| OpenMS 2.5.0

Classes | Static Public Member Functions | Static Private Member Functions | List of all members
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, 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`
| ) |  |

static private

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