Package | Description |
---|---|
com.compomics.util.experiment.identification |
Experiment classes related to identifications.
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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.spectrum_annotators |
Spectrum annotation.
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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.
|
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 |
---|---|
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 | Field and Description |
---|---|
protected HashMap<String,IonMatch> |
SpectrumAnnotator.spectrumAnnotation
The spectrum annotation as a map: theoretic fragment key > ionmatch.
|
Modifier and Type | Method and Description |
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abstract ArrayList<IonMatch> |
SpectrumAnnotator.getCurrentAnnotation(MSnSpectrum spectrum,
AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings)
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 |
---|---|
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 |
---|---|
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> |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings,
MSnSpectrum spectrum,
Peptide peptide,
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments)
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.
|
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 |
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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.
|
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,
double intensityLevel)
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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