JavaDoc API documentation for the jmztab-m data model, io and validation packages.
- mzTab_m_swagger.yml Swagger / OpenAPI REST specification.
- How to use the jmzTab-m object model.
- The jmzTab-m reference implementation.
- The mzTab-M specification homepage.
Package Overview
- API - The data model for the mzTab-M 2.0 data standard format for metabolomics.
- IO - Reading, writing and basic validation of mzTab-M data files in JSON, CSV or object format.
- VALIDATION - semantic validation with rule mapping and controlled vocabular terms.
- VALIDATION RULES - xml mapping file rules object model.
- CLI - the command line interface for reading, validation and conversion of mzTab-M 2.0 JSON and CSV files.
- TEST UTILS - utilities for extracting and testing of mzTab-M test files.
| Package | Description |
|---|---|
| de.isas.lipidomics.mztab2.validation |
This package contains classes that provide the basic validator infrastructure used in the jmztabm-validation module.
|
| de.isas.lipidomics.mztab2.validation.constraints |
This package contains custom validation annotations for the javax.validation framework.
|
| de.isas.lipidomics.mztab2.validation.validators |
This package contains custom validators that implement the
|
| de.isas.mztab2.cli |
This package contains the command line interface for jmzTab-M validation and conversion.
|
| de.isas.mztab2.cvmapping |
This package contains classes for controlled vocabulary term access, comparison, results and external cv parameter resolution.
|
| de.isas.mztab2.io |
This package contains implementations for reading and writing of mzTab-M files.
|
| de.isas.mztab2.io.formats |
This package defines formats for Jackson that define, which serializer should be used for a particular object type.
|
| de.isas.mztab2.io.serialization |
This package contains classes that implement custom Jackson serializers for the mzTab-M model objects.
|
| de.isas.mztab2.io.validators |
This package contains implementations for validation of mzTab-M parts during parsing.
|
| de.isas.mztab2.model |
Base package for the jmztab-m data model, generated from the mzTab_m_swagger.yml specification.
|
| de.isas.mztab2.test.utils |
This package contains custom JUnit Rules for extraction of class path resource files and additional logging for testing.
|
| de.isas.mztab2.validation |
This package contains interfaces and implementations for the semantic validation via CvTerms.
|
| de.isas.mztab2.validation.handlers |
This package contains implementations for the semantic validation controlled vocabulary term rules.
|
| info.psidev.cvmapping |
This package contains the generated Java objects created via XML binding from the PSI-MS mapping file schema.
|
| uk.ac.ebi.pride.jmztab2 |
This package contains jmzTab-M model and utility classes that were adapted from the original jmzTab implementation.
|
| uk.ac.ebi.pride.jmztab2.model |
This package contains model classes for mzTab-M structural features like mandatory and optional columns.
|
| uk.ac.ebi.pride.jmztab2.utils |
This package contains the property file mapping for mzTab-M's validation messages.
|
| uk.ac.ebi.pride.jmztab2.utils.errors |
This package contains error type definitions and related classes used during mzTab validation.
|
| uk.ac.ebi.pride.jmztab2.utils.parser |
This package contains text file line parser implementations for the mzTab-M document sections.
|