public final class MzMLTransformer extends Object
Modifier and Type | Method and Description |
---|---|
static Chromatogram |
transformChromatogram(uk.ac.ebi.jmzml.model.mzml.Chromatogram chroma)
Convert chromatogram
|
static List<CVLookup> |
transformCVList(uk.ac.ebi.jmzml.model.mzml.CVList oldCvList)
Convert cv loopups
|
static CVLookup |
transformCVLookup(uk.ac.ebi.jmzml.model.mzml.CV oldCv)
Convert cv lookups
|
static DataProcessing |
transformDataProcessing(uk.ac.ebi.jmzml.model.mzml.DataProcessing oldDataProcessing)
Convert data processing
|
static List<DataProcessing> |
transformDataProcessingList(uk.ac.ebi.jmzml.model.mzml.DataProcessingList oldDataProcessingList)
Convert a list of data prcessings
|
static CvParam |
transformDateToCvParam(Date creationDate) |
static List<Organization> |
transformFileDescriptionOrganization(uk.ac.ebi.jmzml.model.mzml.FileDescription rawFileDescription)
Method to transform FileDescription in the MzMl file to an Organization Objet List
|
static ParamGroup |
transformFileDescriptionToFileContent(uk.ac.ebi.jmzml.model.mzml.FileDescription rawFileDescription)
Retrieve the file content
|
static List<SourceFile> |
transformFileDescriptionToFileSource(uk.ac.ebi.jmzml.model.mzml.FileDescription rawFileDescription)
Transform FileDescription object to List of SourceFile
|
static List<Person> |
transformFileDescriptionToPerson(uk.ac.ebi.jmzml.model.mzml.FileDescription rawFileDescription)
Method to retrieve the Contact Persons From the FileDescription Object in the MzMl Files
|
static InstrumentConfiguration |
transformInstrumentConfiguration(uk.ac.ebi.jmzml.model.mzml.InstrumentConfiguration oldInstrument)
Convert instrument configuration
|
static List<InstrumentConfiguration> |
transformInstrumentConfigurationList(uk.ac.ebi.jmzml.model.mzml.InstrumentConfigurationList oldInstrumentList)
Convert instrument configuration list
|
static <T extends uk.ac.ebi.jmzml.model.mzml.ParamGroup> |
transformParamGroup(T paramGroup)
Convert param group
|
static <T extends uk.ac.ebi.jmzml.model.mzml.ParamGroup> |
transformParamGroupList(List<T> oldParamGroupList)
Convert a list of param groups
|
static ReferenceableParamGroup |
transformReferenceableParamGroupList(uk.ac.ebi.jmzml.model.mzml.ReferenceableParamGroupList oldRefParamGroupList)
Convert referenceable param group
|
static Sample |
transformSample(uk.ac.ebi.jmzml.model.mzml.Sample oldSample)
Convert sample
|
static List<Sample> |
transformSampleList(uk.ac.ebi.jmzml.model.mzml.SampleList oldSampleList)
Convert sample list
|
static ScanSetting |
transformScanSetting(uk.ac.ebi.jmzml.model.mzml.ScanSettings oldScanSetting)
Convert scan setting
|
static List<ScanSetting> |
transformScanSettingList(uk.ac.ebi.jmzml.model.mzml.ScanSettingsList oldScanSettingsList)
Convert scan settings
|
static Software |
transformSoftware(uk.ac.ebi.jmzml.model.mzml.Software oldSoftware)
Convert software
|
static List<Software> |
transformSoftwareList(uk.ac.ebi.jmzml.model.mzml.SoftwareList oldSoftwareList)
Convert software list
|
static List<SourceFile> |
transformSourceFileList(uk.ac.ebi.jmzml.model.mzml.SourceFileList oldSourceFileList)
Convert source file list
|
static Spectrum |
transformSpectrum(uk.ac.ebi.jmzml.model.mzml.Spectrum spectrum)
Convert spectrum
|
public static Spectrum transformSpectrum(uk.ac.ebi.jmzml.model.mzml.Spectrum spectrum)
spectrum
- jmzML spectrum objectpublic static <T extends uk.ac.ebi.jmzml.model.mzml.ParamGroup> ParamGroup transformParamGroup(T paramGroup)
T
- any jmzml objects which extends param groupparamGroup
- jmzML param grouppublic static <T extends uk.ac.ebi.jmzml.model.mzml.ParamGroup> List<ParamGroup> transformParamGroupList(List<T> oldParamGroupList)
T
- any jmzML objects extends param groupoldParamGroupList
- a list of jmzML param groupspublic static ReferenceableParamGroup transformReferenceableParamGroupList(uk.ac.ebi.jmzml.model.mzml.ReferenceableParamGroupList oldRefParamGroupList)
oldRefParamGroupList
- jmzml referenceable param grouppublic static List<SourceFile> transformSourceFileList(uk.ac.ebi.jmzml.model.mzml.SourceFileList oldSourceFileList)
oldSourceFileList
- jmzml source file listpublic static Chromatogram transformChromatogram(uk.ac.ebi.jmzml.model.mzml.Chromatogram chroma)
chroma
- jmzml chromatogrampublic static List<CVLookup> transformCVList(uk.ac.ebi.jmzml.model.mzml.CVList oldCvList)
oldCvList
- jmzml cv listpublic static CVLookup transformCVLookup(uk.ac.ebi.jmzml.model.mzml.CV oldCv)
oldCv
- jmzml cv lookupspublic static List<Sample> transformSampleList(uk.ac.ebi.jmzml.model.mzml.SampleList oldSampleList)
oldSampleList
- jmzml sample listpublic static Sample transformSample(uk.ac.ebi.jmzml.model.mzml.Sample oldSample)
oldSample
- jmzml samplepublic static List<Software> transformSoftwareList(uk.ac.ebi.jmzml.model.mzml.SoftwareList oldSoftwareList)
oldSoftwareList
- a list of jmzml softwarepublic static Software transformSoftware(uk.ac.ebi.jmzml.model.mzml.Software oldSoftware)
oldSoftware
- jmzml softarepublic static List<ScanSetting> transformScanSettingList(uk.ac.ebi.jmzml.model.mzml.ScanSettingsList oldScanSettingsList)
oldScanSettingsList
- scan setting listpublic static ScanSetting transformScanSetting(uk.ac.ebi.jmzml.model.mzml.ScanSettings oldScanSetting)
oldScanSetting
- jmzml scan settingpublic static List<InstrumentConfiguration> transformInstrumentConfigurationList(uk.ac.ebi.jmzml.model.mzml.InstrumentConfigurationList oldInstrumentList)
oldInstrumentList
- jmzml instrument configuration listpublic static InstrumentConfiguration transformInstrumentConfiguration(uk.ac.ebi.jmzml.model.mzml.InstrumentConfiguration oldInstrument)
oldInstrument
- jmzml instrument configurationpublic static List<DataProcessing> transformDataProcessingList(uk.ac.ebi.jmzml.model.mzml.DataProcessingList oldDataProcessingList)
oldDataProcessingList
- jmzml data processing listpublic static DataProcessing transformDataProcessing(uk.ac.ebi.jmzml.model.mzml.DataProcessing oldDataProcessing)
oldDataProcessing
- jmzml data processingpublic static ParamGroup transformFileDescriptionToFileContent(uk.ac.ebi.jmzml.model.mzml.FileDescription rawFileDescription)
rawFileDescription
- The raw file description objects.public static List<SourceFile> transformFileDescriptionToFileSource(uk.ac.ebi.jmzml.model.mzml.FileDescription rawFileDescription)
rawFileDescription
- jmzml FileDescription Objectpublic static List<Person> transformFileDescriptionToPerson(uk.ac.ebi.jmzml.model.mzml.FileDescription rawFileDescription)
rawFileDescription
- raw file descriptionpublic static List<Organization> transformFileDescriptionOrganization(uk.ac.ebi.jmzml.model.mzml.FileDescription rawFileDescription)
rawFileDescription
- raw file descriptionCopyright © 2015 European Bioinformatics Institute. All Rights Reserved.