| OpenMS 2.5.0

Public Member Functions | Protected Attributes | Private Types | Private Member Functions | List of all members
OnDiscMSExperiment Class Reference
Kernel

Representation of a mass spectrometry experiment on disk. More...

`#include <OpenMS/KERNEL/OnDiscMSExperiment.h>`

## Public Member Functions

| OnDiscMSExperiment ()
| Constructor. More...
bool | openFile (const String &filename, bool skipMetaData=false)
| Open a specific file on disk. More...
| OnDiscMSExperiment (const OnDiscMSExperiment &source)
| Copy constructor. More...
bool | operator== (const OnDiscMSExperiment &rhs) const
| Equality operator. More...
bool | operator!= (const OnDiscMSExperiment &rhs) const
| Inequality operator. More...
bool | isSortedByRT () const
| Checks if all spectra are sorted with respect to ascending RT. More...
Size | size () const
| alias for getNrSpectra More...
bool | empty () const
| returns whether spectra are empty More...
Size | getNrSpectra () const
| get the total number of spectra available More...
Size | getNrChromatograms () const
| get the total number of chromatograms available More...
boost::shared_ptr< const ExperimentalSettings > | getExperimentalSettings () const
| returns the meta information of this experiment (const access) More...
boost::shared_ptr< PeakMap > | getMetaData () const
MSSpectrum | operator[] (Size n)
| alias for getSpectrum More...
MSSpectrum | getSpectrum (Size id)
| returns a single spectrum More...
OpenMS::Interfaces::SpectrumPtr | getSpectrumById (Size id)
| returns a single spectrum More...
MSChromatogram | getChromatogram (Size id)
| returns a single chromatogram More...
OpenMS::Interfaces::ChromatogramPtr | getChromatogramById (Size id)
| returns a single chromatogram More...
void | setSkipXMLChecks (bool skip)
| sets whether to skip some XML checks and be fast instead More...

## Protected Attributes

String | filename_
| The filename of the underlying data file. More...
Internal::IndexedMzMLHandler | indexed_mzml_file_
| The index of the underlying data file. More...
boost::shared_ptr< PeakMap > | meta_ms_experiment_
| The meta-data. More...

## Private Types

typedef ChromatogramPeak | ChromatogramPeakT
typedef Peak1D | PeakT

## Private Member Functions

OnDiscMSExperiment & | operator= (const OnDiscMSExperiment &)
| Private Assignment operator -> we cannot copy file streams in IndexedMzMLHandler. More...
void | loadMetaData_ (const String &filename)

## Detailed Description

Representation of a mass spectrometry experiment on disk.

Note
  This implementation is not thread-safe since it keeps internally a single file access pointer which it moves when accessing a specific data item. Please provide a separate copy to each thread, e.g.

#pragma omp parallel for firstprivate(ondisc_map)

## Member Typedef Documentation

## ◆ ChromatogramPeakT

typedef ChromatogramPeak ChromatogramPeakT

private

## ◆ PeakT

typedef Peak1D PeakT

private

## Constructor & Destructor Documentation

## ◆ OnDiscMSExperiment() [1/2]

OnDiscMSExperiment | ( |  | ) |

inline

Constructor.

This initializes the object, use openFile to open a file.

## ◆ OnDiscMSExperiment() [2/2]

OnDiscMSExperiment | ( | const OnDiscMSExperiment & | source | ) |

inline

Copy constructor.

## Member Function Documentation

## ◆ empty()

bool empty | ( |  | ) | const

inline

returns whether spectra are empty

## ◆ getChromatogram()

MSChromatogram getChromatogram | ( | Size | id | ) |

inline

returns a single chromatogram

Parameters

  id | The index of the chromatogram

Referenced by IndexedMzMLFileLoader::store().

## ◆ getChromatogramById()

OpenMS::Interfaces::ChromatogramPtr getChromatogramById | ( | Size | id | ) |

inline

returns a single chromatogram

## ◆ getExperimentalSettings()

boost::shared_ptr<const ExperimentalSettings> getExperimentalSettings | ( |  | ) | const

inline

returns the meta information of this experiment (const access)

Referenced by IndexedMzMLFileLoader::store().

## ◆ getMetaData()

boost::shared_ptr<PeakMap> getMetaData | ( |  | ) | const

inline

## ◆ getNrChromatograms()

Size getNrChromatograms | ( |  | ) | const

inline

get the total number of chromatograms available

Referenced by IndexedMzMLFileLoader::store().

## ◆ getNrSpectra()

Size getNrSpectra | ( |  | ) | const

inline

get the total number of spectra available

Referenced by IndexedMzMLFileLoader::store().

## ◆ getSpectrum()

MSSpectrum getSpectrum | ( | Size | id | ) |

inline

returns a single spectrum

Parameters

  id | The index of the spectrum

Referenced by IndexedMzMLFileLoader::store().

## ◆ getSpectrumById()

OpenMS::Interfaces::SpectrumPtr getSpectrumById | ( | Size | id | ) |

inline

returns a single spectrum

## ◆ isSortedByRT()

bool isSortedByRT | ( |  | ) | const

inline

Checks if all spectra are sorted with respect to ascending RT.

Note that we cannot check whether all spectra are sorted (except if we were to load them all and check).

## ◆ loadMetaData_()

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

private

## ◆ openFile()

bool openFile | ( | const String & | filename,
|  | bool | skipMetaData = `false`
| ) |  |

inline

Open a specific file on disk.

This tries to read the indexed mzML by parsing the index and then reading the meta information into memory.

Returns
  Whether the parsing of the file was successful (if false, the file most likely was not an indexed mzML file)

Referenced by IndexedMzMLFileLoader::load().

## ◆ operator!=()

bool operator!= | ( | const OnDiscMSExperiment & | rhs | ) | const

inline

Inequality operator.

References KDTree::operator==().

## ◆ operator=()

OnDiscMSExperiment& operator= | ( | const OnDiscMSExperiment & |  | ) |

private

Private Assignment operator -> we cannot copy file streams in IndexedMzMLHandler.

## ◆ operator==()

bool operator== | ( | const OnDiscMSExperiment & | rhs | ) | const

inline

Equality operator.

This only checks whether the underlying file is the same and the parsed meta-information is the same. Note that the file reader (e.g. the std::ifstream of the file) might be in a different state.

References OnDiscMSExperiment::filename_, and OnDiscMSExperiment::meta_ms_experiment_.

## ◆ operator[]()

MSSpectrum operator[] | ( | Size | n | ) |

inline

alias for getSpectrum

## ◆ setSkipXMLChecks()

void setSkipXMLChecks | ( | bool | skip | ) |

inline

sets whether to skip some XML checks and be fast instead

## ◆ size()

Size size | ( |  | ) | const

inline

alias for getNrSpectra

## Member Data Documentation

## ◆ filename_

String filename_

protected

The filename of the underlying data file.

Referenced by OnDiscMSExperiment::operator==().

## ◆ indexed_mzml_file_

Internal::IndexedMzMLHandler indexed_mzml_file_

protected

The index of the underlying data file.

## ◆ meta_ms_experiment_

boost::shared_ptr<PeakMap> meta_ms_experiment_

protected

The meta-data.

Referenced by OnDiscMSExperiment::operator==().