public class CometParameters extends Object implements IdentificationAlgorithmParameter
Modifier and Type | Class and Description |
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static class |
CometParameters.CometOutputFormat
The available output formats.
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Constructor and Description |
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CometParameters()
Constructor.
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Modifier and Type | Method and Description |
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boolean |
equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
Indicates whether another identificationAlgorithmParameter has the same
parameters.
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Advocate |
getAlgorithm()
Returns the identification algorithm.
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Integer |
getBatchSize()
Returns the batch size.
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Integer |
getEnzymeType()
Returns the enzyme type.
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Double |
getFragmentBinOffset()
Returns the fragment ion bin offset.
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Integer |
getIsotopeCorrection()
Returns the isotope correction setting.
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Double |
getLowerClearMzRange()
Returns the lower mass value for the clear mz range.
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Integer |
getMaxFragmentCharge()
Returns the maximum fragment ion charge.
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Double |
getMaxPrecursorMass()
Returns the maximum precursor mass.
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Integer |
getMaxVariableMods()
Returns the maximum number of variable modifications per peptide.
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Double |
getMinPeakIntensity()
Returns the minimum peak intensity.
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Integer |
getMinPeaks()
Returns the minimum number of peaks.
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Double |
getMinPrecursorMass()
Returns the minimum precursor mass.
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Integer |
getNumberOfSpectrumMatches()
Returns the maximum number of spectrum matches.
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boolean |
getPrintExpectScore()
Returns true if the export score is to be printed.
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Boolean |
getRemoveMethionine()
Returns true if n-term methionine is to be removed.
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Integer |
getRemovePrecursor()
Returns if the precursor is to be removed.
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Double |
getRemovePrecursorTolerance()
Returns the precursor removal tolerance.
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boolean |
getRequireVariableMods()
Returns true if at least one variable modification is required per
peptide.
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CometParameters.CometOutputFormat |
getSelectedOutputFormat()
Returns the selected output format.
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Boolean |
getTheoreticalFragmentIonsSumOnly()
Returns true if the theoretical fragment ions are calculated on the sum
in the bin alone.
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Double |
getUpperClearMzRange()
Returns the upper mass value for the clear mz range.
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Boolean |
getUseSparseMatrix()
Deprecated.
from Comet release 2015.02 all searches use this internal
data representation by default
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void |
setBatchSize(Integer batchSize)
Set the batch size.
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void |
setEnzymeType(Integer enzymeType)
Set the enzyme type.
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void |
setFragmentBinOffset(Double fragmentBinOffset)
Set the fragment ion bin offset.
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void |
setIsotopeCorrection(Integer isotopeCorrection)
Set the isotope correction setting.
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void |
setLowerClearMzRange(Double lowerClearMzRange)
Set the lower mass value for the clear mz range.
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void |
setMaxFragmentCharge(Integer maxFragmentCharge)
Set the maximum fragment ion charge.
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void |
setMaxPrecursorMass(Double maxPrecursorMass)
Set the maximum precursor mass.
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void |
setMaxVariableMods(Integer maxVariableMods)
Set the maximum number of variable modifications per peptide.
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void |
setMinPeakIntensity(Double minPeakIntensity)
Set the minimum peak intensity.
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void |
setMinPeaks(Integer minPeaks)
Set the minimum number of peaks.
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void |
setMinPrecursorMass(Double minPrecursorMass)
Set the minimum precursor mass.
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void |
setNumberOfSpectrumMatches(Integer numberOfSpectrumMarches)
Set the maximum number of spectrum matches.
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void |
setPrintExpectScore(boolean printExpectScore)
Set if the export score is to be printed.
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void |
setRemoveMethionine(Boolean removeMethionine)
Sets if n-term methionine is to be removed.
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void |
setRemovePrecursor(Integer removePrecursor)
Set if the precursor is to be removed.
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void |
setRemovePrecursorTolerance(Double removePrecursorTolerance)
Set the precursor removal tolerance.
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void |
setRequireVariableMods(Boolean requireVariableMods)
Set if at least one variable modification is required per peptide.
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void |
setSelectedOutputFormat(CometParameters.CometOutputFormat selectedOutputFormat)
Sets the output format.
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void |
setTheoreticalFragmentIonsSumOnly(Boolean theoreticalFragmentIonsSumOnly)
Set if the theoretical fragment ions are calculated on the sum in the bin
alone.
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void |
setUpperClearMzRange(Double upperClearMzRange)
Set the upper mass value for the clear mz range.
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void |
setUseSparseMatrix(Boolean useSparseMatrix)
Deprecated.
from Comet release 2015.02 all searches use this internal
data representation by default
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String |
toString(boolean html)
Returns the parameters as a string.
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public Advocate getAlgorithm()
IdentificationAlgorithmParameter
getAlgorithm
in interface IdentificationAlgorithmParameter
public boolean equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
IdentificationAlgorithmParameter
equals
in interface IdentificationAlgorithmParameter
identificationAlgorithmParameter
- the other
identificationAlgorithmParameterpublic String toString(boolean html)
IdentificationAlgorithmParameter
toString
in interface IdentificationAlgorithmParameter
html
- use HTML formattingpublic Integer getNumberOfSpectrumMatches()
public void setNumberOfSpectrumMatches(Integer numberOfSpectrumMarches)
numberOfSpectrumMarches
- the numberOfSpectrumMarches to setpublic Integer getMaxVariableMods()
public void setMaxVariableMods(Integer maxVariableMods)
maxVariableMods
- the maxVariableMods to setpublic Integer getMinPeaks()
public void setMinPeaks(Integer minPeaks)
minPeaks
- the minPeaks to setpublic Double getMinPeakIntensity()
public void setMinPeakIntensity(Double minPeakIntensity)
minPeakIntensity
- the minPeakIntensity to setpublic Integer getRemovePrecursor()
public void setRemovePrecursor(Integer removePrecursor)
removePrecursor
- the removePrecursor to setpublic Double getRemovePrecursorTolerance()
public void setRemovePrecursorTolerance(Double removePrecursorTolerance)
removePrecursorTolerance
- the removePrecursorTolerance to setpublic Double getLowerClearMzRange()
public void setLowerClearMzRange(Double lowerClearMzRange)
lowerClearMzRange
- the lowerClearMzRange to setpublic Double getUpperClearMzRange()
public void setUpperClearMzRange(Double upperClearMzRange)
upperClearMzRange
- the upperClearMzRange to setpublic Integer getEnzymeType()
public void setEnzymeType(Integer enzymeType)
enzymeType
- the enzymeType to setpublic Integer getIsotopeCorrection()
public void setIsotopeCorrection(Integer isotopeCorrection)
isotopeCorrection
- the isotopeCorrection to setpublic Double getMinPrecursorMass()
public void setMinPrecursorMass(Double minPrecursorMass)
minPrecursorMass
- the minPrecursorMass to setpublic Double getMaxPrecursorMass()
public void setMaxPrecursorMass(Double maxPrecursorMass)
maxPrecursorMass
- the maxPrecursorMass to setpublic Integer getMaxFragmentCharge()
public void setMaxFragmentCharge(Integer maxFragmentCharge)
maxFragmentCharge
- the maxFragmentCharge to setpublic Boolean getRemoveMethionine()
public void setRemoveMethionine(Boolean removeMethionine)
removeMethionine
- the removeMethionine to setpublic Integer getBatchSize()
public void setBatchSize(Integer batchSize)
batchSize
- the batchSize to setpublic Boolean getTheoreticalFragmentIonsSumOnly()
public void setTheoreticalFragmentIonsSumOnly(Boolean theoreticalFragmentIonsSumOnly)
theoreticalFragmentIonsSumOnly
- the theoreticalFragmentIonsSumOnly
to setpublic Double getFragmentBinOffset()
public void setFragmentBinOffset(Double fragmentBinOffset)
fragmentBinOffset
- the fragmentBinOffset to setpublic Boolean getUseSparseMatrix()
public void setUseSparseMatrix(Boolean useSparseMatrix)
useSparseMatrix
- the useSparseMatrix to setpublic boolean getRequireVariableMods()
public void setRequireVariableMods(Boolean requireVariableMods)
requireVariableMods
- the requireVariableMods to setpublic boolean getPrintExpectScore()
public void setPrintExpectScore(boolean printExpectScore)
printExpectScore
- the printExpectScore to setpublic CometParameters.CometOutputFormat getSelectedOutputFormat()
public void setSelectedOutputFormat(CometParameters.CometOutputFormat selectedOutputFormat)
selectedOutputFormat
- the output formatCopyright © 2016. All rights reserved.