OpenMS
2.6.0
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In-Memory representation of a mass spectrometry experiment. More...
#include <OpenMS/KERNEL/MSExperiment.h>
Classes | |
struct | ContainerAdd_ |
Helper class to add either general data points in set2DData or use mass traces from meta values. More... | |
struct | ContainerAdd_< ContainerValueType, false > |
struct | ContainerAdd_< ContainerValueType, true > |
Public Types | |
typedef Peak1D | PeakT |
typedef ChromatogramPeak | ChromatogramPeakT |
Base type definitions | |
typedef PeakT | PeakType |
Peak type. More... | |
typedef ChromatogramPeakT | ChromatogramPeakType |
Chromatogram peak type. More... | |
typedef DRange< 2 > | AreaType |
Area type. More... | |
typedef PeakType::CoordinateType | CoordinateType |
Coordinate type of peak positions. More... | |
typedef PeakType::IntensityType | IntensityType |
Intensity type of peaks. More... | |
typedef RangeManager< 2 > | RangeManagerType |
RangeManager type. More... | |
typedef MSSpectrum | SpectrumType |
Spectrum Type. More... | |
typedef MSChromatogram | ChromatogramType |
Chromatogram type. More... | |
typedef std::vector< SpectrumType > | Base |
STL base class type. More... | |
Iterator type definitions | |
typedef std::vector< SpectrumType >::iterator | Iterator |
Mutable iterator. More... | |
typedef std::vector< SpectrumType >::const_iterator | ConstIterator |
Non-mutable iterator. More... | |
typedef Internal::AreaIterator< PeakT, PeakT &, PeakT *, Iterator, SpectrumType::Iterator > | AreaIterator |
Mutable area iterator type (for traversal of a rectangular subset of the peaks) More... | |
typedef Internal::AreaIterator< const PeakT, const PeakT &, const PeakT *, ConstIterator, SpectrumType::ConstIterator > | ConstAreaIterator |
Immutable area iterator type (for traversal of a rectangular subset of the peaks) More... | |
Public Types inherited from RangeManager< 2 > | |
enum | |
Dimension of the position range. More... | |
typedef DRange< D > | PositionRangeType |
Position range type. More... | |
typedef DPosition< D > | PositionType |
Position Type. More... | |
typedef DRange< 1 > | IntensityRangeType |
Intensity range type. More... | |
Public Member Functions | |
Conversion to/from 2D data | |
template<class Container > | |
void | get2DData (Container &cont) const |
Reads out a 2D Spectrum. More... | |
template<class Container > | |
void | set2DData (const Container &container) |
Assignment of a data container with RT and MZ to an MSExperiment. More... | |
template<class Container > | |
void | set2DData (const Container &container, const StringList &store_metadata_names) |
Assignment of a data container with RT and MZ to an MSExperiment. More... | |
template<bool add_mass_traces, class Container > | |
void | set2DData (const Container &container) |
Assignment of a data container with RT and MZ to an MSExperiment. More... | |
Iterating ranges and areas | |
AreaIterator | areaBegin (CoordinateType min_rt, CoordinateType max_rt, CoordinateType min_mz, CoordinateType max_mz) |
Returns an area iterator for area . More... | |
AreaIterator | areaEnd () |
Returns an invalid area iterator marking the end of an area. More... | |
ConstAreaIterator | areaBeginConst (CoordinateType min_rt, CoordinateType max_rt, CoordinateType min_mz, CoordinateType max_mz) const |
Returns a non-mutable area iterator for area . More... | |
ConstAreaIterator | areaEndConst () const |
Returns an non-mutable invalid area iterator marking the end of an area. More... | |
ConstIterator | RTBegin (CoordinateType rt) const |
Fast search for spectrum range begin. More... | |
ConstIterator | RTEnd (CoordinateType rt) const |
Fast search for spectrum range end (returns the past-the-end iterator) More... | |
Iterator | RTBegin (CoordinateType rt) |
Fast search for spectrum range begin. More... | |
Iterator | RTEnd (CoordinateType rt) |
Fast search for spectrum range end (returns the past-the-end iterator) More... | |
Range methods | |
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void | updateRanges () override |
Updates minimum and maximum position/intensity. More... | |
void | updateRanges (Int ms_level) |
Updates the m/z, intensity, retention time and MS level ranges of all spectra with a certain ms level. More... | |
CoordinateType | getMinMZ () const |
returns the minimal m/z value More... | |
CoordinateType | getMaxMZ () const |
returns the maximal m/z value More... | |
CoordinateType | getMinRT () const |
returns the minimal retention time value More... | |
CoordinateType | getMaxRT () const |
returns the maximal retention time value More... | |
const AreaType & | getDataRange () const |
Returns RT and m/z range the data lies in. More... | |
UInt64 | getSize () const |
returns the total number of peaks More... | |
const std::vector< UInt > & | getMSLevels () const |
returns an array of MS levels More... | |
Sorting spectra and peaks | |
void | sortSpectra (bool sort_mz=true) |
Sorts the data points by retention time. More... | |
void | sortChromatograms (bool sort_rt=true) |
Sorts the data points of the chromatograms by m/z. More... | |
bool | isSorted (bool check_mz=true) const |
Checks if all spectra are sorted with respect to ascending RT. More... | |
void | reset () |
Resets all internal values. More... | |
bool | clearMetaDataArrays () |
Clears the meta data arrays of all contained spectra (float, integer and string arrays) More... | |
const ExperimentalSettings & | getExperimentalSettings () const |
returns the meta information of this experiment (const access) More... | |
ExperimentalSettings & | getExperimentalSettings () |
returns the meta information of this experiment (mutable access) More... | |
void | getPrimaryMSRunPath (StringList &toFill) const |
get the file path to the first MS run More... | |
ConstIterator | getPrecursorSpectrum (ConstIterator iterator) const |
Returns the precursor spectrum of the scan pointed to by iterator . More... | |
void | swap (MSExperiment &from) |
Swaps the content of this map with the content of from . More... | |
void | setSpectra (const std::vector< MSSpectrum > &spectra) |
sets the spectrum list More... | |
void | addSpectrum (const MSSpectrum &spectrum) |
adds a spectrum to the list More... | |
void | addSpectrum (MSSpectrum &&spectrum) |
const std::vector< MSSpectrum > & | getSpectra () const |
returns the spectrum list More... | |
std::vector< MSSpectrum > & | getSpectra () |
returns the spectrum list (mutable) More... | |
void | setChromatograms (const std::vector< MSChromatogram > &chromatograms) |
sets the chromatogram list More... | |
void | addChromatogram (const MSChromatogram &chromatogram) |
adds a chromatogram to the list More... | |
void | addChromatogram (MSChromatogram &&chrom) |
const std::vector< MSChromatogram > & | getChromatograms () const |
returns the chromatogram list More... | |
std::vector< MSChromatogram > & | getChromatograms () |
returns the chromatogram list (mutable) More... | |
Public Member Functions inherited from RangeManager< 2 > | |
RangeManager () | |
Default constructor. More... | |
RangeManager (const RangeManager &rhs) | |
Copy constructor. More... | |
RangeManager (RangeManager &&) noexcept=default | |
Move constructor. More... | |
virtual | ~RangeManager () |
Destructor. More... | |
RangeManager & | operator= (const RangeManager &rhs) |
Assignment operator. More... | |
bool | operator== (const RangeManager &rhs) const |
Equality operator. More... | |
bool | operator!= (const RangeManager &rhs) const |
Equality operator. More... | |
const PositionType & | getMin () const |
Returns the minimum position. More... | |
const PositionType & | getMax () const |
Returns the maximum position. More... | |
double | getMinInt () const |
Returns the minimum intensity. More... | |
double | getMaxInt () const |
Returns the maximum intensity. More... | |
void | clearRanges () |
Resets the ranges. More... | |
Public Member Functions inherited from ExperimentalSettings | |
ExperimentalSettings ()=default | |
Constructor. More... | |
ExperimentalSettings (const ExperimentalSettings &)=default | |
Copy constructor. More... | |
ExperimentalSettings (ExperimentalSettings &&)=default | |
Move constructor. More... | |
~ExperimentalSettings () override | |
Destructor. More... | |
ExperimentalSettings & | operator= (const ExperimentalSettings &)=default |
Assignment operator. More... | |
ExperimentalSettings & | operator= (ExperimentalSettings &&) &=default |
Move assignment operator. More... | |
bool | operator== (const ExperimentalSettings &rhs) const |
Equality operator. More... | |
bool | operator!= (const ExperimentalSettings &rhs) const |
Equality operator. More... | |
const Sample & | getSample () const |
returns a const reference to the sample description More... | |
Sample & | getSample () |
returns a mutable reference to the sample description More... | |
void | setSample (const Sample &sample) |
sets the sample description More... | |
const std::vector< SourceFile > & | getSourceFiles () const |
returns a const reference to the source data file More... | |
std::vector< SourceFile > & | getSourceFiles () |
returns a mutable reference to the source data file More... | |
void | setSourceFiles (const std::vector< SourceFile > &source_files) |
sets the source data file More... | |
const std::vector< ContactPerson > & | getContacts () const |
returns a const reference to the list of contact persons More... | |
std::vector< ContactPerson > & | getContacts () |
returns a mutable reference to the list of contact persons More... | |
void | setContacts (const std::vector< ContactPerson > &contacts) |
sets the list of contact persons More... | |
const Instrument & | getInstrument () const |
returns a const reference to the MS instrument description More... | |
Instrument & | getInstrument () |
returns a mutable reference to the MS instrument description More... | |
void | setInstrument (const Instrument &instrument) |
sets the MS instrument description More... | |
const HPLC & | getHPLC () const |
returns a const reference to the description of the HPLC run More... | |
HPLC & | getHPLC () |
returns a mutable reference to the description of the HPLC run More... | |
void | setHPLC (const HPLC &hplc) |
sets the description of the HPLC run More... | |
const DateTime & | getDateTime () const |
returns the date the experiment was performed More... | |
void | setDateTime (const DateTime &date) |
sets the date the experiment was performed More... | |
const String & | getComment () const |
returns the free-text comment More... | |
void | setComment (const String &comment) |
sets the free-text comment More... | |
const std::vector< ProteinIdentification > & | getProteinIdentifications () const |
returns a const reference to the protein ProteinIdentification vector More... | |
std::vector< ProteinIdentification > & | getProteinIdentifications () |
returns a mutable reference to the protein ProteinIdentification vector More... | |
void | setProteinIdentifications (const std::vector< ProteinIdentification > &protein_identifications) |
sets the protein ProteinIdentification vector More... | |
const String & | getFractionIdentifier () const |
returns fraction identifier More... | |
void | setFractionIdentifier (const String &fraction_identifier) |
sets the fraction identifier More... | |
Public Member Functions inherited from MetaInfoInterface | |
MetaInfoInterface () | |
Constructor. More... | |
MetaInfoInterface (const MetaInfoInterface &rhs) | |
Copy constructor. More... | |
MetaInfoInterface (MetaInfoInterface &&) noexcept | |
Move constructor. More... | |
~MetaInfoInterface () | |
Destructor. More... | |
MetaInfoInterface & | operator= (const MetaInfoInterface &rhs) |
Assignment operator. More... | |
MetaInfoInterface & | operator= (MetaInfoInterface &&) noexcept |
Move assignment operator. More... | |
bool | operator== (const MetaInfoInterface &rhs) const |
Equality operator. More... | |
bool | operator!= (const MetaInfoInterface &rhs) const |
Equality operator. More... | |
const DataValue & | getMetaValue (const String &name, const DataValue &default_value=DataValue::EMPTY) const |
Returns the value corresponding to a string, or a default value (default: DataValue::EMPTY) if not found. More... | |
const DataValue & | getMetaValue (UInt index, const DataValue &default_value=DataValue::EMPTY) const |
Returns the value corresponding to an index, or a default value (default: DataValue::EMPTY) if not found. More... | |
bool | metaValueExists (const String &name) const |
Returns whether an entry with the given name exists. More... | |
bool | metaValueExists (UInt index) const |
Returns whether an entry with the given index exists. More... | |
void | setMetaValue (const String &name, const DataValue &value) |
Sets the DataValue corresponding to a name. More... | |
void | setMetaValue (UInt index, const DataValue &value) |
Sets the DataValue corresponding to an index. More... | |
void | removeMetaValue (const String &name) |
Removes the DataValue corresponding to name if it exists. More... | |
void | removeMetaValue (UInt index) |
Removes the DataValue corresponding to index if it exists. More... | |
void | addMetaValues (const MetaInfoInterface &from) |
function to copy all meta values from one object to this one More... | |
void | getKeys (std::vector< String > &keys) const |
Fills the given vector with a list of all keys for which a value is set. More... | |
void | getKeys (std::vector< UInt > &keys) const |
Fills the given vector with a list of all keys for which a value is set. More... | |
bool | isMetaEmpty () const |
Returns if the MetaInfo is empty. More... | |
void | clearMetaInfo () |
Removes all meta values. More... | |
Public Member Functions inherited from DocumentIdentifier | |
DocumentIdentifier () | |
Default constructor. More... | |
DocumentIdentifier (const DocumentIdentifier &)=default | |
Copy constructor. More... | |
DocumentIdentifier (DocumentIdentifier &&)=default | |
Move constructor. More... | |
virtual | ~DocumentIdentifier () |
Destructor. More... | |
DocumentIdentifier & | operator= (const DocumentIdentifier &)=default |
Assignment operator. More... | |
DocumentIdentifier & | operator= (DocumentIdentifier &&) &=default |
Move assignment operator. More... | |
bool | operator== (const DocumentIdentifier &rhs) const |
Equality operator. More... | |
void | setIdentifier (const String &id) |
set document identifier (e.g. an LSID) More... | |
const String & | getIdentifier () const |
retrieve document identifier (e.g. an LSID) More... | |
void | swap (DocumentIdentifier &from) |
exchange content with from More... | |
void | setLoadedFilePath (const String &file_name) |
set the file_name_ according to absolute path of the file loaded from preferably done whilst loading More... | |
const String & | getLoadedFilePath () const |
get the file_name_ which is the absolute path to the file loaded from More... | |
void | setLoadedFileType (const String &file_name) |
set the file_type according to the type of the file loaded from (see FileHandler::Type) preferably done whilst loading More... | |
const FileTypes::Type & | getLoadedFileType () const |
get the file_type (e.g. featureXML, consensusXML, mzData, mzXML, mzML, ...) of the file loaded from More... | |
Delegations of calls to the vector of MSSpectra | |
typedef Base::value_type | value_type |
typedef Base::iterator | iterator |
typedef Base::const_iterator | const_iterator |
Size | size () const |
void | resize (Size s) |
bool | empty () const |
void | reserve (Size s) |
SpectrumType & | operator[] (Size n) |
const SpectrumType & | operator[] (Size n) const |
Iterator | begin () |
ConstIterator | begin () const |
Iterator | end () |
ConstIterator | end () const |
void | reserveSpaceSpectra (Size s) |
void | reserveSpaceChromatograms (Size s) |
MSExperiment () | |
Constructor. More... | |
MSExperiment (const MSExperiment &source) | |
Copy constructor. More... | |
MSExperiment (MSExperiment &&)=default | |
Move constructor. More... | |
MSExperiment & | operator= (const MSExperiment &source) |
Assignment operator. More... | |
MSExperiment & | operator= (MSExperiment &&) &=default |
Move assignment operator. More... | |
MSExperiment & | operator= (const ExperimentalSettings &source) |
Assignment operator. More... | |
bool | operator== (const MSExperiment &rhs) const |
Equality operator. More... | |
bool | operator!= (const MSExperiment &rhs) const |
Equality operator. More... | |
Easy Access interface | |
std::vector< UInt > | ms_levels_ |
MS levels of the data. More... | |
UInt64 | total_size_ |
Number of all data points. More... | |
std::vector< MSChromatogram > | chromatograms_ |
chromatograms More... | |
std::vector< SpectrumType > | spectra_ |
spectra More... | |
MSChromatogram & | getChromatogram (Size id) |
returns a single chromatogram More... | |
MSSpectrum & | getSpectrum (Size id) |
returns a single spectrum More... | |
Size | getNrSpectra () const |
get the total number of spectra available More... | |
Size | getNrChromatograms () const |
get the total number of chromatograms available More... | |
const MSChromatogram | getTIC (float rt_bin_size=0) const |
Compute Total Ion Count per MS1 spectrum and applies the resampling algorithm, if a bin size in RT seconds greater than 0 is given. More... | |
void | clear (bool clear_meta_data) |
Clears all data and meta data. More... | |
bool | containsScanOfLevel (size_t ms_level) const |
returns true if at least one of the spectra has the specified level More... | |
bool | hasZeroIntensities (size_t ms_level) const |
returns true if any MS spectra of the specified level contain at least one peak with intensity of 0.0 More... | |
SpectrumType * | createSpec_ (PeakType::CoordinateType rt) |
SpectrumType * | createSpec_ (PeakType::CoordinateType rt, const StringList &metadata_names) |
Additional Inherited Members | |
Static Public Member Functions inherited from MetaInfoInterface | |
static MetaInfoRegistry & | metaRegistry () |
Returns a reference to the MetaInfoRegistry. More... | |
Protected Member Functions inherited from RangeManager< 2 > | |
void | updateRanges_ (const PeakIteratorType &begin, const PeakIteratorType &end) |
Updates the range using data points in the iterator range. More... | |
Protected Member Functions inherited from MetaInfoInterface | |
void | createIfNotExists_ () |
Creates the MetaInfo object if it does not exist. More... | |
Protected Attributes inherited from RangeManager< 2 > | |
IntensityRangeType | int_range_ |
Intensity range (1-dimensional) More... | |
PositionRangeType | pos_range_ |
Position range (D-dimensional) More... | |
Protected Attributes inherited from ExperimentalSettings | |
Sample | sample_ |
std::vector< SourceFile > | source_files_ |
std::vector< ContactPerson > | contacts_ |
Instrument | instrument_ |
HPLC | hplc_ |
DateTime | datetime_ |
String | comment_ |
std::vector< ProteinIdentification > | protein_identifications_ |
String | fraction_identifier_ |
Protected Attributes inherited from MetaInfoInterface | |
MetaInfo * | meta_ |
Pointer to the MetaInfo object (0 by default) More... | |
Protected Attributes inherited from DocumentIdentifier | |
String | id_ |
the ID (e.g. LSID) More... | |
String | file_path_ |
the path to the loaded file More... | |
FileTypes::Type | file_type_ |
the type of the loaded file More... | |
In-Memory representation of a mass spectrometry experiment.
Contains the data and metadata of an experiment performed with an MS (or HPLC and MS). This representation of an MS experiment is organized as list of spectra and chromatograms and provides an in-memory representation of popular mass-spectrometric file formats such as mzXML or mzML. The meta-data associated with an experiment is contained in ExperimentalSettings (by inheritance) while the raw data (as well as spectra and chromatogram level meta data) is stored in objects of type MSSpectrum and MSChromatogram, which are accessible through the getSpectrum and getChromatogram functions.
Be careful 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!
typedef Internal::AreaIterator<PeakT, PeakT&, PeakT*, Iterator, SpectrumType::Iterator> AreaIterator |
Mutable area iterator type (for traversal of a rectangular subset of the peaks)
typedef std::vector<SpectrumType> Base |
STL base class type.
typedef ChromatogramPeak ChromatogramPeakT |
Chromatogram peak type.
typedef MSChromatogram ChromatogramType |
Chromatogram type.
typedef Base::const_iterator const_iterator |
typedef Internal::AreaIterator<const PeakT, const PeakT&, const PeakT*, ConstIterator, SpectrumType::ConstIterator> ConstAreaIterator |
Immutable area iterator type (for traversal of a rectangular subset of the peaks)
typedef std::vector<SpectrumType>::const_iterator ConstIterator |
Non-mutable iterator.
Coordinate type of peak positions.
typedef PeakType::IntensityType IntensityType |
Intensity type of peaks.
typedef std::vector<SpectrumType>::iterator Iterator |
Mutable iterator.
typedef Base::iterator iterator |
typedef RangeManager<2> RangeManagerType |
RangeManager type.
typedef MSSpectrum SpectrumType |
Spectrum Type.
typedef Base::value_type value_type |
MSExperiment | ( | ) |
Constructor.
MSExperiment | ( | const MSExperiment & | source | ) |
Copy constructor.
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default |
Move constructor.
void addChromatogram | ( | const MSChromatogram & | chromatogram | ) |
adds a chromatogram to the list
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void addSpectrum | ( | const MSSpectrum & | spectrum | ) |
adds a spectrum to the list
Referenced by SpectraMerger::averageCentroidSpectra_(), SpectraMerger::averageProfileSpectra_(), TOPPViewBase::copyLayer(), MS2File::load(), MascotInfile::load(), MascotGenericFile::load(), DTA2DFile::load(), SpectraMerger::mergeSpectra_(), OPXLDataStructs::PreprocessedPairSpectra::PreprocessedPairSpectra(), and TOPPViewBase::showSpectrumGenerationDialog().
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AreaIterator areaBegin | ( | CoordinateType | min_rt, |
CoordinateType | max_rt, | ||
CoordinateType | min_mz, | ||
CoordinateType | max_mz | ||
) |
Returns an area iterator for area
.
ConstAreaIterator areaBeginConst | ( | CoordinateType | min_rt, |
CoordinateType | max_rt, | ||
CoordinateType | min_mz, | ||
CoordinateType | max_mz | ||
) | const |
Returns a non-mutable area iterator for area
.
AreaIterator areaEnd | ( | ) |
Returns an invalid area iterator marking the end of an area.
ConstAreaIterator areaEndConst | ( | ) | const |
Returns an non-mutable invalid area iterator marking the end of an area.
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inline |
Referenced by KDTreeFeatureMaps::addMaps(), SpectraMerger::average(), SpectraMerger::averageCentroidSpectra_(), SpectraMerger::averageProfileSpectra_(), IsotopeWaveletTransform< PeakType >::extendBox_(), IDFilter::filterHitsByScore(), MapAlignmentAlgorithmIdentification::getRetentionTimes_(), IDFilter::keepHitsMatchingProteins(), IDFilter::keepNBestHits(), NucleicAcidSearchEngine::main_(), SpectraMerger::mergeSpectra_(), SpectraMerger::mergeSpectraBlockWise(), TwoDOptimization::optimize(), and DTA2DFile::store().
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inline |
void clear | ( | bool | clear_meta_data | ) |
Clears all data and meta data.
clear_meta_data | If true, all meta data is cleared in addition to the data. |
Referenced by SpectraMerger::mergeSpectra_(), PeakPickerIterative::pickExperiment(), and IsotopeWaveletTransform< PeakType >::updateBoxStates().
bool clearMetaDataArrays | ( | ) |
Clears the meta data arrays of all contained spectra (float, integer and string arrays)
bool containsScanOfLevel | ( | size_t | ms_level | ) | const |
returns true if at least one of the spectra has the specified level
Referenced by TOPPViewBase::estimateNoiseFromRandomMS1Scans().
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private |
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private |
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inline |
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inline |
Referenced by KDTreeFeatureMaps::addMaps(), SpectraMerger::average(), SpectraMerger::averageCentroidSpectra_(), SpectraMerger::averageProfileSpectra_(), TOPPViewBase::estimateNoiseFromRandomMS1Scans(), IDFilter::filterHitsByScore(), MapAlignmentAlgorithmIdentification::getRetentionTimes_(), IDFilter::keepHitsMatchingProteins(), IDFilter::keepNBestHits(), NucleicAcidSearchEngine::main_(), SpectraMerger::mergeSpectra_(), SpectraMerger::mergeSpectraBlockWise(), TwoDOptimization::optimize(), and DTA2DFile::store().
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inline |
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Reads out a 2D Spectrum.
Container can be a PeakArray or an STL container of peaks which supports push_back(), end() and back()
MSChromatogram& getChromatogram | ( | Size | id | ) |
returns a single chromatogram
Referenced by GaussFilter::filterExperiment(), and SavitzkyGolayFilter::filterExperiment().
std::vector<MSChromatogram>& getChromatograms | ( | ) |
returns the chromatogram list (mutable)
const std::vector<MSChromatogram>& getChromatograms | ( | ) | const |
returns the chromatogram list
Referenced by GaussFilter::filterExperiment(), and SavitzkyGolayFilter::filterExperiment().
const AreaType& getDataRange | ( | ) | const |
Returns RT and m/z range the data lies in.
RT is dimension 0, m/z is dimension 1
ExperimentalSettings& getExperimentalSettings | ( | ) |
returns the meta information of this experiment (mutable access)
const ExperimentalSettings& getExperimentalSettings | ( | ) | const |
returns the meta information of this experiment (const access)
Referenced by XMassFile::importExperimentalSettings().
CoordinateType getMaxMZ | ( | ) | const |
returns the maximal m/z value
CoordinateType getMaxRT | ( | ) | const |
returns the maximal retention time value
CoordinateType getMinMZ | ( | ) | const |
returns the minimal m/z value
CoordinateType getMinRT | ( | ) | const |
returns the minimal retention time value
const std::vector<UInt>& getMSLevels | ( | ) | const |
returns an array of MS levels
Size getNrChromatograms | ( | ) | const |
get the total number of chromatograms available
Size getNrSpectra | ( | ) | const |
get the total number of spectra available
Referenced by NucleicAcidSearchEngine::main_().
ConstIterator getPrecursorSpectrum | ( | ConstIterator | iterator | ) | const |
Returns the precursor spectrum of the scan pointed to by iterator
.
If there is no precursor scan the past-the-end iterator is returned.
void getPrimaryMSRunPath | ( | StringList & | toFill | ) | const |
get the file path to the first MS run
Referenced by NucleicAcidSearchEngine::main_().
UInt64 getSize | ( | ) | const |
returns the total number of peaks
std::vector<MSSpectrum>& getSpectra | ( | ) |
returns the spectrum list (mutable)
const std::vector<MSSpectrum>& getSpectra | ( | ) | const |
returns the spectrum list
Referenced by SpectraMerger::mergeSpectra_().
MSSpectrum& getSpectrum | ( | Size | id | ) |
returns a single spectrum
const MSChromatogram getTIC | ( | float | rt_bin_size = 0 | ) | const |
Compute Total Ion Count per MS1 spectrum and applies the resampling algorithm, if a bin size in RT seconds greater than 0 is given.
By default, each MS1 spectrum's intensity just gets summed up. Regular RT bins can be obtained by specifying rt_bin_size
.
bin_size | RT bin size in seconds |
Referenced by DTA2DFile::storeTIC().
bool hasZeroIntensities | ( | size_t | ms_level | ) | const |
returns true if any MS spectra of the specified level contain at least one peak with intensity of 0.0
bool isSorted | ( | bool | check_mz = true | ) | const |
Checks if all spectra are sorted with respect to ascending RT.
check_mz | if true, checks if all peaks are sorted with respect to ascending m/z |
bool operator!= | ( | const MSExperiment & | rhs | ) | const |
Equality operator.
MSExperiment& operator= | ( | const ExperimentalSettings & | source | ) |
Assignment operator.
MSExperiment& operator= | ( | const MSExperiment & | source | ) |
Assignment operator.
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default |
Move assignment operator.
bool operator== | ( | const MSExperiment & | rhs | ) | const |
Equality operator.
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inline |
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void reserveSpaceChromatograms | ( | Size | s | ) |
void reserveSpaceSpectra | ( | Size | s | ) |
void reset | ( | ) |
Resets all internal values.
Referenced by InspectOutfile::getExperiment(), MS2File::load(), MascotInfile::load(), MascotGenericFile::load(), and DTA2DFile::load().
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Referenced by PeakPickerIterative::pickExperiment().
Iterator RTBegin | ( | CoordinateType | rt | ) |
Fast search for spectrum range begin.
ConstIterator RTBegin | ( | CoordinateType | rt | ) | const |
Fast search for spectrum range begin.
Returns the first scan which has equal or higher (>=) RT than rt
.
Referenced by TwoDOptimization::getRegionEndpoints_().
Iterator RTEnd | ( | CoordinateType | rt | ) |
Fast search for spectrum range end (returns the past-the-end iterator)
ConstIterator RTEnd | ( | CoordinateType | rt | ) | const |
Fast search for spectrum range end (returns the past-the-end iterator)
Returns the first scan which has higher (>) RT than rt
.
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Assignment of a data container with RT and MZ to an MSExperiment.
Fill MSExperiment with data. Note that all data present (including meta-data) will be deleted prior to adding new data!
container | An iterable type whose elements support getRT(), getMZ() and getIntensity() |
Exception::Precondition | is thrown if the container is not sorted according to retention time (in debug AND release mode) |
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Assignment of a data container with RT and MZ to an MSExperiment.
Fill MSExperiment with data. Note that all data present (including meta-data) will be deleted prior to adding new data!
container | An iterable type whose elements support getRT(), getMZ() and getIntensity() |
add_mass_traces | If true, each container element is searched for the metavalue "num_of_masstraces". If found, "masstrace_intensity" (X>=0) meta values are added as data points (with 13C spacing). This is useful for, e.g., FF-Metabo output. Note that the actual feature will NOT be added if mass traces are found (since MT0 is usually identical) |
Exception::Precondition | is thrown if the container is not sorted according to retention time (in debug AND release mode) OR a "masstrace_intensity" value is expected but not found |
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Assignment of a data container with RT and MZ to an MSExperiment.
Fill MSExperiment with data. Note that all data present (including meta-data) will be deleted prior to adding new data!
container | An iterable type whose elements support getRT(), getMZ() and getIntensity() |
store_metadata_names | [MetaInfoInterface input only] Names of metadata arrays which should be created; data is filled from the metainfointerface of each element of the input container. Currently, only float data is supported! |
Exception::Precondition | is thrown if the container is not sorted according to retention time (in debug AND release mode) |
void setChromatograms | ( | const std::vector< MSChromatogram > & | chromatograms | ) |
sets the chromatogram list
void setSpectra | ( | const std::vector< MSSpectrum > & | spectra | ) |
sets the spectrum list
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Referenced by SpectrumCanvas::addDataProcessing_(), OpenSwathHelper::checkSwathMapAndSelectTransitions(), OpenMS::collapseIMSpectrum(), OpenMS::determineIMType(), TOPPViewBase::estimateNoiseFromRandomMS1Scans(), GaussFilter::filterExperiment(), SavitzkyGolayFilter::filterExperiment(), MorphologicalFilter::filterExperiment(), TwoDOptimization::getRegionEndpoints_(), TOPPViewBase::hasPeptideIdentifications(), NucleicAcidSearchEngine::main_(), IDMapper::mapPrecursorsToIdentifications(), IsotopeWaveletTransform< PeakType >::mapSeeds2Features(), SpectraMerger::mergeSpectra_(), SpectraMerger::mergeSpectraPrecursors(), TwoDOptimization::optimize(), PeakPickerIterative::pickExperiment(), NucleicAcidSearchEngine::preprocessSpectra_(), LinearResampler::rasterExperiment(), DTA2DFile::store(), DTA2DFile::storeTIC(), and IsotopeWaveletTransform< PeakType >::updateBoxStates().
void sortChromatograms | ( | bool | sort_rt = true | ) |
Sorts the data points of the chromatograms by m/z.
sort_rt | if true, chromatograms are sorted by rt position as well |
void sortSpectra | ( | bool | sort_mz = true | ) |
Sorts the data points by retention time.
sort_mz | if true, spectra are sorted by m/z position as well |
Referenced by SpectraMerger::average(), NucleicAcidSearchEngine::main_(), SpectraMerger::mergeSpectraBlockWise(), SpectraMerger::mergeSpectraPrecursors(), and NucleicAcidSearchEngine::preprocessSpectra_().
void swap | ( | MSExperiment & | from | ) |
Swaps the content of this map with the content of from
.
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Updates minimum and maximum position/intensity.
This method is usually implemented by calling clearRanges() and updateRanges_().
Implements RangeManager< 2 >.
void updateRanges | ( | Int | ms_level | ) |
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) |
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chromatograms
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MS levels of the data.
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spectra
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Number of all data points.