pappso::cbor::psm::SageFileReader Class Reference

#include <sagefilereader.h>

Public Member Functions
	SageFileReader (pappso::UiMonitorInterface *p_monitor, pappso::cbor::CborStreamWriter *p_output, const QFileInfo &sage_json_file)
	main function to convert Sage results to CBOR output
virtual	~SageFileReader ()
const QJsonDocument &	getJsonDocument () const
QString	getMsRunSpWithFileName (const QString &msrun_filename) const

Private Member Functions
void	readJson ()

Private Attributes
const QFileInfo	m_sageJsonFile
QJsonDocument	m_jsonData
std::map< QString, QString >	m_mapFilePath2MsRunSp
QString	m_sageVersion
pappso::cbor::CborStreamWriter *	mp_cborWriter
QString	m_decoyTag
bool	m_generateDecoy = false
QStringList	m_targetFastaFile

Detailed Description

Todo

write docs

Definition at line 47 of file sagefilereader.h.

Constructor & Destructor Documentation

SageFileReader()

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

main function to convert Sage results to CBOR output

given the Sage JSON result file, this class reads the TSV output and convert the Sage PSMs to the PSMcbor format

Parameters

p_monitor	pointer to monitor read progress
p_output	cbor output pointer
sage_json_file	Sage JSON result file

Definition at line 47 of file sagefilereader.cpp.

  : m_sageJsonFile(sage_json_file)
{
  qDebug() << m_sageJsonFile.absoluteFilePath() << "'";
  try
    {
 
      mp_cborWriter = p_output;
 
      mp_cborWriter->startMap();
      mp_cborWriter->writeInformations(
        "sage_file_reader", Utils::getVersion(), "psm", "sage reader");
 
      QDir::setCurrent(sage_json_file.absolutePath());
      readJson();
      mp_cborWriter->append("parameter_map");
      mp_cborWriter->startMap();
      mp_cborWriter->append("sage");
      QCborValue::fromJsonValue(m_jsonData.object()).toCbor(*mp_cborWriter);
      mp_cborWriter->endMap();
 
      p_monitor->setStatus(
        QObject::tr("reading Sage json file %1").arg(sage_json_file.absoluteFilePath()));
 
      //  "decoy_tag": "rev_",
      //  "generate_decoys": true,
      // "target_fasta_files": ["zea_mays.fasta", "contaminant.fasta"],
      //"decoy_fasta_files": ["rev_zea_mays.fasta", "rev_contaminant.fasta"],
 
      mp_cborWriter->append("target_fasta_files");
      mp_cborWriter->writeArray(m_targetFastaFile);
 
      SageReader sage_reader(p_monitor, mp_cborWriter, *this, sage_json_file.absoluteFilePath());
      sage_reader.read();
 
      // mp_cborWriter->append("protein_map");
      //  sage_reader.getPsmProteinMap().
 
      mp_cborWriter->endMap();
    }
  catch(pappso::ExceptionNotRecognized &err)
    {
      throw err;
    }
  catch(pappso::PappsoException &other_err)
    {
      throw pappso::PappsoException(QObject::tr("Error reading Sage JSON file %1:\n%2")
                                      .arg(m_sageJsonFile.absoluteFilePath())
                                      .arg(other_err.qwhat()));
    }
}

References pappso::Utils::getVersion(), m_jsonData, m_sageJsonFile, m_targetFastaFile, mp_cborWriter, pappso::PappsoException::qwhat(), pappso::cbor::psm::SageReader::read(), readJson(), and pappso::UiMonitorInterface::setStatus().

~SageFileReader()

pappso::cbor::psm::SageFileReader::~SageFileReader ( )

virtual

Destructor

Definition at line 102 of file sagefilereader.cpp.

{
}

Member Function Documentation

getJsonDocument()

const QJsonDocument & pappso::cbor::psm::SageFileReader::getJsonDocument

(

)

const

Definition at line 160 of file sagefilereader.cpp.

{
  return m_jsonData;
}

References m_jsonData.

getMsRunSpWithFileName()

QString pappso::cbor::psm::SageFileReader::getMsRunSpWithFileName

(

const QString &

msrun_filename

)

const

Definition at line 167 of file sagefilereader.cpp.

{
  auto it = m_mapFilePath2MsRunSp.find(msrun_filename);
  if(it != m_mapFilePath2MsRunSp.end())
    return it->second;
 
 
  throw pappso::PappsoException(QObject::tr("msrun filename %1 not found").arg(msrun_filename));
}

References m_mapFilePath2MsRunSp.

readJson()

void pappso::cbor::psm::SageFileReader::readJson ( )

private

Definition at line 108 of file sagefilereader.cpp.

{
  QFile mfile(m_sageJsonFile.absoluteFilePath());
  if(!mfile.open(QFile::ReadOnly))
    {
      throw pappso::ExceptionNotRecognized(
        QObject::tr("Unable to read Sage JSON file %1").arg(m_sageJsonFile.absoluteFilePath()));
    }
  QByteArray iContents = mfile.readAll();
 
  QJsonParseError parseError;
  m_jsonData = QJsonDocument::fromJson(iContents, &parseError);
  if(parseError.error != QJsonParseError::NoError)
    {
      throw pappso::ExceptionNotRecognized(QObject::tr("Error reading Sage JSON file %1 at %2:%3")
                                             .arg(m_sageJsonFile.absoluteFilePath())
                                             .arg(parseError.offset)
                                             .arg(parseError.errorString()));
    }
 
  QJsonValue mzml_value = m_jsonData.object().value("mzml_paths");
 
  if(mzml_value.isNull())
    {
      throw pappso::ExceptionNotRecognized(
        QObject::tr("Sage JSON file %1 does not contain mzml_paths")
          .arg(m_sageJsonFile.absoluteFilePath()));
    }
  for(const QJsonValue &value : m_jsonData.object().value("mzml_paths").toArray())
    {
      qDebug() << value.toString();
 
      // MsRunSp msrun_sp = p_project->getMsRunStore().getInstance(value.toString());
      m_mapFilePath2MsRunSp.insert(
        {QFileInfo(value.toString()).fileName(), QFileInfo(value.toString()).absoluteFilePath()});
    }
 
 
  m_sageVersion = m_jsonData.object().value("version").toString();
 
 
  QJsonObject sage_object = m_jsonData.object();
 
 
  QJsonObject database = sage_object.value("database").toObject();
 
  m_decoyTag      = database.value("decoy_tag").toString();
  m_generateDecoy = database.value("generate_decoy").toBool();
  m_targetFastaFile << database.value("fasta").toString();
}

References m_decoyTag, m_generateDecoy, m_jsonData, m_mapFilePath2MsRunSp, m_sageJsonFile, m_sageVersion, and m_targetFastaFile.

Referenced by SageFileReader().

Member Data Documentation

m_decoyTag

QString pappso::cbor::psm::SageFileReader::m_decoyTag

private

Definition at line 80 of file sagefilereader.h.

Referenced by readJson().

m_generateDecoy

bool pappso::cbor::psm::SageFileReader::m_generateDecoy = false

private

Definition at line 81 of file sagefilereader.h.

Referenced by readJson().

m_jsonData

QJsonDocument pappso::cbor::psm::SageFileReader::m_jsonData

private

Definition at line 75 of file sagefilereader.h.

Referenced by SageFileReader(), getJsonDocument(), and readJson().

m_mapFilePath2MsRunSp

std::map<QString, QString> pappso::cbor::psm::SageFileReader::m_mapFilePath2MsRunSp

private

Definition at line 77 of file sagefilereader.h.

Referenced by getMsRunSpWithFileName(), and readJson().

m_sageJsonFile

const QFileInfo pappso::cbor::psm::SageFileReader::m_sageJsonFile

private

Definition at line 74 of file sagefilereader.h.

Referenced by SageFileReader(), and readJson().

m_sageVersion

QString pappso::cbor::psm::SageFileReader::m_sageVersion

private

Definition at line 78 of file sagefilereader.h.

Referenced by readJson().

m_targetFastaFile

QStringList pappso::cbor::psm::SageFileReader::m_targetFastaFile

private

Definition at line 82 of file sagefilereader.h.

Referenced by SageFileReader(), and readJson().

mp_cborWriter

pappso::cbor::CborStreamWriter* pappso::cbor::psm::SageFileReader::mp_cborWriter

private

Definition at line 79 of file sagefilereader.h.

Referenced by SageFileReader().

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

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