|
||||||||||
PREV NEXT | FRAMES NO FRAMES |
Packages that use IonMatch | |
---|---|
com.compomics.util.experiment.identification | This package contains experiment classes related to identifications. |
com.compomics.util.experiment.identification.ptm | |
com.compomics.util.experiment.massspectrometry | This package contains experiment classes related to spectra. |
com.compomics.util.experiment.quantification.matches | |
com.compomics.util.gui.spectrum | This package contains GUI classes related to Spectrum and Chromatogram visualization. |
Uses of IonMatch in com.compomics.util.experiment.identification |
---|
Methods in com.compomics.util.experiment.identification that return IonMatch | |
---|---|
IonMatch |
PeptideAssumption.getPrecursorMatch(Peak precursorPeak)
Returns the ion match. |
Methods in com.compomics.util.experiment.identification that return types with arguments of type IonMatch | |
---|---|
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. |
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. |
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. |
Method parameters in com.compomics.util.experiment.identification with type arguments of type IonMatch | |
---|---|
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. |
Uses of IonMatch in com.compomics.util.experiment.identification.ptm |
---|
Methods in com.compomics.util.experiment.identification.ptm that return types with arguments of type IonMatch | |
---|---|
static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> |
PtmtableContent.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. |
Uses of IonMatch in com.compomics.util.experiment.massspectrometry |
---|
Method parameters in com.compomics.util.experiment.massspectrometry with type arguments of type IonMatch | |
---|---|
HashMap<Double,Peak> |
Spectrum.getDesignaledPeakList(ArrayList<IonMatch> matches)
Returns the peak list of this spectrum without matched peaks. |
Uses of IonMatch in com.compomics.util.experiment.quantification.matches |
---|
Methods in com.compomics.util.experiment.quantification.matches that return types with arguments of type IonMatch | |
---|---|
HashMap<Integer,IonMatch> |
PsmQuantification.getReporterMatches()
Getter for the reporter matches. |
Methods in com.compomics.util.experiment.quantification.matches with parameters of type IonMatch | |
---|---|
void |
PsmQuantification.addIonMatch(int reporterIndex,
IonMatch match)
Method to add a match between a peak and a reporter ion. |
Uses of IonMatch in com.compomics.util.gui.spectrum |
---|
Method parameters in com.compomics.util.gui.spectrum with type arguments of type IonMatch | |
---|---|
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, 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 aReverseIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showReverseTags,
double forwardIonPercentHeight,
double reverseIonPercentHeight)
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 aReverseIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showReverseTags,
double forwardIonPercentHeight,
double reverseIonPercentHeight,
boolean excludeFixedPtms)
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 aReverseIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showReverseTags,
double forwardIonPercentHeight,
double reverseIonPercentHeight,
float forwardIonAlphaLevel,
float reverseIonAlphaLevel,
boolean excludeFixedPtms)
Add reference areas annotating the de novo tags. |
Constructor parameters in com.compomics.util.gui.spectrum with type arguments of type IonMatch | |
---|---|
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. |
|
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. |
|
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. |
|
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. |
|
SequenceFragmentationPanel(String aSequence,
ArrayList<IonMatch> aIonMatches,
boolean boolModifiedSequence,
boolean aHighlightModifications,
ModificationProfile modificationProfile)
Deprecated. use the panel with ion selection instead |
|
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. |
|
SequenceFragmentationPanel(String taggedModifiedSequence,
ArrayList<IonMatch> aIonMatches,
boolean aHighlightModifications,
ModificationProfile modificationProfile,
int forwardIon,
int rewindIon)
Creates a new SequenceFragmentationPanel working with B and Y ions. |
|
||||||||||
PREV NEXT | FRAMES NO FRAMES |