TargetedExperiment.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 2002-2018.
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// $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:

    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);

    virtual ~TargetedExperiment();

    TargetedExperiment & operator=(const TargetedExperiment & rhs);

    bool operator==(const TargetedExperiment & rhs) const;

    bool operator!=(const TargetedExperiment & rhs) const;

    TargetedExperiment operator+(const TargetedExperiment & rhs) const;

    TargetedExperiment & operator+=(const TargetedExperiment & rhs);

    void clear(bool clear_meta_data);

    // 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);

    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);

    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);

    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();

    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


} // namespace OpenMS