| OpenMS 2.5.0

Public Types | Public Member Functions | List of all members
SpectrumAccessOpenMSCached Class Reference

An implementation of the Spectrum Access interface using on-disk caching. More...

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

Inheritance diagram for SpectrumAccessOpenMSCached:

## Public Types

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

## Public Member Functions

| SpectrumAccessOpenMSCached (const String &filename)
| Constructor, opens the file stream. More...
| ~SpectrumAccessOpenMSCached () override
| Destructor. More...
| SpectrumAccessOpenMSCached (const SpectrumAccessOpenMSCached &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...
Public Member Functions inherited from CachedmzML
MSSpectrum | getSpectrum (Size id)
MSChromatogram | getChromatogram (Size id)
size_t | getNrSpectra () const
size_t | getNrChromatograms () const
const MSExperiment & | getMetaData () const
| CachedmzML ()
| Default constructor. More...
| CachedmzML (const String &filename)
| CachedmzML (const CachedmzML &rhs)
| Copy constructor. More...
| ~CachedmzML ()
| Default destructor. More...

## Additional Inherited Members

Static Public Member Functions inherited from CachedmzML
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 inherited from CachedmzML
void | load_ (const String &filename)
Protected Attributes inherited from CachedmzML
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 implementation of the Spectrum Access interface using on-disk caching.

This class implements the OpenSWATH Spectrum Access interface (ISpectrumAccess) using the CachedmzML class which is able to read and write a cached mzML file.

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. The caller is responsible to ensure that access is performed atomically.

## Member Typedef Documentation

## ◆ MSExperimentType

typedef OpenMS::PeakMap MSExperimentType

## ◆ MSSpectrumType

typedef OpenMS::MSSpectrum MSSpectrumType

## Constructor & Destructor Documentation

## ◆ SpectrumAccessOpenMSCached() [1/2]

SpectrumAccessOpenMSCached | ( | const String & | filename | ) |

explicit

Constructor, opens the file stream.

Parameters

  filename | The filename of the .mzML file (it is assumed a second file .mzML.cached exists).

Exceptions

  Exception::FileNotFound | is thrown if the file is not found
  Exception::ParseError | is thrown if the file cannot be parsed

## ◆ ~SpectrumAccessOpenMSCached()

~SpectrumAccessOpenMSCached | ( |  | ) |

override

Destructor.

## ◆ SpectrumAccessOpenMSCached() [2/2]

SpectrumAccessOpenMSCached | ( | const SpectrumAccessOpenMSCached & | rhs | ) |

Copy constructor.

## 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)

Implements ISpectrumAccess.