| OpenMS 2.5.0

Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
CachedmzML Class Reference

An class that uses on-disk caching to read and write spectra and chromatograms. More...

`#include <OpenMS/FORMAT/CachedMzML.h>`

Inheritance diagram for CachedmzML:

## Public Member Functions

MSSpectrum | getSpectrum (Size id)
MSChromatogram | getChromatogram (Size id)
size_t | getNrSpectra () const
size_t | getNrChromatograms () const
const MSExperiment & | getMetaData () const
Constructors and Destructor
| CachedmzML ()
| Default constructor. More...
| CachedmzML (const String &filename)
| CachedmzML (const CachedmzML &rhs)
| Copy constructor. More...
| ~CachedmzML ()
| Default destructor. More...

## Static Public Member Functions

static void | store (const String &filename, const PeakMap &map)
| Stores a map in a cached MzML file. More...
static void | load (const String &filename, CachedmzML &map)
| Loads a map from a cached MzML file. More...

## Protected Member Functions

void | load_ (const String &filename)

## Protected Attributes

MSExperiment | meta_ms_experiment_
| Meta data. More...
std::ifstream | ifs_
| Internal filestream. More...
String | filename_
| Name of the mzML file. More...
String | filename_cached_
| Name of the cached mzML file. More...
std::vector< std::streampos > | spectra_index_
| Indices. More...
std::vector< std::streampos > | chrom_index_

## Detailed Description

An class that uses on-disk caching to read and write spectra and chromatograms.

This class provides functions to read and write spectra and chromatograms to disk using a time-efficient format. Reading the data items from disk can be very fast and done in random order (once the in-memory index is built for the file).

## Constructor & Destructor Documentation

## ◆ CachedmzML() [1/3]

CachedmzML | ( |  | ) |

Default constructor.

## ◆ CachedmzML() [2/3]

CachedmzML | ( | const String & | filename | ) |

## ◆ CachedmzML() [3/3]

CachedmzML | ( | const CachedmzML & | rhs | ) |

Copy constructor.

## ◆ ~CachedmzML()

~CachedmzML | ( |  | ) |

Default destructor.

## Member Function Documentation

## ◆ getChromatogram()

MSChromatogram getChromatogram | ( | Size | id | ) |

## ◆ getMetaData()

const MSExperiment& getMetaData | ( |  | ) | const

inline

## ◆ getNrChromatograms()

size_t getNrChromatograms | ( |  | ) | const

## ◆ getNrSpectra()

size_t getNrSpectra | ( |  | ) | const

## ◆ getSpectrum()

MSSpectrum getSpectrum | ( | Size | id | ) |

## ◆ load()

static void load | ( | const String & | filename,
|  | CachedmzML & | map
| ) |  |

static

Loads a map from a cached MzML file.

`filename` The data location (ends in .mzML, expects an adjacent .mzML.cached file) `map` A CachedmzML result object

Exceptions

  Exception::FileNotFound | is thrown if the file could not be opened
  Exception::ParseError | is thrown if an error occurs during parsing

## ◆ load_()

void load_ | ( | const String & | filename | ) |

protected

## ◆ store()

static void store | ( | const String & | filename,
|  | const PeakMap & | map
| ) |  |

static

Stores a map in a cached MzML file.

`filename` The data location (ends in .mzML) `map` has to be an MSExperiment or have the same interface.

Exceptions

  Exception::UnableToCreateFile | is thrown if the file could not be created

## Member Data Documentation

## ◆ chrom_index_

std::vector<std::streampos> chrom_index_

protected

## ◆ filename_

String filename_

protected

Name of the mzML file.

## ◆ filename_cached_

String filename_cached_

protected

Name of the cached mzML file.

## ◆ ifs_

std::ifstream ifs_

protected

Internal filestream.

## ◆ meta_ms_experiment_

MSExperiment meta_ms_experiment_

protected

Meta data.

## ◆ spectra_index_

std::vector<std::streampos> spectra_index_

protected

Indices.