public class ValidationQCPreferences extends Object implements Serializable
Constructor and Description |
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ValidationQCPreferences()
Creates a validation quality control preferences object with default
settings.
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ValidationQCPreferences(ValidationQCPreferences validationQCPreferences)
Creates a validation quality control preferences object based on an other
ValidationQCPreferences.
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Modifier and Type | Method and Description |
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Double |
getConfidenceMargin()
Returns the margin to the threshold to use as factor of the resolution.
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ArrayList<Filter> |
getPeptideFilters()
Returns the list of peptide quality filters.
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ArrayList<Filter> |
getProteinFilters()
Returns the list of protein quality filters.
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ArrayList<Filter> |
getPsmFilters()
Returns the list of PSM quality filters.
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String |
getShortDescription()
Returns a short description of the parameters.
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boolean |
isDbSize()
Indicates whether the database size should be checked.
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boolean |
isFirstDecoy()
Indicates whether the number of hits before the first decoy should be
checked.
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boolean |
isSameAs(ValidationQCPreferences validationQCPreferences)
Returns true if the two ValidationQCPreferences are the same.
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void |
setConfidenceMargin(Double confidenceMargin)
Sets the margin to the threshold to use as factor of the resolution.
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void |
setDbSize(boolean dbSize)
Sets whether the database size should be checked.
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void |
setFirstDecoy(boolean firstDecoy)
Sets whether the number of hits before the first decoy should be checked.
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void |
setPeptideFilters(ArrayList<Filter> peptideFilters)
Sets the list of peptide quality filters.
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void |
setProteinFilters(ArrayList<Filter> proteinFilters)
Sets the list of protein quality filters.
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void |
setPsmFilters(ArrayList<Filter> psmFilters)
Sets the list of PSM quality filters.
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public ValidationQCPreferences()
public ValidationQCPreferences(ValidationQCPreferences validationQCPreferences)
validationQCPreferences
- an other ValidationQCPreferencespublic boolean isDbSize()
public void setDbSize(boolean dbSize)
dbSize
- a boolean indicating whether the database size should be
checkedpublic boolean isFirstDecoy()
public void setFirstDecoy(boolean firstDecoy)
firstDecoy
- a boolean indicating whether the number of hits before
the first decoy should be checked.public Double getConfidenceMargin()
public void setConfidenceMargin(Double confidenceMargin)
confidenceMargin
- the margin to the threshold to use as factor of
the resolutionpublic ArrayList<Filter> getPsmFilters()
public void setPsmFilters(ArrayList<Filter> psmFilters)
psmFilters
- the list of PSM quality filterspublic ArrayList<Filter> getPeptideFilters()
public void setPeptideFilters(ArrayList<Filter> peptideFilters)
peptideFilters
- the list of peptide quality filterspublic ArrayList<Filter> getProteinFilters()
public void setProteinFilters(ArrayList<Filter> proteinFilters)
proteinFilters
- the list of protein quality filterspublic boolean isSameAs(ValidationQCPreferences validationQCPreferences)
validationQCPreferences
- the ValidationQCPreferences to compare topublic String getShortDescription()
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