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

Packages that use Ion
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.experiment.identification.matches This package contains experiment classes releated to matches. 
com.compomics.util.gui.spectrum This package contains GUI classes related to Spectrum and Chromatogram visualization. 
 

Uses of Ion in com.compomics.util.experiment.biology
 

Methods in com.compomics.util.experiment.biology that return Ion
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.
 

Methods in com.compomics.util.experiment.biology that return types with arguments of type Ion
 ArrayList<Ion> IonFactory.getFragmentIons(Peptide peptide)
          This method returns the theoretic ions expected from a peptide.
 

Methods in com.compomics.util.experiment.biology with parameters of type Ion
abstract  boolean Ion.isSameAs(Ion anotherIon)
          Returns a boolean indicating whether the ion is the same as another ion.
 

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

Subclasses of Ion in com.compomics.util.experiment.biology.ions
 class ElementaryIon
          This class represents an elementary ion
 class Glycon
          This class will models a glycon fragment.
 class ImmoniumIon
          Represents an immonium ion.
 class PeptideFragmentIon
          This class models a peptide fragment ion.
 class PrecursorIon
          A precursor ion.
 class ReporterIon
          This class models a reporter ion and is its own factory
 

Methods in com.compomics.util.experiment.biology.ions with parameters of type Ion
 boolean ReporterIon.isSameAs(Ion anotherIon)
           
 boolean PrecursorIon.isSameAs(Ion anotherIon)
           
 boolean PeptideFragmentIon.isSameAs(Ion anotherIon)
           
 boolean ImmoniumIon.isSameAs(Ion anotherIon)
           
 boolean Glycon.isSameAs(Ion anotherIon)
           
 boolean ElementaryIon.isSameAs(Ion anotherIon)
           
 

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

Methods in com.compomics.util.experiment.identification that return types with arguments of type Ion
 HashMap<Integer,ArrayList<Ion>> SpectrumAnnotator.getExpectedIons(HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, Peptide peptide)
          Returns the expected ions in a map indexed by the possible charges.
 

Methods in com.compomics.util.experiment.identification with parameters of type Ion
 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.
 boolean SpectrumAnnotator.isAccounted(NeutralLossesMap neutralLosses, NeutralLoss neutralLoss, Ion ion, Peptide peptide)
          Returns a boolean indicating whether the neutral loss should be accounted for.
 boolean SpectrumAnnotator.lossesValidated(NeutralLossesMap neutralLosses, Ion theoreticIon, Peptide peptide)
          Returns a boolean indicating whether the neutral losses of the given fragment ion are fit the requirement of the given neutral losses map.
 

Uses of Ion in com.compomics.util.experiment.identification.matches
 

Fields in com.compomics.util.experiment.identification.matches declared as Ion
 Ion IonMatch.ion
          The matching ion.
 

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

Constructors in com.compomics.util.experiment.identification.matches with parameters of type Ion
IonMatch(Peak aPeak, Ion anIon, Charge aCharge)
          Constructor for an ion peak.
 

Uses of Ion in com.compomics.util.gui.spectrum
 

Methods in com.compomics.util.gui.spectrum that return Ion
 Ion IonLabelColorTableModel.getIonAtRow(int rowIndex)
          Returns the ion type at the given row.
 

Methods in com.compomics.util.gui.spectrum with parameters of type Ion
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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