Modifier and Type | Method and Description |
---|---|
static Peptide |
Peptide.getNoModPeptide(Peptide peptide,
ArrayList<PTM> ptms)
Returns a version of the peptide which does not contain the inspected
PTMs.
|
Modifier and Type | Method and Description |
---|---|
void |
PTMFactory.checkFixedModifications(ModificationProfile modificationProfile,
Peptide peptide,
SequenceMatchingPreferences sequenceMatchingPreferences)
Removes the fixed modifications of the peptide and remaps the one
searched for according to the ModificationProfile.
|
HashMap<Integer,ArrayList<String>> |
PTMFactory.getExpectedPTMs(ModificationProfile modificationProfile,
Peptide peptide,
double modificationMass,
double ptmMassTolerance,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the expected modifications based on the modification profile, the
peptide found and the modification details.
|
HashMap<Integer,ArrayList<String>> |
PTMFactory.getExpectedPTMs(ModificationProfile modificationProfile,
Peptide peptide,
String ptmName,
Double ptmMassTolerance,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the names of the possibly expected modification based on the name
of the expected modification in a map where the PTM names are indexed by
their potential site on the sequence.
|
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> |
IonFactory.getFragmentIons(Peptide peptide)
This method returns the theoretic ions expected from a peptide.
|
static Peptide |
Peptide.getNoModPeptide(Peptide peptide,
ArrayList<PTM> ptms)
Returns a version of the peptide which does not contain the inspected
PTMs.
|
static String |
Peptide.getTaggedModifiedSequence(ModificationProfile modificationProfile,
Peptide peptide,
HashMap<Integer,ArrayList<String>> confidentModificationSites,
HashMap<Integer,ArrayList<String>> representativeAmbiguousModificationSites,
HashMap<Integer,ArrayList<String>> secondaryAmbiguousModificationSites,
HashMap<Integer,ArrayList<String>> fixedModificationSites,
boolean useHtmlColorCoding,
boolean includeHtmlStartEndTags,
boolean useShortName)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with PTM tags, e.g, <mox>.
|
boolean |
Peptide.isSameModificationStatus(Peptide anotherPeptide)
Indicates whether another peptide has the same variable modifications as
this peptide.
|
boolean |
Peptide.isSameSequence(Peptide anotherPeptide,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns a boolean indicating whether another peptide has the same
sequence as the given peptide
|
boolean |
Peptide.isSameSequenceAndModificationStatus(Peptide anotherPeptide,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether another peptide has the same sequence and modification
status without accounting for modification localization.
|
boolean |
Peptide.sameModificationsAs(Peptide anotherPeptide)
Indicates whether another peptide has the same modifications at the same
localization as this peptide.
|
boolean |
Peptide.sameModificationsAs(Peptide anotherPeptide,
ArrayList<String> ptms)
Indicates whether another peptide has the same modifications at the same
localization as this peptide.
|
Modifier and Type | Method and Description |
---|---|
Peptide |
PeptideAssumption.getPeptide()
Get the theoretic peptide.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<String> |
Identification.getProteinMatches(Peptide peptide)
Returns the keys of the protein matches where a peptide can be found.
|
boolean |
Identification.isUnique(Peptide peptide)
Indicates whether a peptide is found in a single protein match.
|
Constructor and Description |
---|
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.
|
Modifier and Type | Method and Description |
---|---|
Peptide |
PeptideMatch.getTheoreticPeptide()
Getter for the theoretic peptide.
|
Modifier and Type | Method and Description |
---|---|
static String |
ProteinMatch.getProteinMatchKey(Peptide peptide)
Convenience method which returns the protein key of a peptide.
|
void |
PeptideMatch.setTheoreticPeptide(Peptide theoreticPeptide)
Setter for the theoretic peptide.
|
Constructor and Description |
---|
PeptideMatch(Peptide peptide,
String matchKey)
Constructor for the peptide match.
|
PeptideMatch(Peptide peptide,
String spectrumMatchKey,
String matchKey)
Constructor for the peptide match.
|
ProteinMatch(Peptide peptide,
String peptideMatchKey)
Constructor for the protein match.
|
Modifier and Type | Method and Description |
---|---|
HashMap<Peptide,HashMap<String,ArrayList<Integer>>> |
ProteinTree.getProteinMapping(Tag tag,
SequenceMatchingPreferences sequenceMatchingPreferences,
Double massTolerance,
ArrayList<String> fixedModifications,
ArrayList<String> variableModifications,
boolean reportFixedPtms)
Returns the protein mappings for the given peptide sequence.
|
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,
SearchParameters searchParameters,
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,
SearchParameters searchParameters,
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,
SearchParameters searchParameters,
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 |
PrecursorAccuracy.getScore(Peptide peptide,
int identificationCharge,
Precursor precursor,
boolean ppm)
Scores the match between the given peptide and spectrum using the
precursor m/z accuracy.
|
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,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the A-score for the best PTM location accounting for neutral
losses.
|
static Double |
MDScore.getMDScore(SpectrumMatch spectrumMatch,
Peptide peptideCandidate,
ArrayList<String> ptms,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the MD score for the given peptide in a spectrum match.
|
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.
|
Modifier and Type | Method and Description |
---|---|
Peptide |
PeptideSpectrumAnnotator.getCurrentlyLoadedPeptide()
Returns the currently inspected peptide.
|
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.
|
static NeutralLossesMap |
PeptideSpectrumAnnotator.getDefaultLosses(Peptide peptide,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the possible neutral losses expected by default for a given
peptide.
|
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> |
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.
|
void |
PeptideSpectrumAnnotator.setPeptide(Peptide peptide,
int precursorCharge)
Sets a new peptide to match.
|
Modifier and Type | Method and Description |
---|---|
static HashMap<Integer,ArrayList<Peptide>> |
TagMatcher.getPeptideMatches(Tag tag,
String sequence,
int tagIndex,
int componentIndex,
SequenceMatchingPreferences sequenceMatchingPreferences,
double massTolerance,
ArrayList<String> fixedModifications,
ArrayList<String> variableModifications,
boolean reportFixedPtms)
Returns the possible peptides which can be created on this sequence
indexed by their start index.
|
Modifier and Type | Method and Description |
---|---|
HashMap<String,LinkedList<Peptide>> |
IdfileReader.getPeptidesMap()
Returns a map of all the peptides found in this file in a map indexed by
the beginning of the peptide sequence.
|
Modifier and Type | Method and Description |
---|---|
HashMap<String,LinkedList<Peptide>> |
PepxmlIdfileReader.getPeptidesMap() |
HashMap<String,LinkedList<Peptide>> |
PepNovoIdfileReader.getPeptidesMap() |
HashMap<String,LinkedList<Peptide>> |
MzIdentMLIdfileReader.getPeptidesMap() |
HashMap<String,LinkedList<Peptide>> |
MsAmandaIdfileReader.getPeptidesMap() |
HashMap<String,LinkedList<Peptide>> |
DirecTagIdfileReader.getPeptidesMap() |
HashMap<String,LinkedList<Peptide>> |
AndromedaIdfileReader.getPeptidesMap() |
Modifier and Type | Method and Description |
---|---|
void |
SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide,
ArrayList<IonMatch> annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showRewindTags)
Add reference areas annotating the de novo tags, using default percent
height of 0.9 for the forward ions and 1.0 for the reverse ions default
alpha levels of 0.2.
|
void |
SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide,
ArrayList<IonMatch> annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showRewindTags,
double forwardIonPercentHeight,
double rewindIonPercentHeight)
Add reference areas annotating the de novo tags, using default alpha
levels of 0.2.
|
void |
SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide,
ArrayList<IonMatch> annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showRewindTags,
double forwardIonPercentHeight,
double rewindIonPercentHeight,
boolean excludeFixedPtms)
Add reference areas annotating the de novo tags, using default alpha
levels of 0.2.
|
void |
SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide,
ArrayList<IonMatch> annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showRewindTags,
double forwardIonPercentHeight,
double rewindIonPercentHeight,
float forwardIonAlphaLevel,
float rewindIonAlphaLevel,
boolean excludeFixedPtms)
Add reference areas annotating the de novo tags.
|
Constructor and Description |
---|
FragmentIonTable(Peptide currentPeptide,
ArrayList<ArrayList<IonMatch>> allAnnotations,
ArrayList<MSnSpectrum> allSpectra,
HashSet<Integer> currentFragmentIonTypes,
NeutralLossesMap neutralLosses,
boolean singleCharge,
boolean twoCharges)
Creates a novel fragment ion table displaying bar charts with the
intensity of each fragment ion type.
|
FragmentIonTable(Peptide currentPeptide,
ArrayList<ArrayList<IonMatch>> allAnnotations,
HashSet<Integer> currentFragmentIonTypes,
NeutralLossesMap neutralLosses,
boolean singleCharge,
boolean twoCharges)
Creates a traditional fragment ion table with the theoretical mz values
and the detected fragment ions highlighted.
|
Modifier and Type | Method and Description |
---|---|
boolean |
IdFilter.validateModifications(Peptide peptide,
SequenceMatchingPreferences sequenceMatchingPreferences,
ModificationProfile modificationProfile)
Validates the modifications of a peptide.
|
boolean |
IdFilter.validatePeptide(Peptide peptide,
SequenceMatchingPreferences sequenceMatchingPreferences)
Validates the peptide based on the peptide length and share of Xs in the
sequence.
|
boolean |
IdFilter.validateProteins(Peptide peptide,
SequenceMatchingPreferences sequenceMatchingPreferences)
Validates a peptide depending on its protein inference status.
|
boolean |
IdFilter.validateProteins(Peptide peptide,
SequenceMatchingPreferences sequenceMatchingPreferences,
ProteinTree proteinTree)
Validates a peptide depending on its protein inference status.
|
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