#include <OpenMS/KERNEL/DSpectrum.h>
The peak data itself is stored in a container class, which can be a DPeakArray or a STL container like std::list or std::vector.
Some meta information about the spectrum (ms-level, precursor peak, ...) is also stored. If you want to store more meta information see the MSSpectrum and MSExperiment classes.
The interface to the container is wrapped for convenience. Only members and types contained in both std::list and std::vector are available.
Additionally an interface for the minimum and maximum position, and the minimum and maximum intensity of the peaks is provided by RangeManager.
Type definitions | |
enum | { DIMENSION = PeakType::DIMENSION } |
Dimensionality of the peaks. More... | |
typedef ContainerT | ContainerType |
Peak container type. | |
typedef ContainerType::value_type | PeakType |
Peak type. | |
typedef PeakType::CoordinateType | CoordinateType |
Coordinate type. | |
typedef Internal::PrecursorPeak < DIMENSION > | PrecursorPeakType |
Precursor peak type. | |
typedef RangeManager< DIMENSION > | RangeManagerType |
Rangemanger type. | |
class | DSpectrum |
Public Types | |
STL-compliance type definitions of the container interface | |
typedef ContainerType::iterator | iterator |
typedef ContainerType::const_iterator | const_iterator |
typedef ContainerType::reverse_iterator | reverse_iterator |
typedef ContainerType::const_reverse_iterator | const_reverse_iterator |
typedef ContainerType::value_type | value_type |
typedef ContainerType::reference | reference |
typedef ContainerType::const_reference | const_reference |
typedef ContainerType::pointer | pointer |
typedef ContainerType::difference_type | difference_type |
typedef ContainerType::size_type | size_type |
Type definitions of the container interface | |
typedef ContainerType::iterator | Iterator |
Mutable iterator. | |
typedef ContainerType::const_iterator | ConstIterator |
Non-mutable iterator. | |
typedef ContainerType::reverse_iterator | ReverseIterator |
Mutable reverse iterator. | |
typedef ContainerType::const_reverse_iterator | ConstReverseIterator |
Non-mutable reverse iterator. | |
Public Member Functions | |
DSpectrum & | operator= (const DSpectrum &rhs) |
Assignment operator. | |
template<template< typename, typename > class ContainerT2, typename AllocT> | |
DSpectrum & | operator= (const DSpectrum< ContainerT2< PeakType, AllocT > > &rhs) |
Assignment operator for different allocator. | |
bool | operator== (const DSpectrum &rhs) const |
Equality operator. | |
bool | operator!= (const DSpectrum &rhs) const |
Equality operator. | |
virtual void | updateRanges () |
Updates minimum and maximum position/intensity. | |
Constructors and Destructor | |
DSpectrum () | |
Default constructor. | |
DSpectrum (const typename ContainerType::AllocType &alloc) | |
constructor with custom allocator | |
DSpectrum (const DSpectrum &rhs) | |
Copy constructor. | |
template<template< typename, typename > class ContainerT2, typename AllocT2> | |
DSpectrum (const DSpectrum< ContainerT2< PeakType, AllocT2 > > &rhs) | |
Copy constructor for different allocator. | |
template<template< typename, typename > class ContainerT2, typename AllocT2, typename AllocT> | |
DSpectrum (const DSpectrum< ContainerT2< PeakType, AllocT2 > > &rhs, const AllocT &alloc) | |
Copy constructor for different (but unique) allocator. | |
~DSpectrum () | |
Destructor. | |
Wrappers of container accessors | |
const ContainerType & | getContainer () const |
Non-mutable access to the peak container. | |
ContainerType & | getContainer () |
Mutable access to the peak container. | |
void | setContainer (const ContainerType &container) |
Mutable access to the peak container. | |
ConstIterator | begin () const |
Returns the const begin iterator of the container. | |
ConstIterator | end () const |
Returns the const end iterator of the container. | |
Iterator | begin () |
Returns the begin iterator of the container. | |
Iterator | end () |
Returns the end iterator of the container. | |
reference | operator[] (size_type n) |
returns the element with index n | |
const_reference | operator[] (size_type n) const |
returns the element with index n | |
size_type | max_size () const |
returns the maxium size possbile (the number of peaks) | |
UInt | size () const |
returns the size (the number of peaks) | |
bool | empty () const |
Returns if the container is empty. | |
void | swap (ContainerType &rhs) |
Swaps two containers. | |
bool | operator< (const DSpectrum &rhs) |
Comparison of container sizes. | |
bool | operator> (const DSpectrum &rhs) |
Comparison of container sizes. | |
bool | operator<= (const DSpectrum &rhs) |
Comparison of container sizes. | |
bool | operator>= (const DSpectrum &rhs) |
Comparison of container sizes. | |
ReverseIterator | rbegin () |
See STL documentation. | |
ConstReverseIterator | rbegin () const |
See STL documentation. | |
ReverseIterator | rend () |
See STL documentation. | |
ConstReverseIterator | rend () const |
See STL documentation. | |
Iterator | insert (Iterator loc, const value_type &val) |
Inserts an element. | |
void | insert (iterator loc, size_type num, const value_type &val) |
Inserts an element several times. | |
template<class InputIterator> | |
void | insert (iterator loc, InputIterator start, InputIterator end) |
Inserts a range of elements. | |
Iterator | erase (iterator loc) |
Erases an element. | |
Iterator | erase (iterator start, iterator end) |
Erases a range of elements. | |
value_type & | front () |
Returns the first element. | |
const value_type & | front () const |
Returns the first element. | |
value_type & | back () |
Returns the last element. | |
const value_type & | back () const |
Returns the last element. | |
void | pop_back () |
Removes the last element. | |
void | push_back (const value_type &val) |
Inserts an element at the end. | |
void | assign (size_type num, const value_type &val) |
Fills the container with serval copies of a value. | |
template<class InputIterator> | |
void | assign (InputIterator start, InputIterator end) |
Fills the container with a range of values. | |
void | clear () |
Removes all elements. | |
void | resize (size_type num, const value_type &val=value_type()) |
Resizes the container to size num . Uses val to fill up if it is shorter than num . | |
Accessors for meta information | |
const PrecursorPeakType & | getPrecursorPeak () const |
const accessor for the precorsor peak | |
PrecursorPeakType & | getPrecursorPeak () |
accessor for the precorsor peak | |
void | setPrecursorPeak (const PrecursorPeakType &peak) |
sets the precursor peak | |
CoordinateType | getRT () const |
returns the absolute retention time (unit is seconds) | |
void | setRT (CoordinateType rt) |
UInt | getMSLevel () const |
Returns the MS level. | |
void | setMSLevel (UInt ms_level) |
Sets the MS level. | |
String | getName () const |
Returns the name. | |
void | setName (const String &name) |
Sets the name. | |
Searching a peak or peak range | |
UInt | findNearest (CoordinateType mz) const throw (Exception::Precondition) |
Binary search for the peak nearest to a specific m/z. | |
Iterator | MZBegin (CoordinateType mz) |
Binary search for peak range begin. | |
Iterator | MZEnd (CoordinateType mz) |
Binary search for peak range end (returns the past-the-end iterator). | |
ConstIterator | MZBegin (CoordinateType mz) const |
Binary search for peak range begin. | |
ConstIterator | MZEnd (CoordinateType mz) const |
Binary search for peak range end (returns the past-the-end iterator). | |
Protected Attributes | |
ContainerType | container_ |
The container with all the peak data. | |
PrecursorPeakType | precursor_peak_ |
Precursor information. | |
CoordinateType | retention_time_ |
retention time | |
UInt | ms_level_ |
MS level. | |
String | name_ |
Name. |
typedef ContainerT ContainerType |
Peak container type.
typedef ContainerType::value_type PeakType |
Coordinate type.
typedef Internal::PrecursorPeak<DIMENSION> PrecursorPeakType |
Precursor peak type.
typedef RangeManager<DIMENSION> RangeManagerType |
Rangemanger type.
typedef ContainerType::iterator iterator |
typedef ContainerType::const_iterator const_iterator |
typedef ContainerType::reverse_iterator reverse_iterator |
typedef ContainerType::const_reverse_iterator const_reverse_iterator |
typedef ContainerType::value_type value_type |
typedef ContainerType::reference reference |
typedef ContainerType::const_reference const_reference |
typedef ContainerType::pointer pointer |
typedef ContainerType::difference_type difference_type |
typedef ContainerType::size_type size_type |
typedef ContainerType::iterator Iterator |
Mutable iterator.
typedef ContainerType::const_iterator ConstIterator |
Non-mutable iterator.
typedef ContainerType::reverse_iterator ReverseIterator |
Mutable reverse iterator.
typedef ContainerType::const_reverse_iterator ConstReverseIterator |
Non-mutable reverse iterator.
DSpectrum | ( | ) | [inline] |
Default constructor.
DSpectrum | ( | const typename ContainerType::AllocType & | alloc | ) | [inline] |
constructor with custom allocator
Copy constructor for different allocator.
DSpectrum | ( | const DSpectrum< ContainerT2< PeakType, AllocT2 > > & | rhs, | |
const AllocT & | alloc | |||
) | [inline] |
Copy constructor for different (but unique) allocator.
~DSpectrum | ( | ) | [inline] |
Destructor.
Assignment operator for different allocator.
bool operator== | ( | const DSpectrum< ContainerT > & | rhs | ) | const [inline] |
Equality operator.
bool operator!= | ( | const DSpectrum< ContainerT > & | rhs | ) | const [inline] |
Equality operator.
const ContainerType& getContainer | ( | ) | const [inline] |
Non-mutable access to the peak container.
ContainerType& getContainer | ( | ) | [inline] |
Mutable access to the peak container.
void setContainer | ( | const ContainerType & | container | ) | [inline] |
Mutable access to the peak container.
ConstIterator begin | ( | ) | const [inline] |
Returns the const begin iterator of the container.
ConstIterator end | ( | ) | const [inline] |
Returns the const end iterator of the container.
Iterator begin | ( | ) | [inline] |
Returns the begin iterator of the container.
Iterator end | ( | ) | [inline] |
Returns the end iterator of the container.
const_reference operator[] | ( | size_type | n | ) | const [inline] |
returns the element with index n
size_type max_size | ( | ) | const [inline] |
returns the maxium size possbile (the number of peaks)
UInt size | ( | ) | const [inline] |
returns the size (the number of peaks)
bool empty | ( | ) | const [inline] |
Returns if the container is empty.
void swap | ( | ContainerType & | rhs | ) | [inline] |
Swaps two containers.
bool operator< | ( | const DSpectrum< ContainerT > & | rhs | ) | [inline] |
Comparison of container sizes.
bool operator> | ( | const DSpectrum< ContainerT > & | rhs | ) | [inline] |
Comparison of container sizes.
bool operator<= | ( | const DSpectrum< ContainerT > & | rhs | ) | [inline] |
Comparison of container sizes.
bool operator>= | ( | const DSpectrum< ContainerT > & | rhs | ) | [inline] |
Comparison of container sizes.
ReverseIterator rbegin | ( | ) | [inline] |
See STL documentation.
ConstReverseIterator rbegin | ( | ) | const [inline] |
See STL documentation.
ReverseIterator rend | ( | ) | [inline] |
See STL documentation.
ConstReverseIterator rend | ( | ) | const [inline] |
See STL documentation.
Iterator insert | ( | Iterator | loc, | |
const value_type & | val | |||
) | [inline] |
Inserts an element.
void insert | ( | iterator | loc, | |
size_type | num, | |||
const value_type & | val | |||
) | [inline] |
Inserts an element several times.
void insert | ( | iterator | loc, | |
InputIterator | start, | |||
InputIterator | end | |||
) | [inline] |
Inserts a range of elements.
value_type& front | ( | ) | [inline] |
Returns the first element.
const value_type& front | ( | ) | const [inline] |
Returns the first element.
value_type& back | ( | ) | [inline] |
Returns the last element.
const value_type& back | ( | ) | const [inline] |
Returns the last element.
void pop_back | ( | ) | [inline] |
Removes the last element.
void push_back | ( | const value_type & | val | ) | [inline] |
Inserts an element at the end.
void assign | ( | size_type | num, | |
const value_type & | val | |||
) | [inline] |
Fills the container with serval copies of a value.
void assign | ( | InputIterator | start, | |
InputIterator | end | |||
) | [inline] |
Fills the container with a range of values.
void clear | ( | ) | [inline] |
Removes all elements.
void resize | ( | size_type | num, | |
const value_type & | val = value_type() | |||
) | [inline] |
Resizes the container to size num
. Uses val
to fill up if it is shorter than num
.
virtual void updateRanges | ( | ) | [inline, virtual] |
Updates minimum and maximum position/intensity.
This method is usually implemented by calling clearRanges() and updateRanges_() or updateRanges1D_().
Implements RangeManager< ContainerT::value_type::DIMENSION >.
const PrecursorPeakType& getPrecursorPeak | ( | ) | const [inline] |
const accessor for the precorsor peak
PrecursorPeakType& getPrecursorPeak | ( | ) | [inline] |
accessor for the precorsor peak
void setPrecursorPeak | ( | const PrecursorPeakType & | peak | ) | [inline] |
sets the precursor peak
CoordinateType getRT | ( | ) | const [inline] |
returns the absolute retention time (unit is seconds)
void setRT | ( | CoordinateType | rt | ) | [inline] |
Sets the retention time and the start/stop time of the gradient. The latter two are needed for calculating the normalized retention time
UInt getMSLevel | ( | ) | const [inline] |
Returns the MS level.
For survey scans this is 1, for MS/MS scans 2, ...
void setMSLevel | ( | UInt | ms_level | ) | [inline] |
Sets the MS level.
String getName | ( | ) | const [inline] |
Returns the name.
void setName | ( | const String & | name | ) | [inline] |
Sets the name.
UInt findNearest | ( | CoordinateType | mz | ) | const throw (Exception::Precondition) [inline] |
Binary search for the peak nearest to a specific m/z.
mz | The searched for mass-to-charge ratio searched |
Iterator MZBegin | ( | CoordinateType | mz | ) | [inline] |
Binary search for peak range begin.
Iterator MZEnd | ( | CoordinateType | mz | ) | [inline] |
Binary search for peak range end (returns the past-the-end iterator).
ConstIterator MZBegin | ( | CoordinateType | mz | ) | const [inline] |
Binary search for peak range begin.
ConstIterator MZEnd | ( | CoordinateType | mz | ) | const [inline] |
Binary search for peak range end (returns the past-the-end iterator).
friend class DSpectrum [friend] |
ContainerType container_ [protected] |
The container with all the peak data.
PrecursorPeakType precursor_peak_ [protected] |
Precursor information.
CoordinateType retention_time_ [protected] |
retention time
Generated Tue Apr 1 15:36:45 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |