de.mpg.biochem.mars.molecule

Interface Molecule

All Superinterfaces:

JsonConvertibleRecord, MarsRecord

All Known Implementing Classes:

AbstractMolecule, DefaultMolecule, DnaMolecule, MartianObject, SingleMolecule

public interface Molecule
extends JsonConvertibleRecord, MarsRecord

Molecule records act as the storage location for molecule properties. Molecule records are stored in MoleculeArchives to allow for fast and efficient retrieval and optimal organization.

Molecule records are designed to allow for storage of many different kinds of single-molecule time-series data. They contain a primary MarsTable with molecule properties typically with each row containing features of a given time point. This may include position or intensity information. To facilitate efficient and reproducible processing molecule records may also contain calculated parameters, tags, notes, and kinetic change point segment MarsTables generated by KCPCommand. Molecule records are assigned a random UID string at the time of creation derived from a base58 encoded UUID for readability. This serves as their primary identifier within MoleculeArchives and for a range of transformations and merging operations. Molecule records also have a UID string for corresponding MarsMetadata records, which contain the experiments metadata information from.

Molecule records can be saved to Json for storage when done processing. They are then either stored as an array within MoleculeArchive .yama files or as individual sml or json files within .yama.store directories.

Method Summary

Modifier and Type	Method and Description
int	getChannel() Get the channel for this molecule record.
int	getImage() Get the image index for this molecule record.
java.lang.String	getMetadataUID() Get the UID of the MarsMetadata record associated with this molecule.
MarsTable	getSegmentsTable(java.util.List<java.lang.String> tableColumnNames) Retrieve a segments table (MarsTable) generated using x column, y column and region names provided in index positions 0, 1 and 2 of a List, respectively.
MarsTable	getSegmentsTable(java.lang.String xColumn, java.lang.String yColumn) Retrieve a segments table (MarsTable) generated using xColumn and yColumn.
MarsTable	getSegmentsTable(java.lang.String xColumn, java.lang.String yColumn, java.lang.String region) Retrieve a Segments table (MarsTable) generated using xColum, yColumn and region names.
java.util.Set<java.util.List<java.lang.String>>	getSegmentsTableNames() /** Get the set of segment table names as lists of x and y column names.
MarsTable	getTable() Get the MarsTable holding the primary data for this molecule record.
boolean	hasSegmentsTable(java.lang.String xColumn, java.lang.String yColumn) Check if record has a segments table (MarsTable) generated using xColumn and yColumn.
boolean	hasSegmentsTable(java.lang.String xColumn, java.lang.String yColumn, java.lang.String region) Check if record has a Segments table (MarsTable) generated using xColumn, yColumn and region names.
void	merge(Molecule molecule) Used to merge another molecule record into this one.
void	putSegmentsTable(java.lang.String xColumn, java.lang.String yColumn, MarsTable segmentsTable) Add or update a segments table (MarsTable) generated using the x column and y column names.
void	putSegmentsTable(java.lang.String xColumn, java.lang.String yColumn, java.lang.String region, MarsTable segmentsTable) Add or update a segments table (MarsTable) generated using the x column, y column and region names.
void	removeSegmentsTable(java.util.List<java.lang.String> tableColumnNames) Remove the segments table (MarsTable) generated using x column, y column, and region names provided as a list.
void	removeSegmentsTable(java.lang.String xColumn, java.lang.String yColumn) Remove the segments table (MarsTable) generated using xColumn and y Column.
void	removeSegmentsTable(java.lang.String xColumn, java.lang.String yColumn, java.lang.String region) Remove the segments table (MarsTable) generated using x column, y column, and region names provided.
void	setChannel(int channel) Set the channel for this molecule record.
void	setImage(int image) Set the image position for this molecule record.
void	setMetadataUID(java.lang.String metadataUID) Set the UID of the MarsMetadata record associated with this molecule.
void	setTable(MarsTable table) Set the MarsTable holding the primary data for this molecule record.

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

addNote, addTag, getBooleanParameter, getNotes, getParameter, getParameters, getPosition, getPositionNames, getPositions, getRegion, getRegionNames, getRegions, getStringParameter, getTags, getTagsArray, getUID, hasBooleanParameter, hasDoubleParameter, hasNoTags, hasParameter, hasPosition, hasRegion, hasStringParameter, hasTag, merge, putPosition, putRegion, removeAllParameters, removeAllPositions, removeAllRegions, removeAllTags, removeParameter, removePosition, removeRegion, removeTag, setNotes, setParameter, setParameter, setParameter, setParent

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

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

Method Detail

setMetadataUID

void setMetadataUID(java.lang.String metadataUID)

Set the UID of the MarsMetadata record associated with this molecule. The MarsMetadata contains information about the data collection (Timing of frames, colors, collection date, etc...)

Parameters:

metadataUID - The new metadata UID to set.

getMetadataUID

java.lang.String getMetadataUID()

Get the UID of the MarsMetadata record associated with this molecule. The MarsMetadata contains information about the data collection (Timing of frames, colors, collection date, etc...)

Returns:

Return a JSON string representation of the molecule.

setImage

void setImage(int image)

Set the image position for this molecule record.

Parameters:

image - The imageID.

getImage

int getImage()

Get the image index for this molecule record. An integer value starting at zero. If image index is not set this value will be -1.

Returns:

Return the image index for this molecule record.

setChannel

void setChannel(int channel)

Set the channel for this molecule record.

Parameters:

channel - The channel.

getChannel

int getChannel()

Get the channel for this molecule record. An integer value starting at zero. If channel is not set this value will be -1.

Returns:

Return the channel for this molecule record.

getTable

MarsTable getTable()

Get the MarsTable holding the primary data for this molecule record.

Returns:

The primary table for this molecule record.

setTable

void setTable(MarsTable table)

Set the MarsTable holding the primary data for this molecule record. Usually this is tracking or intensity as a function of time.

Parameters:

table - The MarsTable to add or update in the molecule record.

putSegmentsTable

void putSegmentsTable(java.lang.String xColumn,
                      java.lang.String yColumn,
                      MarsTable segmentsTable)

Add or update a segments table (MarsTable) generated using the x column and y column names. The KCPCommand performs kinetic change point analysis generating segments to fit regions of a trace. The information about these segments is added using this method.

Parameters:

xColumn - The name of the column used for x for KCP analysis.

yColumn - The name of the column used for y for KCP analysis.

segmentsTable - The MarsTable to add that contains the segments.

putSegmentsTable

void putSegmentsTable(java.lang.String xColumn,
                      java.lang.String yColumn,
                      java.lang.String region,
                      MarsTable segmentsTable)

Add or update a segments table (MarsTable) generated using the x column, y column and region names. The KCPCommand performs kinetic change point analysis generating segments to fit regions of a trace. The information about these segments is added using this method.

Parameters:

xColumn - The name of the column used for x for KCP analysis.

yColumn - The name of the column used for y for KCP analysis.

region - The name of the region used for analysis.

segmentsTable - The MarsTable to add that contains the segments.

getSegmentsTable

MarsTable getSegmentsTable(java.lang.String xColumn,
                           java.lang.String yColumn)

Retrieve a segments table (MarsTable) generated using xColumn and yColumn.

Parameters:

xColumn - The name of the x column used for analysis.

yColumn - The name of the y column used for analysis.

Returns:

The segments table.

getSegmentsTable

MarsTable getSegmentsTable(java.lang.String xColumn,
                           java.lang.String yColumn,
                           java.lang.String region)

Retrieve a Segments table (MarsTable) generated using xColum, yColumn and region names.

Parameters:

xColumn - The name of the x column used for analysis.

yColumn - The name of the y column used for analysis.

region - The name of the region used for analysis.

Returns:

The segments table generated using the columns specified.

hasSegmentsTable

boolean hasSegmentsTable(java.lang.String xColumn,
                         java.lang.String yColumn)

Check if record has a segments table (MarsTable) generated using xColumn and yColumn.

Parameters:

xColumn - The name of the x column used for analysis.

yColumn - The name of the y column used for analysis.

Returns:

Returns true if the table exists and false if not.

hasSegmentsTable

boolean hasSegmentsTable(java.lang.String xColumn,
                         java.lang.String yColumn,
                         java.lang.String region)

Check if record has a Segments table (MarsTable) generated using xColumn, yColumn and region names.

Parameters:

xColumn - The name of the x column used for analysis.

yColumn - The name of the y column used for analysis.

region - The name of the region used for analysis.

Returns:

Returns true if the table exists and false if not.

getSegmentsTable

MarsTable getSegmentsTable(java.util.List<java.lang.String> tableColumnNames)

Retrieve a segments table (MarsTable) generated using x column, y column and region names provided in index positions 0, 1 and 2 of a List, respectively.

Parameters:

tableColumnNames - The list of x column, y column and region names.

Returns:

The MarsTable generated using the columns specified.

removeSegmentsTable

void removeSegmentsTable(java.util.List<java.lang.String> tableColumnNames)

Remove the segments table (MarsTable) generated using x column, y column, and region names provided as a list.

Parameters:

tableColumnNames - List of xColumn, yColumn, and Region of the segment table to remove.

removeSegmentsTable

void removeSegmentsTable(java.lang.String xColumn,
                         java.lang.String yColumn)

Remove the segments table (MarsTable) generated using xColumn and y Column.

Parameters:

xColumn - The name of the x column used for analysis.

yColumn - The name of the y column used for analysis.

removeSegmentsTable

void removeSegmentsTable(java.lang.String xColumn,
                         java.lang.String yColumn,
                         java.lang.String region)

Remove the segments table (MarsTable) generated using x column, y column, and region names provided.

Parameters:

xColumn - The name of the x column used for analysis.

yColumn - The name of the y column used for analysis.

region - The name of the region used for analysis.

getSegmentsTableNames

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

/** Get the set of segment table names as lists of x and y column names.

Returns:

The set of Lists holding the x and y column and region names at index positions 0, 1 and 2, respectively.

merge

void merge(Molecule molecule)

Used to merge another molecule record into this one.

Parameters:

molecule - Molecule to merge into this one.