public class ModificationtableContent extends Object
Constructor and Description |
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ModificationtableContent()
Constructor.
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Modifier and Type | Method and Description |
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void |
addAll(ModificationtableContent anotherContent)
Add all.
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void |
addIntensity(int nMod,
Integer peptideFragmentIonType,
int aa,
double intensity)
Add intensity.
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int[] |
getHistogram(int nMod,
Integer peptideFragmentIonType,
int aa,
int bins)
Get histogram.
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ArrayList<Double> |
getIntensities(int nMod,
Integer peptideFragmentIonType,
int aa)
Get intensity.
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HashMap<Integer,HashMap<Integer,HashMap<Integer,ArrayList<Double>>>> |
getMap()
Get the map.
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double |
getMaxIntensity()
Returns the max intensity.
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static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> |
getModificationPlotData(Peptide peptide,
Modification modification,
int nMod,
Spectrum spectrum,
AnnotationParameters annotationPreferences,
SpecificAnnotationParameters specificAnnotationPreferences)
Returns the modification plot series in the JFreechart format for one
PSM.
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static ModificationtableContent |
getModificationTableContent(PeptideAssumption peptideAssumption,
Modification modification,
int nMod,
Spectrum spectrum,
AnnotationParameters annotationParameters)
Get the table content.
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Double |
getQuantile(int nMod,
Integer peptideFragmentIonType,
int aa,
double quantile)
Get the quantile.
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void |
normalize()
Normalize intensities.
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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, Spectrum spectrum, AnnotationParameters annotationPreferences, SpecificAnnotationParameters specificAnnotationPreferences)
peptide
- the peptide of interestmodification
- the modification to scorenMod
- the number of times the modification is expectedspectrum
- the corresponding spectrumannotationPreferences
- the annotation preferencesspecificAnnotationPreferences
- the specific annotation preferencespublic static ModificationtableContent getModificationTableContent(PeptideAssumption peptideAssumption, Modification modification, int nMod, Spectrum spectrum, AnnotationParameters annotationParameters)
peptideAssumption
- the peptide assumptionmodification
- the modification to scorenMod
- the number of times the modification is expectedspectrum
- the corresponding spectrumannotationParameters
- the annotation parametersCopyright © 2018. All rights reserved.