ModificationsDB.h

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// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
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#pragma once

#include "OpenMS/CHEMISTRY/AASequence.h"
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/CHEMISTRY/ResidueModification.h>

#include <set>
#include <memory>  // unique_ptr
#include <unordered_map>

namespace OpenMS
{
  // forward declarations
  class ResidueModification;
  class Residue;

  class OPENMS_DLLAPI ModificationsDB
  {
public:

    static ModificationsDB* getInstance();

    static ModificationsDB* initializeModificationsDB(OpenMS::String unimod_file = "CHEMISTRY/unimod.xml", OpenMS::String psimod_file = "CHEMISTRY/PSI-MOD.obo", OpenMS::String xlmod_file = "CHEMISTRY/XLMOD.obo");

    static bool isInstantiated();

    friend class CrossLinksDB;
    // for access to addNewModification_ (without checking presence)
    friend class Residue;
    friend class AASequence;

    Size getNumberOfModifications() const;

    const ResidueModification* getModification(Size index) const;

    void searchModifications(std::set<const ResidueModification*>& mods,
                             const String& mod_name,
                             const String& residue = "",
                             ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const;

   const ResidueModification* searchModification(const ResidueModification& mod_in) const;

    const ResidueModification* searchModificationsFast(const String& mod_name,
                                                       bool& multiple_matches,
                                                       const String& residue = "",
                                                       ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const;

    const ResidueModification* getModification(const String& mod_name, const String& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const;

    bool has(const String& modification) const;

    const ResidueModification* addModification(std::unique_ptr<ResidueModification> new_mod);

    const ResidueModification* addModification(const ResidueModification& new_mod);

    Size findModificationIndex(const String& mod_name) const;

    void searchModificationsByDiffMonoMass(std::vector<String>& mods, double mass, double max_error, const String& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY);
    void searchModificationsByDiffMonoMass(std::vector<const ResidueModification*>& mods, double mass, double max_error, const String& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY);

    void searchModificationsByDiffMonoMassSorted(std::vector<String>& mods, double mass, double max_error, const String& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY);
    void searchModificationsByDiffMonoMassSorted(std::vector<const ResidueModification*>& mods, double mass, double max_error, const String& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY);


    const ResidueModification* getBestModificationByDiffMonoMass(double mass, double max_error, const String& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY);

    void getAllSearchModifications(std::vector<String>& modifications) const;

    void writeTSV(const String& filename);

  protected:

    static bool is_instantiated_;

    std::vector<ResidueModification*> mods_;

    std::unordered_map<String, std::set<const ResidueModification*> > modification_names_;

    bool residuesMatch_(const char residue, const ResidueModification* curr_mod) const;

private:

    explicit ModificationsDB(const OpenMS::String& unimod_file = "CHEMISTRY/unimod.xml", const OpenMS::String& psimod_file = "CHEMISTRY/PSI-MOD.obo", const OpenMS::String& xlmod_file = "CHEMISTRY/XLMOD.obo");

    ModificationsDB(const ModificationsDB& residue_db);

    virtual ~ModificationsDB();

    ModificationsDB & operator=(const ModificationsDB& aa);

    const ResidueModification* addNewModification_(const ResidueModification& new_mod);

    void readFromOBOFile(const String& filename);

    void readFromUnimodXMLFile(const String& filename);
  };
}