de.mpg.biochem.mars.molecule

Class DefaultMoleculeArchive

java.lang.Object

de.mpg.biochem.mars.molecule.AbstractJsonConvertibleRecord

de.mpg.biochem.mars.molecule.AbstractMoleculeArchive<DefaultMolecule,MarsOMEMetadata,DefaultMoleculeArchiveProperties,DefaultMoleculeArchiveIndex>

de.mpg.biochem.mars.molecule.DefaultMoleculeArchive

All Implemented Interfaces:

JsonConvertibleRecord, MoleculeArchive<DefaultMolecule,MarsOMEMetadata,DefaultMoleculeArchiveProperties,DefaultMoleculeArchiveIndex>

public class DefaultMoleculeArchive
extends AbstractMoleculeArchive<DefaultMolecule,MarsOMEMetadata,DefaultMoleculeArchiveProperties,DefaultMoleculeArchiveIndex>

Default implementation of AbstractMoleculeArchive.

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
DefaultMoleculeArchive(java.io.File file) Constructor for loading a MoleculeArchive.
DefaultMoleculeArchive(MoleculeArchiveSource source) Constructor for loading a MoleculeArchive from a MoleculeArchiveSource.
DefaultMoleculeArchive(java.lang.String name) Creates an empty DefaultMoleculeArchive with the given name.
DefaultMoleculeArchive(java.lang.String name, java.io.File file) Constructor for loading a MoleculeArchive.
DefaultMoleculeArchive(java.lang.String name, MarsTable table) Constructor for building a molecule archive from a MarsTable.
DefaultMoleculeArchive(java.net.URI uri) Constructor for loading a MoleculeArchive.

Method Summary

Modifier and Type	Method and Description
DefaultMoleculeArchiveIndex	createIndex() Create empty MoleculeArchiveIndex.
DefaultMoleculeArchiveIndex	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 DefaultMarsImageMetadata record with the metaUID specified.
DefaultMolecule	createMolecule() Create empty DefaultMolecule record.
DefaultMolecule	createMolecule(com.fasterxml.jackson.core.JsonParser jParser) Create DefaultMolecule record using the JsonParser stream given.
DefaultMolecule	createMolecule(java.lang.String UID) Create empty DefaultMolecule record with the UID specified.
DefaultMolecule	createMolecule(java.lang.String UID, MarsTable table) Create DefaultMolecule record using the UID and MarsTable specified.
DefaultMoleculeArchiveProperties	createProperties() Create empty DefaultMoleculeArchiveProperties record.
DefaultMoleculeArchiveProperties	createProperties(com.fasterxml.jackson.core.JsonParser jParser) Create DefaultMoleculeArchiveProperties 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

DefaultMoleculeArchive

public DefaultMoleculeArchive(java.lang.String name)

Creates an empty DefaultMoleculeArchive with the given name.

Parameters:

name - Name of the empty DefaultMoleculeArchive to create.

DefaultMoleculeArchive

public DefaultMoleculeArchive(java.io.File file)
                       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.

MoleculeArchives should typically be opened using the ImportVirtualStoreCommand, which automatically detect the type and open the archive accordingly.

Parameters:

file - The file or directory to load the archive from.

Throws:

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

DefaultMoleculeArchive

public DefaultMoleculeArchive(java.lang.String name,
                              java.io.File file)
                       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. If the MoleculeArchiveService is provided the statusService will be retrieved and when working in Fiji the progress shows up in the bar as molecule records are loaded.

MoleculeArchives should typically be opened using the ImportVirtualStoreCommand, which automatically detect the type and open the archive accordingly.

Parameters:

name - The name of the archive.

file - The file or directory to load the archive from.

Throws:

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

DefaultMoleculeArchive

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

Constructor for building a molecule archive from a MarsTable. The table provided must contain a molecule column. The integer values in the molecule column determine the grouping for creation of molecule records. Status will be reported during processing by retrieving the StatusService from the MoleculeArchiveService instance.

Parameters:

name - The name of the archive.

table - A MarsTable to build the archive from.

DefaultMoleculeArchive

public DefaultMoleculeArchive(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.

DefaultMoleculeArchive

public DefaultMoleculeArchive(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 DefaultMoleculeArchiveProperties createProperties()

Create empty DefaultMoleculeArchiveProperties record.

Specified by:

createProperties in interface MoleculeArchive<DefaultMolecule,MarsOMEMetadata,DefaultMoleculeArchiveProperties,DefaultMoleculeArchiveIndex>

Specified by:

createProperties in class AbstractMoleculeArchive<DefaultMolecule,MarsOMEMetadata,DefaultMoleculeArchiveProperties,DefaultMoleculeArchiveIndex>

Returns:

Empty MoleculeArchiveProperties.

createProperties

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

Create DefaultMoleculeArchiveProperties record using JsonParser stream.

Specified by:

createProperties in interface MoleculeArchive<DefaultMolecule,MarsOMEMetadata,DefaultMoleculeArchiveProperties,DefaultMoleculeArchiveIndex>

Specified by:

createProperties in class AbstractMoleculeArchive<DefaultMolecule,MarsOMEMetadata,DefaultMoleculeArchiveProperties,DefaultMoleculeArchiveIndex>

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<DefaultMolecule,MarsOMEMetadata,DefaultMoleculeArchiveProperties,DefaultMoleculeArchiveIndex>

Specified by:

createMetadata in class AbstractMoleculeArchive<DefaultMolecule,MarsOMEMetadata,DefaultMoleculeArchiveProperties,DefaultMoleculeArchiveIndex>

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)

Create empty DefaultMarsImageMetadata record with the metaUID specified.

Specified by:

createMetadata in interface MoleculeArchive<DefaultMolecule,MarsOMEMetadata,DefaultMoleculeArchiveProperties,DefaultMoleculeArchiveIndex>

Specified by:

createMetadata in class AbstractMoleculeArchive<DefaultMolecule,MarsOMEMetadata,DefaultMoleculeArchiveProperties,DefaultMoleculeArchiveIndex>

Parameters:

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

Returns:

MarsMetadata record.

createMolecule

public DefaultMolecule createMolecule()

Create empty DefaultMolecule record.

Specified by:

createMolecule in interface MoleculeArchive<DefaultMolecule,MarsOMEMetadata,DefaultMoleculeArchiveProperties,DefaultMoleculeArchiveIndex>

Specified by:

createMolecule in class AbstractMoleculeArchive<DefaultMolecule,MarsOMEMetadata,DefaultMoleculeArchiveProperties,DefaultMoleculeArchiveIndex>

Returns:

Empty molecule record.

createMolecule

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

Create DefaultMolecule record using the JsonParser stream given.

Specified by:

createMolecule in interface MoleculeArchive<DefaultMolecule,MarsOMEMetadata,DefaultMoleculeArchiveProperties,DefaultMoleculeArchiveIndex>

Specified by:

createMolecule in class AbstractMoleculeArchive<DefaultMolecule,MarsOMEMetadata,DefaultMoleculeArchiveProperties,DefaultMoleculeArchiveIndex>

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 DefaultMolecule createMolecule(java.lang.String UID)

Create empty DefaultMolecule record with the UID specified.

Specified by:

createMolecule in interface MoleculeArchive<DefaultMolecule,MarsOMEMetadata,DefaultMoleculeArchiveProperties,DefaultMoleculeArchiveIndex>

Specified by:

createMolecule in class AbstractMoleculeArchive<DefaultMolecule,MarsOMEMetadata,DefaultMoleculeArchiveProperties,DefaultMoleculeArchiveIndex>

Parameters:

UID - The UID to use during creation.

Returns:

Empty molecule with the UID given.

createMolecule

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

Create DefaultMolecule record using the UID and MarsTable specified.

Specified by:

createMolecule in interface MoleculeArchive<DefaultMolecule,MarsOMEMetadata,DefaultMoleculeArchiveProperties,DefaultMoleculeArchiveIndex>

Specified by:

createMolecule in class AbstractMoleculeArchive<DefaultMolecule,MarsOMEMetadata,DefaultMoleculeArchiveProperties,DefaultMoleculeArchiveIndex>

Parameters:

UID - The UID to use during molecule creation.

table - The MarsTable set as the DataTable during creation.

Returns:

Molecule created.

createIndex

public DefaultMoleculeArchiveIndex createIndex()

Description copied from class: AbstractMoleculeArchive

Create empty MoleculeArchiveIndex.

Specified by:

createIndex in interface MoleculeArchive<DefaultMolecule,MarsOMEMetadata,DefaultMoleculeArchiveProperties,DefaultMoleculeArchiveIndex>

Specified by:

createIndex in class AbstractMoleculeArchive<DefaultMolecule,MarsOMEMetadata,DefaultMoleculeArchiveProperties,DefaultMoleculeArchiveIndex>

Returns:

An empty MoleculeArchiveIndex.

createIndex

public DefaultMoleculeArchiveIndex 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<DefaultMolecule,MarsOMEMetadata,DefaultMoleculeArchiveProperties,DefaultMoleculeArchiveIndex>

Specified by:

createIndex in class AbstractMoleculeArchive<DefaultMolecule,MarsOMEMetadata,DefaultMoleculeArchiveProperties,DefaultMoleculeArchiveIndex>

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.