OpenMS
SqMassFile Class Reference

An class that uses on-disk SQLite database to read and write spectra and chromatograms. More...

#include <OpenMS/FORMAT/SqMassFile.h>

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Classes

struct  SqMassConfig
 Configuration class for SqMassFile. More...
 

Public Types

typedef MSExperiment MapType
 

Public Member Functions

Constructors and Destructor
 SqMassFile ()
 Default constructor. More...
 
 ~SqMassFile ()
 Default destructor. More...
 

Read / Write a complete mass spectrometric experiment

SqMassConfig config_
 
void load (const String &filename, MapType &map) const
 
void store (const String &filename, MapType &map) const
 Store an MSExperiment in sqMass format. More...
 
void transform (const String &filename_in, Interfaces::IMSDataConsumer *consumer, bool skip_full_count=false, bool skip_first_pass=false) const
 
void setConfig (const SqMassConfig &config)
 

Detailed Description

An class that uses on-disk SQLite database to read and write spectra and chromatograms.

This class provides functions to read and write spectra and chromatograms to disk using a SQLite database and store them in sqMass format. This allows users to access, select and filter spectra and chromatograms on-demand even in a large collection of data.

Spectra and chromatograms with precursor information will additionally load/store the metavalue 'peptide_sequence' from the first precursor (if any).


Class Documentation

◆ OpenMS::SqMassFile::SqMassConfig

struct OpenMS::SqMassFile::SqMassConfig

Configuration class for SqMassFile.

Contains configuration options for SQLite file

Collaboration diagram for SqMassFile::SqMassConfig:
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Class Members
double linear_fp_mass_acc desired mass accuracy for numpress linear encoding (-1 no effect, use 0.0001 for 0.2 ppm accuracy @ 500 m/z)
bool use_lossy_numpress use lossy numpress compression
bool write_full_meta write full meta data

Member Typedef Documentation

◆ MapType

Constructor & Destructor Documentation

◆ SqMassFile()

Default constructor.

◆ ~SqMassFile()

~SqMassFile ( )

Default destructor.

Member Function Documentation

◆ load()

void load ( const String filename,
MapType map 
) const

◆ setConfig()

void setConfig ( const SqMassConfig config)
inline

◆ store()

void store ( const String filename,
MapType map 
) const

Store an MSExperiment in sqMass format.

If you want a specific RUN::ID in the sqMass file, make sure to populate MSExperiment::setSqlRunID(UInt64 id) before.

◆ transform()

void transform ( const String filename_in,
Interfaces::IMSDataConsumer consumer,
bool  skip_full_count = false,
bool  skip_first_pass = false 
) const

Member Data Documentation

◆ config_

SqMassConfig config_
protected