Package de.isas.mztab2.model
Class Metadata
- java.lang.Object
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- de.isas.mztab2.model.Metadata
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@Generated(value="io.swagger.codegen.languages.JavaClientCodegen", date="2021-01-02T19:25:37.430+01:00") public class Metadata extends Object
The metadata section provides additional information about the dataset(s) reported in the mzTab file. All fields in the metadata section are optional apart from those noted as mandatory. The fields in the metadata section MUST be reported in order of the various fields listed here. The field’s name and value MUST be separated by a tab character.mzTab-M specification example(s):
MTD mzTab-version 2.0.0-M MTD mzTab-ID MTBL1234 MTD title Effects of Rapamycin on metabolite profile ...
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
Metadata.PrefixEnum
The metadata section prefix.static class
Metadata.Properties
Property enumeration for Metadata.
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Constructor Summary
Constructors Constructor Description Metadata()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description Metadata
addAssayItem(Assay assayItem)
Add a single assayItem to the assay collection.Metadata
addColunitSmallMoleculeEvidenceItem(ColumnParameterMapping colunitSmallMoleculeEvidenceItem)
Add a single colunitSmallMoleculeEvidenceItem to the colunitSmallMoleculeEvidence collection.Metadata
addColunitSmallMoleculeFeatureItem(ColumnParameterMapping colunitSmallMoleculeFeatureItem)
Add a single colunitSmallMoleculeFeatureItem to the colunitSmallMoleculeFeature collection.Metadata
addColunitSmallMoleculeItem(ColumnParameterMapping colunitSmallMoleculeItem)
Add a single colunitSmallMoleculeItem to the colunitSmallMolecule collection.Metadata
addContactItem(Contact contactItem)
Add a single contactItem to the contact collection.Metadata
addCustomItem(Parameter customItem)
Add a single customItem to the custom collection.Metadata
addCvItem(CV cvItem)
Add a single cvItem to the cv collection.Metadata
addDatabaseItem(Database databaseItem)
Add a single databaseItem to the database collection.Metadata
addDerivatizationAgentItem(Parameter derivatizationAgentItem)
Add a single derivatizationAgentItem to the derivatizationAgent collection.Metadata
addExternalStudyUriItem(Uri externalStudyUriItem)
Add a single externalStudyUriItem to the externalStudyUri collection.Metadata
addIdConfidenceMeasureItem(Parameter idConfidenceMeasureItem)
Add a single idConfidenceMeasureItem to the idConfidenceMeasure collection.Metadata
addInstrumentItem(Instrument instrumentItem)
Add a single instrumentItem to the instrument collection.Metadata
addMsRunItem(MsRun msRunItem)
Add a single msRunItem to the msRun collection.Metadata
addPublicationItem(Publication publicationItem)
Add a single publicationItem to the publication collection.Metadata
addSampleItem(Sample sampleItem)
Add a single sampleItem to the sample collection.Metadata
addSampleProcessingItem(SampleProcessing sampleProcessingItem)
Add a single sampleProcessingItem to the sampleProcessing collection.Metadata
addSoftwareItem(Software softwareItem)
Add a single softwareItem to the software collection.Metadata
addStudyVariableItem(StudyVariable studyVariableItem)
Add a single studyVariableItem to the studyVariable collection.Metadata
addUriItem(Uri uriItem)
Add a single uriItem to the uri collection.Metadata
assay(List<Assay> assay)
Builder method for assay.Metadata
colunitSmallMolecule(List<ColumnParameterMapping> colunitSmallMolecule)
Builder method for colunitSmallMolecule.Metadata
colunitSmallMoleculeEvidence(List<ColumnParameterMapping> colunitSmallMoleculeEvidence)
Builder method for colunitSmallMoleculeEvidence.Metadata
colunitSmallMoleculeFeature(List<ColumnParameterMapping> colunitSmallMoleculeFeature)
Builder method for colunitSmallMoleculeFeature.Metadata
contact(List<Contact> contact)
Builder method for contact.Metadata
custom(List<Parameter> custom)
Builder method for custom.Metadata
cv(List<CV> cv)
Builder method for cv.Metadata
database(List<Database> database)
Builder method for database.Metadata
derivatizationAgent(List<Parameter> derivatizationAgent)
Builder method for derivatizationAgent.Metadata
description(String description)
Builder method for description.boolean
equals(Object o)
Metadata
externalStudyUri(List<Uri> externalStudyUri)
Builder method for externalStudyUri.@NotNull @Valid List<Assay>
getAssay()
Specification of assay.@Valid List<ColumnParameterMapping>
getColunitSmallMolecule()
Defines the used unit for a column in the small molecule section.@Valid List<ColumnParameterMapping>
getColunitSmallMoleculeEvidence()
Defines the used unit for a column in the small molecule evidence section.@Valid List<ColumnParameterMapping>
getColunitSmallMoleculeFeature()
Defines the used unit for a column in the small molecule feature section.@Valid List<Contact>
getContact()
The contact’s name, affiliation and e-mail.@Valid List<Parameter>
getCustom()
Any additional parameters describing the analysis reported.@NotNull @Valid List<CV>
getCv()
Specification of controlled vocabularies. label: A string describing the labels of the controlled vocabularies/ontologies used in the mzTab file as a short-hand e.g.@NotNull @Valid List<Database>
getDatabase()
Specification of databases.@Valid List<Parameter>
getDerivatizationAgent()
A description of derivatization agents applied to small molecules, using userParams or CV terms where possible.String
getDescription()
The file’s human readable description.@Valid List<Uri>
getExternalStudyUri()
A URI pointing to an external file with more details about the study design (e.g., an ISA-TAB file).@NotNull @Valid List<Parameter>
getIdConfidenceMeasure()
The type of small molecule confidence measures or scores MUST be reported as a CV parameter [1-n].@Valid List<Instrument>
getInstrument()
The name, source, analyzer and detector of the instruments used in the experiment.@NotNull @Valid List<MsRun>
getMsRun()
Specification of ms_run.@NotNull String
getMzTabID()
The ID of the mzTab file, this could be supplied by the repository from which it is downloaded or a local identifier from the lab producing the file.@NotNull @Pattern(regexp="^\\d{1}\\.\\d{1}\\.\\d{1}-[A-Z]{1}$") String
getMzTabVersion()
The version of the mzTab file.@NotNull Metadata.PrefixEnum
getPrefix()
The metadata section prefix.@Valid List<Publication>
getPublication()
A publication associated with this file.@NotNull @Valid Parameter
getQuantificationMethod()
The quantification method used in the experiment reported in the file.@Valid List<Sample>
getSample()
Specification of sample.@Valid List<SampleProcessing>
getSampleProcessing()
A list of parameters describing a sample processing, preparation or handling step similar to a biological or analytical methods report.@NotNull @Valid Parameter
getSmallMoleculeFeatureQuantificationUnit()
Defines what type of units are reported in the small molecule feature quantification / abundance fields.@Valid Parameter
getSmallMoleculeIdentificationReliability()
The system used for giving reliability / confidence codes to small molecule identifications MUST be specified if not using the default codes.@NotNull @Valid Parameter
getSmallMoleculeQuantificationUnit()
Defines what type of units are reported in the small molecule summary quantification / abundance fields.@NotNull @Valid List<Software>
getSoftware()
Software used to analyze the data and obtain the reported results.@NotNull @Valid List<StudyVariable>
getStudyVariable()
Specification of study_variable.String
getTitle()
The file’s human readable title.@Valid List<Uri>
getUri()
A URI pointing to the file’s source data (e.g., a MetaboLights records).int
hashCode()
Metadata
idConfidenceMeasure(List<Parameter> idConfidenceMeasure)
Builder method for idConfidenceMeasure.Metadata
instrument(List<Instrument> instrument)
Builder method for instrument.Metadata
msRun(List<MsRun> msRun)
Builder method for msRun.Metadata
mzTabID(String mzTabID)
Builder method for mzTabID.Metadata
mzTabVersion(String mzTabVersion)
Builder method for mzTabVersion.Metadata
prefix(Metadata.PrefixEnum prefix)
Builder method for prefix.Metadata
publication(List<Publication> publication)
Builder method for publication.Metadata
quantificationMethod(Parameter quantificationMethod)
Builder method for quantificationMethod.Metadata
sample(List<Sample> sample)
Builder method for sample.Metadata
sampleProcessing(List<SampleProcessing> sampleProcessing)
Builder method for sampleProcessing.void
setAssay(List<Assay> assay)
Set assay.void
setColunitSmallMolecule(List<ColumnParameterMapping> colunitSmallMolecule)
Set colunitSmallMolecule.void
setColunitSmallMoleculeEvidence(List<ColumnParameterMapping> colunitSmallMoleculeEvidence)
Set colunitSmallMoleculeEvidence.void
setColunitSmallMoleculeFeature(List<ColumnParameterMapping> colunitSmallMoleculeFeature)
Set colunitSmallMoleculeFeature.void
setContact(List<Contact> contact)
Set contact.void
setCustom(List<Parameter> custom)
Set custom.void
setCv(List<CV> cv)
Set cv.void
setDatabase(List<Database> database)
Set database.void
setDerivatizationAgent(List<Parameter> derivatizationAgent)
Set derivatizationAgent.void
setDescription(String description)
Set description.void
setExternalStudyUri(List<Uri> externalStudyUri)
Set externalStudyUri.void
setIdConfidenceMeasure(List<Parameter> idConfidenceMeasure)
Set idConfidenceMeasure.void
setInstrument(List<Instrument> instrument)
Set instrument.void
setMsRun(List<MsRun> msRun)
Set msRun.void
setMzTabID(String mzTabID)
Set mzTabID.void
setMzTabVersion(String mzTabVersion)
Set mzTabVersion.void
setPrefix(Metadata.PrefixEnum prefix)
Set prefix.void
setPublication(List<Publication> publication)
Set publication.void
setQuantificationMethod(Parameter quantificationMethod)
Set quantificationMethod.void
setSample(List<Sample> sample)
Set sample.void
setSampleProcessing(List<SampleProcessing> sampleProcessing)
Set sampleProcessing.void
setSmallMoleculeFeatureQuantificationUnit(Parameter smallMoleculeFeatureQuantificationUnit)
Set smallMoleculeFeatureQuantificationUnit.void
setSmallMoleculeIdentificationReliability(Parameter smallMoleculeIdentificationReliability)
Set smallMoleculeIdentificationReliability.void
setSmallMoleculeQuantificationUnit(Parameter smallMoleculeQuantificationUnit)
Set smallMoleculeQuantificationUnit.void
setSoftware(List<Software> software)
Set software.void
setStudyVariable(List<StudyVariable> studyVariable)
Set studyVariable.void
setTitle(String title)
Set title.void
setUri(List<Uri> uri)
Set uri.Metadata
smallMoleculeFeatureQuantificationUnit(Parameter smallMoleculeFeatureQuantificationUnit)
Builder method for smallMoleculeFeatureQuantificationUnit.Metadata
smallMoleculeIdentificationReliability(Parameter smallMoleculeIdentificationReliability)
Builder method for smallMoleculeIdentificationReliability.Metadata
smallMoleculeQuantificationUnit(Parameter smallMoleculeQuantificationUnit)
Builder method for smallMoleculeQuantificationUnit.Metadata
software(List<Software> software)
Builder method for software.Metadata
studyVariable(List<StudyVariable> studyVariable)
Builder method for studyVariable.Metadata
title(String title)
Builder method for title.String
toString()
Metadata
uri(List<Uri> uri)
Builder method for uri.
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Constructor Detail
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Metadata
public Metadata()
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Method Detail
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prefix
public Metadata prefix(Metadata.PrefixEnum prefix)
Builder method for prefix.- Parameters:
prefix
- aPrefixEnum
parameter.- Returns:
- Metadata
- See Also:
Metadata#setPrefix for specification examples
,Metadata#getPrefix for validation constraints
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getPrefix
@NotNull public @NotNull Metadata.PrefixEnum getPrefix()
The metadata section prefix. MUST always be MTD.- Returns:
- prefix
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setPrefix
public void setPrefix(Metadata.PrefixEnum prefix)
Set prefix.- Parameters:
prefix
- aPrefixEnum
parameter.- See Also:
Metadata#getPrefix for validation constraints
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mzTabVersion
public Metadata mzTabVersion(String mzTabVersion)
Builder method for mzTabVersion.- Parameters:
mzTabVersion
- aString
parameter.- Returns:
- Metadata
- See Also:
Metadata#setMzTabVersion for specification examples
,Metadata#getMzTabVersion for validation constraints
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getMzTabVersion
@NotNull @Pattern(regexp="^\\d{1}\\.\\d{1}\\.\\d{1}-[A-Z]{1}$") public @NotNull @Pattern(regexp="^\\d{1}\\.\\d{1}\\.\\d{1}-[A-Z]{1}$") String getMzTabVersion()
The version of the mzTab file. The suffix MUST be "-M" for mzTab for metabolomics (mzTab-M).- Returns:
- mzTabVersion
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setMzTabVersion
public void setMzTabVersion(String mzTabVersion)
Set mzTabVersion.mzTab-M specification example(s):
MTD mzTab-version 2.0.0-M MTD mzTab-version 2.0.1-M
- Parameters:
mzTabVersion
- aString
parameter.- See Also:
Metadata#getMzTabVersion for validation constraints
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mzTabID
public Metadata mzTabID(String mzTabID)
Builder method for mzTabID.- Parameters:
mzTabID
- aString
parameter.- Returns:
- Metadata
- See Also:
Metadata#setMzTabID for specification examples
,Metadata#getMzTabID for validation constraints
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getMzTabID
@NotNull public @NotNull String getMzTabID()
The ID of the mzTab file, this could be supplied by the repository from which it is downloaded or a local identifier from the lab producing the file. It is not intended to be a globally unique ID but carry some locally useful meaning.- Returns:
- mzTabID
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setMzTabID
public void setMzTabID(String mzTabID)
Set mzTabID.- Parameters:
mzTabID
- aString
parameter.- See Also:
Metadata#getMzTabID for validation constraints
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title
public Metadata title(String title)
Builder method for title.- Parameters:
title
- aString
parameter.- Returns:
- Metadata
- See Also:
Metadata#setTitle for specification examples
,Metadata#getTitle for validation constraints
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setTitle
public void setTitle(String title)
Set title.- Parameters:
title
- aString
parameter.- See Also:
Metadata#getTitle for validation constraints
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description
public Metadata description(String description)
Builder method for description.- Parameters:
description
- aString
parameter.- Returns:
- Metadata
- See Also:
Metadata#setDescription for specification examples
,Metadata#getDescription for validation constraints
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getDescription
public String getDescription()
The file’s human readable description.- Returns:
- description
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setDescription
public void setDescription(String description)
Set description.- Parameters:
description
- aString
parameter.- See Also:
Metadata#getDescription for validation constraints
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contact
public Metadata contact(List<Contact> contact)
Builder method for contact.- Parameters:
contact
- aList<Contact>
parameter.- Returns:
- Metadata
- See Also:
Metadata#setContact for specification examples
,Metadata#getContact for validation constraints
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addContactItem
public Metadata addContactItem(Contact contactItem)
Add a single contactItem to the contact collection.- Parameters:
contactItem
- aContact
parameter.- Returns:
- Metadata
- See Also:
Metadata#getContact for validation constraints
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getContact
@Valid public @Valid List<Contact> getContact()
The contact’s name, affiliation and e-mail. Several contacts can be given by indicating the number in the square brackets after "contact". A contact has to be supplied in the format [first name] [initials] [last name].- Returns:
- contact
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setContact
public void setContact(List<Contact> contact)
Set contact.mzTab-M specification example(s):
MTD contact[1]-name James D. Watson MTD contact[1]-affiliation Cambridge University, UK MTD contact[1]-email watson@cam.ac.uk MTD contact[2]-name Francis Crick MTD contact[2]-affiliation Cambridge University, UK MTD contact[2]-email crick@cam.ac.uk
- Parameters:
contact
- aList<Contact>
parameter.- See Also:
Metadata#getContact for validation constraints
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publication
public Metadata publication(List<Publication> publication)
Builder method for publication.- Parameters:
publication
- aList<Publication>
parameter.- Returns:
- Metadata
- See Also:
Metadata#setPublication for specification examples
,Metadata#getPublication for validation constraints
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addPublicationItem
public Metadata addPublicationItem(Publication publicationItem)
Add a single publicationItem to the publication collection.- Parameters:
publicationItem
- aPublication
parameter.- Returns:
- Metadata
- See Also:
Metadata#getPublication for validation constraints
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getPublication
@Valid public @Valid List<Publication> getPublication()
A publication associated with this file. Several publications can be given by indicating the number in the square brackets after “publication”. PubMed ids must be prefixed by “pubmed:”, DOIs by “doi:”. Multiple identifiers MUST be separated by “|”.- Returns:
- publication
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setPublication
public void setPublication(List<Publication> publication)
Set publication.mzTab-M specification example(s):
MTD publication[1] pubmed:21063943|doi:10.1007/978-1-60761-987-1_6 MTD publication[2] pubmed:20615486|doi:10.1016/j.jprot.2010.06.008
- Parameters:
publication
- aList<Publication>
parameter.- See Also:
Metadata#getPublication for validation constraints
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uri
public Metadata uri(List<Uri> uri)
Builder method for uri.- Parameters:
uri
- aList<Uri>
parameter.- Returns:
- Metadata
- See Also:
Metadata#setUri for specification examples
,Metadata#getUri for validation constraints
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addUriItem
public Metadata addUriItem(Uri uriItem)
Add a single uriItem to the uri collection.- Parameters:
uriItem
- aUri
parameter.- Returns:
- Metadata
- See Also:
Metadata#getUri for validation constraints
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getUri
@Valid public @Valid List<Uri> getUri()
A URI pointing to the file’s source data (e.g., a MetaboLights records).- Returns:
- uri
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setUri
public void setUri(List<Uri> uri)
Set uri.mzTab-M specification example(s):
MTD uri[1] https://www.ebi.ac.uk/metabolights/MTBLS517
- Parameters:
uri
- aList<Uri>
parameter.- See Also:
Metadata#getUri for validation constraints
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externalStudyUri
public Metadata externalStudyUri(List<Uri> externalStudyUri)
Builder method for externalStudyUri.- Parameters:
externalStudyUri
- aList<Uri>
parameter.- Returns:
- Metadata
- See Also:
Metadata#setExternalStudyUri for specification examples
,Metadata#getExternalStudyUri for validation constraints
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addExternalStudyUriItem
public Metadata addExternalStudyUriItem(Uri externalStudyUriItem)
Add a single externalStudyUriItem to the externalStudyUri collection.- Parameters:
externalStudyUriItem
- aUri
parameter.- Returns:
- Metadata
- See Also:
Metadata#getExternalStudyUri for validation constraints
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getExternalStudyUri
@Valid public @Valid List<Uri> getExternalStudyUri()
A URI pointing to an external file with more details about the study design (e.g., an ISA-TAB file).- Returns:
- externalStudyUri
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setExternalStudyUri
public void setExternalStudyUri(List<Uri> externalStudyUri)
Set externalStudyUri.mzTab-M specification example(s):
MTD external_study_uri[1] https://www.ebi.ac.uk/metabolights/MTBLS517/files/i_Investigation.txt
- Parameters:
externalStudyUri
- aList<Uri>
parameter.- See Also:
Metadata#getExternalStudyUri for validation constraints
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instrument
public Metadata instrument(List<Instrument> instrument)
Builder method for instrument.- Parameters:
instrument
- aList<Instrument>
parameter.- Returns:
- Metadata
- See Also:
Metadata#setInstrument for specification examples
,Metadata#getInstrument for validation constraints
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addInstrumentItem
public Metadata addInstrumentItem(Instrument instrumentItem)
Add a single instrumentItem to the instrument collection.- Parameters:
instrumentItem
- aInstrument
parameter.- Returns:
- Metadata
- See Also:
Metadata#getInstrument for validation constraints
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getInstrument
@Valid public @Valid List<Instrument> getInstrument()
The name, source, analyzer and detector of the instruments used in the experiment. Multiple instruments are numbered [1-n].- Returns:
- instrument
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setInstrument
public void setInstrument(List<Instrument> instrument)
Set instrument.mzTab-M specification example(s):
MTD instrument[1]-name [MS, MS:1000449, LTQ Orbitrap,] MTD instrument[1]-source [MS, MS:1000073, ESI,] … MTD instrument[2]-source [MS, MS:1000598, ETD,] MTD instrument[1]-analyzer[1] [MS, MS:1000291, linear ion trap,] … MTD instrument[2]-analyzer[1] [MS, MS:1000484, orbitrap,] MTD instrument[1]-detector [MS, MS:1000253, electron multiplier,] … MTD instrument[2]-detector [MS, MS:1000348, focal plane collector,]
- Parameters:
instrument
- aList<Instrument>
parameter.- See Also:
Metadata#getInstrument for validation constraints
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quantificationMethod
public Metadata quantificationMethod(Parameter quantificationMethod)
Builder method for quantificationMethod.- Parameters:
quantificationMethod
- aParameter
parameter.- Returns:
- Metadata
- See Also:
Metadata#setQuantificationMethod for specification examples
,Metadata#getQuantificationMethod for validation constraints
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getQuantificationMethod
@NotNull @Valid public @NotNull @Valid Parameter getQuantificationMethod()
The quantification method used in the experiment reported in the file.- Returns:
- quantificationMethod
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setQuantificationMethod
public void setQuantificationMethod(Parameter quantificationMethod)
Set quantificationMethod.- Parameters:
quantificationMethod
- aParameter
parameter.- See Also:
Metadata#getQuantificationMethod for validation constraints
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sample
public Metadata sample(List<Sample> sample)
Builder method for sample.- Parameters:
sample
- aList<Sample>
parameter.- Returns:
- Metadata
- See Also:
Metadata#setSample for specification examples
,Metadata#getSample for validation constraints
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addSampleItem
public Metadata addSampleItem(Sample sampleItem)
Add a single sampleItem to the sample collection.- Parameters:
sampleItem
- aSample
parameter.- Returns:
- Metadata
- See Also:
Metadata#getSample for validation constraints
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getSample
@Valid public @Valid List<Sample> getSample()
Specification of sample. (empty) name: A name for each sample to serve as a list of the samples that MUST be reported in the following tables. Samples MUST be reported if a statistical design is being captured (i.e. bio or tech replicates). If the type of replicates are not known, samples SHOULD NOT be reported. species: The respective species of the samples analysed. For more complex cases, such as metagenomics, optional columns and userParams should be used. tissue: The respective tissue(s) of the sample. cell_type: The respective cell type(s) of the sample. disease: The respective disease(s) of the sample. description: A human readable description of the sample. custom: Custom parameters describing the sample’s additional properties. Dates MUST be provided in ISO-8601 format.- Returns:
- sample
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setSample
public void setSample(List<Sample> sample)
Set sample.mzTab-M specification example(s):
COM Experiment where all samples consisted of the same two species MTD sample[1] individual number 1 MTD sample[1]-species[1] [NCBITaxon, NCBITaxon:9606, Homo sapiens, ] MTD sample[1]-tissue[1] [BTO, BTO:0000759, liver, ] MTD sample[1]-cell_type[1] [CL, CL:0000182, hepatocyte, ] MTD sample[1]-disease[1] [DOID, DOID:684, hepatocellular carcinoma, ] MTD sample[1]-disease[2] [DOID, DOID:9451, alcoholic fatty liver, ] MTD sample[1]-description Hepatocellular carcinoma samples. MTD sample[1]-custom[1] [,,Extraction date, 2011-12-21] MTD sample[1]-custom[2] [,,Extraction reason, liver biopsy] MTD sample[2] individual number 2 MTD sample[2]-species[1] [NCBITaxon, NCBITaxon:9606, Homo sapiens, ] MTD sample[2]-tissue[1] [BTO, BTO:0000759, liver, ] MTD sample[2]-cell_type[1] [CL, CL:0000182, hepatocyte, ] MTD sample[2]-description Healthy control samples.
- Parameters:
sample
- aList<Sample>
parameter.- See Also:
Metadata#getSample for validation constraints
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sampleProcessing
public Metadata sampleProcessing(List<SampleProcessing> sampleProcessing)
Builder method for sampleProcessing.- Parameters:
sampleProcessing
- aList<SampleProcessing>
parameter.- Returns:
- Metadata
- See Also:
Metadata#setSampleProcessing for specification examples
,Metadata#getSampleProcessing for validation constraints
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addSampleProcessingItem
public Metadata addSampleProcessingItem(SampleProcessing sampleProcessingItem)
Add a single sampleProcessingItem to the sampleProcessing collection.- Parameters:
sampleProcessingItem
- aSampleProcessing
parameter.- Returns:
- Metadata
- See Also:
Metadata#getSampleProcessing for validation constraints
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getSampleProcessing
@Valid public @Valid List<SampleProcessing> getSampleProcessing()
A list of parameters describing a sample processing, preparation or handling step similar to a biological or analytical methods report. The order of the sample_processing items should reflect the order these processing steps were performed in. If multiple parameters are given for a step these MUST be separated by a “|”. If derivatization was performed, it MUST be reported here as a general step, e.g. 'silylation' and the actual derivatization agens MUST be specified in the Section 6.2.54 part.- Returns:
- sampleProcessing
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setSampleProcessing
public void setSampleProcessing(List<SampleProcessing> sampleProcessing)
Set sampleProcessing.mzTab-M specification example(s):
MTD sample_processing[1] [MSIO, MSIO:0000107, metabolism quenching using precooled 60 percent methanol ammonium bicarbonate buffer,] MTD sample_processing[2] [MSIO, MSIO:0000146, centrifugation,] MTD sample_processing[3] [MSIO, MSIO:0000141, metabolite extraction,] MTD sample_processing[4] [MSIO, MSIO:0000141, silylation,]
- Parameters:
sampleProcessing
- aList<SampleProcessing>
parameter.- See Also:
Metadata#getSampleProcessing for validation constraints
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software
public Metadata software(List<Software> software)
Builder method for software.- Parameters:
software
- aList<Software>
parameter.- Returns:
- Metadata
- See Also:
Metadata#setSoftware for specification examples
,Metadata#getSoftware for validation constraints
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addSoftwareItem
public Metadata addSoftwareItem(Software softwareItem)
Add a single softwareItem to the software collection.- Parameters:
softwareItem
- aSoftware
parameter.- Returns:
- Metadata
- See Also:
Metadata#getSoftware for validation constraints
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getSoftware
@NotNull @Valid public @NotNull @Valid List<Software> getSoftware()
Software used to analyze the data and obtain the reported results. The parameter’s value SHOULD contain the software’s version. The order (numbering) should reflect the order in which the tools were used. A software setting used. This field MAY occur multiple times for a single software. The value of this field is deliberately set as a String, since there currently do not exist CV terms for every possible setting.- Returns:
- software
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setSoftware
public void setSoftware(List<Software> software)
Set software.mzTab-M specification example(s):
MTD software[1] [MS, MS:1002879, Progenesis QI, 3.0] MTD software[1]-setting Fragment tolerance = 0.1 Da … MTD software[2]-setting Parent tolerance = 0.5 Da
- Parameters:
software
- aList<Software>
parameter.- See Also:
Metadata#getSoftware for validation constraints
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derivatizationAgent
public Metadata derivatizationAgent(List<Parameter> derivatizationAgent)
Builder method for derivatizationAgent.- Parameters:
derivatizationAgent
- aList<Parameter>
parameter.- Returns:
- Metadata
- See Also:
Metadata#setDerivatizationAgent for specification examples
,Metadata#getDerivatizationAgent for validation constraints
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addDerivatizationAgentItem
public Metadata addDerivatizationAgentItem(Parameter derivatizationAgentItem)
Add a single derivatizationAgentItem to the derivatizationAgent collection.- Parameters:
derivatizationAgentItem
- aParameter
parameter.- Returns:
- Metadata
- See Also:
Metadata#getDerivatizationAgent for validation constraints
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getDerivatizationAgent
@Valid public @Valid List<Parameter> getDerivatizationAgent()
A description of derivatization agents applied to small molecules, using userParams or CV terms where possible.- Returns:
- derivatizationAgent
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setDerivatizationAgent
public void setDerivatizationAgent(List<Parameter> derivatizationAgent)
Set derivatizationAgent.mzTab-M specification example(s):
MTD derivatization_agent[1] [XLMOD, XLMOD:07014, N-methyl-N-t-butyldimethylsilyltrifluoroacetamide, ]
- Parameters:
derivatizationAgent
- aList<Parameter>
parameter.- See Also:
Metadata#getDerivatizationAgent for validation constraints
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msRun
public Metadata msRun(List<MsRun> msRun)
Builder method for msRun.- Parameters:
msRun
- aList<MsRun>
parameter.- Returns:
- Metadata
- See Also:
Metadata#setMsRun for specification examples
,Metadata#getMsRun for validation constraints
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addMsRunItem
public Metadata addMsRunItem(MsRun msRunItem)
Add a single msRunItem to the msRun collection.- Parameters:
msRunItem
- aMsRun
parameter.- Returns:
- Metadata
- See Also:
Metadata#getMsRun for validation constraints
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getMsRun
@NotNull @Valid public @NotNull @Valid List<MsRun> getMsRun()
Specification of ms_run. location: Location of the external data file e.g. raw files on which analysis has been performed. If the actual location of the MS run is unknown, a “null” MUST be used as a place holder value, since the [1-n] cardinality is referenced elsewhere. If pre-fractionation has been performed, then [1-n] ms_runs SHOULD be created per assay. instrument_ref: If different instruments are used in different runs, instrument_ref can be used to link a specific instrument to a specific run. format: Parameter specifying the data format of the external MS data file. If ms_run[1-n]-format is present, ms_run[1-n]-id_format SHOULD also be present, following the parameters specified in Table 1. id_format: Parameter specifying the id format used in the external data file. If ms_run[1-n]-id_format is present, ms_run[1-n]-format SHOULD also be present. fragmentation_method: The type(s) of fragmentation used in a given ms run. scan_polarity: The polarity mode of a given run. Usually only one value SHOULD be given here except for the case of mixed polarity runs. hash: Hash value of the corresponding external MS data file defined in ms_run[1-n]-location. If ms_run[1-n]-hash is present, ms_run[1-n]-hash_method SHOULD also be present. hash_method: A parameter specifying the hash methods used to generate the String in ms_run[1-n]-hash. Specifics of the hash method used MAY follow the definitions of the mzML format. If ms_run[1-n]-hash is present, ms_run[1-n]-hash_method SHOULD also be present.- Returns:
- msRun
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setMsRun
public void setMsRun(List<MsRun> msRun)
Set msRun.mzTab-M specification example(s):
COM location can be a local or remote URI MTD ms_run[1]-location file:///C:/path/to/my/file.mzML MTD ms_run[1]-instrument_ref instrument[1] MTD ms_run[1]-format [MS, MS:1000584, mzML file, ] MTD ms_run[1]-id_format [MS, MS:1000530, mzML unique identifier, ] MTD ms_run[1]-fragmentation_method[1] [MS, MS:1000133, CID, ] COM for mixed polarity scan scenarios MTD ms_run[1]-scan_polarity[1] [MS, MS:1000130, positive scan, ] MTD ms_run[1]-scan_polarity[2] [MS, MS:1000129, negative scan, ] MTD ms_run[1]-hash_method [MS, MS:1000569, SHA-1, ] MTD ms_run[1]-hash de9f2c7fd25e1b3afad3e85a0bd17d9b100db4b3
- Parameters:
msRun
- aList<MsRun>
parameter.- See Also:
Metadata#getMsRun for validation constraints
-
assay
public Metadata assay(List<Assay> assay)
Builder method for assay.- Parameters:
assay
- aList<Assay>
parameter.- Returns:
- Metadata
- See Also:
Metadata#setAssay for specification examples
,Metadata#getAssay for validation constraints
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addAssayItem
public Metadata addAssayItem(Assay assayItem)
Add a single assayItem to the assay collection.- Parameters:
assayItem
- aAssay
parameter.- Returns:
- Metadata
- See Also:
Metadata#getAssay for validation constraints
-
getAssay
@NotNull @Valid public @NotNull @Valid List<Assay> getAssay()
Specification of assay. (empty) name: A name for each assay, to serve as a list of the assays that MUST be reported in the following tables. custom: Additional custom parameters or values for a given assay. external_uri: An external reference uri to further information about the assay, for example via a reference to an object within an ISA-TAB file. sample_ref: An association from a given assay to the sample analysed. ms_run_ref: An association from a given assay to the source MS run. All assays MUST reference exactly one ms_run unless a workflow with pre-fractionation is being encoded, in which case each assay MUST reference n ms_runs where n fractions have been collected. Multiple assays SHOULD reference the same ms_run to capture multiplexed experimental designs.- Returns:
- assay
-
setAssay
public void setAssay(List<Assay> assay)
Set assay.mzTab-M specification example(s):
MTD assay[1] first assay MTD assay[1]-custom[1] [MS, , Assay operator, Fred Blogs] MTD assay[1]-sample_ref sample[1] MTD assay[1]-ms_run_ref ms_run[1] MTD assay[1]-external_uri https://www.ebi.ac.uk/metabolights/MTBLS517/files/i_Investigation.txt?STUDYASSAY=a_e04_c18pos.txt MTD assay[2] second assay MTD assay[2]-sample_ref sample[2]
- Parameters:
assay
- aList<Assay>
parameter.- See Also:
Metadata#getAssay for validation constraints
-
studyVariable
public Metadata studyVariable(List<StudyVariable> studyVariable)
Builder method for studyVariable.- Parameters:
studyVariable
- aList<StudyVariable>
parameter.- Returns:
- Metadata
- See Also:
Metadata#setStudyVariable for specification examples
,Metadata#getStudyVariable for validation constraints
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addStudyVariableItem
public Metadata addStudyVariableItem(StudyVariable studyVariableItem)
Add a single studyVariableItem to the studyVariable collection.- Parameters:
studyVariableItem
- aStudyVariable
parameter.- Returns:
- Metadata
- See Also:
Metadata#getStudyVariable for validation constraints
-
getStudyVariable
@NotNull @Valid public @NotNull @Valid List<StudyVariable> getStudyVariable()
Specification of study_variable. (empty) name: A name for each study variable (experimental condition or factor), to serve as a list of the study variables that MUST be reported in the following tables. For software that does not capture study variables, a single study variable MUST be reported, linking to all assays. This single study variable MUST have the identifier “undefined“. assay_refs: Bar-separated references to the IDs of assays grouped in the study variable. average_function: The function used to calculate the study variable quantification value and the operation used is not arithmetic mean (default) e.g. “geometric mean”, “median”. The 1-n refers to different study variables. variation_function: The function used to calculate the study variable quantification variation value if it is reported and the operation used is not coefficient of variation (default) e.g. “standard error”. description: A textual description of the study variable. factors: Additional parameters or factors, separated by bars, that are known about study variables allowing the capture of more complex, such as nested designs.- Returns:
- studyVariable
-
setStudyVariable
public void setStudyVariable(List<StudyVariable> studyVariable)
Set studyVariable.mzTab-M specification example(s):
MTD study_variable[1] control MTD study_variable[1]-assay_refs assay[1]| assay[2]| assay[3] MTD study_variable-average_function [MS, MS:1002883, median, ] MTD study_variable-variation_function [MS, MS:1002885, standard error, ] MTD study_variable[1]-description Group B (spike-in 0.74 fmol/uL) MTD study_variable[1]-factors [,,rapamycin dose,0.5mg] MTD study_variable[2] 1 minute
- Parameters:
studyVariable
- aList<StudyVariable>
parameter.- See Also:
Metadata#getStudyVariable for validation constraints
-
custom
public Metadata custom(List<Parameter> custom)
Builder method for custom.- Parameters:
custom
- aList<Parameter>
parameter.- Returns:
- Metadata
- See Also:
Metadata#setCustom for specification examples
,Metadata#getCustom for validation constraints
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addCustomItem
public Metadata addCustomItem(Parameter customItem)
Add a single customItem to the custom collection.- Parameters:
customItem
- aParameter
parameter.- Returns:
- Metadata
- See Also:
Metadata#getCustom for validation constraints
-
getCustom
@Valid public @Valid List<Parameter> getCustom()
Any additional parameters describing the analysis reported.- Returns:
- custom
-
setCustom
public void setCustom(List<Parameter> custom)
Set custom.mzTab-M specification example(s):
MTD custom[1] [,,MS operator, Florian]
- Parameters:
custom
- aList<Parameter>
parameter.- See Also:
Metadata#getCustom for validation constraints
-
cv
public Metadata cv(List<CV> cv)
Builder method for cv.- Parameters:
cv
- aList<CV>
parameter.- Returns:
- Metadata
- See Also:
Metadata#setCv for specification examples
,Metadata#getCv for validation constraints
-
addCvItem
public Metadata addCvItem(CV cvItem)
Add a single cvItem to the cv collection.- Parameters:
cvItem
- aCV
parameter.- Returns:
- Metadata
- See Also:
Metadata#getCv for validation constraints
-
getCv
@NotNull @Valid public @NotNull @Valid List<CV> getCv()
Specification of controlled vocabularies. label: A string describing the labels of the controlled vocabularies/ontologies used in the mzTab file as a short-hand e.g. "MS" for PSI-MS. full_name: A string describing the full names of the controlled vocabularies/ontologies used in the mzTab file. version: A string describing the version of the controlled vocabularies/ontologies used in the mzTab file. uri: A string containing the URIs of the controlled vocabularies/ontologies used in the mzTab file.- Returns:
- cv
-
setCv
public void setCv(List<CV> cv)
Set cv.mzTab-M specification example(s):
MTD cv[1]-label MS MTD cv[1]-full_name PSI-MS controlled vocabulary MTD cv[1]-version 4.1.11 MTD cv[1]-uri https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo
- Parameters:
cv
- aList<CV>
parameter.- See Also:
Metadata#getCv for validation constraints
-
smallMoleculeQuantificationUnit
public Metadata smallMoleculeQuantificationUnit(Parameter smallMoleculeQuantificationUnit)
Builder method for smallMoleculeQuantificationUnit.- Parameters:
smallMoleculeQuantificationUnit
- aParameter
parameter.- Returns:
- Metadata
- See Also:
Metadata#setSmallMoleculeQuantificationUnit for specification examples
,Metadata#getSmallMoleculeQuantificationUnit for validation constraints
-
getSmallMoleculeQuantificationUnit
@NotNull @Valid public @NotNull @Valid Parameter getSmallMoleculeQuantificationUnit()
Defines what type of units are reported in the small molecule summary quantification / abundance fields.- Returns:
- smallMoleculeQuantificationUnit
-
setSmallMoleculeQuantificationUnit
public void setSmallMoleculeQuantificationUnit(Parameter smallMoleculeQuantificationUnit)
Set smallMoleculeQuantificationUnit.- Parameters:
smallMoleculeQuantificationUnit
- aParameter
parameter.- See Also:
Metadata#getSmallMoleculeQuantificationUnit for validation constraints
-
smallMoleculeFeatureQuantificationUnit
public Metadata smallMoleculeFeatureQuantificationUnit(Parameter smallMoleculeFeatureQuantificationUnit)
Builder method for smallMoleculeFeatureQuantificationUnit.- Parameters:
smallMoleculeFeatureQuantificationUnit
- aParameter
parameter.- Returns:
- Metadata
- See Also:
Metadata#setSmallMoleculeFeatureQuantificationUnit for specification examples
,Metadata#getSmallMoleculeFeatureQuantificationUnit for validation constraints
-
getSmallMoleculeFeatureQuantificationUnit
@NotNull @Valid public @NotNull @Valid Parameter getSmallMoleculeFeatureQuantificationUnit()
Defines what type of units are reported in the small molecule feature quantification / abundance fields.- Returns:
- smallMoleculeFeatureQuantificationUnit
-
setSmallMoleculeFeatureQuantificationUnit
public void setSmallMoleculeFeatureQuantificationUnit(Parameter smallMoleculeFeatureQuantificationUnit)
Set smallMoleculeFeatureQuantificationUnit.- Parameters:
smallMoleculeFeatureQuantificationUnit
- aParameter
parameter.- See Also:
Metadata#getSmallMoleculeFeatureQuantificationUnit for validation constraints
-
smallMoleculeIdentificationReliability
public Metadata smallMoleculeIdentificationReliability(Parameter smallMoleculeIdentificationReliability)
Builder method for smallMoleculeIdentificationReliability.- Parameters:
smallMoleculeIdentificationReliability
- aParameter
parameter.- Returns:
- Metadata
- See Also:
Metadata#setSmallMoleculeIdentificationReliability for specification examples
,Metadata#getSmallMoleculeIdentificationReliability for validation constraints
-
getSmallMoleculeIdentificationReliability
@Valid public @Valid Parameter getSmallMoleculeIdentificationReliability()
The system used for giving reliability / confidence codes to small molecule identifications MUST be specified if not using the default codes.- Returns:
- smallMoleculeIdentificationReliability
-
setSmallMoleculeIdentificationReliability
public void setSmallMoleculeIdentificationReliability(Parameter smallMoleculeIdentificationReliability)
Set smallMoleculeIdentificationReliability.- Parameters:
smallMoleculeIdentificationReliability
- aParameter
parameter.- See Also:
Metadata#getSmallMoleculeIdentificationReliability for validation constraints
-
database
public Metadata database(List<Database> database)
Builder method for database.- Parameters:
database
- aList<Database>
parameter.- Returns:
- Metadata
- See Also:
Metadata#setDatabase for specification examples
,Metadata#getDatabase for validation constraints
-
addDatabaseItem
public Metadata addDatabaseItem(Database databaseItem)
Add a single databaseItem to the database collection.- Parameters:
databaseItem
- aDatabase
parameter.- Returns:
- Metadata
- See Also:
Metadata#getDatabase for validation constraints
-
getDatabase
@NotNull @Valid public @NotNull @Valid List<Database> getDatabase()
Specification of databases. (empty): The description of databases used. For cases, where a known database has not been used for identification, a userParam SHOULD be inserted to describe any identification performed e.g. de novo. If no identification has been performed at all then "no database" should be inserted followed by null. prefix: The prefix used in the “identifier” column of data tables. For the “no database” case "null" must be used. version: The database version is mandatory where identification has been performed. This may be a formal version number e.g. “1.4.1”, a date of access “2016-10-27” (ISO-8601 format) or “Unknown” if there is no suitable version that can be annotated. uri: The URI to the database. For the “no database” case, "null" must be reported.- Returns:
- database
-
setDatabase
public void setDatabase(List<Database> database)
Set database.mzTab-M specification example(s):
MTD database[1] [MIRIAM, MIR:00100079, HMDB, ] MTD database[1]-prefix hmdb MTD database[1]-version 3.6 MTD database[1]-uri http://www.hmdb.ca/ MTD database[2] [,, "de novo", ] MTD database[2]-prefix dn MTD database[2]-version Unknown MTD database[2]-uri null MTD database[3] [,, "no database", null ] MTD database[3]-prefix null MTD database[3]-version Unknown MTD database[3]-uri null
- Parameters:
database
- aList<Database>
parameter.- See Also:
Metadata#getDatabase for validation constraints
-
idConfidenceMeasure
public Metadata idConfidenceMeasure(List<Parameter> idConfidenceMeasure)
Builder method for idConfidenceMeasure.- Parameters:
idConfidenceMeasure
- aList<Parameter>
parameter.- Returns:
- Metadata
- See Also:
Metadata#setIdConfidenceMeasure for specification examples
,Metadata#getIdConfidenceMeasure for validation constraints
-
addIdConfidenceMeasureItem
public Metadata addIdConfidenceMeasureItem(Parameter idConfidenceMeasureItem)
Add a single idConfidenceMeasureItem to the idConfidenceMeasure collection.- Parameters:
idConfidenceMeasureItem
- aParameter
parameter.- Returns:
- Metadata
- See Also:
Metadata#getIdConfidenceMeasure for validation constraints
-
getIdConfidenceMeasure
@NotNull @Valid public @NotNull @Valid List<Parameter> getIdConfidenceMeasure()
The type of small molecule confidence measures or scores MUST be reported as a CV parameter [1-n]. The CV parameter definition should formally state whether the ordering is high to low or vice versa. The order of the scores SHOULD reflect their importance for the identification and be used to determine the identification’s rank.- Returns:
- idConfidenceMeasure
-
setIdConfidenceMeasure
public void setIdConfidenceMeasure(List<Parameter> idConfidenceMeasure)
Set idConfidenceMeasure.mzTab-M specification example(s):
MTD id_confidence_measure[1] [MS,MS:1002889,Progenesis MetaScope Score,] MTD id_confidence_measure[2] [MS,MS:1002890,fragmentation score,] MTD id_confidence_measure[3] [MS,MS:1002891,isotopic fit score,]
- Parameters:
idConfidenceMeasure
- aList<Parameter>
parameter.- See Also:
Metadata#getIdConfidenceMeasure for validation constraints
-
colunitSmallMolecule
public Metadata colunitSmallMolecule(List<ColumnParameterMapping> colunitSmallMolecule)
Builder method for colunitSmallMolecule.- Parameters:
colunitSmallMolecule
- aList<ColumnParameterMapping>
parameter.- Returns:
- Metadata
- See Also:
Metadata#setColunitSmallMolecule for specification examples
,Metadata#getColunitSmallMolecule for validation constraints
-
addColunitSmallMoleculeItem
public Metadata addColunitSmallMoleculeItem(ColumnParameterMapping colunitSmallMoleculeItem)
Add a single colunitSmallMoleculeItem to the colunitSmallMolecule collection.- Parameters:
colunitSmallMoleculeItem
- aColumnParameterMapping
parameter.- Returns:
- Metadata
- See Also:
Metadata#getColunitSmallMolecule for validation constraints
-
getColunitSmallMolecule
@Valid public @Valid List<ColumnParameterMapping> getColunitSmallMolecule()
Defines the used unit for a column in the small molecule section. The format of the value has to be \{column name}=\{Parameter defining the unit}. This field MUST NOT be used to define a unit for quantification columns. The unit used for small molecule quantification values MUST be set in small_molecule-quantification_unit.- Returns:
- colunitSmallMolecule
-
setColunitSmallMolecule
public void setColunitSmallMolecule(List<ColumnParameterMapping> colunitSmallMolecule)
Set colunitSmallMolecule.mzTab-M specification example(s):
COM colunit for optional small molecule summary column with the name 'opt_global_cv_MS:MS:1002954_collisional_cross_sectional_area' MTD colunit-small_molecule opt_global_cv_MS:MS:1002954_collisional_cross_sectional_area=[UO,UO:00003241, square angstrom,]
- Parameters:
colunitSmallMolecule
- aList<ColumnParameterMapping>
parameter.- See Also:
Metadata#getColunitSmallMolecule for validation constraints
-
colunitSmallMoleculeFeature
public Metadata colunitSmallMoleculeFeature(List<ColumnParameterMapping> colunitSmallMoleculeFeature)
Builder method for colunitSmallMoleculeFeature.- Parameters:
colunitSmallMoleculeFeature
- aList<ColumnParameterMapping>
parameter.- Returns:
- Metadata
- See Also:
Metadata#setColunitSmallMoleculeFeature for specification examples
,Metadata#getColunitSmallMoleculeFeature for validation constraints
-
addColunitSmallMoleculeFeatureItem
public Metadata addColunitSmallMoleculeFeatureItem(ColumnParameterMapping colunitSmallMoleculeFeatureItem)
Add a single colunitSmallMoleculeFeatureItem to the colunitSmallMoleculeFeature collection.- Parameters:
colunitSmallMoleculeFeatureItem
- aColumnParameterMapping
parameter.- Returns:
- Metadata
- See Also:
Metadata#getColunitSmallMoleculeFeature for validation constraints
-
getColunitSmallMoleculeFeature
@Valid public @Valid List<ColumnParameterMapping> getColunitSmallMoleculeFeature()
Defines the used unit for a column in the small molecule feature section. The format of the value has to be \{column name}=\{Parameter defining the unit}. This field MUST NOT be used to define a unit for quantification columns. The unit used for small molecule quantification values MUST be set in small_molecule_feature-quantification_unit.- Returns:
- colunitSmallMoleculeFeature
-
setColunitSmallMoleculeFeature
public void setColunitSmallMoleculeFeature(List<ColumnParameterMapping> colunitSmallMoleculeFeature)
Set colunitSmallMoleculeFeature.mzTab-M specification example(s):
COM colunit for optional small molecule feature column with the name 'opt_ms_run[1]_cv_MS:MS:1002476_ion_mobility_drift_time' referencing ms_run[1] MTD colunit-small_molecule_feature opt_ms_run[1]_cv_MS:MS:1002476_ion_mobility_drift_time=[UO,UO:0000031, minute,]
- Parameters:
colunitSmallMoleculeFeature
- aList<ColumnParameterMapping>
parameter.- See Also:
Metadata#getColunitSmallMoleculeFeature for validation constraints
-
colunitSmallMoleculeEvidence
public Metadata colunitSmallMoleculeEvidence(List<ColumnParameterMapping> colunitSmallMoleculeEvidence)
Builder method for colunitSmallMoleculeEvidence.- Parameters:
colunitSmallMoleculeEvidence
- aList<ColumnParameterMapping>
parameter.- Returns:
- Metadata
- See Also:
Metadata#setColunitSmallMoleculeEvidence for specification examples
,Metadata#getColunitSmallMoleculeEvidence for validation constraints
-
addColunitSmallMoleculeEvidenceItem
public Metadata addColunitSmallMoleculeEvidenceItem(ColumnParameterMapping colunitSmallMoleculeEvidenceItem)
Add a single colunitSmallMoleculeEvidenceItem to the colunitSmallMoleculeEvidence collection.- Parameters:
colunitSmallMoleculeEvidenceItem
- aColumnParameterMapping
parameter.- Returns:
- Metadata
- See Also:
Metadata#getColunitSmallMoleculeEvidence for validation constraints
-
getColunitSmallMoleculeEvidence
@Valid public @Valid List<ColumnParameterMapping> getColunitSmallMoleculeEvidence()
Defines the used unit for a column in the small molecule evidence section. The format of the value has to be \{column name}=\{Parameter defining the unit}.- Returns:
- colunitSmallMoleculeEvidence
-
setColunitSmallMoleculeEvidence
public void setColunitSmallMoleculeEvidence(List<ColumnParameterMapping> colunitSmallMoleculeEvidence)
Set colunitSmallMoleculeEvidence.mzTab-M specification example(s):
COM colunit for optional small molecule evidence column with the name 'opt_global_mass_error' MTD colunit-small_molecule_evidence opt_global_mass_error=[UO, UO:0000169, parts per million, ]
- Parameters:
colunitSmallMoleculeEvidence
- aList<ColumnParameterMapping>
parameter.- See Also:
Metadata#getColunitSmallMoleculeEvidence for validation constraints
-
-