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
AndValidationHandler	Implements 'AND' logic, meaning all alternative possible terms or term roots for an object must occur.
Assay	Specification of assay.
Assay.Properties	Property enumeration for Assay.
AssayFormat	Format specification for Assay.
AssaySerializer	AssaySerializer implementation for Assay.
AssayValidator	Validates that the quantification method section is present in metadata.
CheckParameter	JAVAX validation compliant annotation.
ClassPathFile	Test files enum to configure test files.
ColumnParameterMapping	Defines the used unit for a column in the mzTab-M file.
ColumnParameterMapping.Properties	Property enumeration for ColumnParameterMapping.
COMLineParser	Comment line parser.
Comment	Comment lines can be placed anywhere in an mzTab file.
Comment.PrefixEnum	Gets or Sets prefix
Comment.Properties	Property enumeration for Comment.
Contact	The contact’s name, affiliation and e-mail.
Contact.Properties	Property enumeration for Contact.
ContactFormat	Format specification for Contact.
ContactSerializer	ContactSerializer implementation for Contact.
CrossCheckErrorType	Provide crosscheck service, that is parse the consistent between current mztab file and some other resource (eg, database, xml file and so on).
CV	Specification of controlled vocabularies. label: A string describing the labels of the controlled vocabularies/ontologies used in the mzTab file as a short-hand e.g.
CV.Properties	Property enumeration for CV.
CvDefinitionValidationHandler	Validates that controlled vocabularies used by parameters are defined in the metadata CV section.
CvFormat	Format specification for CV.
CvMapping	Java-Klasse für anonymous complex type.
CvMapping.CvMappingRuleList	Java-Klasse für anonymous complex type.
CvMapping.CvReferenceList	Java-Klasse für anonymous complex type.
CvMappingRule	Java-Klasse für anonymous complex type.
CvMappingRule.CvTermsCombinationLogic	Java-Klasse für null.
CvMappingRule.RequirementLevel	Java-Klasse für null.
CvMappingUtils	Utility methods for conversion between the mapping file domain and the mzTab domain.
CvMappingValidator	Validator implementation that uses a provided xml mapping file with rules for required, recommended and optional CV parameters to assert that an mzTab follows these rules.
CvParameterLookupService	Abstraction over OLSClient to autoconvert Terms to Parameters and to allow easy matching of Parameters against parent terms and their children.
CvReference	Java-Klasse für anonymous complex type.
CvRuleHandler	Interface for rule logic handling implementations.
CvSerializer	CvSerializer implementation for CV.
CvTerm	Java-Klasse für anonymous complex type.
CvTermSelectionHandler	Interface for JxPath subtree selection handling.
CvTermValidationHandler	Interface for handling of rule evaluation results.
CvValidator	Validates that the controlled vocabulary section is present in metadata and that it is correctly populated.
Database	Specification of databases.
Database.Properties	Property enumeration for Database.
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.
EmptyRuleHandler	Implements handling of rules that have no cv parameter match.
Error	Error
Error.Properties	Property enumeration for Error.
ExtractClassPathFiles	ExtractClassPathFiles class.
ExtraParametersValidationHandler	Implements handling of cv parameters (not user params) that are found at the object.
FormatErrorType	Diagnose different types of format-related (reporting format problems).
IMZTabColumn	IMZTabColumn interface.
IndexedElement	Indexed elements (IDs) define a unique ID for a collection of multiple metadata elements of the same type within the mzTab-M document, e.g. for sample, assay, study variable etc.
IndexedElement.Properties	Property enumeration for IndexedElement.
Instrument	The name, source, analyzer and detector of the instruments used in the experiment.
Instrument.Properties	Property enumeration for Instrument.
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.
JxPathElement	Utility methods for simpler Java 8 compatible handling of JXPath selections and pointers.
LogicalErrorType	Reporting errors related to the logical relationships among the different sections in a file.
LogMethodName	JUnit TestWatcher to LOGGER the executed test method name.
Metadata	The metadata section provides additional information about the dataset(s) reported in the mzTab file.
Metadata.PrefixEnum	The metadata section prefix.
Metadata.Properties	Property enumeration for Metadata.
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.
MetadataValidator<T>	Implementations of the parsing validator are applied to the type object during the parsing process.
MsRun	Specification of ms_run.
MsRun.Properties	Property enumeration for MsRun.
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.
MzTab	mzTab-M is intended as a reporting standard for quantitative results from metabolomics/lipodomics approaches.
MzTab.Properties	Property enumeration for MzTab.
MzTabBeanValidator	This validator used the HibernateValidator bean validation reference implementation.
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.
MZTabCommandLine	MZTabCommandLine class.
MZTabConstants	Define a couple of constants used in the jmzTab API.
MZTabConversionException	Runtime exception for mzTab conversion
MZTabDataLineParser<T>	This class allows the validation and loading of the data into mzTab domain objects.
MZTabError	mzTab files can be validated to ensure that they comply with the latest version of the format specification.
MZTabErrorList	A limit max capacity list, if contains a couple of MZTabError objects.
MZTabErrorOverflowException	If error count great than MZTabProperties.MAX_ERROR_COUNT System will stop validate and throw overflow exception.
MZTabErrorType	MZTabErrorType class.
MZTabErrorType.Category
MZTabErrorType.Level	We classify diagnosis message types into three levels: Info, Warn and Error, all of them coming from the notational conventions of the specification.
MZTabErrorTypeMap	This list class used to storage all types of MZTabError, and provide query service based on the error/warn code.
MZTabException	Wrap a MZTabError.
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.
MZTabProperties	This class will load the properties used by the mzTab-M library for message formatting during validation.
MZTabStringUtils	Provide a couple of functions for translate, parse and print formatted string defined in the mzTab specification.
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.
MzTabValidator	Delegating validator implementation that forwards validation to the provided validator implementations.
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.
ObjectFactory	This object contains factory methods for each Java content interface and Java element interface generated in the info.psidev.cvmapping package.
OptColumnMapping	Additional columns can be added to the end of the small molecule table.
OptColumnMapping.Properties	Property enumeration for OptColumnMapping.
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.
OrValidationHandler	Implements 'OR' logic, meaning alternative possible terms or term roots for an object may be present.
Parameter	mzTab makes use of CV parameters.
Parameter.Properties	Property enumeration for Parameter.
ParameterComparisonResult	Result of a comparison of a CvTerm T defined in a CvRule against the parameter P found via JXPath.
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}.
ParameterValidator	Base interface for parameter validation with default validation method.
PositionMapping	Create and maintain a couple of mappings between physical position and logical position.
Publication	A publication associated with this file.
Publication.Properties	Property enumeration for Publication.
PublicationFormat	Format specification for Publication.
PublicationItem	A publication item, defined by a qualifier and a native accession, e.g. pubmed id.
PublicationItem.Properties	Property enumeration for PublicationItem.
PublicationItem.TypeEnum	The type qualifier of this publication item.
PublicationSerializer	PublicationSerializer implementation for Publication.
QuantificationMethodValidator	Validates that the quantification method section is present in metadata.
RemoveUserParams	Removes user parameters from the provided selection.
ResolvingCvRuleHandler	Implements resolution of cv parameters using the provided lookup service.
RuleEvaluationResult	Captures results of applying a rule to a parameter selection.
Sample	Specification of sample.
Sample.Properties	Property enumeration for Sample.
SampleFormat	Format specification for Sample.
SampleProcessing	A list of parameters describing a sample processing, preparation or handling step similar to a biological or analytical methods report.
SampleProcessing.Properties	Property enumeration for SampleProcessing.
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.
SetOperations	Utility methods for sets with common names.
SFHLineParser	Parse and validate Small Molecule Feature header line into a MZTabColumnFactory.
SharedParametersValidationHandler	Implements support for validating multiple parameters and the intersection between terms as described by the rule and the actually found ones.
SmallMoleculeColumn	Define the stable columns which have stable order in the small molecule header line
SmallMoleculeColumn.Stable	Stable SmallMoleculeColumn definition templates.
SmallMoleculeEvidence	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.
SmallMoleculeEvidence.HeaderPrefixEnum	The small molecule evidence table header prefix.
SmallMoleculeEvidence.PrefixEnum	The small molecule evidence table row prefix.
SmallMoleculeEvidence.Properties	Property enumeration for SmallMoleculeEvidence.
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.
SmallMoleculeFeature	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.
SmallMoleculeFeature.HeaderPrefixEnum	The small molecule feature table header prefix.
SmallMoleculeFeature.PrefixEnum	The small molecule feature table row prefix.
SmallMoleculeFeature.Properties	Property enumeration for SmallMoleculeFeature.
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.
SmallMoleculeSummary	The small molecule summary section is table-based, represented summarized quantitative information across assays and study variables, grouped by identification in rows.
SmallMoleculeSummary.HeaderPrefixEnum	The small molecule table header prefix.
SmallMoleculeSummary.PrefixEnum	The small molecule table row prefix.
SmallMoleculeSummary.Properties	Property enumeration for SmallMoleculeSummary.
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.
Software	Software used to analyze the data and obtain the reported results.
Software.Properties	Property enumeration for Software.
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.
SpectraRef	Reference to a spectrum in a spectrum file, for example a fragmentation spectrum has been used to support the identification.
SpectraRef.Properties	Property enumeration for SpectraRef.
SplitList<E>	This is list which each item split by a split char.
StringList	A typed list of strings.
StudyVariable	Specification of study_variable.
StudyVariable.Properties	Property enumeration for StudyVariable.
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.
Uri	A URI pointing to the file’s source data (e.g., a MetaboLights records) or an external file with more details about the study design.
Uri.Properties	Property enumeration for Uri.
UriConverter	Converter from Uri to String.
UriFormat	Format specification for Uri.
ValidationMessage	ValidationMessage
ValidationMessage.CategoryEnum	Gets or Sets category
ValidationMessage.MessageTypeEnum	Gets or Sets messageType
ValidationMessage.Properties	Property enumeration for ValidationMessage.
Validator<T>	Validator interface.
XorValidationHandler	Implements 'XOR' logic, meaning mutually exclusive alternative possible terms or term roots for an object are allowed.
ZipResourceExtractionException	This runtime exception is thrown when IO exceptions are encountered within the ZipResourceExtractor test rule.
ZipResourceExtractor	ZipResourceExtractor class.