#include <OpenMS/KERNEL/MSExperiment.h>
Contains the data and metadata of an experiment performed with an MS (or HPLC and MS).
Be carefull when changing the order of contained MSSpectrum instances, if tandem-MS data is stored in this class. The only way to find a precursor spectrum of MSSpectrum x is to search for the first spectrum before x that has a lower MS-level!
Public Types | |
typedef MSSpectrum< PeakT, AllocT > | SpectrumType |
Spectrum Type. | |
typedef std::vector< SpectrumType > | Base |
STL base class type. | |
typedef std::vector < SpectrumType >::iterator | Iterator |
Mutable iterator. | |
typedef std::vector < SpectrumType > ::const_iterator | ConstIterator |
Non-mutable iterator. | |
typedef Internal::AreaIterator < PeakT, PeakT &, PeakT *, Iterator, typename SpectrumType::Iterator > | AreaIterator |
Mutable area iterator type (for traversal of a rectangular subset of the peaks). | |
typedef Internal::AreaIterator < const PeakT, const PeakT &, const PeakT *, ConstIterator, typename SpectrumType::ConstIterator > | ConstAreaIterator |
Immutable area iterator type (for traversal of a rectangular subset of the peaks). | |
typedef PeakT | PeakType |
Peak type. | |
typedef DRange< 2 > | AreaType |
Area type. | |
typedef DoubleReal | CoordinateType |
Coordinate type of peak positions. | |
typedef DoubleReal | IntensityType |
Intenstiy type of peaks. | |
typedef RangeManager< 2 > | RangeManagerType |
RangeManager type. | |
typedef SpectrumType::const_reference | ConstPeakReference |
const peak reference type | |
typedef SpectrumType::reference | PeakReference |
peak reference type | |
Public Member Functions | |
MSExperiment () | |
Constructor. | |
MSExperiment (const AllocT &alloc) | |
MSExperiment (const MSExperiment &source) | |
Copy constructor. | |
MSExperiment & | operator= (const MSExperiment &source) |
Assignment operator. | |
void | push_back (const SpectrumType &spec) |
template<typename A> | |
void | push_back (const MSSpectrum< PeakT, A > &spec) |
void | resize (const typename Base::size_type &size) |
reimplement resize, so that new MSSpectra with our unique allocator are created | |
MSExperiment & | operator= (const ExperimentalSettings &source) |
Assignment operator. | |
bool | operator== (const MSExperiment &rhs) const |
Equality operator. | |
bool | operator!= (const MSExperiment &rhs) const |
Equality operator. | |
template<class Container> | |
void | get2DData (Container &cont) const |
Reads out a 2D Spectrum. | |
template<class Container> | |
void | set2DData (const Container &cont) throw (Exception::Precondition) |
Assignment of a 2D spectrum to MSExperiment. | |
AreaIterator | areaBegin (CoordinateType min_rt, CoordinateType max_rt, CoordinateType min_mz, CoordinateType max_mz) |
Returns an area iterator for area . | |
AreaIterator | areaEnd () |
Returns an invalid area iterator marking the end of an area. | |
ConstAreaIterator | areaBeginConst (CoordinateType min_rt, CoordinateType max_rt, CoordinateType min_mz, CoordinateType max_mz) const |
Returns a non-mutable area iterator for area . | |
ConstAreaIterator | areaEndConst () const |
Returns an non-mutable invalid area iterator marking the end of an area. | |
ConstIterator | RTBegin (CoordinateType rt) const |
Fast search for spectrum range begin. | |
ConstIterator | RTEnd (CoordinateType rt) const |
Fast search for spectrum range end (returns the past-the-end iterator). | |
Iterator | RTBegin (CoordinateType rt) |
Fast search for spectrum range begin. | |
Iterator | RTEnd (CoordinateType rt) |
Fast search for spectrum range end (returns the past-the-end iterator). | |
void | sortSpectra (bool sort_mz=true) |
Sorts the data points by retention time. | |
void | reset () |
Resets all internal values. | |
const ExperimentalSettings & | getExperimentalSettings () const |
returns the meta information of this experiment (const access) | |
ExperimentalSettings & | getExperimentalSettings () |
returns the meta information of this experiment (mutable access) | |
ConstIterator | getPrecursorSpectrum (ConstIterator iterator) const |
Returns the precursor spectrum of the scan pointed to by iterator . | |
Range methods | |
| |
virtual void | updateRanges () |
Updates minimum and maximum position/intensity. | |
void | updateRanges (Int ms_level) |
Updates the m/z, intensity, retention time and MS level ranges of all spectra with a certain ms level. | |
CoordinateType | getMinMZ () const |
returns the minimal m/z value | |
CoordinateType | getMaxMZ () const |
returns the maximal m/z value | |
CoordinateType | getMinRT () const |
returns the minimal retention time value | |
CoordinateType | getMaxRT () const |
returns the maximal retention time value | |
const AreaType & | getDataRange () const |
Returns RT and m/z range the data lies in. | |
UInt | getSize () const |
returns the total number of peaks | |
const std::vector< UInt > & | getMSLevels () const |
returns an array of MS levels | |
Protected Types | |
typedef std::vector < MSSpectrum< PeakT, AllocT > > | Base_ |
Base class typedef. | |
Protected Member Functions | |
virtual void | clearChildIds_ () |
Clears the persistence id of all sub-objects. | |
Protected Attributes | |
std::vector< UInt > | ms_levels_ |
MS levels of the data. | |
UInt | total_size_ |
Number of all data points. | |
AllocT | alloc_ |
allocator for MSSpectrum |
typedef MSSpectrum<PeakT, AllocT> SpectrumType |
Spectrum Type.
typedef std::vector<SpectrumType> Base |
STL base class type.
typedef std::vector<SpectrumType>::iterator Iterator |
Mutable iterator.
typedef std::vector<SpectrumType>::const_iterator ConstIterator |
Non-mutable iterator.
typedef Internal::AreaIterator<PeakT, PeakT&, PeakT*, Iterator, typename SpectrumType::Iterator> AreaIterator |
Mutable area iterator type (for traversal of a rectangular subset of the peaks).
typedef Internal::AreaIterator<const PeakT, const PeakT&, const PeakT*, ConstIterator, typename SpectrumType::ConstIterator> ConstAreaIterator |
Immutable area iterator type (for traversal of a rectangular subset of the peaks).
typedef PeakT PeakType |
Peak type.
typedef DoubleReal CoordinateType |
Coordinate type of peak positions.
typedef DoubleReal IntensityType |
typedef RangeManager<2> RangeManagerType |
RangeManager type.
const peak reference type
typedef SpectrumType::reference PeakReference |
peak reference type
typedef std::vector<MSSpectrum<PeakT, AllocT> > Base_ [protected] |
Base class typedef.
MSExperiment | ( | ) | [inline] |
Constructor.
MSExperiment | ( | const AllocT & | alloc | ) | [inline] |
MSExperiment | ( | const MSExperiment< PeakT, AllocT > & | source | ) | [inline] |
Copy constructor.
MSExperiment& operator= | ( | const MSExperiment< PeakT, AllocT > & | source | ) | [inline] |
Assignment operator.
void push_back | ( | const SpectrumType & | spec | ) | [inline] |
void push_back | ( | const MSSpectrum< PeakT, A > & | spec | ) | [inline] |
void resize | ( | const typename Base::size_type & | size | ) | [inline] |
reimplement resize, so that new MSSpectra with our unique allocator are created
MSExperiment& operator= | ( | const ExperimentalSettings & | source | ) | [inline] |
bool operator== | ( | const MSExperiment< PeakT, AllocT > & | rhs | ) | const [inline] |
Equality operator.
bool operator!= | ( | const MSExperiment< PeakT, AllocT > & | rhs | ) | const [inline] |
Equality operator.
void get2DData | ( | Container & | cont | ) | const [inline] |
Reads out a 2D Spectrum.
Container can be a PeakArray or an STL container of peaks which supports insert(), end() and back()
void set2DData | ( | const Container & | cont | ) | throw (Exception::Precondition) [inline] |
Assignment of a 2D spectrum to MSExperiment.
Container can be a PeakArray or an STL container of peaks.
AreaIterator areaBegin | ( | CoordinateType | min_rt, | |
CoordinateType | max_rt, | |||
CoordinateType | min_mz, | |||
CoordinateType | max_mz | |||
) | [inline] |
Returns an area iterator for area
.
AreaIterator areaEnd | ( | ) | [inline] |
Returns an invalid area iterator marking the end of an area.
ConstAreaIterator areaBeginConst | ( | CoordinateType | min_rt, | |
CoordinateType | max_rt, | |||
CoordinateType | min_mz, | |||
CoordinateType | max_mz | |||
) | const [inline] |
Returns a non-mutable area iterator for area
.
ConstAreaIterator areaEndConst | ( | ) | const [inline] |
Returns an non-mutable invalid area iterator marking the end of an area.
ConstIterator RTBegin | ( | CoordinateType | rt | ) | const [inline] |
Fast search for spectrum range begin.
ConstIterator RTEnd | ( | CoordinateType | rt | ) | const [inline] |
Fast search for spectrum range end (returns the past-the-end iterator).
Iterator RTBegin | ( | CoordinateType | rt | ) | [inline] |
Fast search for spectrum range begin.
Iterator RTEnd | ( | CoordinateType | rt | ) | [inline] |
Fast search for spectrum range end (returns the past-the-end iterator).
virtual void updateRanges | ( | ) | [inline, virtual] |
Updates minimum and maximum position/intensity.
This method is usually implemented by calling clearRanges() and updateRanges_() or updateRanges1D_().
Implements RangeManager< 2 >.
void updateRanges | ( | Int | ms_level | ) | [inline] |
Updates the m/z, intensity, retention time and MS level ranges of all spectra with a certain ms level.
ms_level | MS level to consider for m/z range , RT range and intensity range (All MS levels if negative) |
CoordinateType getMinMZ | ( | ) | const [inline] |
returns the minimal m/z value
CoordinateType getMaxMZ | ( | ) | const [inline] |
returns the maximal m/z value
CoordinateType getMinRT | ( | ) | const [inline] |
returns the minimal retention time value
CoordinateType getMaxRT | ( | ) | const [inline] |
returns the maximal retention time value
const AreaType& getDataRange | ( | ) | const [inline] |
Returns RT and m/z range the data lies in.
RT is dimension 0, m/z is dimension 1
UInt getSize | ( | ) | const [inline] |
returns the total number of peaks
const std::vector<UInt>& getMSLevels | ( | ) | const [inline] |
returns an array of MS levels
void sortSpectra | ( | bool | sort_mz = true |
) | [inline] |
Sorts the data points by retention time.
sort_mz
: indicates whether the points should be sorted by m/z as well
void reset | ( | ) | [inline] |
Resets all internal values.
const ExperimentalSettings& getExperimentalSettings | ( | ) | const [inline] |
returns the meta information of this experiment (const access)
ExperimentalSettings& getExperimentalSettings | ( | ) | [inline] |
returns the meta information of this experiment (mutable access)
ConstIterator getPrecursorSpectrum | ( | ConstIterator | iterator | ) | const [inline] |
Returns the precursor spectrum of the scan pointed to by iterator
.
If there is no precursor scan the past-the-end iterator is returned.
virtual void clearChildIds_ | ( | ) | [inline, protected, virtual] |
std::vector<UInt> ms_levels_ [protected] |
MS levels of the data.
UInt total_size_ [protected] |
Number of all data points.
AllocT alloc_ [protected] |
allocator for MSSpectrum
Generated Tue Apr 1 15:36:46 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |