All Classes

Class	Description
AbundanceColumn	If the data exporter wishes to report only final results for 'Summary' files (i.e. following averaging over replicates), then these MUST be reported as quantitative values in the columns associated with the study_variable[1-n] (e.g.
AbundanceColumn.Field
AssayFormat	Format specification for Assay.
AssaySerializer	AssaySerializer implementation for Assay.
AssayValidator	Validates that the quantification method section is present in metadata.
COMLineParser	Comment line parser.
ContactFormat	Format specification for Contact.
ContactSerializer	ContactSerializer implementation for Contact.
CvFormat	Format specification for CV.
CvSerializer	CvSerializer implementation for CV.
CvValidator	Validates that the controlled vocabulary section is present in metadata and that it is correctly populated.
DatabaseFormat	Format specification for Database.
DatabaseSerializer	DatabaseSerializer implementation for Database.
DatabaseValidator	Validates that the database section is present and correctly populated in metadata.
ElementNameMappingException	ElementNameMappingException should be thrown to indicate that the state of the passed in element did not allow mapping to a proper mzTab name.
FieldValidator<T>	Implementations of the field validator are applied to the type object (usually a parsed string element) during the parsing process.
IMZTabColumn	IMZTabColumn interface.
InstrumentFormat	Format specification for Instrument.
InstrumentSerializer	InstrumentSerializer implementation for Instrument.
IOptColumnMappingBuilder	Interface for optional column mapping builders.
ISmallMoleculeColumn	ISmallMoleculeColumn interface.
ISmallMoleculeEvidenceColumn	ISmallMoleculeEvidenceColumn interface.
ISmallMoleculeFeatureColumn	ISmallMoleculeFeatureColumn interface.
MetadataElement	Define all elements used in metadata.
MetadataFormat	Format specification for Metadata.
MetadataProperty	Define a property in metadata, which depend on the MetadataElement.
MetadataSerializer	MetadataSerializer class.
MsRunFormat	Format specification for MsRun.
MsRunSerializer	MsRunSerializer implementation for MsRun.
MsRunValidator	Validates that the ms run section is present in metadata.
MTDLineParser	Parse a metadata line into a element.
MZBoolean	In mzTab, using 0-false, 1-true to express the boolean value.
MZTabColumn	Define a column header which used in Section.Protein_Header, Section.Peptide_Header, Section.PSM_Header, or Section.Small_Molecule_Header.
MZTabColumnFactory	This is a static factory class which used to generate a couple of MZTabColumn objects, and organizes them into "logicalPosition, MZTabColumn" pairs.
MZTabDataLineParser<T>	This class allows the validation and loading of the data into mzTab domain objects.
MzTabFileParser	MZTabFileParser provides reading functionality of the mzTab file.
MZTabHeaderLineParser	A couple of common method used to parse a header line into MZTabColumnFactory structure.
MzTabIdValidator	Validates that mzTab-ID is neither null nor empty.
MZTabLineParser	Common tab split line parser.
MzTabNonValidatingWriter	MzTabNonValidatingWriter allows to write MzTab objects without additional validation checks.
MZTabParserContext	MZTabParserContext is used to keep track of indexed elements and interrelations during parsing.
MZTabUtils	Provide a couple of functions for translating, parsing and printing formatted strings defined in the mzTab specification.
MzTabValidatingWriter	MzTabValidatingWriter allows to write MzTab objects after validation with a custom or default validator.
MzTabValidatingWriter.WriteAndParseValidator	A default validator implemenation that first writes and then parses the created temporary file, performing the parser checks.
MzTabVersionValidator	Validates that mzTab-version is neither null nor empty.
MzTabWriter<T>	Interface for mztab writer implementors.
MzTabWriterDefaults	Default mapper and schema definitions for writing of mzTab files using the Jackson CSV mapper.
OptColumnMappingBuilder	Builder for reusable OptColumnMapping creation for multiple rows.
OptColumnMappingBuilder.GlobalOptColumnMappingBuilder	Create a new OptColumnMappingBuilder for global optional columns.
OptColumnMappingBuilder.IndexedElementOptColumnMappingBuilder	Create a new OptColumnMappingBuilder for IndexedElement.
OptionColumn	Additional columns can be added to the end of the protein table.
ParameterConverter	Parameter to String converter implementation for Parameter.
ParameterFormat	Format specification for Parameter.
ParameterOptionColumn	An kind of OptionColumn which use CV parameter accessions in following the format: opt_{OBJECT_ID}_cv_{accession}_{parameter name}.
PositionMapping	Create and maintain a couple of mappings between physical position and logical position.
PublicationFormat	Format specification for Publication.
PublicationSerializer	PublicationSerializer implementation for Publication.
QuantificationMethodValidator	Validates that the quantification method section is present in metadata.
RefiningValidator<T>	Implementations of the refining validator are applied to the type object after the actual line parsing process, for post-hoc validation.
SampleFormat	Format specification for Sample.
SampleProcessingFormat	Format specification for SampleProcessing.
SampleProcessingSerializer	SampleProcessingSerializer implementation for SampleProcessing.
SampleSerializer	SampleSerializer implementation for Sample.
Section	Every line in an mzTab file MUST start with a three letter code identifying the type of line delimited by a Tab character.
SEHLineParser	Parse and validate Small Molecule Evidence header line into a MZTabColumnFactory.
Serializers	Utility class providing helper methods for other serializers.
SFHLineParser	Parse and validate Small Molecule Feature header line into a MZTabColumnFactory.
SmallMoleculeColumn	Define the stable columns which have stable order in the small molecule header line
SmallMoleculeColumn.Stable	Stable SmallMoleculeColumn definition templates.
SmallMoleculeEvidenceColumn	Define the stable columns which have stable order in the small molecule evidence header line.
SmallMoleculeEvidenceColumn.Stable	Stable SmallMoleculeEvidenceColumn definition templates.
SmallMoleculeEvidenceFormat	Format specification for SmallMoleculeEvidence.
SmallMoleculeEvidenceSerializer	SmallMoleculeEvidenceSerializer implementation for SmallMoleculeEvidence.
SmallMoleculeFeatureColumn	Define the stable columns which have stable order in the small molecule feature header line.
SmallMoleculeFeatureColumn.Stable	Stable SmallMoleculeFeatureColumn definition templates.
SmallMoleculeFeatureFormat	Format specification for SmallMoleculeFeature.
SmallMoleculeFeatureQuantificationUnitValidator	Validates that smallMoleculeFeatureQuantificationUnit is neither null nor empty.
SmallMoleculeFeatureSerializer	SmallMoleculeFeatureSerializer implementation for SmallMoleculeFeature.
SmallMoleculeIdConfidenceMeasureValidator	Validates that smallMolecule identification confidence measure is neither null nor empty.
SmallMoleculeQuantificationUnitValidator	Validates that smallMoleculeQuantificationUnit is neither null nor empty.
SmallMoleculeSummaryFormat	Format specification for SmallMoleculeSummary.
SmallMoleculeSummarySerializer	SmallMoleculeSummarySerializer implementation for SmallMoleculeSummary.
SMELineParser	SMELineParser class.
SMFLineParser	SMFLineParser class.
SMHLineParser	Parse and validate Small Molecule header line into a MZTabColumnFactory.
SMLLineParser	SMLLineParser class.
SoftwareFormat	Format specification for Software.
SoftwareSerializer	SoftwareSerializer implementation for Software.
SoftwareValidator	Validates that the software section is present in metadata and contains at least one item.
SpectraRefValidator
SplitList<E>	This is list which each item split by a split char.
StudyVariableFormat	Format specification for StudyVariable.
StudyVariableSerializer	StudyVariableSerializer implementation for StudyVariable.
StudyVariableValidator	Validates that the study variable section is present in metadata and is linked to all assays and ms runs.
UriConverter	Converter from Uri to String.
UriFormat	Format specification for Uri.