp<?, ?>) - Constructor for class com.chemaxon.overlap.concurrent.BppManager
Construct new instance.
BppManagerMBean - Interface in com.chemaxon.overlap.concurrent
MBean for managing batched paged processor.
BruteForcePagedSimilarity<D extends com.chemaxon.descriptors.common.Descriptor> - Class in com.chemaxon.overlap.bruteforce
Brute force paged similarity search.
BruteForcePagedSimilarity(DescriptorComparator<D>, List<ImmutableList<D>>, List<D>) - Constructor for class com.chemaxon.overlap.bruteforce.BruteForcePagedSimilarity
Construct new immutable reference.
BruteForcePagedSimilarity.DissimResult - Class in com.chemaxon.overlap.bruteforce
 
BruteForcePagedSimilarity.DissimResult(int) - Constructor for class com.chemaxon.overlap.bruteforce.BruteForcePagedSimilarity.DissimResult
 
BruteForcePagedSimilarity.SearchPage<D extends com.chemaxon.descriptors.common.Descriptor> - Class in com.chemaxon.overlap.bruteforce
 
BruteForcePagedSimilarity.SearchPage(DescriptorComparator<D>, List<D>, List<D>, int) - Constructor for class com.chemaxon.overlap.bruteforce.BruteForcePagedSimilarity.SearchPage
 
build() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters.Builder
Build immutable representation.
build() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfParameters.Builder
 
build() - Method in class com.chemaxon.overlap.io.CompactStringStorage.Builder
 
build() - Method in class com.chemaxon.overlap.io.IdProjectors.IdProjectorBuilder
Build serializable, immutable projector.
build() - Method in class com.chemaxon.overlap.io.IdProjectors.IdProjectorMCB
Build serializable, immutable projector.
build() - Method in interface com.chemaxon.overlap.io.MasterStorages.MasterStorageBuilder
Build immutable, serializable storage from the current state.
build() - Method in class com.chemaxon.overlap.io.MasterStorages.MoleculeCallbackBuilder
Create immutable representation.
build() - Method in class com.chemaxon.overlap.io.PropertyCollectorCallback
Create the master storage from the current state.

C

calculateFullMatrix(List<T>, SubProgressObserver, ExecutorService, boolean) - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Calculate full dissimilarity matrix.
calculateSelfKnn(int, int, SubProgressObserver, ExecutorService) - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Brute force find kNN among the contents of the represented descriptors.
call() - Method in class com.chemaxon.overlap.bruteforce.BruteForcePagedSimilarity.SearchPage
 
call() - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap.SearchMostSimilars
 
call() - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap.SearchPage
 
call() - Method in class com.chemaxon.overlap.concurrent.ProcessPage
 
call() - Method in class com.chemaxon.overlap.storage.Process
 
call() - Method in class com.chemaxon.overlap.storage.SerializeTask
 
CharLayout - Class in com.chemaxon.calculations.util
Simple utilities for character based multiline layouts.
CharLayout.HA - Enum in com.chemaxon.calculations.util
Possible horizontal alignments.
close() - Method in class com.chemaxon.overlap.io.StructureRecordIterator
 
CmdlineUtils - Class in com.chemaxon.calculations.util
Command line related utilities.
com.chemaxon.calculations.common - package com.chemaxon.calculations.common
 
com.chemaxon.calculations.util - package com.chemaxon.calculations.util
Various utilities used in calculations, descriptors, clustering and overlap analysis.
com.chemaxon.descriptors.fingerprints.ecfp - package com.chemaxon.descriptors.fingerprints.ecfp
 
com.chemaxon.descriptors.fingerprints.pf2d - package com.chemaxon.descriptors.fingerprints.pf2d
 
com.chemaxon.overlap - package com.chemaxon.overlap
Overlap analysis related codes.
com.chemaxon.overlap.bruteforce - package com.chemaxon.overlap.bruteforce
Brute force similarity search.
com.chemaxon.overlap.concurrent - package com.chemaxon.overlap.concurrent
Concurrency related utilities.
com.chemaxon.overlap.io - package com.chemaxon.overlap.io
 
com.chemaxon.overlap.storage - package com.chemaxon.overlap.storage
 
com.chemaxon.overlap.unguarded - package com.chemaxon.overlap.unguarded
Unguarded descriptor handling.
CompactStringStorage - Class in com.chemaxon.overlap.io
Concatenated UTF-8 byte array backed master String storage.
CompactStringStorage(int, int, List<int[]>, List<byte[]>) - Constructor for class com.chemaxon.overlap.io.CompactStringStorage
Construct.
CompactStringStorage.Builder - Class in com.chemaxon.overlap.io
Builder class.
CompactStringStorage.Builder(int, int) - Constructor for class com.chemaxon.overlap.io.CompactStringStorage.Builder
Construct.
comparator - Variable in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap.SearchMostSimilars
Underlying comparator.
comparator - Variable in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap.SearchPage
Underlying comparator.
computeNext() - Method in class com.chemaxon.overlap.io.StructureRecordIterator
 
ConsolePO - Class in com.chemaxon.calculations.common
Stupid progressObserver to write to console.
ConsolePO(String, long) - Constructor for class com.chemaxon.calculations.common.ConsolePO
Construct a new instance.
ConsolePO(ConsolePO, PrintStream, String, long) - Constructor for class com.chemaxon.calculations.common.ConsolePO
Construct a new instance.
constructEcfpGeneratorImpl() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters
Construct non thread safe Ecfp generator.
constructPdGeneratorImpl() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfParameters
Construct non thread safe Pf generator.
constructPfGenerator(PfParameters) - Method in interface com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfParameters.ConstructPfGenerator
Constructor invocation.
copyTo(int, int, int[], int[], double[]) - Method in class com.chemaxon.overlap.KnnResultsImpl
Low level array copy to target arrays.
countingCallback() - Static method in class com.chemaxon.overlap.io.MoleculeCallbacks
Counting callback.
createBruteForceOverlap(Function<D, T>, UnguardedDissimilarityCalculator<T>) - Method in class com.chemaxon.overlap.storage.PagedDescriptorStorage
Create a brute force overlap calculator from the current state of the storage.
createEmptyStorage() - Method in class com.chemaxon.overlap.OverlapAnalysisContext
Create an empty storage.
createFailedPage() - Method in class com.chemaxon.overlap.concurrent.ProcessPage
Create a page representing the same inputs with all failed state.
createIntermediateResult() - Method in interface com.chemaxon.overlap.AsyncResult
Create a new intermediate result.
createNewBuilder() - Static method in class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfParameters
Construct a builder for this parameter class, initialized to default.
createStringStoreBuilder(int) - Static method in class com.chemaxon.overlap.io.MasterStorages
Create a String storage builder.
createStringStoreBuilder() - Static method in class com.chemaxon.overlap.io.MasterStorages
Create a String storage builder.

D

DEFAULT_IMPORT_PAGESIZE - Static variable in class com.chemaxon.overlap.io.MasterStorages
Page size to use on import.
DEFAULT_PAGESIZE - Static variable in class com.chemaxon.overlap.OverlapAnalysisContext
Default pagesize.
dequeueFinisheds(Queue<Future<List<ProcessQueueItem<D>>>>, MoleculeCallback, ProgressObserver) - Method in class com.chemaxon.overlap.storage.PagedDescriptorStorage
Dequeue finished results if any.
deserialize(ObjectInputStream, SubProgressObserver) - Static method in class com.chemaxon.overlap.io.CompactStringStorage
Deserialize from an object input stream.
deserialize(ObjectInputStream, SubProgressObserver) - Static method in class com.chemaxon.overlap.io.MasterMoleculeStorage
Deserialize from an object input stream.
deserializeUnguarded(int, DescriptorGenerator<D>, Function<D, T>, UnguardedDissimilarityCalculator<T>, ObjectInputStream, SubProgressObserver) - Static method in class com.chemaxon.overlap.storage.PagedDescriptorStorage
Deserialize an UnguardedPagedSimilarity from a binary serialized form.
deserializeUnguardedPagedOverlap(ObjectInputStream, SubProgressObserver) - Method in class com.chemaxon.overlap.OverlapAnalysisContext
Deserialize an UnguardedPagedSimilarity from binary serialized from.
diameter(int) - Method in class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters.Builder
Update diameter.
dissimArray - Variable in class com.chemaxon.overlap.bruteforce.Dissimilarities
Dissimilarity values for the IDs;
Dissimilarities - Class in com.chemaxon.overlap.bruteforce
Multiple dissimilarity result values.
Dissimilarities(int) - Constructor for class com.chemaxon.overlap.bruteforce.Dissimilarities
Initialize with invalid values.
dissimilarity(int[], int[]) - Method in class com.chemaxon.overlap.unguarded.UnguardedBinaryIntManhattan
 
dissimilarity(int[], int[]) - Method in class com.chemaxon.overlap.unguarded.UnguardedBinaryIntTanimoto
 
dissimilarity(long[], long[]) - Method in class com.chemaxon.overlap.unguarded.UnguardedBinaryLongManhattan
 
dissimilarity(long[], long[]) - Method in class com.chemaxon.overlap.unguarded.UnguardedBinaryLongTanimoto
 
dissimilarity(long[], long[]) - Method in class com.chemaxon.overlap.unguarded.UnguardedBinaryLongTversky
 
dissimilarity(T, T) - Method in interface com.chemaxon.overlap.unguarded.UnguardedDissimilarityCalculator
Compare dissimilarity of two objects.
dissimilarity(float[], float[]) - Method in class com.chemaxon.overlap.unguarded.UnguardedFloatVectorEuclidSqr
 
dissimilarity(float[], float[]) - Method in class com.chemaxon.overlap.unguarded.UnguardedFloatVectorManhattan
 
dissimilarity(float[], float[]) - Method in class com.chemaxon.overlap.unguarded.UnguardedFloatVectorMaxDiff
 
dissimilarity(float[], float[]) - Method in class com.chemaxon.overlap.unguarded.UnguardedFloatVectorTanimoto
 
done() - Method in class com.chemaxon.calculations.common.ConsolePO
 

E

enqueueNextBatch(Iterator<StructureRecord>, StandardizerWrapper, Queue<Future<List<ProcessQueueItem<D>>>>, ExecutorService) - Method in class com.chemaxon.overlap.storage.PagedDescriptorStorage
Enqueue next batch of processes.
error(int, S, Throwable) - Method in interface com.chemaxon.overlap.concurrent.ErrorHandler
Process error report.
ErrorHandler<S> - Interface in com.chemaxon.overlap.concurrent
Callback to accept process errors.
ErrorHandlers - Class in com.chemaxon.overlap.concurrent
Utilities related to ErrorHandler.
errorLoggingCallback(Log) - Static method in class com.chemaxon.overlap.io.MoleculeCallbacks
Error logging callback.
errorPropagatingHandler() - Static method in class com.chemaxon.overlap.concurrent.ErrorHandlers
Error propagating handler.
errorVerbosingCallback() - Static method in class com.chemaxon.overlap.io.MoleculeCallbacks
Error verbosing callback.
ExtractFloatFp - Class in com.chemaxon.overlap.unguarded
Extract float [] fp from a FloatVectorDescriptor.
ExtractFloatFp() - Constructor for class com.chemaxon.overlap.unguarded.ExtractFloatFp
 
ExtractIntFp - Class in com.chemaxon.overlap.unguarded
Extract int [] fingerprint from a BinaryVectorDescriptor.
ExtractIntFp() - Constructor for class com.chemaxon.overlap.unguarded.ExtractIntFp
 
ExtractLongFp - Class in com.chemaxon.overlap.unguarded
Extract long [] fp from a BinaryVectorDescriptor.
ExtractLongFp() - Constructor for class com.chemaxon.overlap.unguarded.ExtractLongFp
 

F

fetch(boolean) - Method in class com.chemaxon.overlap.concurrent.ManagedBpp
Fetch next ready result if any.
findMostSimilar(List<D>, SubProgressObserver, ExecutorService) - Method in class com.chemaxon.overlap.bruteforce.BruteForcePagedSimilarity
Brute force find most similar structure for a set of structures.
findMostSimilar(UnguardedPagedOverlap<T>, int, SubProgressObserver, ExecutorService) - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Brute force find most similar structure for a set of structures.
findMostSimilar(List<T>, SubProgressObserver, ExecutorService) - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Brute force find most similar structure for a set of structures.
findMostSimilar(D, SubProgressObserver) - Method in interface com.chemaxon.overlap.Similarity
Look up the most similar node.
findMostSimilar(D, SubProgressObserver, ExecutorService) - Method in interface com.chemaxon.overlap.Similarity
Look up the most similar node.
findMostSimilarOnSingleThread(List<D>, SubProgressObserver) - Method in class com.chemaxon.overlap.bruteforce.BruteForcePagedSimilarity
Single threaded reference for multi query most similar lookup.
findMostSimilarOnSingleThread(D, SubProgressObserver) - Method in class com.chemaxon.overlap.bruteforce.BruteForcePagedSimilarity
Find most similar for a given query structure.
findMostSimilarOnSingleThread(List<T>, SubProgressObserver) - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Single threaded reference for multi query most similar lookup.
findMostSimilarOnSingleThread(T, SubProgressObserver) - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Find most similar for a given query structure.
findMostSimilars(T, int, SubProgressObserver, ExecutorService) - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Find most similar structures for a single query.
findMostSimilars(D, SubProgressObserver, int) - Method in interface com.chemaxon.overlap.Similarity
Look up the most similar nodes.
findMostSimilars(D, SubProgressObserver, int, ExecutorService) - Method in interface com.chemaxon.overlap.Similarity
Look up the most similar nodes.
findMostSimilarsOnSingleThread(D, SubProgressObserver, int) - Method in class com.chemaxon.overlap.bruteforce.BruteForcePagedSimilarity
Find most similars for a given query structure.
findMostSimilarsOnSingleThread(T, SubProgressObserver, int) - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Find most similars for a given query structure.
firstId - Variable in class com.chemaxon.overlap.bruteforce.BruteForcePagedSimilarity.SearchPage
 
firstId - Variable in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap.SearchMostSimilars
ID of the first target in UnguardedPagedOverlap.SearchMostSimilars.pages.
firstId - Variable in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap.SearchPage
ID of the first target in UnguardedPagedOverlap.SearchPage.page.
firstPageToStrings() - Method in class com.chemaxon.overlap.concurrent.ManagedBpp
First page in String[] format.
FORMATS - Static variable in class com.chemaxon.overlap.io.MasterMoleculeStorage
Formats to try to represent structure.
freeze() - Method in class com.chemaxon.overlap.concurrent.BppManager
 
freeze() - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean
Freeze worker.
fromByteArray(byte[]) - Method in class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpGenerator
 
fromByteArray(byte[]) - Method in class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfGenerator
 
fromStandardizerCfgLocation(String) - Static method in class com.chemaxon.overlap.io.StandardizerWrappers
Wrap a Standardizer with config file location.
fromStandardizerConfigXml(String) - Static method in class com.chemaxon.overlap.io.StandardizerWrappers
Wrap a Standardizer with config XML location.
fromString(String) - Method in class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpGenerator
 
fromString(String) - Method in class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfGenerator
 
FullMatrix - Class in com.chemaxon.overlap.bruteforce
Full matrix calculator for unguarded paged storage.
FullMatrix.Calc<T> - Class in com.chemaxon.overlap.bruteforce
Calculator function.
FullMatrix.Calc(List<T>, UnguardedDissimilarityCalculator<T>) - Constructor for class com.chemaxon.overlap.bruteforce.FullMatrix.Calc
Construct.
FullMatrix.Report<T> - Class in com.chemaxon.overlap.bruteforce
Report dissimilarity vectors.
FullMatrix.Report(double[][]) - Constructor for class com.chemaxon.overlap.bruteforce.FullMatrix.Report
Construct.

G

generateDescriptor(Molecule) - Method in class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpGenerator
 
generateDescriptor(Molecule) - Method in class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfGenerator
 
get(int) - Method in class com.chemaxon.overlap.io.CompactStringStorage
 
get(int) - Method in class com.chemaxon.overlap.io.MasterMoleculeStorage
 
get(int) - Method in interface com.chemaxon.overlap.io.MasterStorage
Get given structure identified with an index.
getAbsentCount() - Method in class com.chemaxon.overlap.io.CompactStringStorage
 
getAbsentCount() - Method in class com.chemaxon.overlap.io.MasterMoleculeStorage
 
getAbsentCount() - Method in interface com.chemaxon.overlap.io.MasterStorage
Number of absent structures.
getBareDescriptor(BinaryVectorDescriptor) - Method in class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpGenerator
 
getBareDescriptor(FloatVectorDescriptor) - Method in class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfGenerator
 
getBestdissims() - Method in class com.chemaxon.overlap.bruteforce.BruteForcePagedSimilarity.DissimResult
 
getBestids() - Method in class com.chemaxon.overlap.bruteforce.BruteForcePagedSimilarity.DissimResult
 
getBin(int) - Method in class com.chemaxon.calculations.util.Histo
Get the value from a bin.
getBinCount() - Method in class com.chemaxon.calculations.util.Histo
Get bin count.
getBinIndex(double) - Method in class com.chemaxon.calculations.util.Histo
Look up associated bin.
getBinLowerBound(int) - Method in class com.chemaxon.calculations.util.Histo
Lower bound of a bin.
getBinUpperBound(int) - Method in class com.chemaxon.calculations.util.Histo
Upper bound of a bin.
getClientId(int) - Method in interface com.chemaxon.overlap.io.IdProjector
Associated client ID if present.
getCurrentNonFinishedCount() - Method in class com.chemaxon.overlap.concurrent.ManagedBpp
Number of unfinished items.
getCurrentQueueSize() - Method in class com.chemaxon.overlap.concurrent.ManagedBpp
Current size of the processing queue.
getDefaultComparator() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpGenerator
 
getDefaultComparator() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfGenerator
 
getDescriptor() - Method in class com.chemaxon.overlap.storage.ProcessQueueItem
Calculated descriptor if applicable or null.
getDescriptorAsString(int, boolean) - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Retrieve descriptor as String.
getDescriptorComparator() - Method in class com.chemaxon.overlap.OverlapAnalysisContext
Gets represented descriptor comparator.
getDescriptorGenerator() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters
 
getDescriptorGenerator() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfParameters
 
getDescriptorGenerator() - Method in class com.chemaxon.overlap.OverlapAnalysisContext
Gets represented descriptor generator.
getDiameter() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters
Diameter.
getDissimArray() - Method in class com.chemaxon.overlap.bruteforce.Dissimilarities
Best dissimilarities array.
getDissimilarities(int) - Method in interface com.chemaxon.overlap.KnnResults
Dissimilarity.
getDissimilarities(int) - Method in class com.chemaxon.overlap.KnnResultsImpl
 
getDissimilarity(int) - Method in interface com.chemaxon.overlap.SimilarityResults
Dissimilarity.
getDissimilarity(int) - Method in class com.chemaxon.overlap.SimilarityResultsImpl
 
getDissimiliarity() - Method in class com.chemaxon.overlap.SimilarityResultImpl
 
getDissimiliarity() - Method in interface com.chemaxon.overlap.SimilarityResultNode
Get the represented dissimilarity value.
getElapsedTime() - Method in class com.chemaxon.calculations.common.Timer
Elapsed time.
getError() - Method in class com.chemaxon.overlap.storage.ProcessQueueItem
Represented error if applicable or null.
getFirstPageSources() - Method in class com.chemaxon.overlap.concurrent.BppManager
 
getFirstPageSources() - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean
Inputs represented by the first enqueued page in String format.
getFormat() - Method in class com.chemaxon.overlap.io.StructureRecordIterator
Get format.
getGuardObject() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpGenerator
 
getGuardObject() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfGenerator
 
getHistoBody(int) - Method in class com.chemaxon.calculations.util.Histo
Compose histogram body
getIdArray() - Method in class com.chemaxon.overlap.bruteforce.Dissimilarities
Best IDs array.
getIndexToName() - Method in class com.chemaxon.overlap.io.MoleculeCallbacks.IndexToNameStoringCallback
Get a clone of index to name association.
getInputCount() - Method in class com.chemaxon.overlap.concurrent.BppManager
 
getInputCount() - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean
Number of individual inputs read from the input source.
getInputCount() - Method in class com.chemaxon.overlap.concurrent.ManagedBpp
Total read inputs.
getInvocationCount() - Method in class com.chemaxon.calculations.common.Timer
Get total invocation count.
getK() - Method in interface com.chemaxon.overlap.KnnResults
Value of k.
getK() - Method in class com.chemaxon.overlap.KnnResultsImpl
 
getLowerBound() - Method in class com.chemaxon.calculations.util.Histo
Lower bound of the histogram.
getMasterId(int) - Method in interface com.chemaxon.overlap.io.IdProjector
Master ID from a client ID.
getMaxQueueSize() - Method in class com.chemaxon.overlap.concurrent.BppManager
 
getMaxQueueSize() - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean
Current results queue size limit.
getMaxQueueSize() - Method in class com.chemaxon.overlap.concurrent.ManagedBpp
Max queue size.
getMol() - Method in class com.chemaxon.overlap.storage.ProcessQueueItem
Parsed molecule or null for parse error.
getMolString() - Method in class com.chemaxon.overlap.storage.ProcessQueueItem
Get represented molecule source if present.
getNeighbors(int) - Method in interface com.chemaxon.overlap.KnnResults
ID of the nearest neighbors of query.
getNeighbors(int) - Method in class com.chemaxon.overlap.KnnResultsImpl
 
getNonFinishedCount() - Method in class com.chemaxon.overlap.concurrent.BppManager
 
getNonFinishedCount() - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean
Non finished items in the queue.
getOkCount() - Method in interface com.chemaxon.overlap.io.MoleculeCallbacks.CountingMoleculeCallback
Count of OKs.
getOutputCount() - Method in class com.chemaxon.overlap.concurrent.BppManager
 
getOutputCount() - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean
Number of reported results.
getOutputCount() - Method in class com.chemaxon.overlap.concurrent.ManagedBpp
Total reported outputs.
getPage(int) - Method in class com.chemaxon.overlap.storage.PagedDescriptorStorage
 
getPageCount() - Method in class com.chemaxon.overlap.storage.PagedDescriptorStorage
Count of pages.
getPageSize() - Method in class com.chemaxon.overlap.bruteforce.BruteForcePagedSimilarity.SearchPage
 
getPageSize() - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap.SearchPage
Number of represented targets.
getPageSize() - Method in class com.chemaxon.overlap.concurrent.BppManager
 
getPageSize() - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean
Current page size.
getPagesize() - Method in class com.chemaxon.overlap.concurrent.ManagedBpp
Current page size.
getPagesize() - Method in class com.chemaxon.overlap.OverlapAnalysisContext
Gets represented page size.
getParameters() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpGenerator
 
getParameters() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfGenerator
 
getParseErrorCount() - Method in interface com.chemaxon.overlap.io.MoleculeCallbacks.CountingMoleculeCallback
Parse error count.
getProcessingErrorCount() - Method in interface com.chemaxon.overlap.io.MoleculeCallbacks.CountingMoleculeCallback
Processing error count.
getQueriesCount() - Method in class com.chemaxon.overlap.bruteforce.BruteForcePagedSimilarity.SearchPage
 
getQueriesCount() - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap.SearchPage
Number of queries.
getQuery(int) - Method in interface com.chemaxon.overlap.KnnResults
Query ID.
getQuery(int) - Method in class com.chemaxon.overlap.KnnResultsImpl
 
getQuery(int) - Method in interface com.chemaxon.overlap.SimilarityResults
ID of stored query.
getQuery(int) - Method in class com.chemaxon.overlap.SimilarityResultsImpl
 
getQueryCount() - Method in interface com.chemaxon.overlap.KnnResults
Number of queries stored.
getQueryCount() - Method in class com.chemaxon.overlap.KnnResultsImpl
 
getQueueSize() - Method in class com.chemaxon.overlap.concurrent.BppManager
 
getQueueSize() - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean
Current size of the results queue.
getReadIndex() - Method in interface com.chemaxon.overlap.io.StructureRecord
Represented structure/record index.
getReadIndex() - Method in class com.chemaxon.overlap.io.StructureRecordImpl
 
getReadno() - Method in class com.chemaxon.overlap.storage.ProcessQueueItem
Represented structure index.
getResult() - Method in interface com.chemaxon.overlap.AsyncResult
Get the representation of the long running task.
getSmallestBinsBlock(int) - Method in class com.chemaxon.calculations.util.Histo
Compose the list of smallest bins block.
getSourcesAsStrings() - Method in class com.chemaxon.overlap.concurrent.ProcessPage
Get sources String representation.
getSourcesCount() - Method in class com.chemaxon.overlap.concurrent.ProcessPage
Get number of represented sources.
getStandardizer() - Method in class com.chemaxon.overlap.OverlapAnalysisContext
Gets represented standardizer wrapper.
getStatBlock() - Method in class com.chemaxon.calculations.util.Histo
Compose statistics block.
getStructureSource() - Method in interface com.chemaxon.overlap.io.StructureRecord
Structure source if applicable.
getStructureSource() - Method in class com.chemaxon.overlap.io.StructureRecordImpl
 
getTarget(int) - Method in interface com.chemaxon.overlap.SimilarityResults
ID of the stored target.
getTarget(int) - Method in class com.chemaxon.overlap.SimilarityResultsImpl
 
getTargetID() - Method in class com.chemaxon.overlap.SimilarityResultImpl
 
getTargetID() - Method in interface com.chemaxon.overlap.SimilarityResultNode
Get the internal ID of the represented target structure.
getTotalNotifyCount() - Method in interface com.chemaxon.overlap.io.MoleculeCallbacks.CountingMoleculeCallback
Count of all notify calls.
getTotalTargetCount() - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap.SearchMostSimilars
Get number of total descriptors compared.
getUnguardedDissimilarityCalculator() - Method in class com.chemaxon.overlap.OverlapAnalysisContext
Gets represented unguarded dissimilarty calculator.
getUnguardedExtractor() - Method in class com.chemaxon.overlap.OverlapAnalysisContext
Gets represented unguarded form extractor.
getUpperBound() - Method in class com.chemaxon.calculations.util.Histo
Upper bound of the histogram.
getXmlConfig() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfParameters
The XML configuration string.

H

hasNext() - Method in class com.chemaxon.overlap.concurrent.BppFrontend
Check if has more source to be processed.
Histo - Class in com.chemaxon.calculations.util
Simple histogram of values.
Histo(int, int, int, boolean) - Constructor for class com.chemaxon.calculations.util.Histo
Create a histogram containing integers.
Histo(int, int) - Constructor for class com.chemaxon.calculations.util.Histo
 
Histo(double, double, int, boolean, boolean) - Constructor for class com.chemaxon.calculations.util.Histo
Create a histogram containing real numbers.
Histo(double, double, int) - Constructor for class com.chemaxon.calculations.util.Histo
 

I

idArray - Variable in class com.chemaxon.overlap.bruteforce.Dissimilarities
Represented target IDs.
identityStandardizer() - Static method in class com.chemaxon.overlap.io.StandardizerWrappers
Identity standardization.
IdProjector - Interface in com.chemaxon.overlap.io
ID projection between a master ID and a client ID.
IdProjectors - Class in com.chemaxon.overlap.io
Utilities for ID projection.
IdProjectors.IdProjectorBuilder - Class in com.chemaxon.overlap.io
Plain ID projector builder.
IdProjectors.IdProjectorBuilder() - Constructor for class com.chemaxon.overlap.io.IdProjectors.IdProjectorBuilder
Construct new builder.
IdProjectors.IdProjectorBuilder(int) - Constructor for class com.chemaxon.overlap.io.IdProjectors.IdProjectorBuilder
Construct new builder.
IdProjectors.IdProjectorMCB - Class in com.chemaxon.overlap.io
Projector builder over molecule callbacks.
IdProjectors.IdProjectorMCB() - Constructor for class com.chemaxon.overlap.io.IdProjectors.IdProjectorMCB
Instantiate without forwarding.
IdProjectors.IdProjectorMCB(MoleculeCallback) - Constructor for class com.chemaxon.overlap.io.IdProjectors.IdProjectorMCB
Instantiate with a forwarding callback.
IdProjectors.IdProjectorMCB(int, MoleculeCallback) - Constructor for class com.chemaxon.overlap.io.IdProjectors.IdProjectorMCB
Instantiate with a forwarding callback.
initial(DescriptorGenerator<D>) - Static method in class com.chemaxon.overlap.OverlapAnalysisContext
Empty representation with specified DescriptorGenerator.
initial(DescriptorGenerator<D>, DescriptorComparator<D>) - Static method in class com.chemaxon.overlap.OverlapAnalysisContext
Empty representation with specified DescriptorGenerator and comparator.
inputStreamFromLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Create InputStream from not nullable location.
inputStreamFromNullableLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Create in input stream from nullable location.
insertSorted(double, int) - Method in class com.chemaxon.overlap.bruteforce.Dissimilarities
Merge another ID/dissimilarity value into sorted.
invocation() - Method in class com.chemaxon.calculations.common.AutoThrottle
Sign an invocation to query next throttled event.
invoke(long) - Method in class com.chemaxon.calculations.common.Timer
Register one or multiple invocations.
invoke() - Method in class com.chemaxon.calculations.common.Timer
Register one invoceation.
isCancelled() - Method in class com.chemaxon.calculations.common.ConsolePO
 
isEmpty() - Method in class com.chemaxon.calculations.util.Histo
Check if the histogram is empty.
isEmpty() - Method in class com.chemaxon.overlap.concurrent.ManagedBpp
Check if the results queue is empty.
isFirstPageDone() - Method in class com.chemaxon.overlap.concurrent.ManagedBpp
Check if first page is done.
isFrozen() - Method in class com.chemaxon.overlap.concurrent.BppManager
 
isFrozen() - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean
Check frozen status.
isFrozen() - Method in class com.chemaxon.overlap.concurrent.ManagedBpp
Check frozen status.
isInCurrentBounds(double) - Method in class com.chemaxon.calculations.util.Histo
Check if a bin is associated with the given value.
isParseError() - Method in class com.chemaxon.overlap.storage.ProcessQueueItem
Check if a parse error occured.
isProcessError() - Method in class com.chemaxon.overlap.storage.ProcessQueueItem
Check if process error occured.
iterateDescriptors() - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Iterate descriptors.
iterateDescriptors(int) - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Iterate descriptors.
iteratePages() - Method in class com.chemaxon.overlap.storage.PagedDescriptorStorage
 

J

join(CharLayout.HA, String, List<String>...) - Static method in class com.chemaxon.calculations.util.CharLayout
Join an arbitrary set of multiliners.
join(List<String>, CharLayout.HA, String, List<String>, CharLayout.HA) - Static method in class com.chemaxon.calculations.util.CharLayout
Join two set of multiliners.

K

kill(boolean) - Method in class com.chemaxon.overlap.concurrent.ManagedBpp
Kill one or all pages.
killAllAndFreeze() - Method in class com.chemaxon.overlap.concurrent.BppManager
 
killAllAndFreeze() - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean
Kill first page and freeze worker.
killFirstPage() - Method in class com.chemaxon.overlap.concurrent.BppManager
 
killFirstPage() - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean
Kill first page unconditionally.
killFirstPageIfBlocking() - Method in class com.chemaxon.overlap.concurrent.BppManager
 
killFirstPageIfBlocking() - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean
Kill first page only if all other pages are ready.
KnnResults - Interface in com.chemaxon.overlap
Results of K nearest neighbors calculations.
KnnResultsImpl - Class in com.chemaxon.overlap
Arrays of primitives backed implementation of KnnResults.
KnnResultsImpl(int, int[], int[], double[]) - Constructor for class com.chemaxon.overlap.KnnResultsImpl
Construct.

L

lineIteratorFromLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Create a LineIterator from a not nullable location.

M

ManagedBpp<S,T> - Class in com.chemaxon.overlap.concurrent
Managed batched parallel processor backend functionality.
ManagedBpp(int, int, ListeningExecutorService) - Constructor for class com.chemaxon.overlap.concurrent.ManagedBpp
Construct.
ManagedBpp.Poker<V> - Class in com.chemaxon.overlap.concurrent
Callback interface to notify waiting instance.
ManagedBpp.Poker() - Constructor for class com.chemaxon.overlap.concurrent.ManagedBpp.Poker
 
MasterMoleculeStorage - Class in com.chemaxon.overlap.io
Master molecule storage is a space efficient storage for Molecules.
MasterMoleculeStorage(CompactStringStorage) - Constructor for class com.chemaxon.overlap.io.MasterMoleculeStorage
Construct over valid sources
masterMoleculeStorageFromFile(InputStream, String, int, StandardizerWrapper, ExecutorService, SubProgressObserver, List<? extends MoleculeCallback>) - Static method in class com.chemaxon.overlap.io.MasterStorages
Create storage from a strcuture file.
MasterStorage<T> - Interface in com.chemaxon.overlap.io
Master structure storage represents the molecules from a repository.
MasterStorages - Class in com.chemaxon.overlap.io
Helper method for managing MasterStorages instances.
MasterStorages.MasterStorageBuilder<T> - Interface in com.chemaxon.overlap.io
Builder class for a master storage.
MasterStorages.MoleculeCallbackBuilder - Class in com.chemaxon.overlap.io
Molecule callback based builder.
MasterStorages.MoleculeCallbackBuilder() - Constructor for class com.chemaxon.overlap.io.MasterStorages.MoleculeCallbackBuilder
Construct new empty builder.
max(long[]) - Static method in class com.chemaxon.calculations.util.Histo
Find maximum in an array.
MAX_QUEUE_SIZE - Static variable in class com.chemaxon.overlap.io.MasterStorages
Max queue size for import.
MAX_RESULT_QUEUE_SIZE - Static variable in class com.chemaxon.overlap.storage.PagedDescriptorStorage
Max non reported queue elements.
merge(BruteForcePagedSimilarity.DissimResult) - Method in class com.chemaxon.overlap.bruteforce.BruteForcePagedSimilarity.DissimResult
 
mergeDistinct(Dissimilarities) - Method in class com.chemaxon.overlap.bruteforce.Dissimilarities
Merge another instance with.
mergeSorted(Dissimilarities) - Method in class com.chemaxon.overlap.bruteforce.Dissimilarities
Merge another instance.
mergeSorted(Dissimilarities, int) - Method in class com.chemaxon.overlap.bruteforce.Dissimilarities
Merge another instance.
MoleculeCallback - Interface in com.chemaxon.overlap.io
Callback executed on each molecules.
MoleculeCallbacks - Class in com.chemaxon.overlap.io
MoleculeCallback related utilities.
MoleculeCallbacks.CountingMoleculeCallback - Interface in com.chemaxon.overlap.io
Error counting callback.
MoleculeCallbacks.IndexToNameStoringCallback - Class in com.chemaxon.overlap.io
A callback storing indexes.
MoleculeCallbacks.IndexToNameStoringCallback(MoleculeCallback) - Constructor for class com.chemaxon.overlap.io.MoleculeCallbacks.IndexToNameStoringCallback
Construct.
MoleculeCallbacks.IndexToNameStoringCallback() - Constructor for class com.chemaxon.overlap.io.MoleculeCallbacks.IndexToNameStoringCallback
Construct.
molToHumanReadable(Molecule) - Static method in class com.chemaxon.overlap.io.Util
Convert molecule to human readable string.

N

nextPage(int) - Method in class com.chemaxon.overlap.concurrent.BppFrontend
Create next page to be submitted.
notifyMolecule(int, Optional<String>, Molecule, int) - Method in class com.chemaxon.overlap.io.IdProjectors.IdProjectorMCB
 
notifyMolecule(int, Optional<String>, Molecule, int) - Method in class com.chemaxon.overlap.io.MasterStorages.MoleculeCallbackBuilder
 
notifyMolecule(int, Optional<String>, Molecule, int) - Method in interface com.chemaxon.overlap.io.MoleculeCallback
Introduce new processed molecule.
notifyMolecule(int, Optional<String>, Molecule, int) - Method in class com.chemaxon.overlap.io.MoleculeCallbacks.IndexToNameStoringCallback
 
notifyMolecule(int, Optional<String>, Molecule, int) - Method in class com.chemaxon.overlap.io.PropertyCollectorCallback
 
notifyParseError(int, Optional<String>, Throwable) - Method in class com.chemaxon.overlap.io.IdProjectors.IdProjectorMCB
 
notifyParseError(int, Optional<String>, Throwable) - Method in class com.chemaxon.overlap.io.MasterStorages.MoleculeCallbackBuilder
 
notifyParseError(int, Optional<String>, Throwable) - Method in interface com.chemaxon.overlap.io.MoleculeCallback
Notify a parsing error.
notifyParseError(int, Optional<String>, Throwable) - Method in class com.chemaxon.overlap.io.MoleculeCallbacks.IndexToNameStoringCallback
 
notifyParseError(int, Optional<String>, Throwable) - Method in class com.chemaxon.overlap.io.PropertyCollectorCallback
 
notifyProcessingError(int, Optional<String>, Molecule, Throwable) - Method in class com.chemaxon.overlap.io.IdProjectors.IdProjectorMCB
 
notifyProcessingError(int, Optional<String>, Molecule, Throwable) - Method in class com.chemaxon.overlap.io.MasterStorages.MoleculeCallbackBuilder
 
notifyProcessingError(int, Optional<String>, Molecule, Throwable) - Method in interface com.chemaxon.overlap.io.MoleculeCallback
Notify a processing error.
notifyProcessingError(int, Optional<String>, Molecule, Throwable) - Method in class com.chemaxon.overlap.io.MoleculeCallbacks.IndexToNameStoringCallback
 
notifyProcessingError(int, Optional<String>, Molecule, Throwable) - Method in class com.chemaxon.overlap.io.PropertyCollectorCallback
 
nullCallback() - Static method in class com.chemaxon.overlap.io.MoleculeCallbacks
Null callback.

O

objectInputStreamFromLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Create ObjectInputStream from a not nullable location.
objectInputStreamFromNullableLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Create in object input stream from nullable location.
objectOutputStreamFromLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
ObjectOutputStream from a location.
objectOutputStreamFromNullableLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
ObjectOutputStream from a nullable location.
ok(D) - Method in class com.chemaxon.overlap.storage.ProcessQueueItem
Report successfull processing.
onFailure(Throwable) - Method in class com.chemaxon.overlap.concurrent.ManagedBpp.Poker
 
onSuccess(V) - Method in class com.chemaxon.overlap.concurrent.ManagedBpp.Poker
 
OverlapAnalysisContext<D extends com.chemaxon.descriptors.common.Descriptor,T extends Serializable> - Class in com.chemaxon.overlap
Context for an overlap analysis.

P

pad(String, int, CharLayout.HA) - Static method in class com.chemaxon.calculations.util.CharLayout
Align String to the given length.
page - Variable in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap.SearchPage
Targets.
PagedDescriptorStorage<D extends com.chemaxon.descriptors.common.Descriptor> - Class in com.chemaxon.overlap.storage
Descriptor storage.
PagedDescriptorStorage(int, DescriptorGenerator<D>) - Constructor for class com.chemaxon.overlap.storage.PagedDescriptorStorage
Construct new empty descriptor storage.
PagedDescriptorStorage(int, DescriptorGenerator<D>, ObjectInputStream, SubProgressObserver) - Constructor for class com.chemaxon.overlap.storage.PagedDescriptorStorage
Construct from a byte [] serialized form.
PagedDescriptorStorage(int, DescriptorGenerator<D>, InputStream, SubProgressObserver) - Constructor for class com.chemaxon.overlap.storage.PagedDescriptorStorage
Construct from a String serialized form.
pages - Variable in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap.SearchMostSimilars
Targets.
PAGES_GROUP_SIZE_FOR_SINGLE_QUERY - Static variable in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Number of pages to group when processing single query.
pagesize(int) - Method in class com.chemaxon.overlap.OverlapAnalysisContext
Update pagesize.
parse() - Method in class com.chemaxon.overlap.storage.ProcessQueueItem
Forward molecule parse.
parseMolecule() - Method in interface com.chemaxon.overlap.io.StructureRecord
Parse molecule if not parsed successfully already.
parseMolecule() - Method in class com.chemaxon.overlap.io.StructureRecordImpl
 
poke() - Method in class com.chemaxon.overlap.concurrent.ManagedBpp.Poker
Do the notification.
prefix(String, List<String>) - Static method in class com.chemaxon.calculations.util.CharLayout
Prefix lines.
printStreamFromLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
PrintStream from a location.
printStreamFromNullableLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
PrintStream from a nullable location.
process(int, int, SubProgressObserver, ExecutorService, Iterator<S>, Function<S, T>, ErrorHandler<S>, ResultHandler<S, T>) - Static method in class com.chemaxon.overlap.concurrent.BatchedPagedProcessor
Launch a long running process.
process(BppFrontend<S, T>) - Method in class com.chemaxon.overlap.concurrent.ManagedBpp
Launch a managed long running process.
process(Iterator<S>, Function<S, T>, ErrorHandler<S>, ResultHandler<S, T>) - Method in interface com.chemaxon.overlap.concurrent.Processor
Invoke blocking processing.
Process<D extends com.chemaxon.descriptors.common.Descriptor> - Class in com.chemaxon.overlap.storage
Process a set of PQE elements.
Process(DescriptorGenerator<D>, StandardizerWrapper, List<ProcessQueueItem<D>>) - Constructor for class com.chemaxon.overlap.storage.Process
Construct.
processError(Throwable) - Method in class com.chemaxon.overlap.storage.ProcessQueueItem
Report that process error occured.
processManaged(MBeanServer, ObjectName, int, int, SubProgressObserver, ListeningExecutorService, Iterator<S>, Function<S, T>, ErrorHandler<S>, ResultHandler<S, T>) - Static method in class com.chemaxon.overlap.concurrent.BatchedPagedProcessor
Launch a managed long running process.
Processor - Interface in com.chemaxon.overlap.concurrent
Abstraction of a mass processor.
ProcessPage<S,T> - Class in com.chemaxon.overlap.concurrent
Process a page of inputs.
ProcessPage(int, List<S>, Function<S, T>) - Constructor for class com.chemaxon.overlap.concurrent.ProcessPage
Construct.
ProcessPage(int, List<S>) - Constructor for class com.chemaxon.overlap.concurrent.ProcessPage
Create a failed page.
ProcessQueueItem<D> - Class in com.chemaxon.overlap.storage
Process queue element data object.
ProcessQueueItem(StructureRecord) - Constructor for class com.chemaxon.overlap.storage.ProcessQueueItem
Construct new instance.
processResult(ProcessPage<S, T>) - Method in class com.chemaxon.overlap.concurrent.BppFrontend
Process result.
PropertyCollectorCallback - Class in com.chemaxon.overlap.io
Build storage for molecular properties.
PropertyCollectorCallback() - Constructor for class com.chemaxon.overlap.io.PropertyCollectorCallback
Construct builder to represent molecule name.
PropertyCollectorCallback(String) - Constructor for class com.chemaxon.overlap.io.PropertyCollectorCallback
Construct builder to store a given property.

Q

queries - Variable in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap.SearchPage
Queries.
query - Variable in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap.SearchMostSimilars
Query.

R

removePropertyChangeListener(PropertyChangeListener) - Method in class com.chemaxon.calculations.common.ConsolePO
 
reportResults(ErrorHandler<S>, ResultHandler<S, T>) - Method in class com.chemaxon.overlap.concurrent.ProcessPage
Flush calculated results to sinks.
result(int, ImmutableList<T>, double[][]) - Method in class com.chemaxon.overlap.bruteforce.FullMatrix.Report
 
result(int, ImmutableList<T>, Dissimilarities[]) - Method in class com.chemaxon.overlap.bruteforce.SelfKnn.Report
 
result(int, S, T) - Method in interface com.chemaxon.overlap.concurrent.ResultHandler
Report process result.
ResultHandler<S,T> - Interface in com.chemaxon.overlap.concurrent
Callback to report processing results.

S

SelfKnn - Class in com.chemaxon.overlap.bruteforce
Self kNN calculator for unguarded paged storage.
SelfKnn.Calc<T> - Class in com.chemaxon.overlap.bruteforce
Calculator function.
SelfKnn.Calc(int, List<T>, UnguardedDissimilarityCalculator<T>) - Constructor for class com.chemaxon.overlap.bruteforce.SelfKnn.Calc
Construct.
SelfKnn.Report<T> - Class in com.chemaxon.overlap.bruteforce
Report dissimilarity vectors.
SelfKnn.Report(int, int) - Constructor for class com.chemaxon.overlap.bruteforce.SelfKnn.Report
Construct.
serialize(ObjectOutputStream, SubProgressObserver) - Method in class com.chemaxon.overlap.io.CompactStringStorage
Write into serialized format.
serialize(ObjectOutputStream, SubProgressObserver) - Method in class com.chemaxon.overlap.io.MasterMoleculeStorage
Write into serialized format.
SerializeTask<D extends com.chemaxon.descriptors.common.Descriptor> - Class in com.chemaxon.overlap.storage
Task to serialize a bunch of descriptors into Strings.
SerializeTask(DescriptorGenerator<D>, List<D>) - Constructor for class com.chemaxon.overlap.storage.SerializeTask
Construct new task.
setFrozen(boolean) - Method in class com.chemaxon.overlap.concurrent.ManagedBpp
Set frozen status.
setMaxQueueSize(int) - Method in class com.chemaxon.overlap.concurrent.BppManager
 
setMaxQueueSize(int) - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean
Set new max queue size parameter.
setMaxQueueSize(int) - Method in class com.chemaxon.overlap.concurrent.ManagedBpp
Set max queue size.
setPageSize(int) - Method in class com.chemaxon.overlap.concurrent.BppManager
 
setPageSize(int) - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean
Set new page size.
setPageSize(int) - Method in class com.chemaxon.overlap.concurrent.ManagedBpp
Set page size effective for new submissions.
Similarity<D extends com.chemaxon.descriptors.common.Descriptor> - Interface in com.chemaxon.overlap
Query interface for the similarity subsystem.
SimilarityResultImpl - Class in com.chemaxon.overlap
Similarity result implementation.
SimilarityResultImpl(int, double) - Constructor for class com.chemaxon.overlap.SimilarityResultImpl
Construct.
SimilarityResultNode - Interface in com.chemaxon.overlap
SimilarityResultNode is a simple wrapper for a single structure in a similarity query based result.
SimilarityResults - Interface in com.chemaxon.overlap
Results of similarity calculations.
SimilarityResultsImpl - Class in com.chemaxon.overlap
Arrays of primitives backed implementation of SimilarityResults.
SimilarityResultsImpl(int[], int[], double[]) - Constructor for class com.chemaxon.overlap.SimilarityResultsImpl
Construct.
size() - Method in class com.chemaxon.overlap.bruteforce.BruteForcePagedSimilarity
Total number of descriptors stored.
size() - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Total number of descriptors stored.
size() - Method in class com.chemaxon.overlap.io.CompactStringStorage
 
size() - Method in class com.chemaxon.overlap.io.MasterMoleculeStorage
 
size() - Method in interface com.chemaxon.overlap.io.MasterStorage
Number of structures in the storage.
size() - Method in interface com.chemaxon.overlap.SimilarityResults
Number of stored triplets.
size() - Method in class com.chemaxon.overlap.SimilarityResultsImpl
 
size() - Method in class com.chemaxon.overlap.storage.PagedDescriptorStorage
Stored descriptor count.
split(String) - Static method in class com.chemaxon.calculations.util.CharLayout
Split to lines.
standardize(Molecule) - Method in interface com.chemaxon.overlap.io.StandardizerWrapper
Invoke represented transformation.
standardizer(StandardizerWrapper) - Method in class com.chemaxon.overlap.OverlapAnalysisContext
Update standardizer.
StandardizerWrapper - Interface in com.chemaxon.overlap.io
Wrap Standardizer for the similarity subsystem.
StandardizerWrappers - Class in com.chemaxon.overlap.io
Provide utility methods for StandardizerWrapper.
stop() - Method in class com.chemaxon.calculations.common.Timer
Stop.
stringFromLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Read the contents of a location into a String.
stringFromNullableLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Read the contents of a location when it is not null.
StructureRecord - Interface in com.chemaxon.overlap.io
Wraps an imported molecule.
StructureRecordImpl - Class in com.chemaxon.overlap.io
Simple structure record implementation.
StructureRecordImpl(String, int, String) - Constructor for class com.chemaxon.overlap.io.StructureRecordImpl
Construct.
StructureRecordIterator - Class in com.chemaxon.overlap.io
Class encapsulating MRecordReader.
StructureRecordIterator(InputStream, String) - Constructor for class com.chemaxon.overlap.io.StructureRecordIterator
New instance.
submit(ProcessPage<S, T>) - Method in class com.chemaxon.overlap.concurrent.ManagedBpp
Submit next page for execution.
subTask(String, long) - Method in class com.chemaxon.calculations.common.ConsolePO
 
sum(long[]) - Static method in class com.chemaxon.calculations.util.Histo
Sum the elements of a given array.
switchToDeterminate(long) - Method in class com.chemaxon.calculations.common.ConsolePO
 

T

ThreadLocalizedEcfpGenerator - Class in com.chemaxon.descriptors.fingerprints.ecfp
Create a thread unsafe but ThreadLocal hacked ECFP generator.
ThreadLocalizedEcfpGenerator(ThreadLocalizedEcfpParameters) - Constructor for class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpGenerator
Construct.
ThreadLocalizedEcfpParameters - Class in com.chemaxon.descriptors.fingerprints.ecfp
Parameters class for ThreadLocalizedEcfpGenerator.
ThreadLocalizedEcfpParameters(ThreadLocalizedEcfpParameters.Builder) - Constructor for class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters
Parametrize from a builder.
ThreadLocalizedEcfpParameters() - Constructor for class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters
Construct with default parametrization.
ThreadLocalizedEcfpParameters.Builder - Class in com.chemaxon.descriptors.fingerprints.ecfp
Parameters builder class for ThreadLocalizedEcfpParameters.
ThreadLocalizedEcfpParameters.Builder() - Constructor for class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters.Builder
Construct.
ThreadLocalizedEcfpParameters.Builder(ThreadLocalizedEcfpParameters) - Constructor for class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters.Builder
Construct from the state of a ThreadLocalizedEcfpParameters.
ThreadLocalizedPfGenerator - Class in com.chemaxon.descriptors.fingerprints.pf2d
Create a thread unsafe but ThreadLocal hacked Pd generator.
ThreadLocalizedPfGenerator(ThreadLocalizedPfParameters) - Constructor for class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfGenerator
Construct.
ThreadLocalizedPfParameters - Class in com.chemaxon.descriptors.fingerprints.pf2d
Parameters class for ThreadLocalizedPfGenerator.
ThreadLocalizedPfParameters() - Constructor for class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfParameters
Constructor using the default settings.
ThreadLocalizedPfParameters.Builder - Class in com.chemaxon.descriptors.fingerprints.pf2d
Builder class for the immutable parameter object.
ThreadLocalizedPfParameters.Builder() - Constructor for class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfParameters.Builder
Constructor with default settings.
ThreadLocalizedPfParameters.Builder(ThreadLocalizedPfParameters) - Constructor for class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfParameters.Builder
Constructor based on a parameter object.
ThreadLocalizedPfParameters.ConstructPfGenerator - Interface in com.chemaxon.descriptors.fingerprints.pf2d
Interface representing PF generator constructor.
Timer - Class in com.chemaxon.calculations.common
Simple timer to measure elapsed times, invocation counts.
Timer(String) - Constructor for class com.chemaxon.calculations.common.Timer
Construct started timer.
toByteArray(BinaryVectorDescriptor) - Method in class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpGenerator
 
toByteArray(FloatVectorDescriptor) - Method in class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfGenerator
 
toBytes(ObjectOutputStream, SubProgressObserver) - Method in class com.chemaxon.overlap.storage.PagedDescriptorStorage
Deprecated. Use PagedDescriptorStorage.toBytes(java.io.ObjectOutputStream, com.chemaxon.calculations.common.SubProgressObserver, long) with a sound reset interval.
toBytes(ObjectOutputStream, SubProgressObserver, long) - Method in class com.chemaxon.overlap.storage.PagedDescriptorStorage
Dump descriptors to a binary file.
toHumanReadableTimeUnit(double) - Static method in class com.chemaxon.calculations.common.Timer
Format to nicely interpretable time unit.
toList() - Method in class com.chemaxon.overlap.bruteforce.BruteForcePagedSimilarity.DissimResult
 
toList() - Method in class com.chemaxon.overlap.bruteforce.Dissimilarities
Create list representation.
toSiPrefixedString(long) - Static method in class com.chemaxon.calculations.common.Timer
Format nicely with SI unit prefixes.
toString() - Method in class com.chemaxon.calculations.common.ConsolePO
 
toString(boolean) - Method in class com.chemaxon.calculations.common.Timer
 
toString() - Method in class com.chemaxon.calculations.common.Timer
 
toString(List<String>) - Static method in class com.chemaxon.calculations.util.CharLayout
Collapse into a multiline String.
toString(int, boolean) - Method in class com.chemaxon.calculations.util.Histo
 
toString() - Method in class com.chemaxon.calculations.util.Histo
 
toString(BinaryVectorDescriptor) - Method in class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpGenerator
 
toString() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpGenerator
 
toString() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters
 
toString(FloatVectorDescriptor) - Method in class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfGenerator
 
toString() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfGenerator
 
toString() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfParameters
 
toString() - Method in class com.chemaxon.overlap.io.CompactStringStorage
 
toString() - Method in class com.chemaxon.overlap.io.MasterMoleculeStorage
 
toString() - Method in class com.chemaxon.overlap.io.MoleculeCallbacks.IndexToNameStoringCallback
 
toString() - Method in class com.chemaxon.overlap.io.PropertyCollectorCallback
 
toString() - Method in class com.chemaxon.overlap.io.StructureRecordImpl
 
toString() - Method in class com.chemaxon.overlap.KnnResultsImpl
 
toString(boolean) - Method in class com.chemaxon.overlap.OverlapAnalysisContext
Create String representation.
toString() - Method in class com.chemaxon.overlap.OverlapAnalysisContext
 
toString() - Method in class com.chemaxon.overlap.SimilarityResultImpl
 
toString() - Method in class com.chemaxon.overlap.SimilarityResultsImpl
 
toString() - Method in class com.chemaxon.overlap.storage.ProcessQueueItem
 
toString() - Method in class com.chemaxon.overlap.unguarded.ExtractFloatFp
 
toString() - Method in class com.chemaxon.overlap.unguarded.ExtractIntFp
 
toString() - Method in class com.chemaxon.overlap.unguarded.ExtractLongFp
 
toString() - Method in class com.chemaxon.overlap.unguarded.UnguardedBinaryIntManhattan
 
toString() - Method in class com.chemaxon.overlap.unguarded.UnguardedBinaryIntTanimoto
 
toString() - Method in class com.chemaxon.overlap.unguarded.UnguardedBinaryLongManhattan
 
toString() - Method in class com.chemaxon.overlap.unguarded.UnguardedBinaryLongTanimoto
 
toString() - Method in class com.chemaxon.overlap.unguarded.UnguardedBinaryLongTversky
 
toString() - Method in class com.chemaxon.overlap.unguarded.UnguardedFloatVectorEuclidSqr
 
toString() - Method in class com.chemaxon.overlap.unguarded.UnguardedFloatVectorManhattan
 
toString() - Method in class com.chemaxon.overlap.unguarded.UnguardedFloatVectorMaxDiff
 
toString() - Method in class com.chemaxon.overlap.unguarded.UnguardedFloatVectorTanimoto
 
toStrings(int, boolean) - Method in class com.chemaxon.calculations.util.Histo
Create a String representation.
toStrings() - Method in class com.chemaxon.calculations.util.Histo
 
toStrings(PrintStream, SubProgressObserver) - Method in class com.chemaxon.overlap.io.MoleculeCallbacks.IndexToNameStoringCallback
Print index to name associations into escaped strings.
toStrings(PrintStream, SubProgressObserver) - Method in class com.chemaxon.overlap.storage.PagedDescriptorStorage
Write String representations to a PrintStream.
toStrings(PrintStream, SubProgressObserver, ExecutorService) - Method in class com.chemaxon.overlap.storage.PagedDescriptorStorage
Write String representations to a PrintStream using concurrent conversions.
totalPagesSize - Variable in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap.SearchMostSimilars
Number of total pages size.
transformMolecules(List<Molecule>, SubProgressObserver) - Method in class com.chemaxon.overlap.OverlapAnalysisContext
Transform molecules according to the represented context.
transformPage(Function<D, T>, List<D>) - Static method in class com.chemaxon.overlap.unguarded.Unguardeds
Transform a page of descriptors to unguarded form.
traverse(UnguardedVisitor<T>, SubProgressObserver) - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Traverse storage on single thread.

U

unfreeze() - Method in class com.chemaxon.overlap.concurrent.BppManager
 
unfreeze() - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean
Unfreeze worker.
unguarded(Function<D, N>, UnguardedDissimilarityCalculator<N>) - Method in class com.chemaxon.overlap.OverlapAnalysisContext
Update represented unguarded layer.
UnguardedBinaryIntManhattan - Class in com.chemaxon.overlap.unguarded
Unguarded Manhattan comparator for binary fingerprints represented as int [].
UnguardedBinaryIntManhattan() - Constructor for class com.chemaxon.overlap.unguarded.UnguardedBinaryIntManhattan
 
UnguardedBinaryIntTanimoto - Class in com.chemaxon.overlap.unguarded
Unguarded Tanimoto comparator for binary fingerprints represented as int [].
UnguardedBinaryIntTanimoto() - Constructor for class com.chemaxon.overlap.unguarded.UnguardedBinaryIntTanimoto
 
UnguardedBinaryLongManhattan - Class in com.chemaxon.overlap.unguarded
Unguarded Manhattan comparator for binary fingerprints represented as long [].
UnguardedBinaryLongManhattan() - Constructor for class com.chemaxon.overlap.unguarded.UnguardedBinaryLongManhattan
 
UnguardedBinaryLongTanimoto - Class in com.chemaxon.overlap.unguarded
Unguarded Tanimoto comparator for binary fingerprints represented as long [].
UnguardedBinaryLongTanimoto() - Constructor for class com.chemaxon.overlap.unguarded.UnguardedBinaryLongTanimoto
 
UnguardedBinaryLongTversky - Class in com.chemaxon.overlap.unguarded
Parametrized Tversky comparator for binary fingerprints represented as long [].
UnguardedBinaryLongTversky(double, double) - Constructor for class com.chemaxon.overlap.unguarded.UnguardedBinaryLongTversky
Construct new instance.
UnguardedDissimilarityCalculator<T> - Interface in com.chemaxon.overlap.unguarded
Unguarded dissimilarity calculator.
UnguardedFloatVectorEuclidSqr - Class in com.chemaxon.overlap.unguarded
Unguarded square of euclidean comparator for float[] vectors.
UnguardedFloatVectorEuclidSqr() - Constructor for class com.chemaxon.overlap.unguarded.UnguardedFloatVectorEuclidSqr
 
UnguardedFloatVectorManhattan - Class in com.chemaxon.overlap.unguarded
Unguarded manhattan dissimilarity for float[] vectors.
UnguardedFloatVectorManhattan() - Constructor for class com.chemaxon.overlap.unguarded.UnguardedFloatVectorManhattan
 
UnguardedFloatVectorMaxDiff - Class in com.chemaxon.overlap.unguarded
Unguarded maximum diff dissimilarity for float[] vectors.
UnguardedFloatVectorMaxDiff() - Constructor for class com.chemaxon.overlap.unguarded.UnguardedFloatVectorMaxDiff
 
UnguardedFloatVectorTanimoto - Class in com.chemaxon.overlap.unguarded
Unguarded tanimoto-like comparator for non-negative float[] vectors.
UnguardedFloatVectorTanimoto() - Constructor for class com.chemaxon.overlap.unguarded.UnguardedFloatVectorTanimoto
 
UnguardedPagedOverlap<T extends Serializable> - Class in com.chemaxon.overlap.bruteforce
Brute force paged similarity search.
UnguardedPagedOverlap(UnguardedDissimilarityCalculator<T>, ImmutableList<ImmutableList<T>>, int) - Constructor for class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Construct new immutable reference from prepared storage.
UnguardedPagedOverlap(Function<D, T>, UnguardedDissimilarityCalculator<T>, List<ImmutableList<D>>, List<D>) - Constructor for class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Construct new immutable reference from pages of Descriptor instances.
UnguardedPagedOverlap.SearchMostSimilars<T> - Class in com.chemaxon.overlap.bruteforce
Search multiple pages for most n-most similar structures.
UnguardedPagedOverlap.SearchMostSimilars(UnguardedDissimilarityCalculator<T>, T, List<ImmutableList<T>>, int, int) - Constructor for class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap.SearchMostSimilars
Construct task
UnguardedPagedOverlap.SearchPage<T> - Class in com.chemaxon.overlap.bruteforce
Search one page of descriptors against a set of queries.
UnguardedPagedOverlap.SearchPage(UnguardedDissimilarityCalculator<T>, List<T>, List<T>, int) - Constructor for class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap.SearchPage
Construct.
Unguardeds - Class in com.chemaxon.overlap.unguarded
Utility methods related for unguarded descriptors.
UnguardedVisitor<T> - Interface in com.chemaxon.overlap.unguarded
Simple callback to traverse an unguarded storage.
Updater<D extends com.chemaxon.descriptors.common.Descriptor> - Interface in com.chemaxon.overlap.io
Updater allows the insertion of structures/descriptors to the similarity subsystem.
UTF8ENCODING - Static variable in class com.chemaxon.calculations.util.CmdlineUtils
UTF-8 encoding String literal.
Util - Class in com.chemaxon.overlap.io
IO related utilities.

V

valueOf(String) - Static method in enum com.chemaxon.calculations.util.CharLayout.HA
Returns the enum constant of this type with the specified name.
values() - Static method in enum com.chemaxon.calculations.util.CharLayout.HA
Returns an array containing the constants of this enum type, in the order they are declared.
visitDescriptor(int, T) - Method in interface com.chemaxon.overlap.unguarded.UnguardedVisitor
Visit a single descriptor.
visitDescriptors(int, List<T>) - Method in interface com.chemaxon.overlap.unguarded.UnguardedVisitor
Visit multiple descriptors.

W

withComparator(DescriptorComparator<D>) - Method in class com.chemaxon.overlap.bruteforce.BruteForcePagedSimilarity
Construct another BruteForcePagedSimilarity instance representing a different comparator.
withComparator(UnguardedDissimilarityCalculator<T>) - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Construct another BruteForcePagedSimilarity instance representing a different comparator.
worked(long, boolean) - Method in class com.chemaxon.calculations.common.ConsolePO
Report work unit completion.
worked(long) - Method in class com.chemaxon.calculations.common.ConsolePO
 
wrapComparator(DescriptorComparator<?>) - Static method in class com.chemaxon.overlap.unguarded.Unguardeds
Wrap a DescriptorComparator.
wrapGenerator(DescriptorGenerator<D>) - Static method in class com.chemaxon.overlap.unguarded.Unguardeds
Wrap a DescriptorGenerator as an unguarded extractor Function.

X

xmlConfig(String) - Method in class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfParameters.Builder
Sets configuration xml string.
xmlConfig(Optional<String>) - Method in class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfParameters.Builder
Sets configuration xml string.

A B C D E F G H I J K L M N O P Q R S T U V W X

jklustor-overlap-0.0.2-20140619012940 (ChemAxon)