XIPMParquetConsumer Class Reference

Writes targeted mz/RT/IM peak maps to a Parquet file (.xipm). More...

#include <OpenMS/FORMAT/DATAACCESS/XIPMParquetConsumer.h>

Collaboration diagram for XIPMParquetConsumer:

Public Member Functions
	XIPMParquetConsumer (const std::string &filename, const OpenSwath::LightTargetedExperiment &transition_exp)
	Construct a parquet writer for targeted peak-map export.
	~XIPMParquetConsumer ()
	Destructor flushes pending rows and closes the parquet writer.
void	consumePeakMap (const PeakMapExtractor::ExtractedPeakMap &peak_map, UInt64 run_id, const std::string &source_file, Int64 ms_level)
	Consume one targeted peak map.
void	finalize ()
	Finalize and write the parquet file.
void	setExpectedSize (Size expectedPeakMaps)
	Reserve storage for the expected number of peak maps.

Private Attributes
std::unique_ptr< XIPMParquetConsumerImpl >	impl_

Detailed Description

Writes targeted mz/RT/IM peak maps to a Parquet file (.xipm).

The schema includes run metadata, precursor/transition annotations, extraction window metadata, compressed mz/RT/ion mobility/intensity arrays, and compression flags.

The Parquet output has the following columns (one row per extracted peak map):

Column	Type	Description
RUN_ID	int64	Run identifier
SOURCE_FILE	string (nullable)	Input source filename
MS_LEVEL	int64	MS level (1 for precursor peak maps, 2 for fragment peak maps)
PEAKMAP_TYPE	string	Peak-map type (precursor or transition)
PRECURSOR_ID	int64 (nullable)	Precursor id
TRANSITION_ID	int64 (nullable)	Transition id
MODIFIED_SEQUENCE	string (nullable)	Modified peptide sequence
PRECURSOR_CHARGE	int64 (nullable)	Precursor charge
PRODUCT_CHARGE	int64 (nullable)	Product charge
DETECTING_TRANSITION	int64 (nullable)	Detecting transition flag
PRECURSOR_DECOY	int64 (nullable)	Precursor decoy flag
PRODUCT_DECOY	int64 (nullable)	Product decoy flag
TRANSITION_ORDINAL	int64 (nullable)	Transition ordinal
TRANSITION_TYPE	string (nullable)	Transition type (e.g. y, b)
ANNOTATION	string (nullable)	Transition annotation (e.g. y3^1) or precursor annotation
TARGET_MZ	float64	Extraction target m/z
TARGET_RT	float64 (nullable)	Extraction target RT in the run coordinate system
TARGET_ION_MOBILITY	float64 (nullable)	Extraction target ion mobility
RT_START	float64 (nullable)	Extraction window start in RT
RT_END	float64 (nullable)	Extraction window end in RT
MZ_DATA	binary	Compressed mz array
RT_DATA	binary	Compressed RT array
MOBILITY_DATA	binary	Compressed ion mobility array
INTENSITY_DATA	binary	Compressed intensity array
MZ_COMPRESSION	int64	m/z compression scheme id
RT_COMPRESSION	int64	RT compression scheme id
MOBILITY_COMPRESSION	int64	Ion mobility compression scheme id
INTENSITY_COMPRESSION	int64	Intensity compression scheme id

Compression identifiers:

Column	Value	Description
MZ_COMPRESSION	0	No compression (raw doubles)
MZ_COMPRESSION	1	Zlib-compressed raw doubles
MZ_COMPRESSION	5	MSNumpress (linear) with lossy compression
RT_COMPRESSION	0	No compression (raw doubles)
RT_COMPRESSION	1	Zlib-compressed raw doubles
RT_COMPRESSION	5	MSNumpress (linear) with lossy compression
MOBILITY_COMPRESSION	0	No compression (raw doubles)
MOBILITY_COMPRESSION	1	Zlib-compressed raw doubles
MOBILITY_COMPRESSION	5	MSNumpress (linear) with lossy compression
INTENSITY_COMPRESSION	0	No compression (raw doubles)
INTENSITY_COMPRESSION	1	Zlib-compressed raw doubles
INTENSITY_COMPRESSION	6	MSNumpress (short logged float) with lossy compression

Constructor & Destructor Documentation

XIPMParquetConsumer()

XIPMParquetConsumer	(	const std::string &	filename,
		const OpenSwath::LightTargetedExperiment &	transition_exp
	)

Construct a parquet writer for targeted peak-map export.

Parameters

[in]	filename	Output parquet filename
[in]	transition_exp	Transition metadata used to annotate rows

~XIPMParquetConsumer()

~XIPMParquetConsumer

(

)

Destructor flushes pending rows and closes the parquet writer.

Member Function Documentation

consumePeakMap()

void consumePeakMap	(	const PeakMapExtractor::ExtractedPeakMap &	peak_map,
		UInt64	run_id,
		const std::string &	source_file,
		Int64	ms_level
	)

Consume one targeted peak map.

Parameters

[in]	peak_map	Extracted peak map to append
[in]	run_id	Run identifier
[in]	source_file	Source mzML / raw file name
[in]	ms_level	MS level of the extraction (1 = precursor, 2 = fragment)

finalize()

void finalize

(

)

Finalize and write the parquet file.

setExpectedSize()

void setExpectedSize

(

Size

expectedPeakMaps

)

Reserve storage for the expected number of peak maps.

Parameters

[in]

expectedPeakMaps

The expected number of rows

Member Data Documentation

impl_

std::unique_ptr<XIPMParquetConsumerImpl> impl_

private