MzMLSpectrumDecoder Class Reference

A class to decode input strings that contain an mzML chromatogram or spectrum tag. More...

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

Collaboration diagram for MzMLSpectrumDecoder:

Public Member Functions
	MzMLSpectrumDecoder (bool skip_xml_checks=false)
void	domParseSpectrum (const std::string &in, OpenMS::Interfaces::SpectrumPtr &sptr)
	Extract data from a string which contains a full mzML spectrum. More...
void	domParseSpectrum (const std::string &in, MSSpectrum &s)
	Extract data from a string which contains a full mzML spectrum. More...
void	domParseChromatogram (const std::string &in, MSChromatogram &c)
	Extract data from a string which contains a full mzML chromatogram. More...
void	domParseChromatogram (const std::string &in, OpenMS::Interfaces::ChromatogramPtr &cptr)
	Extract data from a string which contains a full mzML chromatogram. More...
void	setSkipXMLChecks (bool only)
	Whether to skip some XML checks (e.g. removing whitespace inside base64 arrays) and be fast instead. More...

Protected Types
typedef Internal::MzMLHandlerHelper::BinaryData	BinaryData

Protected Member Functions
OpenMS::Interfaces::SpectrumPtr	decodeBinaryDataSpectrum_ (std::vector< BinaryData > &data) const
	decode binary data More...
void	decodeBinaryDataMSSpectrum_ (std::vector< BinaryData > &data, OpenMS::MSSpectrum &s) const
void	decodeBinaryDataMSChrom_ (std::vector< BinaryData > &data, OpenMS::MSChromatogram &c) const
OpenMS::Interfaces::ChromatogramPtr	decodeBinaryDataChrom_ (std::vector< BinaryData > &data) const
	decode binary data More...
void	handleBinaryDataArray_ (xercesc::DOMNode *indexListNode, std::vector< BinaryData > &data)
	Convert a single DOMNode of type binaryDataArray to BinaryData object. More...
std::string	domParseString_ (const std::string &in, std::vector< BinaryData > &data)
	Extract data from a string containing multiple <binaryDataArray> tags. More...

Protected Attributes
bool	skip_xml_checks_
	Whether to skip some XML checks (e.g. removing whitespace inside base64 arrays) and be fast instead. More...

Detailed Description

A class to decode input strings that contain an mzML chromatogram or spectrum tag.

It uses xercesc to parse a string containing either a exactly one mzML spectrum or chromatogram (from <chromatogram> to </chromatogram> or <spectrum> to </spectrum> tag). It returns the data contained in the binaryDataArray for Intensity / mass-to-charge or Intensity / time.

Member Typedef Documentation

BinaryData

typedef Internal::MzMLHandlerHelper::BinaryData BinaryData

protected

Constructor & Destructor Documentation

MzMLSpectrumDecoder()

MzMLSpectrumDecoder ( bool  skip_xml_checks = false )

inlineexplicit

Member Function Documentation

decodeBinaryDataChrom_()

OpenMS::Interfaces::ChromatogramPtr decodeBinaryDataChrom_ ( std::vector< BinaryData > &  data ) const

protected

decode binary data

Todo:

Duplicated code from MzMLHandler, need to clean up see MzMLHandler::fillData_()

decodeBinaryDataMSChrom_()

void decodeBinaryDataMSChrom_ ( std::vector< BinaryData > &  data, OpenMS::MSChromatogram &  c  ) const

protected

decodeBinaryDataMSSpectrum_()

void decodeBinaryDataMSSpectrum_ ( std::vector< BinaryData > &  data, OpenMS::MSSpectrum &  s  ) const

protected

decodeBinaryDataSpectrum_()

OpenMS::Interfaces::SpectrumPtr decodeBinaryDataSpectrum_ ( std::vector< BinaryData > &  data ) const

protected

decode binary data

Todo:

Duplicated code from MzMLHandler, need to clean up see MzMLHandler::fillData_()

domParseChromatogram() [1/2]

void domParseChromatogram	(	const std::string &	in,
		MSChromatogram &	c
	)

Extract data from a string which contains a full mzML chromatogram.

Extracts data from the input string which is expected to contain exactly one <chromatogram> tag (from <chromatogram> to </chromatogram>). This function will extract the contained binaryDataArray and provide the result as Chromatogram.

Parameters

in	Input string containing the raw XML
c	Resulting chromatogram

Precondition

in must have <chromatogram> as root element.

domParseChromatogram() [2/2]

void domParseChromatogram	(	const std::string &	in,
		OpenMS::Interfaces::ChromatogramPtr &	cptr
	)

Extract data from a string which contains a full mzML chromatogram.

Extracts data from the input string which is expected to contain exactly one <chromatogram> tag (from <chromatogram> to </chromatogram>). This function will extract the contained binaryDataArray and provide the result as Chromatogram.

Parameters

in	Input string containing the raw XML
cptr	Resulting chromatogram

Precondition

in must have <chromatogram> as root element.

domParseSpectrum() [1/2]

void domParseSpectrum	(	const std::string &	in,
		MSSpectrum &	s
	)

Extract data from a string which contains a full mzML spectrum.

Extracts data from the input string which is expected to contain exactly one <spectrum> tag (from <spectrum> to </spectrum>). This function will extract the contained binaryDataArray and provide the result as Spectrum.

Parameters

in	Input string containing the raw XML
s	Resulting spectrum

Precondition

in must have <spectrum> as root element.

domParseSpectrum() [2/2]

void domParseSpectrum	(	const std::string &	in,
		OpenMS::Interfaces::SpectrumPtr &	sptr
	)

Extract data from a string which contains a full mzML spectrum.

Extracts data from the input string which is expected to contain exactly one <spectrum> tag (from <spectrum> to </spectrum>). This function will extract the contained binaryDataArray and provide the result as Spectrum.

Parameters

in	Input string containing the raw XML
sptr	Resulting spectrum

Precondition

in must have <spectrum> as root element.

domParseString_()

std::string domParseString_ ( const std::string &  in, std::vector< BinaryData > &  data  )

protected

Extract data from a string containing multiple <binaryDataArray> tags.

This may be a string from <spectrum> to </spectrum> or <chromatogram> to </chromatogram> tag which contains one or more <binaryDataArray>. These XML tags need to conform to the mzML standard. The function will return a vector with all binary data found in the string in the binaryDataArray tags.

Parameters

in	Input string containing the raw XML
data	Binary data extracted from the string

Precondition

in must have <spectrum> or <chromatogram> as root element.

handleBinaryDataArray_()

void handleBinaryDataArray_ ( xercesc::DOMNode *  indexListNode, std::vector< BinaryData > &  data  )

protected

Convert a single DOMNode of type binaryDataArray to BinaryData object.

This function will extract the data from a xerces DOMNode which points to a binaryDataArray tag and store the result as a BinaryData object. The result will be appended to the data vector.

Parameters

in	DOMNode of type binaryDataArray
data	Binary data extracted from the string

setSkipXMLChecks()

void setSkipXMLChecks

(

bool

only

)

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

Member Data Documentation

skip_xml_checks_

bool skip_xml_checks_

protected

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