Package uk.ac.ebi.pride.jmztab2.model

This package contains model classes for mzTab-M structural features like mandatory and optional columns.

Interface Summary

Interface	Description
IMZTabColumn	IMZTabColumn interface.
IOptColumnMappingBuilder	Interface for optional column mapping builders.
ISmallMoleculeColumn	ISmallMoleculeColumn interface.
ISmallMoleculeEvidenceColumn	ISmallMoleculeEvidenceColumn interface.
ISmallMoleculeFeatureColumn	ISmallMoleculeFeatureColumn interface.

Class Summary

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.
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.
MZTabConstants	Define a couple of constants used in the jmzTab API.
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.
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.
ParameterOptionColumn	An kind of OptionColumn which use CV parameter accessions in following the format: opt_{OBJECT_ID}_cv_{accession}_{parameter name}.
SmallMoleculeColumn	Define the stable columns which have stable order in the small molecule header line
SmallMoleculeEvidenceColumn	Define the stable columns which have stable order in the small molecule evidence header line.
SmallMoleculeFeatureColumn	Define the stable columns which have stable order in the small molecule feature header line.
SplitList<E>	This is list which each item split by a split char.

Enum Summary

Enum	Description
AbundanceColumn.Field
MetadataElement	Define all elements used in metadata.
MetadataProperty	Define a property in metadata, which depend on the MetadataElement.
MZBoolean	In mzTab, using 0-false, 1-true to express the boolean value.
Section	Every line in an mzTab file MUST start with a three letter code identifying the type of line delimited by a Tab character.
SmallMoleculeColumn.Stable	Stable SmallMoleculeColumn definition templates.
SmallMoleculeEvidenceColumn.Stable	Stable SmallMoleculeEvidenceColumn definition templates.
SmallMoleculeFeatureColumn.Stable	Stable SmallMoleculeFeatureColumn definition templates.