ModificationDefinitionsSet.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 2002-2018.
//
// 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.
// --------------------------------------------------------------------------
// 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: 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