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.biology.neutrallosses   
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. 
 

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 with parameters of type NeutralLoss
 boolean NeutralLoss.isSameAs(NeutralLoss anotherNeutralLoss)
          Method indicating whether another neutral loss is the same as the one considered
 

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
 ArrayList<NeutralLoss> PeptideFragmentIon.getNeutralLosses()
          Returns the neutral losses for this fragment ion
 

Constructor parameters in com.compomics.util.experiment.biology.ions with type arguments of type NeutralLoss
PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType type, int number, double mass, ArrayList<NeutralLoss> neutralLosses)
          Construction for a peptide fragment with neutral loss.
 

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

Subclasses of NeutralLoss in com.compomics.util.experiment.biology.neutrallosses
 class CH4OS
          Neutral loss CH4OS, likely to be encountered on fragment from peptides containing an oxidized methionine.
 class H2O
          A water loss, likely to be found on fragments from peptides containing the amino-acid D, E, S or T
 class H3PO4
          A phosphorylation loss, likely to be found on fragments from phosphorylated peptides on Y.
 class HPO3
          A phosphorylation loss, likely to be found on fragments from phosphorylated peptides on S or T.
 class NH3
          A nitrium loss, likely to be found on fragments from peptides containing the amino-acid K, N, Q or R.
 

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

Methods in com.compomics.util.experiment.identification that return types with arguments of type NeutralLoss
 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, PeptideFragmentIon fragmentIon, 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 Vector<DefaultSpectrumAnnotation> SpectrumPanel.filterAnnotations(Vector<DefaultSpectrumAnnotation> annotations, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> fragmentIonTypes, ArrayList<NeutralLoss> neutralLosses, boolean singleChargeSelected, boolean doubleChargeSelected, boolean moreThanTwoChargesSelected)
          Filters the annotations and returns the annotations matching the currently selected types.
 



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