36 #ifndef OPENMS_ANALYSIS_TARGETED_PRECURSORIONSELECTION_H 37 #define OPENMS_ANALYSIS_TARGETED_PRECURSORIONSELECTION_H 46 class PrecursorIonSelectionPreprocessing;
47 class PSProteinInference;
89 const double & getMaxScore()
const;
90 void setMaxScore(
const double & max_score);
95 std::binary_function<Feature, Feature, bool>
106 std::binary_function<Feature, Feature, bool>
110 if (left.
getRT() < right.
getRT())
return true;
111 else if (left.
getRT() > right.
getRT())
return false;
137 void getNextPrecursors(std::vector<Int> & solution_indices, std::vector<PSLPFormulation::IndexTriple> & variable_indices, std::set<Int> & measured_variables,
163 void rescore(
FeatureMap & features, std::vector<PeptideIdentification> & new_pep_ids,
164 std::vector<ProteinIdentification> & prot_ids,
178 void simulateRun(
FeatureMap & features, std::vector<PeptideIdentification> & pep_ids,
179 std::vector<ProteinIdentification> & prot_ids,
186 std::cout <<
" LPSolver set to " << solver_ << std::endl;
198 return prot_id_counter_;
203 std::vector<PeptideIdentification> & pep_ids,
204 std::vector<ProteinIdentification> & prot_ids,
208 void simulateRun_(
FeatureMap & features, std::vector<PeptideIdentification> & pep_ids,
209 std::vector<ProteinIdentification> & prot_ids,
217 void updateMembers_();
219 void rescore_(
FeatureMap & features, std::vector<PeptideIdentification> & new_pep_ids,
227 void checkForRequiredUserParams_(
FeatureMap & features);
234 UInt filterProtIds_(std::vector<ProteinIdentification> & prot_ids);
236 std::vector<PeptideIdentification> filterPeptideIds_(std::vector<PeptideIdentification> & pep_ids);
238 void convertPeptideIdScores_(std::vector<PeptideIdentification> & pep_ids);
264 #endif // #ifndef OPENMS_ANALYSIS_ID_PRECURSORIONSELECTION_H Definition: PrecursorIonSelection.h:77
void setLPSolver(LPWrapper::SOLVER solver)
Definition: PrecursorIonSelection.h:183
LPWrapper::SOLVER getLPSolver()
Definition: PrecursorIonSelection.h:189
double max_score_
maximal score in the FeatureMap
Definition: PrecursorIonSelection.h:243
A more convenient string class.
Definition: String.h:57
Size x_variable_number_
Definition: PrecursorIonSelection.h:256
SOLVER
Definition: LPWrapper.h:129
Type type_
precursor ion selection strategy
Definition: PrecursorIonSelection.h:245
A container for features.
Definition: FeatureMap.h:94
unsigned int UInt
Unsigned integer type.
Definition: Types.h:95
Compare by score.
Definition: PrecursorIonSelection.h:105
Definition: PrecursorIonSelection.h:78
Definition: PrecursorIonSelection.h:80
double mz_tolerance_
precursor ion error tolerance
Definition: PrecursorIonSelection.h:251
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Definition: PrecursorIonSelection.h:79
void sortByTotalScore(FeatureMap &features)
Sort features by total score.
Definition: PrecursorIonSelection.h:121
This class implements the database preprocessing needing for precursor ion selection.
Definition: PrecursorIonSelectionPreprocessing.h:56
Type
Precursor ion selection type (iterative, static, upshift, downshift, dynamic exclusion).
Definition: PrecursorIonSelection.h:75
bool operator()(Feature const &left, Feature const &right) const
Definition: PrecursorIonSelection.h:97
bool operator()(Feature const &left, Feature const &right) const
Definition: PrecursorIonSelection.h:108
Base::iterator Iterator
Definition: FeatureMap.h:138
An LC-MS feature.
Definition: Feature.h:70
String mz_tolerance_unit_
precursor ion error tolerance unit (ppm or Da)
Definition: PrecursorIonSelection.h:253
This class implements protein inference for the precursor ion selection strategies.
Definition: PSProteinInference.h:53
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:82
CoordinateType getRT() const
Returns the RT coordinate (index 0)
Definition: Peak2D.h:209
const std::map< String, std::set< String > > & getPeptideProteinCounter()
Definition: PrecursorIonSelection.h:196
std::vector< Size > fraction_counter_
stores the number of selected precursors per fraction
Definition: PrecursorIonSelection.h:249
UInt min_pep_ids_
minimal number of peptides identified for a protein to be declared identified
Definition: PrecursorIonSelection.h:241
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:128
Compare by score.
Definition: PrecursorIonSelection.h:94
UInt max_iteration_
maximal number of iterations
Definition: PrecursorIonSelection.h:255
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
LPWrapper::SOLVER solver_
Definition: PrecursorIonSelection.h:258
std::map< String, std::set< String > > prot_id_counter_
stores the peptide sequences for all protein identifications
Definition: PrecursorIonSelection.h:247
Definition: PrecursorIonSelection.h:81
This class implements different precursor ion selection strategies.
Definition: PrecursorIonSelection.h:53