de.mpg.biochem.mars.molecule

Class SingleMoleculeArchive

java.lang.Object

de.mpg.biochem.mars.molecule.AbstractJsonConvertibleRecord

de.mpg.biochem.mars.molecule.AbstractMoleculeArchive<SingleMolecule,MarsOMEMetadata,SingleMoleculeArchiveProperties,SingleMoleculeArchiveIndex>

de.mpg.biochem.mars.molecule.SingleMoleculeArchive

All Implemented Interfaces:

JsonConvertibleRecord, MoleculeArchive<SingleMolecule,MarsOMEMetadata,SingleMoleculeArchiveProperties,SingleMoleculeArchiveIndex>

public class SingleMoleculeArchive
extends AbstractMoleculeArchive<SingleMolecule,MarsOMEMetadata,SingleMoleculeArchiveProperties,SingleMoleculeArchiveIndex>

Implementation of AbstractMoleculeArchive for default archives used for routine single molecule time-series datasets composed of SingleMolecule molecule records, MarsMetadata metadata records, and SingleMoleculeArchiveProperties archive properties.

For a more extensive explanation of uses and features of molecule archives see 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
SingleMoleculeArchive(java.io.File file) Constructor for loading a SingleMoleculeArchive.
SingleMoleculeArchive(MoleculeArchiveSource source) Constructor for loading a MoleculeArchive from a MoleculeArchiveSource.
SingleMoleculeArchive(java.lang.String name) Creates an empty SingleMoleculeArchive with the given name.
SingleMoleculeArchive(java.lang.String name, java.io.File file) Constructor for loading a SingleMoleculeArchive.
SingleMoleculeArchive(java.lang.String name, MarsTable table) Constructor for building a Molecule Archive from a MarsTable.
SingleMoleculeArchive(java.lang.String name, MarsTable table, java.lang.String indexColumnName) Constructor for building a molecule archive from a MarsTable.
SingleMoleculeArchive(java.net.URI uri) Constructor for loading a MoleculeArchive.

Method Summary

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

SingleMoleculeArchive

public SingleMoleculeArchive(java.lang.String name)

Creates an empty SingleMoleculeArchive with the given name.

Parameters:

name - Name of the empty SingleMoleculeArchive to create.

SingleMoleculeArchive

public SingleMoleculeArchive(java.io.File file)
                      throws java.io.IOException,
                             com.fasterxml.jackson.core.JsonParseException

Constructor for loading a SingleMoleculeArchive. 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:

com.fasterxml.jackson.core.JsonParseException - if there is a problem parsing the file provided.

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

SingleMoleculeArchive

public SingleMoleculeArchive(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.

SingleMoleculeArchive

public SingleMoleculeArchive(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.

SingleMoleculeArchive

public SingleMoleculeArchive(java.lang.String name,
                             java.io.File file)
                      throws com.fasterxml.jackson.core.JsonParseException,
                             java.io.IOException

Constructor for loading a SingleMoleculeArchive. 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:

com.fasterxml.jackson.core.JsonParseException - if there is a parsing exception.

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

SingleMoleculeArchive

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

Constructor for building a Molecule Archive from a MarsTable. The Molecule Archive will contain one Molecule record with the table provided.

Parameters:

name - The name of the archive.

table - A MarsTable to build the archive from.

SingleMoleculeArchive

public SingleMoleculeArchive(java.lang.String name,
                             MarsTable table,
                             java.lang.String indexColumnName)

Constructor for building a molecule archive from a MarsTable. The table provided must contain a column for the molecule index. The integer values in the index 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.

indexColumnName - Molecule index column.

Method Detail

createProperties

public SingleMoleculeArchiveProperties createProperties()

Create empty SingleMoleculeArchiveProperties record.

Specified by:

createProperties in interface MoleculeArchive<SingleMolecule,MarsOMEMetadata,SingleMoleculeArchiveProperties,SingleMoleculeArchiveIndex>

Specified by:

createProperties in class AbstractMoleculeArchive<SingleMolecule,MarsOMEMetadata,SingleMoleculeArchiveProperties,SingleMoleculeArchiveIndex>

Returns:

Empty MoleculeArchiveProperties.

createProperties

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

Create SingleMoleculeArchiveProperties record using JsonParser stream.

Specified by:

createProperties in interface MoleculeArchive<SingleMolecule,MarsOMEMetadata,SingleMoleculeArchiveProperties,SingleMoleculeArchiveIndex>

Specified by:

createProperties in class AbstractMoleculeArchive<SingleMolecule,MarsOMEMetadata,SingleMoleculeArchiveProperties,SingleMoleculeArchiveIndex>

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<SingleMolecule,MarsOMEMetadata,SingleMoleculeArchiveProperties,SingleMoleculeArchiveIndex>

Specified by:

createMetadata in class AbstractMoleculeArchive<SingleMolecule,MarsOMEMetadata,SingleMoleculeArchiveProperties,SingleMoleculeArchiveIndex>

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 MarsOMEMetadata record with the metaUID specified.

Specified by:

createMetadata in interface MoleculeArchive<SingleMolecule,MarsOMEMetadata,SingleMoleculeArchiveProperties,SingleMoleculeArchiveIndex>

Specified by:

createMetadata in class AbstractMoleculeArchive<SingleMolecule,MarsOMEMetadata,SingleMoleculeArchiveProperties,SingleMoleculeArchiveIndex>

Parameters:

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

Returns:

MarsMetadata record.

createMolecule

public SingleMolecule createMolecule()

Create empty SingleMolecule record.

Specified by:

createMolecule in interface MoleculeArchive<SingleMolecule,MarsOMEMetadata,SingleMoleculeArchiveProperties,SingleMoleculeArchiveIndex>

Specified by:

createMolecule in class AbstractMoleculeArchive<SingleMolecule,MarsOMEMetadata,SingleMoleculeArchiveProperties,SingleMoleculeArchiveIndex>

Returns:

Empty molecule record.

createMolecule

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

Create SingleMolecule record using the JsonParser stream given.

Specified by:

createMolecule in interface MoleculeArchive<SingleMolecule,MarsOMEMetadata,SingleMoleculeArchiveProperties,SingleMoleculeArchiveIndex>

Specified by:

createMolecule in class AbstractMoleculeArchive<SingleMolecule,MarsOMEMetadata,SingleMoleculeArchiveProperties,SingleMoleculeArchiveIndex>

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 SingleMolecule createMolecule(java.lang.String UID)

Create empty SingleMolecule record with the UID specified.

Specified by:

createMolecule in interface MoleculeArchive<SingleMolecule,MarsOMEMetadata,SingleMoleculeArchiveProperties,SingleMoleculeArchiveIndex>

Specified by:

createMolecule in class AbstractMoleculeArchive<SingleMolecule,MarsOMEMetadata,SingleMoleculeArchiveProperties,SingleMoleculeArchiveIndex>

Parameters:

UID - The UID to use during creation.

Returns:

Empty molecule with the UID given.

createMolecule

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

Create SingleMolecule record using the UID and MarsTable specified.

Specified by:

createMolecule in interface MoleculeArchive<SingleMolecule,MarsOMEMetadata,SingleMoleculeArchiveProperties,SingleMoleculeArchiveIndex>

Specified by:

createMolecule in class AbstractMoleculeArchive<SingleMolecule,MarsOMEMetadata,SingleMoleculeArchiveProperties,SingleMoleculeArchiveIndex>

Parameters:

UID - The UID to use during molecule creation.

table - The MarsTable set as the DataTable during creation.

Returns:

Molecule created.

createIndex

public SingleMoleculeArchiveIndex createIndex()

Description copied from class: AbstractMoleculeArchive

Create empty MoleculeArchiveIndex.

Specified by:

createIndex in interface MoleculeArchive<SingleMolecule,MarsOMEMetadata,SingleMoleculeArchiveProperties,SingleMoleculeArchiveIndex>

Specified by:

createIndex in class AbstractMoleculeArchive<SingleMolecule,MarsOMEMetadata,SingleMoleculeArchiveProperties,SingleMoleculeArchiveIndex>

Returns:

An empty MoleculeArchiveIndex.

createIndex

public SingleMoleculeArchiveIndex 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<SingleMolecule,MarsOMEMetadata,SingleMoleculeArchiveProperties,SingleMoleculeArchiveIndex>

Specified by:

createIndex in class AbstractMoleculeArchive<SingleMolecule,MarsOMEMetadata,SingleMoleculeArchiveProperties,SingleMoleculeArchiveIndex>

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.