IndexedMzMLHandler Class Reference

A low-level class to read an indexedmzML file. More...

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

Collaboration diagram for IndexedMzMLHandler:

Public Member Functions
	IndexedMzMLHandler ()
	Default constructor. More...
	IndexedMzMLHandler (const String &filename)
	Constructor. More...
	IndexedMzMLHandler (const IndexedMzMLHandler &source)
	Copy constructor. More...
	~IndexedMzMLHandler ()
	Destructor. More...
void	openFile (const String &filename)
	Open a file. More...
bool	getParsingSuccess () const
	Returns whether parsing was successful. More...
size_t	getNrSpectra () const
	Returns the number of spectra available. More...
size_t	getNrChromatograms () const
	Returns the number of chromatograms available. More...
OpenMS::Interfaces::SpectrumPtr	getSpectrumById (int id)
	Retrieve the raw data for the spectrum at position "id". More...
const OpenMS::MSSpectrum	getMSSpectrumById (int id)
	Retrieve the raw data for the spectrum at position "id". More...
void	getMSSpectrumByNativeId (std::string id, OpenMS::MSSpectrum &s)
	Retrieve the raw data for the spectrum with native id "id". More...
void	getMSSpectrumById (int id, OpenMS::MSSpectrum &s)
	Retrieve the raw data for the spectrum at position "id". More...
OpenMS::Interfaces::ChromatogramPtr	getChromatogramById (int id)
	Retrieve the raw data for the chromatogram at position "id". More...
const OpenMS::MSChromatogram	getMSChromatogramById (int id)
	Retrieve the raw data for the chromatogram at position "id". More...
void	getMSChromatogramByNativeId (const std::string &id, OpenMS::MSChromatogram &c)
	Retrieve the raw data for the chromatogram with native id "id". More...
void	getMSChromatogramById (int id, OpenMS::MSChromatogram &c)
	Retrieve the raw data for the chromatogram at position "id". More...
void	setSkipXMLChecks (bool skip)
	Whether to skip some XML checks (removing whitespace from base64 arrays) and be fast instead. More...

Private Member Functions
void	parseFooter_ ()
	Try to parse the footer of the indexedmzML. More...
std::string	getChromatogramById_helper_ (int id)
std::string	getSpectrumById_helper_ (int id)

Private Attributes
String	filename_
	Name of the file. More...
std::vector< std::streampos >	spectra_offsets_
	Binary offsets to all spectra. More...
std::unordered_map< std::string, Size >	spectra_native_ids_
	Mapping of spectra native ids to offsets. More...
std::vector< std::streampos >	chromatograms_offsets_
	Binary offsets to all chromatograms. More...
std::unordered_map< std::string, Size >	chromatograms_native_ids_
	Mapping of chromatogram native ids to offsets. More...
std::streampos	index_offset_
	offset to the <indexList> element More...
bool	spectra_before_chroms_
	Whether spectra are written before chromatograms in this file. More...
std::ifstream	filestream_
	The current filestream (opened by openFile) More...
bool	parsing_success_
	Whether parsing the indexedmzML file was successful. More...
bool	skip_xml_checks_
	Whether to skip XML checks. More...

Detailed Description

A low-level class to read an indexedmzML file.

This class provides low-level access to the underlying data structures, if you simply want to read an indexed mzML file you probably want to use IndexedMzMLFileLoader instead.

This class implements access to an indexedmzML file and the contained spectra and chromatogram data through the getSpectrumById and getChromatogramById functions. It thus allows random access to spectra and chromatograms data without having to read the whole file into memory. It does not provide the same interface as MSExperiment, if this is desired, please use IndexedMzMLFileLoader and OnDiscMSExperiment.

Internally, it uses the IndexedMzMLDecoder for initial parsing and extracting all the offsets of the <chromatogram> and <spectrum> tags. These offsets are stored as members of this class as well as the offset to the <indexList> element

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. The caller is responsible to ensure that access is performed atomically.

Constructor & Destructor Documentation

IndexedMzMLHandler() [1/3]

IndexedMzMLHandler

(

)

Default constructor.

IndexedMzMLHandler() [2/3]

IndexedMzMLHandler ( const String &  filename )

explicit

Constructor.

Tries to parse the file, success can be checked with getParsingSuccess()

IndexedMzMLHandler() [3/3]

IndexedMzMLHandler

(

const IndexedMzMLHandler &

source

)

Copy constructor.

~IndexedMzMLHandler()

~IndexedMzMLHandler

(

)

Destructor.

Member Function Documentation

getChromatogramById()

OpenMS::Interfaces::ChromatogramPtr getChromatogramById

(

int

id

)

Retrieve the raw data for the chromatogram at position "id".

Exceptions

Exception	if getParsingSuccess() returns false
Exception	if id is not within [0, getNrChromatograms()-1]

Returns

The chromatogram at position id

getChromatogramById_helper_()

std::string getChromatogramById_helper_ ( int  id )

private

getMSChromatogramById() [1/2]

const OpenMS::MSChromatogram getMSChromatogramById

(

int

id

)

Retrieve the raw data for the chromatogram at position "id".

Exceptions

Exception	if getParsingSuccess() returns false
Exception	if id is not within [0, getNrChromatograms()-1]

Returns

The chromatogram at position id

getMSChromatogramById() [2/2]

void getMSChromatogramById	(	int	id,
		OpenMS::MSChromatogram &	c
	)

Retrieve the raw data for the chromatogram at position "id".

Exceptions

Exception	if getParsingSuccess() returns false
Exception	if id is not within [0, getNrChromatograms()-1]

Parameters

id	The chromatogram id
c	The chromatogram to be used and filled with data

getMSChromatogramByNativeId()

void getMSChromatogramByNativeId	(	const std::string &	id,
		OpenMS::MSChromatogram &	c
	)

Retrieve the raw data for the chromatogram with native id "id".

Exceptions

Exception	if getParsingSuccess() returns false
Exception	if id cannot be found

Parameters

id	The chromatogram native id
s	The chromatogram to be used and filled with data

getMSSpectrumById() [1/2]

const OpenMS::MSSpectrum getMSSpectrumById

(

int

id

)

Retrieve the raw data for the spectrum at position "id".

Exceptions

Exception	if getParsingSuccess() returns false
Exception	if id is not within [0, getNrSpectra()-1]

Returns

The spectrum at position id

getMSSpectrumById() [2/2]

void getMSSpectrumById	(	int	id,
		OpenMS::MSSpectrum &	s
	)

Retrieve the raw data for the spectrum at position "id".

Exceptions

Exception	if getParsingSuccess() returns false
Exception	if id is not within [0, getNrSpectra()-1]

Parameters

id	The spectrum id
s	The spectrum to be used and filled with data

getMSSpectrumByNativeId()

void getMSSpectrumByNativeId	(	std::string	id,
		OpenMS::MSSpectrum &	s
	)

Retrieve the raw data for the spectrum with native id "id".

Exceptions

Exception	if getParsingSuccess() returns false
Exception	if id cannot be found

Parameters

id	The spectrum native id
s	The spectrum to be used and filled with data

getNrChromatograms()

size_t getNrChromatograms

(

)

const

Returns the number of chromatograms available.

Referenced by TOPPViewBase::addDataFile().

getNrSpectra()

size_t getNrSpectra

(

)

const

Returns the number of spectra available.

Referenced by TOPPViewBase::addDataFile().

getParsingSuccess()

bool getParsingSuccess

(

)

const

Returns whether parsing was successful.

Note

Callable after openFile or the constructor using a filename

It is invalid to call getSpectrumById or getChromatogramById if this function returns false

Returns

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

Referenced by TOPPViewBase::addDataFile().

getSpectrumById()

OpenMS::Interfaces::SpectrumPtr getSpectrumById

(

int

id

)

Retrieve the raw data for the spectrum at position "id".

Exceptions

Exception	if getParsingSuccess() returns false
Exception	if id is not within [0, getNrSpectra()-1]

Returns

The spectrum at position id

getSpectrumById_helper_()

std::string getSpectrumById_helper_ ( int  id )

private

openFile()

void openFile

(

const String &

filename

)

Open a file.

Tries to parse the file, success can be checked with getParsingSuccess()

Referenced by TOPPViewBase::addDataFile().

parseFooter_()

void parseFooter_ ( )

private

Try to parse the footer of the indexedmzML.

Upon success, the chromatogram and spectra offsets will be populated and parsing_success_ will be set to true.

Note

You *need* to check getParsingSuccess after calling this!

setSkipXMLChecks()

void setSkipXMLChecks ( bool  skip )

inline

Whether to skip some XML checks (removing whitespace from base64 arrays) and be fast instead.

Member Data Documentation

chromatograms_native_ids_

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

private

Mapping of chromatogram native ids to offsets.

chromatograms_offsets_

std::vector< std::streampos > chromatograms_offsets_

private

Binary offsets to all chromatograms.

filename_

String filename_

private

Name of the file.

filestream_

std::ifstream filestream_

private

The current filestream (opened by openFile)

index_offset_

std::streampos index_offset_

private

offset to the <indexList> element

parsing_success_

bool parsing_success_

private

Whether parsing the indexedmzML file was successful.

skip_xml_checks_

bool skip_xml_checks_

private

Whether to skip XML checks.

spectra_before_chroms_

bool spectra_before_chroms_

private

Whether spectra are written before chromatograms in this file.

spectra_native_ids_

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

private

Mapping of spectra native ids to offsets.

spectra_offsets_

std::vector< std::streampos > spectra_offsets_

private

Binary offsets to all spectra.