PrecursorIonSelectionPreprocessing.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Alexandra Zerck $
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#ifndef OPENMS_ANALYSIS_TARGETED_PRECURSORIONSELECTIONPREPROCESSING_H
#define OPENMS_ANALYSIS_TARGETED_PRECURSORIONSELECTIONPREPROCESSING_H

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/FORMAT/FASTAFile.h>
#include <OpenMS/KERNEL/FeatureMap.h>

#include <algorithm>
#include <cmath>
#include <set>
#include <fstream>
namespace OpenMS
{

  class OPENMS_DLLAPI PrecursorIonSelectionPreprocessing :
    public DefaultParamHandler
  {
public:
    PrecursorIonSelectionPreprocessing();
    PrecursorIonSelectionPreprocessing(const PrecursorIonSelectionPreprocessing & source);
    ~PrecursorIonSelectionPreprocessing();

    PrecursorIonSelectionPreprocessing & operator=(const PrecursorIonSelectionPreprocessing & source);


    const std::map<String, std::vector<DoubleReal> > & getProtMasses() const;


    const std::vector<DoubleReal> & getMasses(String acc) const;

    const std::map<String, std::vector<DoubleReal> > & getProteinRTMap() const;
    const std::map<String, std::vector<DoubleReal> > & getProteinPTMap() const;
    const std::map<String, std::vector<String> > & getProteinPeptideSequenceMap() const;


    void dbPreprocessing(String db_path, bool save = true);

    void dbPreprocessing(String db_path, String rt_model_path, String dt_model_path, bool save = true);


    void loadPreprocessing();

    DoubleReal getWeight(DoubleReal mass);

    DoubleReal getRT(String prot_id, Size peptide_index);

    DoubleReal getPT(String prot_id, Size peptide_index);

    void setFixedModifications(StringList & modifications);
    const std::map<char, std::vector<String> > & getFixedModifications()
    {
      return fixed_modifications_;
    }

    void setGaussianParameters(DoubleReal mu, DoubleReal sigma);
    DoubleReal getGaussMu()
    {
      return mu_;
    }

    DoubleReal getGaussSigma()
    {
      return sigma_;
    }

    DoubleReal getRTProbability(String prot_id, Size peptide_index, Feature & feature);
    DoubleReal getRTProbability(DoubleReal pred_rt, Feature & feature);

protected:
    void savePreprocessedDB_(String db_path, String path);
    void savePreprocessedDBWithRT_(String db_path, String path);
    void loadPreprocessedDB_(String path);
    void filterTaxonomyIdentifier_(FASTAFile::FASTAEntry & entry);
    Int getScanNumber_(DoubleReal rt);
    DoubleReal getRTProbability_(DoubleReal min_obs_rt, DoubleReal max_obs_rt, DoubleReal pred_rt);
    void updateMembers_();

    std::vector<DoubleReal> masses_;
    std::set<AASequence> sequences_;
    std::map<String, std::vector<DoubleReal> > prot_masses_;
    std::vector<DoubleReal> bin_masses_;
    std::vector<UInt> counter_;
    UInt f_max_;

    bool fixed_mods_;
    std::map<String, std::vector<DoubleReal> > rt_prot_map_;
    std::map<String, std::vector<DoubleReal> > pt_prot_map_;
    std::map<String, std::vector<String> > prot_peptide_seq_map_;
    std::map<char, std::vector<String> > fixed_modifications_;
    DoubleReal sigma_;
    DoubleReal mu_;


  };
}

#endif //#ifndef OPENMS_ANALYSIS_ID_PRECURSORIONSELECTIONPREPROCESSING_H