pappso::TandemWrapperRun Class Reference

#include <tandemwrapperrun.h>

Inheritance diagram for pappso::TandemWrapperRun:

Signals
void	tandemProgressMessage (QString message)

Public Member Functions
	TandemWrapperRun (const QString &tandem_binary, const QString &tmp_dir)
	prepare a tandem run
void	run (UiMonitorInterface &monitor, const QString &tandem_input_file)
	run a tandem job
void	readTandemPresetFile (const QString &tandem_preset_file)
QString	getMs2FilterSuiteString () const
	gets the list of filters used on MS2 spectrum
	~TandemWrapperRun ()

Private Slots
void	readyReadStandardOutput ()
void	readyReadStandardError ()

Private Member Functions
void	setTandemBinaryPath (const QString &tandem_binary_path)
const QString	checkXtandemVersion (const QString &tandem_bin_path)
void	wrapTandemInputFile (const QString &tandem_input_file)
bool	convertOrginalMsData2mzXmlData (const QString &origin, const QString &target)
void	runTandem (const QString &tandem_input_file)
	run a tandem job
void	writeFinalTandemOutput (const QString &tmp_tandem_output, const QString &final_tandem_output, const QString &original_msdata_file_name)
	tandem output modification tandem output is modified to contain the Bruker's file as input and centroidization parameters

Private Attributes
UiMonitorInterface *	mp_monitor
QString	m_tandemBinary
QString	m_tandemVersion
QString	m_tmpDir
int	m_maxTandemRunTimeMs
QProcess *	m_xtProcess = nullptr
std::shared_ptr< FilterSuiteString >	msp_ms2FilterSuiteString = nullptr
QTemporaryDir *	mpa_temporaryDirectory = nullptr
bool	m_convertMzDataUsingSpectrumIndex = false
Enums::MsDataFormat	m_mzFormat = Enums::MsDataFormat::unknown
qint64	m_conversionTime = 0

Detailed Description

Definition at line 61 of file tandemwrapperrun.h.

Constructor & Destructor Documentation

TandemWrapperRun()

pappso::TandemWrapperRun::TandemWrapperRun	(	const QString &	tandem_binary,
		const QString &	tmp_dir )

prepare a tandem run

Parameters

tandem_binary	file path to tandem.exe if not set, a default value is given in QSettings
tmp_dir	temporary directory, where to write mzXML file conversion if not set, a default value is given in QSettings

Definition at line 49 of file tandemwrapperrun.cpp.

{
 
  setTandemBinaryPath(tandem_binary);
 
  if(!tmp_dir.isEmpty())
    {
      mpa_temporaryDirectory = new QTemporaryDir(tmp_dir + "/xtpwrp");
    }
  else
    {
      mpa_temporaryDirectory = new QTemporaryDir(QDir::tempPath() + "/xtpwrp");
    }
  mpa_temporaryDirectory->setAutoRemove(true);
  if(!mpa_temporaryDirectory->isValid())
    {
      throw pappso::PappsoException(
        QObject::tr("ERROR: unable to create temporary directory %1\n Please "
                    "check file system permissions")
          .arg(mpa_temporaryDirectory->path()));
    }
}

References mpa_temporaryDirectory, and setTandemBinaryPath().

~TandemWrapperRun()

pappso::TandemWrapperRun::~TandemWrapperRun

(

)

Destructor

Definition at line 73 of file tandemwrapperrun.cpp.

{
  if(mpa_temporaryDirectory != nullptr)
    {
      delete mpa_temporaryDirectory;
    }
 
  if(m_xtProcess != nullptr)
    {
      m_xtProcess->deleteLater();
    }
}

References m_xtProcess, and mpa_temporaryDirectory.

Member Function Documentation

checkXtandemVersion()

const QString pappso::TandemWrapperRun::checkXtandemVersion ( const QString & tandem_bin_path )

private

Definition at line 107 of file tandemwrapperrun.cpp.

{
  qDebug();
  // check tandem path
  QFileInfo tandem_exe(tandem_bin_path);
  if(!tandem_exe.exists())
    {
      // dir.path() returns the unique directory path
      throw pappso::PappsoException(
        QObject::tr(
          "X!Tandem software not found at %1.\nPlease check the X!Tandem "
          "installation on your computer and set tandem.exe path.")
          .arg(tandem_exe.absoluteFilePath()));
    }
  if(!tandem_exe.isReadable())
    {
      // dir.path() returns the unique directory path
      throw pappso::PappsoException(
        QObject::tr("Please check permissions on X!Tandem software found at %1 "
                    "(file not readable).")
          .arg(tandem_exe.absoluteFilePath()));
    }
  if(!tandem_exe.isExecutable())
    {
      // dir.path() returns the unique directory path
      throw pappso::PappsoException(
        QObject::tr("Please check permissions on X!Tandem software found at %1 "
                    "(file not executable).")
          .arg(tandem_exe.absoluteFilePath()));
    }
 
 
  QString version_return;
  QStringList arguments;
 
  arguments << "-v";
 
  QProcess *xt_process = new QProcess();
  // hk_process->setWorkingDirectory(QFileInfo(_hardklor_exe).absolutePath());
 
  xt_process->start(tandem_bin_path, arguments);
 
  if(!xt_process->waitForStarted())
    {
      throw pappso::PappsoException(
        QObject::tr("X!Tandem %1 process failed to start")
          .arg(m_tandemVersion));
    }
 
  while(xt_process->waitForReadyRead(1000))
    {
    }
  /*
  if (!xt_process->waitForFinished(_max_xt_time_ms)) {
      throw pappso::PappsoException(QObject::tr("can't wait for X!Tandem process
  to finish : timeout at %1").arg(_max_xt_time_ms));
  }
  */
  QByteArray result = xt_process->readAll();
 
 
  qDebug() << result.constData();
 
  // X! TANDEM Jackhammer TPP (2013.06.15.1 - LabKey, Insilicos, ISB)
 
  QRegularExpression parse_version(
    "(.*) TANDEM ([A-Z,a-z, ]+) \\(([^ ,^\\)]*)(.*)");
  qDebug() << parse_version;
  // Pattern patt = Pattern.compile("X! TANDEM [A-Z]+ \\‍((.*)\\‍)",
  //            Pattern.CASE_INSENSITIVE);
  QRegularExpressionMatch match_parse_version =
    parse_version.match(result.constData());
  if(match_parse_version.hasMatch())
    {
      version_return = QString("X!Tandem %1 %2")
                         .arg(match_parse_version.captured(2))
                         .arg(match_parse_version.captured(3)); //.join(" ");
    }
  else
    {
      throw pappso::PappsoException(
        QObject::tr("This executable %1 may not be a valid X!Tandem software. "
                    "Please check your X!Tandem installation.")
          .arg(tandem_bin_path));
    }
 
  QProcess::ExitStatus Status = xt_process->exitStatus();
  delete xt_process;
  if(Status != 0)
    {
      // != QProcess::NormalExit
      throw pappso::PappsoException(
        QObject::tr("error executing X!Tandem Status != 0 : %1 %2\n%3")
          .arg(tandem_bin_path)
          .arg(arguments.join(" ").arg(result.data())));
    }
  qDebug();
  return version_return;
}

References m_tandemVersion.

Referenced by setTandemBinaryPath(), and tandemProgressMessage().

convertOrginalMsData2mzXmlData()

bool pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData ( const QString & origin, const QString & target )

private

Definition at line 439 of file tandemwrapperrun.cpp.

{
  qDebug();
  pappso::MsFileAccessor origin_access(origin, "runa1");
  origin_access.setPreferredFileReaderType(Enums::MsDataFormat::brukerTims,
                                           Enums::FileReaderType::tims_ms2);
  origin_access.getMsRunIds();
  m_mzFormat = origin_access.getFileFormat();
  if(m_mzFormat == Enums::MsDataFormat::unknown)
    {
      throw pappso::PappsoException(
        QObject::tr("%1 file format not known").arg(origin));
    }
 
  if(origin_access.getFileFormat() == Enums::MsDataFormat::brukerTims)
    {
      m_convertMzDataUsingSpectrumIndex = true;
    }
 
  if((origin_access.getFileFormat() == Enums::MsDataFormat::mzML) ||
     (origin_access.getFileFormat() == Enums::MsDataFormat::brukerTims))
    {
      mp_monitor->setStatus(
        QObject::tr("Converting %1 to mzXML %2").arg(origin).arg(target));
      pappso::MsRunReaderSPtr p_reader;
      p_reader =
        origin_access.msRunReaderSPtr(origin_access.getMsRunIds().front());
 
      pappso::TimsMsRunReaderMs2 *tims2_reader =
        dynamic_cast<pappso::TimsMsRunReaderMs2 *>(p_reader.get());
      if(tims2_reader != nullptr)
        {
          qDebug();
          tims2_reader->setMs2BuiltinCentroid(true);
 
          if(msp_ms2FilterSuiteString != nullptr)
            {
              tims2_reader->setMs2FilterCstSPtr(msp_ms2FilterSuiteString);
            }
          qDebug();
        }
 
 
      pappso::MzxmlOutput *p_mzxml_output;
      QFile output_file(target);
      // qDebug() << " TsvDirectoryWriter::writeSheet " <<
      // QFileInfo(*_p_ofile).absoluteFilePath();
      if(output_file.open(QIODevice::WriteOnly))
        {
          QElapsedTimer timer;
          m_conversionTime = 0;
          timer.start();
          p_mzxml_output = new pappso::MzxmlOutput(
            *mp_monitor, QTextStream(&output_file).device());
 
          p_mzxml_output->maskMs1(true);
 
          p_mzxml_output->setReadAhead(true);
 
          p_mzxml_output->write(p_reader.get());
 
          p_mzxml_output->close();
 
          delete p_mzxml_output;
          m_conversionTime = timer.elapsed();
 
          mp_monitor->setStatus(QObject::tr("Conversion finished in %1 seconds")
                                  .arg(m_conversionTime / 1000));
        }
      else
        {
          throw pappso::PappsoException(
            QObject::tr("unable to write into %1 mzXML output file")
              .arg(target));
        }
 
      qDebug();
      return true;
    }
  else
    { // other mz data formats
      return false;
    }
  return true;
}

References pappso::Enums::brukerTims, pappso::MzxmlOutput::close(), pappso::MsFileAccessor::getFileFormat(), pappso::MsFileAccessor::getMsRunIds(), m_conversionTime, m_convertMzDataUsingSpectrumIndex, m_mzFormat, pappso::MzxmlOutput::maskMs1(), mp_monitor, msp_ms2FilterSuiteString, pappso::MsFileAccessor::msRunReaderSPtr(), pappso::Enums::mzML, pappso::TimsMsRunReaderMs2::setMs2BuiltinCentroid(), pappso::TimsMsRunReaderMs2::setMs2FilterCstSPtr(), pappso::MsFileAccessor::setPreferredFileReaderType(), pappso::MzxmlOutput::setReadAhead(), pappso::Enums::tims_ms2, pappso::Enums::unknown, and pappso::MzxmlOutput::write().

Referenced by tandemProgressMessage(), and wrapTandemInputFile().

getMs2FilterSuiteString()

QString pappso::TandemWrapperRun::getMs2FilterSuiteString

(

)

const

gets the list of filters used on MS2 spectrum

Returns

string describing filters and associated parameters

Definition at line 605 of file tandemwrapperrun.cpp.

{
  if(msp_ms2FilterSuiteString == nullptr)
    return "";
  return msp_ms2FilterSuiteString.get()->toString();
}

References msp_ms2FilterSuiteString.

Referenced by writeFinalTandemOutput().

readTandemPresetFile()

void pappso::TandemWrapperRun::readTandemPresetFile

(

const QString &

tandem_preset_file

)

Definition at line 285 of file tandemwrapperrun.cpp.

{
  // get number of threads and centroid parameters from tandem preset
 
  XtandemPresetReader preset_handler;
 
 
  if(preset_handler.readFile(tandem_preset_file))
    {
 
      int ideal_number_of_thread = QThread::idealThreadCount();
      int cpu_number             = preset_handler.getNumberOfThreads();
      qDebug() << " cpu_number=" << cpu_number;
      // QThreadPool::globalInstance()->setMaxThreadCount(1);
      if(cpu_number > ideal_number_of_thread)
        {
          cpu_number = ideal_number_of_thread;
        }
      else
        {
          if(cpu_number > 0)
            {
              QThreadPool::globalInstance()->setMaxThreadCount(cpu_number);
 
              qDebug() << " maxThreadCount="
                       << QThreadPool::globalInstance()->maxThreadCount();
            }
        }
 
      QString ms2_filters_str = preset_handler.getMs2FiltersOptions();
      if(!ms2_filters_str.isEmpty())
        {
          msp_ms2FilterSuiteString =
            std::make_shared<pappso::FilterSuiteString>(ms2_filters_str);
        }
      else
        {
          msp_ms2FilterSuiteString =
            std::make_shared<pappso::FilterSuiteString>(
              "chargeDeconvolution|0.02dalton mzExclusion|0.01dalton");
        }
    }
  else
    {
      throw pappso::PappsoException(
        QObject::tr("Error reading %1 X!Tandem preset file :\n %2")
          .arg(tandem_preset_file)
          .arg(preset_handler.errorString()));
    }
}

References pappso::XmlStreamReaderInterface::errorString(), pappso::XtandemPresetReader::getMs2FiltersOptions(), pappso::XtandemPresetReader::getNumberOfThreads(), msp_ms2FilterSuiteString, and pappso::XmlStreamReaderInterface::readFile().

Referenced by wrapTandemInputFile().

readyReadStandardError

void pappso::TandemWrapperRun::readyReadStandardError ( )

privateslot

Definition at line 229 of file tandemwrapperrun.cpp.

{
  mp_monitor->appendText(m_xtProcess->readAllStandardError());
  if(mp_monitor->shouldIstop())
    {
      m_xtProcess->kill();
      delete m_xtProcess;
      m_xtProcess = nullptr;
      throw pappso::ExceptionInterrupted(
        QObject::tr("X!Tandem stopped by the user"));
    }
}

References m_xtProcess, and mp_monitor.

Referenced by runTandem(), and tandemProgressMessage().

readyReadStandardOutput

void pappso::TandemWrapperRun::readyReadStandardOutput ( )

privateslot

Definition at line 208 of file tandemwrapperrun.cpp.

{
  QString message(m_xtProcess->readAllStandardOutput());
  mp_monitor->appendText(message);
 
  if(message.toLower().contains("error"))
    {
      throw pappso::XtandemError(message);
    }
 
  if(mp_monitor->shouldIstop())
    {
      m_xtProcess->kill();
      delete m_xtProcess;
      m_xtProcess = nullptr;
      throw pappso::ExceptionInterrupted(
        QObject::tr("X!Tandem stopped by the user"));
    }
}

References m_xtProcess, and mp_monitor.

Referenced by runTandem(), and tandemProgressMessage().

run()

void pappso::TandemWrapperRun::run	(	UiMonitorInterface &	monitor,
		const QString &	tandem_input_file )

run a tandem job

The tandem input file should contain an additional input parameter called "spectrum, timstof MS2 filters". The value of this parameters must contain a string describing the FilterSuiteString to apply on TimsTOF MS2. A default value of "chargeDeconvolution|0.02dalton" is recommended for this additional tandem input parameter

Parameters

monitor	user interface monitor
tandem_input_file	tandem xml input file

Definition at line 527 of file tandemwrapperrun.cpp.

{
  mp_monitor = &monitor;
 
  wrapTandemInputFile(tandem_input_file);
  mp_monitor = nullptr;
}

References mp_monitor, and wrapTandemInputFile().

runTandem()

void pappso::TandemWrapperRun::runTandem ( const QString & tandem_input_file )

private

run a tandem job

Parameters

tandem_input_file

tandem xml input file

Definition at line 536 of file tandemwrapperrun.cpp.

{
  if(mp_monitor->shouldIstop())
    {
      throw pappso::ExceptionInterrupted(
        QObject::tr("X!Tandem stopped by the user processing on file %1")
          .arg(tandem_input_file));
    }
  m_xtProcess = new QProcess();
  QStringList arguments;
 
  qDebug() << m_tandemBinary << " " << m_xtProcess->arguments();
 
  arguments << tandem_input_file;
  // hk_process->setWorkingDirectory(QFileInfo(_hardklor_exe).absolutePath());
  m_xtProcess->start(m_tandemBinary, arguments);
 
  qDebug() << m_tandemBinary << " " << m_xtProcess->arguments();
 
  connect(m_xtProcess,
          &QProcess::readyReadStandardOutput,
          this,
          &TandemWrapperRun::readyReadStandardOutput);
  connect(m_xtProcess,
          &QProcess::readyReadStandardError,
          this,
          &TandemWrapperRun::readyReadStandardError);
 
 
  qDebug() << m_tandemBinary << " " << m_xtProcess->arguments();
 
  mp_monitor->setStatus(QObject::tr("Running X!Tandem"));
 
  if(!m_xtProcess->waitForStarted())
    {
      throw pappso::PappsoException(
        QObject::tr("X!Tandem process failed to start"));
    }
 
  qDebug() << m_tandemBinary << " " << m_xtProcess->arguments();
  while(m_xtProcess->waitForFinished(m_maxTandemRunTimeMs) == false)
    {
      //_p_monitor->appendText(xt_process->readAll().data());
      // data.append(xt_process->readAll());
      if(mp_monitor->shouldIstop())
        {
          m_xtProcess->kill();
          delete m_xtProcess;
          m_xtProcess = nullptr;
          throw pappso::ExceptionInterrupted(
            QObject::tr("X!Tandem stopped by the user processing on file %1")
              .arg(tandem_input_file));
        }
    }
 
  QProcess::ExitStatus Status = m_xtProcess->exitStatus();
 
  delete m_xtProcess;
  if(Status != QProcess::ExitStatus::NormalExit)
    {
      // != QProcess::NormalExit
      throw pappso::PappsoException(
        QObject::tr("error executing X!Tandem Status != 0 : %1")
          .arg(m_tandemBinary));
    }
  m_xtProcess = nullptr;
}

References m_maxTandemRunTimeMs, m_tandemBinary, m_xtProcess, mp_monitor, readyReadStandardError(), and readyReadStandardOutput().

Referenced by tandemProgressMessage(), and wrapTandemInputFile().

setTandemBinaryPath()

void pappso::TandemWrapperRun::setTandemBinaryPath ( const QString & tandem_binary_path )

private

Definition at line 87 of file tandemwrapperrun.cpp.

{
 
 
  m_tandemBinary = tandem_binary_path;
  QSettings settings;
  if(m_tandemBinary.isEmpty())
    {
      m_tandemBinary =
        settings.value("path/tandem_binary", "/usr/bin/tandem").toString();
    }
  // check for tandem executable
  m_tandemVersion = checkXtandemVersion(m_tandemBinary);
 
  qDebug() << m_tandemVersion;
  settings.setValue("path/tandem_binary", m_tandemBinary);
}

References checkXtandemVersion(), m_tandemBinary, and m_tandemVersion.

Referenced by TandemWrapperRun(), and tandemProgressMessage().

tandemProgressMessage

void pappso::TandemWrapperRun::tandemProgressMessage ( QString message )

signal

References checkXtandemVersion(), convertOrginalMsData2mzXmlData(), readyReadStandardError(), readyReadStandardOutput(), runTandem(), setTandemBinaryPath(), wrapTandemInputFile(), and writeFinalTandemOutput().

wrapTandemInputFile()

void pappso::TandemWrapperRun::wrapTandemInputFile ( const QString & tandem_input_file )

private

Definition at line 338 of file tandemwrapperrun.cpp.

{
  // read original tandem input file
  // store original ms data file name
  // create new mzXML data file in temporary directory
  // create new tandem input file based on new mzXML file
 
 
  QString mzxml_data_file_name =
    mpa_temporaryDirectory->filePath("msdata.mzxml");
  QString wrapped_tandem_input =
    mpa_temporaryDirectory->filePath("input_tandem.xml");
  QString wrapped_tandem_output =
    mpa_temporaryDirectory->filePath("output_tandem.xml");
 
  WrapTandemInput wrap_tandem_input(
    mzxml_data_file_name, wrapped_tandem_input, wrapped_tandem_output);
 
 
  if(wrap_tandem_input.readFile(tandem_input_file))
    {
    }
  else
    {
      throw pappso::PappsoException(
        QObject::tr("Error reading %1 X!Tandem input file :\n %2")
          .arg(tandem_input_file)
          .arg(wrap_tandem_input.errorString()));
    }
 
 
  if(m_tandemBinary.endsWith("tandemng") ||
     m_tandemBinary.endsWith("tandemng.exe") ||
     m_tandemBinary.endsWith("tandemng2015") ||
     m_tandemBinary.endsWith("tandemng2015.exe") ||
     m_tandemBinary.endsWith("tandemng2015p") ||
     m_tandemBinary.endsWith("tandemng2015p.exe"))
    {
      // no wrapper
      //  launch tandem on original file
      runTandem(tandem_input_file);
    }
  else
    {
      /*
       *
      XtandemInputSaxHandler wrap_input(
        mzxml_data_file_name, wrapped_tandem_input, wrapped_tandem_output);
      QFile qfile(tandem_input_file);
      if(!qfile.exists())
        {
          throw pappso::PappsoException(
            QObject::tr("Tandem input file %1 does not exists")
              .arg(QFileInfo(tandem_input_file).absoluteFilePath()));
        }
      QXmlInputSource xmlInputSource(&qfile);
      QXmlSimpleReader simplereader;
      simplereader.setContentHandler(&wrap_input);
      simplereader.setErrorHandler(&wrap_input);
 
      if(simplereader.parse(xmlInputSource))
        {
        }
      else
        {
          throw pappso::PappsoException(
            QObject::tr("Error reading %1 X!Tandem input file :\n %2")
              .arg(tandem_input_file)
              .arg(wrap_input.errorString()));
        }
    */
      // get number of threads and centroid parameters from tandem preset
      readTandemPresetFile(wrap_tandem_input.getOriginalTandemPresetFileName());
 
 
      // convert to mzXML
      QString original_msdata_file_name =
        wrap_tandem_input.getOriginalMsDataFileName();
      if(convertOrginalMsData2mzXmlData(original_msdata_file_name,
                                        mzxml_data_file_name))
        {
 
 
          // launch tandem
          runTandem(wrapped_tandem_input);
 
          // rewrite tandem result file
          writeFinalTandemOutput(
            wrapped_tandem_output,
            wrap_tandem_input.getOriginalTandemOutputFileName(),
            original_msdata_file_name);
        }
      else
        {
          // launch tandem on original file
          runTandem(tandem_input_file);
        }
    }
}

References convertOrginalMsData2mzXmlData(), pappso::XmlStreamReaderInterface::errorString(), pappso::WrapTandemInput::getOriginalMsDataFileName(), pappso::WrapTandemInput::getOriginalTandemOutputFileName(), pappso::WrapTandemInput::getOriginalTandemPresetFileName(), m_tandemBinary, mpa_temporaryDirectory, pappso::XmlStreamReaderInterface::readFile(), readTandemPresetFile(), runTandem(), and writeFinalTandemOutput().

Referenced by run(), and tandemProgressMessage().

writeFinalTandemOutput()

void pappso::TandemWrapperRun::writeFinalTandemOutput ( const QString & tmp_tandem_output, const QString & final_tandem_output, const QString & original_msdata_file_name )

private

tandem output modification tandem output is modified to contain the Bruker's file as input and centroidization parameters

Parameters

tmp_tandem_output	raw tandem output filename
final_tandem_output	final destination file for modified tandem output

Definition at line 243 of file tandemwrapperrun.cpp.

{
  mp_monitor->setStatus(QObject::tr("Rewriting X!Tandem XML result file"));
 
  WrapTandemResults wrap_output(final_tandem_output, original_msdata_file_name);
 
  wrap_output.setInputParameters("spectrum, timstof MS2 filters",
                                 getMs2FilterSuiteString());
  wrap_output.setInputParameters("spectrum, mzFormat",
                                 QString("%1").arg((int)m_mzFormat));
 
  if(m_convertMzDataUsingSpectrumIndex)
    {
      wrap_output.setInputParameters("output, spectrum index", "true");
    }
  else
    {
    }
 
  if(m_conversionTime != 0)
    {
      wrap_output.setInputParameters(
        "timing, tandemwrapper conversion time (sec)",
        QString("%1").arg(m_conversionTime / 1000));
    }
 
  if(wrap_output.readFile(tmp_tandem_output))
    {
    }
  else
    {
      throw pappso::PappsoException(
        QObject::tr("Error reading %1 X!Tandem output file :\n %2")
          .arg(tmp_tandem_output)
          .arg(wrap_output.errorString()));
    }
}

References pappso::XmlStreamReaderInterface::errorString(), getMs2FilterSuiteString(), m_conversionTime, m_convertMzDataUsingSpectrumIndex, m_mzFormat, mp_monitor, pappso::XmlStreamReaderInterface::readFile(), and pappso::WrapTandemResults::setInputParameters().

Referenced by tandemProgressMessage(), and wrapTandemInputFile().

Member Data Documentation

m_conversionTime

qint64 pappso::TandemWrapperRun::m_conversionTime = 0

private

Definition at line 150 of file tandemwrapperrun.h.

Referenced by convertOrginalMsData2mzXmlData(), and writeFinalTandemOutput().

m_convertMzDataUsingSpectrumIndex

bool pappso::TandemWrapperRun::m_convertMzDataUsingSpectrumIndex = false

private

Definition at line 146 of file tandemwrapperrun.h.

Referenced by convertOrginalMsData2mzXmlData(), and writeFinalTandemOutput().

m_maxTandemRunTimeMs

int pappso::TandemWrapperRun::m_maxTandemRunTimeMs

private

Initial value:

=
    1000

Definition at line 138 of file tandemwrapperrun.h.

Referenced by runTandem().

m_mzFormat

Enums::MsDataFormat pappso::TandemWrapperRun::m_mzFormat = Enums::MsDataFormat::unknown

private

Definition at line 148 of file tandemwrapperrun.h.

Referenced by convertOrginalMsData2mzXmlData(), and writeFinalTandemOutput().

m_tandemBinary

QString pappso::TandemWrapperRun::m_tandemBinary

private

Definition at line 135 of file tandemwrapperrun.h.

Referenced by runTandem(), setTandemBinaryPath(), and wrapTandemInputFile().

m_tandemVersion

QString pappso::TandemWrapperRun::m_tandemVersion

private

Definition at line 136 of file tandemwrapperrun.h.

Referenced by checkXtandemVersion(), and setTandemBinaryPath().

m_tmpDir

QString pappso::TandemWrapperRun::m_tmpDir

private

Definition at line 137 of file tandemwrapperrun.h.

m_xtProcess

QProcess* pappso::TandemWrapperRun::m_xtProcess = nullptr

private

Definition at line 140 of file tandemwrapperrun.h.

Referenced by ~TandemWrapperRun(), readyReadStandardError(), readyReadStandardOutput(), and runTandem().

mp_monitor

UiMonitorInterface* pappso::TandemWrapperRun::mp_monitor

private

Definition at line 134 of file tandemwrapperrun.h.

Referenced by convertOrginalMsData2mzXmlData(), readyReadStandardError(), readyReadStandardOutput(), run(), runTandem(), and writeFinalTandemOutput().

mpa_temporaryDirectory

QTemporaryDir* pappso::TandemWrapperRun::mpa_temporaryDirectory = nullptr

private

Definition at line 144 of file tandemwrapperrun.h.

Referenced by TandemWrapperRun(), ~TandemWrapperRun(), and wrapTandemInputFile().

msp_ms2FilterSuiteString

std::shared_ptr<FilterSuiteString> pappso::TandemWrapperRun::msp_ms2FilterSuiteString = nullptr

private

Definition at line 142 of file tandemwrapperrun.h.

Referenced by convertOrginalMsData2mzXmlData(), getMs2FilterSuiteString(), and readTandemPresetFile().

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

• pappsomspp/core/processing/tandemwrapper/tandemwrapperrun.h
• pappsomspp/core/processing/tandemwrapper/tandemwrapperrun.cpp