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Packages that use NeutralLossesMap | |
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com.compomics.util.experiment.identification | This package contains experiment classes related to identifications. |
com.compomics.util.experiment.identification.ptm | |
com.compomics.util.gui.spectrum | This package contains GUI classes related to Spectrum and Chromatogram visualization. |
Uses of NeutralLossesMap in com.compomics.util.experiment.identification |
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Methods in com.compomics.util.experiment.identification that return NeutralLossesMap | |
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static NeutralLossesMap |
SpectrumAnnotator.getDefaultLosses(Peptide peptide)
Returns the possible neutral losses expected by default for a given peptide. /! |
Methods in com.compomics.util.experiment.identification with parameters of type NeutralLossesMap | |
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ArrayList<IonMatch> |
SpectrumAnnotator.getCurrentAnnotation(ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges)
Returns the currently matched ions with the given settings. |
HashMap<Integer,ArrayList<PeptideFragmentIon>> |
SpectrumAnnotator.getExpectedIons(ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
Peptide peptide)
Returns the expected ions in a map indexed by the possible charges. |
ArrayList<IonMatch> |
SpectrumAnnotator.getSpectrumAnnotation(ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
MSnSpectrum spectrum,
Peptide peptide,
double intensityLimit,
double mzTolerance)
Returns the spectrum annotations of a spectrum in a list of IonMatches. |
boolean |
SpectrumAnnotator.isAccounted(NeutralLossesMap neutralLosses,
NeutralLoss neutralLoss,
PeptideFragmentIon fragmentIon,
Peptide peptide)
Returns a boolean indicating whether the neutral loss should be accounted for. |
boolean |
SpectrumAnnotator.lossesValidated(NeutralLossesMap neutralLosses,
PeptideFragmentIon fragmentIon,
Peptide peptide)
Returns a boolean indicating whether the neutral losses of the given fragment ion are fit the requirement of the given neutral losses map. |
ArrayList<IonMatch> |
SpectrumAnnotator.matchPeak(Peptide peptide,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> iontypes,
ArrayList<Integer> charges,
int precursorCharge,
NeutralLossesMap neutralLosses,
Peak peak,
double massTolerance)
This method matches the potential fragment ions of a given peptide with a given peak. |
Uses of NeutralLossesMap in com.compomics.util.experiment.identification.ptm |
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Methods in com.compomics.util.experiment.identification.ptm with parameters of type NeutralLossesMap | |
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static HashMap<ArrayList<Integer>,Double> |
PTMLocationScores.getAScore(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance)
Returns the A-score for the best PTM location. |
static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> |
PTMLocationScores.getPTMPlotData(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
double intensityLimit)
Returns the ptm plot series in the jfreechart format for one psm. |
static PtmtableContent |
PTMLocationScores.getPTMTableContent(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
double intensityLimit)
Get the PTM table content. |
Uses of NeutralLossesMap in com.compomics.util.gui.spectrum |
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Constructors in com.compomics.util.gui.spectrum with parameters of type NeutralLossesMap | |
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FragmentIonTable(Peptide currentPeptide,
ArrayList<ArrayList<IonMatch>> allAnnotations,
ArrayList<MSnSpectrum> allSpectra,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> 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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FragmentIonTable(Peptide currentPeptide,
ArrayList<IonMatch> annotations,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> 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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