Package de.isas.mztab2.model
Class SmallMoleculeEvidence
- java.lang.Object
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- de.isas.mztab2.model.SmallMoleculeEvidence
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@Generated(value="io.swagger.codegen.languages.JavaClientCodegen", date="2019-08-07T11:09:24.487+02:00") 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.
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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.
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Constructor Summary
Constructors Constructor Description SmallMoleculeEvidence()
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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="^\\[\\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 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.
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Constructor Detail
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SmallMoleculeEvidence
public SmallMoleculeEvidence()
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Method Detail
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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
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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
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smeId
public SmallMoleculeEvidence smeId(Integer smeId)
Builder method for smeId.- Parameters:
smeId
- aInteger
parameter.- Returns:
- SmallMoleculeEvidence
- See Also:
SmallMoleculeEvidence#setSmeId for specification examples
,SmallMoleculeEvidence#getSmeId for validation constraints
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getSmeId
@NotNull public @NotNull Integer getSmeId()
A within file unique identifier for the small molecule evidence result.- Returns:
- smeId
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setSmeId
public void setSmeId(Integer smeId)
Set smeId.mzTab-M specification example(s):
SEH SME_ID … SME 1 …
- Parameters:
smeId
- aInteger
parameter.- See Also:
SmallMoleculeEvidence#getSmeId for validation constraints
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evidenceInputId
public SmallMoleculeEvidence evidenceInputId(String evidenceInputId)
Builder method for evidenceInputId.- Parameters:
evidenceInputId
- aString
parameter.- Returns:
- SmallMoleculeEvidence
- See Also:
SmallMoleculeEvidence#setEvidenceInputId for specification examples
,SmallMoleculeEvidence#getEvidenceInputId for validation constraints
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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
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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
- aString
parameter.- See Also:
SmallMoleculeEvidence#getEvidenceInputId for validation constraints
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databaseIdentifier
public SmallMoleculeEvidence databaseIdentifier(String databaseIdentifier)
Builder method for databaseIdentifier.- Parameters:
databaseIdentifier
- aString
parameter.- Returns:
- SmallMoleculeEvidence
- See Also:
SmallMoleculeEvidence#setDatabaseIdentifier for specification examples
,SmallMoleculeEvidence#getDatabaseIdentifier for validation constraints
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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
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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
- aString
parameter.- See Also:
SmallMoleculeEvidence#getDatabaseIdentifier for validation constraints
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chemicalFormula
public SmallMoleculeEvidence chemicalFormula(String chemicalFormula)
Builder method for chemicalFormula.- Parameters:
chemicalFormula
- aString
parameter.- Returns:
- SmallMoleculeEvidence
- See Also:
SmallMoleculeEvidence#setChemicalFormula for specification examples
,SmallMoleculeEvidence#getChemicalFormula for validation constraints
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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
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setChemicalFormula
public void setChemicalFormula(String chemicalFormula)
Set chemicalFormula.mzTab-M specification example(s):
SEH SME_ID … chemical_formula … SME 1 … C17H20N4O2 …
- Parameters:
chemicalFormula
- aString
parameter.- See Also:
SmallMoleculeEvidence#getChemicalFormula for validation constraints
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smiles
public SmallMoleculeEvidence smiles(String smiles)
Builder method for smiles.- Parameters:
smiles
- aString
parameter.- Returns:
- SmallMoleculeEvidence
- See Also:
SmallMoleculeEvidence#setSmiles for specification examples
,SmallMoleculeEvidence#getSmiles for validation constraints
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getSmiles
public String getSmiles()
The potential molecule’s structure in the simplified molecular-input line-entry system (SMILES) for the small molecule.- Returns:
- smiles
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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
- aString
parameter.- See Also:
SmallMoleculeEvidence#getSmiles for validation constraints
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inchi
public SmallMoleculeEvidence inchi(String inchi)
Builder method for inchi.- Parameters:
inchi
- aString
parameter.- Returns:
- SmallMoleculeEvidence
- See Also:
SmallMoleculeEvidence#setInchi for specification examples
,SmallMoleculeEvidence#getInchi for validation constraints
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getInchi
public String getInchi()
A standard IUPAC International Chemical Identifier (InChI) for the given substance.- Returns:
- inchi
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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
- aString
parameter.- See Also:
SmallMoleculeEvidence#getInchi for validation constraints
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chemicalName
public SmallMoleculeEvidence chemicalName(String chemicalName)
Builder method for chemicalName.- Parameters:
chemicalName
- aString
parameter.- Returns:
- SmallMoleculeEvidence
- See Also:
SmallMoleculeEvidence#setChemicalName for specification examples
,SmallMoleculeEvidence#getChemicalName for validation constraints
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getChemicalName
public String getChemicalName()
The small molecule’s chemical/common name, or general description if a chemical name is unavailable.- Returns:
- chemicalName
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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
- aString
parameter.- See Also:
SmallMoleculeEvidence#getChemicalName for validation constraints
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uri
public SmallMoleculeEvidence uri(String uri)
Builder method for uri.- Parameters:
uri
- aString
parameter.- Returns:
- SmallMoleculeEvidence
- See Also:
SmallMoleculeEvidence#setUri for specification examples
,SmallMoleculeEvidence#getUri for validation constraints
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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
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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
- aString
parameter.- See Also:
SmallMoleculeEvidence#getUri for validation constraints
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derivatizedForm
public SmallMoleculeEvidence derivatizedForm(Parameter derivatizedForm)
Builder method for derivatizedForm.- Parameters:
derivatizedForm
- aParameter
parameter.- Returns:
- SmallMoleculeEvidence
- See Also:
SmallMoleculeEvidence#setDerivatizedForm for specification examples
,SmallMoleculeEvidence#getDerivatizedForm for validation constraints
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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
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setDerivatizedForm
public void setDerivatizedForm(Parameter derivatizedForm)
Set derivatizedForm.- Parameters:
derivatizedForm
- aParameter
parameter.- See Also:
SmallMoleculeEvidence#getDerivatizedForm for validation constraints
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adductIon
public SmallMoleculeEvidence adductIon(String adductIon)
Builder method for adductIon.- Parameters:
adductIon
- aString
parameter.- Returns:
- SmallMoleculeEvidence
- See Also:
SmallMoleculeEvidence#setAdductIon for specification examples
,SmallMoleculeEvidence#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]+, [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
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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
- aString
parameter.- See Also:
SmallMoleculeEvidence#getAdductIon for validation constraints
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expMassToCharge
public SmallMoleculeEvidence expMassToCharge(Double expMassToCharge)
Builder method for expMassToCharge.- Parameters:
expMassToCharge
- aDouble
parameter.- Returns:
- SmallMoleculeEvidence
- See Also:
SmallMoleculeEvidence#setExpMassToCharge for specification examples
,SmallMoleculeEvidence#getExpMassToCharge for validation constraints
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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
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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
- aDouble
parameter.- See Also:
SmallMoleculeEvidence#getExpMassToCharge for validation constraints
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charge
public SmallMoleculeEvidence charge(Integer charge)
Builder method for charge.- Parameters:
charge
- aInteger
parameter.- Returns:
- SmallMoleculeEvidence
- See Also:
SmallMoleculeEvidence#setCharge for specification examples
,SmallMoleculeEvidence#getCharge for validation constraints
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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
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setCharge
public void setCharge(Integer charge)
Set charge.mzTab-M specification example(s):
SEH SME_ID … charge … SME 1 … 1 …
- Parameters:
charge
- aInteger
parameter.- See Also:
SmallMoleculeEvidence#getCharge for validation constraints
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theoreticalMassToCharge
public SmallMoleculeEvidence theoreticalMassToCharge(Double theoreticalMassToCharge)
Builder method for theoreticalMassToCharge.- Parameters:
theoreticalMassToCharge
- aDouble
parameter.- Returns:
- SmallMoleculeEvidence
- See Also:
SmallMoleculeEvidence#setTheoreticalMassToCharge for specification examples
,SmallMoleculeEvidence#getTheoreticalMassToCharge for validation constraints
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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
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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
- aDouble
parameter.- See Also:
SmallMoleculeEvidence#getTheoreticalMassToCharge for validation constraints
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spectraRef
public SmallMoleculeEvidence spectraRef(List<SpectraRef> spectraRef)
Builder method for spectraRef.- Parameters:
spectraRef
- aList<SpectraRef>
parameter.- Returns:
- SmallMoleculeEvidence
- See Also:
SmallMoleculeEvidence#setSpectraRef for specification examples
,SmallMoleculeEvidence#getSpectraRef for validation constraints
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addSpectraRefItem
public SmallMoleculeEvidence addSpectraRefItem(SpectraRef spectraRefItem)
Add a single spectraRefItem to the spectraRef collection.- Parameters:
spectraRefItem
- aSpectraRef
parameter.- Returns:
- SmallMoleculeEvidence
- See Also:
SmallMoleculeEvidence#getSpectraRef for validation constraints
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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
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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
- aList<SpectraRef>
parameter.- See Also:
SmallMoleculeEvidence#getSpectraRef for validation constraints
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identificationMethod
public SmallMoleculeEvidence identificationMethod(Parameter identificationMethod)
Builder method for identificationMethod.- Parameters:
identificationMethod
- aParameter
parameter.- Returns:
- SmallMoleculeEvidence
- See Also:
SmallMoleculeEvidence#setIdentificationMethod for specification examples
,SmallMoleculeEvidence#getIdentificationMethod for validation constraints
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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
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setIdentificationMethod
public void setIdentificationMethod(Parameter identificationMethod)
Set identificationMethod.- Parameters:
identificationMethod
- aParameter
parameter.- See Also:
SmallMoleculeEvidence#getIdentificationMethod for validation constraints
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msLevel
public SmallMoleculeEvidence msLevel(Parameter msLevel)
Builder method for msLevel.- Parameters:
msLevel
- aParameter
parameter.- Returns:
- SmallMoleculeEvidence
- See Also:
SmallMoleculeEvidence#setMsLevel for specification examples
,SmallMoleculeEvidence#getMsLevel for validation constraints
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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
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setMsLevel
public void setMsLevel(Parameter msLevel)
Set msLevel.- Parameters:
msLevel
- aParameter
parameter.- See Also:
SmallMoleculeEvidence#getMsLevel for validation constraints
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idConfidenceMeasure
public SmallMoleculeEvidence idConfidenceMeasure(List<Double> idConfidenceMeasure)
Builder method for idConfidenceMeasure.- Parameters:
idConfidenceMeasure
- aList<Double>
parameter.- Returns:
- SmallMoleculeEvidence
- See Also:
SmallMoleculeEvidence#setIdConfidenceMeasure for specification examples
,SmallMoleculeEvidence#getIdConfidenceMeasure for validation constraints
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addIdConfidenceMeasureItem
public SmallMoleculeEvidence addIdConfidenceMeasureItem(Double idConfidenceMeasureItem)
Add a single idConfidenceMeasureItem to the idConfidenceMeasure collection.- Parameters:
idConfidenceMeasureItem
- aDouble
parameter.- Returns:
- SmallMoleculeEvidence
- See Also:
SmallMoleculeEvidence#getIdConfidenceMeasure for validation constraints
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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
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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
- aList<Double>
parameter.- See Also:
SmallMoleculeEvidence#getIdConfidenceMeasure for validation constraints
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rank
public SmallMoleculeEvidence rank(Integer rank)
Builder method for rank.- Parameters:
rank
- aInteger
parameter.- Returns:
- SmallMoleculeEvidence
- See Also:
SmallMoleculeEvidence#setRank for specification examples
,SmallMoleculeEvidence#getRank for validation constraints
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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
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setRank
public void setRank(Integer rank)
Set rank.mzTab-M specification example(s):
SEH SME_ID … rank … SME 1 … 1 …
- Parameters:
rank
- aInteger
parameter.- See Also:
SmallMoleculeEvidence#getRank for validation constraints
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opt
public SmallMoleculeEvidence opt(List<OptColumnMapping> opt)
Builder method for opt.- Parameters:
opt
- aList<OptColumnMapping>
parameter.- Returns:
- SmallMoleculeEvidence
- See Also:
SmallMoleculeEvidence#setOpt for specification examples
,SmallMoleculeEvidence#getOpt for validation constraints
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addOptItem
public SmallMoleculeEvidence addOptItem(OptColumnMapping optItem)
Add a single optItem to the opt collection.- Parameters:
optItem
- aOptColumnMapping
parameter.- Returns:
- SmallMoleculeEvidence
- See Also:
SmallMoleculeEvidence#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 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
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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
- aList<OptColumnMapping>
parameter.- See Also:
SmallMoleculeEvidence#getOpt for validation constraints
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comment
public SmallMoleculeEvidence comment(List<Comment> comment)
Builder method for comment.- Parameters:
comment
- aList<Comment>
parameter.- Returns:
- SmallMoleculeEvidence
- See Also:
SmallMoleculeEvidence#setComment for specification examples
,SmallMoleculeEvidence#getComment for validation constraints
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addCommentItem
public SmallMoleculeEvidence addCommentItem(Comment commentItem)
Add a single commentItem to the comment collection.- Parameters:
commentItem
- aComment
parameter.- Returns:
- SmallMoleculeEvidence
- See Also:
SmallMoleculeEvidence#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:
SmallMoleculeEvidence#getComment for validation constraints
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