Class ValidationQcParameters
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.advanced.ValidationQcParameters
- All Implemented Interfaces:
Serializable
public class ValidationQcParameters extends ExperimentObject
This class lists the criteria used for quality control of the validated
matches.
- Author:
- Marc Vaudel, Harald Barsnes
- See Also:
- Serialized Form
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Field Summary
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Constructor Summary
Constructors Constructor Description ValidationQcParameters()
Creates a validation quality control preferences object with default settings.ValidationQcParameters(ValidationQcParameters validationQCPreferences)
Creates a validation quality control preferences object based on an other ValidationQCPreferences. -
Method Summary
Modifier and Type Method Description Double
getConfidenceMargin()
Returns the margin to the threshold to use as factor of the resolution.ArrayList<Filter>
getPeptideFilters()
Returns the list of peptide quality filters.ArrayList<Filter>
getProteinFilters()
Returns the list of protein quality filters.ArrayList<Filter>
getPsmFilters()
Returns the list of PSM quality filters.String
getShortDescription()
Returns a short description of the parameters.boolean
isDbSize()
Indicates whether the database size should be checked.boolean
isFirstDecoy()
Indicates whether the number of hits before the first decoy should be checked.boolean
isSameAs(ValidationQcParameters validationQCPreferences)
Returns true if the two ValidationQCPreferences are the same.void
setConfidenceMargin(Double confidenceMargin)
Sets the margin to the threshold to use as factor of the resolution.void
setDbSize(boolean dbSize)
Sets whether the database size should be checked.void
setFirstDecoy(boolean firstDecoy)
Sets whether the number of hits before the first decoy should be checked.void
setPeptideFilters(ArrayList<Filter> peptideFilters)
Sets the list of peptide quality filters.void
setProteinFilters(ArrayList<Filter> proteinFilters)
Sets the list of protein quality filters.void
setPsmFilters(ArrayList<Filter> psmFilters)
Sets the list of PSM quality filters.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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ValidationQcParameters
public ValidationQcParameters()Creates a validation quality control preferences object with default settings. -
ValidationQcParameters
Creates a validation quality control preferences object based on an other ValidationQCPreferences.- Parameters:
validationQCPreferences
- an other ValidationQCPreferences
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Method Details
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isDbSize
public boolean isDbSize()Indicates whether the database size should be checked.- Returns:
- true if the database size should be checked
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setDbSize
public void setDbSize(boolean dbSize)Sets whether the database size should be checked.- Parameters:
dbSize
- a boolean indicating whether the database size should be checked
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isFirstDecoy
public boolean isFirstDecoy()Indicates whether the number of hits before the first decoy should be checked.- Returns:
- true if the number of hits before the first decoy should be checked
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setFirstDecoy
public void setFirstDecoy(boolean firstDecoy)Sets whether the number of hits before the first decoy should be checked.- Parameters:
firstDecoy
- a boolean indicating whether the number of hits before the first decoy should be checked.
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getConfidenceMargin
Returns the margin to the threshold to use as factor of the resolution. e.g. for a threshold of 10% and a resolution of 1%, with a factor of 1 the threshold will be 11%, with a factor of 2.5 the threshold will be 12.5%.- Returns:
- the margin to the threshold to use as factor of the resolution
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setConfidenceMargin
Sets the margin to the threshold to use as factor of the resolution. e.g. for a threshold of 10% and a resolution of 1%, with a factor of 1 the threshold will be 11%, with a factor of 2.5 the threshold will be 12.5%.- Parameters:
confidenceMargin
- the margin to the threshold to use as factor of the resolution
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getPsmFilters
Returns the list of PSM quality filters.- Returns:
- the list of PSM quality filters
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setPsmFilters
Sets the list of PSM quality filters.- Parameters:
psmFilters
- the list of PSM quality filters
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getPeptideFilters
Returns the list of peptide quality filters.- Returns:
- the list of peptide quality filters
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setPeptideFilters
Sets the list of peptide quality filters.- Parameters:
peptideFilters
- the list of peptide quality filters
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getProteinFilters
Returns the list of protein quality filters.- Returns:
- the list of peptide quality filters
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setProteinFilters
Sets the list of protein quality filters.- Parameters:
proteinFilters
- the list of protein quality filters
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isSameAs
Returns true if the two ValidationQCPreferences are the same.- Parameters:
validationQCPreferences
- the ValidationQCPreferences to compare to- Returns:
- true if the two ValidationQCPreferences are the same
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getShortDescription
Returns a short description of the parameters.- Returns:
- a short description of the parameters
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