|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectcom.compomics.util.experiment.identification.PTMLocationScores
public class PTMLocationScores
This class scores PTM locations using various A-scores.
Constructor Summary | |
---|---|
PTMLocationScores()
|
Method Summary | |
---|---|
static HashMap<ArrayList<Integer>,Double> |
getAScore(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
double mzTolerance)
Returns the A-score for the best PTM location. |
static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> |
getPTMPlotData(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
double mzTolerance,
double intensityLimit)
Returns the ptm plot series in the jfreechert format for one psm. |
static HashMap<Integer,MSnSpectrum> |
getReducedSpectra(MSnSpectrum baseSpectrum,
double mzTolerance)
Generates a map containing the spectra filtered on intensity with a basis of 20*mz tolerance indexed by the depth used. |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
---|
public PTMLocationScores()
Method Detail |
---|
public static HashMap<ArrayList<Integer>,Double> getAScore(Peptide peptide, PTM ptm, int nPTM, MSnSpectrum spectrum, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, double mzTolerance)
peptide
- The peptide of interestptm
- The PTM to scorenPTM
- The number of occurrences where this PTM is expected on this peptidespectrum
- The corresponding spectrumexpectedFragmentIons
- The fragment ions to look forneutralLosses
- The neutral losses to look forcharges
- The fragment ions charges to look formzTolerance
- The m/z tolerance to use
public static HashMap<Integer,MSnSpectrum> getReducedSpectra(MSnSpectrum baseSpectrum, double mzTolerance)
baseSpectrum
- the base spectrummzTolerance
- the m/z tolerance
public static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> getPTMPlotData(Peptide peptide, PTM ptm, int nPTM, MSnSpectrum spectrum, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, double mzTolerance, double intensityLimit)
peptide
- The peptide of interestptm
- The PTM to scorenPTM
- The amount of times the PTM is expectedspectrum
- The corresponding spectrumexpectedFragmentIons
- The fragment ions to look forneutralLosses
- The neutral losses to look forcharges
- The fragment ions charges to look formzTolerance
- The m/z tolerance to use
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |