public final class PrideXmlTransformer extends Object
Modifier and Type | Method and Description |
---|---|
static ParamGroup |
transformAdditional(uk.ac.ebi.pride.jaxb.model.Param rawAdditionalParams)
Transform additional params from pride xml to core data model format.
|
static BinaryDataArray |
transformBinaryDataArray(uk.ac.ebi.pride.jaxb.model.PeakListBinary rawArr,
uk.ac.ebi.pride.utilities.term.CvTermReference binaryType)
Transform BinaryDataArray from pride xml to core data model
|
static List<ParamGroup> |
transformContacts(uk.ac.ebi.pride.jaxb.model.Admin rawAdmin)
Transform a list of contacts from pride xml to core data model format
|
static List<Organization> |
transformContactToOrganization(uk.ac.ebi.pride.jaxb.model.Admin rawAdmin)
Transform a list of contacts from person contact
|
static List<Person> |
transformContactToPerson(uk.ac.ebi.pride.jaxb.model.Admin rawAdmin)
Transform a list of contacts from person contact
|
static List<CVLookup> |
transformCvLookups(List<uk.ac.ebi.pride.jaxb.model.CvLookup> rawCvLookups)
Transform a list of cvlookup object from pride Xml format to core data model format.
|
static CvParam |
transformCvParam(uk.ac.ebi.pride.jaxb.model.CvParam rawCvParam)
Transform a cv parameter from pride xml format to core data model format.
|
static List<CvParam> |
transformCvParams(List<uk.ac.ebi.pride.jaxb.model.CvParam> rawCvParams)
Convert a list of cv params
|
static DataProcessing |
transformDataProcessing(uk.ac.ebi.pride.jaxb.model.DataProcessing rawDataProcessing)
Transform data processing from pride xml to core data model format.
|
static Protein |
transformGelFreeIdent(uk.ac.ebi.pride.jaxb.model.GelFreeIdentification rawIdent)
Convert gel free protein identification
|
static Protein |
transformIdentification(uk.ac.ebi.pride.jaxb.model.Identification identification)
Convert protein identification
|
static List<InstrumentConfiguration> |
transformInstrument(uk.ac.ebi.pride.jaxb.model.Instrument rawInstrument,
uk.ac.ebi.pride.jaxb.model.DataProcessing rawDataProcessing)
Transform an instrument from pride xml to core data model format.
|
static ParamGroup |
transformParamGroup(uk.ac.ebi.pride.jaxb.model.Param rawParams)
Transform a paramgroup from pride xml format to core data model format.
|
static Peptide |
transformPeptide(uk.ac.ebi.pride.jaxb.model.PeptideItem rawPeptide,
DBSequence dbSequence,
Comparable index)
Transform peptide from pride xml to core data model.
|
static Precursor |
transformPrecursor(uk.ac.ebi.pride.jaxb.model.Precursor rawPrecursor)
transform precursors from pride xml to core data model
Note: In MzData schema, there are experimentRef, this is not included
in pride xml schema.
|
static List<Precursor> |
transformPrecursorList(uk.ac.ebi.pride.jaxb.model.PrecursorList rawPrecursors)
Convert precursor list
|
static ExperimentProtocol |
transformProtocol(uk.ac.ebi.pride.jaxb.model.Protocol rawProt)
transform protocol from pride xml to core data model.
|
static List<Reference> |
transformReferences(List<uk.ac.ebi.pride.jaxb.model.Reference> rawReferences)
Transform references from pride xml format to core data model format
|
static Sample |
transformSample(uk.ac.ebi.pride.jaxb.model.Admin rawAdmin)
Transform sample from pride xml format to core data model format
|
static Software |
transformSoftware(uk.ac.ebi.pride.jaxb.model.DataProcessing rawDataProcessing)
Transform an software object from pride xml format to core data model format.
|
static SourceFile |
transformSourceFile(uk.ac.ebi.pride.jaxb.model.Admin rawAdmin)
Transform source file from pride xml to core data model
|
static Spectrum |
transformSpectrum(uk.ac.ebi.pride.jaxb.model.Spectrum rawSpec)
Convert spectrum
Note: supDes, supDataArrayBinary are ignored.
|
static Protein |
transformTwoDimIdent(uk.ac.ebi.pride.jaxb.model.TwoDimensionalIdentification rawIdent)
Convert two dimensional identification
ToDo: there are code duplication between transformTwoDimIdent and transformGelFreeIdent
|
static UserParam |
transformUserParam(uk.ac.ebi.pride.jaxb.model.UserParam rawUserParam)
Transform a user parameter from pride xml format to core data model format.
|
static List<UserParam> |
transformUserParams(List<uk.ac.ebi.pride.jaxb.model.UserParam> rawUserParams)
Convert a list of user params
|
public static Spectrum transformSpectrum(uk.ac.ebi.pride.jaxb.model.Spectrum rawSpec)
rawSpec
- pride xml spectrumpublic static List<Precursor> transformPrecursorList(uk.ac.ebi.pride.jaxb.model.PrecursorList rawPrecursors)
rawPrecursors
- pride xml precursor listpublic static Precursor transformPrecursor(uk.ac.ebi.pride.jaxb.model.Precursor rawPrecursor)
rawPrecursor
- pride xml precursorpublic static BinaryDataArray transformBinaryDataArray(uk.ac.ebi.pride.jaxb.model.PeakListBinary rawArr, uk.ac.ebi.pride.utilities.term.CvTermReference binaryType)
rawArr
- pride xml binary data arraybinaryType
- binary typepublic static Protein transformIdentification(uk.ac.ebi.pride.jaxb.model.Identification identification)
identification
- pride xml protein identificationpublic static Protein transformTwoDimIdent(uk.ac.ebi.pride.jaxb.model.TwoDimensionalIdentification rawIdent)
rawIdent
- pride xml two dimensional identificationpublic static Protein transformGelFreeIdent(uk.ac.ebi.pride.jaxb.model.GelFreeIdentification rawIdent)
rawIdent
- pride xml protein identificationpublic static Peptide transformPeptide(uk.ac.ebi.pride.jaxb.model.PeptideItem rawPeptide, DBSequence dbSequence, Comparable index)
rawPeptide
- peptide in pride xml format.public static ExperimentProtocol transformProtocol(uk.ac.ebi.pride.jaxb.model.Protocol rawProt)
rawProt
- protocol from pride xml.public static ParamGroup transformParamGroup(uk.ac.ebi.pride.jaxb.model.Param rawParams)
rawParams
- paramgroup in pride xml format.public static List<UserParam> transformUserParams(List<uk.ac.ebi.pride.jaxb.model.UserParam> rawUserParams)
rawUserParams
- pride xml user paramspublic static UserParam transformUserParam(uk.ac.ebi.pride.jaxb.model.UserParam rawUserParam)
rawUserParam
- a user parameter in pride xml format.public static List<CvParam> transformCvParams(List<uk.ac.ebi.pride.jaxb.model.CvParam> rawCvParams)
rawCvParams
- pride xml cv paramspublic static CvParam transformCvParam(uk.ac.ebi.pride.jaxb.model.CvParam rawCvParam)
rawCvParam
- a cv parameter in pride xml format.public static List<CVLookup> transformCvLookups(List<uk.ac.ebi.pride.jaxb.model.CvLookup> rawCvLookups)
rawCvLookups
- a list of cv lookups in pride xml format.public static Sample transformSample(uk.ac.ebi.pride.jaxb.model.Admin rawAdmin)
rawAdmin
- Admin object in pride xml format, which contains all the details about sample.public static Software transformSoftware(uk.ac.ebi.pride.jaxb.model.DataProcessing rawDataProcessing)
rawDataProcessing
- software object in pride xml format.public static List<InstrumentConfiguration> transformInstrument(uk.ac.ebi.pride.jaxb.model.Instrument rawInstrument, uk.ac.ebi.pride.jaxb.model.DataProcessing rawDataProcessing)
rawInstrument
- instrument object in pride xml format.rawDataProcessing
- data processing object in pride xml format.public static DataProcessing transformDataProcessing(uk.ac.ebi.pride.jaxb.model.DataProcessing rawDataProcessing)
rawDataProcessing
- data processing in pride xml.public static List<ParamGroup> transformContacts(uk.ac.ebi.pride.jaxb.model.Admin rawAdmin)
rawAdmin
- admin object in pride xml.public static List<Person> transformContactToPerson(uk.ac.ebi.pride.jaxb.model.Admin rawAdmin)
rawAdmin
- admin object in pride xml.public static List<Organization> transformContactToOrganization(uk.ac.ebi.pride.jaxb.model.Admin rawAdmin)
rawAdmin
- admin object in pride xml.public static SourceFile transformSourceFile(uk.ac.ebi.pride.jaxb.model.Admin rawAdmin)
rawAdmin
- Admin in pride xml format.public static List<Reference> transformReferences(List<uk.ac.ebi.pride.jaxb.model.Reference> rawReferences)
rawReferences
- a list of references in pride xml format.public static ParamGroup transformAdditional(uk.ac.ebi.pride.jaxb.model.Param rawAdditionalParams)
rawAdditionalParams
- Additional params from pride xmlCopyright © 2015 European Bioinformatics Institute. All Rights Reserved.