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

public class PNovoParameters
extends ExperimentObject
implements IdentificationAlgorithmParameter
pNovo specific parameters.
Author:
Harald Barsnes
See Also:
Serialized Form
  • Constructor Details

  • 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
    • getNumberOfPeptides

      public int getNumberOfPeptides()
      Returns the number of peptides to report per spectrum.
      Returns:
      the number of peptides to report per spectrum
    • setNumberOfPeptides

      public void setNumberOfPeptides​(int numberOfPeptides)
      Set the number of peptides to report per spectrum.
      Parameters:
      numberOfPeptides - the number of peptides to report per spectrum
    • getLowerPrecursorMass

      public int getLowerPrecursorMass()
      Returns the lower precursor mass.
      Returns:
      the lowerPrecursorMass
    • setLowerPrecursorMass

      public void setLowerPrecursorMass​(int lowerPrecursorMass)
      Set the lower precursor mass.
      Parameters:
      lowerPrecursorMass - the lowerPrecursorMass to set
    • getUpperPrecursorMass

      public int getUpperPrecursorMass()
      Returns the upper precursor mass.
      Returns:
      the upperPrecursorMass
    • setUpperPrecursorMass

      public void setUpperPrecursorMass​(int upperPrecursorMass)
      Set the upper precursor mass.
      Parameters:
      upperPrecursorMass - the upperPrecursorMass to set
    • getActicationType

      public String getActicationType()
      Returns the activation type.
      Returns:
      the acticationType
    • setActicationType

      public void setActicationType​(String acticationType)
      Sets the activation type.
      Parameters:
      acticationType - the acticationType to set
    • getPNovoPtmMap

      public HashMap<Character,​String> getPNovoPtmMap()
      Returns the pNovo to utilities PTM map. Null if not set.
      Returns:
      the pNovo to utilities PTM map, null if not set
    • getUtilitiesPtmName

      public String getUtilitiesPtmName​(Character pNovoPtmCharacter)
      Returns the utilities PTM name corresponding to the given pNovo PTM character. Null if not found.
      Parameters:
      pNovoPtmCharacter - the pNovo PTM character
      Returns:
      the utilities PTM name
    • setPNovoPtmMap

      public void setPNovoPtmMap​(HashMap<Character,​String> pNovoPtmMap)
      Set the pNovo to utilities PTM map.
      Parameters:
      pNovoPtmMap - the pNovoPtmMap to set
    • getPNovoPtmResiduesMap

      public HashMap<Character,​Character> getPNovoPtmResiduesMap()
      Returns the pNovo to original amino acids residue map. Null if not set.
      Returns:
      the pNovo to original amino acids residue map, null if not set
    • getPtmResidue

      public Character getPtmResidue​(Character pNovoPtmCharacter)
      Returns the original amino acids residue corresponding to the given pNovo PTM character. Null if not found.
      Parameters:
      pNovoPtmCharacter - the pNovo PTM character
      Returns:
      the original amino acids residue
    • setPNovoPtmResiduesMap

      public void setPNovoPtmResiduesMap​(HashMap<Character,​Character> pNovoResidueMap)
      Set the pNovo to original amino acids residue map.
      Parameters:
      pNovoResidueMap - the pNovoResidueMap to set