ProFormaWriter.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Timo Sachsenberg $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CHEMISTRY/ProFormaData.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/OpenMSConfig.h>
 
#include <iosfwd>
#include <vector>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI ProFormaWriter
  {
  public:
    static String toString(const Peptidoform& peptidoform,
                           ProFormaWriteMode mode = ProFormaWriteMode::LOSSLESS);
 
    static String toString(const PeptidoformIon& ion,
                           ProFormaWriteMode mode = ProFormaWriteMode::LOSSLESS);
 
  private:
    static void writeGlobalMods_(std::ostream& os, const std::vector<GlobalModEntry>& mods, ProFormaWriteMode mode);
 
    static void writeIsotopeReplacement_(std::ostream& os, const IsotopeReplacement& isotope);
 
    static void writeGlobalModification_(std::ostream& os, const GlobalModification& mod, ProFormaWriteMode mode);
 
    static void writeModification_(std::ostream& os, const Modification& mod, ProFormaWriteMode mode);
 
    static void writeModificationTag_(std::ostream& os, const ModificationTag& tag, ProFormaWriteMode mode);
 
    static void writeCvAccession_(std::ostream& os, const CvAccession& cv);
 
    static void writeNamedMod_(std::ostream& os, const NamedMod& named);
 
    static void writeMassDelta_(std::ostream& os, const MassDelta& delta, ProFormaWriteMode mode);
 
    static void writeFormulaTag_(std::ostream& os, const FormulaTag& formula);
 
    static void writeGlycanComposition_(std::ostream& os, const GlycanComposition& glycan);
 
    static void writeInfoTag_(std::ostream& os, const InfoTag& info);
 
    static void writePositionConstraint_(std::ostream& os, const PositionConstraint& pc);
 
    static void writeLabel_(std::ostream& os, const Label& label, ProFormaWriteMode mode);
 
    static void writeUnlocalisedMods_(std::ostream& os, const std::vector<UnlocalisedMod>& mods, ProFormaWriteMode mode);
 
    static void writeLabileModifications_(std::ostream& os, const std::vector<LabileModification>& mods, ProFormaWriteMode mode);
 
    static void writeNTermMods_(std::ostream& os, const std::vector<Modification>& mods, ProFormaWriteMode mode);
 
    static void writeCTermMods_(std::ostream& os, const std::vector<Modification>& mods, ProFormaWriteMode mode);
 
    static void writeSequence_(std::ostream& os, const std::vector<SequenceSection>& seq, ProFormaWriteMode mode);
 
    static void writeSequenceElement_(std::ostream& os, const SequenceElement& elem, ProFormaWriteMode mode);
 
    static void writeAmbiguousRegion_(std::ostream& os, const AmbiguousRegion& region, ProFormaWriteMode mode);
 
    static void writeModifiedRange_(std::ostream& os, const ModifiedRange& range, ProFormaWriteMode mode);
 
    static void writeChargeState_(std::ostream& os, const ChargeState& charge);
 
    static const char* cvDatabaseToString_(CvDatabase db);
 
    static const char* cvDatabaseToHint_(CvDatabase db);
 
    static const char* massSourceToString_(MassDelta::Source source);
  };
 
} // namespace OpenMS