Package | Description |
---|---|
uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl | |
uk.ac.ebi.pride.utilities.data.controller.impl.Transformer | |
uk.ac.ebi.pride.utilities.data.core |
Modifier and Type | Method and Description |
---|---|
List<SourceFile> |
PrideXmlControllerImpl.getSourceFiles()
Get a list of source files.
|
List<SourceFile> |
MzXmlControllerImpl.getSourceFiles()
Get a list of Source Files.
|
List<SourceFile> |
MzTabControllerImpl.getSourceFiles()
Get a list of source files.
|
List<SourceFile> |
MzMLControllerImpl.getSourceFiles()
Get a List of SourceFiles
|
List<SourceFile> |
MzIdentMLControllerImpl.getSourceFiles()
Get a list of source files.
|
List<SourceFile> |
MzDataControllerImpl.getSourceFiles()
Get the information of SourceFiles.
|
Modifier and Type | Method and Description |
---|---|
static SourceFile |
PrideXmlTransformer.transformSourceFile(uk.ac.ebi.pride.jaxb.model.Admin rawAdmin)
Transform source file from pride xml to core data model
|
static SourceFile |
MzTabTransformer.transformSourceFile(uk.ac.ebi.pride.jmztab.model.MsRun msRun)
Convert an msRun to SourceFile
|
Modifier and Type | Method and Description |
---|---|
static List<SourceFile> |
MzMLTransformer.transformFileDescriptionToFileSource(uk.ac.ebi.jmzml.model.mzml.FileDescription rawFileDescription)
Transform FileDescription object to List of SourceFile
|
static List<SourceFile> |
MzXmlTransformer.transformFileSources(List<uk.ac.ebi.pride.tools.mzxml_parser.mzxml.model.ParentFile> rawParentFiles) |
static List<SourceFile> |
MzMLTransformer.transformSourceFileList(uk.ac.ebi.jmzml.model.mzml.SourceFileList oldSourceFileList)
Convert source file list
|
static List<SourceFile> |
MzTabTransformer.transformSourceFiles(Map<Integer,uk.ac.ebi.pride.jmztab.model.MsRun> msRunMap) |
static List<SourceFile> |
MzDataTransformer.transformToFileSource(uk.ac.ebi.pride.tools.mzdata_parser.mzdata.model.SourceFile oldSourceFile)
Transform FileDescription object to List of SourceFile
|
static List<SourceFile> |
MzIdentMLTransformer.transformToSourceFile(List<uk.ac.ebi.jmzidml.model.mzidml.SourceFile> oldSourceFiles) |
Modifier and Type | Method and Description |
---|---|
SourceFile |
Spectrum.getSourceFile() |
SourceFile |
Scan.getSourceFile() |
SourceFile |
Precursor.getSourceFile() |
Modifier and Type | Method and Description |
---|---|
List<SourceFile> |
ScanSetting.getSourceFile() |
List<SourceFile> |
ExperimentMetaData.getSourceFiles() |
Modifier and Type | Method and Description |
---|---|
void |
Spectrum.setSourceFile(SourceFile sourceFile) |
void |
Scan.setSourceFile(SourceFile sourceFile) |
void |
Precursor.setSourceFile(SourceFile sourceFile) |
Modifier and Type | Method and Description |
---|---|
void |
ScanSetting.setSourceFile(List<SourceFile> sourceFile) |
void |
ExperimentMetaData.setSourceFiles(List<SourceFile> sourceFiles) |
Constructor and Description |
---|
Precursor(Spectrum spectrum,
SourceFile sourceFile,
String externalSpectrumID,
ParamGroup isolationWindow,
List<ParamGroup> selectedIon,
ParamGroup activation)
Constructor
|
Scan(String spectrumRef,
String externalSpecRef,
SourceFile sourceFile,
InstrumentConfiguration instrumentConfiguration,
List<ParamGroup> scanWindows,
ParamGroup params)
Constructor
|
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) |
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) |
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) |
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.
|
ScanSetting(String id,
List<SourceFile> sourceFile,
List<ParamGroup> targets,
ParamGroup params)
Constructor
|
Copyright © 2015 European Bioinformatics Institute. All Rights Reserved.