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="2021-01-02T19:26:21.550+01:00") public class SmallMoleculeFeature extends Object
The 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 class
SmallMoleculeFeature.HeaderPrefixEnum
The small molecule feature table header prefix.static class
SmallMoleculeFeature.PrefixEnum
The small molecule feature table row prefix.static class
SmallMoleculeFeature.Properties
Property 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 SmallMoleculeFeature
abundanceAssay(List<Double> abundanceAssay)
Builder method for abundanceAssay.SmallMoleculeFeature
addAbundanceAssayItem(Double abundanceAssayItem)
Add a single abundanceAssayItem to the abundanceAssay collection.SmallMoleculeFeature
addCommentItem(Comment commentItem)
Add a single commentItem to the comment collection.SmallMoleculeFeature
addOptItem(OptColumnMapping optItem)
Add a single optItem to the opt collection.SmallMoleculeFeature
addSmeIdRefsItem(Integer smeIdRefsItem)
Add a single smeIdRefsItem to the smeIdRefs collection.SmallMoleculeFeature
adductIon(String adductIon)
Builder method for adductIon.SmallMoleculeFeature
charge(Integer charge)
Builder method for charge.SmallMoleculeFeature
comment(List<Comment> comment)
Builder method for comment.boolean
equals(Object o)
SmallMoleculeFeature
expMassToCharge(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*[+-]$") 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.@NotNull Integer
getCharge()
The feature’s charge value using positive integers both for positive and negative polarity modes.@Valid List<Comment>
getComment()
Get comment.@NotNull Double
getExpMassToCharge()
The experimental mass/charge value for the feature, by default assumed to be the mean across assays or a representative value.SmallMoleculeFeature.HeaderPrefixEnum
getHeaderPrefix()
The small molecule feature table header prefix.@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.@Valid List<OptColumnMapping>
getOpt()
Additional columns can be added to the end of the small molecule feature table.SmallMoleculeFeature.PrefixEnum
getPrefix()
The small molecule feature table row prefix.Double
getRetentionTimeInSeconds()
The apex of the feature on the retention time axis, in a Master or aggregate MS run.Double
getRetentionTimeInSecondsEnd()
The end time of the feature on the retention time axis, in a Master or aggregate MS run.Double
getRetentionTimeInSecondsStart()
The start time of the feature on the retention time axis, in a Master or aggregate MS run.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.List<Integer>
getSmeIdRefs()
References to the identification evidence (SME elements) via referencing SME_ID values.@NotNull Integer
getSmfId()
A within file unique identifier for the small molecule feature.int
hashCode()
SmallMoleculeFeature
isotopomer(Parameter isotopomer)
Builder method for isotopomer.SmallMoleculeFeature
opt(List<OptColumnMapping> opt)
Builder method for opt.SmallMoleculeFeature
retentionTimeInSeconds(Double retentionTimeInSeconds)
Builder method for retentionTimeInSeconds.SmallMoleculeFeature
retentionTimeInSecondsEnd(Double retentionTimeInSecondsEnd)
Builder method for retentionTimeInSecondsEnd.SmallMoleculeFeature
retentionTimeInSecondsStart(Double retentionTimeInSecondsStart)
Builder method for retentionTimeInSecondsStart.void
setAbundanceAssay(List<Double> abundanceAssay)
Set abundanceAssay.void
setAdductIon(String adductIon)
Set adductIon.void
setCharge(Integer charge)
Set charge.void
setComment(List<Comment> comment)
Set comment.void
setExpMassToCharge(Double expMassToCharge)
Set expMassToCharge.void
setIsotopomer(Parameter isotopomer)
Set isotopomer.void
setOpt(List<OptColumnMapping> opt)
Set opt.void
setRetentionTimeInSeconds(Double retentionTimeInSeconds)
Set retentionTimeInSeconds.void
setRetentionTimeInSecondsEnd(Double retentionTimeInSecondsEnd)
Set retentionTimeInSecondsEnd.void
setRetentionTimeInSecondsStart(Double retentionTimeInSecondsStart)
Set retentionTimeInSecondsStart.void
setSmeIdRefAmbiguityCode(Integer smeIdRefAmbiguityCode)
Set smeIdRefAmbiguityCode.void
setSmeIdRefs(List<Integer> smeIdRefs)
Set smeIdRefs.void
setSmfId(Integer smfId)
Set smfId.SmallMoleculeFeature
smeIdRefAmbiguityCode(Integer smeIdRefAmbiguityCode)
Builder method for smeIdRefAmbiguityCode.SmallMoleculeFeature
smeIdRefs(List<Integer> smeIdRefs)
Builder method for smeIdRefs.SmallMoleculeFeature
smfId(Integer smfId)
Builder method for smfId.String
toString()
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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
- aInteger
parameter.- 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
- aInteger
parameter.- 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
- aInteger
parameter.- 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
- aInteger
parameter.- 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
- aInteger
parameter.- See Also:
SmallMoleculeFeature#getSmeIdRefAmbiguityCode for validation constraints
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adductIon
public SmallMoleculeFeature adductIon(String adductIon)
Builder method for adductIon.- Parameters:
adductIon
- aString
parameter.- 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
- aString
parameter.- See Also:
SmallMoleculeFeature#getAdductIon for validation constraints
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isotopomer
public SmallMoleculeFeature isotopomer(Parameter isotopomer)
Builder method for isotopomer.- Parameters:
isotopomer
- aParameter
parameter.- 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
- aParameter
parameter.- See Also:
SmallMoleculeFeature#getIsotopomer for validation constraints
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expMassToCharge
public SmallMoleculeFeature expMassToCharge(Double expMassToCharge)
Builder method for expMassToCharge.- Parameters:
expMassToCharge
- aDouble
parameter.- 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
- aDouble
parameter.- See Also:
SmallMoleculeFeature#getExpMassToCharge for validation constraints
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charge
public SmallMoleculeFeature charge(Integer charge)
Builder method for charge.- Parameters:
charge
- aInteger
parameter.- 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
- aInteger
parameter.- See Also:
SmallMoleculeFeature#getCharge for validation constraints
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retentionTimeInSeconds
public SmallMoleculeFeature retentionTimeInSeconds(Double retentionTimeInSeconds)
Builder method for retentionTimeInSeconds.- Parameters:
retentionTimeInSeconds
- aDouble
parameter.- 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
- aDouble
parameter.- See Also:
SmallMoleculeFeature#getRetentionTimeInSeconds for validation constraints
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retentionTimeInSecondsStart
public SmallMoleculeFeature retentionTimeInSecondsStart(Double retentionTimeInSecondsStart)
Builder method for retentionTimeInSecondsStart.- Parameters:
retentionTimeInSecondsStart
- aDouble
parameter.- 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
- aDouble
parameter.- See Also:
SmallMoleculeFeature#getRetentionTimeInSecondsStart for validation constraints
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retentionTimeInSecondsEnd
public SmallMoleculeFeature retentionTimeInSecondsEnd(Double retentionTimeInSecondsEnd)
Builder method for retentionTimeInSecondsEnd.- Parameters:
retentionTimeInSecondsEnd
- aDouble
parameter.- 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
- aDouble
parameter.- 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
- aDouble
parameter.- 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
- aOptColumnMapping
parameter.- 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
- aComment
parameter.- 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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