SpectrumCheapDPCorr calculates an optimal alignment on stick spectra. More...
#include <OpenMS/COMPARISON/SPECTRA/SpectrumCheapDPCorr.h>
Public Member Functions | |
| SpectrumCheapDPCorr () | |
| default constructor | |
| SpectrumCheapDPCorr (const SpectrumCheapDPCorr &source) | |
| copy constructor | |
| virtual | ~SpectrumCheapDPCorr () |
| destructor | |
| SpectrumCheapDPCorr & | operator= (const SpectrumCheapDPCorr &source) |
| assignment operator | |
| double | operator() (const PeakSpectrum &a, const PeakSpectrum &b) const |
| function call operator, calculates the similarity | |
| double | operator() (const PeakSpectrum &a) const |
| calculates self similarity | |
Private Member Functions | |
| double | dynprog_ (const PeakSpectrum &, const PeakSpectrum &, int, int, int, int) const |
| O(n^2) dynamical programming. | |
| double | comparepeaks_ (double posa, double posb, double inta, double intb) const |
| similarity of two peaks | |
Private Attributes | |
| PeakSpectrum | lastconsensus_ |
| consensus spectrum of the last comparison | |
| bool | keeppeaks_ |
| should peaks with no alignment partner be kept in the consensus? | |
| double | factor_ |
| weighting factor for the next consensus spectrum | |
| Map< UInt, UInt > | peak_map_ |
| last peak map | |
Static Private Attributes | |
| static const String | info_ |
|
| |
| const PeakSpectrum & | lastconsensus () const |
| return consensus spectrum from last funtion call operator | |
| Map< UInt, UInt > | getPeakMap () const |
| void | setFactor (double f) |
| set weighting of the second spectrum for consensus from next function call operator | |
| static PeakSpectrumCompareFunctor * | create () |
| static const String | getProductName () |
Detailed Description
SpectrumCheapDPCorr calculates an optimal alignment on stick spectra.
to save computing time only Peak Pairs that could get a score > 0 are considered which Peak Pairs could get scores > 0 ?
Peaks get a score depending on the difference in position and the heights of the peaks
pairs with positions that differ more than some limit get score 0
| Name | Type | Default | Restrictions | Description |
|---|---|---|---|---|
| variation | float | 0.001 | Maximum difference in position (in percent of the current m/z). Note that big values of variation ( 1 being the maximum ) result in consideration of all possible pairings which has a running time of O(n*n) |
|
| int_cnt | int | 0 | How the peak heights are used in the score. 0 = product 1 = sqrt(product) 2 = sum 3 = agreeing intensity |
|
| keeppeaks | int | 0 | Flag that states if peaks without alignment partner are kept in the consensus spectrum. |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
Constructor & Destructor Documentation
default constructor
| SpectrumCheapDPCorr | ( | const SpectrumCheapDPCorr & | source | ) |
copy constructor
| virtual ~SpectrumCheapDPCorr | ( | ) | [virtual] |
destructor
Member Function Documentation
similarity of two peaks
| static PeakSpectrumCompareFunctor* create | ( | ) | [inline, static] |
| double dynprog_ | ( | const PeakSpectrum & | , | |
| const PeakSpectrum & | , | |||
| int | , | |||
| int | , | |||
| int | , | |||
| int | ||||
| ) | const [private] |
O(n^2) dynamical programming.
| static const String getProductName | ( | ) | [inline, static] |
Reimplemented from PeakSpectrumCompareFunctor.
| const PeakSpectrum& lastconsensus | ( | ) | const |
return consensus spectrum from last funtion call operator
| double operator() | ( | const PeakSpectrum & | a, | |
| const PeakSpectrum & | b | |||
| ) | const [virtual] |
function call operator, calculates the similarity
Implements PeakSpectrumCompareFunctor.
| double operator() | ( | const PeakSpectrum & | a | ) | const [virtual] |
calculates self similarity
Implements PeakSpectrumCompareFunctor.
| SpectrumCheapDPCorr& operator= | ( | const SpectrumCheapDPCorr & | source | ) |
assignment operator
| void setFactor | ( | double | f | ) |
set weighting of the second spectrum for consensus from next function call operator
Member Data Documentation
bool keeppeaks_ [private] |
should peaks with no alignment partner be kept in the consensus?
PeakSpectrum lastconsensus_ [mutable, private] |
consensus spectrum of the last comparison
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:51 using doxygen 1.7.1 |