de.mpg.biochem.mars.molecule

Class DnaMoleculeArchive

java.lang.Object

de.mpg.biochem.mars.molecule.AbstractJsonConvertibleRecord

de.mpg.biochem.mars.molecule.AbstractMoleculeArchive<DnaMolecule,MarsOMEMetadata,DnaMoleculeArchiveProperties,DnaMoleculeArchiveIndex>

de.mpg.biochem.mars.molecule.DnaMoleculeArchive

All Implemented Interfaces:

JsonConvertibleRecord, MoleculeArchive<DnaMolecule,MarsOMEMetadata,DnaMoleculeArchiveProperties,DnaMoleculeArchiveIndex>

public class DnaMoleculeArchive
extends AbstractMoleculeArchive<DnaMolecule,MarsOMEMetadata,DnaMoleculeArchiveProperties,DnaMoleculeArchiveIndex>

Field Summary

Fields inherited from class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive

archiveIndex, archiveProperties, jFactory, metadataMap, moleculeMap, name, recordLocks, smileEncoding, source, virtual, win

Constructor Summary

Constructors

Constructor and Description
DnaMoleculeArchive(java.io.File file)
DnaMoleculeArchive(MoleculeArchiveSource source) Constructor for loading a MoleculeArchive from a MoleculeArchiveSource.
DnaMoleculeArchive(java.lang.String name)
DnaMoleculeArchive(java.lang.String name, java.io.File file)
DnaMoleculeArchive(java.lang.String name, MarsTable table)
DnaMoleculeArchive(java.net.URI uri) Constructor for loading a MoleculeArchive.

Method Summary

Modifier and Type	Method and Description
DnaMoleculeArchiveIndex	createIndex() Create empty MoleculeArchiveIndex.
DnaMoleculeArchiveIndex	createIndex(com.fasterxml.jackson.core.JsonParser jParser) Create MoleculeArchiveIndex using JsonParser stream.
MarsOMEMetadata	createMetadata(com.fasterxml.jackson.core.JsonParser jParser) Create MarsOMEMetadata record using JsonParser stream.
MarsOMEMetadata	createMetadata(java.lang.String metaUID) Create empty MarsMetadata record with the metaUID specified.
DnaMolecule	createMolecule() Create empty Molecule record.
DnaMolecule	createMolecule(com.fasterxml.jackson.core.JsonParser jParser) Create Molecule record using the JsonParser stream given.
DnaMolecule	createMolecule(java.lang.String UID) Create empty Molecule record with the UID specified.
DnaMolecule	createMolecule(java.lang.String UID, MarsTable table) Create Molecule record using the UID and MarsTable specified.
DnaMoleculeArchiveProperties	createProperties() Create empty MoleculeArchiveProperties record.
DnaMoleculeArchiveProperties	createProperties(com.fasterxml.jackson.core.JsonParser jParser) Create MoleculeArchiveProperties record using JsonParser stream.

Methods inherited from class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive

addMoleculeTags, contains, containsMetadata, createIOMaps, deleteMetadatasWithTag, deleteMoleculesWithTag, detectEncoding, get, get, getChannel, getComments, getImage, getMetadata, getMetadata, getMetadataTagList, getMetadataTagSet, getMetadataUIDforMolecule, getMetadataUIDs, getMoleculeBatch, getMoleculeUIDs, getName, getNumberOfMetadatas, getNumberOfMolecules, getSource, getTagList, getTagSet, getWindow, isVirtual, load, loadVirtualStore, log, logln, metadata, metadataHasTag, moleculeHasNoTags, moleculeHasTag, moleculeHasTags, molecules, moleculeTags, parallelMetadata, parallelMolecules, properties, put, putMetadata, rebuildIndexes, rebuildIndexes, remove, remove, removeMetadata, removeMetadata, save, saveAs, saveAs, saveAsJson, saveAsJson, saveAsJsonVirtualStore, saveAsJsonVirtualStore, saveAsJsonVirtualStore, saveAsJsonVirtualStore, saveAsVirtualStore, saveAsVirtualStore, saveAsVirtualStore, saveAsVirtualStore, saveMetadataToSource, saveMoleculeToSource, setComments, setName, setWindow, toString

Methods inherited from class de.mpg.biochem.mars.molecule.AbstractJsonConvertibleRecord

dumpJSON, fromJSON, getJsonGenerator, getJsonParser, setJsonField, setShowWarnings, toJSON

Methods inherited from class java.lang.Object

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

Methods inherited from interface de.mpg.biochem.mars.molecule.JsonConvertibleRecord

dumpJSON, fromJSON, getJsonGenerator, getJsonParser, setJsonField, setShowWarnings, toJSON

Constructor Detail

DnaMoleculeArchive

public DnaMoleculeArchive(java.lang.String name)

DnaMoleculeArchive

public DnaMoleculeArchive(java.io.File file)
                   throws java.io.IOException

Throws:

java.io.IOException

DnaMoleculeArchive

public DnaMoleculeArchive(java.lang.String name,
                          MarsTable table)

DnaMoleculeArchive

public DnaMoleculeArchive(java.lang.String name,
                          java.io.File file)
                   throws java.io.IOException

Throws:

java.io.IOException

DnaMoleculeArchive

public DnaMoleculeArchive(java.net.URI uri)
                   throws java.io.IOException

Constructor for loading a MoleculeArchive. A yama file can be given or a yama virtual store directory. Virtual mode will automatically be activated if a directory is provided.

Parameters:

uri - The URI to load the archive from.

Throws:

java.io.IOException - if there is a problem with the file location.

DnaMoleculeArchive

public DnaMoleculeArchive(MoleculeArchiveSource source)
                   throws java.io.IOException

Constructor for loading a MoleculeArchive from a MoleculeArchiveSource.

Parameters:

source - The MoleculeArchiveSource to load the archive from.

Throws:

java.io.IOException - if there is a problem with the file location.

Method Detail

createProperties

public DnaMoleculeArchiveProperties createProperties()

Description copied from class: AbstractMoleculeArchive

Create empty MoleculeArchiveProperties record.

Specified by:

createProperties in interface MoleculeArchive<DnaMolecule,MarsOMEMetadata,DnaMoleculeArchiveProperties,DnaMoleculeArchiveIndex>

Specified by:

createProperties in class AbstractMoleculeArchive<DnaMolecule,MarsOMEMetadata,DnaMoleculeArchiveProperties,DnaMoleculeArchiveIndex>

Returns:

Empty MoleculeArchiveProperties.

createProperties

public DnaMoleculeArchiveProperties createProperties(com.fasterxml.jackson.core.JsonParser jParser)
                                              throws java.io.IOException

Description copied from class: AbstractMoleculeArchive

Create MoleculeArchiveProperties record using JsonParser stream.

Specified by:

createProperties in interface MoleculeArchive<DnaMolecule,MarsOMEMetadata,DnaMoleculeArchiveProperties,DnaMoleculeArchiveIndex>

Specified by:

createProperties in class AbstractMoleculeArchive<DnaMolecule,MarsOMEMetadata,DnaMoleculeArchiveProperties,DnaMoleculeArchiveIndex>

Parameters:

jParser - JsonParser to use to create archive properties.

Returns:

MoleculeArchiveProperties created.

Throws:

java.io.IOException - Thrown if unable to read Json from JsonParser stream.

createMetadata

public MarsOMEMetadata createMetadata(com.fasterxml.jackson.core.JsonParser jParser)
                               throws java.io.IOException

Create MarsOMEMetadata record using JsonParser stream.

Specified by:

createMetadata in interface MoleculeArchive<DnaMolecule,MarsOMEMetadata,DnaMoleculeArchiveProperties,DnaMoleculeArchiveIndex>

Specified by:

createMetadata in class AbstractMoleculeArchive<DnaMolecule,MarsOMEMetadata,DnaMoleculeArchiveProperties,DnaMoleculeArchiveIndex>

Parameters:

jParser - JsonParser to use to create metadata.

Returns:

MarsMetadata record created using JsonParser stream.

Throws:

java.io.IOException - Thrown if unable to read Json from JsonParser stream.

createMetadata

public MarsOMEMetadata createMetadata(java.lang.String metaUID)

Description copied from class: AbstractMoleculeArchive

Create empty MarsMetadata record with the metaUID specified.

Specified by:

createMetadata in interface MoleculeArchive<DnaMolecule,MarsOMEMetadata,DnaMoleculeArchiveProperties,DnaMoleculeArchiveIndex>

Specified by:

createMetadata in class AbstractMoleculeArchive<DnaMolecule,MarsOMEMetadata,DnaMoleculeArchiveProperties,DnaMoleculeArchiveIndex>

Parameters:

metaUID - The metaUID to use during creation of the empty MarsMetadata record.

Returns:

MarsMetadata record.

createMolecule

public DnaMolecule createMolecule()

Description copied from class: AbstractMoleculeArchive

Create empty Molecule record.

Specified by:

createMolecule in interface MoleculeArchive<DnaMolecule,MarsOMEMetadata,DnaMoleculeArchiveProperties,DnaMoleculeArchiveIndex>

Specified by:

createMolecule in class AbstractMoleculeArchive<DnaMolecule,MarsOMEMetadata,DnaMoleculeArchiveProperties,DnaMoleculeArchiveIndex>

Returns:

Empty molecule record.

createMolecule

public DnaMolecule createMolecule(com.fasterxml.jackson.core.JsonParser jParser)
                           throws java.io.IOException

Description copied from class: AbstractMoleculeArchive

Create Molecule record using the JsonParser stream given.

Specified by:

createMolecule in interface MoleculeArchive<DnaMolecule,MarsOMEMetadata,DnaMoleculeArchiveProperties,DnaMoleculeArchiveIndex>

Specified by:

createMolecule in class AbstractMoleculeArchive<DnaMolecule,MarsOMEMetadata,DnaMoleculeArchiveProperties,DnaMoleculeArchiveIndex>

Parameters:

jParser - JsonParser to use to create the molecule.

Returns:

Molecule created using the JsonParser stream.

Throws:

java.io.IOException - Thrown if unable to read Json from JsonParser stream.

createMolecule

public DnaMolecule createMolecule(java.lang.String UID)

Description copied from class: AbstractMoleculeArchive

Create empty Molecule record with the UID specified.

Specified by:

createMolecule in interface MoleculeArchive<DnaMolecule,MarsOMEMetadata,DnaMoleculeArchiveProperties,DnaMoleculeArchiveIndex>

Specified by:

createMolecule in class AbstractMoleculeArchive<DnaMolecule,MarsOMEMetadata,DnaMoleculeArchiveProperties,DnaMoleculeArchiveIndex>

Parameters:

UID - The UID to use during creation.

Returns:

Empty molecule with the UID given.

createMolecule

public DnaMolecule createMolecule(java.lang.String UID,
                                  MarsTable table)

Description copied from class: AbstractMoleculeArchive

Create Molecule record using the UID and MarsTable specified.

Specified by:

createMolecule in interface MoleculeArchive<DnaMolecule,MarsOMEMetadata,DnaMoleculeArchiveProperties,DnaMoleculeArchiveIndex>

Specified by:

createMolecule in class AbstractMoleculeArchive<DnaMolecule,MarsOMEMetadata,DnaMoleculeArchiveProperties,DnaMoleculeArchiveIndex>

Parameters:

UID - The UID to use during molecule creation.

table - The MarsTable set as the DataTable during creation.

Returns:

Molecule created.

createIndex

public DnaMoleculeArchiveIndex createIndex()

Description copied from class: AbstractMoleculeArchive

Create empty MoleculeArchiveIndex.

Specified by:

createIndex in interface MoleculeArchive<DnaMolecule,MarsOMEMetadata,DnaMoleculeArchiveProperties,DnaMoleculeArchiveIndex>

Specified by:

createIndex in class AbstractMoleculeArchive<DnaMolecule,MarsOMEMetadata,DnaMoleculeArchiveProperties,DnaMoleculeArchiveIndex>

Returns:

An empty MoleculeArchiveIndex.

createIndex

public DnaMoleculeArchiveIndex createIndex(com.fasterxml.jackson.core.JsonParser jParser)
                                    throws java.io.IOException

Description copied from class: AbstractMoleculeArchive

Create MoleculeArchiveIndex using JsonParser stream.

Specified by:

createIndex in interface MoleculeArchive<DnaMolecule,MarsOMEMetadata,DnaMoleculeArchiveProperties,DnaMoleculeArchiveIndex>

Specified by:

createIndex in class AbstractMoleculeArchive<DnaMolecule,MarsOMEMetadata,DnaMoleculeArchiveProperties,DnaMoleculeArchiveIndex>

Parameters:

jParser - JsonParser to use to create the MoleculeArchiveIndex.

Returns:

MoleculeArchiveIndex created using the JsonParser stream.

Throws:

java.io.IOException - Thrown if unable to read Json from JsonParser stream.