net.sf.basedb.core.data
Class FormulaData

java.lang.Object
  net.sf.basedb.core.data.BasicData
      net.sf.basedb.core.data.OwnedData
          net.sf.basedb.core.data.SharedData
              net.sf.basedb.core.data.CommonData
                  net.sf.basedb.core.data.FormulaData

All Implemented Interfaces:

IdentifiableData, LoggableData, NameableData, OwnableData, RegisteredData, RemovableData, ShareableData

public class FormulaData
extends CommonData
implements RegisteredData, LoggableData

This class holds information about a formula used in the analysis of raw data and bioassay sets.

Version:

2.0

Author:

Nicklas

See Also:

Formula, Data API - Other classes

Hibernate: class

table="`Formulas`" lazy="false"

Field Summary

private int	averageMethod
private int	channels
private ColoringData	coloring
private Date	entryDate
private List<String>	formulas
static int	MAX_FORMULA_LENGTH The maximum allowed length of a formula.
static int	MAX_RAWDATATYPE_LENGTH The maximum allowed length of the raw data type name.
private int	parser
private String	rawDataType
private Integer	resultIntensityTransform
private Integer	sourceIntensityTransform
private int	type
private Integer	valueType

Fields inherited from interface net.sf.basedb.core.data.NameableData

MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH

Constructor Summary

FormulaData()

Method Summary

int	getAverageMethod() The average method for thid formula: 0 = none, Formula.AverageMethod.NONE; no average is defined for this formula 1 = geometric mean, Formula.AverageMethod.GEOMETRIC_MEAN; this formula uses geometric mean 2 = arithmetic mean, Formula.AverageMethod.ARITHMETIC_MEAN; this formula uses arithmetic mean 3 = min, Formula.AverageMethod.MIN; this formula uses the min value as a "mean" 4 = max, Formula.AverageMethod.MAX; this formula uses the max value as a "mean"
int	getChannels() The number of required channels in the experiment to use this formula, or 0 if the number of channels doesn't matter.
ColoringData	getColoring() Get the coloring information for this formula.
Date	getEntryDate() Get the date this item was added to the database.
List<String>	getFormulas() Get the list of formulas.
int	getParser() Which parser to use to convert the formula to an expression or restriction. 1 = JEP
String	getRawDataType() The name of raw data type this formula can be used on, or null if it can be used on any raw data type.
Integer	getResultIntensityTransform() A flag indicating what kind of result spot data this formula generates, or null if it generates the same kind of data that is used as source. 0 = no transformation; 1 = 2-log; 2 = 10-log
Integer	getSourceIntensityTransform() A flag indicating what kind of spot source data that the formula can be used with, or null if the formula can be used with any kind of source data. 0 = no transformation; 1 = 2-log; 2 = 10-log
int	getType() The type of formula: 1 = intensity expression; raw data type required, 1 formula for each channel 2 = intensity transformation; raw data type or channels required, 1 formula for each channel 3 = column expression; raw data type or channels required, 1 formula only 4 = column restriction; raw data type or channels required, 1 formula only
Integer	getValueType() The code for the value type. null = not known or doesn't care.
void	setAverageMethod(int averageMethod)
void	setChannels(int channels)
void	setColoring(ColoringData coloring)
void	setEntryDate(Date entryDate)
(package private) void	setFormulas(List<String> formulas)
void	setParser(int parser)
void	setRawDataType(String rawDataType)
void	setResultIntensityTransform(Integer resultIntensityTransform)
void	setSourceIntensityTransform(Integer sourceIntensityTransform)
void	setType(int type)
void	setValueType(Integer valueType)

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

getDescription, getName, isRemoved, setDescription, setName, setRemoved

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

getItemKey, getProjectKey, setItemKey, setProjectKey

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

getOwner, setOwner

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

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

getOwner, setOwner

Field Detail

entryDate

private Date entryDate

averageMethod

private int averageMethod

type

private int type

valueType

private Integer valueType

sourceIntensityTransform

private Integer sourceIntensityTransform

resultIntensityTransform

private Integer resultIntensityTransform

parser

private int parser

MAX_RAWDATATYPE_LENGTH

public static final int MAX_RAWDATATYPE_LENGTH

The maximum allowed length of the raw data type name.

See Also:

Constant Field Values

rawDataType

private String rawDataType

channels

private int channels

MAX_FORMULA_LENGTH

public static final int MAX_FORMULA_LENGTH

The maximum allowed length of a formula.

See Also:

Constant Field Values

formulas

private List<String> formulas

coloring

private ColoringData coloring

Constructor Detail

FormulaData

public FormulaData()

Method Detail

getEntryDate

public Date getEntryDate()

Description copied from interface: RegisteredData

Get the date this item was added to the database. The value is generated at creation time and can't be modified later.

Specified by:

getEntryDate in interface RegisteredData

setEntryDate

public void setEntryDate(Date entryDate)

getAverageMethod

public int getAverageMethod()

The average method for thid formula:

• 0 = none, Formula.AverageMethod.NONE; no average is defined for this formula
• 1 = geometric mean, Formula.AverageMethod.GEOMETRIC_MEAN; this formula uses geometric mean
• 2 = arithmetic mean, Formula.AverageMethod.ARITHMETIC_MEAN; this formula uses arithmetic mean
• 3 = min, Formula.AverageMethod.MIN; this formula uses the min value as a "mean"
• 4 = max, Formula.AverageMethod.MAX; this formula uses the max value as a "mean"

Since:

2.4

Hibernate: property

column="`average_method`" type="int" not-null="true"

setAverageMethod

public void setAverageMethod(int averageMethod)

getType

public int getType()

The type of formula:

• 1 = intensity expression; raw data type required, 1 formula for each channel
• 2 = intensity transformation; raw data type or channels required, 1 formula for each channel
• 3 = column expression; raw data type or channels required, 1 formula only
• 4 = column restriction; raw data type or channels required, 1 formula only

Hibernate: property

column="`type`" type="int" not-null="true"

setType

public void setType(int type)

getValueType

public Integer getValueType()

The code for the value type. null = not known or doesn't care.

Since:

2.15

Hibernate: property

column="`value_type`" type="int" not-null="false"

setValueType

public void setValueType(Integer valueType)

Since:

2.15

getSourceIntensityTransform

public Integer getSourceIntensityTransform()

A flag indicating what kind of spot source data that the formula can be used with, or null if the formula can be used with any kind of source data. 0 = no transformation; 1 = 2-log; 2 = 10-log

Since:

2.12

Hibernate: property

column="`source_transform`" type="int" not-null="false"

setSourceIntensityTransform

public void setSourceIntensityTransform(Integer sourceIntensityTransform)

Since:

2.12

getResultIntensityTransform

public Integer getResultIntensityTransform()

A flag indicating what kind of result spot data this formula generates, or null if it generates the same kind of data that is used as source. 0 = no transformation; 1 = 2-log; 2 = 10-log

Since:

2.12

Hibernate: property

column="`result_transform`" type="int" not-null="false"

setResultIntensityTransform

public void setResultIntensityTransform(Integer resultIntensityTransform)

Since:

2.12

getParser

public int getParser()

Which parser to use to convert the formula to an expression or restriction. 1 = JEP

Hibernate: property

column="`parser`" type="int" not-null="true"

setParser

public void setParser(int parser)

getRawDataType

public String getRawDataType()

The name of raw data type this formula can be used on, or null if it can be used on any raw data type.

Hibernate: property

column="`rawdatatype`" type="string" length="255" not-null="false"

setRawDataType

public void setRawDataType(String rawDataType)

getChannels

public int getChannels()

The number of required channels in the experiment to use this formula, or 0 if the number of channels doesn't matter.

Hibernate: property

column="`channels`" type="int" not-null="true"

setChannels

public void setChannels(int channels)

getFormulas

public List<String> getFormulas()

Get the list of formulas.

Hibernate: list

table="`FormulaExpressions`" lazy="true"

Hibernate: collection-key

column="`formula_id`"

Hibernate: collection-index

column="`index`" type="int"

Hibernate: collection-element

column="`formula`" type="string" length="255" not-null="true"

setFormulas

void setFormulas(List<String> formulas)

getColoring

public ColoringData getColoring()

Get the coloring information for this formula.

Hibernate: component

setColoring

public void setColoring(ColoringData coloring)