Helper for mzML file format. More...

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

Classes
struct	BinaryData
	Representation for binary data in mzML. More...

Static Public Member Functions
static std::string	getCompressionTerm_ (const PeakFileOptions &opt, MSNumpressCoder::NumpressConfig np_compression, const std::string &indent="", bool use_numpress=false, bool zstd_byte_shuffle=true)
	Returns the appropriate compression term given the PeakFileOptions and the NumpressConfig.

static void	encodeNumericArray (std::vector< float > &in, const PeakFileOptions &opt, std::string &out)
	Encode a numeric array as Base64 string, applying the compression selected in `opt`.

static void	encodeNumericArray (std::vector< double > &in, const PeakFileOptions &opt, std::string &out)
	Encode a numeric array as Base64 string, applying the compression selected in `opt`.

static void	encodeNumericArray (std::vector< Int32 > &in, const PeakFileOptions &opt, std::string &out)
	Encode a numeric array as Base64 string, applying the compression selected in `opt`.

static void	encodeNumericArray (std::vector< Int64 > &in, const PeakFileOptions &opt, std::string &out)
	Encode a numeric array as Base64 string, applying the compression selected in `opt`.

static void	encodeStringArray (const std::vector< std::string > &in, const PeakFileOptions &opt, std::string &out)
	Encode a string array (null-terminated strings) as Base64 string, applying the compression selected in `opt`.

static void	encodeNumpressArray (const std::vector< double > &in, const PeakFileOptions &opt, const MSNumpressCoder::NumpressConfig &config, std::string &out)
	Numpress-encode an array and encode the result as Base64 string, applying the compression selected in `opt`.

static void	encodeNumpressArray (const std::vector< float > &in, const PeakFileOptions &opt, const MSNumpressCoder::NumpressConfig &config, std::string &out)
	Numpress-encode an array and encode the result as Base64 string, applying the compression selected in `opt`.

static void	writeFooter_ (std::ostream &os, const PeakFileOptions &options, const std::vector< std::pair< std::string, Int64 > > &spectra_offsets, const std::vector< std::pair< std::string, Int64 > > &chromatograms_offsets)
	Write the indexed mzML footer the appropriate compression term given the PeakFileOptions and the NumpressConfig.

static void	decodeBase64Arrays (std::vector< BinaryData > &data_, const bool skipXMLCheck=false)
	Decode Base64 arrays and write into data_ array.

static void	computeDataProperties_ (const std::vector< BinaryData > &data_, bool &precision_64, SignedSize &index, const std::string &index_name)
	Identify a data array from a list.

static bool	handleBinaryDataArrayCVParam (std::vector< BinaryData > &data_, const std::string &accession, const std::string &value, const std::string &name, const std::string &unit_accession)
	Handle a given CV parameter found in a binaryDataArray tag.

Static Private Member Functions
static void	warning (int mode, const std::string &msg, UInt line=0, UInt column=0)
	Also display some warning message when appropriate (see XMLHandler)

Detailed Description

Helper for mzML file format.

This class provides common structures and re-useable helper functions for parsing the mzML format. These are mainly used by MzMLHandler and MzMLSpectrumDecoder.

Member Function Documentation

◆ computeDataProperties_()

static void computeDataProperties_	(	const std::vector< BinaryData > &	data_,
		bool &	precision_64,
		SignedSize &	index,
		const std::string &	index_name
	)

static

Identify a data array from a list.

Given a specific array name, find it in the provided list and return its index and precision.

Parameters

[in]	data_	The list of data arrays
[in]	precision_64	Whether the identified array has 64 bit precision
[in]	index	The index of the identified array
[in]	index_name	The name of the array to be identified

◆ decodeBase64Arrays()

static void decodeBase64Arrays	(	std::vector< BinaryData > &	data_,
		const bool	skipXMLCheck = `false`
	)

static

Decode Base64 arrays and write into data_ array.

Parameters

[in,out]	data_	The input and output
[in]	skipXMLCheck	whether to skip cleaning the Base64 arrays and remove whitespaces

◆ encodeNumericArray() [1/4]

static void encodeNumericArray	(	std::vector< double > &	in,
		const PeakFileOptions &	opt,
		std::string &	out
	)

static

Encode a numeric array as Base64 string, applying the compression selected in opt.

If zstd compression is enabled in opt, the array is byte-shuffled and compressed with zstd (MS:1003781), otherwise it is zlib-compressed if requested (MS:1000574). The data is always stored in little-endian byte order.

Parameters

[in,out]	in	The data to encode (may be modified, i.e. endianized)
[in]	opt	The PeakFileOptions used for writing
[out]	out	The resulting Base64 string

◆ encodeNumericArray() [2/4]

static void encodeNumericArray	(	std::vector< float > &	in,
		const PeakFileOptions &	opt,
		std::string &	out
	)

static

Encode a numeric array as Base64 string, applying the compression selected in opt.

If zstd compression is enabled in opt, the array is byte-shuffled and compressed with zstd (MS:1003781), otherwise it is zlib-compressed if requested (MS:1000574). The data is always stored in little-endian byte order.

Parameters

[in,out]	in	The data to encode (may be modified, i.e. endianized)
[in]	opt	The PeakFileOptions used for writing
[out]	out	The resulting Base64 string

◆ encodeNumericArray() [3/4]

static void encodeNumericArray	(	std::vector< Int32 > &	in,
		const PeakFileOptions &	opt,
		std::string &	out
	)

static

Encode a numeric array as Base64 string, applying the compression selected in opt.

If zstd compression is enabled in opt, the array is byte-shuffled and compressed with zstd (MS:1003781), otherwise it is zlib-compressed if requested (MS:1000574). The data is always stored in little-endian byte order.

Parameters

[in,out]	in	The data to encode (may be modified, i.e. endianized)
[in]	opt	The PeakFileOptions used for writing
[out]	out	The resulting Base64 string

◆ encodeNumericArray() [4/4]

static void encodeNumericArray	(	std::vector< Int64 > &	in,
		const PeakFileOptions &	opt,
		std::string &	out
	)

static

Encode a numeric array as Base64 string, applying the compression selected in opt.

If zstd compression is enabled in opt, the array is byte-shuffled and compressed with zstd (MS:1003781), otherwise it is zlib-compressed if requested (MS:1000574). The data is always stored in little-endian byte order.

Parameters

[in,out]	in	The data to encode (may be modified, i.e. endianized)
[in]	opt	The PeakFileOptions used for writing
[out]	out	The resulting Base64 string

◆ encodeNumpressArray() [1/2]

static void encodeNumpressArray	(	const std::vector< double > &	in,
		const PeakFileOptions &	opt,
		const MSNumpressCoder::NumpressConfig &	config,
		std::string &	out
	)

static

Numpress-encode an array and encode the result as Base64 string, applying the compression selected in opt.

If zstd compression is enabled in opt, the numpress output is compressed with zstd (MS:1003783 - MS:1003785), otherwise it is zlib-compressed if requested (MS:1002746 - MS:1002748).

Parameters

[in]	in	The data to encode
[in]	opt	The PeakFileOptions used for writing
[in]	config	The numpress configuration
[out]	out	The resulting Base64 string (empty if numpress encoding failed)

◆ encodeNumpressArray() [2/2]

static void encodeNumpressArray	(	const std::vector< float > &	in,
		const PeakFileOptions &	opt,
		const MSNumpressCoder::NumpressConfig &	config,
		std::string &	out
	)

static

Numpress-encode an array and encode the result as Base64 string, applying the compression selected in opt.

If zstd compression is enabled in opt, the numpress output is compressed with zstd (MS:1003783 - MS:1003785), otherwise it is zlib-compressed if requested (MS:1002746 - MS:1002748).

Parameters

[in]	in	The data to encode
[in]	opt	The PeakFileOptions used for writing
[in]	config	The numpress configuration
[out]	out	The resulting Base64 string (empty if numpress encoding failed)

◆ encodeStringArray()

static void encodeStringArray	(	const std::vector< std::string > &	in,
		const PeakFileOptions &	opt,
		std::string &	out
	)

static

Encode a string array (null-terminated strings) as Base64 string, applying the compression selected in opt.

If zstd compression is enabled in opt, the data is compressed with zstd (MS:1003780), otherwise it is zlib-compressed if requested (MS:1000574).

Parameters

[in]	in	The strings to encode
[in]	opt	The PeakFileOptions used for writing
[out]	out	The resulting Base64 string

◆ getCompressionTerm_()

static std::string getCompressionTerm_	(	const PeakFileOptions &	opt,
		MSNumpressCoder::NumpressConfig	np_compression,
		const std::string &	indent = `""`,
		bool	use_numpress = `false`,
		bool	zstd_byte_shuffle = `true`
	)

static

Returns the appropriate compression term given the PeakFileOptions and the NumpressConfig.

Parameters

[in]	opt	The PeakFileOptions used for writing (zlib or zstd compression)
[in]	np_compression	The numpress configuration of the array
[in]	indent	Indentation prepended to the term
[in]	use_numpress	Whether numpress compression is applied to the array
[in]	zstd_byte_shuffle	Whether the array is byte-shuffled before zstd compression (only used if zstd compression is enabled and numpress is not used)

◆ handleBinaryDataArrayCVParam()

static bool handleBinaryDataArrayCVParam	(	std::vector< BinaryData > &	data_,
		const std::string &	accession,
		const std::string &	value,
		const std::string &	name,
		const std::string &	unit_accession
	)

static

Handle a given CV parameter found in a binaryDataArray tag.

Given a CV parameter, properly set the members of the last entry of data_, this will properly handle all terms describing precision, compression, name of the data and units.

Parameters

[in,out]	data_	The list of data arrays, whose last entry will be changed
[in]	accession	The CV accession
[in]	value	The CV value
[in]	name	The CV name
[in]	unit_accession	The CV unit accession (if a unit tag is present)

◆ warning()

static void warning	(	int	mode,
		const std::string &	msg,
		UInt	line = `0`,
		UInt	column = `0`
	)

staticprivate

Also display some warning message when appropriate (see XMLHandler)

◆ writeFooter_()

static void writeFooter_	(	std::ostream &	os,
		const PeakFileOptions &	options,
		const std::vector< std::pair< std::string, Int64 > > &	spectra_offsets,
		const std::vector< std::pair< std::string, Int64 > > &	chromatograms_offsets
	)

static

Write the indexed mzML footer the appropriate compression term given the PeakFileOptions and the NumpressConfig.

Parameters

[out]	os	The output stream
[in]	options	The PeakFileOptions used for writing
[in]	spectra_offsets	Binary offsets of <spectrum> tags
[in]	chromatograms_offsets	Binary offsets of <chromatogram> tags

Classes

Static Public Member Functions

Static Private Member Functions

Detailed Description

Member Function Documentation

◆ computeDataProperties_()

◆ decodeBase64Arrays()

◆ encodeNumericArray() [1/4]

◆ encodeNumericArray() [2/4]

◆ encodeNumericArray() [3/4]

◆ encodeNumericArray() [4/4]

◆ encodeNumpressArray() [1/2]

◆ encodeNumpressArray() [2/2]

◆ encodeStringArray()

◆ getCompressionTerm_()

◆ handleBinaryDataArrayCVParam()

◆ warning()

◆ writeFooter_()