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OpenMS
2.8.0
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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... | |
| ~IDDecoyProbability () override | |
| Destructor. 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) |
| Converts the forward and reverse identification into probabilities. More... | |
| 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< double > &scores, std::vector< double > &binned, Transformation_ &trafo) |
| double | getProbability_ (const Math::GammaDistributionFitter::GammaDistributionFitResult &result_gamma, const Transformation_ &gamma_trafo, const Math::GaussFitter::GaussFitResult &result_gauss, const Transformation_ &gauss_trafo, double score) |
| void | generateDistributionImage_ (const std::vector< double > &ids, const String &formula, const String &filename) |
| void | generateDistributionImage_ (const std::vector< double > &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< double > &rev_scores, const std::vector< double > &fwd_scores, const std::vector< double > &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 | |
| Static Public Member Functions inherited from DefaultParamHandler | |
| static void | writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="") |
| Writes all parameters to meta values. 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... | |
IDDecoyProbability calculates probabilities using decoy approach.
This class calculates the probabilities using a target decoy 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.
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override |
Destructor.
| void apply | ( | std::vector< PeptideIdentification > & | ids | ) |
| 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 |
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| IDDecoyProbability& operator= | ( | const IDDecoyProbability & | rhs | ) |
assignment operator
1.9.1
