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Packages that use Ion | |
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com.compomics.util.experiment.biology | This package contains experiement classes related to biological entities. |
com.compomics.util.experiment.biology.ions | This package contains experiment classes related to ions. |
com.compomics.util.experiment.identification | This package contains experiment classes related to identifications. |
com.compomics.util.experiment.identification.matches | This package contains experiment classes releated to matches. |
com.compomics.util.gui.spectrum | This package contains GUI classes related to Spectrum and Chromatogram visualization. |
Uses of Ion in com.compomics.util.experiment.biology |
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Methods in com.compomics.util.experiment.biology that return Ion | |
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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,
ArrayList<NeutralLoss> neutralLosses)
Convenience method returning a generic ion based on the given ion type. |
Methods in com.compomics.util.experiment.biology that return types with arguments of type Ion | |
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ArrayList<Ion> |
IonFactory.getFragmentIons(Peptide peptide)
This method returns the theoretic ions expected from a peptide. |
Methods in com.compomics.util.experiment.biology with parameters of type Ion | |
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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 |
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Subclasses of Ion in com.compomics.util.experiment.biology.ions | |
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class |
ElementaryIon
This class represents an elementary ion. |
class |
Glycon
This class will models a glycon fragment. |
class |
ImmoniumIon
Represents an immonium ion. |
class |
PeptideFragmentIon
This class models a peptide fragment ion. |
class |
PrecursorIon
A precursor ion. |
class |
ReporterIon
This class models a reporter ion and is its own factory |
Methods in com.compomics.util.experiment.biology.ions with parameters of type Ion | |
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boolean |
ReporterIon.isSameAs(Ion anotherIon)
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boolean |
PrecursorIon.isSameAs(Ion anotherIon)
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boolean |
PeptideFragmentIon.isSameAs(Ion anotherIon)
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boolean |
ImmoniumIon.isSameAs(Ion anotherIon)
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boolean |
Glycon.isSameAs(Ion anotherIon)
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boolean |
ElementaryIon.isSameAs(Ion anotherIon)
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Uses of Ion in com.compomics.util.experiment.identification |
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Methods in com.compomics.util.experiment.identification that return types with arguments of type Ion | |
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HashMap<Integer,ArrayList<Ion>> |
SpectrumAnnotator.getExpectedIons(HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<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 Ion | |
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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. |
boolean |
SpectrumAnnotator.isAccounted(NeutralLossesMap neutralLosses,
NeutralLoss neutralLoss,
Ion ion,
Peptide peptide)
Returns a boolean indicating whether the neutral loss should be accounted for. |
boolean |
SpectrumAnnotator.lossesValidated(NeutralLossesMap neutralLosses,
Ion theoreticIon,
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 Ion in com.compomics.util.experiment.identification.matches |
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Fields in com.compomics.util.experiment.identification.matches declared as Ion | |
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Ion |
IonMatch.ion
The matching ion. |
Methods in com.compomics.util.experiment.identification.matches with parameters of type Ion | |
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static String |
IonMatch.getPeakAnnotation(boolean html,
Ion ion,
Charge charge)
Returns the annotation to use for a given ion and charge as a String. |
static String |
IonMatch.getPeakAnnotation(Ion ion,
Charge 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 | |
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IonMatch(Peak aPeak,
Ion anIon,
Charge aCharge)
Constructor for an ion peak. |
Uses of Ion in com.compomics.util.gui.spectrum |
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Methods in com.compomics.util.gui.spectrum that return Ion | |
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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 | |
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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. |
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