public class PtmtableContent extends Object
Constructor and Description |
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PtmtableContent()
Constructor.
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Modifier and Type | Method and Description |
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void |
addAll(PtmtableContent 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>> |
getPTMPlotData(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences)
Returns the PTM plot series in the JFreechart format for one PSM.
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static PtmtableContent |
getPTMTableContent(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences)
Get the PTM 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(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, AnnotationSettings annotationPreferences, SpecificAnnotationSettings specificAnnotationPreferences)
peptide
- the peptide of interestptm
- the PTM to scorenPTM
- the amount of times the PTM is expectedspectrum
- the corresponding spectrumannotationPreferences
- the annotation preferencesspecificAnnotationPreferences
- the specific annotation preferencespublic static PtmtableContent getPTMTableContent(Peptide peptide, PTM ptm, int nPTM, MSnSpectrum spectrum, AnnotationSettings annotationPreferences, SpecificAnnotationSettings specificAnnotationPreferences) throws IOException, SQLException, ClassNotFoundException, InterruptedException
peptide
- the peptide of interestptm
- the PTM to scorenPTM
- the amount of times the PTM is expectedspectrum
- the corresponding spectrumannotationPreferences
- the annotation preferencesspecificAnnotationPreferences
- the specific annotation preferencesIOException
- exception thrown whenever an error occurred while
reading a protein sequenceInterruptedException
- exception thrown whenever an error occurred
while reading a protein sequenceClassNotFoundException
- if a ClassNotFoundException occursSQLException
- if an SQLException occursCopyright © 2016. All rights reserved.