MzMLHandlerHelper Class Reference

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, const 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, const 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