SearchEngineBase.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: Chris Bielow $
// $Authors: Chris Bielow $
// --------------------------------------------------------------------------
 
#pragma once
 
#include "OpenMS/METADATA/ProteinIdentification.h"
#include <OpenMS/APPLICATIONS/TOPPBase.h>
 
 
namespace OpenMS
{
  
  class OPENMS_DLLAPI SearchEngineBase : public TOPPBase
  {
  public:
    SearchEngineBase() = delete;
 
    SearchEngineBase(const SearchEngineBase&) = delete;
 
    SearchEngineBase(const String& name, const String& description, bool official = true, const std::vector<Citation>& citations = {}, bool toolhandler_test = true);
 
    ~SearchEngineBase() override;
 
    String getRawfileName(int ms_level = 2) const;
 
 
    String getDBFilename(const String& db = "") const;
 
 
    virtual void registerPeptideIndexingParameter_(Param peptide_indexing_parameter);
 
    virtual SearchEngineBase::ExitCodes reindex_(
      std::vector<ProteinIdentification>& protein_identifications, 
      std::vector<PeptideIdentification>& peptide_identifications) const;
  }; // end SearchEngineBase
 
}   // end NS OpenMS