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

Class DirecTagParameters

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
All Implemented Interfaces:
IdentificationAlgorithmParameter, Serializable
public class DirecTagParameters extends ExperimentObject implements IdentificationAlgorithmParameter
The DirecTag specific parameters.
Author:
Thilo Muth, Harald Barsnes
See Also:

  • Constructor Details

    • DirecTagParameters

      public DirecTagParameters()
      Constructor.

  • Method Details

    • getNumChargeStates

      public int getNumChargeStates()
      Returns the number of charge states.
      Returns:
      numChargeStates the number of charge states

    • setNumChargeStates

      public void setNumChargeStates(int numChargeStates)
      Sets the number of charge states.
      Parameters:
      numChargeStates - the number of charge states

    • getOutputSuffix

      public String getOutputSuffix()
      Returns the output tags suffix.
      Returns:
      the output tags suffix.

    • setOutputSuffix

      public void setOutputSuffix(String outputSuffix)
      Sets the output tags suffix.
      Parameters:
      outputSuffix - the output tags suffix.

    • isUseChargeStateFromMS

      public boolean isUseChargeStateFromMS()
      Indicates whether the charge state from the spectrum should be used.
      Returns:
      boolean indicating whether the charge states from the spectrum should be used

    • setUseChargeStateFromMS

      public void setUseChargeStateFromMS(boolean useChargeStateFromMS)
      Sets whether the charge state from the spectrum should be used.
      Parameters:
      useChargeStateFromMS - boolean indicating whether the charge states from the spectrum should be used

    • isDuplicateSpectra

      public boolean isDuplicateSpectra()
      Indicates whether to use duplicate spectra option.
      Returns:
      boolean indicating whether to use duplicate spectra option

    • setDuplicateSpectra

      public void setDuplicateSpectra(boolean duplicateSpectra)
      Sets whether to use duplicate spectra option.
      Parameters:
      duplicateSpectra - boolean indicating whether to use duplicate spectra option

    • getDeisotopingMode

      public int getDeisotopingMode()
      Returns the deisotoping flag value.
      Returns:
      deisotoping flag value

    • setDeisotopingMode

      public void setDeisotopingMode(int deisotopingMode)
      Sets the deisotoping flag value.
      Parameters:
      deisotopingMode - deisotoping flag value

    • getIsotopeMzTolerance

      public double getIsotopeMzTolerance()
      Returns the deisotoping m/z tolerance.
      Returns:
      deisotoping m/z tolerance

    • setIsotopeMzTolerance

      public void setIsotopeMzTolerance(double isotopeMzTolerance)
      Sets the deisotoping m/z tolerance.
      Parameters:
      isotopeMzTolerance - deisotoping m/z tolerance

    • getComplementMzTolerance

      public double getComplementMzTolerance()
      Returns the complement m/z tolerance.
      Returns:
      the complement m/z tolerance

    • setComplementMzTolerance

      public void setComplementMzTolerance(double complementMzTolerance)
      Sets the complement m/z tolerance.
      Parameters:
      complementMzTolerance - the complement m/z tolerance

    • getTagLength

      public int getTagLength()
      Returns the tag length.
      Returns:
      the tag length

    • setTagLength

      public void setTagLength(int tagLength)
      Sets the tag length.
      Parameters:
      tagLength - the tag length

    • getMaxDynamicMods

      public int getMaxDynamicMods()
      Returns the maximum number of dynamic mods.
      Returns:
      the maximum number of dynamic mods

    • setMaxDynamicMods

      public void setMaxDynamicMods(int maxDynamicMods)
      Sets the maximum number of dynamic mods.
      Parameters:
      maxDynamicMods - the maximum number of dynamic mods

    • getMaxTagCount

      public int getMaxTagCount()
      Returns the maximum number of tags per spectrum to be generated.
      Returns:
      the maximum number of tags per spectrum to be generated

    • setMaxTagCount

      public void setMaxTagCount(int maxTagCount)
      Sets the maximum number of tags per spectrum to be generated.
      Parameters:
      maxTagCount - the maximum number of tags per spectrum to be generated

    • getIntensityScoreWeight

      public double getIntensityScoreWeight()
      Returns the intensity score weight.
      Returns:
      the intensity score weight

    • setIntensityScoreWeight

      public void setIntensityScoreWeight(double intensityScoreWeight)
      Set the intensity score weight.
      Parameters:
      intensityScoreWeight - the intensity score weight

    • getMzFidelityScoreWeight

      public double getMzFidelityScoreWeight()
      Returns the mzFidelity score weight.
      Returns:
      the mzFidelity score weight

    • setMzFidelityScoreWeight

      public void setMzFidelityScoreWeight(double mzFidelityScoreWeight)
      Set the mzFidelity score weight.
      Parameters:
      mzFidelityScoreWeight - the mzFidelity score weight

    • getComplementScoreWeight

      public double getComplementScoreWeight()
      Returns the complement score weight.
      Returns:
      the complement score weight

    • setComplementScoreWeight

      public void setComplementScoreWeight(double complementScoreWeight)
      Set the complement score weight.
      Parameters:
      complementScoreWeight - the complement score weight

    • getTicCutoffPercentage

      public double getTicCutoffPercentage()
      Returns the TIC cutoff in percent. Default is 85%.
      Returns:
      the ticCutoffPercentage

    • setTicCutoffPercentage

      public void setTicCutoffPercentage(double ticCutoffPercentage)
      Set the TIC cutoff in percent. Default is 85%.
      Parameters:
      ticCutoffPercentage - the ticCutoffPercentage to set

    • getMaxPeakCount

      public int getMaxPeakCount()
      Returns the maximum peak count.
      Returns:
      the maxPeakCount

    • setMaxPeakCount

      public void setMaxPeakCount(int maxPeakCount)
      Set the maximum peak count.
      Parameters:
      maxPeakCount - the maxPeakCount to set

    • getNumIntensityClasses

      public int getNumIntensityClasses()
      Returns the number of intensity classes.
      Returns:
      the numIntensityClasses

    • setNumIntensityClasses

      public void setNumIntensityClasses(int numIntensityClasses)
      Sets the number of intensity classes.
      Parameters:
      numIntensityClasses - the numIntensityClasses to set

    • isAdjustPrecursorMass

      public boolean isAdjustPrecursorMass()
      Returns if the precursor mass is to be adjusted.
      Returns:
      the adjustPrecursorMass

    • setAdjustPrecursorMass

      public void setAdjustPrecursorMass(boolean adjustPrecursorMass)
      Set if the precursor mass is to be adjusted.
      Parameters:
      adjustPrecursorMass - the adjustPrecursorMass to set

    • getMinPrecursorAdjustment

      public double getMinPrecursorAdjustment()
      Returns the minimum precursor adjustment.
      Returns:
      the minPrecursorAdjustment

    • setMinPrecursorAdjustment

      public void setMinPrecursorAdjustment(double minPrecursorAdjustment)
      Set the minimum precursor adjustment.
      Parameters:
      minPrecursorAdjustment - the minPrecursorAdjustment to set

    • getMaxPrecursorAdjustment

      public double getMaxPrecursorAdjustment()
      Returns the maximum precursor adjustment.
      Returns:
      the maxPrecursorAdjustment

    • setMaxPrecursorAdjustment

      public void setMaxPrecursorAdjustment(double maxPrecursorAdjustment)
      Set the maximum precursor adjustment.
      Parameters:
      maxPrecursorAdjustment - the maxPrecursorAdjustment to set

    • getPrecursorAdjustmentStep

      public double getPrecursorAdjustmentStep()
      Returns the precursor adjustment step.
      Returns:
      the precursorAdjustmentStep

    • setPrecursorAdjustmentStep

      public void setPrecursorAdjustmentStep(double PrecursorAdjustmentStep)
      Set the precursor adjustment step.
      Parameters:
      PrecursorAdjustmentStep - the precursorAdjustmentStep to set

    • setModifications

      public void setModifications(ArrayList<String> variableModifications)
      Sets the variable modifications searched. The order is the one used by DirecTag and the name is the utilities one.
      Parameters:
      variableModifications - list of the names of the searched variable modifications

    • getUtilitiesModificationName

      public String getUtilitiesModificationName(int index)
      Returns the name of the modification indexed by the given index.
      Parameters:
      index - the index of the modification of interest
      Returns:
      the name of the modification of interest

    • 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