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

public class PepnovoParameters
extends ExperimentObject
implements IdentificationAlgorithmParameter
PepNovo specific parameters.
Author:
Marc Vaudel
See Also:
Serialized Form
  • Constructor Details

  • Method Details

    • getHitListLength

      public Integer getHitListLength()
      Returns the length of the hit list.
      Returns:
      the length of the hit list
    • setHitListLength

      public void setHitListLength​(Integer hitListLength)
      Sets the length of the hit list.
      Parameters:
      hitListLength - the length of the hit list
    • isEstimateCharge

      public Boolean isEstimateCharge()
      Indicates whether the precursor charge shall be estimated for PepNovo.
      Returns:
      a boolean indicating whether the precursor charge shall be estimated for PepNovo
    • setEstimateCharge

      public void setEstimateCharge​(Boolean estimateCharge)
      Sets whether the precursor charge shall be estimated for PepNovo.
      Parameters:
      estimateCharge - a boolean indicating whether the precursor charge shall be estimated for PepNovo
    • isCorrectPrecursorMass

      public Boolean isCorrectPrecursorMass()
      Returns a boolean indicating whether the precursor mass shall be corrected (TagDB setting).
      Returns:
      a boolean indicating whether the precursor mass shall be corrected (TagDB setting)
    • setCorrectPrecursorMass

      public void setCorrectPrecursorMass​(Boolean correctPrecursorMass)
      Sets whether the precursor mass shall be corrected (TagDB setting).
      Parameters:
      correctPrecursorMass - a boolean indicating whether the precursor mass shall be corrected (TagDB setting)
    • getDiscardLowQualitySpectra

      public Boolean getDiscardLowQualitySpectra()
      Returns a boolean indicating whether low quality spectra shall be discarded.
      Returns:
      a boolean indicating whether low quality spectra shall be discarded
    • setDiscardLowQualitySpectra

      public void setDiscardLowQualitySpectra​(Boolean discardLowQualitySpectra)
      Sets whether low quality spectra shall be discarded.
      Parameters:
      discardLowQualitySpectra - a boolean indicating whether low quality spectra shall be discarded
    • getFragmentationModel

      public String getFragmentationModel()
      Returns the name of the fragmentation model.
      Returns:
      the name of the fragmentation model
    • setFragmentationModel

      public void setFragmentationModel​(String fragmentationModel)
      Sets the name of the fragmentation model.
      Parameters:
      fragmentationModel - the name of the fragmentation model
    • generateQuery

      public Boolean generateQuery()
      Returns a boolean indicating whether a blast query shall be generated.
      Returns:
      a boolean indicating whether a blast query shall be generated
    • setGenerateQuery

      public void setGenerateQuery​(Boolean generateQuery)
      Sets a boolean indicating whether a blast query shall be generated.
      Parameters:
      generateQuery - a boolean indicating whether a blast query shall be generated
    • getPepNovoPtmMap

      public Map<String,​String> getPepNovoPtmMap()
      Returns the PepNovo to utilities PTM map. Null if not set.
      Returns:
      the PepNovo to utilities PTM map, null if not set
    • getUtilitiesPtmName

      public String getUtilitiesPtmName​(String pepnovoPtmName)
      Returns the utilities PTM name corresponding to the given PepNovo PTM name. Null if not found.
      Parameters:
      pepnovoPtmName - the PepNovo PTM name
      Returns:
      the utilities PTM name
    • setPepNovoPtmMap

      public void setPepNovoPtmMap​(Map<String,​String> pepNovoPtmMap)
      Set the PepNovo to utilities PTM map.
      Parameters:
      pepNovoPtmMap - the pepNovoPtmMap 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