Package org.rcsb.strucmotif.io

Class StructureDataProviderImpl

java.lang.Object

org.rcsb.strucmotif.io.StructureDataProviderImpl

All Implemented Interfaces:

StructureDataProvider

@Service
public class StructureDataProviderImpl
extends Object
implements StructureDataProvider

Default implementation of a structure data provider.

Constructor Summary

Constructors

Constructor	Description
StructureDataProviderImpl(StructureReader structureReader, StructureWriter structureWriter, MotifSearchConfig motifSearchConfig)	Construct a structure provider.

Method Summary

Modifier and Type	Method	Description
void	deleteRenumbered(String structureIdentifier)	Drop information on a renumbered structure.
InputStream	getOriginalInputStream(String structureIdentifier)	Acquire the input stream of an original structure.
void	initializeRenumberedStructureCache()	If `strucmotif.in-memory-strategy` is active: Initialize caching by reading all structures and keeping them in memory for fast access.
Structure	readFromInputStream(InputStream inputStream)	Read everything from an input stream.
Structure	readOriginal(String structureIdentifier)	Read a selected range from an original structure.
Structure	readRenumbered(String structureIdentifier)	Read a renumbered structure entirely.
Structure	readSome(String structureIdentifier)	Read some structure entirely.
void	writeRenumbered(String structureIdentifier, org.rcsb.cif.schema.mm.MmCifFile mmCifFile)	Write a renumbered structure.

Methods inherited from class java.lang.Object

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

Constructor Details

StructureDataProviderImpl

@Autowired
public StructureDataProviderImpl(StructureReader structureReader,
 StructureWriter structureWriter,
 MotifSearchConfig motifSearchConfig)

Construct a structure provider.

Parameters:

structureReader - the reader

structureWriter - the writer

motifSearchConfig - the config

Method Details

initializeRenumberedStructureCache

public void initializeRenumberedStructureCache()
                                        throws IOException

Description copied from interface: StructureDataProvider

If `strucmotif.in-memory-strategy` is active: Initialize caching by reading all structures and keeping them in memory for fast access.

Specified by:

initializeRenumberedStructureCache in interface StructureDataProvider

Throws:

IOException - reading of structure data failed

getOriginalInputStream

public InputStream getOriginalInputStream(String structureIdentifier)

Description copied from interface: StructureDataProvider

Acquire the input stream of an original structure.

Specified by:

getOriginalInputStream in interface StructureDataProvider

Parameters:

structureIdentifier - the structure identifier to read

Returns:

the corresponding input stream

readFromInputStream

public Structure readFromInputStream(InputStream inputStream)

Description copied from interface: StructureDataProvider

Read everything from an input stream.

Specified by:

readFromInputStream in interface StructureDataProvider

Parameters:

inputStream - the source of data, assumed to be following the mmCIF schema

Returns:

the corresponding Structure

readRenumbered

public Structure readRenumbered(String structureIdentifier)

Description copied from interface: StructureDataProvider

Read a renumbered structure entirely.

Specified by:

readRenumbered in interface StructureDataProvider

Parameters:

structureIdentifier - the structure to read

Returns:

the corresponding Structure

readOriginal

public Structure readOriginal(String structureIdentifier)

Description copied from interface: StructureDataProvider

Read a selected range from an original structure.

Specified by:

readOriginal in interface StructureDataProvider

Parameters:

structureIdentifier - the structure to read

Returns:

the corresponding Structure

readSome

public Structure readSome(String structureIdentifier)

Description copied from interface: StructureDataProvider

Read some structure entirely.

Specified by:

readSome in interface StructureDataProvider

Parameters:

structureIdentifier - the structure to read

Returns:

the corresponding Structure

writeRenumbered

public void writeRenumbered(String structureIdentifier,
 org.rcsb.cif.schema.mm.MmCifFile mmCifFile)

Description copied from interface: StructureDataProvider

Write a renumbered structure.

Specified by:

writeRenumbered in interface StructureDataProvider

Parameters:

structureIdentifier - the structure identifier to write

mmCifFile - the data source

deleteRenumbered

public void deleteRenumbered(String structureIdentifier)

Description copied from interface: StructureDataProvider

Drop information on a renumbered structure.

Specified by:

deleteRenumbered in interface StructureDataProvider

Parameters:

structureIdentifier - the structure identifier to remove