com.chemaxon.overlap.io

Class MasterStorages

java.lang.Object

com.chemaxon.overlap.io.MasterStorages

public final class MasterStorages
extends Object

Helper method for managing MasterStorages instances.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	MasterStorages.MasterStorageBuilder<T> Builder class for a master storage.
static class	MasterStorages.MoleculeCallbackBuilder Molecule callback based builder.

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_IMPORT_PAGESIZE Page size to use on import.
static int	MAX_QUEUE_SIZE Max queue size for import.

Method Summary

Modifier and Type	Method and Description
static MasterMoleculeStorage	allAbsentMasterMoleculeStorage(int size) All absent MMS.
static <T extends Serializable> MasterStorages.MasterStorageBuilder<T>	createArrayStoreBuilder(Class<T> elements) Create a generic array storage builder.
static MasterStorages.MasterStorageBuilder<String>	createCompactStringStoreBuilder()
static MasterStorages.MasterStorageBuilder<Double>	createDoubleStoreBuilder()
static MasterStringStorage	createIndexToStringStorage(int size, String prefix, boolean pad) Create an master storage returning index as strings.
static MasterStorages.MasterStorageBuilder<Integer>	createIntStoreBuilder()
static MasterStorages.MasterStorageBuilder<Long>	createLongStoreBuilder()
static MasterStorages.MasterStorageBuilder<String>	createStringStoreBuilder() Create a String storage builder.
static MasterStorages.MasterStorageBuilder<String>	createStringStoreBuilder(int skip) Create a String storage builder.
static MasterMoleculeStorage	masterMoleculeStorageFromFile(InputStream is, String opts, int count, StandardizerWrapper standardizer, ExecutorService ex, SubProgressObserver po, List<? extends MoleculeCallback> mcb) Create storage from a strcuture file.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_IMPORT_PAGESIZE

public static final int DEFAULT_IMPORT_PAGESIZE

Page size to use on import.

See Also:

Constant Field Values

MAX_QUEUE_SIZE

public static final int MAX_QUEUE_SIZE

Max queue size for import.

See Also:

Constant Field Values

Method Detail

createStringStoreBuilder

public static MasterStorages.MasterStorageBuilder<String> createStringStoreBuilder(int skip)

Create a String storage builder.

Parameters:

skip - Initial skip count

Returns:

A String storage builder

createStringStoreBuilder

public static MasterStorages.MasterStorageBuilder<String> createStringStoreBuilder()

Create a String storage builder.

Returns:

A String storage builder

createArrayStoreBuilder

public static <T extends Serializable> MasterStorages.MasterStorageBuilder<T> createArrayStoreBuilder(Class<T> elements)

Create a generic array storage builder.

Type Parameters:

T - Element type

Parameters:

elements - Element type

Returns:

Builder

createIntStoreBuilder

public static MasterStorages.MasterStorageBuilder<Integer> createIntStoreBuilder()

createLongStoreBuilder

public static MasterStorages.MasterStorageBuilder<Long> createLongStoreBuilder()

createDoubleStoreBuilder

public static MasterStorages.MasterStorageBuilder<Double> createDoubleStoreBuilder()

createCompactStringStoreBuilder

public static MasterStorages.MasterStorageBuilder<String> createCompactStringStoreBuilder()

createIndexToStringStorage

public static MasterStringStorage createIndexToStringStorage(int size,
                                                             String prefix,
                                                             boolean pad)

Create an master storage returning index as strings.

Parameters:

size - Virtual size of storage

prefix - Prefix for returned strings

pad - pad numbers with '0' characters

Returns:

Master storage

allAbsentMasterMoleculeStorage

public static MasterMoleculeStorage allAbsentMasterMoleculeStorage(int size)

All absent MMS.

Parameters:

size - Virtual size

Returns:

MMS created

masterMoleculeStorageFromFile

public static MasterMoleculeStorage masterMoleculeStorageFromFile(InputStream is,
                                                                  String opts,
                                                                  int count,
                                                                  StandardizerWrapper standardizer,
                                                                  ExecutorService ex,
                                                                  SubProgressObserver po,
                                                                  List<? extends MoleculeCallback> mcb)

Create storage from a strcuture file.

This method blocks until completion. Passed stream and progress observer callback is accessed only from the calling thread.

Parameters:

is - InputStream to read from. Will not be closed upon completion/abort.

opts - Options to pass to underlying importer. Use empty string when no import option is used.

count - Max number of structures to input

standardizer - Standardizer to apply on imported structures

ex - ExecutorService to run parsing/converting

po - Observer to track progress. Will be closed by invoking ProgressObserver.done() upon completion/abortion

mcb - Callbacks to also report molecules or null

Returns:

Created master storage