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
This class holds information about a formula used in the analysis of raw data
and bioassay sets.
- Version:
- 2.0
- Author:
- Nicklas
- See Also:
- Hibernate: class
- table="`Formulas`" lazy="false"
-
Field Summary
Modifier and TypeFieldDescriptionprivate int
private int
private ColoringData
private Date
static final int
The maximum allowed length of a formula.static final int
The maximum allowed length of the raw data type name.private int
private String
private Integer
private Integer
private int
private Integer
Fields inherited from interface net.sf.basedb.core.data.NameableData
MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH
-
Constructor Summary
-
Method Summary
Modifier and TypeMethodDescriptionint
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
The number of required channels in the experiment to use this formula, or 0 if the number of channels doesn't matter.Get the coloring information for this formula.Get the date this item was added to the database.Get the list of formulas.int
Which parser to use to convert the formula to an expression or restriction. 1 = JEPThe name of raw data type this formula can be used on, or null if it can be used on any raw data type.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-logA 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 onlyThe 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 Details
-
entryDate
-
averageMethod
private int averageMethod -
type
private int type -
valueType
-
sourceIntensityTransform
-
resultIntensityTransform
-
parser
private int parser -
MAX_RAWDATATYPE_LENGTH
public static final int MAX_RAWDATATYPE_LENGTHThe maximum allowed length of the raw data type name.- See Also:
-
rawDataType
-
channels
private int channels -
MAX_FORMULA_LENGTH
public static final int MAX_FORMULA_LENGTHThe maximum allowed length of a formula.- See Also:
-
formulas
-
coloring
-
-
Constructor Details
-
FormulaData
public FormulaData()
-
-
Method Details
-
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
-
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
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
- Since:
- 2.15
-
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
- Since:
- 2.12
-
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
- 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
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
-
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
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
-
getColoring
Get the coloring information for this formula.- Hibernate: component
-
setColoring
-