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

Class MzDataTransformer

java.lang.Object

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

public final class MzDataTransformer
extends Object

This class provide the functions to convert and transform mzData objects to ms-core-api objetcs.

Author:

Yasset Perez-Riverol Date: 3/15/12 Time: 9:19 AM

Method Summary

Methods

Modifier and Type	Method and Description
static List<CVLookup>	transformCVList(List<uk.ac.ebi.pride.tools.mzdata_parser.mzdata.model.CvLookup> oldCvList) Convert cv loopups
static CVLookup	transformCVLookup(uk.ac.ebi.pride.tools.mzdata_parser.mzdata.model.CvLookup oldCvLookup) Convert cv lookups
static List<DataProcessing>	transformDataProcessing(uk.ac.ebi.pride.tools.mzdata_parser.mzdata.model.DataProcessing oldDataProcessing) Convert data processing
static List<InstrumentConfiguration>	transformInstrumentConfiguration(uk.ac.ebi.pride.tools.mzdata_parser.mzdata.model.InstrumentDescription oldInstrument) Convert instrument configuration
static <T extends uk.ac.ebi.pride.tools.mzdata_parser.mzdata.model.Param> ParamGroup	transformParamGroup(T oldParam) Convert param group
static <T extends uk.ac.ebi.pride.tools.mzdata_parser.mzdata.model.Param> List<ParamGroup>	transformParamGroupList(List<T> oldParamGroupList) Convert a list of param groups
static List<Sample>	transformSampleList(uk.ac.ebi.pride.tools.mzdata_parser.mzdata.model.Admin oldSampleDescription) Convert sample list
static List<Software>	transformSoftware(uk.ac.ebi.pride.tools.mzdata_parser.mzdata.model.Software oldSoftware) Convert software list
static Spectrum	transformSpectrum(uk.ac.ebi.pride.tools.jmzreader.model.Spectrum spectrum) Convert spectrum
static List<SourceFile>	transformToFileSource(uk.ac.ebi.pride.tools.mzdata_parser.mzdata.model.SourceFile oldSourceFile) Transform FileDescription object to List of SourceFile
static List<Person>	transformToPerson(List<uk.ac.ebi.pride.tools.mzdata_parser.mzdata.model.Person> oldPersons) Method to retrieve the Contact Persons From the FileDescription Object in the mzData Files

Methods inherited from class java.lang.Object

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

Method Detail

transformSpectrum

public static Spectrum transformSpectrum(uk.ac.ebi.pride.tools.jmzreader.model.Spectrum spectrum)

Convert spectrum

Parameters:

spectrum - jmzML spectrum object

Returns:

Spectrum spectrum

transformParamGroup

public static <T extends uk.ac.ebi.pride.tools.mzdata_parser.mzdata.model.Param> ParamGroup transformParamGroup(T oldParam)

Convert param group

Type Parameters:

T - any jmzml objects which extends param group

Parameters:

oldParam - jmzML param group

Returns:

ParamGroup param group

transformParamGroupList

public static <T extends uk.ac.ebi.pride.tools.mzdata_parser.mzdata.model.Param> List<ParamGroup> transformParamGroupList(List<T> oldParamGroupList)

Convert a list of param groups

Type Parameters:

T - any jmzML objects extends param group

Parameters:

oldParamGroupList - a list of jmzML param groups

Returns:

ParamGroup param group

transformCVList

public static List<CVLookup> transformCVList(List<uk.ac.ebi.pride.tools.mzdata_parser.mzdata.model.CvLookup> oldCvList)

Convert cv loopups

Parameters:

oldCvList - jmzml cv list

Returns:

List a list of cv lookups

transformCVLookup

public static CVLookup transformCVLookup(uk.ac.ebi.pride.tools.mzdata_parser.mzdata.model.CvLookup oldCvLookup)

Convert cv lookups

Parameters:

oldCvLookup - jmzml cv lookups

Returns:

CVLookup cv lookup

transformSampleList

public static List<Sample> transformSampleList(uk.ac.ebi.pride.tools.mzdata_parser.mzdata.model.Admin oldSampleDescription)

Convert sample list

Parameters:

oldSampleDescription - jmzml sample list

Returns:

List a list of samples

transformSoftware

public static List<Software> transformSoftware(uk.ac.ebi.pride.tools.mzdata_parser.mzdata.model.Software oldSoftware)

Convert software list

Parameters:

oldSoftware - a list of jmzml software

Returns:

List a list of sfotware

transformInstrumentConfiguration

public static List<InstrumentConfiguration> transformInstrumentConfiguration(uk.ac.ebi.pride.tools.mzdata_parser.mzdata.model.InstrumentDescription oldInstrument)

Convert instrument configuration

Parameters:

oldInstrument - mzData instrument configuration

Returns:

Instrumentconfiguration insturment configuration

transformDataProcessing

public static List<DataProcessing> transformDataProcessing(uk.ac.ebi.pride.tools.mzdata_parser.mzdata.model.DataProcessing oldDataProcessing)

Convert data processing

Parameters:

oldDataProcessing - jmzml data processing

Returns:

DataProcessing data processing

transformToFileSource

public static List<SourceFile> transformToFileSource(uk.ac.ebi.pride.tools.mzdata_parser.mzdata.model.SourceFile oldSourceFile)

Transform FileDescription object to List of SourceFile

Parameters:

oldSourceFile - mzData FileDescription Object

Returns:

List List of Source Files used in the MzMl

transformToPerson

public static List<Person> transformToPerson(List<uk.ac.ebi.pride.tools.mzdata_parser.mzdata.model.Person> oldPersons)

Method to retrieve the Contact Persons From the FileDescription Object in the mzData Files

Parameters:

oldPersons - mzData Person Structure to convert to Person Contact

Returns:

List List of Person Contacts