public class MzTabTransformer extends Object
Constructor and Description |
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MzTabTransformer() |
Modifier and Type | Method and Description |
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static ParamGroup |
transformAdditional(List<uk.ac.ebi.pride.jmztab.model.Param> additionalParams) |
static Organization |
transformContactToOrganization(uk.ac.ebi.pride.jmztab.model.Contact contact) |
static List<Organization> |
transformContactToOrganization(Map<Integer,uk.ac.ebi.pride.jmztab.model.Contact> contacts) |
static Person |
transformContactToPerson(uk.ac.ebi.pride.jmztab.model.Contact contact) |
static Collection<Person> |
transformContactToPersons(Map<Integer,uk.ac.ebi.pride.jmztab.model.Contact> contacts) |
static List<SearchDataBase> |
transformDatabases(Set<uk.ac.ebi.pride.utilities.util.Tuple<String,String>> oldDatabases) |
static Protein |
transformIdent(uk.ac.ebi.pride.jmztab.model.Protein rawIdent,
Integer rawIndex,
Map<String,uk.ac.ebi.pride.jmztab.model.PSM> rawPsms,
Map<String,uk.ac.ebi.pride.jmztab.model.Peptide> rawPeptides,
uk.ac.ebi.pride.jmztab.model.Metadata metadata,
boolean hasQuantitation) |
static Protein |
transformIdentification(uk.ac.ebi.pride.jmztab.model.Protein rawIdent,
Integer rawIndex,
Map<String,uk.ac.ebi.pride.jmztab.model.PSM> rawPsms,
Map<String,uk.ac.ebi.pride.jmztab.model.Peptide> rawPeptides,
uk.ac.ebi.pride.jmztab.model.Metadata metadata,
boolean hasQuantitation)
Convert gel free protein identification
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static Collection<InstrumentConfiguration> |
transformInstrument(Map<Integer,uk.ac.ebi.pride.jmztab.model.Instrument> oldInstruments) |
static Map<Comparable,SpectraData> |
transformMsRunMap(Map<Integer,uk.ac.ebi.pride.jmztab.model.MsRun> mRunMap) |
static Peptide |
transformPeptide(uk.ac.ebi.pride.jmztab.model.PSM rawPeptide,
DBSequence dbSequence,
Comparable index,
uk.ac.ebi.pride.jmztab.model.Metadata metadata)
Transform peptide from pride xml to core data model.
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static ExperimentProtocol |
transformProtocol(SortedMap<Integer,uk.ac.ebi.pride.jmztab.model.SplitList<uk.ac.ebi.pride.jmztab.model.Param>> sampleProcession) |
static QuantPeptide |
transformQuantPeptide(uk.ac.ebi.pride.jmztab.model.Peptide rawPeptide,
DBSequence dbSequence,
Comparable index,
uk.ac.ebi.pride.jmztab.model.Metadata metadata)
Transform quantitative peptide from pride xml to core data model.
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static Collection<Reference> |
transformReferences(Map<Integer,uk.ac.ebi.pride.jmztab.model.Publication> publications) |
static List<Sample> |
transformSamples(Map<Integer,uk.ac.ebi.pride.jmztab.model.Sample> oldSamples,
uk.ac.ebi.pride.jmztab.model.Metadata metadata,
boolean hasQuantitation) |
static Software |
transformSoftware(uk.ac.ebi.pride.jmztab.model.Software oldSoftware)
Transform a Software Object
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static List<Software> |
transformSoftwares(Map<Integer,uk.ac.ebi.pride.jmztab.model.Software> dataSoftwares)
Transform a List of softwares
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static SourceFile |
transformSourceFile(uk.ac.ebi.pride.jmztab.model.MsRun msRun)
Convert an msRun to SourceFile
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static List<SourceFile> |
transformSourceFiles(Map<Integer,uk.ac.ebi.pride.jmztab.model.MsRun> msRunMap) |
static Map<Comparable,StudyVariable> |
transformStudyVariables(uk.ac.ebi.pride.jmztab.model.Metadata metadata,
boolean quantitationExperiment) |
public static List<SourceFile> transformSourceFiles(Map<Integer,uk.ac.ebi.pride.jmztab.model.MsRun> msRunMap)
public static SourceFile transformSourceFile(uk.ac.ebi.pride.jmztab.model.MsRun msRun)
msRun
- msRunpublic static Collection<Person> transformContactToPersons(Map<Integer,uk.ac.ebi.pride.jmztab.model.Contact> contacts)
public static Person transformContactToPerson(uk.ac.ebi.pride.jmztab.model.Contact contact)
public static List<Organization> transformContactToOrganization(Map<Integer,uk.ac.ebi.pride.jmztab.model.Contact> contacts)
public static Organization transformContactToOrganization(uk.ac.ebi.pride.jmztab.model.Contact contact)
public static List<Sample> transformSamples(Map<Integer,uk.ac.ebi.pride.jmztab.model.Sample> oldSamples, uk.ac.ebi.pride.jmztab.model.Metadata metadata, boolean hasQuantitation)
public static List<Software> transformSoftwares(Map<Integer,uk.ac.ebi.pride.jmztab.model.Software> dataSoftwares)
dataSoftwares
- mzTab softwarespublic static Software transformSoftware(uk.ac.ebi.pride.jmztab.model.Software oldSoftware)
oldSoftware
- The mzTab Softwarepublic static Collection<Reference> transformReferences(Map<Integer,uk.ac.ebi.pride.jmztab.model.Publication> publications)
public static ParamGroup transformAdditional(List<uk.ac.ebi.pride.jmztab.model.Param> additionalParams)
public static Protein transformIdentification(uk.ac.ebi.pride.jmztab.model.Protein rawIdent, Integer rawIndex, Map<String,uk.ac.ebi.pride.jmztab.model.PSM> rawPsms, Map<String,uk.ac.ebi.pride.jmztab.model.Peptide> rawPeptides, uk.ac.ebi.pride.jmztab.model.Metadata metadata, boolean hasQuantitation)
rawIdent
- mzTab protein identificationpublic static Protein transformIdent(uk.ac.ebi.pride.jmztab.model.Protein rawIdent, Integer rawIndex, Map<String,uk.ac.ebi.pride.jmztab.model.PSM> rawPsms, Map<String,uk.ac.ebi.pride.jmztab.model.Peptide> rawPeptides, uk.ac.ebi.pride.jmztab.model.Metadata metadata, boolean hasQuantitation)
public static Peptide transformPeptide(uk.ac.ebi.pride.jmztab.model.PSM rawPeptide, DBSequence dbSequence, Comparable index, uk.ac.ebi.pride.jmztab.model.Metadata metadata)
rawPeptide
- peptide in pride xml format.public static QuantPeptide transformQuantPeptide(uk.ac.ebi.pride.jmztab.model.Peptide rawPeptide, DBSequence dbSequence, Comparable index, uk.ac.ebi.pride.jmztab.model.Metadata metadata)
rawPeptide
- peptide in pride xml format.public static ExperimentProtocol transformProtocol(SortedMap<Integer,uk.ac.ebi.pride.jmztab.model.SplitList<uk.ac.ebi.pride.jmztab.model.Param>> sampleProcession)
public static Map<Comparable,SpectraData> transformMsRunMap(Map<Integer,uk.ac.ebi.pride.jmztab.model.MsRun> mRunMap)
public static Collection<InstrumentConfiguration> transformInstrument(Map<Integer,uk.ac.ebi.pride.jmztab.model.Instrument> oldInstruments)
public static List<SearchDataBase> transformDatabases(Set<uk.ac.ebi.pride.utilities.util.Tuple<String,String>> oldDatabases)
public static Map<Comparable,StudyVariable> transformStudyVariables(uk.ac.ebi.pride.jmztab.model.Metadata metadata, boolean quantitationExperiment)
Copyright © 2015 European Bioinformatics Institute. All Rights Reserved.