ProFormaParser.cpp

#include "ProFormaParser.h"
#include <sstream>
#include <algorithm>

namespace TopDownProteomics::ProForma {

    ProFormaTerm ProFormaParser::ParseString(const std::string& proFormaString) {
        // Implementation of the ParseString function
        // You need to provide the implementation here
    }

    void ProFormaParser::HandleGlobalModification(
        std::unordered_map<std::string, ProFormaTagGroup>*& tagGroups,
        std::vector<ProFormaGlobalModification>*& globalModifications,
        std::string& sequence, int startRange, int endRange,
        const std::string& tagText) {
        // Implementation of the HandleGlobalModification function
        // You need to provide the implementation here
    }

    void ProFormaParser::ProcessTag(std::string tag, int startIndex, int index, bool inSequenceAmbiguity,
        std::vector<ProFormaTag>*& tags, std::unordered_map<std::string, ProFormaTagGroup>*& tagGroups) {
        // Implementation of the ProcessTag function
        // You need to provide the implementation here
    }

    std::vector<ProFormaDescriptor>* ProFormaParser::ProcessTag(std::string tag, int startIndex, int index,
        std::unordered_map<std::string, ProFormaTagGroup>*& tagGroups) {
        // Implementation of the ProcessTag function
        // You need to provide the implementation here
    }

    std::tuple<ProFormaKey, ProFormaEvidenceType, std::string, std::string, double>
    ProFormaParser::ParseDescriptor(const std::string& text) {
        // Implementation of the ParseDescriptor function
        // You need to provide the implementation here
    }

}