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Packages that use PeptideFragmentIon | |
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com.compomics.util.experiment.biology | This package contains experiement classes related to biological entities. |
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 PeptideFragmentIon in com.compomics.util.experiment.biology |
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Methods in com.compomics.util.experiment.biology that return types with arguments of type PeptideFragmentIon | |
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java.util.ArrayList<PeptideFragmentIon> |
FragmentFactory.getFragmentIons(Peptide peptide)
This method returns the theoretic fragment ions expected from a peptide sequence. |
Uses of PeptideFragmentIon in com.compomics.util.experiment.identification |
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Methods in com.compomics.util.experiment.identification that return types with arguments of type PeptideFragmentIon | |
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java.util.HashMap<java.lang.Integer,java.util.ArrayList<PeptideFragmentIon>> |
SpectrumAnnotator.getExpectedIons(java.util.ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
Peptide peptide)
Returns the expected ions in a map indexed by the possible charges. |
Methods in com.compomics.util.experiment.identification with parameters of type PeptideFragmentIon | |
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boolean |
SpectrumAnnotator.chargeValidated(PeptideFragmentIon fragmentIon,
int charge)
Returns a boolean indicating whether the given charge can be found on the given fragment ion. |
static java.lang.String |
SpectrumAnnotator.getTheoreticFragmentKey(PeptideFragmentIon fragmentIon,
int charge)
Returns the key of a theoretic fragment. |
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. |
Uses of PeptideFragmentIon in com.compomics.util.experiment.identification.ptm |
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Methods in com.compomics.util.experiment.identification.ptm that return types with arguments of type PeptideFragmentIon | |
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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.ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons,
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. |
Uses of PeptideFragmentIon in com.compomics.util.gui.spectrum |
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Methods in com.compomics.util.gui.spectrum with parameters of type PeptideFragmentIon | |
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static java.awt.Color |
SpectrumPanel.determineFragmentIonColor(PeptideFragmentIon fragmentIon)
Returns the peak color to be used for the given peak label. |
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