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

Packages that use Ion.IonType
com.compomics.util.experiment.biology This package contains experiement classes related to biological entities. 
com.compomics.util.experiment.identification This package contains experiment classes related to identifications. 
com.compomics.util.experiment.identification.ptm   
com.compomics.util.experiment.identification.scoring   
com.compomics.util.gui.spectrum This package contains GUI classes related to Spectrum and Chromatogram visualization. 
com.compomics.util.preferences   
 

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

Fields in com.compomics.util.experiment.biology declared as Ion.IonType
protected  Ion.IonType Ion.type
          Type of ion.
 

Methods in com.compomics.util.experiment.biology that return Ion.IonType
 Ion.IonType Ion.getType()
          Returns the ion type.
static Ion.IonType Ion.IonType.valueOf(String name)
          Returns the enum constant of this type with the specified name.
static Ion.IonType[] Ion.IonType.values()
          Returns an array containing the constants of this enum type, in the order they are declared.
 

Methods in com.compomics.util.experiment.biology that return types with arguments of type Ion.IonType
static ArrayList<Ion.IonType> Ion.getImplementedIonTypes()
          Returns the implemented ion types.
 

Methods in com.compomics.util.experiment.biology with parameters of type Ion.IonType
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.
static ArrayList<Integer> Ion.getPossibleSubtypes(Ion.IonType ionType)
          Returns an arraylist of possible subtypes.
static String Ion.getTypeAsString(Ion.IonType type)
          Returns the type of ion as string.
 

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

Method parameters in com.compomics.util.experiment.identification with type arguments of type Ion.IonType
 ArrayList<IonMatch> SpectrumAnnotator.getCurrentAnnotation(HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges)
          Returns the currently matched ions with the given settings.
 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.
 ArrayList<IonMatch> SpectrumAnnotator.getSpectrumAnnotation(HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, MSnSpectrum spectrum, Peptide peptide, double intensityLimit, double mzTolerance, boolean isPpm)
          Returns the spectrum annotations of a spectrum in a list of IonMatches.
 ArrayList<IonMatch> SpectrumAnnotator.matchPeak(Peptide peptide, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, ArrayList<Integer> charges, int precursorCharge, NeutralLossesMap neutralLosses, Peak peak)
          This method matches the potential fragment ions of a given peptide with a given peak.
 

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

Method parameters in com.compomics.util.experiment.identification.ptm with type arguments of type Ion.IonType
static HashMap<ArrayList<Integer>,Double> PTMLocationScores.getAScore(Peptide peptide, ArrayList<PTM> ptms, MSnSpectrum spectrum, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, ArrayList<Integer> charges, int precursorCharge, double mzTolerance)
          Returns the A-score for the best PTM location without accounting for neutral losses.
static HashMap<ArrayList<Integer>,Double> PTMLocationScores.getAScore(Peptide peptide, ArrayList<PTM> ptms, MSnSpectrum spectrum, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, double mzTolerance)
          Returns the A-score for the best PTM location accounting for neutral losses.
static HashMap<ArrayList<Integer>,Double> PTMLocationScores.getAScore(Peptide peptide, ArrayList<PTM> ptms, MSnSpectrum spectrum, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, double mzTolerance, boolean accountNeutralLosses)
          Returns the A-score for the best PTM location.
static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> PTMLocationScores.getPTMPlotData(Peptide peptide, PTM ptm, int nPTM, MSnSpectrum spectrum, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, double mzTolerance, double intensityLimit)
          Returns the PTM plot series in the JFreechart format for one PSM.
static PtmtableContent PTMLocationScores.getPTMTableContent(Peptide peptide, PTM ptm, int nPTM, MSnSpectrum spectrum, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, double mzTolerance, double intensityLimit)
          Get the PTM table content.
 

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

Method parameters in com.compomics.util.experiment.identification.scoring with type arguments of type Ion.IonType
static double PsmScores.getAScorePeptideScore(Peptide peptide, MSnSpectrum spectrum, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, double mzTolerance, boolean accountNeutralLosses)
          Returns a PSM score like the peptide score calculated for the A-score.
 

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

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

Uses of Ion.IonType in com.compomics.util.preferences
 

Methods in com.compomics.util.preferences that return types with arguments of type Ion.IonType
 HashMap<Ion.IonType,ArrayList<Integer>> AnnotationPreferences.getIonTypes()
          Returns the type of ions annotated.
 

Methods in com.compomics.util.preferences with parameters of type Ion.IonType
 void AnnotationPreferences.addIonType(Ion.IonType ionType)
          Adds a new ion type to annotate.
 void AnnotationPreferences.addIonType(Ion.IonType ionType, int subType)
          Adds a new ion type and subtype to annotate.
 



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