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#pragma once
#include <QDebug>
#include <pappsomspp/core/msfile/msfileaccessor.h>
#include <pappsomspp/core/pappsoexception.h>
#include <iostream>
#include <iomanip>
#include <odsstream/odsdocwriter.h>
#include <QJsonDocument>
#include <QJsonArray>
#include <pappsomspp/core/psm/peptidespectrummatch.h>
#include <pappsomspp/core/psm/peptideisotopespectrummatch.h>
#include <pappsomspp/core/amino_acid/aastringcodec.h>
using namespace pappso;
MassSpectrum readMgf(const QString &filename);
QualifiedMassSpectrum readQualifiedMassSpectrumMgf(const QString &filename);
class XicOdsWriter
{
public:
XicOdsWriter(CalcWriterInterface &output) : _output(output)
{
_output.writeCell("rt");
_output.writeCell("intensity");
_output.writeLine();
};
void
write(const Trace &xic)
{
auto it = xic.begin();
while(it != xic.end())
{
_output.writeCell(it->x);
_output.writeCell(it->y);
_output.writeLine();
it++;
}
};
private:
CalcWriterInterface &_output;
};
bool compareTextFiles(const QString &file1, const QString &file2);
std::vector<std::size_t> getMapKeys(const std::map<std::size_t, std::size_t> &map_table);
std::vector<std::size_t> getMapValues(const std::map<std::size_t, std::size_t> &map_table);
void writeJsonTrace(const QString &filepath, Trace &xic);
void writeJsonPsm(const QString &filepath,
const MassSpectrum &mass_spectrum,
const pappso::PeptideSpectrumMatch &psm);
void writeJsonPsmIsotope(const QString &filein,
const MassSpectrum &mass_spectrum,
const pappso::PeptideIsotopeSpectrumMatch &psm);
void writeJsonCodeList(const QString &filein,
const std::vector<uint32_t> code_list,
const pappso::AaStringCodec &aa_codec);
QJsonArray toJson(const std::vector<double> &myVec);
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