de.mpg.biochem.mars.molecule

Class AbstractMoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

java.lang.Object

de.mpg.biochem.mars.molecule.AbstractJsonConvertibleRecord

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

All Implemented Interfaces:

JsonConvertibleRecord, MoleculeArchiveProperties<M,I>

Direct Known Subclasses:

DefaultMoleculeArchiveProperties, DnaMoleculeArchiveProperties, ObjectArchiveProperties, SingleMoleculeArchiveProperties

public abstract class AbstractMoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>
extends AbstractJsonConvertibleRecord
implements MoleculeArchiveProperties<M,I>

Abstract superclass for MoleculeArchiveProperties objects that contain global properties of the MoleculeArchive, including indexing, comments, and many other global properties. Any information you would like to know without having to read the entire archive record-by-record.

Field Summary

Fields

Modifier and Type	Field and Description
protected java.util.Set<java.lang.Integer>	channelSet
protected java.util.Map<java.lang.String,MarsDocument>	documents
protected java.lang.String	inputSchema
protected java.util.Set<java.lang.String>	moleculeDataTableColumnSet
protected java.util.Set<java.util.List<java.lang.String>>	moleculeSegmentTableNames
protected java.util.concurrent.atomic.AtomicInteger	numberOfMolecules
protected java.util.concurrent.atomic.AtomicInteger	numMetadata
protected java.util.Set<java.lang.String>	parameterSet
protected MoleculeArchive<? extends Molecule,? extends MarsMetadata,? extends MoleculeArchiveProperties<?,?>,? extends MoleculeArchiveIndex<?,?>>	parent
protected java.util.Set<java.lang.String>	positionSet
protected java.util.Set<java.lang.String>	regionSet
static java.lang.String	SCHEMA
protected java.util.Set<java.lang.String>	tagSet

Constructor Summary

Constructors

Constructor and Description
AbstractMoleculeArchiveProperties() Creates an empty MoleculeArchiveProperties record.
AbstractMoleculeArchiveProperties(com.fasterxml.jackson.core.JsonParser jParser) Constructor for loading MoleculeArchiveProperties record from a JsonParser stream.

Method Summary

Modifier and Type	Method and Description
void	addAllChannels(java.util.Set<java.lang.Integer> channels) Add molecule channel indexes to the global set that contains a record of all unique channel indexes that are represented in the archive.
void	addAllColumns(java.util.List<java.lang.String> columns) Add column names to the unique set of column names in use in molecule DataTables.
void	addAllColumns(java.util.Set<java.lang.String> columns) Add column names to the unique set of column names in use in molecule DataTables.
void	addAllParameters(java.util.Set<java.lang.String> parameters) Add molecule parameter names to the global set that contains a record of all unique parameter names that are being used.
void	addAllPositions(java.util.Set<java.lang.String> positions) Add molecule position names to the global set that contains a record of all unique position names that are being used.
void	addAllRegions(java.util.Set<java.lang.String> regions) Add molecule region names to the global set that contains a record of all unique region names that are being used.
void	addAllSegmentsTableNames(java.util.Set<java.util.List<java.lang.String>> segmentTableNames) Add segment table names to the unique set of segment table names found in molecule records.
void	addAllTags(java.util.Set<java.lang.String> tags) Add molecule tags to the global set that contains a record of all unique tag names that are being used.
void	addChannel(int channel) Add a channel index to the global set that contains a record of all unique indexes that are represented in the archive.
void	addColumn(java.lang.String column) Add a column name to the unique set of column names in use in molecule DataTables.
void	addComment(java.lang.String comment) Add to archive comments.
void	addMetadataProperties(I metadata) Update global sets to include metadata properties.
void	addMoleculeProperties(M molecule) Update global sets to include molecule properties.
void	addParameter(java.lang.String parameterName) Add a molecule parameter name to the global set that contains a record of all unique parameter names that are being used.
void	addPosition(java.lang.String position) Add a molecule position name to the global set that contains a record of all unique position names that are being used.
void	addRegion(java.lang.String region) Add a molecule region name to the global set that contains a record of all unique region names that are being used.
void	addSegmentsTableNames(java.util.List<java.lang.String> segmentTableName) Add a segment table name to the unique set of segment table names found in molecule records.
void	addTag(java.lang.String tag) Add a molecule tag to the global set that contains a record of all unique tag names that are being used.
void	clear() Clear contents of all global sets and records counts.
protected void	createIOMaps() Must be implemented in subclasses to define how fields, objects, arrays should be saved based on the Jackson streaming API.
java.util.Set<java.lang.Integer>	getChannelSet() Get the set of channel indexes for molecules in the archive.
java.util.Set<java.lang.String>	getColumnSet() Get the unique set of column names in use in molecule DataTables.
java.lang.String	getComments() Get archive comments.
MarsDocument	getDocument(java.lang.String name) Retrieve document.
java.util.Set<java.lang.String>	getDocumentNames() Get the names of all documents.
java.lang.String	getInputSchema() Get the Json input schema for the archive.
int	getNumberOfMetadatas() Get the number of MarsMetadata records in the archive.
int	getNumberOfMolecules() Get the number of molecule in the archive.
java.util.Set<java.lang.String>	getParameterSet() Get the set of molecule parameter names in use.
java.util.Set<java.lang.String>	getPositionSet() Get the set of molecule position names in use.
java.util.Set<java.lang.String>	getRegionSet() Get the set of molecule region names in use.
java.util.Set<java.util.List<java.lang.String>>	getSegmentsTableNames() Get the unique set of segment table names found in molecule records.
java.util.Set<java.lang.String>	getTagSet() Get the set of molecule tag names in use.
void	merge(MoleculeArchiveProperties<?,?> properties, java.lang.String archiveName) Used to during merge MoleculeArchive merge events to merge the properties of another archive into this one.
void	putDocument(MarsDocument document) Add additional comments or reports as documents.
void	putDocument(java.lang.String name, java.lang.String content) Add additional comments or reports as documents.
void	removeAllDocuments() Remove all documents.
void	removeDocument(java.lang.String name) Remove document.
void	setChannelSet(java.util.Set<java.lang.Integer> channelSet) Redefine the set of molecule channels in use.
void	setColumnSet(java.util.Set<java.lang.String> moleculeDataTableColumnSet) Redefine the unique set of column names in use in molecule DataTables.
void	setComments(java.lang.String comments) Overwrite archive comments with new set of comments.
void	setNumberOfMetadatas(int numMetadata) Set the number of MarsMetadata records in the archive.
void	setNumberOfMolecules(int numMolecules) Set the number of molecule in the archive.
void	setParameterSet(java.util.Set<java.lang.String> parameterSet) Redefine the set of parameter names in use.
void	setParent(MoleculeArchive<? extends Molecule,? extends MarsMetadata,? extends MoleculeArchiveProperties<?,?>,? extends MoleculeArchiveIndex<?,?>> archive) Set the parent MoleculeArchive that these MoleculeArchiveProperties belong to.
void	setPositionSet(java.util.Set<java.lang.String> positionSet) Redefine the set of molecule position names in use.
void	setRegionSet(java.util.Set<java.lang.String> regionSet) Redefine the set of molecule region names in use.
void	setSegmentsTableNames(java.util.Set<java.util.List<java.lang.String>> moleculeSegmentTableNames) Redefine the unique set of segment table names found in molecule records.
void	setTagSet(java.util.Set<java.lang.String> tagSet) Redefine the set of molecule tags in use.

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

Field Detail

numberOfMolecules

protected java.util.concurrent.atomic.AtomicInteger numberOfMolecules

numMetadata

protected java.util.concurrent.atomic.AtomicInteger numMetadata

inputSchema

protected java.lang.String inputSchema

documents

protected final java.util.Map<java.lang.String,MarsDocument> documents

SCHEMA

public static final java.lang.String SCHEMA

See Also:

Constant Field Values

tagSet

protected java.util.Set<java.lang.String> tagSet

positionSet

protected java.util.Set<java.lang.String> positionSet

regionSet

protected java.util.Set<java.lang.String> regionSet

parameterSet

protected java.util.Set<java.lang.String> parameterSet

moleculeDataTableColumnSet

protected java.util.Set<java.lang.String> moleculeDataTableColumnSet

channelSet

protected java.util.Set<java.lang.Integer> channelSet

moleculeSegmentTableNames

protected java.util.Set<java.util.List<java.lang.String>> moleculeSegmentTableNames

parent

protected MoleculeArchive<? extends Molecule,? extends MarsMetadata,? extends MoleculeArchiveProperties<?,?>,? extends MoleculeArchiveIndex<?,?>> parent

Constructor Detail

AbstractMoleculeArchiveProperties

public AbstractMoleculeArchiveProperties()

Creates an empty MoleculeArchiveProperties record.

AbstractMoleculeArchiveProperties

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

Constructor for loading MoleculeArchiveProperties record from a JsonParser stream. Used when archives are initially opened.

Parameters:

jParser - A JsonParser at the start of the MoleculeArchiveProperties record.

Throws:

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

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

getInputSchema

public java.lang.String getInputSchema()

Get the Json input schema for the archive. Returns a string with the date for the schema definition using to save the archive that has just been opened. Or null if for archives created with early versions of mars-core.

Specified by:

getInputSchema in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Returns:

The input schema.

merge

public void merge(MoleculeArchiveProperties<?,?> properties,
                  java.lang.String archiveName)

Used to during merge MoleculeArchive merge events to merge the properties of another archive into this one.

Specified by:

merge in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

properties - MoleculeArchiveProperties record to merge into this one.

archiveName - Name of the archive that is being merged with this one.

addTag

public void addTag(java.lang.String tag)

Add a molecule tag to the global set that contains a record of all unique tag names that are being used.

Specified by:

addTag in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

tag - The tag to add.

addAllTags

public void addAllTags(java.util.Set<java.lang.String> tags)

Add molecule tags to the global set that contains a record of all unique tag names that are being used.

Specified by:

addAllTags in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

tags - Set of tags to add.

getTagSet

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

Get the set of molecule tag names in use.

Specified by:

getTagSet in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Returns:

The tag set.

setTagSet

public void setTagSet(java.util.Set<java.lang.String> tagSet)

Redefine the set of molecule tags in use.

Specified by:

setTagSet in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

tagSet - The tag set.

addChannel

public void addChannel(int channel)

Add a channel index to the global set that contains a record of all unique indexes that are represented in the archive.

Specified by:

addChannel in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

channel - The channel for this molecule.

addAllChannels

public void addAllChannels(java.util.Set<java.lang.Integer> channels)

Add molecule channel indexes to the global set that contains a record of all unique channel indexes that are represented in the archive.

Specified by:

addAllChannels in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

channels - The channels to add.

getChannelSet

public java.util.Set<java.lang.Integer> getChannelSet()

Get the set of channel indexes for molecules in the archive.

Specified by:

getChannelSet in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Returns:

The channel set.

setChannelSet

public void setChannelSet(java.util.Set<java.lang.Integer> channelSet)

Redefine the set of molecule channels in use. Integers with an index starting at 0.

Specified by:

setChannelSet in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

channelSet - The set of channels.

addParameter

public void addParameter(java.lang.String parameterName)

Add a molecule parameter name to the global set that contains a record of all unique parameter names that are being used.

Specified by:

addParameter in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

parameterName - The parameter name to add.

addAllParameters

public void addAllParameters(java.util.Set<java.lang.String> parameters)

Add molecule parameter names to the global set that contains a record of all unique parameter names that are being used.

Specified by:

addAllParameters in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

parameters - The parameters to add.

getParameterSet

public java.util.Set<java.lang.String> getParameterSet()

Get the set of molecule parameter names in use.

Specified by:

getParameterSet in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Returns:

The set of parameters.

setParameterSet

public void setParameterSet(java.util.Set<java.lang.String> parameterSet)

Redefine the set of parameter names in use.

Specified by:

setParameterSet in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

parameterSet - The set of parameters.

addPosition

public void addPosition(java.lang.String position)

Add a molecule position name to the global set that contains a record of all unique position names that are being used.

Specified by:

addPosition in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

position - The position name to add.

addAllPositions

public void addAllPositions(java.util.Set<java.lang.String> positions)

Add molecule position names to the global set that contains a record of all unique position names that are being used.

Specified by:

addAllPositions in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

positions - The position names to add.

getPositionSet

public java.util.Set<java.lang.String> getPositionSet()

Get the set of molecule position names in use.

Specified by:

getPositionSet in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Returns:

The position set.

setPositionSet

public void setPositionSet(java.util.Set<java.lang.String> positionSet)

Redefine the set of molecule position names in use.

Specified by:

setPositionSet in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

positionSet - The position set.

addRegion

public void addRegion(java.lang.String region)

Add a molecule region name to the global set that contains a record of all unique region names that are being used.

Specified by:

addRegion in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

region - The region name to add.

addAllRegions

public void addAllRegions(java.util.Set<java.lang.String> regions)

Add molecule region names to the global set that contains a record of all unique region names that are being used.

Specified by:

addAllRegions in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

regions - The region names to add.

getRegionSet

public java.util.Set<java.lang.String> getRegionSet()

Get the set of molecule region names in use.

Specified by:

getRegionSet in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Returns:

The set of region names.

setRegionSet

public void setRegionSet(java.util.Set<java.lang.String> regionSet)

Redefine the set of molecule region names in use.

Specified by:

setRegionSet in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

regionSet - The region set.

setNumberOfMolecules

public void setNumberOfMolecules(int numMolecules)

Set the number of molecule in the archive.

Specified by:

setNumberOfMolecules in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

numMolecules - Total molecule count.

getNumberOfMolecules

public int getNumberOfMolecules()

Get the number of molecule in the archive.

Specified by:

getNumberOfMolecules in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Returns:

Total molecule count.

setNumberOfMetadatas

public void setNumberOfMetadatas(int numMetadata)

Set the number of MarsMetadata records in the archive.

Specified by:

setNumberOfMetadatas in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

numMetadata - Total metadata count.

getNumberOfMetadatas

public int getNumberOfMetadatas()

Get the number of MarsMetadata records in the archive.

Specified by:

getNumberOfMetadatas in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Returns:

Total metadata count.

addColumn

public void addColumn(java.lang.String column)

Add a column name to the unique set of column names in use in molecule DataTables.

Specified by:

addColumn in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

column - The column name to add.

addAllColumns

public void addAllColumns(java.util.Set<java.lang.String> columns)

Add column names to the unique set of column names in use in molecule DataTables.

Specified by:

addAllColumns in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

columns - The set column names to add.

addAllColumns

public void addAllColumns(java.util.List<java.lang.String> columns)

Add column names to the unique set of column names in use in molecule DataTables.

Specified by:

addAllColumns in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

columns - The list of column names to add.

setColumnSet

public void setColumnSet(java.util.Set<java.lang.String> moleculeDataTableColumnSet)

Redefine the unique set of column names in use in molecule DataTables.

Specified by:

setColumnSet in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

moleculeDataTableColumnSet - The set of molecule table columns names.

getColumnSet

public java.util.Set<java.lang.String> getColumnSet()

Get the unique set of column names in use in molecule DataTables.

Specified by:

getColumnSet in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Returns:

The set of column names.

addSegmentsTableNames

public void addSegmentsTableNames(java.util.List<java.lang.String> segmentTableName)

Add a segment table name to the unique set of segment table names found in molecule records.

Specified by:

addSegmentsTableNames in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

segmentTableName - The segment table names.

addAllSegmentsTableNames

public void addAllSegmentsTableNames(java.util.Set<java.util.List<java.lang.String>> segmentTableNames)

Add segment table names to the unique set of segment table names found in molecule records.

Specified by:

addAllSegmentsTableNames in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

segmentTableNames - The segment Table names.

setSegmentsTableNames

public void setSegmentsTableNames(java.util.Set<java.util.List<java.lang.String>> moleculeSegmentTableNames)

Redefine the unique set of segment table names found in molecule records.

Specified by:

setSegmentsTableNames in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

moleculeSegmentTableNames - The molecule segment table names.

getSegmentsTableNames

public java.util.Set<java.util.List<java.lang.String>> getSegmentsTableNames()

Get the unique set of segment table names found in molecule records.

Specified by:

getSegmentsTableNames in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Returns:

The set of lists of segment table names.

getComments

public java.lang.String getComments()

Get archive comments.

Specified by:

getComments in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Returns:

The comments.

addComment

public void addComment(java.lang.String comment)

Add to archive comments.

Specified by:

addComment in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

comment - The comment to add.

setComments

public void setComments(java.lang.String comments)

Overwrite archive comments with new set of comments.

Specified by:

setComments in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

comments - The comments to set.

putDocument

public void putDocument(java.lang.String name,
                        java.lang.String content)

Description copied from interface: MoleculeArchiveProperties

Add additional comments or reports as documents.

Specified by:

putDocument in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

name - Document name.

content - Document content.

putDocument

public void putDocument(MarsDocument document)

Description copied from interface: MoleculeArchiveProperties

Add additional comments or reports as documents.

Specified by:

putDocument in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

document - Document.

getDocument

public MarsDocument getDocument(java.lang.String name)

Description copied from interface: MoleculeArchiveProperties

Retrieve document.

Specified by:

getDocument in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

name - Document name.

Returns:

Document.

removeDocument

public void removeDocument(java.lang.String name)

Description copied from interface: MoleculeArchiveProperties

Remove document.

Specified by:

removeDocument in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

name - Document name.

removeAllDocuments

public void removeAllDocuments()

Description copied from interface: MoleculeArchiveProperties

Remove all documents. The default comments for an archive are not removed.

Specified by:

removeAllDocuments in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

getDocumentNames

public java.util.Set<java.lang.String> getDocumentNames()

Description copied from interface: MoleculeArchiveProperties

Get the names of all documents.

Specified by:

getDocumentNames in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Returns:

Set of document names.

clear

public void clear()

Description copied from interface: MoleculeArchiveProperties

Clear contents of all global sets and records counts. Does not clear comments. Used when rebuilding indexes.

Specified by:

clear in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

addMoleculeProperties

public void addMoleculeProperties(M molecule)

Description copied from interface: MoleculeArchiveProperties

Update global sets to include molecule properties.

Specified by:

addMoleculeProperties in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

molecule - The Molecule to add the properties from.

addMetadataProperties

public void addMetadataProperties(I metadata)

Description copied from interface: MoleculeArchiveProperties

Update global sets to include metadata properties.

Specified by:

addMetadataProperties in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

metadata - The MarsMetadata to add the properties from.

setParent

public void setParent(MoleculeArchive<? extends Molecule,? extends MarsMetadata,? extends MoleculeArchiveProperties<?,?>,? extends MoleculeArchiveIndex<?,?>> archive)

Set the parent MoleculeArchive that these MoleculeArchiveProperties belong to.

Specified by:

setParent in interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

Parameters:

archive - The MoleculeArchive holding this record.