FeatureMapArrowIO Class Reference

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

#include <OpenMS/FORMAT/FeatureMapArrowIO.h>

Static Public Member Functions
static std::shared_ptr< arrow::Table >	exportFeaturesToArrow (const FeatureMap &feature_map)
	Export features to Apache Arrow Table.
static std::shared_ptr< arrow::Table >	exportPSMsToArrow (const FeatureMap &feature_map)
	Export peptide spectrum matches (PSMs) associated with features to Apache Arrow Table.
static bool	exportToParquet (const FeatureMap &feature_map, const String &directory, const ParquetWriteConfig &config=ParquetWriteConfig{})
	Export FeatureMap to a directory of Parquet files.
static bool	importFeaturesFromArrow (const std::shared_ptr< arrow::Table > &table, FeatureMap &feature_map)
	Import features from Apache Arrow Table.
static bool	importPSMsFromArrow (const std::shared_ptr< arrow::Table > &table, FeatureMap &feature_map)
	Import PSMs from Apache Arrow Table.
static bool	importFromParquet (const String &directory, FeatureMap &feature_map)
	Import FeatureMap from a directory of Parquet files.

Detailed Description

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

This class provides static methods to export and import FeatureMap data to/from Apache Arrow Tables and Parquet files. Separate tables are provided for features (with their geometry and metadata) and for peptide spectrum matches (PSMs) associated with features.

Experimental classes:

This API is experimental and may change in future versions.

Member Function Documentation

exportFeaturesToArrow()

static std::shared_ptr< arrow::Table > exportFeaturesToArrow ( const FeatureMap &  feature_map )

static

Export features to Apache Arrow Table.

Each Feature becomes one row with RT, MZ, intensity, charge, quality, convex hull geometry, and metadata columns.

Parameters

[in]

feature_map

The FeatureMap to export

Returns

Shared pointer to Arrow Table, or nullptr on error

exportPSMsToArrow()

static std::shared_ptr< arrow::Table > exportPSMsToArrow ( const FeatureMap &  feature_map )

static

Export peptide spectrum matches (PSMs) associated with features to Apache Arrow Table.

Each PeptideHit from each PeptideIdentification (both feature-level and unassigned) becomes one row.

Parameters

[in]

feature_map

The FeatureMap whose identifications to export

Returns

Shared pointer to Arrow Table, or nullptr on error

exportToParquet()

static bool exportToParquet ( const FeatureMap &  feature_map, const String &  directory, const ParquetWriteConfig &  config = ParquetWriteConfig{}  )

static

Export FeatureMap to a directory of Parquet files.

Writes five Parquet files: features.parquet, psms.parquet, proteins.parquet, protein_groups.parquet, and search_params.parquet into the specified directory. Protein-level data is delegated to ProteinIdentificationArrowIO. FeatureMap-level metadata (DocumentIdentifier, DataProcessing) is stored as file-level key-value metadata in features.parquet.

Parameters

[in]	feature_map	The FeatureMap to export
[in]	directory	Output directory path
[in]	config	Parquet writing options

Returns

true on success, false on error

importFeaturesFromArrow()

static bool importFeaturesFromArrow ( const std::shared_ptr< arrow::Table > &  table, FeatureMap &  feature_map  )

static

Import features from Apache Arrow Table.

Each row becomes a Feature with RT, MZ, intensity, charge, quality, convex hull geometry, and metadata populated.

Parameters

[in]	table	Arrow Table with feature data
[out]	feature_map	FeatureMap to populate

Returns

true on success, false on error

importFromParquet()

static bool importFromParquet ( const String &  directory, FeatureMap &  feature_map  )

static

Import FeatureMap from a directory of Parquet files.

Reads five Parquet files (features.parquet, psms.parquet, proteins.parquet, protein_groups.parquet, search_params.parquet) from the specified directory and reconstructs a complete FeatureMap including feature hierarchy, PSM linkage, protein identifications, and FeatureMap-level metadata.

Parameters

[in]	directory	Input directory path containing Parquet files
[out]	feature_map	FeatureMap to populate

Returns

true on success, false on error

importPSMsFromArrow()

static bool importPSMsFromArrow ( const std::shared_ptr< arrow::Table > &  table, FeatureMap &  feature_map  )

static

Import PSMs from Apache Arrow Table.

Reconstructs PeptideIdentifications and PeptideHits from the table and assigns them to the appropriate features or as unassigned.

Parameters

[in]	table	Arrow Table with PSM data
[out]	feature_map	FeatureMap to populate

Returns

true on success, false on error