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

Class CometParameters

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:

  • Constructor Details

    • CometParameters

      public CometParameters()
      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

    • 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()
      Returns 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