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.
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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 |
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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.
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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.