PSMArrowIO Class Reference

Read and write OpenMS identification data as a parquet bundle (.idparquet). More...

#include <OpenMS/FORMAT/PSMArrowIO.h>

Static Public Member Functions
static bool	exportToParquet (const std::vector< ProteinIdentification > &protein_identifications, const PeptideIdentificationList &peptide_identifications, const std::string &dir, bool export_all_psms=true, const ParquetWriteConfig &config=ParquetWriteConfig{})
	Export protein and peptide identifications to an idparquet directory bundle.
static bool	importFromParquet (const std::string &dir, std::vector< ProteinIdentification > &protein_identifications, PeptideIdentificationList &peptide_identifications)
	Import protein and peptide identifications from an idparquet directory bundle.

Detailed Description

Read and write OpenMS identification data as a parquet bundle (.idparquet).

An idparquet bundle is a directory containing four parquet files:

• psms.parquet (PSMSchema, lossless PeptideIdentification data)
• proteins.parquet (ProteinSchema, ProteinHits)
• protein_groups.parquet (ProteinGroupSchema, indistinguishable groups)
• search_params.parquet (SearchParamsSchema, run-level parameters)

All four files are required for a valid bundle on read.

Member Function Documentation

exportToParquet()

static bool exportToParquet ( const std::vector< ProteinIdentification > &  protein_identifications, const PeptideIdentificationList &  peptide_identifications, const std::string &  dir, bool  export_all_psms = true, const ParquetWriteConfig &  config = ParquetWriteConfig{}  )

static

Export protein and peptide identifications to an idparquet directory bundle.

Writes (and overwrites) the four canonical files inside dir. Other files in dir are left untouched. If dir does not exist it is created (only dir itself; the parent must already exist). If dir exists as a regular file, returns false.

Parameters

[in]	protein_identifications	Protein identifications (run-level metadata, hits, groups, search params)
[in]	peptide_identifications	Peptide identifications (PSMs)
[in]	dir	Output directory path
[in]	export_all_psms	If true, write all hits per PSM; if false, write best hit per spectrum only (default: true — bundle is intended for lossless round-trip)
[in]	config	Parquet writer configuration

Returns

true on success, false on error (errors are logged)

importFromParquet()

static bool importFromParquet ( const std::string &  dir, std::vector< ProteinIdentification > &  protein_identifications, PeptideIdentificationList &  peptide_identifications  )

static

Import protein and peptide identifications from an idparquet directory bundle.

All four canonical files (psms.parquet, proteins.parquet, protein_groups.parquet, search_params.parquet) must be present in dir. Missing any one is an error.

Parameters

[in]	dir	Input directory path
[out]	protein_identifications	Populated from the three protein-side parquet files
[out]	peptide_identifications	Populated from psms.parquet

Returns

true on success, false on error (errors are logged)