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
  • Constructor Details

  • 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
    • getNumberOfSpectrumMatches

      public Integer getNumberOfSpectrumMatches()
      Returns the maximum number of spectrum matches.
      Returns:
      the numberOfSpectrumMarches
    • setNumberOfSpectrumMatches

      public void setNumberOfSpectrumMatches​(Integer numberOfSpectrumMarches)
      Set the maximum number of spectrum matches.
      Parameters:
      numberOfSpectrumMarches - the numberOfSpectrumMarches to set
    • getMaxVariableMods

      public Integer getMaxVariableMods()
      Returns the maximum number of variable modifications per peptide.
      Returns:
      the maxVariableMods
    • setMaxVariableMods

      public void setMaxVariableMods​(Integer maxVariableMods)
      Set the maximum number of variable modifications per peptide.
      Parameters:
      maxVariableMods - the maxVariableMods to set
    • getMinPeaks

      public Integer getMinPeaks()
      Returns the minimum number of peaks.
      Returns:
      the minPeaks
    • setMinPeaks

      public void setMinPeaks​(Integer minPeaks)
      Set the minimum number of peaks.
      Parameters:
      minPeaks - the minPeaks to set
    • getMinPeakIntensity

      public Double getMinPeakIntensity()
      Returns the minimum peak intensity.
      Returns:
      the minPeakIntensity
    • setMinPeakIntensity

      public void setMinPeakIntensity​(Double minPeakIntensity)
      Set the minimum peak intensity.
      Parameters:
      minPeakIntensity - the minPeakIntensity to set
    • getRemovePrecursor

      public Integer getRemovePrecursor()
      Returns if the precursor is to be removed.
      Returns:
      the removePrecursor
    • setRemovePrecursor

      public void setRemovePrecursor​(Integer removePrecursor)
      Set if the precursor is to be removed.
      Parameters:
      removePrecursor - the removePrecursor to set
    • getRemovePrecursorTolerance

      public Double getRemovePrecursorTolerance()
      Returns the precursor removal tolerance.
      Returns:
      the removePrecursorTolerance
    • setRemovePrecursorTolerance

      public void setRemovePrecursorTolerance​(Double removePrecursorTolerance)
      Set the precursor removal tolerance.
      Parameters:
      removePrecursorTolerance - the removePrecursorTolerance to set
    • getLowerClearMzRange

      public Double getLowerClearMzRange()
      Returns the lower mass value for the clear mz range.
      Returns:
      the lowerClearMzRange
    • setLowerClearMzRange

      public void setLowerClearMzRange​(Double lowerClearMzRange)
      Set the lower mass value for the clear mz range.
      Parameters:
      lowerClearMzRange - the lowerClearMzRange to set
    • getUpperClearMzRange

      public Double getUpperClearMzRange()
      Returns the upper mass value for the clear mz range.
      Returns:
      the upperClearMzRange
    • setUpperClearMzRange

      public void setUpperClearMzRange​(Double upperClearMzRange)
      Set the upper mass value for the clear mz range.
      Parameters:
      upperClearMzRange - the upperClearMzRange to set
    • getEnzymeType

      public Integer getEnzymeType()
      Returns the enzyme type.
      Returns:
      the enzymeType
    • setEnzymeType

      public void setEnzymeType​(Integer enzymeType)
      Set the enzyme type.
      Parameters:
      enzymeType - the enzymeType to set
    • getIsotopeCorrection

      public Integer getIsotopeCorrection()
      Returns the isotope correction setting.
      Returns:
      the isotopeCorrection
    • setIsotopeCorrection

      public void setIsotopeCorrection​(Integer isotopeCorrection)
      Set the isotope correction setting.
      Parameters:
      isotopeCorrection - the isotopeCorrection to set
    • getMinPrecursorMass

      public Double getMinPrecursorMass()
      Returns the minimum precursor mass.
      Returns:
      the minPrecursorMass
    • setMinPrecursorMass

      public void setMinPrecursorMass​(Double minPrecursorMass)
      Set the minimum precursor mass.
      Parameters:
      minPrecursorMass - the minPrecursorMass to set
    • getMaxPrecursorMass

      public Double getMaxPrecursorMass()
      Returns the maximum precursor mass.
      Returns:
      the maxPrecursorMass
    • setMaxPrecursorMass

      public void setMaxPrecursorMass​(Double maxPrecursorMass)
      Set the maximum precursor mass.
      Parameters:
      maxPrecursorMass - the maxPrecursorMass to set
    • getMaxFragmentCharge

      public Integer getMaxFragmentCharge()
      Returns the maximum fragment ion charge.
      Returns:
      the maxFragmentCharge
    • setMaxFragmentCharge

      public void setMaxFragmentCharge​(Integer maxFragmentCharge)
      Set the maximum fragment ion charge.
      Parameters:
      maxFragmentCharge - the maxFragmentCharge to set
    • getRemoveMethionine

      public Boolean getRemoveMethionine()
      Returns true if n-term methionine is to be removed.
      Returns:
      the removeMethionine
    • setRemoveMethionine

      public void setRemoveMethionine​(Boolean removeMethionine)
      Sets if n-term methionine is to be removed.
      Parameters:
      removeMethionine - the removeMethionine to set
    • getBatchSize

      public Integer getBatchSize()
      Returns the batch size.
      Returns:
      the batchSize
    • setBatchSize

      public void setBatchSize​(Integer batchSize)
      Set the batch size.
      Parameters:
      batchSize - the batchSize to set
    • getTheoreticalFragmentIonsSumOnly

      public Boolean 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
    • setTheoreticalFragmentIonsSumOnly

      public void setTheoreticalFragmentIonsSumOnly​(Boolean theoreticalFragmentIonsSumOnly)
      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
    • getFragmentBinOffset

      public Double getFragmentBinOffset()
      Returns the fragment ion bin offset.
      Returns:
      the fragmentBinOffset
    • setFragmentBinOffset

      public void setFragmentBinOffset​(Double fragmentBinOffset)
      Set the fragment ion bin offset.
      Parameters:
      fragmentBinOffset - the fragmentBinOffset to set
    • getUseSparseMatrix

      public Boolean getUseSparseMatrix()
      Deprecated.
      from Comet release 2015.02 all searches use this internal data representation by default
      Returns true if a sparse matrix is to be used.
      Returns:
      the useSparseMatrix
    • setUseSparseMatrix

      public void setUseSparseMatrix​(Boolean useSparseMatrix)
      Deprecated.
      from Comet release 2015.02 all searches use this internal data representation by default
      Set if a sparse matrix is to be used.
      Parameters:
      useSparseMatrix - the useSparseMatrix to set
    • getRequireVariableMods

      public boolean getRequireVariableMods()
      Returns true if at least one variable modification is required per peptide.
      Returns:
      the requireVariableMods
    • setRequireVariableMods

      public void setRequireVariableMods​(Boolean requireVariableMods)
      Set if at least one variable modification is required per peptide.
      Parameters:
      requireVariableMods - the requireVariableMods to set
    • getPrintExpectScore

      public boolean getPrintExpectScore()
      Returns true if the export score is to be printed.
      Returns:
      true if the export score is to be printed
    • setPrintExpectScore

      public void setPrintExpectScore​(boolean printExpectScore)
      Set if the export score is to be printed.
      Parameters:
      printExpectScore - the printExpectScore to set
    • getSelectedOutputFormat

      public CometParameters.CometOutputFormat getSelectedOutputFormat()
      Returns the selected output format.
      Returns:
      the selected output format
    • setSelectedOutputFormat

      public void setSelectedOutputFormat​(CometParameters.CometOutputFormat selectedOutputFormat)
      Sets the output format.
      Parameters:
      selectedOutputFormat - the output format
    • getMaxPeptideLength

      public Integer getMaxPeptideLength()
      Returns the maximal peptide length allowed.
      Returns:
      the maximal peptide length allowed
    • setMaxPeptideLength

      public void setMaxPeptideLength​(int maxPeptideLength)
      Sets the maximal peptide length allowed.
      Parameters:
      maxPeptideLength - the maximal peptide length allowed
    • getMinPeptideLength

      public Integer getMinPeptideLength()
      Sets the minimal peptide length allowed.
      Returns:
      the minimal peptide length allowed
    • setMinPeptideLength

      public void setMinPeptideLength​(int minPeptideLength)
      Sets the minimal peptide length allowed.
      Parameters:
      minPeptideLength - the minimal peptide length allowed