| OpenMS 2.5.0

Static Public Member Functions | List of all members
OpenSwathDataAccessHelper Class Reference

Several helpers to convert OpenMS datastructures to structures that implement the OpenSWATH interfaces. More...

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

## Static Public Member Functions

static void | convertToOpenMSSpectrum (const OpenSwath::SpectrumPtr sptr, OpenMS::MSSpectrum &spectrum)
| Convert a SpectrumPtr to an OpenMS Spectrum. More...
static OpenSwath::SpectrumPtr | convertToSpectrumPtr (const OpenMS::MSSpectrum &spectrum)
| Convert an OpenMS Spectrum to an SpectrumPtr. More...
static void | convertToOpenMSChromatogram (const OpenSwath::ChromatogramPtr cptr, OpenMS::MSChromatogram &chromatogram)
| Convert a ChromatogramPtr to an OpenMS Chromatogram. More...
static OpenSwath::ChromatogramPtr | convertToChromatogramPtr (const OpenMS::MSChromatogram &chromatogram)
| Convert an OpenMS Chromatogram to an ChromatogramPtr. More...
static void | convertToOpenMSChromatogramFilter (OpenMS::MSChromatogram &chromatogram, const OpenSwath::ChromatogramPtr cptr, double rt_min, double rt_max)
static void | convertTargetedExp (const OpenMS::TargetedExperiment &transition_exp_, OpenSwath::LightTargetedExperiment &transition_exp)
| convert from the OpenMS TargetedExperiment to the LightTargetedExperiment More...
static void | convertTargetedCompound (const TargetedExperiment::Peptide &pep, OpenSwath::LightCompound &comp)
| convert from the OpenMS TargetedExperiment Peptide to the LightTargetedExperiment Peptide More...
static void | convertTargetedCompound (const TargetedExperiment::Compound &compound, OpenSwath::LightCompound &comp)
| convert from the OpenMS TargetedExperiment Compound to the LightTargetedExperiment Compound More...
static void | convertPeptideToAASequence (const OpenSwath::LightCompound &peptide, AASequence &aa_sequence)
| convert from the LightCompound to an OpenMS AASequence (with correct modifications) More...

## Detailed Description

Several helpers to convert OpenMS datastructures to structures that implement the OpenSWATH interfaces.

## Member Function Documentation

## ◆ convertPeptideToAASequence()

static void convertPeptideToAASequence | ( | const OpenSwath::LightCompound & | peptide,
|  | AASequence & | aa_sequence
| ) |  |

static

convert from the LightCompound to an OpenMS AASequence (with correct modifications)

## ◆ convertTargetedCompound() [1/2]

static void convertTargetedCompound | ( | const TargetedExperiment::Peptide & | pep,
|  | OpenSwath::LightCompound & | comp
| ) |  |

static

convert from the OpenMS TargetedExperiment Peptide to the LightTargetedExperiment Peptide

## ◆ convertTargetedCompound() [2/2]

static void convertTargetedCompound | ( | const TargetedExperiment::Compound & | compound,
|  | OpenSwath::LightCompound & | comp
| ) |  |

static

convert from the OpenMS TargetedExperiment Compound to the LightTargetedExperiment Compound

## ◆ convertTargetedExp()

static void convertTargetedExp | ( | const OpenMS::TargetedExperiment & | transition_exp_,
|  | OpenSwath::LightTargetedExperiment & | transition_exp
| ) |  |

static

convert from the OpenMS TargetedExperiment to the LightTargetedExperiment

Referenced by TOPPOpenSwathBase::loadTransitionList().

## ◆ convertToChromatogramPtr()

static OpenSwath::ChromatogramPtr convertToChromatogramPtr | ( | const OpenMS::MSChromatogram & | chromatogram | ) |

static

Convert an OpenMS Chromatogram to an ChromatogramPtr.

## ◆ convertToOpenMSChromatogram()

static void convertToOpenMSChromatogram | ( | const OpenSwath::ChromatogramPtr | cptr,
|  | OpenMS::MSChromatogram & | chromatogram
| ) |  |

static

Convert a ChromatogramPtr to an OpenMS Chromatogram.

Referenced by ChromatogramExtractor::return_chromatogram().

## ◆ convertToOpenMSChromatogramFilter()

static void convertToOpenMSChromatogramFilter | ( | OpenMS::MSChromatogram & | chromatogram,
|  | const OpenSwath::ChromatogramPtr | cptr,
|  | double | rt_min,
|  | double | rt_max
| ) |  |

static

## ◆ convertToOpenMSSpectrum()

static void convertToOpenMSSpectrum | ( | const OpenSwath::SpectrumPtr | sptr,
|  | OpenMS::MSSpectrum & | spectrum
| ) |  |

static

Convert a SpectrumPtr to an OpenMS Spectrum.

## ◆ convertToSpectrumPtr()

static OpenSwath::SpectrumPtr convertToSpectrumPtr | ( | const OpenMS::MSSpectrum & | spectrum | ) |

static

Convert an OpenMS Spectrum to an SpectrumPtr.