Modifier and Type | Method and Description |
---|---|
Map<SpectraData,File> |
ReferencedIdentificationController.checkMScontrollers(List<File> msIdentMLFiles)
Check if the ms File is supported and match with some of the par of the name in the Spectra Files
This method should be used in high-throughput, when you add different files.
|
List<SpectraData> |
MzTabControllerImpl.getSpectraDataFiles()
Get the List of File Spectra that the Mzidentml use to identified peptides
|
List<SpectraData> |
MzIdentMLControllerImpl.getSpectraDataFiles()
Get the List of File Spectra that the Mzidentml use to identified peptides
|
Map<SpectraData,DataAccessController> |
ReferencedIdentificationController.getSpectraDataMSControllers() |
Map<SpectraData,File> |
ReferencedIdentificationController.getSpectraDataMSFiles()
Get the Spectra Data Map with the corresponding File.
|
Modifier and Type | Method and Description |
---|---|
Integer |
ReferencedIdentificationController.getNumberOfSpectrabySpectraData(SpectraData spectraData)
Get the number of Spectra by File associated with the mzidentml
|
protected boolean |
ReferencedIdentificationController.isSpectraDataSupported(SpectraData spectraData) |
Modifier and Type | Method and Description |
---|---|
void |
ReferencedIdentificationController.addMSController(Map<SpectraData,File> spectraDataFileMap)
Check if the File format is supported and the spectrum Id and add a Set of DataAccessControllers.
|
boolean |
ReferencedIdentificationController.addNewMSController(Map<SpectraData,File> spectraDataFileMap,
Map<Comparable,File> newFiles,
Map<Comparable,String> fileTypes) |
Modifier and Type | Method and Description |
---|---|
static SpectraData |
MzIdentMLTransformer.transformToSpectraData(uk.ac.ebi.jmzidml.model.mzidml.SpectraData oldSpectraData,
boolean mgfTitle) |
Modifier and Type | Method and Description |
---|---|
static Map<Comparable,SpectraData> |
MzTabTransformer.transformMsRunMap(Map<Integer,uk.ac.ebi.pride.jmztab.model.MsRun> mRunMap) |
static List<SpectraData> |
MzIdentMLTransformer.transformToSpectraData(List<uk.ac.ebi.jmzidml.model.mzidml.SpectraData> oldSpectraDatas,
List<Comparable> usedTitle) |
Modifier and Type | Method and Description |
---|---|
SpectraData |
SpectrumIdentification.getSpectraData() |
Modifier and Type | Method and Description |
---|---|
List<SpectraData> |
ExperimentMetaData.getSpectraDatas() |
Modifier and Type | Method and Description |
---|---|
void |
SpectrumIdentification.setSpectraData(SpectraData spectraData) |
Modifier and Type | Method and Description |
---|---|
void |
ExperimentMetaData.setSpectraDatas(List<SpectraData> spectraDatas) |
Constructor and Description |
---|
SpectrumIdentification(Comparable id,
String name,
int chargeState,
double experimentalMassToCharge,
double calculatedMassToCharge,
double calculatedPI,
PeptideSequence peptideSequence,
int rank,
boolean passThreshold,
MassTable massTable,
Sample sample,
List<PeptideEvidence> peptideEvidenceList,
List<FragmentIon> fragmentation,
Score score,
Spectrum spectrum,
SpectraData spectraData)
Spectrum Identification Item
|
SpectrumIdentification(ParamGroup params,
Comparable id,
String name,
int chargeState,
double experimentalMassToCharge,
double calculatedMassToCharge,
double calculatedPI,
PeptideSequence peptideSequence,
int rank,
boolean passThreshold,
MassTable massTable,
Sample sample,
List<PeptideEvidence> peptideEvidenceList,
List<FragmentIon> fragmentation,
Score score,
Spectrum spectrum,
SpectraData spectraData)
Spectrum Identification Item
|
Constructor and Description |
---|
ExperimentMetaData(ParamGroup params,
Comparable id,
String name,
String version,
String shortLabel,
List<Sample> samples,
List<Software> softwares,
List<Person> persons,
List<SourceFile> sourceFiles,
Provider provider,
List<Organization> organizations,
List<Reference> references,
Date creationDate,
Date publicDate,
ExperimentProtocol protocol,
List<SpectraData> spectraDatas) |
ExperimentMetaData(ParamGroup params,
Comparable id,
String name,
String version,
String shortLabel,
List<Sample> samples,
List<Software> softwares,
List<Person> persons,
List<SourceFile> sourceFiles,
Provider provider,
List<Organization> organizations,
List<Reference> references,
Date creationDate,
Date publicDate,
ExperimentProtocol protocol,
List<SpectraData> spectraDatas,
Map<Comparable,StudyVariable> studyVariables)
This controller is specially designed for mzTab files that contains Study Variables with description, etc.
|
Modifier and Type | Method and Description |
---|---|
static Constants.SpecFileFormat |
Constants.getDataFormatFromFileExtension(SpectraData spectradata)
Return the Spectrum File format beased onf the SpectraData object name
|
static List<Constants.SpecFileFormat> |
Constants.getFileTypeSupported(SpectraData spectraData)
Return the set of file format supported for an ambiguous SpectraData Object
|
static String |
MzTabUtils.getOriginalSpectrumId(SpectraData spectraData,
String spectrumID) |
static Constants.SpecFileFormat |
MzTabUtils.getSpectraDataFormat(SpectraData spectraData) |
static Constants.SpecFileFormat |
Constants.getSpectraDataFormat(SpectraData spectraData)
This function returns the Spectrum File format for an specific SpectraData ob object
|
static Constants.SpecIdFormat |
MzTabUtils.getSpectraDataIdFormat(SpectraData spectraData) |
static Constants.SpecIdFormat |
MzIdentMLUtils.getSpectraDataIdFormat(SpectraData spectraData) |
static String |
MzTabUtils.getSpectrumId(SpectraData spectraData,
String spectrumID) |
Copyright © 2015 European Bioinformatics Institute. All Rights Reserved.