Class SpectrumCountingParameters
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
- All Implemented Interfaces:
Serializable
public class SpectrumCountingParameters extends ExperimentObject
This class contains the spectrum counting parameters.
- Author:
- Marc Vaudel, Harald Barsnes
- See Also:
- Serialized Form
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Field Summary
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Constructor Summary
Constructors Constructor Description SpectrumCountingParameters()
Default constructor.SpectrumCountingParameters(SpectrumCountingParameters otherSpectrumCountingPreferences)
Creates new preferences based on other spectrum counting preferences. -
Method Summary
Modifier and Type Method Description Integer
getMatchValidationLevel()
Returns the lowest validation level considered as an integer as indexed in the MatchValidationLevel enum.Boolean
getNormalize()
Indicates whether the spectrum counting index should be normalized.Double
getReferenceMass()
Returns the reference total mass to use for normalization.SpectrumCountingMethod
getSelectedMethod()
Returns the current spectrum counting method.UnitOfMeasurement
getUnit()
Returns the unit used for normalization.boolean
isSameAs(SpectrumCountingParameters anotherSpectrumCountingPreferences)
Compares two spectrum counting preferences.void
setMatchValidationLevel(Integer matchValidationLevel)
Sets the lowest validation level to consider as an integer as indexed in the MatchValidationLevel enum.void
setNormalize(Boolean normalize)
Sets whether the spectrum counting index should be normalized.void
setReferenceMass(Double referenceMass)
Sets the reference total mass to use for normalization.void
setSelectedMethod(SpectrumCountingMethod selectedMethod)
Set the current spectrum counting method.void
setUnit(UnitOfMeasurement unit)
Sets the unit used for normalization.Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
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Constructor Details
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SpectrumCountingParameters
public SpectrumCountingParameters()Default constructor. -
SpectrumCountingParameters
Creates new preferences based on other spectrum counting preferences.- Parameters:
otherSpectrumCountingPreferences
- the other spectrum counting preferences
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Method Details
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getSelectedMethod
Returns the current spectrum counting method.- Returns:
- the current spectrum counting method
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setSelectedMethod
Set the current spectrum counting method.- Parameters:
selectedMethod
- the spectral counting method
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getMatchValidationLevel
Returns the lowest validation level considered as an integer as indexed in the MatchValidationLevel enum.- Returns:
- the lowest validation level considered
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setMatchValidationLevel
Sets the lowest validation level to consider as an integer as indexed in the MatchValidationLevel enum.- Parameters:
matchValidationLevel
- the lowest validation level to consider
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isSameAs
Compares two spectrum counting preferences.- Parameters:
anotherSpectrumCountingPreferences
- another spectrum counting preferences- Returns:
- a boolean indicating whether the other spectrum counting preferences is the same as this one
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getReferenceMass
Returns the reference total mass to use for normalization.- Returns:
- the reference total mass to use for normalization in μg
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setReferenceMass
Sets the reference total mass to use for normalization.- Parameters:
referenceMass
- the reference total mass to use for normalization in μg
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getUnit
Returns the unit used for normalization.- Returns:
- the unit used for normalization
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setUnit
Sets the unit used for normalization.- Parameters:
unit
- the unit used for normalization
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getNormalize
Indicates whether the spectrum counting index should be normalized.- Returns:
- true if the spectrum counting index should be normalized
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setNormalize
Sets whether the spectrum counting index should be normalized.- Parameters:
normalize
- a boolean indicating whether the spectrum counting index should be normalized
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