Package | Description |
---|---|
com.compomics.util.experiment.biology |
Experiment classes related to biological entities.
|
com.compomics.util.experiment.biology.ions |
Experiment classes related to ions.
|
com.compomics.util.experiment.identification.matches |
Experiment classes related to matches.
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com.compomics.util.experiment.identification.spectrum_annotation |
Classes used for ms2 spectrum annotation.
|
com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators |
Spectrum annotation.
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com.compomics.util.gui.spectrum |
Spectrum and Chromatogram visualization GUI classes.
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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,
ArrayList<NeutralLoss> neutralLosses)
Convenience method returning a generic ion based on the given ion type.
|
Modifier and Type | Method and Description |
---|---|
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> |
IonFactory.getFragmentIons(Peptide peptide)
This method returns all the theoretic ions expected from a peptide.
|
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> |
IonFactory.getFragmentIons(Peptide peptide,
SpecificAnnotationSettings specificAnnotationSettings)
This method returns the theoretic ions expected from a peptide.
|
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> |
IonFactory.getFragmentIons(Tag tag)
This method returns the theoretic ions expected from a tag.
|
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 |
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.
|
Modifier and Type | Method and Description |
---|---|
boolean |
TagFragmentIon.isSameAs(Ion anotherIon) |
boolean |
ReporterIon.isSameAs(Ion anotherIon) |
boolean |
RelatedIon.isSameAs(Ion anotherIon) |
boolean |
PrecursorIon.isSameAs(Ion anotherIon) |
boolean |
PeptideFragmentIon.isSameAs(Ion anotherIon) |
boolean |
ImmoniumIon.isSameAs(Ion anotherIon) |
boolean |
Glycan.isSameAs(Ion anotherIon) |
boolean |
ElementaryIon.isSameAs(Ion anotherIon) |
Modifier and Type | Field and Description |
---|---|
Ion |
IonMatch.ion
The matching ion.
|
Modifier and Type | Method and 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,
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.
|
Constructor and Description |
---|
IonMatch(Peak aPeak,
Ion anIon,
Charge aCharge)
Constructor for an ion peak.
|
Modifier and Type | Field and Description |
---|---|
protected HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> |
SpectrumAnnotator.theoreticalFragmentIons
The theoretic fragment ions.
|
Modifier and Type | Method and Description |
---|---|
protected HashMap<Integer,ArrayList<Ion>> |
SpectrumAnnotator.getExpectedIons(SpecificAnnotationSettings specificAnnotationSettings)
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.
|
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 boolean |
SpectrumAnnotator.matchInSpectrum(Ion theoreticIon,
int 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.
|
Modifier and Type | Method and Description |
---|---|
HashMap<Integer,ArrayList<Ion>> |
PeptideSpectrumAnnotator.getExpectedIons(SpecificAnnotationSettings specificAnnotationSettings,
Peptide peptide)
Returns the expected ions in a map indexed by the possible charges.
|
HashMap<Integer,ArrayList<Ion>> |
PeptideSpectrumAnnotator.getExpectedIons(SpecificAnnotationSettings specificAnnotationSettings,
Peptide peptide,
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons)
Returns the expected ions in a map indexed by the possible charges.
|
Modifier and Type | Method and Description |
---|---|
HashMap<Integer,ArrayList<Ion>> |
PeptideSpectrumAnnotator.getExpectedIons(SpecificAnnotationSettings specificAnnotationSettings,
Peptide peptide,
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons)
Returns the expected ions in a map indexed by the possible charges.
|
ArrayList<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings,
MSnSpectrum spectrum,
Peptide peptide,
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
void |
PeptideSpectrumAnnotator.setPeptide(Peptide peptide,
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons,
int precursorCharge,
SpecificAnnotationSettings specificAnnotationSettings)
Sets a new peptide to match.
|
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 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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