PSProteinInference.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Alexandra Zerck $
// $Authors: Alexandra Zerck $
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#ifndef OPENMS_ANALYSIS_TARGETED_PSPROTEININFERENCE_H
#define OPENMS_ANALYSIS_TARGETED_PSPROTEININFERENCE_H

#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/DATASTRUCTURES/LPWrapper.h>

namespace OpenMS
{

  class OPENMS_DLLAPI PSProteinInference
  {
public:

    PSProteinInference();

    virtual ~PSProteinInference();


    Size findMinimalProteinList(const std::vector<PeptideIdentification> & peptide_ids);

    void calculateProteinProbabilities(const std::vector<PeptideIdentification> & ids);

//     DoubleReal getProteinProbability(const String& acc,const std::vector<String>& accessions, const std::vector<DoubleReal>& probabilities);

    DoubleReal getProteinProbability(const String & acc);

    bool isProteinInMinimalList(const String & acc);
    Int getNumberOfProtIds(DoubleReal protein_id_threshold);
    Int getNumberOfProtIdsPeptideRule(Int min_peptides, std::map<String, std::set<String> > & prot_id_counter);

    void setSolver(LPWrapper::SOLVER solver)
    {
      solver_ = solver;
    }

    LPWrapper::SOLVER getSolver()
    {
      return solver_;
    }

private:
    std::vector<String> minimal_protein_list_accessions_;
    std::vector<String> accessions_;
    std::vector<DoubleReal> probabilities_;
    LPWrapper::SOLVER solver_;
  };

}



#endif // #ifndef OPENMS_ANALYSIS_TARGETED_PSPROTEININFERENCE_H