Package | Description |
---|---|
com.compomics.util.experiment.biology |
This package contains experiement classes related to biological entities.
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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.
|
Modifier and Type | Method and 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,
java.util.ArrayList<NeutralLoss> neutralLosses)
Convenience method returning a generic ion based on the given ion type.
|
Modifier and Type | Method and Description |
---|---|
java.util.ArrayList<Ion> |
IonFactory.getFragmentIons(Peptide peptide)
This method returns the theoretic ions expected from a peptide.
|
Modifier and Type | Method and Description |
---|---|
abstract boolean |
Ion.isSameAs(Ion anotherIon)
Returns a boolean indicating whether the ion is the same as another ion.
|
Modifier and Type | Class and Description |
---|---|
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.
|
Modifier and Type | Method and Description |
---|---|
boolean |
ReporterIon.isSameAs(Ion anotherIon) |
boolean |
PrecursorIon.isSameAs(Ion anotherIon) |
boolean |
PeptideFragmentIon.isSameAs(Ion anotherIon) |
boolean |
ImmoniumIon.isSameAs(Ion anotherIon) |
boolean |
Glycon.isSameAs(Ion anotherIon) |
boolean |
ElementaryIon.isSameAs(Ion anotherIon) |
Modifier and Type | Method and Description |
---|---|
java.util.HashMap<java.lang.Integer,java.util.ArrayList<Ion>> |
SpectrumAnnotator.getExpectedIons(java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
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.
|
Modifier and Type | Method and 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.
|
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.
|
Modifier and Type | Field and Description |
---|---|
Ion |
IonMatch.ion
The matching ion.
|
Modifier and Type | Method and Description |
---|---|
static java.lang.String |
IonMatch.getPeakAnnotation(boolean html,
Ion ion,
Charge charge)
Returns the annotation to use for a given ion and charge as a String.
|
static java.lang.String |
IonMatch.getPeakAnnotation(Ion ion,
Charge charge)
Returns the annotation to use for a given ion and charge as a String.
|
Constructor and Description |
---|
IonMatch(Peak aPeak,
Ion anIon,
Charge aCharge)
Constructor for an ion peak.
|
Modifier and Type | Method and Description |
---|---|
Ion |
IonLabelColorTableModel.getIonAtRow(int rowIndex)
Returns the ion type at the given row.
|
Modifier and Type | Method and Description |
---|---|
static java.awt.Color |
SpectrumPanel.determineDefaultFragmentIonColor(Ion ion,
boolean isSpectrum)
Returns the peak color to be used for the given peak label.
|
static java.awt.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,
java.awt.Color color)
Sets an annotation color for the given ion.
|
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