MzMLSpectrumDecoder Class Reference

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

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

Public Member Functions
	MzMLSpectrumDecoder ()
void	domParseSpectrum (const std::string &in, OpenMS::Interfaces::SpectrumPtr &sptr)
	Extract data from a string which contains a full mzML spectrum. 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_)
	decode binary data More...
OpenMS::Interfaces::ChromatogramPtr	decodeBinaryDataChrom_ (std::vector< BinaryData > &data_)
	decode binary data More...
void	handleBinaryDataArray_ (xercesc::DOMNode *indexListNode, std::vector< BinaryData > &data_)
	Convert a single DOMNode of type binaryDataArray to BinaryData object. More...
void	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_

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 ( )

inline

Member Function Documentation

decodeBinaryDataChrom_()

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

protected

decode binary data

Duplicated code from MzMLHandler, need to clean up see void MzMLHandler<MapType>::fillData_()

decodeBinaryDataSpectrum_()

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

protected

decode binary data

Duplicated code from MzMLHandler, need to clean up see void MzMLHandler<MapType>::fillData_()

domParseChromatogram()

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()

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_()

void 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