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

```
@Generated(value="io.swagger.codegen.languages.JavaClientCodegen",
           date="2021-01-02T19:25:37.430+01:00")
public class SmallMoleculeEvidence
extends Object
```
The small molecule evidence section is table-based, representing evidence for identifications of small molecules/features, from database search or any other process used to give putative identifications to molecules. In a typical case, each row represents one result from a single search or intepretation of a piece of evidence e.g. a database search with a fragmentation spectrum. Multiple results from a given input data item (e.g. one fragment spectrum) SHOULD share the same value under evidence_input_id. The small molecule evidence section MUST always come after the Small Molecule Feature 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.

Nested Class Summary

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

Constructor Summary

Constructors
Constructor Description

SmallMoleculeEvidence()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`SmallMoleculeEvidence`	`addCommentItem(Comment commentItem)`	Add a single commentItem to the comment collection.
`SmallMoleculeEvidence`	`addIdConfidenceMeasureItem(Double idConfidenceMeasureItem)`	Add a single idConfidenceMeasureItem to the idConfidenceMeasure collection.
`SmallMoleculeEvidence`	`addOptItem(OptColumnMapping optItem)`	Add a single optItem to the opt collection.
`SmallMoleculeEvidence`	`addSpectraRefItem(SpectraRef spectraRefItem)`	Add a single spectraRefItem to the spectraRef collection.
`SmallMoleculeEvidence`	`adductIon(String adductIon)`	Builder method for adductIon.
`SmallMoleculeEvidence`	`charge(Integer charge)`	Builder method for charge.
`SmallMoleculeEvidence`	`chemicalFormula(String chemicalFormula)`	Builder method for chemicalFormula.
`SmallMoleculeEvidence`	`chemicalName(String chemicalName)`	Builder method for chemicalName.
`SmallMoleculeEvidence`	`comment(List<Comment> comment)`	Builder method for comment.
`SmallMoleculeEvidence`	`databaseIdentifier(String databaseIdentifier)`	Builder method for databaseIdentifier.
`SmallMoleculeEvidence`	`derivatizedForm(Parameter derivatizedForm)`	Builder method for derivatizedForm.
`boolean`	`equals(Object o)`
`SmallMoleculeEvidence`	`evidenceInputId(String evidenceInputId)`	Builder method for evidenceInputId.
`SmallMoleculeEvidence`	`expMassToCharge(Double expMassToCharge)`	Builder method for expMassToCharge.
`@Pattern(regexp="^\\[\\dM([-][\\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 small molecule evidence’s charge value using positive integers both for positive and negative polarity modes.
`String`	`getChemicalFormula()`	The chemical formula of the identified compound e.g. in a database, assumed to match the theoretical mass to charge (in some cases this will be the derivatized form, including adducts and protons).
`String`	`getChemicalName()`	The small molecule’s chemical/common name, or general description if a chemical name is unavailable.
`@Valid List<Comment>`	`getComment()`	Get comment.
`@NotNull String`	`getDatabaseIdentifier()`	The putative identification for the small molecule sourced from an external database, using the same prefix specified in database[1-n]-prefix.
`@Valid Parameter`	`getDerivatizedForm()`	If a derivatized form has been analysed by MS, then the functional group attached to the molecule should be reported here using suitable userParam or CV terms as appropriate.
`@NotNull String`	`getEvidenceInputId()`	A within file unique identifier for the input data used to support this identification e.g. fragment spectrum, RT and m/z pair, isotope profile that was used for the identification process, to serve as a grouping mechanism, whereby multiple rows of results from the same input data share the same ID.
`@NotNull Double`	`getExpMassToCharge()`	The experimental mass/charge value for the precursor ion.
`SmallMoleculeEvidence.HeaderPrefixEnum`	`getHeaderPrefix()`	The small molecule evidence table header prefix.
`List<Double>`	`getIdConfidenceMeasure()`	Any statistical value or score for the identification.
`@NotNull @Valid Parameter`	`getIdentificationMethod()`	The database search, search engine or process that was used to identify this small molecule e.g. the name of software, database or manual curation etc.
`String`	`getInchi()`	A standard IUPAC International Chemical Identifier (InChI) for the given substance.
`@NotNull @Valid Parameter`	`getMsLevel()`	The highest MS level used to inform identification e.g.
`@Valid List<OptColumnMapping>`	`getOpt()`	Additional columns can be added to the end of the small molecule evidence table.
`SmallMoleculeEvidence.PrefixEnum`	`getPrefix()`	The small molecule evidence table row prefix.
`@NotNull @Min(1L) Integer`	`getRank()`	The rank of this identification from this approach as increasing integers from 1 (best ranked identification).
`@NotNull Integer`	`getSmeId()`	A within file unique identifier for the small molecule evidence result.
`String`	`getSmiles()`	The potential molecule’s structure in the simplified molecular-input line-entry system (SMILES) for the small molecule.
`@NotNull @Valid List<SpectraRef>`	`getSpectraRef()`	Reference to a spectrum in a spectrum file, for example a fragmentation spectrum has been used to support the identification.
`@NotNull Double`	`getTheoreticalMassToCharge()`	The theoretical mass/charge value for the small molecule or the database mass/charge value (for a spectral library match).
`String`	`getUri()`	A URI pointing to the small molecule’s entry in a database (e.g., the small molecule’s HMDB, Chebi or KEGG entry).
`int`	`hashCode()`
`SmallMoleculeEvidence`	`idConfidenceMeasure(List<Double> idConfidenceMeasure)`	Builder method for idConfidenceMeasure.
`SmallMoleculeEvidence`	`identificationMethod(Parameter identificationMethod)`	Builder method for identificationMethod.
`SmallMoleculeEvidence`	`inchi(String inchi)`	Builder method for inchi.
`SmallMoleculeEvidence`	`msLevel(Parameter msLevel)`	Builder method for msLevel.
`SmallMoleculeEvidence`	`opt(List<OptColumnMapping> opt)`	Builder method for opt.
`SmallMoleculeEvidence`	`rank(Integer rank)`	Builder method for rank.
`void`	`setAdductIon(String adductIon)`	Set adductIon.
`void`	`setCharge(Integer charge)`	Set charge.
`void`	`setChemicalFormula(String chemicalFormula)`	Set chemicalFormula.
`void`	`setChemicalName(String chemicalName)`	Set chemicalName.
`void`	`setComment(List<Comment> comment)`	Set comment.
`void`	`setDatabaseIdentifier(String databaseIdentifier)`	Set databaseIdentifier.
`void`	`setDerivatizedForm(Parameter derivatizedForm)`	Set derivatizedForm.
`void`	`setEvidenceInputId(String evidenceInputId)`	Set evidenceInputId.
`void`	`setExpMassToCharge(Double expMassToCharge)`	Set expMassToCharge.
`void`	`setIdConfidenceMeasure(List<Double> idConfidenceMeasure)`	Set idConfidenceMeasure.
`void`	`setIdentificationMethod(Parameter identificationMethod)`	Set identificationMethod.
`void`	`setInchi(String inchi)`	Set inchi.
`void`	`setMsLevel(Parameter msLevel)`	Set msLevel.
`void`	`setOpt(List<OptColumnMapping> opt)`	Set opt.
`void`	`setRank(Integer rank)`	Set rank.
`void`	`setSmeId(Integer smeId)`	Set smeId.
`void`	`setSmiles(String smiles)`	Set smiles.
`void`	`setSpectraRef(List<SpectraRef> spectraRef)`	Set spectraRef.
`void`	`setTheoreticalMassToCharge(Double theoreticalMassToCharge)`	Set theoreticalMassToCharge.
`void`	`setUri(String uri)`	Set uri.
`SmallMoleculeEvidence`	`smeId(Integer smeId)`	Builder method for smeId.
`SmallMoleculeEvidence`	`smiles(String smiles)`	Builder method for smiles.
`SmallMoleculeEvidence`	`spectraRef(List<SpectraRef> spectraRef)`	Builder method for spectraRef.
`SmallMoleculeEvidence`	`theoreticalMassToCharge(Double theoreticalMassToCharge)`	Builder method for theoreticalMassToCharge.
`String`	`toString()`
`SmallMoleculeEvidence`	`uri(String uri)`	Builder method for uri.

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

- Constructor Detail
  - SmallMoleculeEvidence
```
public SmallMoleculeEvidence()
```
- Method Detail
  - getPrefix
```
public SmallMoleculeEvidence.PrefixEnum getPrefix()
```
    The small molecule evidence table row prefix. SME MUST be used for rows of the small molecule evidence table.
    
    Returns:
    
    prefix
  - getHeaderPrefix
```
public SmallMoleculeEvidence.HeaderPrefixEnum getHeaderPrefix()
```
    The small molecule evidence table header prefix. SEH MUST be used for the small molecule evidence table header line (the column labels).
    
    Returns:
    
    headerPrefix
  - smeId
```
public SmallMoleculeEvidence smeId(Integer smeId)
```
    Builder method for smeId.
    
    Parameters:
    
    smeId - a Integer parameter.
    
    Returns:
    
    SmallMoleculeEvidence
    
    See Also:
    
    SmallMoleculeEvidence#setSmeId for specification examples, SmallMoleculeEvidence#getSmeId for validation constraints
  - getSmeId
```
@NotNull
public @NotNull Integer getSmeId()
```
    A within file unique identifier for the small molecule evidence result.
    
    Returns:
    
    smeId
  - setSmeId
```
public void setSmeId(Integer smeId)
```
    Set smeId.
    mzTab-M specification example(s):
    
    SEH SME_ID … SME 1 …
    Parameters:
    
    smeId - a Integer parameter.
    
    See Also:
    
    SmallMoleculeEvidence#getSmeId for validation constraints
  - evidenceInputId
```
public SmallMoleculeEvidence evidenceInputId(String evidenceInputId)
```
    Builder method for evidenceInputId.
    
    Parameters:
    
    evidenceInputId - a String parameter.
    
    Returns:
    
    SmallMoleculeEvidence
    
    See Also:
    
    SmallMoleculeEvidence#setEvidenceInputId for specification examples, SmallMoleculeEvidence#getEvidenceInputId for validation constraints
  - getEvidenceInputId
```
@NotNull
public @NotNull String getEvidenceInputId()
```
    A within file unique identifier for the input data used to support this identification e.g. fragment spectrum, RT and m/z pair, isotope profile that was used for the identification process, to serve as a grouping mechanism, whereby multiple rows of results from the same input data share the same ID. The identifiers may be human readable but should not be assumed to be interpretable. For example, if fragmentation spectra have been searched then the ID may be the spectrum reference, or for accurate mass search, the ms_run[2]:458.75.
    
    Returns:
    
    evidenceInputId
  - setEvidenceInputId
```
public void setEvidenceInputId(String evidenceInputId)
```
    Set evidenceInputId.
    mzTab-M specification example(s):
    
    SEH SME_ID evidence_input_id … SME 1 ms_run[1]:mass=278.65;rt=376.5 SME 2 ms_run[1]:mass=278.65;rt=376.5 SME 3 ms_run[1]:mass=278.65;rt=376.5 (in this example three identifications were made from the same accurate mass/RT library search)
    Parameters:
    
    evidenceInputId - a String parameter.
    
    See Also:
    
    SmallMoleculeEvidence#getEvidenceInputId for validation constraints
  - databaseIdentifier
```
public SmallMoleculeEvidence databaseIdentifier(String databaseIdentifier)
```
    Builder method for databaseIdentifier.
    
    Parameters:
    
    databaseIdentifier - a String parameter.
    
    Returns:
    
    SmallMoleculeEvidence
    
    See Also:
    
    SmallMoleculeEvidence#setDatabaseIdentifier for specification examples, SmallMoleculeEvidence#getDatabaseIdentifier for validation constraints
  - getDatabaseIdentifier
```
@NotNull
public @NotNull String getDatabaseIdentifier()
```
    The putative identification for the small molecule sourced from an external database, using the same prefix specified in database[1-n]-prefix. This could include additionally a chemical class or an identifier to a spectral library entity, even if its actual identity is unknown. For the “no database” case, "null" must be used. The unprefixed use of "null" is prohibited for any other case. If no putative identification can be reported for a particular database, it MUST be reported as the database prefix followed by null.
    
    Returns:
    
    databaseIdentifier
  - setDatabaseIdentifier
```
public void setDatabaseIdentifier(String databaseIdentifier)
```
    Set databaseIdentifier.
    mzTab-M specification example(s):
    
    SEH SME_ID identifier … SME 1 CID:00027395 … SME 2 HMDB:HMDB12345 … SME 3 CID:null …
    Parameters:
    
    databaseIdentifier - a String parameter.
    
    See Also:
    
    SmallMoleculeEvidence#getDatabaseIdentifier for validation constraints
  - chemicalFormula
```
public SmallMoleculeEvidence chemicalFormula(String chemicalFormula)
```
    Builder method for chemicalFormula.
    
    Parameters:
    
    chemicalFormula - a String parameter.
    
    Returns:
    
    SmallMoleculeEvidence
    
    See Also:
    
    SmallMoleculeEvidence#setChemicalFormula for specification examples, SmallMoleculeEvidence#getChemicalFormula for validation constraints
  - getChemicalFormula
```
public String getChemicalFormula()
```
    The chemical formula of the identified compound e.g. in a database, assumed to match the theoretical mass to charge (in some cases this will be the derivatized form, including adducts and protons). 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. Charge state is reported by the charge field. Example N-acetylglucosamine would be encoded by the string “C8H15NO6”
    
    Returns:
    
    chemicalFormula
  - setChemicalFormula
```
public void setChemicalFormula(String chemicalFormula)
```
    Set chemicalFormula.
    mzTab-M specification example(s):
    
    SEH SME_ID … chemical_formula … SME 1 … C17H20N4O2 …
    Parameters:
    
    chemicalFormula - a String parameter.
    
    See Also:
    
    SmallMoleculeEvidence#getChemicalFormula for validation constraints
  - smiles
```
public SmallMoleculeEvidence smiles(String smiles)
```
    Builder method for smiles.
    
    Parameters:
    
    smiles - a String parameter.
    
    Returns:
    
    SmallMoleculeEvidence
    
    See Also:
    
    SmallMoleculeEvidence#setSmiles for specification examples, SmallMoleculeEvidence#getSmiles for validation constraints
  - getSmiles
```
public String getSmiles()
```
    The potential molecule’s structure in the simplified molecular-input line-entry system (SMILES) for the small molecule.
    
    Returns:
    
    smiles
  - setSmiles
```
public void setSmiles(String smiles)
```
    Set smiles.
    mzTab-M specification example(s):
    
    SEH SME_ID … chemical_formula smiles … SML 1 … C17H20N4O2 C1=CC=C(C=C1)CCNC(=O)CCNNC(=O)C2=CC=NC=C2 …
    Parameters:
    
    smiles - a String parameter.
    
    See Also:
    
    SmallMoleculeEvidence#getSmiles for validation constraints
  - inchi
```
public SmallMoleculeEvidence inchi(String inchi)
```
    Builder method for inchi.
    
    Parameters:
    
    inchi - a String parameter.
    
    Returns:
    
    SmallMoleculeEvidence
    
    See Also:
    
    SmallMoleculeEvidence#setInchi for specification examples, SmallMoleculeEvidence#getInchi for validation constraints
  - getInchi
```
public String getInchi()
```
    A standard IUPAC International Chemical Identifier (InChI) for the given substance.
    
    Returns:
    
    inchi
  - setInchi
```
public void setInchi(String inchi)
```
    Set inchi.
    mzTab-M specification example(s):
    
    SEH SME_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 String parameter.
    
    See Also:
    
    SmallMoleculeEvidence#getInchi for validation constraints
  - chemicalName
```
public SmallMoleculeEvidence chemicalName(String chemicalName)
```
    Builder method for chemicalName.
    
    Parameters:
    
    chemicalName - a String parameter.
    
    Returns:
    
    SmallMoleculeEvidence
    
    See Also:
    
    SmallMoleculeEvidence#setChemicalName for specification examples, SmallMoleculeEvidence#getChemicalName for validation constraints
  - getChemicalName
```
public String getChemicalName()
```
    The small molecule’s chemical/common name, or general description if a chemical name is unavailable.
    
    Returns:
    
    chemicalName
  - setChemicalName
```
public void setChemicalName(String chemicalName)
```
    Set chemicalName.
    mzTab-M specification example(s):
    
    SEH SME_ID … chemical_name … SML 1 … N-(2-phenylethyl)-3-[2-(pyridine-4-carbonyl)hydrazinyl]propanamide …
    Parameters:
    
    chemicalName - a String parameter.
    
    See Also:
    
    SmallMoleculeEvidence#getChemicalName for validation constraints
  - uri
```
public SmallMoleculeEvidence uri(String uri)
```
    Builder method for uri.
    
    Parameters:
    
    uri - a String parameter.
    
    Returns:
    
    SmallMoleculeEvidence
    
    See Also:
    
    SmallMoleculeEvidence#setUri for specification examples, SmallMoleculeEvidence#getUri for validation constraints
  - getUri
```
public String getUri()
```
    A URI pointing to the small molecule’s entry in a database (e.g., the small molecule’s HMDB, Chebi or KEGG entry).
    
    Returns:
    
    uri
  - setUri
```
public void setUri(String uri)
```
    Set uri.
    mzTab-M specification example(s):
    
    SEH SME_ID … uri … SME 1 … http://www.hmdb.ca/metabolites/HMDB00054
    Parameters:
    
    uri - a String parameter.
    
    See Also:
    
    SmallMoleculeEvidence#getUri for validation constraints
  - derivatizedForm
```
public SmallMoleculeEvidence derivatizedForm(Parameter derivatizedForm)
```
    Builder method for derivatizedForm.
    
    Parameters:
    
    derivatizedForm - a Parameter parameter.
    
    Returns:
    
    SmallMoleculeEvidence
    
    See Also:
    
    SmallMoleculeEvidence#setDerivatizedForm for specification examples, SmallMoleculeEvidence#getDerivatizedForm for validation constraints
  - getDerivatizedForm
```
@Valid
public @Valid Parameter getDerivatizedForm()
```
    If a derivatized form has been analysed by MS, then the functional group attached to the molecule should be reported here using suitable userParam or CV terms as appropriate.
    
    Returns:
    
    derivatizedForm
  - setDerivatizedForm
```
public void setDerivatizedForm(Parameter derivatizedForm)
```
    Set derivatizedForm.
    
    Parameters:
    
    derivatizedForm - a Parameter parameter.
    
    See Also:
    
    SmallMoleculeEvidence#getDerivatizedForm for validation constraints
  - adductIon
```
public SmallMoleculeEvidence adductIon(String adductIon)
```
    Builder method for adductIon.
    
    Parameters:
    
    adductIon - a String parameter.
    
    Returns:
    
    SmallMoleculeEvidence
    
    See Also:
    
    SmallMoleculeEvidence#setAdductIon for specification examples, SmallMoleculeEvidence#getAdductIon for validation constraints
  - 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]+, [M+Na]1+, [M+NH4]1+, [M-H]1-, [M+Cl]1-. If the adduct classification is ambiguous with regards to identification evidence it MAY be null.
    
    Returns:
    
    adductIon
  - setAdductIon
```
public void setAdductIon(String adductIon)
```
    Set adductIon.
    mzTab-M specification example(s):
    
    SEH SME_ID … adduct_ion … SME 1 … [M+H]+ … SME 2 … [M+2Na]2+ … OR (for negative mode): SME 1 … [M-H]- … SME 2 … [M+Cl]- …
    Parameters:
    
    adductIon - a String parameter.
    
    See Also:
    
    SmallMoleculeEvidence#getAdductIon for validation constraints
  - expMassToCharge
```
public SmallMoleculeEvidence expMassToCharge(Double expMassToCharge)
```
    Builder method for expMassToCharge.
    
    Parameters:
    
    expMassToCharge - a Double parameter.
    
    Returns:
    
    SmallMoleculeEvidence
    
    See Also:
    
    SmallMoleculeEvidence#setExpMassToCharge for specification examples, SmallMoleculeEvidence#getExpMassToCharge for validation constraints
  - getExpMassToCharge
```
@NotNull
public @NotNull Double getExpMassToCharge()
```
    The experimental mass/charge value for the precursor ion. If multiple adduct forms have been combined into a single identification event/search, then a single value e.g. for the protonated form SHOULD be reported here.
    
    Returns:
    
    expMassToCharge
  - setExpMassToCharge
```
public void setExpMassToCharge(Double expMassToCharge)
```
    Set expMassToCharge.
    mzTab-M specification example(s):
    
    SEH SME_ID … exp_mass_to_charge … SME 1 … 1234.5 …
    Parameters:
    
    expMassToCharge - a Double parameter.
    
    See Also:
    
    SmallMoleculeEvidence#getExpMassToCharge for validation constraints
  - charge
```
public SmallMoleculeEvidence charge(Integer charge)
```
    Builder method for charge.
    
    Parameters:
    
    charge - a Integer parameter.
    
    Returns:
    
    SmallMoleculeEvidence
    
    See Also:
    
    SmallMoleculeEvidence#setCharge for specification examples, SmallMoleculeEvidence#getCharge for validation constraints
  - getCharge
```
@NotNull
public @NotNull Integer getCharge()
```
    The small molecule evidence’s charge value using positive integers both for positive and negative polarity modes.
    
    Returns:
    
    charge
  - setCharge
```
public void setCharge(Integer charge)
```
    Set charge.
    mzTab-M specification example(s):
    
    SEH SME_ID … charge … SME 1 … 1 …
    Parameters:
    
    charge - a Integer parameter.
    
    See Also:
    
    SmallMoleculeEvidence#getCharge for validation constraints
  - theoreticalMassToCharge
```
public SmallMoleculeEvidence theoreticalMassToCharge(Double theoreticalMassToCharge)
```
    Builder method for theoreticalMassToCharge.
    
    Parameters:
    
    theoreticalMassToCharge - a Double parameter.
    
    Returns:
    
    SmallMoleculeEvidence
    
    See Also:
    
    SmallMoleculeEvidence#setTheoreticalMassToCharge for specification examples, SmallMoleculeEvidence#getTheoreticalMassToCharge for validation constraints
  - getTheoreticalMassToCharge
```
@NotNull
public @NotNull Double getTheoreticalMassToCharge()
```
    The theoretical mass/charge value for the small molecule or the database mass/charge value (for a spectral library match).
    
    Returns:
    
    theoreticalMassToCharge
  - setTheoreticalMassToCharge
```
public void setTheoreticalMassToCharge(Double theoreticalMassToCharge)
```
    Set theoreticalMassToCharge.
    mzTab-M specification example(s):
    
    SEH SME_ID … theoretical_mass_to_charge … SME 1 … 1234.71 …
    Parameters:
    
    theoreticalMassToCharge - a Double parameter.
    
    See Also:
    
    SmallMoleculeEvidence#getTheoreticalMassToCharge for validation constraints
  - spectraRef
```
public SmallMoleculeEvidence spectraRef(List<SpectraRef> spectraRef)
```
    Builder method for spectraRef.
    
    Parameters:
    
    spectraRef - a List<SpectraRef> parameter.
    
    Returns:
    
    SmallMoleculeEvidence
    
    See Also:
    
    SmallMoleculeEvidence#setSpectraRef for specification examples, SmallMoleculeEvidence#getSpectraRef for validation constraints
  - addSpectraRefItem
```
public SmallMoleculeEvidence addSpectraRefItem(SpectraRef spectraRefItem)
```
    Add a single spectraRefItem to the spectraRef collection.
    
    Parameters:
    
    spectraRefItem - a SpectraRef parameter.
    
    Returns:
    
    SmallMoleculeEvidence
    
    See Also:
    
    SmallMoleculeEvidence#getSpectraRef for validation constraints
  - getSpectraRef
```
@NotNull
@Valid
public @NotNull @Valid List<SpectraRef> getSpectraRef()
```
    Reference to a spectrum in a spectrum file, for example a fragmentation spectrum has been used to support the identification. If a separate spectrum file has been used for fragmentation spectrum, this MUST be reported in the metadata section as additional ms_runs. The reference must be in the format ms_run[1-n]:{SPECTRA_REF} where SPECTRA_REF MUST follow the format defined in 5.2 (including references to chromatograms where these are used to inform identification). Multiple spectra MUST be referenced using a “|” delimited list for the (rare) cases in which search engines have combined or aggregated multiple spectra in advance of the search to make identifications. If a fragmentation spectrum has not been used, the value should indicate the ms_run to which is identification is mapped e.g. “ms_run[1]”.
    
    Returns:
    
    spectraRef
  - setSpectraRef
```
public void setSpectraRef(List<SpectraRef> spectraRef)
```
    Set spectraRef.
    mzTab-M specification example(s):
    
    SEH SME_ID … spectra_ref … SME 1 … ms_run[1]:index=5 …
    Parameters:
    
    spectraRef - a List<SpectraRef> parameter.
    
    See Also:
    
    SmallMoleculeEvidence#getSpectraRef for validation constraints
  - identificationMethod
```
public SmallMoleculeEvidence identificationMethod(Parameter identificationMethod)
```
    Builder method for identificationMethod.
    
    Parameters:
    
    identificationMethod - a Parameter parameter.
    
    Returns:
    
    SmallMoleculeEvidence
    
    See Also:
    
    SmallMoleculeEvidence#setIdentificationMethod for specification examples, SmallMoleculeEvidence#getIdentificationMethod for validation constraints
  - getIdentificationMethod
```
@NotNull
@Valid
public @NotNull @Valid Parameter getIdentificationMethod()
```
    The database search, search engine or process that was used to identify this small molecule e.g. the name of software, database or manual curation etc. If manual validation has been performed quality, the following CV term SHOULD be used: 'quality estimation by manual validation' MS:1001058.
    
    Returns:
    
    identificationMethod
  - setIdentificationMethod
```
public void setIdentificationMethod(Parameter identificationMethod)
```
    Set identificationMethod.
    
    Parameters:
    
    identificationMethod - a Parameter parameter.
    
    See Also:
    
    SmallMoleculeEvidence#getIdentificationMethod for validation constraints
  - msLevel
```
public SmallMoleculeEvidence msLevel(Parameter msLevel)
```
    Builder method for msLevel.
    
    Parameters:
    
    msLevel - a Parameter parameter.
    
    Returns:
    
    SmallMoleculeEvidence
    
    See Also:
    
    SmallMoleculeEvidence#setMsLevel for specification examples, SmallMoleculeEvidence#getMsLevel for validation constraints
  - getMsLevel
```
@NotNull
@Valid
public @NotNull @Valid Parameter getMsLevel()
```
    The highest MS level used to inform identification e.g. MS1 (accurate mass only) = “ms level=1” or from an MS2 fragmentation spectrum = “ms level=2”. For direct fragmentation or data independent approaches where fragmentation data is used, appropriate CV terms SHOULD be used .
    
    Returns:
    
    msLevel
  - setMsLevel
```
public void setMsLevel(Parameter msLevel)
```
    Set msLevel.
    
    Parameters:
    
    msLevel - a Parameter parameter.
    
    See Also:
    
    SmallMoleculeEvidence#getMsLevel for validation constraints
  - idConfidenceMeasure
```
public SmallMoleculeEvidence idConfidenceMeasure(List<Double> idConfidenceMeasure)
```
    Builder method for idConfidenceMeasure.
    
    Parameters:
    
    idConfidenceMeasure - a List<Double> parameter.
    
    Returns:
    
    SmallMoleculeEvidence
    
    See Also:
    
    SmallMoleculeEvidence#setIdConfidenceMeasure for specification examples, SmallMoleculeEvidence#getIdConfidenceMeasure for validation constraints
  - addIdConfidenceMeasureItem
```
public SmallMoleculeEvidence addIdConfidenceMeasureItem(Double idConfidenceMeasureItem)
```
    Add a single idConfidenceMeasureItem to the idConfidenceMeasure collection.
    
    Parameters:
    
    idConfidenceMeasureItem - a Double parameter.
    
    Returns:
    
    SmallMoleculeEvidence
    
    See Also:
    
    SmallMoleculeEvidence#getIdConfidenceMeasure for validation constraints
  - getIdConfidenceMeasure
```
public List<Double> getIdConfidenceMeasure()
```
    Any statistical value or score for the identification. The metadata section reports the type of score used, as id_confidence_measure[1-n] of type Param.
    
    Returns:
    
    idConfidenceMeasure
  - setIdConfidenceMeasure
```
public void setIdConfidenceMeasure(List<Double> idConfidenceMeasure)
```
    Set idConfidenceMeasure.
    mzTab-M specification example(s):
    
    MTD id_confidence_measure[1] [MS, MS:1001419, SpectraST:discriminant score F,] … SEH SME_ID … id_confidence_measure[1] … SME 1 … 0.7 …
    Parameters:
    
    idConfidenceMeasure - a List<Double> parameter.
    
    See Also:
    
    SmallMoleculeEvidence#getIdConfidenceMeasure for validation constraints
  - rank
```
public SmallMoleculeEvidence rank(Integer rank)
```
    Builder method for rank.
    
    Parameters:
    
    rank - a Integer parameter.
    
    Returns:
    
    SmallMoleculeEvidence
    
    See Also:
    
    SmallMoleculeEvidence#setRank for specification examples, SmallMoleculeEvidence#getRank for validation constraints
  - getRank
```
@NotNull
@Min(1L)
public @NotNull @Min(1L) Integer getRank()
```
    The rank of this identification from this approach as increasing integers from 1 (best ranked identification). Ties (equal score) are represented by using the same rank – defaults to 1 if there is no ranking system used.
    Minimum: 1
    
    Returns:
    
    rank
  - setRank
```
public void setRank(Integer rank)
```
    Set rank.
    mzTab-M specification example(s):
    
    SEH SME_ID … rank … SME 1 … 1 …
    Parameters:
    
    rank - a Integer parameter.
    
    See Also:
    
    SmallMoleculeEvidence#getRank for validation constraints
  - opt
```
public SmallMoleculeEvidence opt(List<OptColumnMapping> opt)
```
    Builder method for opt.
    
    Parameters:
    
    opt - a List<OptColumnMapping> parameter.
    
    Returns:
    
    SmallMoleculeEvidence
    
    See Also:
    
    SmallMoleculeEvidence#setOpt for specification examples, SmallMoleculeEvidence#getOpt for validation constraints
  - addOptItem
```
public SmallMoleculeEvidence addOptItem(OptColumnMapping optItem)
```
    Add a single optItem to the opt collection.
    
    Parameters:
    
    optItem - a OptColumnMapping parameter.
    
    Returns:
    
    SmallMoleculeEvidence
    
    See Also:
    
    SmallMoleculeEvidence#getOpt for validation constraints
  - getOpt
```
@Valid
public @Valid List<OptColumnMapping> getOpt()
```
    Additional columns can be added to the end of the small molecule evidence 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):
    
    SEH SME_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:
    
    SmallMoleculeEvidence#getOpt for validation constraints
  - comment
```
public SmallMoleculeEvidence comment(List<Comment> comment)
```
    Builder method for comment.
    
    Parameters:
    
    comment - a List<Comment> parameter.
    
    Returns:
    
    SmallMoleculeEvidence
    
    See Also:
    
    SmallMoleculeEvidence#setComment for specification examples, SmallMoleculeEvidence#getComment for validation constraints
  - addCommentItem
```
public SmallMoleculeEvidence addCommentItem(Comment commentItem)
```
    Add a single commentItem to the comment collection.
    
    Parameters:
    
    commentItem - a Comment parameter.
    
    Returns:
    
    SmallMoleculeEvidence
    
    See Also:
    
    SmallMoleculeEvidence#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:
    
    SmallMoleculeEvidence#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 SmallMoleculeEvidence

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

SmallMoleculeEvidence

Method Detail

getPrefix

getHeaderPrefix

smeId

getSmeId

setSmeId

evidenceInputId

getEvidenceInputId

setEvidenceInputId

databaseIdentifier

getDatabaseIdentifier

setDatabaseIdentifier

chemicalFormula

getChemicalFormula

setChemicalFormula

smiles

getSmiles

setSmiles

inchi

getInchi

setInchi

chemicalName

getChemicalName

setChemicalName

uri

getUri

setUri

derivatizedForm

getDerivatizedForm

setDerivatizedForm

adductIon

getAdductIon

setAdductIon

expMassToCharge

getExpMassToCharge

setExpMassToCharge

charge

getCharge

setCharge

theoreticalMassToCharge

getTheoreticalMassToCharge

setTheoreticalMassToCharge

spectraRef

addSpectraRefItem

getSpectraRef

setSpectraRef

identificationMethod

getIdentificationMethod

setIdentificationMethod

msLevel

getMsLevel

setMsLevel

idConfidenceMeasure

addIdConfidenceMeasureItem

getIdConfidenceMeasure

setIdConfidenceMeasure

rank

getRank

setRank

opt

addOptItem

getOpt

setOpt

comment

addCommentItem

getComment

setComment

equals

hashCode

toString