java.lang.Object
- de.isas.mztab2.model.SmallMoleculeSummary

```
@Generated(value="io.swagger.codegen.languages.JavaClientCodegen",
           date="2021-01-02T19:26:21.550+01:00")
public class SmallMoleculeSummary
extends Object
```
The small molecule summary section is table-based, represented summarized quantitative information across assays and study variables, grouped by identification in rows. The small molecule section MUST always come after the metadata section. All table columns MUST be Tab separated. There MUST NOT be any empty cells; missing values MUST be reported using “null” for columns where Is Nullable = “True”. Each row of the small molecule section is intended to report one final result to be communicated in terms of a molecule that has been quantified. In many cases, this may be the molecule of biological interest, although in some cases, the final result could be a derivatized form as appropriate – although it is desirable for the database identifier(s) to reference to the biological (non-derivatized) form. In general, different adduct forms would generally be reported in the Small Molecule Feature section. The order of columns MUST follow the order specified below. All columns are MANDATORY except for “opt_” columns.

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`static class`	`SmallMoleculeSummary.HeaderPrefixEnum`	The small molecule table header prefix.
`static class`	`SmallMoleculeSummary.PrefixEnum`	The small molecule table row prefix.
`static class`	`SmallMoleculeSummary.Properties`	Property enumeration for SmallMoleculeSummary.

Constructor Summary

Constructors
Constructor Description

SmallMoleculeSummary()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`SmallMoleculeSummary`	`abundanceAssay(List<Double> abundanceAssay)`	Builder method for abundanceAssay.
`SmallMoleculeSummary`	`abundanceStudyVariable(List<Double> abundanceStudyVariable)`	Builder method for abundanceStudyVariable.
`SmallMoleculeSummary`	`abundanceVariationStudyVariable(List<Double> abundanceVariationStudyVariable)`	Builder method for abundanceVariationStudyVariable.
`SmallMoleculeSummary`	`addAbundanceAssayItem(Double abundanceAssayItem)`	Add a single abundanceAssayItem to the abundanceAssay collection.
`SmallMoleculeSummary`	`addAbundanceStudyVariableItem(Double abundanceStudyVariableItem)`	Add a single abundanceStudyVariableItem to the abundanceStudyVariable collection.
`SmallMoleculeSummary`	`addAbundanceVariationStudyVariableItem(Double abundanceVariationStudyVariableItem)`	Add a single abundanceVariationStudyVariableItem to the abundanceVariationStudyVariable collection.
`SmallMoleculeSummary`	`addAdductIonsItem(String adductIonsItem)`	Add a single adductIonsItem to the adductIons collection.
`SmallMoleculeSummary`	`addChemicalFormulaItem(String chemicalFormulaItem)`	Add a single chemicalFormulaItem to the chemicalFormula collection.
`SmallMoleculeSummary`	`addChemicalNameItem(String chemicalNameItem)`	Add a single chemicalNameItem to the chemicalName collection.
`SmallMoleculeSummary`	`addCommentItem(Comment commentItem)`	Add a single commentItem to the comment collection.
`SmallMoleculeSummary`	`addDatabaseIdentifierItem(String databaseIdentifierItem)`	Add a single databaseIdentifierItem to the databaseIdentifier collection.
`SmallMoleculeSummary`	`addInchiItem(String inchiItem)`	Add a single inchiItem to the inchi collection.
`SmallMoleculeSummary`	`addOptItem(OptColumnMapping optItem)`	Add a single optItem to the opt collection.
`SmallMoleculeSummary`	`addSmfIdRefsItem(Integer smfIdRefsItem)`	Add a single smfIdRefsItem to the smfIdRefs collection.
`SmallMoleculeSummary`	`addSmilesItem(String smilesItem)`	Add a single smilesItem to the smiles collection.
`SmallMoleculeSummary`	`addTheoreticalNeutralMassItem(Double theoreticalNeutralMassItem)`	Add a single theoreticalNeutralMassItem to the theoreticalNeutralMass collection.
`SmallMoleculeSummary`	`adductIons(List<String> adductIons)`	Builder method for adductIons.
`SmallMoleculeSummary`	`addUriItem(String uriItem)`	Add a single uriItem to the uri collection.
`SmallMoleculeSummary`	`bestIdConfidenceMeasure(Parameter bestIdConfidenceMeasure)`	Builder method for bestIdConfidenceMeasure.
`SmallMoleculeSummary`	`bestIdConfidenceValue(Double bestIdConfidenceValue)`	Builder method for bestIdConfidenceValue.
`SmallMoleculeSummary`	`chemicalFormula(List<String> chemicalFormula)`	Builder method for chemicalFormula.
`SmallMoleculeSummary`	`chemicalName(List<String> chemicalName)`	Builder method for chemicalName.
`SmallMoleculeSummary`	`comment(List<Comment> comment)`	Builder method for comment.
`SmallMoleculeSummary`	`databaseIdentifier(List<String> databaseIdentifier)`	Builder method for databaseIdentifier.
`boolean`	`equals(Object o)`
`List<Double>`	`getAbundanceAssay()`	The small molecule’s abundance in every assay described in the metadata section MUST be reported.
`List<Double>`	`getAbundanceStudyVariable()`	The small molecule’s abundance in all the study variables described in the metadata section (study_variable[1-n]_average_function), calculated using the method as described in the Metadata section (default = arithmetic mean across assays).
`List<Double>`	`getAbundanceVariationStudyVariable()`	A measure of the variability of the study variable abundance measurement, calculated using the method as described in the metadata section (study_variable[1-n]_average_function), with a default = arithmethic co-efficient of variation of the small molecule’s abundance in the given study variable.
`List<String>`	`getAdductIons()`	A “\|” separated list of detected adducts for this this molecule, following the general style in the 2013 IUPAC recommendations on terms relating to MS e.g.
`@Valid Parameter`	`getBestIdConfidenceMeasure()`	The approach or database search that identified this small molecule with highest confidence.
`Double`	`getBestIdConfidenceValue()`	The best confidence measure in identification (for this type of score) for the given small molecule across all assays.
`List<String>`	`getChemicalFormula()`	A list of “\|” separated potential chemical formulae of the reported compound.
`List<String>`	`getChemicalName()`	A list of “\|” separated possible chemical/common names for the small molecule, or general description if a chemical name is unavailable.
`@Valid List<Comment>`	`getComment()`	Get comment.
`List<String>`	`getDatabaseIdentifier()`	A list of “\|” separated possible identifiers for the small molecule; multiple values MUST only be provided to indicate ambiguity in the identification of the molecule and not to demonstrate different identifier types for the same molecule.
`SmallMoleculeSummary.HeaderPrefixEnum`	`getHeaderPrefix()`	The small molecule table header prefix.
`List<String>`	`getInchi()`	A list of “\|” separated potential standard IUPAC International Chemical Identifier (InChI) of the given substance.
`@Valid List<OptColumnMapping>`	`getOpt()`	Additional columns can be added to the end of the small molecule table.
`SmallMoleculeSummary.PrefixEnum`	`getPrefix()`	The small molecule table row prefix.
`String`	`getReliability()`	The reliability of the given small molecule identification.
`List<Integer>`	`getSmfIdRefs()`	References to all the features on which quantitation has been based (SMF elements) via referencing SMF_ID values.
`List<String>`	`getSmiles()`	A list of “\|” separated potential molecule structures in the simplified molecular-input line-entry system (SMILES) for the small molecule.
`@NotNull Integer`	`getSmlId()`	A within file unique identifier for the small molecule.
`List<Double>`	`getTheoreticalNeutralMass()`	The small molecule’s precursor’s theoretical neutral mass.
`List<String>`	`getUri()`	A URI pointing to the small molecule’s entry in a reference database (e.g., the small molecule’s HMDB or KEGG entry).
`int`	`hashCode()`
`SmallMoleculeSummary`	`inchi(List<String> inchi)`	Builder method for inchi.
`SmallMoleculeSummary`	`opt(List<OptColumnMapping> opt)`	Builder method for opt.
`SmallMoleculeSummary`	`reliability(String reliability)`	Builder method for reliability.
`void`	`setAbundanceAssay(List<Double> abundanceAssay)`	Set abundanceAssay.
`void`	`setAbundanceStudyVariable(List<Double> abundanceStudyVariable)`	Set abundanceStudyVariable.
`void`	`setAbundanceVariationStudyVariable(List<Double> abundanceVariationStudyVariable)`	Set abundanceVariationStudyVariable.
`void`	`setAdductIons(List<String> adductIons)`	Set adductIons.
`void`	`setBestIdConfidenceMeasure(Parameter bestIdConfidenceMeasure)`	Set bestIdConfidenceMeasure.
`void`	`setBestIdConfidenceValue(Double bestIdConfidenceValue)`	Set bestIdConfidenceValue.
`void`	`setChemicalFormula(List<String> chemicalFormula)`	Set chemicalFormula.
`void`	`setChemicalName(List<String> chemicalName)`	Set chemicalName.
`void`	`setComment(List<Comment> comment)`	Set comment.
`void`	`setDatabaseIdentifier(List<String> databaseIdentifier)`	Set databaseIdentifier.
`void`	`setInchi(List<String> inchi)`	Set inchi.
`void`	`setOpt(List<OptColumnMapping> opt)`	Set opt.
`void`	`setReliability(String reliability)`	Set reliability.
`void`	`setSmfIdRefs(List<Integer> smfIdRefs)`	Set smfIdRefs.
`void`	`setSmiles(List<String> smiles)`	Set smiles.
`void`	`setSmlId(Integer smlId)`	Set smlId.
`void`	`setTheoreticalNeutralMass(List<Double> theoreticalNeutralMass)`	Set theoreticalNeutralMass.
`void`	`setUri(List<String> uri)`	Set uri.
`SmallMoleculeSummary`	`smfIdRefs(List<Integer> smfIdRefs)`	Builder method for smfIdRefs.
`SmallMoleculeSummary`	`smiles(List<String> smiles)`	Builder method for smiles.
`SmallMoleculeSummary`	`smlId(Integer smlId)`	Builder method for smlId.
`SmallMoleculeSummary`	`theoreticalNeutralMass(List<Double> theoreticalNeutralMass)`	Builder method for theoreticalNeutralMass.
`String`	`toString()`
`SmallMoleculeSummary`	`uri(List<String> uri)`	Builder method for uri.

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - SmallMoleculeSummary
```
public SmallMoleculeSummary()
```
- Method Detail
  - getPrefix
```
public SmallMoleculeSummary.PrefixEnum getPrefix()
```
    The small molecule table row prefix. SML MUST be used for rows of the small molecule table.
    
    Returns:
    
    prefix
  - getHeaderPrefix
```
public SmallMoleculeSummary.HeaderPrefixEnum getHeaderPrefix()
```
    The small molecule table header prefix. SMH MUST be used for the small molecule table header line (the column labels).
    
    Returns:
    
    headerPrefix
  - smlId
```
public SmallMoleculeSummary smlId(Integer smlId)
```
    Builder method for smlId.
    
    Parameters:
    
    smlId - a Integer parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#setSmlId for specification examples, SmallMoleculeSummary#getSmlId for validation constraints
  - getSmlId
```
@NotNull
public @NotNull Integer getSmlId()
```
    A within file unique identifier for the small molecule.
    
    Returns:
    
    smlId
  - setSmlId
```
public void setSmlId(Integer smlId)
```
    Set smlId.
    mzTab-M specification example(s):
    
    SMH SML_ID … SML 1 … SML 2 …
    Parameters:
    
    smlId - a Integer parameter.
    
    See Also:
    
    SmallMoleculeSummary#getSmlId for validation constraints
  - smfIdRefs
```
public SmallMoleculeSummary smfIdRefs(List<Integer> smfIdRefs)
```
    Builder method for smfIdRefs.
    
    Parameters:
    
    smfIdRefs - a List<Integer> parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#setSmfIdRefs for specification examples, SmallMoleculeSummary#getSmfIdRefs for validation constraints
  - addSmfIdRefsItem
```
public SmallMoleculeSummary addSmfIdRefsItem(Integer smfIdRefsItem)
```
    Add a single smfIdRefsItem to the smfIdRefs collection.
    
    Parameters:
    
    smfIdRefsItem - a Integer parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#getSmfIdRefs for validation constraints
  - getSmfIdRefs
```
public List<Integer> getSmfIdRefs()
```
    References to all the features on which quantitation has been based (SMF elements) via referencing SMF_ID values. Multiple values SHOULD be provided as a “|” separated list. This MAY be null only if this is a Summary file.
    
    Returns:
    
    smfIdRefs
  - setSmfIdRefs
```
public void setSmfIdRefs(List<Integer> smfIdRefs)
```
    Set smfIdRefs.
    mzTab-M specification example(s):
    
    SMH SML_ID SMF_ID_REFS SML 1 2|3|11…
    Parameters:
    
    smfIdRefs - a List<Integer> parameter.
    
    See Also:
    
    SmallMoleculeSummary#getSmfIdRefs for validation constraints
  - databaseIdentifier
```
public SmallMoleculeSummary databaseIdentifier(List<String> databaseIdentifier)
```
    Builder method for databaseIdentifier.
    
    Parameters:
    
    databaseIdentifier - a List<String> parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#setDatabaseIdentifier for specification examples, SmallMoleculeSummary#getDatabaseIdentifier for validation constraints
  - addDatabaseIdentifierItem
```
public SmallMoleculeSummary addDatabaseIdentifierItem(String databaseIdentifierItem)
```
    Add a single databaseIdentifierItem to the databaseIdentifier collection.
    
    Parameters:
    
    databaseIdentifierItem - a String parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#getDatabaseIdentifier for validation constraints
  - getDatabaseIdentifier
```
public List<String> getDatabaseIdentifier()
```
    A list of “|” separated possible identifiers for the small molecule; multiple values MUST only be provided to indicate ambiguity in the identification of the molecule and not to demonstrate different identifier types for the same molecule. Alternative identifiers for the same molecule MAY be provided as optional columns. The database identifier must be preceded by the resource description (prefix) followed by a colon, as specified in the metadata section. A null value MAY be provided if the identification is sufficiently ambiguous as to be meaningless for reporting or the small molecule has not been identified.
    
    Returns:
    
    databaseIdentifier
  - setDatabaseIdentifier
```
public void setDatabaseIdentifier(List<String> databaseIdentifier)
```
    Set databaseIdentifier.
    mzTab-M specification example(s):
    
    A list of “|” separated possible identifiers for the small molecule; multiple values MUST only be provided to indicate ambiguity in the identification of the molecule and not to demonstrate different identifier types for the same molecule. Alternative identifiers for the same molecule MAY be provided as optional columns. The database identifier must be preceded by the resource description (prefix) followed by a colon, as specified in the metadata section. A null value MAY be provided if the identification is sufficiently ambiguous as to be meaningless for reporting or the small molecule has not been identified.
    Parameters:
    
    databaseIdentifier - a List<String> parameter.
    
    See Also:
    
    SmallMoleculeSummary#getDatabaseIdentifier for validation constraints
  - chemicalFormula
```
public SmallMoleculeSummary chemicalFormula(List<String> chemicalFormula)
```
    Builder method for chemicalFormula.
    
    Parameters:
    
    chemicalFormula - a List<String> parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#setChemicalFormula for specification examples, SmallMoleculeSummary#getChemicalFormula for validation constraints
  - addChemicalFormulaItem
```
public SmallMoleculeSummary addChemicalFormulaItem(String chemicalFormulaItem)
```
    Add a single chemicalFormulaItem to the chemicalFormula collection.
    
    Parameters:
    
    chemicalFormulaItem - a String parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#getChemicalFormula for validation constraints
  - getChemicalFormula
```
public List<String> getChemicalFormula()
```
    A list of “|” separated potential chemical formulae of the reported compound. The number of values provided MUST match the number of entities reported under “database_identifier”, even if this leads to redundant reporting of information (i.e. if ambiguity can be resolved in the chemical formula), and the validation software will throw an error if the number of “|” symbols does not match. “null” values between bars are allowed. This should be specified in Hill notation (EA Hill 1900), i.e. elements in the order C, H and then alphabetically all other elements. Counts of one may be omitted. Elements should be capitalized properly to avoid confusion (e.g., “CO” vs. “Co”). The chemical formula reported should refer to the neutral form. Example: N-acetylglucosamine would be encoded by the string “C8H15NO6”.
    
    Returns:
    
    chemicalFormula
  - setChemicalFormula
```
public void setChemicalFormula(List<String> chemicalFormula)
```
    Set chemicalFormula.
    mzTab-M specification example(s):
    
    SMH SML_ID … chemical_formula … SML 1 … C17H20N4O2 …
    Parameters:
    
    chemicalFormula - a List<String> parameter.
    
    See Also:
    
    SmallMoleculeSummary#getChemicalFormula for validation constraints
  - smiles
```
public SmallMoleculeSummary smiles(List<String> smiles)
```
    Builder method for smiles.
    
    Parameters:
    
    smiles - a List<String> parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#setSmiles for specification examples, SmallMoleculeSummary#getSmiles for validation constraints
  - addSmilesItem
```
public SmallMoleculeSummary addSmilesItem(String smilesItem)
```
    Add a single smilesItem to the smiles collection.
    
    Parameters:
    
    smilesItem - a String parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#getSmiles for validation constraints
  - getSmiles
```
public List<String> getSmiles()
```
    A list of “|” separated potential molecule structures in the simplified molecular-input line-entry system (SMILES) for the small molecule. The number of values provided MUST match the number of entities reported under “database_identifier”, and the validation software will throw an error if the number of “|” symbols does not match. “null” values between bars are allowed.
    
    Returns:
    
    smiles
  - setSmiles
```
public void setSmiles(List<String> smiles)
```
    Set smiles.
    mzTab-M specification example(s):
    
    SMH SML_ID … chemical_formula smiles … SML 1 … C17H20N4O2 C1=CC=C(C=C1)CCNC(=O)CCNNC(=O)C2=CC=NC=C2 …
    Parameters:
    
    smiles - a List<String> parameter.
    
    See Also:
    
    SmallMoleculeSummary#getSmiles for validation constraints
  - inchi
```
public SmallMoleculeSummary inchi(List<String> inchi)
```
    Builder method for inchi.
    
    Parameters:
    
    inchi - a List<String> parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#setInchi for specification examples, SmallMoleculeSummary#getInchi for validation constraints
  - addInchiItem
```
public SmallMoleculeSummary addInchiItem(String inchiItem)
```
    Add a single inchiItem to the inchi collection.
    
    Parameters:
    
    inchiItem - a String parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#getInchi for validation constraints
  - getInchi
```
public List<String> getInchi()
```
    A list of “|” separated potential standard IUPAC International Chemical Identifier (InChI) of the given substance. The number of values provided MUST match the number of entities reported under “database_identifier”, even if this leads to redundant information being reported (i.e. if ambiguity can be resolved in the InChi), and the validation software will throw an error if the number of “|” symbols does not match. “null” values between bars are allowed.
    
    Returns:
    
    inchi
  - setInchi
```
public void setInchi(List<String> inchi)
```
    Set inchi.
    mzTab-M specification example(s):
    
    SMH SML_ID … chemical_formula … inchi … SML 1 … C17H20N4O2 … InChI=1S/C17H20N4O2/c22-16(19-12-6-14-4-2-1-3-5-14)9-13-20-21-17(23)15-7-10-18-11-8-15/h1-5,7-8,10-11,20H,6,9,12-13H2,(H,19,22)(H,21,23) …
    Parameters:
    
    inchi - a List<String> parameter.
    
    See Also:
    
    SmallMoleculeSummary#getInchi for validation constraints
  - chemicalName
```
public SmallMoleculeSummary chemicalName(List<String> chemicalName)
```
    Builder method for chemicalName.
    
    Parameters:
    
    chemicalName - a List<String> parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#setChemicalName for specification examples, SmallMoleculeSummary#getChemicalName for validation constraints
  - addChemicalNameItem
```
public SmallMoleculeSummary addChemicalNameItem(String chemicalNameItem)
```
    Add a single chemicalNameItem to the chemicalName collection.
    
    Parameters:
    
    chemicalNameItem - a String parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#getChemicalName for validation constraints
  - getChemicalName
```
public List<String> getChemicalName()
```
    A list of “|” separated possible chemical/common names for the small molecule, or general description if a chemical name is unavailable. Multiple names are only to demonstrate ambiguity in the identification. The number of values provided MUST match the number of entities reported under “database_identifier”, and the validation software will throw an error if the number of “|” symbols does not match. “null” values between bars are allowed.
    
    Returns:
    
    chemicalName
  - setChemicalName
```
public void setChemicalName(List<String> chemicalName)
```
    Set chemicalName.
    mzTab-M specification example(s):
    
    SMH SML_ID … description … SML 1 … N-(2-phenylethyl)-3-[2-(pyridine-4-carbonyl)hydrazinyl]propanamide …
    Parameters:
    
    chemicalName - a List<String> parameter.
    
    See Also:
    
    SmallMoleculeSummary#getChemicalName for validation constraints
  - uri
```
public SmallMoleculeSummary uri(List<String> uri)
```
    Builder method for uri.
    
    Parameters:
    
    uri - a List<String> parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#setUri for specification examples, SmallMoleculeSummary#getUri for validation constraints
  - addUriItem
```
public SmallMoleculeSummary addUriItem(String uriItem)
```
    Add a single uriItem to the uri collection.
    
    Parameters:
    
    uriItem - a String parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#getUri for validation constraints
  - getUri
```
public List<String> getUri()
```
    A URI pointing to the small molecule’s entry in a reference database (e.g., the small molecule’s HMDB or KEGG entry). The number of values provided MUST match the number of entities reported under “database_identifier”, and the validation software will throw an error if the number of “|” symbols does not match. “null” values between bars are allowed.
    
    Returns:
    
    uri
  - setUri
```
public void setUri(List<String> uri)
```
    Set uri.
    mzTab-M specification example(s):
    
    SMH SML_ID … uri … SML 1 … http://www.genome.jp/dbget-bin/www_bget?cpd:C00031 … SML 2 … http://www.hmdb.ca/metabolites/HMDB0001847 … SML 3 … http://identifiers.org/hmdb/HMDB0001847 …
    Parameters:
    
    uri - a List<String> parameter.
    
    See Also:
    
    SmallMoleculeSummary#getUri for validation constraints
  - theoreticalNeutralMass
```
public SmallMoleculeSummary theoreticalNeutralMass(List<Double> theoreticalNeutralMass)
```
    Builder method for theoreticalNeutralMass.
    
    Parameters:
    
    theoreticalNeutralMass - a List<Double> parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#setTheoreticalNeutralMass for specification examples, SmallMoleculeSummary#getTheoreticalNeutralMass for validation constraints
  - addTheoreticalNeutralMassItem
```
public SmallMoleculeSummary addTheoreticalNeutralMassItem(Double theoreticalNeutralMassItem)
```
    Add a single theoreticalNeutralMassItem to the theoreticalNeutralMass collection.
    
    Parameters:
    
    theoreticalNeutralMassItem - a Double parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#getTheoreticalNeutralMass for validation constraints
  - getTheoreticalNeutralMass
```
public List<Double> getTheoreticalNeutralMass()
```
    The small molecule’s precursor’s theoretical neutral mass. The number of values provided MUST match the number of entities reported under “database_identifier”, and the validation software will throw an error if the number of “|” symbols does not match. “null” values (in general and between bars) are allowed for molecules that have not been identified only, or for molecules where the neutral mass cannot be calculated. In these cases, the SML entry SHOULD reference features in which exp_mass_to_charge values are captured.
    
    Returns:
    
    theoreticalNeutralMass
  - setTheoreticalNeutralMass
```
public void setTheoreticalNeutralMass(List<Double> theoreticalNeutralMass)
```
    Set theoreticalNeutralMass.
    mzTab-M specification example(s):
    
    SMH SML_ID … theoretical_neutral_mass … SML 1 … 1234.5 …
    Parameters:
    
    theoreticalNeutralMass - a List<Double> parameter.
    
    See Also:
    
    SmallMoleculeSummary#getTheoreticalNeutralMass for validation constraints
  - adductIons
```
public SmallMoleculeSummary adductIons(List<String> adductIons)
```
    Builder method for adductIons.
    
    Parameters:
    
    adductIons - a List<String> parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#setAdductIons for specification examples, SmallMoleculeSummary#getAdductIons for validation constraints
  - addAdductIonsItem
```
public SmallMoleculeSummary addAdductIonsItem(String adductIonsItem)
```
    Add a single adductIonsItem to the adductIons collection.
    
    Parameters:
    
    adductIonsItem - a String parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#getAdductIons for validation constraints
  - getAdductIons
```
public List<String> getAdductIons()
```
    A “|” separated list of detected adducts for this this molecule, 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+. If the adduct classification is ambiguous with regards to identification evidence it MAY be null.
    
    Returns:
    
    adductIons
  - setAdductIons
```
public void setAdductIons(List<String> adductIons)
```
    Set adductIons.
    mzTab-M specification example(s):
    
    SMH SML_ID … adduct_ions … SML 1 … [M+H]1+ | [M+Na]1+ …
    Parameters:
    
    adductIons - a List<String> parameter.
    
    See Also:
    
    SmallMoleculeSummary#getAdductIons for validation constraints
  - reliability
```
public SmallMoleculeSummary reliability(String reliability)
```
    Builder method for reliability.
    
    Parameters:
    
    reliability - a String parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#setReliability for specification examples, SmallMoleculeSummary#getReliability for validation constraints
  - getReliability
```
public String getReliability()
```
    The reliability of the given small molecule identification. This must be supplied by the resource and MUST be reported as an integer between 1-4: identified metabolite (1) putatively annotated compound (2) putatively characterized compound class (3) unknown compound (4) These MAY be replaced using a suitable CV term in the metadata section e.g. to use MSI recommendation levels (see Section 6.2.57 for details). The following CV terms are already available within the PSI MS CV. Future schemes may be implemented by extending the PSI MS CV with new terms and associated levels. The MSI has recently discussed an extension of the original four level scheme into a five level scheme MS:1002896 (compound identification confidence level) with levels isolated, pure compound, full stereochemistry (0) reference standard match or full 2D structure (1) unambiguous diagnostic evidence (literature, database) (2) most likely structure, including isomers, substance class or substructure match (3) unknown compound (4) For high-resolution MS, the following term and its levels may be used: MS:1002955 (hr-ms compound identification confidence level) with levels confirmed structure (1) probable structure (2) unambiguous ms library match (2a) diagnostic evidence (2b) tentative candidates (3) unequivocal molecular formula (4) exact mass (5) A String data type is set to allow for different systems to be specified in the metadata section.
    
    Returns:
    
    reliability
  - setReliability
```
public void setReliability(String reliability)
```
    Set reliability.
    mzTab-M specification example(s):
    
    SMH identifier … reliability … SML 1 … 3 … or MTD small_molecule-identification_reliability [MS, MS:1002896, compound identification confidence level,] … SMH identifier … reliability … SML 1 … 0 … or MTD small_molecule-identification_reliability [MS, MS:1002955, hr-ms compound identification confidence level,] … SMH identifier … reliability … SML 1 … 2a …
    Parameters:
    
    reliability - a String parameter.
    
    See Also:
    
    SmallMoleculeSummary#getReliability for validation constraints
  - bestIdConfidenceMeasure
```
public SmallMoleculeSummary bestIdConfidenceMeasure(Parameter bestIdConfidenceMeasure)
```
    Builder method for bestIdConfidenceMeasure.
    
    Parameters:
    
    bestIdConfidenceMeasure - a Parameter parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#setBestIdConfidenceMeasure for specification examples, SmallMoleculeSummary#getBestIdConfidenceMeasure for validation constraints
  - getBestIdConfidenceMeasure
```
@Valid
public @Valid Parameter getBestIdConfidenceMeasure()
```
    The approach or database search that identified this small molecule with highest confidence.
    
    Returns:
    
    bestIdConfidenceMeasure
  - setBestIdConfidenceMeasure
```
public void setBestIdConfidenceMeasure(Parameter bestIdConfidenceMeasure)
```
    Set bestIdConfidenceMeasure.
    
    Parameters:
    
    bestIdConfidenceMeasure - a Parameter parameter.
    
    See Also:
    
    SmallMoleculeSummary#getBestIdConfidenceMeasure for validation constraints
  - bestIdConfidenceValue
```
public SmallMoleculeSummary bestIdConfidenceValue(Double bestIdConfidenceValue)
```
    Builder method for bestIdConfidenceValue.
    
    Parameters:
    
    bestIdConfidenceValue - a Double parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#setBestIdConfidenceValue for specification examples, SmallMoleculeSummary#getBestIdConfidenceValue for validation constraints
  - getBestIdConfidenceValue
```
public Double getBestIdConfidenceValue()
```
    The best confidence measure in identification (for this type of score) for the given small molecule across all assays. The type of score MUST be defined in the metadata section. If the small molecule was not identified by the specified search engine, “null” MUST be reported. If the confidence measure does not report a numerical confidence value, “null” SHOULD be reported.
    
    Returns:
    
    bestIdConfidenceValue
  - setBestIdConfidenceValue
```
public void setBestIdConfidenceValue(Double bestIdConfidenceValue)
```
    Set bestIdConfidenceValue.
    mzTab-M specification example(s):
    
    SMH SML_ID … best_id_confidence_value … SML 1 … 0.7 …
    Parameters:
    
    bestIdConfidenceValue - a Double parameter.
    
    See Also:
    
    SmallMoleculeSummary#getBestIdConfidenceValue for validation constraints
  - abundanceAssay
```
public SmallMoleculeSummary abundanceAssay(List<Double> abundanceAssay)
```
    Builder method for abundanceAssay.
    
    Parameters:
    
    abundanceAssay - a List<Double> parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#setAbundanceAssay for specification examples, SmallMoleculeSummary#getAbundanceAssay for validation constraints
  - addAbundanceAssayItem
```
public SmallMoleculeSummary addAbundanceAssayItem(Double abundanceAssayItem)
```
    Add a single abundanceAssayItem to the abundanceAssay collection.
    
    Parameters:
    
    abundanceAssayItem - a Double parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#getAbundanceAssay for validation constraints
  - getAbundanceAssay
```
public List<Double> getAbundanceAssay()
```
    The small molecule’s abundance in every assay described in the metadata section MUST be reported. Null or zero values may be reported as appropriate. "null" SHOULD be used to report missing quantities, while zero SHOULD be used to indicate a present but not reliably quantifiable value (e.g. below a minimum noise threshold).
    
    Returns:
    
    abundanceAssay
  - setAbundanceAssay
```
public void setAbundanceAssay(List<Double> abundanceAssay)
```
    Set abundanceAssay.
    mzTab-M specification example(s):
    
    SMH SML_ID … abundance_assay[1] … SML 1 … 0.3 …
    Parameters:
    
    abundanceAssay - a List<Double> parameter.
    
    See Also:
    
    SmallMoleculeSummary#getAbundanceAssay for validation constraints
  - abundanceStudyVariable
```
public SmallMoleculeSummary abundanceStudyVariable(List<Double> abundanceStudyVariable)
```
    Builder method for abundanceStudyVariable.
    
    Parameters:
    
    abundanceStudyVariable - a List<Double> parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#setAbundanceStudyVariable for specification examples, SmallMoleculeSummary#getAbundanceStudyVariable for validation constraints
  - addAbundanceStudyVariableItem
```
public SmallMoleculeSummary addAbundanceStudyVariableItem(Double abundanceStudyVariableItem)
```
    Add a single abundanceStudyVariableItem to the abundanceStudyVariable collection.
    
    Parameters:
    
    abundanceStudyVariableItem - a Double parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#getAbundanceStudyVariable for validation constraints
  - getAbundanceStudyVariable
```
public List<Double> getAbundanceStudyVariable()
```
    The small molecule’s abundance in all the study variables described in the metadata section (study_variable[1-n]_average_function), calculated using the method as described in the Metadata section (default = arithmetic mean across assays). Null or zero values may be reported as appropriate. "null" SHOULD be used to report missing quantities, while zero SHOULD be used to indicate a present but not reliably quantifiable value (e.g. below a minimum noise threshold).
    
    Returns:
    
    abundanceStudyVariable
  - setAbundanceStudyVariable
```
public void setAbundanceStudyVariable(List<Double> abundanceStudyVariable)
```
    Set abundanceStudyVariable.
    mzTab-M specification example(s):
    
    SMH SML_ID … abundance_study_variable[1] … SML 1 … 0.3 …
    Parameters:
    
    abundanceStudyVariable - a List<Double> parameter.
    
    See Also:
    
    SmallMoleculeSummary#getAbundanceStudyVariable for validation constraints
  - abundanceVariationStudyVariable
```
public SmallMoleculeSummary abundanceVariationStudyVariable(List<Double> abundanceVariationStudyVariable)
```
    Builder method for abundanceVariationStudyVariable.
    
    Parameters:
    
    abundanceVariationStudyVariable - a List<Double> parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#setAbundanceVariationStudyVariable for specification examples, SmallMoleculeSummary#getAbundanceVariationStudyVariable for validation constraints
  - addAbundanceVariationStudyVariableItem
```
public SmallMoleculeSummary addAbundanceVariationStudyVariableItem(Double abundanceVariationStudyVariableItem)
```
    Add a single abundanceVariationStudyVariableItem to the abundanceVariationStudyVariable collection.
    
    Parameters:
    
    abundanceVariationStudyVariableItem - a Double parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#getAbundanceVariationStudyVariable for validation constraints
  - getAbundanceVariationStudyVariable
```
public List<Double> getAbundanceVariationStudyVariable()
```
    A measure of the variability of the study variable abundance measurement, calculated using the method as described in the metadata section (study_variable[1-n]_average_function), with a default = arithmethic co-efficient of variation of the small molecule’s abundance in the given study variable.
    
    Returns:
    
    abundanceVariationStudyVariable
  - setAbundanceVariationStudyVariable
```
public void setAbundanceVariationStudyVariable(List<Double> abundanceVariationStudyVariable)
```
    Set abundanceVariationStudyVariable.
    mzTab-M specification example(s):
    
    SMH SML_ID … abundance_study_variable[1] abundance_variation_study_variable[1] … SML 1 … 0.3 0.04 …
    Parameters:
    
    abundanceVariationStudyVariable - a List<Double> parameter.
    
    See Also:
    
    SmallMoleculeSummary#getAbundanceVariationStudyVariable for validation constraints
  - opt
```
public SmallMoleculeSummary opt(List<OptColumnMapping> opt)
```
    Builder method for opt.
    
    Parameters:
    
    opt - a List<OptColumnMapping> parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#setOpt for specification examples, SmallMoleculeSummary#getOpt for validation constraints
  - addOptItem
```
public SmallMoleculeSummary addOptItem(OptColumnMapping optItem)
```
    Add a single optItem to the opt collection.
    
    Parameters:
    
    optItem - a OptColumnMapping parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#getOpt for validation constraints
  - getOpt
```
@Valid
public @Valid List<OptColumnMapping> getOpt()
```
    Additional columns can be added to the end of the small molecule 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
  - setOpt
```
public void setOpt(List<OptColumnMapping> opt)
```
    Set opt.
    mzTab-M specification example(s):
    
    SMH SML_ID … opt_assay[1]_my_value … opt_global_another_value SML 1 … My value … some other value
    Parameters:
    
    opt - a List<OptColumnMapping> parameter.
    
    See Also:
    
    SmallMoleculeSummary#getOpt for validation constraints
  - comment
```
public SmallMoleculeSummary comment(List<Comment> comment)
```
    Builder method for comment.
    
    Parameters:
    
    comment - a List<Comment> parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#setComment for specification examples, SmallMoleculeSummary#getComment for validation constraints
  - addCommentItem
```
public SmallMoleculeSummary addCommentItem(Comment commentItem)
```
    Add a single commentItem to the comment collection.
    
    Parameters:
    
    commentItem - a Comment parameter.
    
    Returns:
    
    SmallMoleculeSummary
    
    See Also:
    
    SmallMoleculeSummary#getComment for validation constraints
  - getComment
```
@Valid
public @Valid List<Comment> getComment()
```
    Get comment.
    
    Returns:
    
    comment
  - setComment
```
public void setComment(List<Comment> comment)
```
    Set comment.
    
    Parameters:
    
    comment - a List<Comment> parameter.
    
    See Also:
    
    SmallMoleculeSummary#getComment 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

Class SmallMoleculeSummary

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

SmallMoleculeSummary

Method Detail

getPrefix

getHeaderPrefix

smlId

getSmlId

setSmlId

smfIdRefs

addSmfIdRefsItem

getSmfIdRefs

setSmfIdRefs

databaseIdentifier

addDatabaseIdentifierItem

getDatabaseIdentifier

setDatabaseIdentifier

chemicalFormula

addChemicalFormulaItem

getChemicalFormula

setChemicalFormula

smiles

addSmilesItem

getSmiles

setSmiles

inchi

addInchiItem

getInchi

setInchi

chemicalName

addChemicalNameItem

getChemicalName

setChemicalName

uri

addUriItem

getUri

setUri

theoreticalNeutralMass

addTheoreticalNeutralMassItem

getTheoreticalNeutralMass

setTheoreticalNeutralMass

adductIons

addAdductIonsItem

getAdductIons

setAdductIons

reliability

getReliability

setReliability

bestIdConfidenceMeasure

getBestIdConfidenceMeasure

setBestIdConfidenceMeasure

bestIdConfidenceValue

getBestIdConfidenceValue

setBestIdConfidenceValue

abundanceAssay

addAbundanceAssayItem

getAbundanceAssay

setAbundanceAssay

abundanceStudyVariable

addAbundanceStudyVariableItem

getAbundanceStudyVariable

setAbundanceStudyVariable

abundanceVariationStudyVariable

addAbundanceVariationStudyVariableItem

getAbundanceVariationStudyVariable

setAbundanceVariationStudyVariable

opt

addOptItem

getOpt

setOpt

comment

addCommentItem

getComment

setComment

equals

hashCode