QPXFile Class Reference

Export PSM (Peptide Spectrum Match) data to Apache Arrow format following QPX PSM schema. More...

#include <OpenMS/FORMAT/QPXFile.h>

Static Public Member Functions
static std::shared_ptr< arrow::Table >	exportToArrow (const std::vector< ProteinIdentification > &protein_identifications, const PeptideIdentificationList &peptide_identifications, bool export_all_psms=false)
	Export PSMs to Arrow table using PSMSchema for lossless round-trips.
static std::shared_ptr< arrow::Table >	exportPSMsToQPXArrow (const std::vector< ProteinIdentification > &protein_identifications, const PeptideIdentificationList &peptide_identifications, bool export_all_psms=false)
	Export PSMs to QPX Parquet eXchange format Arrow table (QPXPSMSchema).
static bool	exportToParquet (const std::vector< ProteinIdentification > &protein_identifications, const PeptideIdentificationList &peptide_identifications, const String &filename, bool export_all_psms=false, const ParquetWriteConfig &config=ParquetWriteConfig{})
	Export PSM data to Parquet file.
static bool	exportToParquet (const std::shared_ptr< arrow::Table > &table, const String &filename, const ParquetWriteConfig &config=ParquetWriteConfig{})
	Write a pre-built QPX PSM Arrow table to a Parquet file.

Detailed Description

Export PSM (Peptide Spectrum Match) data to Apache Arrow format following QPX PSM schema.

This class provides static methods to export PeptideIdentification/ProteinIdentification data to Apache Arrow Tables and Parquet files. The schema follows the QPX (Quantitative Proteomics Exchange) PSM format.

Experimental classes:

This API is experimental and may change in future versions.

Member Function Documentation

exportPSMsToQPXArrow()

static std::shared_ptr< arrow::Table > exportPSMsToQPXArrow ( const std::vector< ProteinIdentification > &  protein_identifications, const PeptideIdentificationList &  peptide_identifications, bool  export_all_psms = false  )

static

Export PSMs to QPX Parquet eXchange format Arrow table (QPXPSMSchema).

Unlike exportToArrow() which produces a PSMSchema table for lossless round-trips, this method produces a QPXPSMSchema table optimized for cross-tool exchange (quantms format).

Parameters

protein_identifications	Protein identifications (for file name lookup)
peptide_identifications	Peptide identifications to export
export_all_psms	If true, export all PSM hits; if false, only best hit per spectrum

Returns

Arrow table with QPXPSMSchema columns, or nullptr on failure

exportToArrow()

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

static

Export PSMs to Arrow table using PSMSchema for lossless round-trips.

Produces a table with PSMSchema columns (score, score_type, rank, etc.) suitable for FeatureMapArrowIO and ConsensusMapArrowIO round-trips. For QPX exchange format output, use exportPSMsToQPXArrow() instead.

exportToParquet() [1/2]

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

static

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

The table is expected to follow QPXPSMSchema (e.g., from exportPSMsToQPXArrow). Attaches QPX file metadata (qpx_version, file_type="psm", 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 PSM Arrow table (must not be null)
[in]	filename	Output file path
[in]	config	Parquet writing options

Returns

true on success, false on error

exportToParquet() [2/2]

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

static

Export PSM data to Parquet file.

Parameters

[in]	protein_identifications	Vector of protein identifications
[in]	peptide_identifications	List of peptide identifications
[in]	filename	Output file path
[in]	export_all_psms	If true, export all hits per spectrum (default: false, only best hit)
[in]	config	Parquet writing options

Returns

true on success, false on error