Class ModificationtableContent

java.lang.Object
com.compomics.util.experiment.identification.modification.ModificationtableContent

public class ModificationtableContent
extends Object
Convenience class for the content of a PTM table.
Author:
Marc Vaudel, Harald Barsnes
  • Constructor Details

  • Method Details

    • addIntensity

      public void addIntensity​(int nMod, Integer peptideFragmentIonType, int aa, double intensity)
      Add intensity.
      Parameters:
      nMod - the modification number
      peptideFragmentIonType - the peptide fragment ion type
      aa - the amino acid
      intensity - the intensity
    • getIntensities

      public ArrayList<Double> getIntensities​(int nMod, Integer peptideFragmentIonType, int aa)
      Get intensity.
      Parameters:
      nMod - the modification number
      peptideFragmentIonType - the peptide fragment ion type
      aa - the amino acid
      Returns:
      the list of intensities
    • getQuantile

      public Double getQuantile​(int nMod, Integer peptideFragmentIonType, int aa, double quantile)
      Get the quantile.
      Parameters:
      nMod - the modification number
      peptideFragmentIonType - the peptide fragment ion type
      aa - the amino acid
      quantile - the quantile
      Returns:
      the quantile
    • getHistogram

      public int[] getHistogram​(int nMod, Integer peptideFragmentIonType, int aa, int bins)
      Get histogram.
      Parameters:
      nMod - the modification number
      peptideFragmentIonType - the peptide fragment ion type
      aa - the amino acid
      bins - the bins
      Returns:
      the histogram
    • getMap

      public HashMap<Integer,​HashMap<Integer,​HashMap<Integer,​ArrayList<Double>>>> getMap()
      Get the map.
      Returns:
      the map
    • addAll

      public void addAll​(ModificationtableContent anotherContent)
      Add all.
      Parameters:
      anotherContent - another table content
    • normalize

      public void normalize()
      Normalize intensities.
    • getMaxIntensity

      public double getMaxIntensity()
      Returns the max intensity.
      Returns:
      the max intensity
    • getModificationPlotData

      public static HashMap<PeptideFragmentIon,​ArrayList<IonMatch>> getModificationPlotData​(Peptide peptide, Modification modification, int nMod, String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationParameters, SpecificAnnotationParameters specificAnnotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
      Returns the modification plot series in the JFreechart format for one PSM.
      Parameters:
      peptide - the peptide of interest
      modification - the modification to score
      nMod - the number of times the modification is expected
      spectrumFile - the file of the spectrum
      spectrumTitle - the title of the spectrum
      spectrum - the spectrum
      annotationParameters - the annotation preferences
      specificAnnotationParameters - the specific annotation preferences
      modificationParameters - the modification parameters
      sequenceProvider - a provider for the protein sequences
      modificationSequenceMatchingParameters - the sequence matching preferences for modification to peptide mapping
      Returns:
      the modification plot series in the JFreechart format for one PSM.
    • getModificationTableContent

      public static ModificationtableContent getModificationTableContent​(PeptideAssumption peptideAssumption, Modification modification, int nMod, String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
      Get the table content.
      Parameters:
      peptideAssumption - the peptide assumption
      modification - the modification to score
      nMod - the number of times the modification is expected
      spectrumFile - the file of the spectrum
      spectrumTitle - the title of the spectrum
      spectrum - the corresponding spectrum
      annotationParameters - the annotation parameters
      modificationParameters - the modification parameters
      sequenceProvider - a provider for the protein sequences
      modificationSequenceMatchingParameters - the sequence matching preferences for modification to peptide mapping
      Returns:
      the table content