The representation of a chromatogram. More...
#include <OpenMS/KERNEL/MSChromatogram.h>
 
  
 | Classes | |
| class | FloatDataArray | 
| Float data array class.  More... | |
| class | IntegerDataArray | 
| Float data array class.  More... | |
| struct | MZLess | 
| Comparator for the retention time.  More... | |
| class | StringDataArray | 
| String data array class.  More... | |
| Public Types | |
| Base type definitions | |
| Peak type | |
| typedef PeakT | PeakType | 
| typedef PeakType::CoordinateType | CoordinateType | 
| Coordinate (RT) type.  More... | |
| typedef std::vector< PeakType > | ContainerType | 
| Chromatogram base type.  More... | |
| typedef std::vector < FloatDataArray > | FloatDataArrays | 
| Float data array vector type.  More... | |
| typedef std::vector < StringDataArray > | StringDataArrays | 
| String data array vector type.  More... | |
| typedef std::vector < IntegerDataArray > | IntegerDataArrays | 
| Integer data array vector type.  More... | |
| Peak container iterator type definitions | |
| typedef ContainerType::iterator | Iterator | 
| Mutable iterator.  More... | |
| typedef ContainerType::const_iterator | ConstIterator | 
| Non-mutable iterator.  More... | |
| typedef ContainerType::reverse_iterator | ReverseIterator | 
| Mutable reverse iterator.  More... | |
| typedef ContainerType::const_reverse_iterator | ConstReverseIterator | 
| Non-mutable reverse iterator.  More... | |
|  Public Types inherited from RangeManager< 1 > | |
| 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 Types inherited from ChromatogramSettings | |
| enum | ChromatogramType { MASS_CHROMATOGRAM = 0, TOTAL_ION_CURRENT_CHROMATOGRAM, SELECTED_ION_CURRENT_CHROMATOGRAM, BASEPEAK_CHROMATOGRAM, SELECTED_ION_MONITORING_CHROMATOGRAM, SELECTED_REACTION_MONITORING_CHROMATOGRAM, ELECTROMAGNETIC_RADIATION_CHROMATOGRAM, ABSORPTION_CHROMATOGRAM, EMISSION_CHROMATOGRAM, SIZE_OF_CHROMATOGRAM_TYPE } | 
| Public Member Functions | |
| MSChromatogram () | |
| Constructor.  More... | |
| MSChromatogram (const MSChromatogram &source) | |
| Copy constructor.  More... | |
| virtual | ~MSChromatogram () | 
| Destructor.  More... | |
| MSChromatogram & | operator= (const MSChromatogram &source) | 
| Assignment operator.  More... | |
| bool | operator== (const MSChromatogram &rhs) const | 
| Equality operator.  More... | |
| bool | operator!= (const MSChromatogram &rhs) const | 
| Equality operator.  More... | |
| virtual void | updateRanges () | 
| Updates minimum and maximum position/intensity.  More... | |
| DoubleReal | getMZ () const | 
| returns the mz of the product entry, makes sense especially for MRM scans  More... | |
| Accessors for meta information | |
| Returns the name | |
| const String & | getName () const | 
| void | setName (const String &name) | 
| Sets the name.  More... | |
| Peak data array methods | |
| These methods are used to annotate each peak in a chromatogram with meta information. It is an intermediate way between storing the information in the peak's MetaInfoInterface and deriving a new peak type with members for this information. These statements should help you chose which approach to use 
 | |
| const FloatDataArrays & | getFloatDataArrays () const | 
| FloatDataArrays & | getFloatDataArrays () | 
| Returns a mutable reference to the float meta data arrays.  More... | |
| const StringDataArrays & | getStringDataArrays () const | 
| Returns a const reference to the string meta data arrays.  More... | |
| StringDataArrays & | getStringDataArrays () | 
| Returns a mutable reference to the string meta data arrays.  More... | |
| const IntegerDataArrays & | getIntegerDataArrays () const | 
| Returns a const reference to the integer meta data arrays.  More... | |
| IntegerDataArrays & | getIntegerDataArrays () | 
| Returns a mutable reference to the integer meta data arrays.  More... | |
| Sorting peaks | |
| void | sortByIntensity (bool reverse=false) | 
| Lexicographically sorts the peaks by their intensity.  More... | |
| void | sortByPosition () | 
| Lexicographically sorts the peaks by their position.  More... | |
| bool | isSorted () const | 
| Checks if all peaks are sorted with respect to ascending RT.  More... | |
| Searching a peak or peak range | |
| Size | findNearest (CoordinateType rt) const | 
| Binary search for the peak nearest to a specific RT.  More... | |
| Iterator | RTBegin (CoordinateType rt) | 
| Binary search for peak range begin.  More... | |
| Iterator | RTBegin (Iterator begin, CoordinateType rt, Iterator end) | 
| Binary search for peak range begin.  More... | |
| Iterator | RTEnd (CoordinateType rt) | 
| Binary search for peak range end (returns the past-the-end iterator)  More... | |
| Iterator | RTEnd (Iterator begin, CoordinateType rt, Iterator end) | 
| Binary search for peak range end (returns the past-the-end iterator)  More... | |
| ConstIterator | RTBegin (CoordinateType rt) const | 
| Binary search for peak range begin.  More... | |
| ConstIterator | RTBegin (ConstIterator begin, CoordinateType rt, ConstIterator end) const | 
| Binary search for peak range begin.  More... | |
| ConstIterator | RTEnd (CoordinateType rt) const | 
| Binary search for peak range end (returns the past-the-end iterator)  More... | |
| ConstIterator | RTEnd (ConstIterator begin, CoordinateType rt, ConstIterator end) const | 
| Binary search for peak range end (returns the past-the-end iterator)  More... | |
| void | clear (bool clear_meta_data) | 
| Clears all data and meta data.  More... | |
|  Public Member Functions inherited from RangeManager< 1 > | |
| 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 ChromatogramSettings | |
| ChromatogramSettings () | |
| Constructor.  More... | |
| ChromatogramSettings (const ChromatogramSettings &source) | |
| Copy constructor.  More... | |
| virtual | ~ChromatogramSettings () | 
| Destructor.  More... | |
| ChromatogramSettings & | operator= (const ChromatogramSettings &source) | 
| bool | operator== (const ChromatogramSettings &rhs) const | 
| Equality operator.  More... | |
| bool | operator!= (const ChromatogramSettings &rhs) const | 
| Equality operator.  More... | |
| const String & | getNativeID () const | 
| returns the native identifier for the spectrum, used by the acquisition software.  More... | |
| void | setNativeID (const String &native_id) | 
| sets the native identifier for the spectrum, used by the acquisition software.  More... | |
| const String & | getComment () const | 
| returns the free-text comment  More... | |
| void | setComment (const String &comment) | 
| sets the free-text comment  More... | |
| const InstrumentSettings & | getInstrumentSettings () const | 
| returns a const reference to the instrument settings of the current spectrum  More... | |
| InstrumentSettings & | getInstrumentSettings () | 
| returns a mutable reference to the instrument settings of the current spectrum  More... | |
| void | setInstrumentSettings (const InstrumentSettings &instrument_settings) | 
| sets the instrument settings of the current spectrum  More... | |
| const AcquisitionInfo & | getAcquisitionInfo () const | 
| returns a const reference to the acquisition info  More... | |
| AcquisitionInfo & | getAcquisitionInfo () | 
| returns a mutable reference to the acquisition info  More... | |
| void | setAcquisitionInfo (const AcquisitionInfo &acquisition_info) | 
| sets the acquisition info  More... | |
| const SourceFile & | getSourceFile () const | 
| returns a const reference to the source file  More... | |
| SourceFile & | getSourceFile () | 
| returns a mutable reference to the source file  More... | |
| void | setSourceFile (const SourceFile &source_file) | 
| sets the source file  More... | |
| const Precursor & | getPrecursor () const | 
| returns a const reference to the precursors  More... | |
| Precursor & | getPrecursor () | 
| returns a mutable reference to the precursors  More... | |
| void | setPrecursor (const Precursor &precursor) | 
| sets the precursors  More... | |
| const Product & | getProduct () const | 
| returns a const reference to the products  More... | |
| Product & | getProduct () | 
| returns a mutable reference to the products  More... | |
| void | setProduct (const Product &product) | 
| sets the products  More... | |
| const std::vector < DataProcessing > & | getDataProcessing () const | 
| returns a const reference to the description of the applied processing  More... | |
| std::vector< DataProcessing > & | getDataProcessing () | 
| returns a mutable reference to the description of the applied processing  More... | |
| void | setDataProcessing (const std::vector< DataProcessing > &data_processing) | 
| sets the description of the applied processing  More... | |
| ChromatogramType | getChromatogramType () const | 
| returns the chromatogram type, e.g. a SRM chromatogram  More... | |
| void | setChromatogramType (ChromatogramType type) | 
| sets the chromatogram type  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 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< 1 > | |
| 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 | |
| String | name_ | 
| Name.  More... | |
| FloatDataArrays | float_data_arrays_ | 
| Float data arrays.  More... | |
| StringDataArrays | string_data_arrays_ | 
| String data arrays.  More... | |
| IntegerDataArrays | integer_data_arrays_ | 
| Intager data arrays.  More... | |
|  Protected Attributes inherited from RangeManager< 1 > | |
| IntensityRangeType | int_range_ | 
| Intensity range (1-dimensional)  More... | |
| PositionRangeType | pos_range_ | 
| Position range (D-dimensional)  More... | |
|  Protected Attributes inherited from ChromatogramSettings | |
| String | native_id_ | 
| String | comment_ | 
| InstrumentSettings | instrument_settings_ | 
| SourceFile | source_file_ | 
| AcquisitionInfo | acquisition_info_ | 
| Precursor | precursor_ | 
| Product | product_ | 
| std::vector< DataProcessing > | data_processing_ | 
| ChromatogramType | type_ | 
|  Protected Attributes inherited from MetaInfoInterface | |
| MetaInfo * | meta_ | 
| pointer to the MetaInfo object. 0 by default  More... | |
|  Protected Attributes inherited from PersistentObject | |
| UID | persistence_id_ | 
| A persistence id used to refer the data back to the source.  More... | |
| Additional Inherited Members | |
|  Static Public Member Functions inherited from MetaInfoInterface | |
| static MetaInfoRegistry & | metaRegistry () | 
| retuns a reference to the MetaInfoRegistry  More... | |
|  Public Attributes inherited from vector< T > | |
| T | elements | 
| STL member.  More... | |
|  Static Public Attributes inherited from ChromatogramSettings | |
| static const char *const | ChromatogramNames [SIZE_OF_CHROMATOGRAM_TYPE+1] | 
| Names of chromatogram types corresponding to enum ChromatogramType.  More... | |
The representation of a chromatogram.
| typedef ContainerType::const_iterator ConstIterator | 
Non-mutable iterator.
| typedef ContainerType::const_reverse_iterator ConstReverseIterator | 
Non-mutable reverse iterator.
| typedef std::vector<PeakType> ContainerType | 
Chromatogram base type.
Coordinate (RT) type.
| typedef std::vector<FloatDataArray> FloatDataArrays | 
Float data array vector type.
| typedef std::vector<IntegerDataArray> IntegerDataArrays | 
Integer data array vector type.
| typedef ContainerType::iterator Iterator | 
Mutable iterator.
| typedef ContainerType::reverse_iterator ReverseIterator | 
Mutable reverse iterator.
| typedef std::vector<StringDataArray> StringDataArrays | 
String data array vector type.
| 
 | inline | 
Constructor.
| 
 | inline | 
Copy constructor.
| 
 | inlinevirtual | 
Destructor.
| 
 | inline | 
Clears all data and meta data.
| clear_meta_data | If true, all meta data is cleared in addition to the data. | 
Referenced by GaussFilter::filter(), SavitzkyGolayFilter::filter(), and PeakPickerHiRes::pick().
| 
 | inlineprotectedvirtual | 
Clears the persistence id of all sub-objects.
Implements PersistentObject.
| 
 | inline | 
Binary search for the peak nearest to a specific RT.
| rt | The searched for mass-to-charge ratio searched | 
| Exception::Precondition | is thrown if the chromatogram is empty (not only in debug mode) | 
| 
 | inline | 
Returns a const reference to the float meta data arrays
Referenced by MzMLHandler< MapType >::writeChromatogram_().
| 
 | inline | 
Returns a mutable reference to the float meta data arrays.
| 
 | inline | 
Returns a const reference to the integer meta data arrays.
Referenced by MzMLHandler< MapType >::writeChromatogram_().
| 
 | inline | 
Returns a mutable reference to the integer meta data arrays.
| 
 | inline | 
returns the mz of the product entry, makes sense especially for MRM scans
Referenced by MSChromatogram< PeakT >::MZLess::operator()().
| 
 | inline | 
Referenced by PeakPickerHiRes::pick().
| 
 | inline | 
Returns a const reference to the string meta data arrays.
Referenced by MzMLHandler< MapType >::writeChromatogram_().
| 
 | inline | 
Returns a mutable reference to the string meta data arrays.
| 
 | inline | 
Checks if all peaks are sorted with respect to ascending RT.
| 
 | inline | 
Equality operator.
| 
 | inline | 
Assignment operator.
| 
 | inline | 
Equality operator.
Referenced by MSChromatogram< ChromatogramPeakType >::operator!=().
| 
 | inline | 
Binary search for peak range begin.
Referenced by MSChromatogram< ChromatogramPeakType >::findNearest().
| 
 | inline | 
Binary search for peak range begin.
| 
 | inline | 
Binary search for peak range begin.
| 
 | inline | 
Binary search for peak range begin.
| 
 | inline | 
Binary search for peak range end (returns the past-the-end iterator)
| 
 | inline | 
Binary search for peak range end (returns the past-the-end iterator)
| 
 | inline | 
Binary search for peak range end (returns the past-the-end iterator)
| 
 | inline | 
Binary search for peak range end (returns the past-the-end iterator)
| 
 | inline | 
Sets the name.
Referenced by PeakPickerHiRes::pick().
| 
 | inline | 
Lexicographically sorts the peaks by their intensity.
Sorts the peaks according to ascending intensity. Meta data arrays will be sorted accordingly.
| 
 | inline | 
Lexicographically sorts the peaks by their position.
The chromatogram is sorted with respect to position. Meta data arrays will be sorted accordingly.
| 
 | inlinevirtual | 
Updates minimum and maximum position/intensity.
This method is usually implemented by calling clearRanges() and updateRanges_().
Implements RangeManager< 1 >.
| 
 | protected | 
Float data arrays.
Referenced by MSChromatogram< ChromatogramPeakType >::clear(), MSChromatogram< ChromatogramPeakType >::getFloatDataArrays(), MSChromatogram< ChromatogramPeakType >::operator=(), MSChromatogram< ChromatogramPeakType >::operator==(), MSChromatogram< ChromatogramPeakType >::sortByIntensity(), and MSChromatogram< ChromatogramPeakType >::sortByPosition().
| 
 | protected | 
Intager data arrays.
Referenced by MSChromatogram< ChromatogramPeakType >::clear(), MSChromatogram< ChromatogramPeakType >::getIntegerDataArrays(), MSChromatogram< ChromatogramPeakType >::operator=(), MSChromatogram< ChromatogramPeakType >::operator==(), MSChromatogram< ChromatogramPeakType >::sortByIntensity(), and MSChromatogram< ChromatogramPeakType >::sortByPosition().
| 
 | protected | 
| 
 | protected | 
String data arrays.
Referenced by MSChromatogram< ChromatogramPeakType >::clear(), MSChromatogram< ChromatogramPeakType >::getStringDataArrays(), MSChromatogram< ChromatogramPeakType >::operator=(), MSChromatogram< ChromatogramPeakType >::operator==(), MSChromatogram< ChromatogramPeakType >::sortByIntensity(), and MSChromatogram< ChromatogramPeakType >::sortByPosition().
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:32 using doxygen 1.8.5 |