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java.lang.Objectcom.compomics.util.experiment.identification.ptm.PtmtableContent
public class PtmtableContent
Convenience class for the content of a PTM table.
Constructor Summary | |
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PtmtableContent()
Constructor. |
Method Summary | |
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void |
addAll(PtmtableContent anotherContent)
Add all. |
void |
addIntensity(int nMod,
Integer peptideFragmentIonType,
int aa,
double intensity)
Add intensity. |
int[] |
getHistogram(int nMod,
Integer peptideFragmentIonType,
int aa,
int bins)
Get histogram. |
ArrayList<Double> |
getIntensities(int nMod,
Integer peptideFragmentIonType,
int aa)
Get intensity. |
HashMap<Integer,HashMap<Integer,HashMap<Integer,ArrayList<Double>>>> |
getMap()
Get the map. |
double |
getMaxIntensity()
Returns the max intensity. |
static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> |
getPTMPlotData(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
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 |
getPTMTableContent(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
double intensityLimit)
Get the PTM table content. |
Double |
getQuantile(int nMod,
Integer peptideFragmentIonType,
int aa,
double quantile)
Get the quantile. |
void |
normalize()
Normalize intensities. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public PtmtableContent()
Method Detail |
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public void addIntensity(int nMod, Integer peptideFragmentIonType, int aa, double intensity)
nMod
- peptideFragmentIonType
- aa
- intensity
- public ArrayList<Double> getIntensities(int nMod, Integer peptideFragmentIonType, int aa)
nMod
- peptideFragmentIonType
- aa
-
public Double getQuantile(int nMod, Integer peptideFragmentIonType, int aa, double quantile)
nMod
- peptideFragmentIonType
- aa
- quantile
-
public int[] getHistogram(int nMod, Integer peptideFragmentIonType, int aa, int bins)
nMod
- peptideFragmentIonType
- aa
- bins
-
public HashMap<Integer,HashMap<Integer,HashMap<Integer,ArrayList<Double>>>> getMap()
public void addAll(PtmtableContent anotherContent)
anotherContent
- public void normalize()
public double getMaxIntensity()
public static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> getPTMPlotData(Peptide peptide, PTM ptm, int nPTM, MSnSpectrum spectrum, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, double mzTolerance, double intensityLimit)
peptide
- The peptide of interestptm
- The PTM to scorenPTM
- The amount of times the PTM is expectedspectrum
- The corresponding spectrumiontypes
- The fragment ions to look forneutralLosses
- The neutral losses to look forcharges
- The fragment ions charges to look forprecursorCharge
- The precursor chargemzTolerance
- The m/z tolerance to useintensityLimit
-
public static PtmtableContent getPTMTableContent(Peptide peptide, PTM ptm, int nPTM, MSnSpectrum spectrum, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, double mzTolerance, double intensityLimit)
peptide
- The peptide of interestptm
- The PTM to scorenPTM
- The amount of times the PTM is expectedspectrum
- The corresponding spectrumiontypes
- The fragment ions to look forneutralLosses
- The neutral losses to look forcharges
- The fragment ions charges to look forprecursorCharge
- The precursor chargemzTolerance
- The m/z tolerance to useintensityLimit
-
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