public class IdMatchValidationPreferences extends Object implements Serializable
Constructor and Description |
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IdMatchValidationPreferences()
Constructor for default settings.
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IdMatchValidationPreferences(IdMatchValidationPreferences idMatchValidationPreferences)
Creates a new IdMatchValidationPreferences based on the values of the
given IdMatchValidationPreferences.
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Modifier and Type | Method and Description |
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boolean |
equals(IdMatchValidationPreferences otherIdMatchValidationPreferences)
Returns true if the objects have identical settings.
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double |
getDefaultPeptideFDR()
Returns the default peptide FDR.
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double |
getDefaultProteinFDR()
Returns the default protein FDR.
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double |
getDefaultPsmFDR()
Returns the default PSM FDR.
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Boolean |
getMergeSmallSubgroups()
Indicates whether small subgroups of matches should be merged.
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Boolean |
getSeparatePeptides()
Returns a boolean indicating whether Peptides should be grouped according
to their modification status.
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Boolean |
getSeparatePsms()
Returns a boolean indicating whether PSMs should be grouped according to
their modification status.
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String |
getShortDescription()
Returns a short description of the parameters.
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ValidationQCPreferences |
getValidationQCPreferences()
Returns the validation QC preferences.
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void |
setDefaultPeptideFDR(double defaultPeptideFDR)
Sets the default peptide FDR.
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void |
setDefaultProteinFDR(double defaultProteinFDR)
Sets the default protein FDR.
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void |
setDefaultPsmFDR(double defaultPsmFDR)
Sets the default PSM FDR.
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void |
setMergeSmallSubgroups(Boolean mergeSmallSubgroups)
Sets whether small subgroups of matches should be merged.
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void |
setSeparatePeptides(Boolean separatePeptides)
Sets whether Peptides should be grouped according to their modification
status.
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void |
setSeparatePsms(Boolean separatePsms)
Sets whether PSMs should be grouped according to their modification
status.
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void |
setValidationQCPreferences(ValidationQCPreferences validationQCPreferences)
Sets the validation QC preferences.
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public IdMatchValidationPreferences()
public IdMatchValidationPreferences(IdMatchValidationPreferences idMatchValidationPreferences)
idMatchValidationPreferences
- an IdMatchValidationPreferences to
take default values from.public double getDefaultProteinFDR()
public void setDefaultProteinFDR(double defaultProteinFDR)
defaultProteinFDR
- the default protein FDRpublic double getDefaultPeptideFDR()
public void setDefaultPeptideFDR(double defaultPeptideFDR)
defaultPeptideFDR
- the default peptide FDRpublic double getDefaultPsmFDR()
public void setDefaultPsmFDR(double defaultPsmFDR)
defaultPsmFDR
- the default PSM FDRpublic ValidationQCPreferences getValidationQCPreferences()
public void setValidationQCPreferences(ValidationQCPreferences validationQCPreferences)
validationQCPreferences
- the validation QC preferencespublic Boolean getMergeSmallSubgroups()
public void setMergeSmallSubgroups(Boolean mergeSmallSubgroups)
mergeSmallSubgroups
- a boolean indicating whether small subgroups
of matches should be mergedpublic Boolean getSeparatePeptides()
public void setSeparatePeptides(Boolean separatePeptides)
separatePeptides
- a boolean indicating whether Peptides should be
grouped according to their modification statuspublic Boolean getSeparatePsms()
public void setSeparatePsms(Boolean separatePsms)
separatePsms
- a boolean indicating whether PSMs should be grouped
according to their modification statuspublic String getShortDescription()
public boolean equals(IdMatchValidationPreferences otherIdMatchValidationPreferences)
otherIdMatchValidationPreferences
- the IdMatchValidationPreferences
to compare toCopyright © 2016. All rights reserved.