Contaminants Class Reference

This class is a metric for the QualityControl TOPP tool. More...

#include <OpenMS/QC/Contaminants.h>

Inheritance diagram for Contaminants:

Collaboration diagram for Contaminants:

Classes
struct	ContaminantsSummary
	structure for storing results More...

Public Member Functions
	Contaminants ()=default
	Constructor. More...
virtual	~Contaminants ()=default
	Destructor. More...
void	compute (FeatureMap &features, const std::vector< FASTAFile::FASTAEntry > &contaminants)
	Checks if the peptides are in the contaminant database. More...
const String &	getName () const override
	returns the name of the metric More...
const std::vector< Contaminants::ContaminantsSummary > &	getResults ()
	returns results More...
Status	requires () const override
	Returns the input data requirements of the compute(...) function. More...
Public Member Functions inherited from QCBase
bool	isRunnable (const Status &s) const

Private Member Functions
void	compare_ (const String &key, PeptideHit &pep_hit, Int64 &total, Int64 &cont, double &sum_total, double &sum_cont, double intensity)
	checks if the peptide is in the contaminant database More...

Private Attributes
const String	name_ = "Contaminants"
	name of the metric More...
std::vector< Contaminants::ContaminantsSummary >	results_
	container that stores results More...
std::unordered_set< String >	digested_db_
	unordered set that contains the contaminant sequences More...

Additional Inherited Members
Public Types inherited from QCBase
enum class	Requires : UInt64 {   NOTHING , RAWMZML , POSTFDRFEAT , PREFDRFEAT ,   CONTAMINANTS , TRAFOALIGN , ID , SIZE_OF_REQUIRES }
	Enum to encode a file type as a bit. More...
enum class	ToleranceUnit { AUTO , PPM , DA , SIZE_OF_TOLERANCEUNIT }
using	Status = FlagSet< Requires >
Static Public Member Functions inherited from QCBase
static bool	isLabeledExperiment (const ConsensusMap &cm)
	check if the IsobaricAnalyzer TOPP tool was used to create this ConsensusMap More...
template<typename MAP >
static bool	hasPepID (const MAP &fmap)
	does the container have a PeptideIdentification in its members or as unassignedPepID ? More...
Static Public Attributes inherited from QCBase
static const std::string	names_of_requires []
	strings corresponding to enum Requires More...
static const std::string	names_of_toleranceUnit []
	strings corresponding to enum ToleranceUnit More...

Detailed Description

This class is a metric for the QualityControl TOPP tool.

This class checks whether a peptide is a contaminant (given a protein DB) and adds that result as metavalue "is_contaminant" to the first hit of each PeptideIdentification.

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Class Documentation

OpenMS::Contaminants::ContaminantsSummary

struct OpenMS::Contaminants::ContaminantsSummary

structure for storing results

Collaboration diagram for Contaminants::ContaminantsSummary:

Class Members
double	all_contaminants_ratio	(#all contaminants/ #peptides in all)
double	assigned_contaminants_intensity_ratio	(intensity of contaminants in assigned/ intensity of peptides in assigned)
double	assigned_contaminants_ratio	(#contaminants in assigned/ #peptides in assigned)
pair< Int64, Int64 >	empty_features	(features without peptideidentification or with peptideidentifications but without hits; all features)
double	unassigned_contaminants_ratio	(#contaminants in unassigned/ #peptides in unassigned)

Constructor & Destructor Documentation

Contaminants()

Contaminants ( )

default

Constructor.

~Contaminants()

virtual ~Contaminants ( )

virtualdefault

Destructor.

Member Function Documentation

compare_()

void compare_ ( const String &  key, PeptideHit &  pep_hit, Int64 &  total, Int64 &  cont, double &  sum_total, double &  sum_cont, double  intensity  )

private

checks if the peptide is in the contaminant database

Parameters

key	String that will be the key for searching in the unordered set
pep_hit	PeptideHit to store the result "is_contaminant = 0/1"
total	counter of all checked peptides
cont	counter of all checked peptides that are contaminants
sum_total	intensity of all checked peptides
sum_cont	intensity of all checked peptides that are contaminants
intensity	intensity of current peptide

compute()

void compute	(	FeatureMap &	features,
		const std::vector< FASTAFile::FASTAEntry > &	contaminants
	)

Checks if the peptides are in the contaminant database.

"is_contaminant" metavalue is added to the first hit of each PeptideIdentification of each feature and to the first hit of all unsigned PeptideIdentifications. The enzyme and number of missed cleavages used to digest the given protein DB is taken from the ProteinIdentification[0].getSearchParameters() within the given FeatureMap.

Parameters

features	Input FeatureMap with peptideidentifications of features
contaminants	Vector of FASTAEntries that need to be digested to check whether a peptide is a contaminant or not

Exceptions

Exception::MissingInformation	if the contaminants database is empty
Exception::MissingInformation	if no enzyme is given
Exception::MissingInformation	if proteinidentification of FeatureMap is empty

Warning

LOG_WARN if the FeatureMap is empty

getName()

const String& getName ( ) const

overridevirtual

returns the name of the metric

Implements QCBase.

getResults()

const std::vector<Contaminants::ContaminantsSummary>& getResults

(

)

returns results

requires()

Status requires ( ) const

overridevirtual

Returns the input data requirements of the compute(...) function.

Returns

Status for POSTFDRFEAT and CONTAMINANTS

Implements QCBase.

Member Data Documentation

digested_db_

std::unordered_set<String> digested_db_

private

unordered set that contains the contaminant sequences

name_

const String name_ = "Contaminants"

private

name of the metric

results_

std::vector<Contaminants::ContaminantsSummary> results_

private

container that stores results