|
||||||||||
PREV NEXT | FRAMES NO FRAMES |
Packages that use PTM | |
---|---|
com.compomics.util.experiment.biology | This package contains experiement classes related to biological entities. |
com.compomics.util.experiment.identification | This package contains experiment classes related to identifications. |
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,
java.lang.String location,
java.lang.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(java.lang.String name)
Returns the PTM indexed by its name |
Methods in com.compomics.util.experiment.biology that return types with arguments of type PTM | |
---|---|
java.util.Iterator<PTM> |
PTMFactory.getPtmIterator()
returns an iterator on the imported PTM |
java.util.HashMap<java.lang.Integer,PTM> |
PTMFactory.getPtmMap()
getter for the index to PTM map |
Uses of PTM in com.compomics.util.experiment.identification |
---|
Methods in com.compomics.util.experiment.identification with parameters of type PTM | |
---|---|
static java.util.HashMap<java.lang.Integer,java.lang.Double> |
AScore.getAScore(Peptide peptide,
PTM ptm,
MSnSpectrum spectrum,
java.util.ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons,
java.util.HashMap<NeutralLoss,java.lang.Integer> neutralLosses,
java.util.ArrayList<java.lang.Integer> charges,
double intensityLimit,
double mzTolerance)
|
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 |
|
||||||||||
PREV NEXT | FRAMES NO FRAMES |