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Packages that use PTM | |
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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 |
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Fields in com.compomics.util.experiment.biology declared as PTM | |
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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 | |
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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 | |
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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 |
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Methods in com.compomics.util.experiment.identification.ptm with parameters of type PTM | |
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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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