Package com.compomics.util.experiment.identification

Class SpectrumIdentificationAssumption

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
All Implemented Interfaces:
Serializable
Direct Known Subclasses:
PeptideAssumption, TagAssumption
public abstract class SpectrumIdentificationAssumption extends ExperimentObject
Spectrum identification assumption made by an identification algorithm.
Author:
Marc Vaudel, Dominik Kopczynski
See Also:

  • Field Details

    • rank

      protected int rank
      The rank of the peptide assumption for the given spectrum.

    • advocate

      protected int advocate
      The advocate supporting this assumption.

    • identificationCharge

      protected int identificationCharge
      The charge used for identification.

    • score

      protected double score
      The (advocate specific) score used to rank this assumption.

    • identificationFile

      protected String identificationFile
      The identification file.

    • rawScore

      protected double rawScore
      The raw score as provided by the identification algorithm.

    • aminoAcidScores

      protected ArrayList<double[]> aminoAcidScores
      The individual amino acid scores. Null if not set.

  • Constructor Details

    • SpectrumIdentificationAssumption

      public SpectrumIdentificationAssumption()
      Empty default constructor.

  • Method Details

    • getRank

      public int getRank()
      Get the identification rank.
      Returns:
      the identification rank

    • setRank

      public void setRank(int rank)
      Set the rank of the PeptideAssumption.
      Parameters:
      rank - the rank of the PeptideAssumption

    • getAdvocate

      public int getAdvocate()
      Get the used advocate.
      Returns:
      the advocate index

    • setAdvocate

      public void setAdvocate(int advocate)
      Sets the advocate id.
      Parameters:
      advocate - The advocate id.

    • getScore

      public double getScore()
      Returns the score assigned by the advocate.
      Returns:
      the score

    • setScore

      public void setScore(double score)
      Sets the score. Note: if PsmScores.scoreRoundingDecimal is not null the scored will be floored accordingly.
      Parameters:
      score - the score

    • getIdentificationFile

      public String getIdentificationFile()
      Returns the identification file.
      Returns:
      the identification file

    • setIdentificationFile

      public void setIdentificationFile(String identificationFile)
      Sets the identification file.
      Parameters:
      identificationFile - The identification file.

    • getIdentificationCharge

      public int getIdentificationCharge()
      Returns the charge used for identification.
      Returns:
      the charge used for identification

    • setIdentificationCharge

      public void setIdentificationCharge(int identificationCharge)
      Sets the identification charge.
      Parameters:
      identificationCharge - the identification charge

    • getTheoreticMass

      public abstract double getTheoreticMass()
      Returns the theoretic mass of the given assumption.
      Returns:
      the theoretic mass of the given assumption

    • getTheoreticMz

      public double getTheoreticMz()
      Returns the theoretic m/z.
      Returns:
      the theoretic m/z

    • getDeltaMz

      public double getDeltaMz(double measuredMZ, boolean ppm, int minIsotope, int maxIsotope)
      Returns the precursor m/z error (in ppm or absolute). Note that the value is returns as (experimental mass - theoretical mass) and that negative values thus can occur. The isotopic error can subtracted and retrieved by the function getIsotopeNumber().
      Parameters:
      measuredMZ - the precursor m/z
      ppm - if true the error is returns in ppm, false returns the error in Da
      minIsotope - the minimal isotope
      maxIsotope - the maximal isotope
      Returns:
      the precursor mass error

    • getIsotopeNumber

      public int getIsotopeNumber(double measuredMZ, int minIsotope, int maxIsotope)
      Returns the precursor isotope number according to the number of protons.
      Parameters:
      measuredMZ - the measured m/z value
      minIsotope - the minimal isotope
      maxIsotope - the maximal isotope
      Returns:
      the precursor isotope number according to the number of protons

    • getPrecursorMatch

      public IonMatch getPrecursorMatch(double precursorMz, double precursorIntensity)
      Returns the ion match.
      Parameters:
      precursorMz - The precursor measured m/z.
      precursorIntensity - The precursor measured intensity.
      Returns:
      the ion match

    • getRawScore

      public double getRawScore()
      Returns the raw score as provided by the identification algorithm.
      Returns:
      the raw score as provided by the identification algorithm

    • setRawScore

      public void setRawScore(double rawScore)
      Sets the raw score as provided by the identification algorithm.
      Parameters:
      rawScore - the raw score as provided by the identification algorithm

    • getAminoAcidScores

      public ArrayList<double[]> getAminoAcidScores()
      Returns the amino acid scores. Null of not set. For Peptide objects the list only contains one element, while for Tag objects the list will be indexed in identically to the TagComponent list.
      Returns:
      the amino acid scores

    • setAminoAcidScores

      public void setAminoAcidScores(ArrayList<double[]> aminoAcidScores)
      Set the amino acid scores. For Peptide objects the list should only contain one element, while for Tag objects the list should be indexed in identical to the TagComponent list.
      Parameters:
      aminoAcidScores - the amino acid scores