com.compomics.util.experiment.identification.ptm
Class PtmtableContent

java.lang.Object
  extended by com.compomics.util.experiment.identification.ptm.PtmtableContent

public class PtmtableContent
extends Object

Convenience class for the content of a PTM table.

Author:
Marc Vaudel, Harald Barsnes

Constructor Summary
PtmtableContent()
          Constructor.
 
Method Summary
 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
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

PtmtableContent

public PtmtableContent()
Constructor.

Method Detail

addIntensity

public void addIntensity(int nMod,
                         Integer peptideFragmentIonType,
                         int aa,
                         double intensity)
Add intensity.

Parameters:
nMod -
peptideFragmentIonType -
aa -
intensity -

getIntensities

public ArrayList<Double> getIntensities(int nMod,
                                        Integer peptideFragmentIonType,
                                        int aa)
Get intensity.

Parameters:
nMod -
peptideFragmentIonType -
aa -
Returns:
the list of intensities

getQuantile

public Double getQuantile(int nMod,
                          Integer peptideFragmentIonType,
                          int aa,
                          double quantile)
Get the quantile.

Parameters:
nMod -
peptideFragmentIonType -
aa -
quantile -
Returns:
the quantile

getHistogram

public int[] getHistogram(int nMod,
                          Integer peptideFragmentIonType,
                          int aa,
                          int bins)
Get histogram.

Parameters:
nMod -
peptideFragmentIonType -
aa -
bins -
Returns:
the histogram

getMap

public HashMap<Integer,HashMap<Integer,HashMap<Integer,ArrayList<Double>>>> getMap()
Get the map.

Returns:
the map

addAll

public void addAll(PtmtableContent anotherContent)
Add all.

Parameters:
anotherContent -

normalize

public void normalize()
Normalize intensities.


getMaxIntensity

public double getMaxIntensity()
Returns the max intensity.

Returns:
the max intensity

getPTMPlotData

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)
Returns the PTM plot series in the JFreechart format for one PSM.

Parameters:
peptide - The peptide of interest
ptm - The PTM to score
nPTM - The amount of times the PTM is expected
spectrum - The corresponding spectrum
iontypes - The fragment ions to look for
neutralLosses - The neutral losses to look for
charges - The fragment ions charges to look for
precursorCharge - The precursor charge
mzTolerance - The m/z tolerance to use
intensityLimit -
Returns:
the PTM plot series in the JFreechart format for one PSM.

getPTMTableContent

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)
Get the PTM table content.

Parameters:
peptide - The peptide of interest
ptm - The PTM to score
nPTM - The amount of times the PTM is expected
spectrum - The corresponding spectrum
iontypes - The fragment ions to look for
neutralLosses - The neutral losses to look for
charges - The fragment ions charges to look for
precursorCharge - The precursor charge
mzTolerance - The m/z tolerance to use
intensityLimit -
Returns:
the PtmtableContent object


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