de.mpg.biochem.mars.molecule

Class AbstractMolecule

java.lang.Object

de.mpg.biochem.mars.molecule.AbstractJsonConvertibleRecord

de.mpg.biochem.mars.molecule.AbstractMarsRecord

de.mpg.biochem.mars.molecule.AbstractMolecule

All Implemented Interfaces:

JsonConvertibleRecord, MarsRecord, Molecule

Direct Known Subclasses:

DefaultMolecule, DnaMolecule, MartianObject, SingleMolecule

public abstract class AbstractMolecule
extends AbstractMarsRecord
implements Molecule

Abstract superclass for molecule records. 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.

Field Summary

Fields inherited from class de.mpg.biochem.mars.molecule.AbstractMarsRecord

parent

Constructor Summary

Constructors

Constructor and Description
AbstractMolecule() Constructor for creating an empty Molecule record.
AbstractMolecule(com.fasterxml.jackson.core.JsonParser jParser) Constructor for loading a Molecule record from a file.
AbstractMolecule(java.lang.String UID) Constructor for creating an empty Molecule record with the specified UID.
AbstractMolecule(java.lang.String UID, MarsTable table) Constructor for creating a new Molecule record with the specified UID and the MarsTable given as the DataTable.

Method Summary

Modifier and Type	Method and Description
void	addTag(java.lang.String tag) Add a string tag to the record.
protected void	createIOMaps() Must be implemented in subclasses to define how fields, objects, arrays should be saved based on the Jackson streaming API.
int	getChannel() Get the channel for these molecules.
int	getImage() Get the image index for this molecule.
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 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	putPosition(MarsPosition positionOfInterest) Add or update a MarsPosition.
void	putRegion(MarsRegion regionOfInterest) Add or update a MarsRegion.
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.
void	removeSegmentsTable(java.lang.String xColumn, java.lang.String yColumn) Remove the Segments table (MarsTable) generated using xColumn and yColumn.
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.
void	setImage(int image) Set the image index for this molecule.
void	setMetadataUID(java.lang.String metadataUID) Set the UID of the MarsMetadata record associated with this molecule.
void	setParameter(java.lang.String parameter, boolean value) Add or update a parameter value.
void	setParameter(java.lang.String parameter, double value) Add or update a parameter value.
void	setParameter(java.lang.String parameter, java.lang.String value) Add or update a parameter value.
void	setTable(MarsTable table) Set the MarsTable holding the primary data for this record.

Methods inherited from class de.mpg.biochem.mars.molecule.AbstractMarsRecord

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

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.MarsRecord

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

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

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

Constructor Detail

AbstractMolecule

public AbstractMolecule()

Constructor for creating an empty Molecule record.

AbstractMolecule

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

Constructor for loading a Molecule record from a file. Typically, used when streaming records into memory when loading a AbstractMoleculeArchive or when a record is retrieved from the virtual store.

Parameters:

jParser - A JsonParser at the start of the molecule record Json for loading the molecule record from a file.

Throws:

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

AbstractMolecule

public AbstractMolecule(java.lang.String UID)

Constructor for creating an empty Molecule record with the specified UID.

Parameters:

UID - The unique identifier for this Molecule record.

AbstractMolecule

public AbstractMolecule(java.lang.String UID,
                        MarsTable table)

Constructor for creating a new Molecule record with the specified UID and the MarsTable given as the DataTable.

Parameters:

UID - The unique identifier for this Molecule record.

table - The MarsTable to use for initialization.

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.

Overrides:

createIOMaps in class AbstractMarsRecord

setImage

public void setImage(int image)

Set the image index for this molecule. Format is 0 to (image count) - 1. Set to -1 for no image index.

Specified by:

setImage in interface Molecule

Parameters:

image - Integer value for the image index.

getImage

public int getImage()

Get the image index for this molecule. If the molecule does not have image information this parameter will be set to -1. Format is 0 to (image count) - 1.

Specified by:

getImage in interface Molecule

Returns:

The image integer or -1 if not set.

setChannel

public void setChannel(int channel)

Set the channel for this molecule. Format is 0 to (channel count) - 1. Set to -1 for no channel.

Specified by:

setChannel in interface Molecule

Parameters:

channel - Integer value for the channel.

getChannel

public int getChannel()

Get the channel for these molecules. If the molecule does not have channel information this parameter will be set to -1. Format is 0 to (channel count) - 1.

Specified by:

getChannel in interface Molecule

Returns:

The channel integer or -1 if not set.

setParameter

public void setParameter(java.lang.String parameter,
                         double value)

Add or update a parameter value. Parameters are used to store single values associated with the record.

Specified by:

setParameter in interface MarsRecord

Overrides:

setParameter in class AbstractMarsRecord

Parameters:

parameter - The string parameter name.

value - The double value to set for the parameter name.

setParameter

public void setParameter(java.lang.String parameter,
                         java.lang.String value)

Add or update a parameter value.

Specified by:

setParameter in interface MarsRecord

Overrides:

setParameter in class AbstractMarsRecord

Parameters:

parameter - The string parameter name.

value - The string value to set for the parameter name.

setParameter

public void setParameter(java.lang.String parameter,
                         boolean value)

Add or update a parameter value.

Specified by:

setParameter in interface MarsRecord

Overrides:

setParameter in class AbstractMarsRecord

Parameters:

parameter - The string parameter name.

value - The boolean value to set for the parameter name.

addTag

public void addTag(java.lang.String tag)

Add a string tag to the record. Tags are used for marking individual record to sorting and processing with subsets of molecules.

Specified by:

addTag in interface MarsRecord

Overrides:

addTag in class AbstractMarsRecord

Parameters:

tag - The string tag to be added.

putRegion

public void putRegion(MarsRegion regionOfInterest)

Add or update a MarsRegion. This can be a region of interest for further analysis steps: slope calculations or KCP calculations KCPCommand. Region names are unique. If a region that has this name already exists in the record it will be overwritten by this method.

Specified by:

putRegion in interface MarsRecord

Overrides:

putRegion in class AbstractMarsRecord

Parameters:

regionOfInterest - The region to add to the record.

putPosition

public void putPosition(MarsPosition positionOfInterest)

Add or update a MarsPosition. This can be a position of interest for further analysis steps. Position names are unique. If a position with has this name already exists in the record it will be overwritten by this method.

Specified by:

putPosition in interface MarsRecord

Overrides:

putPosition in class AbstractMarsRecord

Parameters:

positionOfInterest - The position to add to the record.

getTable

public MarsTable getTable()

Get the MarsTable holding the primary data for this record.

Specified by:

getTable in interface Molecule

Returns:

Table for this record.

setTable

public void setTable(MarsTable table)

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

Specified by:

setTable in interface Molecule

Parameters:

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

setMetadataUID

public 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...)

Specified by:

setMetadataUID in interface Molecule

Parameters:

metadataUID - The new MarsMetadata UID to set.

getMetadataUID

public 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...)

Specified by:

getMetadataUID in interface Molecule

Returns:

Return UID string of the metadata record associated with this molecule.

putSegmentsTable

public 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.

Specified by:

putSegmentsTable in interface Molecule

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

public 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.

Specified by:

putSegmentsTable in interface Molecule

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

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

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

Specified by:

getSegmentsTable in interface Molecule

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

public 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.

Specified by:

getSegmentsTable in interface Molecule

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

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

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

Specified by:

hasSegmentsTable in interface Molecule

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

public 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.

Specified by:

hasSegmentsTable in interface Molecule

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

public 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.

Specified by:

getSegmentsTable in interface Molecule

Parameters:

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

Returns:

The MarsTable generated using the columns specified.

removeSegmentsTable

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

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

Specified by:

removeSegmentsTable in interface Molecule

Parameters:

tableColumnNames - List of the x column, y column, and region names of the segment table to remove.

removeSegmentsTable

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

Remove the Segments table (MarsTable) generated using xColumn and yColumn.

Specified by:

removeSegmentsTable in interface Molecule

Parameters:

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

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

removeSegmentsTable

public 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.

Specified by:

removeSegmentsTable in interface Molecule

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

public 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.

Specified by:

getSegmentsTableNames in interface Molecule

Returns:

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

merge

public void merge(Molecule molecule)

Used to merge another molecule record into this one.

Specified by:

merge in interface Molecule

Parameters:

molecule - Molecule to merge into this one.