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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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Methods in com.compomics.util.experiment.biology that return PTM | |
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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 | |
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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 |
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Methods in com.compomics.util.experiment.identification.ptm with parameters of type PTM | |
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static HashMap<ArrayList<Integer>,Double> |
PTMLocationScores.getAScore(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons,
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,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons,
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,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
double intensityLimit)
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