com.chemaxon.overlap.io

Interface Updater<D extends Descriptor>

Type Parameters:

D - Represented descriptor

All Known Implementing Classes:

PagedDescriptorStorage

public interface Updater<D extends Descriptor>

Updater allows the insertion of structures/descriptors to the similarity subsystem.

An updater allows partially filled descriptor space in order to allow incremental/short updates.

Method Summary

Modifier and Type	Method and Description
void	addAll(InputStream is, String opts, int skipCount, int maxProcessCount, StandardizerWrapper standardizer, SubProgressObserver po, ExecutorService e, MoleculeCallback moleculeCallback) Read all molecules from a structure file into the similarity subsystem.
int	addDescriptor(D d) Add a single descriptor to the similarity subsystem.
int	addMolecule(Molecule m) Add a single molecule to the similarity subsystem.

Method Detail

addAll

void addAll(InputStream is,
            String opts,
            int skipCount,
            int maxProcessCount,
            StandardizerWrapper standardizer,
            SubProgressObserver po,
            ExecutorService e,
            MoleculeCallback moleculeCallback)

Read all molecules from a structure file into the similarity subsystem.

Consecutive members of a structure file have consecutive indexes associated. Usually first molecule in the file have index value 0 associated. To allow segmented reading, this method can be called multiple times to append additional structures.

Consistency considerations: the storage is left in a consistent state in case of the following abnormal or unexpected terminations:

• Cancellation through the supplied SubProgressObserver
• Error thrown from the supplied {@link MoleculeCallback
• Processing error from structures
• IO error from file reading (this kind of errors are re-thrown)

Notes on multithreading:

• This method blocks until the execution completes, aborts or fails
• File reading, accessing callbacks (Supplied progress observer, supplied moleculeCallback) is done on the calling thread.
• Molecule standardization and descriptor generation is executed using the supplied ExecutorService

TODO: shorten parameters list using a builder

Parameters:

is - Input stream to read from. Note that the stream is not closed when returning.

opts - Input options or null to pass to underlying MFileFormatUtil.createRecordReader(java.io.InputStream, java.lang.String)

skipCount - Skip given number of structures. Skipped structures are also reported to the given progress observer like ordinary processed structures, however they wont generate calls into the supplied MoleculeCallback.

maxProcessCount - Read at most given number of structures. Count starts after skipping structures.

standardizer - Standardizer to apply on molecules. See StandardizerWrappers for utility methods. Note that supplied wrapper must be thread safe.

po - ProgressObserver to track file read. Total reported work units are assigned to read and processed/skipped molecules count. The given observer

is closed

upon returning

e - ExecutorService to run descriptor generation for pages

moleculeCallback - Callback to report back assigned indexes/processing errors.

Throws:

IllegalArgumentException - When an IO error occurs during file reading or structure importing throws an exception

addMolecule

int addMolecule(Molecule m)

Add a single molecule to the similarity subsystem.

Note that the given molecule must be standardized before calling this method.

Parameters:

m - Molecule to be added

Returns:

Associated index of the structure

Throws:

IllegalArgumentException - in case of processing error. If exception thrown the storage is kept in a consistent state.

addDescriptor

int addDescriptor(D d)

Add a single descriptor to the similarity subsystem.

Note that descriptors have a compatibility related API contract (currently references returned by Descriptor#getDescriptorGenerator() must be equal for compatible descriptors) which must be satisfied by the passed descriptor.

Parameters:

d - Descriptor to be added

Returns:

Associated index of the represented structure

Throws:

IllegalArgumentException - when passed descriptor is not compatible. If exception thrown the storage is kept in a consistent state