Package de.isas.mztab2.model
Class MsRun
- java.lang.Object
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- de.isas.mztab2.model.MsRun
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@Generated(value="io.swagger.codegen.languages.JavaClientCodegen", date="2021-01-02T19:26:21.550+01:00") public class MsRun extends Object
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.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
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
MsRun.Properties
Property enumeration for MsRun.
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Constructor Summary
Constructors Constructor Description MsRun()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description MsRun
addFragmentationMethodItem(Parameter fragmentationMethodItem)
Add a single fragmentationMethodItem to the fragmentationMethod collection.MsRun
addScanPolarityItem(Parameter scanPolarityItem)
Add a single scanPolarityItem to the scanPolarity collection.boolean
equals(Object o)
MsRun
format(Parameter format)
Builder method for format.MsRun
fragmentationMethod(List<Parameter> fragmentationMethod)
Builder method for fragmentationMethod.@Valid Parameter
getFormat()
The msRun's file format.@Valid List<Parameter>
getFragmentationMethod()
The fragmentation methods applied during this msRun.String
getHash()
The file hash value of this msRun's data file.@Valid Parameter
getHashMethod()
The hash method used to calculate the file hash.@NotNull @Min(1L) Integer
getId()
Get id.@Valid Parameter
getIdFormat()
The msRun's mass spectra id format.@Valid Instrument
getInstrumentRef()
The instrument on which this msRun was measured.@NotNull String
getLocation()
The msRun's location URI.String
getName()
The msRun's name.@Valid List<Parameter>
getScanPolarity()
The scan polarity/polarities used during this msRun.MsRun
hash(String hash)
Builder method for hash.int
hashCode()
MsRun
hashMethod(Parameter hashMethod)
Builder method for hashMethod.MsRun
id(Integer id)
Builder method for id.MsRun
idFormat(Parameter idFormat)
Builder method for idFormat.MsRun
instrumentRef(Instrument instrumentRef)
Builder method for instrumentRef.MsRun
location(String location)
Builder method for location.MsRun
name(String name)
Builder method for name.MsRun
scanPolarity(List<Parameter> scanPolarity)
Builder method for scanPolarity.void
setFormat(Parameter format)
Set format.void
setFragmentationMethod(List<Parameter> fragmentationMethod)
Set fragmentationMethod.void
setHash(String hash)
Set hash.void
setHashMethod(Parameter hashMethod)
Set hashMethod.void
setId(Integer id)
Set id.void
setIdFormat(Parameter idFormat)
Set idFormat.void
setInstrumentRef(Instrument instrumentRef)
Set instrumentRef.void
setLocation(String location)
Set location.void
setName(String name)
Set name.void
setScanPolarity(List<Parameter> scanPolarity)
Set scanPolarity.String
toString()
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Constructor Detail
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MsRun
public MsRun()
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Method Detail
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id
public MsRun id(Integer id)
Builder method for id.- Parameters:
id
- aInteger
parameter.- Returns:
- MsRun
- See Also:
MsRun#setId for specification examples
,MsRun#getId for validation constraints
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setId
public void setId(Integer id)
Set id.- Parameters:
id
- aInteger
parameter.- See Also:
MsRun#getId for validation constraints
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name
public MsRun name(String name)
Builder method for name.- Parameters:
name
- aString
parameter.- Returns:
- MsRun
- See Also:
MsRun#setName for specification examples
,MsRun#getName for validation constraints
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setName
public void setName(String name)
Set name.- Parameters:
name
- aString
parameter.- See Also:
MsRun#getName for validation constraints
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location
public MsRun location(String location)
Builder method for location.- Parameters:
location
- aString
parameter.- Returns:
- MsRun
- See Also:
MsRun#setLocation for specification examples
,MsRun#getLocation for validation constraints
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getLocation
@NotNull public @NotNull String getLocation()
The msRun's location URI.- Returns:
- location
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setLocation
public void setLocation(String location)
Set location.- Parameters:
location
- aString
parameter.- See Also:
MsRun#getLocation for validation constraints
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instrumentRef
public MsRun instrumentRef(Instrument instrumentRef)
Builder method for instrumentRef.- Parameters:
instrumentRef
- aInstrument
parameter.- Returns:
- MsRun
- See Also:
MsRun#setInstrumentRef for specification examples
,MsRun#getInstrumentRef for validation constraints
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getInstrumentRef
@Valid public @Valid Instrument getInstrumentRef()
The instrument on which this msRun was measured.- Returns:
- instrumentRef
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setInstrumentRef
public void setInstrumentRef(Instrument instrumentRef)
Set instrumentRef.- Parameters:
instrumentRef
- aInstrument
parameter.- See Also:
MsRun#getInstrumentRef for validation constraints
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format
public MsRun format(Parameter format)
Builder method for format.- Parameters:
format
- aParameter
parameter.- Returns:
- MsRun
- See Also:
MsRun#setFormat for specification examples
,MsRun#getFormat for validation constraints
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setFormat
public void setFormat(Parameter format)
Set format.- Parameters:
format
- aParameter
parameter.- See Also:
MsRun#getFormat for validation constraints
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idFormat
public MsRun idFormat(Parameter idFormat)
Builder method for idFormat.- Parameters:
idFormat
- aParameter
parameter.- Returns:
- MsRun
- See Also:
MsRun#setIdFormat for specification examples
,MsRun#getIdFormat for validation constraints
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getIdFormat
@Valid public @Valid Parameter getIdFormat()
The msRun's mass spectra id format.- Returns:
- idFormat
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setIdFormat
public void setIdFormat(Parameter idFormat)
Set idFormat.- Parameters:
idFormat
- aParameter
parameter.- See Also:
MsRun#getIdFormat for validation constraints
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fragmentationMethod
public MsRun fragmentationMethod(List<Parameter> fragmentationMethod)
Builder method for fragmentationMethod.- Parameters:
fragmentationMethod
- aList<Parameter>
parameter.- Returns:
- MsRun
- See Also:
MsRun#setFragmentationMethod for specification examples
,MsRun#getFragmentationMethod for validation constraints
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addFragmentationMethodItem
public MsRun addFragmentationMethodItem(Parameter fragmentationMethodItem)
Add a single fragmentationMethodItem to the fragmentationMethod collection.- Parameters:
fragmentationMethodItem
- aParameter
parameter.- Returns:
- MsRun
- See Also:
MsRun#getFragmentationMethod for validation constraints
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getFragmentationMethod
@Valid public @Valid List<Parameter> getFragmentationMethod()
The fragmentation methods applied during this msRun.- Returns:
- fragmentationMethod
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setFragmentationMethod
public void setFragmentationMethod(List<Parameter> fragmentationMethod)
Set fragmentationMethod.- Parameters:
fragmentationMethod
- aList<Parameter>
parameter.- See Also:
MsRun#getFragmentationMethod for validation constraints
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scanPolarity
public MsRun scanPolarity(List<Parameter> scanPolarity)
Builder method for scanPolarity.- Parameters:
scanPolarity
- aList<Parameter>
parameter.- Returns:
- MsRun
- See Also:
MsRun#setScanPolarity for specification examples
,MsRun#getScanPolarity for validation constraints
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addScanPolarityItem
public MsRun addScanPolarityItem(Parameter scanPolarityItem)
Add a single scanPolarityItem to the scanPolarity collection.- Parameters:
scanPolarityItem
- aParameter
parameter.- Returns:
- MsRun
- See Also:
MsRun#getScanPolarity for validation constraints
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getScanPolarity
@Valid public @Valid List<Parameter> getScanPolarity()
The scan polarity/polarities used during this msRun.- Returns:
- scanPolarity
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setScanPolarity
public void setScanPolarity(List<Parameter> scanPolarity)
Set scanPolarity.- Parameters:
scanPolarity
- aList<Parameter>
parameter.- See Also:
MsRun#getScanPolarity for validation constraints
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hash
public MsRun hash(String hash)
Builder method for hash.- Parameters:
hash
- aString
parameter.- Returns:
- MsRun
- See Also:
MsRun#setHash for specification examples
,MsRun#getHash for validation constraints
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setHash
public void setHash(String hash)
Set hash.- Parameters:
hash
- aString
parameter.- See Also:
MsRun#getHash for validation constraints
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hashMethod
public MsRun hashMethod(Parameter hashMethod)
Builder method for hashMethod.- Parameters:
hashMethod
- aParameter
parameter.- Returns:
- MsRun
- See Also:
MsRun#setHashMethod for specification examples
,MsRun#getHashMethod for validation constraints
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getHashMethod
@Valid public @Valid Parameter getHashMethod()
The hash method used to calculate the file hash.- Returns:
- hashMethod
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setHashMethod
public void setHashMethod(Parameter hashMethod)
Set hashMethod.- Parameters:
hashMethod
- aParameter
parameter.- See Also:
MsRun#getHashMethod for validation constraints
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