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   
com.compomics.util.gui.dialogs This package contains GUI dialogs. 
 

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, String location, String sequence)
          Getter for a ptm according to its measured characteristics /!
 PTM PTMFactory.getPTM(int index)
          Get a PTM according to its omssa index.
 PTM PTMFactory.getPTM(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 ArrayList<Integer> Peptide.getPotentialModificationSites(String sequence, PTM ptm)
          Returns the potential modification sites as an ordered list of string. 0 is the first aa.
 boolean PTM.isSameAs(PTM anotherPTM)
          Compares two PTMs
 void PTMFactory.replacePTM(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 HashMap<ArrayList<Integer>,Double> PTMLocationScores.getAPlusScore(Peptide peptide, PTM ptm, int nPTM, MSnSpectrum spectrum, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, double mzTolerance)
          Returns an alternative version of the A-score for the best PTM location.
static HashMap<ArrayList<Integer>,Double> PTMLocationScores.getAScore(Peptide peptide, PTM ptm, int nPTM, MSnSpectrum spectrum, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, 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, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<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, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, double mzTolerance, double intensityLimit)
          Get the PTM table content.
 

Uses of PTM in com.compomics.util.gui.dialogs
 

Constructors in com.compomics.util.gui.dialogs with parameters of type PTM
PtmDialog(JDialog parent, PtmDialogParent ptmDialogParent, PtmToPrideMap ptmToPrideMap, PTM currentPTM, boolean editable)
          Creates a new PTM dialog.
PtmDialog(JFrame parent, PtmDialogParent ptmDialogParent, PtmToPrideMap ptmToPrideMap, PTM currentPTM, boolean editable)
          Creates a new PTM dialog.
 



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