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#include "common.h"
#include <pappsomspp/core/exception/exceptionnotrecognized.h>
#include <pappsomspp/core/utils.h>
#include <QJsonObject>
#include <QJsonArray>
#include "tests/tests-config.h"
using namespace pappso;
MassSpectrum
readMgf(const QString &filename)
{
try
{
qDebug();
MsFileAccessor accessor(filename, "msrun");
qDebug();
std::vector<MsRunIdCstSPtr> msrun_ids = accessor.getMsRunIds();
if(accessor.getFileFormat() == Enums::MsDataFormat::unknown)
{
throw pappso::ExceptionNotRecognized("file format not recognized");
}
if(msrun_ids.size() == 0)
{
throw pappso::PappsoException("msrun_ids.size() == 0");
}
MsRunReaderSPtr reader = accessor.msRunReaderSPtr(msrun_ids.front());
qDebug() << msrun_ids.front().get()->getXmlId();
std::cout << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< reader->spectrumListSize() << std::endl;
MassSpectrumSPtr spectrum_sp = reader->massSpectrumSPtr(0);
std::cout << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< spectrum_sp.get()->size() << std::endl;
// spectrum_sp.get()->debugPrintValues();
spectrum_sp.get()->sortMz();
return *(spectrum_sp.get());
}
catch(pappso::PappsoException &error)
{
std::cout << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
<< QString("ERROR reading file %1 :").arg(filename).toStdString().c_str() << " "
<< error.what();
throw error;
}
}
QualifiedMassSpectrum
readQualifiedMassSpectrumMgf(const QString &filename)
{
try
{
qDebug();
MsFileAccessor accessor(filename, "msrun");
std::vector<MsRunIdCstSPtr> msrun_ids = accessor.getMsRunIds();
if(accessor.getFileFormat() == Enums::MsDataFormat::unknown)
{
throw pappso::ExceptionNotRecognized("file format not recognized");
}
if(msrun_ids.size() == 0)
{
throw pappso::PappsoException("msrun_ids.size() == 0");
}
qDebug();
MsRunReaderSPtr reader = accessor.msRunReaderSPtr(msrun_ids.front());
qDebug() << msrun_ids.front().get()->getXmlId();
std::cout << reader->spectrumListSize() << std::endl;
QualifiedMassSpectrum spectrum_sp = reader->qualifiedMassSpectrum(0, true);
return spectrum_sp;
}
catch(pappso::PappsoException &error)
{
std::cout << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
<< QString("ERROR reading file %1 : %2")
.arg(filename)
.arg(error.qwhat())
.toStdString()
.c_str();
throw error;
}
}
bool
compareTextFiles(const QString &file1, const QString &file2)
{
QFile fnew(file1);
fnew.open(QFile::ReadOnly | QFile::Text);
// REQUIRE(fnew.errorString().toStdString() == "");
QTextStream infnew(&fnew);
QFile fold(file2);
fold.open(QFile::ReadOnly | QFile::Text);
QTextStream infold(&fold);
return (infold.readAll().toStdString() == infnew.readAll().toStdString());
}
std::vector<std::size_t>
getMapKeys(const std::map<std::size_t, std::size_t> &map_table)
{
std::vector<std::size_t> vector;
for(auto &&pair : map_table)
vector.push_back(pair.first);
return vector;
}
std::vector<std::size_t>
getMapValues(const std::map<std::size_t, std::size_t> &map_table)
{
std::vector<std::size_t> vector;
for(auto &&pair : map_table)
vector.push_back(pair.second);
return vector;
}
QJsonArray
toJson(const std::vector<double> &myVec)
{
QJsonArray result;
for(auto i = myVec.begin(); i != myVec.end(); i++)
{
result.push_back((*i));
}
return result;
}
void
writeJsonTrace(const QString &filein, Trace &xic)
{
QString filepath = QString(CMAKE_SOURCE_DIR).append("/tests/typst/data/").append(filein);
qDebug() << filepath;
QFile jsonf(filepath);
if(jsonf.open(QIODevice::WriteOnly))
{
QJsonDocument doc;
QJsonObject trace_json;
trace_json.insert("x", toJson(xic.xValues()));
trace_json.insert("y", toJson(xic.yValues()));
doc.setObject(trace_json);
jsonf.write(doc.toJson());
jsonf.close();
}
else
{
throw pappso::PappsoException(
QObject::tr("Unable to write JSON output file %1").arg(filepath));
}
qDebug() << filepath;
}
void
writeJsonPsm(const QString &filein,
const MassSpectrum &mass_spectrum,
const pappso::PeptideSpectrumMatch &psm)
{
qDebug() << filein;
QString filepath = QString(CMAKE_SOURCE_DIR).append("/tests/typst/data/").append(filein);
QFile jsonf(filepath);
if(jsonf.open(QIODevice::WriteOnly))
{
QJsonDocument doc;
QJsonObject psm_json;
struct data_plot
{
pappso::DataPoint point;
double mz_th;
int charge;
int size;
};
std::map<Enums::PeptideIon, std::vector<data_plot>> ion_map;
QJsonObject spectrum_json;
spectrum_json.insert("mz", toJson(mass_spectrum.xValues()));
spectrum_json.insert("intensity", toJson(mass_spectrum.yValues()));
for(const PeakIonMatch &peakion_match : psm)
{
auto it = ion_map.insert({peakion_match.getPeptideIonType(), {}});
it.first->second.push_back(
{peakion_match.getPeak(),
peakion_match.getPeptideFragmentIonSp().get()->getMz(peakion_match.getCharge()),
(int)peakion_match.getCharge(),
(int)peakion_match.getPeptideFragmentIonSp().get()->size()});
}
QJsonObject psm_ion_json;
for(auto &cle_valeur : ion_map)
{
std::vector<data_plot> ¤t_vector = cle_valeur.second;
std::sort(current_vector.begin(),
current_vector.end(),
[](const data_plot &a, const data_plot &b) { return a.point.x < b.point.y; });
QJsonArray current_ion_json_arr;
for(const data_plot &one_point : current_vector)
{
QJsonObject current_ion;
current_ion.insert("mz", one_point.point.x);
current_ion.insert("mzth", one_point.mz_th);
current_ion.insert("intensity", one_point.point.y);
current_ion.insert("size", one_point.size);
current_ion.insert("charge", one_point.charge);
current_ion_json_arr.push_back(current_ion);
}
psm_ion_json.insert(Utils::toString(cle_valeur.first), current_ion_json_arr);
}
psm_json.insert("ion-series", psm_ion_json);
psm_json.insert("spectra", spectrum_json);
doc.setObject(psm_json);
jsonf.write(doc.toJson());
jsonf.close();
}
else
{
throw pappso::PappsoException(
QObject::tr("Unable to write JSON output file %1").arg(filepath));
}
qDebug() << filepath;
}
void
writeJsonPsmIsotope(const QString &filein,
const pappso::MassSpectrum &mass_spectrum,
const pappso::PeptideIsotopeSpectrumMatch &psm)
{
qDebug() << filein;
QString filepath = QString(CMAKE_SOURCE_DIR).append("/tests/typst/data/").append(filein);
QFile jsonf(filepath);
QJsonDocument doc;
QJsonObject psm_json;
QJsonObject spectrum_json;
QJsonObject psm_ion_json;
struct data_plot
{
pappso::DataPoint point;
double mz_th;
int charge;
int size;
int isotope_number;
int isotope_rank;
};
std::map<Enums::PeptideIon, std::vector<data_plot>> ion_map;
if(jsonf.open(QIODevice::WriteOnly))
{
spectrum_json.insert("mz", toJson(mass_spectrum.xValues()));
spectrum_json.insert("intensity", toJson(mass_spectrum.yValues()));
psm_json.insert("spectra", spectrum_json);
for(const PeakIonIsotopeMatch &peakion_match : psm)
{
auto it = ion_map.insert({peakion_match.getPeptideIonType(), {}});
it.first->second.push_back({
peakion_match.getPeak(),
peakion_match.getPeptideFragmentIonSp().get()->getMz(peakion_match.getCharge()),
(int)peakion_match.getCharge(),
(int)peakion_match.getPeptideFragmentIonSp().get()->size(),
(int)peakion_match.getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber(),
(int)peakion_match.getPeptideNaturalIsotopeAverageSp().get()->getIsotopeRank(),
});
}
for(auto &cle_valeur : ion_map)
{
std::vector<data_plot> ¤t_vector = cle_valeur.second;
std::sort(current_vector.begin(),
current_vector.end(),
[](const data_plot &a, const data_plot &b) { return a.point.x < b.point.y; });
QJsonArray current_ion_json_arr;
for(const data_plot &one_point : current_vector)
{
QJsonObject current_ion;
current_ion.insert("mz", one_point.point.x);
current_ion.insert("mzth", one_point.mz_th);
current_ion.insert("intensity", one_point.point.y);
current_ion.insert("size", one_point.size);
current_ion.insert("charge", one_point.charge);
current_ion.insert("isotope", one_point.isotope_number);
current_ion.insert("rank", one_point.isotope_rank);
current_ion_json_arr.push_back(current_ion);
}
psm_ion_json.insert(Utils::toString(cle_valeur.first), current_ion_json_arr);
}
psm_json.insert("ion-series", psm_ion_json);
qWarning();
doc.setObject(psm_json);
qWarning();
jsonf.write(doc.toJson());
qWarning();
jsonf.flush();
qWarning();
jsonf.close();
qWarning();
}
else
{
throw pappso::PappsoException(
QObject::tr("Unable to write JSON output file %1").arg(filepath));
}
qWarning();
qDebug() << filepath;
}
void
writeJsonCodeList(const QString &filein,
const std::vector<uint32_t> code_list,
const pappso::AaStringCodec &aa_codec)
{
qDebug() << filein;
QString filepath = QString(CMAKE_SOURCE_DIR).append("/tests/typst/data/").append(filein);
QFile jsonf(filepath);
if(jsonf.open(QIODevice::WriteOnly))
{
QJsonDocument doc;
QJsonObject code_list_json;
QJsonArray arr_code;
QJsonArray arr_mass;
QJsonArray arr_str;
for(auto &code : code_list)
{
arr_code.push_back((int32_t)code);
arr_mass.push_back(aa_codec.getMass(code));
arr_str.push_back(aa_codec.decode(code));
}
code_list_json.insert("arr_code", arr_code);
code_list_json.insert("arr_mass", arr_mass);
code_list_json.insert("arr_sequence", arr_str);
doc.setObject(code_list_json);
jsonf.write(doc.toJson());
jsonf.close();
}
else
{
throw pappso::PappsoException(
QObject::tr("Unable to write JSON output file %1").arg(filepath));
}
}
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