ConsensusMapArrowExport Class Reference

Export ConsensusMap feature data to Apache Arrow format following QPX feature schema. More...

#include <OpenMS/FORMAT/ConsensusMapArrowExport.h>

Static Public Member Functions
static std::shared_ptr< arrow::Table >	exportToArrow (const ConsensusMap &cmap)
	Export ConsensusMap to Apache Arrow Table.
static bool	exportToParquet (const ConsensusMap &cmap, const std::string &filename, const ParquetWriteConfig &config=ParquetWriteConfig{})
	Export ConsensusMap to Parquet file.
static bool	exportToParquetStreaming (const ConsensusMap &cmap, const std::string &filename, size_t batch_size=1000000, const ParquetWriteConfig &config=ParquetWriteConfig{}, int n_threads=1)
	Stream a ConsensusMap to a Parquet file in row batches (bounded peak memory)

Detailed Description

Export ConsensusMap feature data to Apache Arrow format following QPX feature schema.

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

Experimental classes:

This API is experimental and may change in future versions.

Member Function Documentation

exportToArrow()

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

static

Export ConsensusMap to Apache Arrow Table.

Exports consensus features following the QPX feature schema. Each ConsensusFeature becomes one row with identification, quantification, and protein group information.

Parameters

[in]

cmap

The ConsensusMap to export

Returns

Shared pointer to Arrow Table, or nullptr on error

exportToParquet()

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

static

Export ConsensusMap to Parquet file.

Parameters

[in]	cmap	The ConsensusMap to export
[in]	filename	Output file path
[in]	config	Parquet writing options

Returns

true on success, false on error

exportToParquetStreaming()

static bool exportToParquetStreaming ( const ConsensusMap &  cmap, const std::string &  filename, size_t  batch_size = 1000000, const ParquetWriteConfig &  config = ParquetWriteConfig{}, int  n_threads = 1  )

static

Stream a ConsensusMap to a Parquet file in row batches (bounded peak memory)

Functionally equivalent to exportToParquet() but builds and flushes the feature table one batch_size -sized range at a time through a persistent parquet::arrow::FileWriter, instead of materializing the whole ~N-row Arrow table in memory before a single write. For isobaric data (one consensus feature per PSM) N can be in the millions, where the one-shot path's transient peak drives the process into swap / OOM; here peak memory stays bounded by one batch.

Each batch is optionally partitioned and built in parallel with OpenMP and written in index order (the Parquet writer stays serial), so the written rows and their order are identical to exportToParquet() and deterministic for any thread count; only the Parquet row-group layout may differ.

Parameters

[in]	cmap	The ConsensusMap to export
[in]	filename	Output file path
[in]	batch_size	Consensus features materialized per batch (0 is treated as the default)
[in]	config	Parquet writing options
[in]	n_threads	OpenMP threads for the per-batch build: 1 = serial (default), 0 = all available cores (honors OMP_NUM_THREADS), N = fixed

Returns

true on success, false on error