Package de.isas.mztab2.io

Class MzTabWriterDefaults

  • public class MzTabWriterDefaults
extends Object
    Default mapper and schema definitions for writing of mzTab files using the Jackson CSV mapper.
    Author:
    nilshoffmann

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      com.fasterxml.jackson.dataformat.csv.CsvMapper defaultMapper()
      Create a default csv mapper instance.
      com.fasterxml.jackson.dataformat.csv.CsvSchema defaultSchemaForBuilder​(com.fasterxml.jackson.dataformat.csv.CsvSchema.Builder builder)
      Apply the default csv schema to the provided builder.
      com.fasterxml.jackson.dataformat.csv.CsvMapper metadataMapper()
      Create a metadata section csv mapper.
      com.fasterxml.jackson.dataformat.csv.CsvSchema metaDataSchema​(com.fasterxml.jackson.dataformat.csv.CsvMapper mapper)
      Creates the csv schema for the metadata section (column names, value separators, array element separators, etc.).
      com.fasterxml.jackson.dataformat.csv.CsvMapper smallMoleculeEvidenceMapper()
      Create a small molecule evidence section csv mapper.
      com.fasterxml.jackson.dataformat.csv.CsvSchema smallMoleculeEvidenceSchema​(com.fasterxml.jackson.dataformat.csv.CsvMapper mapper, de.isas.mztab2.model.MzTab mzTabFile)
      Creates the csv schema (column names and types) for the small molecule feature section.
      com.fasterxml.jackson.dataformat.csv.CsvMapper smallMoleculeFeatureMapper()
      Create a small molecule feature section csv mapper.
      com.fasterxml.jackson.dataformat.csv.CsvSchema smallMoleculeFeatureSchema​(com.fasterxml.jackson.dataformat.csv.CsvMapper mapper, de.isas.mztab2.model.MzTab mzTabFile)
      Creates the csv schema (column names and types) for the small molecule feature section.
      com.fasterxml.jackson.dataformat.csv.CsvMapper smallMoleculeSummaryMapper()
      Create a small molecule summary section csv mapper.
      com.fasterxml.jackson.dataformat.csv.CsvSchema smallMoleculeSummarySchema​(com.fasterxml.jackson.dataformat.csv.CsvMapper mapper, de.isas.mztab2.model.MzTab mzTabFile)
      Creates the csv schema (column names and types) for the small molecule summary section.

    • Method Detail

      • defaultMapper

        public com.fasterxml.jackson.dataformat.csv.CsvMapper defaultMapper()
        Create a default csv mapper instance.
        Returns:
        the csv mapper

      • metadataMapper

        public com.fasterxml.jackson.dataformat.csv.CsvMapper metadataMapper()
        Create a metadata section csv mapper. This registers mixins for serialization of all objects that are part of the metadata section.
        Returns:
        the metadata section csv mapper.

      • metaDataSchema

        public com.fasterxml.jackson.dataformat.csv.CsvSchema metaDataSchema​(com.fasterxml.jackson.dataformat.csv.CsvMapper mapper)
        Creates the csv schema for the metadata section (column names, value separators, array element separators, etc.).
        Parameters:
        mapper - the configured csv mapper
        Returns:
        the metadata csv schema

      • smallMoleculeSummaryMapper

        public com.fasterxml.jackson.dataformat.csv.CsvMapper smallMoleculeSummaryMapper()
        Create a small molecule summary section csv mapper. This registers mixins for serialization of all objects that are part of the small molecule summary section.
        Returns:
        the small molecule summary section csv mapper.

      • smallMoleculeFeatureMapper

        public com.fasterxml.jackson.dataformat.csv.CsvMapper smallMoleculeFeatureMapper()
        Create a small molecule feature section csv mapper. This registers mixins for serialization of all objects that are part of the small molecule feature section.
        Returns:
        the small molecule feature section csv mapper.

      • smallMoleculeEvidenceMapper

        public com.fasterxml.jackson.dataformat.csv.CsvMapper smallMoleculeEvidenceMapper()
        Create a small molecule evidence section csv mapper. This registers mixins for serialization of all objects that are part of the small molecule evidence section.
        Returns:
        the small molecule evidence section csv mapper.

      • defaultSchemaForBuilder

        public com.fasterxml.jackson.dataformat.csv.CsvSchema defaultSchemaForBuilder​(com.fasterxml.jackson.dataformat.csv.CsvSchema.Builder builder)
        Apply the default csv schema to the provided builder.
        Parameters:
        builder - the builder to use for schema configuration
        Returns:
        the configured csv schema

      • smallMoleculeSummarySchema

        public com.fasterxml.jackson.dataformat.csv.CsvSchema smallMoleculeSummarySchema​(com.fasterxml.jackson.dataformat.csv.CsvMapper mapper,
                                                                                 de.isas.mztab2.model.MzTab mzTabFile)
                                                                          throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException
        Creates the csv schema (column names and types) for the small molecule summary section.
        Parameters:
        mapper - the csv mapper
        mzTabFile - the mztab object
        Returns:
        the configured csv schema for the small molecule summary section
        Throws:
        uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

      • smallMoleculeFeatureSchema

        public com.fasterxml.jackson.dataformat.csv.CsvSchema smallMoleculeFeatureSchema​(com.fasterxml.jackson.dataformat.csv.CsvMapper mapper,
                                                                                 de.isas.mztab2.model.MzTab mzTabFile)
                                                                          throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException
        Creates the csv schema (column names and types) for the small molecule feature section.
        Parameters:
        mapper - the csv mapper
        mzTabFile - the mztab object
        Returns:
        the configured csv schema for the small molecule feature section
        Throws:
        uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

      • smallMoleculeEvidenceSchema

        public com.fasterxml.jackson.dataformat.csv.CsvSchema smallMoleculeEvidenceSchema​(com.fasterxml.jackson.dataformat.csv.CsvMapper mapper,
                                                                                  de.isas.mztab2.model.MzTab mzTabFile)
                                                                           throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException
        Creates the csv schema (column names and types) for the small molecule feature section.
        Parameters:
        mapper - the csv mapper
        mzTabFile - the mztab object
        Returns:
        the configured csv schema for the small molecule feature section
        Throws:
        uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException