public class ModificationtableContent extends Object
Constructor and Description |
---|
ModificationtableContent()
Constructor.
|
Modifier and Type | Method and Description |
---|---|
void |
addAll(ModificationtableContent 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>> |
getModificationPlotData(Peptide peptide,
Modification modification,
int nMod,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
AnnotationParameters annotationParameters,
SpecificAnnotationParameters specificAnnotationParameters,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters)
Returns the modification plot series in the JFreechart format for one
PSM.
|
static ModificationtableContent |
getModificationTableContent(PeptideAssumption peptideAssumption,
Modification modification,
int nMod,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
AnnotationParameters annotationParameters,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters)
Get the 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(ModificationtableContent anotherContent)
anotherContent
- another table contentpublic void normalize()
public double getMaxIntensity()
public static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> getModificationPlotData(Peptide peptide, Modification modification, int nMod, String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationParameters, SpecificAnnotationParameters specificAnnotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
peptide
- the peptide of interestmodification
- the modification to scorenMod
- the number of times the modification is expectedspectrumFile
- the file of the spectrumspectrumTitle
- the title of the spectrumspectrum
- the spectrumannotationParameters
- the annotation preferencesspecificAnnotationParameters
- the specific annotation preferencesmodificationParameters
- the modification parameterssequenceProvider
- a provider for the protein sequencesmodificationSequenceMatchingParameters
- the sequence matching
preferences for modification to peptide mappingpublic static ModificationtableContent getModificationTableContent(PeptideAssumption peptideAssumption, Modification modification, int nMod, String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
peptideAssumption
- the peptide assumptionmodification
- the modification to scorenMod
- the number of times the modification is expectedspectrumFile
- the file of the spectrumspectrumTitle
- the title of the spectrumspectrum
- the corresponding spectrumannotationParameters
- the annotation parametersmodificationParameters
- the modification parameterssequenceProvider
- a provider for the protein sequencesmodificationSequenceMatchingParameters
- the sequence matching
preferences for modification to peptide mappingCopyright © 2021. All rights reserved.