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 String	getCompressionTerm_ (const PeakFileOptions &opt, MSNumpressCoder::NumpressConfig np_compression, String indent="", bool use_numpress=false)
	Returns the appropriate compression term given the PeakFileOptions and the NumpressConfig. More...

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. More...

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

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

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

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

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 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

data_	The list of data arrays
precision_64	Whether the identified array has 64 bit precision
index	The index of the identified array
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

data_	The input and output
skipXMLCheck	whether to skip cleaning the Base64 arrays and remove whitespaces

◆ getCompressionTerm_()

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

static

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

◆ handleBinaryDataArrayCVParam()

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

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

◆ warning()

static void warning	(	int	mode,
		const 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

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

Classes

Static Public Member Functions

Static Private Member Functions

Detailed Description

Member Function Documentation

◆ computeDataProperties_()

◆ decodeBase64Arrays()

◆ getCompressionTerm_()

◆ handleBinaryDataArrayCVParam()

◆ warning()

◆ writeFooter_()