MRMFeature.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 2002-2020.
//
// 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: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/Feature.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathScores.h>
 
namespace OpenMS
{
  class OPENMS_DLLAPI MRMFeature :
    public Feature
  {
public:
 
 
    typedef std::vector<Feature> FeatureListType;
 
 
    MRMFeature();
 
    MRMFeature(const MRMFeature &rhs);
 
    MRMFeature(MRMFeature &&rhs) = default;
 
    MRMFeature & operator=(const MRMFeature & rhs);
 
    MRMFeature& operator=(MRMFeature&&) & = default;
 
    ~MRMFeature() override;
 
 
 
    const OpenSwath_Scores & getScores() const;
 
    OpenSwath_Scores & getScores();
 
    Feature & getFeature(const String& key);
 
    const Feature & getFeature(const String& key) const;
 
    void setScores(const OpenSwath_Scores & scores);
 
    void addScore(const String & score_name, double score);
 
    void addFeature(const Feature & feature, const String& key);
 
    void addFeature(Feature && feature, const String& key);
 
    const std::vector<Feature> & getFeatures() const;
 
    void getFeatureIDs(std::vector<String> & result) const;
 
    void addPrecursorFeature(const Feature & feature, const String& key);
 
    void addPrecursorFeature(Feature && feature, const String& key);
 
    void getPrecursorFeatureIDs(std::vector<String> & result) const;
 
    Feature & getPrecursorFeature(String key);
 
    const Feature & getPrecursorFeature(String key) const;
 
    void IDScoresAsMetaValue(bool decoy, const OpenSwath_Ind_Scores& idscores);
 
protected:
 
    FeatureListType features_;
 
    FeatureListType precursor_features_;
 
    OpenSwath_Scores pg_scores_;
 
    std::map<String, int> feature_map_;
 
    std::map<String, int> precursor_feature_map_;
 
  };
}