pappso::XtandemPresetReader Class Reference

#include <xtandempresetreader.h>

Inheritance diagram for pappso::XtandemPresetReader:

Public Member Functions
	XtandemPresetReader ()
virtual	~XtandemPresetReader ()
int	getNumberOfThreads () const
const QString	getMs2FiltersOptions () const
int	getCountNote () const
Public Member Functions inherited from pappso::XmlStreamReaderInterface
	XmlStreamReaderInterface ()
virtual	~XmlStreamReaderInterface ()
virtual bool	readFile (const QString &fileName)
bool	read (QIODevice *device)
bool	read (const QString &xml_content)
QString	errorString () const

Protected Member Functions
virtual void	readStream () override
Protected Member Functions inherited from pappso::XmlStreamReaderInterface
void	cloneStartElement (QXmlStreamWriter &output) const
void	cloneElement (QXmlStreamWriter &output)
void	cloneNode (QXmlStreamWriter &output)

Private Member Functions
void	read_note ()

Private Attributes
int	m_countNote = -1
int	m_threads = -1
Enums::PrecisionUnit	m_ms2precisionUnit = Enums::PrecisionUnit::dalton
double	m_ms2precisionValue = 0

Additional Inherited Members
Protected Attributes inherited from pappso::XmlStreamReaderInterface
QXmlStreamReader	m_qxmlStreamReader

Detailed Description

Definition at line 39 of file xtandempresetreader.h.

Constructor & Destructor Documentation

XtandemPresetReader()

pappso::XtandemPresetReader::XtandemPresetReader

(

)

Default constructor

Definition at line 35 of file xtandempresetreader.cpp.

{
}

~XtandemPresetReader()

pappso::XtandemPresetReader::~XtandemPresetReader ( )

virtual

Destructor

Definition at line 39 of file xtandempresetreader.cpp.

{
}

Member Function Documentation

getCountNote()

int pappso::XtandemPresetReader::getCountNote

(

)

const

Definition at line 162 of file xtandempresetreader.cpp.

{
  return m_countNote;
}

References m_countNote.

getMs2FiltersOptions()

const QString pappso::XtandemPresetReader::getMs2FiltersOptions

(

)

const

Definition at line 110 of file xtandempresetreader.cpp.

{
  QString filter_suite;
  PrecisionPtr precision = PrecisionFactory::getPrecisionPtrInstance(
    m_ms2precisionUnit, m_ms2precisionValue);
  QString charge_decon_filter = QString("chargeDeconvolution|%1")
                                  .arg(precision->toString().replace(" ", ""));
 
  PrecisionPtr precision_exclu = PrecisionFactory::getPrecisionPtrInstance(
    m_ms2precisionUnit, m_ms2precisionValue / 2);
  QString mz_exclusion_filter =
    QString("mzExclusion|%1").arg(precision_exclu->toString().replace(" ", ""));
  filter_suite = charge_decon_filter + " " + mz_exclusion_filter;
  return filter_suite;
}

References pappso::PrecisionFactory::getPrecisionPtrInstance(), m_ms2precisionUnit, m_ms2precisionValue, and pappso::PrecisionBase::toString().

Referenced by pappso::TandemWrapperRun::readTandemPresetFile().

getNumberOfThreads()

int pappso::XtandemPresetReader::getNumberOfThreads

(

)

const

Definition at line 103 of file xtandempresetreader.cpp.

{
  return m_threads;
}

References m_threads.

Referenced by pappso::TandemWrapperRun::readTandemPresetFile().

read_note()

void pappso::XtandemPresetReader::read_note ( )

private

Definition at line 45 of file xtandempresetreader.cpp.

{
  // <note type="input"
  // label="output,path">/gorgone/pappso/jouy/users/Celine/2019_Lumos/20191222_107_Juste_APD/metapappso_condor/test_run/20191222_18_EF1_third_step_test_condor_22janv.xml</note>
  if(m_qxmlStreamReader.name().toString() != "note")
    {
      m_qxmlStreamReader.skipCurrentElement();
      return;
    }
  Q_ASSERT(m_qxmlStreamReader.name().toString() == "note");
  QString label;
 
 
  m_countNote++;
  if((m_qxmlStreamReader.attributes().hasAttribute("type")) &&
     (m_qxmlStreamReader.attributes().value("type").toString() == "input"))
    {
      if(m_qxmlStreamReader.attributes().hasAttribute("label"))
        {
          label = m_qxmlStreamReader.attributes().value("label").toString();
        }
    }
  if(label.isEmpty())
    {
    }
  else
    {
      if(label == "spectrum, timstof MS2 filters")
        {
        }
      else if(label == "spectrum, threads")
        {
          m_threads = m_qxmlStreamReader.readElementText().toInt();
          return;
        }
      else if(label == "spectrum, fragment monoisotopic mass error units")
        {
 
          m_ms2precisionUnit = Enums::PrecisionUnit::dalton;
          if(m_qxmlStreamReader.readElementText().trimmed().toLower() == "ppm")
            {
              m_ms2precisionUnit = Enums::PrecisionUnit::ppm;
            }
          return;
        }
      else if(label == "spectrum, fragment monoisotopic mass error")
        {
          m_ms2precisionValue = m_qxmlStreamReader.readElementText().toDouble();
          return;
        }
    }
  m_qxmlStreamReader.skipCurrentElement();
  // qDebug() << "end ";
  //
}

References pappso::Enums::dalton, m_countNote, m_ms2precisionUnit, m_ms2precisionValue, pappso::XmlStreamReaderInterface::m_qxmlStreamReader, m_threads, and pappso::Enums::ppm.

Referenced by readStream().

readStream()

void pappso::XtandemPresetReader::readStream ( )

overrideprotectedvirtual

Implements pappso::XmlStreamReaderInterface.

Definition at line 128 of file xtandempresetreader.cpp.

{
  qDebug();
  m_countNote         = 0;
  m_threads           = -1;
  m_ms2precisionUnit  = Enums::PrecisionUnit::dalton;
  m_ms2precisionValue = -1;
  if(m_qxmlStreamReader.readNextStartElement())
    {
      if(m_qxmlStreamReader.name().toString() == "bioml")
        {
          qDebug();
          while(m_qxmlStreamReader.readNextStartElement())
            {
              // qDebug() << m_qxmlStreamReader.name();
              read_note();
            }
        }
      else
        {
          m_qxmlStreamReader.raiseError(
            QObject::tr("Not an X!Tandem preset file"));
          m_qxmlStreamReader.skipCurrentElement();
        }
    }
  if(m_threads == -1)
    {
      qDebug();
      m_qxmlStreamReader.raiseError(QObject::tr("Not an X!Tandem preset file"));
    }
  qDebug();
}

References pappso::Enums::dalton, m_countNote, m_ms2precisionUnit, m_ms2precisionValue, pappso::XmlStreamReaderInterface::m_qxmlStreamReader, m_threads, and read_note().

Member Data Documentation

m_countNote

int pappso::XtandemPresetReader::m_countNote = -1

private

Definition at line 63 of file xtandempresetreader.h.

Referenced by getCountNote(), read_note(), and readStream().

m_ms2precisionUnit

Enums::PrecisionUnit pappso::XtandemPresetReader::m_ms2precisionUnit = Enums::PrecisionUnit::dalton

private

Definition at line 66 of file xtandempresetreader.h.

Referenced by getMs2FiltersOptions(), read_note(), and readStream().

m_ms2precisionValue

double pappso::XtandemPresetReader::m_ms2precisionValue = 0

private

Definition at line 67 of file xtandempresetreader.h.

Referenced by getMs2FiltersOptions(), read_note(), and readStream().

m_threads

int pappso::XtandemPresetReader::m_threads = -1

private

Definition at line 64 of file xtandempresetreader.h.

Referenced by getNumberOfThreads(), read_note(), and readStream().

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

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