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<Software> |
PrideXmlControllerImpl.getSoftwares()
Get a list of software
|
List<Software> |
MzXmlControllerImpl.getSoftwares()
The softwares on mzXml are annotated with their names, the type, and the execution
time processing the data.
|
List<Software> |
MzTabControllerImpl.getSoftwares()
Get a list of software
|
List<Software> |
MzMLControllerImpl.getSoftwares()
Get a List of Softwares
|
List<Software> |
MzIdentMLControllerImpl.getSoftwares()
Get a list of softwares
|
List<Software> |
MzDataControllerImpl.getSoftwares()
Get a List of Software
|
Modifier and Type | Method and Description |
---|---|
static Software |
PrideXmlTransformer.transformSoftware(uk.ac.ebi.pride.jaxb.model.DataProcessing rawDataProcessing)
Transform an software object from pride xml format to core data model format.
|
static Software |
MzXmlTransformer.transformSoftware(uk.ac.ebi.pride.tools.mzxml_parser.mzxml.model.Software rawSoftware) |
static Software |
MzTabTransformer.transformSoftware(uk.ac.ebi.pride.jmztab.model.Software oldSoftware)
Transform a Software Object
|
static Software |
MzMLTransformer.transformSoftware(uk.ac.ebi.jmzml.model.mzml.Software oldSoftware)
Convert software
|
static Software |
MzIdentMLTransformer.transformToSoftware(uk.ac.ebi.jmzidml.model.mzidml.AnalysisSoftware oldSoftware) |
Modifier and Type | Method and Description |
---|---|
static List<Software> |
MzDataTransformer.transformSoftware(uk.ac.ebi.pride.tools.mzdata_parser.mzdata.model.Software oldSoftware)
Convert software list
|
static List<Software> |
MzMLTransformer.transformSoftwareList(uk.ac.ebi.jmzml.model.mzml.SoftwareList oldSoftwareList)
Convert software list
|
static List<Software> |
MzXmlTransformer.transformSoftwares(List<uk.ac.ebi.pride.tools.mzxml_parser.mzxml.model.Software> rawSoftwares) |
static List<Software> |
MzTabTransformer.transformSoftwares(Map<Integer,uk.ac.ebi.pride.jmztab.model.Software> dataSoftwares)
Transform a List of softwares
|
static List<Software> |
MzIdentMLTransformer.transformToSoftware(List<uk.ac.ebi.jmzidml.model.mzidml.AnalysisSoftware> oldSoftwares) |
Modifier and Type | Method and Description |
---|---|
Software |
Protocol.getAnalysisSoftware() |
Software |
Provider.getSoftware() |
Software |
ProcessingMethod.getSoftware() |
Software |
InstrumentConfiguration.getSoftware() |
Modifier and Type | Method and Description |
---|---|
List<Software> |
ExperimentMetaData.getSoftwares() |
Modifier and Type | Method and Description |
---|---|
void |
Protocol.setAnalysisSoftware(Software analysisSoftware) |
void |
Provider.setSoftware(Software software) |
void |
ProcessingMethod.setSoftware(Software software) |
void |
InstrumentConfiguration.setSoftware(Software software) |
Modifier and Type | Method and Description |
---|---|
void |
ExperimentMetaData.setSoftwares(List<Software> softwares) |
Constructor and Description |
---|
InstrumentConfiguration(String id,
ScanSetting scanSetting,
Software software,
List<InstrumentComponent> source,
List<InstrumentComponent> analyzer,
List<InstrumentComponent> detector,
ParamGroup params)
Constructor
|
ProcessingMethod(int order,
Software software,
ParamGroup params)
Constructor
|
Protocol(ParamGroup analysisParam,
Comparable id,
String name,
Software analysisSoftware,
ParamGroup threshold) |
Provider(Comparable id,
String name,
Software software,
Contact contact,
CvParam role) |
SpectrumIdentificationProtocol(Comparable id,
String name,
Software analysisSoftware,
ParamGroup analysisParam,
ParamGroup threshold,
ParamGroup searchType,
List<SearchModification> searchModifications,
boolean enzymeIndependent,
List<Enzyme> enzymes,
List<MassTable> massTables,
List<CvParam> fragmentTolerance,
List<CvParam> parentTolerance,
List<Filter> filters,
DataBaseTranslation dataBaseTranslation) |
SpectrumIdentificationProtocol(ParamGroup analysisParam,
Comparable id,
String name,
Software analysisSoftware,
ParamGroup threshold,
ParamGroup searchType,
List<SearchModification> searchModifications,
boolean enzymeIndependent,
List<Enzyme> enzymes,
List<MassTable> massTables,
List<CvParam> fragmentTolerance,
List<CvParam> parentTolerance,
List<Filter> filters,
DataBaseTranslation dataBaseTranslation) |
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.
|
Copyright © 2015 European Bioinformatics Institute. All Rights Reserved.