ModificationsDB.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/DATASTRUCTURES/StringUtils.h>
#include <OpenMS/CHEMISTRY/ResidueModification.h>
#include <OpenMS/CHEMISTRY/ModificationDataProvider.h>
 
#include <set>
#include <memory>  // unique_ptr
#include <unordered_map>
 
namespace OpenMS
{
  // forward declarations
  class ResidueModification;
  class Residue;
 
  class OPENMS_DLLAPI ModificationsDB
  {
public:
 
    static const ModificationsDB* getInstance();
 
    static const ModificationsDB* initializeModificationsDB(std::string unimod_file = "CHEMISTRY/unimod.xml", std::string custommod_file = "CHEMISTRY/custom_mods.xml", std::string psimod_file = "CHEMISTRY/PSI-MOD.obo", std::string xlmod_file = "CHEMISTRY/XLMOD.obo");
 
    static bool isInstantiated();
 
    explicit ModificationsDB(std::vector<std::unique_ptr<ModificationDataProvider>> providers);
 
    virtual ~ModificationsDB();
 
    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 std::string& mod_name,
                             const std::string& residue = "",
                             ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const;
 
   const ResidueModification* searchModification(const ResidueModification& mod_in) const;
 
    const ResidueModification* searchModificationsFast(const std::string& mod_name,
                                                       bool& multiple_matches,
                                                       const std::string& residue = "",
                                                       ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const;
 
    const ResidueModification* getModification(const std::string& mod_name, const std::string& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const;
 
    bool has(const std::string& modification) const;
 
    const ResidueModification* addModification(std::unique_ptr<ResidueModification> new_mod) const;
 
    const ResidueModification* addModification(const ResidueModification& new_mod) const;
 
    Size findModificationIndex(const std::string& mod_name) const;
 
    void searchModificationsByDiffMonoMass(std::vector<std::string>& mods, double mass, double max_error, const std::string& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const;
    void searchModificationsByDiffMonoMass(std::vector<const ResidueModification*>& mods, double mass, double max_error, const std::string& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const;
 
    void searchModificationsByDiffMonoMassSorted(std::vector<std::string>& mods, double mass, double max_error, const std::string& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const;
    void searchModificationsByDiffMonoMassSorted(std::vector<const ResidueModification*>& mods, double mass, double max_error, const std::string& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const;
 
 
    const ResidueModification* getBestModificationByDiffMonoMass(double mass, double max_error, const std::string& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const;
 
    void getAllSearchModifications(std::vector<std::string>& modifications) const;
 
    void writeTSV(const std::string& filename) const;
 
  protected:
 
    static bool is_instantiated_;
 
    mutable std::vector<ResidueModification*> mods_;
 
    mutable std::unordered_map<std::string, std::set<const ResidueModification*> > modification_names_;
 
    bool residuesMatch_(const char residue, const ResidueModification* curr_mod) const;
 
private:
 
    ModificationsDB(const ModificationsDB& residue_db);
 
    ModificationsDB & operator=(const ModificationsDB& aa);
 
    const ResidueModification* addNewModification_(const ResidueModification& new_mod) const;
 
    void loadFromProviders_(std::vector<std::unique_ptr<ModificationDataProvider>>& providers);
  };
}