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OpenMS
2.5.0
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Go to the documentation of this file.
40 #include <unordered_set>
95 void compute(
FeatureMap& features,
const std::vector<FASTAFile::FASTAEntry>& contaminants);
98 const String& getName()
const override;
101 const std::vector<Contaminants::ContaminantsSummary>& getResults();
107 Status requires()
const override;
114 std::vector<Contaminants::ContaminantsSummary>
results_;
130 void compare_(
const String& key,
PeptideHit& pep_hit,
Int64& total,
Int64& cont,
double& sum_total,
double& sum_cont,
double intensity);
Storing a status of available/needed inputs (i.e. a set of Requires) as UInt64.
Definition: QCBase.h:118
A more convenient string class.
Definition: String.h:58
OPENMS_INT64_TYPE Int64
Signed integer type (64bit)
Definition: Types.h:70
double unassigned_contaminants_ratio
(# contaminants in unassigned/ #peptides in unassigned)
Definition: Contaminants.h:62
structure for storing results
Definition: Contaminants.h:56
std::pair< Int64, Int64 > empty_features
(features without peptideidentification or with peptideidentifications but without hits; all features...
Definition: Contaminants.h:71
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
std::vector< Contaminants::ContaminantsSummary > results_
container that stores results
Definition: Contaminants.h:114
double assigned_contaminants_ratio
(# contaminants in assigned/ #peptides in assigned)
Definition: Contaminants.h:59
This class serves as an abstract base class for all QC classes.
Definition: QCBase.h:52
double all_contaminants_ratio
(# all contaminants/ #peptides in all)
Definition: Contaminants.h:65
double assigned_contaminants_intensity_ratio
(intensity of contaminants in assigned/ intensity of peptides in assigned)
Definition: Contaminants.h:68
This class is a metric for the QualityControl TOPP tool.
Definition: Contaminants.h:52
A container for features.
Definition: FeatureMap.h:95
std::unordered_set< String > digested_db_
unordered set that contains the contaminant sequences
Definition: Contaminants.h:117
Representation of a peptide hit.
Definition: PeptideHit.h:54