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.matches This package contains experiment classes releated to matches. e.g., pepties, proteins, modifications and spectra. 
 

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
 

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

Methods in com.compomics.util.experiment.identification.matches that return PTM
 PTM ModificationMatch.getTheoreticPtm()
          getter for the theoretic PTM
 

Methods in com.compomics.util.experiment.identification.matches with parameters of type PTM
 void ModificationMatch.setTheoreticPtm(PTM ptm)
          Sets the theoretic PTM
 

Constructors in com.compomics.util.experiment.identification.matches with parameters of type PTM
ModificationMatch(PTM theoreticPtm, boolean variable, int modifiedSite)
          constructor for a modification match
 



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