de.mpg.biochem.mars.molecule

Class AbstractMoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

java.lang.Object

de.mpg.biochem.mars.molecule.AbstractJsonConvertibleRecord

de.mpg.biochem.mars.molecule.AbstractMoleculeArchive<M,I,P,X>

Type Parameters:

M - Molecule type.

I - MarsMetadata type.

P - MoleculeArchiveProperties type.

All Implemented Interfaces:

JsonConvertibleRecord, MoleculeArchive<M,I,P,X>

Direct Known Subclasses:

DefaultMoleculeArchive, DnaMoleculeArchive, ObjectArchive, SingleMoleculeArchive

public abstract class AbstractMoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>
extends AbstractJsonConvertibleRecord
implements MoleculeArchive<M,I,P,X>

Abstract superclass for the primary storage structure of Mars datasets. MoleculeArchives provides an optimal structure for storing single-molecule time-series data. Time-series data for each molecule in a dataset are stored in the form of Molecule records, which may also contain calculated parameters, tags, notes, and kinetic change point segments. These records are assigned a UID string at the time of creation. This string provides universal molecule uniqueness throughout all datasets. MoleculeArchives contain a collection of molecule records associated with a given experimental condition or analysis pipeline.

MarsMetadata records containing data collection information are also stored in MoleculeArchives. They are identified using metaUID strings. Molecule records associated with a given data collection have a metaUID string linking them to the correct MarsMetadata record within the same MoleculeArchive. Global properties of the MoleculeArchive, including indexing, comments, etc.., are stored in a MoleculeArchiveProperties record also contained within the MoleculeArchive.

Multiple MoleculeArchives can easily be merged with all Molecule records preserving uniqueness due to their UIDs and unique MarsMetadata information. After a merge the archive will then have additional Molecule records and MarsMetadata records.

Most Molecule Archive methods support multithreaded applications. threads and get and put records simultaneously. Molecule Archives allows for virtual storage in which molecule and metadata records are stored as individual files within an archive folder. These records are loaded and saved as needed with only a few records residing in memory at any given time.

MoleculeArchives are generated by several Mars commands, including PeakTrackerCommand, MoleculeIntegratorMultiViewCommand and BuildArchiveFromTableCommand. Required input for all commands in the molecule package, including RegionDifferenceCalculatorCommand, VarianceCalculatorCommand, DriftCorrectorCommand as well as commands in the kcp package, including KCPCommand, and SigmaCalculatorCommand.

MoleculeArchives can be saved in json (or smile) format as a single file or in a virtual store using the saveAs(File) and saveAsVirtualStore(File) methods, respectively. These files and folders will have a .yama extension for Yet Another MoleculeArchive or .yama.store extension to indicate a virtual store. The files have a json or smile format with the .yama extension indicating they contain certain expected field names and value types.

MoleculeArchive of different types can be opened using the ImportVirtualStoreCommand. This import command will automatically detect the type and load the archive in accordingly.

MoleculeArchives can be loaded using the constructors AbstractMoleculeArchive(File) or AbstractMoleculeArchive(String, File). Otherwise, MoleculeArchives can be loaded using the Mars command ImportVirtualStoreCommand through the GUI or in scripts.

Field Summary

Fields

Modifier and Type	Field and Description
protected MoleculeArchiveIndex<M,I>	archiveIndex Record index used for virtual archives.
protected P	archiveProperties Archive properties.
protected com.fasterxml.jackson.core.JsonFactory	jFactory JsonFactory instance used.
protected java.util.concurrent.ConcurrentSkipListMap<java.lang.String,I>	metadataMap Map from metadata UID to MarsMetadata object.
protected java.util.concurrent.ConcurrentSkipListMap<java.lang.String,M>	moleculeMap Map from molecule UID to Molecule object.
protected java.lang.String	name
protected java.util.concurrent.ConcurrentMap<java.lang.String,java.util.concurrent.locks.ReentrantLock>	recordLocks Map from molecule UID to ReentrantLock to ensure thread blocking when accessing molecule files in virtual mode.
protected boolean	smileEncoding Encoding.
protected MoleculeArchiveSource	source The archive IO Source.
protected boolean	virtual Set to true if working from a virtual store.
protected MoleculeArchiveWindow	win

Constructor Summary

Constructors

Constructor and Description
AbstractMoleculeArchive(java.io.File file) Constructor for loading a MoleculeArchive.
AbstractMoleculeArchive(MoleculeArchiveSource source) Constructor for loading a MoleculeArchive from a MoleculeArchiveSource.
AbstractMoleculeArchive(java.lang.String name) Constructor for creating an empty MoleculeArchive.
AbstractMoleculeArchive(java.lang.String name, java.io.File file) Constructor for loading a MoleculeArchive.
AbstractMoleculeArchive(java.lang.String name, MarsTable table) Constructor for building a Molecule Archive from a MarsTable.
AbstractMoleculeArchive(java.lang.String name, MarsTable table, java.lang.String indexColumnName) Constructor for building a molecule archive from a MarsTable.
AbstractMoleculeArchive(java.net.URI uri) Constructor for loading a MoleculeArchive.

Method Summary

Modifier and Type	Method and Description
void	addMoleculeTags(java.util.Map<java.lang.String,java.lang.String> tagMap) Add tags to molecules using UID to tag map.
boolean	contains(java.lang.String UID) Used to check if there is a molecule record with the UID given.
boolean	containsMetadata(java.lang.String UID) Used to check if there is a MarsMetadata record with the UID given.
abstract X	createIndex() Create empty MoleculeArchiveIndex.
abstract X	createIndex(com.fasterxml.jackson.core.JsonParser jParser) Create MoleculeArchiveIndex using JsonParser stream.
protected void	createIOMaps() Must be implemented in subclasses to define how fields, objects, arrays should be saved based on the Jackson streaming API.
abstract I	createMetadata(com.fasterxml.jackson.core.JsonParser jParser) Create MarsMetadata record using JsonParser stream.
abstract I	createMetadata(java.lang.String metaUID) Create empty MarsMetadata record with the metaUID specified.
abstract M	createMolecule() Create empty Molecule record.
abstract M	createMolecule(com.fasterxml.jackson.core.JsonParser jParser) Create Molecule record using the JsonParser stream given.
abstract M	createMolecule(java.lang.String UID) Create empty Molecule record with the UID specified.
abstract M	createMolecule(java.lang.String UID, MarsTable table) Create Molecule record using the UID and MarsTable specified.
abstract P	createProperties() Create empty MoleculeArchiveProperties record.
abstract P	createProperties(com.fasterxml.jackson.core.JsonParser jParser) Create MoleculeArchiveProperties record using JsonParser stream.
void	deleteMetadatasWithTag(java.lang.String tag) Removes all MarsMetadata records with the tag provided.
void	deleteMoleculesWithTag(java.lang.String tag) Removes all molecule records with the tag provided.
protected com.fasterxml.jackson.core.JsonParser	detectEncoding(java.io.InputStream inputStream)
M	get(int index) Retrieves the molecule record at the provided index.
M	get(java.lang.String UID) Get the molecule record with the given UID.
int	getChannel(java.lang.String UID) Channel for the molecule with the given UID.
java.lang.String	getComments() Global comments.
int	getImage(java.lang.String UID) Image index for the molecule with the given UID.
I	getMetadata(int index) Retrieves an MarsMetadata record.
I	getMetadata(java.lang.String metaUID) Retrieves a MarsMetadata record.
java.lang.String	getMetadataTagList(java.lang.String UID) Comma separated list of tags for the MarsMetadata record with the given UID.
java.util.Set<java.lang.String>	getMetadataTagSet(java.lang.String UID) Tags for the MarsMetadata record with the given UID.
java.lang.String	getMetadataUIDforMolecule(java.lang.String UID) Get the UID of the metadata for a molecule record.
java.util.List<java.lang.String>	getMetadataUIDs() Retrieves the list of UIDs of all MarsMetadata records.
java.util.List<double[][]>	getMoleculeBatch(java.util.List<java.lang.String> UIDs, java.lang.String tColumn, java.lang.String signalColumn, int rangeStart, int rangeEnd, java.util.List<java.lang.String> tagsToLearn, int threads) Utility function to generate batches of molecules data in an optimal format for machine learning using keras.
java.util.List<java.lang.String>	getMoleculeUIDs() Retrieves the list of UIDs for all Molecule records.
java.lang.String	getName() Get the name of the archive.
int	getNumberOfMetadatas() Number of MarsMetadata records in the MoleculeArchive.
int	getNumberOfMolecules() Number of molecule records in the MoleculeArchive.
MoleculeArchiveSource	getSource() MoleculeArchiveSource backing the MoleculeArchive.
java.lang.String	getTagList(java.lang.String UID) Comma separated list of tags for the molecule with the given UID.
java.util.Set<java.lang.String>	getTagSet(java.lang.String UID) Tags for the molecule with the given UID.
MoleculeArchiveWindow	getWindow() Returns the MoleculeArchiveWindow holding this archive, if one exists.
boolean	isVirtual() True if the archive is virtual, false if not.
protected void	load(MoleculeArchiveSource source)
protected void	loadVirtualStore(MoleculeArchiveSource virtualSource)
void	log(java.lang.String message) Add a log message to all metadata records.
void	logln(java.lang.String message) Add a log message to all metadata records.
java.util.stream.Stream<I>	metadata() Convenience method to retrieve a metadata stream.
boolean	metadataHasTag(java.lang.String UID, java.lang.String tag) Check if a MarsMetadata record has a tag.
boolean	moleculeHasNoTags(java.lang.String UID) Check if a molecule record has a tag.
boolean	moleculeHasTag(java.lang.String UID, java.lang.String tag) Check if a molecule record has a tag.
boolean	moleculeHasTags(java.lang.String UID) Check if a molecule record has tags.
java.util.stream.Stream<M>	molecules() Convenience method to retrieve a Molecule stream.
java.util.Set<java.lang.String>	moleculeTags(java.lang.String UID) Retrieve the list of tags for a molecule.
java.util.stream.Stream<I>	parallelMetadata() Convenience method to retrieve a metadata stream.
java.util.stream.Stream<M>	parallelMolecules() Convenience method to retrieve a multithreaded Molecule stream.
P	properties() Get the MoleculeArchiveProperties which contain general information about the archive.
void	put(M molecule) Adds a molecule to the archive.
void	putMetadata(I metadata) Adds a metadata record to the archive.
void	rebuildIndexes() Rebuild all indexes by inspecting the contents of store directories.
void	rebuildIndexes(int nThreads) Rebuild all indexes by inspecting the contents of store directories.
void	remove(M molecule) Removes the molecule record provided.
void	remove(java.lang.String UID) Removes the molecule record with the given UID.
void	removeMetadata(I meta) The Metadata record given is removed from the archive.
void	removeMetadata(java.lang.String metaUID) The metadata record with the UID given is removed from the archive.
void	save() Saves the MoleculeArchive to the file from which it was opened.
java.io.File	saveAs(java.io.File file) Saves MoleculeArchive to the given file destination.
java.lang.String	saveAs(java.lang.String url) Saves MoleculeArchive to the given file destination.
java.io.File	saveAsJson(java.io.File file) Saves MoleculeArchive to the given file destination in json format.
java.lang.String	saveAsJson(java.lang.String url) Saves MoleculeArchive to the given file destination in json format.
java.io.File	saveAsJsonVirtualStore(java.io.File virtualDirectory) Creates the directory given and a virtual store inside with all files in json format with .json file extension.
java.io.File	saveAsJsonVirtualStore(java.io.File virtualDirectory, int nThreads) Creates the directory given and a virtual store inside with all files in json format with .json file extension.
java.lang.String	saveAsJsonVirtualStore(java.lang.String url) Creates the directory given and a virtual store inside with all files in json format with .json file extension.
java.lang.String	saveAsJsonVirtualStore(java.lang.String url, int nThreads) Creates the directory given and a virtual store inside with all files in json format with .json file extension.
java.io.File	saveAsVirtualStore(java.io.File virtualDirectory) Creates the directory given and a virtual store inside with all files in smile format with .sml file extension.
java.io.File	saveAsVirtualStore(java.io.File virtualDirectory, int nThreads) Creates the directory given and a virtual store inside with all files in smile format with .sml file extension.
java.lang.String	saveAsVirtualStore(java.lang.String url) Creates the directory given and a virtual store inside with all files in smile format with .sml file extension.
java.lang.String	saveAsVirtualStore(java.lang.String url, int nThreads) Creates the directory given and a virtual store inside with all files in smile format with .sml file extension.
protected void	saveMetadataToSource(MoleculeArchiveSource virtualSource, I metadata, com.fasterxml.jackson.core.JsonFactory jFactory) Saves a MarsMetadata record as a json file.
protected void	saveMoleculeToSource(MoleculeArchiveSource virtualSource, M molecule, com.fasterxml.jackson.core.JsonFactory jFactory) Saves a molecule record as a json file.
void	setComments(java.lang.String comments) Sets the global comments.
void	setName(java.lang.String name) Set the name of the archive.
void	setWindow(MoleculeArchiveWindow win) Set the window containing this archive.
java.lang.String	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

Field Detail

name

protected java.lang.String name

win

protected MoleculeArchiveWindow win

source

protected MoleculeArchiveSource source

The archive IO Source.

jFactory

protected com.fasterxml.jackson.core.JsonFactory jFactory

JsonFactory instance used. Can be either smile or json.

archiveProperties

protected P extends MoleculeArchiveProperties<M,I> archiveProperties

Archive properties.

archiveIndex

protected MoleculeArchiveIndex<M extends Molecule,I extends MarsMetadata> archiveIndex

Record index used for virtual archives.

metadataMap

protected java.util.concurrent.ConcurrentSkipListMap<java.lang.String,I extends MarsMetadata> metadataMap

Map from metadata UID to MarsMetadata object.

moleculeMap

protected java.util.concurrent.ConcurrentSkipListMap<java.lang.String,M extends Molecule> moleculeMap

Map from molecule UID to Molecule object.

recordLocks

protected java.util.concurrent.ConcurrentMap<java.lang.String,java.util.concurrent.locks.ReentrantLock> recordLocks

Map from molecule UID to ReentrantLock to ensure thread blocking when accessing molecule files in virtual mode.

virtual

protected final boolean virtual

Set to true if working from a virtual store.

smileEncoding

protected boolean smileEncoding

Encoding.

Constructor Detail

AbstractMoleculeArchive

public AbstractMoleculeArchive(java.lang.String name)

Constructor for creating an empty MoleculeArchive.

Parameters:

name - The name archive.

AbstractMoleculeArchive

public AbstractMoleculeArchive(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.

Parameters:

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

Throws:

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

AbstractMoleculeArchive

public AbstractMoleculeArchive(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.

AbstractMoleculeArchive

public AbstractMoleculeArchive(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.

AbstractMoleculeArchive

public AbstractMoleculeArchive(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.

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.

AbstractMoleculeArchive

public AbstractMoleculeArchive(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.

AbstractMoleculeArchive

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

Constructor for building a molecule archive from a MarsTable. The index column specified defines the rows that belong to each Molecule record using either unique numbering or id strings.

Parameters:

name - The name of the archive.

table - A MarsTable to build the archive from.

indexColumnName - Molecule index column.

Method Detail

detectEncoding

protected com.fasterxml.jackson.core.JsonParser detectEncoding(java.io.InputStream inputStream)
                                                        throws java.io.IOException

Throws:

java.io.IOException

loadVirtualStore

protected void loadVirtualStore(MoleculeArchiveSource virtualSource)
                         throws java.io.IOException

Throws:

java.io.IOException

load

protected void load(MoleculeArchiveSource source)
             throws java.io.IOException

Throws:

java.io.IOException

rebuildIndexes

public void rebuildIndexes()
                    throws java.io.IOException

Rebuild all indexes by inspecting the contents of store directories. Then save the new indexes to the indexes.json file in the store.

Specified by:

rebuildIndexes in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Throws:

java.io.IOException - if something goes wrong saving the indexes.

rebuildIndexes

public void rebuildIndexes(int nThreads)
                    throws java.io.IOException

Rebuild all indexes by inspecting the contents of store directories. Then save the new indexes to the indexes.json file in the store. Use the number of threads specified.

Specified by:

rebuildIndexes in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

nThreads - The thread count.

Throws:

java.io.IOException - if something goes wrong saving the indexes.

save

public void save()
          throws java.io.IOException

Saves the MoleculeArchive to the file from which it was opened.

Specified by:

save in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Throws:

java.io.IOException - if something goes wrong saving the data.

saveAs

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

Saves MoleculeArchive to the given file destination.

Specified by:

saveAs in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

file - a yama file destination. If the .yama is not present it will be added.

Returns:

File with correct extensions where archive was saved.

Throws:

java.io.IOException - if something goes wrong saving the data.

saveAs

public java.lang.String saveAs(java.lang.String url)
                        throws java.io.IOException

Saves MoleculeArchive to the given file destination.

Specified by:

saveAs in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

url - a url destination. If the .yama is not present it will be added.

Returns:

File with correct extensions where archive was saved.

Throws:

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

saveAsJson

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

Description copied from interface: MoleculeArchive

Saves MoleculeArchive to the given file destination in json format.

Specified by:

saveAsJson in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

file - a yama.json file destination. If the .yama.json is not present it will be added.

Returns:

File with correct extensions where archive was saved.

Throws:

java.io.IOException - if something goes wrong saving the data.

saveAsJson

public java.lang.String saveAsJson(java.lang.String url)
                            throws java.io.IOException

Description copied from interface: MoleculeArchive

Saves MoleculeArchive to the given file destination in json format.

Specified by:

saveAsJson in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

url - a yama.json file destination. If the .yama.json is not present it will be added.

Returns:

url with correct extensions where archive was saved.

Throws:

java.io.IOException - if something goes wrong saving the data.

createIOMaps

protected void createIOMaps()

Description copied from class: AbstractJsonConvertibleRecord

Must be implemented in subclasses to define how fields, objects, arrays should be saved based on the Jackson streaming API.

Specified by:

createIOMaps in class AbstractJsonConvertibleRecord

saveAsJsonVirtualStore

public java.io.File saveAsJsonVirtualStore(java.io.File virtualDirectory)
                                    throws java.io.IOException

Creates the directory given and a virtual store inside with all files in json format with .json file extension. Indexes are rebuilt while saving if the archive was loaded from a virtual store.

Specified by:

saveAsJsonVirtualStore in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

virtualDirectory - a directory destination for the virtual store.

Returns:

the directory where the store was saved.

Throws:

java.io.IOException - if something goes wrong creating the virtual store.

saveAsJsonVirtualStore

public java.lang.String saveAsJsonVirtualStore(java.lang.String url)
                                        throws java.io.IOException

Creates the directory given and a virtual store inside with all files in json format with .json file extension. Indexes are rebuilt while saving if the archive was loaded from a virtual store.

Specified by:

saveAsJsonVirtualStore in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

url - a url destination for the virtual store.

Returns:

the url where the store was saved.

Throws:

java.io.IOException - if something goes wrong creating the virtual store.

saveAsJsonVirtualStore

public java.lang.String saveAsJsonVirtualStore(java.lang.String url,
                                               int nThreads)
                                        throws java.io.IOException

Creates the directory given and a virtual store inside with all files in json format with .json file extension. Indexes are rebuilt while saving if the archive was loaded from a virtual store.

Specified by:

saveAsJsonVirtualStore in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

url - a url destination for the virtual store.

nThreads - The thread count.

Returns:

the url where the store was saved.

Throws:

java.io.IOException - if something goes wrong creating the virtual store.

saveAsJsonVirtualStore

public java.io.File saveAsJsonVirtualStore(java.io.File virtualDirectory,
                                           int nThreads)
                                    throws java.io.IOException

Creates the directory given and a virtual store inside with all files in json format with .json file extension. Indexes are rebuilt while saving * if the archive was loaded from a virtual store.

Specified by:

saveAsJsonVirtualStore in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

virtualDirectory - a directory destination for the virtual store.

nThreads - The thread count.

Returns:

the directory where the store was saved.

Throws:

java.io.IOException - if something goes wrong creating the virtual store.

saveAsVirtualStore

public java.io.File saveAsVirtualStore(java.io.File virtualDirectory)
                                throws java.io.IOException

Creates the directory given and a virtual store inside with all files in smile format with .sml file extension. This is the default format. Indexes are rebuilt while saving if the archive was loaded from a virtual store.

Specified by:

saveAsVirtualStore in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

virtualDirectory - a directory destination for the virtual store.

Returns:

the directory where the store was saved.

Throws:

java.io.IOException - if something goes wrong creating the virtual store.

saveAsVirtualStore

public java.lang.String saveAsVirtualStore(java.lang.String url)
                                    throws java.io.IOException

Creates the directory given and a virtual store inside with all files in smile format with .sml file extension. This is the default format. Indexes are rebuilt while saving if the archive was loaded from a virtual store.

Specified by:

saveAsVirtualStore in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

url - the destination for the virtual store.

Returns:

the directory where the store was saved.

Throws:

java.io.IOException - if something goes wrong creating the virtual store.

saveAsVirtualStore

public java.lang.String saveAsVirtualStore(java.lang.String url,
                                           int nThreads)
                                    throws java.io.IOException

Creates the directory given and a virtual store inside with all files in smile format with .sml file extension. This is the default format. Indexes are rebuilt while saving if the archive was loaded from a virtual store.

Specified by:

saveAsVirtualStore in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

url - the destination for the virtual store.

nThreads - The thread count.

Returns:

the directory where the store was saved.

Throws:

java.io.IOException - if something goes wrong creating the virtual store.

saveAsVirtualStore

public java.io.File saveAsVirtualStore(java.io.File virtualDirectory,
                                       int nThreads)
                                throws java.io.IOException

Creates the directory given and a virtual store inside with all files in smile format with .sml file extension. This is the default format. Indexes are rebuilt while saving if the archive was loaded from a virtual store.

Specified by:

saveAsVirtualStore in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

virtualDirectory - a directory destination for the virtual store.

nThreads - The thread count.

Returns:

the directory where the store was saved.

Throws:

java.io.IOException - if something goes wrong creating the virtual store.

put

public void put(M molecule)

Adds a molecule to the archive. If a molecule with the same UID is already in the archive, the record is updated. All indexes are updated with the properties of the molecule added.

Specified by:

put in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

molecule - a record to add or update.

putMetadata

public void putMetadata(I metadata)

Adds a metadata record to the archive. If a metadata record with the same UID is already in the archive, the record is updated. All indexes are updated with the properties of the metadata record added.

Specified by:

putMetadata in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

metadata - a metadata record to add or update.

removeMetadata

public void removeMetadata(java.lang.String metaUID)

The metadata record with the UID given is removed from the archive. All indexes are updated to reflect the change.

Specified by:

removeMetadata in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

metaUID - the UID of the metadata record to remove.

removeMetadata

public void removeMetadata(I meta)

The Metadata record given is removed from the archive. All indexes are updated to reflect the change.

Specified by:

removeMetadata in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

meta - Metadata record to remove.

getMetadata

public I getMetadata(int index)

Retrieves an MarsMetadata record.

Specified by:

getMetadata in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

index - The index of the MarsMetadata record to retrieve.

Returns:

A MarsMetadata record.

getMetadata

public I getMetadata(java.lang.String metaUID)

Retrieves a MarsMetadata record.

Specified by:

getMetadata in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

metaUID - The UID of the MarsMetadata record to retrieve.

Returns:

A MarsMetadata record.

getMetadataUIDs

public final java.util.List<java.lang.String> getMetadataUIDs()

Retrieves the list of UIDs of all MarsMetadata records. Useful for stream().forEach(...) operations.

Specified by:

getMetadataUIDs in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Returns:

The list of all MarsMetadata UIDs.

getNumberOfMolecules

public int getNumberOfMolecules()

Number of molecule records in the MoleculeArchive.

Specified by:

getNumberOfMolecules in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Returns:

The integer number of molecule records.

getNumberOfMetadatas

public int getNumberOfMetadatas()

Number of MarsMetadata records in the MoleculeArchive.

Specified by:

getNumberOfMetadatas in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Returns:

The integer number of MarsMetadata records.

getComments

public java.lang.String getComments()

Global comments.

Specified by:

getComments in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Returns:

The global comments String.

setComments

public void setComments(java.lang.String comments)

Sets the global comments. This replaces all current comments with those given.

Specified by:

setComments in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

comments - A string of global comments to set.

isVirtual

public boolean isVirtual()

True if the archive is virtual, false if not.

Specified by:

isVirtual in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Returns:

A boolean which is true if working from a virtual store.

get

public M get(int index)

Retrieves the molecule record at the provided index. Molecule records are stored in a map and not a List, so this method creates a new UID list every time it is called, reducing performance. The molecules() method and get(UID) methods offer better performance. If a list is required the getMoleculeUIDs() method should be used once and then the list can be iterated.

Specified by:

get in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

index - The integer index position of the molecule record.

Returns:

A Molecule record.

remove

public void remove(java.lang.String UID)

Removes the molecule record with the given UID.

Specified by:

remove in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

UID - The UID of the molecule record to remove.

remove

public void remove(M molecule)

Removes the molecule record provided.

Specified by:

remove in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

molecule - The molecule record to remove.

getMoleculeUIDs

public final java.util.List<java.lang.String> getMoleculeUIDs()

Retrieves the list of UIDs for all Molecule records. Useful for stream().forEach(...) operations.

Specified by:

getMoleculeUIDs in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Returns:

The list with all Molecule UIDs.

getTagList

public java.lang.String getTagList(java.lang.String UID)

Comma separated list of tags for the molecule with the given UID.

Specified by:

getTagList in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

UID - The UID of the molecule to retrieve the tag list for.

Returns:

A String containing a comma separated list of tags.

getTagSet

public java.util.Set<java.lang.String> getTagSet(java.lang.String UID)

Tags for the molecule with the given UID.

Specified by:

getTagSet in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

UID - The UID of the molecule to retrieve the tag set for.

Returns:

A set containing all tags for the given molecule.

getChannel

public int getChannel(java.lang.String UID)

Channel for the molecule with the given UID.

Specified by:

getChannel in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

UID - The UID of the molecule to retrieve the channel of.

Returns:

The channel index of the molecule in question.

getImage

public int getImage(java.lang.String UID)

Image index for the molecule with the given UID.

Specified by:

getImage in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

UID - The UID of the molecule to retrieve the image index of.

Returns:

The image index of the molecule in question.

getMetadataTagList

public java.lang.String getMetadataTagList(java.lang.String UID)

Comma separated list of tags for the MarsMetadata record with the given UID.

Specified by:

getMetadataTagList in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

UID - The UID of the MarsMetadata record to retrieve the tag list for.

Returns:

A String containing a comma separated list of tags.

getMetadataTagSet

public java.util.Set<java.lang.String> getMetadataTagSet(java.lang.String UID)

Tags for the MarsMetadata record with the given UID.

Specified by:

getMetadataTagSet in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

UID - The UID of the MarsMetadata record to retrieve the tag list for.

Returns:

The set of tags for the given MarsMetadata record.

getSource

public MoleculeArchiveSource getSource()

Description copied from interface: MoleculeArchive

MoleculeArchiveSource backing the MoleculeArchive.

Specified by:

getSource in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Returns:

MoleculeArchiveSource.

saveMoleculeToSource

protected void saveMoleculeToSource(MoleculeArchiveSource virtualSource,
                                    M molecule,
                                    com.fasterxml.jackson.core.JsonFactory jFactory)
                             throws java.io.IOException

Saves a molecule record as a json file.

Parameters:

virtualSource - The source to save the file to.

molecule - The molecule record to save.

jFactory - the JsonFactory to use when saving. Determines if smile or text encoding is used.

Throws:

java.io.IOException - if the molecule can't be saved to the file given.

saveMetadataToSource

protected void saveMetadataToSource(MoleculeArchiveSource virtualSource,
                                    I metadata,
                                    com.fasterxml.jackson.core.JsonFactory jFactory)
                             throws java.io.IOException

Saves a MarsMetadata record as a json file.

Parameters:

virtualSource - The source to save the file to.

metadata - The MarsMetadata record to save.

jFactory - the JsonFactory to use when saving. Determines if smile or text encoding is used.

Throws:

java.io.IOException - if the MarsMetadata can't be saved to the file given.

getMoleculeBatch

public java.util.List<double[][]> getMoleculeBatch(java.util.List<java.lang.String> UIDs,
                                                   java.lang.String tColumn,
                                                   java.lang.String signalColumn,
                                                   int rangeStart,
                                                   int rangeEnd,
                                                   java.util.List<java.lang.String> tagsToLearn,
                                                   int threads)

Utility function to generate batches of molecules data in an optimal format for machine learning using keras. Region goes from rangeStart to 1 - rangeEnd.

Specified by:

getMoleculeBatch in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

UIDs - The list of UIDs for the molecule to review data from.

tColumn - Name of the T column.

signalColumn - Name of the signal column.

rangeStart - Index of start of range in T column.

rangeEnd - Index of end of range in T column.

tagsToLearn - List of tags to use to build labels.

threads - Number of thread to use when building data.

Returns:

Returns batch of molecule data.

moleculeHasTag

public boolean moleculeHasTag(java.lang.String UID,
                              java.lang.String tag)

Check if a molecule record has a tag. This offers optimal performance for virtual mode because only the tag index is checked without retrieving all virtual records.

Specified by:

moleculeHasTag in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

UID - The UID of the molecule to check for the tag.

tag - The tag to check for.

Returns:

Returns true if the molecule has the tag and false if not.

moleculeHasNoTags

public boolean moleculeHasNoTags(java.lang.String UID)

Check if a molecule record has a tag. This offers optimal performance for virtual mode because only the tag index is checked without retrieving all virtual records.

Specified by:

moleculeHasNoTags in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

UID - The UID of the molecule to check for the tag.

Returns:

Returns true if the molecule has the tag and false if not.

moleculeTags

public java.util.Set<java.lang.String> moleculeTags(java.lang.String UID)

Retrieve the list of tags for a molecule. Will retrieve the list from the index if working in virtual memory.

Specified by:

moleculeTags in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

UID - The UID of the molecule to retrieve the tags of.

Returns:

Returns the set of for the molecule with UID.

moleculeHasTags

public boolean moleculeHasTags(java.lang.String UID)

Check if a molecule record has tags. This offers optimal performance for virtual mode because only the tag index is checked without retrieving all virtual records.

Specified by:

moleculeHasTags in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

UID - The UID of the molecule to check.

Returns:

Returns true if the molecule has tags and false if not.

metadataHasTag

public boolean metadataHasTag(java.lang.String UID,
                              java.lang.String tag)

Check if a MarsMetadata record has a tag. This offers optimal performance for virtual mode because only the tag index is checked without retrieving all virtual records.

Specified by:

metadataHasTag in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

UID - The UID of the MarsMetadata record to check for the tag.

tag - The tag to check for.

Returns:

Returns true if the MarsMetadata record has the tag and false if not.

addMoleculeTags

public void addMoleculeTags(java.util.Map<java.lang.String,java.lang.String> tagMap)

Add tags to molecules using UID to tag map. This offers optimal performance by using multiple threads. Provides a way to add tags resulting from machine learning using python. In virtual mode, this adds tags directly to the records as well as the index.

Specified by:

addMoleculeTags in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

tagMap - The UID to tag map for add to molecules.

deleteMoleculesWithTag

public void deleteMoleculesWithTag(java.lang.String tag)

Removes all molecule records with the tag provided.

Specified by:

deleteMoleculesWithTag in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

tag - Molecule records with this tag will be removed.

deleteMetadatasWithTag

public void deleteMetadatasWithTag(java.lang.String tag)

Removes all MarsMetadata records with the tag provided.

Specified by:

deleteMetadatasWithTag in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

tag - MarsMetadata records with this tag will be removed.

contains

public boolean contains(java.lang.String UID)

Used to check if there is a molecule record with the UID given.

Specified by:

contains in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

UID - Check for a molecule record with this UID.

Returns:

True if the archive contains the molecule record with the provided UID and false if not.

containsMetadata

public boolean containsMetadata(java.lang.String UID)

Used to check if there is a MarsMetadata record with the UID given.

Specified by:

containsMetadata in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

UID - Check for a MarsMetadata record with this UID.

Returns:

True if the archive contains a MarsMetadata record with the provided UID and false if not.

get

public M get(java.lang.String UID)

Get the molecule record with the given UID.

Specified by:

get in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

UID - The UID of the record to retrieve.

Returns:

The Molecule record with the UID given or null if none is located.

molecules

public java.util.stream.Stream<M> molecules()

Convenience method to retrieve a Molecule stream. Can be used to iterate over all molecules using forEach.

Specified by:

molecules in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Returns:

Molecule stream.

metadata

public java.util.stream.Stream<I> metadata()

Convenience method to retrieve a metadata stream. Can be used to iterate over all metadata using forEach.

Specified by:

metadata in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Returns:

Molecule stream.

parallelMetadata

public java.util.stream.Stream<I> parallelMetadata()

Convenience method to retrieve a metadata stream. Can be used to iterate over all metadata using forEach.

Specified by:

parallelMetadata in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Returns:

Molecule stream.

parallelMolecules

public java.util.stream.Stream<M> parallelMolecules()

Convenience method to retrieve a multithreaded Molecule stream. Can be used to iterate over all molecules using forEach in a multithreaded manner.

Specified by:

parallelMolecules in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Returns:

Molecule stream.

getMetadataUIDforMolecule

public java.lang.String getMetadataUIDforMolecule(java.lang.String UID)

Get the UID of the metadata for a molecule record. If working from a virtual store, this will use an index providing optimal performance. If working in memory this is the same as retrieving the molecule record and the metadata UID from it directly.

Specified by:

getMetadataUIDforMolecule in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

UID - The UID of the molecule to get the metadata UID for.

Returns:

The UID string of the metadata record corresponding to the molecule record whose UID was provided.

setName

public void setName(java.lang.String name)

Set the name of the archive.

Specified by:

setName in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

name - The new name of the archive.

getName

public java.lang.String getName()

Get the name of the archive.

Specified by:

getName in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Returns:

The String name of the archive.

getWindow

public MoleculeArchiveWindow getWindow()

Returns the MoleculeArchiveWindow holding this archive, if one exists. Otherwise, null is returned.

Specified by:

getWindow in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Returns:

The MoleculeArchiveWindow containing this archive.

setWindow

public void setWindow(MoleculeArchiveWindow win)

Set the window containing this archive.

Specified by:

setWindow in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

win - Set the MoleculeArchiveWindow that contains this archive.

logln

public void logln(java.lang.String message)

Add a log message to all metadata records. Used by Mars commands to keep a record of the sequence of processing steps during analysis. Start a new line after adding the message.

Specified by:

logln in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

message - The String message to add to all metadata logs.

log

public void log(java.lang.String message)

Add a log message to all metadata records. Used by Mars commands to keep a record of the sequence of processing steps during analysis. Start a new line after adding the message. Do not start a new line after adding the message.

Specified by:

log in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

message - The String message to add to all metadata logs.

properties

public P properties()

Get the MoleculeArchiveProperties which contain general information about the archive. This includes numbers of records, comments, file locations, and global lists of table columns, tags, and parameters.

Specified by:

properties in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Returns:

The MoleculeArchiveProperties for this AbstractMoleculeArchive.

createIndex

public abstract X createIndex()

Create empty MoleculeArchiveIndex.

Specified by:

createIndex in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Returns:

An empty MoleculeArchiveIndex.

createIndex

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

Create MoleculeArchiveIndex using JsonParser stream.

Specified by:

createIndex in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

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.

createProperties

public abstract P createProperties()

Create empty MoleculeArchiveProperties record.

Specified by:

createProperties in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Returns:

Empty MoleculeArchiveProperties.

createProperties

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

Create MoleculeArchiveProperties record using JsonParser stream.

Specified by:

createProperties in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

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 abstract I createMetadata(com.fasterxml.jackson.core.JsonParser jParser)
                          throws java.io.IOException

Create MarsMetadata record using JsonParser stream.

Specified by:

createMetadata in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

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 abstract I createMetadata(java.lang.String metaUID)

Create empty MarsMetadata record with the metaUID specified.

Specified by:

createMetadata in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

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

Returns:

MarsMetadata record.

createMolecule

public abstract M createMolecule()

Create empty Molecule record.

Specified by:

createMolecule in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Returns:

Empty molecule record.

createMolecule

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

Create Molecule record using the JsonParser stream given.

Specified by:

createMolecule in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

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 abstract M createMolecule(java.lang.String UID)

Create empty Molecule record with the UID specified.

Specified by:

createMolecule in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

UID - The UID to use during creation.

Returns:

Empty molecule with the UID given.

createMolecule

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

Create Molecule record using the UID and MarsTable specified.

Specified by:

createMolecule in interface MoleculeArchive<M extends Molecule,I extends MarsMetadata,P extends MoleculeArchiveProperties<M,I>,X extends MoleculeArchiveIndex<M,I>>

Parameters:

UID - The UID to use during molecule creation.

table - The MarsTable set as the DataTable during creation.

Returns:

Molecule created.

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object