SpectrumCheapDPCorr calculates an optimal alignment on stick spectra. More...
#include <OpenMS/COMPARISON/SPECTRA/SpectrumCheapDPCorr.h>
 
  
 | Public Member Functions | |
| SpectrumCheapDPCorr () | |
| default constructor  More... | |
| SpectrumCheapDPCorr (const SpectrumCheapDPCorr &source) | |
| copy constructor  More... | |
| virtual | ~SpectrumCheapDPCorr () | 
| destructor  More... | |
| SpectrumCheapDPCorr & | operator= (const SpectrumCheapDPCorr &source) | 
| assignment operator  More... | |
| double | operator() (const PeakSpectrum &a, const PeakSpectrum &b) const | 
| function call operator, calculates the similarity  More... | |
| double | operator() (const PeakSpectrum &a) const | 
| calculates self similarity  More... | |
|  Public Member Functions inherited from PeakSpectrumCompareFunctor | |
| PeakSpectrumCompareFunctor () | |
| default constructor  More... | |
| PeakSpectrumCompareFunctor (const PeakSpectrumCompareFunctor &source) | |
| copy constructor  More... | |
| virtual | ~PeakSpectrumCompareFunctor () | 
| destructor  More... | |
| PeakSpectrumCompareFunctor & | operator= (const PeakSpectrumCompareFunctor &source) | 
| assignment operator  More... | |
|  Public Member Functions inherited from DefaultParamHandler | |
| DefaultParamHandler (const String &name) | |
| Constructor with name that is displayed in error messages.  More... | |
| DefaultParamHandler (const DefaultParamHandler &rhs) | |
| Copy constructor.  More... | |
| virtual | ~DefaultParamHandler () | 
| Destructor.  More... | |
| virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) | 
| Assignment operator.  More... | |
| virtual bool | operator== (const DefaultParamHandler &rhs) const | 
| Equality operator.  More... | |
| void | setParameters (const Param ¶m) | 
| Sets the parameters.  More... | |
| const Param & | getParameters () const | 
| Non-mutable access to the parameters.  More... | |
| const Param & | getDefaults () const | 
| Non-mutable access to the default parameters.  More... | |
| const String & | getName () const | 
| Non-mutable access to the name.  More... | |
| void | setName (const String &name) | 
| Mutable access to the name.  More... | |
| const std::vector< String > & | getSubsections () const | 
| Non-mutable access to the registered subsections.  More... | |
| Private Member Functions | |
| double | dynprog_ (const PeakSpectrum &, const PeakSpectrum &, int, int, int, int) const | 
| O(n^2) dynamical programming.  More... | |
| double | comparepeaks_ (double posa, double posb, double inta, double intb) const | 
| similarity of two peaks  More... | |
| Private Attributes | |
| PeakSpectrum | lastconsensus_ | 
| consensus spectrum of the last comparison  More... | |
| bool | keeppeaks_ | 
| should peaks with no alignment partner be kept in the consensus?  More... | |
| double | factor_ | 
| weighting factor for the next consensus spectrum  More... | |
| Map< UInt, UInt > | peak_map_ | 
| last peak map  More... | |
| Static Private Attributes | |
| static const String | info_ | 
| const PeakSpectrum & | lastconsensus () const | 
| return consensus spectrum from last funtion call operator  More... | |
| Map< UInt, UInt > | getPeakMap () const | 
| void | setFactor (double f) | 
| set weighting of the second spectrum for consensus from next function call operator  More... | |
| static PeakSpectrumCompareFunctor * | create () | 
| static const String | getProductName () | 
| Additional Inherited Members | |
|  Static Public Member Functions inherited from PeakSpectrumCompareFunctor | |
| static void | registerChildren () | 
| registers all derived products  More... | |
| static const String | getProductName () | 
|  Protected Member Functions inherited from DefaultParamHandler | |
| virtual void | updateMembers_ () | 
| This method is used to update extra member variables at the end of the setParameters() method.  More... | |
| void | defaultsToParam_ () | 
| Updates the parameters after the defaults have been set in the constructor.  More... | |
|  Protected Attributes inherited from DefaultParamHandler | |
| Param | param_ | 
| Container for current parameters.  More... | |
| Param | defaults_ | 
| Container for default parameters. This member should be filled in the constructor of derived classes!  More... | |
| std::vector< String > | subsections_ | 
| Container for registered subsections. This member should be filled in the constructor of derived classes!  More... | |
| String | error_name_ | 
| Name that is displayed in error messages during the parameter checking.  More... | |
| bool | check_defaults_ | 
| If this member is set to false no checking if parameters in done;.  More... | |
| bool | warn_empty_defaults_ | 
| If this member is set to false no warning is emitted when defaults are empty;.  More... | |
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. | 
default constructor
| SpectrumCheapDPCorr | ( | const SpectrumCheapDPCorr & | source | ) | 
copy constructor
| 
 | virtual | 
destructor
similarity of two peaks
| 
 | inlinestatic | 
| 
 | private | 
O(n^2) dynamical programming.
| 
 | inlinestatic | 
| const PeakSpectrum& lastconsensus | ( | ) | const | 
return consensus spectrum from last funtion call operator
| 
 | virtual | 
function call operator, calculates the similarity
Implements PeakSpectrumCompareFunctor.
| 
 | 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
| 
 | mutableprivate | 
weighting factor for the next consensus spectrum
| 
 | staticprivate | 
| 
 | private | 
should peaks with no alignment partner be kept in the consensus?
| 
 | mutableprivate | 
consensus spectrum of the last comparison
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:28 using doxygen 1.8.5 |