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.
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com.compomics.util.experiment.identification |
This package contains experiment classes related to identifications.
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com.compomics.util.gui.spectrum |
This package contains GUI classes related to Spectrum and Chromatogram visualization.
|
com.compomics.util.preferences |
Modifier and Type | Field and Description |
---|---|
static NeutralLoss |
NeutralLoss.CH4OS
CH4OS loss.
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static NeutralLoss |
NeutralLoss.H2O
H2O loss.
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static NeutralLoss |
NeutralLoss.H3PO4
H3PO4 loss.
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static NeutralLoss |
NeutralLoss.HPO3
H3PO3 loss.
|
static NeutralLoss |
NeutralLoss.NH3
NH3 loss.
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Modifier and Type | Method and Description |
---|---|
static ArrayList<ArrayList<NeutralLoss>> |
IonFactory.getAccountedNeutralLosses(ArrayList<NeutralLoss> possibleNeutralLosses)
Convenience method returning the possible neutral losses combination as
accounted by the factory, i.e., for now up to two neutral losses per
peak.
|
ArrayList<NeutralLoss> |
IonFactory.getDefaultNeutralLosses()
Returns the default neutral losses.
|
ArrayList<NeutralLoss> |
PTM.getNeutralLosses()
Returns the neutral losses possibly encountered with this modification.
|
abstract ArrayList<NeutralLoss> |
Ion.getNeutralLosses()
Returns the possible neutral losses of this ion type.
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Modifier and Type | Method and Description |
---|---|
void |
IonFactory.addDefaultNeutralLoss(NeutralLoss newNeutralLoss)
Adds a default neutral loss to the default neutral losses if the
corresponding loss was not here already.
|
void |
PTM.addNeutralLoss(NeutralLoss neutralLoss)
Adds a neutral loss.
|
boolean |
NeutralLoss.isSameAs(NeutralLoss anotherNeutralLoss)
Method indicating whether another neutral loss is the same as the one
considered.
|
Modifier and Type | Method and Description |
---|---|
static ArrayList<ArrayList<NeutralLoss>> |
IonFactory.getAccountedNeutralLosses(ArrayList<NeutralLoss> possibleNeutralLosses)
Convenience method returning the possible neutral losses combination as
accounted by the factory, i.e., for now up to two neutral losses per
peak.
|
static Ion |
Ion.getGenericIon(Ion.IonType ionType,
int subType,
ArrayList<NeutralLoss> neutralLosses)
Convenience method returning a generic ion based on the given ion type.
|
static double |
IonFactory.getLossesMass(ArrayList<NeutralLoss> neutralLosses)
Convenience summing the masses of various neutral losses.
|
static String |
Ion.getNeutralLossesAsString(ArrayList<NeutralLoss> neutralLosses)
Returns the neutral loss (if any), the empty string if no loss.
|
void |
PTM.setNeutralLosses(ArrayList<NeutralLoss> neutralLosses)
Sets the neutral losses possibly encountered with this modification.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<NeutralLoss> |
TagFragmentIon.getNeutralLosses() |
ArrayList<NeutralLoss> |
ReporterIon.getNeutralLosses() |
ArrayList<NeutralLoss> |
PrecursorIon.getNeutralLosses() |
ArrayList<NeutralLoss> |
PeptideFragmentIon.getNeutralLosses() |
ArrayList<NeutralLoss> |
ImmoniumIon.getNeutralLosses() |
ArrayList<NeutralLoss> |
Glycon.getNeutralLosses() |
ArrayList<NeutralLoss> |
ElementaryIon.getNeutralLosses() |
Constructor and Description |
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PeptideFragmentIon(int fragmentType,
ArrayList<NeutralLoss> neutralLosses)
Constructor for a generic ion.
|
PeptideFragmentIon(int fragmentType,
int number,
double mass,
ArrayList<NeutralLoss> neutralLosses)
Constructor.
|
PrecursorIon(ArrayList<NeutralLoss> neutralLosses)
Constructor for a generic ion.
|
PrecursorIon(double theoreticMass,
ArrayList<NeutralLoss> neutralLosses)
Constructor.
|
TagFragmentIon(int fragmentType,
ArrayList<NeutralLoss> neutralLosses)
Constructor for a generic ion.
|
TagFragmentIon(int fragmentType,
int number,
int subNumber,
double mass,
ArrayList<NeutralLoss> neutralLosses,
double massGap)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<NeutralLoss> |
NeutralLossesMap.getAccountedNeutralLosses()
Returns an arraylist of implemented neutral losses.
|
Modifier and Type | Method and Description |
---|---|
void |
NeutralLossesMap.addNeutralLoss(NeutralLoss neutralLoss,
int bStart,
int yStart)
Adds a new neutral loss to the map.
|
boolean |
NeutralLossesMap.containsLoss(NeutralLoss neutralLoss)
Returns a boolean indicating whether a loss is implemented in the
mapping.
|
int |
NeutralLossesMap.getBStart(NeutralLoss neutralLoss)
Returns the amino acid where a neutral loss should start being accounted
for when predicting b ions (counting from N-terminus, first aa is 1).
|
int |
NeutralLossesMap.getYStart(NeutralLoss neutralLoss)
Returns the amino acid where a neutral loss should start being accounted
for when predicting b ions (counting from N-terminus, first aa is 1).
|
boolean |
SpectrumAnnotator.isAccounted(NeutralLossesMap neutralLosses,
NeutralLoss neutralLoss,
Ion ion)
Returns a boolean indicating whether the neutral loss should be accounted
for.
|
Modifier and Type | Method and Description |
---|---|
static Vector<SpectrumAnnotation> |
SpectrumPanel.filterAnnotations(Vector<SpectrumAnnotation> annotations,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
ArrayList<NeutralLoss> neutralLosses,
boolean singleChargeSelected,
boolean doubleChargeSelected,
boolean moreThanTwoChargesSelected)
Deprecated.
don't use method based on the peak labels but on the data
type
|
Constructor and Description |
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IonLabelColorTableModel(HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
ArrayList<NeutralLoss> neutralLosses)
Constructor which sets a new table.
|
Modifier and Type | Method and Description |
---|---|
void |
AnnotationPreferences.addNeutralLoss(NeutralLoss neutralLoss)
Adds a neutral loss.
|
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