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 name if it exists. More... | |
| void | removeMetaValue (UInt index) |
Removes the DataValue corresponding to index if 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.
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inline |
Constructor.
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Copy constructor.
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Destructor.
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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 GaussFilter::filter(), SavitzkyGolayFilter::filter(), and PeakPickerHiRes::pick().
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Clears the persistence id of all sub-objects.
Implements PersistentObject.
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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) |
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Returns a const reference to the float meta data arrays
Referenced by MzMLHandler< MapType >::writeChromatogram_().
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Returns a mutable reference to the float meta data arrays.
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Returns a const reference to the integer meta data arrays.
Referenced by MzMLHandler< MapType >::writeChromatogram_().
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Returns a mutable reference to the integer meta data arrays.
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returns the mz of the product entry, makes sense especially for MRM scans
Referenced by MSChromatogram< PeakT >::MZLess::operator()().
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Referenced by PeakPickerHiRes::pick().
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Returns a const reference to the string meta data arrays.
Referenced by MzMLHandler< MapType >::writeChromatogram_().
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Returns a mutable reference to the string meta data arrays.
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Checks if all peaks are sorted with respect to ascending RT.
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Equality operator.
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Assignment operator.
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inline |
Equality operator.
Referenced by MSChromatogram< ChromatogramPeakType >::operator!=().
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Binary search for peak range begin.
Referenced by MSChromatogram< ChromatogramPeakType >::findNearest().
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Binary search for peak range begin.
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Binary search for peak range begin.
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Binary search for peak range begin.
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inline |
Binary search for peak range end (returns the past-the-end iterator)
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Binary search for peak range end (returns the past-the-end iterator)
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inline |
Binary search for peak range end (returns the past-the-end iterator)
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Binary search for peak range end (returns the past-the-end iterator)
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Sets the name.
Referenced by PeakPickerHiRes::pick().
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Lexicographically sorts the peaks by their intensity.
Sorts the peaks according to ascending intensity. Meta data arrays will be sorted accordingly.
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inline |
Lexicographically sorts the peaks by their position.
The chromatogram is sorted with respect to position. Meta data arrays will be sorted accordingly.
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inlinevirtual |
Updates minimum and maximum position/intensity.
This method is usually implemented by calling clearRanges() and updateRanges_().
Implements RangeManager< 1 >.
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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().
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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().
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protected |
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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 |