net.sf.basedb.core.data
Class RawData

java.lang.Object
  net.sf.basedb.core.data.BasicData
      net.sf.basedb.core.data.RawData

All Implemented Interfaces:

BatchableData, ExtendableData, IdentifiableData

Direct Known Subclasses:

BaseFileImporter.RawDataProxy

public class RawData
extends BasicData
implements BatchableData, ExtendableData

Represents the measurements for single raw data spot. A raw data entry consists of two parts, coordinate/reporter information and measured values (intensities, etc.) What kind of measurements are available are defined by the RawDataType of the raw bioassay.

Version:

2.0

Author:

Nicklas

See Also:

RawDataBatcher, RawDataUtil, Hybridzations and raw data overview

Last modified

$Date: 2009-04-06 14:52:39 +0200 (Mon, 06 Apr 2009) $

Field Summary

private Integer	block
private Integer	column
private Map<String,Object>	extendedProperties
private FeatureData	feature
private Integer	metaGridX
private Integer	metaGridY
private int	position
private RawBioAssayData	rawBioAssay
private ReporterData	reporter
private Integer	row
private Float	x
private Float	y

Constructor Summary

RawData()

RawData(RawBioAssayData rawBioAssay)

Method Summary

Map<String,Object>	getAllExtended()
Integer	getBlock()
Integer	getColumn()
Object	getExtended(String name) Get the value of an extended property.
FeatureData	getFeature() The feature this raw data is connected with.
Integer	getMetaGridX()
Integer	getMetaGridY()
int	getPosition()
(package private) RawBioAssayData	getRawBioAssay() The raw bioassay this raw data spot belongs to.
ReporterData	getReporter() The reporter this raw data is connected with.
Integer	getRow()
Float	getX()
Float	getY()
void	setBlock(Integer block)
void	setColumn(Integer column)
void	setExtended(String name, Object value) Set the value of an extended property.
(package private) void	setFeature(FeatureData feature)
void	setMetaGridX(Integer metaGridX)
void	setMetaGridY(Integer metaGridY)
void	setPosition(int position) This method was private before 2.6.
(package private) void	setRawBioAssay(RawBioAssayData rawBioAssay)
void	setReporter(ReporterData reporter)
void	setRow(Integer row)
void	setX(Float x)
void	setY(Float y)

Methods inherited from class net.sf.basedb.core.data.BasicData

equals, getId, getVersion, hashCode, setId, setVersion, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface net.sf.basedb.core.data.IdentifiableData

getId, getVersion

Field Detail

extendedProperties

private Map<String,Object> extendedProperties

rawBioAssay

private RawBioAssayData rawBioAssay

feature

private FeatureData feature

reporter

private ReporterData reporter

position

private int position

x

private Float x

y

private Float y

block

private Integer block

metaGridX

private Integer metaGridX

metaGridY

private Integer metaGridY

row

private Integer row

column

private Integer column

Constructor Detail

RawData

public RawData()

RawData

public RawData(RawBioAssayData rawBioAssay)

Method Detail

getExtended

public Object getExtended(String name)

Description copied from interface: ExtendableData

Get the value of an extended property.

Specified by:

getExtended in interface ExtendableData

Parameters:

name - The name of the property

Returns:

The value of the property or null if not found

setExtended

public void setExtended(String name,
                        Object value)

Description copied from interface: ExtendableData

Set the value of an extended property.

Specified by:

setExtended in interface ExtendableData

Parameters:

name - The name of the property

value - The new value for the property

getRawBioAssay

RawBioAssayData getRawBioAssay()

The raw bioassay this raw data spot belongs to. Cannot be public since we don't want to expose data objects to clients.

setRawBioAssay

void setRawBioAssay(RawBioAssayData rawBioAssay)

getFeature

public FeatureData getFeature()

The feature this raw data is connected with.

setFeature

void setFeature(FeatureData feature)

getReporter

public ReporterData getReporter()

The reporter this raw data is connected with. If a feature is also connected the reporter must be the same as the feature's reporter.

setReporter

public void setReporter(ReporterData reporter)

getPosition

public int getPosition()

setPosition

public void setPosition(int position)

This method was private before 2.6. If the raw bioassay is connected to an array design which uses the POSITION feature identifier method a value must be set. If the raw bioassay is connected to an array design which uses another feature identifier method this value will be overwritten with the position value from the feature. If the raw bioassay is not connected to an array design a position will be automatically generated if no value has been set, ie. if the value is 0. The value must be a positive integer.

Parameters:

position - The position number of the spot

Since:

2.6

getX

public Float getX()

setX

public void setX(Float x)

getY

public Float getY()

setY

public void setY(Float y)

getBlock

public Integer getBlock()

setBlock

public void setBlock(Integer block)

getMetaGridX

public Integer getMetaGridX()

setMetaGridX

public void setMetaGridX(Integer metaGridX)

getMetaGridY

public Integer getMetaGridY()

setMetaGridY

public void setMetaGridY(Integer metaGridY)

getRow

public Integer getRow()

setRow

public void setRow(Integer row)

getColumn

public Integer getColumn()

setColumn

public void setColumn(Integer column)

getAllExtended

public Map<String,Object> getAllExtended()