36 #ifndef OPENMS_ANALYSIS_TARGETED_PRECURSORIONSELECTION_H 
   37 #define OPENMS_ANALYSIS_TARGETED_PRECURSORIONSELECTION_H 
   46   class PrecursorIonSelectionPreprocessing;
 
   47   class PSProteinInference;
 
   90     void setMaxScore(
const DoubleReal & 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
A more convenient string class. 
Definition: String.h:56
Size x_variable_number_
Definition: PrecursorIonSelection.h:256
SOLVER
Definition: LPWrapper.h:124
Type type_
precursor ion selection strategy 
Definition: PrecursorIonSelection.h:245
Compare by score. 
Definition: PrecursorIonSelection.h:105
Definition: PrecursorIonSelection.h:78
Definition: PrecursorIonSelection.h:80
CoordinateType getRT() const 
Returns the RT coordinate (index 0) 
Definition: Peak2D.h:203
Definition: PrecursorIonSelection.h:79
DoubleReal max_score_
maximal score in the FeatureMap 
Definition: PrecursorIonSelection.h:243
void sortByTotalScore(FeatureMap<> &features)
Sort features by total score. 
Definition: PrecursorIonSelection.h:121
bool operator()(Feature const &left, Feature const &right) const 
Definition: PrecursorIonSelection.h:97
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:108
An LC-MS feature. 
Definition: Feature.h:66
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
Representation of a mass spectrometry experiment. 
Definition: MSExperiment.h:68
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:144
Compare by score. 
Definition: PrecursorIonSelection.h:94
UInt max_iteration_
maximal number of iterations 
Definition: PrecursorIonSelection.h:255
DoubleReal mz_tolerance_
precursor ion error tolerance 
Definition: PrecursorIonSelection.h:251
A base class for all classes handling default parameters. 
Definition: DefaultParamHandler.h:90
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
double DoubleReal
Double-precision real type. 
Definition: Types.h:118