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

Class XtandemParameters

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:

  • Constructor Details

    • XtandemParameters

      public XtandemParameters()
      Constructor.

  • 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