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<Sample> |
PrideXmlControllerImpl.getSamples()
Get a list of samples
|
List<Sample> |
MzTabControllerImpl.getSamples()
Get a list of samples
|
List<Sample> |
MzMLControllerImpl.getSamples()
Get a list of samples by checking the cache first
|
List<Sample> |
MzIdentMLControllerImpl.getSamples()
Get a list of samples
|
List<Sample> |
MzDataControllerImpl.getSamples()
Get a list of samples by checking the cache first
|
Collection<Sample> |
AbstractDataAccessController.getSamples() |
Modifier and Type | Method and Description |
---|---|
static Sample |
PrideXmlTransformer.transformSample(uk.ac.ebi.pride.jaxb.model.Admin rawAdmin)
Transform sample from pride xml format to core data model format
|
static Sample |
MzMLTransformer.transformSample(uk.ac.ebi.jmzml.model.mzml.Sample oldSample)
Convert sample
|
static Sample |
MzIdentMLTransformer.transformToSample(uk.ac.ebi.jmzidml.model.mzidml.Sample oldSample) |
Modifier and Type | Method and Description |
---|---|
static List<Sample> |
MzDataTransformer.transformSampleList(uk.ac.ebi.pride.tools.mzdata_parser.mzdata.model.Admin oldSampleDescription)
Convert sample list
|
static List<Sample> |
MzMLTransformer.transformSampleList(uk.ac.ebi.jmzml.model.mzml.SampleList oldSampleList)
Convert sample list
|
static List<Sample> |
MzTabTransformer.transformSamples(Map<Integer,uk.ac.ebi.pride.jmztab.model.Sample> oldSamples,
uk.ac.ebi.pride.jmztab.model.Metadata metadata,
boolean hasQuantitation) |
static List<Sample> |
MzIdentMLTransformer.transformSubSampleToSample(List<uk.ac.ebi.jmzidml.model.mzidml.SubSample> oldSamples) |
static List<Sample> |
MzIdentMLTransformer.transformToSample(List<uk.ac.ebi.jmzidml.model.mzidml.Sample> oldSamples)
Transform old Samples to Samples
|
Modifier and Type | Method and Description |
---|---|
Sample |
SpectrumIdentification.getSample() |
Sample |
Assay.getSample() |
Modifier and Type | Method and Description |
---|---|
List<Sample> |
Sample.getParentSample() |
List<Sample> |
StudyVariable.getSamples() |
List<Sample> |
ExperimentMetaData.getSamples() |
Modifier and Type | Method and Description |
---|---|
void |
SpectrumIdentification.setSample(Sample sample) |
void |
Assay.setSample(Sample sample) |
Modifier and Type | Method and Description |
---|---|
void |
Sample.setParentSample(List<Sample> subSamples) |
void |
StudyVariable.setSamples(List<Sample> samples) |
void |
ExperimentMetaData.setSamples(List<Sample> samples) |
Constructor and Description |
---|
Assay(Comparable id,
String name,
Sample sample) |
Assay(ParamGroup params,
Comparable id,
String name,
Sample sample) |
Assay(ParamGroup params,
Comparable id,
String name,
Sample sample,
CvParam reagent) |
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) |
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.
|
Sample(ParamGroup params,
String id,
String name,
List<Sample> subSamples,
Map<Contact,CvParam> contactRoles) |
Copyright © 2015 European Bioinformatics Institute. All Rights Reserved.