EnzymesDB.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
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// $Maintainer: Xiao Liang $
// $Authors: Xiao Liang, Chris Bielow $
// --------------------------------------------------------------------------

#ifndef OPENMS_CHEMISTRY_ENZYMESDB_H
#define OPENMS_CHEMISTRY_ENZYMESDB_H

#include <OpenMS/DATASTRUCTURES/Map.h>
#include <boost/unordered_map.hpp>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <set>

namespace OpenMS
{
  // forward declarations
  class Enzyme;

  class OPENMS_DLLAPI EnzymesDB
  {
public:

    typedef std::set<const Enzyme*>::const_iterator ConstEnzymeIterator;
    typedef std::set<const Enzyme*>::iterator EnzymeIterator;

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

    virtual ~EnzymesDB();

    const Enzyme* getEnzyme(const String& name) const;

    const Enzyme* getEnzymeByRegEx(const String& cleavage_regex) const;

    void setEnzymes(const String& filename);

    void addEnzyme(const Enzyme& enzyme);

    void clear();

    void getAllNames(std::vector<String>& all_names) const;

    void getAllXTandemNames(std::vector<String>& all_names) const;

    void getAllCometNames(std::vector<String>& all_names) const;

    void getAllOMSSANames(std::vector<String>& all_names) const;

    void getAllMSGFNames(std::vector<String>& all_names) const;




    bool hasEnzyme(const String& name) const;

    bool hasRegEx(const String& cleavage_regex) const;

    bool hasEnzyme(const Enzyme* enzyme) const;

    inline ConstEnzymeIterator beginEnzyme() const { return const_enzymes_.begin(); }  // we only allow constant iterators -- this DB is not meant to be modifiable
    inline ConstEnzymeIterator endEnzyme() const { return const_enzymes_.end(); }

protected:
    EnzymesDB();

    EnzymesDB(const EnzymesDB& enzyme_db);

    EnzymesDB& operator=(const EnzymesDB& enzymes_db);

    void readEnzymesFromFile_(const String& filename);

    const Enzyme* parseEnzyme_(Map<String, String>& values) const;

    // add to internal data; also update indices for search by name and regex
    void addEnzyme_(const Enzyme* enzyme);

    boost::unordered_map<String, const Enzyme*> enzyme_names_;  // index by names

    Map<String, const Enzyme*> enzyme_regex_; // index by regex

    std::set<const Enzyme*> const_enzymes_; // set of enzymes

  };
}
#endif