java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.tool_specific.XtandemParameters
All Implemented Interfaces:
IdentificationAlgorithmParameter, Serializable

public class XtandemParameters
extends ExperimentObject
implements IdentificationAlgorithmParameter
The X!Tandem specific parameters.
Author:
Marc Vaudel
See Also:
Serialized Form
  • Constructor Details

  • Method Details

    • getDynamicRange

      public double getDynamicRange()
      Returns the dynamic range for spectrum filtering.
      Returns:
      the dynamic range for spectrum filtering
    • setDynamicRange

      public void setDynamicRange​(double dynamicRange)
      Sets the dynamic range for spectrum filtering.
      Parameters:
      dynamicRange - the dynamic range for spectrum filtering
    • getnPeaks

      public int getnPeaks()
      Returns the number of most intense peaks to consider.
      Returns:
      the number of most intense peaks to consider
    • setnPeaks

      public void setnPeaks​(int nPeaks)
      Sets the number of most intense peaks to consider.
      Parameters:
      nPeaks - the number of most intense peaks to consider
    • getMinPrecursorMass

      public double getMinPrecursorMass()
      Returns the minimal precursor mass.
      Returns:
      the minimal precursor mass
    • setMinPrecursorMass

      public void setMinPrecursorMass​(double minPrecursorMass)
      Sets the minimal precursor mass.
      Parameters:
      minPrecursorMass - the minimal precursor mass
    • getMinFragmentMz

      public double getMinFragmentMz()
      Returns the minimal fragment m/z.
      Returns:
      the minimal fragment m/z
    • setMinFragmentMz

      public void setMinFragmentMz​(double minFragmentMz)
      Sets the minimal fragment m/z.
      Parameters:
      minFragmentMz - the minimal fragment m/z
    • getMinPeaksPerSpectrum

      public int getMinPeaksPerSpectrum()
      Returns the minimal number of peaks per spectrum.
      Returns:
      the minimal number of peaks per spectrum
    • setMinPeaksPerSpectrum

      public void setMinPeaksPerSpectrum​(int minPeaksPerSpectrum)
      Sets the minimal number of peaks per spectrum.
      Parameters:
      minPeaksPerSpectrum - the minimal number of peaks per spectrum
    • isProteinQuickAcetyl

      public boolean isProteinQuickAcetyl()
      Indicates whether the protein quick acetylation option should be triggered.
      Returns:
      true if the protein quick acetylation option should be triggered
    • setProteinQuickAcetyl

      public void setProteinQuickAcetyl​(boolean proteinQuickAcetyl)
      Sets whether the protein quick acetylation option should be triggered.
      Parameters:
      proteinQuickAcetyl - true if the protein quick acetylation option should be triggered
    • isQuickPyrolidone

      public boolean isQuickPyrolidone()
      Returns whether the quick pyrolidone option should be triggered.
      Returns:
      true if the quick pyrolidone option should be triggered
    • setQuickPyrolidone

      public void setQuickPyrolidone​(boolean quickPyrolidone)
      Sets whether the quick pyrolidone option should be triggered.
      Parameters:
      quickPyrolidone - the quick pyrolidone option should be triggered
    • isRefine

      public boolean isRefine()
      Returns whether the second pass search should be triggered.
      Returns:
      true if the second pass search should be triggered
    • setRefine

      public void setRefine​(boolean refine)
      Sets whether the second pass search should be triggered.
      Parameters:
      refine - true if the second pass search should be triggered
    • isStpBias

      public boolean isStpBias()
      Returns whether the stP bias should be triggered.
      Returns:
      true if the stP bias should be triggered
    • setStpBias

      public void setStpBias​(boolean stpBias)
      Sets whether the stP bias should be triggered
      Parameters:
      stpBias - true if the stP bias should be triggered
    • getMaxEValue

      public double getMaxEValue()
      Returns the maximal e-value searched for.
      Returns:
      the maximal e-value searched for
    • setMaxEValue

      public void setMaxEValue​(double maxEValue)
      Sets the maximal e-value searched for.
      Parameters:
      maxEValue - the maximal e-value searched for
    • isRefineSemi

      public boolean isRefineSemi()
      Indicates whether the semi enzymatic option of the second pass search should be triggered.
      Returns:
      true if the semi enzymatic option of the second pass search should be triggered
    • setRefineSemi

      public void setRefineSemi​(boolean refineSemi)
      Sets whether the semi enzymatic option of the second pass search should be triggered.
      Parameters:
      refineSemi - true if the semi enzymatic option of the second pass search should be triggered
    • isRefinePointMutations

      public boolean isRefinePointMutations()
      Indicates whether point mutations should be looked for during the refinement process.
      Returns:
      true if point mutations should be looked for during the refinement process
    • setRefinePointMutations

      public void setRefinePointMutations​(boolean refinePointMutations)
      Sets whether point mutations should be looked for during the refinement process.
      Parameters:
      refinePointMutations - true if point mutations should be looked for during the refinement process
    • isRefineSpectrumSynthesis

      public boolean isRefineSpectrumSynthesis()
      Indicates whether the spectrum synthesis option should be used during the refinement process.
      Returns:
      true if the spectrum synthesis option should be used during the refinement process
    • setRefineSpectrumSynthesis

      public void setRefineSpectrumSynthesis​(boolean refineSpectrumSynthesis)
      Sets whether the spectrum synthesis option should be used during the refinement process.
      Parameters:
      refineSpectrumSynthesis - true if the spectrum synthesis option should be used during the refinement process
    • isRefineUnanticipatedCleavages

      public boolean isRefineUnanticipatedCleavages()
      Returns whether the unanticipated cleavages option should be used during the refinement process.
      Returns:
      true if the unanticipated cleavages option should be used during the refinement process
    • setRefineUnanticipatedCleavages

      public void setRefineUnanticipatedCleavages​(boolean refineUnanticipatedCleavages)
      Sets whether the unanticipated cleavages option should be used during the refinement process.
      Parameters:
      refineUnanticipatedCleavages - true if the unanticipated cleavages option should be used during the refinement process
    • getMaximumExpectationValueRefinement

      public double getMaximumExpectationValueRefinement()
      Returns the maximum expectation value to use for refinement.
      Returns:
      the maximum expectation value to use for refinement
    • setMaximumExpectationValueRefinement

      public void setMaximumExpectationValueRefinement​(double maximumExpectationValue)
      Sets the maximum expectation value to use for refinement.
      Parameters:
      maximumExpectationValue - the maximum expectation value to use for refinement
    • isPotentialModificationsForFullRefinment

      public boolean isPotentialModificationsForFullRefinment()
      Indicates whether the refinement modifications should be used for the full refinement.
      Returns:
      true if the refinement modifications should be used for the full refinement
    • setPotentialModificationsForFullRefinment

      public void setPotentialModificationsForFullRefinment​(boolean potentialModificationsForFullRefinment)
      Sets whether the refinement modifications should be used for the full refinement
      Parameters:
      potentialModificationsForFullRefinment - true if the refinement modifications should be used for the full refinement
    • getSkylinePath

      public String getSkylinePath()
      Returns the skyline path.
      Returns:
      the skyline path
    • setSkylinePath

      public void setSkylinePath​(String skylinePath)
      Sets the skyline path.
      Parameters:
      skylinePath - the skyline path
    • isOutputProteins

      public boolean isOutputProteins()
      Indicates whether the protein bloc should be included in the export.
      Returns:
      true if the protein bloc should be included in the export
    • setOutputProteins

      public void setOutputProteins​(boolean outputProteins)
      Sets whether the protein bloc should be included in the export.
      Parameters:
      outputProteins - the protein bloc should be included in the export
    • isOutputSequences

      public boolean isOutputSequences()
      Returns whether the protein sequences should be included in the protein block of the export.
      Returns:
      true if the protein sequences should be included in the protein block of the export
    • setOutputSequences

      public void setOutputSequences​(boolean outputSequences)
      Sets whether the protein sequences should be included in the protein block of the export.
      Parameters:
      outputSequences - true if the protein sequences should be included in the protein block of the export
    • isOutputSpectra

      public boolean isOutputSpectra()
      Indicate whether the spectra should be exported in the result file.
      Returns:
      true if the spectra should be exported in the result file
    • setOutputSpectra

      public void setOutputSpectra​(boolean outputSpectra)
      Sets whether the spectra should be exported in the result file.
      Parameters:
      outputSpectra - true if the spectra should be exported in the result file
    • isOutputHistograms

      public boolean isOutputHistograms()
      Indicates whether histograms should be written in the result file.
      Returns:
      true if histograms should be written in the result file
    • setOutputHistograms

      public void setOutputHistograms​(boolean outputHistograms)
      Sets whether histograms should be written in the result file
      Parameters:
      outputHistograms - true if histograms should be written in the result file
    • isUseNoiseSuppression

      public boolean isUseNoiseSuppression()
      Indicates whether noise suppression should be used when importing spectra. Note: ignored in X!Tandem VENGEANCE (2015.12.15) and newer
      Returns:
      true if noise suppression should be used when importing spectra
    • setUseNoiseSuppression

      public void setUseNoiseSuppression​(boolean useNoiseSuppression)
      Sets whether noise suppression should be used when importing spectra. Note: ignored in X!Tandem VENGEANCE (2015.12.15) and newer
      Parameters:
      useNoiseSuppression - true if noise suppression should be used when importing spectra
    • isRefineSnaps

      public boolean isRefineSnaps()
      Sets whether snAPs should be used during the refinement process.
      Returns:
      true if snAPs should be used during the refinement process
    • setRefineSnaps

      public void setRefineSnaps​(boolean refineSnaps)
      Sets whether snAPs should be used during the refinement process.
      Parameters:
      refineSnaps - true if snAPs should be used during the refinement process
    • getOutputResults

      public String getOutputResults()
      Returns the output results filter.
      Returns:
      the outputResults
    • setOutputResults

      public void setOutputResults​(String outputResults)
      Set the output results filter.
      Parameters:
      outputResults - the outputResults to set
    • getProteinPtmComplexity

      public double getProteinPtmComplexity()
      Returns the proteinPtmComplexity.
      Returns:
      the proteinPtmComplexity
    • setProteinPtmComplexity

      public void setProteinPtmComplexity​(double proteinPtmComplexity)
      Set the proteinPtmComplexity.
      Parameters:
      proteinPtmComplexity - the proteinPtmComplexity to set
    • 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
    • getParentMonoisotopicMassIsotopeError

      public boolean getParentMonoisotopicMassIsotopeError()
      Returns true if the parent ion mass tolerance is expanded by opening up multiple tolerance windows centered on the first and second 13C isotope peaks for a peptide.
      Returns:
      the parentMonoisotopicMassIsotopeError
    • setParentMonoisotopicMassIsotopeError

      public void setParentMonoisotopicMassIsotopeError​(boolean parentMonoisotopicMassIsotopeError)
      Sets whether the parent ion mass tolerance is expanded by opening up multiple tolerance windows centered on the first and second 13C isotope peaks for a peptide.
      Parameters:
      parentMonoisotopicMassIsotopeError - the parentMonoisotopicMassIsotopeError to set