Representation of a mass spectrometry experiment. More...
#include <OpenMS/KERNEL/MSExperiment.h>
 
  
 | Public Types | |
| 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 | 
| Intenstiy type of peaks.  More... | |
| typedef RangeManager< 2 > | RangeManagerType | 
| RangeManager type.  More... | |
| typedef MSSpectrum< PeakType > | SpectrumType | 
| Spectrum Type.  More... | |
| typedef MSChromatogram < ChromatogramPeakType > | 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, typename 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, typename 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 | |
| void | reserveSpaceSpectra (Size s) | 
| void | reserveSpaceChromatograms (Size s) | 
| MSExperiment () | |
| Constructor.  More... | |
| MSExperiment (const MSExperiment &source) | |
| Copy constructor.  More... | |
| MSExperiment & | operator= (const MSExperiment &source) | 
| 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... | |
| 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... | |
| 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< PeakT > > &spectra) | 
| sets the spectra list  More... | |
| void | addSpectrum (const MSSpectrum< PeakT > &spectrum) | 
| adds a spectra to the list  More... | |
| const std::vector< MSSpectrum < PeakT > > & | getSpectra () const | 
| returns the spectra list  More... | |
| std::vector< MSSpectrum< PeakT > > & | getSpectra () | 
| returns the spectra list  More... | |
| void | setChromatograms (const std::vector< MSChromatogram< ChromatogramPeakType > > &chromatograms) | 
| sets the chromatogram list  More... | |
| void | addChromatogram (const MSChromatogram< ChromatogramPeakType > &chromatogram) | 
| adds a chromatogram to the list  More... | |
| const std::vector < MSChromatogram < ChromatogramPeakType > > & | getChromatograms () const | 
| returns the chromatogram list  More... | |
| MSChromatogram < ChromatogramPeakType > & | getChromatogram (Size id) | 
| returns a single chromatogram  More... | |
| const MSChromatogram < ChromatogramPeakType > | getTIC () const | 
| returns the total ion chromatogram (TIC)  More... | |
| void | clear (bool clear_meta_data) | 
| Clears all data and meta data.  More... | |
| 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 &cont) | 
| Assignment of a 2D spectrum to 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 | |
| 
 | |
| virtual void | updateRanges () | 
| 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... | |
|  Public Member Functions inherited from RangeManager< 2 > | |
| RangeManager () | |
| Default constructor.  More... | |
| RangeManager (const RangeManager &rhs) | |
| Copy 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... | |
| DoubleReal | getMinInt () const | 
| Returns the minimum intensity.  More... | |
| DoubleReal | getMaxInt () const | 
| Returns the maximum intensity.  More... | |
| void | clearRanges () | 
| Resets the ranges.  More... | |
|  Public Member Functions inherited from ExperimentalSettings | |
| ExperimentalSettings () | |
| Constructor.  More... | |
| ExperimentalSettings (const ExperimentalSettings &source) | |
| Copy constructor.  More... | |
| ~ExperimentalSettings () | |
| Destructor.  More... | |
| ExperimentalSettings & | operator= (const ExperimentalSettings &source) | 
| 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 () | |
| destructor  More... | |
| MetaInfoInterface & | operator= (const MetaInfoInterface &rhs) | 
| 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 | 
| returns the value corresponding to a string  More... | |
| const DataValue & | getMetaValue (UInt index) const | 
| returns the value corresponding to an index  More... | |
| bool | metaValueExists (const String &name) const | 
| returns if this MetaInfo is set  More... | |
| bool | metaValueExists (UInt index) const | 
| returns if this MetaInfo is set  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 nameif it exists.  More... | |
| void | removeMetaValue (UInt index) | 
| Removes the DataValue corresponding to indexif it exists.  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 &source) | |
| Copy constructor.  More... | |
| DocumentIdentifier & | operator= (const DocumentIdentifier &source) | 
| Assignment operator.  More... | |
| bool | operator== (const DocumentIdentifier &rhs) const | 
| Equality operator.  More... | |
| virtual | ~DocumentIdentifier () | 
| destructor  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 fromMore... | |
| 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... | |
|  Public Member Functions inherited from PersistentObject | |
| PersistentObject () | |
| Default constructor.  More... | |
| virtual | ~PersistentObject () | 
| Destructor.  More... | |
| PersistentObject & | operator= (const PersistentObject &rhs) | 
| Assignment operator.  More... | |
| const UID & | getPersistenceId () const | 
| Returns the persistence id.  More... | |
| void | setPersistenceId (const UID &persistence_id) | 
| Sets the persistence id.  More... | |
| void | clearId (bool deep=true) | 
| Clears the persistence id.  More... | |
| Protected Member Functions | |
| virtual void | clearChildIds_ () | 
| Clears the persistence id of all sub-objects.  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 | |
| std::vector< UInt > | ms_levels_ | 
| MS levels of the data.  More... | |
| UInt64 | total_size_ | 
| Number of all data points.  More... | |
| std::vector< MSChromatogram < ChromatogramPeakType > > | chromatograms_ | 
| chromatograms  More... | |
| std::vector< SpectrumType > | spectra_ | 
| spectra  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... | |
|  Protected Attributes inherited from PersistentObject | |
| UID | persistence_id_ | 
| A persistence id used to refer the data back to the source.  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 | 
| Additional Inherited Members | |
|  Static Public Member Functions inherited from MetaInfoInterface | |
| static MetaInfoRegistry & | metaRegistry () | 
| retuns a reference to the MetaInfoRegistry  More... | |
Representation of a mass spectrometry experiment.
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!
| 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 std::vector<SpectrumType> Base | 
STL base class type.
| typedef ChromatogramPeakT ChromatogramPeakType | 
Chromatogram peak type.
Chromatogram type.
| typedef Base::const_iterator const_iterator | 
| 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 std::vector<SpectrumType>::const_iterator ConstIterator | 
Non-mutable iterator.
Coordinate type of peak positions.
| typedef PeakType::IntensityType IntensityType | 
Intenstiy type of peaks.
| typedef std::vector<SpectrumType>::iterator Iterator | 
Mutable iterator.
| typedef Base::iterator iterator | 
| typedef RangeManager<2> RangeManagerType | 
RangeManager type.
| typedef MSSpectrum<PeakType> SpectrumType | 
Spectrum Type.
| typedef Base::value_type value_type | 
| 
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Constructor.
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Copy constructor.
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adds a chromatogram to the list
Referenced by PeakPickerHiRes::pickExperiment().
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adds a spectra to the list
Referenced by IDEvaluationBase::addSearchFile(), TOPPViewBase::copyLayer(), TOPPRNPxl::main_(), OfflinePrecursorIonSelection::makePrecursorSelectionForKnownLCMSMap(), CachedmzML::readMemdump(), and TOPPViewBase::showSpectrumGenerationDialog().
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Returns an area iterator for area. 
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Returns a non-mutable area iterator for area. 
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
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Returns an invalid area iterator marking the end of an area.
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Returns an non-mutable invalid area iterator marking the end of an area.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
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Referenced by TOPPViewBase::annotateWithID(), InternalCalibration::calibrateMapGlobally(), IsotopeWaveletTransform< PeakType >::extendBox_(), OfflinePrecursorIonSelection::getMassRanges(), TwoDOptimization::getRegionEndpoints_(), TOPPRNPxl::main_(), OfflinePrecursorIonSelection::makePrecursorSelectionForKnownLCMSMap(), TwoDOptimization::optimize(), TwoDOptimization::optimizeRegionsScanwise_(), and FeatureFinder::run().
| 
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| 
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Clears all data and meta data.
| clear_meta_data | If true, all meta data is cleared in addition to the data. | 
Referenced by PeakPickerHiRes::pickExperiment(), IsotopeWaveletTransform< PeakType >::updateBoxStates(), and CachedmzML::writeMetadata().
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Clears the persistence id of all sub-objects.
Implements PersistentObject.
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Clears the meta data arrays of all contained spectra (float, integer and string arrays)
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Referenced by IDMapper::annotate(), InternalCalibration::calibrateMapGlobally(), InternalCalibration::calibrateMapSpectrumwise(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findIsotope_(), OfflinePrecursorIonSelection::getMassRanges(), TOPPViewBase::hasPeptideIdentifications(), TwoDOptimization::optimize(), and FeatureFinder::run().
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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()
Referenced by ConsensusMap::convert().
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returns a single chromatogram
Referenced by GaussFilter::filterExperiment(), and SavitzkyGolayFilter::filterExperiment().
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returns the chromatogram list
Referenced by TOPPBase::addDataProcessing_(), GaussFilter::filterExperiment(), SavitzkyGolayFilter::filterExperiment(), PeakPickerHiRes::pickExperiment(), FeatureFinder::run(), FeatureFinderAlgorithmMRM< PeakType, FeatureType >::run(), FileHandler::storeExperiment(), and CachedmzML::writeMetadata().
| 
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Returns RT and m/z range the data lies in.
RT is dimension 0, m/z is dimension 1
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returns the meta information of this experiment (const access)
Referenced by XMassFile::importExperimentalSettings().
| 
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returns the meta information of this experiment (mutable access)
| 
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returns the maximal m/z value
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
| 
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returns the maximal retention time value
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
| 
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returns the minimal m/z value
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensityScore_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
| 
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returns the minimal retention time value
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensityScore_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
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returns an array of MS levels
Referenced by FeatureFinder::run().
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Returns the precursor spectrum of the scan pointed to by iterator. 
If there is no precursor scan the past-the-end iterator is returned.
| 
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returns the total number of peaks
Referenced by ConsensusMap::convert(), and FeatureFinder::run().
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returns the spectra list
Referenced by MSExperiment< SimPointType >::swap().
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returns the spectra list
| 
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returns the total ion chromatogram (TIC)
| 
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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 | 
Referenced by MSExperiment< SimPointType >::areaBeginConst(), MSExperiment< SimPointType >::isSorted(), and FeatureFinder::run().
| 
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Equality operator.
| 
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Assignment operator.
| 
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Assignment operator.
| 
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Equality operator.
Referenced by MSExperiment< SimPointType >::operator!=().
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Referenced by CachedmzML::readMemdump().
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Resets all internal values.
Referenced by InspectOutfile::getExperiment(), and FileHandler::loadExperiment().
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Fast search for spectrum range begin.
Returns the first scan which has equal or higher (>=) RT than rt.
Referenced by MSExperiment< SimPointType >::areaBeginConst(), InternalCalibration::calibrateMapGlobally(), OfflinePrecursorIonSelection::getMassRanges(), TwoDOptimization::getRegionEndpoints_(), OfflinePrecursorIonSelection::makePrecursorSelectionForKnownLCMSMap(), and FeatureFinder::run().
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Fast search for spectrum range begin.
| 
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Fast search for spectrum range end (returns the past-the-end iterator)
Returns the first scan which has higher (>) RT than rt.
Referenced by MSExperiment< SimPointType >::areaBeginConst(), and OfflinePrecursorIonSelection::makePrecursorSelectionForKnownLCMSMap().
| 
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Fast search for spectrum range end (returns the past-the-end iterator)
| 
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Assignment of a 2D spectrum to MSExperiment.
Container can be a PeakArray or an STL container of peaks.
| Exception::Precondition | is thrown if the container is not sorted according to retention time (not only in debug mode) | 
| 
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sets the chromatogram list
Referenced by TOPPBase::addDataProcessing_(), CachedmzML::readMemdump(), and CachedmzML::writeMetadata().
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sets the spectra list
| 
 | inline | 
Referenced by TOPPBase::addDataProcessing_(), SpectrumCanvas::addDataProcessing_(), IDMapper::annotate(), OfflinePrecursorIonSelection::calculateXICs_(), TOFCalibration::calibrate(), InternalCalibration::calibrateMapGlobally(), InternalCalibration::calibrateMapSpectrumwise(), OpenSwathHelper::checkSwathMapAndSelectTransitions(), TOPPViewBase::containsMS1Scans(), TOPPViewBase::countMS1Zeros(), PSLPFormulation::createAndSolveCombinedLPForKnownLCMSMapFeatureBased(), PSLPFormulation::createAndSolveILPForKnownLCMSMapFeatureBased(), TOPPViewBase::estimateNoiseFromRandomMS1Scans(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTrace_(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTraces_(), GaussFilter::filterExperiment(), SavitzkyGolayFilter::filterExperiment(), MorphologicalFilter::filterExperiment(), IDFilter::filterIdentificationsByBestNHits(), IDFilter::filterIdentificationsByProteins(), IDFilter::filterIdentificationsByScores(), IDFilter::filterIdentificationsByThresholds(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findIsotope_(), OfflinePrecursorIonSelection::getMassRanges(), FeaFiModule< PeakType, FeatureType >::getNextMz(), FeaFiModule< PeakType, FeatureType >::getNextRt(), FeaFiModule< PeakType, FeatureType >::getPeakIntensity(), FeaFiModule< PeakType, FeatureType >::getPeakMz(), FeaFiModule< PeakType, FeatureType >::getPeakRt(), FeaFiModule< PeakType, FeatureType >::getPrevMz(), FeaFiModule< PeakType, FeatureType >::getPrevRt(), TwoDOptimization::getRegionEndpoints_(), TOPPViewBase::hasPeptideIdentifications(), TOPPRNPxl::main_(), OfflinePrecursorIonSelection::makePrecursorSelectionForKnownLCMSMap(), IsotopeWaveletTransform< PeakType >::mapSeeds2Features(), TwoDOptimization::optimize(), PeakPickerHiRes::pickExperiment(), LinearResampler::rasterExperiment(), FeatureFinder::run(), FeatureFinderAlgorithmMRM< PeakType, FeatureType >::run(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::run(), FeatureFinderAlgorithmSH< PeakType, FeatureType >::run(), IsotopeWaveletTransform< PeakType >::updateBoxStates(), and CachedmzML::writeMetadata().
| 
 | inline | 
Sorts the data points of the chromatograms by m/z.
| sort_rt | if true, chromatograms are sorted by rt position as well | 
Referenced by FeatureFinder::run().
| 
 | inline | 
Sorts the data points by retention time.
| sort_mz | if true, spectra are sorted by m/z position as well | 
Referenced by FeatureFinder::run().
| 
 | inline | 
Swaps the content of this map with the content of from. 
| 
 | inlinevirtual | 
Updates minimum and maximum position/intensity.
This method is usually implemented by calling clearRanges() and updateRanges_().
Implements RangeManager< 2 >.
Referenced by ConsensusMap::convert(), and MSExperiment< SimPointType >::updateRanges().
| 
 | 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) | 
| 
 | protected | 
chromatograms
Referenced by MSExperiment< SimPointType >::addChromatogram(), MSExperiment< SimPointType >::clear(), MSExperiment< SimPointType >::getChromatogram(), MSExperiment< SimPointType >::getChromatograms(), MSExperiment< SimPointType >::operator=(), MSExperiment< SimPointType >::operator==(), MSExperiment< SimPointType >::reserveSpaceChromatograms(), MSExperiment< SimPointType >::setChromatograms(), MSExperiment< SimPointType >::sortChromatograms(), MSExperiment< SimPointType >::swap(), and MSExperiment< SimPointType >::updateRanges().
| 
 | protected | 
| 
 | protected | 
spectra
Referenced by MSExperiment< SimPointType >::addSpectrum(), MSExperiment< SimPointType >::areaBeginConst(), MSExperiment< SimPointType >::begin(), MSExperiment< SimPointType >::clear(), MSExperiment< SimPointType >::clearChildIds_(), MSExperiment< SimPointType >::clearMetaDataArrays(), MSExperiment< SimPointType >::empty(), MSExperiment< SimPointType >::end(), MSExperiment< SimPointType >::get2DData(), MSExperiment< SimPointType >::getPrecursorSpectrum(), MSExperiment< SimPointType >::getSpectra(), MSExperiment< SimPointType >::getTIC(), MSExperiment< SimPointType >::isSorted(), MSExperiment< SimPointType >::operator=(), MSExperiment< SimPointType >::operator==(), MSExperiment< SimPointType >::operator[](), MSExperiment< SimPointType >::reserve(), MSExperiment< SimPointType >::reserveSpaceSpectra(), MSExperiment< SimPointType >::reset(), MSExperiment< SimPointType >::resize(), MSExperiment< SimPointType >::RTBegin(), MSExperiment< SimPointType >::RTEnd(), MSExperiment< SimPointType >::set2DData(), MSExperiment< SimPointType >::setSpectra(), MSExperiment< SimPointType >::size(), MSExperiment< SimPointType >::sortSpectra(), MSExperiment< SimPointType >::swap(), and MSExperiment< SimPointType >::updateRanges().
| 
 | protected | 
Number of all data points.
Referenced by MSExperiment< SimPointType >::clear(), MSExperiment< SimPointType >::getSize(), MSExperiment< SimPointType >::operator=(), MSExperiment< SimPointType >::swap(), and MSExperiment< SimPointType >::updateRanges().
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:32 using doxygen 1.8.5 |