Package de.isas.mztab2.io
Class MzTabWriterDefaults
- java.lang.Object
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- de.isas.mztab2.io.MzTabWriterDefaults
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public class MzTabWriterDefaults extends Object
Default mapper and schema definitions for writing of mzTab files using the Jackson CSV mapper.- Author:
- nilshoffmann
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Constructor Summary
Constructors Constructor Description MzTabWriterDefaults()
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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, 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, 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, MzTab mzTabFile)
Creates the csv schema (column names and types) for the small molecule summary section.
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Constructor Detail
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MzTabWriterDefaults
public MzTabWriterDefaults()
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Method Detail
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defaultMapper
public com.fasterxml.jackson.dataformat.csv.CsvMapper defaultMapper()
Create a default csv mapper instance.- Returns:
- the csv mapper
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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.
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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
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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.
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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.
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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.
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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
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smallMoleculeSummarySchema
public com.fasterxml.jackson.dataformat.csv.CsvSchema smallMoleculeSummarySchema(com.fasterxml.jackson.dataformat.csv.CsvMapper mapper, MzTab mzTabFile) throws MZTabException
Creates the csv schema (column names and types) for the small molecule summary section.- Parameters:
mapper
- the csv mappermzTabFile
- the mztab object- Returns:
- the configured csv schema for the small molecule summary section
- Throws:
MZTabException
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smallMoleculeFeatureSchema
public com.fasterxml.jackson.dataformat.csv.CsvSchema smallMoleculeFeatureSchema(com.fasterxml.jackson.dataformat.csv.CsvMapper mapper, MzTab mzTabFile) throws MZTabException
Creates the csv schema (column names and types) for the small molecule feature section.- Parameters:
mapper
- the csv mappermzTabFile
- the mztab object- Returns:
- the configured csv schema for the small molecule feature section
- Throws:
MZTabException
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smallMoleculeEvidenceSchema
public com.fasterxml.jackson.dataformat.csv.CsvSchema smallMoleculeEvidenceSchema(com.fasterxml.jackson.dataformat.csv.CsvMapper mapper, MzTab mzTabFile) throws MZTabException
Creates the csv schema (column names and types) for the small molecule feature section.- Parameters:
mapper
- the csv mappermzTabFile
- the mztab object- Returns:
- the configured csv schema for the small molecule feature section
- Throws:
MZTabException
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