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#include "proteincode_lib.h"
#include <pappsomspp/core/utils.h>
#include "tests/tests-config.h"
#include <QJsonDocument>
#include <QJsonObject>
#include <QJsonArray>
#include <pappsomspp/core/pappsoexception.h>
#include <pappsomspp/core/protein/proteinintegercode.h>
void
FastaProteinArrayHandler::setSequence(const QString &description_in, const QString &sequence_in)
{
m_proteinArray.push_back({description_in, sequence_in});
}
const std::vector<pappso::Protein> &
FastaProteinArrayHandler::getProteinArray() const
{
return m_proteinArray;
};
void
writeProteinConvolutionScore(const QString &filename,
const pappso::Protein &protein,
const pappso::ProteinPresenceAbsenceMatrix *pmatrix,
const std::vector<double> &convolution_score)
{
QFile file(filename);
// file.open(QIODevice::WriteOnly);
OdsDocWriter writer(&file);
writer.writeSheet(protein.getAccession());
writer.writeCell("sequence");
for(long long i = 0; i < protein.getSequence().size(); i++)
{
writer.writeCell(protein.getSequence()[i]);
}
writer.writeLine();
writer.writeCell("convolution score");
for(long long i = 0; i < protein.getSequence().size(); i++)
{
writer.writeCell(convolution_score[i]);
}
writer.writeLine();
if(pmatrix != nullptr)
{
auto matrix = pmatrix->getPresenceAbsenceMatrix();
for(long long j = 0; j < 5; j++)
{
writer.writeCell(QString("%1aa").arg(j + 1));
for(long long i = 0; i < protein.getSequence().size(); i++)
{
if(matrix(i, j) ==
pappso::ProteinPresenceAbsenceMatrix::ProteinPresenceAbsenceMatrixElement::present)
{
writer.writeCell("X");
}
else
{
writer.writeEmptyCell();
}
}
writer.writeLine();
}
}
writer.close();
}
void
writeProteinConvolutionScoreJson(const QString &filein,
const pappso::Protein &protein,
const pappso::ProteinIntegerCode &protein_code,
const pappso::ProteinPresenceAbsenceMatrix *pmatrix,
const std::vector<double> &convolution_score)
{
qDebug() << filein;
QString filepath = QString(CMAKE_SOURCE_DIR).append("/tests/typst/data/").append(filein);
QFile jsonf(filepath);
if(jsonf.open(QIODevice::WriteOnly))
{
qWarning();
QJsonDocument doc;
QJsonObject protein_conv;
protein_conv.insert("accession", protein.getAccession());
protein_conv.insert("description", protein.getDescription());
QJsonArray sequence_json;
for(long long i = 0; i < protein.getSequence().size(); i++)
{
sequence_json.push_back((QString)protein.getSequence()[i].toLatin1());
}
qWarning();
protein_conv.insert("sequence", sequence_json);
QJsonArray matrix_code_json;
QJsonArray matrix_single_code_json;
for(int code : protein_code.getSeqAaCode())
{
matrix_single_code_json.push_back(code);
}
matrix_code_json.push_back(matrix_single_code_json);
QJsonArray matrix_2mer_code_json;
for (int code: protein_code.getPeptideCodedFragment(2)) {
matrix_2mer_code_json.push_back(code);
}
matrix_code_json.push_back(matrix_2mer_code_json);
QJsonArray matrix_3mer_code_json;
for (int code: protein_code.getPeptideCodedFragment(3)) {
matrix_3mer_code_json.push_back(code);
}
matrix_code_json.push_back(matrix_3mer_code_json);
QJsonArray matrix_4mer_code_json;
for (int code: protein_code.getPeptideCodedFragment(4)) {
matrix_4mer_code_json.push_back(code);
}
matrix_code_json.push_back(matrix_4mer_code_json);
protein_conv.insert("protein_matrix_code", matrix_code_json);
qWarning();
QJsonArray convolution_score_json;
for(long long i = 0; i < protein.getSequence().size(); i++)
{
convolution_score_json.push_back(convolution_score[i]);
}
protein_conv.insert("convolution_score", convolution_score_json);
qWarning();
if(pmatrix != nullptr)
{
qWarning() << "coucou";
QJsonArray pmatrix_json;
auto matrix = pmatrix->getPresenceAbsenceMatrix();
for(long long j = 0; j < 5; j++)
{
QJsonArray pmatrix_seq_kmer_json;
for(long long i = 0; i < protein.getSequence().size(); i++)
{
if(matrix(i, j) == pappso::ProteinPresenceAbsenceMatrix::
ProteinPresenceAbsenceMatrixElement::present)
{
pmatrix_seq_kmer_json.push_back(true);
}
else
{
pmatrix_seq_kmer_json.push_back(false);
}
}
pmatrix_json.push_back(pmatrix_seq_kmer_json);
}
protein_conv.insert("presence_matrix", pmatrix_json);
}
doc.setObject(protein_conv);
jsonf.write(doc.toJson());
jsonf.close();
qWarning() << "coucou";
}
else
{
throw pappso::PappsoException(
QObject::tr("Unable to write JSON output file %1").arg(filepath));
}
}
void
writeSelfSpectrum(const QString &filename,
const pappso::specself::SelfSpectrum &self_spectrum,
const pappso::AaStringCodec &aa_codec)
{
qDebug();
QFile file(filename);
// file.open(QIODevice::WriteOnly);
OdsDocWriter writer(&file);
writer.writeSheet("spectrum_matrix");
const pappso::specself::SelfSpectrumMatrix &matrix = self_spectrum.getMatrix();
const pappso::Trace &trace = self_spectrum.getTrace();
writer.writeLine();
writer.writeEmptyCell();
writer.writeEmptyCell();
for(auto datapoint : trace)
{
writer.writeCell(datapoint.x);
}
auto it_trace = trace.begin();
for(auto itmi = ++matrix.begin1(); itmi != matrix.end1(); ++itmi, ++it_trace)
{
writer.writeLine();
writer.writeCell(it_trace->x);
writer.writeCell(it_trace->y);
for(auto itmj = ++itmi.begin(); itmj != itmi.end(); itmj++)
{
writer.writeCell(aa_codec.decode((*itmj).aaCodeList).join(" "));
}
}
qDebug();
writer.close();
}
void
writeSpectralAlignmentMatrix(const QString &filename,
const pappso::specglob::SpectralAlignment &spectral_alignment)
{
QFile file(filename);
// file.open(QIODevice::WriteOnly);
OdsDocWriter writer(&file);
const matrix<pappso::specglob::SpectralAlignmentDataPoint> &matrix =
spectral_alignment.getMatrix();
pappso::PeptideSp peptide_sp = spectral_alignment.getPeptideSpectraCsp().get()->getPeptideSp();
writer.writeSheet("score");
std::size_t i = 0;
// output_stream << "\n" << getExpeSpec().getMassList());
for(auto itr1 = matrix.begin1(); itr1 != matrix.end1(); ++itr1, i++)
{
if(i < peptide_sp.get()->size())
writer.writeCell(peptide_sp.get()->getConstAa(i).toProForma());
else
writer.writeEmptyCell();
for(auto itr2 = itr1.begin(); itr2 != itr1.end(); itr2++)
{
writer.writeCell((*itr2).score);
}
writer.writeLine();
}
writer.writeSheet("alignment_type");
for(auto itr1 = matrix.begin1(); itr1 != matrix.end1(); ++itr1)
{
for(auto itr2 = itr1.begin(); itr2 != itr1.end(); itr2++)
{
writer.writeCell(QString("[%1,%2]")
.arg(pappso::Utils::toString((*itr2).alignment_type))
.arg((*itr2).origin_column_indices));
}
writer.writeLine();
}
writer.writeSheet("mass_difference");
for(auto itr1 = matrix.begin1(); itr1 != matrix.end1(); ++itr1)
{
for(auto itr2 = itr1.begin(); itr2 != itr1.end(); itr2++)
{
writer.writeCell((*itr2).mass_difference);
}
writer.writeLine();
}
writer.close();
}
void
writeJsonAaCode(const QString &filein, const pappso::AaCode &aa_code)
{
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 aacode_json;
QJsonArray aa_list;
aa_list.push_back("");
for(auto &aa : aa_code.getAaCollection())
{
aa_list.push_back((QString)aa.getLetter());
}
QJsonArray code_list;
code_list.push_back(0);
for(auto &aa : aa_code.getAaCollection())
{
code_list.push_back(aa_code.getAaCode(aa.getLetter()));
}
QJsonArray mass_list;
mass_list.push_back(0);
for(auto &aa : aa_code.getAaCollection())
{
mass_list.push_back(aa.getMass());
}
aacode_json.insert("aa", aa_list);
aacode_json.insert("code", code_list);
aacode_json.insert("mass", mass_list);
doc.setObject(aacode_json);
jsonf.write(doc.toJson());
jsonf.close();
}
else
{
throw pappso::PappsoException(
QObject::tr("Unable to write JSON output file %1").arg(filepath));
}
qDebug() << filepath;
}
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