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Packages that use Ion.IonType | |
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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 |
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Fields in com.compomics.util.experiment.biology declared as Ion.IonType | |
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protected Ion.IonType |
Ion.type
Type of ion. |
Methods in com.compomics.util.experiment.biology that return Ion.IonType | |
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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 | |
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static ArrayList<Ion.IonType> |
Ion.getImplementedIonTypes()
Returns the implemented ion types. |
Methods in com.compomics.util.experiment.biology with parameters of type Ion.IonType | |
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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 |
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Method parameters in com.compomics.util.experiment.identification with type arguments of type Ion.IonType | |
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HashMap<Integer,ArrayList<IonMatch>> |
SpectrumAnnotator.getCoveredAminoAcids(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 ion matches corresponding to fragment ions indexed by amino acid number in the sequence. |
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 |
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Method parameters in com.compomics.util.experiment.identification.ptm with type arguments of type Ion.IonType | |
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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 |
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Method parameters in com.compomics.util.experiment.identification.scoring with type arguments of type Ion.IonType | |
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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 |
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Method parameters in com.compomics.util.gui.spectrum with type arguments of type Ion.IonType | |
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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 | |
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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 |
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Methods in com.compomics.util.preferences that return types with arguments of type Ion.IonType | |
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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 | |
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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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