Package de.isas.mztab2.model
Class StudyVariable
- java.lang.Object
-
- de.isas.mztab2.model.StudyVariable
-
@Generated(value="io.swagger.codegen.languages.JavaClientCodegen", date="2021-01-02T19:25:37.430+01:00") public class StudyVariable extends Object
Specification of study_variable. (empty) name: A name for each study variable (experimental condition or factor), to serve as a list of the study variables that MUST be reported in the following tables. For software that does not capture study variables, a single study variable MUST be reported, linking to all assays. This single study variable MUST have the identifier “undefined“. assay_refs: Bar-separated references to the IDs of assays grouped in the study variable. average_function: The function used to calculate the study variable quantification value and the operation used is not arithmetic mean (default) e.g. “geometric mean”, “median”. The 1-n refers to different study variables. variation_function: The function used to calculate the study variable quantification variation value if it is reported and the operation used is not coefficient of variation (default) e.g. “standard error”. description: A textual description of the study variable. factors: Additional parameters or factors, separated by bars, that are known about study variables allowing the capture of more complex, such as nested designs.mzTab-M specification example(s):
MTD study_variable[1] control MTD study_variable[1]-assay_refs assay[1]| assay[2]| assay[3] MTD study_variable-average_function [MS, MS:1002883, median, ] MTD study_variable-variation_function [MS, MS:1002885, standard error, ] MTD study_variable[1]-description Group B (spike-in 0.74 fmol/uL) MTD study_variable[1]-factors [,,time point, 1 minute]|[,,rapamycin dose,0.5mg] MTD study_variable[2] 1 minute 0.5mg rapamycin
-
-
Nested Class Summary
Nested Classes Modifier and Type Class Description static class
StudyVariable.Properties
Property enumeration for StudyVariable.
-
Constructor Summary
Constructors Constructor Description StudyVariable()
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description StudyVariable
addAssayRefsItem(Assay assayRefsItem)
Add a single assayRefsItem to the assayRefs collection.StudyVariable
addFactorsItem(Parameter factorsItem)
Add a single factorsItem to the factors collection.StudyVariable
assayRefs(List<Assay> assayRefs)
Builder method for assayRefs.StudyVariable
averageFunction(Parameter averageFunction)
Builder method for averageFunction.StudyVariable
description(String description)
Builder method for description.boolean
equals(Object o)
StudyVariable
factors(List<Parameter> factors)
Builder method for factors.@Valid List<Assay>
getAssayRefs()
The assays referenced by this study variable.@Valid Parameter
getAverageFunction()
The function used to calculate summarised small molecule quantities over the assays referenced by this study variable.String
getDescription()
A free-form description of this study variable.@Valid List<Parameter>
getFactors()
Parameters indicating which factors were used for the assays referenced by this study variable, and at which levels.@NotNull @Min(1L) Integer
getId()
Get id.@NotNull String
getName()
The study variable name.@Valid Parameter
getVariationFunction()
The function used to calculate the variation of small molecule quantities over the assays referenced by this study variable.int
hashCode()
StudyVariable
id(Integer id)
Builder method for id.StudyVariable
name(String name)
Builder method for name.void
setAssayRefs(List<Assay> assayRefs)
Set assayRefs.void
setAverageFunction(Parameter averageFunction)
Set averageFunction.void
setDescription(String description)
Set description.void
setFactors(List<Parameter> factors)
Set factors.void
setId(Integer id)
Set id.void
setName(String name)
Set name.void
setVariationFunction(Parameter variationFunction)
Set variationFunction.String
toString()
StudyVariable
variationFunction(Parameter variationFunction)
Builder method for variationFunction.
-
-
-
Constructor Detail
-
StudyVariable
public StudyVariable()
-
-
Method Detail
-
id
public StudyVariable id(Integer id)
Builder method for id.- Parameters:
id
- aInteger
parameter.- Returns:
- StudyVariable
- See Also:
StudyVariable#setId for specification examples
,StudyVariable#getId for validation constraints
-
setId
public void setId(Integer id)
Set id.- Parameters:
id
- aInteger
parameter.- See Also:
StudyVariable#getId for validation constraints
-
name
public StudyVariable name(String name)
Builder method for name.- Parameters:
name
- aString
parameter.- Returns:
- StudyVariable
- See Also:
StudyVariable#setName for specification examples
,StudyVariable#getName for validation constraints
-
setName
public void setName(String name)
Set name.- Parameters:
name
- aString
parameter.- See Also:
StudyVariable#getName for validation constraints
-
assayRefs
public StudyVariable assayRefs(List<Assay> assayRefs)
Builder method for assayRefs.- Parameters:
assayRefs
- aList<Assay>
parameter.- Returns:
- StudyVariable
- See Also:
StudyVariable#setAssayRefs for specification examples
,StudyVariable#getAssayRefs for validation constraints
-
addAssayRefsItem
public StudyVariable addAssayRefsItem(Assay assayRefsItem)
Add a single assayRefsItem to the assayRefs collection.- Parameters:
assayRefsItem
- aAssay
parameter.- Returns:
- StudyVariable
- See Also:
StudyVariable#getAssayRefs for validation constraints
-
getAssayRefs
@Valid public @Valid List<Assay> getAssayRefs()
The assays referenced by this study variable.- Returns:
- assayRefs
-
setAssayRefs
public void setAssayRefs(List<Assay> assayRefs)
Set assayRefs.- Parameters:
assayRefs
- aList<Assay>
parameter.- See Also:
StudyVariable#getAssayRefs for validation constraints
-
averageFunction
public StudyVariable averageFunction(Parameter averageFunction)
Builder method for averageFunction.- Parameters:
averageFunction
- aParameter
parameter.- Returns:
- StudyVariable
- See Also:
StudyVariable#setAverageFunction for specification examples
,StudyVariable#getAverageFunction for validation constraints
-
getAverageFunction
@Valid public @Valid Parameter getAverageFunction()
The function used to calculate summarised small molecule quantities over the assays referenced by this study variable.- Returns:
- averageFunction
-
setAverageFunction
public void setAverageFunction(Parameter averageFunction)
Set averageFunction.- Parameters:
averageFunction
- aParameter
parameter.- See Also:
StudyVariable#getAverageFunction for validation constraints
-
variationFunction
public StudyVariable variationFunction(Parameter variationFunction)
Builder method for variationFunction.- Parameters:
variationFunction
- aParameter
parameter.- Returns:
- StudyVariable
- See Also:
StudyVariable#setVariationFunction for specification examples
,StudyVariable#getVariationFunction for validation constraints
-
getVariationFunction
@Valid public @Valid Parameter getVariationFunction()
The function used to calculate the variation of small molecule quantities over the assays referenced by this study variable.- Returns:
- variationFunction
-
setVariationFunction
public void setVariationFunction(Parameter variationFunction)
Set variationFunction.- Parameters:
variationFunction
- aParameter
parameter.- See Also:
StudyVariable#getVariationFunction for validation constraints
-
description
public StudyVariable description(String description)
Builder method for description.- Parameters:
description
- aString
parameter.- Returns:
- StudyVariable
- See Also:
StudyVariable#setDescription for specification examples
,StudyVariable#getDescription for validation constraints
-
getDescription
public String getDescription()
A free-form description of this study variable.- Returns:
- description
-
setDescription
public void setDescription(String description)
Set description.- Parameters:
description
- aString
parameter.- See Also:
StudyVariable#getDescription for validation constraints
-
factors
public StudyVariable factors(List<Parameter> factors)
Builder method for factors.- Parameters:
factors
- aList<Parameter>
parameter.- Returns:
- StudyVariable
- See Also:
StudyVariable#setFactors for specification examples
,StudyVariable#getFactors for validation constraints
-
addFactorsItem
public StudyVariable addFactorsItem(Parameter factorsItem)
Add a single factorsItem to the factors collection.- Parameters:
factorsItem
- aParameter
parameter.- Returns:
- StudyVariable
- See Also:
StudyVariable#getFactors for validation constraints
-
getFactors
@Valid public @Valid List<Parameter> getFactors()
Parameters indicating which factors were used for the assays referenced by this study variable, and at which levels.- Returns:
- factors
-
setFactors
public void setFactors(List<Parameter> factors)
Set factors.- Parameters:
factors
- aList<Parameter>
parameter.- See Also:
StudyVariable#getFactors for validation constraints
-
-