Class CometParameters
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.tool_specific.CometParameters
- All Implemented Interfaces:
IdentificationAlgorithmParameter
,Serializable
public class CometParameters extends ExperimentObject implements IdentificationAlgorithmParameter
The Comet specific parameters.
- Author:
- Harald Barsnes
- See Also:
- Serialized Form
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
CometParameters.CometOutputFormat
The available output formats. -
Field Summary
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Constructor Summary
Constructors Constructor Description CometParameters()
Constructor. -
Method Summary
Modifier and Type Method Description boolean
equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
Indicates whether another identificationAlgorithmParameter has the same parameters.Advocate
getAlgorithm()
Returns the identification algorithm.Integer
getBatchSize()
Returns the batch size.Integer
getEnzymeType()
Returns the enzyme type.Double
getFragmentBinOffset()
Returns the fragment ion bin offset.Integer
getIsotopeCorrection()
Returns the isotope correction setting.Double
getLowerClearMzRange()
Returns the lower mass value for the clear mz range.Integer
getMaxFragmentCharge()
Returns the maximum fragment ion charge.Integer
getMaxPeptideLength()
Returns the maximal peptide length allowed.Double
getMaxPrecursorMass()
Returns the maximum precursor mass.Integer
getMaxVariableMods()
Returns the maximum number of variable modifications per peptide.Double
getMinPeakIntensity()
Returns the minimum peak intensity.Integer
getMinPeaks()
Returns the minimum number of peaks.Integer
getMinPeptideLength()
Sets the minimal peptide length allowed.Double
getMinPrecursorMass()
Returns the minimum precursor mass.Integer
getNumberOfSpectrumMatches()
Returns the maximum number of spectrum matches.boolean
getPrintExpectScore()
Returns true if the export score is to be printed.Boolean
getRemoveMethionine()
Returns true if n-term methionine is to be removed.Integer
getRemovePrecursor()
Returns if the precursor is to be removed.Double
getRemovePrecursorTolerance()
Returns the precursor removal tolerance.boolean
getRequireVariableMods()
Returns true if at least one variable modification is required per peptide.CometParameters.CometOutputFormat
getSelectedOutputFormat()
Returns the selected output format.Boolean
getTheoreticalFragmentIonsSumOnly()
Returns true if the theoretical fragment ions are calculated on the sum in the bin alone.Double
getUpperClearMzRange()
Returns the upper mass value for the clear mz range.Boolean
getUseSparseMatrix()
Deprecated.from Comet release 2015.02 all searches use this internal data representation by defaultvoid
setBatchSize(Integer batchSize)
Set the batch size.void
setEnzymeType(Integer enzymeType)
Set the enzyme type.void
setFragmentBinOffset(Double fragmentBinOffset)
Set the fragment ion bin offset.void
setIsotopeCorrection(Integer isotopeCorrection)
Set the isotope correction setting.void
setLowerClearMzRange(Double lowerClearMzRange)
Set the lower mass value for the clear mz range.void
setMaxFragmentCharge(Integer maxFragmentCharge)
Set the maximum fragment ion charge.void
setMaxPeptideLength(int maxPeptideLength)
Sets the maximal peptide length allowed.void
setMaxPrecursorMass(Double maxPrecursorMass)
Set the maximum precursor mass.void
setMaxVariableMods(Integer maxVariableMods)
Set the maximum number of variable modifications per peptide.void
setMinPeakIntensity(Double minPeakIntensity)
Set the minimum peak intensity.void
setMinPeaks(Integer minPeaks)
Set the minimum number of peaks.void
setMinPeptideLength(int minPeptideLength)
Sets the minimal peptide length allowed.void
setMinPrecursorMass(Double minPrecursorMass)
Set the minimum precursor mass.void
setNumberOfSpectrumMatches(Integer numberOfSpectrumMarches)
Set the maximum number of spectrum matches.void
setPrintExpectScore(boolean printExpectScore)
Set if the export score is to be printed.void
setRemoveMethionine(Boolean removeMethionine)
Sets if n-term methionine is to be removed.void
setRemovePrecursor(Integer removePrecursor)
Set if the precursor is to be removed.void
setRemovePrecursorTolerance(Double removePrecursorTolerance)
Set the precursor removal tolerance.void
setRequireVariableMods(Boolean requireVariableMods)
Set if at least one variable modification is required per peptide.void
setSelectedOutputFormat(CometParameters.CometOutputFormat selectedOutputFormat)
Sets the output format.void
setTheoreticalFragmentIonsSumOnly(Boolean theoreticalFragmentIonsSumOnly)
Set if the theoretical fragment ions are calculated on the sum in the bin alone.void
setUpperClearMzRange(Double upperClearMzRange)
Set the upper mass value for the clear mz range.void
setUseSparseMatrix(Boolean useSparseMatrix)
Deprecated.from Comet release 2015.02 all searches use this internal data representation by defaultString
toString(boolean html)
Returns the parameters as a string.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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CometParameters
public CometParameters()Constructor.
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Method Details
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getAlgorithm
Description copied from interface:IdentificationAlgorithmParameter
Returns the identification algorithm.- Specified by:
getAlgorithm
in interfaceIdentificationAlgorithmParameter
- Returns:
- the identification algorithm
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equals
Description copied from interface:IdentificationAlgorithmParameter
Indicates whether another identificationAlgorithmParameter has the same parameters.- Specified by:
equals
in interfaceIdentificationAlgorithmParameter
- Parameters:
identificationAlgorithmParameter
- the other identificationAlgorithmParameter- Returns:
- true if the algorithm and parameters are the same
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toString
Description copied from interface:IdentificationAlgorithmParameter
Returns the parameters as a string.- Specified by:
toString
in interfaceIdentificationAlgorithmParameter
- Parameters:
html
- use HTML formatting- Returns:
- the parameters as a string
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getNumberOfSpectrumMatches
Returns the maximum number of spectrum matches.- Returns:
- the numberOfSpectrumMarches
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setNumberOfSpectrumMatches
Set the maximum number of spectrum matches.- Parameters:
numberOfSpectrumMarches
- the numberOfSpectrumMarches to set
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getMaxVariableMods
Returns the maximum number of variable modifications per peptide.- Returns:
- the maxVariableMods
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setMaxVariableMods
Set the maximum number of variable modifications per peptide.- Parameters:
maxVariableMods
- the maxVariableMods to set
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getMinPeaks
Returns the minimum number of peaks.- Returns:
- the minPeaks
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setMinPeaks
Set the minimum number of peaks.- Parameters:
minPeaks
- the minPeaks to set
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getMinPeakIntensity
Returns the minimum peak intensity.- Returns:
- the minPeakIntensity
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setMinPeakIntensity
Set the minimum peak intensity.- Parameters:
minPeakIntensity
- the minPeakIntensity to set
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getRemovePrecursor
Returns if the precursor is to be removed.- Returns:
- the removePrecursor
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setRemovePrecursor
Set if the precursor is to be removed.- Parameters:
removePrecursor
- the removePrecursor to set
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getRemovePrecursorTolerance
Returns the precursor removal tolerance.- Returns:
- the removePrecursorTolerance
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setRemovePrecursorTolerance
Set the precursor removal tolerance.- Parameters:
removePrecursorTolerance
- the removePrecursorTolerance to set
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getLowerClearMzRange
Returns the lower mass value for the clear mz range.- Returns:
- the lowerClearMzRange
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setLowerClearMzRange
Set the lower mass value for the clear mz range.- Parameters:
lowerClearMzRange
- the lowerClearMzRange to set
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getUpperClearMzRange
Returns the upper mass value for the clear mz range.- Returns:
- the upperClearMzRange
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setUpperClearMzRange
Set the upper mass value for the clear mz range.- Parameters:
upperClearMzRange
- the upperClearMzRange to set
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getEnzymeType
Returns the enzyme type.- Returns:
- the enzymeType
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setEnzymeType
Set the enzyme type.- Parameters:
enzymeType
- the enzymeType to set
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getIsotopeCorrection
Returns the isotope correction setting.- Returns:
- the isotopeCorrection
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setIsotopeCorrection
Set the isotope correction setting.- Parameters:
isotopeCorrection
- the isotopeCorrection to set
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getMinPrecursorMass
Returns the minimum precursor mass.- Returns:
- the minPrecursorMass
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setMinPrecursorMass
Set the minimum precursor mass.- Parameters:
minPrecursorMass
- the minPrecursorMass to set
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getMaxPrecursorMass
Returns the maximum precursor mass.- Returns:
- the maxPrecursorMass
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setMaxPrecursorMass
Set the maximum precursor mass.- Parameters:
maxPrecursorMass
- the maxPrecursorMass to set
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getMaxFragmentCharge
Returns the maximum fragment ion charge.- Returns:
- the maxFragmentCharge
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setMaxFragmentCharge
Set the maximum fragment ion charge.- Parameters:
maxFragmentCharge
- the maxFragmentCharge to set
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getRemoveMethionine
Returns true if n-term methionine is to be removed.- Returns:
- the removeMethionine
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setRemoveMethionine
Sets if n-term methionine is to be removed.- Parameters:
removeMethionine
- the removeMethionine to set
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getBatchSize
Returns the batch size.- Returns:
- the batchSize
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setBatchSize
Set the batch size.- Parameters:
batchSize
- the batchSize to set
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getTheoreticalFragmentIonsSumOnly
Returns true if the theoretical fragment ions are calculated on the sum in the bin alone. False means that flanking bins are used as well.- Returns:
- the theoreticalFragmentIonsSumOnly
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setTheoreticalFragmentIonsSumOnly
Set if the theoretical fragment ions are calculated on the sum in the bin alone. False means that flanking bins are used as well.- Parameters:
theoreticalFragmentIonsSumOnly
- the theoreticalFragmentIonsSumOnly to set
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getFragmentBinOffset
Returns the fragment ion bin offset.- Returns:
- the fragmentBinOffset
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setFragmentBinOffset
Set the fragment ion bin offset.- Parameters:
fragmentBinOffset
- the fragmentBinOffset to set
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getUseSparseMatrix
Deprecated.from Comet release 2015.02 all searches use this internal data representation by defaultReturns true if a sparse matrix is to be used.- Returns:
- the useSparseMatrix
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setUseSparseMatrix
Deprecated.from Comet release 2015.02 all searches use this internal data representation by defaultSet if a sparse matrix is to be used.- Parameters:
useSparseMatrix
- the useSparseMatrix to set
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getRequireVariableMods
public boolean getRequireVariableMods()Returns true if at least one variable modification is required per peptide.- Returns:
- the requireVariableMods
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setRequireVariableMods
Set if at least one variable modification is required per peptide.- Parameters:
requireVariableMods
- the requireVariableMods to set
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getPrintExpectScore
public boolean getPrintExpectScore()Returns true if the export score is to be printed.- Returns:
- true if the export score is to be printed
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setPrintExpectScore
public void setPrintExpectScore(boolean printExpectScore)Set if the export score is to be printed.- Parameters:
printExpectScore
- the printExpectScore to set
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getSelectedOutputFormat
Returns the selected output format.- Returns:
- the selected output format
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setSelectedOutputFormat
Sets the output format.- Parameters:
selectedOutputFormat
- the output format
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getMaxPeptideLength
Returns the maximal peptide length allowed.- Returns:
- the maximal peptide length allowed
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setMaxPeptideLength
public void setMaxPeptideLength(int maxPeptideLength)Sets the maximal peptide length allowed.- Parameters:
maxPeptideLength
- the maximal peptide length allowed
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getMinPeptideLength
Sets the minimal peptide length allowed.- Returns:
- the minimal peptide length allowed
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setMinPeptideLength
public void setMinPeptideLength(int minPeptideLength)Sets the minimal peptide length allowed.- Parameters:
minPeptideLength
- the minimal peptide length allowed
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