de.mpg.biochem.mars.molecule

Interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>

All Superinterfaces:

JsonConvertibleRecord

All Known Implementing Classes:

AbstractMoleculeArchiveProperties, DefaultMoleculeArchiveProperties, DnaMoleculeArchiveProperties, ObjectArchiveProperties, SingleMoleculeArchiveProperties

public interface MoleculeArchiveProperties<M extends Molecule,I extends MarsMetadata>
extends JsonConvertibleRecord

Global properties of Molecule Archives are stored in MoleculeArchiveProperties including comments, number of each record type, as well as tag, parameter, Table column, region and position name indexes. Information you would like to know without having to read the entire archive record-by-record.

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 Tables.
void	addAllColumns(java.util.Set<java.lang.String> columns) Add column names to the unique set of column names in use in molecule Tables.
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.
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 Tables.
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 Tables.
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 molecule parameter names in use.
void	setParent(MoleculeArchive<? extends Molecule,? extends MarsMetadata,? extends MoleculeArchiveProperties<?,?>,? extends MoleculeArchiveIndex<?,?>> archive) Set the parent MoleculeArchive that this record is stored in.
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 interface de.mpg.biochem.mars.molecule.JsonConvertibleRecord

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

Method Detail

getInputSchema

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.

Returns:

The input schema.

addTag

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.

Parameters:

tag - The tag to add.

addAllTags

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.

Parameters:

tags - Set of tags to add.

getTagSet

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

Get the set of molecule tag names in use.

Returns:

The tag set.

setTagSet

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

Redefine the set of molecule tags in use.

Parameters:

tagSet - The tag set.

addChannel

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.

Parameters:

channel - The channel for this molecule.

addAllChannels

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.

Parameters:

channels - The channels to add.

getChannelSet

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

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

Returns:

The channel set.

setChannelSet

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

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

Parameters:

channelSet - The set of channels.

addParameter

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.

Parameters:

parameterName - The parameter name to add.

addAllParameters

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.

Parameters:

parameters - The parameters to add.

getParameterSet

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

Get the set of molecule parameter names in use.

Returns:

The set of parameters.

setParameterSet

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

Redefine the set of molecule parameter names in use.

Parameters:

parameterSet - The set of parameters.

addPosition

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.

Parameters:

position - The position name to add.

addAllPositions

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.

Parameters:

positions - The position names to add.

getPositionSet

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

Get the set of molecule position names in use.

Returns:

The position set.

setPositionSet

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

Redefine the set of molecule position names in use.

Parameters:

positionSet - The position set.

addRegion

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.

Parameters:

region - The region name to add.

addAllRegions

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.

Parameters:

regions - The region names to add.

getRegionSet

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

Get the set of molecule region names in use.

Returns:

The set of region names.

setRegionSet

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

Redefine the set of molecule region names in use.

Parameters:

regionSet - The region set.

setNumberOfMolecules

void setNumberOfMolecules(int numMolecules)

Set the number of molecule in the archive.

Parameters:

numMolecules - Total molecule count.

getNumberOfMolecules

int getNumberOfMolecules()

Get the number of molecule in the archive.

Returns:

Total molecule count.

setNumberOfMetadatas

void setNumberOfMetadatas(int numMetadata)

Set the number of MarsMetadata records in the archive.

Parameters:

numMetadata - Total metadata count.

getNumberOfMetadatas

int getNumberOfMetadatas()

Get the number of MarsMetadata records in the archive.

Returns:

Total metadata count.

addColumn

void addColumn(java.lang.String column)

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

Parameters:

column - The column name to add.

addAllColumns

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

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

Parameters:

columns - The set column names to add.

addAllColumns

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

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

Parameters:

columns - The list of column names to add.

setColumnSet

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

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

Parameters:

moleculeDataTableColumnSet - The set of molecule table columns names.

getColumnSet

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

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

Returns:

The set of column names.

addSegmentsTableNames

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.

Parameters:

segmentTableName - The segment table names.

addAllSegmentsTableNames

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.

Parameters:

segmentTableNames - The segment Table names.

setSegmentsTableNames

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

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

Parameters:

moleculeSegmentTableNames - The molecule segment table names.

getSegmentsTableNames

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

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

Returns:

The set of lists of segment table names.

getComments

java.lang.String getComments()

Get archive comments.

Returns:

The comments.

addComment

void addComment(java.lang.String comment)

Add to archive comments.

Parameters:

comment - The comment to add.

setComments

void setComments(java.lang.String comments)

Overwrite archive comments with new set of comments.

Parameters:

comments - The comments to set.

putDocument

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

Add additional comments or reports as documents.

Parameters:

name - Document name.

content - Document content.

putDocument

void putDocument(MarsDocument document)

Add additional comments or reports as documents.

Parameters:

document - Document.

getDocument

MarsDocument getDocument(java.lang.String name)

Retrieve document.

Parameters:

name - Document name.

Returns:

Document.

removeDocument

void removeDocument(java.lang.String name)

Remove document.

Parameters:

name - Document name.

removeAllDocuments

void removeAllDocuments()

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

getDocumentNames

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

Get the names of all documents.

Returns:

Set of document names.

merge

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.

Parameters:

properties - MoleculeArchiveProperties record to merge into this one.

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

clear

void clear()

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

addMoleculeProperties

void addMoleculeProperties(M molecule)

Update global sets to include molecule properties.

Parameters:

molecule - The Molecule to add the properties from.

addMetadataProperties

void addMetadataProperties(I metadata)

Update global sets to include metadata properties.

Parameters:

metadata - The MarsMetadata to add the properties from.

setParent

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

Set the parent MoleculeArchive that this record is stored in.

Parameters:

archive - The MoleculeArchive holding this record.