OpenMS  2.6.0
Classes | Static Public Member Functions | Private Types | List of all members
DecoyHelper Class Reference

Helper class for calculcations on decoy proteins. More...

#include <OpenMS/DATASTRUCTURES/FASTAContainer.h>

Classes

struct  Result
 

Static Public Member Functions

template<typename T >
static Result findDecoyString (FASTAContainer< T > &proteins)
 Heuristic to determine the decoy string given a set of protein names. More...
 

Private Types

using DecoyStringToAffixCount = std::map< std::string, std::pair< int, int > >
 
using CaseInsensitiveToCaseSensitiveDecoy = std::map< std::string, std::string >
 

Detailed Description

Helper class for calculcations on decoy proteins.


Class Documentation

◆ OpenMS::DecoyHelper::Result

struct OpenMS::DecoyHelper::Result
Collaboration diagram for DecoyHelper::Result:
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Class Members
bool is_prefix
String name
bool success

Member Typedef Documentation

◆ CaseInsensitiveToCaseSensitiveDecoy

using CaseInsensitiveToCaseSensitiveDecoy = std::map<std::string, std::string>
private

◆ DecoyStringToAffixCount

using DecoyStringToAffixCount = std::map<std::string, std::pair<int, int> >
private

Member Function Documentation

◆ findDecoyString()

static Result findDecoyString ( FASTAContainer< T > &  proteins)
inlinestatic

Heuristic to determine the decoy string given a set of protein names.

Tested decoy strings are "decoy", "dec", "reverse", "rev", "__id_decoy", "xxx", "shuffled", "shuffle", "pseudo" and "random". Both prefix and suffix is tested and if one of the candidates above is found in at least 40% of all proteins, it is returned as the winner (see DecoyHelper::Result).

References OPENMS_LOG_DEBUG, OPENMS_LOG_ERROR, OPENMS_LOG_WARN, StringUtils::prefix(), StringUtils::suffix(), and String::toLower().

Referenced by PeptideIndexing::run().