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. 
 

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 /!\ This method can generate inconsistent results in case a measurement matches to various PTMs.
 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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