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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 | This package contains experiment classes related to identifications. |
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 index |
PTM |
PTMFactory.getPTM(String name)
Returns the PTM indexed by its name |
Methods in com.compomics.util.experiment.biology that return types with arguments of type PTM | |
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Iterator<PTM> |
PTMFactory.getPtmIterator()
returns an iterator on the imported PTM |
HashMap<Integer,PTM> |
PTMFactory.getPtmMap()
getter for the index to PTM map |
Methods in com.compomics.util.experiment.biology with parameters of type PTM | |
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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. |
void |
PTMFactory.replacePTM(String oldName,
PTM newPTM)
replaces an old ptm by a new |
Uses of PTM in com.compomics.util.experiment.identification |
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Methods in com.compomics.util.experiment.identification with parameters of type PTM | |
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static HashMap<ArrayList<Integer>,Double> |
AScore.getAScore(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons,
HashMap<NeutralLoss,Integer> neutralLosses,
ArrayList<Integer> charges,
double mzTolerance)
Returns the A-score for the best PTM location. |
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