Package com.compomics.util.parameters.identification.tool_specific

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:

  • Constructor Details

    • MetaMorpheusParameters

      public MetaMorpheusParameters()
      Constructor.

  • Method Details

    • getAlgorithm

      public Advocate getAlgorithm()
      Description copied from interface: IdentificationAlgorithmParameter
      Returns the identification algorithm.
      Specified by:
      getAlgorithm in interface IdentificationAlgorithmParameter
      Returns:
      the identification algorithm

    • equals

      public boolean equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
      Description copied from interface: IdentificationAlgorithmParameter
      Indicates whether another identificationAlgorithmParameter has the same parameters.
      Specified by:
      equals in interface IdentificationAlgorithmParameter
      Parameters:
      identificationAlgorithmParameter - the other identificationAlgorithmParameter
      Returns:
      true if the algorithm and parameters are the same

    • toString

      public String toString(boolean html)
      Description copied from interface: IdentificationAlgorithmParameter
      Returns the parameters as a string.
      Specified by:
      toString in interface IdentificationAlgorithmParameter
      Parameters:
      html - use HTML formatting
      Returns:
      the parameters as a string

    • getMinPeptideLength

      public Integer getMinPeptideLength()
      Returns the minimum peptide length.
      Returns:
      the the minimum peptide length

    • setMinPeptideLength

      public void setMinPeptideLength(Integer minPeptideLength)
      Set the minimum peptide length.
      Parameters:
      minPeptideLength - the minimum peptide length

    • getMaxPeptideLength

      public Integer getMaxPeptideLength()
      Returns the maximum peptide length.
      Returns:
      the the maximum peptide length

    • setMaxPeptideLength

      public void setMaxPeptideLength(Integer maxPeptideLength)
      Set the maximum peptide length.
      Parameters:
      maxPeptideLength - the maximum peptide length

    • getSearchType

      public MetaMorpheusParameters.MetaMorpheusSearchType getSearchType()
      Returns the search type.
      Returns:
      the searchType

    • setSearchType

      public void setSearchType(MetaMorpheusParameters.MetaMorpheusSearchType searchType)
      Set the search type.
      Parameters:
      searchType - the searchType to set

    • getTotalPartitions

      public Integer getTotalPartitions()
      Returns total partitions.
      Returns:
      the totalPartitions

    • setTotalPartitions

      public void setTotalPartitions(Integer totalPartitions)
      Set the total partitions.
      Parameters:
      totalPartitions - the totalPartitions to set

    • getDissociationType

      public MetaMorpheusParameters.MetaMorpheusDissociationType getDissociationType()
      Returns the dissociation type.
      Returns:
      the dissociationType

    • setDissociationType

      public void setDissociationType(MetaMorpheusParameters.MetaMorpheusDissociationType dissociationType)
      Set the dissociation type.
      Parameters:
      dissociationType - the dissociationType to set

    • getMaxModsForPeptide

      public Integer getMaxModsForPeptide()
      Returns the max mods for peptide.
      Returns:
      the maxModsForPeptide

    • setMaxModsForPeptide

      public void setMaxModsForPeptide(Integer maxModsForPeptide)
      Set the max mods for peptide.
      Parameters:
      maxModsForPeptide - the maxModsForPeptide to set

    • getInitiatorMethionineBehavior

      public MetaMorpheusParameters.MetaMorpheusInitiatorMethionineBehaviorType getInitiatorMethionineBehavior()
      Returns the initiator methionine behavior.
      Returns:
      the initiatorMethionineBehavior

    • setInitiatorMethionineBehavior

      public void setInitiatorMethionineBehavior(MetaMorpheusParameters.MetaMorpheusInitiatorMethionineBehaviorType initiatorMethionineBehavior)
      Set the initiator methionine behavior.
      Parameters:
      initiatorMethionineBehavior - the initiatorMethionineBehavior to set

    • getScoreCutoff

      public Double getScoreCutoff()
      Returns the score cut-off.
      Returns:
      the scoreCutoff

    • setScoreCutoff

      public void setScoreCutoff(Double scoreCutoff)
      Set the score cut-off.
      Parameters:
      scoreCutoff - the scoreCutoff to set

    • getUseDeltaScore

      public boolean getUseDeltaScore()
      Returns true of delta score is to be used.
      Returns:
      the useDeltaScore

    • setUseDeltaScore

      public void setUseDeltaScore(boolean useDeltaScore)
      Set whether delta score is to be used.
      Parameters:
      useDeltaScore - the useDeltaScore to set

    • getFragmentationTerminus

      public MetaMorpheusParameters.MetaMorpheusFragmentationTerminusType getFragmentationTerminus()
      Returns the fragmentation terminus.
      Returns:
      the fragmentationTerminus

    • setFragmentationTerminus

      public void setFragmentationTerminus(MetaMorpheusParameters.MetaMorpheusFragmentationTerminusType fragmentationTerminus)
      Set the fragmentation terminus.
      Parameters:
      fragmentationTerminus - the fragmentationTerminus to set

    • getMaxFragmentSize

      public Double getMaxFragmentSize()
      Returns the max fragmentation size.
      Returns:
      the maxFragmentSize

    • setMaxFragmentSize

      public void setMaxFragmentSize(Double maxFragmentSize)
      Set the max fragmentation size.
      Parameters:
      maxFragmentSize - the maxFragmentSize to set

    • getMinAllowedInternalFragmentLength

      public Integer getMinAllowedInternalFragmentLength()
      Returns the minimum allowed internal fragment length. 0 means "no internal fragments".
      Returns:
      the minAllowedInternalFragmentLength

    • setMinAllowedInternalFragmentLength

      public void setMinAllowedInternalFragmentLength(Integer minAllowedInternalFragmentLength)
      Set the minimum allowed internal fragment length. 0 means "no internal fragments".
      Parameters:
      minAllowedInternalFragmentLength - the minAllowedInternalFragmentLength to set

    • getMassDiffAcceptorType

      public MetaMorpheusParameters.MetaMorpheusMassDiffAcceptorType getMassDiffAcceptorType()
      Returns the mass difference acceptor type.
      Returns:
      the massDiffAcceptorType

    • setMassDiffAcceptorType

      public void setMassDiffAcceptorType(MetaMorpheusParameters.MetaMorpheusMassDiffAcceptorType massDiffAcceptorType)
      Set the mass difference acceptor type.
      Parameters:
      massDiffAcceptorType - the massDiffAcceptorType to set

    • getWriteMzId

      public Boolean getWriteMzId()
      Returns true if mzId output is to be created.
      Returns:
      the writeMzId

    • setWriteMzId

      public void setWriteMzId(Boolean writeMzId)
      Set whether mzId output is to be created.
      Parameters:
      writeMzId - the writeMzId to set

    • getWritePepXml

      public Boolean getWritePepXml()
      Returns true if pepXML output is to be created.
      Returns:
      the writePepXml

    • setWritePepXml

      public void setWritePepXml(Boolean writePepXml)
      Set whether pepXML output is to be created.
      Parameters:
      writePepXml - the writePepXml to set

    • getUseProvidedPrecursorInfo

      public Boolean getUseProvidedPrecursorInfo()
      Returns true of the provided precursor info is to be used.
      Returns:
      the useProvidedPrecursorInfo

    • setUseProvidedPrecursorInfo

      public void setUseProvidedPrecursorInfo(Boolean useProvidedPrecursorInfo)
      Set whether the provided precursor info is to be used.
      Parameters:
      useProvidedPrecursorInfo - the useProvidedPrecursorInfo to set

    • getDoPrecursorDeconvolution

      public Boolean getDoPrecursorDeconvolution()
      Returns true if precursor deconvolution is to be carried out.
      Returns:
      the doPrecursorDeconvolution

    • setDoPrecursorDeconvolution

      public void setDoPrecursorDeconvolution(Boolean doPrecursorDeconvolution)
      Set whether precursor deconvolution is to be carried out.
      Parameters:
      doPrecursorDeconvolution - the doPrecursorDeconvolution to set

    • getDeconvolutionIntensityRatio

      public Double getDeconvolutionIntensityRatio()
      Returns the deconvolution intensity ratio.
      Returns:
      the deconvolutionIntensityRatio

    • setDeconvolutionIntensityRatio

      public void setDeconvolutionIntensityRatio(Double deconvolutionIntensityRatio)
      Set the deconvolution intensity ratio.
      Parameters:
      deconvolutionIntensityRatio - the deconvolutionIntensityRatio to set

    • getDeconvolutionMassTolerance

      public Double getDeconvolutionMassTolerance()
      Returns the deconvolution mass tolerance.
      Returns:
      the deconvolutionMassTolerance

    • setDeconvolutionMassTolerance

      public void setDeconvolutionMassTolerance(Double deconvolutionMassTolerance)
      Set the deconvolution mass tolerance.
      Parameters:
      deconvolutionMassTolerance - the deconvolutionMassTolerance to set

    • getDeconvolutionMassToleranceType

      public MetaMorpheusParameters.MetaMorpheusToleranceType getDeconvolutionMassToleranceType()
      Returns the deconvolution mass tolerance type.
      Returns:
      the deconvolutionMassToleranceType

    • setDeconvolutionMassToleranceType

      public void setDeconvolutionMassToleranceType(MetaMorpheusParameters.MetaMorpheusToleranceType deconvolutionMassToleranceType)
      Set the deconvolution mass tolerance type.
      Parameters:
      deconvolutionMassToleranceType - the deconvolutionMassToleranceType to set

    • getTrimMs1Peaks

      public Boolean getTrimMs1Peaks()
      Returns true if Ms1 peaks are to be trimmed.
      Returns:
      the trimMs1Peaks

    • setTrimMs1Peaks

      public void setTrimMs1Peaks(Boolean trimMs1Peaks)
      Set whether Ms1 peaks are to be trimmed.
      Parameters:
      trimMs1Peaks - the trimMs1Peaks to set

    • getTrimMsMsPeaks

      public Boolean getTrimMsMsPeaks()
      Returns true if MsMs peaks are to be trimmed.
      Returns:
      the trimMsMsPeaks

    • setTrimMsMsPeaks

      public void setTrimMsMsPeaks(Boolean trimMsMsPeaks)
      Set whether MsMs peaks are to be trimmed.
      Parameters:
      trimMsMsPeaks - the trimMsMsPeaks to set

    • getNumberOfPeaksToKeepPerWindow

      public Integer getNumberOfPeaksToKeepPerWindow()
      Return the number of peaks to keep per window.
      Returns:
      the numberOfPeaksToKeepPerWindow

    • setNumberOfPeaksToKeepPerWindow

      public void setNumberOfPeaksToKeepPerWindow(Integer numberOfPeaksToKeepPerWindow)
      Set the number of peaks to keep per window.
      Parameters:
      numberOfPeaksToKeepPerWindow - the numberOfPeaksToKeepPerWindow to set

    • getMinAllowedIntensityRatioToBasePeak

      public Double getMinAllowedIntensityRatioToBasePeak()
      Returns the minimum allowed intensity ratio to base peak.
      Returns:
      the minAllowedIntensityRatioToBasePeak

    • setMinAllowedIntensityRatioToBasePeak

      public void setMinAllowedIntensityRatioToBasePeak(Double minAllowedIntensityRatioToBasePeak)
      Set the minimum allowed intensity ratio to base peak.
      Parameters:
      minAllowedIntensityRatioToBasePeak - the minAllowedIntensityRatioToBasePeak to set

    • getWindowWidthThomsons

      public Double getWindowWidthThomsons()
      Returns the window width in Thomson. Null if not set.
      Returns:
      the windowWidthThomson

    • setWindowWidthThomsons

      public void setWindowWidthThomsons(Double windowWidthThomsons)
      Set the window width in Thomson.
      Parameters:
      windowWidthThomsons - the windowWidthThomson to set

    • getNumberOfWindows

      public Integer getNumberOfWindows()
      Returns the number of windows. Null if not set.
      Returns:
      the numberOfWindows

    • setNumberOfWindows

      public void setNumberOfWindows(Integer numberOfWindows)
      Set the number of windows.
      Parameters:
      numberOfWindows - the numberOfWindows to set

    • getNormalizePeaksAcrossAllWindows

      public Boolean getNormalizePeaksAcrossAllWindows()
      Returns the normalize peaks across all windows.
      Returns:
      the normalizePeaksAcrossAllWindows

    • setNormalizePeaksAcrossAllWindows

      public void setNormalizePeaksAcrossAllWindows(Boolean normalizePeaksAcrossAllWindows)
      Set the normalize peaks across all windows.
      Parameters:
      normalizePeaksAcrossAllWindows - the normalizePeaksAcrossAllWindows to set

    • getModPeptidesAreDifferent

      public Boolean getModPeptidesAreDifferent()
      Returns true if modified peptides are considered different.
      Returns:
      the modPeptidesAreDifferent

    • setModPeptidesAreDifferent

      public void setModPeptidesAreDifferent(Boolean modPeptidesAreDifferent)
      Set whether modified peptides are considered different.
      Parameters:
      modPeptidesAreDifferent - the modPeptidesAreDifferent to set

    • getNoOneHitWonders

      public Boolean getNoOneHitWonders()
      Returns true if one hit wonders are excluded.
      Returns:
      the noOneHitWonders

    • setNoOneHitWonders

      public void setNoOneHitWonders(Boolean noOneHitWonders)
      Set whether one hit wonders are to be excluded.
      Parameters:
      noOneHitWonders - the noOneHitWonders to set

    • getSearchTarget

      public Boolean getSearchTarget()
      Returns true if target sequences are to be searched.
      Returns:
      the searchTarget

    • setSearchTarget

      public void setSearchTarget(Boolean searchTarget)
      Set whether target sequences are to be searched.
      Parameters:
      searchTarget - the searchTarget to set

    • getDecoyType

      public MetaMorpheusParameters.MetaMorpheusDecoyType getDecoyType()
      Returns the decoy type.
      Returns:
      the decoyType

    • setDecoyType

      public void setDecoyType(MetaMorpheusParameters.MetaMorpheusDecoyType decoyType)
      Set the decoy type.
      Parameters:
      decoyType - the decoyType to set

    • getMaxModificationIsoforms

      public Integer getMaxModificationIsoforms()
      Returns the max modification isoforms.
      Returns:
      the maxModificationIsoforms

    • setMaxModificationIsoforms

      public void setMaxModificationIsoforms(Integer maxModificationIsoforms)
      Set the max modification isoforms.
      Parameters:
      maxModificationIsoforms - the maxModificationIsoforms to set

    • getMinVariantDepth

      public Integer getMinVariantDepth()
      Returns the min variant depth.
      Returns:
      the minVariantDepth

    • setMinVariantDepth

      public void setMinVariantDepth(Integer minVariantDepth)
      Set the min variant depth.
      Parameters:
      minVariantDepth - the minVariantDepth to set

    • getMaxHeterozygousVariants

      public Integer getMaxHeterozygousVariants()
      Returns the max heterozygous variants.
      Returns:
      the maxHeterozygousVariants

    • setMaxHeterozygousVariants

      public void setMaxHeterozygousVariants(Integer maxHeterozygousVariants)
      Set the max heterozygous variants.
      Parameters:
      maxHeterozygousVariants - the maxHeterozygousVariants to set

    • 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

    • 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

    • getGPtmCategories

      public ArrayList<ModificationCategory> getGPtmCategories()
      Returns the modification categories to include in the G-PTM search.
      Returns:
      the modification categories to include in the G-PTM search

    • setGPtmCategories

      public void setGPtmCategories(ArrayList<ModificationCategory> gPtmCategories)
      Set the modification categories to include in the G-PTM search.
      Parameters:
      gPtmCategories - the gPtmCategories to set