pappso::cbor::psm::SageTsvHandler Class Reference

#include <sagetsvhandler.h>

Inheritance diagram for pappso::cbor::psm::SageTsvHandler:

Classes
struct	Line
struct	Psm
struct	Sample
struct	Scan

Public Types
enum class	Columns : std::int8_t {   psm_id , peptide , proteins , protein_groups ,   num_proteins , num_protein_groups , filename , scannr ,   rank , label , expmass , calcmass ,   charge , peptide_len , missed_cleavages , semi_enzymatic ,   isotope_error , precursor_ppm , fragment_ppm , hyperscore ,   delta_next , delta_best , rt , aligned_rt ,   predicted_rt , delta_rt_model , ion_mobility , predicted_mobility ,   delta_mobility , matched_peaks , longest_b , longest_y ,   longest_y_pct , matched_intensity_pct , scored_candidates , poisson ,   sage_discriminant_score , posterior_error , spectrum_q , peptide_q ,   protein_q , protein_group_q , ms2_intensity }

Public Member Functions
	SageTsvHandler (pappso::UiMonitorInterface *p_monitor, const SageReader &sage_reader, PsmProteinMap &psm_protein_map)
virtual	~SageTsvHandler ()
virtual void	startSheet (const QString &sheet_name) override
virtual void	endSheet () override
virtual void	startLine () override
virtual void	endLine () override
virtual void	setCell (const OdsCell &cell) override
virtual void	endDocument () override
void	writeSampleList ()

Private Member Functions
void	parsePeptide (const QString &peptide_str)
void	parseProteins (const QString &proteins_str)
bool	parseScanNrColumn (const QString &spectrum_string_id)
void	parseMsRunFilename (const QString &msrun_filename)
void	recordLine ()
void	writeSample (const Sample &one_sample)
void	writeScan (const Scan &one_scan)
void	writePsm (const Psm &one_psm)

Private Attributes
const SageReader &	m_sageReader
PsmProteinMap &	m_psmProteinMap
pappso::UiMonitorInterface *	mp_monitor = nullptr
std::size_t	m_progressIndex = 0
std::size_t	m_lineNumber = 0
std::size_t	m_columnNumber = 0
std::vector< Columns >	m_columnTypeList
pappso::PeptideSp	msp_peptide
std::vector< SageReader::SageModification >	m_staticModificationList
std::vector< SageReader::SageModification >	m_variableModificationList
std::size_t	m_spectrumIndex
std::size_t	m_scanNumber
bool	m_scanNumberIsOk
Line	m_line
QString	m_decoyTag
QStringList	m_proteinList
QString	m_spectrumNativeId
std::map< QString, Sample >	m_sampleMap
Sample *	mp_currentSample

Detailed Description

Todo:

write docs

Definition at line 49 of file sagetsvhandler.h.

Member Enumeration Documentation

Columns

enum class pappso::cbor::psm::SageTsvHandler::Columns : std::int8_t

strong

Enumerator
psm_id
peptide
proteins
protein_groups
num_proteins
num_protein_groups
filename
scannr
rank
label
expmass
calcmass
charge
peptide_len
missed_cleavages
semi_enzymatic
isotope_error
precursor_ppm
fragment_ppm
hyperscore
delta_next
delta_best
rt
aligned_rt
predicted_rt
delta_rt_model
ion_mobility
predicted_mobility
delta_mobility
matched_peaks
longest_b
longest_y
longest_y_pct
matched_intensity_pct
scored_candidates
poisson
sage_discriminant_score
posterior_error
spectrum_q
peptide_q
protein_q
protein_group_q
ms2_intensity

Definition at line 52 of file sagetsvhandler.h.

  {
    psm_id,
    peptide,
    proteins,
    protein_groups,
    num_proteins,
    num_protein_groups,
    filename,
    scannr,
    rank,
    label,
    expmass,
    calcmass,
    charge,
    peptide_len,
    missed_cleavages,
    semi_enzymatic,
    isotope_error,
    precursor_ppm,
    fragment_ppm,
    hyperscore,
    delta_next,
    delta_best,
    rt,
    aligned_rt,
    predicted_rt,
    delta_rt_model,
    ion_mobility,
    predicted_mobility,
    delta_mobility,
    matched_peaks,
    longest_b,
    longest_y,
    longest_y_pct,
    matched_intensity_pct,
    scored_candidates,
    poisson,
    sage_discriminant_score,
    posterior_error,
    spectrum_q,
    peptide_q,
    protein_q,
    protein_group_q,
    ms2_intensity,
  };

Constructor & Destructor Documentation

SageTsvHandler()

pappso::cbor::psm::SageTsvHandler::SageTsvHandler	(	pappso::UiMonitorInterface *	p_monitor,
		const SageReader &	sage_reader,
		PsmProteinMap &	psm_protein_map
	)

Default constructor

Definition at line 49 of file sagetsvhandler.cpp.

  : m_sageReader(sage_reader), m_psmProteinMap(psm_protein_map)
{
  mp_monitor                 = p_monitor;
  m_staticModificationList   = sage_reader.getStaticModificationList();
  m_variableModificationList = sage_reader.getVariableModificationList();
  m_decoyTag                 = sage_reader.getDecoyTag();
}

References pappso::cbor::psm::SageReader::getDecoyTag(), pappso::cbor::psm::SageReader::getStaticModificationList(), pappso::cbor::psm::SageReader::getVariableModificationList(), m_decoyTag, m_staticModificationList, m_variableModificationList, and mp_monitor.

~SageTsvHandler()

pappso::cbor::psm::SageTsvHandler::~SageTsvHandler ( )

virtual

Destructor

Definition at line 60 of file sagetsvhandler.cpp.

{
}

Member Function Documentation

endDocument()

void pappso::cbor::psm::SageTsvHandler::endDocument ( )

overridevirtual

Definition at line 443 of file sagetsvhandler.cpp.

{
}

endLine()

void pappso::cbor::psm::SageTsvHandler::endLine ( )

overridevirtual

callback that indicates a line ending. Override it if needed.

Definition at line 74 of file sagetsvhandler.cpp.

{
  if(m_line.charge != 0)
    recordLine();
  m_lineNumber++;
}

References pappso::cbor::psm::SageTsvHandler::Line::charge, m_line, m_lineNumber, and recordLine().

endSheet()

void pappso::cbor::psm::SageTsvHandler::endSheet ( )

overridevirtual

callback that indicates the end of the current data sheet. Override it if needed

Definition at line 82 of file sagetsvhandler.cpp.

{
}

parseMsRunFilename()

void pappso::cbor::psm::SageTsvHandler::parseMsRunFilename ( const QString &  msrun_filename )

private

Definition at line 586 of file sagetsvhandler.cpp.

{
 
 
  // find the sample :
  auto it_insert   = m_sampleMap.insert({msrun_filename, {}});
  mp_currentSample = &(it_insert.first->second);
  if(it_insert.second)
    {
      // new sample
      it_insert.first->second.name = msrun_filename;
      QCborMap ms_file;
      QCborMap identification_file;
 
      it_insert.first->second.cbor_core_sample.insert(QString("name"),
                                                      QFileInfo(msrun_filename).baseName());
 
      // identification_file_list
      QCborArray identification_file_list;
      identification_file.insert(QString("name"), m_sageReader.getmJsonAbsoluteFilePath());
      identification_file_list.push_back(identification_file);
      it_insert.first->second.cbor_core_sample.insert(QString("identification_file_list"),
                                                      identification_file_list);
 
 
      ms_file.insert(QString("name"), m_sageReader.getMzmlPath(msrun_filename));
      it_insert.first->second.cbor_core_sample.insert(QString("peaklist_file"), ms_file);
    }
 
  /*
  msp_msrun = m_sageReader.getSageFileReader().getMsRunSpWithFileName(msrun_filename);
  qDebug() << msp_msrun.get()->getFileName();
 
  msp_identificationSageJsonFileSp =
    m_sageReader.getSageFileReader().getIdentificationSageJsonFileSpWithFileName(msrun_filename);
 
  mp_identificationGroup =
    m_sageReader.getSageFileReader().getIdentificationGroupPtrWithFileName(msrun_filename);
  qDebug() << msp_msrun.get()->getFileName();
  */
}

References pappso::cbor::psm::SageReader::getmJsonAbsoluteFilePath(), pappso::cbor::psm::SageReader::getMzmlPath(), m_sageReader, m_sampleMap, mp_currentSample, and pappso::cbor::psm::SageTsvHandler::Sample::name.

Referenced by setCell().

parsePeptide()

void pappso::cbor::psm::SageTsvHandler::parsePeptide ( const QString &  peptide_str )

private

Definition at line 460 of file sagetsvhandler.cpp.

{
  qDebug();
  QString peptide_str_verif = peptide_str;
  // fixed modifications :
  for(SageReader::SageModification modif : m_staticModificationList)
    {
      qDebug() << modif.strModification;
      qDebug() << modif.modification->getAccession();
      peptide_str_verif = peptide_str_verif.replace(
        modif.strModification, QString("[%1]").arg(modif.modification->getAccession()));
    }
  // variable modifications :
  for(SageReader::SageModification modif : m_variableModificationList)
    {
      qDebug() << modif.strModification;
      qDebug() << modif.modification->getAccession();
      peptide_str_verif = peptide_str_verif.replace(
        modif.strModification, QString("[%1]").arg(modif.modification->getAccession()));
    }
 
  qDebug() << peptide_str_verif;
  // LPMFGC[+57.0216]NDATQVYK
  msp_peptide = pappso::PeptideProFormaParser::parseString(peptide_str_verif);
  qDebug();
  // variable modifications :
  /*
  setVariableModifications(peptide_sp,
                           peptide_line.peptide_string_list.at(6));
*/
  qDebug() << msp_peptide.get()->toProForma();
}

References m_staticModificationList, m_variableModificationList, msp_peptide, and pappso::PeptideProFormaParser::parseString().

Referenced by setCell().

parseProteins()

void pappso::cbor::psm::SageTsvHandler::parseProteins ( const QString &  proteins_str )

private

Definition at line 495 of file sagetsvhandler.cpp.

{
 
  m_proteinList.clear();
  m_proteinList = proteins_str.split(";");
  for(QString accession : m_proteinList)
    {
 
      PsmProtein psm_protein;
      psm_protein.protein_sp = std::make_shared<pappso::Protein>(accession, "");
      psm_protein.isTarget   = true;
      if(accession.startsWith(m_decoyTag))
        {
          psm_protein.isTarget = false;
        }
 
      m_psmProteinMap.insert(psm_protein);
    }
}

References pappso::cbor::psm::PsmProteinMap::insert(), pappso::cbor::psm::PsmProtein::isTarget, m_decoyTag, m_proteinList, m_psmProteinMap, and pappso::cbor::psm::PsmProtein::protein_sp.

Referenced by setCell().

parseScanNrColumn()

bool pappso::cbor::psm::SageTsvHandler::parseScanNrColumn ( const QString &  spectrum_string_id )

private

Definition at line 516 of file sagetsvhandler.cpp.

{
  m_spectrumNativeId = spectrum_string_id;
  qDebug() << spectrum_string_id;
  m_scanNumber     = 0;
  bool is_ok       = false;
  m_scanNumberIsOk = false;
  // controllerType=0 controllerNumber=1 scan=176056
  if(mp_currentSample->name.endsWith(".d"))
    { // assume this is a Bruker's timTOF sample
      // 200ngHeLaPASEF_2min_compressed.d   2005
      std::size_t precursor_number = spectrum_string_id.toULongLong(&is_ok);
      if(is_ok)
        {
          // precursor=2006 idxms2=4011
          m_scanNumberIsOk   = is_ok;
          m_spectrumIndex    = precursor_number * 2 + 1;
          m_spectrumNativeId = QString("precursor=%1 idxms2=%2")
                                 .arg(precursor_number + 1)
                                 .arg(precursor_number * 2 + 1);
        }
    }
 
  if(!is_ok)
    {
      QStringList scan_list = spectrum_string_id.split("scan=");
      if(scan_list.size() == 2)
        {
          // we bet that there is a scan number, easy to parse
          m_scanNumber     = scan_list.at(1).toULongLong(&is_ok);
          m_scanNumberIsOk = is_ok;
          if(m_scanNumber > 0)
            m_spectrumIndex = m_scanNumber - 1;
        }
      if(is_ok == false)
        {
          ;
          QStringList scan_list = spectrum_string_id.split(QRegularExpression("[^\\d]"));
          if(scan_list.size() == 2)
            {
              m_scanNumber     = scan_list.at(0).toULongLong(&is_ok);
              m_scanNumberIsOk = is_ok;
              if(m_scanNumber > 0)
                m_spectrumIndex = m_scanNumber - 1;
            }
          /*
         if(msp_previousMsrun != msp_msrun)
           {
             mp_monitor->setStatus(
               QObject::tr("Reading mz data file %1").arg(msp_msrun.get()->getFileName()));
             msp_previousMsrun = msp_msrun;
           }
 
         pappso::MsRunReader *msrunreader_p = msp_msrun.get()->getMsRunReaderSPtr().get();
         if(msrunreader_p->getMsRunId()->getMsDataFormat() == pappso::MsDataFormat::brukerTims)
           {
             m_spectrumIndex = spectrum_string_id.toInt() * 2 - 1;
           }
         else
           {
             m_spectrumIndex =
               msrunreader_p->spectrumStringIdentifier2SpectrumIndex(spectrum_string_id);
           }*/
        }
    }
  qDebug() << spectrum_string_id;
  return is_ok;
}

References m_scanNumber, m_scanNumberIsOk, m_spectrumIndex, m_spectrumNativeId, mp_currentSample, and pappso::cbor::psm::SageTsvHandler::Sample::name.

Referenced by setCell().

recordLine()

void pappso::cbor::psm::SageTsvHandler::recordLine ( )

private

Definition at line 629 of file sagetsvhandler.cpp.

{
  qDebug();
 
  for(const QString &accession : m_proteinList)
    {
      PsmProtein psm_protein;
      psm_protein.protein_sp = std::make_shared<pappso::Protein>(accession, "");
 
      QCborMap sage_eval;
      sage_eval.insert(QString("protein_q"), m_line.protein_q);
 
      auto it = m_psmProteinMap.insert(psm_protein);
      it.first->second.cborEval.insert(QString("sage"), sage_eval);
    }
  /*
  PeptideEvidence pe(msp_msrun.get(), m_spectrumIndex, true);
  pe.setCharge(m_line.charge);
  pe.setChecked(true);
  pe.setExperimentalMass(m_line.expmass);
  pe.setPeptideXtpSp(msp_peptide);
  pe.setIdentificationDataSource(msp_identificationSageJsonFileSp.get());
  pe.setIdentificationEngine(m_identificationEngine);
  pe.setRetentionTime(m_line.rt);
  pe.setParam(PeptideEvidenceParam::tandem_hyperscore, m_line.hyperscore);
  pe.setParam(PeptideEvidenceParam::sage_sage_discriminant_score,
              m_line.sage_discriminant_score);
  pe.setParam(PeptideEvidenceParam::sage_peptide_q, m_line.peptide_q);
  pe.setParam(PeptideEvidenceParam::sage_posterior_error, m_line.posterior_error);
  pe.setParam(PeptideEvidenceParam::sage_spectrum_q, m_line.spectrum_q);
  pe.setParam(PeptideEvidenceParam::sage_predicted_rt, m_line.predicted_rt);
  pe.setParam(PeptideEvidenceParam::sage_isotope_error, m_line.isotope_error);
 
 
  PeptideMatch peptide_match;
  // peptide_match.setStart(mz_peptide_evidence.start);
  peptide_match.setPeptideEvidenceSp(
    msp_identificationSageJsonFileSp.get()->getPeptideEvidenceStore().getInstance(&pe));
    */
 
  // find the scan in sample
  auto it_insert            = mp_currentSample->scan_map.insert({m_spectrumNativeId, Scan()});
  Scan *current_cbor_scan_p = &(it_insert.first->second);
  if(it_insert.second)
    {
      // new scan
      QCborMap &scan_id = it_insert.first->second.cbor_id;
      if(m_scanNumberIsOk)
        {
          scan_id.insert(QString("index"), (qint64)m_spectrumIndex);
          if(m_scanNumber > 0)
            scan_id.insert(QString("scan"), (qint64)m_scanNumber);
        }
      scan_id.insert(QString("native_id"), m_spectrumNativeId);
 
      QCborMap &scan_ms2 = it_insert.first->second.cbor_ms2;
      scan_ms2.insert(QString("rt"), m_line.rt);
 
      QCborMap &scan_precursor = it_insert.first->second.cbor_precursor;
      scan_precursor.insert(QString("z"), m_line.charge);
      double mh = m_line.expmass + MHPLUS;
      scan_precursor.insert(QString("mh"), mh);
      double exp_mz = (m_line.expmass + (MHPLUS * m_line.charge)) / m_line.charge;
      scan_precursor.insert(QString("mz"), exp_mz);
    }
 
  Psm one_psm;
  one_psm.peptide_sequence_li = msp_peptide.get()->getSequenceLi();
  one_psm.proforma            = msp_peptide.get()->toProForma();
  one_psm.protein_list        = m_proteinList;
 
 
  one_psm.cbor_eval.insert(QString("aligned_rt"), m_line.aligned_rt);
  one_psm.cbor_eval.insert(QString("calcmass"), m_line.calcmass);
  one_psm.cbor_eval.insert(QString("delta_best"), m_line.delta_best);
  one_psm.cbor_eval.insert(QString("delta_mobility"), m_line.delta_mobility);
  one_psm.cbor_eval.insert(QString("delta_next"), m_line.delta_next);
  one_psm.cbor_eval.insert(QString("delta_rt_model"), m_line.delta_rt_model);
  one_psm.cbor_eval.insert(QString("fragment_ppm"), m_line.fragment_ppm);
  one_psm.cbor_eval.insert(QString("hyperscore"), m_line.hyperscore);
  one_psm.cbor_eval.insert(QString("ion_mobility"), m_line.ion_mobility);
  one_psm.cbor_eval.insert(QString("isotope_error"), m_line.isotope_error);
  one_psm.cbor_eval.insert(QString("label"), m_line.label);
  one_psm.cbor_eval.insert(QString("longest_b"), (qint64)m_line.longest_b);
  one_psm.cbor_eval.insert(QString("longest_y"), (qint64)m_line.longest_y);
  one_psm.cbor_eval.insert(QString("longest_y_pct"), m_line.longest_y_pct);
  one_psm.cbor_eval.insert(QString("matched_intensity_pct"), m_line.matched_intensity_pct);
  one_psm.cbor_eval.insert(QString("matched_peaks"), (qint64)m_line.matched_peaks);
  one_psm.cbor_eval.insert(QString("missed_cleavages"), m_line.missed_cleavages);
  one_psm.cbor_eval.insert(QString("ms2_intensity"), m_line.ms2_intensity);
  one_psm.cbor_eval.insert(QString("peptide_len"), (qint64)m_line.peptide_len);
  one_psm.cbor_eval.insert(QString("peptide_q"), m_line.peptide_q);
  one_psm.cbor_eval.insert(QString("poisson"), m_line.poisson);
  one_psm.cbor_eval.insert(QString("posterior_error"), m_line.posterior_error);
  one_psm.cbor_eval.insert(QString("precursor_ppm"), m_line.precursor_ppm);
  one_psm.cbor_eval.insert(QString("predicted_mobility"), m_line.predicted_mobility);
  one_psm.cbor_eval.insert(QString("predicted_rt"), m_line.predicted_rt);
  one_psm.cbor_eval.insert(QString("protein_q"), m_line.protein_q);
  one_psm.cbor_eval.insert(QString("rank"), m_line.rank);
  one_psm.cbor_eval.insert(QString("sage_discriminant_score"), m_line.sage_discriminant_score);
  one_psm.cbor_eval.insert(QString("scored_candidates"), (qint64)m_line.scored_candidates);
  one_psm.cbor_eval.insert(QString("semi_enzymatic"), m_line.semi_enzymatic);
  one_psm.cbor_eval.insert(QString("spectrum_q"), m_line.spectrum_q);
 
  current_cbor_scan_p->psm_list.emplace_back(one_psm);
 
 
  std::size_t progress = m_lineNumber / 10000;
  if(progress > m_progressIndex)
    {
      if(mp_monitor->shouldIstop())
        {
          throw pappso::ExceptionInterrupted(
            QObject::tr("Sage TSV data reading process interrupted"));
        }
      m_progressIndex = progress;
      mp_monitor->setStatus(QString("%1K ").arg(m_progressIndex * 10));
    }
}

References pappso::cbor::psm::SageTsvHandler::Line::aligned_rt, pappso::cbor::psm::SageTsvHandler::Line::calcmass, pappso::cbor::psm::SageTsvHandler::Psm::cbor_eval, pappso::cbor::psm::SageTsvHandler::Scan::cbor_id, pappso::cbor::psm::SageTsvHandler::Line::charge, pappso::cbor::psm::SageTsvHandler::Line::delta_best, pappso::cbor::psm::SageTsvHandler::Line::delta_mobility, pappso::cbor::psm::SageTsvHandler::Line::delta_next, pappso::cbor::psm::SageTsvHandler::Line::delta_rt_model, pappso::cbor::psm::SageTsvHandler::Line::expmass, pappso::cbor::psm::SageTsvHandler::Line::fragment_ppm, pappso::cbor::psm::SageTsvHandler::Line::hyperscore, pappso::cbor::psm::PsmProteinMap::insert(), pappso::cbor::psm::SageTsvHandler::Line::ion_mobility, pappso::cbor::psm::SageTsvHandler::Line::isotope_error, pappso::cbor::psm::SageTsvHandler::Line::label, pappso::cbor::psm::SageTsvHandler::Line::longest_b, pappso::cbor::psm::SageTsvHandler::Line::longest_y, pappso::cbor::psm::SageTsvHandler::Line::longest_y_pct, m_line, m_lineNumber, m_progressIndex, m_proteinList, m_psmProteinMap, m_scanNumber, m_scanNumberIsOk, m_spectrumIndex, m_spectrumNativeId, pappso::cbor::psm::SageTsvHandler::Line::matched_intensity_pct, pappso::cbor::psm::SageTsvHandler::Line::matched_peaks, pappso::MHPLUS(), pappso::cbor::psm::SageTsvHandler::Line::missed_cleavages, mp_currentSample, mp_monitor, pappso::cbor::psm::SageTsvHandler::Line::ms2_intensity, msp_peptide, pappso::cbor::psm::SageTsvHandler::Line::peptide_len, pappso::cbor::psm::SageTsvHandler::Line::peptide_q, pappso::cbor::psm::SageTsvHandler::Psm::peptide_sequence_li, pappso::cbor::psm::SageTsvHandler::Line::poisson, pappso::cbor::psm::SageTsvHandler::Line::posterior_error, pappso::cbor::psm::SageTsvHandler::Line::precursor_ppm, pappso::cbor::psm::SageTsvHandler::Line::predicted_mobility, pappso::cbor::psm::SageTsvHandler::Line::predicted_rt, pappso::cbor::psm::SageTsvHandler::Psm::proforma, pappso::cbor::psm::SageTsvHandler::Psm::protein_list, pappso::cbor::psm::SageTsvHandler::Line::protein_q, pappso::cbor::psm::PsmProtein::protein_sp, pappso::cbor::psm::SageTsvHandler::Scan::psm_list, pappso::cbor::psm::SageTsvHandler::Line::rank, pappso::cbor::psm::SageTsvHandler::Line::rt, pappso::cbor::psm::SageTsvHandler::Line::sage_discriminant_score, pappso::cbor::psm::SageTsvHandler::Sample::scan_map, pappso::cbor::psm::SageTsvHandler::Line::scored_candidates, pappso::cbor::psm::SageTsvHandler::Line::semi_enzymatic, pappso::UiMonitorInterface::setStatus(), pappso::UiMonitorInterface::shouldIstop(), and pappso::cbor::psm::SageTsvHandler::Line::spectrum_q.

Referenced by endLine().

setCell()

void pappso::cbor::psm::SageTsvHandler::setCell ( const OdsCell &  cell )

overridevirtual

callback that report the content of the current cell in a dedicated Cell object. Override it if you need to retrieve cell content.

Definition at line 87 of file sagetsvhandler.cpp.

{
  if(m_lineNumber == 0)
    {
      // header
      QString tag = cell.getStringValue();
      if(tag == "psm_id")
        {
          m_columnTypeList.push_back(Columns::psm_id);
        }
      else if(tag == "peptide")
        {
          m_columnTypeList.push_back(Columns::peptide);
        }
      else if(tag == "proteins")
        {
          m_columnTypeList.push_back(Columns::proteins);
        }
      else if(tag == "protein_groups")
        {
          m_columnTypeList.push_back(Columns::protein_groups);
        }
      else if(tag == "num_protein_groups")
        {
          m_columnTypeList.push_back(Columns::num_protein_groups);
        }
      else if(tag == "num_proteins")
        {
          m_columnTypeList.push_back(Columns::num_proteins);
        }
      else if(tag == "filename")
        {
          m_columnTypeList.push_back(Columns::filename);
        }
      else if(tag == "scannr")
        {
          m_columnTypeList.push_back(Columns::scannr);
        }
      else if(tag == "rank")
        {
          m_columnTypeList.push_back(Columns::rank);
        }
      else if(tag == "label")
        {
          m_columnTypeList.push_back(Columns::label);
        }
      else if(tag == "expmass")
        {
          m_columnTypeList.push_back(Columns::expmass);
        }
 
      else if(tag == "calcmass")
        {
          m_columnTypeList.push_back(Columns::calcmass);
        }
      else if(tag == "charge")
        {
          m_columnTypeList.push_back(Columns::charge);
        }
      else if(tag == "peptide_len")
        {
          m_columnTypeList.push_back(Columns::peptide_len);
        }
      else if(tag == "missed_cleavages")
        {
          m_columnTypeList.push_back(Columns::missed_cleavages);
        }
      else if(tag == "semi_enzymatic")
        {
          m_columnTypeList.push_back(Columns::semi_enzymatic);
        }
      else if(tag == "isotope_error")
        {
          m_columnTypeList.push_back(Columns::isotope_error);
        }
      else if(tag == "precursor_ppm")
        {
          m_columnTypeList.push_back(Columns::precursor_ppm);
        }
      else if(tag == "fragment_ppm")
        {
          m_columnTypeList.push_back(Columns::fragment_ppm);
        }
      else if(tag == "hyperscore")
        {
          m_columnTypeList.push_back(Columns::hyperscore);
        }
      else if(tag == "delta_next")
        {
          m_columnTypeList.push_back(Columns::delta_next);
        }
      else if(tag == "delta_best")
        {
          m_columnTypeList.push_back(Columns::delta_best);
        }
      else if(tag == "rt")
        {
          m_columnTypeList.push_back(Columns::rt);
        }
      else if(tag == "aligned_rt")
        {
          m_columnTypeList.push_back(Columns::aligned_rt);
        }
      else if(tag == "predicted_rt")
        {
          m_columnTypeList.push_back(Columns::predicted_rt);
        }
      else if(tag == "delta_rt_model")
        {
          m_columnTypeList.push_back(Columns::delta_rt_model);
        }
      else if(tag == "ion_mobility")
        {
          m_columnTypeList.push_back(Columns::ion_mobility);
        }
      else if(tag == "predicted_mobility")
        {
          m_columnTypeList.push_back(Columns::predicted_mobility);
        }
      else if(tag == "delta_mobility")
        {
          m_columnTypeList.push_back(Columns::delta_mobility);
        }
      else if(tag == "matched_peaks")
        {
          m_columnTypeList.push_back(Columns::matched_peaks);
        }
      else if(tag == "longest_b")
        {
          m_columnTypeList.push_back(Columns::longest_b);
        }
      else if(tag == "longest_y")
        {
          m_columnTypeList.push_back(Columns::longest_y);
        }
      else if(tag == "longest_y_pct")
        {
          m_columnTypeList.push_back(Columns::longest_y_pct);
        }
      else if(tag == "matched_intensity_pct")
        {
          m_columnTypeList.push_back(Columns::matched_intensity_pct);
        }
      else if(tag == "scored_candidates")
        {
          m_columnTypeList.push_back(Columns::scored_candidates);
        }
      else if(tag == "poisson")
        {
          m_columnTypeList.push_back(Columns::poisson);
        }
      else if(tag == "sage_discriminant_score")
        {
          m_columnTypeList.push_back(Columns::sage_discriminant_score);
        }
      else if(tag == "posterior_error")
        {
          m_columnTypeList.push_back(Columns::posterior_error);
        }
      else if(tag == "spectrum_q")
        {
          m_columnTypeList.push_back(Columns::spectrum_q);
        }
      else if(tag == "peptide_q")
        {
          m_columnTypeList.push_back(Columns::peptide_q);
        }
      else if(tag == "protein_q")
        {
          m_columnTypeList.push_back(Columns::protein_q);
        }
      else if(tag == "protein_group_q")
        {
          m_columnTypeList.push_back(Columns::protein_group_q);
        }
      else if(tag == "ms2_intensity")
        {
          m_columnTypeList.push_back(Columns::ms2_intensity);
        }
      else
        {
          throw pappso::ExceptionNotPossible(QObject::tr("column \"%1\" not defined").arg(tag));
        }
    }
  else
    {
      if(m_columnNumber >= m_columnTypeList.size())
        {
          throw pappso::ExceptionOutOfRange(
            QObject::tr("the value %1 is out of range").arg(cell.getStringValue()));
        }
      Columns column_type = m_columnTypeList[m_columnNumber];
      switch(column_type)
        {
          case Columns::psm_id:
            break;
          case Columns::protein_groups:
            break;
          case Columns::num_protein_groups:
            break;
          case Columns::protein_group_q:
            break;
          case Columns::peptide:
            parsePeptide(cell.toString());
            break;
          case Columns::proteins:
            parseProteins(cell.toString());
            break;
          case Columns::num_proteins:
            if((std::size_t)cell.getDoubleValue() != (std::size_t)m_proteinList.size())
              {
                throw pappso::PappsoException(
                  QObject::tr("column \"num_proteins\"!=%1").arg(m_proteinList.size()));
              }
            break;
          case Columns::filename:
            parseMsRunFilename(cell.toString());
            break;
          case Columns::scannr:
            parseScanNrColumn(cell.toString());
            break;
          case Columns::rank:
            m_line.rank = cell.getDoubleValue();
            break;
          case Columns::label:
            m_line.label = cell.getDoubleValue();
            break;
          case Columns::expmass:
            m_line.expmass = cell.getDoubleValue();
            break;
          case Columns::calcmass:
            m_line.calcmass = cell.getDoubleValue();
            break;
          case Columns::charge:
            m_line.charge = cell.getDoubleValue();
            break;
          case Columns::peptide_len:
            m_line.peptide_len = cell.getDoubleValue();
            break;
          case Columns::missed_cleavages:
            m_line.missed_cleavages = cell.getDoubleValue();
            break;
          case Columns::semi_enzymatic:
            m_line.semi_enzymatic = cell.getDoubleValue();
            break;
          case Columns::isotope_error:
            m_line.isotope_error = cell.getDoubleValue();
            break;
 
          case Columns::precursor_ppm:
            m_line.precursor_ppm = cell.getDoubleValue();
            break;
          case Columns::fragment_ppm:
            m_line.fragment_ppm = cell.getDoubleValue();
            break;
          case Columns::hyperscore:
            m_line.hyperscore = cell.getDoubleValue();
            break;
          case Columns::delta_next:
            m_line.delta_next = cell.getDoubleValue();
            break;
          case Columns::delta_best:
            m_line.delta_best = cell.getDoubleValue();
            break;
          case Columns::rt:
            m_line.rt = cell.getDoubleValue() * 60; // to convert retention time in seconds
            break;
          case Columns::aligned_rt:
            m_line.aligned_rt = cell.getDoubleValue();
            break;
          case Columns::predicted_rt:
            m_line.predicted_rt = cell.getDoubleValue();
            break;
          case Columns::delta_rt_model:
            m_line.delta_rt_model = cell.getDoubleValue();
            break;
          case Columns::ion_mobility:
            m_line.ion_mobility = cell.getDoubleValue();
            break;
          case Columns::predicted_mobility:
            m_line.predicted_mobility = cell.getDoubleValue();
            break;
          case Columns::delta_mobility:
            m_line.delta_mobility = cell.getDoubleValue();
            break;
          case Columns::matched_peaks:
            m_line.matched_peaks = cell.getDoubleValue();
            break;
          case Columns::longest_b:
            m_line.longest_b = cell.getDoubleValue();
            break;
          case Columns::longest_y:
            m_line.longest_y = cell.getDoubleValue();
            break;
          case Columns::longest_y_pct:
            m_line.longest_y_pct = cell.getDoubleValue();
            break;
          case Columns::matched_intensity_pct:
            m_line.matched_intensity_pct = cell.getDoubleValue();
            break;
          case Columns::scored_candidates:
            m_line.scored_candidates = cell.getDoubleValue();
            break;
          case Columns::poisson:
            m_line.poisson = cell.getDoubleValue();
            break;
          case Columns::sage_discriminant_score:
            m_line.sage_discriminant_score = cell.getDoubleValue();
            break;
          case Columns::posterior_error:
            m_line.posterior_error = cell.getDoubleValue();
            break;
          case Columns::spectrum_q:
            m_line.spectrum_q = cell.getDoubleValue();
            break;
          case Columns::peptide_q:
            m_line.peptide_q = cell.getDoubleValue();
            break;
          case Columns::protein_q:
            m_line.protein_q = cell.getDoubleValue();
            break;
          case Columns::ms2_intensity:
            m_line.ms2_intensity = cell.getDoubleValue();
            break;
          default:
            qDebug() << "m_line.calcmass=" << m_line.calcmass;
            throw pappso::ExceptionNotImplemented(
              QObject::tr("column type %1 not implemented").arg((std::uint8_t)column_type));
            break;
        }
 
      /*
 
    2333    TMISDSDYTEFENFTK
    GRMZM2G018197_P01;GRMZM2G068952_P01;GRMZM5G822976_P01   3
    20120906_balliau_extract_1_A01_urnb-1.mzML  controllerType=0
    controllerNumber=1 scan=12542   1   1   1926.8225   1926.8193   2   16  0   0
    0.0 1.6471838   1.9796097   54.06803492297634   28.049970383419556  0.0 38.192993
    0.76385987  0.7671368   0.0032769442    0.0 0.0 0.0 16  2   14  0.875   32.54396 380
    -13.375352220427656 1.1570586   -34.13482   0.00016041065   0.00022231363
    0.00040124074   1271951.1
    */
    }
  m_columnNumber++;
}

References aligned_rt, pappso::cbor::psm::SageTsvHandler::Line::aligned_rt, calcmass, pappso::cbor::psm::SageTsvHandler::Line::calcmass, charge, pappso::cbor::psm::SageTsvHandler::Line::charge, delta_best, pappso::cbor::psm::SageTsvHandler::Line::delta_best, delta_mobility, pappso::cbor::psm::SageTsvHandler::Line::delta_mobility, delta_next, pappso::cbor::psm::SageTsvHandler::Line::delta_next, delta_rt_model, pappso::cbor::psm::SageTsvHandler::Line::delta_rt_model, expmass, pappso::cbor::psm::SageTsvHandler::Line::expmass, filename, fragment_ppm, pappso::cbor::psm::SageTsvHandler::Line::fragment_ppm, hyperscore, pappso::cbor::psm::SageTsvHandler::Line::hyperscore, ion_mobility, pappso::cbor::psm::SageTsvHandler::Line::ion_mobility, isotope_error, pappso::cbor::psm::SageTsvHandler::Line::isotope_error, label, pappso::cbor::psm::SageTsvHandler::Line::label, longest_b, pappso::cbor::psm::SageTsvHandler::Line::longest_b, longest_y, pappso::cbor::psm::SageTsvHandler::Line::longest_y, longest_y_pct, pappso::cbor::psm::SageTsvHandler::Line::longest_y_pct, m_columnNumber, m_columnTypeList, m_line, m_lineNumber, m_proteinList, matched_intensity_pct, pappso::cbor::psm::SageTsvHandler::Line::matched_intensity_pct, matched_peaks, pappso::cbor::psm::SageTsvHandler::Line::matched_peaks, missed_cleavages, pappso::cbor::psm::SageTsvHandler::Line::missed_cleavages, ms2_intensity, pappso::cbor::psm::SageTsvHandler::Line::ms2_intensity, num_protein_groups, num_proteins, parseMsRunFilename(), parsePeptide(), parseProteins(), parseScanNrColumn(), peptide, peptide_len, pappso::cbor::psm::SageTsvHandler::Line::peptide_len, peptide_q, pappso::cbor::psm::SageTsvHandler::Line::peptide_q, poisson, pappso::cbor::psm::SageTsvHandler::Line::poisson, posterior_error, pappso::cbor::psm::SageTsvHandler::Line::posterior_error, precursor_ppm, pappso::cbor::psm::SageTsvHandler::Line::precursor_ppm, predicted_mobility, pappso::cbor::psm::SageTsvHandler::Line::predicted_mobility, predicted_rt, pappso::cbor::psm::SageTsvHandler::Line::predicted_rt, protein_group_q, protein_groups, protein_q, pappso::cbor::psm::SageTsvHandler::Line::protein_q, proteins, psm_id, rank, pappso::cbor::psm::SageTsvHandler::Line::rank, rt, pappso::cbor::psm::SageTsvHandler::Line::rt, sage_discriminant_score, pappso::cbor::psm::SageTsvHandler::Line::sage_discriminant_score, scannr, scored_candidates, pappso::cbor::psm::SageTsvHandler::Line::scored_candidates, semi_enzymatic, pappso::cbor::psm::SageTsvHandler::Line::semi_enzymatic, spectrum_q, and pappso::cbor::psm::SageTsvHandler::Line::spectrum_q.

startLine()

void pappso::cbor::psm::SageTsvHandler::startLine ( )

overridevirtual

callback that indicates a new line start. Override it if needed.

Definition at line 434 of file sagetsvhandler.cpp.

{
  m_columnNumber = 0;
  msp_peptide    = nullptr;
  m_proteinList.clear();
  m_line = Line();
}

References m_columnNumber, m_line, m_proteinList, and msp_peptide.

startSheet()

void pappso::cbor::psm::SageTsvHandler::startSheet ( const QString &  sheet_name )

overridevirtual

callback that indicates the begining of a data sheet. Override it in order to retrieve information about the current data sheet.

Definition at line 447 of file sagetsvhandler.cpp.

{
  m_columnNumber = 0;
  m_lineNumber   = 0;
  mp_monitor->setStatus(QObject::tr("reading Sage TSV file"));
 
  if(mp_monitor->shouldIstop())
    {
      throw pappso::ExceptionInterrupted(QObject::tr("Sage TSV data reading process interrupted"));
    }
}

References m_columnNumber, m_lineNumber, mp_monitor, pappso::UiMonitorInterface::setStatus(), and pappso::UiMonitorInterface::shouldIstop().

writePsm()

void pappso::cbor::psm::SageTsvHandler::writePsm ( const Psm &  one_psm )

private

Definition at line 800 of file sagetsvhandler.cpp.

{
  m_sageReader.getCborStreamWriter().startMap();
  m_sageReader.getCborStreamWriter().append("proforma");
  m_sageReader.getCborStreamWriter().append(one_psm.proforma);
  m_sageReader.getCborStreamWriter().append("protein_list");
 
  QCborArray cbor_protein_list;
  for(const QString &accession : one_psm.protein_list)
    {
      // qWarning() << "accession=" << accession;
      QCborMap cbor_protein;
      cbor_protein.insert(QString("accession"), accession);
 
 
      // start/end positions
      QString protein_sequence =
        QString(m_psmProteinMap.getByAccession(accession).protein_sp.get()->getSequence())
          .replace("L", "I");
      int position = protein_sequence.indexOf(one_psm.peptide_sequence_li);
 
      QCborArray positions;
      while(position >= 0)
        {
          positions.push_back(position);
          position = protein_sequence.indexOf(one_psm.peptide_sequence_li, position + 1);
        }
 
      cbor_protein.insert(QString("positions"), positions);
 
      cbor_protein_list.append(cbor_protein);
    }
 
 
  QCborValue(cbor_protein_list).toCbor(m_sageReader.getCborStreamWriter());
 
  m_sageReader.getCborStreamWriter().append("eval");
  m_sageReader.getCborStreamWriter().startMap();
  m_sageReader.getCborStreamWriter().append("sage");
  QCborValue(one_psm.cbor_eval).toCbor(m_sageReader.getCborStreamWriter());
  m_sageReader.getCborStreamWriter().endMap();
 
  m_sageReader.getCborStreamWriter().endMap();
}

References pappso::cbor::psm::SageTsvHandler::Psm::cbor_eval, pappso::cbor::psm::PsmProteinMap::getByAccession(), pappso::cbor::psm::SageReader::getCborStreamWriter(), m_psmProteinMap, m_sageReader, pappso::cbor::psm::SageTsvHandler::Psm::peptide_sequence_li, pappso::cbor::psm::SageTsvHandler::Psm::proforma, pappso::cbor::psm::SageTsvHandler::Psm::protein_list, and pappso::cbor::psm::PsmProtein::protein_sp.

Referenced by writeScan().

writeSample()

void pappso::cbor::psm::SageTsvHandler::writeSample ( const Sample &  one_sample )

private

Definition at line 750 of file sagetsvhandler.cpp.

{
  m_sageReader.getCborStreamWriter().startMap();
  m_sageReader.getCborStreamWriter().append("name");
  one_sample.cbor_core_sample.value("name").toCbor(m_sageReader.getCborStreamWriter());
 
  m_sageReader.getCborStreamWriter().append("identification_file_list");
  one_sample.cbor_core_sample.value("identification_file_list")
    .toCbor(m_sageReader.getCborStreamWriter());
 
 
  m_sageReader.getCborStreamWriter().append("peaklist_file");
  one_sample.cbor_core_sample.value("peaklist_file").toCbor(m_sageReader.getCborStreamWriter());
  //"scan_list": [
 
  m_sageReader.getCborStreamWriter().append("scan_list");
  m_sageReader.getCborStreamWriter().startArray(one_sample.scan_map.size());
  for(auto &it_scan : one_sample.scan_map)
    {
      writeScan(it_scan.second);
    }
  m_sageReader.getCborStreamWriter().endArray();
 
 
  m_sageReader.getCborStreamWriter().endMap();
}

References pappso::cbor::psm::SageTsvHandler::Sample::cbor_core_sample, pappso::cbor::psm::SageReader::getCborStreamWriter(), m_sageReader, pappso::cbor::psm::SageTsvHandler::Sample::scan_map, and writeScan().

Referenced by writeSampleList().

writeSampleList()

void pappso::cbor::psm::SageTsvHandler::writeSampleList

(

)

Definition at line 65 of file sagetsvhandler.cpp.

{
  for(auto it_sample_map : m_sampleMap)
    {
      writeSample(it_sample_map.second);
    }
}

References m_sampleMap, and writeSample().

Referenced by pappso::cbor::psm::SageReader::readTsvFile().

writeScan()

void pappso::cbor::psm::SageTsvHandler::writeScan ( const Scan &  one_scan )

private

Definition at line 778 of file sagetsvhandler.cpp.

{
  m_sageReader.getCborStreamWriter().startMap();
  m_sageReader.getCborStreamWriter().append("id");
  QCborValue(one_scan.cbor_id).toCbor(m_sageReader.getCborStreamWriter());
  m_sageReader.getCborStreamWriter().append("precursor");
  QCborValue(one_scan.cbor_precursor).toCbor(m_sageReader.getCborStreamWriter());
  m_sageReader.getCborStreamWriter().append("ms2");
  QCborValue(one_scan.cbor_ms2).toCbor(m_sageReader.getCborStreamWriter());
 
  m_sageReader.getCborStreamWriter().append("psm_list");
  m_sageReader.getCborStreamWriter().startArray(one_scan.psm_list.size());
  for(auto &it_psm : one_scan.psm_list)
    {
      writePsm(it_psm);
    }
  m_sageReader.getCborStreamWriter().endArray();
 
  m_sageReader.getCborStreamWriter().endMap();
}

References pappso::cbor::psm::SageTsvHandler::Scan::cbor_id, pappso::cbor::psm::SageTsvHandler::Scan::cbor_ms2, pappso::cbor::psm::SageTsvHandler::Scan::cbor_precursor, pappso::cbor::psm::SageReader::getCborStreamWriter(), m_sageReader, pappso::cbor::psm::SageTsvHandler::Scan::psm_list, and writePsm().

Referenced by writeSample().

Member Data Documentation

m_columnNumber

std::size_t pappso::cbor::psm::SageTsvHandler::m_columnNumber = 0

private

Definition at line 221 of file sagetsvhandler.h.

Referenced by setCell(), startLine(), and startSheet().

m_columnTypeList

std::vector<Columns> pappso::cbor::psm::SageTsvHandler::m_columnTypeList

private

Definition at line 222 of file sagetsvhandler.h.

Referenced by setCell().

m_decoyTag

QString pappso::cbor::psm::SageTsvHandler::m_decoyTag

private

Definition at line 232 of file sagetsvhandler.h.

Referenced by SageTsvHandler(), and parseProteins().

m_line

Line pappso::cbor::psm::SageTsvHandler::m_line

private

Definition at line 231 of file sagetsvhandler.h.

Referenced by endLine(), recordLine(), setCell(), and startLine().

m_lineNumber

std::size_t pappso::cbor::psm::SageTsvHandler::m_lineNumber = 0

private

Definition at line 220 of file sagetsvhandler.h.

Referenced by endLine(), recordLine(), setCell(), and startSheet().

m_progressIndex

std::size_t pappso::cbor::psm::SageTsvHandler::m_progressIndex = 0

private

Definition at line 219 of file sagetsvhandler.h.

Referenced by recordLine().

m_proteinList

QStringList pappso::cbor::psm::SageTsvHandler::m_proteinList

private

Definition at line 233 of file sagetsvhandler.h.

Referenced by parseProteins(), recordLine(), setCell(), and startLine().

m_psmProteinMap

PsmProteinMap& pappso::cbor::psm::SageTsvHandler::m_psmProteinMap

private

Definition at line 217 of file sagetsvhandler.h.

Referenced by parseProteins(), recordLine(), and writePsm().

m_sageReader

const SageReader& pappso::cbor::psm::SageTsvHandler::m_sageReader

private

Definition at line 216 of file sagetsvhandler.h.

Referenced by parseMsRunFilename(), writePsm(), writeSample(), and writeScan().

m_sampleMap

std::map<QString, Sample> pappso::cbor::psm::SageTsvHandler::m_sampleMap

private

Definition at line 235 of file sagetsvhandler.h.

Referenced by parseMsRunFilename(), and writeSampleList().

m_scanNumber

std::size_t pappso::cbor::psm::SageTsvHandler::m_scanNumber

private

Definition at line 228 of file sagetsvhandler.h.

Referenced by parseScanNrColumn(), and recordLine().

m_scanNumberIsOk

bool pappso::cbor::psm::SageTsvHandler::m_scanNumberIsOk

private

Definition at line 229 of file sagetsvhandler.h.

Referenced by parseScanNrColumn(), and recordLine().

m_spectrumIndex

std::size_t pappso::cbor::psm::SageTsvHandler::m_spectrumIndex

private

Definition at line 227 of file sagetsvhandler.h.

Referenced by parseScanNrColumn(), and recordLine().

m_spectrumNativeId

QString pappso::cbor::psm::SageTsvHandler::m_spectrumNativeId

private

Definition at line 234 of file sagetsvhandler.h.

Referenced by parseScanNrColumn(), and recordLine().

m_staticModificationList

std::vector<SageReader::SageModification> pappso::cbor::psm::SageTsvHandler::m_staticModificationList

private

Definition at line 225 of file sagetsvhandler.h.

Referenced by SageTsvHandler(), and parsePeptide().

m_variableModificationList

std::vector<SageReader::SageModification> pappso::cbor::psm::SageTsvHandler::m_variableModificationList

private

Definition at line 226 of file sagetsvhandler.h.

Referenced by SageTsvHandler(), and parsePeptide().

mp_currentSample

Sample* pappso::cbor::psm::SageTsvHandler::mp_currentSample

private

Definition at line 236 of file sagetsvhandler.h.

Referenced by parseMsRunFilename(), parseScanNrColumn(), and recordLine().

mp_monitor

pappso::UiMonitorInterface* pappso::cbor::psm::SageTsvHandler::mp_monitor = nullptr

private

Definition at line 218 of file sagetsvhandler.h.

Referenced by SageTsvHandler(), recordLine(), and startSheet().

msp_peptide

pappso::PeptideSp pappso::cbor::psm::SageTsvHandler::msp_peptide

private

Definition at line 224 of file sagetsvhandler.h.

Referenced by parsePeptide(), recordLine(), and startLine().

---

The documentation for this class was generated from the following files:

• pappsomspp/core/processing/cbor/psm/sage/sagetsvhandler.h
• pappsomspp/core/processing/cbor/psm/sage/sagetsvhandler.cpp