DigestionEnzymeProtein.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Xiao Liang $
// $Authors: Xiao Liang $
// --------------------------------------------------------------------------
//
 
#pragma once
 
#include <OpenMS/CHEMISTRY/DigestionEnzyme.h>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI DigestionEnzymeProtein :
    public DigestionEnzyme
  {
  public:
 
 
    DigestionEnzymeProtein();
 
    explicit DigestionEnzymeProtein(const DigestionEnzyme& d);
 
    DigestionEnzymeProtein(const DigestionEnzymeProtein&) = default;
 
    DigestionEnzymeProtein(DigestionEnzymeProtein&&) = default;
 
    explicit DigestionEnzymeProtein(const String& name,
                                    const String& cleavage_regex,
                                    const std::set<String>& synonyms = std::set<String>(),
                                    String regex_description = "",
                                    EmpiricalFormula n_term_gain = EmpiricalFormula("H"),
                                    EmpiricalFormula c_term_gain = EmpiricalFormula("OH"),
                                    String psi_id = "",
                                    String xtandem_id = "",
                                    Int comet_id = -1,
                                    Int msgf_id = -1,
                                    Int omssa_id = -1);
 
    ~DigestionEnzymeProtein() override;
 
    DigestionEnzymeProtein& operator=(const DigestionEnzymeProtein&) = default;
 
    DigestionEnzymeProtein& operator=(DigestionEnzymeProtein&&) & = default;
 
    void setNTermGain(const EmpiricalFormula& value);
 
    EmpiricalFormula getNTermGain() const;
 
    void setCTermGain(const EmpiricalFormula& value);
 
    EmpiricalFormula getCTermGain() const;
 
    void setPSIID(const String& value);
 
    String getPSIID() const;
 
    void setXTandemID(const String& value);
 
    String getXTandemID() const;
 
    void setCometID(Int value);
 
    Int getCometID() const;
 
    void setMSGFID(Int value);
 
    Int getMSGFID() const;
 
    void setOMSSAID(Int value);
 
    Int getOMSSAID() const;
 
 
    bool operator==(const DigestionEnzymeProtein& enzyme) const;
 
    bool operator!=(const DigestionEnzymeProtein& enzyme) const;
 
    // Note: comparison operator is not inherited. TODO rename and make virtual
    bool operator==(const String& cleavage_regex) const;
 
    bool operator!=(const String& cleavage_regex) const;
 
    bool operator<(const DigestionEnzymeProtein& enzyme) const;
 
    bool setValueFromFile(const String& key, const String& value) override;
 
    friend OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const DigestionEnzymeProtein& enzyme);
 
  protected:
    EmpiricalFormula n_term_gain_;
 
    EmpiricalFormula c_term_gain_;
 
    String psi_id_;
 
    String xtandem_id_;
 
    Int comet_id_;
 
    Int msgf_id_;
 
    Int omssa_id_;
 
  };
 
  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const DigestionEnzymeProtein& enzyme);
 
  typedef DigestionEnzymeProtein Protease;
}