Package | Description |
---|---|
com.compomics.util.experiment.identification |
Experiment classes related to identifications.
|
com.compomics.util.experiment.identification.modification |
Modification mapping and localization.
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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.spectrum_annotation |
Classes used for ms2 spectrum annotation.
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com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators |
This package contains implementations of the SimpleAnnotator allowing the annotation of specific sets of ions.
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com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators |
This package contains implementations of the SpectrumAnnotator allowing the annotation of all ions.
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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 |
---|---|
IonMatch |
SpectrumIdentificationAssumption.getPrecursorMatch(double precursorMz,
double precursorIntensity)
Returns the ion match.
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Modifier and Type | Method and Description |
---|---|
static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> |
ModificationtableContent.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.
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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,
ArrayList<IonMatch> ionMatchesList)
Returns the score.
|
double |
SnrScore.getScore(Peptide peptide,
Spectrum spectrum,
HashMap<Double,ArrayList<IonMatch>> ionMatches)
Returns the score.
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Modifier and Type | Method and Description |
---|---|
IonMatch[] |
SpectrumAnnotator.getCurrentAnnotation(String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters)
Returns the currently matched ions with the given settings using the
intensity filter.
|
abstract IonMatch[] |
SpectrumAnnotator.getCurrentAnnotation(String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
boolean useIntensityFilter)
Returns the currently matched ions with the given settings.
|
protected IonMatch |
SpectrumAnnotator.matchInSpectrum(double[] spectrumMz,
double[] spectrumIntensity,
Ion theoreticIon,
Integer inspectedCharge)
Matches a theoretic ion in the spectrum.
|
protected IonMatch |
SpectrumAnnotator.setBestPeak(double[] spectrumMz,
double[] spectrumIntensity,
int[] matchedPeaksIndexes,
IonMatch ionMatch)
Returns the peak to retain of the matched peaks according to the ties
resolution setting.
|
Modifier and Type | Method and Description |
---|---|
protected ArrayList<IonMatch> |
SpectrumAnnotator.matchPeak(SpecificAnnotationParameters specificAnnotationSettings,
double peakMz,
double peakIntensity)
This method matches the potential fragment ions of a given peptide with a
given peak.
|
static ArrayList<IonMatch> |
SpectrumAnnotator.matchReporterIon(Ion theoreticIon,
int charge,
Spectrum spectrum,
double massTolerance)
Convenience method to match a reporter ion in a spectrum.
|
Modifier and Type | Method and Description |
---|---|
static Vector<SpectrumAnnotation> |
SpectrumAnnotator.getSpectrumAnnotation(IonMatch[] ionMatches)
Translates the list of ion matches into a vector of annotations which can
be read by the SpectrumPanel.
|
protected IonMatch |
SpectrumAnnotator.setBestPeak(double[] spectrumMz,
double[] spectrumIntensity,
int[] matchedPeaksIndexes,
IonMatch ionMatch)
Returns the peak to retain of the matched peaks according to the ties
resolution setting.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<IonMatch> |
ReporterIonAnnotator.getIonMatches(SpectrumIndex spectrumIndex)
Returns the ions matched in the given spectrum.
|
ArrayList<IonMatch> |
ImmoniumIonAnnotator.getIonMatches(SpectrumIndex spectrumIndex)
Returns the ions matched in the given spectrum.
|
ArrayList<IonMatch> |
FragmentAnnotatorNL.getIonMatches(SpectrumIndex spectrumIndex,
int peptideCharge)
Returns the ions matched in the given spectrum at the given charge.
|
ArrayList<IonMatch> |
FragmentAnnotator.getIonMatches(SpectrumIndex spectrumIndex,
int peptideCharge)
Returns the ions matched in the given spectrum at the given charge.
|
ArrayList<IonMatch> |
PrecursorAnnotator.getIonMatches(SpectrumIndex spectrumIndex,
int peptideCharge,
int isotopeMax)
Returns the ions matched in the given spectrum at the given charge.
|
Modifier and Type | Method and Description |
---|---|
IonMatch[] |
TagSpectrumAnnotator.getCurrentAnnotation(String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
boolean useIntensityFilter) |
IonMatch[] |
PeptideSpectrumAnnotator.getCurrentAnnotation(String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
boolean useIntensityFilter) |
IonMatch[] |
TagSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
ModificationParameters modificationParameters,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Tag tag)
Returns the spectrum annotations of a spectrum in a list of IonMatches
using an intensity filter.
|
IonMatch[] |
TagSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
ModificationParameters modificationParameters,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Tag tag,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
IonMatch[] |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters)
Returns the spectrum annotations of a spectrum in a list of IonMatches
using the intensity filter.
|
IonMatch[] |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
IonMatch[] |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in an array of IonMatches.
|
Modifier and Type | Method and Description |
---|---|
Map<Integer,ArrayList<IonMatch>> |
PeptideSpectrumAnnotator.getCoveredAminoAcids(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
boolean useIntensityFilter)
Returns the ion matches corresponding to fragment ions indexed by amino
acid number in the sequence.
|
ArrayList<IonMatch> |
SimplePeptideAnnotator.getIonMatches(SpectrumIndex spectrumIndex,
int peptideCharge,
int precursorIsotopeMax)
Returns the ion matches for the given spectrum.
|
java.util.stream.Stream<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotationStream(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters)
Returns the spectrum annotations of a spectrum in a list of IonMatches
using the intensity filter.
|
java.util.stream.Stream<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotationStream(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
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,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a stream of IonMatches.
|
ArrayList<IonMatch> |
PeptideSpectrumAnnotator.matchPeak(Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
SpecificAnnotationParameters specificAnnotationSettings,
double peakMz,
double peakIntensity)
This method matches the potential fragment ions of a given peptide with a
given peak according to the annotation settings.
|
Modifier and Type | Method and Description |
---|---|
void |
SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide,
IonMatch[] annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showRewindTags,
boolean mirrored,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters)
Add reference areas annotating the de novo tags, using default percent
height of 0.9 for the forward ions and 1.0 for the reverse ions default
alpha levels of 0.2.
|
void |
SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide,
IonMatch[] annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showRewindTags,
double forwardIonPercentHeight,
double rewindIonPercentHeight,
ArrayList<float[]> alphaLevels,
boolean excludeFixedModifications,
boolean mirrored,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters)
Add reference areas annotating the de novo tags.
|
void |
SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide,
IonMatch[] annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showRewindTags,
double forwardIonPercentHeight,
double rewindIonPercentHeight,
boolean excludeFixedModifications,
boolean mirrored,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters)
Add reference areas annotating the de novo tags, using default alpha
levels of 0.2.
|
void |
SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide,
IonMatch[] annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showRewindTags,
double forwardIonPercentHeight,
double rewindIonPercentHeight,
boolean mirrored,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters)
Add reference areas annotating the de novo tags, using default alpha
levels of 0.2.
|
void |
SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide,
IonMatch[] annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showRewindTags,
double forwardIonPercentHeight,
double rewindIonPercentHeight,
float forwardIonAlphaLevel,
float rewindIonAlphaLevel,
ArrayList<float[]> alphaLevels,
boolean excludeFixedModifications,
boolean mirrored,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters)
Add reference areas annotating the de novo tags.
|
void |
SpectrumPanel.addAutomaticDeNovoSequencing(Tag tag,
IonMatch[] annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showRewindTags,
boolean mirrored)
Add reference areas annotating the de novo tags, using default percent
height of 0.9 for the forward ions and 1.0 for the reverse ions default
alpha levels of 0.2.
|
void |
SpectrumPanel.addAutomaticDeNovoSequencing(Tag tag,
IonMatch[] annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showRewindTags,
double forwardIonPercentHeight,
double rewindIonPercentHeight,
ArrayList<float[]> alphaLevels,
boolean excludeFixedModifications,
boolean mirrored)
Add reference areas annotating the de novo tags, using default alpha
levels of 0.2.
|
void |
SpectrumPanel.addAutomaticDeNovoSequencing(Tag tag,
IonMatch[] annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showRewindTags,
double forwardIonPercentHeight,
double rewindIonPercentHeight,
boolean mirrored)
Add reference areas annotating the de novo tags, using default alpha
levels of 0.2.
|
void |
SpectrumPanel.addAutomaticDeNovoSequencing(Tag tag,
IonMatch[] annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showReverseTags,
double forwardIonPercentHeight,
double rewindIonPercentHeight,
float forwardIonAlphaLevel,
float rewindIonAlphaLevel,
ArrayList<float[]> alphaLevels,
boolean excludeFixedModifications,
boolean mirrored)
Add reference areas annotating the de novo tags.
|
void |
SequenceFragmentationPanel.setIonMatches(IonMatch[] lIonMatches)
Set the ArrayList with FragmentIon matches.
|
Modifier and Type | Method and Description |
---|---|
static void |
MassErrorBubblePlot.addFragmentIonTypeMarkers(HashMap<IonMatch,ArrayList<XYZDataPoint>> data,
org.jfree.chart.JFreeChart chart,
boolean showMarkers)
Adds interval markers for all the fragment ion types.
|
org.jfree.data.xy.DefaultXYZDataset |
MassErrorBubblePlot.addXYZDataSeries(HashMap<IonMatch,ArrayList<XYZDataPoint>> data)
Adds the provided data series to an XYZ data set.
|
Constructor and Description |
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IntensityHistogram(IonMatch[] annotations,
Spectrum currentSpectrum,
double intensityThreshold)
Creates an IntensityHistogram plot
|
MassErrorPlot(IonMatch[] annotations,
Spectrum currentSpectrum,
double massTolerance)
Creates a new MassErrorPlot.
|
MassErrorPlot(IonMatch[] annotations,
Spectrum currentSpectrum,
double massTolerance,
boolean useRelativeError)
Creates a new MassErrorPlot.
|
SequenceFragmentationPanel(String aSequence,
IonMatch[] aIonMatches,
boolean boolModifiedSequence,
boolean aHighlightModifications,
ModificationParameters modificationProfile,
int forwardIon,
int rewindIon)
Creates a new SequenceFragmentationPanel working with B and Y ions.
|
SequenceFragmentationPanel(String taggedModifiedSequence,
IonMatch[] aIonMatches,
boolean aHighlightModifications,
ModificationParameters modificationProfile,
int forwardIon,
int rewindIon)
Creates a new SequenceFragmentationPanel working with B and Y ions.
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