com.chemaxon.overlap.io

Class MasterMoleculeStorageImpl

java.lang.Object

com.chemaxon.overlap.io.MasterMoleculeStorageImpl

All Implemented Interfaces:

MasterMoleculeStorage, MasterStorage<Molecule>, IndirectSerializable<MasterMoleculeStorage>, Serializable

public final class MasterMoleculeStorageImpl
extends Object
implements MasterMoleculeStorage

Master molecule storage is a space efficient storage for Molecules.

This class is immutable, thread safe and Serializable.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
MasterMoleculeStorageImpl(CompactStringStorage sources) Construct over valid sources.
MasterMoleculeStorageImpl(CompactStringStorage sources, String importOptsOrNull) Construct over valid sources.

Method Summary

Modifier and Type	Method and Description
static String	bestEffortConvert(Molecule mol) Convert Molecule to String multiple formats.
static MasterMoleculeStorageImpl	deserialize(ObjectInputStream ois, SubProgressObserver po) Deserialize from an object input stream.
Optional<Molecule>	get(int index) Get given structure identified with an index.
int	getAbsentCount() Number of absent structures.
Optional<String>	getSource(int index) Return given structure source as stored.
Class<Molecule>	getStoredType() Represented type.
boolean	isPresent(int index) Check if given entity is present.
void	serialize(ObjectOutputStream oos, SubProgressObserver po) Write into serialized format.
int	size() Number of structures in the storage.
String	toString()
void	writeIndirected(ObjectOutputStream oos, SubProgressObserver po) Write Deserializer conform representation.

Methods inherited from class java.lang.Object

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

Methods inherited from interface com.chemaxon.overlap.io.MasterStorage

areAllAbsent

Constructor Detail

MasterMoleculeStorageImpl

public MasterMoleculeStorageImpl(CompactStringStorage sources)

Construct over valid sources. The passed sources are expected to conform with MolImporter.importMol(java.lang.String).

Parameters:

sources - Sources to construct

MasterMoleculeStorageImpl

public MasterMoleculeStorageImpl(CompactStringStorage sources,
                                 String importOptsOrNull)

Construct over valid sources. The passed sources are expected to conform with MolImporter.importMol(java.lang.String).

Parameters:

sources - Sources to construct

importOptsOrNull - Options to pass to MolImporter.importMol(java.lang.String, java.lang.String).

Method Detail

getStoredType

public Class<Molecule> getStoredType()

Description copied from interface: MasterStorage

Represented type.

Specified by:

getStoredType in interface MasterStorage<Molecule>

Returns:

represented type

size

public int size()

Description copied from interface: MasterStorage

Number of structures in the storage.

Specified by:

size in interface MasterStorage<Molecule>

Returns:

Number of structures in the storage

getAbsentCount

public int getAbsentCount()

Description copied from interface: MasterStorage

Number of absent structures.

Specified by:

getAbsentCount in interface MasterStorage<Molecule>

Returns:

Number of absent structures.

get

public Optional<Molecule> get(int index)

Description copied from interface: MasterStorage

Get given structure identified with an index.

Specified by:

get in interface MasterStorage<Molecule>

Parameters:

index - Structure index

Returns:

Structure if present

bestEffortConvert

public static String bestEffortConvert(Molecule mol)

Convert Molecule to String multiple formats.

Parameters:

mol - Molecule to represent

Returns:

First format structure possible to represent

Throws:

IllegalArgumentException - When none of the formats were applicable

toString

public String toString()

Overrides:

toString in class Object

serialize

public void serialize(ObjectOutputStream oos,
                      SubProgressObserver po)
               throws IOException

Write into serialized format.

Parameters:

oos - Stream to write to

po - Progress observer to track progress. Work units reflect non-skipped stored entities. Will be closed upon completion.

Throws:

IOException - re-thrown

deserialize

public static MasterMoleculeStorageImpl deserialize(ObjectInputStream ois,
                                                    SubProgressObserver po)
                                             throws IOException,
                                                    ClassNotFoundException

Deserialize from an object input stream.

Parameters:

ois - Stream to read from

po - Progress observer to track progress. Work units reflect non-skipped stored entities. Will be closed upon completion.

Returns:

deserialized instance

Throws:

IOException - propagated from underlying deserialization

ClassNotFoundException - propagated from underlying deserialization

getSource

public Optional<String> getSource(int index)
                           throws IndexOutOfBoundsException

Description copied from interface: MasterMoleculeStorage

Return given structure source as stored.

Specified by:

getSource in interface MasterMoleculeStorage

Parameters:

index - Structure index

Returns:

Structur source as stored if available.

Throws:

IndexOutOfBoundsException - in case of error

isPresent

public boolean isPresent(int index)
                  throws IndexOutOfBoundsException

Description copied from interface: MasterStorage

Check if given entity is present.

Specified by:

isPresent in interface MasterStorage<Molecule>

Parameters:

index - Structure index

Returns:

true when structure is present

Throws:

IndexOutOfBoundsException - when index is less than 0 or greater or equal than MasterStorage.size()

writeIndirected

public void writeIndirected(ObjectOutputStream oos,
                            SubProgressObserver po)
                     throws IOException

Description copied from interface: IndirectSerializable

Write Deserializer conform representation. First a Deserializer instance is written to the stream using ObjectOutputStream.writeObject(java.lang.Object). This instance is capable of deserializing the content written next.

Specified by:

writeIndirected in interface IndirectSerializable<MasterMoleculeStorage>

Parameters:

oos - Stream to write to

po - Observer to track progress; will be closed upon finishing

Throws:

IOException - delegated from underlying ObjectOutputStream accesses