Package chemaxon.standardizer.concurrent

Class StandardizerRunner

java.lang.Object

chemaxon.standardizer.concurrent.StandardizerRunner

@PublicAPI
public class StandardizerRunner
extends Object

Concurrent executor of the standardizer

Since:

6.0

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	StandardizerRunner.ErrorHandlingPolicy	Policy for error handling

Constructor Summary

Constructors

Constructor	Description
StandardizerRunner(Iterator<Molecule> input, StandardizerConfiguration configuration)	Deprecated. Won't be public in the future
StandardizerRunner(Iterator<Molecule> input, StandardizerConfiguration configuration, int threadCount)	Deprecated. Won't be public in the future
StandardizerRunner(Iterator<Molecule> input, StandardizerConfiguration configuration, int threadCount, String reportPropertyName)	Deprecated. Won't be public in the future

Method Summary

Modifier and Type	Method	Description
protected static Molecule	evaluate(StandardizerRunner.ErrorHandlingPolicy policy, StandardizerResult result)
static Iterator<Molecule>	iterator(Iterator<Molecule> iterator, StandardizerConfiguration configuration, int threadCount, StandardizerRunner.ErrorHandlingPolicy policy, String reportPropertyName)	Returns an iterator that will wrap the specified iterator and standardizes all molecules.
static Iterator<StandardizerResult>	resultIterator(Iterator<Molecule> iterator, StandardizerConfiguration configuration, int threadCount, String reportPropertyName)	Returns an iterator that will wrap the specified iterator and standardizes all molecules.
static Iterator<StandardizerResult>	resultIterator(Iterator<Molecule> iterator, StandardizerConfiguration configuration, int threadCount, String reportPropertyName, boolean saveChangeList)	Returns an iterator that will wrap the specified iterator and standardizes all molecules.
static void	standardize(MolImporter importer, MolExporter exporter, StandardizerConfiguration configuration, int threadCount, StandardizerRunner.ErrorHandlingPolicy policy, String reportPropertyName)	Reads the molecules from the importer, standardizes them, and writes to the exporter.

Methods inherited from class java.lang.Object

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

Constructor Detail

StandardizerRunner

@Deprecated
public StandardizerRunner(Iterator<Molecule> input,
                          StandardizerConfiguration configuration)

Deprecated.

Won't be public in the future

Constructs a parallel standardizer runner based on the available processor number.

Parameters:

input - the input molecule iterator

configuration - the standardizer configuration to apply concurrently

StandardizerRunner

@Deprecated
public StandardizerRunner(Iterator<Molecule> input,
                          StandardizerConfiguration configuration,
                          int threadCount)

Deprecated.

Won't be public in the future

Constructs a parallel standardizer runner that will use specified number of threads for standardization.

Parameters:

input - the input molecule iterator

configuration - the standardizer configuration to apply concurrently

threadCount - the number of standardizer threads

StandardizerRunner

@Deprecated
public StandardizerRunner(Iterator<Molecule> input,
                          StandardizerConfiguration configuration,
                          int threadCount,
                          String reportPropertyName)

Deprecated.

Won't be public in the future

Constructs a parallel standardizer runner that will use specified number of threads for standardization.

Parameters:

input - the input molecule iterator

configuration - the standardizer configuration to apply concurrently

threadCount - the number of standardizer threads

reportPropertyName - the property name to report the applied actions to

Method Detail

iterator

public static Iterator<Molecule> iterator(Iterator<Molecule> iterator,
                                          StandardizerConfiguration configuration,
                                          int threadCount,
                                          StandardizerRunner.ErrorHandlingPolicy policy,
                                          String reportPropertyName)

Returns an iterator that will wrap the specified iterator and standardizes all molecules.
IMPORTANT NOTE: in case of StandardizerRunner.ErrorHandlingPolicy.HALT the method Iterator.next() of the resulted molecule iterator may throw IllegalArgumentException, if exception occurred during standardization. The thrown exception wraps the original exception.
NOTE: the returned iterator not supports Iterator.remove().

Parameters:

iterator - the iterator containing the molecules to be standardized

configuration - the configuration to apply on the iterator

threadCount - the number of threads to use for standardization

policy - the error handling policy

reportPropertyName - the name of the property to report applied standardizer actions to

Returns:

an iterator that iterates through the standardized molecules of the original iterator

resultIterator

public static Iterator<StandardizerResult> resultIterator(Iterator<Molecule> iterator,
                                                          StandardizerConfiguration configuration,
                                                          int threadCount,
                                                          String reportPropertyName)

Returns an iterator that will wrap the specified iterator and standardizes all molecules. NOTE: the returned iterator not supports Iterator.remove().

Parameters:

iterator - the iterator to wrap

configuration - the configuration to apply on the iterator

threadCount - the number of threads to use for standardization

reportPropertyName - the name of the property to report applied standardizer actions to

Returns:

an iterator that iterates through the standardization results of the original iterator

resultIterator

public static Iterator<StandardizerResult> resultIterator(Iterator<Molecule> iterator,
                                                          StandardizerConfiguration configuration,
                                                          int threadCount,
                                                          String reportPropertyName,
                                                          boolean saveChangeList)

Returns an iterator that will wrap the specified iterator and standardizes all molecules. NOTE: the returned iterator does not support Iterator.remove().

Parameters:

iterator - the iterator to wrap

configuration - the configuration to apply on the iterator

threadCount - the number of threads to use for standardization

reportPropertyName - the name of the property to report applied standardizer actions to

saveChangeList - sets to save the molecule modifications of each performed standardizer action; if true then the changes will be saved

Returns:

an iterator that iterates through the standardization results of the original iterator

Since:

JChem 6.4

standardize

public static void standardize(MolImporter importer,
                               MolExporter exporter,
                               StandardizerConfiguration configuration,
                               int threadCount,
                               StandardizerRunner.ErrorHandlingPolicy policy,
                               String reportPropertyName)
                        throws MolExportException,
                               IOException

Reads the molecules from the importer, standardizes them, and writes to the exporter.

Parameters:

importer - the importer to read molecules from

exporter - the exporter to write standardized molecules to

configuration - the configuration to be applied on the molecules

threadCount - the number of threads to use for standardization

policy - the error handling policy

reportPropertyName - the name of the property to report applied standardizer actions to

Throws:

MolExportException - on export failure

IOException - on export failure

evaluate

protected static Molecule evaluate(StandardizerRunner.ErrorHandlingPolicy policy,
                                   StandardizerResult result)
                            throws Exception

Throws:

Exception