ModificationDefinitionsSet.h

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// Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: $
// --------------------------------------------------------------------------
//
 
#pragma once
 
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/CHEMISTRY/ModificationDefinition.h>
#include <OpenMS/CONCEPT/Types.h> // for "UInt"
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/DATASTRUCTURES/ListUtils.h> // for "StringList"
#include <OpenMS/DATASTRUCTURES/StringListUtils.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
 
#include <set>
 
namespace OpenMS
{
  class OPENMS_DLLAPI ModificationDefinitionsSet
  {
public:
 
    ModificationDefinitionsSet();
 
    ModificationDefinitionsSet(const ModificationDefinitionsSet& rhs);
 
    ModificationDefinitionsSet(const StringList& fixed_modifications, const StringList& variable_modifications);
 
    virtual ~ModificationDefinitionsSet();
 
    void setMaxModifications(Size max_mod);
 
    Size getMaxModifications() const;
 
    Size getNumberOfModifications() const;
 
    Size getNumberOfFixedModifications() const;
 
    Size getNumberOfVariableModifications() const;
 
    void addModification(const ModificationDefinition& mod_def);
 
    void setModifications(const std::set<ModificationDefinition>& mod_defs);
 
    void setModifications(const String& fixed_modifications, const String& variable_modifications);
 
    void setModifications(const StringList& fixed_modifications, const StringList& variable_modifications);
 
    std::set<ModificationDefinition> getModifications() const;
 
    const std::set<ModificationDefinition>& getFixedModifications() const;
 
    const std::set<ModificationDefinition>& getVariableModifications() const;
 
    std::set<String> getModificationNames() const;
 
    void getModificationNames(StringList& fixed_modifications, StringList& variable_modifications) const;
 
    std::set<String> getFixedModificationNames() const;
 
    std::set<String> getVariableModificationNames() const;
 
    ModificationDefinitionsSet& operator=(const ModificationDefinitionsSet& element);
 
    bool isCompatible(const AASequence& peptide) const;
 
    bool operator==(const ModificationDefinitionsSet& rhs) const;
 
    bool operator!=(const ModificationDefinitionsSet& rhs) const;
 
    void findMatches(std::multimap<double, ModificationDefinition>& matches, double mass, const String& residue = "", ResidueModification::TermSpecificity term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY, bool consider_fixed = true, bool consider_variable = true, bool is_delta = true, double tolerance = 0.01) const;
 
    void inferFromPeptides(const std::vector<PeptideIdentification>& peptides);
 
protected:
 
    std::set<ModificationDefinition> variable_mods_;
 
    std::set<ModificationDefinition> fixed_mods_;
 
    Size max_mods_per_peptide_;
 
    static void addMatches_(std::multimap<double, ModificationDefinition>& matches, double mass, const String& residue, ResidueModification::TermSpecificity term_spec, const std::set<ModificationDefinition>& source, bool is_delta, double tolerance);
 
  };
 
} // namespace OpenMS