Uses of Class
com.compomics.util.experiment.biology.PTM

Packages that use PTM
com.compomics.util.experiment.biology This package contains experiement classes related to biological entities. 
com.compomics.util.experiment.identification This package contains experiment classes related to identifications. 
 

Uses of PTM in com.compomics.util.experiment.biology
 

Methods in com.compomics.util.experiment.biology that return PTM
 PTM PTMFactory.getPTM(double mass, String location, String sequence)
          getter for a ptm according to its measured characteristics /!
 PTM PTMFactory.getPTM(int index)
          get a PTM according to its index
 PTM PTMFactory.getPTM(String name)
          Returns the PTM indexed by its name
 

Methods in com.compomics.util.experiment.biology that return types with arguments of type PTM
 Iterator<PTM> PTMFactory.getPtmIterator()
          returns an iterator on the imported PTM
 HashMap<Integer,PTM> PTMFactory.getPtmMap()
          getter for the index to PTM map
 

Methods in com.compomics.util.experiment.biology with parameters of type PTM
static ArrayList<Integer> Peptide.getPotentialModificationSites(String sequence, PTM ptm)
          returns the potential modification sites as an ordered list of string. 0 is the first aa.
 void PTMFactory.replacePTM(String oldName, PTM newPTM)
          replaces an old ptm by a new
 

Uses of PTM in com.compomics.util.experiment.identification
 

Methods in com.compomics.util.experiment.identification with parameters of type PTM
static HashMap<ArrayList<Integer>,Double> PTMLocationScores.getAScore(Peptide peptide, PTM ptm, int nPTM, MSnSpectrum spectrum, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, double mzTolerance)
          Returns the A-score for the best PTM location.
static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> PTMLocationScores.getPTMPlotData(Peptide peptide, PTM ptm, int nPTM, MSnSpectrum spectrum, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, double mzTolerance, double intensityLimit)
          Returns the ptm plot series in the jfreechert format for one psm.
 



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