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)
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 46 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 )

Default constructor

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 74 of file sagefilereader.h.

Referenced by readJson().

m_generateDecoy

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

private

Definition at line 75 of file sagefilereader.h.

Referenced by readJson().

m_jsonData

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

private

Definition at line 69 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 71 of file sagefilereader.h.

Referenced by getMsRunSpWithFileName(), and readJson().

m_sageJsonFile

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

private

Definition at line 68 of file sagefilereader.h.

Referenced by SageFileReader(), and readJson().

m_sageVersion

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

private

Definition at line 72 of file sagefilereader.h.

Referenced by readJson().

m_targetFastaFile

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

private

Definition at line 76 of file sagefilereader.h.

Referenced by SageFileReader(), and readJson().

mp_cborWriter

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

private

Definition at line 73 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