Package | Description |
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com.compomics.util.experiment.identification.psm_scoring |
Main PSM scoring class.
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com.compomics.util.experiment.identification.psm_scoring.psm_scores |
Main PTM scoring classes.
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com.compomics.util.experiment.identification.ptm |
Additional PSM scoring classes.
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com.compomics.util.experiment.identification.ptm.ptmscores |
PTM scores.
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com.compomics.util.experiment.identification.spectrum_annotation |
Classes used for ms2 spectrum annotation.
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com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators |
Spectrum annotation.
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com.compomics.util.experiment.io.massspectrometry |
Reading and indexing of mgf files.
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com.compomics.util.experiment.io.massspectrometry.export |
Experiment classes related to exporting mass spectrometry files.
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com.compomics.util.gui.spectrum |
Spectrum and Chromatogram visualization GUI classes.
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Modifier and Type | Method and Description |
---|---|
static double |
PsmScores.getDecreasingScore(Peptide peptide,
Integer peptideCharge,
MSnSpectrum spectrum,
ShotgunProtocol shotgunProtocol,
IdentificationParameters identificationParameters,
SpecificAnnotationSettings specificAnnotationPreferences,
int scoreIndex)
Scores the match between the given peptide and spectrum using the given score.
|
static double |
PsmScores.getScore(Peptide peptide,
Integer peptideCharge,
MSnSpectrum spectrum,
ShotgunProtocol shotgunProtocol,
IdentificationParameters identificationParameters,
SpecificAnnotationSettings specificAnnotationPreferences,
int scoreIndex)
Scores the match between the given peptide and spectrum using the given score.
|
static double |
PsmScores.getScore(Peptide peptide,
Integer peptideCharge,
MSnSpectrum spectrum,
ShotgunProtocol shotgunProtocol,
IdentificationParameters identificationParameters,
SpecificAnnotationSettings specificAnnotationPreferences,
PsmScores psmScore)
Scores the match between the given peptide and spectrum using the given score.
|
Modifier and Type | Method and Description |
---|---|
static double |
MS2MzFidelityScore.getScore(Peptide peptide,
MSnSpectrum spectrum,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences)
Scores the match between the given peptide and spectrum using an m/z
fidelity score.
|
static double |
IntensityRankScore.getScore(Peptide peptide,
MSnSpectrum spectrum,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences)
Scores the match between the given peptide and spectrum using the
intensity rank of the matched peaks.
|
static double |
ComplementarityScore.getScore(Peptide peptide,
MSnSpectrum spectrum,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences)
Scores the match between the given peptide and spectrum using the
complementarity of the matched peaks.
|
static double |
AAMS2MzFidelityScore.getScore(Peptide peptide,
MSnSpectrum spectrum,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences)
Scores the match between the given peptide and spectrum using an m/z
fidelity score.
|
static double |
AAIntensityRankScore.getScore(Peptide peptide,
MSnSpectrum spectrum,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences)
Scores the match between the given peptide and spectrum using the
intensity rank of the matched peaks.
|
static double |
MS2MzFidelityScore.getScore(Peptide peptide,
MSnSpectrum spectrum,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences,
PeptideSpectrumAnnotator peptideSpectrumAnnotator)
Scores the match between the given peptide and spectrum using an m/z
fidelity score.
|
static double |
IntensityRankScore.getScore(Peptide peptide,
MSnSpectrum spectrum,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences,
PeptideSpectrumAnnotator peptideSpectrumAnnotator)
Scores the match between the given peptide and spectrum using the
intensity rank of the matched peaks.
|
static double |
ComplementarityScore.getScore(Peptide peptide,
MSnSpectrum spectrum,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences,
PeptideSpectrumAnnotator peptideSpectrumAnnotator)
Scores the match between the given peptide and spectrum using the
complementarity of the matched peaks.
|
static double |
AAMS2MzFidelityScore.getScore(Peptide peptide,
MSnSpectrum spectrum,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences,
PeptideSpectrumAnnotator peptideSpectrumAnnotator)
Scores the match between the given peptide and spectrum using an m/z
fidelity score.
|
static double |
AAIntensityRankScore.getScore(Peptide peptide,
MSnSpectrum spectrum,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences,
PeptideSpectrumAnnotator peptideSpectrumAnnotator)
Scores the match between the given peptide and spectrum using the
intensity rank of the matched peaks.
|
Modifier and Type | Method and Description |
---|---|
static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> |
PtmtableContent.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.
|
static PtmtableContent |
PtmtableContent.getPTMTableContent(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences)
Get the PTM table content.
|
Modifier and Type | Method and Description |
---|---|
static HashMap<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 HashMap<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 |
---|---|
static HashMap<Integer,Double> |
AScore.getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator,
MathContext mathContext)
Returns the A-score for the best PTM location.
|
static HashMap<Integer,HashMap<Integer,BigDecimal>> |
AScore.getPositionToScoreMap(Peptide peptide,
Peptide noModPeptide,
ArrayList<Integer> possibleSites,
MSnSpectrum spectrum,
HashMap<Integer,MSnSpectrum> spectrumMap,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences,
PeptideSpectrumAnnotator spectrumAnnotator,
PTM refPTM,
MathContext mathContext)
Returns a map PTM localization > score.
|
static HashMap<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 HashMap<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 HashMap<Integer,Double> |
PhosphoRS.getSequenceProbabilities(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator,
MathContext mathContext)
Returns the PhosphoRS sequence probabilities for the PTM possible
locations.
|
Modifier and Type | Method and Description |
---|---|
static HashMap<Integer,HashMap<Integer,BigDecimal>> |
AScore.getPositionToScoreMap(Peptide peptide,
Peptide noModPeptide,
ArrayList<Integer> possibleSites,
MSnSpectrum spectrum,
HashMap<Integer,MSnSpectrum> spectrumMap,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences,
PeptideSpectrumAnnotator spectrumAnnotator,
PTM refPTM,
MathContext mathContext)
Returns a map PTM localization > score.
|
Modifier and Type | Method and Description |
---|---|
abstract ArrayList<IonMatch> |
SpectrumAnnotator.getCurrentAnnotation(MSnSpectrum spectrum,
AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings)
Returns the currently matched ions with the given settings.
|
protected void |
SpectrumAnnotator.setSpectrum(MSnSpectrum spectrum,
double intensityLimit)
Sets a new spectrum to annotate.
|
Modifier and Type | Method and Description |
---|---|
HashMap<Integer,ArrayList<IonMatch>> |
PeptideSpectrumAnnotator.getCoveredAminoAcids(AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings,
MSnSpectrum spectrum,
Peptide peptide)
Returns the ion matches corresponding to fragment ions indexed by amino
acid number in the sequence.
|
ArrayList<IonMatch> |
TagSpectrumAnnotator.getCurrentAnnotation(MSnSpectrum spectrum,
AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings) |
ArrayList<IonMatch> |
PeptideSpectrumAnnotator.getCurrentAnnotation(MSnSpectrum spectrum,
AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings) |
ArrayList<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings,
MSnSpectrum spectrum,
Peptide peptide)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
ArrayList<IonMatch> |
TagSpectrumAnnotator.getSpectrumAnnotation(AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings,
MSnSpectrum spectrum,
Tag tag)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
Modifier and Type | Method and Description |
---|---|
static MSnSpectrum |
MgfReader.getSpectrum(uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile bufferedRandomAccessFile,
long index,
String fileName)
Returns the next spectrum starting from the given index.
|
static MSnSpectrum |
MgfReader.getSpectrum(BufferedReader br,
String fileName)
Returns the next spectrum found in the mgf file.
|
MSnSpectrum |
MgfFileIterator.next()
Returns the next spectrum in the file.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<MSnSpectrum> |
MgfReader.getSpectra(File aFile)
Reads an MGF file and retrieves a list of spectra.
|
Modifier and Type | Method and Description |
---|---|
static void |
AplExporter.writeSpectrum(BufferedWriter bw,
MSnSpectrum spectrum,
FragmentationMethod fragmentationMethod,
int charge)
Writes the given spectrum in ms2 format.
|
static void |
Ms2Exporter.writeSpectrum(BufferedWriter bw,
MSnSpectrum spectrum,
Integer defaultScanNumber)
Writes the given spectrum in ms2 format.
|
Constructor and Description |
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IntensityHistogram(ArrayList<IonMatch> annotations,
MSnSpectrum currentSpectrum,
double intensityLevel)
Creates an IntensityHistogram plot
|
MassErrorPlot(ArrayList<IonMatch> annotations,
MSnSpectrum currentSpectrum,
double massTolerance)
Creates a new MassErrorPlot.
|
MassErrorPlot(ArrayList<IonMatch> annotations,
MSnSpectrum currentSpectrum,
double massTolerance,
boolean useRelativeError)
Creates a new MassErrorPlot.
|
Constructor and Description |
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FragmentIonTable(Peptide currentPeptide,
ArrayList<ArrayList<IonMatch>> allAnnotations,
ArrayList<MSnSpectrum> 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<MSnSpectrum> currentSpectra,
double massTolerance,
boolean fragmentIonLabels,
boolean addMarkers)
Creates a new MassErrorBubblePlot.
|
MassErrorBubblePlot(ArrayList<String> dataIndexes,
ArrayList<ArrayList<IonMatch>> annotations,
ArrayList<MSnSpectrum> currentSpectra,
double massTolerance,
boolean fragmentIonLabels,
boolean addMarkers,
boolean useRelativeError)
Creates a new MassErrorBubblePlot.
|
MassErrorBubblePlot(ArrayList<String> dataIndexes,
ArrayList<ArrayList<IonMatch>> annotations,
ArrayList<MSnSpectrum> currentSpectra,
double massTolerance,
double bubbleScale,
boolean fragmentIonLabels,
boolean addMarkers,
boolean useRelativeError)
Creates a new MassErrorBubblePlot.
|
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