Package de.isas.mztab2.model

Class SmallMoleculeSummary

  • @Generated(value="io.swagger.codegen.languages.JavaClientCodegen",
           date="2019-08-07T11:19:54.315+02:00")
public class SmallMoleculeSummary
extends java.lang.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.

    • 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

      • getSmlId

        @NotNull
public @NotNull java.lang.Integer getSmlId()
        A within file unique identifier for the small molecule.
        Returns:
        smlId

      • getSmfIdRefs

        public java.util.List<java.lang.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​(java.util.List<java.lang.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

      • getDatabaseIdentifier

        public java.util.List<java.lang.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​(java.util.List<java.lang.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

      • getChemicalFormula

        public java.util.List<java.lang.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​(java.util.List<java.lang.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

      • getSmiles

        public java.util.List<java.lang.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​(java.util.List<java.lang.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

      • getInchi

        public java.util.List<java.lang.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​(java.util.List<java.lang.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

      • getChemicalName

        public java.util.List<java.lang.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​(java.util.List<java.lang.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

      • getUri

        public java.util.List<java.lang.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​(java.util.List<java.lang.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

      • getTheoreticalNeutralMass

        public java.util.List<java.lang.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​(java.util.List<java.lang.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

      • getAdductIons

        public java.util.List<java.lang.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​(java.util.List<java.lang.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

      • getReliability

        public java.lang.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​(java.lang.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

      • getBestIdConfidenceMeasure

        @Valid
public @Valid Parameter getBestIdConfidenceMeasure()
        The approach or database search that identified this small molecule with highest confidence.
        Returns:
        bestIdConfidenceMeasure

      • getBestIdConfidenceValue

        public java.lang.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​(java.lang.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

      • getAbundanceAssay

        public java.util.List<java.lang.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​(java.util.List<java.lang.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

      • getAbundanceStudyVariable

        public java.util.List<java.lang.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​(java.util.List<java.lang.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

      • getAbundanceVariationStudyVariable

        public java.util.List<java.lang.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​(java.util.List<java.lang.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

      • getOpt

        @Valid
public @Valid java.util.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

      • getComment

        @Valid
public @Valid java.util.List<Comment> getComment()

        Get comment.

        Returns:
        comment

      • equals

        public boolean equals​(java.lang.Object o)
        Overrides:
        equals in class java.lang.Object

      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class java.lang.Object

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object