Package | Description |
---|---|
com.compomics.util.experiment.identification |
Experiment classes related to identifications.
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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.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.experiment.massspectrometry |
Experiment classes related to spectra.
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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(Peak precursorPeak)
Returns the ion match.
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Modifier and Type | Method and Description |
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double |
HyperScore.getScore(Peptide peptide,
int charge,
MSnSpectrum spectrum,
ArrayList<IonMatch> ionMatches)
Returns the hyperscore.
|
double |
SnrScore.getScore(Peptide peptide,
MSnSpectrum spectrum,
ArrayList<IonMatch> ionMatchesList)
Returns the score.
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double |
SnrScore.getScore(Peptide peptide,
MSnSpectrum spectrum,
HashMap<Double,ArrayList<IonMatch>> ionMatches)
Returns the score.
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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.
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Modifier and Type | Method and Description |
---|---|
protected IonMatch |
SpectrumAnnotator.matchInSpectrum(Ion theoreticIon,
Integer inspectedCharge)
Matches a theoretic ion in the spectrum.
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Modifier and Type | Method and Description |
---|---|
ArrayList<IonMatch> |
SpectrumAnnotator.getCurrentAnnotation(MSnSpectrum spectrum,
AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings)
Returns the currently matched ions with the given settings using the intensity filter.
|
abstract ArrayList<IonMatch> |
SpectrumAnnotator.getCurrentAnnotation(MSnSpectrum spectrum,
AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings,
boolean useIntensityFilter)
Returns the currently matched ions with the given settings.
|
protected ArrayList<IonMatch> |
SpectrumAnnotator.matchPeak(SpecificAnnotationSettings specificAnnotationSettings,
Peak peak)
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 |
---|---|
protected Peak |
SpectrumAnnotator.getBestPeak(ArrayList<Peak> matchedPeaks,
IonMatch ionMatch)
Returns the peak to retain of the matched peaks according to the ties
resolution setting.
|
Modifier and Type | Method and Description |
---|---|
static Vector<SpectrumAnnotation> |
SpectrumAnnotator.getSpectrumAnnotation(ArrayList<IonMatch> ionMatches)
Translates the list of ion matches into a vector of annotations which can
be read by the SpectrumPanel.
|
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 |
---|---|
HashMap<Integer,ArrayList<IonMatch>> |
PeptideSpectrumAnnotator.getCoveredAminoAcids(AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings,
MSnSpectrum 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(MSnSpectrum spectrum,
AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings,
boolean useIntensityFilter) |
ArrayList<IonMatch> |
PeptideSpectrumAnnotator.getCurrentAnnotation(MSnSpectrum spectrum,
AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings,
boolean useIntensityFilter) |
ArrayList<IonMatch> |
SimplePeptideAnnotator.getIonMatches(SpectrumIndex spectrumIndex,
int peptideCharge,
int precursorIsotopeMax)
Returns the ion matches for the given spectrum.
|
ArrayList<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings,
MSnSpectrum spectrum,
Peptide peptide)
Returns the spectrum annotations of a spectrum in a list of IonMatches
using the intensity filter.
|
ArrayList<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings,
MSnSpectrum spectrum,
Peptide peptide,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
ArrayList<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings,
MSnSpectrum 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(AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings,
MSnSpectrum spectrum,
Tag tag)
Returns the spectrum annotations of a spectrum in a list of IonMatches using an intensity filter.
|
ArrayList<IonMatch> |
TagSpectrumAnnotator.getSpectrumAnnotation(AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings,
MSnSpectrum spectrum,
Tag tag,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
ArrayList<IonMatch> |
PeptideSpectrumAnnotator.matchPeak(Peptide peptide,
SpecificAnnotationSettings specificAnnotationSettings,
Peak peak)
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 |
---|---|
HashMap<Double,Peak> |
Spectrum.getDesignaledPeakList(ArrayList<IonMatch> matches)
Returns the peak list of this spectrum without matched peaks.
|
Modifier and Type | Method and Description |
---|---|
void |
SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide,
ArrayList<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(Peptide currentPeptide,
ArrayList<IonMatch> annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showRewindTags,
double forwardIonPercentHeight,
double rewindIonPercentHeight,
ArrayList<float[]> alphaLevels,
boolean excludeFixedPtms,
boolean mirrored)
Add reference areas annotating the de novo tags.
|
void |
SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide,
ArrayList<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(Peptide currentPeptide,
ArrayList<IonMatch> annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showRewindTags,
double forwardIonPercentHeight,
double rewindIonPercentHeight,
boolean excludeFixedPtms,
boolean mirrored)
Add reference areas annotating the de novo tags, using default alpha
levels of 0.2.
|
void |
SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide,
ArrayList<IonMatch> annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showRewindTags,
double forwardIonPercentHeight,
double rewindIonPercentHeight,
float forwardIonAlphaLevel,
float rewindIonAlphaLevel,
ArrayList<float[]> alphaLevels,
boolean excludeFixedPtms,
boolean mirrored)
Add reference areas annotating the de novo tags.
|
void |
SpectrumPanel.addAutomaticDeNovoSequencing(Tag tag,
ArrayList<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,
ArrayList<IonMatch> annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showRewindTags,
double forwardIonPercentHeight,
double rewindIonPercentHeight,
ArrayList<float[]> alphaLevels,
boolean excludeFixedPtms,
boolean mirrored)
Add reference areas annotating the de novo tags, using default alpha
levels of 0.2.
|
void |
SpectrumPanel.addAutomaticDeNovoSequencing(Tag tag,
ArrayList<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,
ArrayList<IonMatch> annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showReverseTags,
double forwardIonPercentHeight,
double rewindIonPercentHeight,
float forwardIonAlphaLevel,
float rewindIonAlphaLevel,
ArrayList<float[]> alphaLevels,
boolean excludeFixedPtms,
boolean mirrored)
Add reference areas annotating the de novo tags.
|
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 |
---|
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.
|
FragmentIonTable(Peptide currentPeptide,
ArrayList<ArrayList<IonMatch>> allAnnotations,
HashSet<Integer> currentFragmentIonTypes,
NeutralLossesMap neutralLosses,
boolean singleCharge,
boolean twoCharges)
Creates a traditional fragment ion table with the theoretical mz values
and the detected fragment ions highlighted.
|
IntensityHistogram(ArrayList<IonMatch> annotations,
MSnSpectrum currentSpectrum,
AnnotationSettings.IntensityThresholdType intensityThresholdType,
double intensityThreshold)
Creates an IntensityHistogram plot
|
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.
|
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.
|
SequenceFragmentationPanel(String aSequence,
ArrayList<IonMatch> aIonMatches,
boolean boolModifiedSequence,
boolean aHighlightModifications,
PtmSettings modificationProfile)
Deprecated.
use the panel with ion selection instead
|
SequenceFragmentationPanel(String aSequence,
ArrayList<IonMatch> aIonMatches,
boolean boolModifiedSequence,
boolean aHighlightModifications,
PtmSettings modificationProfile,
int forwardIon,
int rewindIon)
Creates a new SequenceFragmentationPanel working with B and Y ions.
|
SequenceFragmentationPanel(String taggedModifiedSequence,
ArrayList<IonMatch> aIonMatches,
boolean aHighlightModifications,
PtmSettings modificationProfile,
int forwardIon,
int rewindIon)
Creates a new SequenceFragmentationPanel working with B and Y ions.
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