#include <OpenMS/COMPARISON/CLUSTERING/BinnedRep.h>
Bin Dimensions:
BinSize = size of the bins
BinSpread > 0 adds peaks to more bins
expample:
spread 0: | => #
spread 1: | => ###
spread 2: | =? #####
since small binsizes tend to produce very sparse Vectors ( < 1%) a sparse Vector is used
Public Types | |
typedef SparseVector::const_iterator | const_iterator |
typedef SparseVector::iterator | iterator |
typedef SparseVector::const_iterator | ConstIterator |
typedef SparseVector::iterator | Iterator |
Public Member Functions | |
void | normalize () |
scale all peaks from 0 to 1 | |
Constructors and destructors | |
BinnedRep () | |
default constructor | |
BinnedRep (double, uint=0) | |
detailed constructor with declaration of bin dimensions | |
BinnedRep (const PeakSpectrum &spec, double binsize=1.0, uint binspread=0) | |
detailed constructor with PeakSpectrum and bin settings | |
BinnedRep (const BinnedRep &source) | |
copy constructor | |
virtual | ~BinnedRep () |
destructor | |
Accessors | |
BinnedRep & | operator= (const BinnedRep &source) |
assignment operator | |
uint | id () const |
returns the id of the spectrum | |
double | getBinSize () const |
returns the bin size of the spectrum | |
double | max () const |
returns the maximum of the m/z values | |
double | min () const |
returns the minimum of the m/z values | |
double | getRT () const |
returns the retention time | |
unsigned int | getBinSpread () const |
returns the spreading of the bins | |
double | getParentmz () const |
returns the mass-to-charge ratio of the parent ion | |
unsigned int | getPrecursorPeakCharge () const |
returns the charge of the parent ion | |
unsigned int | size () const |
returns the number of bins | |
String | str () const |
converts it to a string | |
Iterator | begin () |
returns an iterator pointing at the first bin | |
Iterator | end () |
returns an end iterator | |
ConstIterator | begin () const |
returns an constant begin iterator | |
ConstIterator | end () const |
returns an constant end Iterator | |
intensity | operator[] (int) const |
access to a bin with bracket operator | |
Private Member Functions | |
void | clear_ () |
clears all data | |
Private Attributes | |
SparseVector | bins_ |
sparse vector containing the summed intensity | |
double | binsize_ |
size of the bins | |
unsigned int | spread_ |
spreading of the bins | |
double | begin_ |
first m/z | |
double | end_ |
last m/z | |
unsigned int | id_ |
the spectrum id | |
double | retention_ |
retention time of the spectrum | |
double | parent_m_z_ |
the m/z of the parent ion | |
unsigned int | precursorpeakcharge_ |
charge of the parent ion | |
Friends | |
void | operator<< (BinnedRep &bin_rep, const PeakSpectrum &spec) |
fill bins with stick spectrum |
typedef SparseVector::iterator iterator |
typedef SparseVector::iterator Iterator |
BinnedRep | ( | ) |
default constructor
BinnedRep | ( | double | , | |
uint | = 0 | |||
) |
detailed constructor with declaration of bin dimensions
BinnedRep | ( | const PeakSpectrum & | spec, | |
double | binsize = 1.0 , |
|||
uint | binspread = 0 | |||
) |
detailed constructor with PeakSpectrum and bin settings
virtual ~BinnedRep | ( | ) | [virtual] |
destructor
uint id | ( | ) | const [inline] |
returns the id of the spectrum
double getBinSize | ( | ) | const [inline] |
returns the bin size of the spectrum
double max | ( | ) | const [inline] |
returns the maximum of the m/z values
double min | ( | ) | const [inline] |
returns the minimum of the m/z values
double getRT | ( | ) | const [inline] |
returns the retention time
unsigned int getBinSpread | ( | ) | const [inline] |
returns the spreading of the bins
double getParentmz | ( | ) | const [inline] |
returns the mass-to-charge ratio of the parent ion
unsigned int getPrecursorPeakCharge | ( | ) | const [inline] |
returns the charge of the parent ion
unsigned int size | ( | ) | const [inline] |
returns the number of bins
String str | ( | ) | const |
converts it to a string
Iterator begin | ( | ) | [inline] |
returns an iterator pointing at the first bin
Iterator end | ( | ) | [inline] |
returns an end iterator
ConstIterator begin | ( | ) | const [inline] |
returns an constant begin iterator
ConstIterator end | ( | ) | const [inline] |
returns an constant end Iterator
intensity operator[] | ( | int | ) | const |
access to a bin with bracket operator
void normalize | ( | ) |
scale all peaks from 0 to 1
void clear_ | ( | ) | [private] |
clears all data
void operator<< | ( | BinnedRep & | bin_rep, | |
const PeakSpectrum & | spec | |||
) | [friend] |
fill bins with stick spectrum
SparseVector bins_ [private] |
sparse vector containing the summed intensity
double binsize_ [private] |
size of the bins
unsigned int spread_ [private] |
spreading of the bins
double begin_ [private] |
first m/z
double end_ [private] |
last m/z
unsigned int id_ [private] |
the spectrum id
double retention_ [private] |
retention time of the spectrum
double parent_m_z_ [private] |
the m/z of the parent ion
unsigned int precursorpeakcharge_ [private] |
charge of the parent ion
Generated Tue Apr 1 15:36:43 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |