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OpenMS
2.5.0
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The representation of a chromatogram. More...
#include <OpenMS/KERNEL/MSChromatogram.h>
Classes | |
| struct | MZLess |
| Comparator for the retention time. More... | |
Public Member Functions | |
| double | getMZ () const |
| returns the mz of the product entry, makes sense especially for MRM scans More... | |
Export methods from std::vector | |
| MSChromatogram ()=default | |
| Constructor. More... | |
| MSChromatogram (const MSChromatogram &)=default | |
| Copy constructor. More... | |
| MSChromatogram (MSChromatogram &&)=default | |
| Move constructor. More... | |
| ~MSChromatogram () override | |
| Destructor. More... | |
| MSChromatogram & | operator= (const MSChromatogram &source) |
| Assignment operator. More... | |
| MSChromatogram & | operator= (MSChromatogram &&) &=default |
| Move assignment operator. More... | |
| bool | operator== (const MSChromatogram &rhs) const |
| Equality operator. More... | |
| bool | operator!= (const MSChromatogram &rhs) const |
| Equality operator. More... | |
| void | updateRanges () override |
| Updates minimum and maximum position/intensity. 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
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| const FloatDataArrays & | getFloatDataArrays () const |
| FloatDataArrays & | getFloatDataArrays () |
| Returns a mutable reference to the float meta data arrays. More... | |
| void | setFloatDataArrays (const FloatDataArrays &fda) |
| Sets 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... | |
| void | setStringDataArrays (const StringDataArrays &sda) |
| Sets 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... | |
| void | setIntegerDataArrays (const IntegerDataArrays &ida) |
| Sets 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 | MZEnd (CoordinateType rt) const |
| ConstIterator | RTEnd (ConstIterator begin, CoordinateType rt, ConstIterator end) const |
| Binary search for peak range end (returns the past-the-end iterator) More... | |
| Iterator | PosBegin (CoordinateType rt) |
| Binary search for peak range begin. More... | |
| Iterator | PosBegin (Iterator begin, CoordinateType rt, Iterator end) |
| Binary search for peak range begin. More... | |
| ConstIterator | PosBegin (CoordinateType rt) const |
| Binary search for peak range begin. More... | |
| ConstIterator | PosBegin (ConstIterator begin, CoordinateType rt, ConstIterator end) const |
| Binary search for peak range begin. More... | |
| Iterator | PosEnd (CoordinateType rt) |
| Binary search for peak range end (returns the past-the-end iterator) More... | |
| Iterator | PosEnd (Iterator begin, CoordinateType rt, Iterator end) |
| Binary search for peak range end (returns the past-the-end iterator) More... | |
| ConstIterator | PosEnd (CoordinateType rt) const |
| Binary search for peak range end (returns the past-the-end iterator) More... | |
| ConstIterator | PosEnd (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... | |
| 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 ChromatogramSettings | |
| ChromatogramSettings () | |
| Constructor. More... | |
| ChromatogramSettings (const ChromatogramSettings &)=default | |
| Copy constructor. More... | |
| ChromatogramSettings (ChromatogramSettings &&)=default | |
| Move constructor. More... | |
| virtual | ~ChromatogramSettings () |
| Destructor. More... | |
| ChromatogramSettings & | operator= (const ChromatogramSettings &)=default |
| ChromatogramSettings & | operator= (ChromatogramSettings &&) &=default |
| Move assignment operator. More... | |
| 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... | |
| ChromatogramType | getChromatogramType () const |
| returns the chromatogram type, e.g. a SRM chromatogram More... | |
| void | setChromatogramType (ChromatogramType type) |
| sets the chromatogram type More... | |
| void | setDataProcessing (const std::vector< DataProcessingPtr > &data_processing) |
| sets the description of the applied processing More... | |
| std::vector< DataProcessingPtr > & | getDataProcessing () |
| returns a mutable reference to the description of the applied processing More... | |
| const std::vector< boost::shared_ptr< const DataProcessing > > | getDataProcessing () const |
| returns a const reference to the description of the applied processing 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 | 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... | |
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_ |
| Integer 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< DataProcessingPtr > | data_processing_ |
| ChromatogramType | type_ |
Protected Attributes inherited from MetaInfoInterface | |
| MetaInfo * | meta_ |
| Pointer to the MetaInfo object (0 by default) More... | |
Additional Inherited Members | |
Static Public Member Functions inherited from MetaInfoInterface | |
| static MetaInfoRegistry & | metaRegistry () |
| Returns a reference to the MetaInfoRegistry. 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... | |
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... | |
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.
Float data array vector type.
| typedef std::vector<FloatDataArray> FloatDataArrays |
Integer data array vector type.
| typedef std::vector<IntegerDataArray> IntegerDataArrays |
| typedef ContainerType::iterator Iterator |
Mutable iterator.
| typedef ChromatogramPeak PeakType |
| typedef ContainerType::reverse_iterator ReverseIterator |
Mutable reverse iterator.
String data array vector type.
| typedef std::vector<StringDataArray> StringDataArrays |
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default |
Constructor.
|
default |
Copy constructor.
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default |
Move constructor.
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inlineoverride |
Destructor.
| 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. |
| Size findNearest | ( | CoordinateType | rt | ) | const |
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) |
| FloatDataArrays& getFloatDataArrays | ( | ) |
Returns a mutable reference to the float meta data arrays.
| const FloatDataArrays& getFloatDataArrays | ( | ) | const |
Returns a const reference to the float meta data arrays
| IntegerDataArrays& getIntegerDataArrays | ( | ) |
Returns a mutable reference to the integer meta data arrays.
| const IntegerDataArrays& getIntegerDataArrays | ( | ) | const |
Returns a const reference to the integer meta data arrays.
| double getMZ | ( | ) | const |
returns the mz of the product entry, makes sense especially for MRM scans
Referenced by GaussFilter::filter().
| const String& getName | ( | ) | const |
| StringDataArrays& getStringDataArrays | ( | ) |
Returns a mutable reference to the string meta data arrays.
| const StringDataArrays& getStringDataArrays | ( | ) | const |
Returns a const reference to the string meta data arrays.
| bool isSorted | ( | ) | const |
Checks if all peaks are sorted with respect to ascending RT.
| ConstIterator MZEnd | ( | CoordinateType | rt | ) | const |
|
inline |
Equality operator.
References KDTree::operator==().
| MSChromatogram& operator= | ( | const MSChromatogram & | source | ) |
Assignment operator.
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default |
Move assignment operator.
| bool operator== | ( | const MSChromatogram & | rhs | ) | const |
Equality operator.
| ConstIterator PosBegin | ( | ConstIterator | begin, |
| CoordinateType | rt, | ||
| ConstIterator | end | ||
| ) | const |
Binary search for peak range begin.
Alias for RTBegin()
| Iterator PosBegin | ( | CoordinateType | rt | ) |
Binary search for peak range begin.
Alias for RTBegin()
| ConstIterator PosBegin | ( | CoordinateType | rt | ) | const |
Binary search for peak range begin.
Alias for RTBegin()
| Iterator PosBegin | ( | Iterator | begin, |
| CoordinateType | rt, | ||
| Iterator | end | ||
| ) |
Binary search for peak range begin.
Alias for RTBegin()
| ConstIterator PosEnd | ( | ConstIterator | begin, |
| CoordinateType | rt, | ||
| ConstIterator | end | ||
| ) | const |
Binary search for peak range end (returns the past-the-end iterator)
Alias for RTEnd()
| Iterator PosEnd | ( | CoordinateType | rt | ) |
Binary search for peak range end (returns the past-the-end iterator)
Alias for RTEnd()
| ConstIterator PosEnd | ( | CoordinateType | rt | ) | const |
Binary search for peak range end (returns the past-the-end iterator)
Alias for RTEnd()
| Iterator PosEnd | ( | Iterator | begin, |
| CoordinateType | rt, | ||
| Iterator | end | ||
| ) |
Binary search for peak range end (returns the past-the-end iterator)
Alias for RTEnd()
| ConstIterator RTBegin | ( | ConstIterator | begin, |
| CoordinateType | rt, | ||
| ConstIterator | end | ||
| ) | const |
Binary search for peak range begin.
| Iterator RTBegin | ( | CoordinateType | rt | ) |
Binary search for peak range begin.
| ConstIterator RTBegin | ( | CoordinateType | rt | ) | const |
Binary search for peak range begin.
| Iterator RTBegin | ( | Iterator | begin, |
| CoordinateType | rt, | ||
| Iterator | end | ||
| ) |
Binary search for peak range begin.
| ConstIterator RTEnd | ( | ConstIterator | begin, |
| CoordinateType | rt, | ||
| ConstIterator | end | ||
| ) | const |
Binary search for peak range end (returns the past-the-end iterator)
| Iterator RTEnd | ( | CoordinateType | rt | ) |
Binary search for peak range end (returns the past-the-end iterator)
| ConstIterator RTEnd | ( | CoordinateType | rt | ) | const |
Binary search for peak range end (returns the past-the-end iterator)
| Iterator RTEnd | ( | Iterator | begin, |
| CoordinateType | rt, | ||
| Iterator | end | ||
| ) |
Binary search for peak range end (returns the past-the-end iterator)
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inline |
Sets the float meta data arrays.
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inline |
Sets the integer meta data arrays.
| void setName | ( | const String & | name | ) |
Sets the name.
|
inline |
Sets the string meta data arrays.
| void sortByIntensity | ( | bool | reverse = false | ) |
Lexicographically sorts the peaks by their intensity.
Sorts the peaks according to ascending intensity. Meta data arrays will be sorted accordingly.
Referenced by MRMTransitionGroupPicker::pickTransitionGroup().
| void sortByPosition | ( | ) |
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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inlineoverridevirtual |
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.
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protected |
Integer data arrays.
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protected |
Name.
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protected |
String data arrays.
1.8.16