public class MetaMorpheusParameters extends ExperimentObject implements IdentificationAlgorithmParameter
Modifier and Type | Class and Description |
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static class |
MetaMorpheusParameters.MetaMorpheusDecoyType
The available decoy types.
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static class |
MetaMorpheusParameters.MetaMorpheusDissociationType
The available dissociation types.
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static class |
MetaMorpheusParameters.MetaMorpheusFragmentationTerminusType
The available fragmentation terminus types.
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static class |
MetaMorpheusParameters.MetaMorpheusInitiatorMethionineBehaviorType
The available initiator methionine behavior types.
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static class |
MetaMorpheusParameters.MetaMorpheusMassDiffAcceptorType
The available mass difference acceptor types.
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static class |
MetaMorpheusParameters.MetaMorpheusSearchType
The available search types.
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static class |
MetaMorpheusParameters.MetaMorpheusToleranceType
The available decoy types.
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NO_KEY
Constructor and Description |
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MetaMorpheusParameters()
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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Double |
getDeconvolutionIntensityRatio()
Returns the deconvolution intensity ratio.
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Double |
getDeconvolutionMassTolerance()
Returns the deconvolution mass tolerance.
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MetaMorpheusParameters.MetaMorpheusToleranceType |
getDeconvolutionMassToleranceType()
Returns the deconvolution mass tolerance type.
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MetaMorpheusParameters.MetaMorpheusDecoyType |
getDecoyType()
Returns the decoy type.
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MetaMorpheusParameters.MetaMorpheusDissociationType |
getDissociationType()
Returns the dissociation type.
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Boolean |
getDoPrecursorDeconvolution()
Returns true if precursor deconvolution is to be carried out.
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MetaMorpheusParameters.MetaMorpheusFragmentationTerminusType |
getFragmentationTerminus()
Returns the fragmentation terminus.
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ArrayList<ModificationCategory> |
getGPtmCategories()
Returns the modification categories to include in the G-PTM search.
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MetaMorpheusParameters.MetaMorpheusInitiatorMethionineBehaviorType |
getInitiatorMethionineBehavior()
Returns the initiator methionine behavior.
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MetaMorpheusParameters.MetaMorpheusMassDiffAcceptorType |
getMassDiffAcceptorType()
Returns the mass difference acceptor type.
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Double |
getMaxFragmentSize()
Returns the max fragmentation size.
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Integer |
getMaxHeterozygousVariants()
Returns the max heterozygous variants.
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Integer |
getMaxModificationIsoforms()
Returns the max modification isoforms.
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Integer |
getMaxModsForPeptide()
Returns the max mods for peptide.
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Integer |
getMaxPeptideLength()
Returns the maximum peptide length.
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Double |
getMinAllowedIntensityRatioToBasePeak()
Returns the minimum allowed intensity ratio to base peak.
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Integer |
getMinPeptideLength()
Returns the minimum peptide length.
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Integer |
getMinVariantDepth()
Returns the min variant depth.
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Boolean |
getModPeptidesAreDifferent()
Returns true if modified peptides are considered different.
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Boolean |
getNoOneHitWonders()
Returns true if one hit wonders are excluded.
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Boolean |
getNormalizePeaksAcrossAllWindows()
Returns the normalize peaks across all windows.
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Integer |
getNumberOfPeaksToKeepPerWindow()
Return the number of peaks to keep per window.
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Integer |
getNumberOfWindows()
Returns the number of windows.
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Double |
getScoreCutoff()
Returns the score cut-off.
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Boolean |
getSearchTarget()
Returns true if target sequences are to be searched.
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MetaMorpheusParameters.MetaMorpheusSearchType |
getSearchType()
Returns the search type.
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Integer |
getTotalPartitions()
Returns total partitions.
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Boolean |
getTrimMs1Peaks()
Returns true if Ms1 peaks are to be trimmed.
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Boolean |
getTrimMsMsPeaks()
Returns true if MsMs peaks are to be trimmed.
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boolean |
getUseDeltaScore()
Returns true of delta score is to be used.
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Boolean |
getUseProvidedPrecursorInfo()
Returns true of the provided precursor info is to be used.
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Double |
getWindowWidthThomsons()
Returns the window width in Thomson.
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Boolean |
getWriteMzId()
Returns true if mzId output is to be created.
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Boolean |
getWritePepXml()
Returns true if pepXML output is to be created.
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boolean |
runGptm()
Returns true if the G-PTM search is to be performed.
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void |
setDeconvolutionIntensityRatio(Double deconvolutionIntensityRatio)
Set the deconvolution intensity ratio.
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void |
setDeconvolutionMassTolerance(Double deconvolutionMassTolerance)
Set the deconvolution mass tolerance.
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void |
setDeconvolutionMassToleranceType(MetaMorpheusParameters.MetaMorpheusToleranceType deconvolutionMassToleranceType)
Set the deconvolution mass tolerance type.
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void |
setDecoyType(MetaMorpheusParameters.MetaMorpheusDecoyType decoyType)
Set the decoy type.
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void |
setDissociationType(MetaMorpheusParameters.MetaMorpheusDissociationType dissociationType)
Set the dissociation type.
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void |
setDoPrecursorDeconvolution(Boolean doPrecursorDeconvolution)
Set whether precursor deconvolution is to be carried out.
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void |
setFragmentationTerminus(MetaMorpheusParameters.MetaMorpheusFragmentationTerminusType fragmentationTerminus)
Set the fragmentation terminus.
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void |
setGPtmCategories(ArrayList<ModificationCategory> gPtmCategories)
Set the modification categories to include in the G-PTM search.
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void |
setInitiatorMethionineBehavior(MetaMorpheusParameters.MetaMorpheusInitiatorMethionineBehaviorType initiatorMethionineBehavior)
Set the initiator methionine behavior.
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void |
setMassDiffAcceptorType(MetaMorpheusParameters.MetaMorpheusMassDiffAcceptorType massDiffAcceptorType)
Set the mass difference acceptor type.
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void |
setMaxFragmentSize(Double maxFragmentSize)
Set the max fragmentation size.
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void |
setMaxHeterozygousVariants(Integer maxHeterozygousVariants)
Set the max heterozygous variants.
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void |
setMaxModificationIsoforms(Integer maxModificationIsoforms)
Set the max modification isoforms.
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void |
setMaxModsForPeptide(Integer maxModsForPeptide)
Set the max mods for peptide.
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void |
setMaxPeptideLength(Integer maxPeptideLength)
Set the maximum peptide length.
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void |
setMinAllowedIntensityRatioToBasePeak(Double minAllowedIntensityRatioToBasePeak)
Set the minimum allowed intensity ratio to base peak.
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void |
setMinPeptideLength(Integer minPeptideLength)
Set the minimum peptide length.
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void |
setMinVariantDepth(Integer minVariantDepth)
Set the min variant depth.
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void |
setModPeptidesAreDifferent(Boolean modPeptidesAreDifferent)
Set whether modified peptides are considered different.
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void |
setNoOneHitWonders(Boolean noOneHitWonders)
Set whether one hit wonders are to be excluded.
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void |
setNormalizePeaksAcrossAllWindows(Boolean normalizePeaksAcrossAllWindows)
Set the normalize peaks across all windows.
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void |
setNumberOfPeaksToKeepPerWindow(Integer numberOfPeaksToKeepPerWindow)
Set the number of peaks to keep per window.
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void |
setNumberOfWindows(Integer numberOfWindows)
Set the number of windows.
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void |
setRunGptm(boolean runGptm)
Set whether the G-PTM search is to be performed.
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void |
setScoreCutoff(Double scoreCutoff)
Set the score cut-off.
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void |
setSearchTarget(Boolean searchTarget)
Set whether target sequences are to be searched.
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void |
setSearchType(MetaMorpheusParameters.MetaMorpheusSearchType searchType)
Set the search type.
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void |
setTotalPartitions(Integer totalPartitions)
Set the total partitions.
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void |
setTrimMs1Peaks(Boolean trimMs1Peaks)
Set whether Ms1 peaks are to be trimmed.
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void |
setTrimMsMsPeaks(Boolean trimMsMsPeaks)
Set whether MsMs peaks are to be trimmed.
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void |
setUseDeltaScore(boolean useDeltaScore)
Set whether delta score is to be used.
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void |
setUseProvidedPrecursorInfo(Boolean useProvidedPrecursorInfo)
Set whether the provided precursor info is to be used.
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void |
setWindowWidthThomsons(Double windowWidthThomsons)
Set the window width in Thomson.
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void |
setWriteMzId(Boolean writeMzId)
Set whether mzId output is to be created.
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void |
setWritePepXml(Boolean writePepXml)
Set whether pepXML output is to be created.
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String |
toString(boolean html)
Returns the parameters as a string.
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addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
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 getMinPeptideLength()
public void setMinPeptideLength(Integer minPeptideLength)
minPeptideLength
- the minimum peptide lengthpublic Integer getMaxPeptideLength()
public void setMaxPeptideLength(Integer maxPeptideLength)
maxPeptideLength
- the maximum peptide lengthpublic MetaMorpheusParameters.MetaMorpheusSearchType getSearchType()
public void setSearchType(MetaMorpheusParameters.MetaMorpheusSearchType searchType)
searchType
- the searchType to setpublic Integer getTotalPartitions()
public void setTotalPartitions(Integer totalPartitions)
totalPartitions
- the totalPartitions to setpublic MetaMorpheusParameters.MetaMorpheusDissociationType getDissociationType()
public void setDissociationType(MetaMorpheusParameters.MetaMorpheusDissociationType dissociationType)
dissociationType
- the dissociationType to setpublic Integer getMaxModsForPeptide()
public void setMaxModsForPeptide(Integer maxModsForPeptide)
maxModsForPeptide
- the maxModsForPeptide to setpublic MetaMorpheusParameters.MetaMorpheusInitiatorMethionineBehaviorType getInitiatorMethionineBehavior()
public void setInitiatorMethionineBehavior(MetaMorpheusParameters.MetaMorpheusInitiatorMethionineBehaviorType initiatorMethionineBehavior)
initiatorMethionineBehavior
- the initiatorMethionineBehavior to setpublic Double getScoreCutoff()
public void setScoreCutoff(Double scoreCutoff)
scoreCutoff
- the scoreCutoff to setpublic boolean getUseDeltaScore()
public void setUseDeltaScore(boolean useDeltaScore)
useDeltaScore
- the useDeltaScore to setpublic MetaMorpheusParameters.MetaMorpheusFragmentationTerminusType getFragmentationTerminus()
public void setFragmentationTerminus(MetaMorpheusParameters.MetaMorpheusFragmentationTerminusType fragmentationTerminus)
fragmentationTerminus
- the fragmentationTerminus to setpublic Double getMaxFragmentSize()
public void setMaxFragmentSize(Double maxFragmentSize)
maxFragmentSize
- the maxFragmentSize to setpublic MetaMorpheusParameters.MetaMorpheusMassDiffAcceptorType getMassDiffAcceptorType()
public void setMassDiffAcceptorType(MetaMorpheusParameters.MetaMorpheusMassDiffAcceptorType massDiffAcceptorType)
massDiffAcceptorType
- the massDiffAcceptorType to setpublic Boolean getWriteMzId()
public void setWriteMzId(Boolean writeMzId)
writeMzId
- the writeMzId to setpublic Boolean getWritePepXml()
public void setWritePepXml(Boolean writePepXml)
writePepXml
- the writePepXml to setpublic Boolean getUseProvidedPrecursorInfo()
public void setUseProvidedPrecursorInfo(Boolean useProvidedPrecursorInfo)
useProvidedPrecursorInfo
- the useProvidedPrecursorInfo to setpublic Boolean getDoPrecursorDeconvolution()
public void setDoPrecursorDeconvolution(Boolean doPrecursorDeconvolution)
doPrecursorDeconvolution
- the doPrecursorDeconvolution to setpublic Double getDeconvolutionIntensityRatio()
public void setDeconvolutionIntensityRatio(Double deconvolutionIntensityRatio)
deconvolutionIntensityRatio
- the deconvolutionIntensityRatio to setpublic Double getDeconvolutionMassTolerance()
public void setDeconvolutionMassTolerance(Double deconvolutionMassTolerance)
deconvolutionMassTolerance
- the deconvolutionMassTolerance to setpublic MetaMorpheusParameters.MetaMorpheusToleranceType getDeconvolutionMassToleranceType()
public void setDeconvolutionMassToleranceType(MetaMorpheusParameters.MetaMorpheusToleranceType deconvolutionMassToleranceType)
deconvolutionMassToleranceType
- the deconvolutionMassToleranceType
to setpublic Boolean getTrimMs1Peaks()
public void setTrimMs1Peaks(Boolean trimMs1Peaks)
trimMs1Peaks
- the trimMs1Peaks to setpublic Boolean getTrimMsMsPeaks()
public void setTrimMsMsPeaks(Boolean trimMsMsPeaks)
trimMsMsPeaks
- the trimMsMsPeaks to setpublic Integer getNumberOfPeaksToKeepPerWindow()
public void setNumberOfPeaksToKeepPerWindow(Integer numberOfPeaksToKeepPerWindow)
numberOfPeaksToKeepPerWindow
- the numberOfPeaksToKeepPerWindow to
setpublic Double getMinAllowedIntensityRatioToBasePeak()
public void setMinAllowedIntensityRatioToBasePeak(Double minAllowedIntensityRatioToBasePeak)
minAllowedIntensityRatioToBasePeak
- the
minAllowedIntensityRatioToBasePeak to setpublic Double getWindowWidthThomsons()
public void setWindowWidthThomsons(Double windowWidthThomsons)
windowWidthThomsons
- the windowWidthThomson to setpublic Integer getNumberOfWindows()
public void setNumberOfWindows(Integer numberOfWindows)
numberOfWindows
- the numberOfWindows to setpublic Boolean getNormalizePeaksAcrossAllWindows()
public void setNormalizePeaksAcrossAllWindows(Boolean normalizePeaksAcrossAllWindows)
normalizePeaksAcrossAllWindows
- the normalizePeaksAcrossAllWindows
to setpublic Boolean getModPeptidesAreDifferent()
public void setModPeptidesAreDifferent(Boolean modPeptidesAreDifferent)
modPeptidesAreDifferent
- the modPeptidesAreDifferent to setpublic Boolean getNoOneHitWonders()
public void setNoOneHitWonders(Boolean noOneHitWonders)
noOneHitWonders
- the noOneHitWonders to setpublic Boolean getSearchTarget()
public void setSearchTarget(Boolean searchTarget)
searchTarget
- the searchTarget to setpublic MetaMorpheusParameters.MetaMorpheusDecoyType getDecoyType()
public void setDecoyType(MetaMorpheusParameters.MetaMorpheusDecoyType decoyType)
decoyType
- the decoyType to setpublic Integer getMaxModificationIsoforms()
public void setMaxModificationIsoforms(Integer maxModificationIsoforms)
maxModificationIsoforms
- the maxModificationIsoforms to setpublic Integer getMinVariantDepth()
public void setMinVariantDepth(Integer minVariantDepth)
minVariantDepth
- the minVariantDepth to setpublic Integer getMaxHeterozygousVariants()
public void setMaxHeterozygousVariants(Integer maxHeterozygousVariants)
maxHeterozygousVariants
- the maxHeterozygousVariants to setpublic boolean runGptm()
public void setRunGptm(boolean runGptm)
runGptm
- set to true if the G-PTM search is to be performedpublic ArrayList<ModificationCategory> getGPtmCategories()
public void setGPtmCategories(ArrayList<ModificationCategory> gPtmCategories)
gPtmCategories
- the gPtmCategories to setCopyright © 2021. All rights reserved.