| OpenMS 2.5.0

Public Types | Public Member Functions | Private Attributes | List of all members
SpectrumAccessOpenMS Class Reference

An implementation of the OpenSWATH Spectrum Access interface using OpenMS. More...

`#include <OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMS.h>`

Inheritance diagram for SpectrumAccessOpenMS:

## Public Types

typedef OpenMS::PeakMap | MSExperimentType
typedef OpenMS::MSSpectrum | MSSpectrumType
typedef OpenMS::MSChromatogram | MSChromatogramType

## Public Member Functions

| SpectrumAccessOpenMS (boost::shared_ptr< MSExperimentType > ms_experiment)
| Constructor. More...
| ~SpectrumAccessOpenMS () override
| Destructor. More...
| SpectrumAccessOpenMS (const SpectrumAccessOpenMS &rhs)
| Copy constructor. More...
boost::shared_ptr< OpenSwath::ISpectrumAccess > | lightClone () const override
| Light clone operator (actual data will not get copied) More...
OpenSwath::SpectrumPtr | getSpectrumById (int id) override
| Return a pointer to a spectrum at the given id. More...
OpenSwath::SpectrumMeta | getSpectrumMetaById (int id) const override
| Returns the meta information for a spectrum. More...
std::vector< std::size_t > | getSpectraByRT (double RT, double deltaRT) const override
| Return a vector of ids of spectra that are within RT +/- deltaRT. More...
size_t | getNrSpectra () const override
| Returns the number of spectra available. More...
SpectrumSettings | getSpectraMetaInfo (int id) const
OpenSwath::ChromatogramPtr | getChromatogramById (int id) override
| Return a pointer to a chromatogram at the given id. More...
size_t | getNrChromatograms () const override
| Returns the number of chromatograms available. More...
ChromatogramSettings | getChromatogramMetaInfo (int id) const
std::string | getChromatogramNativeID (int id) const override
| Returns the native id of the chromatogram at the given id. More...
Public Member Functions inherited from ISpectrumAccess
virtual | ~ISpectrumAccess ()
| Destructor. More...

## Private Attributes

boost::shared_ptr< MSExperimentType > | ms_experiment_

## Detailed Description

An implementation of the OpenSWATH Spectrum Access interface using OpenMS.

## Member Typedef Documentation

## ◆ MSChromatogramType

typedef OpenMS::MSChromatogram MSChromatogramType

## ◆ MSExperimentType

typedef OpenMS::PeakMap MSExperimentType

## ◆ MSSpectrumType

typedef OpenMS::MSSpectrum MSSpectrumType

## Constructor & Destructor Documentation

## ◆ SpectrumAccessOpenMS() [1/2]

SpectrumAccessOpenMS | ( | boost::shared_ptr< MSExperimentType > | ms_experiment | ) |

explicit

Constructor.

## ◆ ~SpectrumAccessOpenMS()

~SpectrumAccessOpenMS | ( |  | ) |

override

Destructor.

## ◆ SpectrumAccessOpenMS() [2/2]

SpectrumAccessOpenMS | ( | const SpectrumAccessOpenMS & | rhs | ) |

Copy constructor.

Performs a light copy operation when another SpectrumAccessOpenMS instance is given: only a copy of the pointer to the underlying MSExperiment is stored, so after this, both instances (rhs and *this) will point to the same MSExperiment.

## Member Function Documentation

## ◆ getChromatogramById()

OpenSwath::ChromatogramPtr getChromatogramById | ( | int | id | ) |

override virtual

Return a pointer to a chromatogram at the given id.

Implements ISpectrumAccess.

## ◆ getChromatogramMetaInfo()

ChromatogramSettings getChromatogramMetaInfo | ( | int | id | ) | const

## ◆ getChromatogramNativeID()

std::string getChromatogramNativeID | ( | int | id | ) | const

override virtual

Returns the native id of the chromatogram at the given id.

Implements ISpectrumAccess.

## ◆ getNrChromatograms()

size_t getNrChromatograms | ( |  | ) | const

override virtual

Returns the number of chromatograms available.

Implements ISpectrumAccess.

## ◆ getNrSpectra()

size_t getNrSpectra | ( |  | ) | const

override virtual

Returns the number of spectra available.

Implements ISpectrumAccess.

## ◆ getSpectraByRT()

std::vector<std::size_t> getSpectraByRT | ( | double | RT,
|  | double | deltaRT
| ) |  | const

override virtual

Return a vector of ids of spectra that are within RT +/- deltaRT.

Implements ISpectrumAccess.

## ◆ getSpectraMetaInfo()

SpectrumSettings getSpectraMetaInfo | ( | int | id | ) | const

## ◆ getSpectrumById()

OpenSwath::SpectrumPtr getSpectrumById | ( | int | id | ) |

override virtual

Return a pointer to a spectrum at the given id.

Implements ISpectrumAccess.

## ◆ getSpectrumMetaById()

OpenSwath::SpectrumMeta getSpectrumMetaById | ( | int | id | ) | const

override virtual

Returns the meta information for a spectrum.

Implements ISpectrumAccess.

## ◆ lightClone()

boost::shared_ptr<OpenSwath::ISpectrumAccess> lightClone | ( |  | ) | const

override virtual

Light clone operator (actual data will not get copied)

Creates a light clone of the current instance, with the clone pointing to the same underlying MSExperiment.

Implements ISpectrumAccess.

## Member Data Documentation

## ◆ ms_experiment_

boost::shared_ptr<MSExperimentType> ms_experiment_

private