#include <sagereader.h>

Classes
struct	SageModification
class	FastaSeq

Public Member Functions
	SageReader (pappso::UiMonitorInterface p_monitor, pappso::cbor::CborStreamWriter p_output, const SageFileReader &sage_file_reader, const QString &sage_json_file)
void	read ()
virtual	~SageReader ()
std::vector< SageModification >	getStaticModificationList () const
std::vector< SageModification >	getVariableModificationList () const
QString	getDecoyTag () const
const SageFileReader &	getSageFileReader () const
pappso::cbor::CborStreamWriter &	getCborStreamWriter () const
const QString &	getmJsonAbsoluteFilePath () const
const QString &	getMzmlPath (const QString &file_msrun) const

Private Member Functions
void	readTsvFile ()
void	extractMzmlPathList (const QJsonDocument &json_doc)
QString	getTsvFilePath (const QJsonDocument &json_doc)
QString	getFastaFilePath (const QJsonDocument &json_doc)
QString	convertToLocalFileOrDie (const QString &file_str) const

Private Attributes
const SageFileReader &	m_sageFileReader
pappso::UiMonitorInterface *	mp_monitor
pappso::cbor::CborStreamWriter *	mp_cborWriter
PsmProteinMap	m_psmProteinMap
QString	m_jsonAbsoluteFilePath
QStringList	m_mzmlPathList

Detailed Description

Todo: write docs

Definition at line 42 of file sagereader.h.

Constructor & Destructor Documentation

◆ SageReader()

pappso::cbor::psm::SageReader::SageReader	(	pappso::UiMonitorInterface *	p_monitor,
		pappso::cbor::CborStreamWriter *	p_output,
		const SageFileReader &	sage_file_reader,
		const QString &	sage_json_file )

Default constructor

Definition at line 47 of file sagereader.cpp.

  : m_sageFileReader(sage_file_reader)
{
  mp_monitor             = p_monitor;
  mp_cborWriter          = p_output;
  m_jsonAbsoluteFilePath = sage_json_file;
}

References m_jsonAbsoluteFilePath, m_sageFileReader, mp_cborWriter, and mp_monitor.

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

◆ ~SageReader()

pappso::cbor::psm::SageReader::~SageReader ( )

virtual

Destructor

Definition at line 58 of file sagereader.cpp.

59{

60}

Member Function Documentation

◆ convertToLocalFileOrDie()

QString pappso::cbor::psm::SageReader::convertToLocalFileOrDie ( const QString & file_str ) const

private

Definition at line 254 of file sagereader.cpp.

{
 
  // if we have an URL : convert it to local file
  qDebug() << path;
  if(path.startsWith("file:") || path.startsWith("http:") || path.startsWith("https:"))
    {
      QUrl tsv_url(path);
      if(tsv_url.isValid())
        {
          qDebug() << "tsv_url.isValid()";
          if(tsv_url.isLocalFile())
            {
              qDebug() << "tsv_url.isLocalFile()";
              return tsv_url.toLocalFile();
            }
          else
            {
              throw pappso::PappsoException(
                QObject::tr("Unable to load data from remote URL %1").arg(tsv_url.toString()));
            }
        }
    }
  return path;
}

Referenced by extractMzmlPathList(), getFastaFilePath(), and getTsvFilePath().

◆ extractMzmlPathList()

void pappso::cbor::psm::SageReader::extractMzmlPathList ( const QJsonDocument & json_doc )

private

Definition at line 174 of file sagereader.cpp.

{
 
  QJsonObject sage_object        = json_doc.object();
  QJsonValue json_mzml_path_list = sage_object.value("mzml_paths");
  if(json_mzml_path_list.isUndefined())
    {
      throw pappso::ExceptionNotFound(QObject::tr("mzml_paths not found in Sage json document"));
    }
  m_mzmlPathList.clear();
 
  for(auto path_mzml : json_mzml_path_list.toArray())
    {
      m_mzmlPathList << convertToLocalFileOrDie(path_mzml.toString());
    }
}

References convertToLocalFileOrDie(), and m_mzmlPathList.

Referenced by readTsvFile().

◆ getCborStreamWriter()

pappso::cbor::CborStreamWriter & pappso::cbor::psm::SageReader::getCborStreamWriter ( ) const

Definition at line 115 of file sagereader.cpp.

{
  return *mp_cborWriter;
}

References mp_cborWriter.

◆ getDecoyTag()

QString pappso::cbor::psm::SageReader::getDecoyTag ( ) const

Definition at line 406 of file sagereader.cpp.

{
  QString path;
  QJsonObject sage_object = m_sageFileReader.getJsonDocument().object();
  QJsonValue database     = sage_object.value("database");
  if(database.isUndefined())
    {
      throw pappso::ExceptionNotFound(QObject::tr("database not found in Sage json document"));
    }
  path = database.toObject().value("decoy_tag").toString();
  if(path.isEmpty())
    {
      throw pappso::ExceptionNotFound(QObject::tr("decoy_tag value is empty"));
    }
  return path;
}

References m_sageFileReader.

Referenced by pappso::cbor::psm::SageTsvHandler::SageTsvHandler().

◆ getFastaFilePath()

QString pappso::cbor::psm::SageReader::getFastaFilePath ( const QJsonDocument & json_doc )

private

Definition at line 234 of file sagereader.cpp.

{
  QString path;
  QJsonObject sage_object = json_doc.object();
  QJsonValue database     = sage_object.value("database");
  if(database.isUndefined())
    {
      throw pappso::ExceptionNotFound(QObject::tr("database not found in Sage json document"));
    }
  path = database.toObject().value("fasta").toString();
  if(path.isEmpty())
    {
      throw pappso::ExceptionNotFound(QObject::tr("fasta value is empty"));
    }
 
 
  return convertToLocalFileOrDie(path);
}

References convertToLocalFileOrDie().

Referenced by readTsvFile().

◆ getmJsonAbsoluteFilePath()

const QString & pappso::cbor::psm::SageReader::getmJsonAbsoluteFilePath ( ) const

Definition at line 63 of file sagereader.cpp.

{
  return m_jsonAbsoluteFilePath;
}

References m_jsonAbsoluteFilePath.

◆ getMzmlPath()

const QString & pappso::cbor::psm::SageReader::getMzmlPath ( const QString & file_msrun ) const

Definition at line 192 of file sagereader.cpp.

{
  for(auto &file_path : m_mzmlPathList)
    {
      if(file_path.endsWith(file_msrun))
        return file_path;
    }
  throw pappso::ExceptionNotFound(
    QObject::tr("MS run %1 not found in Sage json document").append(file_msrun));
}

References m_mzmlPathList.

◆ getSageFileReader()

const pappso::cbor::psm::SageFileReader & pappso::cbor::psm::SageReader::getSageFileReader ( ) const

Definition at line 424 of file sagereader.cpp.

{
  return m_sageFileReader;
}

References m_sageFileReader.

◆ getStaticModificationList()

std::vector< pappso::cbor::psm::SageReader::SageModification > pappso::cbor::psm::SageReader::getStaticModificationList ( ) const

Definition at line 281 of file sagereader.cpp.

{
  std::vector<SageReader::SageModification> list;
  QJsonObject sage_object = m_sageFileReader.getJsonDocument().object();
  QJsonValue database     = sage_object.value("database");
  if(database.isUndefined())
    {
      throw pappso::ExceptionNotFound(QObject::tr("database not found in Sage json document"));
    }
 
  QJsonValue static_mods = database.toObject().value("static_mods");
  if(static_mods.isUndefined())
    {
      throw pappso::ExceptionNotFound(QObject::tr("static_mods not found in Sage json document"));
    }
  for(QString residue_str : static_mods.toObject().keys())
    {
      SageModification modif;
      modif.residue      = (Enums::AminoAcidChar)residue_str.at(0).toLatin1();
      modif.modification = pappso::Utils::guessAaModificationPbyMonoisotopicMassDelta(
        modif.residue, static_mods.toObject().value(residue_str).toDouble());
      modif.strModification =
        QString::number(static_mods.toObject().value(residue_str).toDouble(), 'f', 6);
      if(modif.strModification.isEmpty())
        {
          throw pappso::PappsoException(QObject::tr(" modif.strModification is empty"));
        }
      if(modif.modification->getMass() < 0)
        {
          modif.strModification = QString("[%1]").arg(modif.strModification);
        }
      else
        {
          modif.strModification = QString("[+%1]").arg(modif.strModification);
        }
      list.push_back(modif);
    }
  return list;
}

References pappso::AaModification::getMass(), pappso::Utils::guessAaModificationPbyMonoisotopicMassDelta(), m_sageFileReader, pappso::cbor::psm::SageReader::SageModification::modification, pappso::cbor::psm::SageReader::SageModification::residue, and pappso::cbor::psm::SageReader::SageModification::strModification.

Referenced by pappso::cbor::psm::SageTsvHandler::SageTsvHandler().

◆ getTsvFilePath()

QString pappso::cbor::psm::SageReader::getTsvFilePath ( const QJsonDocument & json_doc )

private

Definition at line 205 of file sagereader.cpp.

{
  QString path;
  QJsonObject sage_object = json_doc.object();
  QJsonValue output_path  = sage_object.value("output_paths");
  if(output_path.isUndefined())
    {
      throw pappso::ExceptionNotFound(QObject::tr("output_paths not found in Sage json document"));
    }
 
  if(!output_path.isArray())
    {
      throw pappso::ExceptionNotFound(QObject::tr("output_paths is not an array"));
    }
  for(auto element : output_path.toArray())
    {
      if(element.isString())
        {
          if(element.toString().endsWith(".tsv"))
            {
              path = element.toString();
            }
        }
    }
 
  return convertToLocalFileOrDie(path);
}

References convertToLocalFileOrDie().

Referenced by readTsvFile().

◆ getVariableModificationList()

std::vector< pappso::cbor::psm::SageReader::SageModification > pappso::cbor::psm::SageReader::getVariableModificationList ( ) const

Definition at line 322 of file sagereader.cpp.

{
  std::vector<SageReader::SageModification> list;
  QJsonObject sage_object = m_sageFileReader.getJsonDocument().object();
  QJsonValue database     = sage_object.value("database");
  if(database.isUndefined())
    {
      throw pappso::ExceptionNotFound(QObject::tr("database not found in Sage json document"));
    }
 
  QJsonValue var_mods = database.toObject().value("variable_mods");
  if(var_mods.isUndefined())
    {
      throw pappso::ExceptionNotFound(QObject::tr("variable_mods not found in Sage json document"));
    }
  for(QString residue_str : var_mods.toObject().keys())
    {
      qDebug() << residue_str;
      SageModification modif;
      modif.residue = (Enums::AminoAcidChar)residue_str.at(0).toLatin1();
      if(!Utils::isAminoAcidChar(modif.residue))
        {
          qDebug() << "not amino acid";
          QChar pos = residue_str.at(0).toLatin1();
          qDebug() << residue_str << "not amino acid " << pos;
          if(pos == '^')
            {
              modif.position = pos;
              modif.residue  = (Enums::AminoAcidChar)residue_str.at(1).toLatin1();
              qDebug() << (char)modif.residue;
              if(!Utils::isAminoAcidChar(modif.residue))
                {
                  throw pappso::PappsoException(QObject::tr("unable to parse %1").arg(residue_str));
                }
            }
          else if((pos == '[') || (pos == ']'))
            {
              modif.position = pos;
              // modif.residue  = (Enums::AminoAcidChar)residue_str.at(1).toLatin1();
              // qDebug() << (char)modif.residue;
            }
          else
            {
              throw pappso::PappsoException(QObject::tr("unable to parse %1").arg(residue_str));
            }
          qDebug() << (char)modif.residue;
 
          qDebug() << (char)modif.residue;
        }
 
      // Enums::AminoAcidChar aa = (Enums::AminoAcidChar)modif.residue.toLatin1();
      qDebug() << residue_str << " " << (char)modif.residue;
      for(QJsonValue one_mass : var_mods.toObject().value(residue_str).toArray())
        {
          modif.modification = pappso::Utils::guessAaModificationPbyMonoisotopicMassDelta(
            modif.residue, one_mass.toDouble(), modif.position);
          qDebug() << modif.modification->getAccession();
          modif.strModification = QString::number(one_mass.toDouble(), 'f', 6);
          if(modif.strModification.isEmpty())
            {
              throw pappso::PappsoException(QObject::tr(" modif.strModification is empty"));
            }
          if(modif.modification->getMass() < 0)
            {
              modif.strModification = QString("[%1]").arg(modif.strModification);
            }
          else
            {
              modif.strModification = QString("[+%1]").arg(modif.strModification);
            }
 
          qDebug() << modif.strModification;
          list.push_back(modif);
          qDebug() << modif.strModification;
        }
      qDebug() << list.size();
    }
 
  qDebug() << list.size();
 
  return list;
}

References pappso::AaModification::getAccession(), pappso::AaModification::getMass(), pappso::Utils::guessAaModificationPbyMonoisotopicMassDelta(), pappso::Utils::isAminoAcidChar(), m_sageFileReader, pappso::cbor::psm::SageReader::SageModification::modification, pappso::cbor::psm::SageReader::SageModification::position, pappso::cbor::psm::SageReader::SageModification::residue, and pappso::cbor::psm::SageReader::SageModification::strModification.

Referenced by pappso::cbor::psm::SageTsvHandler::SageTsvHandler().

◆ read()

void pappso::cbor::psm::SageReader::read ( )

Definition at line 70 of file sagereader.cpp.

{
  readTsvFile();
}

References readTsvFile().

Referenced by pappso::cbor::psm::SageFileReader::SageFileReader().

◆ readTsvFile()

void pappso::cbor::psm::SageReader::readTsvFile ( )

private

Definition at line 122 of file sagereader.cpp.

{
 
  extractMzmlPathList(m_sageFileReader.getJsonDocument());
  // getTsvFilePath(mp_identificationDataSource->getJsonDocument().object());
  QString file_str = getTsvFilePath(m_sageFileReader.getJsonDocument());
  QFileInfo tsv_file_info(file_str);
  SageTsvHandler handler(mp_monitor, *this, m_psmProteinMap);
  try
    {
      TsvReader tsv_reader(handler);
 
      QFile tsv_file(tsv_file_info.absoluteFilePath());
      tsv_reader.parse(tsv_file);
      tsv_file.close();
    }
  catch(OdsException &error_ods)
    {
      throw pappso::PappsoException(QObject::tr("Error reading %1 file:\n %2")
                                      .arg(tsv_file_info.absoluteFilePath())
                                      .arg(error_ods.qwhat()));
    }
 
 
  // collect protein sequences
  QFile fastaFile(getFastaFilePath(m_sageFileReader.getJsonDocument()));
  SageReader::FastaSeq seq(this);
  pappso::FastaReader reader(seq);
  reader.parse(fastaFile);
 
  qDebug();
  mp_cborWriter->append("protein_map");
  m_psmProteinMap.writeMap(*mp_cborWriter);
 
 
  mp_cborWriter->append("sample_list");
  mp_cborWriter->startArray();
  try
    {
      handler.writeSampleList();
    }
  catch(OdsException &error_ods)
    {
      throw pappso::PappsoException(QObject::tr("Error reading %1 file:\n %2")
                                      .arg(tsv_file_info.absoluteFilePath())
                                      .arg(error_ods.qwhat()));
    }
 
  mp_cborWriter->endArray();
}

References extractMzmlPathList(), getFastaFilePath(), getTsvFilePath(), m_psmProteinMap, m_sageFileReader, mp_cborWriter, mp_monitor, pappso::FastaReader::parse(), and pappso::cbor::psm::SageTsvHandler::writeSampleList().

Referenced by read().

Member Data Documentation

◆ m_jsonAbsoluteFilePath

QString pappso::cbor::psm::SageReader::m_jsonAbsoluteFilePath

private

Definition at line 118 of file sagereader.h.

Referenced by SageReader(), and getmJsonAbsoluteFilePath().

◆ m_mzmlPathList

QStringList pappso::cbor::psm::SageReader::m_mzmlPathList

private

Definition at line 119 of file sagereader.h.

Referenced by extractMzmlPathList(), and getMzmlPath().

◆ m_psmProteinMap

PsmProteinMap pappso::cbor::psm::SageReader::m_psmProteinMap

private

Definition at line 117 of file sagereader.h.

Referenced by readTsvFile().

◆ m_sageFileReader

const SageFileReader& pappso::cbor::psm::SageReader::m_sageFileReader

private

Definition at line 114 of file sagereader.h.

Referenced by SageReader(), getDecoyTag(), getSageFileReader(), getStaticModificationList(), getVariableModificationList(), and readTsvFile().

◆ mp_cborWriter

pappso::cbor::CborStreamWriter* pappso::cbor::psm::SageReader::mp_cborWriter

private

Definition at line 116 of file sagereader.h.

Referenced by SageReader(), getCborStreamWriter(), and readTsvFile().

◆ mp_monitor

pappso::UiMonitorInterface* pappso::cbor::psm::SageReader::mp_monitor

private

Definition at line 115 of file sagereader.h.

Referenced by SageReader(), and readTsvFile().

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

pappsomspp/core/processing/cbor/psm/sage/sagereader.h
pappsomspp/core/processing/cbor/psm/sage/sagereader.cpp

Classes

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SageReader()

◆ ~SageReader()

Member Function Documentation

◆ convertToLocalFileOrDie()

◆ extractMzmlPathList()

◆ getCborStreamWriter()

◆ getDecoyTag()

◆ getFastaFilePath()

◆ getmJsonAbsoluteFilePath()

◆ getMzmlPath()

◆ getSageFileReader()

◆ getStaticModificationList()

◆ getTsvFilePath()

◆ getVariableModificationList()

◆ read()

◆ readTsvFile()

Member Data Documentation

◆ m_jsonAbsoluteFilePath

◆ m_mzmlPathList

◆ m_psmProteinMap

◆ m_sageFileReader

◆ mp_cborWriter

◆ mp_monitor