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