Uses of Class
com.compomics.util.experiment.massspectrometry.Charge

Packages that use Charge
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.experiment.massspectrometry This package contains experiment classes related to spectra. 
 

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

Methods in com.compomics.util.experiment.identification that return Charge
 Charge PeptideAssumption.getIdentificationCharge()
          Returns the charge used for identification.
 Charge SearchParameters.getMaxChargeSearched()
          Returns the maximal charge searched.
 Charge SearchParameters.getMinChargeSearched()
          Returns the minimal charge searched.
 Charge SearchParameters.getMinimalChargeForMultipleChargedFragments()
          Returns the minimal precursor charge to account for multiply charged fragments in OMSSA.
 

Methods in com.compomics.util.experiment.identification with parameters of type Charge
 void SearchParameters.setMaxChargeSearched(Charge maxChargeSearched)
          Sets the maximal charge searched.
 void SearchParameters.setMinChargeSearched(Charge minChargeSearched)
          Sets the minimal charge searched.
 void SearchParameters.setMinimalChargeForMultipleChargedFragments(Charge minimalChargeForMultipleChargedFragments)
          Sets the minimal precursor charge to account for multiply charged fragments in OMSSA.
 

Constructors in com.compomics.util.experiment.identification with parameters of type Charge
PeptideAssumption(Peptide aPeptide, int rank, int advocate, Charge identificationCharge, double score)
          Constructor for a peptide assumption.
PeptideAssumption(Peptide aPeptide, int rank, int advocate, Charge identificationCharge, double score, String identificationFile)
          Constructor for a peptide assumption.
 

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

Fields in com.compomics.util.experiment.identification.matches declared as Charge
 Charge IonMatch.charge
          The supposed charge of the ion.
 

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

Uses of Charge in com.compomics.util.experiment.massspectrometry
 

Methods in com.compomics.util.experiment.massspectrometry that return types with arguments of type Charge
 ArrayList<Charge> Precursor.getPossibleCharges()
          Getter for the possible charges.
 

Constructor parameters in com.compomics.util.experiment.massspectrometry with type arguments of type Charge
Precursor(double rt, double mz, ArrayList<Charge> possibleCharges)
          Constructor for the precursor.
Precursor(double mz, double intensity, ArrayList<Charge> possibleCharges, double rtMin, double rtMax)
          Cronstructor with rt window and no reference rt.
Precursor(double rt, double mz, double intensity, ArrayList<Charge> possibleCharges)
          Constructor for the precursor.
Precursor(double rt, double mz, double intensity, ArrayList<Charge> possibleCharges, double rtMin, double rtMax)
          Cronstructor with rt window.
 



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