ProteinGroupArrowExport Class Reference

Export protein group data to Apache Arrow format following QPX pg schema. More...

#include <OpenMS/FORMAT/ProteinGroupArrowExport.h>

Static Public Member Functions
static std::shared_ptr< arrow::Table >	exportToArrow (const ConsensusMap &cmap)
	Export protein group data to Apache Arrow Table.
static bool	exportToParquet (const ConsensusMap &cmap, const String &filename, const ParquetWriteConfig &config=ParquetWriteConfig{})
	Export protein group data to Parquet file.
static std::shared_ptr< arrow::Table >	exportToArrow (const std::vector< ProteinIdentification > &protein_identifications, const PeptideIdentificationList &peptide_identifications)
	Export protein group data to Arrow table from identification data (no quantification)
static bool	exportToParquet (const std::vector< ProteinIdentification > &protein_identifications, const PeptideIdentificationList &peptide_identifications, const String &filename, const ParquetWriteConfig &config=ParquetWriteConfig{})
	Export protein group data to Parquet file from identification data (no quantification)
static bool	exportToParquet (const std::shared_ptr< arrow::Table > &table, const String &filename, const ParquetWriteConfig &config=ParquetWriteConfig{})
	Write a pre-built QPX protein group Arrow table to a Parquet file.

Detailed Description

Export protein group data to Apache Arrow format following QPX pg schema.

This class provides static methods to export protein group quantification data from a ConsensusMap to Apache Arrow Tables and Parquet files. The schema follows the QPX (Quantitative Proteomics Exchange) protein group format.

Protein groups must have quantification annotated via PeptideAndProteinQuant::annotateQuantificationsToProteins() before export.

Experimental classes:

This API is experimental and may change in future versions.

Member Function Documentation

exportToArrow() [1/2]

static std::shared_ptr< arrow::Table > exportToArrow ( const ConsensusMap &  cmap )

static

Export protein group data to Apache Arrow Table.

Exports indistinguishable protein groups following the QPX pg schema. One row is emitted per protein group per run file.

Parameters

[in]

cmap

The ConsensusMap with annotated protein group quantification

Returns

Shared pointer to Arrow Table, or nullptr on error

exportToArrow() [2/2]

static std::shared_ptr< arrow::Table > exportToArrow ( const std::vector< ProteinIdentification > &  protein_identifications, const PeptideIdentificationList &  peptide_identifications  )

static

Export protein group data to Arrow table from identification data (no quantification)

For search-engine output where no ConsensusMap is available. Populates required QPX pg fields (pg_accessions, anchor_protein, run_file_name, is_decoy, peptides) and sets quantification columns (intensities, additional_intensities) to null.

Parameters

[in]	protein_identifications	Protein identifications with protein groups
[in]	peptide_identifications	Peptide identifications (for peptide-per-protein counts)

Returns

Shared pointer to Arrow Table (empty table if no groups, never nullptr)

exportToParquet() [1/3]

static bool exportToParquet ( const ConsensusMap &  cmap, const String &  filename, const ParquetWriteConfig &  config = ParquetWriteConfig{}  )

static

Export protein group data to Parquet file.

Parameters

[in]	cmap	The ConsensusMap with annotated protein group quantification
[in]	filename	Output file path
[in]	config	Parquet writing options

Returns

true on success, false on error

exportToParquet() [2/3]

static bool exportToParquet ( const std::shared_ptr< arrow::Table > &  table, const String &  filename, const ParquetWriteConfig &  config = ParquetWriteConfig{}  )

static

Write a pre-built QPX protein group Arrow table to a Parquet file.

The table is expected to follow QPXPgSchema (e.g., from exportToArrow). Attaches QPX file metadata (qpx_version, file_type="pg", UUID, creation_date) before writing. Use this overload when the caller already has the table built (e.g., for merged output) to avoid rebuilding it.

Parameters

[in]	table	QPX pg Arrow table (must not be null)
[in]	filename	Output file path
[in]	config	Parquet writing options

Returns

true on success, false on error

exportToParquet() [3/3]

static bool exportToParquet ( const std::vector< ProteinIdentification > &  protein_identifications, const PeptideIdentificationList &  peptide_identifications, const String &  filename, const ParquetWriteConfig &  config = ParquetWriteConfig{}  )

static

Export protein group data to Parquet file from identification data (no quantification)

Parameters

[in]	protein_identifications	Protein identifications with protein groups
[in]	peptide_identifications	Peptide identifications (for peptide-per-protein counts)
[in]	filename	Output file path
[in]	config	Parquet writing options

Returns

true on success, false on error