Package | Description |
---|---|
com.compomics.util.experiment.biology |
This package contains experiement classes related to biological entities.
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com.compomics.util.experiment.identification |
This package contains experiment classes related to identifications.
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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.
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com.compomics.util.preferences |
Modifier and Type | Field and Description |
---|---|
protected Ion.IonType |
Ion.type
Type of ion.
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Modifier and Type | Method and Description |
---|---|
Ion.IonType |
Ion.getType()
Returns the ion type.
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static Ion.IonType |
Ion.IonType.valueOf(java.lang.String name)
Returns the enum constant of this type with the specified name.
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static Ion.IonType[] |
Ion.IonType.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
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Modifier and Type | Method and Description |
---|---|
static java.util.ArrayList<Ion.IonType> |
Ion.getImplementedIonTypes()
Returns the implemented ion types.
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Modifier and Type | Method and Description |
---|---|
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,
java.util.ArrayList<NeutralLoss> neutralLosses)
Convenience method returning a generic ion based on the given ion type.
|
static java.util.ArrayList<java.lang.Integer> |
Ion.getPossibleSubtypes(Ion.IonType ionType)
Returns an arraylist of possible subtypes.
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static java.lang.String |
Ion.getTypeAsString(Ion.IonType type)
Returns the type of ion as string.
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Modifier and Type | Method and Description |
---|---|
java.util.HashMap<java.lang.Integer,java.util.ArrayList<IonMatch>> |
SpectrumAnnotator.getCoveredAminoAcids(java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.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.
|
java.util.ArrayList<IonMatch> |
SpectrumAnnotator.getCurrentAnnotation(java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.Integer> charges)
Returns the currently matched ions with the given settings.
|
java.util.HashMap<java.lang.Integer,java.util.ArrayList<Ion>> |
SpectrumAnnotator.getExpectedIons(java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
Peptide peptide)
Returns the expected ions in a map indexed by the possible charges.
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java.util.ArrayList<IonMatch> |
SpectrumAnnotator.getSpectrumAnnotation(java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.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.
|
java.util.ArrayList<IonMatch> |
SpectrumAnnotator.matchPeak(Peptide peptide,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
NeutralLossesMap neutralLosses,
Peak peak)
This method matches the potential fragment ions of a given peptide with a
given peak.
|
Modifier and Type | Method and Description |
---|---|
static java.util.HashMap<java.util.ArrayList<java.lang.Integer>,java.lang.Double> |
PTMLocationScores.getAScore(Peptide peptide,
java.util.ArrayList<PTM> ptms,
MSnSpectrum spectrum,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
double mzTolerance)
Returns the A-score for the best PTM location without accounting for
neutral losses.
|
static java.util.HashMap<java.util.ArrayList<java.lang.Integer>,java.lang.Double> |
PTMLocationScores.getAScore(Peptide peptide,
java.util.ArrayList<PTM> ptms,
MSnSpectrum spectrum,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
double mzTolerance)
Returns the A-score for the best PTM location accounting for neutral
losses.
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static java.util.HashMap<java.util.ArrayList<java.lang.Integer>,java.lang.Double> |
PTMLocationScores.getAScore(Peptide peptide,
java.util.ArrayList<PTM> ptms,
MSnSpectrum spectrum,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses)
Returns the A-score for the best PTM location.
|
static java.util.HashMap<PeptideFragmentIon,java.util.ArrayList<IonMatch>> |
PTMLocationScores.getPTMPlotData(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.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,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
double mzTolerance,
double intensityLimit)
Get the PTM table content.
|
Modifier and Type | Method and Description |
---|---|
static double |
PsmScores.getAScorePeptideScore(Peptide peptide,
MSnSpectrum spectrum,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses)
Returns a PSM score like the peptide score calculated for the A-score.
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Modifier and Type | Method and Description |
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static java.util.Vector<DefaultSpectrumAnnotation> |
SpectrumPanel.filterAnnotations(java.util.Vector<DefaultSpectrumAnnotation> annotations,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
java.util.ArrayList<NeutralLoss> neutralLosses,
boolean singleChargeSelected,
boolean doubleChargeSelected,
boolean moreThanTwoChargesSelected)
Deprecated.
don't use method based on the peak labels but on the data
type
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Constructor and Description |
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IonLabelColorTableModel(java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
java.util.ArrayList<NeutralLoss> neutralLosses)
Constructor which sets a new table.
|
Modifier and Type | Method and Description |
---|---|
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> |
AnnotationPreferences.getIonTypes()
Returns the type of ions annotated.
|
Modifier and Type | Method and Description |
---|---|
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.
|
Copyright © 2013. All Rights Reserved.