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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java.util.ArrayList<IonMatch> |
SpectrumAnnotator.getCurrentAnnotation(java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.Integer> charges)
Returns the currently matched ions with the given settings.
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java.util.ArrayList<IonMatch> |
SpectrumAnnotator.getSpectrumAnnotation(java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.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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java.util.ArrayList<IonMatch> |
SpectrumAnnotator.matchPeak(Peptide peptide,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
NeutralLossesMap neutralLosses,
Peak peak)
This method matches the potential fragment ions of a given peptide with a
given peak.
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Modifier and Type | Method and Description |
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static java.util.Vector<DefaultSpectrumAnnotation> |
SpectrumAnnotator.getSpectrumAnnotation(java.util.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 java.util.HashMap<PeptideFragmentIon,java.util.ArrayList<IonMatch>> |
PTMLocationScores.getPTMPlotData(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.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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java.util.HashMap<java.lang.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,
java.util.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,
java.util.ArrayList<java.util.ArrayList<IonMatch>> allAnnotations,
java.util.ArrayList<java.lang.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,
java.util.ArrayList<java.util.ArrayList<IonMatch>> allAnnotations,
java.util.ArrayList<MSnSpectrum> allSpectra,
java.util.ArrayList<java.lang.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(java.util.ArrayList<IonMatch> annotations,
java.util.ArrayList<java.lang.Integer> currentFragmentIons,
MSnSpectrum currentSpectrum,
double intensityLevel,
boolean includeSinglyCharge,
boolean includeDoublyCharge,
boolean includeMoreThanTwoCharges)
Creates an IntensityHistogram plot
//@TODO improve charge compatibility
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MassErrorBubblePlot(java.util.ArrayList<java.lang.String> dataIndexes,
java.util.ArrayList<java.util.ArrayList<IonMatch>> annotations,
java.util.ArrayList<java.lang.Integer> currentFragmentIons,
java.util.ArrayList<MSnSpectrum> currentSpectra,
double massTolerance,
boolean includeSinglyCharge,
boolean includeDoublyCharge,
boolean includeMoreThanTwoCharges,
boolean fragmentIonLabels,
boolean addMarkers)
Creates a new MassErrorBubblePlot.
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MassErrorBubblePlot(java.util.ArrayList<java.lang.String> dataIndexes,
java.util.ArrayList<java.util.ArrayList<IonMatch>> annotations,
java.util.ArrayList<java.lang.Integer> currentFragmentIons,
java.util.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(java.util.ArrayList<java.lang.String> dataIndexes,
java.util.ArrayList<java.util.ArrayList<IonMatch>> annotations,
java.util.ArrayList<java.lang.Integer> currentFragmentIons,
java.util.ArrayList<MSnSpectrum> currentSpectra,
double massTolerance,
double bubbleScale,
boolean includeSinglyCharge,
boolean includeDoublyCharge,
boolean includeMoreThanTwoCharges,
boolean fragmentIonLabels,
boolean addMarkers,
boolean useRelativeError)
Creates a new MassErrorBubblePlot.
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MassErrorPlot(java.util.ArrayList<IonMatch> annotations,
java.util.ArrayList<java.lang.Integer> currentFragmentIons,
MSnSpectrum currentSpectrum,
double massTolerance,
boolean includeSinglyCharge,
boolean includeDoublyCharge,
boolean includeMoreThanTwoCharges)
Creates a new MassErrorPlot.
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MassErrorPlot(java.util.ArrayList<IonMatch> annotations,
java.util.ArrayList<java.lang.Integer> currentFragmentIons,
MSnSpectrum currentSpectrum,
double massTolerance,
boolean includeSinglyCharge,
boolean includeDoublyCharge,
boolean includeMoreThanTwoCharges,
boolean useRelativeError)
Creates a new MassErrorPlot.
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SequenceFragmentationPanel(java.lang.String aSequence,
java.util.ArrayList<IonMatch> aIonMatches,
boolean boolModifiedSequence,
boolean aHighlightModifications,
ModificationProfile modificationProfile)
Deprecated.
use the panel with ion selection instead
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SequenceFragmentationPanel(java.lang.String aSequence,
java.util.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(java.lang.String taggedModifiedSequence,
java.util.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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