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(PtmSettings modificationProfile,
Peptide peptide,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences)
Removes the fixed modifications of the peptide and remaps the one
searched for according to the ModificationProfile.
|
HashMap<Integer,ArrayList<String>> |
PTMFactory.getExpectedPTMs(PtmSettings modificationProfile,
Peptide peptide,
double modificationMass,
double ptmMassTolerance,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences)
Returns the expected modifications based on the modification profile, the
peptide found and the modification details.
|
HashMap<Integer,ArrayList<String>> |
PTMFactory.getExpectedPTMs(PtmSettings modificationProfile,
Peptide peptide,
String ptmName,
Double ptmMassTolerance,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences)
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 all the theoretic ions expected from a peptide.
|
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> |
IonFactory.getFragmentIons(Peptide peptide,
SpecificAnnotationSettings specificAnnotationSettings)
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.getPeptideModificationsAsString(Peptide peptide,
boolean variablePtms)
Returns the peptide modifications as a string.
|
static String |
Peptide.getTaggedModifiedSequence(PtmSettings 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 |
---|---|
HashSet<String> |
Identification.getProteinMatches(Peptide peptide)
Returns the keys of the protein matches where a peptide can be found.
|
boolean |
Identification.isUniqueInDatabase(Peptide peptide)
Indicates whether a peptide is found in a single protein match.
|
Modifier and Type | Method and Description |
---|---|
HashMap<Integer,ArrayList<Peptide>> |
TagMatcher.buildPeptides(String sequence,
ArrayList<SequenceSegment> nTermPossibleSequences,
String seedSequence,
ArrayList<SequenceSegment> cTermPossibleSequences,
HashMap<Integer,ArrayList<ModificationMatch>> modificationsAtIndex,
int mutationsAtIndex)
Builds the possible peptides based on the given terminal segments and the
seed sequence.
|
HashMap<Integer,ArrayList<Peptide>> |
TagMatcher.getPeptideMatches(Tag tag,
String accession,
String sequence,
Integer tagIndex,
Integer componentIndex,
double massTolerance)
Returns the possible peptides which can be created on this sequence
indexed by their start index.
|
Modifier and Type | Method and Description |
---|---|
boolean |
PeptideAssumptionFilter.validateModifications(Peptide peptide,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences,
PtmSettings modificationProfile)
Validates the modifications of a peptide.
|
boolean |
PeptideAssumptionFilter.validatePeptide(Peptide peptide,
SequenceMatchingPreferences sequenceMatchingPreferences,
Enzyme enzyme)
Validates the peptide based on the peptide length, the share of X's in
the sequence and the allowed number of missed cleavages.
|
boolean |
PeptideAssumptionFilter.validateProteins(Peptide peptide,
SequenceMatchingPreferences sequenceMatchingPreferences)
Validates a peptide depending on its protein inference status.
|
boolean |
PeptideAssumptionFilter.validateProteins(Peptide peptide,
SequenceMatchingPreferences sequenceMatchingPreferences,
ProteinTree proteinTree)
Validates a peptide depending on its protein inference status.
|
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.
|
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,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences,
Double massTolerance)
Returns the protein mappings for the given peptide sequence.
|
Modifier and Type | Method and Description |
---|---|
static double |
PsmScores.getDecreasingScore(Peptide peptide,
Integer peptideCharge,
MSnSpectrum spectrum,
ShotgunProtocol shotgunProtocol,
IdentificationParameters identificationParameters,
SpecificAnnotationSettings specificAnnotationPreferences,
int scoreIndex)
Scores the match between the given peptide and spectrum using the given
score.
|
static double |
PsmScores.getScore(Peptide peptide,
Integer peptideCharge,
MSnSpectrum spectrum,
ShotgunProtocol shotgunProtocol,
IdentificationParameters identificationParameters,
SpecificAnnotationSettings specificAnnotationPreferences,
int scoreIndex)
Scores the match between the given peptide and spectrum using the given
score.
|
static double |
PsmScores.getScore(Peptide peptide,
Integer peptideCharge,
MSnSpectrum spectrum,
ShotgunProtocol shotgunProtocol,
IdentificationParameters identificationParameters,
SpecificAnnotationSettings specificAnnotationPreferences,
PsmScores psmScore)
Scores the match between the given peptide and spectrum using the given
score.
|
Modifier and Type | Method and Description |
---|---|
static double |
PrecursorAccuracy.getScore(Peptide peptide,
int identificationCharge,
Precursor precursor,
boolean ppm,
int minIsotope,
int maxIsotope)
Scores the match between the given peptide and spectrum using the
precursor m/z accuracy.
|
static double |
MS2MzFidelityScore.getScore(Peptide peptide,
MSnSpectrum spectrum,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences)
Scores the match between the given peptide and spectrum using an m/z
fidelity score.
|
static double |
IntensityRankScore.getScore(Peptide peptide,
MSnSpectrum spectrum,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences)
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,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences)
Scores the match between the given peptide and spectrum using the
complementarity of the matched peaks.
|
static double |
AAMS2MzFidelityScore.getScore(Peptide peptide,
MSnSpectrum spectrum,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences)
Scores the match between the given peptide and spectrum using an m/z
fidelity score.
|
static double |
AAIntensityRankScore.getScore(Peptide peptide,
MSnSpectrum spectrum,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences)
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,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences,
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,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences,
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,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences,
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,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences,
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,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences,
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,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences)
Returns the PTM plot series in the JFreechart format for one PSM.
|
static PtmtableContent |
PtmtableContent.getPTMTableContent(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences)
Get the PTM table content.
|
Modifier and Type | Method and Description |
---|---|
static HashMap<Integer,Double> |
AScore.getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator)
Returns the A-score for the best PTM location.
|
static Double |
MDScore.getMDScore(ArrayList<SpectrumIdentificationAssumption> mascotAssumptions,
Peptide peptideCandidate,
ArrayList<String> ptms,
SequenceMatchingPreferences sequenceMatchingPreferences,
Integer rounding)
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,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences,
PeptideSpectrumAnnotator spectrumAnnotator,
PTM refPTM)
Returns a map PTM localization > score.
|
static HashMap<Integer,Double> |
PhosphoRS.getSequenceProbabilities(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences,
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(AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings,
MSnSpectrum spectrum,
Peptide peptide)
Returns the ion matches corresponding to fragment ions indexed by amino
acid number in the sequence.
|
static NeutralLossesMap |
PeptideSpectrumAnnotator.getDefaultLosses(Peptide peptide,
SequenceMatchingPreferences sequenceMatchingSettings,
SequenceMatchingPreferences ptmSequenceMatchingSettings)
Returns the possible neutral losses expected by default for a given
peptide.
|
HashMap<Integer,ArrayList<Ion>> |
PeptideSpectrumAnnotator.getExpectedIons(SpecificAnnotationSettings specificAnnotationSettings,
Peptide peptide)
Returns the expected ions in a map indexed by the possible charges.
|
HashMap<Integer,ArrayList<Ion>> |
PeptideSpectrumAnnotator.getExpectedIons(SpecificAnnotationSettings specificAnnotationSettings,
Peptide peptide,
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons)
Returns the expected ions in a map indexed by the possible charges.
|
ArrayList<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings,
MSnSpectrum spectrum,
Peptide peptide)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
ArrayList<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings,
MSnSpectrum spectrum,
Peptide peptide,
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
ArrayList<IonMatch> |
PeptideSpectrumAnnotator.matchPeak(Peptide peptide,
SpecificAnnotationSettings specificAnnotationSettings,
Peak peak)
This method matches the potential fragment ions of a given peptide with a
given peak according to the annotation settings.
|
void |
PeptideSpectrumAnnotator.setPeptide(Peptide peptide,
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons,
int precursorCharge,
SpecificAnnotationSettings specificAnnotationSettings)
Sets a new peptide to match.
|
void |
PeptideSpectrumAnnotator.setPeptide(Peptide peptide,
int precursorCharge,
SpecificAnnotationSettings specificAnnotationSettings)
Sets a new peptide to match.
|
Modifier and Type | Method and Description |
---|---|
Peptide |
PeptideAssumption.getPeptide()
Get the theoretic peptide.
|
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 |
---|---|
void |
SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide,
ArrayList<IonMatch> annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showRewindTags,
boolean mirrored)
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,
ArrayList<float[]> alphaLevels,
boolean excludeFixedPtms,
boolean mirrored)
Add reference areas annotating the de novo tags.
|
void |
SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide,
ArrayList<IonMatch> annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showRewindTags,
double forwardIonPercentHeight,
double rewindIonPercentHeight,
boolean mirrored)
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,
boolean mirrored)
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,
ArrayList<float[]> alphaLevels,
boolean excludeFixedPtms,
boolean mirrored)
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.
|
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