Modifier and Type | Method and Description |
---|---|
static Peptide |
DataAccessUtilities.getPeptide(Protein ident,
int index)
This is convenient method for accessing peptide.
|
Modifier and Type | Method and Description |
---|---|
static Map<PeptideEvidence,List<Peptide>> |
DataAccessUtilities.getPeptideEvidence(List<Peptide> peptides)
Get peptide Evidence for a Lis of Peptide Identifications
|
Modifier and Type | Method and Description |
---|---|
static int |
DataAccessUtilities.getNumberOfPTMs(Peptide peptide)
Get the number of the modification of a peptide
|
static int |
DataAccessUtilities.getNumberOfSubstitutionPTMs(Peptide peptide)
Get the number of substitution modification of a peptide
|
static boolean |
DataAccessUtilities.hasFragmentIon(Peptide peptide)
Check whether peptide has fragment ion information
|
Modifier and Type | Method and Description |
---|---|
static Map<PeptideEvidence,List<Peptide>> |
DataAccessUtilities.getPeptideEvidence(List<Peptide> peptides)
Get peptide Evidence for a Lis of Peptide Identifications
|
Modifier and Type | Method and Description |
---|---|
Peptide |
PeptideDataAccess.getPeptideByIndex(Comparable proteinId,
Comparable peptideId)
This is convenient method for accessing peptide.
|
Modifier and Type | Method and Description |
---|---|
List<Peptide> |
MzGraphDataAccess.getPeptidesBySpectrum(Comparable specId)
Retrieve the Identified Peptides related with one spectrum
|
Modifier and Type | Method and Description |
---|---|
Peptide |
CachedDataAccessController.getPeptideByIndex(Comparable proteinId,
Comparable index) |
Peptide |
AbstractDataAccessController.getPeptideByIndex(Comparable proteinId,
Comparable index) |
Peptide |
ReferencedIdentificationController.getPeptideByIndex(Comparable proteinId,
Comparable index,
boolean useCache)
Get peptide using a given identification id and a given peptide index
|
Peptide |
PrideXmlControllerImpl.getPeptideByIndex(Comparable proteinId,
Comparable index,
boolean useCache)
Get peptide using a given identification id and a given peptide index
|
Peptide |
CachedDataAccessController.getPeptideByIndex(Comparable proteinId,
Comparable index,
boolean useCache) |
Modifier and Type | Method and Description |
---|---|
List<Peptide> |
ReferencedIdentificationController.getPeptidesBySpectrum(Comparable specId)
Retrieve the Identified Peptides related with one spectrum
|
List<Peptide> |
CachedDataAccessController.getPeptidesBySpectrum(Comparable specId)
Retrieve the Identified Peptides related with one spectrum
|
List<Peptide> |
AbstractDataAccessController.getPeptidesBySpectrum(Comparable specId)
Retrieve the Identified Peptides related with one spectrum
|
Modifier and Type | Method and Description |
---|---|
static Peptide |
PrideXmlTransformer.transformPeptide(uk.ac.ebi.pride.jaxb.model.PeptideItem rawPeptide,
DBSequence dbSequence,
Comparable index)
Transform peptide from pride xml to core data model.
|
static Peptide |
MzTabTransformer.transformPeptide(uk.ac.ebi.pride.jmztab.model.PSM rawPeptide,
DBSequence dbSequence,
Comparable index,
uk.ac.ebi.pride.jmztab.model.Metadata metadata)
Transform peptide from pride xml to core data model.
|
Modifier and Type | Method and Description |
---|---|
static List<Peptide> |
MzIdentMLTransformer.transformToPeptideIdentificationsFromSpectrumItems(List<uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem> spectrumIdentificationItems) |
Modifier and Type | Class and Description |
---|---|
class |
QuantPeptide
Quantitative Peptide is a Peptide with Quantitation information and is used in mzTab file formats.
|
Modifier and Type | Method and Description |
---|---|
List<Peptide> |
Spectrum.getPeptide() |
List<Peptide> |
Protein.getPeptides() |
List<Peptide> |
SpectrumIdentificationList.getSpectrumIdentificationResultList() |
Modifier and Type | Method and Description |
---|---|
void |
Spectrum.setPeptide(List<Peptide> peptide) |
void |
Protein.setPeptides(List<Peptide> peptides) |
void |
SpectrumIdentificationList.setSpectrumIdentificationResultList(List<Peptide> spectrumIdentificationItemList) |
Constructor and Description |
---|
Protein(Comparable id,
String name,
DBSequence dbSequence,
boolean passThreshold,
List<Peptide> peptides,
Score score,
double threshold,
double sequenceCoverage,
Gel gel)
Constructor for Protein Entity Identification
|
Protein(ParamGroup params,
Comparable id,
String name,
DBSequence dbSequence,
boolean passThreshold,
List<Peptide> peptides,
Score score,
double threshold,
double sequenceCoverage,
Gel gel)
Constructor for Protein Entity Identification with CVParams
|
Protein(ParamGroup params,
Comparable id,
String name,
DBSequence dbSequence,
boolean passThreshold,
List<Peptide> peptides,
Score score,
double threshold,
double sequenceCoverage,
Gel gel,
QuantScore quantScore)
Constructor for Protein Entity Identification with CVParams and Quantitation Score based on mzTab model
|
Protein(ParamGroup params,
Comparable id,
String name,
DBSequence dbSequence,
boolean passThreshold,
List<Peptide> peptides,
Score score,
double threshold,
double sequenceCoverage,
Gel gel,
QuantScore quantScore,
List<QuantPeptide> quantPeptides)
Constructor for Protein Entity Identification with CVParams and Quantitation Score based on mzTab model
|
Spectrum(Comparable id,
String name,
int index,
DataProcessing defaultDataProcessing,
int defaultArrayLength,
List<BinaryDataArray> binaryDataArrays,
String spotID,
SourceFile sourceFile,
ScanList scanList,
List<Precursor> precursors,
List<ParamGroup> products,
List<Peptide> peptide) |
Spectrum(ParamGroup params,
Comparable id,
String name,
int index,
DataProcessing defaultDataProcessing,
int defaultArrayLength,
List<BinaryDataArray> binaryDataArrays,
String spotID,
SourceFile sourceFile,
ScanList scanList,
List<Precursor> precursors,
List<ParamGroup> products,
List<Peptide> peptide) |
SpectrumIdentificationList(Comparable id,
String name,
int numSequenceSearched,
List<IdentifiableParamGroup> fragmentationTable,
List<Peptide> spectrumIdentificationList) |
SpectrumIdentificationList(ParamGroup params,
Comparable id,
String name,
int numSequenceSearched,
List<IdentifiableParamGroup> fragmentationTable,
List<Peptide> spectrumIdentificationList) |
Modifier and Type | Method and Description |
---|---|
protected static String |
AbstractMzTabConverter.generateAccession(Peptide identification) |
Modifier and Type | Method and Description |
---|---|
protected void |
MzIdentMLMzTabConverter.loadModifications(uk.ac.ebi.pride.jmztab.model.Protein protein,
List<Peptide> items) |
protected uk.ac.ebi.pride.jmztab.model.Protein |
MzIdentMLMzTabConverter.loadProtein(Protein msProtein,
List<Peptide> peptides) |
protected List<uk.ac.ebi.pride.jmztab.model.PSM> |
MzIdentMLMzTabConverter.loadPSMs(Protein protein,
List<Peptide> peptides)
Converts the passed Identification object into an MzTab PSM.
|
Modifier and Type | Method and Description |
---|---|
List<Peptide> |
ThresholdPeptideFilter.filter(List<Peptide> peptides) |
List<Peptide> |
RankOnePeptideFilter.filter(List<Peptide> peptides) |
List<Peptide> |
PeptideFilter.filter(List<Peptide> peptides) |
List<Peptide> |
NoPeptideFilter.filter(List<Peptide> peptides) |
Modifier and Type | Method and Description |
---|---|
List<Peptide> |
ThresholdPeptideFilter.filter(List<Peptide> peptides) |
List<Peptide> |
RankOnePeptideFilter.filter(List<Peptide> peptides) |
List<Peptide> |
PeptideFilter.filter(List<Peptide> peptides) |
List<Peptide> |
NoPeptideFilter.filter(List<Peptide> peptides) |
Copyright © 2015 European Bioinformatics Institute. All Rights Reserved.