#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathOSWParquetWriter.h>

Collaboration diagram for OpenSwathOSWParquetWriter:

Public Member Functions
void	write (const String &output_path, const OpenSwath::LightTargetedExperiment &assay_library, const FeatureMap &feature_map, UInt64 run_id, const String &input_filename, bool enable_uis_scoring) const
	Write an OSW parquet directory or zip archive.

void	setPreserveExisting (bool preserve)
	Set whether the writer should preserve (append) existing archives.

Private Attributes
bool	preserve_existing_ = false

Detailed Description

@brief Write OpenSwathWorkflow output to an OSW Parquet directory (.oswpq).

This writer mirrors the OSW SQLite tables in Parquet:
- runs.parquet
- features.parquet
- feature_precursor.parquet
- feature_transition.parquet (including UIS rows when present)

The output is a directory or zip archive with the following layout:
@code
<output>.oswpq
├── metadata.json
├── library/
│   ├── precursors.parquet
│   └── transitions.parquet
└── runs/
  ├── runs.parquet
  └── run_id=&lt;id&gt;/
    ├── features.parquet
    ├── feature_precursor.parquet
    └── feature_transition.parquet
@endcode

If the output directory already exists, the writer will append a new run partition under runs/run_id=<id>/, update runs.parquet, and refresh metadata.json. Existing runs are not modified.

Member Function Documentation

◆ setPreserveExisting()

void setPreserveExisting ( bool preserve )

Set whether the writer should preserve (append) existing archives.

Parameters

[in] preserve If true, the writer will append to existing .oswpq archives instead of overwriting them.

◆ write()

void write	(	const String &	output_path,
		const OpenSwath::LightTargetedExperiment &	assay_library,
		const FeatureMap &	feature_map,
		UInt64	run_id,
		const String &	input_filename,
		bool	enable_uis_scoring
	)		const

Write an OSW parquet directory or zip archive.

Writes the assay library (precursors + transitions) and scored features for a single run into the Parquet directory layout. If the output directory already exists, the new run is appended under a fresh run_id= partition.

Parameters

[in]	output_path	Path to the output directory (.oswpq)
[in]	assay_library	The transition library used for extraction
[in]	feature_map	Scored features for this run
[in]	run_id	Unique identifier for this run
[in]	input_filename	Original input filename (stored in metadata)
[in]	enable_uis_scoring	Whether UIS (identification) transitions are included

Exceptions

Exception::MissingFeature	if built without Parquet support
Exception::MissingInformation	if a feature is missing required meta values
Exception::InvalidValue	if a run_id already exists in the output

Member Data Documentation

◆ preserve_existing_

bool preserve_existing_ = false

mutableprivate