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Packages that use NeutralLoss | |
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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.gui.spectrum | This package contains GUI classes related to Spectrum and Chromatogram visualization. |
com.compomics.util.preferences |
Uses of NeutralLoss in com.compomics.util.experiment.biology |
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Fields in com.compomics.util.experiment.biology declared as NeutralLoss | |
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static NeutralLoss |
NeutralLoss.CH4OS
CH4OS loss. |
static NeutralLoss |
NeutralLoss.H2O
H2O loss. |
static NeutralLoss |
NeutralLoss.H3PO4
H3PO4 loss. |
static NeutralLoss |
NeutralLoss.HPO3
H3PO3 loss. |
static NeutralLoss |
NeutralLoss.NH3
NH3 loss. |
Methods in com.compomics.util.experiment.biology that return types with arguments of type NeutralLoss | |
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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. |
Methods in com.compomics.util.experiment.biology with parameters of type NeutralLoss | |
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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. |
Method parameters in com.compomics.util.experiment.biology with type arguments of type NeutralLoss | |
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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. |
Uses of NeutralLoss in com.compomics.util.experiment.biology.ions |
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Methods in com.compomics.util.experiment.biology.ions that return types with arguments of type NeutralLoss | |
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ArrayList<NeutralLoss> |
ReporterIon.getNeutralLosses()
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ArrayList<NeutralLoss> |
PrecursorIon.getNeutralLosses()
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ArrayList<NeutralLoss> |
PeptideFragmentIon.getNeutralLosses()
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ArrayList<NeutralLoss> |
ImmoniumIon.getNeutralLosses()
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ArrayList<NeutralLoss> |
Glycon.getNeutralLosses()
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ArrayList<NeutralLoss> |
ElementaryIon.getNeutralLosses()
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Constructor parameters in com.compomics.util.experiment.biology.ions with type arguments of type NeutralLoss | |
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PeptideFragmentIon(int fragmentType,
ArrayList<NeutralLoss> neutralLosses)
Constructor for a generic ion. |
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PeptideFragmentIon(int fragmentType,
int number,
double mass,
ArrayList<NeutralLoss> neutralLosses)
Constructor. |
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PrecursorIon(ArrayList<NeutralLoss> neutralLosses)
Constructor for a generic ion. |
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PrecursorIon(double theoreticMass,
ArrayList<NeutralLoss> neutralLosses)
Constructor. |
Uses of NeutralLoss in com.compomics.util.experiment.identification |
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Methods in com.compomics.util.experiment.identification that return types with arguments of type NeutralLoss | |
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ArrayList<NeutralLoss> |
NeutralLossesMap.getAccountedNeutralLosses()
Returns an arraylist of implemented neutral losses. |
Methods in com.compomics.util.experiment.identification with parameters of type NeutralLoss | |
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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,
Peptide peptide)
Returns a boolean indicating whether the neutral loss should be accounted for. |
Uses of NeutralLoss in com.compomics.util.gui.spectrum |
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Method parameters in com.compomics.util.gui.spectrum with type arguments of type NeutralLoss | |
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static Vector<DefaultSpectrumAnnotation> |
SpectrumPanel.filterAnnotations(Vector<DefaultSpectrumAnnotation> 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 parameters in com.compomics.util.gui.spectrum with type arguments of type NeutralLoss | |
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IonLabelColorTableModel(HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
ArrayList<NeutralLoss> neutralLosses)
Constructor which sets a new table. |
Uses of NeutralLoss in com.compomics.util.preferences |
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Methods in com.compomics.util.preferences with parameters of type NeutralLoss | |
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void |
AnnotationPreferences.addNeutralLoss(NeutralLoss neutralLoss)
Adds a neutral loss. |
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