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.ptm   
com.compomics.util.preferences   
 

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)
          Deprecated. This method can generate inconsistent results in case a measurement matches to various PTMs.
 PTM PTMFactory.getPTM(ModificationProfile modificationProfile, int index)
          Get a PTM according to its omssa index.
 PTM PTMFactory.getPTM(java.lang.String name)
          Returns the PTM indexed by its name.
 PTM PTMFactory.getSearchedPTM(PTM modification)
          Returns the standard search compatible PTM corresponding to this pattern.
 PTM PTMFactory.getSearchedPTM(java.lang.String modificationName)
          Returns the standard search compatible PTM corresponding to this pattern, i.e., a pattern targeting a single amino-acid and not a complex pattern.
 

Methods in com.compomics.util.experiment.biology with parameters of type PTM
 void PTMFactory.addUserPTM(PTM ptm)
          Adds a new user modification.
 java.util.ArrayList<java.lang.Integer> Peptide.getPotentialModificationSites(PTM ptm)
          Returns the potential modification sites as an ordered list of string.
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.
 PTM PTMFactory.getSearchedPTM(PTM modification)
          Returns the standard search compatible PTM corresponding to this pattern.
 boolean Peptide.isModifiable(PTM ptm)
          Indicates whether the given modification can be found on the peptide.
 boolean PTM.isSameAs(PTM anotherPTM)
          Compares two PTMs.
 

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<PeptideFragmentIon,java.util.ArrayList<IonMatch>> PTMLocationScores.getPTMPlotData(Peptide peptide, PTM ptm, int nPTM, MSnSpectrum spectrum, java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, 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.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, NeutralLossesMap neutralLosses, java.util.ArrayList<java.lang.Integer> charges, int precursorCharge, double mzTolerance, double intensityLimit)
          Get the PTM table content.
 

Method parameters in com.compomics.util.experiment.identification.ptm with type arguments of type PTM
static java.util.HashMap<java.util.ArrayList<java.lang.Integer>,java.lang.Double> PTMLocationScores.getAScore(Peptide peptide, java.util.ArrayList<PTM> ptms, MSnSpectrum spectrum, java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, java.util.ArrayList<java.lang.Integer> charges, int precursorCharge, double mzTolerance)
          Returns the A-score for the best PTM location without accounting for neutral losses.
static java.util.HashMap<java.util.ArrayList<java.lang.Integer>,java.lang.Double> PTMLocationScores.getAScore(Peptide peptide, java.util.ArrayList<PTM> ptms, MSnSpectrum spectrum, java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, NeutralLossesMap neutralLosses, java.util.ArrayList<java.lang.Integer> charges, int precursorCharge, double mzTolerance)
          Returns the A-score for the best PTM location accounting for neutral losses.
static java.util.HashMap<java.util.ArrayList<java.lang.Integer>,java.lang.Double> PTMLocationScores.getAScore(Peptide peptide, java.util.ArrayList<PTM> ptms, MSnSpectrum spectrum, java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, NeutralLossesMap neutralLosses, java.util.ArrayList<java.lang.Integer> charges, int precursorCharge, double mzTolerance, boolean accountNeutralLosses)
          Returns the A-score for the best PTM location.
 

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

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

Uses of PTM in com.compomics.util.preferences
 

Methods in com.compomics.util.preferences that return PTM
 PTM ModificationProfile.getPtm(java.lang.String modName)
          Returns the back-ed up PTM with the given name.
 

Methods in com.compomics.util.preferences with parameters of type PTM
 void ModificationProfile.addFixedModification(PTM modification)
          Adds a fixed modification.
 void ModificationProfile.addRefinementModification(PTM modification)
          Adds a refinement modification.
 void ModificationProfile.addVariableModification(PTM modification)
          Adds a variable modification.
 



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