Modifier and Type | Method and Description |
---|---|
static List<CvParam> |
DataAccessUtilities.getCvParam(ParamGroup paramGroup,
String cvLabel,
String accession)
Get cv param by accession number and cv label.
|
static List<Parameter> |
DataAccessUtilities.getParamByName(ParamGroup paramGroup,
String name)
Get a list parameters using a given name.
|
static Integer |
DataAccessUtilities.getPrecursorChargeParamGroup(ParamGroup paramGroup)
Get precursor charge from param group
|
static double |
DataAccessUtilities.getPrecursorMz(ParamGroup paramGroup)
Get precursor m/z value
|
static Score |
DataAccessUtilities.getScore(ParamGroup params) |
static List<uk.ac.ebi.pride.utilities.term.SearchEngineCvTermReference> |
DataAccessUtilities.getSearchEngineCvTermReference(ParamGroup paramGroup) |
static List<uk.ac.ebi.pride.utilities.term.SearchEngineScoreCvTermReference> |
DataAccessUtilities.getSearchEngineScoresCvTermReference(ParamGroup paramGroup) |
static List<uk.ac.ebi.pride.utilities.term.SearchEngineCvTermReference> |
DataAccessUtilities.getSearchEngineTypes(ParamGroup paramGroup)
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
ParamGroup |
PrideXmlControllerImpl.getAdditional()
Get additional parameters
|
ParamGroup |
MzXmlControllerImpl.getAdditional()
Get additional details, the mzXML is like mzML the Additional is the combination of FileContent
and StartTime.
|
ParamGroup |
MzTabControllerImpl.getAdditional()
Get custom parameters
|
ParamGroup |
MzMLControllerImpl.getAdditional()
In case of mzMl the additional parameters are related with the getFileContent
This are a set of CVTerms related with the Content in the MzML File.
|
ParamGroup |
MzIdentMLControllerImpl.getAdditional()
Additional is a concept that comes from PRIDE XML Files.
|
ParamGroup |
AbstractDataAccessController.getAdditional() |
ParamGroup |
MzXmlControllerImpl.getFileContent()
This will be summarize the different parent file formats.
|
ParamGroup |
MzMLControllerImpl.getFileContent()
This summarizes the different types of spectra that can be expected
in the file.
|
ParamGroup |
MzDataControllerImpl.getFileContent()
File Content is extra parameters related with Source Files in case of mzData.
|
Modifier and Type | Method and Description |
---|---|
static ParamGroup |
MzTabTransformer.transformAdditional(List<uk.ac.ebi.pride.jmztab.model.Param> additionalParams) |
static ParamGroup |
PrideXmlTransformer.transformAdditional(uk.ac.ebi.pride.jaxb.model.Param rawAdditionalParams)
Transform additional params from pride xml to core data model format.
|
static ParamGroup |
MzMLTransformer.transformFileDescriptionToFileContent(uk.ac.ebi.jmzml.model.mzml.FileDescription rawFileDescription)
Retrieve the file content
|
static ParamGroup |
PrideXmlTransformer.transformParamGroup(uk.ac.ebi.pride.jaxb.model.Param rawParams)
Transform a paramgroup from pride xml format to core data model format.
|
static <T extends uk.ac.ebi.jmzml.model.mzml.ParamGroup> |
MzMLTransformer.transformParamGroup(T paramGroup)
Convert param group
|
static <T extends uk.ac.ebi.pride.tools.mzdata_parser.mzdata.model.Param> |
MzDataTransformer.transformParamGroup(T oldParam)
Convert param group
|
Modifier and Type | Method and Description |
---|---|
static List<ParamGroup> |
PrideXmlTransformer.transformContacts(uk.ac.ebi.pride.jaxb.model.Admin rawAdmin)
Transform a list of contacts from pride xml to core data model format
|
static <T extends uk.ac.ebi.jmzml.model.mzml.ParamGroup> |
MzMLTransformer.transformParamGroupList(List<T> oldParamGroupList)
Convert a list of param groups
|
static <T extends uk.ac.ebi.pride.tools.mzdata_parser.mzdata.model.Param> |
MzDataTransformer.transformParamGroupList(List<T> oldParamGroupList)
Convert a list of param groups
|
Modifier and Type | Class and Description |
---|---|
class |
AbundanceAssay
Abundance Assay is the Class to storage the abundance variables for each Protein.
|
class |
Assay
Assay In the mzTab experiment with the corresponding Reagent and sample
|
class |
BinaryDataArray
BinaryDataArray is a slim down version of binaryDataArray in mzML
ParamGroup of this object must have the followings in mzML 1.1.0.1 definition:
For Chromatograms (once each):
1.
|
class |
Chromatogram
Chromatogram object.
|
class |
Contact
This class is just to organize the code, the ConstantRole class have to kind of instance,
one of then is Organization and the Other one if the person both objects extend the IdentifiableParamGroup
in order to organize the code we create a new abstract class named AbstractContact to separate the Contacts types
from the IdentifiableParamGroup.
|
class |
DBSequence
A database sequence from the specified SearchDatabase (nucleic acid or amino acid).
|
class |
ExperimentMetaData
General descriptions shared or used for the whole file.
|
class |
ExperimentProtocol
Protocol used to generate the dataset, added by PRIDE XML 2.0.
|
class |
FragmentIon
FragmentIon stores details about peptide fragment ion information.
|
class |
Gel
Gel is a class to Describe the Gel Spot for each Protein.
|
class |
IdentifiableParamGroup
Other classes in the model can be specified as sub-classes, inheriting from IdentifiablePraramGroup.
|
class |
IdentificationMetaData
This class is used to manage and store the information of the metadata for protein and spectrum
identifications.
|
class |
InstrumentComponent
InstrumentComponent is key to keep the order of different instrument
component.
|
class |
InstrumentConfiguration
Description of a particular hardware configuration of a mass spectrometer.
|
class |
MassTable |
class |
Modification
A molecule modification specification.
|
class |
MzGraph
Abstract object can be extended by both Spectrum and Chromatogram.
|
class |
MzGraphMetaData
This class storage the information related with metadata at the spectrum level.
|
class |
Organization
Organizations are entities like companies, universities, government agencies.
|
class |
PeptideEvidence
PeptideEvidence links a specific Peptide Element to a specific position in a DBSequence.
|
class |
PeptideSequence
One (poly)peptide (a sequence with modifications).
|
class |
Person
A person's name and contact details.
|
class |
ProcessingMethod
Description of the default peak processing method.
|
class |
Protein
Abstract class for both GelFreeIdentification and TwoDimIdentification
|
class |
ProteinGroup
A set of logically related results from a protein detection, for example to represent conflicting assignments of
peptides to proteins
|
class |
Protocol
The collection of protocols which include the parameters and settings of the performed analyses.
|
class |
QuantScore
The QuantScore is the List of StudyVariable Scores and the Abundance by Assays.
|
class |
Reference
Reference is added by PRIDE XML 2.0., also a generic reference for mzIdentML References.
|
class |
Sample
Description of the sample used to generate the Dataset.
|
class |
Scan
Scan or acquisition from original raw file used to create this
peak list, as specified in sourceFile.
|
class |
ScanList
List and descriptions of scans.
|
class |
ScanSetting
Description of the acquisition settings or the instrument prior to the start of
the run.
|
class |
Software
Software details.
|
class |
SourceFile
Description of source file, including identification file, location and type.
|
class |
Spectrum
A peak list including the underlying acquisitions.
|
class |
SpectrumIdentification
PSM Spectrum identification match.
|
class |
SpectrumIdentificationList
Represents the set of all search results from SpectrumIdentification.
|
class |
SpectrumIdentificationProtocol
The parameters and settings of a SpectrumIdentification analysis.
|
class |
StudyVariable
Study variable is use for Quantitation on mzTab files.
|
Modifier and Type | Method and Description |
---|---|
ParamGroup |
Precursor.getActivation() |
ParamGroup |
ExperimentMetaData.getAdditional() |
ParamGroup |
Protocol.getAnalysisParam() |
ParamGroup |
Enzyme.getEnzymeName() |
ParamGroup |
Filter.getExclude() |
ParamGroup |
MzGraphMetaData.getFileContent() |
ParamGroup |
ExperimentMetaData.getFileContent() |
ParamGroup |
Filter.getFilterType() |
ParamGroup |
Filter.getInclude() |
ParamGroup |
Precursor.getIsolationWindow() |
ParamGroup |
SearchDataBase.getNameDatabase() |
ParamGroup |
ReferenceableParamGroup.getRefParamGroup(String ref) |
ParamGroup |
SpectrumIdentificationProtocol.getSearchType() |
ParamGroup |
Protocol.getThreshold() |
Modifier and Type | Method and Description |
---|---|
Map<String,ParamGroup> |
MassTable.getAmbiguousResidues() |
List<ParamGroup> |
Spectrum.getProducts() |
List<ParamGroup> |
ExperimentProtocol.getProtocolSteps() |
Map<String,ParamGroup> |
ReferenceableParamGroup.getRefMap() |
List<ParamGroup> |
Scan.getScanWindows() |
List<ParamGroup> |
Precursor.getSelectedIons() |
List<ParamGroup> |
ScanSetting.getTargets() |
Modifier and Type | Method and Description |
---|---|
void |
ReferenceableParamGroup.addRefParamGroup(String ref,
ParamGroup params) |
void |
Precursor.setActivation(ParamGroup activation) |
void |
Protocol.setAnalysisParam(ParamGroup analysisParam) |
void |
Enzyme.setEnzymeName(ParamGroup enzymeName) |
void |
Filter.setExclude(ParamGroup exclude) |
void |
MzGraphMetaData.setFileContent(ParamGroup fileContent) |
void |
Filter.setFilterType(ParamGroup filterType) |
void |
Filter.setInclude(ParamGroup include) |
void |
Precursor.setIsolationWindow(ParamGroup isolationWindow) |
void |
SearchDataBase.setNameDatabase(ParamGroup nameDatabase) |
void |
SpectrumIdentificationProtocol.setSearchType(ParamGroup searchType) |
void |
Protocol.setThreshold(ParamGroup threshold) |
Modifier and Type | Method and Description |
---|---|
void |
MassTable.setAmbiguousResidues(Map<String,ParamGroup> ambiguousResidues) |
void |
Spectrum.setProducts(List<ParamGroup> products) |
void |
ExperimentProtocol.setProtocolSteps(List<ParamGroup> protocolSteps) |
void |
ReferenceableParamGroup.setRefMap(Map<String,ParamGroup> refMap) |
void |
Scan.setScanWindows(List<ParamGroup> scanWindows) |
void |
Precursor.setSelectedIons(List<ParamGroup> selectedIon) |
void |
ScanSetting.setTargets(List<ParamGroup> targets) |
Constructor and Description |
---|
AbundanceAssay(ParamGroup params,
Comparable id,
String name) |
AbundanceAssay(ParamGroup params,
Comparable id,
String name,
Assay assay,
Double value) |
Assay(ParamGroup params,
Comparable id,
String name) |
Assay(ParamGroup params,
Comparable id,
String name,
Sample sample) |
Assay(ParamGroup params,
Comparable id,
String name,
Sample sample,
CvParam reagent) |
BinaryDataArray(DataProcessing dataProcessing,
double[] binaryDoubleArr,
ParamGroup params)
Constructor
|
Chromatogram(ParamGroup params,
Comparable id,
String name,
int index,
DataProcessing defaultDataProcessing,
int defaultArrayLength,
List<BinaryDataArray> binaryDataArrays) |
Contact(ParamGroup params,
Comparable id,
String name) |
DBSequence(ParamGroup params,
Comparable id,
String name,
int length,
String accession,
SearchDataBase searchDataBase,
String sequence,
String accessionVersion,
String spliceIsoform) |
Enzyme(String id,
String name,
boolean semiSpecific,
int missedCleavages,
int minDistance,
ParamGroup enzymeName,
String siteRegExp) |
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.
|
ExperimentProtocol(ParamGroup params,
String id,
String name,
List<ParamGroup> protocolSteps) |
Filter(ParamGroup filterType,
ParamGroup include,
ParamGroup exclude) |
FragmentIon(ParamGroup params)
Constructor
|
Gel(ParamGroup params,
String gelLink,
Double xCoordinate,
Double yCoordinate,
Double molecularWeight,
Double pI)
Constructor
|
IdentifiableParamGroup(ParamGroup params,
Comparable id,
String name) |
IdentificationMetaData(ParamGroup params,
Comparable id,
String name,
List<SpectrumIdentificationProtocol> spectrumIdentificationProtocols,
Protocol proteinDetectionProtocol,
List<SearchDataBase> searchDataBases) |
InstrumentComponent(int order,
ParamGroup params)
constructor
|
InstrumentConfiguration(String id,
ScanSetting scanSetting,
Software software,
List<InstrumentComponent> source,
List<InstrumentComponent> analyzer,
List<InstrumentComponent> detector,
ParamGroup params)
Constructor
|
Modification(ParamGroup params,
String id,
String name,
int location,
List<String> residues,
List<Double> avgMassDelta,
List<Double> monoisotopicMassDelta,
String modDatabase,
String modDatabaseVersion)
Constructor for Modification Objects
|
MzGraph(ParamGroup params,
Comparable id,
String name,
int index,
DataProcessing defaultDataProcessing,
int defaultArrayLength,
List<BinaryDataArray> binaryDataArrays) |
MzGraphMetaData(ParamGroup params,
Comparable id,
String name,
List<ScanSetting> scanSettings,
List<InstrumentConfiguration> instrumentConfigurations,
List<DataProcessing> dataProcessings) |
Organization(ParamGroup params,
Comparable id,
String name,
Organization parentOrganization,
String mail) |
Organization(ParamGroup params,
String name,
String mail) |
ParamGroup(ParamGroup params) |
PeptideEvidence(ParamGroup params,
String id,
String name,
Integer startPosition,
Integer endPosition,
boolean decoy,
PeptideSequence peptideSequence,
DBSequence dbSequence) |
PeptideSequence(ParamGroup params,
String id,
String name,
String sequence,
List<Modification> modifications) |
PeptideSequence(ParamGroup params,
String id,
String name,
String sequence,
List<Modification> modifications,
List<SubstitutionModification> substitutionModifications) |
Person(ParamGroup params,
Comparable id,
String name,
String lastname,
String firstname,
String midInitials,
List<Organization> affiliation,
String contactInfo) |
Person(ParamGroup params,
String firstname,
String contactInfo) |
Precursor(Spectrum spectrum,
SourceFile sourceFile,
String externalSpectrumID,
ParamGroup isolationWindow,
List<ParamGroup> selectedIon,
ParamGroup activation)
Constructor
|
ProcessingMethod(int order,
Software software,
ParamGroup params)
Constructor
|
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
|
ProteinGroup(ParamGroup params,
Comparable id,
String name,
List<Protein> proteinDetectionHypothesis) |
Protocol(Comparable id,
String name,
ParamGroup analysisParam) |
Protocol(ParamGroup analysisParam,
Comparable id,
String name,
Software analysisSoftware,
ParamGroup threshold) |
QuantScore(ParamGroup params,
Comparable id,
String name,
Map<Comparable,Double> studyVariableScores,
Map<Comparable,Double> assayAbundance)
Default Constructor for QuantScore.
|
Reference(ParamGroup params,
String fullReference) |
Reference(ParamGroup params,
String id,
String name,
String doi,
String title,
String pages,
String issue,
String volume,
String year,
String editor,
String publisher,
String publication,
String authors,
String fullReference) |
Sample(ParamGroup params,
String id,
String name) |
Sample(ParamGroup params,
String id,
String name,
List<Sample> subSamples,
Map<Contact,CvParam> contactRoles) |
Scan(String spectrumRef,
String externalSpecRef,
SourceFile sourceFile,
InstrumentConfiguration instrumentConfiguration,
List<ParamGroup> scanWindows,
ParamGroup params)
Constructor
|
ScanList(List<Scan> scans,
ParamGroup params)
Constructor
|
ScanSetting(String id,
List<SourceFile> sourceFile,
List<ParamGroup> targets,
ParamGroup params)
Constructor
|
SearchDataBase(String name,
String databaseVersion,
ParamGroup param)
Database with name, version, DatabaseName in the form of CvParam
|
SearchDataBase(String id,
String name,
String location,
CvParam fileFormat,
String externalFormatDocumentationURI,
String version,
String releaseDate,
int numDatabaseSequence,
long numDatabaseResidue,
ParamGroup nameDatabase,
List<CvParam> description) |
Software(ParamGroup params,
Comparable id,
String name,
Contact contact,
String customization,
String uri,
String version) |
SourceFile(ParamGroup params,
String id,
String name,
String path) |
SourceFile(ParamGroup params,
String id,
String name,
String path,
CvParam fileFormat,
String externalFormatDocumentationURI) |
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) |
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
|
SpectrumIdentificationList(ParamGroup params,
Comparable id,
String name,
int numSequenceSearched,
List<IdentifiableParamGroup> fragmentationTable,
List<Peptide> spectrumIdentificationList) |
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) |
StudyVariable(ParamGroup params,
Comparable id,
String name) |
Constructor and Description |
---|
ExperimentProtocol(ParamGroup params,
String id,
String name,
List<ParamGroup> protocolSteps) |
MassTable(List<Integer> msLevel,
Map<String,Float> residues,
Map<String,ParamGroup> ambiguousResidues) |
Precursor(Spectrum spectrum,
SourceFile sourceFile,
String externalSpectrumID,
ParamGroup isolationWindow,
List<ParamGroup> selectedIon,
ParamGroup activation)
Constructor
|
ReferenceableParamGroup(Map<String,ParamGroup> refMap) |
Scan(String spectrumRef,
String externalSpecRef,
SourceFile sourceFile,
InstrumentConfiguration instrumentConfiguration,
List<ParamGroup> scanWindows,
ParamGroup params)
Constructor
|
ScanSetting(String id,
List<SourceFile> sourceFile,
List<ParamGroup> targets,
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) |
Modifier and Type | Method and Description |
---|---|
static String |
CvUtilities.getMailFromCvParam(ParamGroup person) |
static boolean |
CvUtilities.isDecoyHit(ParamGroup paramGroup)
Checks whether the passed identification object is a decoy hit.
|
Copyright © 2015 European Bioinformatics Institute. All Rights Reserved.