Package de.isas.mztab2.model

Class Assay

java.lang.Object

de.isas.mztab2.model.Assay

@Generated(value="io.swagger.codegen.languages.JavaClientCodegen",
           date="2021-01-02T19:26:21.550+01:00")
public class Assay
extends Object

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.

mzTab-M specification example(s):

MTD     assay[1]        first assay
MTD     assay[1]-custom[1]      [MS, , Assay operator, Fred Blogs]
MTD     assay[1]-external_uri   https://www.ebi.ac.uk/metabolights/MTBLS517/files/i_Investigation.txt?STUDYASSAY=a_e04_c18pos.txt
MTD     assay[1]-sample_ref     sample[1]
MTD     assay[1]-ms_run_ref     ms_run[1]

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	Assay.Properties	Property enumeration for Assay.

Constructor Summary

Constructors

Constructor	Description
Assay()

Method Summary

Modifier and Type	Method	Description
Assay	addCustomItem(Parameter customItem)	Add a single customItem to the custom collection.
Assay	addMsRunRefItem(MsRun msRunRefItem)	Add a single msRunRefItem to the msRunRef collection.
Assay	custom(List<Parameter> custom)	Builder method for custom.
boolean	equals(Object o)
Assay	externalUri(String externalUri)	Builder method for externalUri.
@Valid List<Parameter>	getCustom()	Additional user or cv parameters.
String	getExternalUri()	An external URI to further information about this assay.
@Min(1L) Integer	getId()	Get id.
@NotNull @Valid @Size(min=1) List<MsRun>	getMsRunRef()	The ms run(s) referenced by this assay.
@NotNull String	getName()	The assay name.
@Valid Sample	getSampleRef()	The sample referenced by this assay.
int	hashCode()
Assay	id(Integer id)	Builder method for id.
Assay	msRunRef(List<MsRun> msRunRef)	Builder method for msRunRef.
Assay	name(String name)	Builder method for name.
Assay	sampleRef(Sample sampleRef)	Builder method for sampleRef.
void	setCustom(List<Parameter> custom)	Set custom.
void	setExternalUri(String externalUri)	Set externalUri.
void	setId(Integer id)	Set id.
void	setMsRunRef(List<MsRun> msRunRef)	Set msRunRef.
void	setName(String name)	Set name.
void	setSampleRef(Sample sampleRef)	Set sampleRef.
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

Assay

public Assay()

Method Detail

id

public Assay id(Integer id)

Builder method for id.

Parameters:

id - a Integer parameter.

Returns:

Assay

See Also:

Assay#setId for specification examples, Assay#getId for validation constraints

getId

@Min(1L)
public @Min(1L) Integer getId()

Get id.

Minimum: 1

Returns:

id

setId

public void setId(Integer id)

Set id.

Parameters:

id - a Integer parameter.

See Also:

Assay#getId for validation constraints

name

public Assay name(String name)

Builder method for name.

Parameters:

name - a String parameter.

Returns:

Assay

See Also:

Assay#setName for specification examples, Assay#getName for validation constraints

getName

@NotNull
public @NotNull String getName()

The assay name.

Returns:

name

setName

public void setName(String name)

Set name.

Parameters:

name - a String parameter.

See Also:

Assay#getName for validation constraints

custom

public Assay custom(List<Parameter> custom)

Builder method for custom.

Parameters:

custom - a List<Parameter> parameter.

Returns:

Assay

See Also:

Assay#setCustom for specification examples, Assay#getCustom for validation constraints

addCustomItem

public Assay addCustomItem(Parameter customItem)

Add a single customItem to the custom collection.

Parameters:

customItem - a Parameter parameter.

Returns:

Assay

See Also:

Assay#getCustom for validation constraints

getCustom

@Valid
public @Valid List<Parameter> getCustom()

Additional user or cv parameters.

Returns:

custom

setCustom

public void setCustom(List<Parameter> custom)

Set custom.

Parameters:

custom - a List<Parameter> parameter.

See Also:

Assay#getCustom for validation constraints

externalUri

public Assay externalUri(String externalUri)

Builder method for externalUri.

Parameters:

externalUri - a String parameter.

Returns:

Assay

See Also:

Assay#setExternalUri for specification examples, Assay#getExternalUri for validation constraints

getExternalUri

public String getExternalUri()

An external URI to further information about this assay.

Returns:

externalUri

setExternalUri

public void setExternalUri(String externalUri)

Set externalUri.

Parameters:

externalUri - a String parameter.

See Also:

Assay#getExternalUri for validation constraints

sampleRef

public Assay sampleRef(Sample sampleRef)

Builder method for sampleRef.

Parameters:

sampleRef - a Sample parameter.

Returns:

Assay

See Also:

Assay#setSampleRef for specification examples, Assay#getSampleRef for validation constraints

getSampleRef

@Valid
public @Valid Sample getSampleRef()

The sample referenced by this assay.

Returns:

sampleRef

setSampleRef

public void setSampleRef(Sample sampleRef)

Set sampleRef.

Parameters:

sampleRef - a Sample parameter.

See Also:

Assay#getSampleRef for validation constraints

msRunRef

public Assay msRunRef(List<MsRun> msRunRef)

Builder method for msRunRef.

Parameters:

msRunRef - a List<MsRun> parameter.

Returns:

Assay

See Also:

Assay#setMsRunRef for specification examples, Assay#getMsRunRef for validation constraints

addMsRunRefItem

public Assay addMsRunRefItem(MsRun msRunRefItem)

Add a single msRunRefItem to the msRunRef collection.

Parameters:

msRunRefItem - a MsRun parameter.

Returns:

Assay

See Also:

Assay#getMsRunRef for validation constraints

getMsRunRef

@NotNull
@Valid
@Size(min=1)
public @NotNull @Valid @Size(min=1) List<MsRun> getMsRunRef()

The ms run(s) referenced by this assay.

Returns:

msRunRef

setMsRunRef

public void setMsRunRef(List<MsRun> msRunRef)

Set msRunRef.

Parameters:

msRunRef - a List<MsRun> parameter.

See Also:

Assay#getMsRunRef for validation constraints

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object