Package | Description |
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com.compomics.util.experiment.identification |
This package contains experiment classes related to identifications.
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com.compomics.util.experiment.identification.ptm | |
com.compomics.util.experiment.identification.ptm.ptmscores | |
com.compomics.util.experiment.identification.scoring | |
com.compomics.util.experiment.io.massspectrometry | |
com.compomics.util.gui.spectrum |
This package contains GUI classes related to Spectrum and Chromatogram visualization.
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Modifier and Type | Method and Description |
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java.util.HashMap<java.lang.Integer,java.util.ArrayList<IonMatch>> |
SpectrumAnnotator.getCoveredAminoAcids(java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
MSnSpectrum spectrum,
Peptide peptide,
double intensityLimit,
double mzTolerance,
boolean isPpm)
Returns the ion matches corresponding to fragment ions indexed by amino
acid number in the sequence.
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java.util.ArrayList<IonMatch> |
SpectrumAnnotator.getSpectrumAnnotation(java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
MSnSpectrum spectrum,
Peptide peptide,
double intensityLimit,
double mzTolerance,
boolean isPpm)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
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Modifier and Type | Method and Description |
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static java.util.HashMap<PeptideFragmentIon,java.util.ArrayList<IonMatch>> |
PtmtableContent.getPTMPlotData(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
double mzTolerance,
double intensityLimit)
Returns the PTM plot series in the JFreechart format for one PSM.
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static PtmtableContent |
PtmtableContent.getPTMTableContent(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
double mzTolerance,
double intensityLimit)
Get the PTM table content.
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Modifier and Type | Method and Description |
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static java.util.HashMap<java.lang.Integer,MSnSpectrum> |
AScore.getReducedSpectra(MSnSpectrum baseSpectrum,
double mzTolerance)
Generates a map containing the spectra filtered on intensity with a basis
of 20*m/z tolerance indexed by the depth used.
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static java.util.HashMap<java.lang.Integer,MSnSpectrum> |
AScore.getReducedSpectra(MSnSpectrum baseSpectrum,
double mzTolerance,
int depthMax)
Generates a map containing the spectra filtered on intensity with a basis
of 20*m/z tolerance indexed by the depth used.
|
Modifier and Type | Method and Description |
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static java.util.HashMap<java.util.ArrayList<java.lang.Integer>,java.lang.Double> |
AScore.getAScore(Peptide peptide,
java.util.ArrayList<PTM> ptms,
MSnSpectrum spectrum,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
double mzTolerance)
Returns the A-score for the best PTM location without accounting for
neutral losses.
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static java.util.HashMap<java.util.ArrayList<java.lang.Integer>,java.lang.Double> |
AScore.getAScore(Peptide peptide,
java.util.ArrayList<PTM> ptms,
MSnSpectrum spectrum,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
double mzTolerance)
Returns the A-score for the best PTM location accounting for neutral
losses.
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static java.util.HashMap<java.util.ArrayList<java.lang.Integer>,java.lang.Double> |
AScore.getAScore(Peptide peptide,
java.util.ArrayList<PTM> ptms,
MSnSpectrum spectrum,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses)
Returns the A-score for the best PTM location.
|
static java.util.HashMap<java.lang.Integer,java.util.HashMap<java.lang.Integer,java.lang.Double>> |
AScore.getPositionToScoreMap(Peptide peptide,
Peptide noModPeptide,
java.util.ArrayList<java.lang.Integer> possibleSites,
MSnSpectrum spectrum,
java.util.HashMap<java.lang.Integer,MSnSpectrum> spectrumMap,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap scoringLossesMap,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
double mzTolerance,
SpectrumAnnotator spectrumAnnotator,
PTM refPTM)
Returns a map PTM localization -> score.
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static java.util.HashMap<java.lang.Integer,MSnSpectrum> |
AScore.getReducedSpectra(MSnSpectrum baseSpectrum,
double mzTolerance)
Generates a map containing the spectra filtered on intensity with a basis
of 20*m/z tolerance indexed by the depth used.
|
static java.util.HashMap<java.lang.Integer,MSnSpectrum> |
AScore.getReducedSpectra(MSnSpectrum baseSpectrum,
double mzTolerance,
int depthMax)
Generates a map containing the spectra filtered on intensity with a basis
of 20*m/z tolerance indexed by the depth used.
|
static java.util.HashMap<java.util.ArrayList<java.lang.Integer>,java.lang.Double> |
PhosphoRS.getSequenceProbabilities(Peptide peptide,
java.util.ArrayList<PTM> ptms,
MSnSpectrum spectrum,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses)
Returns the PhosphoRS sequence probabilities for the PTM possible
locations.
|
Modifier and Type | Method and Description |
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static java.util.HashMap<java.lang.Integer,java.util.HashMap<java.lang.Integer,java.lang.Double>> |
AScore.getPositionToScoreMap(Peptide peptide,
Peptide noModPeptide,
java.util.ArrayList<java.lang.Integer> possibleSites,
MSnSpectrum spectrum,
java.util.HashMap<java.lang.Integer,MSnSpectrum> spectrumMap,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap scoringLossesMap,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
double mzTolerance,
SpectrumAnnotator spectrumAnnotator,
PTM refPTM)
Returns a map PTM localization -> score.
|
Modifier and Type | Method and Description |
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static java.util.HashMap<java.lang.Integer,MSnSpectrum> |
PsmScores.getReducedSpectra(MSnSpectrum baseSpectrum,
double mzTolerance)
Generates a map containing the spectra filtered on intensity with a basis
of 20*mz tolerance indexed by the depth used.
|
static java.util.HashMap<java.lang.Integer,MSnSpectrum> |
PsmScores.getReducedSpectra(MSnSpectrum baseSpectrum,
double mzTolerance,
int depthMax)
Generates a map containing the spectra filtered on intensity with a basis
of 20*mz tolerance indexed by the depth used.
|
Modifier and Type | Method and Description |
---|---|
static double |
PsmScores.getAScorePeptideScore(Peptide peptide,
MSnSpectrum spectrum,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses)
Returns a PSM score like the peptide score calculated for the A-score.
|
static java.util.HashMap<java.lang.Integer,MSnSpectrum> |
PsmScores.getReducedSpectra(MSnSpectrum baseSpectrum,
double mzTolerance)
Generates a map containing the spectra filtered on intensity with a basis
of 20*mz tolerance indexed by the depth used.
|
static java.util.HashMap<java.lang.Integer,MSnSpectrum> |
PsmScores.getReducedSpectra(MSnSpectrum baseSpectrum,
double mzTolerance,
int depthMax)
Generates a map containing the spectra filtered on intensity with a basis
of 20*mz tolerance indexed by the depth used.
|
Modifier and Type | Method and Description |
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static MSnSpectrum |
MgfReader.getSpectrum(uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile bufferedRandomAccessFile,
long index,
java.lang.String fileName)
Returns the next spectrum starting from the given index.
|
Modifier and Type | Method and Description |
---|---|
java.util.ArrayList<MSnSpectrum> |
MgfReader.getSpectra(java.io.File aFile)
Reads an MGF file and retrieves a list of spectra.
|
Constructor and Description |
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IntensityHistogram(java.util.ArrayList<IonMatch> annotations,
MSnSpectrum currentSpectrum,
double intensityLevel)
Creates an IntensityHistogram plot
|
MassErrorPlot(java.util.ArrayList<IonMatch> annotations,
MSnSpectrum currentSpectrum,
double massTolerance)
Creates a new MassErrorPlot.
|
MassErrorPlot(java.util.ArrayList<IonMatch> annotations,
MSnSpectrum currentSpectrum,
double massTolerance,
boolean useRelativeError)
Creates a new MassErrorPlot.
|
Constructor and Description |
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FragmentIonTable(Peptide currentPeptide,
java.util.ArrayList<java.util.ArrayList<IonMatch>> allAnnotations,
java.util.ArrayList<MSnSpectrum> allSpectra,
java.util.ArrayList<java.lang.Integer> currentFragmentIonTypes,
NeutralLossesMap neutralLosses,
boolean singleCharge,
boolean twoCharges)
Creates a novel fragment ion table displaying bar charts with the
intensity of each fragment ion type.
|
MassErrorBubblePlot(java.util.ArrayList<java.lang.String> dataIndexes,
java.util.ArrayList<java.util.ArrayList<IonMatch>> annotations,
java.util.ArrayList<MSnSpectrum> currentSpectra,
double massTolerance,
boolean fragmentIonLabels,
boolean addMarkers)
Creates a new MassErrorBubblePlot.
|
MassErrorBubblePlot(java.util.ArrayList<java.lang.String> dataIndexes,
java.util.ArrayList<java.util.ArrayList<IonMatch>> annotations,
java.util.ArrayList<MSnSpectrum> currentSpectra,
double massTolerance,
boolean fragmentIonLabels,
boolean addMarkers,
boolean useRelativeError)
Creates a new MassErrorBubblePlot.
|
MassErrorBubblePlot(java.util.ArrayList<java.lang.String> dataIndexes,
java.util.ArrayList<java.util.ArrayList<IonMatch>> annotations,
java.util.ArrayList<MSnSpectrum> currentSpectra,
double massTolerance,
double bubbleScale,
boolean fragmentIonLabels,
boolean addMarkers,
boolean useRelativeError)
Creates a new MassErrorBubblePlot.
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