ModificationsDB.h

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// $Maintainer: Stephan Aiche $
// $Authors: Andreas Bertsch $
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#ifndef OPENMS_CHEMISTRY_MODIFICATIONSDB_H
#define OPENMS_CHEMISTRY_MODIFICATIONSDB_H

#include <OpenMS/DATASTRUCTURES/Map.h>
#include <OpenMS/CHEMISTRY/ResidueModification.h>

#include <set>

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

  class OPENMS_DLLAPI ModificationsDB
  {
public:

    inline static ModificationsDB * getInstance()
    {
      static ModificationsDB * db_ = 0;
      if (db_ == 0)
      {
        db_ = new ModificationsDB;
      }
      return db_;
    }

    Size getNumberOfModifications() const;

    const ResidueModification & getModification(Size index) const;

    void searchTerminalModifications(std::set<const ResidueModification *> & mods, const String & name, ResidueModification::Term_Specificity term_spec) const;

    void searchModifications(std::set<const ResidueModification *> & mods, const String & orgin, const String & mod_name, ResidueModification::Term_Specificity term_spec) const;

    void searchModifications(std::set<const ResidueModification *> & mods, const String & mod_name, ResidueModification::Term_Specificity term_spec) const;

    const ResidueModification & getTerminalModification(const String & name, ResidueModification::Term_Specificity term_spec) const;

    const ResidueModification & getModification(const String & residue_name, const String & mod_name, ResidueModification::Term_Specificity term_spec) const;

    const ResidueModification & getModification(const String & modification) const;

    Size findModificationIndex(const String & mod_name) const;

    void getTerminalModificationsByDiffMonoMass(std::vector<String> & mods, DoubleReal mass, DoubleReal error, ResidueModification::Term_Specificity term_spec);

    void getModificationsByDiffMonoMass(std::vector<String> & mods, DoubleReal mass, DoubleReal error = 0.0);

    void getModificationsByDiffMonoMass(std::vector<String> & mods, const String & residue, DoubleReal mass, DoubleReal error = 0.0);

    void readFromOBOFile(const String & filename);

    void readFromUnimodXMLFile(const String & filename);

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

protected:

    std::vector<ResidueModification *> mods_;

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


private:


    ModificationsDB();

    ModificationsDB(const ModificationsDB & residue_db);

    virtual ~ModificationsDB();


    ModificationsDB & operator=(const ModificationsDB & aa);
  };
}
#endif