Modifier and Type | Method and Description |
---|---|
static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> |
ModificationtableContent.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.
|
static ModificationtableContent |
ModificationtableContent.getModificationTableContent(PeptideAssumption peptideAssumption,
Modification modification,
int nMod,
Spectrum spectrum,
AnnotationParameters annotationParameters)
Get the table content.
|
Modifier and Type | Method and Description |
---|---|
static HashMap<Integer,Double> |
PhosphoRS.getSequenceProbabilities(Peptide peptide,
ArrayList<Modification> modifications,
Spectrum spectrum,
SequenceProvider sequenceProvider,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
boolean accountNeutralLosses,
SequenceMatchingParameters sequenceMatchingPreferences,
SequenceMatchingParameters modificationSequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator)
Returns the PhosphoRS sequence probabilities for the modification
possible locations.
|
Modifier and Type | Method and Description |
---|---|
double |
PsmScoresEstimator.getDecreasingScore(Peptide peptide,
Integer peptideCharge,
Spectrum spectrum,
IdentificationParameters identificationParameters,
SpecificAnnotationParameters specificAnnotationPreferences,
PeptideSpectrumAnnotator peptideSpectrumAnnotator,
int scoreIndex)
Scores the match between the given peptide and spectrum using the given
score.
|
double |
PsmScoresEstimator.getScore(Peptide peptide,
Integer peptideCharge,
Spectrum spectrum,
IdentificationParameters identificationParameters,
SpecificAnnotationParameters specificAnnotationPreferences,
PeptideSpectrumAnnotator peptideSpectrumAnnotator,
int scoreIndex)
Scores the match between the given peptide and spectrum using the given
score.
|
double |
PsmScoresEstimator.getScore(Peptide peptide,
Integer peptideCharge,
Spectrum spectrum,
IdentificationParameters identificationParameters,
SpecificAnnotationParameters specificAnnotationPreferences,
PeptideSpectrumAnnotator peptideSpectrumAnnotator,
PsmScore psmScore)
Scores the match between the given peptide and spectrum using the given
score.
|
Modifier and Type | Method and Description |
---|---|
double |
HyperScore.getScore(Peptide peptide,
int charge,
Spectrum spectrum,
ArrayList<IonMatch> ionMatches)
Returns the hyperscore.
|
double |
SnrScore.getScore(Peptide peptide,
Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
PeptideSpectrumAnnotator peptideSpectrumAnnotator)
Returns the score.
|
double |
HyperScore.getScore(Peptide peptide,
Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
PeptideSpectrumAnnotator peptideSpectrumAnnotator)
Returns the hyperscore.
|
double |
SnrScore.getScore(Peptide peptide,
Spectrum spectrum,
ArrayList<IonMatch> ionMatchesList)
Returns the score.
|
double |
SnrScore.getScore(Peptide peptide,
Spectrum spectrum,
HashMap<Double,ArrayList<IonMatch>> ionMatches)
Returns the score.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<IonMatch> |
SpectrumAnnotator.getCurrentAnnotation(Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings)
Returns the currently matched ions with the given settings using the intensity filter.
|
abstract ArrayList<IonMatch> |
SpectrumAnnotator.getCurrentAnnotation(Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
boolean useIntensityFilter)
Returns the currently matched ions with the given settings.
|
static ArrayList<IonMatch> |
SpectrumAnnotator.matchReporterIon(Ion theoreticIon,
int charge,
Spectrum spectrum,
double massTolerance)
Convenience method to match a reporter ion in a spectrum.
|
protected void |
SpectrumAnnotator.setSpectrum(Spectrum spectrum,
double intensityLimit)
Sets a new spectrum to annotate.
|
Modifier and Type | Method and Description |
---|---|
Map<Integer,ArrayList<IonMatch>> |
PeptideSpectrumAnnotator.getCoveredAminoAcids(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
Spectrum spectrum,
Peptide peptide,
boolean useIntensityFilter)
Returns the ion matches corresponding to fragment ions indexed by amino
acid number in the sequence.
|
ArrayList<IonMatch> |
TagSpectrumAnnotator.getCurrentAnnotation(Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
boolean useIntensityFilter) |
ArrayList<IonMatch> |
PeptideSpectrumAnnotator.getCurrentAnnotation(Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
boolean useIntensityFilter) |
java.util.stream.Stream<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
Spectrum spectrum,
Peptide peptide)
Returns the spectrum annotations of a spectrum in a list of IonMatches
using the intensity filter.
|
ArrayList<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
Spectrum spectrum,
Peptide peptide,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
java.util.stream.Stream<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
Spectrum spectrum,
Peptide peptide,
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
ArrayList<IonMatch> |
TagSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
Spectrum spectrum,
Tag tag)
Returns the spectrum annotations of a spectrum in a list of IonMatches using an intensity filter.
|
ArrayList<IonMatch> |
TagSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
Spectrum spectrum,
Tag tag,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
java.util.stream.Stream<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotationStream(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
Spectrum spectrum,
Peptide peptide,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
Modifier and Type | Method and Description |
---|---|
static void |
AplExporter.writeSpectrum(BufferedWriter bw,
Spectrum spectrum,
FragmentationMethod fragmentationMethod,
int charge)
Writes the given spectrum in ms2 format.
|
static void |
Ms2Exporter.writeSpectrum(BufferedWriter bw,
Spectrum spectrum,
Integer defaultScanNumber)
Writes the given spectrum in ms2 format.
|
Modifier and Type | Method and Description |
---|---|
static Spectrum |
MgfReader.getSpectrum(uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile bufferedRandomAccessFile,
long index,
String fileName)
Returns the next spectrum starting from the given index.
|
static Spectrum |
MgfReader.getSpectrum(BufferedReader br,
String fileName)
Returns the next spectrum found in the mgf file.
|
Spectrum |
MgfFileIterator.next()
Returns the next spectrum in the file.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<Spectrum> |
MgfReader.getSpectra(File aFile)
Reads an MGF file and retrieves a list of spectra.
|
Modifier and Type | Method and Description |
---|---|
static Spectrum |
MspReader.getSpectrum(uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile bufferedRandomAccessFile,
long index,
String fileName)
Returns the next spectrum starting from the given index.
|
static Spectrum |
MspReader.getSpectrum(BufferedReader br,
String fileName)
The function returns the next spectrum found in the msp file.
|
Spectrum |
MspFileIterator.next()
Returns the next spectrum in the file.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<Spectrum> |
MspReader.getSpectra(File aFile)
Reads an MSP file and retrieves a list of spectra.
|
Modifier and Type | Method and Description |
---|---|
Spectrum |
SpectrumFactory.getSpectrum(String spectrumKey)
Returns the desired spectrum.
|
Spectrum |
SpectrumFactory.getSpectrum(String spectrumFile,
String spectrumTitle)
Returns the desired spectrum.
|
Constructor and Description |
---|
IntensityHistogram(ArrayList<IonMatch> annotations,
Spectrum currentSpectrum,
AnnotationParameters.IntensityThresholdType intensityThresholdType,
double intensityThreshold)
Creates an IntensityHistogram plot
|
MassErrorPlot(ArrayList<IonMatch> annotations,
Spectrum currentSpectrum,
double massTolerance)
Creates a new MassErrorPlot.
|
MassErrorPlot(ArrayList<IonMatch> annotations,
Spectrum currentSpectrum,
double massTolerance,
boolean useRelativeError)
Creates a new MassErrorPlot.
|
Constructor and Description |
---|
FragmentIonTable(Peptide currentPeptide,
ArrayList<ArrayList<IonMatch>> allAnnotations,
ArrayList<Spectrum> allSpectra,
HashSet<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(ArrayList<String> dataIndexes,
ArrayList<ArrayList<IonMatch>> annotations,
ArrayList<Spectrum> currentSpectra,
double massTolerance,
boolean fragmentIonLabels,
boolean addMarkers)
Creates a new MassErrorBubblePlot.
|
MassErrorBubblePlot(ArrayList<String> dataIndexes,
ArrayList<ArrayList<IonMatch>> annotations,
ArrayList<Spectrum> currentSpectra,
double massTolerance,
boolean fragmentIonLabels,
boolean addMarkers,
boolean useRelativeError)
Creates a new MassErrorBubblePlot.
|
MassErrorBubblePlot(ArrayList<String> dataIndexes,
ArrayList<ArrayList<IonMatch>> annotations,
ArrayList<Spectrum> currentSpectra,
double massTolerance,
double bubbleScale,
boolean fragmentIonLabels,
boolean addMarkers,
boolean useRelativeError)
Creates a new MassErrorBubblePlot.
|
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