ThermoRawScanReader Class Reference

Scan-by-scan conversion of a Thermo RAW file into OpenMS spectra (private). More...

#include <OpenMS/FORMAT/HANDLERS/ThermoRawScanReader.h>

Classes
class	Accessor
	Converts scans independently of each other (random access). More...
struct	ScanInfo
	Scan header values needed to select scans before converting them. More...
struct	ScanRecord
	Everything of a scan that depends on the scans before it (see header()). More...

Public Types
using	Options = ThermoRawFile::Options
using	ParentLookup = std::function< const MSSpectrum *(int scan)>
	Returns the converted (peak-sorted) spectrum of a scan or nullptr if it is not available.

Public Member Functions
	ThermoRawScanReader (const std::string &path, const Options &options)
	Open path.
	~ThermoRawScanReader ()
	ThermoRawScanReader (const ThermoRawScanReader &)=delete
ThermoRawScanReader &	operator= (const ThermoRawScanReader &)=delete
bool	hasMSData () const
	True if the file contains a mass spectrometer controller.
int	firstScan () const
	First MS scan number (only valid if hasMSData()).
int	lastScan () const
	Last MS scan number (only valid if hasMSData()).
void	fillSettings (ExperimentalSettings &settings) const
	Write run-level settings into settings (instrument configurations are added by convert() and addInstrumentConfigurations()).
const ScanInfo &	header (int scan, bool with_peaks=false)
	Read the header of scan; must be called for every scan in increasing order.
void	readAhead (int last_scan, int peaks_from)
	Read the following scans up to last_scan on worker threads ahead of header().
void	scanHeaders (int first, int last, bool precursors, const std::function< bool(const ScanInfo &)> &visit)
	Visit the headers of scans first to last ahead of header(), without peaks.
void	convert (MSSpectrum &spectrum, ExperimentalSettings &settings, const ParentLookup &parent, bool peaks)
	Convert the scan of the last header() call.
void	addInstrumentConfigurations (ExperimentalSettings &settings)
	Add the instrument configurations of all scans read by header() so far to settings.
ScanRecord	record () const
	Record of the scan whose header was read last (by header()).
std::unique_ptr< Accessor >	accessor () const
	Random access converter for scans whose records were taken.
std::shared_ptr< DataProcessing >	dataProcessing () const
	Data processing attached to every converted spectrum and chromatogram.
MSChromatogram	ticChromatogram () const
	TIC chromatogram as reported by the vendor library (reads every scan header).
void	readDetectors (std::vector< MSChromatogram > &chromatograms, std::vector< MSSpectrum > &spectra)
	Detector (UV/PDA/analog) chromatograms and PDA spectra (Options::all_detectors); may be called at any time.

Private Attributes
std::unique_ptr< Impl >	impl_

Detailed Description

Scan-by-scan conversion of a Thermo RAW file into OpenMS spectra (private).

Shared by ThermoRawFile::load() and by later streaming and random access readers. A reader opens the RAW file once; all calls must come from one thread.

Usage:

1. fillSettings() writes the run-level settings (source file, sample, instrument, data processing).
2. header() must be called for every MS scan in acquisition order, from firstScan() on, because the precursor of an MSn scan is reconstructed from the scans before it. It reads only the scan header, unless the caller asks for the peaks as well because it will convert the scan anyway (one vendor read instead of two).
3. convert() turns the scan whose header was read last into an MSSpectrum. Scans that are not needed can simply be skipped (no peaks are read for them).

The precursor intensity estimate of an MSn scan sums peaks of its parent scan. convert() asks the ParentLookup for the parent spectrum first (e.g. the already loaded experiment); if it returns nullptr, the reader decodes the parent peaks itself, so filtered loads give the same precursors as a full load.

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Class Documentation

OpenMS::Internal::ThermoRawScanReader::ScanInfo

struct OpenMS::Internal::ThermoRawScanReader::ScanInfo

Scan header values needed to select scans before converting them.

Class Members
int	ms_level = 0	MS level (0 for unknown or non-MS controllers)
double	precursor_mz = 0.0	m/z of the first precursor (NaN if there is none)
double	rt = 0.0	retention time in seconds
int	scan = 0	scan number
double	tic = 0.0	total ion current (NaN if the vendor reports none)

OpenMS::Internal::ThermoRawScanReader::ScanRecord

struct OpenMS::Internal::ThermoRawScanReader::ScanRecord

Everything of a scan that depends on the scans before it (see header()).

With a record, Accessor::convert() converts the scan in any order and on any thread.

Class Members
string	configuration_id	instrument configuration id
ScanInfo	info
string	native_id
vector< ThermoPrecursor >	precursors	resolved in acquisition order

Member Typedef Documentation

Options

using Options = ThermoRawFile::Options

ParentLookup

using ParentLookup = std::function<const MSSpectrum*(int scan)>

Returns the converted (peak-sorted) spectrum of a scan or nullptr if it is not available.

Constructor & Destructor Documentation

ThermoRawScanReader() [1/2]

ThermoRawScanReader	(	const std::string &	path,
		const Options &	options
	)

Open path.

Parameters

[in]	path	Thermo RAW file (symbolic links are resolved for the vendor library), or a ZIP archive that holds one .raw file ('.zip' suffix), which is extracted into a temporary directory that lives as long as the reader and its accessors
[in]	options	Conversion options; ms_levels / rt / scan ranges are not applied here

Exceptions

Exception::FileNotFound	if path does not exist
Exception::ParseError	if path is gzip- or bzip2-compressed ('.gz', '.bz2' suffix), or a ZIP archive that holds no .raw file or more than one
Exception::InvalidValue	if the .raw file cannot be extracted (e.g. not enough free space)
std::exception	if the bridge cannot open the file

~ThermoRawScanReader()

~ThermoRawScanReader

(

)

ThermoRawScanReader() [2/2]

ThermoRawScanReader ( const ThermoRawScanReader &  )

delete

Member Function Documentation

accessor()

std::unique_ptr< Accessor > accessor

(

)

const

Random access converter for scans whose records were taken.

Call it after the header() pass: precursor intensity estimates use parents from the first scan visited by header() on, as a sequential conversion does.

addInstrumentConfigurations()

void addInstrumentConfigurations

(

ExperimentalSettings &

settings

)

Add the instrument configurations of all scans read by header() so far to settings.

Configuration ids are assigned in the order of all scans read, independent of which scans are converted. Call this after the last header() so that configurations of scans that were not converted are also listed, as in a load without scan selection.

convert()

void convert	(	MSSpectrum &	spectrum,
		ExperimentalSettings &	settings,
		const ParentLookup &	parent,
		bool	peaks
	)

Convert the scan of the last header() call.

Parameters

[out]	spectrum	The converted spectrum (peaks sorted by m/z)
[in,out]	settings	Receives instrument configurations as they appear
[in]	parent	Lookup of already converted parent spectra (may be empty)
[in]	peaks	If false, no peaks or auxiliary arrays are read (metadata only)

dataProcessing()

std::shared_ptr< DataProcessing > dataProcessing

(

)

const

Data processing attached to every converted spectrum and chromatogram.

fillSettings()

void fillSettings

(

ExperimentalSettings &

settings

)

const

Write run-level settings into settings (instrument configurations are added by convert() and addInstrumentConfigurations()).

firstScan()

int firstScan

(

)

const

First MS scan number (only valid if hasMSData()).

hasMSData()

bool hasMSData

(

)

const

True if the file contains a mass spectrometer controller.

header()

const ScanInfo & header	(	int	scan,
		bool	with_peaks = false
	)

Read the header of scan; must be called for every scan in increasing order.

Parameters

[in]	scan	Scan number, the successor of the previous call's scan
[in]	with_peaks	Also read the peaks for a following convert() call. Saves a second vendor read of the scan when the caller already knows it will convert it.

lastScan()

int lastScan

(

)

const

Last MS scan number (only valid if hasMSData()).

operator=()

ThermoRawScanReader & operator= ( const ThermoRawScanReader &  )

delete

readAhead()

void readAhead	(	int	last_scan,
		int	peaks_from
	)

Read the following scans up to last_scan on worker threads ahead of header().

Uses up to three threads besides the calling one, limited by the OpenMP thread count (none if it is 1). Output is unchanged; header() takes the scans from the read-ahead buffer, which holds a bounded number of scans.

Parameters

[in]	last_scan	Last scan to read ahead
[in]	peaks_from	Scans from this number on are read with peaks (as header(scan, true))

readDetectors()

void readDetectors	(	std::vector< MSChromatogram > &	chromatograms,
		std::vector< MSSpectrum > &	spectra
	)

Detector (UV/PDA/analog) chromatograms and PDA spectra (Options::all_detectors); may be called at any time.

record()

ScanRecord record

(

)

const

Record of the scan whose header was read last (by header()).

scanHeaders()

void scanHeaders	(	int	first,
		int	last,
		bool	precursors,
		const std::function< bool(const ScanInfo &)> &	visit
	)

Visit the headers of scans first to last ahead of header(), without peaks.

A cheap pass, e.g. to count the scans a filtered conversion selects before streaming them or to index a file for random access. Instrument configurations are registered in the same order as header() would register them (so ids match a single pass), and the state of header() and convert() is not changed otherwise.

Parameters

[in]	first	First scan number; use firstScan() if precursors are resolved
[in]	last	Last scan number
[in]	precursors	Also set ScanInfo::precursor_mz. Reads the trailers and resolves the precursors from first on (slower); otherwise precursor_mz is NaN.
[in]	visit	Called for every scan in order; returning false stops the pass

ticChromatogram()

MSChromatogram ticChromatogram

(

)

const

TIC chromatogram as reported by the vendor library (reads every scan header).

Member Data Documentation

impl_

std::unique_ptr<Impl> impl_

private