Package 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
, Developer documentation: Other classes- Hibernate: class
- table="`Formulas`" lazy="false"
-
-
Field Summary
Fields Modifier and Type Field Description 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
Constructors Constructor Description FormulaData()
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description 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 = JEPString
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-logInteger
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-logint
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 onlyInteger
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, getRemovedBy, setDescription, setName, setRemovedBy
-
Methods inherited from class net.sf.basedb.core.data.SharedData
getItemKey, getProjectKey, setItemKey, setProjectKey
-
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
-
coloring
private ColoringData coloring
-
-
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 interfaceRegisteredData
-
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"
- 0 = none,
-
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"
-
getColoring
public ColoringData getColoring()
Get the coloring information for this formula.- Hibernate: component
-
setColoring
public void setColoring(ColoringData coloring)
-
-