TargetedExperiment.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 2002-2022.
//
// 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: Andreas Bertsch $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/ANALYSIS/MRM/ReactionMonitoringTransition.h>
#include <OpenMS/ANALYSIS/TARGETED/IncludeExcludeTarget.h>
#include <OpenMS/METADATA/CVTerm.h>
#include <OpenMS/METADATA/CVTermList.h>
#include <OpenMS/METADATA/Software.h>
#include <OpenMS/METADATA/SourceFile.h>
#include <OpenMS/ANALYSIS/TARGETED/TargetedExperimentHelper.h>
 
#include <vector>
 
namespace OpenMS
{
  class OPENMS_DLLAPI TargetedExperiment
  {
public:
    
    struct OPENMS_DLLAPI SummaryStatistics
    {
      Size protein_count;
      Size peptide_count;
      Size compound_count;
      Size transition_count;
      std::map<ReactionMonitoringTransition::DecoyTransitionType, size_t> decoy_counts; 
      bool contains_invalid_references;
    };
 
 
    typedef TargetedExperimentHelper::CV CV;
    typedef TargetedExperimentHelper::Protein Protein;
    typedef TargetedExperimentHelper::RetentionTime RetentionTime;
    typedef TargetedExperimentHelper::Compound Compound;
    typedef TargetedExperimentHelper::Peptide Peptide;
    typedef TargetedExperimentHelper::Contact Contact;
    typedef TargetedExperimentHelper::Publication Publication;
    typedef TargetedExperimentHelper::Instrument Instrument;
    typedef TargetedExperimentHelper::Prediction Prediction;
    typedef TargetedExperimentHelper::Interpretation Interpretation;
    typedef ReactionMonitoringTransition Transition;
    typedef Residue IonType; // IonType enum of Interpretation class
 
    typedef std::map<String, const Protein *> ProteinReferenceMapType;
    typedef std::map<String, const Peptide *> PeptideReferenceMapType;
    typedef std::map<String, const Compound *> CompoundReferenceMapType;
 
    TargetedExperiment();
 
    TargetedExperiment(const TargetedExperiment & rhs);
 
    TargetedExperiment(TargetedExperiment && rhs) noexcept;
 
    virtual ~TargetedExperiment();
 
    TargetedExperiment & operator=(const TargetedExperiment & rhs);
 
    TargetedExperiment & operator=(TargetedExperiment && rhs) noexcept;
 
    bool operator==(const TargetedExperiment & rhs) const;
 
    bool operator!=(const TargetedExperiment & rhs) const;
 
    TargetedExperiment operator+(const TargetedExperiment & rhs) const;
 
    TargetedExperiment& operator+=(const TargetedExperiment & rhs);
    TargetedExperiment& operator+=(TargetedExperiment && rhs);
 
    void clear(bool clear_meta_data);
 
    SummaryStatistics getSummary() const;
 
    // cv list
    void setCVs(const std::vector<CV> & cvs);
 
    const std::vector<CV> & getCVs() const;
 
    void addCV(const CV & cv);
 
    // contact list
    void setContacts(const std::vector<Contact> & contacts);
 
    const std::vector<Contact> & getContacts() const;
 
    void addContact(const Contact & contact);
 
    // publication list
    void setPublications(const std::vector<Publication> & publications);
 
    const std::vector<Publication> & getPublications() const;
 
    void addPublication(const Publication & publication);
 
    // target list
    void setTargetCVTerms(const CVTermList & cv_terms);
 
    const CVTermList & getTargetCVTerms() const;
 
    void addTargetCVTerm(const CVTerm & cv_term);
 
    void setTargetMetaValue(const String & name, const DataValue & value);
 
    // instrument list
    void setInstruments(const std::vector<Instrument> & instruments);
 
    const std::vector<Instrument> & getInstruments() const;
 
    void addInstrument(const Instrument & instrument);
 
    // software list
    void setSoftware(const std::vector<Software> & software);
 
    const std::vector<Software> & getSoftware() const;
 
    void addSoftware(const Software & software);
 
    // protein list
    void setProteins(const std::vector<Protein> & proteins);
    void setProteins(std::vector<Protein> && proteins);
 
    const std::vector<Protein> & getProteins() const;
 
    const Protein & getProteinByRef(const String & ref) const;
 
    bool hasProtein(const String & ref) const;
 
    void addProtein(const Protein & protein);
 
    // compound list
    void setCompounds(const std::vector<Compound> & rhs);
 
    const std::vector<Compound> & getCompounds() const;
 
    void addCompound(const Compound & rhs);
 
    void setPeptides(const std::vector<Peptide> & rhs);
    void setPeptides(std::vector<Peptide> && rhs);
 
    const std::vector<Peptide> & getPeptides() const;
 
    bool hasPeptide(const String & ref) const;
 
    const Peptide & getPeptideByRef(const String & ref) const;
 
    bool hasCompound(const String & ref) const;
 
    const Compound & getCompoundByRef(const String & ref) const;
 
    void addPeptide(const Peptide & rhs);
 
    void setTransitions(const std::vector<ReactionMonitoringTransition> & transitions);
    void setTransitions(std::vector<ReactionMonitoringTransition> && transitions);
 
    const std::vector<ReactionMonitoringTransition> & getTransitions() const;
 
    void addTransition(const ReactionMonitoringTransition & transition);
 
    void setIncludeTargets(const std::vector<IncludeExcludeTarget> & targets);
 
    const std::vector<IncludeExcludeTarget> & getIncludeTargets() const;
 
    void addIncludeTarget(const IncludeExcludeTarget & target);
 
    void setExcludeTargets(const std::vector<IncludeExcludeTarget> & targets);
 
    const std::vector<IncludeExcludeTarget> & getExcludeTargets() const;
 
    void addExcludeTarget(const IncludeExcludeTarget & target);
 
    void setSourceFiles(const std::vector<SourceFile> & source_files);
 
    const std::vector<SourceFile> & getSourceFiles() const;
 
    void addSourceFile(const SourceFile & source_file);
 
 
 
    void sortTransitionsByProductMZ();
 
 
 
    void sortTransitionsByName();
 
    bool containsInvalidReferences() const;
 
protected:
 
    void createProteinReferenceMap_() const;
 
    void createPeptideReferenceMap_() const;
 
    void createCompoundReferenceMap_() const;
 
    std::vector<CV> cvs_;
 
    std::vector<Contact> contacts_;
 
    std::vector<Publication> publications_;
 
    std::vector<Instrument> instruments_;
 
    CVTermList targets_;
 
    std::vector<Software> software_;
 
    std::vector<Protein> proteins_;
 
    std::vector<Compound> compounds_;
 
    std::vector<Peptide> peptides_;
 
    std::vector<ReactionMonitoringTransition> transitions_;
 
    std::vector<IncludeExcludeTarget> include_targets_;
 
    std::vector<IncludeExcludeTarget> exclude_targets_;
 
    std::vector<SourceFile> source_files_;
 
    mutable ProteinReferenceMapType protein_reference_map_;
 
    mutable bool protein_reference_map_dirty_;
 
    mutable PeptideReferenceMapType peptide_reference_map_;
 
    mutable bool peptide_reference_map_dirty_;
 
    mutable CompoundReferenceMapType compound_reference_map_;
 
    mutable bool compound_reference_map_dirty_;
 
  };
 
  namespace TargetedExperimentHelper
  {
  } // namespace TargetedExperimentHelper
 
  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const TargetedExperiment::SummaryStatistics& s);
 
 
} // namespace OpenMS