Uses of Class
com.compomics.util.experiment.biology.NeutralLoss

Packages that use NeutralLoss
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
 

Fields in com.compomics.util.experiment.biology declared as NeutralLoss
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
static java.util.ArrayList<java.util.ArrayList<NeutralLoss>> IonFactory.getAccountedNeutralLosses(java.util.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.
 java.util.ArrayList<NeutralLoss> IonFactory.getDefaultNeutralLosses()
          Returns the default neutral losses.
 java.util.ArrayList<NeutralLoss> PTM.getNeutralLosses()
          Returns the neutral losses possibly encountered with this modification.
abstract  java.util.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
 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
static java.util.ArrayList<java.util.ArrayList<NeutralLoss>> IonFactory.getAccountedNeutralLosses(java.util.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, java.util.ArrayList<NeutralLoss> neutralLosses)
          Convenience method returning a generic ion based on the given ion type.
static double IonFactory.getLossesMass(java.util.ArrayList<NeutralLoss> neutralLosses)
          Convenience summing the masses of various neutral losses.
static java.lang.String Ion.getNeutralLossesAsString(java.util.ArrayList<NeutralLoss> neutralLosses)
          Returns the neutral loss (if any), the empty string if no loss.
 void PTM.setNeutralLosses(java.util.ArrayList<NeutralLoss> neutralLosses)
          Sets the neutral losses possibly encountered with this modification.
 

Uses of NeutralLoss in com.compomics.util.experiment.biology.ions
 

Methods in com.compomics.util.experiment.biology.ions that return types with arguments of type NeutralLoss
 java.util.ArrayList<NeutralLoss> ReporterIon.getNeutralLosses()
           
 java.util.ArrayList<NeutralLoss> PrecursorIon.getNeutralLosses()
           
 java.util.ArrayList<NeutralLoss> PeptideFragmentIon.getNeutralLosses()
           
 java.util.ArrayList<NeutralLoss> ImmoniumIon.getNeutralLosses()
           
 java.util.ArrayList<NeutralLoss> Glycon.getNeutralLosses()
           
 java.util.ArrayList<NeutralLoss> ElementaryIon.getNeutralLosses()
           
 

Constructor parameters in com.compomics.util.experiment.biology.ions with type arguments of type NeutralLoss
PeptideFragmentIon(int fragmentType, java.util.ArrayList<NeutralLoss> neutralLosses)
          Constructor for a generic ion.
PeptideFragmentIon(int fragmentType, int number, double mass, java.util.ArrayList<NeutralLoss> neutralLosses)
          Constructor.
PrecursorIon(java.util.ArrayList<NeutralLoss> neutralLosses)
          Constructor for a generic ion.
PrecursorIon(double theoreticMass, java.util.ArrayList<NeutralLoss> neutralLosses)
          Constructor.
 

Uses of NeutralLoss in com.compomics.util.experiment.identification
 

Methods in com.compomics.util.experiment.identification that return types with arguments of type NeutralLoss
 java.util.ArrayList<NeutralLoss> NeutralLossesMap.getAccountedNeutralLosses()
          Returns an arraylist of implemented neutral losses.
 

Methods in com.compomics.util.experiment.identification with parameters of type NeutralLoss
 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
 

Method parameters in com.compomics.util.gui.spectrum with type arguments of type NeutralLoss
static java.util.Vector<DefaultSpectrumAnnotation> SpectrumPanel.filterAnnotations(java.util.Vector<DefaultSpectrumAnnotation> annotations, java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, java.util.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
IonLabelColorTableModel(java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, java.util.ArrayList<NeutralLoss> neutralLosses)
          Constructor which sets a new table.
 

Uses of NeutralLoss in com.compomics.util.preferences
 

Methods in com.compomics.util.preferences with parameters of type NeutralLoss
 void AnnotationPreferences.addNeutralLoss(NeutralLoss neutralLoss)
          Adds a neutral loss.
 



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