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

```
@Generated(value="io.swagger.codegen.languages.JavaClientCodegen",
           date="2020-02-11T15:12:05.057+01:00")
public class MzTab
extends Object
```
mzTab-M is intended as a reporting standard for quantitative results from metabolomics/lipodomics approaches. This format is further intended to provide local LIMS systems as well as MS metabolomics repositories a simple way to share and combine basic information. The mzTab-M format consists of four cross-referenced data tables: Metadata (MTD), Small Molecule (SML), Small Molecule Feature (SMF) and the Small Molecule Evidence (SME). The MTD and SML tables are mandatory, and for a file to contain any evidence about how molecules were quantified or identified by software, then all four tables must be present. The tables must follow the order MTD, SML, SMF and SME, with a blank line separating each table. The structure of each table, in terms of the rows and columns that must be present is tightly specified and formally defined and explained in the mzTab-M specification document. mzTab-M files MUST have one Metadata (MTD) section and one Small Molecule (SML) Section. In practice, we expect that most files SHOULD also include one Small Molecule Feature (SMF) section, and one Small Molecule Evidence (SME) Section. Files lacking SMF and SME sections can only present summary data about quantified molecules, without any evidence trail for how those values were derived. It will be left to reading software to determine whether additional validation will be requested such that SMF and SME tables MUST be present.

Nested Class Summary

Nested Classes
Modifier and Type Class Description

static class MzTab.Properties
Property enumeration for MzTab.

Constructor Summary

Constructors
Constructor Description

MzTab()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`MzTab`	`addCommentItem(Comment commentItem)`	Add a single commentItem to the comment collection.
`MzTab`	`addSmallMoleculeEvidenceItem(SmallMoleculeEvidence smallMoleculeEvidenceItem)`	Add a single smallMoleculeEvidenceItem to the smallMoleculeEvidence collection.
`MzTab`	`addSmallMoleculeFeatureItem(SmallMoleculeFeature smallMoleculeFeatureItem)`	Add a single smallMoleculeFeatureItem to the smallMoleculeFeature collection.
`MzTab`	`addSmallMoleculeSummaryItem(SmallMoleculeSummary smallMoleculeSummaryItem)`	Add a single smallMoleculeSummaryItem to the smallMoleculeSummary collection.
`MzTab`	`comment(List<Comment> comment)`	Builder method for comment.
`boolean`	`equals(Object o)`
`@Valid List<Comment>`	`getComment()`	Comment lines can be placed anywhere in an mzTab file.
`@NotNull @Valid Metadata`	`getMetadata()`	Get metadata.
`@NotNull @Valid List<SmallMoleculeEvidence>`	`getSmallMoleculeEvidence()`	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.
`@NotNull @Valid List<SmallMoleculeFeature>`	`getSmallMoleculeFeature()`	The small molecule feature section is table-based, representing individual MS regions (generally considered to be the elution profile for all isotopomers formed from a single charge state of a molecule), that have been measured/quantified.
`@NotNull @Valid @Size(min=1) List<SmallMoleculeSummary>`	`getSmallMoleculeSummary()`	The small molecule section is table-based.
`int`	`hashCode()`
`MzTab`	`metadata(Metadata metadata)`	Builder method for metadata.
`void`	`setComment(List<Comment> comment)`	Set comment.
`void`	`setMetadata(Metadata metadata)`	Set metadata.
`void`	`setSmallMoleculeEvidence(List<SmallMoleculeEvidence> smallMoleculeEvidence)`	Set smallMoleculeEvidence.
`void`	`setSmallMoleculeFeature(List<SmallMoleculeFeature> smallMoleculeFeature)`	Set smallMoleculeFeature.
`void`	`setSmallMoleculeSummary(List<SmallMoleculeSummary> smallMoleculeSummary)`	Set smallMoleculeSummary.
`MzTab`	`smallMoleculeEvidence(List<SmallMoleculeEvidence> smallMoleculeEvidence)`	Builder method for smallMoleculeEvidence.
`MzTab`	`smallMoleculeFeature(List<SmallMoleculeFeature> smallMoleculeFeature)`	Builder method for smallMoleculeFeature.
`MzTab`	`smallMoleculeSummary(List<SmallMoleculeSummary> smallMoleculeSummary)`	Builder method for smallMoleculeSummary.
`String`	`toString()`

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

- Constructor Detail
  - MzTab
```
public MzTab()
```
- Method Detail
  - metadata
```
public MzTab metadata(Metadata metadata)
```
    Builder method for metadata.
    
    Parameters:
    
    metadata - a Metadata parameter.
    
    Returns:
    
    MzTab
    
    See Also:
    
    MzTab#setMetadata for specification examples, MzTab#getMetadata for validation constraints
  - getMetadata
```
@NotNull
@Valid
public @NotNull @Valid Metadata getMetadata()
```
    Get metadata.
    
    Returns:
    
    metadata
  - setMetadata
```
public void setMetadata(Metadata metadata)
```
    Set metadata.
    
    Parameters:
    
    metadata - a Metadata parameter.
    
    See Also:
    
    MzTab#getMetadata for validation constraints
  - smallMoleculeSummary
```
public MzTab smallMoleculeSummary(List<SmallMoleculeSummary> smallMoleculeSummary)
```
    Builder method for smallMoleculeSummary.
    
    Parameters:
    
    smallMoleculeSummary - a List<SmallMoleculeSummary> parameter.
    
    Returns:
    
    MzTab
    
    See Also:
    
    MzTab#setSmallMoleculeSummary for specification examples, MzTab#getSmallMoleculeSummary for validation constraints
  - addSmallMoleculeSummaryItem
```
public MzTab addSmallMoleculeSummaryItem(SmallMoleculeSummary smallMoleculeSummaryItem)
```
    Add a single smallMoleculeSummaryItem to the smallMoleculeSummary collection.
    
    Parameters:
    
    smallMoleculeSummaryItem - a SmallMoleculeSummary parameter.
    
    Returns:
    
    MzTab
    
    See Also:
    
    MzTab#getSmallMoleculeSummary for validation constraints
  - getSmallMoleculeSummary
```
@NotNull
@Valid
@Size(min=1)
public @NotNull @Valid @Size(min=1) List<SmallMoleculeSummary> getSmallMoleculeSummary()
```
    The small molecule section is table-based. 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.
    
    Returns:
    
    smallMoleculeSummary
  - setSmallMoleculeSummary
```
public void setSmallMoleculeSummary(List<SmallMoleculeSummary> smallMoleculeSummary)
```
    Set smallMoleculeSummary.
    
    Parameters:
    
    smallMoleculeSummary - a List<SmallMoleculeSummary> parameter.
    
    See Also:
    
    MzTab#getSmallMoleculeSummary for validation constraints
  - smallMoleculeFeature
```
public MzTab smallMoleculeFeature(List<SmallMoleculeFeature> smallMoleculeFeature)
```
    Builder method for smallMoleculeFeature.
    
    Parameters:
    
    smallMoleculeFeature - a List<SmallMoleculeFeature> parameter.
    
    Returns:
    
    MzTab
    
    See Also:
    
    MzTab#setSmallMoleculeFeature for specification examples, MzTab#getSmallMoleculeFeature for validation constraints
  - addSmallMoleculeFeatureItem
```
public MzTab addSmallMoleculeFeatureItem(SmallMoleculeFeature smallMoleculeFeatureItem)
```
    Add a single smallMoleculeFeatureItem to the smallMoleculeFeature collection.
    
    Parameters:
    
    smallMoleculeFeatureItem - a SmallMoleculeFeature parameter.
    
    Returns:
    
    MzTab
    
    See Also:
    
    MzTab#getSmallMoleculeFeature for validation constraints
  - getSmallMoleculeFeature
```
@NotNull
@Valid
public @NotNull @Valid List<SmallMoleculeFeature> getSmallMoleculeFeature()
```
    The small molecule feature section is table-based, representing individual MS regions (generally considered to be the elution profile for all isotopomers formed from a single charge state of a molecule), that have been measured/quantified. However, for approaches that quantify individual isotopomers e.g. stable isotope labelling/flux studies, then each SMF row SHOULD represent a single isotopomer. Different adducts or derivatives and different charge states of individual molecules should be reported as separate SMF rows. The small molecule feature section MUST always come after the Small Molecule Table. All table columns MUST be Tab separated. There MUST NOT be any empty cells. Missing values MUST be reported using “null”. The order of columns MUST follow the order specified below. All columns are MANDATORY except for “opt_” columns.
    
    Returns:
    
    smallMoleculeFeature
  - setSmallMoleculeFeature
```
public void setSmallMoleculeFeature(List<SmallMoleculeFeature> smallMoleculeFeature)
```
    Set smallMoleculeFeature.
    
    Parameters:
    
    smallMoleculeFeature - a List<SmallMoleculeFeature> parameter.
    
    See Also:
    
    MzTab#getSmallMoleculeFeature for validation constraints
  - smallMoleculeEvidence
```
public MzTab smallMoleculeEvidence(List<SmallMoleculeEvidence> smallMoleculeEvidence)
```
    Builder method for smallMoleculeEvidence.
    
    Parameters:
    
    smallMoleculeEvidence - a List<SmallMoleculeEvidence> parameter.
    
    Returns:
    
    MzTab
    
    See Also:
    
    MzTab#setSmallMoleculeEvidence for specification examples, MzTab#getSmallMoleculeEvidence for validation constraints
  - addSmallMoleculeEvidenceItem
```
public MzTab addSmallMoleculeEvidenceItem(SmallMoleculeEvidence smallMoleculeEvidenceItem)
```
    Add a single smallMoleculeEvidenceItem to the smallMoleculeEvidence collection.
    
    Parameters:
    
    smallMoleculeEvidenceItem - a SmallMoleculeEvidence parameter.
    
    Returns:
    
    MzTab
    
    See Also:
    
    MzTab#getSmallMoleculeEvidence for validation constraints
  - getSmallMoleculeEvidence
```
@NotNull
@Valid
public @NotNull @Valid List<SmallMoleculeEvidence> getSmallMoleculeEvidence()
```
    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.
    
    Returns:
    
    smallMoleculeEvidence
  - setSmallMoleculeEvidence
```
public void setSmallMoleculeEvidence(List<SmallMoleculeEvidence> smallMoleculeEvidence)
```
    Set smallMoleculeEvidence.
    
    Parameters:
    
    smallMoleculeEvidence - a List<SmallMoleculeEvidence> parameter.
    
    See Also:
    
    MzTab#getSmallMoleculeEvidence for validation constraints
  - comment
```
public MzTab comment(List<Comment> comment)
```
    Builder method for comment.
    
    Parameters:
    
    comment - a List<Comment> parameter.
    
    Returns:
    
    MzTab
    
    See Also:
    
    MzTab#setComment for specification examples, MzTab#getComment for validation constraints
  - addCommentItem
```
public MzTab addCommentItem(Comment commentItem)
```
    Add a single commentItem to the comment collection.
    
    Parameters:
    
    commentItem - a Comment parameter.
    
    Returns:
    
    MzTab
    
    See Also:
    
    MzTab#getComment for validation constraints
  - getComment
```
@Valid
public @Valid List<Comment> getComment()
```
    Comment lines can be placed anywhere in an mzTab file. These lines must start with the three-letter code COM and are ignored by most parsers. Empty lines can also occur anywhere in an mzTab file and are ignored.
    
    Returns:
    
    comment
  - setComment
```
public void setComment(List<Comment> comment)
```
    Set comment.
    
    Parameters:
    
    comment - a List<Comment> parameter.
    
    See Also:
    
    MzTab#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 MzTab

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

MzTab

Method Detail

metadata

getMetadata

setMetadata

smallMoleculeSummary

addSmallMoleculeSummaryItem

getSmallMoleculeSummary

setSmallMoleculeSummary

smallMoleculeFeature

addSmallMoleculeFeatureItem

getSmallMoleculeFeature

setSmallMoleculeFeature

smallMoleculeEvidence

addSmallMoleculeEvidenceItem

getSmallMoleculeEvidence

setSmallMoleculeEvidence

comment

addCommentItem

getComment

setComment

equals

hashCode

toString