uk.ac.ebi.pride.utilities.data.controller.impl.Transformer

Class MzIdentMLTransformer

java.lang.Object

uk.ac.ebi.pride.utilities.data.controller.impl.Transformer.MzIdentMLTransformer

public final class MzIdentMLTransformer
extends Object

This class is the Transformer class from a jmzidml object to a core object. It is used by MzIdentMLTransformer to convert jmzidml native objects to the ms-core-api Objects.

Author:

Yasset Perez-Riverol Date: 19/09/11 Time: 16:08

Method Summary

Methods

Modifier and Type	Method and Description
static void	setCvLookupMap(Map<String,CVLookup> cvLookupList)
static void	setFragmentationTable(Map<String,IdentifiableParamGroup> fragTable)
static List<Organization>	transformAffiliationToOrganization(List<uk.ac.ebi.jmzidml.model.mzidml.Affiliation> oldAffiliations)
static List<CVLookup>	transformCVList(List<uk.ac.ebi.jmzidml.model.mzidml.Cv> cvList)
static CvParam	transformDateToCvParam(Date creationDate)
static ProteinGroup	transformProteinAmbiguityGroupToProteinGroup(uk.ac.ebi.jmzidml.model.mzidml.ProteinAmbiguityGroup proteinAmbiguityGroup)
static Protein	transformProteinHypothesisToIdentification(uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionHypothesis oldIdent)
static Protein	transformSpectrumIdentificationItemToIdentification(uk.ac.ebi.jmzidml.model.mzidml.DBSequence oldDbSequence, List<uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem> spectrumIdentificationItemList)
static List<Sample>	transformSubSampleToSample(List<uk.ac.ebi.jmzidml.model.mzidml.SubSample> oldSamples)
static CVLookup	transformToCVLookup(uk.ac.ebi.jmzidml.model.mzidml.Cv oldCv)
static Map<String,IdentifiableParamGroup>	transformToFragmentationTable(uk.ac.ebi.jmzidml.model.mzidml.FragmentationTable oldFragmentationTable)
static List<Organization>	transformToOrganization(List<uk.ac.ebi.jmzidml.model.mzidml.Organization> oldOrganizations)
static Organization	transformToOrganization(uk.ac.ebi.jmzidml.model.mzidml.Organization oldOrganization)
static SpectrumIdentification	transformToPeptideIdentification(uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem oldSpectrumIdentification)
static List<Peptide>	transformToPeptideIdentificationsFromSpectrumItems(List<uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem> spectrumIdentificationItems)
static List<Person>	transformToPerson(List<uk.ac.ebi.jmzidml.model.mzidml.Person> oldPersons)
static Person	transformToPerson(uk.ac.ebi.jmzidml.model.mzidml.Person oldPerson)
static Protocol	transformToProteinDetectionProtocol(uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionProtocol oldProteinDetectionProtocol)
static Provider	transformToProvider(uk.ac.ebi.jmzidml.model.mzidml.Provider oldProvider)
static List<Reference>	transformToReference(Iterator<uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference> it)
static List<Sample>	transformToSample(List<uk.ac.ebi.jmzidml.model.mzidml.Sample> oldSamples) Transform old Samples to Samples
static Sample	transformToSample(uk.ac.ebi.jmzidml.model.mzidml.Sample oldSample)
static List<SearchDataBase>	transformToSearchDataBase(List<uk.ac.ebi.jmzidml.model.mzidml.SearchDatabase> oldSearchDatabases)
static Software	transformToSoftware(uk.ac.ebi.jmzidml.model.mzidml.AnalysisSoftware oldSoftware)
static List<Software>	transformToSoftware(List<uk.ac.ebi.jmzidml.model.mzidml.AnalysisSoftware> oldSoftwares)
static List<SourceFile>	transformToSourceFile(List<uk.ac.ebi.jmzidml.model.mzidml.SourceFile> oldSourceFiles)
static List<SpectraData>	transformToSpectraData(List<uk.ac.ebi.jmzidml.model.mzidml.SpectraData> oldSpectraDatas, List<Comparable> usedTitle)
static SpectraData	transformToSpectraData(uk.ac.ebi.jmzidml.model.mzidml.SpectraData oldSpectraData, boolean mgfTitle)
static List<SpectrumIdentificationProtocol>	transformToSpectrumIdentificationProtocol(List<uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol> oldSpecProtocol)
static SpectrumIdentificationProtocol	transformToSpectrumIdentificationProtocol(uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol oldProtocol)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

setCvLookupMap

public static void setCvLookupMap(Map<String,CVLookup> cvLookupList)

setFragmentationTable

public static void setFragmentationTable(Map<String,IdentifiableParamGroup> fragTable)

transformToSourceFile

public static List<SourceFile> transformToSourceFile(List<uk.ac.ebi.jmzidml.model.mzidml.SourceFile> oldSourceFiles)

transformToOrganization

public static List<Organization> transformToOrganization(List<uk.ac.ebi.jmzidml.model.mzidml.Organization> oldOrganizations)

transformToOrganization

public static Organization transformToOrganization(uk.ac.ebi.jmzidml.model.mzidml.Organization oldOrganization)

transformAffiliationToOrganization

public static List<Organization> transformAffiliationToOrganization(List<uk.ac.ebi.jmzidml.model.mzidml.Affiliation> oldAffiliations)

transformToPerson

public static List<Person> transformToPerson(List<uk.ac.ebi.jmzidml.model.mzidml.Person> oldPersons)

transformToPerson

public static Person transformToPerson(uk.ac.ebi.jmzidml.model.mzidml.Person oldPerson)

transformToSample

public static List<Sample> transformToSample(List<uk.ac.ebi.jmzidml.model.mzidml.Sample> oldSamples)

Transform old Samples to Samples

Parameters:

oldSamples - old Samples Objects from jmzidentml

Returns:

List of Samples

transformSubSampleToSample

public static List<Sample> transformSubSampleToSample(List<uk.ac.ebi.jmzidml.model.mzidml.SubSample> oldSamples)

transformToSample

public static Sample transformToSample(uk.ac.ebi.jmzidml.model.mzidml.Sample oldSample)

transformToSoftware

public static List<Software> transformToSoftware(List<uk.ac.ebi.jmzidml.model.mzidml.AnalysisSoftware> oldSoftwares)

transformToSoftware

public static Software transformToSoftware(uk.ac.ebi.jmzidml.model.mzidml.AnalysisSoftware oldSoftware)

transformToReference

public static List<Reference> transformToReference(Iterator<uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference> it)

transformProteinHypothesisToIdentification

public static Protein transformProteinHypothesisToIdentification(uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionHypothesis oldIdent)

transformSpectrumIdentificationItemToIdentification

public static Protein transformSpectrumIdentificationItemToIdentification(uk.ac.ebi.jmzidml.model.mzidml.DBSequence oldDbSequence,
                                                          List<uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem> spectrumIdentificationItemList)

transformToFragmentationTable

public static Map<String,IdentifiableParamGroup> transformToFragmentationTable(uk.ac.ebi.jmzidml.model.mzidml.FragmentationTable oldFragmentationTable)

transformToPeptideIdentificationsFromSpectrumItems

public static List<Peptide> transformToPeptideIdentificationsFromSpectrumItems(List<uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem> spectrumIdentificationItems)

transformToPeptideIdentification

public static SpectrumIdentification transformToPeptideIdentification(uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem oldSpectrumIdentification)

transformCVList

public static List<CVLookup> transformCVList(List<uk.ac.ebi.jmzidml.model.mzidml.Cv> cvList)

transformToCVLookup

public static CVLookup transformToCVLookup(uk.ac.ebi.jmzidml.model.mzidml.Cv oldCv)

transformToProvider

public static Provider transformToProvider(uk.ac.ebi.jmzidml.model.mzidml.Provider oldProvider)

transformToSpectrumIdentificationProtocol

public static List<SpectrumIdentificationProtocol> transformToSpectrumIdentificationProtocol(List<uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol> oldSpecProtocol)

transformToSpectrumIdentificationProtocol

public static SpectrumIdentificationProtocol transformToSpectrumIdentificationProtocol(uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol oldProtocol)

transformToProteinDetectionProtocol

public static Protocol transformToProteinDetectionProtocol(uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionProtocol oldProteinDetectionProtocol)

transformToSearchDataBase

public static List<SearchDataBase> transformToSearchDataBase(List<uk.ac.ebi.jmzidml.model.mzidml.SearchDatabase> oldSearchDatabases)

transformToSpectraData

public static SpectraData transformToSpectraData(uk.ac.ebi.jmzidml.model.mzidml.SpectraData oldSpectraData,
                                 boolean mgfTitle)

transformToSpectraData

public static List<SpectraData> transformToSpectraData(List<uk.ac.ebi.jmzidml.model.mzidml.SpectraData> oldSpectraDatas,
                                       List<Comparable> usedTitle)

transformDateToCvParam

public static CvParam transformDateToCvParam(Date creationDate)

transformProteinAmbiguityGroupToProteinGroup

public static ProteinGroup transformProteinAmbiguityGroupToProteinGroup(uk.ac.ebi.jmzidml.model.mzidml.ProteinAmbiguityGroup proteinAmbiguityGroup)