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.ptm   
 

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

Fields in com.compomics.util.experiment.biology declared as PTM
static PTM PTMFactory.unknownPTM
          unknown modification to be returned when the modification is not found
 

Methods in com.compomics.util.experiment.biology that return PTM
 PTM PTMFactory.getPTM(double mass, java.lang.String location, java.lang.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 omssa index
 PTM PTMFactory.getPTM(java.lang.String name)
          Returns the PTM indexed by its name
 

Methods in com.compomics.util.experiment.biology with parameters of type PTM
 void PTMFactory.addUserPTM(PTM ptm)
          Adds a new user modification
static java.util.ArrayList<java.lang.Integer> Peptide.getPotentialModificationSites(java.lang.String sequence, PTM ptm)
          Returns the potential modification sites as an ordered list of string.
 boolean PTM.isSameAs(PTM anotherPTM)
          Compares two PTMs
 void PTMFactory.replacePTM(java.lang.String oldName, PTM newPTM)
          replaces an old ptm by a new
 

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

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



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