public class PtmtableContent extends Object
Constructor and Description |
---|
PtmtableContent()
Constructor.
|
Modifier and Type | Method and Description |
---|---|
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,HashSet<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,HashSet<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.
|
public void addIntensity(int nMod, Integer peptideFragmentIonType, int aa, double intensity)
nMod
- the modification numberpeptideFragmentIonType
- the peptide fragment ion typeaa
- the amino acidintensity
- the intensitypublic ArrayList<Double> getIntensities(int nMod, Integer peptideFragmentIonType, int aa)
nMod
- the modification numberpeptideFragmentIonType
- the peptide fragment ion typeaa
- the amino acidpublic Double getQuantile(int nMod, Integer peptideFragmentIonType, int aa, double quantile)
nMod
- the modification numberpeptideFragmentIonType
- the peptide fragment ion typeaa
- the amino acidquantile
- the quantilepublic int[] getHistogram(int nMod, Integer peptideFragmentIonType, int aa, int bins)
nMod
- the modification numberpeptideFragmentIonType
- the peptide fragment ion typeaa
- the amino acidbins
- the binspublic HashMap<Integer,HashMap<Integer,HashMap<Integer,ArrayList<Double>>>> getMap()
public void addAll(PtmtableContent anotherContent)
anotherContent
- another PTM table contentpublic void normalize()
public double getMaxIntensity()
public static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> getPTMPlotData(Peptide peptide, PTM ptm, int nPTM, MSnSpectrum spectrum, HashMap<Ion.IonType,HashSet<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
- the intensity limitpublic static PtmtableContent getPTMTableContent(Peptide peptide, PTM ptm, int nPTM, MSnSpectrum spectrum, HashMap<Ion.IonType,HashSet<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
- the intensity limitCopyright © 2015. All rights reserved.