pappso::cbor::psm::SageReader Class Reference

#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 41 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 45 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 56 of file sagereader.cpp.

{
}

Member Function Documentation

convertToLocalFileOrDie()

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

private

Definition at line 246 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 166 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 107 of file sagereader.cpp.

{
  return *mp_cborWriter;
}

References mp_cborWriter.

getDecoyTag()

QString pappso::cbor::psm::SageReader::getDecoyTag

(

)

const

Definition at line 358 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 226 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 61 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 184 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 376 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 273 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      = residue_str.at(0);
      modif.modification = pappso::Utils::guessAaModificationPbyMonoisotopicMassDelta(
        (Enums::AminoAcidChar)modif.residue.toLatin1(),
        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 197 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 315 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("static_mods not found in Sage json document"));
    }
  for(QString residue_str : var_mods.toObject().keys())
    {
      SageModification modif;
      modif.residue = residue_str.at(0);
      for(QJsonValue one_mass : var_mods.toObject().value(residue_str).toArray())
        {
          modif.modification = pappso::Utils::guessAaModificationPbyMonoisotopicMassDelta(
            (Enums::AminoAcidChar)modif.residue.toLatin1(), one_mass.toDouble());
          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);
            }
          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().

read()

void pappso::cbor::psm::SageReader::read

(

)

Definition at line 68 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 114 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 102 of file sagereader.h.

Referenced by SageReader(), and getmJsonAbsoluteFilePath().

m_mzmlPathList

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

private

Definition at line 103 of file sagereader.h.

Referenced by extractMzmlPathList(), and getMzmlPath().

m_psmProteinMap

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

private

Definition at line 101 of file sagereader.h.

Referenced by readTsvFile().

m_sageFileReader

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

private

Definition at line 98 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 100 of file sagereader.h.

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

mp_monitor

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

private

Definition at line 99 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