ProteinIdentificationArrowIO Class Reference

Import and export ProteinIdentification data to/from Apache Arrow format. More...

#include <OpenMS/FORMAT/ProteinIdentificationArrowIO.h>

Static Public Member Functions
static std::shared_ptr< arrow::Table >	exportProteinsToArrow (const std::vector< ProteinIdentification > &protein_identifications)
	Export protein hits to Apache Arrow Table.
static bool	exportProteinsToParquet (const std::vector< ProteinIdentification > &protein_identifications, const String &filename, const ParquetWriteConfig &config=ParquetWriteConfig{})
	Export protein hits to Parquet file.
static std::shared_ptr< arrow::Table >	exportProteinGroupsToArrow (const std::vector< ProteinIdentification > &protein_identifications)
	Export protein groups to Apache Arrow Table.
static bool	exportProteinGroupsToParquet (const std::vector< ProteinIdentification > &protein_identifications, const String &filename, const ParquetWriteConfig &config=ParquetWriteConfig{})
	Export protein groups to Parquet file.
static std::shared_ptr< arrow::Table >	exportSearchParamsToArrow (const std::vector< ProteinIdentification > &protein_identifications)
	Export search parameters to Apache Arrow Table.
static bool	exportSearchParamsToParquet (const std::vector< ProteinIdentification > &protein_identifications, const String &filename, const ParquetWriteConfig &config=ParquetWriteConfig{})
	Export search parameters to Parquet file.
static bool	importFromParquet (const String &proteins_filename, const String &protein_groups_filename, const String &search_params_filename, std::vector< ProteinIdentification > &protein_identifications)
	Import all three Parquet files and reconstruct ProteinIdentifications.
static bool	importSearchParamsFromArrow (const std::shared_ptr< arrow::Table > &table, std::vector< ProteinIdentification > &protein_identifications)
	Import search parameters from Arrow Table.
static bool	importProteinsFromArrow (const std::shared_ptr< arrow::Table > &table, std::vector< ProteinIdentification > &protein_identifications)
	Import protein hits from Arrow Table.
static bool	importProteinGroupsFromArrow (const std::shared_ptr< arrow::Table > &table, std::vector< ProteinIdentification > &protein_identifications)
	Import protein groups from Arrow Table.
static bool	importSearchParamsFromParquet (const String &filename, std::vector< ProteinIdentification > &protein_identifications)
	Import search parameters from Parquet file.
static bool	importProteinsFromParquet (const String &filename, std::vector< ProteinIdentification > &protein_identifications)
	Import protein hits from Parquet file.
static bool	importProteinGroupsFromParquet (const String &filename, std::vector< ProteinIdentification > &protein_identifications)
	Import protein groups from Parquet file.

Detailed Description

Import and export ProteinIdentification data to/from Apache Arrow format.

This class provides static methods to export and import ProteinIdentification data to/from Apache Arrow Tables and Parquet files. Separate tables are provided for protein hits, protein groups, and search parameters.

Experimental classes:

This API is experimental and may change in future versions.

Member Function Documentation

exportProteinGroupsToArrow()

static std::shared_ptr< arrow::Table > exportProteinGroupsToArrow ( const std::vector< ProteinIdentification > &  protein_identifications )

static

Export protein groups to Apache Arrow Table.

Each ProteinGroup becomes one row with group probability and member accessions.

Parameters

[in]

protein_identifications

Vector of protein identifications

Returns

Shared pointer to Arrow Table, or nullptr on error

exportProteinGroupsToParquet()

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

static

Export protein groups to Parquet file.

Parameters

[in]	protein_identifications	Vector of protein identifications
[in]	filename	Output file path
[in]	config	Parquet writing options

Returns

true on success, false on error

exportProteinsToArrow()

static std::shared_ptr< arrow::Table > exportProteinsToArrow ( const std::vector< ProteinIdentification > &  protein_identifications )

static

Export protein hits to Apache Arrow Table.

Each ProteinHit becomes one row with identification, score, and metadata.

Parameters

[in]

protein_identifications

Vector of protein identifications

Returns

Shared pointer to Arrow Table, or nullptr on error

exportProteinsToParquet()

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

static

Export protein hits to Parquet file.

Parameters

[in]	protein_identifications	Vector of protein identifications
[in]	filename	Output file path
[in]	config	Parquet writing options

Returns

true on success, false on error

exportSearchParamsToArrow()

static std::shared_ptr< arrow::Table > exportSearchParamsToArrow ( const std::vector< ProteinIdentification > &  protein_identifications )

static

Export search parameters to Apache Arrow Table.

Each ProteinIdentification's SearchParameters becomes one row.

Parameters

[in]

protein_identifications

Vector of protein identifications

Returns

Shared pointer to Arrow Table, or nullptr on error

exportSearchParamsToParquet()

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

static

Export search parameters to Parquet file.

Parameters

[in]	protein_identifications	Vector of protein identifications
[in]	filename	Output file path
[in]	config	Parquet writing options

Returns

true on success, false on error

importFromParquet()

static bool importFromParquet ( const String &  proteins_filename, const String &  protein_groups_filename, const String &  search_params_filename, std::vector< ProteinIdentification > &  protein_identifications  )

static

Import all three Parquet files and reconstruct ProteinIdentifications.

Reads the three Parquet files and reconstructs a vector of ProteinIdentification objects with hits, groups, and search parameters.

Parameters

[in]	proteins_filename	Path to proteins Parquet file
[in]	protein_groups_filename	Path to protein groups Parquet file
[in]	search_params_filename	Path to search params Parquet file
[out]	protein_identifications	Reconstructed protein identifications

Returns

true on success, false on error

importProteinGroupsFromArrow()

static bool importProteinGroupsFromArrow ( const std::shared_ptr< arrow::Table > &  table, std::vector< ProteinIdentification > &  protein_identifications  )

static

Import protein groups from Arrow Table.

Adds ProteinGroups and IndistinguishableProteins to matching ProteinIdentifications by run_identifier.

Parameters

[in]	table	Arrow Table with protein groups
[out]	protein_identifications	Protein identifications to populate

Returns

true on success, false on error

importProteinGroupsFromParquet()

static bool importProteinGroupsFromParquet ( const String &  filename, std::vector< ProteinIdentification > &  protein_identifications  )

static

Import protein groups from Parquet file.

Parameters

[in]	filename	Path to Parquet file
[out]	protein_identifications	Protein identifications to populate

Returns

true on success, false on error

importProteinsFromArrow()

static bool importProteinsFromArrow ( const std::shared_ptr< arrow::Table > &  table, std::vector< ProteinIdentification > &  protein_identifications  )

static

Import protein hits from Arrow Table.

Adds ProteinHits to matching ProteinIdentifications by run_identifier. If no matching ProteinIdentification exists, creates new ones.

Parameters

[in]	table	Arrow Table with protein hits
[out]	protein_identifications	Protein identifications to populate

Returns

true on success, false on error

importProteinsFromParquet()

static bool importProteinsFromParquet ( const String &  filename, std::vector< ProteinIdentification > &  protein_identifications  )

static

Import protein hits from Parquet file.

Parameters

[in]	filename	Path to Parquet file
[out]	protein_identifications	Protein identifications to populate

Returns

true on success, false on error

importSearchParamsFromArrow()

static bool importSearchParamsFromArrow ( const std::shared_ptr< arrow::Table > &  table, std::vector< ProteinIdentification > &  protein_identifications  )

static

Import search parameters from Arrow Table.

Each row becomes a ProteinIdentification shell with run-level metadata and SearchParameters populated.

Parameters

[in]	table	Arrow Table with search parameters
[out]	protein_identifications	Reconstructed protein identifications

Returns

true on success, false on error

importSearchParamsFromParquet()

static bool importSearchParamsFromParquet ( const String &  filename, std::vector< ProteinIdentification > &  protein_identifications  )

static

Import search parameters from Parquet file.

Parameters

[in]	filename	Path to Parquet file
[out]	protein_identifications	Reconstructed protein identifications

Returns

true on success, false on error