Modifier and Type | Method and Description |
---|---|
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,
SpecificAnnotationParameters specificAnnotationSettings)
This method returns the theoretic ions expected from a peptide.
|
Modifier and Type | Method and Description |
---|---|
Peptide |
Peptide.getNoModPeptide(HashSet<String> forbiddenModifications)
Returns a version of the peptide which does not contain the given list of
modifications.
|
Modifier and Type | Method and Description |
---|---|
boolean |
Peptide.isSameModificationStatus(Peptide anotherPeptide)
Indicates whether another peptide has the same variable modifications as
this peptide.
|
boolean |
Peptide.isSameSequence(Peptide anotherPeptide,
SequenceMatchingParameters sequenceMatchingPreferences)
Returns a boolean indicating whether another peptide has the same
sequence as the given peptide
|
boolean |
Peptide.isSameSequenceAndModificationStatus(Peptide anotherPeptide,
SequenceMatchingParameters 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> modifications)
Indicates whether another peptide has the same modifications at the same
localization as this peptide.
|
Modifier and Type | Method and Description |
---|---|
HashSet<Long> |
Identification.getProteinMatches(Peptide peptide)
Returns the keys of the protein matches where a peptide can be found.
|
Modifier and Type | Method and Description |
---|---|
boolean |
PeptideAssumptionFilter.validateModifications(Peptide peptide,
SequenceMatchingParameters sequenceMatchingPreferences,
SequenceMatchingParameters modificationSequenceMatchingPreferences,
ModificationParameters modificationProfile)
Verifies that the definition of every modification name is available.
|
boolean |
PeptideAssumptionFilter.validatePeptide(Peptide peptide,
SequenceMatchingParameters sequenceMatchingPreferences,
DigestionParameters digestionPreferences)
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,
SequenceMatchingParameters sequenceMatchingPreferences,
SequenceProvider sequenceProvider)
Validates a peptide depending on its protein inference status.
|
Modifier and Type | Method and Description |
---|---|
Peptide |
PeptideMatch.getPeptide()
Getter for the peptide.
|
Modifier and Type | Method and Description |
---|---|
static long |
ProteinMatch.getProteinMatchKey(Peptide peptide)
Convenience method which returns the protein key from a peptide.
|
void |
PeptideMatch.setPeptide(Peptide peptide)
Setter for the peptide.
|
Constructor and Description |
---|
PeptideMatch(Peptide peptide,
long matchKey,
long spectrumMatchKey)
Constructor for the peptide match.
|
ProteinMatch(Peptide peptide,
long peptideMatchKey)
Constructor for the protein match.
|
Modifier and Type | Method and Description |
---|---|
static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> |
ModificationtableContent.getModificationPlotData(Peptide peptide,
Modification modification,
int nMod,
Spectrum spectrum,
AnnotationParameters annotationPreferences,
SpecificAnnotationParameters specificAnnotationPreferences)
Returns the modification plot series in the JFreechart format for one
PSM.
|
Modifier and Type | Method and Description |
---|---|
static Double |
MDScore.getMDScore(ArrayList<SpectrumIdentificationAssumption> mascotAssumptions,
Peptide peptideCandidate,
ArrayList<String> ptms,
SequenceMatchingParameters sequenceMatchingPreferences,
Integer rounding)
Returns the MD score for the given peptide in a spectrum match.
|
static HashMap<Integer,Double> |
PhosphoRS.getSequenceProbabilities(Peptide peptide,
ArrayList<Modification> modifications,
Spectrum spectrum,
SequenceProvider sequenceProvider,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
boolean accountNeutralLosses,
SequenceMatchingParameters sequenceMatchingPreferences,
SequenceMatchingParameters modificationSequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator)
Returns the PhosphoRS sequence probabilities for the modification
possible locations.
|
Modifier and Type | Method and Description |
---|---|
int[] |
FeaturesGenerator.getComplementaryIonsFeatures(Peptide peptide,
int charge,
int ionIndex)
Returns the ms2pip features for the complementary ions of the given
peptide at the given charge.
|
int[] |
FeaturesGenerator.getForwardIonsFeatures(Peptide peptide,
int charge,
int ionIndex)
Returns the ms2pip features for the forward ions of the given peptide at
the given charge.
|
Modifier and Type | Method and Description |
---|---|
static Collection<Peptide> |
PeptideProteinMapping.getPeptides(ArrayList<PeptideProteinMapping> peptideProteinMappings,
SequenceMatchingParameters sequenceMatchingPreferences)
Aggregates the given mapping into a list of peptides.
|
Modifier and Type | Method and Description |
---|---|
Peptide |
PeptideWithPosition.getPeptide()
Returns the peptide.
|
Peptide |
PeptideDraft.getPeptide(double massMin,
double massMax)
Returns a peptide from the peptide draft.
|
Peptide |
PeptideDraft.getPeptide(double massMin,
double massMax,
BoxedObject<Boolean> smallMass)
Returns a peptide from the peptide draft.
|
Peptide |
ProteinIteratorUtils.getPeptideFromProtein(char[] proteinSequence,
int indexOnProtein,
double massMin,
double massMax)
Returns a peptide from the given sequence.
|
Peptide |
ProteinIteratorUtils.getPeptideFromProtein(char[] peptideSequence,
String proteinSequence,
int indexOnProtein,
Double massMin,
Double massMax)
Returns a peptide from the given sequence on the given protein.
|
Peptide |
ProteinIteratorUtils.getPeptideFromProtein(char[] peptideSequence,
String proteinSequence,
int indexOnProtein,
Double massMin,
Double massMax,
BoxedObject<Boolean> smallMass)
Returns a peptide from the given sequence on the given protein.
|
Constructor and Description |
---|
PeptideWithPosition(Peptide peptide,
int position)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
double |
PsmScoresEstimator.getDecreasingScore(Peptide peptide,
Integer peptideCharge,
Spectrum spectrum,
IdentificationParameters identificationParameters,
SpecificAnnotationParameters specificAnnotationPreferences,
PeptideSpectrumAnnotator peptideSpectrumAnnotator,
int scoreIndex)
Scores the match between the given peptide and spectrum using the given
score.
|
double |
PsmScoresEstimator.getScore(Peptide peptide,
Integer peptideCharge,
Spectrum spectrum,
IdentificationParameters identificationParameters,
SpecificAnnotationParameters specificAnnotationPreferences,
PeptideSpectrumAnnotator peptideSpectrumAnnotator,
int scoreIndex)
Scores the match between the given peptide and spectrum using the given
score.
|
double |
PsmScoresEstimator.getScore(Peptide peptide,
Integer peptideCharge,
Spectrum spectrum,
IdentificationParameters identificationParameters,
SpecificAnnotationParameters specificAnnotationPreferences,
PeptideSpectrumAnnotator peptideSpectrumAnnotator,
PsmScore psmScore)
Scores the match between the given peptide and spectrum using the given
score.
|
Modifier and Type | Method and Description |
---|---|
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.
|
double |
HyperScore.getScore(Peptide peptide,
int charge,
Spectrum spectrum,
ArrayList<IonMatch> ionMatches)
Returns the hyperscore.
|
double |
SnrScore.getScore(Peptide peptide,
Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
PeptideSpectrumAnnotator peptideSpectrumAnnotator)
Returns the score.
|
double |
HyperScore.getScore(Peptide peptide,
Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
PeptideSpectrumAnnotator peptideSpectrumAnnotator)
Returns the hyperscore.
|
double |
SnrScore.getScore(Peptide peptide,
Spectrum spectrum,
ArrayList<IonMatch> ionMatchesList)
Returns the score.
|
double |
SnrScore.getScore(Peptide peptide,
Spectrum spectrum,
HashMap<Double,ArrayList<IonMatch>> ionMatches)
Returns the score.
|
Constructor and Description |
---|
FragmentAnnotator(Peptide peptide,
SimplePeptideAnnotator.IonSeries ionSeries)
Constructor.
|
FragmentAnnotator(Peptide peptide,
SimplePeptideAnnotator.IonSeries ionSeries,
boolean forward,
boolean complementary)
Constructor.
|
FragmentAnnotatorNL(Peptide peptide,
SimplePeptideAnnotator.IonSeries ionSeries,
boolean sequenceDependent)
Constructor.
|
FragmentAnnotatorNL(Peptide peptide,
SimplePeptideAnnotator.IonSeries ionSeries,
boolean sequenceDependent,
boolean forward,
boolean complementary)
Constructor.
|
PrecursorAnnotator(Peptide peptide)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
Peptide |
PeptideSpectrumAnnotator.getCurrentlyLoadedPeptide()
Returns the currently inspected peptide.
|
Modifier and Type | Method and Description |
---|---|
Map<Integer,ArrayList<IonMatch>> |
PeptideSpectrumAnnotator.getCoveredAminoAcids(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
Spectrum spectrum,
Peptide peptide,
boolean useIntensityFilter)
Returns the ion matches corresponding to fragment ions indexed by amino
acid number in the sequence.
|
static NeutralLossesMap |
PeptideSpectrumAnnotator.getDefaultLosses(Peptide peptide)
Returns the possible neutral losses expected by default for a given
peptide.
|
HashMap<Integer,ArrayList<Ion>> |
PeptideSpectrumAnnotator.getExpectedIons(SpecificAnnotationParameters specificAnnotationSettings,
Peptide peptide)
Returns the expected ions in a map indexed by the possible charges.
|
HashMap<Integer,ArrayList<Ion>> |
PeptideSpectrumAnnotator.getExpectedIons(SpecificAnnotationParameters specificAnnotationSettings,
Peptide peptide,
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons)
Returns the expected ions in a map indexed by the possible charges.
|
java.util.stream.Stream<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
Spectrum spectrum,
Peptide peptide)
Returns the spectrum annotations of a spectrum in a list of IonMatches
using the intensity filter.
|
ArrayList<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
Spectrum spectrum,
Peptide peptide,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
java.util.stream.Stream<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
Spectrum spectrum,
Peptide peptide,
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
java.util.stream.Stream<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotationStream(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
Spectrum spectrum,
Peptide peptide,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
ArrayList<IonMatch> |
PeptideSpectrumAnnotator.matchPeak(Peptide peptide,
SpecificAnnotationParameters 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,
SpecificAnnotationParameters specificAnnotationSettings)
Sets a new peptide to annotate.
|
void |
PeptideSpectrumAnnotator.setPeptide(Peptide peptide,
int precursorCharge,
SpecificAnnotationParameters specificAnnotationSettings)
Sets a new peptide to annotate.
|
Constructor and Description |
---|
SimplePeptideAnnotator(Peptide peptide,
int charge,
AnnotationParameters annotationSettings)
Constructor.
|
SimplePeptideAnnotator(Peptide peptide,
int charge,
boolean a,
boolean b,
boolean c,
boolean x,
boolean y,
boolean z,
boolean precursor,
boolean immonium,
boolean related,
boolean reporter,
boolean neutralLosses,
boolean neutralLossesSequenceDependent,
ReporterIon[] reporterIons)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
Peptide |
PeptideAssumption.getPeptide()
Get the theoretic peptide.
|
Modifier and Type | Method and Description |
---|---|
void |
PeptideAssumption.setPeptide(Peptide peptide) |
Constructor and Description |
---|
PeptideAssumption(Peptide peptide,
int identificationCharge)
Constructor for a simple peptide assumption containing only the
information necessary for spectrum annotation.
|
PeptideAssumption(Peptide peptide,
int rank,
int advocate,
int identificationCharge,
double score)
Constructor for a peptide assumption.
|
PeptideAssumption(Peptide peptide,
int rank,
int advocate,
int identificationCharge,
double score,
String identificationFile)
Constructor for a peptide assumption.
|
Modifier and Type | Method and Description |
---|---|
static TreeMap<String,String[]> |
PeptideUtils.getAaAfter(Peptide peptide,
int nAa,
SequenceProvider sequenceProvider)
Returns the amino acids before the given peptide as a string in a map
based on the peptide protein mapping.
|
static String |
PeptideUtils.getAaAfter(Peptide peptide,
String accession,
int index,
int nAa,
SequenceProvider sequenceProvider)
Returns the amino acids before the given peptide as a string.
|
static TreeMap<String,String[]> |
PeptideUtils.getAaBefore(Peptide peptide,
int nAa,
SequenceProvider sequenceProvider)
Returns the amino acids before the given peptide as a string in a map
based on the peptide protein mapping.
|
static String |
PeptideUtils.getAaBefore(Peptide peptide,
String accession,
int index,
int nAa,
SequenceProvider sequenceProvider)
Returns the amino acids before the given peptide as a string in a map
based on the peptide protein mapping.
|
static String |
PeptideUtils.getPeptideModificationsAsString(Peptide peptide,
boolean variable)
Returns the peptide modifications as a string.
|
static String |
PeptideUtils.getTaggedModifiedSequence(Peptide peptide,
ModificationParameters modificationProfile,
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 Modification tags, e.g,
<mox>.
|
static boolean |
PeptideUtils.isDecoy(Peptide peptide,
SequenceProvider sequenceProvider)
Returns a boolean indicating whether the peptide matches a decoy
sequence.
|
static boolean |
PeptideUtils.isEnzymatic(Peptide peptide,
SequenceProvider sequenceProvider,
ArrayList<Enzyme> enzymes)
Returns a boolean indicating whether the peptide is enzymatic in at least one protein using one of the given enzymes.
|
static boolean |
PeptideUtils.isEnzymatic(Peptide peptide,
String proteinAccession,
String proteinSequence,
ArrayList<Enzyme> enzymes)
Returns a boolean indicating whether the peptide is enzymatic using one of the given enzymes.
|
static boolean |
PeptideUtils.isVariant(Peptide peptide,
String accession)
Returns a boolean indicating whether the peptide needs variants to be mapped to the given protein.
|
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 excludeFixedModifications,
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 excludeFixedModifications,
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 excludeFixedModifications,
boolean mirrored)
Add reference areas annotating the de novo tags.
|
Constructor and Description |
---|
FragmentIonTable(Peptide currentPeptide,
ArrayList<ArrayList<IonMatch>> allAnnotations,
ArrayList<Spectrum> 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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