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

Class PNovoParameters

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:

  • Constructor Details

    • PNovoParameters

      public PNovoParameters()
      Constructor.

  • 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