IDDecoyProbability calculates probabilities using decoy approach. More...
#include <OpenMS/ANALYSIS/ID/IDDecoyProbability.h>
 
  
 | Classes | |
| struct | Transformation_ | 
| struct to be used to store a transformation (used for fitting)  More... | |
| Public Member Functions | |
| IDDecoyProbability () | |
| Default constructor.  More... | |
| IDDecoyProbability (const IDDecoyProbability &rhs) | |
| Copy constructor.  More... | |
| virtual | ~IDDecoyProbability () | 
| Desctructor.  More... | |
| IDDecoyProbability & | operator= (const IDDecoyProbability &rhs) | 
| assignment operator  More... | |
| void | apply (std::vector< PeptideIdentification > &prob_ids, const std::vector< PeptideIdentification > &fwd_ids, const std::vector< PeptideIdentification > &rev_ids) | 
| void | apply (std::vector< PeptideIdentification > &ids) | 
|  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... | |
| Protected Member Functions | |
| void | normalizeBins_ (const std::vector< DoubleReal > &scores, std::vector< DoubleReal > &binned, Transformation_ &trafo) | 
| DoubleReal | getProbability_ (const Math::GammaDistributionFitter::GammaDistributionFitResult &result_gamma, const Transformation_ &gamma_trafo, const Math::GaussFitter::GaussFitResult &result_gauss, const Transformation_ &gauss_trafo, DoubleReal score) | 
| void | generateDistributionImage_ (const std::vector< DoubleReal > &ids, const String &formula, const String &filename) | 
| void | generateDistributionImage_ (const std::vector< DoubleReal > &all_ids, const Transformation_ &all_trans, const String &fwd_formula, const String &rev_formula, const String &filename) | 
| void | apply_ (std::vector< PeptideIdentification > &ids, const std::vector< DoubleReal > &rev_scores, const std::vector< DoubleReal > &fwd_scores, const std::vector< DoubleReal > &all_scores) | 
|  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... | |
| Additional Inherited Members | |
|  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... | |
IDDecoyProbability calculates probabilities using decoy approach.
This class calcalates the probabilities using a target deocy approach. Like in peptide prophet the forward distribution is modeled using a gaussian distribution the reverse scores are modeled using a gamma distribution.
Default constructor.
| IDDecoyProbability | ( | const IDDecoyProbability & | rhs | ) | 
Copy constructor.
| 
 | virtual | 
Desctructor.
| void apply | ( | std::vector< PeptideIdentification > & | prob_ids, | 
| const std::vector< PeptideIdentification > & | fwd_ids, | ||
| const std::vector< PeptideIdentification > & | rev_ids | ||
| ) | 
converts the forward and reverse identification into probabilities
| prob_ids | Output of the algorithm which includes identifications with probability based scores | 
| fwd_ids | Input parameter which represents the identifications of the forward search | 
| rev_ids | Input parameter which represents the identifications of the reversed search | 
| void apply | ( | std::vector< PeptideIdentification > & | ids | ) | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
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 | protected | 
| IDDecoyProbability& operator= | ( | const IDDecoyProbability & | rhs | ) | 
assignment operator
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:26 using doxygen 1.8.5 |