Class ModificationtableContent
java.lang.Object
com.compomics.util.experiment.identification.modification.ModificationtableContent
public class ModificationtableContent extends Object
Convenience class for the content of a PTM table.
- Author:
- Marc Vaudel, Harald Barsnes
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Constructor Summary
Constructors Constructor Description ModificationtableContent()
Constructor. -
Method Summary
Modifier and Type Method 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.
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Constructor Details
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ModificationtableContent
public ModificationtableContent()Constructor.
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Method Details
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addIntensity
Add intensity.- Parameters:
nMod
- the modification numberpeptideFragmentIonType
- the peptide fragment ion typeaa
- the amino acidintensity
- the intensity
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getIntensities
Get intensity.- Parameters:
nMod
- the modification numberpeptideFragmentIonType
- the peptide fragment ion typeaa
- the amino acid- Returns:
- the list of intensities
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getQuantile
Get the quantile.- Parameters:
nMod
- the modification numberpeptideFragmentIonType
- the peptide fragment ion typeaa
- the amino acidquantile
- the quantile- Returns:
- the quantile
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getHistogram
Get histogram.- Parameters:
nMod
- the modification numberpeptideFragmentIonType
- the peptide fragment ion typeaa
- the amino acidbins
- the bins- Returns:
- the histogram
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getMap
Get the map.- Returns:
- the map
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addAll
Add all.- Parameters:
anotherContent
- another table content
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normalize
public void normalize()Normalize intensities. -
getMaxIntensity
public double getMaxIntensity()Returns the max intensity.- Returns:
- the max intensity
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getModificationPlotData
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)Returns the modification plot series in the JFreechart format for one PSM.- Parameters:
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 mapping- Returns:
- the modification plot series in the JFreechart format for one PSM.
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getModificationTableContent
public 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.- Parameters:
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 mapping- Returns:
- the table content
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