de.mpg.biochem.mars.molecule

Class AbstractMoleculeArchiveIndex<M extends Molecule,I extends MarsMetadata>

java.lang.Object

de.mpg.biochem.mars.molecule.AbstractJsonConvertibleRecord

de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveIndex<M,I>

All Implemented Interfaces:

JsonConvertibleRecord, MoleculeArchiveIndex<M,I>

Direct Known Subclasses:

DefaultMoleculeArchiveIndex, DnaMoleculeArchiveIndex, ObjectArchiveIndex, SingleMoleculeArchiveIndex

public abstract class AbstractMoleculeArchiveIndex<M extends Molecule,I extends MarsMetadata>
extends AbstractJsonConvertibleRecord
implements MoleculeArchiveIndex<M,I>

Constructor Summary

Constructors

Constructor and Description
AbstractMoleculeArchiveIndex()
AbstractMoleculeArchiveIndex(com.fasterxml.jackson.core.JsonParser jParser)

Method Summary

Modifier and Type	Method and Description
void	addMetadata(I metadata)
void	addMolecule(M molecule)
boolean	containsMetadataUID(java.lang.String metadataUID)
boolean	containsMoleculeUID(java.lang.String UID)
protected void	createIOMaps() Must be implemented in subclasses to define how fields, objects, arrays should be saved based on the Jackson streaming API.
java.lang.String	getMetadataUIDforMolecule(java.lang.String UID)
java.util.concurrent.ConcurrentSkipListSet<java.lang.String>	getMetadataUIDSet()
java.util.Map<java.lang.String,java.util.Set<java.lang.String>>	getMetadataUIDtoTagListMap()
java.util.concurrent.ConcurrentSkipListSet<java.lang.String>	getMoleculeUIDSet()
java.util.Map<java.lang.String,java.lang.Integer>	getMoleculeUIDtoChannelMap()
java.util.Map<java.lang.String,java.lang.Integer>	getMoleculeUIDtoImageMap()
java.util.Map<java.lang.String,java.lang.String>	getMoleculeUIDtoMetadataUIDMap()
java.util.Map<java.lang.String,java.util.Set<java.lang.String>>	getMoleculeUIDtoTagListMap()
void	removeMetadata(I metadata)
void	removeMetadata(java.lang.String metadataUID)
void	removeMolecule(Molecule molecule)
void	removeMolecule(java.lang.String UID)

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, toString, wait, wait, wait

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

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

Constructor Detail

AbstractMoleculeArchiveIndex

public AbstractMoleculeArchiveIndex()

AbstractMoleculeArchiveIndex

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

Throws:

java.io.IOException

Method Detail

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

addMolecule

public void addMolecule(M molecule)

Specified by:

addMolecule in interface MoleculeArchiveIndex<M extends Molecule,I extends MarsMetadata>

removeMolecule

public void removeMolecule(Molecule molecule)

Specified by:

removeMolecule in interface MoleculeArchiveIndex<M extends Molecule,I extends MarsMetadata>

removeMolecule

public void removeMolecule(java.lang.String UID)

Specified by:

removeMolecule in interface MoleculeArchiveIndex<M extends Molecule,I extends MarsMetadata>

addMetadata

public void addMetadata(I metadata)

Specified by:

addMetadata in interface MoleculeArchiveIndex<M extends Molecule,I extends MarsMetadata>

removeMetadata

public void removeMetadata(I metadata)

Specified by:

removeMetadata in interface MoleculeArchiveIndex<M extends Molecule,I extends MarsMetadata>

removeMetadata

public void removeMetadata(java.lang.String metadataUID)

Specified by:

removeMetadata in interface MoleculeArchiveIndex<M extends Molecule,I extends MarsMetadata>

containsMoleculeUID

public boolean containsMoleculeUID(java.lang.String UID)

Specified by:

containsMoleculeUID in interface MoleculeArchiveIndex<M extends Molecule,I extends MarsMetadata>

containsMetadataUID

public boolean containsMetadataUID(java.lang.String metadataUID)

Specified by:

containsMetadataUID in interface MoleculeArchiveIndex<M extends Molecule,I extends MarsMetadata>

getMoleculeUIDSet

public java.util.concurrent.ConcurrentSkipListSet<java.lang.String> getMoleculeUIDSet()

Specified by:

getMoleculeUIDSet in interface MoleculeArchiveIndex<M extends Molecule,I extends MarsMetadata>

getMetadataUIDSet

public java.util.concurrent.ConcurrentSkipListSet<java.lang.String> getMetadataUIDSet()

Specified by:

getMetadataUIDSet in interface MoleculeArchiveIndex<M extends Molecule,I extends MarsMetadata>

getMetadataUIDtoTagListMap

public java.util.Map<java.lang.String,java.util.Set<java.lang.String>> getMetadataUIDtoTagListMap()

Specified by:

getMetadataUIDtoTagListMap in interface MoleculeArchiveIndex<M extends Molecule,I extends MarsMetadata>

getMoleculeUIDtoTagListMap

public java.util.Map<java.lang.String,java.util.Set<java.lang.String>> getMoleculeUIDtoTagListMap()

Specified by:

getMoleculeUIDtoTagListMap in interface MoleculeArchiveIndex<M extends Molecule,I extends MarsMetadata>

getMoleculeUIDtoImageMap

public java.util.Map<java.lang.String,java.lang.Integer> getMoleculeUIDtoImageMap()

Specified by:

getMoleculeUIDtoImageMap in interface MoleculeArchiveIndex<M extends Molecule,I extends MarsMetadata>

getMoleculeUIDtoChannelMap

public java.util.Map<java.lang.String,java.lang.Integer> getMoleculeUIDtoChannelMap()

Specified by:

getMoleculeUIDtoChannelMap in interface MoleculeArchiveIndex<M extends Molecule,I extends MarsMetadata>

getMetadataUIDforMolecule

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

Specified by:

getMetadataUIDforMolecule in interface MoleculeArchiveIndex<M extends Molecule,I extends MarsMetadata>

getMoleculeUIDtoMetadataUIDMap

public java.util.Map<java.lang.String,java.lang.String> getMoleculeUIDtoMetadataUIDMap()

Specified by:

getMoleculeUIDtoMetadataUIDMap in interface MoleculeArchiveIndex<M extends Molecule,I extends MarsMetadata>