ResidueModification.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// 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.
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// 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
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------
//

#pragma once

#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/CHEMISTRY/EmpiricalFormula.h>

#include <set>

namespace OpenMS
{
  // forward declaration
  class Residue;

  class OPENMS_DLLAPI ResidueModification
  {
public:

    enum TermSpecificity
    {
      ANYWHERE = 0,
      C_TERM = 1,
      N_TERM = 2,
      PROTEIN_C_TERM = 3,
      PROTEIN_N_TERM = 4,
      NUMBER_OF_TERM_SPECIFICITY
    };

    enum SourceClassification
    {
      ARTIFACT = 0,
      HYPOTHETICAL,
      NATURAL,
      POSTTRANSLATIONAL,
      MULTIPLE,
      CHEMICAL_DERIVATIVE,
      ISOTOPIC_LABEL,
      PRETRANSLATIONAL,
      OTHER_GLYCOSYLATION,
      NLINKED_GLYCOSYLATION,
      AA_SUBSTITUTION,
      OTHER,
      NONSTANDARD_RESIDUE,
      COTRANSLATIONAL,
      OLINKED_GLYCOSYLATION,
      UNKNOWN,
      NUMBER_OF_SOURCE_CLASSIFICATIONS
    };

    ResidueModification();

    ResidueModification(const ResidueModification& modification);

    virtual ~ResidueModification();

    ResidueModification& operator=(const ResidueModification& modification);

    void setId(const String& id);

    const String& getId() const;

    void setFullId(const String& full_id = "");


    const String& getFullId() const;

    void setUniModRecordId(const Int& id);

    const Int& getUniModRecordId() const;

    const String getUniModAccession() const;

    void setPSIMODAccession(const String& id);

    const String& getPSIMODAccession() const;

    void setFullName(const String& full_name);

    const String& getFullName() const;

    void setName(const String& name);

    const String& getName() const;

    void setTermSpecificity(TermSpecificity term_spec);

    void setTermSpecificity(const String& name);

    TermSpecificity getTermSpecificity() const;

    String getTermSpecificityName(TermSpecificity term_spec = NUMBER_OF_TERM_SPECIFICITY) const;

    void setOrigin(char origin);

    char getOrigin() const;

    void setSourceClassification(const String& classification);

    void setSourceClassification(SourceClassification classification);

    SourceClassification getSourceClassification() const;

    String getSourceClassificationName(SourceClassification classification = NUMBER_OF_SOURCE_CLASSIFICATIONS) const;

    void setAverageMass(double mass);

    double getAverageMass() const;

    void setMonoMass(double mass);

    double getMonoMass() const;

    void setDiffAverageMass(double mass);

    double getDiffAverageMass() const;

    void setDiffMonoMass(double mass);

    double getDiffMonoMass() const;

    void setFormula(const String& composition);

    const String& getFormula() const;

    void setDiffFormula(const EmpiricalFormula& diff_formula);

    const EmpiricalFormula& getDiffFormula() const;

    void setSynonyms(const std::set<String>& synonyms);

    void addSynonym(const String& synonym);

    const std::set<String>& getSynonyms() const;

    void setNeutralLossDiffFormula(const EmpiricalFormula& loss);

    const EmpiricalFormula& getNeutralLossDiffFormula() const;

    void setNeutralLossMonoMass(double mono_mass);

    double getNeutralLossMonoMass() const;

    void setNeutralLossAverageMass(double average_mass);

    double getNeutralLossAverageMass() const;

    bool hasNeutralLoss() const;

    bool isUserDefined() const;

    bool operator==(const ResidueModification& modification) const;

    bool operator!=(const ResidueModification& modification) const;

    bool operator<(const ResidueModification& modification) const;

protected:

    String id_;

    String full_id_;

    String psi_mod_accession_;

    // The UniMod record id (an integer)
    Int unimod_record_id_;

    String full_name_;

    String name_;

    TermSpecificity term_spec_;

    char origin_;

    SourceClassification classification_;

    double average_mass_;

    double mono_mass_;

    double diff_average_mass_;

    double diff_mono_mass_;

    String formula_;

    EmpiricalFormula diff_formula_;

    std::set<String> synonyms_;

    EmpiricalFormula neutral_loss_diff_formula_;

    double neutral_loss_mono_mass_;

    double neutral_loss_average_mass_;
  };
}