MobilogramParquetConsumer Class Reference

Writes Mobilograms (ion-mobility traces) to a Parquet file using a PyProphet-compatible-like schema. More...

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

Collaboration diagram for MobilogramParquetConsumer:

Public Member Functions
	MobilogramParquetConsumer (const String &filename, UInt64 run_id, const String &source_file, const OpenSwath::LightTargetedExperiment &transition_exp)
	Construct a parquet consumer for mobilogram export.
	~MobilogramParquetConsumer ()
	Destructor flushes pending data and closes the parquet writer.
void	consumeMobilogram (const Mobilogram &m, const String &mobilogram_type="", Int64 ms_level=-1, Int64 transition_id=-1, const String &transition_native_id="", double feature_rt=std::numeric_limits< double >::quiet_NaN(), Int64 feature_id=-1)
	Consume a mobilogram and write it to the parquet file.
void	finalize ()
	Finalize and write the parquet file. Call to surface write errors.
void	setExpectedSize (Size expectedMobilograms)
	Reserve storage for expected number of mobilograms.

Private Attributes
std::unique_ptr< MobilogramParquetConsumerImpl >	impl_

Detailed Description

Writes Mobilograms (ion-mobility traces) to a Parquet file using a PyProphet-compatible-like schema.

Constructor & Destructor Documentation

MobilogramParquetConsumer()

MobilogramParquetConsumer	(	const String &	filename,
		UInt64	run_id,
		const String &	source_file,
		const OpenSwath::LightTargetedExperiment &	transition_exp
	)

Construct a parquet consumer for mobilogram export.

Parameters

[in]	filename	Output parquet filename.
[in]	run_id	Run identifier to store with each mobilogram.
[in]	source_file	Source mzML filename to store with each mobilogram.
[in]	transition_exp	Optional transition experiment used to annotate mobilograms. Note: the signature takes a const reference, so a caller that does not want any transition annotations must pass an empty OpenSwath::LightTargetedExperiment (i.e. one with no compounds/transitions). A null pointer is not accepted.

~MobilogramParquetConsumer()

~MobilogramParquetConsumer

(

)

Destructor flushes pending data and closes the parquet writer.

Member Function Documentation

consumeMobilogram()

void consumeMobilogram	(	const Mobilogram &	m,
		const String &	mobilogram_type = "",
		Int64	ms_level = -1,
		Int64	transition_id = -1,
		const String &	transition_native_id = "",
		double	feature_rt = std::numeric_limits< double >::quiet_NaN(),
		Int64	feature_id = -1
	)

Consume a mobilogram and write it to the parquet file.

Parameters

[in]	m	The mobilogram to consume (read-only; the caller retains ownership and the mobilogram is not modified)
[in]	mobilogram_type	The type of the mobilogram (e.g. "precursor" or "fragment")
[in]	ms_level	The MS level of the mobilogram (e.g. 1 for precursor, 2 for fragment)
[in]	transition_id	The id of the corresponding transition in the transition experiment (nullable: -1 means not set)
[in]	transition_native_id	The native id of the corresponding transition in the transition experiment (nullable: empty string means not set)
[in]	feature_rt	Optional retention time apex that the mobilogram corresponds to (nullable: NaN means not set)
[in]	feature_id	Optional feature id associated with the mobilogram (nullable: -1 means not set)

finalize()

void finalize

(

)

Finalize and write the parquet file. Call to surface write errors.

setExpectedSize()

void setExpectedSize

(

Size

expectedMobilograms

)

Reserve storage for expected number of mobilograms.

Must be called before any concurrent consumeMobilogram() calls (e.g. from an OpenMP parallel loop). Calling it after concurrent writes have started is undefined behaviour.

Parameters

[in]

expectedMobilograms

The expected number of mobilograms

Member Data Documentation

impl_

std::unique_ptr<MobilogramParquetConsumerImpl> impl_

private