Package de.isas.mztab2.model
Class SmallMoleculeFeature
- java.lang.Object
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- de.isas.mztab2.model.SmallMoleculeFeature
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@Generated(value="io.swagger.codegen.languages.JavaClientCodegen", date="2021-01-02T19:25:37.430+01:00") public class SmallMoleculeFeature extends ObjectThe small molecule feature section is table-based, representing individual MS regions (generally considered to be the elution profile for all isotopomers formed from a single charge state of a molecule), that have been measured/quantified. However, for approaches that quantify individual isotopomers e.g. stable isotope labelling/flux studies, then each SMF row SHOULD represent a single isotopomer. Different adducts or derivatives and different charge states of individual molecules should be reported as separate SMF rows. The small molecule feature section MUST always come after the Small Molecule Table. All table columns MUST be Tab separated. There MUST NOT be any empty cells. Missing values MUST be reported using “null”. The order of columns MUST follow the order specified below. All columns are MANDATORY except for “opt_” columns.
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Nested Class Summary
Nested Classes Modifier and Type Class Description static classSmallMoleculeFeature.HeaderPrefixEnumThe small molecule feature table header prefix.static classSmallMoleculeFeature.PrefixEnumThe small molecule feature table row prefix.static classSmallMoleculeFeature.PropertiesProperty enumeration for SmallMoleculeFeature.
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Constructor Summary
Constructors Constructor Description SmallMoleculeFeature()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description SmallMoleculeFeatureabundanceAssay(List<Double> abundanceAssay)Builder method for abundanceAssay.SmallMoleculeFeatureaddAbundanceAssayItem(Double abundanceAssayItem)Add a single abundanceAssayItem to the abundanceAssay collection.SmallMoleculeFeatureaddCommentItem(Comment commentItem)Add a single commentItem to the comment collection.SmallMoleculeFeatureaddOptItem(OptColumnMapping optItem)Add a single optItem to the opt collection.SmallMoleculeFeatureaddSmeIdRefsItem(Integer smeIdRefsItem)Add a single smeIdRefsItem to the smeIdRefs collection.SmallMoleculeFeatureadductIon(String adductIon)Builder method for adductIon.SmallMoleculeFeaturecharge(Integer charge)Builder method for charge.SmallMoleculeFeaturecomment(List<Comment> comment)Builder method for comment.booleanequals(Object o)SmallMoleculeFeatureexpMassToCharge(Double expMassToCharge)Builder method for expMassToCharge.List<Double>getAbundanceAssay()The feature’s abundance in every assay described in the metadata section MUST be reported.@Pattern(regexp="^\\[\\d*M([+-][\\w]*)\\]\\d*[+-]$") StringgetAdductIon()The assumed classification of this molecule’s adduct ion after detection, following the general style in the 2013 IUPAC recommendations on terms relating to MS e.g.@NotNull IntegergetCharge()The feature’s charge value using positive integers both for positive and negative polarity modes.@Valid List<Comment>getComment()Get comment.@NotNull DoublegetExpMassToCharge()The experimental mass/charge value for the feature, by default assumed to be the mean across assays or a representative value.SmallMoleculeFeature.HeaderPrefixEnumgetHeaderPrefix()The small molecule feature table header prefix.@Valid ParametergetIsotopomer()If de-isotoping has not been performed, then the isotopomer quantified MUST be reported here e.g. “+1”, “+2”, “13C peak” using CV terms, otherwise (i.e. for approaches where SMF rows are de-isotoped features) this MUST be null.@Valid List<OptColumnMapping>getOpt()Additional columns can be added to the end of the small molecule feature table.SmallMoleculeFeature.PrefixEnumgetPrefix()The small molecule feature table row prefix.DoublegetRetentionTimeInSeconds()The apex of the feature on the retention time axis, in a Master or aggregate MS run.DoublegetRetentionTimeInSecondsEnd()The end time of the feature on the retention time axis, in a Master or aggregate MS run.DoublegetRetentionTimeInSecondsStart()The start time of the feature on the retention time axis, in a Master or aggregate MS run.IntegergetSmeIdRefAmbiguityCode()If multiple values are given under SME_ID_REFS, one of the following codes MUST be provided. 1=Ambiguous identification; 2=Only different evidence streams for the same molecule with no ambiguity; 3=Both ambiguous identification and multiple evidence streams.List<Integer>getSmeIdRefs()References to the identification evidence (SME elements) via referencing SME_ID values.@NotNull IntegergetSmfId()A within file unique identifier for the small molecule feature.inthashCode()SmallMoleculeFeatureisotopomer(Parameter isotopomer)Builder method for isotopomer.SmallMoleculeFeatureopt(List<OptColumnMapping> opt)Builder method for opt.SmallMoleculeFeatureretentionTimeInSeconds(Double retentionTimeInSeconds)Builder method for retentionTimeInSeconds.SmallMoleculeFeatureretentionTimeInSecondsEnd(Double retentionTimeInSecondsEnd)Builder method for retentionTimeInSecondsEnd.SmallMoleculeFeatureretentionTimeInSecondsStart(Double retentionTimeInSecondsStart)Builder method for retentionTimeInSecondsStart.voidsetAbundanceAssay(List<Double> abundanceAssay)Set abundanceAssay.voidsetAdductIon(String adductIon)Set adductIon.voidsetCharge(Integer charge)Set charge.voidsetComment(List<Comment> comment)Set comment.voidsetExpMassToCharge(Double expMassToCharge)Set expMassToCharge.voidsetIsotopomer(Parameter isotopomer)Set isotopomer.voidsetOpt(List<OptColumnMapping> opt)Set opt.voidsetRetentionTimeInSeconds(Double retentionTimeInSeconds)Set retentionTimeInSeconds.voidsetRetentionTimeInSecondsEnd(Double retentionTimeInSecondsEnd)Set retentionTimeInSecondsEnd.voidsetRetentionTimeInSecondsStart(Double retentionTimeInSecondsStart)Set retentionTimeInSecondsStart.voidsetSmeIdRefAmbiguityCode(Integer smeIdRefAmbiguityCode)Set smeIdRefAmbiguityCode.voidsetSmeIdRefs(List<Integer> smeIdRefs)Set smeIdRefs.voidsetSmfId(Integer smfId)Set smfId.SmallMoleculeFeaturesmeIdRefAmbiguityCode(Integer smeIdRefAmbiguityCode)Builder method for smeIdRefAmbiguityCode.SmallMoleculeFeaturesmeIdRefs(List<Integer> smeIdRefs)Builder method for smeIdRefs.SmallMoleculeFeaturesmfId(Integer smfId)Builder method for smfId.StringtoString()
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Constructor Detail
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SmallMoleculeFeature
public SmallMoleculeFeature()
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Method Detail
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getPrefix
public SmallMoleculeFeature.PrefixEnum getPrefix()
The small molecule feature table row prefix. SMF MUST be used for rows of the small molecule feature table.- Returns:
- prefix
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getHeaderPrefix
public SmallMoleculeFeature.HeaderPrefixEnum getHeaderPrefix()
The small molecule feature table header prefix. SFH MUST be used for the small molecule feature table header line (the column labels).- Returns:
- headerPrefix
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smfId
public SmallMoleculeFeature smfId(Integer smfId)
Builder method for smfId.- Parameters:
smfId- aIntegerparameter.- Returns:
- SmallMoleculeFeature
- See Also:
SmallMoleculeFeature#setSmfId for specification examples,SmallMoleculeFeature#getSmfId for validation constraints
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getSmfId
@NotNull public @NotNull Integer getSmfId()
A within file unique identifier for the small molecule feature.- Returns:
- smfId
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setSmfId
public void setSmfId(Integer smfId)
Set smfId.mzTab-M specification example(s):
SFH SMF_ID … SMF 1 … SMF 2 …- Parameters:
smfId- aIntegerparameter.- See Also:
SmallMoleculeFeature#getSmfId for validation constraints
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smeIdRefs
public SmallMoleculeFeature smeIdRefs(List<Integer> smeIdRefs)
Builder method for smeIdRefs.- Parameters:
smeIdRefs- aList<Integer>parameter.- Returns:
- SmallMoleculeFeature
- See Also:
SmallMoleculeFeature#setSmeIdRefs for specification examples,SmallMoleculeFeature#getSmeIdRefs for validation constraints
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addSmeIdRefsItem
public SmallMoleculeFeature addSmeIdRefsItem(Integer smeIdRefsItem)
Add a single smeIdRefsItem to the smeIdRefs collection.- Parameters:
smeIdRefsItem- aIntegerparameter.- Returns:
- SmallMoleculeFeature
- See Also:
SmallMoleculeFeature#getSmeIdRefs for validation constraints
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getSmeIdRefs
public List<Integer> getSmeIdRefs()
References to the identification evidence (SME elements) via referencing SME_ID values. Multiple values MAY be provided as a “|” separated list to indicate ambiguity in the identification or to indicate that different types of data supported the identifiction (see SME_ID_REF_ambiguity_code). For the case of a consensus approach where multiple adduct forms are used to infer the SML ID, different features should just reference the same SME_ID value(s).- Returns:
- smeIdRefs
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setSmeIdRefs
public void setSmeIdRefs(List<Integer> smeIdRefs)
Set smeIdRefs.mzTab-M specification example(s):
SFH SMF_ID SME_ID_REFS SMF 1 5|6|12…- Parameters:
smeIdRefs- aList<Integer>parameter.- See Also:
SmallMoleculeFeature#getSmeIdRefs for validation constraints
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smeIdRefAmbiguityCode
public SmallMoleculeFeature smeIdRefAmbiguityCode(Integer smeIdRefAmbiguityCode)
Builder method for smeIdRefAmbiguityCode.- Parameters:
smeIdRefAmbiguityCode- aIntegerparameter.- Returns:
- SmallMoleculeFeature
- See Also:
SmallMoleculeFeature#setSmeIdRefAmbiguityCode for specification examples,SmallMoleculeFeature#getSmeIdRefAmbiguityCode for validation constraints
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getSmeIdRefAmbiguityCode
public Integer getSmeIdRefAmbiguityCode()
If multiple values are given under SME_ID_REFS, one of the following codes MUST be provided. 1=Ambiguous identification; 2=Only different evidence streams for the same molecule with no ambiguity; 3=Both ambiguous identification and multiple evidence streams. If there are no or one value under SME_ID_REFs, this MUST be reported as null.- Returns:
- smeIdRefAmbiguityCode
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setSmeIdRefAmbiguityCode
public void setSmeIdRefAmbiguityCode(Integer smeIdRefAmbiguityCode)
Set smeIdRefAmbiguityCode.mzTab-M specification example(s):
SFH SMF_ID SME_ID_REFS SME_ID_REF_ambiguity_code SMF 1 5|6|12… 1- Parameters:
smeIdRefAmbiguityCode- aIntegerparameter.- See Also:
SmallMoleculeFeature#getSmeIdRefAmbiguityCode for validation constraints
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adductIon
public SmallMoleculeFeature adductIon(String adductIon)
Builder method for adductIon.- Parameters:
adductIon- aStringparameter.- Returns:
- SmallMoleculeFeature
- See Also:
SmallMoleculeFeature#setAdductIon for specification examples,SmallMoleculeFeature#getAdductIon for validation constraints
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getAdductIon
@Pattern(regexp="^\\[\\d*M([+-][\\w]*)\\]\\d*[+-]$") public @Pattern(regexp="^\\[\\d*M([+-][\\w]*)\\]\\d*[+-]$") String getAdductIon()
The assumed classification of this molecule’s adduct ion after detection, following the general style in the 2013 IUPAC recommendations on terms relating to MS e.g. [M+H]1+, [M+Na]1+, [M+NH4]1+, [M-H]1-, [M+Cl]1-, [M+H]1+.- Returns:
- adductIon
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setAdductIon
public void setAdductIon(String adductIon)
Set adductIon.mzTab-M specification example(s):
SFH SMF_ID … adduct_ion … SMF 1 … [M+H]+ … SMF 2 … [M+2Na]2+ …- Parameters:
adductIon- aStringparameter.- See Also:
SmallMoleculeFeature#getAdductIon for validation constraints
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isotopomer
public SmallMoleculeFeature isotopomer(Parameter isotopomer)
Builder method for isotopomer.- Parameters:
isotopomer- aParameterparameter.- Returns:
- SmallMoleculeFeature
- See Also:
SmallMoleculeFeature#setIsotopomer for specification examples,SmallMoleculeFeature#getIsotopomer for validation constraints
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getIsotopomer
@Valid public @Valid Parameter getIsotopomer()
If de-isotoping has not been performed, then the isotopomer quantified MUST be reported here e.g. “+1”, “+2”, “13C peak” using CV terms, otherwise (i.e. for approaches where SMF rows are de-isotoped features) this MUST be null.- Returns:
- isotopomer
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setIsotopomer
public void setIsotopomer(Parameter isotopomer)
Set isotopomer.- Parameters:
isotopomer- aParameterparameter.- See Also:
SmallMoleculeFeature#getIsotopomer for validation constraints
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expMassToCharge
public SmallMoleculeFeature expMassToCharge(Double expMassToCharge)
Builder method for expMassToCharge.- Parameters:
expMassToCharge- aDoubleparameter.- Returns:
- SmallMoleculeFeature
- See Also:
SmallMoleculeFeature#setExpMassToCharge for specification examples,SmallMoleculeFeature#getExpMassToCharge for validation constraints
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getExpMassToCharge
@NotNull public @NotNull Double getExpMassToCharge()
The experimental mass/charge value for the feature, by default assumed to be the mean across assays or a representative value. For approaches that report isotopomers as SMF rows, then the m/z of the isotopomer MUST be reported here.- Returns:
- expMassToCharge
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setExpMassToCharge
public void setExpMassToCharge(Double expMassToCharge)
Set expMassToCharge.mzTab-M specification example(s):
SFH SMF_ID … exp_mass_to_charge … SMF 1 … 1234.5 …- Parameters:
expMassToCharge- aDoubleparameter.- See Also:
SmallMoleculeFeature#getExpMassToCharge for validation constraints
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charge
public SmallMoleculeFeature charge(Integer charge)
Builder method for charge.- Parameters:
charge- aIntegerparameter.- Returns:
- SmallMoleculeFeature
- See Also:
SmallMoleculeFeature#setCharge for specification examples,SmallMoleculeFeature#getCharge for validation constraints
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getCharge
@NotNull public @NotNull Integer getCharge()
The feature’s charge value using positive integers both for positive and negative polarity modes.- Returns:
- charge
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setCharge
public void setCharge(Integer charge)
Set charge.mzTab-M specification example(s):
SFH SMF_ID … charge … SMF 1 … 1 …- Parameters:
charge- aIntegerparameter.- See Also:
SmallMoleculeFeature#getCharge for validation constraints
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retentionTimeInSeconds
public SmallMoleculeFeature retentionTimeInSeconds(Double retentionTimeInSeconds)
Builder method for retentionTimeInSeconds.- Parameters:
retentionTimeInSeconds- aDoubleparameter.- Returns:
- SmallMoleculeFeature
- See Also:
SmallMoleculeFeature#setRetentionTimeInSeconds for specification examples,SmallMoleculeFeature#getRetentionTimeInSeconds for validation constraints
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getRetentionTimeInSeconds
public Double getRetentionTimeInSeconds()
The apex of the feature on the retention time axis, in a Master or aggregate MS run. Retention time MUST be reported in seconds. Retention time values for individual MS runs (i.e. before alignment) MAY be reported as optional columns. Retention time SHOULD only be null in the case of direct infusion MS or other techniques where a retention time value is absent or unknown. Relative retention time or retention time index values MAY be reported as optional columns, and could be considered for inclusion in future versions of mzTab as appropriate.- Returns:
- retentionTimeInSeconds
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setRetentionTimeInSeconds
public void setRetentionTimeInSeconds(Double retentionTimeInSeconds)
Set retentionTimeInSeconds.mzTab-M specification example(s):
SFH SMF_ID … retention_time_in_seconds … SMF 1 … 1345.7 …- Parameters:
retentionTimeInSeconds- aDoubleparameter.- See Also:
SmallMoleculeFeature#getRetentionTimeInSeconds for validation constraints
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retentionTimeInSecondsStart
public SmallMoleculeFeature retentionTimeInSecondsStart(Double retentionTimeInSecondsStart)
Builder method for retentionTimeInSecondsStart.- Parameters:
retentionTimeInSecondsStart- aDoubleparameter.- Returns:
- SmallMoleculeFeature
- See Also:
SmallMoleculeFeature#setRetentionTimeInSecondsStart for specification examples,SmallMoleculeFeature#getRetentionTimeInSecondsStart for validation constraints
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getRetentionTimeInSecondsStart
public Double getRetentionTimeInSecondsStart()
The start time of the feature on the retention time axis, in a Master or aggregate MS run. Retention time MUST be reported in seconds. Retention time start and end SHOULD only be null in the case of direct infusion MS or other techniques where a retention time value is absent or unknown and MAY be reported in optional columns.- Returns:
- retentionTimeInSecondsStart
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setRetentionTimeInSecondsStart
public void setRetentionTimeInSecondsStart(Double retentionTimeInSecondsStart)
Set retentionTimeInSecondsStart.mzTab-M specification example(s):
SFH SMF_ID … retention_time_in_seconds_start … SMF 1 … 1327.0 …- Parameters:
retentionTimeInSecondsStart- aDoubleparameter.- See Also:
SmallMoleculeFeature#getRetentionTimeInSecondsStart for validation constraints
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retentionTimeInSecondsEnd
public SmallMoleculeFeature retentionTimeInSecondsEnd(Double retentionTimeInSecondsEnd)
Builder method for retentionTimeInSecondsEnd.- Parameters:
retentionTimeInSecondsEnd- aDoubleparameter.- Returns:
- SmallMoleculeFeature
- See Also:
SmallMoleculeFeature#setRetentionTimeInSecondsEnd for specification examples,SmallMoleculeFeature#getRetentionTimeInSecondsEnd for validation constraints
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getRetentionTimeInSecondsEnd
public Double getRetentionTimeInSecondsEnd()
The end time of the feature on the retention time axis, in a Master or aggregate MS run. Retention time MUST be reported in seconds. Retention time start and end SHOULD only be null in the case of direct infusion MS or other techniques where a retention time value is absent or unknown and MAY be reported in optional columns..- Returns:
- retentionTimeInSecondsEnd
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setRetentionTimeInSecondsEnd
public void setRetentionTimeInSecondsEnd(Double retentionTimeInSecondsEnd)
Set retentionTimeInSecondsEnd.mzTab-M specification example(s):
SFH SMF_ID … retention_time_in_seconds_end … SMF 1 … 1327.8 …- Parameters:
retentionTimeInSecondsEnd- aDoubleparameter.- See Also:
SmallMoleculeFeature#getRetentionTimeInSecondsEnd for validation constraints
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abundanceAssay
public SmallMoleculeFeature abundanceAssay(List<Double> abundanceAssay)
Builder method for abundanceAssay.- Parameters:
abundanceAssay- aList<Double>parameter.- Returns:
- SmallMoleculeFeature
- See Also:
SmallMoleculeFeature#setAbundanceAssay for specification examples,SmallMoleculeFeature#getAbundanceAssay for validation constraints
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addAbundanceAssayItem
public SmallMoleculeFeature addAbundanceAssayItem(Double abundanceAssayItem)
Add a single abundanceAssayItem to the abundanceAssay collection.- Parameters:
abundanceAssayItem- aDoubleparameter.- Returns:
- SmallMoleculeFeature
- See Also:
SmallMoleculeFeature#getAbundanceAssay for validation constraints
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getAbundanceAssay
public List<Double> getAbundanceAssay()
The feature’s abundance in every assay described in the metadata section MUST be reported. Null or zero values may be reported as appropriate.- Returns:
- abundanceAssay
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setAbundanceAssay
public void setAbundanceAssay(List<Double> abundanceAssay)
Set abundanceAssay.mzTab-M specification example(s):
SMH SML_ID … abundance_assay[1] … SMF 1 … 38648 …- Parameters:
abundanceAssay- aList<Double>parameter.- See Also:
SmallMoleculeFeature#getAbundanceAssay for validation constraints
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opt
public SmallMoleculeFeature opt(List<OptColumnMapping> opt)
Builder method for opt.- Parameters:
opt- aList<OptColumnMapping>parameter.- Returns:
- SmallMoleculeFeature
- See Also:
SmallMoleculeFeature#setOpt for specification examples,SmallMoleculeFeature#getOpt for validation constraints
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addOptItem
public SmallMoleculeFeature addOptItem(OptColumnMapping optItem)
Add a single optItem to the opt collection.- Parameters:
optItem- aOptColumnMappingparameter.- Returns:
- SmallMoleculeFeature
- See Also:
SmallMoleculeFeature#getOpt for validation constraints
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getOpt
@Valid public @Valid List<OptColumnMapping> getOpt()
Additional columns can be added to the end of the small molecule feature table. These column headers MUST start with the prefix “opt_” followed by the {identifier} of the object they reference: assay, study variable, MS run or “global” (if the value relates to all replicates). Column names MUST only contain the following characters: ‘A’-‘Z’, ‘a’-‘z’, ‘0’-‘9’, ‘’, ‘-’, ‘[’, ‘]’, and ‘:’. CV parameter accessions MAY be used for optional columns following the format: opt{identifier}_cv_{accession}_\{parameter name}. Spaces within the parameter’s name MUST be replaced by ‘_’.- Returns:
- opt
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setOpt
public void setOpt(List<OptColumnMapping> opt)
Set opt.mzTab-M specification example(s):
SFH SMF_ID … opt_assay[1]_my_value … opt_global_another_value SMF 1 … My value … some other value- Parameters:
opt- aList<OptColumnMapping>parameter.- See Also:
SmallMoleculeFeature#getOpt for validation constraints
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comment
public SmallMoleculeFeature comment(List<Comment> comment)
Builder method for comment.- Parameters:
comment- aList<Comment>parameter.- Returns:
- SmallMoleculeFeature
- See Also:
SmallMoleculeFeature#setComment for specification examples,SmallMoleculeFeature#getComment for validation constraints
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addCommentItem
public SmallMoleculeFeature addCommentItem(Comment commentItem)
Add a single commentItem to the comment collection.- Parameters:
commentItem- aCommentparameter.- Returns:
- SmallMoleculeFeature
- See Also:
SmallMoleculeFeature#getComment for validation constraints
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getComment
@Valid public @Valid List<Comment> getComment()
Get comment.
- Returns:
- comment
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setComment
public void setComment(List<Comment> comment)
Set comment.- Parameters:
comment- aList<Comment>parameter.- See Also:
SmallMoleculeFeature#getComment for validation constraints
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