Package | Description |
---|---|
com.compomics.util.experiment.biology |
Experiment classes related to biological entities.
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com.compomics.util.experiment.identification |
Experiment classes related to identifications.
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com.compomics.util.experiment.identification.psm_scoring |
Main PSM scoring class.
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com.compomics.util.experiment.identification.psm_scoring.psm_scores |
Main PTM scoring classes.
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com.compomics.util.experiment.identification.ptm |
Additional PSM scoring classes.
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com.compomics.util.experiment.identification.ptm.ptmscores |
PTM scores.
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com.compomics.util.experiment.identification.spectrum_annotators |
Spectrum annotation.
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com.compomics.util.gui.spectrum |
Spectrum and Chromatogram visualization GUI classes.
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com.compomics.util.preferences |
Utilities preferences classes.
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Modifier and Type | Field and Description |
---|---|
protected Ion.IonType |
Ion.type
Type of ion.
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Modifier and Type | Method and Description |
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Ion.IonType |
Ion.getType()
Returns the ion type.
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static Ion.IonType |
Ion.IonType.valueOf(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.
|
Modifier and Type | Method and Description |
---|---|
static 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,
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.
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static String |
Ion.getTypeAsString(Ion.IonType type)
Returns the type of ion as string.
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Modifier and Type | Method and Description |
---|---|
abstract ArrayList<IonMatch> |
SpectrumAnnotator.getCurrentAnnotation(MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
boolean pickMostAccuratePeak)
Returns the currently matched ions with the given settings.
|
protected HashMap<Integer,ArrayList<Ion>> |
SpectrumAnnotator.getExpectedIons(HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge)
Returns the expected ions in a map indexed by the possible charges.
|
protected ArrayList<IonMatch> |
SpectrumAnnotator.matchPeak(HashMap<Ion.IonType,HashSet<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.
|
Modifier and Type | Method and Description |
---|---|
static double |
PsmScores.getDecreasingScore(Peptide peptide,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int identificationCharge,
ShotgunProtocol shotgunProtocol,
int scoreIndex)
Scores the match between the given peptide and spectrum using an m/z
fidelity score.
|
static double |
PsmScores.getScore(Peptide peptide,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int identificationCharge,
ShotgunProtocol shotgunProtocol,
int scoreIndex)
Scores the match between the given peptide and spectrum using an m/z
fidelity score.
|
static double |
PsmScores.getScore(Peptide peptide,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int identificationCharge,
ShotgunProtocol shotgunProtocol,
PsmScores psmScore)
Scores the match between the given peptide and spectrum using an m/z
fidelity score.
|
Modifier and Type | Method and Description |
---|---|
static double |
MS2MzFidelityScore.getScore(Peptide peptide,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int identificationCharge,
double mzTolerance)
Scores the match between the given peptide and spectrum using an m/z
fidelity score.
|
static double |
IntensityRankScore.getScore(Peptide peptide,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int identificationCharge,
double mzTolerance)
Scores the match between the given peptide and spectrum using the
intensity rank of the matched peaks.
|
static double |
ComplementarityScore.getScore(Peptide peptide,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int identificationCharge,
double mzTolerance)
Scores the match between the given peptide and spectrum using the
complementarity of the matched peaks.
|
static double |
AAMS2MzFidelityScore.getScore(Peptide peptide,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int identificationCharge,
double mzTolerance)
Scores the match between the given peptide and spectrum using an m/z
fidelity score.
|
static double |
AAIntensityRankScore.getScore(Peptide peptide,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int identificationCharge,
double mzTolerance)
Scores the match between the given peptide and spectrum using the
intensity rank of the matched peaks.
|
static double |
MS2MzFidelityScore.getScore(Peptide peptide,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int identificationCharge,
double mzTolerance,
PeptideSpectrumAnnotator peptideSpectrumAnnotator)
Scores the match between the given peptide and spectrum using an m/z
fidelity score.
|
static double |
IntensityRankScore.getScore(Peptide peptide,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int identificationCharge,
double mzTolerance,
PeptideSpectrumAnnotator peptideSpectrumAnnotator)
Scores the match between the given peptide and spectrum using the
intensity rank of the matched peaks.
|
static double |
ComplementarityScore.getScore(Peptide peptide,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int identificationCharge,
double mzTolerance,
PeptideSpectrumAnnotator peptideSpectrumAnnotator)
Scores the match between the given peptide and spectrum using the
complementarity of the matched peaks.
|
static double |
AAMS2MzFidelityScore.getScore(Peptide peptide,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int identificationCharge,
double mzTolerance,
PeptideSpectrumAnnotator peptideSpectrumAnnotator)
Scores the match between the given peptide and spectrum using an m/z
fidelity score.
|
static double |
AAIntensityRankScore.getScore(Peptide peptide,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int identificationCharge,
double mzTolerance,
PeptideSpectrumAnnotator peptideSpectrumAnnotator)
Scores the match between the given peptide and spectrum using the
intensity rank of the matched peaks.
|
Modifier and Type | Method and Description |
---|---|
static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> |
PtmtableContent.getPTMPlotData(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<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 |
PtmtableContent.getPTMTableContent(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
double intensityLimit)
Get the PTM table content.
|
Modifier and Type | Method and Description |
---|---|
static HashMap<Integer,Double> |
AScore.getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the A-score for the best PTM location without accounting for
neutral losses.
|
static HashMap<Integer,Double> |
AScore.getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the A-score for the best PTM location.
|
static HashMap<Integer,Double> |
AScore.getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator)
Returns the A-score for the best PTM location.
|
static HashMap<Integer,Double> |
AScore.getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator,
Integer rounding)
Returns the A-score for the best PTM location.
|
static HashMap<Integer,Double> |
AScore.getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the A-score for the best PTM location accounting for neutral
losses.
|
static HashMap<Integer,HashMap<Integer,Double>> |
AScore.getPositionToScoreMap(Peptide peptide,
Peptide noModPeptide,
ArrayList<Integer> possibleSites,
MSnSpectrum spectrum,
HashMap<Integer,MSnSpectrum> spectrumMap,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap scoringLossesMap,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
PeptideSpectrumAnnotator spectrumAnnotator,
PTM refPTM)
Returns a map PTM localization > score.
|
static HashMap<Integer,Double> |
PhosphoRS.getSequenceProbabilities(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the PhosphoRS sequence probabilities for the PTM possible
locations.
|
static HashMap<Integer,Double> |
PhosphoRS.getSequenceProbabilities(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator)
Returns the PhosphoRS sequence probabilities for the PTM possible
locations.
|
static HashMap<Integer,Double> |
PhosphoRS.getSequenceProbabilities(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator,
Integer ptmScoreScale)
Returns the PhosphoRS sequence probabilities for the PTM possible
locations.
|
Modifier and Type | Method and Description |
---|---|
HashMap<Integer,ArrayList<IonMatch>> |
PeptideSpectrumAnnotator.getCoveredAminoAcids(HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
MSnSpectrum spectrum,
Peptide peptide,
double intensityLimit,
double mzTolerance,
boolean isPpm,
boolean pickMostAccuratePeak)
Returns the ion matches corresponding to fragment ions indexed by amino
acid number in the sequence.
|
ArrayList<IonMatch> |
TagSpectrumAnnotator.getCurrentAnnotation(MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
boolean pickMostAccuratePeak) |
ArrayList<IonMatch> |
PeptideSpectrumAnnotator.getCurrentAnnotation(MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
boolean pickMostAccuratePeak) |
HashMap<Integer,ArrayList<Ion>> |
PeptideSpectrumAnnotator.getExpectedIons(HashMap<Ion.IonType,HashSet<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> |
PeptideSpectrumAnnotator.getSpectrumAnnotation(HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
MSnSpectrum spectrum,
Peptide peptide,
double intensityLimit,
double mzTolerance,
boolean isPpm,
boolean pickMostAccuratePeak)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
ArrayList<IonMatch> |
TagSpectrumAnnotator.getSpectrumAnnotation(HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
MSnSpectrum spectrum,
Tag tag,
double intensityLimit,
double mzTolerance,
boolean isPpm,
boolean pickMostAccuratePeak)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
ArrayList<IonMatch> |
PeptideSpectrumAnnotator.matchPeak(Peptide peptide,
HashMap<Ion.IonType,HashSet<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.
|
Modifier and Type | Method and Description |
---|---|
static Vector<SpectrumAnnotation> |
SpectrumPanel.filterAnnotations(Vector<SpectrumAnnotation> 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 and Description |
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IonLabelColorTableModel(HashMap<Ion.IonType,HashSet<Integer>> iontypes,
ArrayList<NeutralLoss> neutralLosses)
Constructor which sets a new table.
|
Modifier and Type | Method and Description |
---|---|
HashMap<Ion.IonType,HashSet<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.
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Copyright © 2014. All rights reserved.