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) |
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| 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
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inlinestatic |
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private |
O(n^2) dynamical programming.
|
inlinestatic |
| const PeakSpectrum& lastconsensus | ( | ) | const |
return consensus spectrum from last funtion call operator
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virtual |
function call operator, calculates the similarity
Implements PeakSpectrumCompareFunctor.
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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
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mutableprivate |
weighting factor for the next consensus spectrum
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staticprivate |
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private |
should peaks with no alignment partner be kept in the consensus?
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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 |