Uses of Class
com.compomics.util.experiment.biology.ions.Ion
Package | Description |
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com.compomics.util.experiment.biology.ions |
Experiment classes related to ions.
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com.compomics.util.experiment.biology.ions.impl |
Ion implementations.
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com.compomics.util.experiment.identification.matches |
Experiment classes related to matches.
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com.compomics.util.experiment.identification.peptide_fragmentation |
Peptide fragment intensities.
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com.compomics.util.experiment.identification.peptide_fragmentation.models |
Predictors for peptide fragment intensities.
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com.compomics.util.experiment.identification.spectrum_annotation |
Classes used for ms2 spectrum annotation.
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com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators |
This package contains implementations of the SpectrumAnnotator allowing the annotation of all ions.
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com.compomics.util.gui.spectrum |
Spectrum and Chromatogram visualization GUI classes.
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Uses of Ion in com.compomics.util.experiment.biology.ions
Methods in com.compomics.util.experiment.biology.ions that return Ion Modifier and Type Method Description static Ion
Ion. getGenericIon(Ion.IonType ionType, int subType)
Convenience method returning a generic ion based on the given ion type without neutral losses.static Ion
Ion. getGenericIon(Ion.IonType ionType, int subType, NeutralLoss[] neutralLosses)
Convenience method returning a generic ion based on the given ion type.Methods in com.compomics.util.experiment.biology.ions that return types with arguments of type Ion Modifier and Type Method Description HashMap<Integer,HashMap<Integer,ArrayList<Ion>>>
IonFactory. getFragmentIons(Peptide peptide, SpecificAnnotationParameters specificAnnotationSettings, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)
This method returns the theoretic ions expected from a peptide.HashMap<Integer,HashMap<Integer,ArrayList<Ion>>>
IonFactory. getFragmentIons(Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)
This method returns all the theoretic ions expected from a peptide.HashMap<Integer,HashMap<Integer,ArrayList<Ion>>>
IonFactory. getFragmentIons(Tag tag, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters)
This method returns the theoretic ions expected from a tag.Methods in com.compomics.util.experiment.biology.ions with parameters of type Ion Modifier and Type Method Description abstract boolean
Ion. isSameAs(Ion anotherIon)
Returns a boolean indicating whether the ion is the same as another ion. -
Uses of Ion in com.compomics.util.experiment.biology.ions.impl
Subclasses of Ion in com.compomics.util.experiment.biology.ions.impl Modifier and Type Class Description class
ElementaryIon
This class represents an elementary ion.class
Glycan
This class represents a glycan.class
ImmoniumIon
Represents an immonium ion.class
PeptideFragmentIon
This class models a peptide fragment ion.class
PrecursorIon
A precursor ion.class
RelatedIon
Represents a related ion, i.e., an ion that is related to a given amino acid, and is its own factory.class
ReporterIon
This class models a reporter ion and is its own factory.class
TagFragmentIon
A fragment ion obtained from a tag.Methods in com.compomics.util.experiment.biology.ions.impl with parameters of type Ion Modifier and Type Method Description boolean
ElementaryIon. isSameAs(Ion anotherIon)
boolean
Glycan. isSameAs(Ion anotherIon)
boolean
ImmoniumIon. isSameAs(Ion anotherIon)
boolean
PeptideFragmentIon. isSameAs(Ion anotherIon)
boolean
PrecursorIon. isSameAs(Ion anotherIon)
boolean
RelatedIon. isSameAs(Ion anotherIon)
boolean
ReporterIon. isSameAs(Ion anotherIon)
boolean
TagFragmentIon. isSameAs(Ion anotherIon)
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Uses of Ion in com.compomics.util.experiment.identification.matches
Fields in com.compomics.util.experiment.identification.matches declared as Ion Modifier and Type Field Description Ion
IonMatch. ion
The matching ion.Methods in com.compomics.util.experiment.identification.matches with parameters of type Ion Modifier and Type Method Description static String
IonMatch. getMatchKey(Ion ion, int charge)
Returns the key for the ion match uniquely representing a peak annotation.static String
IonMatch. getMatchKey(Ion ion, int charge, IonMatchKeysCache ionMatchKeysCache)
Returns the key for the ion match uniquely representing a peak annotation.static String
IonMatch. getPeakAnnotation(boolean html, Ion ion, int charge)
Returns the annotation to use for a given ion and charge as a String.static String
IonMatch. getPeakAnnotation(Ion ion, int charge)
Returns the annotation to use for a given ion and charge as a String.Constructors in com.compomics.util.experiment.identification.matches with parameters of type Ion Constructor Description IonMatch(double peakMz, double peakIntensity, Ion ion, int charge)
Constructor for an ion match. -
Uses of Ion in com.compomics.util.experiment.identification.peptide_fragmentation
Methods in com.compomics.util.experiment.identification.peptide_fragmentation with parameters of type Ion Modifier and Type Method Description Double
FragmentItensityPredictor. getIntentisy(Ion ion)
Returns the intensity expected for the given peak. -
Uses of Ion in com.compomics.util.experiment.identification.peptide_fragmentation.models
Methods in com.compomics.util.experiment.identification.peptide_fragmentation.models with parameters of type Ion Modifier and Type Method Description static Double
SequestFragmentationModel. getIntensity(Ion ion)
Returns the intensity expected for the given ion. -
Uses of Ion in com.compomics.util.experiment.identification.spectrum_annotation
Fields in com.compomics.util.experiment.identification.spectrum_annotation with type parameters of type Ion Modifier and Type Field Description protected HashMap<Integer,HashMap<Integer,ArrayList<Ion>>>
SpectrumAnnotator. theoreticalFragmentIons
The theoretic fragment ions.Methods in com.compomics.util.experiment.identification.spectrum_annotation that return types with arguments of type Ion Modifier and Type Method Description protected HashMap<Integer,ArrayList<Ion>>
SpectrumAnnotator. getExpectedIons(SpecificAnnotationParameters specificAnnotationSettings)
Returns the expected ions in a map indexed by the possible charges.Methods in com.compomics.util.experiment.identification.spectrum_annotation with parameters of type Ion Modifier and Type Method Description boolean
SpectrumAnnotator. chargeValidated(Ion theoreticIon, int charge, int precursorCharge)
Returns a boolean indicating whether the given charge can be found on the given fragment ion.String
IonMatchKeysCache. getMatchKey(Ion ion, int charge)
Returns the key for the ion match uniquely representing a peak annotation.boolean
SpectrumAnnotator. isAccounted(NeutralLossesMap neutralLosses, NeutralLoss neutralLoss, Ion ion)
Returns a boolean indicating whether the neutral loss should be accounted for.boolean
SpectrumAnnotator. lossesValidated(NeutralLossesMap neutralLosses, Ion theoreticIon)
Returns a boolean indicating whether the neutral losses of the given fragment ion fit the requirement of the given neutral losses map.protected IonMatch
SpectrumAnnotator. matchInSpectrum(double[] spectrumMz, double[] spectrumIntensity, Ion theoreticIon, Integer inspectedCharge)
Matches a theoretic ion in the spectrum.static ArrayList<IonMatch>
SpectrumAnnotator. matchReporterIon(Ion theoreticIon, int charge, Spectrum spectrum, double massTolerance)
Convenience method to match a reporter ion in a spectrum. -
Uses of Ion in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators
Methods in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators that return types with arguments of type Ion Modifier and Type Method Description HashMap<Integer,ArrayList<Ion>>
PeptideSpectrumAnnotator. getExpectedIons(SpecificAnnotationParameters specificAnnotationSettings, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)
Returns the expected ions in a map indexed by the possible charges.HashMap<Integer,ArrayList<Ion>>
PeptideSpectrumAnnotator. getExpectedIons(SpecificAnnotationParameters specificAnnotationSettings, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons)
Returns the expected ions in a map indexed by the possible charges.Method parameters in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators with type arguments of type Ion Modifier and Type Method Description HashMap<Integer,ArrayList<Ion>>
PeptideSpectrumAnnotator. getExpectedIons(SpecificAnnotationParameters specificAnnotationSettings, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons)
Returns the expected ions in a map indexed by the possible charges.IonMatch[]
PeptideSpectrumAnnotator. getSpectrumAnnotation(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments, boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in an array of IonMatches.java.util.stream.Stream<IonMatch>
PeptideSpectrumAnnotator. getSpectrumAnnotationStream(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments, boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a stream of IonMatches.void
PeptideSpectrumAnnotator. setPeptide(Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons, int precursorCharge, SpecificAnnotationParameters specificAnnotationSettings)
Sets a new peptide to annotate. -
Uses of Ion in com.compomics.util.gui.spectrum
Methods in com.compomics.util.gui.spectrum that return Ion Modifier and Type Method Description Ion
IonLabelColorTableModel. getIonAtRow(int rowIndex)
Returns the ion type at the given row.Methods in com.compomics.util.gui.spectrum with parameters of type Ion Modifier and Type Method Description static Color
SpectrumPanel. determineDefaultFragmentIonColor(Ion ion, boolean isSpectrum)
Returns the peak color to be used for the given peak label.static Color
SpectrumPanel. determineFragmentIonColor(Ion ion, boolean isSpectrum)
Returns the peak color to be used for the given peak label according to the color map.static void
SpectrumPanel. setIonColor(Ion ion, Color color)
Sets an annotation color for the given ion.