OnDiscMSExperiment Class Reference

Representation of a mass spectrometry experiment on disk. More...

#include <OpenMS/KERNEL/OnDiscMSExperiment.h>

Inheritance diagram for OnDiscMSExperiment:

Public Member Functions
	OnDiscMSExperiment ()=default
	Constructor.
bool	openFile (const std::string &filename, bool skipMetaData=false)
	Open a specific file on disk.
	OnDiscMSExperiment (const OnDiscMSExperiment &source)
	Copy constructor.
bool	operator== (const OnDiscMSExperiment &rhs) const
	Equality operator.
bool	operator!= (const OnDiscMSExperiment &rhs) const
	Inequality operator.
bool	isSortedByRT () const override
	Checks if all spectra are sorted with respect to ascending RT.
Size	getNrSpectra () const override
	get the total number of spectra available
Size	getNrChromatograms () const override
	get the total number of chromatograms available
std::shared_ptr< const ExperimentalSettings >	getExperimentalSettings () const override
	returns the meta information of this experiment (const access)
std::shared_ptr< PeakMap >	getMetaData () const
MSSpectrum	operator[] (Size n)
	alias for getSpectrum
MSSpectrum	getSpectrum (Size id) override
	returns a single spectrum
MSSpectrum	getSpectrumMetadata (Size id) override
	returns a single spectrum without peaks and data arrays
double	getSpectrumRT (Size id) const override
	Retention time of spectrum id, from the meta data.
UInt	getSpectrumMSLevel (Size id) const override
	MS level of spectrum id, from the meta data.
std::unique_ptr< IMSExperimentRandomAccess >	clone () const override
	A copy with its own file stream (see the copy constructor)
OpenMS::Interfaces::SpectrumPtr	getSpectrumById (Size id)
	returns a single spectrum (without applying PeakFileOptions filters)
MSChromatogram	getChromatogram (Size id) override
	returns a single chromatogram
MSChromatogram	getChromatogramByNativeId (const std::string &id)
	returns a single chromatogram
MSSpectrum	getSpectrumByNativeId (const std::string &id)
	returns a single spectrum
OpenMS::Interfaces::ChromatogramPtr	getChromatogramById (Size id)
	returns a single chromatogram
void	setSkipXMLChecks (bool skip)
	sets whether to skip some XML checks and be fast instead
PeakFileOptions &	getOptions ()
	Mutable access to the options for loading/storing.
const PeakFileOptions &	getOptions () const
	Non-mutable access to the options for loading/storing.
void	setOptions (const PeakFileOptions &options)
	set options for loading/storing
Public Member Functions inherited from IMSExperimentRandomAccess
virtual	~IMSExperimentRandomAccess ()
Size	size () const
	Alias for getNrSpectra()
bool	empty () const
	True if there are no spectra.
virtual MSSpectrum	getSpectrumPeaks (Size index)
	Peaks and data arrays of spectrum index; other metadata may be missing.
virtual Size	findFirstRT (double rt) const
	Index of the first spectrum with retention time >= rt.

Protected Attributes
std::string	filename_
	The filename of the underlying data file.
Internal::IndexedMzMLHandler	indexed_mzml_file_
	The index of the underlying data file (mutable: reading moves the file stream)
std::shared_ptr< PeakMap >	meta_ms_experiment_
	The meta-data.
std::unordered_map< std::string, Size >	chromatograms_native_ids_
	Mapping of chromatogram native ids to offsets.
std::unordered_map< std::string, Size >	spectra_native_ids_
	Mapping of spectra native ids to offsets.
PeakFileOptions	options_
	Options for loading / storing.

Private Types
typedef ChromatogramPeak	ChromatogramPeakT
typedef Peak1D	PeakT

Private Member Functions
OnDiscMSExperiment &	operator= (const OnDiscMSExperiment &)
	Private Assignment operator -> we cannot copy file streams in IndexedMzMLHandler.
void	loadMetaData_ (const std::string &filename)
MSChromatogram	getMetaChromatogramById_ (const std::string &id)
MSSpectrum	getMetaSpectrumById_ (const std::string &id)

Additional Inherited Members
Protected Member Functions inherited from IMSExperimentRandomAccess
	IMSExperimentRandomAccess ()=default
	IMSExperimentRandomAccess (const IMSExperimentRandomAccess &)=default
IMSExperimentRandomAccess &	operator= (const IMSExperimentRandomAccess &)=default

Detailed Description

Representation of a mass spectrometry experiment on disk.

This class allows random access to spectra and chromatograms in indexed mzML files without loading the entire file into memory.

Filtering with PeakFileOptions

PeakFileOptions can be used to filter data when retrieving spectra/chromatograms:

• RT range, MS level, and precursor m/z range filters: Checked BEFORE loading peak data (skips I/O)
• m/z range and intensity filters: Applied AFTER loading peak data

Note

Unlike in-memory loading (FileHandler), where filtered spectra are completely removed from the container, OnDiscMSExperiment preserves all indices. When a spectrum doesn't pass RT range or MS level filters, getSpectrum() returns the spectrum with metadata but no peaks (I/O is skipped). This preserves the index mapping to the file.

Example:

OnDiscMSExperiment exp;
exp.openFile("data.mzML");
exp.getOptions().setMSLevels({2});  // Only want MS2
exp.getOptions().setRTRange(DRange<1>(100, 200));
 
for (Size i = 0; i < exp.size(); ++i)
{
  MSSpectrum s = exp.getSpectrum(i);
  if (s.empty()) continue;  // Filtered out, no I/O was performed
  // Process MS2 spectrum in RT range...
}

Note

This implementation is not thread-safe since it keeps internally a single file access pointer which it moves when accessing a specific data item. Please provide a separate copy to each thread, e.g.

#pragma omp parallel for firstprivate(ondisc_map)

Member Typedef Documentation

ChromatogramPeakT

typedef ChromatogramPeak ChromatogramPeakT

private

PeakT

typedef Peak1D PeakT

private

Constructor & Destructor Documentation

OnDiscMSExperiment() [1/2]

OnDiscMSExperiment ( )

default

Constructor.

This initializes the object, use openFile to open a file.

OnDiscMSExperiment() [2/2]

OnDiscMSExperiment ( const OnDiscMSExperiment &  source )

inline

Copy constructor.

Member Function Documentation

clone()

std::unique_ptr< IMSExperimentRandomAccess > clone ( ) const

overridevirtual

A copy with its own file stream (see the copy constructor)

Implements IMSExperimentRandomAccess.

getChromatogram()

MSChromatogram getChromatogram ( Size  id )

overridevirtual

returns a single chromatogram

If PeakFileOptions has RT or intensity range set, the chromatogram will be filtered accordingly.

Parameters

[in]

id

The index of the chromatogram

Implements IMSExperimentRandomAccess.

getChromatogramById()

OpenMS::Interfaces::ChromatogramPtr getChromatogramById

(

Size

id

)

returns a single chromatogram

getChromatogramByNativeId()

MSChromatogram getChromatogramByNativeId

(

const std::string &

id

)

returns a single chromatogram

Parameters

[in]

id

The native identifier of the chromatogram

getExperimentalSettings()

std::shared_ptr< const ExperimentalSettings > getExperimentalSettings ( ) const

inlineoverridevirtual

returns the meta information of this experiment (const access)

Implements IMSExperimentRandomAccess.

getMetaChromatogramById_()

MSChromatogram getMetaChromatogramById_ ( const std::string &  id )

private

getMetaData()

std::shared_ptr< PeakMap > getMetaData ( ) const

inline

getMetaSpectrumById_()

MSSpectrum getMetaSpectrumById_ ( const std::string &  id )

private

getNrChromatograms()

Size getNrChromatograms ( ) const

inlineoverridevirtual

get the total number of chromatograms available

Implements IMSExperimentRandomAccess.

getNrSpectra()

Size getNrSpectra ( ) const

inlineoverridevirtual

get the total number of spectra available

Implements IMSExperimentRandomAccess.

getOptions() [1/2]

PeakFileOptions & getOptions

(

)

Mutable access to the options for loading/storing.

getOptions() [2/2]

const PeakFileOptions & getOptions

(

)

const

Non-mutable access to the options for loading/storing.

getSpectrum()

MSSpectrum getSpectrum ( Size  id )

overridevirtual

returns a single spectrum

If PeakFileOptions has m/z or intensity range set, the spectrum will be filtered accordingly.

Parameters

[in]

id

The index of the spectrum

Implements IMSExperimentRandomAccess.

getSpectrumById()

OpenMS::Interfaces::SpectrumPtr getSpectrumById ( Size  id )

inline

returns a single spectrum (without applying PeakFileOptions filters)

getSpectrumByNativeId()

MSSpectrum getSpectrumByNativeId

(

const std::string &

id

)

returns a single spectrum

Parameters

[in]

id

The native identifier of the spectrum

getSpectrumMetadata()

MSSpectrum getSpectrumMetadata ( Size  id )

overridevirtual

returns a single spectrum without peaks and data arrays

Needs the meta data: a file opened with skipMetaData has no RT, MS level or precursors in memory. PeakFileOptions filters are not applied.

Parameters

[in]

id

The index of the spectrum

Exceptions

Exception::IndexOverflow	if id >= getNrSpectra()
Exception::IllegalArgument	if the file was opened with skipMetaData

Implements IMSExperimentRandomAccess.

getSpectrumMSLevel()

UInt getSpectrumMSLevel ( Size  id ) const

overridevirtual

MS level of spectrum id, from the meta data.

Exceptions

Exception::IndexOverflow	if id >= getNrSpectra()
Exception::IllegalArgument	if the file was opened with skipMetaData

Implements IMSExperimentRandomAccess.

getSpectrumRT()

double getSpectrumRT ( Size  id ) const

overridevirtual

Retention time of spectrum id, from the meta data.

Exceptions

Exception::IndexOverflow	if id >= getNrSpectra()
Exception::IllegalArgument	if the file was opened with skipMetaData

Implements IMSExperimentRandomAccess.

isSortedByRT()

bool isSortedByRT ( ) const

inlineoverridevirtual

Checks if all spectra are sorted with respect to ascending RT.

Note that we cannot check whether all spectra are sorted (except if we were to load them all and check).

Implements IMSExperimentRandomAccess.

loadMetaData_()

void loadMetaData_ ( const std::string &  filename )

private

openFile()

bool openFile	(	const std::string &	filename,
		bool	skipMetaData = false
	)

Open a specific file on disk.

This tries to read the indexed mzML by parsing the index and then reading the meta information into memory.

Returns

Whether the parsing of the file was successful (if false, the file most likely was not an indexed mzML file)

operator!=()

bool operator!= ( const OnDiscMSExperiment &  rhs ) const

inline

Inequality operator.

References OpenMS::Internal::operator==().

operator=()

OnDiscMSExperiment & operator= ( const OnDiscMSExperiment &  )

private

Private Assignment operator -> we cannot copy file streams in IndexedMzMLHandler.

operator==()

bool operator== ( const OnDiscMSExperiment &  rhs ) const

inline

Equality operator.

This only checks whether the underlying file is the same and the parsed meta-information is the same. Note that the file reader (e.g. the std::ifstream of the file) might be in a different state.

References OnDiscMSExperiment::filename_, and OnDiscMSExperiment::meta_ms_experiment_.

operator[]()

MSSpectrum operator[] ( Size  n )

inline

alias for getSpectrum

setOptions()

void setOptions

(

const PeakFileOptions &

options

)

set options for loading/storing

setSkipXMLChecks()

void setSkipXMLChecks

(

bool

skip

)

sets whether to skip some XML checks and be fast instead

Member Data Documentation

chromatograms_native_ids_

std::unordered_map< std::string, Size > chromatograms_native_ids_

protected

Mapping of chromatogram native ids to offsets.

filename_

std::string filename_

protected

The filename of the underlying data file.

Referenced by OnDiscMSExperiment::operator==().

indexed_mzml_file_

Internal::IndexedMzMLHandler indexed_mzml_file_

mutableprotected

The index of the underlying data file (mutable: reading moves the file stream)

meta_ms_experiment_

std::shared_ptr<PeakMap> meta_ms_experiment_

protected

The meta-data.

Referenced by OnDiscMSExperiment::operator==().

options_

PeakFileOptions options_

protected

Options for loading / storing.

spectra_native_ids_

std::unordered_map< std::string, Size > spectra_native_ids_

protected

Mapping of spectra native ids to offsets.