Package | Description |
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com.compomics.util.experiment.identification |
This package contains experiment classes related to identifications.
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com.compomics.util.experiment.identification.ptm | |
com.compomics.util.experiment.quantification.matches | |
com.compomics.util.gui.spectrum |
This package contains GUI classes related to Spectrum and Chromatogram visualization.
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Modifier and Type | Method and Description |
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IonMatch |
PeptideAssumption.getPrecursorMatch(Peak precursorPeak)
Returns the ion match.
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Modifier and Type | Method and Description |
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HashMap<Integer,ArrayList<IonMatch>> |
SpectrumAnnotator.getCoveredAminoAcids(HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
MSnSpectrum spectrum,
Peptide peptide,
double intensityLimit,
double mzTolerance,
boolean isPpm)
Returns the ion matches corresponding to fragment ions indexed by amino
acid number in the sequence.
|
ArrayList<IonMatch> |
SpectrumAnnotator.getCurrentAnnotation(HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges)
Returns the currently matched ions with the given settings.
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ArrayList<IonMatch> |
SpectrumAnnotator.getSpectrumAnnotation(HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
MSnSpectrum spectrum,
Peptide peptide,
double intensityLimit,
double mzTolerance,
boolean isPpm)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
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ArrayList<IonMatch> |
SpectrumAnnotator.matchPeak(Peptide peptide,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
ArrayList<Integer> charges,
int precursorCharge,
NeutralLossesMap neutralLosses,
Peak peak)
This method matches the potential fragment ions of a given peptide with a
given peak.
|
Modifier and Type | Method and Description |
---|---|
static Vector<DefaultSpectrumAnnotation> |
SpectrumAnnotator.getSpectrumAnnotation(ArrayList<IonMatch> ionMatches)
Translates the list of ion matches into a vector of annotations which can
be read by the SpectrumPanel.
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Modifier and Type | Method and Description |
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static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> |
PTMLocationScores.getPTMPlotData(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
double intensityLimit)
Returns the PTM plot series in the JFreechart format for one PSM.
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Modifier and Type | Method and Description |
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HashMap<Integer,IonMatch> |
PsmQuantification.getReporterMatches()
Getter for the reporter matches.
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Modifier and Type | Method and Description |
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void |
PsmQuantification.addIonMatch(int reporterIndex,
IonMatch match)
Method to add a match between a peak and a reporter ion.
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Modifier and Type | Method and Description |
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void |
SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide,
ArrayList<IonMatch> annotations,
int aForwardIon,
int aReverseIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showReverseTags)
Add reference areas annotating the de novo tags.
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Constructor and Description |
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FragmentIonTable(Peptide currentPeptide,
ArrayList<ArrayList<IonMatch>> allAnnotations,
ArrayList<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.
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FragmentIonTable(Peptide currentPeptide,
ArrayList<ArrayList<IonMatch>> allAnnotations,
ArrayList<MSnSpectrum> allSpectra,
ArrayList<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.
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IntensityHistogram(ArrayList<IonMatch> annotations,
ArrayList<Integer> currentFragmentIons,
MSnSpectrum currentSpectrum,
double intensityLevel,
boolean includeSinglyCharge,
boolean includeDoublyCharge,
boolean includeMoreThanTwoCharges)
Creates an IntensityHistogram plot
//@TODO improve charge compatibility
|
MassErrorBubblePlot(ArrayList<String> dataIndexes,
ArrayList<ArrayList<IonMatch>> annotations,
ArrayList<Integer> currentFragmentIons,
ArrayList<MSnSpectrum> currentSpectra,
double massTolerance,
boolean includeSinglyCharge,
boolean includeDoublyCharge,
boolean includeMoreThanTwoCharges,
boolean fragmentIonLabels,
boolean addMarkers)
Creates a new MassErrorBubblePlot.
|
MassErrorBubblePlot(ArrayList<String> dataIndexes,
ArrayList<ArrayList<IonMatch>> annotations,
ArrayList<Integer> currentFragmentIons,
ArrayList<MSnSpectrum> currentSpectra,
double massTolerance,
boolean includeSinglyCharge,
boolean includeDoublyCharge,
boolean includeMoreThanTwoCharges,
boolean fragmentIonLabels,
boolean addMarkers,
boolean useRelativeError)
Creates a new MassErrorBubblePlot.
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MassErrorBubblePlot(ArrayList<String> dataIndexes,
ArrayList<ArrayList<IonMatch>> annotations,
ArrayList<Integer> currentFragmentIons,
ArrayList<MSnSpectrum> currentSpectra,
double massTolerance,
double bubbleScale,
boolean includeSinglyCharge,
boolean includeDoublyCharge,
boolean includeMoreThanTwoCharges,
boolean fragmentIonLabels,
boolean addMarkers,
boolean useRelativeError)
Creates a new MassErrorBubblePlot.
|
MassErrorPlot(ArrayList<IonMatch> annotations,
ArrayList<Integer> currentFragmentIons,
MSnSpectrum currentSpectrum,
double massTolerance,
boolean includeSinglyCharge,
boolean includeDoublyCharge,
boolean includeMoreThanTwoCharges)
Creates a new MassErrorPlot.
|
MassErrorPlot(ArrayList<IonMatch> annotations,
ArrayList<Integer> currentFragmentIons,
MSnSpectrum currentSpectrum,
double massTolerance,
boolean includeSinglyCharge,
boolean includeDoublyCharge,
boolean includeMoreThanTwoCharges,
boolean useRelativeError)
Creates a new MassErrorPlot.
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SequenceFragmentationPanel(String aSequence,
ArrayList<IonMatch> aIonMatches,
boolean boolModifiedSequence,
boolean aHighlightModifications,
ModificationProfile modificationProfile)
Deprecated.
use the panel with ion selection instead
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SequenceFragmentationPanel(String aSequence,
ArrayList<IonMatch> aIonMatches,
boolean boolModifiedSequence,
boolean aHighlightModifications,
ModificationProfile modificationProfile,
int forwardIon,
int rewindIon)
Creates a new SequenceFragmentationPanel working with B and Y ions.
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SequenceFragmentationPanel(String taggedModifiedSequence,
ArrayList<IonMatch> aIonMatches,
boolean aHighlightModifications,
ModificationProfile modificationProfile,
int forwardIon,
int rewindIon)
Creates a new SequenceFragmentationPanel working with B and Y ions.
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