DecoyHelper Class Reference

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

#include <OpenMS/DATASTRUCTURES/FASTAContainer.h>

Collaboration diagram for DecoyHelper:

Classes
struct	DecoyStatistics
	struct for intermediate results needed for calculations on decoy proteins More...
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...
template<typename T >
static DecoyStatistics	countDecoys (FASTAContainer< T > &proteins)
	Function to count the occurrences of decoy strings in a given set of protein names. More...

Static Public Attributes
static const std::vector< std::string >	affixes = { "decoy", "dec", "reverse", "rev", "reversed", "__id_decoy", "xxx", "shuffled", "shuffle", "pseudo", "random" }
static const std::string	regexstr_prefix = std::string("^(") + ListUtils::concatenate<std::string>(affixes, "_*|") + "_*)"
static const std::string	regexstr_suffix = std::string("(_") + ListUtils::concatenate<std::string>(affixes, "*|_") + ")$"

Private Types
using	DecoyStringToAffixCount = std::unordered_map< std::string, std::pair< Size, Size > >
using	CaseInsensitiveToCaseSensitiveDecoy = std::unordered_map< std::string, std::string >

Detailed Description

Helper class for calculations on decoy proteins.

Member Typedef Documentation

CaseInsensitiveToCaseSensitiveDecoy

using CaseInsensitiveToCaseSensitiveDecoy = std::unordered_map<std::string, std::string>

private

DecoyStringToAffixCount

using DecoyStringToAffixCount = std::unordered_map<std::string, std::pair<Size, Size> >

private

Member Function Documentation

countDecoys()

static DecoyStatistics countDecoys ( FASTAContainer< T > &  proteins )

inlinestatic

Function to count the occurrences of decoy strings in a given set of protein names.

For tested decoy strings see DecoyHelper::affixes. Returns all data needed for interpretation (see DecoyHelper::DecoyStatistics).

References DecoyHelper::DecoyStatistics::all_prefix_occur, DecoyHelper::DecoyStatistics::all_proteins_count, DecoyHelper::DecoyStatistics::all_suffix_occur, DecoyHelper::DecoyStatistics::decoy_case_sensitive, DecoyHelper::DecoyStatistics::decoy_count, OpenMS::StringUtils::prefix(), DecoyHelper::regexstr_prefix, DecoyHelper::regexstr_suffix, OpenMS::StringUtils::suffix(), and String::toLower().

Referenced by DecoyHelper::findDecoyString().

findDecoyString()

static Result findDecoyString ( FASTAContainer< T > &  proteins )

inlinestatic

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

For tested decoy strings see DecoyHelper::affixes. 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 DecoyHelper::DecoyStatistics::all_prefix_occur, DecoyHelper::DecoyStatistics::all_proteins_count, DecoyHelper::DecoyStatistics::all_suffix_occur, DecoyHelper::countDecoys(), DecoyHelper::DecoyStatistics::decoy_case_sensitive, DecoyHelper::DecoyStatistics::decoy_count, OPENMS_LOG_DEBUG, OPENMS_LOG_ERROR, and OPENMS_LOG_WARN.

Member Data Documentation

affixes

const std::vector<std::string> affixes = { "decoy", "dec", "reverse", "rev", "reversed", "__id_decoy", "xxx", "shuffled", "shuffle", "pseudo", "random" }

inlinestatic

regexstr_prefix

const std::string regexstr_prefix = std::string("^(") + ListUtils::concatenate<std::string>(affixes, "_*|") + "_*)"

inlinestatic

Referenced by DecoyHelper::countDecoys().

regexstr_suffix

const std::string regexstr_suffix = std::string("(_") + ListUtils::concatenate<std::string>(affixes, "*|_") + ")$"

inlinestatic

Referenced by DecoyHelper::countDecoys().